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Cisneros-Villanueva M, Fonseca-Montaño MA, Ríos-Romero M, López-Camarillo C, Jiménez-Morales S, Langley E, Rosette-Rueda AS, Cedro-Tanda A, Hernández-Sotelo D, Hidalgo-Miranda A. LncRNA SOX9-AS1 triggers a transcriptional program involved in lipid metabolic reprogramming, cell migration and invasion in triple-negative breast cancer. Sci Rep 2024; 14:1483. [PMID: 38233470 PMCID: PMC10794186 DOI: 10.1038/s41598-024-51947-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 01/11/2024] [Indexed: 01/19/2024] Open
Abstract
At the molecular level, triple-negative breast cancer (TNBC) is frequently categorized as PAM50 basal-like subtype, but despite the advances in molecular analyses, the clinical outcome for these subtypes is uncertain. Long non-coding RNAs (lncRNAs) are master regulators of genes involved in hallmarks of cancer, which makes them suitable biomarkers for breast cancer (BRCA) diagnosis and prognosis. Here, we evaluated the regulatory role of lncRNA SOX9-AS1 in these subtypes. Using the BRCA-TCGA cohort, we observed that SOX9-AS1 was significantly overexpressed in basal-like and TNBC in comparison with other BRCA subtypes. Survival analyzes showed that SOX9-AS1 overexpression was associated with a favorable prognosis in TNBC and basal-like patients. To study the functions of SOX9-AS1, we determined the expression levels in a panel of nine BRCA cell lines finding increased levels in MDA-MB-468 and HCC1187 TNBC. Using subcellular fractionation in these cell lines, we ascertained that SOX9-AS1 was located in the cytoplasmic compartment. In addition, we performed SOX9-AS1 gene silencing using two short-harping constructs, which were transfected in both cell models and performed a genome-wide RNA-seq analysis. Data showed that 351 lncRNAs and 740 mRNAs were differentially expressed in MDA-MB-468 while 56 lncRNAs and 100 mRNAs were modulated in HCC1187 cells (Log2FC < - 1.5 and > 1.5, p.adj value < 0.05). Pathway analysis revealed that the protein-encoding genes potentially regulate lipid metabolic reprogramming, and epithelial-mesenchymal transition (EMT). Expression of lipid metabolic-related genes LIPE, REEP6, GABRE, FBP1, SCD1, UGT2B11, APOC1 was confirmed by RT-qPCR. Functional analysis demonstrated that the knockdown of SOX9-AS1 increases the triglyceride synthesis, cell migration and invasion in both two TNBC cell lines. In conclusion, high SOX9-AS1 expression predicts an improved clinical course in patients, while the loss of SOX9-AS1 expression enhances the aggressiveness of TNBC cells.
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Affiliation(s)
- Mireya Cisneros-Villanueva
- Laboratorio Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), 14610, Mexico, México
- Programa de Doctorado en Ciencias Biomédicas, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero (UAGro), Chilpancingo de los Bravo, Guerrero, México
- Laboratorio de Epigenética del Cáncer, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero (UAGro), Chilpancingo de los Bravo, Guerrero, México
| | - Marco Antonio Fonseca-Montaño
- Laboratorio Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), 14610, Mexico, México
- Programa de Doctorado, Posgrado en Ciencias Biológicas, Unidad de Posgrado, Universidad Nacional Autónoma de México (UNAM), 04510, Mexico, México
| | - Magdalena Ríos-Romero
- Laboratorio Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), 14610, Mexico, México
| | - César López-Camarillo
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico, México
| | - Silvia Jiménez-Morales
- Laboratorio Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), 14610, Mexico, México
| | - Elizabeth Langley
- Laboratorio de Cáncer Hormono Regulado, Instituto Nacional de Cancerología (INCan), 14080, Mexico, México
| | - Alan Sajid Rosette-Rueda
- Laboratorio Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), 14610, Mexico, México
| | | | - Daniel Hernández-Sotelo
- Laboratorio de Epigenética del Cáncer, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero (UAGro), Chilpancingo de los Bravo, Guerrero, México.
| | - Alfredo Hidalgo-Miranda
- Laboratorio Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), 14610, Mexico, México.
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Pérez-Saldivar ML, Flores-García MK, Núñez-Villegas N, Fajardo-Gutiérrez A, Medina-Sanson A, Jiménez-Hernández E, Martín-Trejo JA, López-Santiago N, Peñaloza-González JG, Cortés-Herrera B, Merino-Pasaye LE, Amador-Sánchez R, García-López LR, Pérez-Lorenzana H, Román-Zepeda PF, Castañeda-Echevarría A, López-Caballero MG, Martínez-Silva SI, Rivera-González J, Granados-Kraulles J, Flores-Botello J, Medrano-López F, Rodríguez-Vázquez MA, Torres-Valle D, Mora-Rico K, Mora-Ríos FG, R.García‐Cortés L, Salcedo-Lozada P, Flores-Lujano J, Núñez-Enríquez JC, Bekker-Méndez VC, Mata-Rocha M, Rosas-Vargas H, Duarte-Rodríguez DA, Jiménez-Morales S, Hidalgo-Miranda A, López-Carrillo L, Mejía-Aranguré JM. Maternal diet in pregnancy and acute leukemia in infants: a case-control study in Mexico City. Front Oncol 2024; 13:1165323. [PMID: 38260836 PMCID: PMC10802844 DOI: 10.3389/fonc.2023.1165323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 12/08/2023] [Indexed: 01/24/2024] Open
Abstract
Introduction Epidemiological studies around the world on acute leukemia (AL) and risk factors in infants are scarce. Infant AL has been proposed to originate in utero, which facilitates its study by establishing a short exposure time in pregnant women to environmental and dietary factors that could contribute to the risk of or protection against leukemia. We hypothesized that maternal diet during pregnancy may be an important factor involved in AL in offspring. Methods We conducted a hospital-based case-control study from 2010 to 2019 on maternal diet during pregnancy in nine high-specialty public hospitals of different health institutions that diagnose and offer treatment to children with AL in Mexico City. Cases (n=109) were children ≤24 months of age with de novo diagnosis of AL, and controls (n=252) were children obtained in hospitals from second-level medical care matched for age, sex, and health institution. Maternal diet during pregnancy was obtained by a semiquantitative food frequency questionnaire. Unconditional logistic regression models were used to assess the association between food groups and infant AL. Potential confounders were assessed by constructing directed acyclic graphs (DAGs) with Dagitty software in which adjusted options were identified for the construction of unconditional logistic regression models. Results Cases were slightly predominantly female (52.3%). The years of education of the mother in cases and controls was 0-9 on average, and those who reported smoking cigarettes and consuming alcohol during pregnancy did so at a low frequency. Regarding the mother's diet, the main findings were that the consumption of allium vegetables during pregnancy was inversely associated with AL for medium and high consumption (OR=0.26, 95% CI 0.14-0.46; P-trend< 0.001). In contrast, the high consumption of high-fat dairy products had a positive association with AL (OR=2.37, 95% CI 1.30-4.34; P-trend<0.001). No association was found between consumption of topoisomerase II inhibitor foods during pregnancy and AL. Conclusion The results suggest that maternal intake during pregnancy of allium vegetables, specifically garlic, is inversely associated with the development of AL in children ≤24 months old. On the other hand, consumption of high-fat dairy products is positively associated with AL in children ≤24 months old.
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Affiliation(s)
- María Luisa Pérez-Saldivar
- Unidad de Investigación Médica en Epidemiología Clínica, Unidad Médica de Alta Especialidad (Unidad Médica de Alta Especialidad (UMAE)) Hospital de Pediatría, Centro Médico Nacional (Centro Médico Nacional (CMN)) Siglo XXI, Instituto Mexicano del Seguro Social (Instituto Mexicano del Seguro Social (IMSS)), Mexico City, Mexico
| | | | - Nancy Núñez-Villegas
- Servicio de Hematología Pediátrica, Hospital General “Gaudencio González Garza”, Centro Médico Nacional (CMN) “La Raza”, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Arturo Fajardo-Gutiérrez
- Unidad de Investigación Médica en Epidemiología Clínica, Unidad Médica de Alta Especialidad (Unidad Médica de Alta Especialidad (UMAE)) Hospital de Pediatría, Centro Médico Nacional (Centro Médico Nacional (CMN)) Siglo XXI, Instituto Mexicano del Seguro Social (Instituto Mexicano del Seguro Social (IMSS)), Mexico City, Mexico
| | - Aurora Medina-Sanson
- Departamento de Hemato-Oncología, Hospital Infantil de México Federico Gómez, Secretaria de Salud (Secretaría de Salud (SSA)), Mexico City, Mexico
| | - Elva Jiménez-Hernández
- Servicio de Oncología, Hospital Pediátrico Moctezuma, Secretaría de Salud de la Ciudad de México (Secretaría de Salud de la Ciudad de México (SSCDMX)), Mexico City, Mexico
| | - Jorge Alfonso Martín-Trejo
- Servicio de Hematología, Unidad Médica de Alta Especialidad (UMAE) Hospital de Pediatría, Centro Médico Nacional (CMN) “Siglo XXI”, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Norma López-Santiago
- Servicio de Hematología, Instituto Nacional de Pediatría (INP), Secretaría de Salud (SSA), Mexico City, Mexico
| | | | - Beatriz Cortés-Herrera
- Servicio de Hematología Pediátrica, Hospital General de México, Secretaría de Salud (SSA), Mexico City, Mexico
| | - Laura Elizabeth Merino-Pasaye
- Servicio de Hematología Pediátrica, Centro Médico Nacional (CMN)”20 de Noviembre”, Instituto de Seguridad Social al Servicio de los Trabajadores del Estado (Instituto de Seguridad Social al Servicio de los Trabajadores del Estado (ISSSTE)), Mexico City, Mexico
| | - Raquel Amador-Sánchez
- Servicio de Hematología Pediátrica, HGR No. 1 “Dr. Carlos Mac Gregor Sánchez Navarro” Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Luis Ramiro García-López
- Servicio de Pediatría, Hospital Pediátrico de Tacubaya, Secretaría de Salud de la Ciudad de México (SSCDMX), Mexico City, Mexico
| | - Héctor Pérez-Lorenzana
- Servicio de Cirugía Pediátrica, Hospital General “Gaudencio González Garza”, Centro Médico Nacional (CMN) “La Raza”, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Pedro Francisco Román-Zepeda
- Servicio de Cirugía Pediátrica, Hospital General Regional (HGR) No. 1 “Dr. Carlos Mac Gregor Sánchez Navarro” Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Alejandro Castañeda-Echevarría
- Servicio de Pediatría, Hospital General de Zona Regional (HGZR) No. 25 Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - María Guadalupe López-Caballero
- Coordinación Clínica y Pediatría, Hospital Pediátrico de Coyoacán, Secretaría de Salud de la Ciudad de México (SSCDMX), Mexico City, Mexico
| | - Sofía Irene Martínez-Silva
- Hospital Pediátrico de Iztapalapa, Secretaría de Salud de la Ciudad de México (SSCDMX), Mexico City, Mexico
| | - Juan Rivera-González
- Hospital General Dr. “Gustavo Baz Prada”, Instituto de Salud del Estado de México (ISEM), Estado de México, Mexico
| | - Jorge Granados-Kraulles
- Coordinación Clínica y Pediatría del Hospital General de Zona 76 Instituto Mexicano del Seguro Social (IMSS), Estado de México, Mexico
| | - Jesús Flores-Botello
- Coordinación Clínica y Pediatría, Hospital General “La Perla” ISEM, Estado de México, Mexico
| | - Francisco Medrano-López
- Coordinación Clínica y Pediatría, HGR No. 72 “Dr. Vicente Santos Guajardo”, Instituto Mexicano del Seguro Social (IMSS), Estado de México, Mexico
| | - María Adriana Rodríguez-Vázquez
- Coordinación Clínica y Pediatría del Hospital General de Zona 68, Instituto Mexicano del Seguro Social (IMSS), Estado de México, Mexico
| | - Delfino Torres-Valle
- Coordinación Clínica y Pediatría del Hospital General de Zona 71, Instituto Mexicano del Seguro Social (IMSS), Estado de México, Mexico
| | - Karina Mora-Rico
- Servicio de Cirugía Pediátrica, HGR 1° Octubre, Instituto de Seguridad Social al Servicio de los Trabajadores del Estado (ISSSTE), Mexico City, Mexico
| | - Félix G. Mora-Ríos
- Cirugía Pediátrica del Hospital Regional “General Ignacio Zaragoza”, Instituto de Seguridad Social al Servicio de los Trabajadores del Estado (ISSSTE), Mexico City, Mexico
| | - Luis R.García‐Cortés
- Delegación Regional Estado de México Oriente, Instituto Mexicano del Seguro Social (IMSS), Estado de México, Mexico
| | | | - Janet Flores-Lujano
- Unidad de Investigación Médica en Epidemiología Clínica, Unidad Médica de Alta Especialidad (Unidad Médica de Alta Especialidad (UMAE)) Hospital de Pediatría, Centro Médico Nacional (Centro Médico Nacional (CMN)) Siglo XXI, Instituto Mexicano del Seguro Social (Instituto Mexicano del Seguro Social (IMSS)), Mexico City, Mexico
| | - Juan Carlos Núñez-Enríquez
- Unidad de Investigación Médica en Epidemiología Clínica, Unidad Médica de Alta Especialidad (Unidad Médica de Alta Especialidad (UMAE)) Hospital de Pediatría, Centro Médico Nacional (Centro Médico Nacional (CMN)) Siglo XXI, Instituto Mexicano del Seguro Social (Instituto Mexicano del Seguro Social (IMSS)), Mexico City, Mexico
| | - Vilma Carolina Bekker-Méndez
- Unidad de Investigación Médica en Inmunología e Infectología, Hospital de Infectología “Dr. Daniel Méndez Hernández”, Centro Médico Nacional (CMN) “La Raza”, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Minerva Mata-Rocha
- Laboratorio de Biología Molecular de las Leucemias, Unidad de Investigación en Genética Humana, Unidad Médica de Alta Especialidad (UMAE), Hospital de Pediatría, Centro Médico Nacional (CMN) “Siglo XXI”, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Haydeé Rosas-Vargas
- Laboratorio de Genética, Unidad Médica de Alta Especialidad (Unidad Médica de Alta Especialidad (UMAE)) Hospital de Pediatría, Centro Médico Nacional (Centro Médico Nacional (CMN)) Siglo XXI, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - David Aldebarán Duarte-Rodríguez
- Unidad de Investigación Médica en Epidemiología Clínica, Unidad Médica de Alta Especialidad (Unidad Médica de Alta Especialidad (UMAE)) Hospital de Pediatría, Centro Médico Nacional (Centro Médico Nacional (CMN)) Siglo XXI, Instituto Mexicano del Seguro Social (Instituto Mexicano del Seguro Social (IMSS)), Mexico City, Mexico
| | - Silvia Jiménez-Morales
- Laboratorio de Innovación y Medicina de Precisión, Núcleo A. Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
| | - Alfredo Hidalgo-Miranda
- Laboratorio de Innovación y Medicina de Precisión, Núcleo A. Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
| | | | - Juan Manuel Mejía-Aranguré
- Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
- Laboratorio Genómica Funcional del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
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Fonseca-Montaño MA, Vázquez-Santillán KI, Hidalgo-Miranda A. The current advances of lncRNAs in breast cancer immunobiology research. Front Immunol 2023; 14:1194300. [PMID: 37342324 PMCID: PMC10277570 DOI: 10.3389/fimmu.2023.1194300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 05/24/2023] [Indexed: 06/22/2023] Open
Abstract
Breast cancer is the most frequently diagnosed malignancy and the leading cause of cancer-related death in women worldwide. Breast cancer development and progression are mainly associated with tumor-intrinsic alterations in diverse genes and signaling pathways and with tumor-extrinsic dysregulations linked to the tumor immune microenvironment. Significantly, abnormal expression of lncRNAs affects the tumor immune microenvironment characteristics and modulates the behavior of different cancer types, including breast cancer. In this review, we provide the current advances about the role of lncRNAs as tumor-intrinsic and tumor-extrinsic modulators of the antitumoral immune response and the immune microenvironment in breast cancer, as well as lncRNAs which are potential biomarkers of tumor immune microenvironment and clinicopathological characteristics in patients, suggesting that lncRNAs are potential targets for immunotherapy in breast cancer.
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Affiliation(s)
- Marco Antonio Fonseca-Montaño
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
- Programa de Doctorado, Posgrado en Ciencias Biológicas, Unidad de Posgrado, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | | | - Alfredo Hidalgo-Miranda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
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Fonseca-Montaño MA, Cisneros-Villanueva M, Coales I, Hidalgo-Miranda A. LINC00426 is a potential immune phenotype-related biomarker and an overall survival predictor in PAM50 luminal B breast cancer. Front Genet 2023; 14:1034569. [PMID: 37260772 PMCID: PMC10228735 DOI: 10.3389/fgene.2023.1034569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 05/03/2023] [Indexed: 06/02/2023] Open
Abstract
Background: Breast cancer (BRCA) represents the most frequent diagnosed malignancy in women worldwide. Despite treatment advances, BRCAs eventually develop resistance to targeted therapies, resulting in poor prognosis. The identification of new biomarkers, like immune-related long non-coding RNAs (lncRNAs), could contribute to the clinical management of BRCA patients. In this report, we evaluated the LINC00426 expression in PAM50 BRCA subtypes from two clinical independent cohorts (BRCA-TCGA and GEO-GSE96058 datasets). Methods and results: Using Cox regression models and Kaplan-Meier survival analyses, we identified that LINC00426 expression was a consistent overall survival (OS) predictor in luminal B (LB) BRCA patients. Subsequently, differential gene expression and gene set enrichment analyses identified that LINC00426 expression was associated with different immune-related and cancer-related pathways and processes in LB BRCA. Additionally, the LINC00426 expression was correlated with the infiltration level of diverse immune cell populations, alongside immune checkpoint and cytolytic activity-related gene expression. Conclusion: This evidence suggests that LINC00426 is a potential biomarker of immune phenotype and an OS predictor in PAM50 LB BRCA.
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Affiliation(s)
- Marco Antonio Fonseca-Montaño
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
- Programa de Doctorado, Posgrado en Ciencias Biológicas, Unidad de Posgrado, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Mireya Cisneros-Villanueva
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
| | - Isabelle Coales
- Centre for Host Microbiome Interactions, King’s College London, London, United Kingdom
| | - Alfredo Hidalgo-Miranda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
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Nambo-Venegas R, Palacios-González B, Mas-Oliva J, Aurioles-Amozurrutia AK, Cruz-Rangel A, Moreno A, Hidalgo-Miranda A, Rodríguez-Dorantes M, Vadillo-Ortega F, Xicohtencatl-Cortes J, Ruiz-Olmedo MI, Reyes-Grajeda JP. Conversion of M1 Macrophages to Foam Cells: Transcriptome Differences Determined by Sex. Biomedicines 2023; 11:biomedicines11020490. [PMID: 36831031 PMCID: PMC9953229 DOI: 10.3390/biomedicines11020490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/27/2023] [Accepted: 01/30/2023] [Indexed: 02/11/2023] Open
Abstract
BACKGROUND M1 macrophages involved in pro-inflammatory processes can be induced by low-density lipoproteins (LDL), giving rise to foam cells. In the atheroma plaque, it has been identified that males present more advanced lesions associated with infiltration. Therefore, our study aims to investigate sex-related changes in the transcriptome of M1 macrophages during the internalization process of LDL particles. METHODS Peripheral blood mononuclear cells (PBMCs) from healthy male and female subjects were separated using Hystopaque, and monocytes were isolated from PBMCs using a positive selection of CD14+ cells. Cells were stimulated with LDL 10 µg/mL, and the transcriptional profile of M1 macrophages performed during LDL internalization was determined using a Clariom D platform array. RESULTS Chromosome Y influences the immune system and inflammatory responses in males expressing 43% of transcripts in response to LDL treatment. Males and females share 15 transcripts, where most correspond to non-coding elements involved in oxidative stress and endothelial damage. CONCLUSIONS During LDL internalization, male monocyte-derived M1 macrophages display more marked proinflammatory gene expression. In contrast, female M1 macrophages display a more significant number of markers associated with cell damage.
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Affiliation(s)
- Rafael Nambo-Venegas
- Laboratorio de Estructura de Proteínas, Instituto Nacional de Medicina Genómica, Mexico City 14600, Mexico
| | - Berenice Palacios-González
- Laboratorio de Envejecimiento Saludable, Centro de Investigación Sobre Envejecimiento (CIE-CINVESTAV Sur), Instituto Nacional de Medicina Genómica, Mexico City 14330, Mexico
| | - Jaime Mas-Oliva
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | | | - Armando Cruz-Rangel
- Laboratorio de Estructura de Proteínas, Instituto Nacional de Medicina Genómica, Mexico City 14600, Mexico
| | - Abel Moreno
- Instituto de Química, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Alfredo Hidalgo-Miranda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City 14600, Mexico
| | | | - Felipe Vadillo-Ortega
- Unidad de Vinculación Científica de la Facultad de Medicina UNAM en INMEGEN, Instituto Nacional de Medicina Genómica, Mexico City 14600, Mexico
| | - Juan Xicohtencatl-Cortes
- Laboratorio de Bacteriología Intestinal, Hospital Infantil de México Federico Gómez, Mexico City 06720, Mexico
| | | | - Juan Pablo Reyes-Grajeda
- Laboratorio de Estructura de Proteínas, Instituto Nacional de Medicina Genómica, Mexico City 14600, Mexico
- Correspondence:
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Fonseca-Montaño MA, Blancas S, Herrera-Montalvo LA, Hidalgo-Miranda A. Cancer Genomics. Arch Med Res 2022; 53:723-731. [PMID: 36460546 DOI: 10.1016/j.arcmed.2022.11.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/17/2022] [Accepted: 11/22/2022] [Indexed: 12/04/2022]
Abstract
In the past decade, genomics has fundamentally changed our view of cancer biology, allowing comprehensive analyses of mutations, copy number alterations, structural variants, gene expression and DNA methylation profiles in large-scale studies across different cancer types. Efforts like The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) have fostered international collaborations for cancer genomic analyses and have generated public databases that give scientists around the world access to thoroughly curated data, which have been extensively used as a tool for further hypothesis driven research on several aspects of cancer biology. In parallel, some of these findings are being translated into specific clinical benefits for cancer patients. In this review, we provide a brief historical description of the evolution of international public cancer genome projects and related databases, as well as we discuss about their impact on general cancer research.
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Affiliation(s)
- Marco A Fonseca-Montaño
- Instituto Nacional de Medicina Genómica, Ciudad de México, México; Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Ciudad de México, México
| | - Susana Blancas
- Instituto Nacional de Medicina Genómica, Ciudad de México, México; Cátedras Consejo Nacional de Ciencia y Tecnología, Ciudad de México, México; Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Ciudad de México, México
| | | | - Alfredo Hidalgo-Miranda
- Instituto Nacional de Medicina Genómica, Ciudad de México, México; Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Ciudad de México, México.
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López-Sánchez GN, Montalvo-Javé E, Domínguez-Perez M, Antuna-Puente B, Beltrán-Anaya FO, Hidalgo-Miranda A, Chávez-Tapia NC, Uribe M, Nuño-Lámbarri N. Hepatic mir-122-3p, mir-140-5p and mir-148b-5p expressions are correlated with cytokeratin-18 serum levels in MAFLD. Ann Hepatol 2022; 27:100756. [PMID: 36096296 DOI: 10.1016/j.aohep.2022.100756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/23/2022] [Accepted: 08/25/2022] [Indexed: 02/04/2023]
Abstract
INTRODUCTION AND OBJECTIVES Metabolic-associated fatty liver disease (MAFLD) is defined by steatosis in more than 5% of hepatocytes without other liver diseases. Patients with this disease can progress to multiple stages like liver fibrosis, cirrhosis, and hepatocellular carcinoma. miRNAs are single-stranded molecules that regulate metabolic homeostasis; their differential expression postulates them as potential circulating biomarkers for MAFLD. Previous research reported that hsa-miR-140-5p, hsa-miR-148-5p, and hsa-miR-122-3p have a differential expression in patients with MAFLD. This study aimed to investigate the correlation between liver hsa-miR-140-5p, hsa-miR-148-5p, and hsa-miR-122-3p and serum biomarkers CK-18, APOB, IL-6, IL-32, and TNF-α in patients with MAFLD compared with control patients. MATERIALS AND METHODS A cross-sectional study was carried out with 16 patients of both sexes, aged between 18-60 years, to determine the association between the levels of hsa-miR-140-5p, hsa-miR-148-5p, and hsa-miR-122-3p with MAFLD in liver biopsies of patients who underwent laparoscopic cholecystectomy. RESULTS Twelve patients presented MAFLD, four without hepatic steatosis. Circulating levels of CK-18 showed a significant difference in patients with MAFLD, and a strong correlation was found between hsa-miR-122-3p, hsa-miR-140-5p, and hsa-miR-148b-5p versus the CAP value. CONCLUSION There is a correlation between elevated tissue expression of hsa-miR-122-3p, hsa-miR-140-5p, and hsa-miR-148b-3p with plasma levels of CK-18 in patients with simple steatosis compared with patients without the disease.
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Affiliation(s)
| | - Eduardo Montalvo-Javé
- Department of Surgery, Faculty of Medicine, The National Autonomous University of Mexico (UNAM), Mexico City, Mexico; Hepato Pancreato and Biliary Clinic, Department of General Surgery, "Hospital General de Mexico", Dr. Eduardo Liceaga. Mexico City, Mexico; Obesity and Digestive Diseases Unit, Medica Sur Clinic & Foundation, Mexico City, Mexico
| | - Mayra Domínguez-Perez
- Genomics of Cardiovascular Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Barbara Antuna-Puente
- Infection Disease Division, Department of Medicine, Queen's University, Kingston, ON, Canada
| | - Fredy O Beltrán-Anaya
- Virology Laboratory, Faculty of Chemical Biological Sciences, UAGro. Lázaro Cárdenas
| | - Alfredo Hidalgo-Miranda
- Genomics of Cancer Diseases Laboratory, National Institute of Genomic Medicine. Mexico City, Mexico
| | - Norberto C Chávez-Tapia
- Traslational Research Unit, Medica Sur Clinic & Foundation, Mexico City, Mexico; Obesity and Digestive Diseases Unit, Medica Sur Clinic & Foundation, Mexico City, Mexico
| | - Misael Uribe
- Obesity and Digestive Diseases Unit, Medica Sur Clinic & Foundation, Mexico City, Mexico.
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8
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Valenzuela-Vázquez L, Nuñez-Enriquez JC, Sánchez-Herrera J, Medina-Sanson A, Pérez-Saldivar ML, Jiménez-Hernández E, Martiín-Trejo JA, Del Campo-Martínez MDLÁ, Flores-Lujano J, Amador-Sánchez R, Mora-Ríos FG, Peñaloza-González JG, Duarte-Rodríguez DA, Torres-Nava JR, Espinosa-Elizondo RM, Cortés-Herrera B, Flores-Villegas LV, Merino-Pasaye LE, Almeida-Hernández C, Ramírez-Colorado R, Solís-Labastida KA, Medrano-López F, Pérez-Gómez JA, Velázquez-Aviña MM, Martínez-Ríos A, Aguilar-De los Santos A, Santillán-Juárez JD, Gurrola-Silva A, García-Velázquez AJ, Mata-Rocha M, Hernández-Echáurregui GA, Sepúlveda-Robles OA, Rosas-Vargas H, Mancilla-Herrera I, Jimenez-Morales S, Hidalgo-Miranda A, Martinez-Duncker I, Waight JD, Hance KW, Madauss KP, Mejía-Aranguré JM, Cruz-Munoz ME. NK cells with decreased expression of multiple activating receptors is a dominant phenotype in pediatric patients with acute lymphoblastic leukemia. Front Oncol 2022; 12:1023510. [PMID: 36419901 PMCID: PMC9677112 DOI: 10.3389/fonc.2022.1023510] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 10/17/2022] [Indexed: 11/09/2022] Open
Abstract
NK cells have unique attributes to react towards cells undergoing malignant transformation or viral infection. This reactivity is regulated by activating or inhibitory germline encoded receptors. An impaired NK cell function may result from an aberrant expression of such receptors, a condition often seen in patients with hematological cancers. Acute lymphoblastic leukemia (ALL) is the most common pediatric cancer worldwide and NK cells have emerged as crucial targets for developing immunotherapies. However, there are important gaps concerning the phenotype and behavior of NK cells during emergence of ALL. In this study we analyze the phenotype and function of NK cells from peripheral blood in pediatric patients with ALL at diagnosis. Our results showed that NK cells exhibited an altered phenotype highlighted by a significant reduction in the overall expression and percent representation of activating receptors compared to age-matched controls. No significant differences were found for the expression of inhibitory receptors. Moreover, NK cells with a concurrent reduced expression in various activating receptors, was the dominant phenotype among patients. An alteration in the relative frequencies of NK cells expressing NKG2A and CD57 within the mature NK cell pool was also observed. In addition, NK cells from patients displayed a significant reduction in the ability to sustain antibody-dependent cellular cytotoxicity (ADCC). Finally, an aberrant expression of activating receptors is associated with the phenomenon of leukemia during childhood.
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Affiliation(s)
- Lucero Valenzuela-Vázquez
- Facultad de Medicina, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
- Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Juan Carlos Nuñez-Enriquez
- Unidad de Investigación Médica en Epidemiología Clínica, Unidad Médica de Alta Especialidad (UMAE) Hospital de Pediatría, Centro Médico Nacional (CMN) “Siglo XXI”, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Jacqueline Sánchez-Herrera
- Facultad de Medicina, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
- Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Aurora Medina-Sanson
- Servicio de Oncología Pediátrica, Hospital Infantil de México, “Dr. Federico Gómez Sántos”, Secretaria de Salud, Ciudad de México, Mexico
| | - María Luisa Pérez-Saldivar
- Unidad de Investigación Médica en Epidemiología Clínica, Unidad Médica de Alta Especialidad (UMAE) Hospital de Pediatría, Centro Médico Nacional (CMN) “Siglo XXI”, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Elva Jiménez-Hernández
- Servicio de Hematología Pediátrica, Hospital General “Gaudencio González Garza”, Centro Médico Nacional (CMN) “La Raza”, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Jorge Alfonso Martiín-Trejo
- Servicio de Hematología Pediátrica, Unidad Médica de Alta Especialidad (UMAE) Hospital de Pediatría, Centro Médico Nacional (CMN) “Siglo XXI”, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - María de Los Ángeles Del Campo-Martínez
- Servicio de Hematología Pediátrica, Hospital General “Gaudencio González Garza”, Centro Médico Nacional (CMN) “La Raza”, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Janet Flores-Lujano
- Unidad de Investigación Médica en Epidemiología Clínica, Unidad Médica de Alta Especialidad (UMAE) Hospital de Pediatría, Centro Médico Nacional (CMN) “Siglo XXI”, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Raquel Amador-Sánchez
- Hospital General Regional No. 1 “Carlos McGregor Sánchez Navarro”, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Félix Gustavo Mora-Ríos
- Departamento de Hematología, Hospital General Regional Ignacio Zaragoza del Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado (ISSSTE), Mexico City, Mexico
| | | | - David Aldebarán Duarte-Rodríguez
- Unidad de Investigación Médica en Epidemiología Clínica, Unidad Médica de Alta Especialidad (UMAE) Hospital de Pediatría, Centro Médico Nacional (CMN) “Siglo XXI”, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - José Refugio Torres-Nava
- Servicio de Oncología, Hospital Pediátrico de Moctezuma, Secretaría de Salud de la Ciudad de México (CDMX), Mexico City, Mexico
| | | | - Beatriz Cortés-Herrera
- Servicio de Hematología Pediátrica, Hospital General de México, Secretaria de Salud (SS), Mexico City, Mexico
| | - Luz Victoria Flores-Villegas
- Servicio de Hematología Pediátrica, Centro Médico Nacional (CMN) “20 de Noviembre”, Instituto de Seguridad Social al Servicio de los Trabajadores del Estado (ISSSTE), Mexico City, Mexico
| | - Laura Elizabeth Merino-Pasaye
- Servicio de Hematología Pediátrica, Centro Médico Nacional (CMN) “20 de Noviembre”, Instituto de Seguridad Social al Servicio de los Trabajadores del Estado (ISSSTE), Mexico City, Mexico
| | - Carolina Almeida-Hernández
- Hospital General de Ecatepec “Las Américas”, Instituto de Salud del Estado de México (ISEM), Mexico City, Mexico
| | - Rosario Ramírez-Colorado
- Hospital Pediátrico La Villa, Secretaría de Salud de la Ciudad de México (SSCDMX), Mexico City, Mexico
| | - Karina Anastacia Solís-Labastida
- Servicio de Hematología Pediátrica, Unidad Médica de Alta Especialidad (UMAE) Hospital de Pediatría, Centro Médico Nacional (CMN) “Siglo XXI”, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Francisco Medrano-López
- Hospital General Regional (HGR) No. 72 “Dr. Vicente Santos Guajardo”, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Jessica Arleet Pérez-Gómez
- Hospital General Regional (HGR) No. 72 “Dr. Vicente Santos Guajardo”, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | | | - Annel Martínez-Ríos
- Departamento de Hematología, Hospital General Regional Ignacio Zaragoza del Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado (ISSSTE), Mexico City, Mexico
| | | | - Jessica Denisse Santillán-Juárez
- Servicio de Hemato-oncología Pediátrica, Hospital Regional No. 1° de Octubre, Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado (ISSSTE), Mexico City, Mexico
| | - Alma Gurrola-Silva
- Hospital Regional Tipo B de Alta Especialidad Bicentenario de la Independencia, Instituto de Seguridad Social al Servicio de los Trabajadores del Estado, Mexico City, Mexico
| | - Alejandra Jimena García-Velázquez
- Servicio de Hemato-oncología Pediátrica, Hospital Regional No. 1° de Octubre, Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado (ISSSTE), Mexico City, Mexico
| | - Minerva Mata-Rocha
- Unidad de Investigación Médica en Epidemiología Clínica, Unidad Médica de Alta Especialidad (UMAE) Hospital de Pediatría, Centro Médico Nacional (CMN) “Siglo XXI”, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | | | - Omar Alejandro Sepúlveda-Robles
- Unidad de Investigación Médica en Genética Humana, Unidad Médica de Alta Especialidad (UMAE) Hospital de Pediatría, Centro Médico Nacional (CMN) “Siglo XXI”, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Haydeé Rosas-Vargas
- Unidad de Investigación Médica en Genética Humana, Unidad Médica de Alta Especialidad (UMAE) Hospital de Pediatría, Centro Médico Nacional (CMN) “Siglo XXI”, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Ismael Mancilla-Herrera
- Departamento de Infectología e Inmunología, Instituto Nacional de Perinatología, Mexico City, Mexico
| | - Silvia Jimenez-Morales
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Alfredo Hidalgo-Miranda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Ivan Martinez-Duncker
- Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | | | | | | | - Juan Manuel Mejía-Aranguré
- Unidad de Investigación Médica en Genética Humana, Unidad Médica de Alta Especialidad (UMAE) Hospital de Pediatría, Centro Médico Nacional (CMN) “Siglo XXI”, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
- Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
- *Correspondence: Juan Manuel Mejía-Aranguré, ; Mario Ernesto Cruz-Munoz,
| | - Mario Ernesto Cruz-Munoz
- Facultad de Medicina, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
- *Correspondence: Juan Manuel Mejía-Aranguré, ; Mario Ernesto Cruz-Munoz,
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9
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Flores-Lujano J, Duarte-Rodríguez DA, Jiménez-Hernández E, Martín-Trejo JA, Allende-López A, Peñaloza-González JG, Pérez-Saldivar ML, Medina-Sanson A, Torres-Nava JR, Solís-Labastida KA, Flores-Villegas LV, Espinosa-Elizondo RM, Amador-Sánchez R, Velázquez-Aviña MM, Merino-Pasaye LE, Núñez-Villegas NN, González-Ávila AI, del Campo-Martínez MDLÁ, Alvarado-Ibarra M, Bekker-Méndez VC, Cárdenas-Cardos R, Jiménez-Morales S, Rivera-Luna R, Rosas-Vargas H, López-Santiago NC, Rangel-López A, Hidalgo-Miranda A, Vega E, Mata-Rocha M, Sepúlveda-Robles OA, Arellano-Galindo J, Núñez-Enríquez JC, Mejía-Aranguré JM. Persistently high incidence rates of childhood acute leukemias from 2010 to 2017 in Mexico City: A population study from the MIGICCL. Front Public Health 2022; 10:918921. [PMID: 36187646 PMCID: PMC9518605 DOI: 10.3389/fpubh.2022.918921] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 08/09/2022] [Indexed: 01/22/2023] Open
Abstract
Introduction Over the years, the Hispanic population living in the United States has consistently shown high incidence rates of childhood acute leukemias (AL). Similarly, high AL incidence was previously observed in Mexico City (MC). Here, we estimated the AL incidence rates among children under 15 years of age in MC during the period 2010-2017. Methods The Mexican Interinstitutional Group for the Identification of the Causes of Childhood Leukemia conducted a study gathering clinical and epidemiological information regarding children newly diagnosed with AL at public health institutions of MC. Crude age incidence rates (cAIR) were obtained. Age-standardized incidence rates worldwide (ASIRw) and by municipalities (ASIRm) were calculated by the direct and indirect methods, respectively. These were reported per million population <15 years of age; stratified by age group, sex, AL subtypes, immunophenotype and gene rearrangements. Results A total of 903 AL cases were registered. The ASIRw was 63.3 (cases per million) for AL, 53.1 for acute lymphoblastic leukemia (ALL), and 9.4 for acute myeloblastic leukemia. The highest cAIR for AL was observed in the age group between 1 and 4 years (male: 102.34 and female: 82.73). By immunophenotype, the ASIRw was 47.3 for B-cell and 3.7 for T-cell. The incidence did not show any significant trends during the study period. The ASIRm for ALL were 68.6, 66.6 and 62.8 at Iztacalco, Venustiano Carranza and Benito Juárez, respectively, whereas, other municipalities exhibited null values mainly for AML. Conclusion The ASIRw for childhood AL in MC is among the highest reported worldwide. We observed spatial heterogeneity of rates by municipalities. The elevated AL incidence observed in Mexican children may be explained by a combination of genetic background and exposure to environmental risk factors.
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Affiliation(s)
- Janet Flores-Lujano
- Unidad de Investigación Médica en Epidemiología Clínica, Unidad Médica de Alta Especialidad, Hospital de Pediatría “Dr. Silvestre Frenk Freund, ” Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - David Aldebarán Duarte-Rodríguez
- Unidad de Investigación Médica en Epidemiología Clínica, Unidad Médica de Alta Especialidad, Hospital de Pediatría “Dr. Silvestre Frenk Freund, ” Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Elva Jiménez-Hernández
- Servicio de Hematología Pediátrica, Centro Médico Nacional “La Raza, ” Hospital General “Gaudencio González Garza, ” Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico,Servicio de Oncología, Hospital Pediátrico de Moctezuma, Secretaría de Salud de la Ciudad de México (SSCDMX), Mexico City, Mexico
| | - Jorge Alfonso Martín-Trejo
- Servicio de Hematología Pediátrica, Unidad Médica de Alta Especialidad, Hospital de Pediatría “Dr. Silvestre Frenk Freund, ” Centro Médico Nacional “Siglo XXI, ” Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Aldo Allende-López
- Unidad de Investigación Médica en Epidemiología Clínica, Unidad Médica de Alta Especialidad, Hospital de Pediatría “Dr. Silvestre Frenk Freund, ” Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | | | - María Luisa Pérez-Saldivar
- Unidad de Investigación Médica en Epidemiología Clínica, Unidad Médica de Alta Especialidad, Hospital de Pediatría “Dr. Silvestre Frenk Freund, ” Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Aurora Medina-Sanson
- Departamento de HematoOncología, Hospital Infantil de México Federico Gómez, Secretaría de Salud (SS), Mexico City, Mexico
| | - José Refugio Torres-Nava
- Servicio de Oncología, Hospital Pediátrico de Moctezuma, Secretaría de Salud de la Ciudad de México (SSCDMX), Mexico City, Mexico
| | - Karina Anastacia Solís-Labastida
- Servicio de Hematología Pediátrica, Unidad Médica de Alta Especialidad, Hospital de Pediatría “Dr. Silvestre Frenk Freund, ” Centro Médico Nacional “Siglo XXI, ” Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Luz Victoria Flores-Villegas
- Servicio de Hematología Pediátrica, Centro Médico Nacional “20 de Noviembre, ” Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado (ISSSTE), Mexico City, Mexico
| | | | - Raquel Amador-Sánchez
- Servicio de Hematología Pediátrica, Hospital General Regional 1 “Dr. Carlos McGregor Sánchez Navarro, ” Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | | | - Laura Elizabeth Merino-Pasaye
- Servicio de Hematología Pediátrica, Centro Médico Nacional “20 de Noviembre, ” Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado (ISSSTE), Mexico City, Mexico
| | - Nora Nancy Núñez-Villegas
- Servicio de Hematología Pediátrica, Centro Médico Nacional “La Raza, ” Hospital General “Gaudencio González Garza, ” Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Ana Itamar González-Ávila
- Servicio de Hematología Pediátrica, Hospital General Regional 1 “Dr. Carlos McGregor Sánchez Navarro, ” Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - María de los Ángeles del Campo-Martínez
- Servicio de Hematología Pediátrica, Centro Médico Nacional “La Raza, ” Hospital General “Gaudencio González Garza, ” Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Martha Alvarado-Ibarra
- Servicio de Hematología Pediátrica, Centro Médico Nacional “20 de Noviembre, ” Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado (ISSSTE), Mexico City, Mexico
| | - Vilma Carolina Bekker-Méndez
- Hospital de Infectología “Dr. Daniel Méndez Hernández, ” “La Raza, ” Instituto Mexicano del Seguro Social (IMSS), Unidad de Investigación Médica en Inmunología e Infectología, Mexico City, Mexico
| | - Rocío Cárdenas-Cardos
- Servicio de Oncología Pediátrica, Instituto Nacional de Pediatría, Secretaría de Salud (SS), Mexico City, Mexico
| | - Silvia Jiménez-Morales
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
| | - Roberto Rivera-Luna
- Servicio de Oncología Pediátrica, Instituto Nacional de Pediatría, Secretaría de Salud (SS), Mexico City, Mexico
| | - Haydee Rosas-Vargas
- Unidad de Investigación Médica en Genética Humana, Unidad Médica de Alta Especialidad, Hospital de Pediatría “Dr. Silvestre Frenk Freund, ” Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Norma C. López-Santiago
- Servicio de Hematología Pediátrica, Instituto Nacional de Pediatría, Secretaría de Salud (SS), Mexico City, Mexico
| | - Angélica Rangel-López
- Coordinación de Investigación en Salud, Unidad Habilitada de Apoyo al Predictamen, Centro Médico Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Alfredo Hidalgo-Miranda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
| | - Elizabeth Vega
- Instituto de Ciencias de la Atmósfera y Cambio Climático, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Minerva Mata-Rocha
- Unidad de Investigación Médica en Genética Humana, Unidad Médica de Alta Especialidad, Hospital de Pediatría “Dr. Silvestre Frenk Freund, ” Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Omar Alejandro Sepúlveda-Robles
- Unidad de Investigación Médica en Genética Humana, Unidad Médica de Alta Especialidad, Hospital de Pediatría “Dr. Silvestre Frenk Freund, ” Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - José Arellano-Galindo
- Unidad de Investigación en Enfermedades Infecciosas, Laboratorio de Virología Clínica y Experimental, Hospital Infantil de México Federico Gómez, Secretaría de Salud (SS), Mexico City, Mexico
| | - Juan Carlos Núñez-Enríquez
- Unidad de Investigación Médica en Epidemiología Clínica, Unidad Médica de Alta Especialidad, Hospital de Pediatría “Dr. Silvestre Frenk Freund, ” Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico,Juan Carlos Núñez-Enríquez
| | - Juan Manuel Mejía-Aranguré
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico,Unidad de Investigación Médica en Genética Humana, Unidad Médica de Alta Especialidad, Hospital de Pediatría “Dr. Silvestre Frenk Freund, ” Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico,Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico,*Correspondence: Juan Manuel Mejía-Aranguré
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10
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May-Hau DI, Bárcenas-López DA, Núñez-Enríquez JC, Bekker-Méndez VC, Beltrán-Anaya FO, Jiménez-Hernández E, Ortíz-Maganda MP, Guerra-Castillo FX, Medina-Sanson A, Flores-Lujano J, Martín-Trejo JA, Peñaloza-González JG, Velázquez-Aviña MM, Torres-Nava JR, Hernández-Echáurregui GA, Espinosa-Elizondo RM, Gutiérrez-Rivera MDL, Sanchez-Hernandez R, Pérez-Saldívar ML, Flores-Villegas LV, Merino-Pasaye LE, Duarte-Rodríguez DA, Mata-Rocha M, Sepúlveda-Robles OA, Rosas-Vargas H, Hidalgo-Miranda A, Mejía-Aranguré JM, Jiménez-Morales S. Underexpression of LINC00173 in TCF3/PBX1-Positive Cases Is Associated With Poor Prognosis in Children With B-Cell Precursor Acute Lymphoblastic Leukemia. Front Oncol 2022; 12:887766. [PMID: 35719952 PMCID: PMC9201104 DOI: 10.3389/fonc.2022.887766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 04/21/2022] [Indexed: 11/13/2022] Open
Abstract
Background B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is the most frequent pediatric cancer worldwide. Despite improvements in treatment regimens, approximately 20% of the cases cannot be cured, highlighting the necessity for identifying new biomarkers to improve the current clinical and molecular risk stratification schemes. We aimed to investigate whether LINC00173 is a biomarker in ALL and to explore its expression level in other human cancer types. Methods A nested case-control study including Mexican children with BCP-ALL was conducted. LINC00173 expression was evaluated by qRT-PCR using hydrolysis probes. To validate our findings, RNA-seq expression data from BCP-ALL and normal tissues were retrieved from Therapeutically Applicable Research to Generate Effective Treatments (TARGET) and Genotype-Tissue Expression (GTEx) repositories, respectively. LINC00173 expression was also evaluated in solid tumors by downloading available data from The Cancer Genome Atlas (TCGA). Results A lower expression of LINC00173 in BCP-ALL cases compared to normal subjects was observed (p < 0.05). ALL patients who carry the TCF3/PBX1 fusion gene displayed lower expression of LINC00173 in contrast to other BCP-ALL molecular subtypes (p < 0.04). LINC00173 underexpression was associated with a high risk to relapse (HR = 1.946, 95% CI = 1.213-3.120) and die (HR = 2.073, 95% CI = 1.211-3.547). Patients with TCF3/PBX1 and underexpression of LINC00173 had the worst prognosis (DFS: HR = 12.24, 95% CI = 5.04-29.71; OS: HR = 11.19, 95% CI = 26-32). TCGA data analysis revealed that underexpression of LINC00173 is also associated with poor clinical outcomes in six new reported tumor types. Conclusion Our findings suggest that LINC00173 is a biomarker of poor prognosis in BCP-ALL and other types of cancer. We observed an association between the expression of LINC00173 and TCF3/PBX1 and the risk to relapse and die in BCP-ALL, which is worse in TCF3/PBX1-positive cases displaying underexpression of LINC00173. Experimental studies are needed to provide insight into the LINC00173 and TCF3/PBX relationship.
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Affiliation(s)
- Didier Ismael May-Hau
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico.,Programa de Maestría en Investigación Clínica Experimental en Salud, Universidad Nacional Autónoma de Mexico, México City, Mexico
| | - Diego Alberto Bárcenas-López
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico.,Programa de Doctorado, Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Juan Carlos Núñez-Enríquez
- Unidad de Investigación Médica en Epidemiología Clínica, Hospital de Pediatría "Dr. Silvestre Frenk Freund", Centro Médico Nacional "Siglo XXI", Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Vilma Carolina Bekker-Méndez
- Unidad de Investigación Médica en Inmunología e Infectología, Hospital de Infectología "Dr. Daniel Méndez Hernández", Centro Médico Nacional "La Raza", Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Fredy Omar Beltrán-Anaya
- Laboratorio de Epidemiología Clínica y Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo, Mexico
| | - Elva Jiménez-Hernández
- Servicio de Hematología Pediátrica, Hospital General "Gaudencio González Garza", Centro Médico Nacional "La Raza", Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Mónica Patricia Ortíz-Maganda
- Unidad de Investigación Médica en Inmunología e Infectología, Hospital de Infectología "Dr. Daniel Méndez Hernández", Centro Médico Nacional "La Raza", Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Francisco Xavier Guerra-Castillo
- Unidad de Investigación Médica en Inmunología e Infectología, Hospital de Infectología "Dr. Daniel Méndez Hernández", Centro Médico Nacional "La Raza", Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Aurora Medina-Sanson
- Departamento de Hemato-Oncología, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Janet Flores-Lujano
- Unidad de Investigación Médica en Epidemiología Clínica, Hospital de Pediatría "Dr. Silvestre Frenk Freund", Centro Médico Nacional "Siglo XXI", Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Jorge Alfonso Martín-Trejo
- Servicio de Hematología Pediátrica, Hospital de Pediatría "Dr. Silvestre Frenk Freund", Centro Médico Nacional "Siglo XXI", Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | | | | | - José Refugio Torres-Nava
- Servicio de Oncología, Hospital Pediátrico de Moctezuma, Secretaría de Salud de la Ciudad de México, Mexico City, Mexico
| | | | | | - María de Lourdes Gutiérrez-Rivera
- Servicio de Oncología Pediátrica, Hospital de Pediatría "Dr. Silvestre Frenk Freund", Centro Médico Nacional "Siglo XXI", Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Rodrigo Sanchez-Hernandez
- Servicio de Oncología Pediátrica, Hospital de Pediatría "Dr. Silvestre Frenk Freund", Centro Médico Nacional "Siglo XXI", Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - María Luisa Pérez-Saldívar
- Unidad de Investigación Médica en Epidemiología Clínica, Hospital de Pediatría "Dr. Silvestre Frenk Freund", Centro Médico Nacional "Siglo XXI", Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Luz Victoria Flores-Villegas
- Servicio de Hematología Pediátrica, Centro Médico Nacional "20 de Noviembre", Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado, Mexico City, Mexico
| | - Laura Elizabeth Merino-Pasaye
- Servicio de Hematología Pediátrica, Centro Médico Nacional "20 de Noviembre", Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado, Mexico City, Mexico
| | - David Aldebarán Duarte-Rodríguez
- Unidad de Investigación Médica en Epidemiología Clínica, Hospital de Pediatría "Dr. Silvestre Frenk Freund", Centro Médico Nacional "Siglo XXI", Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Minerva Mata-Rocha
- Unidad de Investigación Médica en Genética Humana, Hospital de Pediatría "Dr. Silvestre Frenk Freund", Centro Médico Nacional "Siglo XXI", Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Omar Alejandro Sepúlveda-Robles
- Unidad de Investigación Médica en Genética Humana, Hospital de Pediatría "Dr. Silvestre Frenk Freund", Centro Médico Nacional "Siglo XXI", Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Haydeé Rosas-Vargas
- Unidad de Investigación Médica en Genética Humana, Hospital de Pediatría "Dr. Silvestre Frenk Freund", Centro Médico Nacional "Siglo XXI", Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Alfredo Hidalgo-Miranda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Juan Manuel Mejía-Aranguré
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico.,Medicine Faculty, Universidad Autónoma de México, Mexico City, Mexico
| | - Silvia Jiménez-Morales
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
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Mata-Rocha M, Rangel-López A, Jimenez-Hernandez E, Nuñez-Enríquez JC, Morales-Castillo BA, Sánchez-Escobar N, Sepúlveda-Robles OA, Bravata-Alcántara JC, Nájera-Cortés AS, Pérez-Saldivar ML, Flores-Lujano J, Duarte-Rodríguez DA, Oviedo de Anda NA, Romero Tlalolini MDLA, Alaez Verson C, Martín-Trejo JA, Muñoz Medina JE, Gonzalez-Bonilla CR, Hernandez Cueto MDLA, Bekker-Méndez VC, Jiménez-Morales S, Medina-Sansón A, Amador-Sánchez R, Peñaloza-González JG, Torres-Nava JR, Espinosa-Elizondo RM, Cortés-Herrera B, Flores-Villegas LV, Merino-Pasaye LE, Gutierrez-Rivera MDL, Velazquez-Aviña MM, Santillan-Juarez JD, Gurrola-Silva A, Hernández Echáurregui GA, Hidalgo-Miranda A, Arellano Galindo J, Rosas-Vargas H, Mejía-Aranguré JM. Low Prevalence of ETV6::RUNX1 Fusion Gene in a Hispanic Population. Front Pediatr 2022; 10:837656. [PMID: 35685921 PMCID: PMC9171364 DOI: 10.3389/fped.2022.837656] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 04/06/2022] [Indexed: 11/13/2022] Open
Abstract
ETV6::RUNX1 is a genetic rearrangement of good prognosis in children with acute lymphoblastic leukemia (ALL). In Mexico, its prevalence is low in comparison with Caucasian populations. We developed a novel TaqMan one-step RT-qPCR approach to assess the prevalence of four genetic rearrangements in a cohort of Hispanic children with ALL from Mexico City. The prevalence of common fusion gene transcripts was as follows: TCF3::PBX1 7.7%; BCR::ABL1p 190 3.3%; and KMT2A::AFF1 2.8%, and ETV6::RUNX1was observed with low prevalence (10.5%) in comparison to that reported for developed countries. This is consistent with previous findings on Mexican children with ALL and similar to those reported on children from Hispanic populations. The confirmation of a low prevalence of ETV6::RUNX1 in children of a Hispanic origin represents an advancement in the description of genetic factors of ALL in these populations.
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Affiliation(s)
- Minerva Mata-Rocha
- CONACyT-Unidad de Investigacion Medica en Genetica Humana, Hospital de Pediatria, Centro Medico Nacional Siglo XXI, IMSS, Mexico City, Mexico
| | - Angelica Rangel-López
- Coordinacion de Investigacion en Salud, Unidad Habilitada de Apoyo al Predictamen, Centro Medico Siglo XXI, IMSS, Mexico City, Mexico
| | - Elva Jimenez-Hernandez
- Servicio de Hematologia Pediatrica, Hospital General “Gaudencio González Garza”, Centro Medico Nacional (CMN) “La Raza”, IMSS, Mexico City, Mexico
| | - Juan Carlos Nuñez-Enríquez
- Unidad de Investigacion Medica en Epidemiologia Clinica, Hospital de Pediatria, Centro Medico Nacional Siglo XXI, IMSS, Mexico City, Mexico
| | - Blanca Angélica Morales-Castillo
- Unidad de Investigacion Medica en Genética Humana, Hospital de Pediatria, Centro Medico Nacional Siglo XXI, IMSS, Mexico City, Mexico
| | - Norberto Sánchez-Escobar
- Unidad de Investigacion Medica en Genética Humana, Hospital de Pediatria, Centro Medico Nacional Siglo XXI, IMSS, Mexico City, Mexico
- Facultad de Medicina y Cirugía, UABJO, Oaxaca, Mexico
| | - Omar Alejandro Sepúlveda-Robles
- Unidad de Investigacion Medica en Genética Humana, Hospital de Pediatria, Centro Medico Nacional Siglo XXI, IMSS, Mexico City, Mexico
| | - Juan Carlos Bravata-Alcántara
- Laboratorio de Genética y Diagnóstico Molecular, Hospital Juárez de México, Secretaría de Salud (SSa), Mexico City, Mexico
| | - Alan Steve Nájera-Cortés
- Laboratorio de Genética y Diagnóstico Molecular, Hospital Juárez de México, Secretaría de Salud (SSa), Mexico City, Mexico
| | - María Luisa Pérez-Saldivar
- Unidad de Investigacion Medica en Epidemiologia Clinica, Hospital de Pediatria, Centro Medico Nacional Siglo XXI, IMSS, Mexico City, Mexico
| | - Janet Flores-Lujano
- Unidad de Investigacion Medica en Epidemiologia Clinica, Hospital de Pediatria, Centro Medico Nacional Siglo XXI, IMSS, Mexico City, Mexico
| | - David Aldebarán Duarte-Rodríguez
- Unidad de Investigacion Medica en Epidemiologia Clinica, Hospital de Pediatria, Centro Medico Nacional Siglo XXI, IMSS, Mexico City, Mexico
| | | | | | - Carmen Alaez Verson
- Laboratorio de Diagnóstico Genómico, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
| | - Jorge Alfonso Martín-Trejo
- Servicio de Hematologia, UMAE Hospital de Pediatria, Centro Medico Nacional Siglo XXI, IMSS, Mexico City, Mexico
| | - Jose Esteban Muñoz Medina
- Laboratorio Central de Epidemiología, Centro Médico Nacional “La Raza”, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | | | - Maria de los Angeles Hernandez Cueto
- Centro Médico Nacional La Raza, División de Laboratorios de Vigilancia e Investigación Epidemiológica, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - VC. Bekker-Méndez
- UIM en Inmunología e Infectología, Centro Médico Nacional “La Raza”, IMSS, Mexico City, Mexico
| | - Silvia Jiménez-Morales
- Laboratorio de Genomica del Cancer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Aurora Medina-Sansón
- Servicio de Oncología, Hospital Infantil de Mexico Federico Gómez, Secretaria de Salud, Mexico City, Mexico
| | - Raquel Amador-Sánchez
- Servicio de Hematologia Pediatrica, Hospital General Regional “Carlos McGregor Sanchez Navarro”, IMSS, Mexico City, Mexico
| | | | - José Refugio Torres-Nava
- Servicio de Oncología, Hospital Pediatrico de Moctezuma, Secretaria de Salud de la Ciudad de Mexico (SSCDMX), Mexico City, Mexico
| | | | - Beatriz Cortés-Herrera
- Servicio de Hematologia Pediatrica, Hospital General de Mexico, Secretaria de Salud, Mexico City, Mexico
| | | | | | | | | | | | - Alma Gurrola-Silva
- Servicio de Pediatría, Hospital Regional Tipo B de Alta Especialidad Bicentenario de la Independencia, Instituto de Seguridad Social al Servicio de los Trabajadores del Estado, Mexico City, Mexico
| | | | - Alfredo Hidalgo-Miranda
- Laboratorio de Genomica del Cancer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - José Arellano Galindo
- Unidad de Investigación en Enfermedades Infecciosas, Laboratorio de Virologia Clínica y Experimental, Hospital Infantil de Mexico Federico Gómez, Secretaria de Salud, Mexico City, Mexico
| | - Haydeé Rosas-Vargas
- Unidad de Investigacion Medica en Genética Humana, Hospital de Pediatria, Centro Medico Nacional Siglo XXI, IMSS, Mexico City, Mexico
| | - Juan Manuel Mejía-Aranguré
- Unidad de Investigacion Medica en Genética Humana, Hospital de Pediatria, Centro Medico Nacional Siglo XXI, IMSS, Mexico City, Mexico
- Laboratorio de Genomica del Cancer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
- Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
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12
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Dircio-Maldonado R, Castro-Oropeza R, Flores-Guzman P, Cedro-Tanda A, Beltran-Anaya FO, Hidalgo-Miranda A, Mayani H. Gene expression profiles and cytokine environments determine the in vitro proliferation and expansion capacities of human hematopoietic stem and progenitor cells. Hematology 2022; 27:476-487. [PMID: 35413231 DOI: 10.1080/16078454.2022.2061108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
OBJECTIVE The interplay between intrinsic and extrinsic elements involved in the physiology of hematopoietic cells is not completely understood. In the present study, we analyzed the transcriptional profiles of human cord blood-derived hematopoietic stem cells (HSCs), as well as myeloid (MPCs) and erythroid (EPCs) progenitors, and assessed their proliferation and expansion kinetics in vitro. METHODS All cell populations were obtained by cell-sorting, and were cultured in liquid cultures supplemented with different cytokine combinations. Their gene expression profiles were determined by RNA microarrays right after cell-sorting, before culture. RESULTS HSCs showed the highest proliferation and expansion capacities in culture, and were found to be more closely related, in transcriptional terms, to MPCs than to EPCs. This correlated with the fact that after 30 days, only cultures initiated with HSCs and MPCs were sustained. Expression of cell cycle and cell division-related genes was enriched in EPCs. Such cells showed significantly higher proliferation than MPCs, however, their expansion potential was reduced, so that cultures initiated with EPCs declined after 15 days and became exhausted by day 30. Proliferation and expansion of HSCs and EPCs were higher in the presence of a cytokine combination that favors erythropoiesis, whereas the growth of MPCs was higher under a cytokine combination that favors myelopoiesis. CONCLUSION This study shows a correlation between the transcriptional profiles of HSCs, MPCs, and EPCs, and their respective in vitro growth under particular culture conditions. These results may be relevant in the development of ex vivo systems for the expansion of hematopoietic cells for clinical application.
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Affiliation(s)
- Roberto Dircio-Maldonado
- Hematopoietic Stem Cells Laboratory, IMSS National Medical Center, Oncology Research Unit, Oncology Hospital, Mexico City, Mexico
| | - Rosario Castro-Oropeza
- Hematopoietic Stem Cells Laboratory, IMSS National Medical Center, Oncology Research Unit, Oncology Hospital, Mexico City, Mexico
| | - Patricia Flores-Guzman
- Hematopoietic Stem Cells Laboratory, IMSS National Medical Center, Oncology Research Unit, Oncology Hospital, Mexico City, Mexico
| | - Alberto Cedro-Tanda
- National Institute of Genomic Medicine, National Ministry of Health, Mexico City, Mexico
| | | | | | - Hector Mayani
- Hematopoietic Stem Cells Laboratory, IMSS National Medical Center, Oncology Research Unit, Oncology Hospital, Mexico City, Mexico
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13
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Cedro-Tanda A, Gómez-Romero L, de Anda-Jauregui G, Garnica-López D, Alfaro-Mora Y, Sánchez-Xochipa S, García-García EF, Mendoza-Vargas A, Frías-Jiménez EJ, Moreno B, Campos-Romero A, Moreno-Camacho JL, Alcantar-Fernández J, Ortíz-Ramírez J, Benitez-González M, Trejo-González R, Aguirre-Chavarría D, Núñez-Martínez ME, Uribe-Figueroa L, Angulo O, Ruiz R, Hidalgo-Miranda A, Herrera LA. Early Genomic, Epidemiological, and Clinical Description of the SARS-CoV-2 Omicron Variant in Mexico City. Viruses 2022; 14:545. [PMID: 35336952 PMCID: PMC8950183 DOI: 10.3390/v14030545] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 02/26/2022] [Accepted: 03/02/2022] [Indexed: 01/27/2023] Open
Abstract
Omicron is the most mutated SARS-CoV-2 variant-a factor that can affect transmissibility, disease severity, and immune evasiveness. Its genomic surveillance is important in cities with millions of inhabitants and an economic center, such as Mexico City. Results. From 16 November to 31 December 2021, we observed an increase of 88% in Omicron prevalence in Mexico City. We explored the R346K substitution, prevalent in 42% of Omicron variants, known to be associated with immune escape by monoclonal antibodies. In a phylogenetic analysis, we found several independent exchanges between Mexico and the world, and there was an event followed by local transmission that gave rise to most of the Omicron diversity in Mexico City. A haplotype analysis revealed that there was no association between haplotype and vaccination status. Among the 66% of patients who have been vaccinated, no reported comorbidities were associated with Omicron; the presence of odynophagia and the absence of dysgeusia were significant predictor symptoms for Omicron, and the RT-qPCR Ct values were lower for Omicron. Conclusions. Genomic surveillance is key to detecting the emergence and spread of SARS-CoV-2 variants in a timely manner, even weeks before the onset of an infection wave, and can inform public health decisions and detect the spread of any mutation that may affect therapeutic efficacy.
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Affiliation(s)
- Alberto Cedro-Tanda
- Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (G.d.A.-J.); (D.G.-L.); (Y.A.-M.); (S.S.-X.); (E.F.G.-G.); (A.M.-V.); (E.J.F.-J.); (B.M.)
| | - Laura Gómez-Romero
- Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (G.d.A.-J.); (D.G.-L.); (Y.A.-M.); (S.S.-X.); (E.F.G.-G.); (A.M.-V.); (E.J.F.-J.); (B.M.)
| | - Guillermo de Anda-Jauregui
- Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (G.d.A.-J.); (D.G.-L.); (Y.A.-M.); (S.S.-X.); (E.F.G.-G.); (A.M.-V.); (E.J.F.-J.); (B.M.)
- Researchers for Mexico (Previously Cátedras CONACYT para Jóvenes Investigadores), Av. de los Insurgentes Sur 1582, Crédito Constructor, Benito Juárez, Mexico City 03940, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México (UNAM), Circuito Centro Cultural S/N, Cd. Universitaria, Delegación Coyoacán, Mexico City 04510, Mexico
| | - Dora Garnica-López
- Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (G.d.A.-J.); (D.G.-L.); (Y.A.-M.); (S.S.-X.); (E.F.G.-G.); (A.M.-V.); (E.J.F.-J.); (B.M.)
| | - Yair Alfaro-Mora
- Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (G.d.A.-J.); (D.G.-L.); (Y.A.-M.); (S.S.-X.); (E.F.G.-G.); (A.M.-V.); (E.J.F.-J.); (B.M.)
| | - Sonia Sánchez-Xochipa
- Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (G.d.A.-J.); (D.G.-L.); (Y.A.-M.); (S.S.-X.); (E.F.G.-G.); (A.M.-V.); (E.J.F.-J.); (B.M.)
| | - Eulices F. García-García
- Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (G.d.A.-J.); (D.G.-L.); (Y.A.-M.); (S.S.-X.); (E.F.G.-G.); (A.M.-V.); (E.J.F.-J.); (B.M.)
| | - Alfredo Mendoza-Vargas
- Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (G.d.A.-J.); (D.G.-L.); (Y.A.-M.); (S.S.-X.); (E.F.G.-G.); (A.M.-V.); (E.J.F.-J.); (B.M.)
| | - Emmanuel J. Frías-Jiménez
- Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (G.d.A.-J.); (D.G.-L.); (Y.A.-M.); (S.S.-X.); (E.F.G.-G.); (A.M.-V.); (E.J.F.-J.); (B.M.)
| | - Bernardo Moreno
- Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (G.d.A.-J.); (D.G.-L.); (Y.A.-M.); (S.S.-X.); (E.F.G.-G.); (A.M.-V.); (E.J.F.-J.); (B.M.)
| | - Abraham Campos-Romero
- Innovation and Research Department, Salud Digna, Culiacan 80000, Mexico; (A.C.-R.); (J.A.-F.)
| | | | | | - Jesús Ortíz-Ramírez
- Hospital General Ajusco Medio, Secretaría de Salud de la Ciudad de México (SEDESA), Encinos 41, Miguel Hidalgo 4ta Secc, Tlalpan, Mexico City 14250, Mexico; (J.O.-R.); (M.B.-G.)
| | - Mariana Benitez-González
- Hospital General Ajusco Medio, Secretaría de Salud de la Ciudad de México (SEDESA), Encinos 41, Miguel Hidalgo 4ta Secc, Tlalpan, Mexico City 14250, Mexico; (J.O.-R.); (M.B.-G.)
| | - Roxana Trejo-González
- Centro Médico ABC, Av. Carlos Fernández Graef 154, Santa Fe, Contadero, Cuajimalpa de Morelos, Mexico City 05330, Mexico; (R.T.-G.); (D.A.-C.); (M.E.N.-M.)
| | - Daniel Aguirre-Chavarría
- Centro Médico ABC, Av. Carlos Fernández Graef 154, Santa Fe, Contadero, Cuajimalpa de Morelos, Mexico City 05330, Mexico; (R.T.-G.); (D.A.-C.); (M.E.N.-M.)
| | - Marcela E. Núñez-Martínez
- Centro Médico ABC, Av. Carlos Fernández Graef 154, Santa Fe, Contadero, Cuajimalpa de Morelos, Mexico City 05330, Mexico; (R.T.-G.); (D.A.-C.); (M.E.N.-M.)
| | - Laura Uribe-Figueroa
- Laboratorio Arion Genética, Margaritas 440-Bis, Hacienda de Guadalupe Chimalistac, Chimalistac, Álvaro Obregón, Mexico City 01050, Mexico;
| | - Ofelia Angulo
- Secretaría de Educación, Ciencia, Tecnología e Innovación de la Ciudad de México (SECTEI), Av Chapultepec 49, Colonia Centro, Cuauhtémoc, Mexico City 06010, Mexico; (O.A.); (R.R.)
| | - Rosaura Ruiz
- Secretaría de Educación, Ciencia, Tecnología e Innovación de la Ciudad de México (SECTEI), Av Chapultepec 49, Colonia Centro, Cuauhtémoc, Mexico City 06010, Mexico; (O.A.); (R.R.)
| | - Alfredo Hidalgo-Miranda
- Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (G.d.A.-J.); (D.G.-L.); (Y.A.-M.); (S.S.-X.); (E.F.G.-G.); (A.M.-V.); (E.J.F.-J.); (B.M.)
| | - Luis A. Herrera
- Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (G.d.A.-J.); (D.G.-L.); (Y.A.-M.); (S.S.-X.); (E.F.G.-G.); (A.M.-V.); (E.J.F.-J.); (B.M.)
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Av. San Fernando 22, Belisario Domínguez Secc 16, Tlalpan, Mexico City 14080, Mexico
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14
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Cisneros-Villanueva M, Hidalgo-Pérez L, Rios-Romero M, Cedro-Tanda A, Ruiz-Villavicencio CA, Page K, Hastings R, Fernandez-Garcia D, Allsopp R, Fonseca-Montaño MA, Jimenez-Morales S, Padilla-Palma V, Shaw JA, Hidalgo-Miranda A. Cell-free DNA analysis in current cancer clinical trials: a review. Br J Cancer 2022; 126:391-400. [PMID: 35027672 PMCID: PMC8810765 DOI: 10.1038/s41416-021-01696-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 12/06/2021] [Accepted: 12/23/2021] [Indexed: 12/13/2022] Open
Abstract
Cell-free DNA (cfDNA) analysis represents a promising method for the diagnosis, treatment selection and clinical follow-up of cancer patients. Although its general methodological feasibility and usefulness has been demonstrated, several issues related to standardisation and technical validation must be addressed for its routine clinical application in cancer. In this regard, most cfDNA clinical applications are still limited to clinical trials, proving its value in several settings. In this paper, we review the current clinical trials involving cfDNA/ctDNA analysis and highlight those where it has been useful for patient stratification, treatment follow-up or development of novel approaches for early diagnosis. Our query included clinical trials, including the terms 'cfDNA', 'ctDNA', 'liquid biopsy' AND 'cancer OR neoplasm' in the FDA and EMA public databases. We identified 1370 clinical trials (FDA = 1129, EMA = 241) involving liquid-biopsy analysis in cancer. These clinical trials show promising results for the early detection of cancer and confirm cfDNA as a tool for real-time monitoring of acquired therapy resistance, accurate disease-progression surveillance and improvement of treatment, situations that result in a better quality of life and extended overall survival for cancer patients.
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Affiliation(s)
- M Cisneros-Villanueva
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de Mexico, 14610, Mexico City, Mexico
| | - L Hidalgo-Pérez
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de Mexico, 14610, Mexico City, Mexico
| | - M Rios-Romero
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de Mexico, 14610, Mexico City, Mexico
| | - A Cedro-Tanda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de Mexico, 14610, Mexico City, Mexico
| | - C A Ruiz-Villavicencio
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de Mexico, 14610, Mexico City, Mexico
| | - K Page
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - R Hastings
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - D Fernandez-Garcia
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - R Allsopp
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - M A Fonseca-Montaño
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de Mexico, 14610, Mexico City, Mexico
| | - S Jimenez-Morales
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de Mexico, 14610, Mexico City, Mexico
| | - V Padilla-Palma
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de Mexico, 14610, Mexico City, Mexico
| | - J A Shaw
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK.
| | - A Hidalgo-Miranda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de Mexico, 14610, Mexico City, Mexico.
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15
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Meneses-Medina MI, Hernandez-Felix JH, Anaya-Sánchez LG, Valenzuela-Vidales AK, Rosas-Camargo V, Martos-Armendariz EO, Torres-Valdiviezo LI, Cedro-Tanda A, Noguez-Ramos A, Herrera-Montalvo LA, Hidalgo-Miranda A, Valdez-Echeverria RD, Galindo-Fraga A, Huitzil-Meléndez FD. SARS-CoV-2 Infection Rate in Patients With Cancer and Health Care Workers in a Chemoradiotherapy Unit During the Pandemic: A Prospective Cohort in Mexico. JCO Glob Oncol 2021; 7:1639-1646. [PMID: 34898237 PMCID: PMC8667990 DOI: 10.1200/go.21.00207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Cancer treatment during the COVID-19 pandemic represents a challenge. Hospital visits to receive treatment and interaction with health care workers (HCW) represent potential contagious events. We aimed to determine SARS-CoV-2 infection rate among patients with cancer and HCW of a chemoradiotherapy unit localized in a center designated as a COVID-19 priority facility in Mexico City. We also determined the diagnostic performance of a clinical questionnaire (CQ) as a screening tool and anti–SARS-CoV-2 antibody seroconversion rate. Biweekly RT-PCR for SARS-CoV-2 detects asymptomatic infections and prevents transmission in an oncological unit![]()
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Affiliation(s)
- Monica Isabel Meneses-Medina
- Departamento de Hematología y Oncología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México, México
| | - Jorge Humberto Hernandez-Felix
- Departamento de Hematología y Oncología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México, México.,Facultad de Medicina, Universidad Autónoma de Coahuila Unidad Torreón, Torreón, México
| | - Luis Guillermo Anaya-Sánchez
- Departamento de Hematología y Oncología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México, México.,Escuela de Ciencias, Departamento de Ciencias de la Salud, Universidad de las Américas Puebla, Puebla, México
| | - Ana Karen Valenzuela-Vidales
- Departamento de Hematología y Oncología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México, México
| | - Vanessa Rosas-Camargo
- Departamento de Hematología y Oncología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México, México
| | - Edgar Omar Martos-Armendariz
- Departamento de Hematología y Oncología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México, México.,Facultad de Ciencias de la Salud, Universidad Juárez del Estado de Durango, Gómez Palacio, México
| | - Lucero Itzel Torres-Valdiviezo
- Departamento de Hematología y Oncología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México, México.,Escuela de Ciencias, Departamento de Ciencias de la Salud, Universidad de las Américas Puebla, Puebla, México
| | | | - Alejandro Noguez-Ramos
- Departamento de Hematología y Oncología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México, México
| | - Luis Alonso Herrera-Montalvo
- Instituto Nacional de Medicina Genómica, Ciudad de México, México.,Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autonoma de México, Ciudad de México, México
| | | | - Raymundo David Valdez-Echeverria
- Departamento de Hematología y Oncología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México, México
| | - Arturo Galindo-Fraga
- Subdirección de Epidemiología Hospitalaria, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México, México
| | - Fidel David Huitzil-Meléndez
- Departamento de Hematología y Oncología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México, México
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16
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Jiménez-Morales S, Núñez-Enríquez JC, Cruz-Islas J, Bekker-Méndez VC, Jiménez-Hernández E, Medina-Sanson A, Olarte-Carrillo I, Martínez-Tovar A, Flores-Lujano J, Ramírez-Bello J, Pérez-Saldívar ML, Martín-Trejo JA, Pérez-Lorenzana H, Amador-Sánchez R, Mora-Ríos FG, Peñaloza-González JG, Duarte-Rodríguez DA, Torres-Nava JR, Flores-Bautista JE, Espinosa-Elizondo RM, Román-Zepeda PF, Flores-Villegas LV, Tamez-Gómez EL, López-García VH, Lara-Ramos JR, González-Ulivarri JE, Martínez-Silva SI, Espinoza-Anrubio G, Almeida-Hernández C, Ramírez-Colorado R, Hernández-Mora L, García-López LR, Cruz-Ojeda GA, Godoy-Esquivel AE, Contreras-Hernández I, Medina-Hernández A, López-Caballero MG, Hernández-Pineda NA, Granados-Kraulles J, Rodríguez-Vázquez MA, Torres-Valle D, Cortés-Reyes C, Medrano-López F, Pérez-Gómez JA, Martínez-Ríos A, Aguilar-De-Los-Santos A, Serafin-Díaz B, Gutiérrez-Rivera MDL, Merino-Pasaye LE, Vargas-Alarcón G, Mata-Rocha M, Sepúlveda-Robles OA, Rosas-Vargas H, Hidalgo-Miranda A, Mejía-Aranguré JM. Association Analysis Between the Functional Single Nucleotide Variants in miR-146a, miR-196a-2, miR-499a, and miR-612 With Acute Lymphoblastic Leukemia. Front Oncol 2021; 11:762063. [PMID: 34804964 PMCID: PMC8602911 DOI: 10.3389/fonc.2021.762063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/12/2021] [Indexed: 01/26/2023] Open
Abstract
Background Acute lymphoblastic leukemia (ALL) is characterized by an abnormal proliferation of immature lymphocytes, in whose development involves both environmental and genetic factors. It is well known that single nucleotide polymorphisms (SNPs) in coding and noncoding genes contribute to the susceptibility to ALL. This study aims to determine whether SNPs in miR-146a, miR-196a-2, miR-499a, and miR-612 genes are associated with the risk to ALL in pediatric Mexican population. Methods A multicenter case-control study was carried out including patients with de novo diagnosis of ALL and healthy subjects as control group. The DNA samples were obtained from saliva and peripheral blood, and the genotyping of rs2910164, rs12803915, rs11614913, and rs3746444 was performed using the 5′exonuclease technique. Gene-gene interaction was evaluated by the multifactor dimensionality reduction (MDR) software. Results miR-499a rs3746444 showed significant differences among cases and controls. The rs3746444G allele was found as a risk factor to ALL (OR, 1.6 [95% CI, 1.05–2.5]; p = 0.028). The homozygous GG genotype of rs3746444 confers higher risk to ALL than the AA genotype (OR, 5.3 [95% CI, 1.23–23.4]; p = 0.01). Moreover, GG genotype highly increases the risk to ALL in male group (OR, 17.6 [95% CI, 1.04–298.9]; p = 0.00393). In addition, an association in a gender-dependent manner among SNPs located in miR-146a and miR-196a-2 genes and ALL susceptibility was found. Conclusion Our findings suggest that SNP located in miR-499a, miR-146a, and miR-196a-2 genes confer risk to ALL in Mexican children. Experimental analysis to decipher the role of these SNPs in human hematopoiesis could improve our understanding of the molecular mechanism underlying the development of ALL.
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Affiliation(s)
- Silvia Jiménez-Morales
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Juan Carlos Núñez-Enríquez
- Unidad de Investigación Médica en Epidemiología Clínica, Unidad Medica de Alta Especialidad (UMAE) Hospital de Pediatría "Dr. Silvestre Frenk Freund", Centro Médico Nacional "Siglo XXI", Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Jazmín Cruz-Islas
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Vilma Carolina Bekker-Méndez
- Unidad de Investigación Médica en Inmunología e Infectología, Hospital de Infectología "Dr. Daniel Méndez Hernández", "La Raza", IMSS, Mexico City, Mexico
| | - Elva Jiménez-Hernández
- Servicio de Hematología Pediátrica, Hospital General "Gaudencio González Garza", Centro Médico Nacional "La Raza", IMSS, Mexico City, Mexico
| | - Aurora Medina-Sanson
- Departamento de Hemato-Oncología, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Irma Olarte-Carrillo
- Servicio de Hematología, Departamento de Investigación, Hospital General de México Dr. Eduardo Liceaga, Mexico City, Mexico
| | - Adolfo Martínez-Tovar
- Servicio de Hematología, Departamento de Investigación, Hospital General de México Dr. Eduardo Liceaga, Mexico City, Mexico
| | - Janet Flores-Lujano
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Julian Ramírez-Bello
- Departamento de Endocrinología, Instituto Nacional de Cardiología, Ignacio Chávez, México City, Mexico
| | | | - Jorge Alfonso Martín-Trejo
- Servicio de Hematología Pediátrica Unidad Medica de Alta Especialidad (UMAE) Hospital de Pediatría "Dr. Silvestre Frenk Freund", Centro Médico Nacional "Siglo XXI", IMSS, Mexico City, Mexico
| | - Héctor Pérez-Lorenzana
- Servicio de Cirugía Pediátrica, Hospital General "Gaudencio González Garza", Centro Médico Nacional (CMN) "La Raza", IMSS, Mexico City, Mexico
| | - Raquel Amador-Sánchez
- Servicio de Hematología Pediátrica, Hospital General Regional "Carlos McGregor Sánchez Navarro", IMSS, Mexico City, Mexico
| | - Felix Gustavo Mora-Ríos
- Cirugía Pediátrica, Hospital Regional "General Ignacio Zaragoza", Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado (ISSSTE), Mexico City, Mexico
| | | | | | - José Refugio Torres-Nava
- Servicio de Oncología, Hospital Pediátrico de Moctezuma, Secretaría de Salud de la Ciudad de México (SSCDMX), Mexico City, Mexico
| | | | | | - Pedro Francisco Román-Zepeda
- Coordinación Clínica y Servicio de Cirugía Pediátrica, Hospital General Regional (HGR) No. 1 "Dr. Carlos Mac Gregor Sánchez Navarro", IMSS, Mexico City, Mexico
| | | | | | | | | | | | | | - Gilberto Espinoza-Anrubio
- Servicio de Pediatría, Hospital General Zona (HGZ) No. 8 "Dr. Gilberto Flores Izquierdo" IMSS, Mexico City, Mexico
| | - Carolina Almeida-Hernández
- Jefatura de Enseñanza, Hospital General de Ecatepec "Las Américas", Instituto de Salud del Estado de México (ISEM), Mexico City, Mexico
| | | | - Luis Hernández-Mora
- Jefatura de Enseñanza, Hospital Pediátrico San Juan de Aragón, Secretaría de Salud (SS), Mexico City, Mexico
| | | | | | | | | | | | | | | | | | | | - Delfino Torres-Valle
- Coordinación Clínica y Pediatría del Hospital General de Zona 71, IMSS, Mexico City, Mexico
| | - Carlos Cortés-Reyes
- Pediatría, Hospital General Dr. Darío Fernández Fierro, ISSSTE, Mexico City, Mexico
| | - Francisco Medrano-López
- Coordinación Clínica y Servicio de Pediatría, HGR No. 72 "Dr. Vicente Santos Guajardo", IMSS, Mexico City, Mexico
| | - Jessica Arleet Pérez-Gómez
- Coordinación Clínica y Servicio de Pediatría, HGR No. 72 "Dr. Vicente Santos Guajardo", IMSS, Mexico City, Mexico
| | - Annel Martínez-Ríos
- Cirugía Pediátrica del Hospital Regional "General Ignacio Zaragoza", ISSSTE, Mexico City, Mexico
| | | | - Berenice Serafin-Díaz
- Coordinación Clínica y Pediatría del Hospital General de Zona 57, IMSS, Mexico City, Mexico
| | - María de Lourdes Gutiérrez-Rivera
- Servicio de Oncología Pediátrica Unidad Medica de Alta Especialidad (UMAE) Hospital de Pediatría "Dr. Silvestre Frenk Freund", IMSS, Mexico City, Mexico
| | | | - Gilberto Vargas-Alarcón
- Departamento of Biología Molecular, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, Mexico
| | - Minerva Mata-Rocha
- Unidad de Investigación Médica en Genética Humana, Unidad Medica de Alta Especialidad (UMAE) Hospital de Pediatría "Dr. Silvestre Frenk Freund", Centro Médico Nacional "Siglo XXI", IMSS, Mexico City, Mexico
| | - Omar Alejandro Sepúlveda-Robles
- Unidad de Investigación Médica en Genética Humana, Unidad Medica de Alta Especialidad (UMAE) Hospital de Pediatría "Dr. Silvestre Frenk Freund", Centro Médico Nacional "Siglo XXI", IMSS, Mexico City, Mexico
| | - Haydeé Rosas-Vargas
- Unidad de Investigación Médica en Genética Humana, Unidad Medica de Alta Especialidad (UMAE) Hospital de Pediatría "Dr. Silvestre Frenk Freund", Centro Médico Nacional "Siglo XXI", IMSS, Mexico City, Mexico
| | - Alfredo Hidalgo-Miranda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Juan Manuel Mejía-Aranguré
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico.,Unidad de Investigación Médica en Genética Humana, Unidad Medica de Alta Especialidad (UMAE) Hospital de Pediatría "Dr. Silvestre Frenk Freund", Centro Médico Nacional "Siglo XXI", IMSS, Mexico City, Mexico.,Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
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17
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Jiménez-Morales S, Aranda-Uribe IS, Pérez-Amado CJ, Ramírez-Bello J, Hidalgo-Miranda A. Mechanisms of Immunosuppressive Tumor Evasion: Focus on Acute Lymphoblastic Leukemia. Front Immunol 2021; 12:737340. [PMID: 34867958 PMCID: PMC8636671 DOI: 10.3389/fimmu.2021.737340] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 10/27/2021] [Indexed: 01/05/2023] Open
Abstract
Acute lymphoblastic leukemia (ALL) is a malignancy with high heterogeneity in its biological features and treatments. Although the overall survival (OS) of patients with ALL has recently improved considerably, owing to the application of conventional chemo-therapeutic agents, approximately 20% of the pediatric cases and 40-50% of the adult patients relapse during and after the treatment period. The potential mechanisms that cause relapse involve clonal evolution, innate and acquired chemoresistance, and the ability of ALL cells to escape the immune-suppressive tumor response. Currently, immunotherapy in combination with conventional treatment is used to enhance the immune response against tumor cells, thereby significantly improving the OS in patients with ALL. Therefore, understanding the mechanisms of immune evasion by leukemia cells could be useful for developing novel therapeutic strategies.
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Affiliation(s)
- Silvia Jiménez-Morales
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Ivan Sammir Aranda-Uribe
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
- Departamento de Farmacología, División de Ciencias de la Salud, Universidad de Quintana Roo, Quintana Roo, Mexico
| | - Carlos Jhovani Pérez-Amado
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
- Programa de Doctorado en Ciencias Bioquímicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Julian Ramírez-Bello
- Departamento de Endocrinología, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, Mexico
| | - Alfredo Hidalgo-Miranda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
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18
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Cedro-Tanda A, Gómez-Romero L, Alcaraz N, de Anda-Jauregui G, Peñaloza F, Moreno B, Escobar-Arrazola MA, Ramirez-Vega OA, Munguia-Garza P, Garcia-Cardenas F, Cisneros-Villanueva M, Moreno-Camacho JL, Rodriguez-Gallegos J, Luna-Ruiz Esparza MA, Fernández Rojas MA, Mendoza-Vargas A, Reyes-Grajeda JP, Campos-Romero A, Angulo O, Ruiz R, Sheinbaum-Pardo C, Sifuentes-Osornio J, Kershenobich D, Hidalgo-Miranda A, Herrera LA. The Evolutionary Landscape of SARS-CoV-2 Variant B.1.1.519 and Its Clinical Impact in Mexico City. Viruses 2021; 13:2182. [PMID: 34834987 PMCID: PMC8617872 DOI: 10.3390/v13112182] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/21/2021] [Accepted: 10/25/2021] [Indexed: 12/15/2022] Open
Abstract
The SARS-CoV-2 pandemic is one of the most concerning health problems around the globe. We reported the emergence of SARS-CoV-2 variant B.1.1.519 in Mexico City. We reported the effective reproduction number (Rt) of B.1.1.519 and presented evidence of its geographical origin based on phylogenetic analysis. We also studied its evolution via haplotype analysis and identified the most recurrent haplotypes. Finally, we studied the clinical impact of B.1.1.519. The B.1.1.519 variant was predominant between November 2020 and May 2021, reaching 90% of all cases sequenced in February 2021. It is characterized by three amino acid changes in the spike protein: T478K, P681H, and T732A. Its Rt varies between 0.5 and 2.9. Its geographical origin remain to be investigated. Patients infected with variant B.1.1.519 showed a highly significant adjusted odds ratio (aOR) increase of 1.85 over non-B.1.1.519 patients for developing a severe/critical outcome (p = 0.000296, 1.33-2.6 95% CI) and a 2.35-fold increase for hospitalization (p = 0.005, 1.32-4.34 95% CI). The continuous monitoring of this and other variants will be required to control the ongoing pandemic as it evolves.
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Affiliation(s)
- Alberto Cedro-Tanda
- Instituto Nacional de Medicina Genómica, INMEGEN, Periferico Sur 4809, Arenal Tepepan, Tlalpan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (N.A.); (G.d.A.-J.); (F.P.); (B.M.); (F.G.-C.); (M.C.-V.); (A.M.-V.); (J.P.R.-G.)
| | - Laura Gómez-Romero
- Instituto Nacional de Medicina Genómica, INMEGEN, Periferico Sur 4809, Arenal Tepepan, Tlalpan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (N.A.); (G.d.A.-J.); (F.P.); (B.M.); (F.G.-C.); (M.C.-V.); (A.M.-V.); (J.P.R.-G.)
| | - Nicolás Alcaraz
- Instituto Nacional de Medicina Genómica, INMEGEN, Periferico Sur 4809, Arenal Tepepan, Tlalpan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (N.A.); (G.d.A.-J.); (F.P.); (B.M.); (F.G.-C.); (M.C.-V.); (A.M.-V.); (J.P.R.-G.)
| | - Guillermo de Anda-Jauregui
- Instituto Nacional de Medicina Genómica, INMEGEN, Periferico Sur 4809, Arenal Tepepan, Tlalpan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (N.A.); (G.d.A.-J.); (F.P.); (B.M.); (F.G.-C.); (M.C.-V.); (A.M.-V.); (J.P.R.-G.)
- Cátedras CONACYT para Jóvenes Investigadores, CONACYT, Av. de los Insurgentes Sur 1582, Crédito Constructor, Benito Juárez, Mexico City 03940, Mexico
| | - Fernando Peñaloza
- Instituto Nacional de Medicina Genómica, INMEGEN, Periferico Sur 4809, Arenal Tepepan, Tlalpan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (N.A.); (G.d.A.-J.); (F.P.); (B.M.); (F.G.-C.); (M.C.-V.); (A.M.-V.); (J.P.R.-G.)
| | - Bernardo Moreno
- Instituto Nacional de Medicina Genómica, INMEGEN, Periferico Sur 4809, Arenal Tepepan, Tlalpan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (N.A.); (G.d.A.-J.); (F.P.); (B.M.); (F.G.-C.); (M.C.-V.); (A.M.-V.); (J.P.R.-G.)
| | - Marco A. Escobar-Arrazola
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Av. San Fernando 22, Belisario Domínguez Secc 16, Tlalpan, Mexico City 14080, Mexico; (M.A.E.-A.); (O.A.R.-V.); (P.M.-G.)
| | - Oscar A. Ramirez-Vega
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Av. San Fernando 22, Belisario Domínguez Secc 16, Tlalpan, Mexico City 14080, Mexico; (M.A.E.-A.); (O.A.R.-V.); (P.M.-G.)
| | - Paulina Munguia-Garza
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Av. San Fernando 22, Belisario Domínguez Secc 16, Tlalpan, Mexico City 14080, Mexico; (M.A.E.-A.); (O.A.R.-V.); (P.M.-G.)
| | - Francisco Garcia-Cardenas
- Instituto Nacional de Medicina Genómica, INMEGEN, Periferico Sur 4809, Arenal Tepepan, Tlalpan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (N.A.); (G.d.A.-J.); (F.P.); (B.M.); (F.G.-C.); (M.C.-V.); (A.M.-V.); (J.P.R.-G.)
| | - Mireya Cisneros-Villanueva
- Instituto Nacional de Medicina Genómica, INMEGEN, Periferico Sur 4809, Arenal Tepepan, Tlalpan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (N.A.); (G.d.A.-J.); (F.P.); (B.M.); (F.G.-C.); (M.C.-V.); (A.M.-V.); (J.P.R.-G.)
| | - Jose L. Moreno-Camacho
- Clinical Laboratory Division, Salud Digna, Culiacan, Sinaloa 80000, Mexico; (J.L.M.-C.); (J.R.-G.)
| | - Jorge Rodriguez-Gallegos
- Clinical Laboratory Division, Salud Digna, Culiacan, Sinaloa 80000, Mexico; (J.L.M.-C.); (J.R.-G.)
- Molecular Biology Laboratory, National Reference Center, Salud Digna, Tlalnepantla de Baz, Estado de Mexico 54075, Mexico
| | - Marco A. Luna-Ruiz Esparza
- Innovation and Research Department, Salud Digna, Culiacan, Sinaloa 80000, Mexico; (M.A.L.-R.E.); (M.A.F.R.); (A.C.-R.)
| | - Miguel A. Fernández Rojas
- Innovation and Research Department, Salud Digna, Culiacan, Sinaloa 80000, Mexico; (M.A.L.-R.E.); (M.A.F.R.); (A.C.-R.)
| | - Alfredo Mendoza-Vargas
- Instituto Nacional de Medicina Genómica, INMEGEN, Periferico Sur 4809, Arenal Tepepan, Tlalpan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (N.A.); (G.d.A.-J.); (F.P.); (B.M.); (F.G.-C.); (M.C.-V.); (A.M.-V.); (J.P.R.-G.)
| | - Juan Pablo Reyes-Grajeda
- Instituto Nacional de Medicina Genómica, INMEGEN, Periferico Sur 4809, Arenal Tepepan, Tlalpan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (N.A.); (G.d.A.-J.); (F.P.); (B.M.); (F.G.-C.); (M.C.-V.); (A.M.-V.); (J.P.R.-G.)
| | - Abraham Campos-Romero
- Innovation and Research Department, Salud Digna, Culiacan, Sinaloa 80000, Mexico; (M.A.L.-R.E.); (M.A.F.R.); (A.C.-R.)
| | - Ofelia Angulo
- Secretaría de Educación, Ciencia, Tecnología e Innovacion, Av Chapultepec 49, Colonia Centro, Cuauhtémoc, Mexico City 06010, Mexico; (O.A.); (R.R.)
| | - Rosaura Ruiz
- Secretaría de Educación, Ciencia, Tecnología e Innovacion, Av Chapultepec 49, Colonia Centro, Cuauhtémoc, Mexico City 06010, Mexico; (O.A.); (R.R.)
| | - Claudia Sheinbaum-Pardo
- Gobierno de la Ciudad de México, Antiguo Palacio del Ayuntamiento, Avenida Plaza de la Constitución 2, Colonia Centro, Mexico City 06010, Mexico;
| | - José Sifuentes-Osornio
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Vasco de Quiroga 15, Belisario Domínguez Secc 16, Tlalpan, Mexico City 14080, Mexico; (J.S.-O.); (D.K.)
| | - David Kershenobich
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Vasco de Quiroga 15, Belisario Domínguez Secc 16, Tlalpan, Mexico City 14080, Mexico; (J.S.-O.); (D.K.)
| | - Alfredo Hidalgo-Miranda
- Instituto Nacional de Medicina Genómica, INMEGEN, Periferico Sur 4809, Arenal Tepepan, Tlalpan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (N.A.); (G.d.A.-J.); (F.P.); (B.M.); (F.G.-C.); (M.C.-V.); (A.M.-V.); (J.P.R.-G.)
| | - Luis A. Herrera
- Instituto Nacional de Medicina Genómica, INMEGEN, Periferico Sur 4809, Arenal Tepepan, Tlalpan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (N.A.); (G.d.A.-J.); (F.P.); (B.M.); (F.G.-C.); (M.C.-V.); (A.M.-V.); (J.P.R.-G.)
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Av. San Fernando 22, Belisario Domínguez Secc 16, Tlalpan, Mexico City 14080, Mexico; (M.A.E.-A.); (O.A.R.-V.); (P.M.-G.)
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19
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Rodríguez-Maldonado AP, Vázquez-Pérez JA, Cedro-Tanda A, Taboada B, Boukadida C, Wong-Arámbula C, Nuñez-García TE, Cruz-Ortiz N, Barrera-Badillo G, Hernández-Rivas L, López-Martínez I, Mendoza-Vargas A, Reyes-Grajeda JP, Alcaraz N, Peñaloza-Figueroa F, Gonzalez-Barrera D, Rangel-DeLeon D, Herrera-Montalvo LA, Mejía-Nepomuceno F, Hernández-Terán A, Mújica-Sánchez M, Becerril-Vargas E, Martínez-Orozco JA, Pérez-Padilla R, Salas-Hernández J, Sanchez-Flores A, Isa P, Matías-Florentino M, Ávila-Ríos S, Muñoz-Medina JE, Grajales-Muñiz C, Salas-Lais AG, Santos Coy-Arechavaleta A, Hidalgo-Miranda A, Arias CF, Ramírez-González JE. Emergence and spread of the potential variant of interest (VOI) B.1.1.519 of SARS-CoV-2 predominantly present in Mexico. Arch Virol 2021; 166:3173-3177. [PMID: 34448936 PMCID: PMC8390838 DOI: 10.1007/s00705-021-05208-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/27/2021] [Indexed: 11/28/2022]
Abstract
SARS-CoV-2 variants emerged in late 2020, and at least three variants of concern (B.1.1.7, B.1.351, and P1) have been reported by WHO. These variants have several substitutions in the spike protein that affect receptor binding; they exhibit increased transmissibility and may be associated with reduced vaccine effectiveness. In the present work, we report the identification of a potential variant of interest, harboring the mutations T478K, P681H, and T732A in the spike protein, within the newly named lineage B.1.1.519, that rapidly outcompeted the preexisting variants in Mexico and has been the dominant virus in the country during the first trimester of 2021.
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Affiliation(s)
- Abril Paulina Rodríguez-Maldonado
- Dirección General de Epidemiología, Instituto de Diagnóstico y Referencia Epidemiológicos "Dr. Manuel Martínez Báez, Mexico City, Mexico
| | | | | | - Blanca Taboada
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Celia Boukadida
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias "Ismael Cosío Villegas", Mexico City, Mexico
| | - Claudia Wong-Arámbula
- Dirección General de Epidemiología, Instituto de Diagnóstico y Referencia Epidemiológicos "Dr. Manuel Martínez Báez, Mexico City, Mexico
| | - Tatiana Ernestina Nuñez-García
- Dirección General de Epidemiología, Instituto de Diagnóstico y Referencia Epidemiológicos "Dr. Manuel Martínez Báez, Mexico City, Mexico
| | - Natividad Cruz-Ortiz
- Dirección General de Epidemiología, Instituto de Diagnóstico y Referencia Epidemiológicos "Dr. Manuel Martínez Báez, Mexico City, Mexico
| | - Gisela Barrera-Badillo
- Dirección General de Epidemiología, Instituto de Diagnóstico y Referencia Epidemiológicos "Dr. Manuel Martínez Báez, Mexico City, Mexico
| | - Lucía Hernández-Rivas
- Dirección General de Epidemiología, Instituto de Diagnóstico y Referencia Epidemiológicos "Dr. Manuel Martínez Báez, Mexico City, Mexico
| | - Irma López-Martínez
- Dirección General de Epidemiología, Instituto de Diagnóstico y Referencia Epidemiológicos "Dr. Manuel Martínez Báez, Mexico City, Mexico
| | | | | | - Nicolas Alcaraz
- Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | | | | | | | | | | | | | | | | | | | | | | | - Alejandro Sanchez-Flores
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Pavel Isa
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Margarita Matías-Florentino
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias "Ismael Cosío Villegas", Mexico City, Mexico
| | - Santiago Ávila-Ríos
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias "Ismael Cosío Villegas", Mexico City, Mexico
| | | | | | | | | | | | - Carlos F Arias
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias "Ismael Cosío Villegas", Mexico City, Mexico.
| | - José Ernesto Ramírez-González
- Dirección General de Epidemiología, Instituto de Diagnóstico y Referencia Epidemiológicos "Dr. Manuel Martínez Báez, Mexico City, Mexico.
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20
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Martínez-Rivera V, Cárdenas-Monroy CA, Millan-Catalan O, González-Corona J, Huerta-Pacheco NS, Martínez-Gutiérrez A, Villavicencio-Queijeiro A, Pedraza-Lara C, Hidalgo-Miranda A, Bravo-Gómez ME, Pérez-Plasencia C, Guardado-Estrada M. Dysregulation of miR-381-3p and miR-23b-3p in skeletal muscle could be a possible estimator of early post-mortem interval in rats. PeerJ 2021; 9:e11102. [PMID: 33986977 PMCID: PMC8086579 DOI: 10.7717/peerj.11102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 02/22/2021] [Indexed: 01/01/2023] Open
Abstract
Background The post-mortem interval (PMI) is the time elapsed since the dead of an individual until the body is found, which is relevant for forensic purposes. The miRNAs regulate the expression of some genes; and due to their small size, they can better support degradation, which makes them suitable for forensic analysis. In the present work, we evaluated the gene expression of miR-381-3p, miR-23b-3p, and miR-144-3p in skeletal muscle in a murine model at the early PMI. Methods We designed a rat model to evaluate the early PMI under controlled conditions. This model consisted in 25 rats divided into five groups of rats, that correspond to the 0, 3, 6, 12 and 24 hours of PMI. The 0 h-PMI was considered as the control group. Muscle samples were taken from each rat to analyze the expression of miR-381-3p, miR-23b-3p, and miR-144-3p by quantitative RT-PCR. The gene expression of each miRNA was expressed as Fold Change (FC) and compared among groups. To find the targets of these miRNAs and the pathways where they participate, we performed an in-silico analysis. From the gene targets of miR-381-3p identified in the silico analysis, the EPC1 gene was selected for gene expression analysis by quantitative RT-PCR in these samples. Also, to evaluate if miR-381-3p could predict the early PMI, a mixed effects model was calculated using its gene expression. Results An upregulation of miR-381-3p was found at 24 h-PMI compared with the control group of 0 h-PMI and (FC = 1.02 vs. FC = 1.96; p = 0.0079). This was the opposite for miR-23b-3p, which had a down-regulation at 24 h-PMI compared to 0 h-PMI (FC = 1.22 vs. FC = 0.13; p = 0.0079). Moreover, the gene expression of miR-381-3p increased throughout the first 24 h of PMI, contrary to miR-23b-3p. The targets of these two miRNAs, participate in biological pathways related to hypoxia, apoptosis, and RNA metabolism. The gene expression of EPC1 was found downregulated at 3 and 12 h of PMI, whereas it remained unchanged at 6 h and 24 h of PMI. Using a multivariate analysis, it was possible to predict the FC of miR-381-3p of all but 6 h-PMI analyzed PMIs. Discussion The present results suggest that miR-23b-3p and miR-381-3p participate at the early PMI, probably regulating the expression of some genes related to the autolysis process as EPC1 gene. Although the miR-381-3p gene expression is a potential estimator of PMI, further studies will be required to obtain better estimates.
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Affiliation(s)
- Vanessa Martínez-Rivera
- Laboratorio de Genética, Ciencia Forense, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Christian A Cárdenas-Monroy
- Laboratorio de Genética, Ciencia Forense, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Oliver Millan-Catalan
- Unidad de Investigación Biomédica en Cáncer, Laboratorio de Genómica, Instituo Nacional de Cancerologia, Ciudad de México, México.,Unidad de Investigación Biomédica en Cáncer, Laboratorio de Genómica, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Jessica González-Corona
- Laboratorio de Genética, Ciencia Forense, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - N Sofia Huerta-Pacheco
- Cátedras CONACYT-Ciencia Forense, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Antonio Martínez-Gutiérrez
- Unidad de Investigación Biomédica en Cáncer, Laboratorio de Genómica, Instituo Nacional de Cancerologia, Ciudad de México, México
| | - Alexa Villavicencio-Queijeiro
- Laboratorio de Genética, Ciencia Forense, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Carlos Pedraza-Lara
- Laboratorio de Entomología, Ciencia Forense, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Alfredo Hidalgo-Miranda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Nacional de Medicina Genomica, Ciudad de México, México
| | - María Elena Bravo-Gómez
- Laboratorio de Toxicología, Ciencia Forense, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Carlos Pérez-Plasencia
- Unidad de Investigación Biomédica en Cáncer, Laboratorio de Genómica, Instituo Nacional de Cancerologia, Ciudad de México, México.,Unidad de Investigación Biomédica en Cáncer, Laboratorio de Genómica, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Mariano Guardado-Estrada
- Laboratorio de Genética, Ciencia Forense, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
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21
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Martínez-Greene JA, Hernández-Ortega K, Quiroz-Baez R, Resendis-Antonio O, Pichardo-Casas I, Sinclair DA, Budnik B, Hidalgo-Miranda A, Uribe-Querol E, Ramos-Godínez MDP, Martínez-Martínez E. Quantitative proteomic analysis of extracellular vesicle subgroups isolated by an optimized method combining polymer-based precipitation and size exclusion chromatography. J Extracell Vesicles 2021; 10:e12087. [PMID: 33936570 PMCID: PMC8077108 DOI: 10.1002/jev2.12087] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 03/17/2021] [Accepted: 04/09/2021] [Indexed: 12/20/2022] Open
Abstract
The molecular characterization of extracellular vesicles (EVs) has revealed a great heterogeneity in their composition at a cellular and tissue level. Current isolation methods fail to efficiently separate EV subtypes for proteomic and functional analysis. The aim of this study was to develop a reproducible and scalable isolation workflow to increase the yield and purity of EV preparations. Through a combination of polymer‐based precipitation and size exclusion chromatography (Pre‐SEC), we analyzed two subsets of EVs based on their CD9, CD63 and CD81 content and elution time. EVs were characterized using transmission electron microscopy, nanoparticle tracking analysis, and Western blot assays. To evaluate differences in protein composition between the early‐ and late‐eluting EV fractions, we performed a quantitative proteomic analysis of MDA‐MB‐468‐derived EVs. We identified 286 exclusive proteins in early‐eluting fractions and 148 proteins with a differential concentration between early‐ and late‐eluting fractions. A density gradient analysis further revealed EV heterogeneity within each analyzed subgroup. Through a systems biology approach, we found significant interactions among proteins contained in the EVs which suggest the existence of functional clusters related to specific biological processes. The workflow presented here allows the study of EV subtypes within a single cell type and contributes to standardizing the EV isolation for functional studies.
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Affiliation(s)
- Juan A Martínez-Greene
- Laboratory of Cell Communication & Extracellular Vesicles Instituto Nacional de Medicina Genómica Mexico City Mexico
| | - Karina Hernández-Ortega
- Departamento de Biología Facultad de Química Universidad Nacional Autónoma de México Ciudad de México México
| | - Ricardo Quiroz-Baez
- Departamento de Investigación Básica Instituto Nacional de Geriatría Mexico City Mexico
| | - Osbaldo Resendis-Antonio
- Human Systems Biology Laboratory Instituto Nacional de Medicina Genómica Mexico City Mexico.,Coordinación de la Investigación Científica-Red de Apoyo a la Investigación Universidad Nacional Autónoma de México Mexico City Mexico
| | - Israel Pichardo-Casas
- Department of Genetics Paul F. Glenn Labs for the Biology of Aging Harvard Medical School Boston Massachusetts USA
| | - David A Sinclair
- Department of Genetics Paul F. Glenn Labs for the Biology of Aging Harvard Medical School Boston Massachusetts USA
| | - Bogdan Budnik
- Mass Spectrometry and Proteomics Resource Laboratory Division of Science Harvard University Cambridge Massachusetts USA
| | - Alfredo Hidalgo-Miranda
- Laboratorio de Genómica del Cáncer Instituto Nacional de Medicina Genómica Mexico City Mexico
| | - Eileen Uribe-Querol
- Laboratorio de Biología del Desarrollo División de Estudios de Posgrado e Investigación Facultad de Odontología Universidad Nacional Autónoma de México Mexico City Mexico
| | | | - Eduardo Martínez-Martínez
- Laboratory of Cell Communication & Extracellular Vesicles Instituto Nacional de Medicina Genómica Mexico City Mexico
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22
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Cisneros-Villanueva M, Hidalgo-Pérez L, Cedro-Tanda A, Peña-Luna M, Mancera-Rodríguez MA, Hurtado-Cordova E, Rivera-Salgado I, Martínez-Aguirre A, Jiménez-Morales S, Alfaro-Ruiz LA, Arellano-Llamas R, Tenorio-Torres A, Domínguez-Reyes C, Villegas-Carlos F, Ríos-Romero M, Hidalgo-Miranda A. LINC00460 Is a Dual Biomarker That Acts as a Predictor for Increased Prognosis in Basal-Like Breast Cancer and Potentially Regulates Immunogenic and Differentiation-Related Genes. Front Oncol 2021; 11:628027. [PMID: 33912452 PMCID: PMC8074675 DOI: 10.3389/fonc.2021.628027] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 03/10/2021] [Indexed: 12/23/2022] Open
Abstract
Breast cancer (BRCA) is a serious public health problem, as it is the most frequent malignant tumor in women worldwide. BRCA is a molecularly heterogeneous disease, particularly at gene expression (mRNAs) level. Recent evidence shows that coding RNAs represent only 34% of the total transcriptome in a human cell. The rest of the 66% of RNAs are non−coding, so we might be missing relevant biological, clinical or regulatory information. In this report, we identified two novel tumor types from TCGA with LINC00460 deregulation. We used survival analysis to demonstrate that LINC00460 expression is a marker for poor overall (OS), relapse-free (RFS) and distant metastasis-free survival (DMFS) in basal-like BRCA patients. LINC00460 expression is a potential marker for aggressive phenotypes in distinct tumors, including HPV-negative HNSC, stage IV KIRC, locally advanced lung cancer and basal-like BRCA. We show that the LINC00460 prognostic expression effect is tissue-specific, since its upregulation can predict poor OS in some tumors, but also predicts an improved clinical course in BRCA patients. We found that the LINC00460 expression is significantly enriched in the Basal-like 2 (BL2) TNBC subtype and potentially regulates the WNT differentiation pathway. LINC00460 can also modulate a plethora of immunogenic related genes in BRCA, such as SFRP5, FOSL1, IFNK, CSF2, DUSP7 and IL1A and interacts with miR-103-a-1, in-silico, which, in turn, can no longer target WNT7A. Finally, LINC00460:WNT7A ratio constitutes a composite marker for decreased OS and DMFS in Basal-like BRCA, and can predict anthracycline therapy response in ER-BRCA patients. This evidence confirms that LINC00460 is a master regulator in BRCA molecular circuits and influences clinical outcome.
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Affiliation(s)
- Mireya Cisneros-Villanueva
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, México.,Laboratorio de Epigenética del Cáncer, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo, Mexico
| | - Lizbett Hidalgo-Pérez
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, México.,Programa de Doctorado en Ciencias Biomédicas, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, Mexico
| | - Alberto Cedro-Tanda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, México
| | - Mónica Peña-Luna
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, México
| | | | - Eduardo Hurtado-Cordova
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, México
| | - Irene Rivera-Salgado
- Departamento de Anatomía Patológica, Hospital Central Sur de Alta Especialidad, Petróleos Mexicanos, Ciudad de México, México
| | - Alejandro Martínez-Aguirre
- Departamento de Anatomía Patológica, Hospital Central Sur de Alta Especialidad, Petróleos Mexicanos, Ciudad de México, México
| | - Silvia Jiménez-Morales
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, México
| | - Luis Alberto Alfaro-Ruiz
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, México
| | - Rocío Arellano-Llamas
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, México
| | | | | | | | - Magdalena Ríos-Romero
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, México.,Posgrado en Ciencias Biológicas, Unidad de Posgrado, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México
| | - Alfredo Hidalgo-Miranda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, México
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23
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Espinosa M, Lizárraga F, Vázquez-Santillán K, Hidalgo-Miranda A, Piña-Sánchez P, Torres J, García-Ramírez RA, Maldonado V, Melendez-Zajgla J, Ceballos-Cancino G. Coexpression of Smac/DIABLO and Estrogen Receptor in breast cancer. Cancer Biomark 2021; 30:429-446. [PMID: 33492282 DOI: 10.3233/cbm-200535] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND Smac/DIABLO is a proapoptotic protein deregulated in breast cancer, with a controversial role as a tumor marker, possibly due to a lack of correlative mRNA and protein analyses. OBJECTIVE To investigate the association of Smac/DIABLO gene and protein levels with clinical variables in breast cancer patients. METHODS Smac/DIABLO mRNA expression was analyzed by qPCR in 57 frozen tissues, whereas protein levels were assessed by immunohistochemistry in 82 paraffin-embedded tissues. Survivin mRNA levels were also measured. In vitro assays were performed to investigate possible regulators of Smac/DIABLO. RESULTS Higher levels of Smac/DIABLO mRNA and protein were found in estrogen receptor (ER)-positive samples (p= 0.0054 and p= 0.0043, respectively) in comparison to ER-negative tumors. A negligible positive association was found between Smac/DIABLO and survivin expression. In vitro assays showed that Smac/DIABLO is not regulated by ER and, conversely, it does not participate in ER expression modulation. CONCLUSIONS mRNA and protein levels of Smac/DIABLO were increased in ER-positive breast tumors in comparison with ER-negative samples, although the mechanism of this regulation is still unknown. Public databases showed a possible clinical relevance for this association.
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Affiliation(s)
- Magali Espinosa
- Instituto Nacional de Medicina Genómica, Department of Basic Research, Functional Cancer Genomics Laboratory, Mexico City, Mexico
| | - Floria Lizárraga
- Instituto Nacional de Medicina Genómica, Department of Basic Research, Epigenetic Laboratory, Mexico City, Mexico
| | - Karla Vázquez-Santillán
- Instituto Nacional de Medicina Genómica, Department of Basic Research, Epigenetic Laboratory, Mexico City, Mexico
| | - Alfredo Hidalgo-Miranda
- Instituto Nacional de Medicina Genómica, Department of Basic Research, Cancer Genomics Laboratory, Mexico City, Mexico
| | - Patricia Piña-Sánchez
- Instituto Mexicano del Seguro Social, CMN S XXI, Oncology Research Unit, Molecular Oncology Laboratory, Mexico City, Mexico
| | - Javier Torres
- Instituto Mexicano del Seguro Social, CMN S XXI, Unity of Research in Infectious Diseases, Mexico City, Mexico
| | - Román A García-Ramírez
- Instituto Nacional de Medicina Genómica, Department of Basic Research, Functional Cancer Genomics Laboratory, Mexico City, Mexico
| | - Vilma Maldonado
- Instituto Nacional de Medicina Genómica, Department of Basic Research, Epigenetic Laboratory, Mexico City, Mexico
| | - Jorge Melendez-Zajgla
- Instituto Nacional de Medicina Genómica, Department of Basic Research, Functional Cancer Genomics Laboratory, Mexico City, Mexico
| | - Gisela Ceballos-Cancino
- Instituto Nacional de Medicina Genómica, Department of Basic Research, Functional Cancer Genomics Laboratory, Mexico City, Mexico
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24
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Herrera LA, Hidalgo-Miranda A, Reynoso-Noverón N, Meneses-García AA, Mendoza-Vargas A, Reyes-Grajeda JP, Vadillo-Ortega F, Cedro-Tanda A, Peñaloza F, Frías-Jimenez E, Arriaga-Canon C, Ruiz R, Angulo O, López-Villaseñor I, Amador-Bedolla C, Vilar-Compte D, Cornejo P, Cisneros-Villanueva M, Hurtado-Cordova E, Cendejas-Orozco M, Hernández-Morales JS, Moreno B, Hernández-Cruz IA, Herrera CA, García F, González-Woge MA, Munguía-Garza P, Luna-Maldonado F, Sánchez-Vizcarra A, Osnaya VG, Medina-Molotla N, Alfaro-Mora Y, Cáceres-Gutiérrez RE, Tolentino-García L, Rosas-Escobar P, Román-González SA, Escobar-Arrazola MA, Canseco-Méndez JC, Ortiz-Soriano DR, Domínguez-Ortiz J, González-Barrera AD, Aparicio-Bautista DI, Cruz-Rangel A, Alarcón-Zendejas AP, Contreras-Espinosa L, González R, Guerra-Calderas L, Meraz-Rodríguez MA, Montalvo-Casimiro M, Montiel-Manríquez R, Torres-Arciga K, Venegas D, Juárez-González V, Guajardo-Barreto X, Monroy-Martínez V, Guillén D, Fernández J, Herrera J, León-Rodriguez R, Canela-Pérez I, Ruíz-Ordaz BH, Valdez-Vazquez R, Bertin-Montoya J, Niembro-Ortega M, Villegas-Acosta L, López-Castillo D, Soriano-Ríos A, Gastelum-Ramos M, Zamora-Barandas T, Morales-Baez J, García-Rodríguez M, García-Martínez M, Nieto-Patlán E, Quirasco-Baruch M, López-Martínez I, Ramírez-Gonzalez E, Olivera-Díaz H, Escobar-Escamilla N. Saliva is a reliable and accessible source for the detection of SARS-CoV-2. Int J Infect Dis 2021; 105:83-90. [PMID: 33581365 PMCID: PMC7876483 DOI: 10.1016/j.ijid.2021.02.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 02/02/2021] [Accepted: 02/04/2021] [Indexed: 01/08/2023] Open
Abstract
OBJECTIVES The aim of this study was to investigate the feasibility of saliva sampling as a non-invasive and safer tool to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and to compare its reproducibility and sensitivity with nasopharyngeal swab samples (NPS). The use of sample pools was also investigated. METHODS A total of 2107 paired samples were collected from asymptomatic healthcare and office workers in Mexico City. Sixty of these samples were also analyzed in two other independent laboratories for concordance analysis. Sample processing and analysis of virus genetic material were performed according to standard protocols described elsewhere. A pooling analysis was performed by analyzing the saliva pool and the individual pool components. RESULTS The concordance between NPS and saliva results was 95.2% (kappa 0.727, p = 0.0001) and 97.9% without considering inconclusive results (kappa 0.852, p = 0.0001). Saliva had a lower number of inconclusive results than NPS (0.9% vs 1.9%). Furthermore, saliva showed a significantly higher concentration of both total RNA and viral copies than NPS. Comparison of our results with those of the other two laboratories showed 100% and 97% concordance. Saliva samples are stable without the use of any preservative, and a positive SARS-CoV-2 sample can be detected 5, 10, and 15 days after collection when the sample is stored at 4 °C. CONCLUSIONS The study results indicate that saliva is as effective as NPS for the identification of SARS-CoV-2-infected asymptomatic patients. Sample pooling facilitates the analysis of a larger number of samples, with the benefit of cost reduction.
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Affiliation(s)
- Luis A Herrera
- Instituto Nacional de Medicina Genómica, INMEGEN, Mexico City, Mexico; Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico.
| | - Alfredo Hidalgo-Miranda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, INMEGEN, Mexico City, Mexico.
| | - Nancy Reynoso-Noverón
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | | | - Alfredo Mendoza-Vargas
- Unidad de Secuenciación, Instituto Nacional de Medicina Genómica, INMEGEN, Mexico City, Mexico
| | - Juan P Reyes-Grajeda
- Unidad de Secuenciación, Instituto Nacional de Medicina Genómica, INMEGEN, Mexico City, Mexico
| | | | | | - Fernando Peñaloza
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | | | - Cristian Arriaga-Canon
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Rosaura Ruiz
- Secretaria de Educación, Ciencia, Tecnología e Innovación, Mexico City, Mexico
| | - Ofelia Angulo
- Secretaria de Educación, Ciencia, Tecnología e Innovación, Mexico City, Mexico
| | - Imelda López-Villaseñor
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Carlos Amador-Bedolla
- Departamento de Física y Química Teórica, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | | | | | - Mireya Cisneros-Villanueva
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, INMEGEN, Mexico City, Mexico
| | - Eduardo Hurtado-Cordova
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, INMEGEN, Mexico City, Mexico
| | - Mariana Cendejas-Orozco
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, INMEGEN, Mexico City, Mexico
| | | | - Bernardo Moreno
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Irwin A Hernández-Cruz
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - César A Herrera
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Francisco García
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Miguel A González-Woge
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Paulina Munguía-Garza
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Fernando Luna-Maldonado
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Antonia Sánchez-Vizcarra
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Vincent G Osnaya
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Nelly Medina-Molotla
- Unidad de Secuenciación, Instituto Nacional de Medicina Genómica, INMEGEN, Mexico City, Mexico
| | - Yair Alfaro-Mora
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Rodrigo E Cáceres-Gutiérrez
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Laura Tolentino-García
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Patricia Rosas-Escobar
- Unidad de Secuenciación, Instituto Nacional de Medicina Genómica, INMEGEN, Mexico City, Mexico
| | | | - Marco A Escobar-Arrazola
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Julio C Canseco-Méndez
- Unidad de Secuenciación, Instituto Nacional de Medicina Genómica, INMEGEN, Mexico City, Mexico
| | | | - Julieta Domínguez-Ortiz
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | | | | | | | - Ana Paula Alarcón-Zendejas
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Laura Contreras-Espinosa
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Rodrigo González
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Lissania Guerra-Calderas
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Marco A Meraz-Rodríguez
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Michel Montalvo-Casimiro
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Rogelio Montiel-Manríquez
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Karla Torres-Arciga
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Daniela Venegas
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Vasti Juárez-González
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Xiadani Guajardo-Barreto
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Verónica Monroy-Martínez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Daniel Guillén
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Jacquelina Fernández
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Juliana Herrera
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Renato León-Rodriguez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Israel Canela-Pérez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Blanca H Ruíz-Ordaz
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | | | | | | | | | | | | | | | | | | | | | | | - Erik Nieto-Patlán
- Unidad de Investigación Preclínica, Facultad de Química, Mexico City, Mexico
| | - Maricarmen Quirasco-Baruch
- Departamento de Alimentos y Biotecnología, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Irma López-Martínez
- Instituto de Diagnóstico y Referencia Epidemiológicos, InDRE, Mexico City, Mexico
| | | | - Hiram Olivera-Díaz
- Instituto de Diagnóstico y Referencia Epidemiológicos, InDRE, Mexico City, Mexico
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Alvarez-Gomez RM, De la Fuente-Hernandez MA, Herrera-Montalvo L, Hidalgo-Miranda A. Challenges of diagnostic genomics in Latin America. Curr Opin Genet Dev 2021; 66:101-109. [PMID: 33517184 DOI: 10.1016/j.gde.2020.12.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/11/2020] [Accepted: 12/16/2020] [Indexed: 12/24/2022]
Abstract
Cancer genome sequencing methods have now become essential for diagnostic purposes, for devising treatment strategies, and for monitoring disease regression and progression. However, access to these benefits has not permeated homogeneously throughout the world; certain regions, such as Latin America, have been slower at adopting these technologies in terms of their routine use, development and patient access. There are also differences among Latin American subregions with respect to their prioritized types of neoplasia and the drugs that are available and approved in them. An overview of the current situation, including the status of genomics for cancer diagnostics and efforts by type of cancer is presented. In addition, we discuss the perspective of initiatives, alliances, and educational/research programs that pledge to make cancer genomics diagnosis a reality for Latin American individuals' health.
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Affiliation(s)
- Rosa Maria Alvarez-Gomez
- National Institute of Genomic Medicine, Periferico Sur 4809, Arenal Tepepan, Tlalpan, 14610, Mexico City, Mexico; National Cancer Institute, San Fernando 22, Seccion XVI, Tlalpan, Mexico City, Mexico
| | - Marcela Angelica De la Fuente-Hernandez
- National Institute of Genomic Medicine, Periferico Sur 4809, Arenal Tepepan, Tlalpan, 14610, Mexico City, Mexico; Doctoral Program in Biological Sciences, National Autonomous University of Mexico, C.U., Coyoacan, 04510, Mexico City, Mexico
| | - Luis Herrera-Montalvo
- National Institute of Genomic Medicine, Periferico Sur 4809, Arenal Tepepan, Tlalpan, 14610, Mexico City, Mexico
| | - Alfredo Hidalgo-Miranda
- National Institute of Genomic Medicine, Periferico Sur 4809, Arenal Tepepan, Tlalpan, 14610, Mexico City, Mexico.
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Bárcenas-López DA, Mendiola-Soto DK, Núñez-Enríquez JC, Mejía-Aranguré JM, Hidalgo-Miranda A, Jiménez-Morales S. Promising genes and variants to reduce chemotherapy adverse effects in acute lymphoblastic leukemia. Transl Oncol 2021; 14:100978. [PMID: 33290991 PMCID: PMC7720095 DOI: 10.1016/j.tranon.2020.100978] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/17/2020] [Accepted: 11/25/2020] [Indexed: 12/12/2022] Open
Abstract
Almost two decades ago, the sequencing of the human genome and high throughput technologies came to revolutionize the clinical and therapeutic approaches of patients with complex human diseases. In acute lymphoblastic leukemia (ALL), the most frequent childhood malignancy, these technologies have enabled to characterize the genomic landscape of the disease and have significantly improved the survival rates of ALL patients. Despite this, adverse reactions from treatment such as toxicity, drug resistance and secondary tumors formation are still serious consequences of chemotherapy, and the main obstacles to reduce ALL-related mortality. It is well known that germline variants and somatic mutations in genes involved in drug metabolism impact the efficacy of drugs used in oncohematological diseases therapy. So far, a broader spectrum of clinically actionable alterations that seems to be crucial for the progression and treatment response have been identified. Although these results are promising, it is necessary to put this knowledge into the clinics to help physician make medical decisions and generate an impact in patients' health. This review summarizes the gene variants and clinically actionable mutations that modify the efficacy of antileukemic drugs. Therefore, knowing their genetic status before treatment is critical to reduce severe adverse effects, toxicities and life-threatening consequences in ALL patients.
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Affiliation(s)
- Diego Alberto Bárcenas-López
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Del. Tlalpan, Mexico City 14610, Mexico; Programa de Doctorado, Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Diana Karen Mendiola-Soto
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Del. Tlalpan, Mexico City 14610, Mexico; Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Juan Carlos Núñez-Enríquez
- Unidad de Investigación Médica en Epidemiología Clínica, Hospital de Pediatría, CMNSXXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Juan Manuel Mejía-Aranguré
- Unidad de Investigación Médica en Epidemiología Clínica, Hospital de Pediatría, CMNSXXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico; Coordinación de Investigación en Salud, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Alfredo Hidalgo-Miranda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Del. Tlalpan, Mexico City 14610, Mexico
| | - Silvia Jiménez-Morales
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Del. Tlalpan, Mexico City 14610, Mexico.
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27
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Romero-Cordoba SL, Salido-Guadarrama I, Rebollar-Vega R, Tenorio-Flores A, Bautista-Piña V, Villegas-Carlos F, Dominguez-Reyes C, Hidalgo-Miranda A. Abstract PO-220: Comprehensive "omic" portraits of breast cancer in Mexican-Hispanic women. Cancer Epidemiol Biomarkers Prev 2020. [DOI: 10.1158/1538-7755.disp20-po-220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Abstract
Breast cancer is a relevant public health problem that affects millions of women worldwide. Breast tumors are recognized as a clinically and molecular heterogeneous pathology, but the genomic basis of its variability remains poorly understood, mainly regarding the comprehensive of ethnicity/racial disparities and their consequences in genomics studies. Moreover, most of the comprehensive molecular characterizations are predominantly centered on Caucasian population. Thus, we deeply characterized the molecular architecture of breast cancer in a set of Mexican patients through genomic and transcriptomic portraits. We explored the molecular features of breast cancers in Mexican-Hispanic (HM) women and compared them with public multi-ethnic datasets. HM patients presented an earlier onset of the disease, in particular in the aggressive Basal-like/triple negative and Luminal B subtypes. The significant E17K hotspot mutation in AKT1 gene occurred in 8% of the HM tumors, an enriched prevalence exclusively seen in this dataset. An integrative analysis also revealed an important role of the AKT1/PIK3CA axis as a potentially druggable target and indicate an aggressive biology. Computational analysis allowed us to identify age-related COSMIC (v2) signature 1 to be present in a much broader spectrum of HM women than in those from other ethnicities. On the basis of transcriptome immunogenomic analysis across human population we identified that luminal breast tumors with HM ancestry presented an enhanced immunogenic phenotype than their Asiatic and Caucasian counterparts. To the best of our knowledge, this dataset represents the largest breast cancer genomics characterization of breast tumors in Mexican women, and, provides novel insights into molecular phenotypes and mechanisms underlying carcinogenesis in a group of Mexican Hispanic women. In conclusion, this study provides a conceptual framework to better understand ethnic disparities of breast cancer.
Citation Format: Sandra Lorena Romero-Cordoba, Ivan Salido-Guadarrama, Rosa Rebollar-Vega, Alberto Tenorio-Flores, Verónica Bautista-Piña, Felipe Villegas-Carlos, Carlos Dominguez-Reyes, Alfredo Hidalgo-Miranda. Comprehensive "omic" portraits of breast cancer in Mexican-Hispanic women [abstract]. In: Proceedings of the AACR Virtual Conference: Thirteenth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2020 Oct 2-4. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(12 Suppl):Abstract nr PO-220.
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Pérez-Amado CJ, Tovar H, Gómez-Romero L, Beltrán-Anaya FO, Bautista-Piña V, Dominguez-Reyes C, Villegas-Carlos F, Tenorio-Torres A, Alfaro-Ruíz LA, Hidalgo-Miranda A, Jiménez-Morales S. Mitochondrial DNA Mutation Analysis in Breast Cancer: Shifting From Germline Heteroplasmy Toward Homoplasmy in Tumors. Front Oncol 2020; 10:572954. [PMID: 33194675 PMCID: PMC7653098 DOI: 10.3389/fonc.2020.572954] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/18/2020] [Indexed: 12/24/2022] Open
Abstract
Studies have suggested a potential role of somatic mitochondrial mutations in cancer development. To analyze the landscape of somatic mitochondrial mutation in breast cancer and to determine whether mitochondrial DNA (mtDNA) mutational burden is correlated with overall survival (OS), we sequenced whole mtDNA from 92 matched-paired primary breast tumors and peripheral blood. A total of 324 germline variants and 173 somatic mutations were found in the tumors. The most common germline allele was 663G (12S), showing lower heteroplasmy levels in peripheral blood lymphocytes than in their matched tumors, even reaching homoplasmic status in several cases. The heteroplasmy load was higher in tumors than in their paired normal tissues. Somatic mtDNA mutations were found in 73.9% of breast tumors; 59% of these mutations were located in the coding region (66.7% non-synonymous and 33.3% synonymous). Although the CO1 gene presented the highest number of mutations, tRNA genes (T,C, and W), rRNA 12S, and CO1 and ATP6 exhibited the highest mutation rates. No specific mtDNA mutational profile was associated with molecular subtypes of breast cancer, and we found no correlation between mtDNA mutational burden and OS. Future investigations will provide insight into the molecular mechanisms through which mtDNA mutations and heteroplasmy shifting contribute to breast cancer development.
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Affiliation(s)
- Carlos Jhovani Pérez-Amado
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico.,Programa de Doctorado, Posgrado en Ciencias Bioquímicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Hugo Tovar
- Genómica Computacional, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Laura Gómez-Romero
- Genómica Computacional, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Fredy Omar Beltrán-Anaya
- Laboratorio de Investigación en Epidemiología Clínica y Molecular, Facultad de Ciencias Químico-Biológicas, Universidad Autónoma de Guerrero, Chilpancingo, Mexico
| | | | | | | | | | - Luis Alberto Alfaro-Ruíz
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Alfredo Hidalgo-Miranda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Silvia Jiménez-Morales
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
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29
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Medina-Sanson A, Núñez-Enríquez JC, Hurtado-Cordova E, Pérez-Saldivar ML, Martínez-García A, Jiménez-Hernández E, Fernández-López JC, Martín-Trejo JA, Pérez-Lorenzana H, Flores-Lujano J, Amador-Sánchez R, Mora-Ríos FG, Peñaloza-González JG, Duarte-Rodríguez DA, Torres-Nava JR, Flores-Bautista JE, Espinosa-Elizondo RM, Román-Zepeda PF, Flores-Villegas LV, González-Ulivarri JE, Martínez-Silva SI, Espinoza-Anrubio G, Almeida-Hernández C, Ramírez-Colorado R, Hernández-Mora L, García-López LR, Cruz-Ojeda GA, Godoy-Esquivel AE, Contreras-Hernández I, Medina-Hernández A, López-Caballero MG, Hernández-Pineda NA, Granados-Kraulles J, Rodríguez-Vázquez MA, Torres-Valle D, Cortés-Reyes C, Medrano-López F, Pérez-Gómez JA, Martínez-Ríos A, Aguilar-De Los Santos A, Serafin-Díaz B, Bekker-Méndez VC, Mata-Rocha M, Morales-Castillo BA, Sepúlveda-Robles OA, Ramírez-Bello J, Rosas-Vargas H, Hidalgo-Miranda A, Mejía-Aranguré JM, Jiménez-Morales S. Genotype-Environment Interaction Analysis of NQO1, CYP2E1, and NAT2 Polymorphisms and the Risk of Childhood Acute Lymphoblastic Leukemia: A Report From the Mexican Interinstitutional Group for the Identification of the Causes of Childhood Leukemia. Front Oncol 2020; 10:571869. [PMID: 33072605 PMCID: PMC7537417 DOI: 10.3389/fonc.2020.571869] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 08/17/2020] [Indexed: 11/26/2022] Open
Abstract
Background: Acute lymphoblastic leukemia (ALL) is the main type of cancer in children. In Mexico and other Hispanic populations, the incidence of this neoplasm is one of the highest reported worldwide. Functional polymorphisms of various enzymes involved in the metabolism of xenobiotics have been associated with an increased risk of developing ALL, and the risk is different by ethnicity. The aims of the present study were to identify whether NQO1, CYP2E1, and NAT2 polymorphisms or some genotype-environmental interactions were associated with ALL risk in Mexican children. Methods: We conducted a case-control study including 478 pediatric patients diagnosed with ALL and 284 controls (children without leukemia). Ancestry composition of a subset of cases and controls was assessed using 32 ancestry informative markers. Genetic-environmental interactions for the exposure to hydrocarbons were assessed by logistic regression analysis. Results: The polymorphisms rs1801280 (OR 1.54, 95% CI 1.21–1.93), rs1799929 (OR 1.96, 95% CI 1.55–2.49), and rs1208 (OR 1.44, 95% CI 1.14–1.81) were found to increase the risk of ALL; being the risks higher under a recessive model (OR 2.20, 95% CI 1.30–1.71, OR 3.87, 95% CI 2.20–6.80, and OR 2.26, 95% CI 1.32–3.87, respectively). Gene-environment interaction analysis showed that NAT2 rs1799929 TT genotype confers high risk to ALL under exposure to fertilizers, insecticides, hydrocarbon derivatives, and parental tobacco smoking. No associations among NQO1, CYP2E1, and ALL were observed. Conclusion: Our study provides evidence for the association between NAT2 polymorphisms/gene-environment interactions, and the risk of childhood ALL in Mexican children.
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Affiliation(s)
- Aurora Medina-Sanson
- Departamento de Hemato-Oncología, Hospital Infantil de México Federico Gómez, Secretaría de Salud, Mexico City, Mexico.,Programa de Maestría y Doctorado en Ciencias Médicas de la Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM)Mexico City, Mexico
| | - Juan Carlos Núñez-Enríquez
- Unidad de Investigación Médica en Epidemiología Clínica, Unidad Médica de Alta Especialidad Hospital de Pediatría "Dr. Silvestre Frenk Freund", Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Eduardo Hurtado-Cordova
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico.,Universidad Xochicalco, Campos Tijuana, Tijuana, Mexico
| | - María Luisa Pérez-Saldivar
- Unidad de Investigación Médica en Epidemiología Clínica, Unidad Médica de Alta Especialidad Hospital de Pediatría "Dr. Silvestre Frenk Freund", Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Anayeli Martínez-García
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico.,Facultad de Estudios Superiores Zaragoza, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Elva Jiménez-Hernández
- Servicio de Hematología Pediátrica, Centro Médico Nacional "La Raza", Hospital General "Gaudencio González Garza", Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | | | - Jorge Alfonso Martín-Trejo
- Servicio de Hematología Pediátrica, Centro Médico Nacional "Siglo XXI", UMAE Hospital de Pediatría "Dr. Silvestre Frenk Freund", Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Héctor Pérez-Lorenzana
- Servicio de Cirugía Pediátrica, Hospital General "Gaudencio González Garza", Centro Médico Nacional Siglo XXI (CMN) "La Raza", Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Janet Flores-Lujano
- Unidad de Investigación Médica en Epidemiología Clínica, Unidad Médica de Alta Especialidad Hospital de Pediatría "Dr. Silvestre Frenk Freund", Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Raquel Amador-Sánchez
- Servicio de Hematología Pediátrica, Hospital General Regional "Carlos McGregor Sánchez Navarro", Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Felix Gustavo Mora-Ríos
- Cirugía Pediátrica del Hospital Regional "General Ignacio Zaragoza", Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado (ISSSTE), Mexico City, Mexico
| | | | - David Aldebarán Duarte-Rodríguez
- Unidad de Investigación Médica en Epidemiología Clínica, Unidad Médica de Alta Especialidad Hospital de Pediatría "Dr. Silvestre Frenk Freund", Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - José Refugio Torres-Nava
- Servicio de Oncología, Hospital Pediátrico de Moctezuma, Secretaría de Salud de la Ciudad de México (SSCDMX), Mexico City, Mexico
| | | | | | - Pedro Francisco Román-Zepeda
- Coordinación Clínica y Servicio de Cirugía pediátrica, Hospital General Regional (HGR) No. 1 "Dr. Carlos Mac Gregor Sánchez Navarro", Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Luz Victoria Flores-Villegas
- Servicio de Hematología Pediátrica, Centro Médico Nacional "20 de Noviembre", Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado (ISSSTE), Mexico City, Mexico
| | - Juana Esther González-Ulivarri
- Jefatura de Enseñanza, Hospital Pediátrico de Iztacalco, Secretaría de Salud de la Ciudad de México (SSCDMX), Mexico City, Mexico
| | - Sofía Irene Martínez-Silva
- Jefatura de Enseñanza, Hospital Pediátrico de Iztapalapa, Secretaría de Salud de la Ciudad de México (SSCDMX), Mexico City, Mexico
| | - Gilberto Espinoza-Anrubio
- Servicio de Pediatría, Hospital General Zona (HGZ) No. 8 "Dr. Gilberto Flores Izquierdo", Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Carolina Almeida-Hernández
- Jefatura de Enseñanza, Hospital General de Ecatepec "Las Américas", Instituto de Salud del Estado de México (ISEM), Mexico City, Mexico
| | - Rosario Ramírez-Colorado
- Jefatura de Enseñanza, Hospital Pediátrico La Villa, Secretaría de Salud de la Ciudad de México (SSCDMX), Mexico City, Mexico
| | - Luis Hernández-Mora
- Jefatura de Enseñanza, Hospital Pediátrico San Juan de Aragón, Secretaría de Salud (SS), Mexico City, Mexico
| | - Luis Ramiro García-López
- Servicio de Pediatría, Hospital Pediátrico de Tacubaya, Secretaría de Salud de la Ciudad de México (SSCDMX), Mexico City, Mexico
| | - Gabriela Adriana Cruz-Ojeda
- Coordinación Clínica de Educación e Investigación en Salud, Hospital General de Zona (HGZ) No. 47, IMSS, Mexico City, Mexico
| | - Arturo Emilio Godoy-Esquivel
- Servicio de Cirugía Pediátrica, Hospital Pediátrico de Moctezuma, Secretaría de Salud de la Ciudad de México (SSCDMX), Mexico City, Mexico
| | - Iris Contreras-Hernández
- Coordinación de Investigación en Salud, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Abraham Medina-Hernández
- Pediatría, Hospital Materno-Pediátrico de Xochimilco, Secretaría de Salud de la Ciudad de México (SSCDMX), Mexico City, Mexico
| | - María Guadalupe López-Caballero
- Jefatura de Enseñanza, Hospital Pediátrico de Coyoacán, Secretaría de Salud de la Ciudad de México (SSCDMX), Mexico City, Mexico
| | - Norma Angélica Hernández-Pineda
- Coordinación Clínica y Pediatría del Hospital General de Zona 76, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Jorge Granados-Kraulles
- Coordinación Clínica y Pediatría del Hospital General de Zona 76, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - María Adriana Rodríguez-Vázquez
- Coordinación Clínica y Pediatría del Hospital General de Zona 68, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Delfino Torres-Valle
- Coordinación Clínica y Pediatría del Hospital General de Zona 71, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Carlos Cortés-Reyes
- Pediatría, Hospital General Dr. Darío Fernández Fierro, Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado (ISSSTE), Mexico City, Mexico
| | - Francisco Medrano-López
- Coordinación Clínica y Servicio de Pediatría, Hospital General Regional (HGR) No. 72 "Dr. Vicente Santos Guajardo", Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Jessica Arleet Pérez-Gómez
- Coordinación Clínica y Servicio de Pediatría, Hospital General Regional (HGR) No. 72 "Dr. Vicente Santos Guajardo", Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Annel Martínez-Ríos
- Cirugía Pediátrica del Hospital Regional "General Ignacio Zaragoza", Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado (ISSSTE), Mexico City, Mexico
| | - Antonio Aguilar-De Los Santos
- Coordinación Clínica y Pediatría del Hospital General de Zona 98, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Berenice Serafin-Díaz
- Coordinación Clínica y Pediatría del Hospital General de Zona 57, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Vilma Carolina Bekker-Méndez
- Hospital de Infectología "Dr. Daniel Méndez Hernández", "La Raza", Instituto Mexicano del Seguro Social (IMSS), Unidad de Investigación Médica en Inmunología e Infectología, Mexico City, Mexico
| | - Minerva Mata-Rocha
- Unidad de Investigación Médica en Genética Humana, UMAE Hospital de Pediatría "Dr. Silvestre Frenk Freund", Centro Médico Nacional "Siglo XXI", Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Blanca Angélica Morales-Castillo
- Unidad de Investigación Médica en Genética Humana, UMAE Hospital de Pediatría "Dr. Silvestre Frenk Freund", Centro Médico Nacional "Siglo XXI", Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Omar Alejandro Sepúlveda-Robles
- Unidad de Investigación Médica en Genética Humana, UMAE Hospital de Pediatría "Dr. Silvestre Frenk Freund", Centro Médico Nacional "Siglo XXI", Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | | | - Haydeé Rosas-Vargas
- Unidad de Investigación Médica en Genética Humana, UMAE Hospital de Pediatría "Dr. Silvestre Frenk Freund", Centro Médico Nacional "Siglo XXI", Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Alfredo Hidalgo-Miranda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
| | - Juan Manuel Mejía-Aranguré
- Unidad de Investigación Médica en Epidemiología Clínica, Unidad Médica de Alta Especialidad Hospital de Pediatría "Dr. Silvestre Frenk Freund", Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico.,Coordinación de Investigación en Salud, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Silvia Jiménez-Morales
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
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30
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Ríos-Romero M, Cedro-Tanda A, Peña-Luna M, Mancera-Rodríguez MA, Hidalgo-Pérez L, Cisneros-Villanueva M, Beltrán-Anaya FO, Arellano-Llamas R, Jiménez-Morales S, Alfaro-Ruíz LA, Tenorio-Torres A, Domínguez-Reyes C, Villegas-Carlos F, Ochoa-Mendoza E, Hidalgo-Miranda A. FAM83H-AS1 is a potential modulator of cancer driver genes across different tumors and a prognostic marker for ER/PR + BRCA patients. Sci Rep 2020; 10:14145. [PMID: 32839509 PMCID: PMC7445275 DOI: 10.1038/s41598-020-71062-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 08/10/2020] [Indexed: 12/24/2022] Open
Abstract
Breast cancer (BRCA) is a serious public health problem, as it is the most frequent malignant tumor in women worldwide. BRCA is a molecularly heterogenic disease, particularly at gene expression (mRNAs) level. Recent evidence shows that coding RNAs represent only 34% of the total transcriptome in a human cell. The rest of the 66% of RNAs are non-coding, so we might be missing relevant biological, clinical or regulatory information. In this report, we identified nine novel tumor types from TCGA with FAM83H-AS1 deregulation. We used survival analysis to demonstrate that FAM83H-AS1 expression is a marker for poor survival in IHC-detected ER and PR positive BRCA patients and found a significant correlation between FAM83H-AS1 overexpression and tamoxifen resistance. Estrogen and Progesterone receptor expression levels interact with FAM83H-AS1 to potentiate its effect in OS prediction. FAM83H-AS1 silencing impairs two important breast cancer related pathways: cell migration and cell death. Among the most relevant potential FAM83H-AS1 gene targets, we found p63 and claudin 1 (CLDN1) to be deregulated after FAM83H-AS1 knockdown. Using correlation analysis, we show that FAM83H-AS1 can regulate a plethora of cancer-related genes across multiple tumor types, including BRCA. This evidence suggests that FAM83H-AS1 is a master regulator in different cancer types, and BRCA in particular.
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Affiliation(s)
- Magdalena Ríos-Romero
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Tlalpan, Arenal Tepepan, 14610, Ciudad de México (CDMX), Mexico.,Programa de Doctorado de Ciencias Biológicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Alberto Cedro-Tanda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Tlalpan, Arenal Tepepan, 14610, Ciudad de México (CDMX), Mexico
| | - Mónica Peña-Luna
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Tlalpan, Arenal Tepepan, 14610, Ciudad de México (CDMX), Mexico
| | - Marco Antonio Mancera-Rodríguez
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Tlalpan, Arenal Tepepan, 14610, Ciudad de México (CDMX), Mexico
| | - Lizbett Hidalgo-Pérez
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Tlalpan, Arenal Tepepan, 14610, Ciudad de México (CDMX), Mexico
| | - Mireya Cisneros-Villanueva
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Tlalpan, Arenal Tepepan, 14610, Ciudad de México (CDMX), Mexico
| | - Fredy Omar Beltrán-Anaya
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Tlalpan, Arenal Tepepan, 14610, Ciudad de México (CDMX), Mexico
| | - Rocío Arellano-Llamas
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Tlalpan, Arenal Tepepan, 14610, Ciudad de México (CDMX), Mexico
| | - Silvia Jiménez-Morales
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Tlalpan, Arenal Tepepan, 14610, Ciudad de México (CDMX), Mexico
| | - Luis Alberto Alfaro-Ruíz
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Tlalpan, Arenal Tepepan, 14610, Ciudad de México (CDMX), Mexico
| | | | | | | | - Elsa Ochoa-Mendoza
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Tlalpan, Arenal Tepepan, 14610, Ciudad de México (CDMX), Mexico
| | - Alfredo Hidalgo-Miranda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Tlalpan, Arenal Tepepan, 14610, Ciudad de México (CDMX), Mexico.
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31
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Bárcenas-López DA, Núñez-Enríquez JC, Hidalgo-Miranda A, Beltrán-Anaya FO, May-Hau DI, Jiménez-Hernández E, Bekker-Méndez VC, Flores-Lujano J, Medina-Sansón A, Tamez-Gómez EL, López-García VH, Lara-Ramos JR, Núñez-Villegas NN, Peñaloza-González JG, Flores-Villegas LV, Amador-Sánchez R, Espinosa-Elizondo RM, Martín-Trejo JA, Velázquez-Aviña MM, Merino-Pasaye LE, Pérez-Saldívar ML, Duarte-Rodríguez DA, Torres-Nava JR, Cortés-Herrera B, Solís-Labastida KA, González-Ávila AI, Santillán-Juárez JD, García-Velázquez AJ, Rosas-Vargas H, Mata-Rocha M, Sepúlveda-Robles OA, Mejía-Aranguré JM, Jiménez-Morales S. Transcriptome Analysis Identifies LINC00152 as a Biomarker of Early Relapse and Mortality in Acute Lymphoblastic Leukemia. Genes (Basel) 2020; 11:genes11030302. [PMID: 32183133 PMCID: PMC7140896 DOI: 10.3390/genes11030302] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/10/2020] [Accepted: 03/12/2020] [Indexed: 12/16/2022] Open
Abstract
Evidence showing the role of long non-coding RNAs (lncRNAs) in leukemogenesis have emerged in the last decade. It has been proposed that these genes can be used as diagnosis and/or prognosis biomarkers in childhood acute lymphoblastic leukemia (ALL). To know if lncRNAs are associated with early relapse and early mortality, a microarray-based gene expression analysis in children with B-lineage ALL (B-ALL) was conducted. Cox regression analyses were performed. Hazard ratios (HR) and 95% confidence intervals (95% CI) were calculated. LINC00152 and LINC01013 were among the most differentially expressed genes in patients with early relapse and early mortality. For LINC00152 high expression, the risks of relapse and death were HR: 4.16 (95% CI: 1.46–11.86) and HR: 1.99 (95% CI: 0.66–6.02), respectively; for LINC01013 low expression, the risks of relapse and death were HR: 3.03 (95% CI: 1.14–8.05) and HR: 6.87 (95% CI: 1.50–31.48), respectively. These results were adjusted by NCI risk criteria and chemotherapy regimen. The lncRNA–mRNA co-expression analysis showed that LINC00152 potentially regulates genes involved in cell substrate adhesion and peptidyl–tyrosine autophosphorylation biological processes. The results of the present study point out that LINC00152 could be a potential biomarker of relapse in children with B-ALL.
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Affiliation(s)
- Diego Alberto Bárcenas-López
- Programa de Doctorado, Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
| | - Juan Carlos Núñez-Enríquez
- Unidad de Investigación Médica en Epidemiologia Clínica, UMAE Hospital de Pediatría “Dr. Silvestre Frenk Freund”, Centro Médico Nacional “Siglo XXI”, Instituto Mexicano del Seguro Social, Mexico City 06720, Mexico; (J.C.N.-E.); (J.F.-L.); (M.L.P.-S.); (D.A.D.-R.)
| | - Alfredo Hidalgo-Miranda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico;
| | - Fredy Omar Beltrán-Anaya
- Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
| | - Didier Ismael May-Hau
- Programa de Maestría en Investigación Clínica Experimental en Salud, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
| | - Elva Jiménez-Hernández
- Servicio de Hematología Pediátrica, Hospital General “Gaudencio González Garza”, Centro Médico Nacional “La Raza”, IMSS, Mexico City 02990, Mexico; (E.J.-H.); (N.N.N.-V.)
| | - Vilma Carolina Bekker-Méndez
- Unidad de Investigación Médica en Inmunología e Infectología, Hospital de Infectología “Dr. Daniel Méndez Hernández”, Centro Médico Nacional “La Raza”, IMSS, Mexico City 02990, Mexico;
| | - Janet Flores-Lujano
- Unidad de Investigación Médica en Epidemiologia Clínica, UMAE Hospital de Pediatría “Dr. Silvestre Frenk Freund”, Centro Médico Nacional “Siglo XXI”, Instituto Mexicano del Seguro Social, Mexico City 06720, Mexico; (J.C.N.-E.); (J.F.-L.); (M.L.P.-S.); (D.A.D.-R.)
| | - Aurora Medina-Sansón
- Servicio de Hemato-Oncologia, Hospital Infantil de México Federico Gómez, Secretaria de Salud (SS), Mexico City 06720, Mexico;
| | - Edna Liliana Tamez-Gómez
- Servicio de Hemato-Oncología Hospital Infantil de Tamaulipas, Secretaría de Salud (SS), Cd. Victoria Tamaulipas 87070, Mexico;
| | - Víctor Hugo López-García
- Servicio de Ortopedia Pediátrica, Hospital Infantil de Tamaulipas, Secretaría de Salud (SS), Cd. Victoria Tamaulipas 87070, Mexico;
| | - José Ramón Lara-Ramos
- Departamento de Genética, Hospital Infantil de Tamaulipas, Secretaría de Salud (SS), Cd. Victoria Tamaulipas 87070, Mexico;
| | - Nora Nancy Núñez-Villegas
- Servicio de Hematología Pediátrica, Hospital General “Gaudencio González Garza”, Centro Médico Nacional “La Raza”, IMSS, Mexico City 02990, Mexico; (E.J.-H.); (N.N.N.-V.)
| | - José Gabriel Peñaloza-González
- Servicio de Onco-Pediatría, Hospital Juárez de México, Secretaría de Salud (SS), Mexico City 07760, Mexico; (J.G.P.-G.); (M.M.V.-A.)
| | - Luz Victoria Flores-Villegas
- Servicio de Hematología Pediátrica, Centro Médico Nacional “20 de Noviembre”, Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado (ISSSTE), Mexico City 03100, Mexico; (L.V.F.-V.); (L.E.M.-P.)
| | - Raquel Amador-Sánchez
- Hospital General Regional 1 “Dr. Carlos McGregor Sánchez Navarro”, IMSS, Mexico City 03103, Mexico; (R.A.-S.); (A.I.G.-Á.)
| | - Rosa Martha Espinosa-Elizondo
- Servicio de Hematología Pediátrica, Hospital General de México “Dr. Eduardo Liceaga”, Secretaría de Salud (SS), Mexico City 06720, Mexico; (R.M.E.-E.); (B.C.-H.)
| | - Jorge Alfonso Martín-Trejo
- Servicio de Hematología Pediátrica UMAE Hospital de Pediatría “Dr. Silvestre Frenk Freund”, Centro Médico Nacional “Siglo XXI”, IMSS, Mexico City 06720, Mexico; (J.A.M.-T.); (K.A.S.-L.)
| | - Martha Margarita Velázquez-Aviña
- Servicio de Onco-Pediatría, Hospital Juárez de México, Secretaría de Salud (SS), Mexico City 07760, Mexico; (J.G.P.-G.); (M.M.V.-A.)
| | - Laura Elizabeth Merino-Pasaye
- Servicio de Hematología Pediátrica, Centro Médico Nacional “20 de Noviembre”, Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado (ISSSTE), Mexico City 03100, Mexico; (L.V.F.-V.); (L.E.M.-P.)
| | - María Luisa Pérez-Saldívar
- Unidad de Investigación Médica en Epidemiologia Clínica, UMAE Hospital de Pediatría “Dr. Silvestre Frenk Freund”, Centro Médico Nacional “Siglo XXI”, Instituto Mexicano del Seguro Social, Mexico City 06720, Mexico; (J.C.N.-E.); (J.F.-L.); (M.L.P.-S.); (D.A.D.-R.)
| | - David Aldebarán Duarte-Rodríguez
- Unidad de Investigación Médica en Epidemiologia Clínica, UMAE Hospital de Pediatría “Dr. Silvestre Frenk Freund”, Centro Médico Nacional “Siglo XXI”, Instituto Mexicano del Seguro Social, Mexico City 06720, Mexico; (J.C.N.-E.); (J.F.-L.); (M.L.P.-S.); (D.A.D.-R.)
| | - José Refugio Torres-Nava
- Servicio de Oncología, Hospital Pediátrico de Moctezuma, Secretaria de Salud del D.F., Mexico City 15530, Mexico;
| | - Beatriz Cortés-Herrera
- Servicio de Hematología Pediátrica, Hospital General de México “Dr. Eduardo Liceaga”, Secretaría de Salud (SS), Mexico City 06720, Mexico; (R.M.E.-E.); (B.C.-H.)
| | - Karina Anastacia Solís-Labastida
- Servicio de Hematología Pediátrica UMAE Hospital de Pediatría “Dr. Silvestre Frenk Freund”, Centro Médico Nacional “Siglo XXI”, IMSS, Mexico City 06720, Mexico; (J.A.M.-T.); (K.A.S.-L.)
| | - Ana Itamar González-Ávila
- Hospital General Regional 1 “Dr. Carlos McGregor Sánchez Navarro”, IMSS, Mexico City 03103, Mexico; (R.A.-S.); (A.I.G.-Á.)
| | - Jessica Denisse Santillán-Juárez
- Servicio de Hemato-Oncología Pediátrica, Hospital Regional No. 1 de Octubre, ISSSTE, Mexico City 07300, Mexico; (J.D.S.-J.); (A.J.G.-V.)
| | - Alejandra Jimena García-Velázquez
- Servicio de Hemato-Oncología Pediátrica, Hospital Regional No. 1 de Octubre, ISSSTE, Mexico City 07300, Mexico; (J.D.S.-J.); (A.J.G.-V.)
| | - Haydee Rosas-Vargas
- Unidad de Investigación en Genética Humana, UMAE Hospital de Pediatría “Dr. Silvestre Frenk Freund”, Centro Médico Nacional “Siglo XXI”, IMSS, Mexico City 06720, Mexico; (H.R.-V.); (M.M.-R.); (O.A.S.-R.)
| | - Minerva Mata-Rocha
- Unidad de Investigación en Genética Humana, UMAE Hospital de Pediatría “Dr. Silvestre Frenk Freund”, Centro Médico Nacional “Siglo XXI”, IMSS, Mexico City 06720, Mexico; (H.R.-V.); (M.M.-R.); (O.A.S.-R.)
| | - Omar Alejandro Sepúlveda-Robles
- Unidad de Investigación en Genética Humana, UMAE Hospital de Pediatría “Dr. Silvestre Frenk Freund”, Centro Médico Nacional “Siglo XXI”, IMSS, Mexico City 06720, Mexico; (H.R.-V.); (M.M.-R.); (O.A.S.-R.)
| | - Juan Manuel Mejía-Aranguré
- Unidad de Investigación Médica en Epidemiologia Clínica, UMAE Hospital de Pediatría “Dr. Silvestre Frenk Freund”, Centro Médico Nacional “Siglo XXI”, Instituto Mexicano del Seguro Social, Mexico City 06720, Mexico; (J.C.N.-E.); (J.F.-L.); (M.L.P.-S.); (D.A.D.-R.)
- Coordinación de Investigación en Salud, IMSS, Mexico City 06720, Mexico
- Correspondence: or (J.M.M.-A.); (S.J.-M.); Tel.: +52–55–5350–1900 (ext. 1155) (S.J.-M.)
| | - Silvia Jiménez-Morales
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico;
- Correspondence: or (J.M.M.-A.); (S.J.-M.); Tel.: +52–55–5350–1900 (ext. 1155) (S.J.-M.)
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Castro-Muñoz LJ, Manzo-Merino J, Muñoz-Bello JO, Olmedo-Nieva L, Cedro-Tanda A, Alfaro-Ruiz LA, Hidalgo-Miranda A, Madrid-Marina V, Lizano M. The Human Papillomavirus (HPV) E1 protein regulates the expression of cellular genes involved in immune response. Sci Rep 2019; 9:13620. [PMID: 31541186 PMCID: PMC6754496 DOI: 10.1038/s41598-019-49886-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 08/29/2019] [Indexed: 02/07/2023] Open
Abstract
The Human Papillomavirus (HPV) E1 protein is the only viral protein with enzymatic activity. The main known function of this protein is the regulation of the viral DNA replication. Nevertheless, it has been demonstrated that the ablation of HPV18 E1 mRNA in HeLa cells promotes a deregulation of several genes, particularly those involved in host defense mechanisms against viral infections; however, the specific contribution of E1 protein in HPV-independent context has not been studied. The aim of this work was to determine the effect of the HPV E1 protein in the regulation of cellular gene expression profiles evaluated through RNA-seq. We found that E1 proteins from HPV16 and 18 induced an overexpression of different set of genes associated with proliferation and differentiation processes, as well as downregulation of immune response genes, including IFNβ1 and IFNλ1 and Interferon-stimulated gene (ISG), which are important components involved in the antiviral immune response. Together, our results indicate that HR-(High-Risk) and LR-(Low-Risk) HPV E1 proteins play an important role in inhibiting the anti-viral immune response.
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Affiliation(s)
- Leonardo Josué Castro-Muñoz
- Programa de Doctorado en Ciencias Biomédicas, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Circuito Escolar S/N, Ciudad Universitaria, Delegación Coyoacán, 04500, Mexico City, Mexico.,Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología, México/Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Av. San Fernando No. 22, Col. Sección XVI, Tlalpan, 14080, Mexico City, Mexico
| | - Joaquín Manzo-Merino
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología, México/Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Av. San Fernando No. 22, Col. Sección XVI, Tlalpan, 14080, Mexico City, Mexico.,Cátedras CONACyT-Instituto Nacional de Cancerología, San Fernando No. 22, Col. Sección XVI, Tlalpan, México City, Mexico
| | - J Omar Muñoz-Bello
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología, México/Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Av. San Fernando No. 22, Col. Sección XVI, Tlalpan, 14080, Mexico City, Mexico
| | - Leslie Olmedo-Nieva
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología, México/Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Av. San Fernando No. 22, Col. Sección XVI, Tlalpan, 14080, Mexico City, Mexico
| | - Alberto Cedro-Tanda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, México City, Mexico
| | - Luis Alberto Alfaro-Ruiz
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, México City, Mexico
| | - Alfredo Hidalgo-Miranda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, México City, Mexico
| | - Vicente Madrid-Marina
- Dirección de Infecciones Crónicas y Cáncer. Centro de Investigación sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública, Av. Universidad 655, Santa María Ahuacatitlán, Cuernavaca, Morelos, 62100, Mexico
| | - Marcela Lizano
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología, México/Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Av. San Fernando No. 22, Col. Sección XVI, Tlalpan, 14080, Mexico City, Mexico. .,Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Ciudad de México, Mexico.
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Dominguez-Gomez G, Cortez-Pedroza D, Chavez-Blanco A, Taja-Chayeb L, Hidalgo-Miranda A, Cedro-Tanda A, Beltran-Anaya F, Diaz-Chavez J, Schcolnik-Cabrera A, Gonzalez-Fierro A, Dueñas-Gonzalez A. Growth inhibition and transcriptional effects of ribavirin in lymphoma. Oncol Rep 2019; 42:1248-1256. [PMID: 31322273 DOI: 10.3892/or.2019.7240] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Accepted: 06/20/2019] [Indexed: 11/06/2022] Open
Abstract
Ribavirin exhibits inhibitory effects on the epigenetic enzyme enhancer of zeste homolog 2 (EZH2), which participates in lymphomagenesis. Additionally, preclinical and clinical studies have demonstrated the anti‑lymphoma activity of this drug. To further investigate the potential of ribavirin as an anticancer treatment for lymphoma, the tumor‑suppressive effects of ribavirin were analyzed in lymphoma cell lines. The effects of ribavirin on the viability and clonogenicity of the B‑cell lymphoma cell line Pfeiffer (EZH2‑mutant), Toledo (EZH2 wild‑type) and cutaneous T‑cell lymphoma Hut78 cell line were assessed. Expression of EZH2 and trimethylation status of histone 3, lysine 27 trimethylated (H3K27m3) was also determined in response to ribavirin. The transcriptional effects of ribavirin on Hut78 cells were analyzed by microarray expression and the results were validated by reverse transcription‑quantitative polymerase chain reaction, western blotting and knockout of signal transducer and activator of transcription 1 (STAT1). The results of the present study demonstrated that ribavirin suppressed the growth and clonogenicity of cells in a dose‑dependent manner. Ribavirin did not affect the expression of EZH2 nor altered its activity as evaluated by H3K27 trimethylation status. Furthermore, the results of transcriptome analysis indicated that the majority of the canonical pathways affected by ribavirin were associated with the immune system, including 'antigen presentation', 'communication between innate and adaptive immune cells' and 'cross‑talk between dendritic and natural killer cells'. The results of gene expression analysis were confirmed, by demonstrating at the RNA and protein levels, downregulation of stearoyl‑CoA desaturase and upregulation of STAT1. Depletion of STAT1, which was proposed as a key regulator of the aforementioned pathways, exerted growth inhibitory effects almost to the same extent as ribavirin. In conclusion, ribavirin was proposed to exert growth inhibitory effects on lymphoma cell lines, particularly Hut78 cells, a cutaneous T‑cell lymphoma cell line. Of note, these effects may depend on, at least in part, the activation of canonical immune pathways regulated by the key factors STAT1 and interferon‑γ. Our results provide insight into the anti‑lymphoma potential of ribavirin; however, further investigations in preclinical and clinical studies are required to determine the effectiveness of ribavirin as a therapeutic agent for treating lymphoma.
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Affiliation(s)
| | | | - Alma Chavez-Blanco
- Division of Basic Research, National Cancer Institute (INCAN), Mexico City 14080, Mexico
| | - Lucia Taja-Chayeb
- Division of Basic Research, National Cancer Institute (INCAN), Mexico City 14080, Mexico
| | - Alfredo Hidalgo-Miranda
- Cancer Genomics Laboratory, National Institute of Genomic Medicine (INMEGEN), Mexico City 14610, Mexico
| | - Alberto Cedro-Tanda
- Cancer Genomics Laboratory, National Institute of Genomic Medicine (INMEGEN), Mexico City 14610, Mexico
| | - Fredy Beltran-Anaya
- Cancer Genomics Laboratory, National Institute of Genomic Medicine (INMEGEN), Mexico City 14610, Mexico
| | - Jose Diaz-Chavez
- Division of Basic Research, National Cancer Institute (INCAN), Mexico City 14080, Mexico
| | | | - Aurora Gonzalez-Fierro
- Division of Basic Research, National Cancer Institute (INCAN), Mexico City 14080, Mexico
| | - Alfonso Dueñas-Gonzalez
- Unit of Biomedical Research, Institute of Biomedical Research, National Autonomous University of Mexico (UNAM)/INCAN, Mexico City 14080, Mexico
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Beltrán-Anaya FO, Romero-Córdoba S, Rebollar-Vega R, Arrieta O, Bautista-Piña V, Dominguez-Reyes C, Villegas-Carlos F, Tenorio-Torres A, Alfaro-Riuz L, Jiménez-Morales S, Cedro-Tanda A, Ríos-Romero M, Reyes-Grajeda JP, Tagliabue E, Iorio MV, Hidalgo-Miranda A. Expression of long non-coding RNA ENSG00000226738 (LncKLHDC7B) is enriched in the immunomodulatory triple-negative breast cancer subtype and its alteration promotes cell migration, invasion, and resistance to cell death. Mol Oncol 2019; 13:909-927. [PMID: 30648789 PMCID: PMC6441920 DOI: 10.1002/1878-0261.12446] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 11/29/2018] [Accepted: 12/30/2018] [Indexed: 12/31/2022] Open
Abstract
Triple negative breast cancer (TNBC) represents an aggressive phenotype with poor prognosis compared with ER, PR, and HER2‐positive tumors. TNBC is a heterogeneous disease, and gene expression analysis has identified seven molecular subtypes. Accumulating evidence demonstrates that long non‐coding RNA (lncRNA) are involved in regulation of gene expression and cancer biology, contributing to essential cancer cell functions. In this study, we analyzed the expression profile of lncRNA in TNBC subtypes from 156 TNBC samples, and then characterized the functional role of LncKLHDC7B (ENSG00000226738). A total of 710 lncRNA were found to be differentially expressed between TNBC subtypes, and a subset of these altered lncRNA were independently validated. We discovered that LncKLHDC7B (ENSG00000226738) acts as a transcriptional modulator of its neighboring coding gene KLHDC7B in the immunomodulatory subtype. Furthermore, LncKLHDC7B knockdown enhanced migration and invasion, and promoted resistance to cellular death. Our findings confirmed the contribution of LncKLHDC7B to induction of apoptosis and inhibition of cell migration and invasion, suggesting that TNBC tumors with enrichment of LncKLHDC7B may exhibit distinct regulatory activity, or that this may be a generalized process in breast cancer. Additionally, in silico analysis confirmed for the first time that the low expression of KLHDC7B and LncKLHDC7B is associated with poor prognosis in patients with breast cancer.
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Affiliation(s)
- Fredy Omar Beltrán-Anaya
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico.,Programa de Doctorado en Ciencias Biomédicas, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Sandra Romero-Córdoba
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico.,Department of Experimental Oncology and Molecular Medicine, Istituto Nazionale dei Tumori, Milan, Italy
| | - Rosa Rebollar-Vega
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Oscar Arrieta
- Thoracic Oncology Unit, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
| | | | | | | | | | - Luis Alfaro-Riuz
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Silvia Jiménez-Morales
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Alberto Cedro-Tanda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico.,Programa de Doctorado en Ciencias Biomédicas, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Magdalena Ríos-Romero
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | | | - Elda Tagliabue
- Department of Experimental Oncology and Molecular Medicine, Istituto Nazionale dei Tumori, Milan, Italy
| | - Marilena V Iorio
- Department of Experimental Oncology and Molecular Medicine, Istituto Nazionale dei Tumori, Milan, Italy
| | - Alfredo Hidalgo-Miranda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
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Fernández-Lopez JC, Romero-Córdoba S, Rebollar-Vega R, Alfaro-Ruiz LA, Jiménez-Morales S, Beltrán-Anaya F, Arellano-Llamas R, Cedro-Tanda A, Rios-Romero M, Ramirez-Florencio M, Bautista-Piña V, Dominguez-Reyes C, Villegas-Carlos F, Tenorio-Torres A, Hidalgo-Miranda A. Population and breast cancer patients' analysis reveals the diversity of genomic variation of the BRCA genes in the Mexican population. Hum Genomics 2019; 13:3. [PMID: 30630528 PMCID: PMC6327376 DOI: 10.1186/s40246-018-0188-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 12/18/2018] [Indexed: 01/08/2023] Open
Abstract
Interpretation of variants of unknown significance (VUS) in genetic tests is complicated in ethnically diverse populations, given the lack of information regarding the common spectrum of genetic variation in clinically relevant genes. Public availability of data obtained from high-throughput genotyping and/or exome massive parallel sequencing (MPS)-based projects from several thousands of outbred samples might become useful tools to evaluate the pathogenicity of a VUS, based on its frequency in different populations. In the case of the Mexican and other Latino populations, several thousands of samples have been genotyped or sequenced during the last few years as part of different efforts to identify common variants associated to common diseases. In this report, we analyzed Mexican population data from a sample of 3985 outbred individuals, and additional 66 hereditary breast cancer patients were analyzed in order to better define the spectrum of common genomic variation of the BRCA1 and BRCA2 genes. Our analyses identified the most common genetic variants in these clinically relevant genes as well as the presence and frequency of specific pathogenic mutations present in the Mexican population. Analysis of the 3985 population samples by MPS identified three pathogenic mutations in BRCA1, only one population sample showed a BRCA1 exon 16-17 deletion by MLPA. This resulted in a basal prevalence of deleterious mutations of 0.10% (1:996) for BRCA1 and 11 pathogenic mutations in BRCA2, resulting in a basal prevalence of deleterious mutations of 0.276% (1:362) for BRCA2, combined of 0.376% (1:265). Separate analysis of the breast cancer patients identified the presence of pathogenic mutations in 18% (12 pathogenic mutations in 66 patients) of the samples by MPS and 13 additional alterations by MLPA. These results will support a better interpretation of clinical studies focused on the detection of BRCA mutations in Mexican and Latino populations and will help to define the general prevalence of deleterious mutations within these populations.
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Affiliation(s)
- J C Fernández-Lopez
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Perfiérico Sur, 4809, Arenal Tepepan, 14610, Mexico City, CP, Mexico
| | - S Romero-Córdoba
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Perfiérico Sur, 4809, Arenal Tepepan, 14610, Mexico City, CP, Mexico
| | - R Rebollar-Vega
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Perfiérico Sur, 4809, Arenal Tepepan, 14610, Mexico City, CP, Mexico
| | - L A Alfaro-Ruiz
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Perfiérico Sur, 4809, Arenal Tepepan, 14610, Mexico City, CP, Mexico
| | - S Jiménez-Morales
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Perfiérico Sur, 4809, Arenal Tepepan, 14610, Mexico City, CP, Mexico
| | - F Beltrán-Anaya
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Perfiérico Sur, 4809, Arenal Tepepan, 14610, Mexico City, CP, Mexico
| | - R Arellano-Llamas
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Perfiérico Sur, 4809, Arenal Tepepan, 14610, Mexico City, CP, Mexico
| | - A Cedro-Tanda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Perfiérico Sur, 4809, Arenal Tepepan, 14610, Mexico City, CP, Mexico
| | - M Rios-Romero
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Perfiérico Sur, 4809, Arenal Tepepan, 14610, Mexico City, CP, Mexico
| | - M Ramirez-Florencio
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Perfiérico Sur, 4809, Arenal Tepepan, 14610, Mexico City, CP, Mexico
| | - V Bautista-Piña
- Instituto de Enfermedades la Mama FUCAM, Avenida El Bordo 100, Santa Ursula Coapa, 04980, Mexico City, CP, Mexico
| | - C Dominguez-Reyes
- Instituto de Enfermedades la Mama FUCAM, Avenida El Bordo 100, Santa Ursula Coapa, 04980, Mexico City, CP, Mexico
| | - F Villegas-Carlos
- Instituto de Enfermedades la Mama FUCAM, Avenida El Bordo 100, Santa Ursula Coapa, 04980, Mexico City, CP, Mexico
| | - A Tenorio-Torres
- Instituto de Enfermedades la Mama FUCAM, Avenida El Bordo 100, Santa Ursula Coapa, 04980, Mexico City, CP, Mexico
| | - A Hidalgo-Miranda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Perfiérico Sur, 4809, Arenal Tepepan, 14610, Mexico City, CP, Mexico.
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Huerta-Chagoya A, Moreno-Macías H, Fernández-López JC, Ordóñez-Sánchez ML, Rodríguez-Guillén R, Contreras A, Hidalgo-Miranda A, Alfaro-Ruíz LA, Salazar-Fernandez EP, Moreno-Estrada A, Aguilar-Salinas CA, Tusié-Luna T. A panel of 32 AIMs suitable for population stratification correction and global ancestry estimation in Mexican mestizos. BMC Genet 2019; 20:5. [PMID: 30621578 PMCID: PMC6323778 DOI: 10.1186/s12863-018-0707-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 12/18/2018] [Indexed: 11/16/2022] Open
Abstract
Background Association studies are useful to unravel the genetic basis of common human diseases. However, the presence of undetected population structure can lead to both false positive results and failures to detect genuine associations. Even when most of the approaches to deal with population stratification require genome-wide data, the use of a well-selected panel of ancestry informative markers (AIMs) may appropriately correct for population stratification. Few panels of AIMs have been developed for Latino populations and most contain a high number of markers (> 100 AIMs). For some association studies such as candidate gene approaches, it may be unfeasible to genotype a numerous set of markers to avoid false positive results. In such cases, methods that use fewer AIMs may be appropriate. Results We validated an accurate and cost-effective panel of AIMs, for use in population stratification correction of association studies and global ancestry estimation in Mexicans, as well as in populations having large proportions of both European and Native American ancestries. Based on genome-wide data from 1953 Mexican individuals, we performed a PCA and SNP weights were calculated to select subsets of unlinked AIMs within percentiles 0.10 and 0.90, ensuring that all chromosomes were represented. Correlations between PC1 calculated using genome-wide data versus each subset of AIMs (16, 32, 48 and 64) were r2 = 0.923, 0.959, 0.972 and 0.978, respectively. When evaluating PCs performance as population stratification adjustment covariates, no correlation was found between P values obtained from uncorrected and genome-wide corrected association analyses (r2 = 0.141), highlighting that population stratification correction is compulsory for association analyses in admixed populations. In contrast, high correlations were found when adjusting for both PC1 and PC2 for either subset of AIMs (r2 > 0.900). After multiple validations, including an independent sample, we selected a minimal panel of 32 AIMs, which are highly informative of the major ancestral components of Mexican mestizos, namely European and Native American ancestries. Finally, the correlation between the global ancestry proportions calculated using genome-wide data and our panel of 32 AIMs was r2 = 0.972. Conclusions Our panel of 32 AIMs accurately estimated global ancestry and corrected for population stratification in association studies in Mexican individuals. Electronic supplementary material The online version of this article (10.1186/s12863-018-0707-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alicia Huerta-Chagoya
- CONACYT, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de Mexico, Mexico
| | | | | | - María Luisa Ordóñez-Sánchez
- Unidad de Biología Molecular y Medicina Genómica, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de Mexico, Mexico
| | - Rosario Rodríguez-Guillén
- Unidad de Biología Molecular y Medicina Genómica, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de Mexico, Mexico
| | - Alejandra Contreras
- Instituto Nacional de Medicina Genómica, Ciudad de Mexico, Mexico.,Fox Chase Cancer Center, Philadelphia, USA
| | - Alfredo Hidalgo-Miranda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Ciudad de Mexico, Mexico
| | - Luis Alberto Alfaro-Ruíz
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Ciudad de Mexico, Mexico
| | | | - Andrés Moreno-Estrada
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO-UGA), CINVESTAV, Iraputato, Guanajuato, Mexico
| | - Carlos Alberto Aguilar-Salinas
- Departamento de Endocrinología y Metabolismo, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de Mexico, Mexico
| | - Teresa Tusié-Luna
- Unidad de Biología Molecular y Medicina Genómica, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de Mexico, Mexico. .,Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, UNAM, Ciudad de Mexico, Mexico.
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Romero-Cordoba SL, Rodriguez-Cuevas S, Bautista-Pina V, Maffuz-Aziz A, D'Ippolito E, Cosentino G, Baroni S, Iorio MV, Hidalgo-Miranda A. Loss of function of miR-342-3p results in MCT1 over-expression and contributes to oncogenic metabolic reprogramming in triple negative breast cancer. Sci Rep 2018; 8:12252. [PMID: 30115973 PMCID: PMC6095912 DOI: 10.1038/s41598-018-29708-9] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 07/17/2018] [Indexed: 12/20/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is a heterogeneous and aggressive neoplasia lacking the expression of hormonal receptors and human epidermal growth factor receptor-2. Accumulating evidence has highlighted the importance of miRNAs dysregulation in the establishment of cancer programs, but the functional role of many miRNAs remains unclear. The description of miRNAs roles might provide novel strategies for treatment. In the present work, an integrated analysis of miRNA transcriptional landscape was performed (N = 132), identifying the significant down-modulation of miR-342-3p in TNBC, probably because of the aberrant activity of estrogen receptor, which serves as a transcription factor of the miRNA, as demonstrated by a siRNA-knockdown approach. The enhanced expression of miR-342-3p significantly decreased cell proliferation, viability and migration rates of diverse TN cells in vitro. Bioinformatic and functional analyses revealed that miR-342-3p directly targets the monocarboxylate transporter 1 (MCT1), which promotes lactate and glucose fluxes alteration, thus disrupting the metabolic homeostasis of tumor cells. Optical metabolic imaging assay defined a higher optical redox ratio in glycolytic cells overexpressing miR-342-3p. Furthermore, we found that hypoxic conditions and glucose starvation attenuate miR-342-3p expression, suggesting a crosstalk program between these metabolic factors. Consistently, miR-342-3p down-modulation is associated with an increased MCT1 expression level and glycolytic score in human triple negative tumors. Overall, we described for the first time the regulatory activity of miR-342-3p on relevant metabolic carcinogenic pathways in TN breast cancers.
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Affiliation(s)
- Sandra L Romero-Cordoba
- Cancer Genomics Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
- Start Up Unit, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | | | | | | | - Elvira D'Ippolito
- Start Up Unit, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Giulia Cosentino
- Start Up Unit, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Sara Baroni
- Start Up Unit, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Marilena V Iorio
- Start Up Unit, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy.
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Jiménez-Morales S, Pérez-Amado CJ, Langley E, Hidalgo-Miranda A. Overview of mitochondrial germline variants and mutations in human disease: Focus on breast cancer (Review). Int J Oncol 2018; 53:923-936. [PMID: 30015870 DOI: 10.3892/ijo.2018.4468] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 05/18/2018] [Indexed: 11/06/2022] Open
Abstract
High lactate production in cells during growth under oxygen-rich conditions (aerobic glycolysis) is a hallmark of tumor cells, indicating the role of mitochondrial function in tumorigenesis. In fact, enhanced mitochondrial biogenesis and impaired quality control are frequently observed in cancer cells. Mitochondrial DNA (mtDNA) encodes 13 subunits of oxidative phosphorylation (OXPHOS), is present in thousands of copies per cell, and has a very high mutation rate. Mutations in mtDNA and nuclear DNA (nDNA) genes encoding proteins that are important players in mitochondrial biogenesis and function are involved in oncogenic processes. A wide range of germline mtDNA polymorphisms, as well as tumor mtDNA somatic mutations have been identified in diverse cancer types. Approximately 72% of supposed tumor-specific somatic mtDNA mutations reported, have also been found as polymorphisms in the general population. The ATPase 6 and NADH dehydrogenase subunit genes of mtDNA are the most commonly mutated genes in breast cancer (BC). Furthermore, nuclear genes playing a role in mitochondrial biogenesis and function, such as peroxisome proliferators-activated receptor gamma coactivator-1 (PGC-1), fumarate hydratase (FH) and succinate dehydrogenase (SDH) are frequently mutated in cancer. In this review, we provide an overview of the mitochondrial germline variants and mutations in cancer, with particular focus on those found in BC.
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Affiliation(s)
- Silvia Jiménez-Morales
- Laboratory of Cancer Genomics, National Institute of Genomic Medicine, 14610 Mexico City, Mexico
| | - Carlos J Pérez-Amado
- Biochemistry Sciences Program, National Autonomous University of Mexico, 04510 Mexico City, Mexico
| | - Elizabeth Langley
- Department of Basic Research, National Cancer Institute, 14080 Mexico City, Mexico
| | - Alfredo Hidalgo-Miranda
- Laboratory of Cancer Genomics, National Institute of Genomic Medicine, 14610 Mexico City, Mexico
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Munguía-Moreno JA, Díaz-Chavéz J, García-Villa E, Albino-Sanchez ME, Mendoza-Villanueva D, Ocadiz-Delgado R, Bonilla-Delgado J, Marín-Flores A, Cortés-Malagón EM, Alvarez-Rios E, Hidalgo-Miranda A, Üren A, Çelik H, Lambert PF, Gariglio P. Early synergistic interactions between the HPV16‑E7 oncoprotein and 17β-oestradiol for repressing the expression of Granzyme B in a cervical cancer model. Int J Oncol 2018; 53:579-591. [PMID: 29901186 PMCID: PMC6017153 DOI: 10.3892/ijo.2018.4432] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 02/23/2018] [Indexed: 12/18/2022] Open
Abstract
Although high-risk human papillomavirus (HR‑HPV) infection has a prominent role in the aetiology of cervical cancer (CC), sex steroid hormones may also be involved in this process; however, the cooperation between oestrogen and HR‑HPV in the early stages of cervical carcinogenesis is poorly understood. Since 17β-oestradiol (E2) and the HPV type 16‑E7 oncoprotein induce CC in transgenic mice, a microarray analysis was performed in the present study to generate global gene expression profiles from 2‑month‑old FVB (non‑transgenic) and K14E7 (transgenic) mice who were left untreated or were treated for 1 month with E2. Upregulation of cancer-related genes that have not been previously reported in the context of CC, including glycerophosphodiester phosphodiesterase domain containing 3, interleukin 1 receptor type II, natriuretic peptide type C, MGAT4 family member C, lecithin-retinol acyltransferase (phosphatidylcholine-retinol-O-acyltransferase) and glucoside xylosyltransferase 2, was observed. Notably, upregulation of the serine (or cysteine) peptidase inhibitor clade B member 9 gene and downregulation of the Granzyme gene family were observed; the repression of the Granzyme B pathway may be a novel mechanism of immune evasion by cancer cells. The present results provide the basis for further studies on early biomarkers of CC risk and synergistic interactions between HR‑HPV and oestrogen.
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Affiliation(s)
- J Antonio Munguía-Moreno
- Department of Genetics and Molecular Biology, Centre for Research and Advanced Studies of the National Polytechnic Institute, México City 07360, México
| | - José Díaz-Chavéz
- Biomedical Unit for Cancer Research, National Autonomous University of Mexico/National Institute of Cancer, México City 14080, México
| | - Enrique García-Villa
- Department of Genetics and Molecular Biology, Centre for Research and Advanced Studies of the National Polytechnic Institute, México City 07360, México
| | - M Estela Albino-Sanchez
- Department of Genetics and Molecular Biology, Centre for Research and Advanced Studies of the National Polytechnic Institute, México City 07360, México
| | - Daniel Mendoza-Villanueva
- Laboratory of Cell and Developmental Signalling, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Rodolfo Ocadiz-Delgado
- Department of Genetics and Molecular Biology, Centre for Research and Advanced Studies of the National Polytechnic Institute, México City 07360, México
| | - José Bonilla-Delgado
- Research Unit of Genetics and Cancer, Juárez Hospital, México City 07760, México
| | - Armando Marín-Flores
- Department of Genetics and Molecular Biology, Centre for Research and Advanced Studies of the National Polytechnic Institute, México City 07360, México
| | | | - Elizabeth Alvarez-Rios
- Department of Genetics and Molecular Biology, Centre for Research and Advanced Studies of the National Polytechnic Institute, México City 07360, México
| | - Alfredo Hidalgo-Miranda
- Department of Oncogenomics, National Institute of Genomic Medicine, México City 14610, México, México
| | - Aykut Üren
- Department of Oncology, Lombardi Comprehensive Cancer Centre, Georgetown University Medical Centre, Washington, DC 20057, USA
| | - Haydar Çelik
- Department of Oncology, Lombardi Comprehensive Cancer Centre, Georgetown University Medical Centre, Washington, DC 20057, USA
| | - Paul F Lambert
- McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Patricio Gariglio
- Department of Genetics and Molecular Biology, Centre for Research and Advanced Studies of the National Polytechnic Institute, México City 07360, México
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Avilés-Vázquez S, Chávez-González A, Hidalgo-Miranda A, Moreno-Lorenzana D, Arriaga-Pizano L, Sandoval-Esquivel MÁ, Ayala-Sánchez M, Aguilar R, Alfaro-Ruiz L, Mayani H. Global gene expression profiles of hematopoietic stem and progenitor cells from patients with chronic myeloid leukemia: the effect of in vitro culture with or without imatinib. Cancer Med 2017; 6:2942-2956. [PMID: 29030909 PMCID: PMC5727298 DOI: 10.1002/cam4.1187] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 08/11/2017] [Accepted: 08/14/2017] [Indexed: 01/04/2023] Open
Abstract
In this study, we determined the gene expression profiles of bone marrow‐derived cell fractions, obtained from normal subjects and Chronic Myeloid Leukemia (CML) patients, that were highly enriched for hematopoietic stem (HSCs) and progenitor (HPCs) cells. Our results indicate that the profiles of CML HSCs and HPCs were closer to that of normal progenitors, whereas normal HSCs showed the most different expression profile of all. We found that the expression profiles of HSCs and HPCs from CML marrow were closer to each other than those of HSCs and HPCs from normal marrow. The major biologic processes dysregulated in CML cells included DNA repair, cell cycle, chromosome condensation, cell adhesion, and the immune response. We also determined the genomic changes in both normal and CML progenitor cells under culture conditions, and found that several genes involved in cell cycle, steroid biosynthesis, and chromosome segregation were upregulated, whereas genes involved in transcription regulation and apoptosis were downregulated. Interestingly, these changes were the same, regardless of the addition of Imatinib (IM) to the culture. Finally, we identified three genes—PIEZO2, RXFP1, and MAMDC2‐ that are preferentially expressed by CML primitive cells and that encode for cell membrane proteins; thus, they could be used as biomarkers for CML stem cells.
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Affiliation(s)
- Sócrates Avilés-Vázquez
- Oncology Research Unit, Oncology Hospital, National Medical Center, Mexican Institute for Social Security, Mexico City, Mexico
| | - Antonieta Chávez-González
- Oncology Research Unit, Oncology Hospital, National Medical Center, Mexican Institute for Social Security, Mexico City, Mexico
| | | | - Dafne Moreno-Lorenzana
- Oncology Research Unit, Oncology Hospital, National Medical Center, Mexican Institute for Social Security, Mexico City, Mexico
| | - Lourdes Arriaga-Pizano
- Immunochemistry Research Unit, National Medical Center, Mexican Institute for Social Security, Mexico City, Mexico
| | - Miguel Á Sandoval-Esquivel
- Oncology Research Unit, Oncology Hospital, National Medical Center, Mexican Institute for Social Security, Mexico City, Mexico
| | - Manuel Ayala-Sánchez
- Department of Hematology, La Raza Medical Center, Mexican Institute for Social Security, Mexico City, Mexico
| | - Rafael Aguilar
- Department of Hip Surgery, Villa Coapa General Hospital, Mexican Institute for Social Security, Mexico City, Mexico
| | | | - Hector Mayani
- Oncology Research Unit, Oncology Hospital, National Medical Center, Mexican Institute for Social Security, Mexico City, Mexico
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41
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Magaña-Aguirre J, Borgonio-Cuadra V, Valdéz-Vargas C, Romero-Córdoba S, Hidalgo-Miranda A, García-Sierra F, Hernandez-Hernandez O, Cisneros B. miRNA expression profiles in plasma patients with spinocerebellar ataxia type 7 (SCA7). J Neurol Sci 2017. [DOI: 10.1016/j.jns.2017.08.881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Arellano-Llamas R, Alfaro-Ruiz L, Arriaga Canon C, Imaz Rosshandler I, Cruz-Lagunas A, Zúñiga J, Rebollar Vega R, Wong CW, Maurer-Stroh S, Romero Córdoba S, Liu ET, Hidalgo-Miranda A, Vázquez-Pérez JA. Molecular features of influenza A (H1N1)pdm09 prevalent in Mexico during winter seasons 2012-2014. PLoS One 2017; 12:e0180419. [PMID: 28692701 PMCID: PMC5503254 DOI: 10.1371/journal.pone.0180419] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 05/23/2017] [Indexed: 12/28/2022] Open
Abstract
Since the emergence of the pandemic H1N1pdm09 virus in Mexico and California, biannual increases in the number of cases have been detected in Mexico. As observed in previous seasons, pandemic A/H1N1 09 virus was detected in severe cases during the 2011-2012 winter season and finally, during the 2013-2014 winter season it became the most prevalent influenza virus. Molecular and phylogenetic analyses of the whole viral genome are necessary to determine the antigenic and pathogenic characteristics of influenza viruses that cause severe outcomes of the disease. In this paper, we analyzed the evolution, antigenic and genetic drift of Mexican isolates from 2009, at the beginning of the pandemic, to 2014. We found a clear variation of the virus in Mexico from the 2011-2014 season due to different markers and in accordance with previous reports. In this study, we identified 13 novel substitutions with important biological effects, including virulence, T cell epitope presented by MHC and host specificity shift and some others substitutions might have more than one biological function. The systematic monitoring of mutations on whole genome of influenza A pH1N1 (2009) virus circulating at INER in Mexico City might provide valuable information to predict the emergence of new pathogenic influenza virus.
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Affiliation(s)
| | | | | | | | - Alfredo Cruz-Lagunas
- Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Joaquín Zúñiga
- Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | | | | | | | | | - Edison T. Liu
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | | | - Joel A. Vázquez-Pérez
- Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
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43
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Núñez-Enríquez JC, Bárcenas-López DA, Hidalgo-Miranda A, Jiménez-Hernández E, Bekker-Méndez VC, Flores-Lujano J, Solis-Labastida KA, Martínez-Morales GB, Sánchez-Muñoz F, Espinoza-Hernández LE, Velázquez-Aviña MM, Merino-Pasaye LE, García Velázquez AJ, Pérez-Saldívar ML, Mojica-Espinoza R, Ramírez-Bello J, Jiménez-Morales S, Mejía-Aranguré JM. Gene Expression Profiling of Acute Lymphoblastic Leukemia in Children with Very Early Relapse. Arch Med Res 2017; 47:644-655. [PMID: 28476192 DOI: 10.1016/j.arcmed.2016.12.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 11/24/2016] [Indexed: 10/19/2022]
Abstract
BACKGROUND AND AIMS Acute lymphoblastic leukemia (ALL) is the most common childhood cancer worldwide. Mexican patients have high mortality rates, low frequency of good prognosis biomarkers (i.e., ETV6-RUNX1) and a high proportion is classified at the time of diagnosis with a high risk to relapse according to clinical features. In addition, very early relapses are more frequently observed than in other populations. The aim of the study was to identify new potential biomarkers associated with very early relapse in Mexican ALL children through transcriptome analysis. METHODS Microarray gene expression profiling on bone marrow samples of 54 pediatric ALL patients, collected at time of diagnosis and/or at relapse, was performed. Eleven patients presented relapse within the first 18 months after diagnosis. Affymetrix Human Transcriptome Array 2.0 (HTA 2.0) was used to perform gene expression analysis. Annotation and functional enrichment analyses were carried out using Gene Ontology, KEGG pathway analysis and Ingenuity Pathway Analysis tools. RESULTS BLVRB, ZCCHC7, PAX5, EBF1, TMOD1 and BLNK were differentially expressed (fold-change >2.0 and p value <0.01) between relapsed and non-relapsed patients. Functional analysis of abnormally expressed genes revealed their important role in cellular processes related to the development of hematological diseases, cancer, cell death and survival and in cell-to-cell signaling interaction. CONCLUSIONS Our data support previous findings showing the relevance of PAX5, EBF1 and ZCCHC7 as potential biomarkers to identify a subgroup of ALL children in high risk to relapse.
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Affiliation(s)
- Juan Carlos Núñez-Enríquez
- Unidad de Investigación Médica en Epidemiología Clínica, UMAE Hospital de Pediatría, Centro Médico Nacional (CMN) "Siglo XXI", Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | | | - Alfredo Hidalgo-Miranda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
| | - Elva Jiménez-Hernández
- Servicio de Hematología Pediátrica, Hospital General "Gaudencio González Garza", Centro Médico Nacional (CMN) "La Raza", IMSS, Mexico City, Mexico
| | - Vilma Carolina Bekker-Méndez
- Unidad de Investigación Médica en Inmunología e Infectología, Hospital de Infectología "Dr. Daniel Méndez Hernández", "La Raza", IMSS, Mexico City, Mexico
| | - Janet Flores-Lujano
- Unidad de Investigación Médica en Epidemiología Clínica, UMAE Hospital de Pediatría, Centro Médico Nacional (CMN) "Siglo XXI", Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Karina Anastacia Solis-Labastida
- Servicio de Hematología Pediátrica, UMAE Hospital de Pediatría, Centro Médico Nacional (CMN) "Siglo XXI", Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Gabriela Bibiana Martínez-Morales
- Unidad de Investigación Médica en Epidemiología Clínica, UMAE Hospital de Pediatría, Centro Médico Nacional (CMN) "Siglo XXI", Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Fausto Sánchez-Muñoz
- Departamento de Inmunología, Instituto Nacional de Cardiología "Ignacio Chávez" (INCICh), Mexico City, Mexico
| | - Laura Eugenia Espinoza-Hernández
- Servicio de Hematología Pediátrica, Hospital General "Gaudencio González Garza", Centro Médico Nacional (CMN) "La Raza", IMSS, Mexico City, Mexico
| | | | - Laura Elizabeth Merino-Pasaye
- Servicio de Hematología Pediátrica, Centro Médico Nacional (CMN) "20 de Noviembre", Instituto de Seguridad Social al Servicio de los Trabajadores del Estado (ISSSTE), Mexico City, Mexico
| | | | - María Luisa Pérez-Saldívar
- Unidad de Investigación Médica en Epidemiología Clínica, UMAE Hospital de Pediatría, Centro Médico Nacional (CMN) "Siglo XXI", Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Raúl Mojica-Espinoza
- Unidad de Genotipificación y Análisis de Expresión, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Julián Ramírez-Bello
- Unidad de Investigación de Enfermedades Metabólicas y Endócrinas, Hospital Juárez de México, Mexico City, Mexico
| | - Silvia Jiménez-Morales
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico.
| | - Juan Manuel Mejía-Aranguré
- Unidad de Investigación Médica en Epidemiología Clínica, UMAE Hospital de Pediatría, Centro Médico Nacional (CMN) "Siglo XXI", Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico; Coordinación de Investigación en Salud, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico.
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- Mexican Inter-Institutional Group for the Identification of the Causes of Childhood Leukaemia, Instituto Mexicano del Seguro Social, Instituto de Seguridad Social al Servicio de los Trabajadores del Estado, Secretaría de Salud, Secretaría de Salud del Gobierno del Distrito Federal, Mexico City, México
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Jiménez-Morales S, Ramírez-Florencio M, Mejía-Aranguré JM, Núñez-Enríquez JC, Bekker-Mendez C, Torres-Escalante JL, Flores-Lujano J, Jiménez-Hernández E, Del Carmen Rodríguez-Zepeda M, Leal YA, González-Montalvo PM, Pantoja-Guillen F, Peñaloza-Gonzalez JG, Gutiérrez-Juárez EI, Núñez-Villegas NN, Pérez-Saldivar ML, Guerra-Castillo FX, Flores-Villegas LV, Ramos-Cervantes MT, Fragoso JM, García-Escalante MG, Del Carmen Pinto-Escalante D, Ramírez-Bello J, Hidalgo-Miranda A. Analysis of Thiopurine S-Methyltransferase Deficient Alleles in Acute Lymphoblastic Leukemia Patients in Mexican Patients. Arch Med Res 2017; 47:615-622. [PMID: 28476189 DOI: 10.1016/j.arcmed.2016.11.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 11/23/2016] [Indexed: 11/27/2022]
Abstract
BACKGROUND AND AIMS It has been demonstrated that heterozygote and homozygote thiopurine S-methyltransferase (TPMT) mutant allele carriers are at high risk to develop severe and potentially fatal hematopoietic toxicity after treatment with standard doses of 6-mercaptopurine (6-MP) and methotrexate (MX). Those drugs are the backbone of acute lymphoblastic leukemia (ALL) and several autoimmune disease treatments. We undertook this study to determine the frequency of the TPMT deficient alleles in children with ALL and non-ALL subjects from Mexico City and Yucatan, Mexico. METHODS We included 849 unrelated subjects, of which 368 ALL children and 342 non-ALL subjects were from Mexico City, and 60 ALL cases and 79 non-ALL individuals were from Yucatan. Genotyping of the rs1800462, rs1800460 and rs1142345 SNPs was performed by 5'exonuclease technique using TaqMan probes (Life Technologies Foster City, CA). RESULTS The mutant TPMT alleles were present in 4.8% (81/1698 chromosomes) and only 0.2% were homozygote TPMT*3A/TPMT*3A. We did not find statistically significant differences in the distribution of the mutant alleles between patients from Mexico City and Yucatan in either ALL cases or non-ALL. Nonetheless, the TPMT*3C frequency in ALL patients was higher than non-ALL subjects (p = 0.03). To note, the null homozygous TPMT*3A/TPMT*3A genotype was found in 2.5% of the non-ALL subjects. CONCLUSIONS TPMT mutant alleles did not exhibit differential distribution between both evaluated populations; however, TPMT*3C is overrepresented in ALL cases in comparison with non-ALL group. Assessing the TPMT mutant alleles could benefit the ALL children and those undergoing 6-MP and MX treatment.
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Affiliation(s)
- Silvia Jiménez-Morales
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, México.
| | - Mireya Ramírez-Florencio
- Facultad de Estudios Superiores Zaragoza, Universidad Nacional Autónoma de México, Mexico City, México
| | - Juan Manuel Mejía-Aranguré
- Unidad de Investigación Médica en Epidemiología Clínica, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, México; Coordinación de Investigación en Salud, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, México
| | - Juan Carlos Núñez-Enríquez
- Unidad de Investigación Médica en Epidemiología Clínica, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, México
| | - Carolina Bekker-Mendez
- Unidad de Investigación en Inmunología e Infectología Hospital de Infectologia, Centro Médico Nacional La Raza, Instituto Mexicano del Seguro Social, Mexico City, México
| | - José Luis Torres-Escalante
- Servicio de Pediatría de la UMAE, IMSS, Yucatán, Mexico; Facultad de Medicina, Universidad Autónoma de Yucatán, Yucatán, Mexico
| | - Janet Flores-Lujano
- Unidad de Investigación Médica en Epidemiología Clínica, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, México
| | - Elva Jiménez-Hernández
- Servicio de Hematología Pediátrica, Hospital General "Gaudencio González Garza", CMN "La Raza", IMSS, Ciudad de México, México
| | | | - Yelda A Leal
- Unidad de Investigación Médica Yucatán (UIMY), Registro de Cáncer Unidad Médica de Alta Especialidad UMAE-IMSS, Yucatán, México
| | - Pablo Miguel González-Montalvo
- Facultad de Medicina, Universidad Autónoma de Yucatán, Yucatán, Mexico; Servicio de Oncología Pediátrica del Hospital ÓHorán, SS, Yucatán, Mexico
| | - Francisco Pantoja-Guillen
- Facultad de Medicina, Universidad Autónoma de Yucatán, Yucatán, Mexico; Servicio de Oncología Pediátrica del Hospital ÓHorán, SS, Yucatán, Mexico
| | | | | | - Nora Nancy Núñez-Villegas
- Servicio de Hematología Pediátrica, Hospital General "Gaudencio González Garza", CMN "La Raza", IMSS, Ciudad de México, México
| | - Maria Luisa Pérez-Saldivar
- Unidad de Investigación Médica en Epidemiología Clínica, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, México
| | - Francisco Xavier Guerra-Castillo
- Unidad de Investigación en Inmunología e Infectología Hospital de Infectologia, Centro Médico Nacional La Raza, Instituto Mexicano del Seguro Social, Mexico City, México
| | - Luz Victoria Flores-Villegas
- Servicio de Hematología Pediátrica, CMN "20 de Noviembre", Instituto de Seguridad Social al Servicio de los Trabajadores del Estado (ISSSTE), Ciudad de México, México
| | - María Teresa Ramos-Cervantes
- Unidad de Investigación en Inmunología e Infectología Hospital de Infectologia, Centro Médico Nacional La Raza, Instituto Mexicano del Seguro Social, Mexico City, México
| | - José Manuel Fragoso
- Departamento de Biología Molecular, Instituto Nacional de Cardiología, Ignacio Chávez, Ciudad de México, Mexico
| | - María Guadalupe García-Escalante
- Laboratorio de Genética, Centro de Investigaciones Regionales Dr. Hideyo Noguchi, Universidad Autónoma de Yucatán, Yucatán, México
| | - Doris Del Carmen Pinto-Escalante
- Laboratorio de Genética, Centro de Investigaciones Regionales Dr. Hideyo Noguchi, Universidad Autónoma de Yucatán, Yucatán, México
| | - Julián Ramírez-Bello
- Laboratorio de la Unidad de Investigación en Enfermedades Metabólicas y Endócrinas del Hospital Juárez de México, Ciudad de México, Mexico
| | - Alfredo Hidalgo-Miranda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, México.
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Rheinbay E, Parasuraman P, Grimsby J, Tiao G, Engreitz JM, Kim J, Lawrence MS, Taylor-Weiner A, Rodriguez-Cuevas S, Rosenberg M, Hess J, Stewart C, Maruvka YE, Stojanov P, Cortes ML, Seepo S, Cibulskis C, Tracy A, Pugh TJ, Lee J, Zheng Z, Ellisen LW, Iafrate AJ, Boehm JS, Gabriel SB, Meyerson M, Golub TR, Baselga J, Hidalgo-Miranda A, Shioda T, Bernards A, Lander ES, Getz G. Recurrent and functional regulatory mutations in breast cancer. Nature 2017; 547:55-60. [PMID: 28658208 DOI: 10.1038/nature22992] [Citation(s) in RCA: 211] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 05/28/2017] [Indexed: 12/24/2022]
Abstract
Genomic analysis of tumours has led to the identification of hundreds of cancer genes on the basis of the presence of mutations in protein-coding regions. By contrast, much less is known about cancer-causing mutations in non-coding regions. Here we perform deep sequencing in 360 primary breast cancers and develop computational methods to identify significantly mutated promoters. Clear signals are found in the promoters of three genes. FOXA1, a known driver of hormone-receptor positive breast cancer, harbours a mutational hotspot in its promoter leading to overexpression through increased E2F binding. RMRP and NEAT1, two non-coding RNA genes, carry mutations that affect protein binding to their promoters and alter expression levels. Our study shows that promoter regions harbour recurrent mutations in cancer with functional consequences and that the mutations occur at similar frequencies as in coding regions. Power analyses indicate that more such regions remain to be discovered through deep sequencing of adequately sized cohorts of patients.
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Affiliation(s)
- Esther Rheinbay
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02124, USA.,Massachusetts General Hospital Center for Cancer Research, Charlestown, Massachusetts 02129, USA
| | - Prasanna Parasuraman
- Massachusetts General Hospital Center for Cancer Research, Charlestown, Massachusetts 02129, USA
| | - Jonna Grimsby
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02124, USA
| | - Grace Tiao
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02124, USA
| | - Jesse M Engreitz
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02124, USA.,Division of Health Sciences and Technology, MIT, Cambridge, Massachusetts 02139, USA
| | - Jaegil Kim
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02124, USA
| | - Michael S Lawrence
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02124, USA.,Massachusetts General Hospital Center for Cancer Research, Charlestown, Massachusetts 02129, USA
| | | | | | - Mara Rosenberg
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02124, USA
| | - Julian Hess
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02124, USA
| | - Chip Stewart
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02124, USA
| | - Yosef E Maruvka
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02124, USA.,Massachusetts General Hospital Center for Cancer Research, Charlestown, Massachusetts 02129, USA
| | - Petar Stojanov
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02124, USA
| | - Maria L Cortes
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02124, USA
| | - Sara Seepo
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02124, USA
| | - Carrie Cibulskis
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02124, USA
| | - Adam Tracy
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02124, USA
| | - Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network and the Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Jesse Lee
- Massachusetts General Hospital Center for Cancer Research, Charlestown, Massachusetts 02129, USA
| | - Zongli Zheng
- Massachusetts General Hospital Center for Cancer Research, Charlestown, Massachusetts 02129, USA
| | - Leif W Ellisen
- Massachusetts General Hospital Center for Cancer Research, Charlestown, Massachusetts 02129, USA.,Harvard Medical School, Boston, Massachusetts 02115, USA
| | - A John Iafrate
- Massachusetts General Hospital Center for Cancer Research, Charlestown, Massachusetts 02129, USA
| | - Jesse S Boehm
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02124, USA
| | - Stacey B Gabriel
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02124, USA
| | - Matthew Meyerson
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02124, USA.,Harvard Medical School, Boston, Massachusetts 02115, USA.,Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Todd R Golub
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02124, USA.,Harvard Medical School, Boston, Massachusetts 02115, USA.,Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Jose Baselga
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | | | - Toshi Shioda
- Massachusetts General Hospital Center for Cancer Research, Charlestown, Massachusetts 02129, USA
| | - Andre Bernards
- Massachusetts General Hospital Center for Cancer Research, Charlestown, Massachusetts 02129, USA
| | - Eric S Lander
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02124, USA
| | - Gad Getz
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02124, USA.,Massachusetts General Hospital Center for Cancer Research, Charlestown, Massachusetts 02129, USA.,Harvard Medical School, Boston, Massachusetts 02115, USA.,Massachusetts General Hospital, Department of Pathology, Boston, Massachusetts 02114, USA
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Ruvalcaba-Limon E, Rodriguez-Cuevas S, Hidalgo-Miranda A, Villa-Romero A, Bautista-Piña V, Rebollar-Vega R, Fernandez-Lopez JC, Morales-Vasquez F. Abstract P6-09-18: Predictive factors of pathologic complete response to neoadjuvant chemotherapy in patients with Luminal HER2(-) local advanced breast cancer using the DMET microarray. Cancer Res 2017. [DOI: 10.1158/1538-7445.sabcs16-p6-09-18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction
Patients with similar local advanced breast cancer (LABC) could respond different to neoadjuvant chemotherapy (NC). Luminal HER2(-) tumors have pathologic complete response (pCR) by 5-7%. Ki67, tumor grade and hormonal receptors, could be helpful but not enough to choice between NC vs. initial surgery. Response to drugs depends on enzymes involved in absorption, distribution, metabolism and elimination (ADME); the drug-metabolizing enzyme and transporter platform (DMET), could identify 1936 single nucleotide polymorphism (SNP) from 225 genes involved in ADME proccess.
Objective
To identify predictive factors to pCR in patients with Luminal HER2(-) LABC underwent NC, to distinguish wish patients could have a real benefit from NC.
Material and Methods
This is a prospective nested case control study (1:4) with LABC patients, pure invasive ductal carcinoma Luminal HER2(-) subtypes, and sequential NC (anthracyclines and taxanes). Cases were defined as patients with pCR (Residual Cancer Burden=0), and controls those without pCR. SNPs were evaluated from DNA of leucocytes using DMET microarrays by Affymetrix.
Bivariate analyses were used as appropriate. Microarrays were processed by the DMET analyzer console. OR and 95%CI were used to test association between pCR and variables with a non-conditional logistic regression analysis; p value ≤0.05 was considered statistically significant (two-sided).
Results
From 2005 to 2014, of 3762 treated patients, 287 women met inclusion criteria. We included 117 patients, 21 cases and 96 controls. Patients with pCR were 5 years younger than controls (45.4 vs 49.4), have more grade-3 tumors, (66.7 vs 22.3%), more Luminal B subtypes (90.5 vs 64.6%), lower expression of estrogen receptor (60 vs 80%) and higher Ki67 expression (65 vs 12%), all with p≤0.05. No differences in toxicity existed between groups.
In an initial screening procedure, 13 SNPs were identified, but only 4 SNPs (4 genes) are known to participate in ADME of antineoplastic agents. All pCR cases did not have the C/C allelic variant in the rs2072671 SNP (CDA gene); while in rs1883322 SNP (PPARD gene) all had T/T variant
SNPs identified in DMET microarray known to participate with antineoplastic agentsGENESNPAllelic variantpCR, n=21No pCR, n=96pDPYDrs17376848T/T13 (61.9%)83 (86.4%)0.007 C/T8 (38.1%)11 (11.4%) CDArs2072671A/A6 (28.5%)51 (53.1%)0.013 A/C15 (71.4%)36 (37.5%) C/C09 (9.3%) PPARDrs1883322T/T21 (100%)69 (71.8%)0.022 C/T022 (22.9%) C/C05 (5.2%) GSTM3rs7483A/A7 (33.3%)20 (20.8%)0.024 A/G13 (61.9%)43 (44.7%) G/G1 (4.7%)33 (34.3%) pCR= pathologic complete response
After logistic regression analysis, pCR predictive factors were the presence of grade-3 tumors OR=6.66 (95%CI=1.67-26.56), Ki67 ≥14% OR=15.45 (95%CI=1.71–138.86), premenopausal status OR=6.540 (95%CI=1.50–28.38) and A/A or A/G allele in rs7483 SNP (GSTM3 gene) OR=19.16 (95%CI=1.97–185.93).
Conclusions
Genetic variability encoded in the DMET-chip, could be helpful as a predictive factor of pCR in patients with Luminal HER2(-) LABC, but only in combination with other factors such as grade-3 tumors, elevated Ki67, and premenopausal status.
Citation Format: Ruvalcaba-Limon E, Rodriguez-Cuevas S, Hidalgo-Miranda A, Villa-Romero A, Bautista-Piña V, Rebollar-Vega R, Fernandez-Lopez JC, Morales-Vasquez F. Predictive factors of pathologic complete response to neoadjuvant chemotherapy in patients with Luminal HER2(-) local advanced breast cancer using the DMET microarray [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P6-09-18.
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Affiliation(s)
- E Ruvalcaba-Limon
- Breast Diseases Institute and Breast Cancer Fundation (IEM-FUCAM), Coyoacan, Mexico City, Mexico; Cancer Genomics Laboratory, National Genomics Institution, Tlalpan, Mexico City, Mexico; Faculty of Medicine, Autonomous National University of Mexico (UNAM), Mexico City, Mexico
| | - S Rodriguez-Cuevas
- Breast Diseases Institute and Breast Cancer Fundation (IEM-FUCAM), Coyoacan, Mexico City, Mexico; Cancer Genomics Laboratory, National Genomics Institution, Tlalpan, Mexico City, Mexico; Faculty of Medicine, Autonomous National University of Mexico (UNAM), Mexico City, Mexico
| | - A Hidalgo-Miranda
- Breast Diseases Institute and Breast Cancer Fundation (IEM-FUCAM), Coyoacan, Mexico City, Mexico; Cancer Genomics Laboratory, National Genomics Institution, Tlalpan, Mexico City, Mexico; Faculty of Medicine, Autonomous National University of Mexico (UNAM), Mexico City, Mexico
| | - A Villa-Romero
- Breast Diseases Institute and Breast Cancer Fundation (IEM-FUCAM), Coyoacan, Mexico City, Mexico; Cancer Genomics Laboratory, National Genomics Institution, Tlalpan, Mexico City, Mexico; Faculty of Medicine, Autonomous National University of Mexico (UNAM), Mexico City, Mexico
| | - V Bautista-Piña
- Breast Diseases Institute and Breast Cancer Fundation (IEM-FUCAM), Coyoacan, Mexico City, Mexico; Cancer Genomics Laboratory, National Genomics Institution, Tlalpan, Mexico City, Mexico; Faculty of Medicine, Autonomous National University of Mexico (UNAM), Mexico City, Mexico
| | - R Rebollar-Vega
- Breast Diseases Institute and Breast Cancer Fundation (IEM-FUCAM), Coyoacan, Mexico City, Mexico; Cancer Genomics Laboratory, National Genomics Institution, Tlalpan, Mexico City, Mexico; Faculty of Medicine, Autonomous National University of Mexico (UNAM), Mexico City, Mexico
| | - JC Fernandez-Lopez
- Breast Diseases Institute and Breast Cancer Fundation (IEM-FUCAM), Coyoacan, Mexico City, Mexico; Cancer Genomics Laboratory, National Genomics Institution, Tlalpan, Mexico City, Mexico; Faculty of Medicine, Autonomous National University of Mexico (UNAM), Mexico City, Mexico
| | - F Morales-Vasquez
- Breast Diseases Institute and Breast Cancer Fundation (IEM-FUCAM), Coyoacan, Mexico City, Mexico; Cancer Genomics Laboratory, National Genomics Institution, Tlalpan, Mexico City, Mexico; Faculty of Medicine, Autonomous National University of Mexico (UNAM), Mexico City, Mexico
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Flores-Pérez A, Marchat LA, Rodríguez-Cuevas S, Bautista-Piña V, Hidalgo-Miranda A, Ocampo EA, Martínez MS, Palma-Flores C, Fonseca-Sánchez MA, Astudillo-de la Vega H, Ruíz-García E, González-Barrios JA, Pérez-Plasencia C, Streber ML, López-Camarillo C. Dual targeting of ANGPT1 and TGFBR2 genes by miR-204 controls angiogenesis in breast cancer. Sci Rep 2016; 6:34504. [PMID: 27703260 PMCID: PMC5050489 DOI: 10.1038/srep34504] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 09/15/2016] [Indexed: 12/22/2022] Open
Abstract
Deregulated expression of microRNAs has been associated with angiogenesis. Studying the miRNome of locally advanced breast tumors we unsuspectedly found a dramatically repression of miR-204, a small non-coding RNA with no previous involvement in tumor angiogenesis. Downregulation of miR-204 was confirmed in an independent cohort of patients and breast cancer cell lines. Gain-of-function analysis indicates that ectopic expression of miR-204 impairs cell proliferation, anchorage-independent growth, migration, invasion, and the formation of 3D capillary networks in vitro. Likewise, in vivo vascularization and angiogenesis were suppressed by miR-204 in a nu/nu mice model. Genome-wide profiling of MDA-MB-231 cells expressing miR-204 revealed changes in the expression of hundred cancer-related genes. Of these, we focused on the study of pro-angiogenic ANGPT1 and TGFβR2. Functional analysis using luciferase reporter and rescue assays confirmed that ANGPT1 and TGFβR2 are novel effectors downstream of miR-204. Accordingly, an inverse correlation between miR-204 and ANGPT1/TGFβR2 expression was found in breast tumors. Knockdown of TGFβR2, but not ANGPT1, impairs cell proliferation and migration whereas inhibition of both genes inhibits angiogenesis. Taken altogether, our findings reveal a novel role for miR-204/ANGPT1/TGFβR2 axis in tumor angiogenesis. We propose that therapeutic manipulation of miR-204 levels may represent a promising approach in breast cancer.
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Affiliation(s)
- Ali Flores-Pérez
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Ciudad de México, México
| | - Laurence A Marchat
- Programa en Biomedicina Molecular y Red de Biotecnología, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Ciudad de México, México
| | | | | | | | - Elena Aréchaga Ocampo
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana, Ciudad de México, México
| | - Mónica Sierra Martínez
- Laboratorio de Genética y Diagnóstico Molecular, Hospital Juárez, Ciudad de México, México
| | - Carlos Palma-Flores
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Ciudad de México, México
| | - Miguel A Fonseca-Sánchez
- Departamento de Genética Humana, Hospital General de Mexico "Dr Eduardo Liceaga", Ciudad de México, México
| | - Horacio Astudillo-de la Vega
- Laboratorio de Investigación en Cáncer Translacional y Terapia Celular, Centro Médico Siglo XXI, Ciudad de México, México
| | - Erika Ruíz-García
- Laboratorio de Medicina Translacional, Instituto Nacional de Cancerología, Ciudad de México, México
| | | | - Carlos Pérez-Plasencia
- Laboratorio de Genómica, Instituto Nacional de Cancerología, Ciudad de México, México; Universidad Nacional Autónoma de México UNAM, FES-Iztacala, UBIMED, Tlalnepantla, Estado de México, México
| | - María L Streber
- Laboratorio de Investigación Experimental y Animal. Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México, México
| | - César López-Camarillo
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Ciudad de México, México
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Beltrán-Anaya FO, Cedro-Tanda A, Hidalgo-Miranda A, Romero-Cordoba SL. Insights into the Regulatory Role of Non-coding RNAs in Cancer Metabolism. Front Physiol 2016; 7:342. [PMID: 27551267 PMCID: PMC4976125 DOI: 10.3389/fphys.2016.00342] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 07/25/2016] [Indexed: 12/12/2022] Open
Abstract
Cancer represents a complex disease originated from alterations in several genes leading to disturbances in important signaling pathways in tumor biology, favoring heterogeneity that promotes adaptability and pharmacological resistance of tumor cells. Metabolic reprogramming has emerged as an important hallmark of cancer characterized by the presence of aerobic glycolysis, increased glutaminolysis and fatty acid biosynthesis, as well as an altered mitochondrial energy production. The metabolic switches that support energetic requirements of cancer cells are closely related to either activation of oncogenes or down-modulation of tumor-suppressor genes, finally leading to dysregulation of cell proliferation, metastasis and drug resistance signals. Non-coding RNAs (ncRNAs) have emerged as one important kind of molecules that can regulate altered genes contributing, to the establishment of metabolic reprogramming. Moreover, diverse metabolic signals can regulate ncRNA expression and activity at genetic, transcriptional, or epigenetic levels. The regulatory landscape of ncRNAs may provide a new approach for understanding and treatment of different types of malignancies. In this review we discuss the regulatory role exerted by ncRNAs on metabolic enzymes and pathways involved in glucose, lipid, and amino acid metabolism. We also review how metabolic stress conditions and tumoral microenvironment influence ncRNA expression and activity. Furthermore, we comment on the therapeutic potential of metabolism-related ncRNAs in cancer.
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Affiliation(s)
- Fredy O Beltrán-Anaya
- Cancer Genomics Laboratory, National Institute of Genomic Medicine Mexico City, Mexico
| | - Alberto Cedro-Tanda
- Cancer Genomics Laboratory, National Institute of Genomic Medicine Mexico City, Mexico
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Srivastava AK, Wang Y, Huang R, Skinner C, Thompson T, Pollard L, Wood T, Luo F, Stevenson R, Polimanti R, Gelernter J, Lin X, Lim IY, Wu Y, Teh AL, Chen L, Aris IM, Soh SE, Tint MT, MacIsaac JL, Yap F, Kwek K, Saw SM, Kobor MS, Meaney MJ, Godfrey KM, Chong YS, Holbrook JD, Lee YS, Gluckman PD, Karnani N, Kapoor A, Lee D, Chakravarti A, Maercker C, Graf F, Boutros M, Stamoulis G, Santoni F, Makrythanasis P, Letourneau A, Guipponi M, Panousis N, Garieri M, Ribaux P, Falconnet E, Borel C, Antonarakis SE, Kumar S, Curran J, Blangero J, Chatterjee S, Kapoor A, Akiyama J, Auer D, Berrios C, Pennacchio L, Chakravarti A, Donti TR, Cappuccio G, Miller M, Atwal P, Kennedy A, Cardon A, Bacino C, Emrick L, Hertecant J, Baumer F, Porter B, Bainbridge M, Bonnen P, Graham B, Sutton R, Sun Q, Elsea S, Hu Z, Wang P, Zhu Y, Zhao J, Xiong M, Bennett DA, Hidalgo-Miranda A, Romero-Cordoba S, Rodriguez-Cuevas S, Rebollar-Vega R, Tagliabue E, Iorio M, D’Ippolito E, Baroni S, Kaczkowski B, Tanaka Y, Kawaji H, Sandelin A, Andersson R, Itoh M, Lassmann T, Hayashizaki Y, Carninci P, Forrest ARR, Semple CA, Rosenthal EA, Shirts B, Amendola L, Gallego C, Horike-Pyne M, Burt A, Robertson P, Beyers P, Nefcy C, Veenstra D, Hisama F, Bennett R, Dorschner M, Nickerson D, Smith J, Patterson K, Crosslin D, Nassir R, Zubair N, Harrison T, Peters U, Jarvik G, Menghi F, Inaki K, Woo X, Kumar P, Grzeda K, Malhotra A, Kim H, Ucar D, Shreckengast P, Karuturi K, Keck J, Chuang J, Liu ET, Ji B, Tyler A, Ananda G, Carter G, Nikbakht H, Montagne M, Zeinieh M, Harutyunyan A, Mcconechy M, Jabado N, Lavigne P, Majewski J, Goldstein JB, Overman M, Varadhachary G, Shroff R, Wolff R, Javle M, Futreal A, Fogelman D, Bravo L, Fajardo W, Gomez H, Castaneda C, Rolfo C, Pinto JA, Akdemir KC, Chin L, Futreal A, Patterson S, Statz C, Mockus S, Nikolaev SN, Bonilla XI, Parmentier L, King B, Bezrukov F, Kaya G, Zoete V, Seplyarskiy V, Sharpe H, McKee T, Letourneau A, Ribaux P, Popadin K, Basset-Seguin N, Chaabene RB, Santoni F, Andrianova M, Guipponi M, Garieri M, Verdan C, Grosdemange K, Sumara O, Eilers M, Aifantis I, Michielin O, de Sauvage F, Antonarakis S, Likhitrattanapisal S, Lincoln S, Kurian A, Desmond A, Yang S, Kobayashi Y, Ford J, Ellisen L, Peters TL, Alvarez KR, Hollingsworth EF, Lopez-Terrada DH, Hastie A, Dzakula Z, Pang AW, Lam ET, Anantharaman T, Saghbini M, Cao H, Gonzaga-Jauregui C, Ma L, King A, Rosenzweig EB, Krishnan U, Reid JG, Overton JD, Dewey F, Chung WK, Small K, DeLuca A, Cremers F, Lewis RA, Puech V, Bakall B, Silva-Garcia R, Rohrschneider K, Leys M, Shaya FS, Stone E, Sobreira NL, Schiettecatte F, Ling H, Pugh E, Witmer D, Hetrick K, Zhang P, Doheny K, Valle D, Hamosh A, Jhangiani SN, Akdemir ZC, Bainbridge MN, Charng W, Wiszniewski W, Gambin T, Karaca E, Bayram Y, Eldomery MK, Posey J, Doddapaneni H, Hu J, Sutton VR, Muzny DM, Boerwinkle EA, Valle D, Lupski JR, Gibbs RA, Shekar S, Salerno W, English A, Mangubat A, Bruestle J, Thorogood A, Knoppers BM, Takahashi H, Nitta KR, Kozhuharova A, Suzuki AM, Sharma H, Cotella D, Santoro C, Zucchelli S, Gustincich S, Carninci P, Mulvihill JJ, Baynam G, Gahl W, Groft SC, Kosaki K, Lasko P, Melegh B, Taruscio D, Ghosh R, Plon S, Scherer S, Qin X, Sanghvi R, Walker K, Chiang T, Muzny D, Wang L, Black J, Boerwinkle E, Weinshilboum R, Gibbs R, Karpinets T, Calderone T, Wani K, Yu X, Creasy C, Haymaker C, Forget M, Nanda V, Roszik J, Wargo J, Haydu L, Song X, Lazar A, Gershenwald J, Davies M, Bernatchez C, Zhang J, Futreal A, Woodman S, Chesler EJ, Reynolds T, Bubier JA, Phillips C, Langston MA, Baker EJ, Xiong M, Ma L, Lin N, Amos C, Lin N, Wang P, Zhu Y, Zhao J, Calhoun V, Xiong M, Dobretsberger O, Egger M, Leimgruber F, Sadedin S, Oshlack A, Antonio VAA, Ono N, Ahmed Z, Bolisetty M, Zeeshan S, Anguiano E, Ucar D, Sarkar A, Nandineni MR, Zeng C, Shao J, Cao H, Hastie A, Pang AW, Lam ET, Liang T, Pham K, Saghbini M, Dzakula Z, Chee-Wei Y, Dongsheng L, Lai-Ping W, Lian D, Hee ROT, Yunus Y, Aghakhanian F, Mokhtar SS, Lok-Yung CV, Bhak J, Phipps M, Shuhua X, Yik-Ying T, Kumar V, Boon-Peng H, Campbell I, Young MA, James P, Rain M, Mohammad G, Kukreti R, Pasha Q, Akilzhanova AR, Guelly C, Abilova Z, Rakhimova S, Akhmetova A, Kairov U, Trajanoski S, Zhumadilov Z, Bekbossynova M, Schumacher C, Sandhu S, Harkins T, Makarov V, Doddapaneni H, Glenn R, Momin Z, Dilrukshi B, Chao H, Meng Q, Gudenkauf B, Kshitij R, Jayaseelan J, Nessner C, Lee S, Blankenberg K, Lewis L, Hu J, Han Y, Dinh H, Jireh S, Walker K, Boerwinkle E, Muzny D, Gibbs R, Hu J, Walker K, Buhay C, Liu X, Wang Q, Sanghvi R, Doddapaneni H, Ding Y, Veeraraghavan N, Yang Y, Boerwinkle E, Beaudet AL, Eng CM, Muzny DM, Gibbs RA, Worley KCC, Liu Y, Hughes DST, Murali SC, Harris RA, English AC, Qin X, Hampton OA, Larsen P, Beck C, Han Y, Wang M, Doddapaneni H, Kovar CL, Salerno WJ, Yoder A, Richards S, Rogers J, Lupski JR, Muzny DM, Gibbs RA, Meng Q, Bainbridge M, Wang M, Doddapaneni H, Han Y, Muzny D, Gibbs R, Harris RA, Raveenedran M, Xue C, Dahdouli M, Cox L, Fan G, Ferguson B, Hovarth J, Johnson Z, Kanthaswamy S, Kubisch M, Platt M, Smith D, Vallender E, Wiseman R, Liu X, Below J, Muzny D, Gibbs R, Yu F, Rogers J, Lin J, Zhang Y, Ouyang Z, Moore A, Wang Z, Hofmann J, Purdue M, Stolzenberg-Solomon R, Weinstein S, Albanes D, Liu CS, Cheng WL, Lin TT, Lan Q, Rothman N, Berndt S, Chen ES, Bahrami H, Khoshzaban A, Keshal SH, Bahrami H, Khoshzaban A, Keshal SH, Alharbi KKR, Zhalbinova M, Akilzhanova A, Rakhimova S, Bekbosynova M, Myrzakhmetova S, Matar M, Mili N, Molinari R, Ma Y, Guerrier S, Elhawary N, Tayeb M, Bogari N, Qotb N, McClymont SA, Hook PW, Goff LA, McCallion A, Kong Y, Charette JR, Hicks WL, Naggert JK, Zhao L, Nishina PM, Edrees BM, Athar M, Al-Allaf FA, Taher MM, Khan W, Bouazzaoui A, Harbi NA, Safar R, Al-Edressi H, Anazi A, Altayeb N, Ahmed MA, Alansary K, Abduljaleel Z, Kratz A, Beguin P, Poulain S, Kaneko M, Takahiko C, Matsunaga A, Kato S, Suzuki AM, Bertin N, Lassmann T, Vigot R, Carninci P, Plessy C, Launey T, Graur D, Lee D, Kapoor A, Chakravarti A, Friis-Nielsen J, Izarzugaza JM, Brunak S, Chakraborty A, Basak J, Mukhopadhyay A, Soibam BS, Das D, Biswas N, Das S, Sarkar S, Maitra A, Panda C, Majumder P, Morsy H, Gaballah A, Samir M, Shamseya M, Mahrous H, Ghazal A, Arafat W, Hashish M, Gruber JJ, Jaeger N, Snyder M, Patel K, Bowman S, Davis T, Kraushaar D, Emerman A, Russello S, Henig N, Hendrickson C, Zhang K, Rodriguez-Dorantes M, Cruz-Hernandez CD, Garcia-Tobilla CDP, Solorzano-Rosales S, Jäger N, Chen J, Haile R, Hitchins M, Brooks JD, Snyder M, Jiménez-Morales S, Ramírez M, Nuñez J, Bekker V, Leal Y, Jiménez E, Medina A, Hidalgo A, Mejía J, Halytskiy V, Naggert J, Collin GB, DeMauro K, Hanusek R, Nishina PM, Belhassa K, Belhassan K, Bouguenouch L, Samri I, Sayel H, moufid FZ, El Bouchikhi I, Trhanint S, Hamdaoui H, Elotmani I, Khtiri I, Kettani O, Quibibo L, Ahagoud M, Abbassi M, Ouldim K, Marusin AV, Kornetov AN, Swarovskaya M, Vagaiceva K, Stepanov V, De La Paz EMC, Sy R, Nevado J, Reganit P, Santos L, Magno JD, Punzalan FE, Ona D, Llanes E, Santos-Cortes RL, Tiongco R, Aherrera J, Abrahan L, Pagauitan-Alan P, Morelli KH, Domire JS, Pyne N, Harper S, Burgess R, Zhalbinova M, Akilzhanova A, Rakhimova S, Bekbosynova M, Myrzakhmetova S, Gari MA, Dallol A, Alsehli H, Gari A, Gari M, Abuzenadah A, Thomas M, Sukhai M, Garg S, Misyura M, Zhang T, Schuh A, Stockley T, Kamel-Reid S, Sherry S, Xiao C, Slotta D, Rodarmer K, Feolo M, Kimelman M, Godynskiy G, O’Sullivan C, Yaschenko E, Xiao C, Yaschenko E, Sherry S, Rangel-Escareño C, Rueda-Zarate H, Tayubi IA, Mohammed R, Ahmed I, Ahmed T, Seth S, Amin S, Song X, Mao X, Sun H, Verhaak RG, Futreal A, Zhang J, Whiite SJ, Chiang T, English A, Farek J, Kahn Z, Salerno W, Veeraraghavan N, Boerwinkle E, Gibbs R, Kasukawa T, Lizio M, Harshbarger J, Hisashi S, Severin J, Imad A, Sahin S, Freeman TC, Baillie K, Sandelin A, Carninci P, Forrest ARR, Kawaji H, Salerno W, English A, Shekar SN, Mangubat A, Bruestle J, Boerwinkle E, Gibbs RA, Salem AH, Ali M, Ibrahim A, Ibrahim M, Barrera HA, Garza L, Torres JA, Barajas V, Ulloa-Aguirre A, Kershenobich D, Mortaji S, Guizar P, Loera E, Moreno K, De León A, Monsiváis D, Gómez J, Cardiel R, Fernandez-Lopez JC, Bonifaz-Peña V, Rangel-Escareño C, Hidalgo-Miranda A, Contreras AV, Polfus L, Wang X, Philip V, Carter G, Abuzenadah AA, Gari M, Turki R, Dallol A, Uyar A, Kaygun A, Zaman S, Marquez E, George J, Ucar D, Hendrickson CL, Emerman A, Kraushaar D, Bowman S, Henig N, Davis T, Russello S, Patel K, Starr DB, Baird M, Kirkpatrick B, Sheets K, Nitsche R, Prieto-Lafuente L, Landrum M, Lee J, Rubinstein W, Maglott D, Thavanati PKR, de Dios AE, Hernandez REN, Aldrate MEA, Mejia MRR, Kanala KRR, Abduljaleel Z, Khan W, Al-Allaf FA, Athar M, Taher MM, Shahzad N, Bouazzaoui A, Huber E, Dan A, Al-Allaf FA, Herr W, Sprotte G, Köstler J, Hiergeist A, Gessner A, Andreesen R, Holler E, Al-Allaf F, Alashwal A, Abduljaleel Z, Taher M, Bouazzaoui A, Abalkhail H, Al-Allaf A, Bamardadh R, Athar M, Filiptsova O, Kobets M, Kobets Y, Burlaka I, Timoshyna I, Filiptsova O, Kobets MN, Kobets Y, Burlaka I, Timoshyna I, Filiptsova O, Kobets MN, Kobets Y, Burlaka I, Timoshyna I, Al-allaf FA, Mohiuddin MT, Zainularifeen A, Mohammed A, Abalkhail H, Owaidah T, Bouazzaoui A. Human genome meeting 2016 : Houston, TX, USA. 28 February - 2 March 2016. Hum Genomics 2016; 10 Suppl 1:12. [PMID: 27294413 PMCID: PMC4896275 DOI: 10.1186/s40246-016-0063-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
O1 The metabolomics approach to autism: identification of biomarkers for early detection of autism spectrum disorder A. K. Srivastava, Y. Wang, R. Huang, C. Skinner, T. Thompson, L. Pollard, T. Wood, F. Luo, R. Stevenson O2 Phenome-wide association study for smoking- and drinking-associated genes in 26,394 American women with African, Asian, European, and Hispanic descents R. Polimanti, J. Gelernter O3 Effects of prenatal environment, genotype and DNA methylation on birth weight and subsequent postnatal outcomes: findings from GUSTO, an Asian birth cohort X. Lin, I. Y. Lim, Y. Wu, A. L. Teh, L. Chen, I. M. Aris, S. E. Soh, M. T. Tint, J. L. MacIsaac, F. Yap, K. Kwek, S. M. Saw, M. S. Kobor, M. J. Meaney, K. M. Godfrey, Y. S. Chong, J. D. Holbrook, Y. S. Lee, P. D. Gluckman, N. Karnani, GUSTO study group O4 High-throughput identification of specific qt interval modulating enhancers at the SCN5A locus A. Kapoor, D. Lee, A. Chakravarti O5 Identification of extracellular matrix components inducing cancer cell migration in the supernatant of cultivated mesenchymal stem cells C. Maercker, F. Graf, M. Boutros O6 Single cell allele specific expression (ASE) IN T21 and common trisomies: a novel approach to understand DOWN syndrome and other aneuploidies G. Stamoulis, F. Santoni, P. Makrythanasis, A. Letourneau, M. Guipponi, N. Panousis, M. Garieri, P. Ribaux, E. Falconnet, C. Borel, S. E. Antonarakis O7 Role of microRNA in LCL to IPSC reprogramming S. Kumar, J. Curran, J. Blangero O8 Multiple enhancer variants disrupt gene regulatory network in Hirschsprung disease S. Chatterjee, A. Kapoor, J. Akiyama, D. Auer, C. Berrios, L. Pennacchio, A. Chakravarti O9 Metabolomic profiling for the diagnosis of neurometabolic disorders T. R. Donti, G. Cappuccio, M. Miller, P. Atwal, A. Kennedy, A. Cardon, C. Bacino, L. Emrick, J. Hertecant, F. Baumer, B. Porter, M. Bainbridge, P. Bonnen, B. Graham, R. Sutton, Q. Sun, S. Elsea O10 A novel causal methylation network approach to Alzheimer’s disease Z. Hu, P. Wang, Y. Zhu, J. Zhao, M. Xiong, David A Bennett O11 A microRNA signature identifies subtypes of triple-negative breast cancer and reveals MIR-342-3P as regulator of a lactate metabolic pathway A. Hidalgo-Miranda, S. Romero-Cordoba, S. Rodriguez-Cuevas, R. Rebollar-Vega, E. Tagliabue, M. Iorio, E. D’Ippolito, S. Baroni O12 Transcriptome analysis identifies genes, enhancer RNAs and repetitive elements that are recurrently deregulated across multiple cancer types B. Kaczkowski, Y. Tanaka, H. Kawaji, A. Sandelin, R. Andersson, M. Itoh, T. Lassmann, the FANTOM5 consortium, Y. Hayashizaki, P. Carninci, A. R. R. Forrest O13 Elevated mutation and widespread loss of constraint at regulatory and architectural binding sites across 11 tumour types C. A. Semple O14 Exome sequencing provides evidence of pathogenicity for genes implicated in colorectal cancer E. A. Rosenthal, B. Shirts, L. Amendola, C. Gallego, M. Horike-Pyne, A. Burt, P. Robertson, P. Beyers, C. Nefcy, D. Veenstra, F. Hisama, R. Bennett, M. Dorschner, D. Nickerson, J. Smith, K. Patterson, D. Crosslin, R. Nassir, N. Zubair, T. Harrison, U. Peters, G. Jarvik, NHLBI GO Exome Sequencing Project O15 The tandem duplicator phenotype as a distinct genomic configuration in cancer F. Menghi, K. Inaki, X. Woo, P. Kumar, K. Grzeda, A. Malhotra, H. Kim, D. Ucar, P. Shreckengast, K. Karuturi, J. Keck, J. Chuang, E. T. Liu O16 Modeling genetic interactions associated with molecular subtypes of breast cancer B. Ji, A. Tyler, G. Ananda, G. Carter O17 Recurrent somatic mutation in the MYC associated factor X in brain tumors H. Nikbakht, M. Montagne, M. Zeinieh, A. Harutyunyan, M. Mcconechy, N. Jabado, P. Lavigne, J. Majewski O18 Predictive biomarkers to metastatic pancreatic cancer treatment J. B. Goldstein, M. Overman, G. Varadhachary, R. Shroff, R. Wolff, M. Javle, A. Futreal, D. Fogelman O19 DDIT4 gene expression as a prognostic marker in several malignant tumors L. Bravo, W. Fajardo, H. Gomez, C. Castaneda, C. Rolfo, J. A. Pinto O20 Spatial organization of the genome and genomic alterations in human cancers K. C. Akdemir, L. Chin, A. Futreal, ICGC PCAWG Structural Alterations Group O21 Landscape of targeted therapies in solid tumors S. Patterson, C. Statz, S. Mockus O22 Genomic analysis reveals novel drivers and progression pathways in skin basal cell carcinoma S. N. Nikolaev, X. I. Bonilla, L. Parmentier, B. King, F. Bezrukov, G. Kaya, V. Zoete, V. Seplyarskiy, H. Sharpe, T. McKee, A. Letourneau, P. Ribaux, K. Popadin, N. Basset-Seguin, R. Ben Chaabene, F. Santoni, M. Andrianova, M. Guipponi, M. Garieri, C. Verdan, K. Grosdemange, O. Sumara, M. Eilers, I. Aifantis, O. Michielin, F. de Sauvage, S. Antonarakis O23 Identification of differential biomarkers of hepatocellular carcinoma and cholangiocarcinoma via transcriptome microarray meta-analysis S. Likhitrattanapisal O24 Clinical validity and actionability of multigene tests for hereditary cancers in a large multi-center study S. Lincoln, A. Kurian, A. Desmond, S. Yang, Y. Kobayashi, J. Ford, L. Ellisen O25 Correlation with tumor ploidy status is essential for correct determination of genome-wide copy number changes by SNP array T. L. Peters, K. R. Alvarez, E. F. Hollingsworth, D. H. Lopez-Terrada O26 Nanochannel based next-generation mapping for interrogation of clinically relevant structural variation A. Hastie, Z. Dzakula, A. W. Pang, E. T. Lam, T. Anantharaman, M. Saghbini, H. Cao, BioNano Genomics O27 Mutation spectrum in a pulmonary arterial hypertension (PAH) cohort and identification of associated truncating mutations in TBX4 C. Gonzaga-Jauregui, L. Ma, A. King, E. Berman Rosenzweig, U. Krishnan, J. G. Reid, J. D. Overton, F. Dewey, W. K. Chung O28 NORTH CAROLINA macular dystrophy (MCDR1): mutations found affecting PRDM13 K. Small, A. DeLuca, F. Cremers, R. A. Lewis, V. Puech, B. Bakall, R. Silva-Garcia, K. Rohrschneider, M. Leys, F. S. Shaya, E. Stone O29 PhenoDB and genematcher, solving unsolved whole exome sequencing data N. L. Sobreira, F. Schiettecatte, H. Ling, E. Pugh, D. Witmer, K. Hetrick, P. Zhang, K. Doheny, D. Valle, A. Hamosh O30 Baylor-Johns Hopkins Center for Mendelian genomics: a four year review S. N. Jhangiani, Z. Coban Akdemir, M. N. Bainbridge, W. Charng, W. Wiszniewski, T. Gambin, E. Karaca, Y. Bayram, M. K. Eldomery, J. Posey, H. Doddapaneni, J. Hu, V. R. Sutton, D. M. Muzny, E. A. Boerwinkle, D. Valle, J. R. Lupski, R. A. Gibbs O31 Using read overlap assembly to accurately identify structural genetic differences in an ashkenazi jewish trio S. Shekar, W. Salerno, A. English, A. Mangubat, J. Bruestle O32 Legal interoperability: a sine qua non for international data sharing A. Thorogood, B. M. Knoppers, Global Alliance for Genomics and Health - Regulatory and Ethics Working Group O33 High throughput screening platform of competent sineups: that can enhance translation activities of therapeutic target H. Takahashi, K. R. Nitta, A. Kozhuharova, A. M. Suzuki, H. Sharma, D. Cotella, C. Santoro, S. Zucchelli, S. Gustincich, P. Carninci O34 The undiagnosed diseases network international (UDNI): clinical and laboratory research to meet patient needs J. J. Mulvihill, G. Baynam, W. Gahl, S. C. Groft, K. Kosaki, P. Lasko, B. Melegh, D. Taruscio O36 Performance of computational algorithms in pathogenicity predictions for activating variants in oncogenes versus loss of function mutations in tumor suppressor genes R. Ghosh, S. Plon O37 Identification and electronic health record incorporation of clinically actionable pharmacogenomic variants using prospective targeted sequencing S. Scherer, X. Qin, R. Sanghvi, K. Walker, T. Chiang, D. Muzny, L. Wang, J. Black, E. Boerwinkle, R. Weinshilboum, R. Gibbs O38 Melanoma reprogramming state correlates with response to CTLA-4 blockade in metastatic melanoma T. Karpinets, T. Calderone, K. Wani, X. Yu, C. Creasy, C. Haymaker, M. Forget, V. Nanda, J. Roszik, J. Wargo, L. Haydu, X. Song, A. Lazar, J. Gershenwald, M. Davies, C. Bernatchez, J. Zhang, A. Futreal, S. Woodman O39 Data-driven refinement of complex disease classification from integration of heterogeneous functional genomics data in GeneWeaver E. J. Chesler, T. Reynolds, J. A. Bubier, C. Phillips, M. A. Langston, E. J. Baker O40 A general statistic framework for genome-based disease risk prediction M. Xiong, L. Ma, N. Lin, C. Amos O41 Integrative large-scale causal network analysis of imaging and genomic data and its application in schizophrenia studies N. Lin, P. Wang, Y. Zhu, J. Zhao, V. Calhoun, M. Xiong O42 Big data and NGS data analysis: the cloud to the rescue O. Dobretsberger, M. Egger, F. Leimgruber O43 Cpipe: a convergent clinical exome pipeline specialised for targeted sequencing S. Sadedin, A. Oshlack, Melbourne Genomics Health Alliance O44 A Bayesian classification of biomedical images using feature extraction from deep neural networks implemented on lung cancer data V. A. A. Antonio, N. Ono, Clark Kendrick C. Go O45 MAV-SEQ: an interactive platform for the Management, Analysis, and Visualization of sequence data Z. Ahmed, M. Bolisetty, S. Zeeshan, E. Anguiano, D. Ucar O47 Allele specific enhancer in EPAS1 intronic regions may contribute to high altitude adaptation of Tibetans C. Zeng, J. Shao O48 Nanochannel based next-generation mapping for structural variation detection and comparison in trios and populations H. Cao, A. Hastie, A. W. Pang, E. T. Lam, T. Liang, K. Pham, M. Saghbini, Z. Dzakula O49 Archaic introgression in indigenous populations of Malaysia revealed by whole genome sequencing Y. Chee-Wei, L. Dongsheng, W. Lai-Ping, D. Lian, R. O. Twee Hee, Y. Yunus, F. Aghakhanian, S. S. Mokhtar, C. V. Lok-Yung, J. Bhak, M. Phipps, X. Shuhua, T. Yik-Ying, V. Kumar, H. Boon-Peng O50 Breast and ovarian cancer prevention: is it time for population-based mutation screening of high risk genes? I. Campbell, M.-A. Young, P. James, Lifepool O53 Comprehensive coverage from low DNA input using novel NGS library preparation methods for WGS and WGBS C. Schumacher, S. Sandhu, T. Harkins, V. Makarov O54 Methods for large scale construction of robust PCR-free libraries for sequencing on Illumina HiSeqX platform H. DoddapaneniR. Glenn, Z. Momin, B. Dilrukshi, H. Chao, Q. Meng, B. Gudenkauf, R. Kshitij, J. Jayaseelan, C. Nessner, S. Lee, K. Blankenberg, L. Lewis, J. Hu, Y. Han, H. Dinh, S. Jireh, K. Walker, E. Boerwinkle, D. Muzny, R. Gibbs O55 Rapid capture methods for clinical sequencing J. Hu, K. Walker, C. Buhay, X. Liu, Q. Wang, R. Sanghvi, H. Doddapaneni, Y. Ding, N. Veeraraghavan, Y. Yang, E. Boerwinkle, A. L. Beaudet, C. M. Eng, D. M. Muzny, R. A. Gibbs O56 A diploid personal human genome model for better genomes from diverse sequence data K. C. C. Worley, Y. Liu, D. S. T. Hughes, S. C. Murali, R. A. Harris, A. C. English, X. Qin, O. A. Hampton, P. Larsen, C. Beck, Y. Han, M. Wang, H. Doddapaneni, C. L. Kovar, W. J. Salerno, A. Yoder, S. Richards, J. Rogers, J. R. Lupski, D. M. Muzny, R. A. Gibbs O57 Development of PacBio long range capture for detection of pathogenic structural variants Q. Meng, M. Bainbridge, M. Wang, H. Doddapaneni, Y. Han, D. Muzny, R. Gibbs O58 Rhesus macaques exhibit more non-synonymous variation but greater impact of purifying selection than humans R. A. Harris, M. Raveenedran, C. Xue, M. Dahdouli, L. Cox, G. Fan, B. Ferguson, J. Hovarth, Z. Johnson, S. Kanthaswamy, M. Kubisch, M. Platt, D. Smith, E. Vallender, R. Wiseman, X. Liu, J. Below, D. Muzny, R. Gibbs, F. Yu, J. Rogers O59 Assessing RNA structure disruption induced by single-nucleotide variation J. Lin, Y. Zhang, Z. Ouyang P1 A meta-analysis of genome-wide association studies of mitochondrial dna copy number A. Moore, Z. Wang, J. Hofmann, M. Purdue, R. Stolzenberg-Solomon, S. Weinstein, D. Albanes, C.-S. Liu, W.-L. Cheng, T.-T. Lin, Q. Lan, N. Rothman, S. Berndt P2 Missense polymorphic genetic combinations underlying down syndrome susceptibility E. S. Chen P4 The evaluation of alteration of ELAM-1 expression in the endometriosis patients H. Bahrami, A. Khoshzaban, S. Heidari Keshal P5 Obesity and the incidence of apolipoprotein E polymorphisms in an assorted population from Saudi Arabia population K. K. R. Alharbi P6 Genome-associated personalized antithrombotical therapy for patients with high risk of thrombosis and bleeding M. Zhalbinova, A. Akilzhanova, S. Rakhimova, M. Bekbosynova, S. Myrzakhmetova P7 Frequency of Xmn1 polymorphism among sickle cell carrier cases in UAE population M. Matar P8 Differentiating inflammatory bowel diseases by using genomic data: dimension of the problem and network organization N. Mili, R. Molinari, Y. Ma, S. Guerrier P9 Vulnerability of genetic variants to the risk of autism among Saudi children N. Elhawary, M. Tayeb, N. Bogari, N. Qotb P10 Chromatin profiles from ex vivo purified dopaminergic neurons establish a promising model to support studies of neurological function and dysfunction S. A. McClymont, P. W. Hook, L. A. Goff, A. McCallion P11 Utilization of a sensitized chemical mutagenesis screen to identify genetic modifiers of retinal dysplasia in homozygous Nr2e3rd7 mice Y. Kong, J. R. Charette, W. L. Hicks, J. K. Naggert, L. Zhao, P. M. Nishina P12 Ion torrent next generation sequencing of recessive polycystic kidney disease in Saudi patients B. M. Edrees, M. Athar, F. A. Al-Allaf, M. M. Taher, W. Khan, A. Bouazzaoui, N. A. Harbi, R. Safar, H. Al-Edressi, A. Anazi, N. Altayeb, M. A. Ahmed, K. Alansary, Z. Abduljaleel P13 Digital expression profiling of Purkinje neurons and dendrites in different subcellular compartments A. Kratz, P. Beguin, S. Poulain, M. Kaneko, C. Takahiko, A. Matsunaga, S. Kato, A. M. Suzuki, N. Bertin, T. Lassmann, R. Vigot, P. Carninci, C. Plessy, T. Launey P14 The evolution of imperfection and imperfection of evolution: the functional and functionless fractions of the human genome D. Graur P16 Species-independent identification of known and novel recurrent genomic entities in multiple cancer patients J. Friis-Nielsen, J. M. Izarzugaza, S. Brunak P18 Discovery of active gene modules which are densely conserved across multiple cancer types reveal their prognostic power and mutually exclusive mutation patterns B. S. Soibam P19 Whole exome sequencing of dysplastic leukoplakia tissue indicates sequential accumulation of somatic mutations from oral precancer to cancer D. Das, N. Biswas, S. Das, S. Sarkar, A. Maitra, C. Panda, P. Majumder P21 Epigenetic mechanisms of carcinogensis by hereditary breast cancer genes J. J. Gruber, N. Jaeger, M. Snyder P22 RNA direct: a novel RNA enrichment strategy applied to transcripts associated with solid tumors K. Patel, S. Bowman, T. Davis, D. Kraushaar, A. Emerman, S. Russello, N. Henig, C. Hendrickson P23 RNA sequencing identifies gene mutations for neuroblastoma K. Zhang P24 Participation of SFRP1 in the modulation of TMPRSS2-ERG fusion gene in prostate cancer cell lines M. Rodriguez-Dorantes, C. D. Cruz-Hernandez, C. D. P. Garcia-Tobilla, S. Solorzano-Rosales P25 Targeted Methylation Sequencing of Prostate Cancer N. Jäger, J. Chen, R. Haile, M. Hitchins, J. D. Brooks, M. Snyder P26 Mutant TPMT alleles in children with acute lymphoblastic leukemia from México City and Yucatán, Mexico S. Jiménez-Morales, M. Ramírez, J. Nuñez, V. Bekker, Y. Leal, E. Jiménez, A. Medina, A. Hidalgo, J. Mejía P28 Genetic modifiers of Alström syndrome J. Naggert, G. B. Collin, K. DeMauro, R. Hanusek, P. M. Nishina P31 Association of genomic variants with the occurrence of angiotensin-converting-enzyme inhibitor (ACEI)-induced coughing among Filipinos E. M. Cutiongco De La Paz, R. Sy, J. Nevado, P. Reganit, L. Santos, J. D. Magno, F. E. Punzalan , D. Ona , E. Llanes, R. L. Santos-Cortes , R. Tiongco, J. Aherrera, L. Abrahan, P. Pagauitan-Alan; Philippine Cardiogenomics Study Group P32 The use of “humanized” mouse models to validate disease association of a de novo GARS variant and to test a novel gene therapy strategy for Charcot-Marie-Tooth disease type 2D K. H. Morelli, J. S. Domire, N. Pyne, S. Harper, R. Burgess P34 Molecular regulation of chondrogenic human induced pluripotent stem cells M. A. Gari, A. Dallol, H. Alsehli, A. Gari, M. Gari, A. Abuzenadah P35 Molecular profiling of hematologic malignancies: implementation of a variant assessment algorithm for next generation sequencing data analysis and clinical reporting M. Thomas, M. Sukhai, S. Garg, M. Misyura, T. Zhang, A. Schuh, T. Stockley, S. Kamel-Reid P36 Accessing genomic evidence for clinical variants at NCBI S. Sherry, C. Xiao, D. Slotta, K. Rodarmer, M. Feolo, M. Kimelman, G. Godynskiy, C. O’Sullivan, E. Yaschenko P37 NGS-SWIFT: a cloud-based variant analysis framework using control-accessed sequencing data from DBGAP/SRA C. Xiao, E. Yaschenko, S. Sherry P38 Computational assessment of drug induced hepatotoxicity through gene expression profiling C. Rangel-Escareño, H. Rueda-Zarate P40 Flowr: robust and efficient pipelines using a simple language-agnostic approach;ultraseq; fast modular pipeline for somatic variation calling using flowr S. Seth, S. Amin, X. Song, X. Mao, H. Sun, R. G. Verhaak, A. Futreal, J. Zhang P41 Applying “Big data” technologies to the rapid analysis of heterogenous large cohort data S. J. Whiite, T. Chiang, A. English, J. Farek, Z. Kahn, W. Salerno, N. Veeraraghavan, E. Boerwinkle, R. Gibbs P42 FANTOM5 web resource for the large-scale genome-wide transcription start site activity profiles of wide-range of mammalian cells T. Kasukawa, M. Lizio, J. Harshbarger, S. Hisashi, J. Severin, A. Imad, S. Sahin, T. C. Freeman, K. Baillie, A. Sandelin, P. Carninci, A. R. R. Forrest, H. Kawaji, The FANTOM Consortium P43 Rapid and scalable typing of structural variants for disease cohorts W. Salerno, A. English, S. N. Shekar, A. Mangubat, J. Bruestle, E. Boerwinkle, R. A. Gibbs P44 Polymorphism of glutathione S-transferases and sulphotransferases genes in an Arab population A. H. Salem, M. Ali, A. Ibrahim, M. Ibrahim P46 Genetic divergence of CYP3A5*3 pharmacogenomic marker for native and admixed Mexican populations J. C. Fernandez-Lopez, V. Bonifaz-Peña, C. Rangel-Escareño, A. Hidalgo-Miranda, A. V. Contreras P47 Whole exome sequence meta-analysis of 13 white blood cell, red blood cell, and platelet traits L. Polfus, CHARGE and NHLBI Exome Sequence Project Working Groups P48 Association of adipoq gene with type 2 diabetes and related phenotypes in african american men and women: The jackson heart study S. Davis, R. Xu, S. Gebeab, P Riestra, A Gaye, R. Khan, J. Wilson, A. Bidulescu P49 Common variants in casr gene are associated with serum calcium levels in koreans S. H. Jung, N. Vinayagamoorthy, S. H. Yim, Y. J. Chung P50 Inference of multiple-wave population admixture by modeling decay of linkage disequilibrium with multiple exponential functions Y. Zhou, S. Xu P51 A Bayesian framework for generalized linear mixed models in genome-wide association studies X. Wang, V. Philip, G. Carter P52 Targeted sequencing approach for the identification of the genetic causes of hereditary hearing impairment A. A. Abuzenadah, M. Gari, R. Turki, A. Dallol P53 Identification of enhancer sequences by ATAC-seq open chromatin profiling A. Uyar, A. Kaygun, S. Zaman, E. Marquez, J. George, D. Ucar P54 Direct enrichment for the rapid preparation of targeted NGS libraries C. L. Hendrickson, A. Emerman, D. Kraushaar, S. Bowman, N. Henig, T. Davis, S. Russello, K. Patel P56 Performance of the Agilent D5000 and High Sensitivity D5000 ScreenTape assays for the Agilent 4200 Tapestation System R. Nitsche, L. Prieto-Lafuente P57 ClinVar: a multi-source archive for variant interpretation M. Landrum, J. Lee, W. Rubinstein, D. Maglott P59 Association of functional variants and protein physical interactions of human MUTY homolog linked with familial adenomatous polyposis and colorectal cancer syndrome Z. Abduljaleel, W. Khan, F. A. Al-Allaf, M. Athar , M. M. Taher, N. Shahzad P60 Modification of the microbiom constitution in the gut using chicken IgY antibodies resulted in a reduction of acute graft-versus-host disease after experimental bone marrow transplantation A. Bouazzaoui, E. Huber, A. Dan, F. A. Al-Allaf, W. Herr, G. Sprotte, J. Köstler, A. Hiergeist, A. Gessner, R. Andreesen, E. Holler P61 Compound heterozygous mutation in the LDLR gene in Saudi patients suffering severe hypercholesterolemia F. Al-Allaf, A. Alashwal, Z. Abduljaleel, M. Taher, A. Bouazzaoui, H. Abalkhail, A. Al-Allaf, R. Bamardadh, M. Athar
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Affiliation(s)
| | - Y. Wang
- School of Computing, Clemson University, Clemson, SC USA
| | - R. Huang
- Biochemical Genetics Laboratory, Greenwood Genetic Center, Greenwood, SC USA
| | - C. Skinner
- JCSRI, Greenwood Genetic Center, Greenwood, SC USA
| | - T. Thompson
- Biochemical Genetics Laboratory, Greenwood Genetic Center, Greenwood, SC USA
| | - L. Pollard
- Biochemical Genetics Laboratory, Greenwood Genetic Center, Greenwood, SC USA
| | - T. Wood
- Biochemical Genetics Laboratory, Greenwood Genetic Center, Greenwood, SC USA
| | - F. Luo
- School of Computing, Clemson University, Clemson, SC USA
| | - R. Stevenson
- JCSRI, Greenwood Genetic Center, Greenwood, SC USA
| | - R. Polimanti
- Department Psychiatry, Yale Sch Med and VA CT Healthcare Center, West Haven, CT USA
| | - J. Gelernter
- Department Psychiatry, Yale Sch Med and VA CT Healthcare Center, West Haven, CT USA
- Department Genetics, Yale Sch Med and VA CT Healthcare Center, West Haven, CT USA
- Department Neurobiology, Yale Sch Med and VA CT Healthcare Center, West Haven, CT USA
| | - X. Lin
- Singapore Institute for Clinical Sciences, Singapore, Singapore
| | - I. Y. Lim
- Singapore Institute for Clinical Sciences, Singapore, Singapore
| | - Y. Wu
- Singapore Institute for Clinical Sciences, Singapore, Singapore
| | - A. L. Teh
- Singapore Institute for Clinical Sciences, Singapore, Singapore
| | - L. Chen
- Singapore Institute for Clinical Sciences, Singapore, Singapore
| | - I. M. Aris
- Singapore Institute for Clinical Sciences, Singapore, Singapore
| | - S. E. Soh
- Singapore Institute for Clinical Sciences, Singapore, Singapore
| | - M. T. Tint
- National University of Singapore, Singapore, Singapore
| | - J. L. MacIsaac
- University of British Columbia, Vancouver, British Columbia Canada
| | - F. Yap
- KK Women’s and Children’s Hospital, Singapore, Singapore
| | - K. Kwek
- KK Women’s and Children’s Hospital, Singapore, Singapore
| | - S. M. Saw
- National University of Singapore, Singapore, Singapore
| | - M. S. Kobor
- University of British Columbia, Vancouver, British Columbia Canada
| | - M. J. Meaney
- Singapore Institute for Clinical Sciences, Singapore, Singapore
| | - K. M. Godfrey
- University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Y. S. Chong
- Singapore Institute for Clinical Sciences, Singapore, Singapore
| | - J. D. Holbrook
- Singapore Institute for Clinical Sciences, Singapore, Singapore
| | - Y. S. Lee
- Singapore Institute for Clinical Sciences, Singapore, Singapore
| | - P. D. Gluckman
- Singapore Institute for Clinical Sciences, Singapore, Singapore
- University of Auckland, Auckland, New Zealand
| | - N. Karnani
- Singapore Institute for Clinical Sciences, Singapore, Singapore
| | | | - A. Kapoor
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - D. Lee
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - A. Chakravarti
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - C. Maercker
- Esslingen University of Applied Sciences, Esslingen, Germany
| | - F. Graf
- German Cancer Research Center, Heidelberg, Germany
| | - M. Boutros
- German Cancer Research Center, Heidelberg, Germany
| | - G. Stamoulis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - F. Santoni
- Geneva University Hospitals-HUG, Service of Genetic Medicine, Geneva, Switzerland
| | - P. Makrythanasis
- Geneva University Hospitals-HUG, Service of Genetic Medicine, Geneva, Switzerland
| | - A. Letourneau
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - M. Guipponi
- Geneva University Hospitals-HUG, Service of Genetic Medicine, Geneva, Switzerland
| | - N. Panousis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - M. Garieri
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - P. Ribaux
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - E. Falconnet
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - C. Borel
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - S. E. Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Geneva University Hospitals-HUG, Service of Genetic Medicine, Geneva, Switzerland
- iGE3 Institute of Genetics and Genomics of Geneva, University of Geneva Medical School, Geneva, Switzerland
| | - S. Kumar
- South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio-Grande Valley, Edinburg, TX USA
| | - J. Curran
- South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio-Grande Valley, Brownsville, TX USA
| | - J. Blangero
- South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio-Grande Valley, Brownsville, TX USA
| | - S. Chatterjee
- Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD USA
| | - A. Kapoor
- Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD USA
| | - J. Akiyama
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - D. Auer
- Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD USA
| | - C. Berrios
- Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD USA
| | - L. Pennacchio
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - A. Chakravarti
- Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD USA
| | - T. R. Donti
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - G. Cappuccio
- Department of Translational Medical Sciences, Federico II University, Naples, Italy
| | - M. Miller
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - P. Atwal
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | | | - A. Cardon
- Section of Pediatric Neurology and Neuroscience, Baylor College of Medicine, Houston, TX USA
| | - C. Bacino
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - L. Emrick
- Section of Pediatric Neurology and Neuroscience, Baylor College of Medicine, Houston, TX USA
| | | | - F. Baumer
- Stanford Medical School, Stanford, CA USA
| | - B. Porter
- Stanford Medical School, Stanford, CA USA
| | - M. Bainbridge
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - P. Bonnen
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - B. Graham
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - R. Sutton
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - Q. Sun
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - S. Elsea
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - Z. Hu
- School of Public Health, Houston Health Science Center, Houston, TX USA
| | - P. Wang
- University of Texas, Houston Health Science Center, Houston, TX USA
| | - Y. Zhu
- Tulane University, New Orleans, LO USA
| | - J. Zhao
- Tulane University, New Orleans, LO USA
| | - M. Xiong
- University of Texas, Houston Health Science Center, Houston, TX USA
| | - David A. Bennett
- Rush Alzheimer’s Disease Center, Rush University, Chicago, IL USA
| | - A. Hidalgo-Miranda
- Cancer Genomics Laboratory, National Institute of Genomic Medicine (INMEGEN), Mexico City, Mexico
| | - S. Romero-Cordoba
- Cancer Genomics Laboratory, National Institute of Genomic Medicine (INMEGEN), Mexico City, Mexico
| | | | - R. Rebollar-Vega
- Cancer Genomics Laboratory, National Institute of Genomic Medicine (INMEGEN), Mexico City, Mexico
| | | | - M. Iorio
- National Tumor Institute, Milan, Italy
| | | | - S. Baroni
- National Tumor Institute, Milan, Italy
| | - B. Kaczkowski
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Y. Tanaka
- Preventive Medicine and Applied Genomics unit, RIKEN Advanced Center for Computing and Communication, Yokohama, Japan
| | - H. Kawaji
- Preventive Medicine and Applied Genomics unit, RIKEN Advanced Center for Computing and Communication, Yokohama, Japan
| | - A. Sandelin
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - R. Andersson
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - M. Itoh
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - T. Lassmann
- Telethon Kids Institute, The University of Western Australia, Perth, Australia
| | | | - Y. Hayashizaki
- RIKEN Preventive Medicine & Diagnosis Innovation Program, Wako, Japan
| | - P. Carninci
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - A. R. R. Forrest
- Harry Perkins Institute of Medical Research, The University of Western Australia, Nedlands, Australia
| | - C. A. Semple
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, Edinburgh, UK
| | | | | | | | - C. Gallego
- University of Michigan, Ann Arbor, MI USA
| | | | - A. Burt
- Univ of Washington, Seattle, WA USA
| | | | | | - C. Nefcy
- Univ of Washington, Seattle, WA USA
| | | | | | | | | | | | - J. Smith
- Univ of Washington, Seattle, WA USA
| | | | | | - R. Nassir
- University California, Davis, CA USA
| | | | | | - U. Peters
- Univ of Washington, Seattle, WA USA
- Fred Hutch, Seattle, WA USA
| | | | | | - F. Menghi
- The Jackson Laboratory, Farmington, CT USA
| | - K. Inaki
- The Jackson Laboratory, Farmington, CT USA
| | - X. Woo
- The Jackson Laboratory, Farmington, CT USA
| | - P. Kumar
- The Jackson Laboratory, Farmington, CT USA
| | - K. Grzeda
- The Jackson Laboratory, Farmington, CT USA
| | | | - H. Kim
- The Jackson Laboratory, Farmington, CT USA
| | - D. Ucar
- The Jackson Laboratory, Farmington, CT USA
| | | | | | - J. Keck
- The Jackson Laboratory, Sacramento, CA USA
| | - J. Chuang
- The Jackson Laboratory, Farmington, CT USA
| | - E. T. Liu
- The Jackson Laboratory, Farmington, CT USA
| | - B. Ji
- The Jackson Laboratory, Bar Harbor, ME USA
| | - A. Tyler
- The Jackson Laboratory, Bar Harbor, ME USA
| | - G. Ananda
- The Jackson Laboratory, Bar Harbor, ME USA
| | - G. Carter
- The Jackson Laboratory, Bar Harbor, ME USA
| | - H. Nikbakht
- Human Genetics, McGill University, Montreal, Quebec Canada
| | - M. Montagne
- Biochemistry, Sherbrooke University, Sherbrooke, Quebec Canada
| | - M. Zeinieh
- Human Genetics, McGill University, Montreal, Quebec Canada
| | - A. Harutyunyan
- Human Genetics, McGill University, Montreal, Quebec Canada
| | - M. Mcconechy
- Human Genetics, McGill University, Montreal, Quebec Canada
| | - N. Jabado
- Pediatrics, McGill University, Montreal, Quebec Canada
| | - P. Lavigne
- Biochemistry, Sherbrooke University, Sherbrooke, Quebec Canada
| | - J. Majewski
- Human Genetics, McGill University, Montreal, Quebec Canada
| | - J. B. Goldstein
- Genomic Medicine, MD Anderson Cancer Center, Houston, TX USA
| | - M. Overman
- Gastrointestinal Medical Oncology, MD Anderson Cancer Center, Houston, TX USA
| | - G. Varadhachary
- Gastrointestinal Medical Oncology, MD Anderson Cancer Center, Houston, TX USA
| | - R. Shroff
- Gastrointestinal Medical Oncology, MD Anderson Cancer Center, Houston, TX USA
| | - R. Wolff
- Gastrointestinal Medical Oncology, MD Anderson Cancer Center, Houston, TX USA
| | - M. Javle
- Gastrointestinal Medical Oncology, MD Anderson Cancer Center, Houston, TX USA
| | - A. Futreal
- Genomic Medicine, MD Anderson Cancer Center, Houston, TX USA
| | - D. Fogelman
- Gastrointestinal Medical Oncology, MD Anderson Cancer Center, Houston, TX USA
| | - L. Bravo
- Escuela de Medicina Humana, Universidad Privada San Juan Bautista, Lima, Peru
| | - W. Fajardo
- Escuela de Medicina Humana, Universidad Privada San Juan Bautista, Lima, Peru
| | - H. Gomez
- Unidad de Investigación Básica y Traslacional, Oncosalud-AUNA, Lima, Peru
| | - C. Castaneda
- Unidad de Investigación Básica y Traslacional, Oncosalud-AUNA, Lima, Peru
| | - C. Rolfo
- Oncology Department, University Hospital Antwerp, Antwerp, Belgium
| | - J. A. Pinto
- Unidad de Investigación Básica y Traslacional, Oncosalud-AUNA, Lima, Peru
| | - K. C. Akdemir
- Genomic Medicine, MD Anderson Cancer Center, Houston, TX USA
| | - L. Chin
- University of Texas System, Houston, TX USA
| | - A. Futreal
- Genomic Medicine, MD Anderson Cancer Center, Houston, TX USA
| | | | - S. Patterson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT USA
| | - C. Statz
- The Jackson Laboratory for Genomic Medicine, Farmington, CT USA
| | - S. Mockus
- The Jackson Laboratory for Genomic Medicine, Farmington, CT USA
| | - S. N. Nikolaev
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
| | - X. I. Bonilla
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
| | - L. Parmentier
- Department of Dermatology, Hospital of Valais, Sion, Switzerland
| | - B. King
- Department of Pathology, NYU School of Medicine, New York, NY USA
| | - F. Bezrukov
- Department of Physics, University of Connecticut, Connecticut, USA
| | - G. Kaya
- Department of Dermatology, University Hospitals of Geneva, Geneva, Switzerland
| | - V. Zoete
- Swiss Institute of Bioinformatics, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - V. Seplyarskiy
- Institute of Information Transmission Problems, Russian Academy of Sciences, Moscow, Russian Federation
| | - H. Sharpe
- Department of Molecular Oncology, Genentech Inc, San Francisco, CA USA
| | - T. McKee
- Service of Clinical Pathology, University Hospitals of Geneva, Geneva, Switzerland
| | - A. Letourneau
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - P. Ribaux
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - K. Popadin
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | | | - R. Ben Chaabene
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - F. Santoni
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - M. Andrianova
- Institute of Information Transmission Problems, Russian Academy of Sciences, Moscow, Russian Federation
| | - M. Guipponi
- Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - M. Garieri
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - C. Verdan
- Service of Clinical Pathology, University Hospitals of Geneva, Geneva, Switzerland
| | - K. Grosdemange
- Department of Dermatology, University Hospitals of Geneva, Geneva, Switzerland
| | - O. Sumara
- Department of Biochemistry and Molecular Biology, University of Würzburg, Würzburg, Germany
| | - M. Eilers
- Department of Biochemistry and Molecular Biology, University of Würzburg, Würzburg, Germany
| | - I. Aifantis
- Department of Pathology, NYU School of Medicine, New York, NY USA
| | - O. Michielin
- Swiss Institute of Bioinformatics, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - F. de Sauvage
- Department of Molecular Oncology, Genentech Inc, San Francisco, CA USA
| | - S. Antonarakis
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
| | | | | | - A. Kurian
- Stanford Medical Center, Palo Alto, CA USA
| | - A. Desmond
- Massachusetts General Hospital, Boston, MA USA
| | - S. Yang
- Invitae, San Francisco, CA USA
| | | | - J. Ford
- Stanford Medical Center, San Francisco, CA USA
| | - L. Ellisen
- Massachusetts General Hospital, Boston, MA USA
| | - T. L. Peters
- Pathology & Immunology, Baylor College of Medicine, Houston, TX USA
| | - K. R. Alvarez
- Pathology, Texas Children’s Hospital, Houston, TX USA
| | | | - D. H. Lopez-Terrada
- Pathology & Immunology, Baylor College of Medicine, Houston, TX USA
- Pathology, Texas Children’s Hospital, Houston, TX USA
| | - A. Hastie
- BioNano Genomics, Inc, San Diego, CA USA
| | - Z. Dzakula
- BioNano Genomics, Inc, San Diego, CA USA
| | - A. W. Pang
- BioNano Genomics, Inc, San Diego, CA USA
| | - E. T. Lam
- BioNano Genomics, Inc, San Diego, CA USA
| | | | | | - H. Cao
- BioNano Genomics, Inc, San Diego, CA USA
| | | | - C. Gonzaga-Jauregui
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, New York, NY USA
| | - L. Ma
- Department of Pediatrics, New York, NY USA
| | - A. King
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, New York, NY USA
| | - E. Berman Rosenzweig
- Department of Pediatrics, New York, NY USA
- Department of Medicine, Columbia University Medical Center, New York, NY USA
| | | | - J. G. Reid
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, New York, NY USA
| | - J. D. Overton
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, New York, NY USA
| | - F. Dewey
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, New York, NY USA
| | - W. K. Chung
- Department of Pediatrics, New York, NY USA
- Department of Medicine, Columbia University Medical Center, New York, NY USA
| | - K. Small
- Molecular Insight Research Foundation, Glendale, ᅟ
| | - A. DeLuca
- Ophthalmology, University of Iowa, Iowa City, IA USA
| | - F. Cremers
- Biology, Raboud University Medical Center, Nijmegen, Netherlands
| | - R. A. Lewis
- Ophthalmology, Baylor College of Medicine, Houston, TX USA
| | - V. Puech
- Service d’Exploration de la vision et Neuro-ophtalmologie CHRU, Service d’Exploration de la vision et Neuro-ophtalmologie CHRU, Lille, France
| | - B. Bakall
- Associated Retina Consultants, University of Arizona College of Medicine, Phoenix, TX USA
| | | | | | - M. Leys
- WVU Eye Institute, Morgantown, WV USA
| | - F. S. Shaya
- Molecular Insight Research Foundation, Glendale, ᅟ
| | - E. Stone
- University of Iowa, Iowa City, IA USA
| | - N. L. Sobreira
- Johns Hopkins University School of Medicine, Baltimore, MD USA
| | | | - H. Ling
- Center for Inherited Disease Research, JHUSOM, Baltimore, MD USA
| | - E. Pugh
- Center for Inherited Disease Research, JHUSOM, Baltimore, MD USA
| | - D. Witmer
- Center for Inherited Disease Research, JHUSOM, Baltimore, MD USA
| | - K. Hetrick
- Center for Inherited Disease Research, JHUSOM, Baltimore, MD USA
| | - P. Zhang
- Center for Inherited Disease Research, JHUSOM, Baltimore, MD USA
| | - K. Doheny
- Center for Inherited Disease Research, JHUSOM, Baltimore, MD USA
| | - D. Valle
- Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - A. Hamosh
- Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - S. N. Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - Z. Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - M. N. Bainbridge
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - W. Charng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - W. Wiszniewski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - T. Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - E. Karaca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - Y. Bayram
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - M. K. Eldomery
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - J. Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - H. Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - J. Hu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - V. R. Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - D. M. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - E. A. Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - D. Valle
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD USA
| | - J. R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - R. A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | | | - W. Salerno
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - A. English
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | | | | | - A. Thorogood
- Centre of Genomics and Policy, McGill University, Montreal, Quebec Canada
| | - B. M. Knoppers
- Centre of Genomics and Policy, McGill University, Montreal, Quebec Canada
| | | | - H. Takahashi
- Center for Life Science Technologies, Division of Genomic Technologies, RIKEN, Yokohama, Japan
| | - K. R. Nitta
- Center for Life Science Technologies, Division of Genomic Technologies, RIKEN, Yokohama, Japan
| | - A. Kozhuharova
- Center for Life Science Technologies, Division of Genomic Technologies, RIKEN, Yokohama, Japan
| | - A. M. Suzuki
- Center for Life Science Technologies, Division of Genomic Technologies, RIKEN, Yokohama, Japan
| | - H. Sharma
- Center for Life Science Technologies, Division of Genomic Technologies, RIKEN, Yokohama, Japan
| | - D. Cotella
- Dipartimento di Scienze della Salute, Universita’ del Piemonte Orientale, Novara, Italy
| | - C. Santoro
- Dipartimento di Scienze della Salute, Universita’ del Piemonte Orientale, Novara, Italy
| | - S. Zucchelli
- Area of Neuroscience, SISSA, International School for Advanced Studies, Trieste, Italy
| | - S. Gustincich
- Area of Neuroscience, SISSA, International School for Advanced Studies, Trieste, Italy
| | - P. Carninci
- Center for Life Science Technologies, Division of Genomic Technologies, RIKEN, Yokohama, Japan
| | - J. J. Mulvihill
- Division of Genomic Medicine, National Human Genome Research Institute, Bethesda, MD USA
| | - G. Baynam
- Office of Population Health, Department of Health, Perth, Australia
| | - W. Gahl
- Undiagnosed Diseases Program, National Human Genome Research Institute, Bethesda, MD USA
| | - S. C. Groft
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD USA
| | - K. Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - P. Lasko
- Department of Biology, McGill University, Montreal, Quebec Canada
| | - B. Melegh
- Department of Medical Genetics, University of Pecs, Pecs, Hungary
| | - D. Taruscio
- National Center for Rare Diseases, Istituto Superiore di Sanita, Rome, Italy
| | - R. Ghosh
- Pediatrics-Oncology, Baylor College of Medicine, Houston, TX USA
| | - S. Plon
- Pediatrics-Oncology, Baylor College of Medicine, Houston, TX USA
| | - S. Scherer
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - X. Qin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - R. Sanghvi
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - K. Walker
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - T. Chiang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - D. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - L. Wang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, NY USA
| | - J. Black
- Department of Psychiatry, Mayo Clinic, Rochester, NY USA
| | - E. Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | | | - R. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | | | | | - K. Wani
- MD Anderson Cancer Center, Houston, USA
| | - X. Yu
- MD Anderson Cancer Center, Houston, USA
| | - C. Creasy
- MD Anderson Cancer Center, Houston, USA
| | | | - M. Forget
- MD Anderson Cancer Center, Houston, USA
| | - V. Nanda
- MD Anderson Cancer Center, Houston, USA
| | - J. Roszik
- MD Anderson Cancer Center, Houston, USA
| | - J. Wargo
- MD Anderson Cancer Center, Houston, USA
| | - L. Haydu
- MD Anderson Cancer Center, Houston, USA
| | - X. Song
- MD Anderson Cancer Center, Houston, USA
| | - A. Lazar
- MD Anderson Cancer Center, Houston, USA
| | | | - M. Davies
- MD Anderson Cancer Center, Houston, USA
| | | | - J. Zhang
- MD Anderson Cancer Center, Houston, USA
| | | | | | | | | | | | | | | | | | - M. Xiong
- University of Texas School of Public Health, Houston, TX USA
| | - L. Ma
- University of Texas School of Public Health, Houston, TX USA
| | - N. Lin
- University of Texas School of Public Health, Houston, TX USA
| | - C. Amos
- Geisel School of Medicine at Dartmouth, Hanover, NH USA
| | - N. Lin
- Biostatistics, University of Texas Health Science Center at Houston, Houston, TX USA
| | - P. Wang
- Biostatistics, University of Texas Health Science Center at Houston, Houston, TX USA
| | - Y. Zhu
- Tulane University, New Orleans, LO USA
| | - J. Zhao
- Tulane University, New Orleans, LO USA
| | - V. Calhoun
- University of New Mexico, Albuquerque, NM USA
| | - M. Xiong
- University of Texas Health Science Center at Houston, Houston, TX USA
| | | | - M. Egger
- EPS Software Corp, Spring, TX USA
| | | | - S. Sadedin
- Bioinformatics, Murdoch Childrens Research Institute, Parkville, Australia
| | - A. Oshlack
- Bioinformatics, Murdoch Childrens Research Institute, Parkville, Australia
| | | | - V. A. A. Antonio
- Computational Systems Biology Laboratory, Nara Institute of Science and Technology, Ikoma-cho, Japan
| | - N. Ono
- Computational Systems Biology Laboratory, Nara Institute of Science and Technology, Ikoma-cho, Japan
| | | | - Z. Ahmed
- The Jackson Laboratory for Genomic Medicine, Farmington, CT USA
| | - M. Bolisetty
- The Jackson Laboratory for Genomic Medicine, Farmington, CT USA
| | - S. Zeeshan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT USA
| | - E. Anguiano
- The Jackson Laboratory for Genomic Medicine, Farmington, CT USA
| | - D. Ucar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT USA
| | - A. Sarkar
- Laboratory of Genomics and Profiling Applications, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - M. R. Nandineni
- Laboratory of Genomics and Profiling Applications, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - C. Zeng
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - J. Shao
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - H. Cao
- BioNano Genomics, Inc, San Diego, CA USA
| | - A. Hastie
- BioNano Genomics, Inc, San Diego, CA USA
| | - A. W. Pang
- BioNano Genomics, Inc, San Diego, CA USA
| | - E. T. Lam
- BioNano Genomics, Inc, San Diego, CA USA
| | - T. Liang
- BioNano Genomics, Inc, San Diego, CA USA
| | - K. Pham
- BioNano Genomics, Inc, San Diego, CA USA
| | | | - Z. Dzakula
- BioNano Genomics, Inc, San Diego, CA USA
| | - Y. Chee-Wei
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu, Malaysia
| | - L. Dongsheng
- Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences Shanghai, Shanghai, China
| | - W. Lai-Ping
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - D. Lian
- Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences Shanghai, Shanghai, China
| | - R. O. Twee Hee
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Y. Yunus
- Institute of Medical Molecular Biotechnology, Universiti Teknologi MARA, Sungai Buloh, ᅟ
| | - F. Aghakhanian
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Sunway Campus, Petaling Jaya, Malaysia
| | - S. S. Mokhtar
- Institute of Medical Molecular Biotechnology, Universiti Teknologi MARA, Sungai Buloh, ᅟ
| | - C. V. Lok-Yung
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu, Malaysia
| | - J. Bhak
- Personal Genomics Institute, Genome Research Foundation, Suwon, Republic Of Korea
| | - M. Phipps
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Sunway Campu, Petaling Jaya, Malaysia
| | - X. Shuhua
- Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences Shanghai, Shanghai, China
| | - T. Yik-Ying
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - V. Kumar
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu, Malaysia
| | - H. Boon-Peng
- UCSI University, Kuala Lumpur, Kuala Lumpur, Malaysia
| | - I. Campbell
- Research Division, Peter Maccallum Cancer Centre, East Melbourne, Australia
| | - M. -A. Young
- Familial Cancer Centre, Peter Maccallum Cancer Centre, East Melbourne, Australia
| | - P. James
- Familial Cancer Centre, Peter Maccallum Cancer Centre, East Melbourne, Australia
| | | | - M. Rain
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - G. Mohammad
- Department of Medicine, Sonam Norbu Memorial Hospital, Leh, Ladakh India
| | - R. Kukreti
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Q. Pasha
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - A. R. Akilzhanova
- Nazarbayev University, National Laboratory Astana, Center for Life Sciences, Astana, Kazakhstan
| | - C. Guelly
- Center of Medical Research, Medical University of Graz, Graz, Austria
| | - Z. Abilova
- Nazarbayev University, National Laboratory Astana, Center for Life Sciences, Astana, Kazakhstan
| | - S. Rakhimova
- Nazarbayev University, National Laboratory Astana, Center for Life Sciences, Astana, Kazakhstan
| | - A. Akhmetova
- Nazarbayev University, National Laboratory Astana, Center for Life Sciences, Astana, Kazakhstan
| | - U. Kairov
- Nazarbayev University, National Laboratory Astana, Center for Life Sciences, Astana, Kazakhstan
| | - S. Trajanoski
- Center of Medical Research, Medical University of Graz, Graz, Austria
| | - Z. Zhumadilov
- Nazarbayev University, National Laboratory Astana, Center for Life Sciences, Astana, Kazakhstan
| | - M. Bekbossynova
- National Scientific Cardiac Surgery Center, Astana, Kazakhstan
| | | | - S. Sandhu
- Swift Biosciences Inc, Ann Arbor, MI USA
| | - T. Harkins
- Swift Biosciences Inc, Ann Arbor, MI USA
| | - V. Makarov
- Swift Biosciences Inc, Ann Arbor, MI USA
| | - H. Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - R. Glenn
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - Z. Momin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - B. Dilrukshi
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - H. Chao
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - Q. Meng
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - B. Gudenkauf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - R. Kshitij
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - J. Jayaseelan
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - C. Nessner
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - S. Lee
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - K. Blankenberg
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - L. Lewis
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - J. Hu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - Y. Han
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - H. Dinh
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - S. Jireh
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - K. Walker
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - E. Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - D. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - R. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - J. Hu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - K. Walker
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - C. Buhay
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - X. Liu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - Q. Wang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - R. Sanghvi
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - H. Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - Y. Ding
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - N. Veeraraghavan
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - Y. Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - E. Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX USA
| | - A. L. Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - C. M. Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - D. M. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - R. A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - K. C. C. Worley
- Human Genome Sequencing Center, Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - Y. Liu
- Human Genome Sequencing Center, Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - D. S. T. Hughes
- Human Genome Sequencing Center, Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - S. C. Murali
- Human Genome Sequencing Center, Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - R. A. Harris
- Human Genome Sequencing Center, Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - A. C. English
- Human Genome Sequencing Center, Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - X. Qin
- Human Genome Sequencing Center, Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - O. A. Hampton
- Human Genome Sequencing Center, Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - P. Larsen
- Department of Biology, Duke University, Durham, NC USA
| | - C. Beck
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - Y. Han
- Human Genome Sequencing Center, Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - M. Wang
- Human Genome Sequencing Center, Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - H. Doddapaneni
- Human Genome Sequencing Center, Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - C. L. Kovar
- Human Genome Sequencing Center, Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - W. J. Salerno
- Human Genome Sequencing Center, Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - A. Yoder
- Department of Biology, Duke University, Durham, NC USA
| | - S. Richards
- Human Genome Sequencing Center, Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - J. Rogers
- Human Genome Sequencing Center, Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - J. R. Lupski
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - D. M. Muzny
- Human Genome Sequencing Center, Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - R. A. Gibbs
- Human Genome Sequencing Center, Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - Q. Meng
- HGSC, Baylor College of Medicine, Houston, TX USA
| | | | - M. Wang
- HGSC, Baylor College of Medicine, Houston, TX USA
| | | | - Y. Han
- HGSC, Baylor College of Medicine, Houston, TX USA
| | - D. Muzny
- HGSC, Baylor College of Medicine, Houston, TX USA
| | - R. Gibbs
- HGSC, Baylor College of Medicine, Houston, TX USA
| | - R. A. Harris
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - M. Raveenedran
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - C. Xue
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - M. Dahdouli
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - L. Cox
- Genetics, Southwest National Primate Research Center, San Antonio, TX USA
| | - G. Fan
- Human Genetics, Univeristy of California Los Angeles, Los Angeles, CA USA
| | - B. Ferguson
- Division of Neuroscience, Oregon National Primate Research Center, Beaverton, OR USA
| | - J. Hovarth
- Genomics & Microbiology Research Laboratory, NC Museum of Natural Sciences, Raleigh, NC USA
| | - Z. Johnson
- Yerkes Nonhuman Primate Genomics Core, Yerkes National Primate Research Center, Atlanta, GA USA
| | - S. Kanthaswamy
- Environmental Toxicology, California National Primate Research Center, Davis, CA USA
| | - M. Kubisch
- Physiology, Tulane National Primate Research Center, New Orleans, LO USA
| | - M. Platt
- Neuroscience, University of Pennsylvania, Philadelphia, PA USA
| | - D. Smith
- Anthropology, University of California Davis, Davis, CA USA
| | - E. Vallender
- Psychiatry and Human Behavior, University of Mississippi Medical Center, Jackson, MS USA
| | - R. Wiseman
- Genetics, Wisconsin National Primate Research Center, Madison, WI USA
| | - X. Liu
- Epidemiology, Human Genetics & Environmental Sciences, ᅟ, ᅟ
| | - J. Below
- Epidemiology and Disease Control Human Genetics Center, University of Texas Health Science Center, Houston, TX USA
| | - D. Muzny
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - R. Gibbs
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - F. Yu
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - J. Rogers
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - J. Lin
- The Jackson Laboratory for Genomic Medicine, Farmington, CT USA
| | - Y. Zhang
- Department of Statistics, University of Connecticut, Storrs, CT USA
| | - Z. Ouyang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT USA
| | - A. Moore
- National Cancer Institute, Rockville, USA
| | - Z. Wang
- St. Jude Children’s Research Hospital, Memphis, USA
| | - J. Hofmann
- National Cancer Institute, NIH, DHHS, Rockville, USA
| | - M. Purdue
- National Cancer Institute, Rockville, USA
| | | | | | - D. Albanes
- National Cancer Institute, Rockville, USA
| | - C. S. Liu
- Changhua Christian Hospital, Changhua, Taiwan Province of China
| | - W. L. Cheng
- Changhua Christian Hospital, Changhua, Taiwan Province of China
| | - T. T. Lin
- Changhua Christian Hospital, Changhua, Taiwan Province of China
| | - Q. Lan
- National Cancer Institute, Rockville, USA
| | - N. Rothman
- National Cancer Institute, Rockville, USA
| | - S. Berndt
- National Cancer Institute, Rockville, USA
| | - E. S. Chen
- Biochemistry, National University of Singapore, Singapore, Singapore
| | - H. Bahrami
- Proteomics, Faraby Eye Hospital, Tehran, Iran Islamic Republic Of
- R & D, MIB Co., Tehran, Iran Islamic Republic Of
| | | | | | - H. Bahrami
- Proteomics, Faraby Eye Hospital, Tehran, Iran Islamic Republic Of
- R & D, MIB Co., Tehran, Iran Islamic Republic Of
| | | | | | - K. K. R. Alharbi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - M. Zhalbinova
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, ᅟ, Kazakhstan
| | - A. Akilzhanova
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, ᅟ, Kazakhstan
| | - S. Rakhimova
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, ᅟ, Kazakhstan
| | - M. Bekbosynova
- Cardiology, JSC “National Research Cardiac Surgery Center”, National medical holding, Astana, Kazakhstan
| | - S. Myrzakhmetova
- Cardiology, JSC “National Research Cardiac Surgery Center”, National medical holding, Astana, Kazakhstan
| | - M. Matar
- UAE Genetic Diseases Association, Dubai, United Arab Emirates
| | - N. Mili
- Research Center for Statistics, University of Geneva, Switzerland, Geneva Switzerland
| | - R. Molinari
- Research Center for Statistics, University of Geneva, Switzerland, Geneva Switzerland
| | - Y. Ma
- Department of Statistics, University of South Carolina, Columbia, USA
| | - S. Guerrier
- Department of Statistics, University of Illinois at Urbana Champaign, Champaign, USA
| | - N. Elhawary
- Department of Molecular Genetics, Medical Genetics Center, Ain Shams University, Cairo, Egypt
- Department of Medical Genetics, Umm Al-Qura University, ᅟ, Saudi Arabia
| | - M. Tayeb
- Department of Medical Genetics, Umm Al-Qura University, ᅟ, Saudi Arabia
| | - N. Bogari
- Department of Medical Genetics, Umm Al-Qura University, ᅟ, Saudi Arabia
| | - N. Qotb
- Department of Psychology, Umm Al-Qura University, Faculty of Education, Mecca, Saudi Arabia
| | - S. A. McClymont
- Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, USA
| | - P. W. Hook
- Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, USA
| | - L. A. Goff
- Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, USA
| | - A. McCallion
- Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, USA
| | - Y. Kong
- The Jackson Laboratory, Bar Harbor, USA
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, USA
| | | | | | | | - L. Zhao
- The Jackson Laboratory, Bar Harbor, USA
| | - P. M. Nishina
- The Jackson Laboratory, Bar Harbor, USA
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, USA
| | - B. M. Edrees
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - M. Athar
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - F. A. Al-Allaf
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - M. M. Taher
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - W. Khan
- Department of Basic Sciences, College of Science and Health Professions, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - A. Bouazzaoui
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - N. A. Harbi
- Department of Pediatric, King Faisal Specialist Hospital and Research Centre, Jeddah, Saudi Arabia
| | - R. Safar
- Department of Pediatric, Madinah Maternity and Children’s Hospital, Madinah, Saudi Arabia
| | - H. Al-Edressi
- Department of Pediatric, Madinah Maternity and Children’s Hospital, Madinah, Saudi Arabia
| | - A. Anazi
- Pediatric, King Fahad Medical City, Riyadh, Saudi Arabia
| | - N. Altayeb
- Molecular Diagnostics Unit, Department of Laboratory and Blood Bank, King Abdullah Medical City, Makkah, Saudi Arabia
| | - M. A. Ahmed
- Medical Genetics, King Salman Armed Forces Hospital, Tabuk, Saudi Arabia
| | - K. Alansary
- Medical Genetics, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Z. Abduljaleel
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - A. Kratz
- Center for Life Science Technologies, RIKEN Yokohama, Yokohama City, Kanagawa Japan
| | - P. Beguin
- Brain Science Institute (BSI), Launey Research Unit, RIKEN Wako, Wako, Japan
| | - S. Poulain
- Center for Life Science Technologies, RIKEN Yokohama, Yokohama City, Kanagawa Japan
| | - M. Kaneko
- Brain Science Institute (BSI), Launey Research Unit, RIKEN Wako, Wako, Japan
| | - C. Takahiko
- Brain Science Institute (BSI), Launey Research Unit, RIKEN Wako, Wako, Japan
| | - A. Matsunaga
- Brain Science Institute (BSI), Launey Research Unit, RIKEN Wako, Wako, Japan
| | - S. Kato
- Center for Life Science Technologies, RIKEN Yokohama, Yokohama City, Kanagawa Japan
| | - A. M. Suzuki
- Center for Life Science Technologies, RIKEN Yokohama, Yokohama City, Kanagawa Japan
| | - N. Bertin
- Center for Life Science Technologies, RIKEN Yokohama, Yokohama City, Kanagawa Japan
| | - T. Lassmann
- Center for Life Science Technologies, RIKEN Yokohama, Yokohama City, Kanagawa Japan
| | - R. Vigot
- Center for Life Science Technologies, RIKEN Yokohama, Yokohama City, Kanagawa Japan
| | - P. Carninci
- Center for Life Science Technologies, RIKEN Yokohama, Yokohama City, Kanagawa Japan
| | - C. Plessy
- Center for Life Science Technologies, RIKEN Yokohama, Yokohama City, Kanagawa Japan
| | - T. Launey
- Brain Science Institute (BSI), Launey Research Unit, RIKEN Wako, Wako, Japan
| | - D. Graur
- Biology and Biochemistry, University of Houston, Houston, USA
| | - D. Lee
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
| | - A. Kapoor
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
| | - A. Chakravarti
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
| | - J. Friis-Nielsen
- Technical University of Denmark, Center for Biological Sequence Analysis, Lyngby, Denmark
| | - J. M. Izarzugaza
- Technical University of Denmark, Center for Biological Sequence Analysis, Lyngby, Denmark
| | - S. Brunak
- Technical University of Denmark, Center for Biological Sequence Analysis, Lyngby, Denmark
| | - A. Chakraborty
- Molecular Biology, Netaji Subhas Chandra Bose Cancer Research Institute, Kolkata, India
| | - J. Basak
- Molecular Biology, Netaji Subhas Chandra Bose Cancer Research Institute, Kolkata, India
| | - A. Mukhopadhyay
- Medical Oncology, Netaji Subhas Chandra Bose Cancer Research Institute, Kolkata, India
| | | | - D. Das
- National Institute of Biomedical Genomics, Kalyani, India
| | - N. Biswas
- National Institute of Biomedical Genomics, Kalyani, India
| | - S. Das
- National Institute of Biomedical Genomics, Kalyani, India
| | - S. Sarkar
- Chittaranjan National Cancer Institute, Kolkata, India
| | - A. Maitra
- National Institute of Biomedical Genomics, Kalyani, India
| | - C. Panda
- Chittaranjan National Cancer Institute, Kolkata, India
| | - P. Majumder
- National Institute of Biomedical Genomics, Kalyani, India
| | - H. Morsy
- Human Genetics, Faculty of Medicine, Alexandria, Egypt
| | - A. Gaballah
- Microbiology, Faculty of Medicine, Alexandria, Egypt
| | - M. Samir
- Clinical and Experimental Surgery, Faculty of Medicine, Alexandria, Egypt
| | - M. Shamseya
- Clinical and Experimental Internal Medicine, Medical Research Institute, Faculty of Medicine, Alexandria, Egypt
| | - H. Mahrous
- Human Genetics, Faculty of Medicine, Alexandria, Egypt
| | - A. Ghazal
- Microbiology, Faculty of Medicine, Alexandria, Egypt
| | - W. Arafat
- Clinical Oncology and Nuclear Medicine, Faculty of Medicine, Alexandria, Egypt
| | - M. Hashish
- Human Genetics, Faculty of Medicine, Alexandria, Egypt
| | | | - N. Jaeger
- Genetics, Stanford University, Palo Alto, USA
| | - M. Snyder
- Genetics, Stanford University, Palo Alto, USA
| | | | | | - T. Davis
- New England Biolabs, Ipswich, USA
| | | | | | | | | | | | - K. Zhang
- Pathology, University of North Dakota, Grand Forks, USA
| | | | | | | | | | - N. Jäger
- Genetics, Stanford University, Palo Alto, USA
| | - J. Chen
- Genetics, Stanford University, Palo Alto, USA
| | - R. Haile
- Stanford Cancer Institute, Stanford University, Palo Alto, USA
| | - M. Hitchins
- Stanford Cancer Institute, Stanford University, Palo Alto, USA
| | | | - M. Snyder
- Genetics, Stanford University, Palo Alto, USA
| | - S. Jiménez-Morales
- Cancer Genomic Laboratory, National Institute of Genomic Medicine (INMEGEN), ᅟ, Mexico
| | - M. Ramírez
- Biología, FES -Iztacala, UNAM, ᅟ, Mexico
| | - J. Nuñez
- Hospital de Pediatría, CMN SXXI, IMSS, ᅟ, Mexico
| | - V. Bekker
- Investigación Médica en Inmunología, CMN La Raza, IMSS, ᅟ, Mexico
| | - Y. Leal
- Diagnóstico Molecular H1N1-Influenza , UMAE-IMSS, Mérida, Yucatán Mexico
| | - E. Jiménez
- Hematología Pediátrica, CMN La Raza, IMSS, ᅟ, Mexico
| | - A. Medina
- Hemato-Oncología, Hospital Infantil de México, ᅟ, Mexico
| | - A. Hidalgo
- Cancer Genomics Laboratory, INMEGEN, ᅟ, Mexico
| | - J. Mejía
- Coordinación de Investigación en Salud, IMSS, ᅟ, Mexico
| | - V. Halytskiy
- Molecular Immunology Department, Palladin Institute of Biochemistry of the National Academy of Sciences of Ukraine, Kiev, Ukraine
| | | | | | | | | | | | - K. Belhassa
- Department of Medical Genetics and Oncogene, Morocco; Medical Genetics, CHU Hassan II Fes, Fes, Morocco
| | - K. Belhassan
- Department of Medical Genetics and Oncogene, Morocco; Medical Genetics, CHU Hassan II Fes, Fes, Morocco
| | - L. Bouguenouch
- Department of Medical Genetics and Oncogene, Morocco; Medical Genetics, CHU Hassan II Fes, Fes, Morocco
| | - I. Samri
- Department of Medical Genetics and Oncogene, Morocco; Medical Genetics, CHU Hassan II Fes, Fes, Morocco
| | - H. Sayel
- Department of Medical Genetics and Oncogene, Morocco; Medical Genetics, CHU Hassan II Fes, Fes, Morocco
| | - FZ. moufid
- Department of Medical Genetics and Oncogene, Morocco; Medical Genetics, CHU Hassan II Fes, Fes, Morocco
| | - I. El Bouchikhi
- Department of Medical Genetics and Oncogene, Morocco; Medical Genetics, CHU Hassan II Fes, Fes, Morocco
| | - S. Trhanint
- Department of Medical Genetics and Oncogene, Morocco; Medical Genetics, CHU Hassan II Fes, Fes, Morocco
| | - H. Hamdaoui
- Department of Medical Genetics and Oncogene, Morocco; Medical Genetics, CHU Hassan II Fes, Fes, Morocco
| | - I. Elotmani
- Department of Medical Genetics and Oncogene, Morocco; Medical Genetics, CHU Hassan II Fes, Fes, Morocco
| | - I. Khtiri
- Department of Medical Genetics and Oncogene, Morocco; Medical Genetics, CHU Hassan II Fes, Fes, Morocco
| | - O. Kettani
- Department of Medical Genetics and Oncogene, Morocco; Medical Genetics, CHU Hassan II Fes, Fes, Morocco
| | - L. Quibibo
- Department of Medical Genetics and Oncogene, Morocco; Medical Genetics, CHU Hassan II Fes, Fes, Morocco
| | - M. Ahagoud
- Department of Medical Genetics and Oncogene, Morocco; Medical Genetics, CHU Hassan II Fes, Fes, Morocco
| | - M. Abbassi
- Department of Medical Genetics and Oncogene, Morocco; Medical Genetics, CHU Hassan II Fes, Fes, Morocco
| | - K. Ouldim
- Department of Medical Genetics and Oncogene, Morocco; Medical Genetics, CHU Hassan II Fes, Fes, Morocco
| | - A. V. Marusin
- Evolutionary Genetics, Institute of Medical Genetics, ᅟ, Russian Federation
| | - A. N. Kornetov
- Siberian State Medical University, Tomsk, Russian Federation
| | - M. Swarovskaya
- Evolutionary Genetics, Institute of Medical Genetics, ᅟ, Russian Federation
| | - K. Vagaiceva
- Evolutionary Genetics, Institute of Medical Genetics, ᅟ, Russian Federation
| | - V. Stepanov
- Evolutionary Genetics, Institute of Medical Genetics, ᅟ, Russian Federation
| | - E. M. Cutiongco De La Paz
- National Institutes of Health, University of the Philippines, Manila, Philippines
- Philippine Genome Center, University of the Philippines, Quezon City, Philippines
| | - R. Sy
- College of Medicine, University of the Philippines, Manila, Philippines
| | - J. Nevado
- National Institutes of Health, University of the Philippines, Manila, Philippines
| | - P. Reganit
- College of Medicine, University of the Philippines, Manila, Philippines
| | - L. Santos
- College of Medicine, University of the Philippines, Manila, Philippines
| | - J. D. Magno
- College of Medicine, University of the Philippines, Manila, Philippines
| | - F. E. Punzalan
- College of Medicine, University of the Philippines, Manila, Philippines
| | - D. Ona
- College of Medicine, University of the Philippines, Manila, Philippines
| | - E. Llanes
- College of Medicine, University of the Philippines, Manila, Philippines
| | - R. L. Santos-Cortes
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX United States
| | - R. Tiongco
- College of Medicine, University of the Philippines, Manila, Philippines
| | - J. Aherrera
- Philippine General Hospital, University of the Philippines, Manila, Philippines
| | - L. Abrahan
- Philippine General Hospital, University of the Philippines, Manila, Philippines
| | - P. Pagauitan-Alan
- Philippine General Hospital, University of the Philippines, Manila, Philippines
| | | | - K. H. Morelli
- The Jackson Laboratory, Bar Harbor, USA
- Graduate School of Biomedical Sciences & Engineering, The University of Maine, Orono, USA
| | - J. S. Domire
- Center For Gene Therapy, The Research Institute at Nationwide Children’s Hospital, Columbus, Ohio USA
| | - N. Pyne
- Center For Gene Therapy, The Research Institute at Nationwide Children’s Hospital, Columbus, Ohio USA
| | - S. Harper
- Center For Gene Therapy, The Research Institute at Nationwide Children’s Hospital, Columbus, Ohio USA
| | - R. Burgess
- Graduate School of Biomedical Sciences & Engineering, The University of Maine, Orono, USA
| | - M. Zhalbinova
- Laboratory of Genomic and Personalized Medicine, National Laboratory Astana, Nazarbayev University, ᅟ, Kazakhstan
| | - A. Akilzhanova
- Laboratory of Genomic and Personalized Medicine, National Laboratory Astana, Nazarbayev University, ᅟ, Kazakhstan
| | - S. Rakhimova
- Laboratory of Genomic and Personalized Medicine, National Laboratory Astana, Nazarbayev University, ᅟ, Kazakhstan
| | - M. Bekbosynova
- Cardiology, JSC “National Research Cardiac Surgery Center”, National Medical Holding, Astana, Kazakhstan
| | - S. Myrzakhmetova
- Cardiology, JSC “National Research Cardiac Surgery Center”, National Medical Holding, Astana, Kazakhstan
| | - M. A. Gari
- Medical Laboratory Technology, ᅟ, Saudi Arabia
| | - A. Dallol
- Center of Innovation in Personalized Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - H. Alsehli
- Center of Innovation in Personalized Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - A. Gari
- Center of Innovation in Personalized Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - M. Gari
- Center of Innovation in Personalized Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - A. Abuzenadah
- Center of Innovation in Personalized Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - M. Thomas
- Advanced Molecular Diagnostics Laboratory, ᅟ, Canada
| | - M. Sukhai
- Advanced Molecular Diagnostics Laboratory, ᅟ, Canada
| | - S. Garg
- Advanced Molecular Diagnostics Laboratory, ᅟ, Canada
| | - M. Misyura
- Advanced Molecular Diagnostics Laboratory, ᅟ, Canada
| | - T. Zhang
- Advanced Molecular Diagnostics Laboratory, ᅟ, Canada
| | - A. Schuh
- Princess Margaret Cancer Centre, Toronto, Canada
| | - T. Stockley
- Advanced Molecular Diagnostics Laboratory, ᅟ, Canada
| | - S. Kamel-Reid
- Advanced Molecular Diagnostics Laboratory, ᅟ, Canada
| | | | | | | | | | | | | | | | | | | | - C. Xiao
- National Institutes of Health, Bethesda, USA
| | | | - S. Sherry
- National Institutes of Health, Bethesda, USA
| | - C. Rangel-Escareño
- Computational Genomics, National Institute of Genomic Medicine, Mexico City, Mexico
| | - H. Rueda-Zarate
- Computational Genomics, National Institute of Genomic Medicine, Mexico City, Mexico
| | - I. A. Tayubi
- Computer Science, Faculty of Computing and Information Technology, King AbdulAziz University, Rabigh, Saudi Arabia
| | - R. Mohammed
- Computer Science, Faculty of Computing and Information Technology, King AbdulAziz University, Rabigh, Saudi Arabia
| | | | - I. Ahmed
- Computer Science, Faculty of Computing and Information Technology, King AbdulAziz University, Rabigh, Saudi Arabia
| | - T. Ahmed
- Computer Science, Faculty of Computing and Information Technology, King AbdulAziz University, Rabigh, Saudi Arabia
| | - S. Seth
- Institute of Applied Cancer Science, ᅟ, USA
| | - S. Amin
- Genomic Medicine, University of Texas, ᅟ, ᅟ
| | - X. Song
- Institute of Applied Cancer Science, ᅟ, USA
| | - X. Mao
- Genomic Medicine, University of Texas, ᅟ, ᅟ
| | - H. Sun
- MD Anderson Cancer Center, Houston, USA
| | | | - A. Futreal
- Genomic Medicine, University of Texas, ᅟ, ᅟ
| | - J. Zhang
- Institute of Applied Cancer Science, ᅟ, USA
| | - S. J. Whiite
- Human Genome Sequencing Center, Baylor College of Medicine, ᅟ, USA
| | - T. Chiang
- Human Genome Sequencing Center, Baylor College of Medicine, ᅟ, USA
| | - A. English
- Human Genome Sequencing Center, Baylor College of Medicine, ᅟ, USA
| | - J. Farek
- Human Genome Sequencing Center, Baylor College of Medicine, ᅟ, USA
| | - Z. Kahn
- Human Genome Sequencing Center, Baylor College of Medicine, ᅟ, USA
| | - W. Salerno
- Human Genome Sequencing Center, Baylor College of Medicine, ᅟ, USA
| | - N. Veeraraghavan
- Human Genome Sequencing Center, Baylor College of Medicine, ᅟ, USA
| | - E. Boerwinkle
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, USA
| | - R. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, ᅟ, USA
| | - T. Kasukawa
- Center for Life Science Technologies, RIKEN, Yokohama, Japan
| | - M. Lizio
- Center for Life Science Technologies, RIKEN, Yokohama, Japan
| | - J. Harshbarger
- Center for Life Science Technologies, RIKEN, Yokohama, Japan
| | - S. Hisashi
- Center for Life Science Technologies, RIKEN, Yokohama, Japan
- Preventive Medicine and Diagnosis Innovation Program, RIKEN, Wako, Japan
| | - J. Severin
- Center for Life Science Technologies, RIKEN, Yokohama, Japan
| | - A. Imad
- Center for Life Science Technologies, RIKEN, Yokohama, Japan
| | - S. Sahin
- Center for Life Science Technologies, RIKEN, Yokohama, Japan
| | - T. C. Freeman
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - K. Baillie
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - A. Sandelin
- Department of Biology & Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - P. Carninci
- Center for Life Science Technologies, RIKEN, Yokohama, Japan
| | | | - H. Kawaji
- Center for Life Science Technologies, RIKEN, Yokohama, Japan
- Preventive Medicine and Diagnosis Innovation Program, RIKEN, Wako, Japan
- Advanced Center for Computing and Communication, RIKEN, Yokohama, Japan
| | | | - W. Salerno
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas USA
| | - A. English
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas USA
| | | | | | | | - E. Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas USA
- Human Genetics Center and Department of Epidemiology, UT School of Public Health, Houston, Texas USA
| | - R. A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas USA
| | - A. H. Salem
- Anatomy, Arabian Gulf University, Manama, Bahrain
| | - M. Ali
- Biochemistry, Arabian Gulf University, Manama, Bahrain
| | - A. Ibrahim
- Central Laboratory, Ministry of Science and Technology, ᅟ, Sudan
| | - M. Ibrahim
- College of Animal Production Science and Technology, Sudan University of Science and Technology, Khartoum, Sudan
| | - H. A. Barrera
- Bioquimica y Medicina Molecular, Universidad Autónoma de Nuevo León, Monterrey, Mexico
| | - L. Garza
- Bioquimica y Medicina Molecular, Universidad Autónoma de Nuevo León, Monterrey, Mexico
| | - J. A. Torres
- Bioquimica y Medicina Molecular, Universidad Autónoma de Nuevo León, Monterrey, Mexico
| | - V. Barajas
- Bioquimica y Medicina Molecular, Universidad Autónoma de Nuevo León, Monterrey, Mexico
| | | | - D. Kershenobich
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Distrito Federal, Mexico
| | - Shahroj Mortaji
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Distrito Federal, Mexico
| | - Pedro Guizar
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Distrito Federal, Mexico
| | - Eliezer Loera
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Distrito Federal, Mexico
| | - Karen Moreno
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Distrito Federal, Mexico
| | - Adriana De León
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Distrito Federal, Mexico
| | - Daniela Monsiváis
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Distrito Federal, Mexico
| | - Jackeline Gómez
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Distrito Federal, Mexico
| | - Raquel Cardiel
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Distrito Federal, Mexico
| | | | - V. Bonifaz-Peña
- Computational Genomics, Nacional de Medicina Genomica, Mexico City, Mexico
| | - C. Rangel-Escareño
- Computational Genomics, Nacional de Medicina Genomica, Mexico City, Mexico
| | - A. Hidalgo-Miranda
- Cancer Genomics Laboratory, Nacional de Medicina Genomica, Mexico City, Mexico
| | - A. V. Contreras
- Nutrigenetics and Nutrigenomics Laboratory, Instituto Nacional de Medicina Genomica, Mexico City, Mexico
| | - L. Polfus
- Human Genetics Center, University of Texas Health Science Center, Houston, USA
| | | | - X. Wang
- System Genetics, The Jackson Laboratory, Bar Harbor, USA
| | - V. Philip
- System Genetics, The Jackson Laboratory, Bar Harbor, USA
| | - G. Carter
- System Genetics, The Jackson Laboratory, Bar Harbor, USA
| | - A. A. Abuzenadah
- Center of Innovation in Personalized Medicine, Faculty of Applied Medical Sciences, King Abdulaziz University, ᅟ, Saudi Arabia
| | - M. Gari
- Center of Innovation in Personalized Medicine, Faculty of Applied Medical Sciences, King Abdulaziz University, ᅟ, Saudi Arabia
| | - R. Turki
- Ob/Gyn, King Abdulaziz University Hospital, Jeddah, Saudi Arabia
| | - A. Dallol
- Center of Innovation in Personalized Medicine, Faculty of Applied Medical Sciences, King Abdulaziz University, ᅟ, Saudi Arabia
| | - A. Uyar
- The Jackson Laboratory for Genomic Medicine, Farmington, USA
| | - A. Kaygun
- Department of Mathematical Engineering, Istanbul Technical University, Istanbul, Turkey
| | - S. Zaman
- Department of Biomedical Engineering, University of Connecticut, Storrs, USA
| | - E. Marquez
- The Jackson Laboratory for Genomic Medicine, Farmington, USA
| | - J. George
- The Jackson Laboratory for Genomic Medicine, Farmington, USA
| | - D. Ucar
- The Jackson Laboratory for Genomic Medicine, Farmington, USA
| | | | | | | | | | | | - T. Davis
- New England Biolabs, Ipswich, USA
| | | | | | - D. B. Starr
- Genetics, Stanford University, Stanford, USA
| | - M. Baird
- DNA Diagnostics Center, Fairfield, USA
| | | | - K. Sheets
- Vibrant Gene Consulting, Cambridge, USA
| | - R. Nitsche
- Agilent Technologies, Agilent Technologies, Waldbronn, Germany
| | - L. Prieto-Lafuente
- Agilent Technologies UK Ltd, Agilent Technologies UK Ltd., Edinburgh, UK
| | | | - J. Lee
- NIH/NLM/NCBI, Bethesda, USA
| | | | | | - P. K. R. Thavanati
- Institute of Human Genetics, Department of Molecular Biology & Genomics, Centre for Health Sciences, ᅟ, Mexico
| | - A. Escoto de Dios
- Institute of Human Genetics, Department of Molecular Biology & Genomics, Centre for Health Sciences, ᅟ, Mexico
| | | | | | - M. R. Ruiz Mejia
- Biochemistry, Centre for Health Sciences, University of Guadalajara, Guadalajara, Mexico
| | - K. R. R. Kanala
- Human Genetics Unit, Department Anthropology, Sri Venkateswara University, Tirupati, India
| | - Z. Abduljaleel
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - W. Khan
- Department of Basic Sciences, College of Science and Health Professions, King Saud Bin Abdul Aziz University for Health Sciences, Riyadh, Saudi Arabia
| | - F. A. Al-Allaf
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - M. Athar
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - M. M. Taher
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - N. Shahzad
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - A. Bouazzaoui
- Science and Technology Unit, Umm Al Qura University, Mecca, Saudi Arabia
- Department of Medical Genetics, Umm Al Qura University, Mecca, Saudi Arabia
- Medical Clinic 3 – Hematology/Oncology, University Hospital Regensburg, Regensburg, Germany
| | - E. Huber
- Department of Pathology, University Hospital Regensburg, Regensburg, Germany
| | - A. Dan
- IgNova GmbH, Oberursel, Germany
| | - F. A. Al-Allaf
- Science and Technology Unit, Umm Al Qura University, Mecca, Saudi Arabia
- Department of Medical Genetics Faculty of Medicine, Umm Al Qura University, Mecca, Saudi Arabia
| | - W. Herr
- Medical Clinic 3 – Hematology/Oncology, University Hospital Regensburg, Regensburg, Germany
| | - G. Sprotte
- Department of Ansethesiologie, University of Würzburg Medical School, Würzburg, Germany
| | - J. Köstler
- Department of microbiology, University Hospital Regensburg, Regensburg, Germany
| | - A. Hiergeist
- Department of microbiology, University Hospital Regensburg, Regensburg, Germany
| | - A. Gessner
- Department of microbiology, University Hospital Regensburg, Regensburg, Germany
| | - R. Andreesen
- Medical Clinic 3 – Hematology/Oncology, University Hospital Regensburg, Regensburg, Germany
| | - E. Holler
- Medical Clinic 3 – Hematology/Oncology, University Hospital Regensburg, Regensburg, Germany
| | - F. Al-Allaf
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, ᅟ, Saudi Arabia
- Science and Technology Unit, Umm Al-Qura University, ᅟ, Saudi Arabia
- Molecular Diagnostics Unit, Department of Laboratory and Blood Bank, King Abdullah Medical City, Makkah, Saudi Arabia
| | - A. Alashwal
- King Faisal Specialist Hospital and Research Centre, ᅟ, Saudi Arabia
| | - Z. Abduljaleel
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, ᅟ, Saudi Arabia
- Science and Technology Unit, Umm Al-Qura University, ᅟ, Saudi Arabia
| | - M. Taher
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, ᅟ, Saudi Arabia
- Science and Technology Unit, Umm Al-Qura University, ᅟ, Saudi Arabia
| | - A. Bouazzaoui
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, ᅟ, Saudi Arabia
- Science and Technology Unit, Umm Al-Qura University, ᅟ, Saudi Arabia
| | - H. Abalkhail
- King Faisal Specialist Hospital and Research Centre, ᅟ, Saudi Arabia
| | - A. Al-Allaf
- Faculty of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - R. Bamardadh
- Science and Technology Unit, Umm Al-Qura University, ᅟ, Saudi Arabia
| | - M. Athar
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, ᅟ, Saudi Arabia
- Science and Technology Unit, Umm Al-Qura University, ᅟ, Saudi Arabia
| | - O. Filiptsova
- Biology, National University of Pharmacy, Kharkiv, Ukraine
| | - M. Kobets
- Pharmaceutical Marketing and Management, National University of Pharmacy, Kharkiv, Ukraine
| | - Y. Kobets
- Pharmaceutical Marketing and Management, National University of Pharmacy, Kharkiv, Ukraine
| | - I. Burlaka
- Biology, National University of Pharmacy, Kharkiv, Ukraine
| | - I. Timoshyna
- Human Physiology and Anatomy, National University of Pharmacy, Kharkiv, Ukraine
| | - O. Filiptsova
- Biology, National University of Pharmacy, Kharkiv, Ukraine
| | - M. N. Kobets
- Pharmaceutical Marketing and Management, National University of Pharmacy, Kharkiv, Ukraine
| | - Y. Kobets
- Pharmaceutical Marketing and Management, National University of Pharmacy, Kharkiv, Ukraine
| | - I. Burlaka
- Biology, National University of Pharmacy, Kharkiv, Ukraine
| | - I. Timoshyna
- Human Physiology and Anatomy, National University of Pharmacy, Kharkiv, Ukraine
| | - O. Filiptsova
- Biology, National University of Pharmacy, Kharkiv, Ukraine
| | - M. N. Kobets
- Pharmaceutical Marketing and Management, National University of Pharmacy, Kharkiv, Ukraine
| | - Y. Kobets
- Pharmaceutical Marketing and Management, National University of Pharmacy, Kharkiv, Ukraine
| | - I. Burlaka
- Biology, National University of Pharmacy, Kharkiv, Ukraine
| | - I. Timoshyna
- Human Physiology and Anatomy, National University of Pharmacy, Kharkiv, Ukraine
| | - F. A. Al-allaf
- Department of Medical Genetics Faculty of Medicine, Umm Al Qura University, Mecca, Saudi Arabia
- Science and Technology Unit, Umm Al Qura University, Mecca, Saudi Arabia
- Molecular Diagnostics Unit Department of Laboratory Medicine and Blood Bank, King Abdullah Medical City, ᅟ, Saudi Arabia
| | - M. T. Mohiuddin
- Department of Medical Genetics Faculty of Medicine, Umm Al Qura University, Mecca, Saudi Arabia
- Science and Technology Unit, Umm Al Qura University, Mecca, Saudi Arabia
| | - A. Zainularifeen
- Department of Medical Genetics Faculty of Medicine, Umm Al Qura University, Mecca, Saudi Arabia
- Science and Technology Unit, Umm Al Qura University, Mecca, Saudi Arabia
| | - A. Mohammed
- Department of Medical Genetics Faculty of Medicine, Umm Al Qura University, Mecca, Saudi Arabia
- Science and Technology Unit, Umm Al Qura University, Mecca, Saudi Arabia
| | - H. Abalkhail
- Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - T. Owaidah
- Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - A. Bouazzaoui
- Department of Medical Genetics Faculty of Medicine, Umm Al Qura University, Mecca, Saudi Arabia
- Science and Technology Unit, Umm Al Qura University, Mecca, Saudi Arabia
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Luna-Aguirre CM, de la Luz Martinez-Fierro M, Mar-Aguilar F, Garza-Veloz I, Treviño-Alvarado V, Rojas-Martinez A, Jaime-Perez JC, Malagon-Santiago GI, Gutierrez-Aguirre CH, Gonzalez-Llano O, Salazar-Riojas R, Hidalgo-Miranda A, Martinez-Rodriguez HG, Gomez-Almaguer D, Ortiz-Lopez R. Circulating microRNA expression profile in B-cell acute lymphoblastic leukemia. Cancer Biomark 2016; 15:299-310. [PMID: 26406572 DOI: 10.3233/cbm-150465] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND Acute lymphoblastic leukemia (ALL) is a highly diverse disease characterized by cytogenetic and molecular abnormalities, including altered microRNA (miRNA) expression signatures. AIM We perform and validate a plasma miRNA expression profiling to identify potential miRNA involved in leukemogenesis METHODS MiRNA expression profiling assay was realized in 39 B-ALL and 7 normal control plasma samples using TaqMan Low Density Array (TLDA) plates on Applied Biosystems 7900 HT Fast Real-Time PCR System. MiRNA validation was done for six miRNA differentially expressed by quantitative real-time PCR. RESULTS Seventy-seven circulating miRNA differentially expressed: hsa-miR-511, -222, and -34a were overexpressed, whereas hsa-miR-199a-3p, -223, -221, and -26a were underexpressed (p values < 0.005 for both sets). According to operating characteristic curve analysis, hsa-miR-511 was the most valuable biomarker for distinguishing B-ALL from normal controls, with an area under curve value of 1 and 100% for sensitivity, and specificity respectively. CONCLUSIONS Measuring circulating levels of specific miRNA implicated in regulation of cell differentiation and/or cell proliferation such as hsa-miRNA-511, offers high sensitivity and specificity in B-ALL detection and may be potentially useful for detection of disease progression, as indicator of therapeutic response, and in the assessment of biological and/or therapeutic targets for patients with B-ALL.
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Affiliation(s)
- Claudia Maribel Luna-Aguirre
- Departamento de Bioquímica y Medicina Molecular, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey NL, México
| | - Margarita de la Luz Martinez-Fierro
- Laboratorio de Medicina Molecular, Unidad Académica de Medicina Humana y Ciencias de la Salud, Universidad Autónoma de Zacatecas, Zacatecas, México
| | - Fermín Mar-Aguilar
- Departamento de Biología Celular y Genética, Facultad de Ciencias Biológicas, Monterrey NL, México
| | - Idalia Garza-Veloz
- Laboratorio de Medicina Molecular, Unidad Académica de Medicina Humana y Ciencias de la Salud, Universidad Autónoma de Zacatecas, Zacatecas, México
| | | | - Augusto Rojas-Martinez
- Departamento de Bioquímica y Medicina Molecular, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey NL, México.,Centro de Investigación y Desarrollo en Ciencias de la Salud, Universidad Autónoma de Nuevo León, Monterrey, México
| | - Jose Carlos Jaime-Perez
- Servicio de Hematología, Hospital Universitario Universidad Autónoma de Nuevo León, Monterrey NL, México
| | | | | | - Oscar Gonzalez-Llano
- Servicio de Hematología, Hospital Universitario Universidad Autónoma de Nuevo León, Monterrey NL, México
| | - Rosario Salazar-Riojas
- Servicio de Hematología, Hospital Universitario Universidad Autónoma de Nuevo León, Monterrey NL, México
| | | | | | - David Gomez-Almaguer
- Servicio de Hematología, Hospital Universitario Universidad Autónoma de Nuevo León, Monterrey NL, México
| | - Rocio Ortiz-Lopez
- Departamento de Bioquímica y Medicina Molecular, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey NL, México.,Centro de Investigación y Desarrollo en Ciencias de la Salud, Universidad Autónoma de Nuevo León, Monterrey, México
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