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Mariscal-Ramos C, Cortes-Trujllo I, Martínez-Cortés G, Arana IN, Rangel-Villalobos H. Population expansion, larger, and more homogeneous native American ancestry among Mexican mestizo populations based on 10 X-chromosome STR loci (X-STR decaplex system). Am J Hum Biol 2024:e24124. [PMID: 38978431 DOI: 10.1002/ajhb.24124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 07/10/2024] Open
Abstract
OBJECTIVE To evaluate the genetic diversity, admixture, genetic relationships, and sex-biased demographic processes in Mexican Mestizo (admixed) populations based on 10 X-chromosome STRs (X-STRs). METHODS We analyzed the X-STRs Decaplex system in 104 Mexican Native Americans to obtain the ancestral reference needed to complete the demographic analyses above mentioned. We included reported Iberian and Latin American (admixed) populations from Central and South America, as well as datasets from Mexican Mestizos based on Y-linked STRs (Y-STRs), autosomal STRs (A-STRs), and mtDNA. RESULTS Higher X-linked Native American ancestry was observed among Latin American populations regarding that reported from A-STRs and Y-STRs. The interpopulation differentiation based on ancestry among Mexican Mestizos diminished according to the inheritance pattern: Y-STRs (highest), A-STRs, X-STRs, and mtDNA (lowest). This finding is related to the peculiar admixture process that occurred during and after the Spanish Conquest of Mexico (and most of Latin America), involving a large number of Spanish men (Y-chromosomes) with a lesser proportion of X-chromosomes than autosomes; besides to the limited number of Spanish women (XX) arrived in the Americas in subsequent and shorter periods. Population expansion was detected in Mexican Mestizos from all the country, except those from the southeast region characterized by elevated indigenous ancestry, marginalization, and poorness. CONCLUSIONS Population growth was detected in most Mexican Mestizos, besides more homogeneous and larger Native American ancestry based on X-linked inheritance than that based on autosomal STRs and Y-STRs.
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Affiliation(s)
- Christian Mariscal-Ramos
- Instituto de Investigación en Genética Molecular, Centro Universitario de la Ciénega, Universidad de Guadalajara (CUCiénega-UdeG), Ocotlán, Jalisco, Mexico
| | - Irán Cortes-Trujllo
- Instituto de Investigación en Genética Molecular, Centro Universitario de la Ciénega, Universidad de Guadalajara (CUCiénega-UdeG), Ocotlán, Jalisco, Mexico
| | - Gabriela Martínez-Cortés
- Instituto de Investigación en Genética Molecular, Centro Universitario de la Ciénega, Universidad de Guadalajara (CUCiénega-UdeG), Ocotlán, Jalisco, Mexico
| | - Ismael Nuño Arana
- Centro de Investigación Multidisciplinario en Salud, Departamento de Salud y Enfermedad, Centro Universitario de Tonalá, Universidad de Guadalajara (CUCiénega-UdeG), Guadalajara, Jalisco, Mexico
| | - Héctor Rangel-Villalobos
- Instituto de Investigación en Genética Molecular, Centro Universitario de la Ciénega, Universidad de Guadalajara (CUCiénega-UdeG), Ocotlán, Jalisco, Mexico
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Peña-Espinoza BI, Torre-Horta E, Ortiz-López MG, Menjivar M. ABCA1 variant rs9282541 is associated with metabolic syndrome in Maya children. Ann Hum Genet 2024; 88:279-286. [PMID: 38192238 DOI: 10.1111/ahg.12546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 11/17/2023] [Accepted: 12/04/2023] [Indexed: 01/10/2024]
Abstract
INTRODUCTION Metabolic syndrome (MetS) is a metabolic disorder encompassing risk factors for cardiovascular disease and type 2 diabetes (T2D). In Mexico, the MetS is a national health problem in adults and children. Environmental and genetic factors condition the MetS. However, studies to elucidate the contribution of genetic factors to MetS in Mexico are scarce. A recent study showed that variant rs9282541 (A-allele) in ATP-binding cassette transporter A1 (ABCA1) was associated with T2D in the Maya population in addition to low levels of high-density lipoprotein cholesterol (HDL-C). Thus, this study aimed to determine whether the genetic variant of ABCA1 A-allele (rs9282541, NM_005502.4:c.688C > T, NP_005493.2:p.Arg230Cys) is associated with MetS and its components in Mexican Maya children. METHODS The study was conducted in 508 children aged 9-13 from the Yucatán Peninsula. MetS was identified according to the de Ferranti criteria. Genotyping was performed using TaqMan assay by real-time PCR. Evaluation of genetic ancestry group was included. RESULTS The frequency of MetS and overweight-obesity was 45.9% and 41.6%, respectively. The genetic variant rs9282541 was associated with low HDL-C and high glucose concentrations. Remarkably, for the first time, this study showed the association of ABCA1 rs9282541 with MetS in Maya children with an OR of 3.076 (95% CI = 1.16-8.13 p = 0.023). Finally, this study reveals a high prevalence of MetS and suggests that variant rs9282541 of the ABCA1 gene plays an important role in the developing risk of MetS in Maya children.
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Affiliation(s)
- Barbara I Peña-Espinoza
- Laboratorio de Genómica de la Diabetes, Facultad de Química en la Unidad Académica de Ciencia y Tecnología de la UNAM en Yucatán, Ciudad de Mexico, Mexico
| | | | - María G Ortiz-López
- Laboratorio de Endocrinología, Hospital Juárez de México, Mexico City, Mexico
| | - Marta Menjivar
- Laboratorio de Genómica de la Diabetes, Facultad de Química en la Unidad Académica de Ciencia y Tecnología de la UNAM en Yucatán, Ciudad de Mexico, Mexico
- Laboratorio de diabetes, Facultad de Química de la Universidad Nacional Autónoma de México, Mexico City, Mexico
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Arrieta O, Caballé-Pérez E, Hernández-Pedro N, Romero-Nuñez E, Lucio-Lozada J, Castillo-Ruiz C, Acevedo-Castillo K, María Álvarez-Gómez R, Molina-Garay C, Jiménez-Olivares M, Carrillo-Sánchez K, Cristina Mendoza-Caamal E, Cardona AF, Remon J, Alaez-Verson C. Prevalence of pathogenic or likely pathogenic germline variants in cancer predisposition genes among selected patients with lung adenocarcinoma: The GERMLUNG study. Lung Cancer 2024; 194:107864. [PMID: 38945003 DOI: 10.1016/j.lungcan.2024.107864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/23/2024] [Accepted: 06/24/2024] [Indexed: 07/02/2024]
Abstract
INTRODUCTION Pathogenic or likely pathogenic germline variants (PGVs) in cancer predisposition genes may play a role in lung cancer (LC) susceptibility. However, determining an eligible population for genetic testing remains uncertain. This study aimed to assess the prevalence of PGVs in a selected cohort of individuals with lung adenocarcinoma. METHODS A cross-sectional cohort study was conducted to assess the PGVs rate in lung adenocarcinoma patients with a family history of LC, young-onset presentation, history of never/light smoking, or actionable genomic alterations (AGAs). Sequencing was performed using Sophia Hereditary Cancer Solution panel F, including 144 cancer predisposition genes. Variants classified as pathogenic or likely pathogenic were included for further analysis. RESULTS Of 201 patients, 43 (21.4 %) exhibited PGVs, among which 64.5 % were DNA damage repair genes, and 86.1 % were clinically actionable. The main PGVs were in ATM (9.3 %), TP53 (6.9 %), BRCA2 (6.9 %), and CHEK2 (6.9 %) genes. PGVs were associated with male sex (adjusted odds ratio [aOR] 2.46, 95 % CI 1.15-5.32, p = 0.021), along with a trend toward association with AGAs (aOR 6.04, 95 % CI 0.77-49.74, p = 0.094). CONCLUSIONS In this study, a high PGVs prevalence was identified based on our selection criteria, which represents an effective strategy to identify candidates for germline genomic testing, potential screening strategies in close relatives, and personalized therapeutic modalities. Our results warrant further exploration in other populations to confirm them.
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Affiliation(s)
- Oscar Arrieta
- Thoracic Oncology Unit, Instituto Nacional de Cancerología (INCan), Mexico City 14080, Mexico; Personalized Medicine Laboratory, Instituto Nacional de Cancerología (INCan), Mexico City 14080, Mexico.
| | - Enrique Caballé-Pérez
- Thoracic Oncology Unit, Instituto Nacional de Cancerología (INCan), Mexico City 14080, Mexico.
| | - Norma Hernández-Pedro
- Personalized Medicine Laboratory, Instituto Nacional de Cancerología (INCan), Mexico City 14080, Mexico.
| | - Eunice Romero-Nuñez
- Personalized Medicine Laboratory, Instituto Nacional de Cancerología (INCan), Mexico City 14080, Mexico.
| | - José Lucio-Lozada
- Personalized Medicine Laboratory, Instituto Nacional de Cancerología (INCan), Mexico City 14080, Mexico.
| | - Cesar Castillo-Ruiz
- Personalized Medicine Laboratory, Instituto Nacional de Cancerología (INCan), Mexico City 14080, Mexico.
| | - Karla Acevedo-Castillo
- Genomic Diagnosis Laboratory, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico.
| | - Rosa María Álvarez-Gómez
- Hereditary Cancer Clinic, Instituto Nacional de Cancerología (INCan), Mexico City 14080, Mexico.
| | - Carolina Molina-Garay
- Genomic Diagnosis Laboratory, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico.
| | - Marco Jiménez-Olivares
- Genomic Diagnosis Laboratory, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico.
| | - Karol Carrillo-Sánchez
- Genomic Diagnosis Laboratory, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico.
| | | | - Andrés F Cardona
- Thoracic Oncology Unit and Direction of Research, Science and Education, Luis Carlos Sarmiento Angulo, Cancer Treatment and Research Center (CTIC), Bogotá, Colombia.
| | - Jordi Remon
- Gustave Roussy Cancer Campus, Medical Oncology Department, 114 Rue Edouard Vaillant, 94805 Villejuif, France.
| | - Carmen Alaez-Verson
- Genomic Diagnosis Laboratory, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico.
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Panduro A, Roman S, Mariscal-Martinez IM, Jose-Abrego A, Gonzalez-Aldaco K, Ojeda-Granados C, Ramos-Lopez O, Torres-Reyes LA. Personalized medicine and nutrition in hepatology for preventing chronic liver disease in Mexico. Front Nutr 2024; 11:1379364. [PMID: 38784134 PMCID: PMC11113077 DOI: 10.3389/fnut.2024.1379364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 04/01/2024] [Indexed: 05/25/2024] Open
Abstract
Chronic liver disease is a global health issue. Patients with chronic liver disease require a fresh approach that focuses on the genetic and environmental factors that contribute to disease initiation and progression. Emerging knowledge in the fields of Genomic Medicine and Genomic Nutrition demonstrates differences between countries in terms of genetics and lifestyle risk factors such as diet, physical activity, and mental health in chronic liver disease, which serves as the foundation for the implementation of Personalized Medicine and Nutrition (PerMed-Nut) strategies. Most of the world's populations have descended from various ethnic groupings. Mexico's population has a tripartite ancestral background, consisting of Amerindian, European, and African lineages, which is common across Latin America's regional countries. The purpose of this review is to discuss the genetic and environmental components that could be incorporated into a PerMed-Nut model for metabolic-associated liver disease, viral hepatitis B and C, and hepatocellular carcinoma in Mexico. Additionally, the implementation of the PerMed-Nut approach will require updated medicine and nutrition education curricula. Training and equipping future health professionals and researchers with new clinical and investigative abilities focused on preventing liver illnesses in the field of genomic hepatology globally is a vision that clinicians and nutritionists should be concerned about.
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Affiliation(s)
- Arturo Panduro
- Department of Genomic Medicine in Hepatology, Civil Hospital of Guadalajara, Fray Antonio Alcalde, Health Sciences Center, University of Guadalajara, Guadalajara, Jalisco, Mexico
| | - Sonia Roman
- Department of Genomic Medicine in Hepatology, Civil Hospital of Guadalajara, Fray Antonio Alcalde, Health Sciences Center, University of Guadalajara, Guadalajara, Jalisco, Mexico
| | - Irene M. Mariscal-Martinez
- Department of Genomic Medicine in Hepatology, Civil Hospital of Guadalajara, Fray Antonio Alcalde, Health Sciences Center, University of Guadalajara, Guadalajara, Jalisco, Mexico
| | - Alexis Jose-Abrego
- Department of Genomic Medicine in Hepatology, Civil Hospital of Guadalajara, Fray Antonio Alcalde, Health Sciences Center, University of Guadalajara, Guadalajara, Jalisco, Mexico
| | - Karina Gonzalez-Aldaco
- Department of Genomic Medicine in Hepatology, Civil Hospital of Guadalajara, Fray Antonio Alcalde, Health Sciences Center, University of Guadalajara, Guadalajara, Jalisco, Mexico
| | - Claudia Ojeda-Granados
- Department of Medical and Surgical Sciences and Advanced Technologies “GF Ingrassia”, University of Catania, Catania, Italy
| | - Omar Ramos-Lopez
- Medicine and Psychology School, Autonomous University of Baja California, Tijuana, Baja California, Mexico
| | - Luis A. Torres-Reyes
- Department of Genomic Medicine in Hepatology, Civil Hospital of Guadalajara, Fray Antonio Alcalde, Health Sciences Center, University of Guadalajara, Guadalajara, Jalisco, Mexico
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Nakazawa-Ueji YE, Valencia-Pacheco G, González-Herrera LJ, Chan-Chalé L, Velasco-Cárdenas RMH, Carreño-Gonzalez MJ, Pérez-Mendoza G, Amaro-Adrián GI, Rodríguez-Dzul EA, Quintal-Ortiz IG, Angulo-Ramírez AV, López-Villanueva RF. Association of the polymorphisms rs179008 ( TLR7), rs2004640 ( IRF5), rs1800795 ( IL-6) and rs2280788 ( CCL5) with systemic lupus erythematosus in women of Mayan ethnicity from Yucatan. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2024:1-17. [PMID: 38459707 DOI: 10.1080/15257770.2024.2325438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 02/24/2024] [Indexed: 03/10/2024]
Abstract
Introduction: IFN-α is the main cytokine in SLE, and single nucleotide polymorphisms (SNP) in different genes could induce it. Aim: To determine the association of rs2004640 (IRF5), rs179008 (TLR7), rs1800795 (IL-6) and rs2280788 (CCL5) with SLE in Mexican women with Mayan ethnicity. Methods: DNA and RNA were isolated from the peripheral blood of 110 patients and 200 healthy control subjects. SNP genotyping and gene expression analysis of IRF5, TLR7, IL-6 and IFN-α were determined by real-time PCR and analyzed with SNP Stat, Stata 10.1 and Graph Pad Prism v5. Results: rs2004640, rs179008, and rs1800795 in both groups were according to Hardy-Weinberg equilibrium. Risk alleles rs179008T and rs2004640T frequencies were higher in controls (p = 0.015 and p = 0.028, respectively), whereas rs179008A frequency was higher in patients (p = 0.015). Allelic combination AGT frequency was higher in patients (p = 0.001). IL-6 rs1800795C > G and CCL5 rs2280788G > C frequencies did not show significant differences (p > 0.05), being rs2280788G (CCL5) monomorphic in controls. SLE patients showed higher TLR7, IRF5, IL6, and IFN-α mRNA levels. IRF5 expression was higher in SLE patients homozygous for rs2004640T (IRF5). Conclusion: This work showed the contribution of TLR7 and IRF5 in SLE pathogenesis in Mayan females from Yucatan.
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Affiliation(s)
- Yumi Elena Nakazawa-Ueji
- Hematology Laboratory, Regional Research Center, Autonomous University of Yucatan, Yucatan, Mexico
| | | | | | - Laureano Chan-Chalé
- Hematology Laboratory, Regional Research Center, Autonomous University of Yucatan, Yucatan, Mexico
| | | | | | - Gerardo Pérez-Mendoza
- Hematology Laboratory, Regional Research Center, Autonomous University of Yucatan, Yucatan, Mexico
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Vacek M, Zárraga Vargas LC, González Domínguez E, Garcia Rodriguez L, Tello Teran OA, Mojica Cardoso C, Ocampo Roosens LV, Acevedo Fernandez JJ, Li W, Lee B, Olalla Tapia JS, Flatt T. Increased Incidence of TdT-negative Pre-B Acute Lymphoblastic Leukemia Associated With Poor Prognostic Features Among Mexican Children in Central Mexico. J Pediatr Hematol Oncol 2024; 46:e131-e136. [PMID: 38132672 DOI: 10.1097/mph.0000000000002802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 11/16/2023] [Indexed: 12/23/2023]
Abstract
Mexican and Hispanic children in Mexico and the United States, respectively, have the highest incidence and worst outcomes of pre-B acute lymphoblastic leukemia (ALL) compared with other racial/ethnic groups. Terminal deoxynucleotidyl transferase (TdT) is an intranuclear DNA polymerase normally present on immature lymphocytes (TdT-positive) and distinguishes ALL from mature lymphoid malignancies. We performed a multisite retrospective study to determine the incidence of TdT-negative precursor B-cell acute lymphoblastic leukemia (pre-B ALL) among Mexican, Caucasian, and US-born Hispanic children to correlate TdT expression with patient characteristics and known prognostic factors. Fisher exact test was performed for categorical variables and the Wilcoxon rank-sum test was used for continuous variables. TdT-negative pre-B ALL was most frequently identified in patients with National Cancer Institute high-risk disease ( P =0.014). TdT-negative expression was also most frequently associated with hypodiploid pre-B ALL ( P =0.001) and KMT2A gene rearrangement ( P =0.0012). Mexican children had the highest incidence of TdT-negative ALL compared with Caucasians and US Hispanics ( P <0.001), with an increased incidence of poor prognostic features as well. This study demonstrates significant differences in TdT-negative expression, genomic alterations, and leukemic ploidy based on race and ethnicity.
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Affiliation(s)
- Meagan Vacek
- Department of Pediatric Hematology-Oncology, Children's Mercy Hospital, Kansas City, MO
| | - Laura C Zárraga Vargas
- Stem Cell Biology Lab, Autonomous University of Morelos State, Cuernavaca
- The Dr. Ruy Perez Tamayo Diagnostic and Molecular Medicine Unit, Hospital del Niño Morelense, Emiliano Zapata
| | | | | | | | | | | | | | | | - Brian Lee
- Division of Health Services and Outcomes Research, Children's Mercy Hospital, Kansas City, MO
| | - Jesús S Olalla Tapia
- Stem Cell Biology Lab, Autonomous University of Morelos State, Cuernavaca
- The Dr. Ruy Perez Tamayo Diagnostic and Molecular Medicine Unit, Hospital del Niño Morelense, Emiliano Zapata
| | - Terrie Flatt
- Department of Pediatric Hematology-Oncology, Children's Mercy Hospital, Kansas City, MO
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7
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Nuñez NA, Coombes BJ, Beaupre LM, Ozerdem A, Resendez MG, Romo-Nava F, Bond DJ, Veldic M, Singh B, Moore KM, Betcher HK, Kung S, Prieto ML, Fuentes M, Ercis M, Miola A, Sanchez Ruiz JA, Jenkins G, Batzler A, Leung JG, Cuellar-Barboza A, Tye SJ, McElroy SL, Biernacka JM, Frye MA. Pharmacogenomic overlap between antidepressant treatment response in major depression & antidepressant associated treatment emergent mania in bipolar disorder. Transl Psychiatry 2024; 14:93. [PMID: 38351009 PMCID: PMC10864308 DOI: 10.1038/s41398-024-02798-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 01/08/2024] [Accepted: 01/17/2024] [Indexed: 02/16/2024] Open
Abstract
There is increasing interest in individualizing treatment selection for more than 25 regulatory approved treatments for major depressive disorder (MDD). Despite an inconclusive efficacy evidence base, antidepressants (ADs) are prescribed for the depressive phase of bipolar disorder (BD) with oftentimes, an inadequate treatment response and or clinical concern for mood destabilization. This study explored the relationship between antidepressant response in MDD and antidepressant-associated treatment emergent mania (TEM) in BD. We conducted a genome-wide association study (GWAS) and polygenic score analysis of TEM and tested its association in a subset of BD-type I patients treated with SSRIs or SNRIs. Our results did not identify any genome-wide significant variants although, we found that a higher polygenic score (PGS) for antidepressant response in MDD was associated with higher odds of TEM in BD. Future studies with larger transdiagnostic depressed cohorts treated with antidepressants are encouraged to identify a neurobiological mechanism associated with a spectrum of depression improvement from response to emergent mania.
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Affiliation(s)
- Nicolas A Nuñez
- Department of Psychiatry & Psychology, Mayo Clinic, Rochester, MN, USA
| | - Brandon J Coombes
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | | | - Aysegul Ozerdem
- Department of Psychiatry & Psychology, Mayo Clinic, Rochester, MN, USA
| | - Manuel Gardea Resendez
- Department of Psychiatry & Psychology, Mayo Clinic, Rochester, MN, USA
- Department of Psychiatry, Universidad Autónoma de Nuevo León, Monterrey, México
| | | | - David J Bond
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins University, Baltimore, MD, USA
| | - Marin Veldic
- Department of Psychiatry & Psychology, Mayo Clinic, Rochester, MN, USA
| | - Balwinder Singh
- Department of Psychiatry & Psychology, Mayo Clinic, Rochester, MN, USA
| | - Katherine M Moore
- Department of Psychiatry & Psychology, Mayo Clinic, Rochester, MN, USA
| | - Hannah K Betcher
- Department of Psychiatry & Psychology, Mayo Clinic, Rochester, MN, USA
| | - Simon Kung
- Department of Psychiatry & Psychology, Mayo Clinic, Rochester, MN, USA
| | - Miguel L Prieto
- Department of Psychiatry, Faculty of Medicine, Universidad de Los Andes, Santiago, Chile
| | - Manuel Fuentes
- Department of Psychiatry & Psychology, Mayo Clinic, Rochester, MN, USA
| | - Mete Ercis
- Department of Psychiatry & Psychology, Mayo Clinic, Rochester, MN, USA
| | - Alessandro Miola
- Department of Psychiatry & Psychology, Mayo Clinic, Rochester, MN, USA
| | | | - Gregory Jenkins
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Anthony Batzler
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | | | | | - Susannah J Tye
- Department of Psychiatry & Psychology, Mayo Clinic, Rochester, MN, USA
- Queensland Brain Institute, The University of Queensland, St. Lucia, QLD, Australia
| | - Susan L McElroy
- Lindner Center of HOPE/University of Cincinnati, Cincinnati, OH, USA
| | - Joanna M Biernacka
- Department of Psychiatry & Psychology, Mayo Clinic, Rochester, MN, USA
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Mark A Frye
- Department of Psychiatry & Psychology, Mayo Clinic, Rochester, MN, USA.
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Zenteno JC, Chacón-Camacho OF, Ordoñez-Labastida V, Miranda-Duarte A, Del Castillo C, Nava J, Mendoza F, Montes-Almanza L, Mora-Roldán G, Gazarian K. Identification of Genetic Variants for Diabetic Retinopathy Risk Applying Exome Sequencing in Extreme Phenotypes. BIOMED RESEARCH INTERNATIONAL 2024; 2024:2052766. [PMID: 38249632 PMCID: PMC10799704 DOI: 10.1155/2024/2052766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/16/2023] [Accepted: 12/23/2023] [Indexed: 01/23/2024]
Abstract
Background Diabetic retinopathy (DR) risk has been shown to vary depending on ethnic backgrounds, and thus, it is worthy that underrepresented populations are analyzed for the potential identification of DR-associated genetic variants. We conducted a case-control study for the identification of DR-risk variants in Mexican population. Methods We ascertained 60 type 2 diabetes mellitus (T2DM) patients. Cases (n = 30) were patients with advanced proliferative DR (PDR) with less than 15 years after a T2DM diagnosis while controls (n = 30) were patients with no DR 15 years after the diagnosis of T2DM. Exome sequencing was performed in all patients, and the frequency of rare variants was compared. In addition, the frequency of variants occurring in a set of 169 DR-associated genes were compared. Results Statistically significant differences were identified for rare missense and splice variants and for rare splice variants occurring more than once in either group. A strong statistical difference was observed when the number of rare missense variants with an aggregated prediction of pathogenicity and occurring more than once in either group was compared (p = 0.0035). Moreover, 8 variants identified more than once in either group, occurring in previously identified DR-associated genes were recognized. The p.Pro234Ser KIR2DS4 variant showed a strong protective effect (OR = 0.04 [0.001-0.36]; p = 0.04). Conclusions Our study showed an enrichment of rare splice acceptor/donor variants in patients with PDR and identified a potential protective variant in KIR2DS4. Although statistical significance was not reached, our results support the replication of 8 previously identified DR-associated genes.
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Affiliation(s)
- Juan C. Zenteno
- Department of Genetics, Institute of Ophthalmology “Conde de Valenciana”, Mexico City, Mexico
- Faculty of Medicine, Department of Biochemistry, National Autonomous University of Mexico (UNAM), Mexico City, Mexico
- Rare Disease Diagnostic Unit, Faculty of Medicine, UNAM, Mexico City, Mexico
| | - Oscar F. Chacón-Camacho
- Department of Genetics, Institute of Ophthalmology “Conde de Valenciana”, Mexico City, Mexico
- Laboratorio 5 Edificio A-4, Carrera de Médico Cirujano, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Mexico
| | - Vianey Ordoñez-Labastida
- Department of Genetics, Institute of Ophthalmology “Conde de Valenciana”, Mexico City, Mexico
- Rare Disease Diagnostic Unit, Faculty of Medicine, UNAM, Mexico City, Mexico
- Faculty of Medicine, Autonomous University of the State of Morelos (UAEM), Morelos, Mexico
| | - Antonio Miranda-Duarte
- Department of Genomic Medicine, Instituto Nacional de Rehabilitación “Luis Guillermo Ibarra Ibarra”, Mexico City, Mexico
| | - Camila Del Castillo
- Retina Department, Institute of Ophthalmology “Conde de Valenciana”, Mexico City, Mexico
| | - Jessica Nava
- Department of Genetics, Institute of Ophthalmology “Conde de Valenciana”, Mexico City, Mexico
| | - Fatima Mendoza
- Department of Genetics, Institute of Ophthalmology “Conde de Valenciana”, Mexico City, Mexico
| | - Luis Montes-Almanza
- Department of Genetics, Institute of Ophthalmology “Conde de Valenciana”, Mexico City, Mexico
| | - Germán Mora-Roldán
- Department of Genetics, Institute of Ophthalmology “Conde de Valenciana”, Mexico City, Mexico
| | - Karlen Gazarian
- Biomedical Research Institute, Department of Genomic Medicine, National Autonomous University of Mexico, Mexico City, Mexico
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9
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de Smith AJ, Jiménez-Morales S, Mejía-Aranguré JM. The genetic risk of acute lymphoblastic leukemia and its implications for children of Latin American origin. Front Oncol 2024; 13:1299355. [PMID: 38264740 PMCID: PMC10805326 DOI: 10.3389/fonc.2023.1299355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 12/12/2023] [Indexed: 01/25/2024] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most common cancer in children, and disproportionately affects children of Hispanic/Latino ethnicity in the United States, who have the highest incidence of disease compared with other racial/ethnic groups. Incidence of childhood ALL is similarly high in several Latin American countries, notably in Mexico, and of concern is the rising incidence of childhood ALL in some Hispanic/Latino populations that may further widen this disparity. Prior studies have implicated common germline genetic variants in the increased risk of ALL among Hispanic/Latino children. In this review, we describe the known disparities in ALL incidence as well as patient outcomes that disproportionately affect Hispanic/Latino children across the Americas, and we focus on the role of genetic variation as well as Indigenous American ancestry in the etiology of these disparities. Finally, we discuss future avenues of research to further our understanding of the causes of the disparities in ALL incidence and outcomes in children of Latin American origin, which will be required for future precision prevention efforts.
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Affiliation(s)
- Adam J. de Smith
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA, United States
- USC Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, CA, United States
| | - Silvia Jiménez-Morales
- Laboratorio de Innovación y Medicina de Precisión, Núcleo A, Instituto Nacional de Medicina Genómica, Ciudad de México, Mexico
| | - Juan Manuel Mejía-Aranguré
- Laboratorio de Genómica Funcional del Cáncer, Instituto Nacional de Medicina Genómica, Ciudad de México, Mexico
- Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
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10
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Alonso‐Luna O, Mercado‐Celis GE, Melendez‐Zajgla J, Barquera R, Zapata‐Tarres M, Juárez‐Villegas LE, Mendoza‐Caamal EC, Rey‐Helo E, Borges‐Yañez SA. Germline mutations in pediatric cancer cohort with mixed-ancestry Mexicans. Mol Genet Genomic Med 2024; 12:e2332. [PMID: 38093606 PMCID: PMC10767611 DOI: 10.1002/mgg3.2332] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/11/2023] [Accepted: 11/28/2023] [Indexed: 01/07/2024] Open
Abstract
BACKGROUND Childhood cancer is one of the primary causes of disease-related death in 5- to 14-year-old children and currently no prevention strategies exist to reduce the incidence of this disease. Childhood cancer has a larger hereditary component compared with cancer in adults. Few genetic studies have been conducted on children with cancer. Additionally, Latin American populations are underrepresented in genomic studies compared with other populations. Therefore, the aim of this study is to analyze germline mutations in a group of mixed-ancestry Mexican pediatric patients with solid and hematological cancers. METHODS We analyzed genetic variants from 40 Mexican childhood cancer patients and their relatives. DNA from saliva or blood samples was used for whole-exome sequencing. All variants were identified following GATK best practices. RESULTS We found that six patients (15%) were carriers of germline mutations in CDKN2A, CHEK2, DICER1, FANCA, MSH6, MUTYH, NF1, and SBDS cancer predisposition genes, and additional new variants predicted to be deleterious by in silico algorithms. A population genetics analysis detected five components consistent with the demographic models assumed for modern mixed-ancestry Mexicans. CONCLUSIONS This report identifies potential genetic risk factors and provides a better understanding of the underlying mechanisms of childhood cancer in this population.
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Grants
- 365882 Consejo Nacional de Ciencia y Tecnología, CONACyT, Mexico
- 253316 Consejo Nacional de Ciencia y Tecnología, CONACyT, Mexico
- Fundacion Carlos Slim as part of the inaugural phase of Slim Initiative in Genomic Medicine for the Americas, SIGMA
- Broad Institute of MIT and Harvard
- Instituto Nacional de Medicina Genomica (INMEGEN)
- Division de Estudios de Posgrado e Investigacion de la Facultad de Odontologia
- Programa de Maestria y Doctorado en Ciencias Medicas, Odontologicas y de la Salud, UNAM
- "Aqui nadie se rinde, ANSER (I.A.P)
- Max Planck Institute for Evolutionary Anthropology (MPI-EVA)
- Consejo Nacional de Ciencia y Tecnología, CONACyT, Mexico
- Max Planck Institute for Evolutionary Anthropology (MPI‐EVA)
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Affiliation(s)
- Oscar Alonso‐Luna
- Programa de Maestria y Doctorado en Ciencias Medicas, Odontologicas y de la SaludCiudad Universitaria, Universidad Nacional Autonoma de MexicoMexico CityMexico
| | | | - Jorge Melendez‐Zajgla
- Laboratorio de Genomica Funcional del CancerInstituto Nacional de Medicina GenomicaMexico CityMexico
| | - Rodrigo Barquera
- Department of ArchaeogeneticsMax Plank Institute for Evolutionary Anthropology (MPI‐EVA)LeipzigGermany
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11
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Zollner L, Torres D, Briceno I, Gilbert M, Torres-Mejía G, Dennis J, Bolla MK, Wang Q, Hamann U, Lorenzo Bermejo J. Native American ancestry and breast cancer risk in Colombian and Mexican women: ruling out potential confounding through ancestry-informative markers. Breast Cancer Res 2023; 25:111. [PMID: 37784177 PMCID: PMC10544431 DOI: 10.1186/s13058-023-01713-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 09/18/2023] [Indexed: 10/04/2023] Open
Abstract
BACKGROUND Latin American and Hispanic women are less likely to develop breast cancer (BC) than women of European descent. Observational studies have found an inverse relationship between the individual proportion of Native American ancestry and BC risk. Here, we use ancestry-informative markers to rule out potential confounding of this relationship, estimating the confounder-free effect of Native American ancestry on BC risk. METHODS AND STUDY POPULATION We used the informativeness for assignment measure to select robust instrumental variables for the individual proportion of Native American ancestry. We then conducted separate Mendelian randomization (MR) analyses based on 1401 Colombian women, most of them from the central Andean regions of Cundinamarca and Huila, and 1366 Mexican women from Mexico City, Monterrey and Veracruz, supplemented by sensitivity and stratified analyses. RESULTS The proportion of Colombian Native American ancestry showed a putatively causal protective effect on BC risk (inverse variance-weighted odds ratio [OR] = 0.974 per 1% increase in ancestry proportion, 95% confidence interval [CI] 0.970-0.978, p = 3.1 × 10-40). The corresponding OR for Mexican Native American ancestry was 0.988 (95% CI 0.987-0.990, p = 1.4 × 10-44). Stratified analyses revealed a stronger association between Native American ancestry and familial BC (Colombian women: OR = 0.958, 95% CI 0.952-0.964; Mexican women: OR = 0.973, 95% CI 0.969-0.978), and stronger protective effects on oestrogen receptor (ER)-positive BC than on ER-negative and triple-negative BC. CONCLUSIONS The present results point to an unconfounded protective effect of Native American ancestry on BC risk in both Colombian and Mexican women which appears to be stronger for familial and ER-positive BC. These findings provide a rationale for personalised prevention programmes that take genetic ancestry into account, as well as for future admixture mapping studies.
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Affiliation(s)
- Linda Zollner
- Statistical Genetics Research Group, Institute of Medical Biometry, Heidelberg University, Heidelberg, Germany
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Diana Torres
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
- Institute of Human Genetics, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Ignacio Briceno
- Instituto de Genética Humana, Universidad de la Sabana, Bogotá, Colombia
| | - Michael Gilbert
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Gabriela Torres-Mejía
- Center for Population Health Research, National Institute of Public Health, Cuernavaca, Morelos, Mexico
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany.
| | - Justo Lorenzo Bermejo
- Statistical Genetics Research Group, Institute of Medical Biometry, Heidelberg University, Heidelberg, Germany
- Department of Biostatistics for Precision Oncology, Institut de Cancérologie Strasbourg Europe, Strasbourg, France
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12
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Nava-Quiroz KJ, Rojas-Serrano J, Pérez-Rubio G, Buendia-Roldan I, Mejía M, Fernández-López JC, Rodríguez-Henríquez P, Ayala-Alcantar N, Ramos-Martínez E, López-Flores LA, Del Ángel-Pablo AD, Falfán-Valencia R. Molecular Factors in PAD2 ( PADI2) and PAD4 ( PADI4) Are Associated with Interstitial Lung Disease Susceptibility in Rheumatoid Arthritis Patients. Cells 2023; 12:2235. [PMID: 37759458 PMCID: PMC10527441 DOI: 10.3390/cells12182235] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 08/26/2023] [Accepted: 09/01/2023] [Indexed: 09/29/2023] Open
Abstract
Around 50% of rheumatoid arthritis (RA) patients show some extra-articular manifestation, with the lung a usually affected organ; in addition, the presence of anti-citrullinated protein antibodies (ACPA) is a common feature, which is caused by protein citrullination modifications, catalyzed by the peptidyl arginine deiminases (PAD) enzymes. We aimed to identify single nucleotide variants (SNV) in PADI2 and PADI4 genes (PAD2 and PAD4 proteins, respectively) associated with susceptibility to interstitial lung disease (ILD) in RA patients and the PAD2 and PAD4 levels. Material and methods: 867 subjects were included: 118 RA-ILD patients, 133 RA patients, and 616 clinically healthy subjects (CHS). Allelic discrimination was performed in eight SNVs using qPCR, four in PADI2 and four in PADI4. The ELISA technique determined PAD2 and PAD4 levels in serum and bronchoalveolar lavage (BAL) samples, and the population structure was evaluated using 14 informative ancestry markers. Results: The rs1005753-GG (OR = 4.9) in PADI2 and rs11203366-AA (OR = 3.08), rs11203367-GG (OR = 2.4) in PADI4 are associated with genetic susceptibility to RA-ILD as well as the ACTC haplotype (OR = 2.64). In addition, the PAD4 protein is increased in RA-ILD individuals harboring the minor allele homozygous genotype in PADI4 SNVs. Moreover, rs1748033 in PADI4, rs2057094, and rs2076615 in PADI2 are associated with RA susceptibility. In conclusion, in RA patients, single nucleotide variants in PADI4 and PADI2 are associated with ILD susceptibility. The rs1748033 in PADI4 and two different SNVs in PADI2 are associated with RA development but not ILD. PAD4 serum levels are increased in RA-ILD patients.
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Affiliation(s)
- Karol J. Nava-Quiroz
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Tlalpan, Mexico City 14080, Mexico; (K.J.N.-Q.); (G.P.-R.)
- Programa de Maestría y Doctorado en Ciencias Médicas Odontológicas y de la Salud, Universidad Nacional Autónoma de México (UNAM), Mexico City 04100, Mexico
| | - Jorge Rojas-Serrano
- Rheumatology Clinic, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Tlalpan, Mexico City 14080, Mexico
| | - Gloria Pérez-Rubio
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Tlalpan, Mexico City 14080, Mexico; (K.J.N.-Q.); (G.P.-R.)
| | - Ivette Buendia-Roldan
- Translational Research Laboratory on Aging and Pulmonary Fibrosis, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Tlalpan, Mexico City 14080, Mexico
| | - Mayra Mejía
- Diffuse Interstitial Lung Disease Clinic, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Tlalpan, Mexico City 14080, Mexico
| | - Juan Carlos Fernández-López
- Consorcio de Genómica Computacional, Instituto Nacional de Medicina Genómica (INMEGEN), Tlalpan, Mexico City 14610, Mexico
| | - Pedro Rodríguez-Henríquez
- Department of Rheumatology, Hospital General Dr. Manuel Gea González, Tlalpan, Mexico City 14080, Mexico
| | - Noé Ayala-Alcantar
- Banco de Sangre, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Tlalpan, Mexico City 14080, Mexico
| | - Espiridión Ramos-Martínez
- Experimental Medicine Research Unit, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City 06720, Mexico
| | - Luis Alberto López-Flores
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Tlalpan, Mexico City 14080, Mexico; (K.J.N.-Q.); (G.P.-R.)
| | - Alma D. Del Ángel-Pablo
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Tlalpan, Mexico City 14080, Mexico; (K.J.N.-Q.); (G.P.-R.)
| | - Ramcés Falfán-Valencia
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Tlalpan, Mexico City 14080, Mexico; (K.J.N.-Q.); (G.P.-R.)
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13
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Vargas-Robles D, Romaguera J, Alvarado-Velez I, Tosado-Rodríguez E, Dominicci-Maura A, Sanchez M, Wiggin KJ, Martinez-Ferrer M, Gilbert JA, Forney LJ, Godoy-Vitorino F. The cervical microbiota of Hispanics living in Puerto Rico is nonoptimal regardless of HPV status. mSystems 2023; 8:e0035723. [PMID: 37534938 PMCID: PMC10469956 DOI: 10.1128/msystems.00357-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 06/26/2023] [Indexed: 08/04/2023] Open
Abstract
The cervicovaginal microbiota is influenced by host physiology, immunology, lifestyle, and ethnicity. We hypothesized that there would be differences in the cervicovaginal microbiota among pregnant, nonpregnant, and menopausal women living in Puerto Rico (PR) with and without human papillomavirus (HPV) infection and cervical cancer. We specifically wanted to determine if the microbiota is associated with variations in cervical cytology. A total of 294 women, including reproductive-age nonpregnant (N = 196), pregnant (N = 37), and menopausal (N = 61) women, were enrolled. The cervicovaginal bacteria were characterized by 16S rRNA amplicon sequencing, the HPV was genotyped with SPF10-LiPA, and cervical cytology was quantified. High-risk HPV (HR-HPV, 67.3%) was prevalent, including genotypes not covered by the 9vt HPV vaccine. Cervical lesions (34%) were also common. The cervical microbiota was dominated by Lactobacillus iners. Pregnant women in the second and third trimesters exhibited a decrease in diversity and abundance of microbes associated with bacterial vaginosis. Women in menopause had greater alpha diversity, a greater proportion of facultative and strictly anaerobic bacteria, and higher cervicovaginal pH than premenopausal women. Cervical lesions were associated with greater alpha diversity. However, no significant associations between the microbiota and HPV infection (HR or LR-HPV types) were found. The cervicovaginal microbiota of women living in Puerto Rican were either dominated by L. iners or diverse microbial communities regardless of a woman's physiological stage. We postulate that the microbiota and the high prevalence of HR-HPV increase the risk of cervical lesions among women living in PR. IMPORTANCE In the enclosed manuscript, we provide the first in-depth characterization of the cervicovaginal microbiota of Hispanic women living in Puerto Rico (PR), using a 16S rRNA approach, and include women of different physiological stages. Surprisingly we found that high-risk HPV was ubiquitous with a prevalence of 67.3%, including types not covered by the 9vt HPV vaccine. We also found highly diverse microbial communities across women groups-with a reduction in pregnant women, but dominated by nonoptimal Lactobacillus iners. Additionally, we found vaginosis-associated bacteria as Dialister spp., Gardnerella spp., Clostridium, or Prevotella among most women. We believe this is a relevant and timely article expanding knowledge on the cervicovaginal microbiome of PR women, where we postulate that these highly diverse communities are conducive to cervical disease.
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Affiliation(s)
- Daniela Vargas-Robles
- Department of Microbiology and Medical Zoology, University of Puerto Rico School of Medicine, Medical Sciences Campus, San Juan, Puerto Rico
| | - Josefina Romaguera
- Department of Obstetrics and Gynecology, University of Puerto Rico School of Medicine, Medical Sciences Campus, San Juan, Puerto Rico
| | - Ian Alvarado-Velez
- Department of Microbiology and Medical Zoology, University of Puerto Rico School of Medicine, Medical Sciences Campus, San Juan, Puerto Rico
| | - Eduardo Tosado-Rodríguez
- Department of Microbiology and Medical Zoology, University of Puerto Rico School of Medicine, Medical Sciences Campus, San Juan, Puerto Rico
| | - Anelisse Dominicci-Maura
- Department of Microbiology and Medical Zoology, University of Puerto Rico School of Medicine, Medical Sciences Campus, San Juan, Puerto Rico
| | - Maria Sanchez
- University of Puerto Rico Comprehensive Cancer Center, San Juan, Puerto Rico
| | - Kara J. Wiggin
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | | | - Jack A. Gilbert
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Larry J. Forney
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA
| | - Filipa Godoy-Vitorino
- Department of Microbiology and Medical Zoology, University of Puerto Rico School of Medicine, Medical Sciences Campus, San Juan, Puerto Rico
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14
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Schmulson MJ, Puentes-Leal GA, Bustos-Fernández L, Francisconi C, Hani A, López-Colombo A, Palsson OS, Bangdiwala SI, Sperber AD. Comparison of the epidemiology of disorders of gut-brain interaction in four Latin American countries: Results of The Rome Foundation Global Epidemiology Study. Neurogastroenterol Motil 2023; 35:e14569. [PMID: 36989176 DOI: 10.1111/nmo.14569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/01/2023] [Accepted: 03/12/2023] [Indexed: 03/30/2023]
Abstract
BACKGROUND In Latin America, there are scarce data on the epidemiology of DGBI. The Rome Foundation Global Epidemiology Study (RFGES) Internet survey included 26 countries, four from Latin America: Argentina, Brazil, Colombia, and Mexico, with a 40.3% prevalence of Rome IV DGBI. We aimed at comparing the prevalence of DGBI and associated factors among these countries. METHODS The frequency of DGBI by anatomical region, specific diagnoses, sex, age, diet, healthcare access, anxiety, depression, and HRQOL, were analyzed and compared. RESULTS Subjects included Argentina n = 2057, Brazil = 2004, Colombia = 2007, and Mexico = 2001. The most common DGBI were bowel (35.5%), gastroduodenal (11.9%), and anorectal (10.0%). Argentina had the highest prevalence of functional diarrhea (p = 0.006) and IBS-D; Brazil, esophageal, gastroduodenal disorders, and functional dyspepsia; Mexico functional heartburn (all <0.001). Overall, DGBI were more common in women vs. men and decreased with age. Bowel disorders were more common in the 18-39 (46%) vs. 40-64-year (39%) groups. Diet was also different between those with DGBI vs. those without with subtle differences between countries. Subjects endorsing criteria for esophageal, gastroduodenal, and anorectal disorders from Mexico, more commonly consulted physicians for bowel symptoms vs. those from Argentina, Brazil, and Colombia. General practitioners were the most frequently consulted, by Mexicans (50.42%) and Colombians (40.80%), followed by gastroenterologists. Anxiety and depression were more common in DGBI individuals in Argentina and Brazil vs. Mexico and Colombia, and they had lower HRQOL. CONCLUSIONS The prevalence of upper and lower DGBI, as well as the burden of illness, psychological impact and HRQOL, differ between these Latin American countries.
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Affiliation(s)
- Max J Schmulson
- Laboratory of Liver, Pancreas and Motility (HIPAM)-Unit of Research in Experimental Medicine, Faculty of Medicine, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Gerardo A Puentes-Leal
- Unit of Gastroenterology, Centro Hospitalario Serena del Mar, Cartagena de Indias, Colombia
| | | | - Carlos Francisconi
- Gastroenterology Division, Hospital de Clínicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Albis Hani
- Gastroenterology Unit, Hospital Universitario San Ignacio, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Aurelio López-Colombo
- UMAE Hospital de Especialidades Centro Médico Nacional Manuel Avila Camacho, Puebla, Mexico
| | - Olafur S Palsson
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - Ami D Sperber
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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15
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Zhou Y, Nevosadová L, Eliasson E, Lauschke VM. Global distribution of functionally important CYP2C9 alleles and their inferred metabolic consequences. Hum Genomics 2023; 17:15. [PMID: 36855170 PMCID: PMC9976394 DOI: 10.1186/s40246-023-00461-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/16/2023] [Indexed: 03/02/2023] Open
Abstract
BACKGROUND Genetic variability in the cytochrome P450 CYP2C9 constitutes an important predictor for efficacy and safety of various commonly prescribed drugs, including coumarin anticoagulants, phenytoin and multiple non-steroidal anti-inflammatory drugs (NSAIDs). A global map of CYP2C9 variability and its inferred functional consequences has been lacking. RESULTS Frequencies of eight functionally relevant CYP2C9 alleles (*2, *3, *5, *6, *8, *11, *13 and *14) were analyzed. In total, 108 original articles were identified that included genotype data from a total of 81,662 unrelated individuals across 70 countries and 40 unique ethnic groups. The results revealed that CYP2C9*2 was most abundant in Europe and the Middle East, whereas CYP2C9*3 was the main reason for reduced CYP2C9 activity across South Asia. Our data show extensive variation within superpopulations with up to tenfold differences between geographically adjacent populations in Malaysia, Thailand and Vietnam. Translation of genetic CYP2C9 variability into functional consequences indicates that up to 40% of patients in Southern Europe and the Middle East might benefit from warfarin and phenytoin dose reductions, while 3% of patients in Southern Europe and Israel are recommended to reduce starting doses of NSAIDs. CONCLUSIONS This study provides a comprehensive map of the genetic and functional variability of CYP2C9 with high ethnogeographic resolution. The presented data can serve as a useful resource for CYP2C9 allele and phenotype frequencies and might guide the optimization of genotyping strategies, particularly for indigenous and founder populations with distinct genetic profiles.
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Affiliation(s)
- Yitian Zhou
- Division of Clinical Pharmacology, Department of Laboratory Medicine, Karolinska Institutet, 141 52, Huddinge, Sweden.
| | - Lenka Nevosadová
- grid.4714.60000 0004 1937 0626Department of Physiology and Pharmacology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Erik Eliasson
- grid.4714.60000 0004 1937 0626Division of Clinical Pharmacology, Department of Laboratory Medicine, Karolinska Institutet, 141 52 Huddinge, Sweden ,grid.24381.3c0000 0000 9241 5705Medical Diagnostics, Clinical Pharmacology, Karolinska University Hospital, 141 86 Stockholm, Sweden
| | - Volker M. Lauschke
- grid.4714.60000 0004 1937 0626Department of Physiology and Pharmacology, Karolinska Institutet, 171 77 Stockholm, Sweden ,grid.502798.10000 0004 0561 903XDr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany ,grid.10392.390000 0001 2190 1447University of Tübingen, Tübingen, Germany
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16
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Aguilar-Troncoso J, Díaz-Zavala RG, Antúnez-Román LE, Robles-Sardín AE, Valencia ME. Body Composition in Youths Aged 10‒17 Years by Deuterium Oxide Dilution, Air Displacement Plethysmography, and DXA: Validation of the Medical Body Composition Analyzer Bioimpedance Device by a 4-Compartment Model. J Nutr 2023; 153:443-450. [PMID: 36894237 DOI: 10.1016/j.tjnut.2022.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/12/2022] [Accepted: 12/21/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The medical body composition analyzer (mBCA) incorporates advances in multifrequency technology and has been validated using a 4-compartment (4C) model in adults but not in youths aged <18 y. OBJECTIVES This study aimed to formulate a 4C model based on 3 reference methods and develop and validate a body composition prediction equation for the mBCA in youths aged 10‒17 y. METHODS The body density of 60 female and male youths was measured by air displacement plethysmography, total body water by deuterium oxide dilution, and BMC by DXA. Data from the equation group (n = 30) were used to formulate a 4C model. The all-possible-regressions method was used to select variables. The model was validated in a second cohort (n = 30) in a random split design. The accuracy, precision, and potential bias were evaluated by the Bland and Altman procedure. RESULTS Mean age, weight (W), height (H), waist circumference, and z-score of BMI were 13.6 ± 2.3 y, 54.5 ± 15.5 kg, 156 ± 11.9 cm, 75.5 ± 10.9 cm, and 0.70 ± 1.32 z, respectively. The prediction equation was as follows: FFM in kg (FFMkg) = ([0.2081] ∗ [W] + [0.8814] ∗ [H2cm/RΩ] + [0.2055 ∗ XcΩ])-15.343; R2 = 0.96; standardized root-mean-square error (SRMSE) = 2.18 kg. FFM did not differ between the 4C method (38.9 ± 12.0 kg) and the mBCA (38.4 ± 11.4 kg) (P > 0.05). The relationship between these 2 variables did not deviate from the identity line, was not significantly different from 0, and the slope was not significantly different from 1.0. In the precision prediction model of mBCA, the R2 value was 0.98 and SRMSE was 2.1. No significant bias was found when regressing differences between methods and their means (P = 0.08). CONCLUSIONS The equation for the mBCA was accurate, precise, had no significant bias, had substantial strength of agreement and could be used in this age group when subjects were preferentially within the constraints of a specified body size.
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Affiliation(s)
| | - Rolando G Díaz-Zavala
- Department of Chemical and Biological Sciences, University of Sonora, Hermosillo, Sonora, Mexico
| | - Lesley E Antúnez-Román
- Department of Chemical and Biological Sciences, University of Sonora, Hermosillo, Sonora, Mexico
| | - Alma E Robles-Sardín
- Coordinación de Nutrición, Centro de Investigación en Alimentación y Desarrollo, A.C. Hermosillo, Sonora, Mexico
| | - Mauro E Valencia
- Department of Chemical and Biological Sciences, University of Sonora, Hermosillo, Sonora, Mexico.
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López-Villanueva RF, Valencia-Pacheco G, Zapata-Vázquez R, López-Suárez R, Castro-Sansores C. Follow-up of clinical activity and accumulated organic damage in a cohort of patients with systemic lupus erythematosus from the Yucatán Peninsula, Mexico (1995-2016). REUMATOLOGIA CLINICA 2023; 19:106-113. [PMID: 35753952 DOI: 10.1016/j.reumae.2021.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 12/16/2021] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Systemic lupus erythematosus (SLE) is an autoimmune with variable severity, common in Hispanic and African-American individuals. OBJECTIVE To know the clinical activity and the accumulated damage, as well as the prevalence and incidence, in a dynamic cohort of patients with SLE from the Yucatan Peninsula (1995-2016). PATIENTS AND METHODS A cohort of 200 patients with SLE, medical service beneficiaries of the ISSSTE Regional Hospital of Mérida, Yucatán, was analysed for 22 years. Disease activity and accumulated damage were evaluated using the MEX-SLEDAI scale and the SLICC-ACR-DI, respectively, and its correlation with clinical and demographic variables. RESULTS 185 female and 15 male patients were analysed. Average accumulated damage and activity indices during follow-up were 4.63 and 1.10, respectively. The activity index was significantly lower in females compared to males (4.36 vs 7.43), and the accumulated damage did not present a difference by sex. The manifestations associated with greater activity were the mucocutaneous and articular ones, and the organs with the greatest accumulated damage were the musculoskeletal, neurological and gonadal. A relationship between the indices was found with the evolution time, remissions/reactivations, and persistent activity. Mortality was related to persistent activity due to systemic vascular complications and kidney and liver failure. The annual incidence and prevalence of SLE calculated was 2.86% and 48.43% in Yucatán Peninsula. CONCLUSIONS The patients presented persistent activity, with mild to moderate reactivations, and accumulated damage more aggressive in men. The clinical activity decreases and increases the accumulated damage at a longer evolution time, with less kidney disease and greater survival, which suggests a more benign course in the population of the Yucatan Peninsula.
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Affiliation(s)
| | - Guillermo Valencia-Pacheco
- Laboratorio de Hematología, Centro de Investigaciones Regionales Dr. Hideyo Noguchi, Universidad Autónoma de Yucatán, Unidad de Ciencias Biomédicas Inalámbrica, Campus de Ciencias de la Salud, Mérida, Yucatán, Mexico
| | - Rita Zapata-Vázquez
- Facultad de Medicina, Universidad Autónoma de Yucatán, Mérida, Yucatán, Mexico
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18
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De Oliveira TC, Secolin R, Lopes-Cendes I. A review of ancestrality and admixture in Latin America and the caribbean focusing on native American and African descendant populations. Front Genet 2023; 14:1091269. [PMID: 36741309 PMCID: PMC9893294 DOI: 10.3389/fgene.2023.1091269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 01/09/2023] [Indexed: 01/21/2023] Open
Abstract
Genomics can reveal essential features about the demographic evolution of a population that may not be apparent from historical elements. In recent years, there has been a significant increase in the number of studies applying genomic epidemiological approaches to understand the genetic structure and diversity of human populations in the context of demographic history and for implementing precision medicine. These efforts have traditionally been applied predominantly to populations of European origin. More recently, initiatives in the United States and Africa are including more diverse populations, establishing new horizons for research in human populations with African and/or Native ancestries. Still, even in the most recent projects, the under-representation of genomic data from Latin America and the Caribbean (LAC) is remarkable. In addition, because the region presents the most recent global miscegenation, genomics data from LAC may add relevant information to understand population admixture better. Admixture in LAC started during the colonial period, in the 15th century, with intense miscegenation between European settlers, mainly from Portugal and Spain, with local indigenous and sub-Saharan Africans brought through the slave trade. Since, there are descendants of formerly enslaved and Native American populations in the LAC territory; they are considered vulnerable populations because of their history and current living conditions. In this context, studying LAC Native American and African descendant populations is important for several reasons. First, studying human populations from different origins makes it possible to understand the diversity of the human genome better. Second, it also has an immediate application to these populations, such as empowering communities with the knowledge of their ancestral origins. Furthermore, because knowledge of the population genomic structure is an essential requirement for implementing genomic medicine and precision health practices, population genomics studies may ensure that these communities have access to genomic information for risk assessment, prevention, and the delivery of optimized treatment; thus, helping to reduce inequalities in the Western Hemisphere. Hoping to set the stage for future studies, we review different aspects related to genetic and genomic research in vulnerable populations from LAC countries.
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Affiliation(s)
- Thais C. De Oliveira
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil,The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil
| | - Rodrigo Secolin
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil,The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil
| | - Iscia Lopes-Cendes
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil,The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil,*Correspondence: Iscia Lopes-Cendes,
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19
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López-Armas GDC, Ramos-Márquez ME, Navarro-Meza M, Macías-Islas MÁ, Saldaña-Cruz AM, Zepeda-Moreno A, Siller-López F, Cruz-Ramos JA. Leukocyte Telomere Length Predicts Severe Disability in Relapsing-Remitting Multiple Sclerosis and Correlates with Mitochondrial DNA Copy Number. Int J Mol Sci 2023; 24:ijms24020916. [PMID: 36674427 PMCID: PMC9862686 DOI: 10.3390/ijms24020916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/12/2022] [Accepted: 12/21/2022] [Indexed: 01/06/2023] Open
Abstract
Multiple sclerosis (MS) is a chronic autoimmune inflammatory disease that affects the nervous system. Peripheral blood leukocyte telomere length (LTL) and mitochondrial DNA copy number (mtDNA-CN) are potential biomarkers of neurological disability and neural damage. Our objective was to assess the LTL and mtDNA-CN in relapsing-remitting MS (RRMS). We included 10 healthy controls, 75 patients with RRMS, 50 of whom had an Expanded Disability Status Scale (EDSS) from 0 to 3 (mild to moderate disability), and 25 had an EDSS of 3.5 to 7 (severe disability). We use the Real-Time Polymerase Chain Reaction (qPCR) technique to quantify absolute LTL and absolute mtDNA-CN. ANOVA test show differences between healthy control vs. severe disability RRMS and mild-moderate RRMS vs. severe disability RRMS (p = 0.0130). LTL and mtDNA-CN showed a linear correlation in mild-moderate disability RRMS (r = 0.378, p = 0.007). Furthermore, we analyzed LTL between RRMS groups with a ROC curve, and LTL can predict severe disability (AUC = 0.702, p = 0.0018, cut-off < 3.0875 Kb, sensitivity = 75%, specificity = 62%), whereas the prediction is improved with a logistic regression model including LTL plus age (AUC = 0.762, p = 0.0001, sensitivity = 79.17%, specificity = 80%). These results show that LTL is a biomarker of disability in RRMS and is correlated with mtDNA-CN in mild-moderate RRMS patients.
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Affiliation(s)
- Gabriela del Carmen López-Armas
- Laboratorio de Biomédica-Mecatrónica, Subdirección de Investigación y Extensión, Centro de Enseñanza Técnica Industrial Plantel Colomos, Guadalajara 44638, Mexico
| | - Martha Eloisa Ramos-Márquez
- Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico
| | - Mónica Navarro-Meza
- Laboratorio C. de Neuronutrición y Memoria, Departamento de Promoción, Preservación y Desarrollo de la Salud, Centro Universitario del Sur, Universidad de Guadalajara, Ciudad Guzmán 49000, Mexico
| | - Miguel Ángel Macías-Islas
- Departamento de Neurociencias, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico
| | - Ana Miriam Saldaña-Cruz
- Departamento de Fisiología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico
| | - Abraham Zepeda-Moreno
- Departamento de Clínicas de la Reproducción Humana, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico
| | - Fernando Siller-López
- Programa de Bacteriología, Facultad de Ciencias de la Salud, Universidad Católica de Manizales, Manizales 170002, Colombia
| | - José Alfonso Cruz-Ramos
- Departamento de Clínicas Médicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico
- Coordinación de Investigación, Instituto Jalisciense de Cancerología, Guadalajara 44280, Mexico
- Correspondence:
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20
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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] [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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21
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Ilori T, Watanabe A, Ng KH, Solarin A, Sinha A, Gbadegesin R. Genetics of Chronic Kidney Disease in Low-Resource Settings. Semin Nephrol 2022; 42:151314. [PMID: 36801667 PMCID: PMC10272019 DOI: 10.1016/j.semnephrol.2023.151314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
Advances in kidney genomics in the past 20 years has opened the door for more precise diagnosis of kidney disease and identification of new and specific therapeutic agents. Despite these advances, an imbalance exists between low-resource and affluent regions of the world. Individuals of European ancestry from the United States, United Kingdom, and Iceland account for 16% of the world's population, but represent more than 80% of all genome-wide association studies. South Asia, Southeast Asia, Latin America, and Africa together account for 57% of the world population but less than 5% of genome-wide association studies. Implications of this difference include limitations in new variant discovery, inaccurate interpretation of the effect of genetic variants in non-European populations, and unequal access to genomic testing and novel therapies in resource-poor regions. It also further introduces ethical, legal, and social pitfalls, and ultimately may propagate global health inequities. Ongoing efforts to reduce the imbalance in low-resource regions include funding and capacity building, population-based genome sequencing, population-based genome registries, and genetic research networks. More funding, training, and capacity building for infrastructure and expertise is needed in resource-poor regions. Focusing on this will ensure multiple-fold returns on investments in genomic research and technology.
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Affiliation(s)
- Titilayo Ilori
- Division of Nephrology, Boston University School of Medicine, Boston, MA
| | - Andreia Watanabe
- Division of Molecular Medicine, Department of Pediatrics, University of São Paulo School of Medicine, São Paulo, Brazil
| | - Kar-Hui Ng
- Department of Pediatrics, Yong Loo Lin School of Medicine, Singapore
| | - Adaobi Solarin
- Department of Pediatrics and Child Health, Lagos State University College of Medicine, Ikeja, Lagos, Nigeria
| | - Aditi Sinha
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Rasheed Gbadegesin
- Division of Nephrology, Department of Pediatrics, Duke University School of Medicine, Durham, NC.
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22
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Elhaik E. Principal Component Analyses (PCA)-based findings in population genetic studies are highly biased and must be reevaluated. Sci Rep 2022; 12:14683. [PMID: 36038559 PMCID: PMC9424212 DOI: 10.1038/s41598-022-14395-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 06/06/2022] [Indexed: 12/29/2022] Open
Abstract
Principal Component Analysis (PCA) is a multivariate analysis that reduces the complexity of datasets while preserving data covariance. The outcome can be visualized on colorful scatterplots, ideally with only a minimal loss of information. PCA applications, implemented in well-cited packages like EIGENSOFT and PLINK, are extensively used as the foremost analyses in population genetics and related fields (e.g., animal and plant or medical genetics). PCA outcomes are used to shape study design, identify, and characterize individuals and populations, and draw historical and ethnobiological conclusions on origins, evolution, dispersion, and relatedness. The replicability crisis in science has prompted us to evaluate whether PCA results are reliable, robust, and replicable. We analyzed twelve common test cases using an intuitive color-based model alongside human population data. We demonstrate that PCA results can be artifacts of the data and can be easily manipulated to generate desired outcomes. PCA adjustment also yielded unfavorable outcomes in association studies. PCA results may not be reliable, robust, or replicable as the field assumes. Our findings raise concerns about the validity of results reported in the population genetics literature and related fields that place a disproportionate reliance upon PCA outcomes and the insights derived from them. We conclude that PCA may have a biasing role in genetic investigations and that 32,000-216,000 genetic studies should be reevaluated. An alternative mixed-admixture population genetic model is discussed.
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Affiliation(s)
- Eran Elhaik
- Department of Biology, Lund University, 22362, Lund, Sweden.
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23
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Torres-Machorro A, Lerma C, Lozano-Corona R, Grimaldo-Gómez FA. Acute Venous Disease Anomalies in Critically Ill COVID-19 Patients. Cureus 2022; 14:e27067. [PMID: 35936165 PMCID: PMC9348511 DOI: 10.7759/cureus.27067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/19/2022] [Indexed: 11/26/2022] Open
Abstract
Introduction: Other entities besides deep vein thrombosis (DVT) affecting the venous system, such as superficial vein phlebitis (SVP) and superficial vein thrombophlebitis (SVT), receive poor attention in the literature. However, both entities may propagate proximally into the deep venous system and progress to a DVT. To our knowledge, the relevance of other venous findings such as SVP or SVT in coronavirus disease 2019 (COVID-19) patients has not been evaluated. This work aimed to assess the clinical, biochemical, and hematological variables associated with the incidence of acute venous diseases, such as DVT, SVP, and SVT, in a cohort of 74 critically ill COVID-19 patients and their association with mortality. Methods: Given the high thrombotic risk, all patients underwent venous imaging with bedside ultrasound. Clinical variables were obtained from medical records. Comparisons were made by the chi-square test or Fisher’s exact test. We constructed Kaplan-Meier curves and used Cox proportional hazard models to calculate hazard ratios for dichotomized risk factors to identify predictors of mortality. SPSS version 21.0 (IBM Corp., Armonk, NY) was used for statistical analysis. Results: SVP occurred in 28 patients (37.8%), DVT in 22 patients (29.7%), and 28 patients died (37.8%). Elevated D-dimer was associated with DVT but not with SVP. Neither SVP nor DVT was associated with mortality. After adjusting for age, elevated troponins (OR: 2.4, 95% CI: 1.1-5.4), platelets < 244 cell/mm3 (2.4, 1.1-5.6), and IMPROVE (International Medical Prevention Registry on Venous Thromboembolism) bleeding score > 7 (2.8, 1.3-6.3) were predictors of mortality. Conclusions: Acute venous findings such as SVP and DVT are highly prevalent and independent of mortality in critically ill COVID-19 patients. These entities are not related, although they may occur synchronically. DVT is frequently presented as an asymptomatic distal bilateral finding associated with elevated D-dimer, decreased ferritin, and higher vasoactive drug use but independent from chronic venous disease. Interestingly, elevated troponins, decreased platelets, and a prognostic value > 7 of the IMPROVE bleeding score were predictors of mortality in this group of critically ill COVID-19 patients.
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Minutti-Zanella C, Villarreal-Martínez L, Ruiz-Argüelles GJ. Primary Thrombophilia XVII: A Narrative Review of Sticky Platelet Syndrome in México. J Clin Med 2022; 11:jcm11144100. [PMID: 35887863 PMCID: PMC9315593 DOI: 10.3390/jcm11144100] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 07/12/2022] [Accepted: 07/14/2022] [Indexed: 02/01/2023] Open
Abstract
Sticky Platelet Syndrome (SPS) is a disorder characterized by platelet hyperaggregability, diagnosed by studying in vitro platelet aggregation with ADP and epinephrine. It is the second most common cause of thrombophilia in Mexican Mestizos and manifests as an autosomal dominant trait which, combined with other coagulopathies, contributes significantly to the morbidity and mortality of patients with primary thrombophilia. It is easily treatable with antiplatelet drugs; however, the methods for diagnosis are not readily available in all clinical laboratories and the disorder is often overlooked by most clinicians. Herein, we present the results of more than 20 years of Mexican experience with the study of SPS in a Mestizo population.
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Affiliation(s)
- Claudia Minutti-Zanella
- Laboratorios RUIZ-Escuela de Ciencias Médicas, Universidad Popular Autónoma del Estado de Puebla (UPAEP), Puebla 72530, Mexico;
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Ponce-Gallegos MA, Partida-Zavala N, Castro-Castaneda CR, Navarro-Arregui D, Garcia-Hernandez DA, García-Loza BA, Alvarado-Castillo B, Navarro-Partida J. The rs1800795 single nucleotide polymorphism in the IL6 gene is not associated with primary open angle glaucoma in Mexican population. ARCHIVOS DE LA SOCIEDAD ESPANOLA DE OFTALMOLOGIA 2022; 97:363-369. [PMID: 35577741 DOI: 10.1016/j.oftale.2022.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 11/10/2021] [Indexed: 06/15/2023]
Abstract
PURPOSE Interleukin-6 (IL-6) is a proinflammatory cytokine with pleiotropic effects which has been related to primary open angle glaucoma (POAG) due to its particular effect of protecting the retinal ganglion cells (RGc) from the apoptosis. Different single nucleotide polymorphisms (SNP) have been associated with POAG. The aim of this study was to determine whether an association between IL-6 rs1800795 (-174 G>C) SNP and a higher risk for POAG is present in western Mexican population. METHODS One hundred and sixty-five unrelated Mexican mestizo patients with POAG and 108 control subjects were included. Genomic DNA was extracted from leukocytes and purified, followed by genotyping and amplification by polymerase chain reaction (PCR) with Taqman Biosystem probes. Allelic and genotypic diversity was evaluated between cases and control subjects. RESULTS There was no statistically significant association between allele and genotype frequencies, neither with dominant nor recessive genetic association models (p > 0.05). CONCLUSION Even though there is a role of IL6 in the pathophysiology of POAG, our results ruled out the association between IL-6 and the rs1800795 SNP showing not to be an index of higher risk for POAG in Mexican population.
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Affiliation(s)
- M A Ponce-Gallegos
- Unidad Académica de Medicina, Universidad Autónoma de Nayarit, Tepic, Nayarit, Mexico
| | - N Partida-Zavala
- Unidad Académica de Medicina, Universidad Autónoma de Nayarit, Tepic, Nayarit, Mexico
| | - C R Castro-Castaneda
- Tecnológico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Campus Guadalajara, Zapopan, Jalisco, Mexico
| | - D Navarro-Arregui
- Tecnológico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Campus Guadalajara, Zapopan, Jalisco, Mexico
| | - D A Garcia-Hernandez
- Unidad Académica de Medicina, Universidad Autónoma de Nayarit, Tepic, Nayarit, Mexico
| | - B A García-Loza
- Tecnológico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Campus Guadalajara, Zapopan, Jalisco, Mexico
| | - B Alvarado-Castillo
- Instituto Oftalmológico Guillermo Avalos Urzua, Guadalajara, Jalisco, Mexico; Instituto Mexicano del Seguro Social, Centro Médico Nacional de Occidente, Jalisco, Mexico
| | - J Navarro-Partida
- Tecnológico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Campus Guadalajara, Zapopan, Jalisco, Mexico.
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Melo G, Uscanga K, Mauro LA, David AV, Pablo HR, Héctor RV, Aquino P, Meza, Jiménez C, Denis P, Nayali LB. Use of Investigator 24plex GO! to analyse allele frequencies of 21 autosomal STRs in the population of Veracruz state, Mexico. Ann Hum Biol 2022; 49:164-169. [PMID: 35380906 DOI: 10.1080/03014460.2022.2062050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
BackgroundMexican population databases for autosomal STRs are scarce, and no previous studies have been performed with the Qiagen Investigator 24plex GO! Aim: To analyse the frequency of 21 autosomal short tandem repeat (STR) loci and forensic parameters in individuals from Veracruz state, Mexico. Subjects and methods: A total of 234 unrelated individuals were analysed with the Investigator 24plex GO! Kit, which includes the following autosomal STRs: TH01, D3S1358, vWA, D21S11, TPOX, D1S1656, D12S391, SE33, D10S1248, D22S1045, D19S433, D8S133879, D2S1338, D2S441, D18S51, FGA, D16S539, CSF1PO, D13S317, D5S818, and D7S820. Allele frequencies, forensic parameters, and relationships with neighbouring Mexican populations were estimated. Results: The STRs analysed were in Hardy-Weinberg Equilibrium (HWE). The combined matching probability and combined PE were 1.5266 E-24 and 0.999999988711, respectively. The D18S51 and SE33 loci presented the highest Ho (0.8974 and 0.8932) and PE (0.7902 and 0.7815), respectively. The highest PIC (0.9337) and PD (0.9894) values corresponded to SE33. Conversely, D22S1045 had the lowest PIC and PE (0.5533 y 0.3546, respectively). A population cluster among southern Mexican populations, which included non-differentiation between Guerrero and Veracruz states was detected. Conclusion: The forensic efficacy of the 21 STRs analysed by the Investigator 24plex GO! Kit was evaluated in the Veracruz state. Moreover, new population clusters that have not been yet been described and are related to geographic regions were identified, and these are in agreement with previously reported ancestral differences.
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Affiliation(s)
- Guadalupe Melo
- UV-GC-212 "Ciencias Forenses" Instituto de Medicina Forense, Universidad Veracruzana, Boca del Río, México
| | - Keren Uscanga
- Maestría en Medicina Forense, Instituto de Medicina Forense, Universidad Veracruzana, Boca del Río, México
| | - López-Armenta Mauro
- Laboratorio de Genética, Instituto de Servicios Periciales y Ciencias Forenses del Poder Judicial de la CDMX, Ciudad de México, Mexico
| | - Avilés-Villada David
- Posgrado en Ciencias Biológicas. Universidad Nacional Autónoma de México. Ciudad de México, Mexico
| | - Hernández-Romano Pablo
- Centro Estatal de la Transfusión Sanguínea del Estado de Veracruz, Veracruz, México.,Laboratorio de Genética, Hospital de Alta Especialidad de Veracruz, Veracruz, México
| | - Rangel-Villalobos Héctor
- Instituto de Investigación en Genética Molecular, Centro Universitario de la Ciénega, Universidad de Guadalajara (CUCiénega-UdeG), Ocotlán, Jalisco, México
| | - P Aquino
- Facultad de Medicina, Universidad Veracruzana, Veracruz, México
| | - Meza
- Facultad de Medicina, Universidad Veracruzana, Veracruz, México
| | - Carlos Jiménez
- UV-GC-212 "Ciencias Forenses" Instituto de Medicina Forense, Universidad Veracruzana, Boca del Río, México
| | - Patricia Denis
- UV-GC-212 "Ciencias Forenses" Instituto de Medicina Forense, Universidad Veracruzana, Boca del Río, México
| | - López-Balderas Nayali
- UV-GC-212 "Ciencias Forenses" Instituto de Medicina Forense, Universidad Veracruzana, Boca del Río, México
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Fanconi Anemia Patients from an Indigenous Community in Mexico Carry a New Founder Pathogenic Variant in FANCG. Int J Mol Sci 2022; 23:ijms23042334. [PMID: 35216452 PMCID: PMC8877758 DOI: 10.3390/ijms23042334] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/06/2022] [Accepted: 01/08/2022] [Indexed: 12/15/2022] Open
Abstract
Fanconi anemia (FA) is a rare genetic disorder caused by pathogenic variants (PV) in at least 22 genes, which cooperate in the Fanconi anemia/Breast Cancer (FA/BRCA) pathway to maintain genome stability. PV in FANCA, FANCC, and FANCG account for most cases (~90%). This study evaluated the chromosomal, molecular, and physical phenotypic findings of a novel founder FANCG PV, identified in three patients with FA from the Mixe community of Oaxaca, Mexico. All patients presented chromosomal instability and a homozygous PV, FANCG: c.511-3_511-2delCA, identified by next-generation sequencing analysis. Bioinformatic predictions suggest that this deletion disrupts a splice acceptor site promoting the exon 5 skipping. Analysis of Cytoscan 750 K arrays for haplotyping and global ancestry supported the Mexican origin and founder effect of the variant, reaffirming the high frequency of founder PV in FANCG. The degree of bone marrow failure and physical findings (described through the acronyms VACTERL-H and PHENOS) were used to depict the phenotype of the patients. Despite having a similar frequency of chromosomal aberrations and genetic constitution, the phenotype showed a wide spectrum of severity. The identification of a founder PV could help for a systematic and accurate genetic screening of patients with FA suspicion in this population.
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Copy Number Variation and Frequency of rs179008 in TLR7 Gene Associated with Systemic Lupus Erythematosus in Two Mexican Populations. J Immunol Res 2022; 2022:2553901. [PMID: 35083340 PMCID: PMC8786460 DOI: 10.1155/2022/2553901] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 11/23/2021] [Accepted: 12/09/2021] [Indexed: 11/17/2022] Open
Abstract
Systemic Lupus Erythematosus (SLE) is an autoimmune disease in which genetic factors play a role in the susceptibility to develop it. Genes related to the synthesis of interferons such as TLR7 and genetics factors such as single nucleotide polymorphisms (SNPs) or copies number variation (CNV) in the gene have been involved with the development of the disease. The genetic differences between the populations contribute to the complexity of LES. Mexico has a mestizo population with a genetic load of at least three origins: Amerindian, Caucasian, and African. The mestizo of Yucatán is the only group whose contribution Amerindian is mainly Mayan, geographically distant from other Mexican Amerindians. We analyzed the CNV and the frequency of SNP rs179008 of the TLR7 as genetic risk factors in developing the disease in patients from Yucatán and Central Mexico. Results show that 14% of the cases of the Yucatecan population showed significantly >2 CNV and a higher risk of developing the disease (OR: 34.364), concerning 4% of those coming from Central Mexico (OR: 10.855). T allele and the A/T and T/T risk genotypes of rs179008 were more frequent in patients of Central Mexico than in those of Yucatán (50% vs. 30%, 93% vs. 30%, 4% vs. 1%), and association with susceptibility to develop SLE was observed (OR: 1.5 vs. 0.58, 9.54 vs. 0.66, 12 vs. 0.14). Data support the genetic differences between and within Mexican mestizo populations and the role of the TLR7 in the pathogenesis of SLE.
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Gómez R, Tapia-Guerrero YS, Cisneros B, Orozco L, Cerecedo-Zapata C, Mendoza-Caamal E, Leyva-Gómez G, Leyva-García N, Velázquez-Pérez L, Magaña JJ. Genetic Distribution of Five Spinocerebellar Ataxia Microsatellite Loci in Mexican Native American Populations and Its Impact on Contemporary Mestizo Populations. Genes (Basel) 2022; 13:genes13010157. [PMID: 35052497 PMCID: PMC8775409 DOI: 10.3390/genes13010157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/04/2022] [Accepted: 01/13/2022] [Indexed: 12/17/2022] Open
Abstract
Spinocerebellar ataxias (SCAs) conform a heterogeneous group of neurodegenerative disorders with autosomal dominant inheritance. Five of the most frequent SCAs are caused by a CAG repeat expansion in the exons of specific genes. The SCAs incidence and the distribution of polymorphic CAG alleles vary among populations and ethnicities. Thus, characterization of the genetic architecture of ethnically diverse populations, which have undergone recent admixture and demographic events, could facilitate the identification of genetic risk factors. Owing to the great ethnic diversity of the Mexican population, this study aimed to analyze the allele frequencies of five SCA microsatellite loci (SCA1, SCA2, SCA3, SCA6, and SCA7) in eleven Mexican Native American (MNA) populations. Data from the literature were used to compare the allelic distribution of SCA loci with worldwide populations. The SCA loci allelic frequencies evidenced a certain genetic homogeneity in the MNA populations, except for Mayans, who exhibited distinctive genetic profiles. Neither pathological nor large normal alleles were found in MNA populations, except for the SCA2 pre-mutated allele in the Zapotec population. Collectively, our findings demonstrated the contribution of the MNA ancestry in shaping the genetic structure of contemporary Mexican Mestizo populations. Our results also suggest that Native American ancestry has no impact on the origin of SCAs in the Mexican population. Instead, the acquisition of pathological SCA alleles could be associated with European migration.
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Affiliation(s)
- Rocío Gómez
- Department of Toxicology, CINVESTAV-IPN, Mexico City 07360, Mexico;
| | - Yessica S. Tapia-Guerrero
- Laboratory of Genomic Medicine, Department of Genetics, National Rehabilitation Institute-Luis Guillermo Ibarra Ibarra (INR-LGII), Mexico City 14389, Mexico; (Y.S.T.-G.); (C.C.-Z.); (N.L.-G.)
| | - Bulmaro Cisneros
- Department of Genetics and Molecular Biology, CINVESTAV-IPN, Mexico City 07360, Mexico;
| | - Lorena Orozco
- Laboratory of Immunogenomics and Metabolic Diseases, National Genomic Medicine Institute (INMEGEN), Mexico City 14610, Mexico; (L.O.); (E.M.-C.)
| | - César Cerecedo-Zapata
- Laboratory of Genomic Medicine, Department of Genetics, National Rehabilitation Institute-Luis Guillermo Ibarra Ibarra (INR-LGII), Mexico City 14389, Mexico; (Y.S.T.-G.); (C.C.-Z.); (N.L.-G.)
- Rehabilitation and Social Inclusion Center of Veracruz (CRIS-DIF), Xalapa, Veracruz 91097, Mexico
| | - Elvia Mendoza-Caamal
- Laboratory of Immunogenomics and Metabolic Diseases, National Genomic Medicine Institute (INMEGEN), Mexico City 14610, Mexico; (L.O.); (E.M.-C.)
| | - Gerardo Leyva-Gómez
- Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México (UNAM); Mexico City 04510, Mexico;
| | - Norberto Leyva-García
- Laboratory of Genomic Medicine, Department of Genetics, National Rehabilitation Institute-Luis Guillermo Ibarra Ibarra (INR-LGII), Mexico City 14389, Mexico; (Y.S.T.-G.); (C.C.-Z.); (N.L.-G.)
| | | | - Jonathan J. Magaña
- Laboratory of Genomic Medicine, Department of Genetics, National Rehabilitation Institute-Luis Guillermo Ibarra Ibarra (INR-LGII), Mexico City 14389, Mexico; (Y.S.T.-G.); (C.C.-Z.); (N.L.-G.)
- Department of Bioengineering, School of Engineering and Sciences, Tecnologico de Monterrey, Campus Ciudad de México (ITESM-CCM), Mexico City 14380, Mexico
- Correspondence: ; Tel.: +52-(55)-5999-1000 (ext. 14708)
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Quintas-Granados LI, Cortés H, Carmen MGD, Leyva-Gómez G, Bustamante-Montes LP, Rodríguez-Morales M, Villegas-Vazquez EY, López-Reyes I, Alcaraz-Estrada SL, Sandoval-Basilio J, Soto-Reyes E, Sharifi-Rad J, Figueroa-González G, Reyes-Hernández OD. The high methylation level of a novel 151-bp CpG island in the ESR1 gene promoter is associated with a poor breast cancer prognosis. Cancer Cell Int 2021; 21:649. [PMID: 34863151 PMCID: PMC8645138 DOI: 10.1186/s12935-021-02343-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 11/15/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The ESR1 gene suffers methylation changes in many types of cancers, including breast cancer (BC), the most frequently diagnosed cancer in women that is also present in men. Methylation at promoter A of ESR1 is the worse prognosis in terms of overall survival; thus, the early detection, prognostic, and prediction of therapy involve some methylation biomarkers. METHODS Therefore, our study aimed to examine the methylation levels at the ESR1 gene in samples from Mexican BC patients and its possible association with menopausal status. RESULTS We identified a novel 151-bp CpG island in the promoter A of the ESR1 gene. Interestingly, methylation levels at this CpG island in positive ERα tumors were approximately 50% less than negative ERα or control samples. Furthermore, methylation levels at ESR1 were associated with menopausal status. In postmenopausal patients, the methylation levels were 1.5-fold higher than in premenopausal patients. Finally, according to tumor malignancy, triple-negative cancer subtypes had higher ESR1 methylation levels than luminal/HER2+ or luminal A subtypes. CONCLUSIONS Our findings suggest that methylation at this novel CpG island might be a promising prognosis marker.
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Affiliation(s)
| | - Hernán Cortés
- Laboratorio de Medicina Genómica, Departamento de Genómica, Instituto Nacional de Rehabilitación Luis Guillermo Ibarra Ibarra, 14389, Mexico City, Mexico
| | | | - Gerardo Leyva-Gómez
- Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | | | | | - Edgar Yebran Villegas-Vazquez
- Departamento de Biotecnología y Bioingeniería del Centro de Investigación y de Estudios Avanzados del IPN, Mexico City, Mexico
| | - Israel López-Reyes
- Colegio de Ciencias y Humanidades, Plantel Cuautepec, Universidad Autónoma de la Ciudad de México, Mexico City, Mexico
| | - Sofía Lizeth Alcaraz-Estrada
- División de Medicina Genomica, Centro Médico Nacional "20 de Noviembre"-ISSSTE, Mexico, 03100, Mexico City, Mexico
| | - Jorge Sandoval-Basilio
- Laboratorio de Biología Molecular, Universidad Hipócrates, Acapulco, Gro., México
- Laboratorio de Investigación Clínica, Facultad de Medicina, Universidad Autónoma de Guerrero, Acapulco, Gro., México
| | - Ernesto Soto-Reyes
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana-Cuajimalpa (UAM-C), Mexico City, Mexico
| | | | - Gabriela Figueroa-González
- Laboratorio de Farmacogenética, UMIEZ, Facultad de Estudios Superiores Zaragoza, Universidad Nacional Autónoma de México, 09230, Mexico City, México.
| | - Octavio Daniel Reyes-Hernández
- Laboratorio de Biología Molecular del Cáncer, UMIEZ, Facultad de Estudios Superiores Zaragoza, Universidad Nacional Autónoma de México, 09230, Mexico City, México.
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Camarena B, Atkinson EG, Baker M, Becerra-Palars C, Chibnik LB, Escamilla-Orozco R, Jiménez-Pavón J, Koenig Z, Márquez-Luna C, Martin AR, Morales-Cedillo IP, Olivares AM, Ortega-Ortiz H, Rodriguez-Ramírez AM, Saracco-Alvarez R, Basaldua RE, Sena BF, Koenen KC. Neuropsychiatric Genetics of Psychosis in the Mexican Population: A Genome-Wide Association Study Protocol for Schizophrenia, Schizoaffective, and Bipolar Disorder Patients and Controls. Complex Psychiatry 2021; 7:60-70. [PMID: 36017067 PMCID: PMC8740081 DOI: 10.1159/000518926] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 08/03/2021] [Indexed: 11/12/2023] Open
Abstract
No large-scale genome-wide association studies (GWASs) of psychosis have been conducted in Mexico or Latin America to date. Schizophrenia and bipolar disorder in particular have been found to be highly heritable and genetically influenced. However, understanding of the biological basis of psychosis in Latin American populations is limited as previous genomic studies have almost exclusively relied on participants of Northern European ancestry. With the goal of expanding knowledge on the genomic basis of psychotic disorders within the Mexican population, the National Institute of Psychiatry Ramón de la Fuente Muñiz (INPRFM), the Harvard T.H. Chan School of Public Health, and the Broad Institute's Stanley Center for Psychiatric Research launched the Neuropsychiatric Genetics Research of Psychosis in Mexican Populations (NeuroMex) project to collect and analyze case-control psychosis samples from 5 states across Mexico. This article describes the planned sample collection and GWAS protocol for the NeuroMex study. The 4-year study will span from April 2018 to 2022 and aims to recruit 9,208 participants: 4,604 cases and 4,604 controls. Study sites across Mexico were selected to ensure collected samples capture the genomic diversity within the Mexican population. Blood samples and phenotypic data will be collected during the participant interview process and will contribute to the development of a local biobank in Mexico. DNA extraction will be done locally and genetic analysis will take place at the Broad Institute in Cambridge, MA. We will collect extensive phenotypic information using several clinical scales. All study materials including phenotypic instruments utilized are openly available in Spanish and English. The described study represents a long-term collaboration of a number of institutions from across Mexico and the Boston area, including clinical psychiatrists, clinical researchers, computational biologists, and managers at the 3 collaborating institutions. The development of relevant data management, quality assurance, and analysis plans are the primary considerations in this protocol article. Extensive management and analysis processes were developed for both the phenotypic and genetic data collected. Capacity building, partnerships, and training between and among the collaborating institutions are intrinsic components to this study and its long-term success.
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Affiliation(s)
- Beatriz Camarena
- Pharmacogenetics Department, National Institute of Psychiatry Ramón de la Fuente Muñiz, Mexico City, Mexico
| | - Elizabeth G. Atkinson
- Broad Institute of MIT and Harvard, Stanley Center for Psychiatric Research, Cambridge, Massachusetts, USA
- Analytical and Translational Genetics Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Mark Baker
- Broad Institute of MIT and Harvard, Stanley Center for Psychiatric Research, Cambridge, Massachusetts, USA
| | - Claudia Becerra-Palars
- National Institute of Psychiatry Ramón de la Fuente Muñiz, Clinical Services Direction, Mexico City, Mexico
| | - Lori B. Chibnik
- Broad Institute of MIT and Harvard, Stanley Center for Psychiatric Research, Cambridge, Massachusetts, USA
- Analytical and Translational Genetics Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Raúl Escamilla-Orozco
- National Institute of Psychiatry Ramón de la Fuente Muñiz, Clinical Services Direction, Mexico City, Mexico
| | - Joanna Jiménez-Pavón
- National Institute of Psychiatry Ramón de la Fuente Muñiz, Clinical Services Direction, Mexico City, Mexico
| | - Zan Koenig
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Carla Márquez-Luna
- Charles R. Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Alicia R. Martin
- Broad Institute of MIT and Harvard, Stanley Center for Psychiatric Research, Cambridge, Massachusetts, USA
- Analytical and Translational Genetics Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | | | - Ana Maria Olivares
- Broad Institute of MIT and Harvard, Stanley Center for Psychiatric Research, Cambridge, Massachusetts, USA
| | - Hiram Ortega-Ortiz
- National Institute of Psychiatry Ramón de la Fuente Muñiz, Clinical Services Direction, Mexico City, Mexico
| | | | - Ricardo Saracco-Alvarez
- National Institute of Psychiatry Ramon de la Fuente Muñiz, Clinical Research Sub-direction, Mexico City, Mexico
| | - Rebecca E. Basaldua
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Brena F. Sena
- Broad Institute of MIT and Harvard, Stanley Center for Psychiatric Research, Cambridge, Massachusetts, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Karestan C. Koenen
- Broad Institute of MIT and Harvard, Stanley Center for Psychiatric Research, Cambridge, Massachusetts, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
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Osteopontin Gene Polymorphisms Are Associated with Cardiovascular Risk Factors in Patients with Premature Coronary Artery Disease. Biomedicines 2021; 9:biomedicines9111600. [PMID: 34829826 PMCID: PMC8615378 DOI: 10.3390/biomedicines9111600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/30/2021] [Accepted: 10/31/2021] [Indexed: 11/20/2022] Open
Abstract
Osteopontin (OPN) is considered a clinical predictor of cardiovascular disease. We aimed to evaluate the association of the OPN gene polymorphisms rs2728127 and rs11730582 with the development of premature coronary artery disease (pCAD), cardiovascular risk factors, and cardiometabolic parameters. We evaluated 1142 patients with pCAD and 1073 controls. Both polymorphisms were determined by Taqman assays. Similar allele and genotype frequencies were observed in both groups; additionally, an association of these polymorphisms with CAD and cardiometabolic parameters was observed in both groups. In patients with pCAD, the rs11730582 was associated with a high risk of hypoadiponectinemia (OR = 1.300, P additive = 0.003), low risk of hypertension (OR = 0.709, P codominant 1 = 0.030), and low risk of having high non-HDL cholesterol (OR = 0.637, P additive = 0.038). In the control group, the rs2728127 was associated with a low risk of fatty liver (OR = 0.766, P additive = 0.038); while the rs11730582 was associated with a low risk of hypoadiponectinemia (OR = 0.728, P dominant = 0.022), and risk of having elevated apolipoprotein B (OR = 1.400, P dominant = 0.031). Our results suggest that in Mexican individuals, the rs11730582 and rs2728127 OPN gene polymorphisms are associated with some abnormal metabolic variables in patients with pCAD and controls.
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The genomic landscape of Mexican Indigenous populations brings insights into the peopling of the Americas. Nat Commun 2021; 12:5942. [PMID: 34642312 PMCID: PMC8511047 DOI: 10.1038/s41467-021-26188-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 09/22/2021] [Indexed: 12/30/2022] Open
Abstract
The genetic makeup of Indigenous populations inhabiting Mexico has been strongly influenced by geography and demographic history. Here, we perform a genome-wide analysis of 716 newly genotyped individuals from 60 of the 68 recognized ethnic groups in Mexico. We show that the genetic structure of these populations is strongly influenced by geography, and our demographic reconstructions suggest a decline in the population size of all tested populations in the last 15-30 generations. We find evidence that Aridoamerican and Mesoamerican populations diverged roughly 4-9.9 ka, around the time when sedentary farming started in Mesoamerica. Comparisons with ancient genomes indicate that the Upward Sun River 1 (USR1) individual is an outgroup to Mexican/South American Indigenous populations, whereas Anzick-1 was more closely related to Mesoamerican/South American populations than to those from Aridoamerica, showing an even more complex history of divergence than recognized so far.
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Bodner M, Perego UA, Gomez JE, Cerda-Flores RM, Rambaldi Migliore N, Woodward SR, Parson W, Achilli A. The Mitochondrial DNA Landscape of Modern Mexico. Genes (Basel) 2021; 12:genes12091453. [PMID: 34573435 PMCID: PMC8467843 DOI: 10.3390/genes12091453] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/15/2021] [Accepted: 09/16/2021] [Indexed: 12/16/2022] Open
Abstract
Mexico is a rich source for anthropological and population genetic studies with high diversity in ethnic and linguistic groups. The country witnessed the rise and fall of major civilizations, including the Maya and Aztec, but resulting from European colonization, the population landscape has dramatically changed. Today, the majority of Mexicans do not identify themselves as Indigenous but as admixed, and appear to have very little in common with their pre-Columbian predecessors. However, when the maternally inherited mitochondrial (mt)DNA is investigated in the modern Mexican population, this is not the case. Control region sequences of 2021 samples deriving from all over the country revealed an overwhelming Indigenous American legacy, with almost 90% of mtDNAs belonging to the four major pan-American haplogroups A2, B2, C1, and D1. This finding supports a very low European contribution to the Mexican gene pool by female colonizers and confirms the effectiveness of employing uniparental markers as a tool to reconstruct a country’s history. In addition, the distinct frequency and dispersal patterns of Indigenous American and West Eurasian clades highlight the benefit such large and country-wide databases provide for studying the impact of colonialism from a female perspective and population stratification. The importance of geographical database subsets not only for forensic application is clearly demonstrated.
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Affiliation(s)
- Martin Bodner
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria;
| | - Ugo A. Perego
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (U.A.P.); (N.R.M.)
- Sorenson Molecular Genealogy Foundation, Salt Lake City, UT 84115, USA; (J.E.G.); (S.R.W.)
- Department of Math and Science, Southeastern Community College, Burlington, IA 52655, USA
| | - J. Edgar Gomez
- Sorenson Molecular Genealogy Foundation, Salt Lake City, UT 84115, USA; (J.E.G.); (S.R.W.)
- FamilySearch Int., Salt Lake City, UT 84150, USA
| | | | - Nicola Rambaldi Migliore
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (U.A.P.); (N.R.M.)
| | - Scott R. Woodward
- Sorenson Molecular Genealogy Foundation, Salt Lake City, UT 84115, USA; (J.E.G.); (S.R.W.)
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria;
- Forensic Science Program, Penn State University, University Park, State College, PA 16802, USA
- Correspondence: (W.P.); (A.A.)
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (U.A.P.); (N.R.M.)
- Correspondence: (W.P.); (A.A.)
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Suárez D, Cruz R, Torres M, Mogollón F, Moncada J, Carracedo A, Usaquén W. Ancestry analysis using autosomal SNPs in northern South America, reveals interpretation differences between an AIM panel and an identification panel. Forensic Sci Int 2021; 326:110934. [PMID: 34404021 DOI: 10.1016/j.forsciint.2021.110934] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/14/2021] [Accepted: 07/23/2021] [Indexed: 12/20/2022]
Abstract
Current human populations are studied to elucidate their ancestry composition and to obtain reference values for an array of genetic markers for forensic practice. This study compared the 79 ancestry informative markers (AIMs) panel with the SNPforID 52plex set used in forensic identification, using samples belonging to Continental Caribbean populations from Colombia with a high percentage of locals self-determined as Native American descendants. The results show a bias in the individual estimation made with the identification markers, which disregards the Native American ancestry component and overestimates the African ancestry component. Also, the analysis made with the Bayesian Classification Algorithm shows better likelihoods for individual assignment with AIMs than with SNPforID 52plex.
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Affiliation(s)
- Dayana Suárez
- Populations Genetics and Identification Group, Institute of Genetics, National University of Colombia, Bogotá, Colombia.
| | - Raquel Cruz
- CIBERER, Genomic Medicine Group, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - María Torres
- Galician Public Foundation of Genomic Medicine (SERGAS)-CIBERER, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Fernanda Mogollón
- Populations Genetics and Identification Group, Institute of Genetics, National University of Colombia, Bogotá, Colombia
| | - Julie Moncada
- Populations Genetics and Identification Group, Institute of Genetics, National University of Colombia, Bogotá, Colombia
| | - Angel Carracedo
- CIBERER, Genomic Medicine Group, University of Santiago de Compostela, Santiago de Compostela, Spain; Galician Public Foundation of Genomic Medicine (SERGAS)-CIBERER, University of Santiago de Compostela, Santiago de Compostela, Spain; Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - William Usaquén
- Populations Genetics and Identification Group, Institute of Genetics, National University of Colombia, Bogotá, Colombia.
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Exchanging fluids The sociocultural implications of microbial, cultural, and ethnic admixture in Latin America. Politics Life Sci 2021; 39:56-86. [PMID: 32697057 DOI: 10.1017/pls.2020.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Knowledge of evolutionary influences on patterns of human mating, social interactions, and differential health is increasing, yet these insights have rarely been applied to historical analyses of human population dynamics. The genetic and evolutionary forces behind biases in interethnic mating and in the health of individuals of different ethnic groups in Latin America and the Caribbean since the European colonization of America are still largely ignored. We discuss how historical and contemporary sociocultural interactions and practices are strongly influenced by population-level evolutionary forces. Specifically, we discuss the historical implications of functional (de facto) polygyny, sex-biased admixture, and assortative mating in Latin America. We propose that these three evolutionary mechanisms influenced mating patterns, shaping the genetic and cultural landscape across Latin America and the Caribbean. Further, we discuss how genetic differences between the original populations that migrated at different times into Latin America contributed to their accommodation to and survival in the different local ecologies and interethnic interactions. Relevant medical and social implications follow from the genetic and cultural changes reviewed.
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Ortega-Mora EI, Caballero-Sánchez U, Román-López TV, Rosas-Escobar CB, González-Barrios JA, Romero-Hidalgo S, Méndez-Díaz M, Prospéro-García OE, Ruiz-Contreras AE. Allele-dosage genetic polymorphisms of cannabinoid receptor 1 predict attention, but not working memory performance in humans. Acta Psychol (Amst) 2021; 216:103299. [PMID: 33799104 DOI: 10.1016/j.actpsy.2021.103299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 03/05/2021] [Accepted: 03/17/2021] [Indexed: 11/29/2022] Open
Abstract
Attention and working memory (WM) are under high genetic regulation. Single nucleotide polymorphisms (SNPs) of the CNR1 gene, that encode for CB1R, have previously been shown to be related with individual differences in attentional control and WM. However, it remains unclear whether there is an allele-dosage or a dominant contribution of polymorphisms of CNR1 affecting attention and WM performance. This study evaluated the associations between attention and WM performance and three SNPs of CNR1: rs1406977, rs2180619, and rs1049353, previously associated with both processes. Healthy volunteers (n = 127) were asked to perform the Attention Network Task (ANT) to evaluate their overall attention and alerting, orienting, and executive systems, and the n-back task for evaluating their WM. All subjects were genotyped using qPCR with TaqMan assays; and dominant and additive models were assessed using the risk alleles of each SNP as the predictor variable. Results showed an individual association of the three SNPs with attention performance, but the composite genotype by the three alleles had the greatest contribution. Moreover, the additive-dosage model showed that for each G-allele added to the genotypic configuration, there was an increase in the percentage of correct responses respect to carriers who have no risk alleles in their genotypic configuration. The number of risk alleles in the genotypic configurations did not predict efficiency in any of the attention systems, nor in WM performance. Our model showed a contribution of three single nucleotide polymorphisms of the CNR1 gene to explain 9% of the variance of attention in an additive manner.
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Affiliation(s)
- Elsa Ivett Ortega-Mora
- Lab. Neurogenómica Cognitiva, Coord. Psicobiología y Neurociencias, Fac. Psicología, Universidad Nacional Autónoma de México (UNAM), Mexico
| | - Ulises Caballero-Sánchez
- Lab. Neurogenómica Cognitiva, Coord. Psicobiología y Neurociencias, Fac. Psicología, Universidad Nacional Autónoma de México (UNAM), Mexico
| | - Talía V Román-López
- Lab. Neurogenómica Cognitiva, Coord. Psicobiología y Neurociencias, Fac. Psicología, Universidad Nacional Autónoma de México (UNAM), Mexico
| | - Cintia B Rosas-Escobar
- Lab. Neurogenómica Cognitiva, Coord. Psicobiología y Neurociencias, Fac. Psicología, Universidad Nacional Autónoma de México (UNAM), Mexico
| | - Juan Antonio González-Barrios
- Lab. Medicina Genómica, Hospital Regional 1o de Octubre, Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado (ISSSTE), Mexico
| | - Sandra Romero-Hidalgo
- Departamento de Genómica Computacional, Instituto Nacional de Medicina Genómica, Mexico
| | | | | | - Alejandra E Ruiz-Contreras
- Lab. Neurogenómica Cognitiva, Coord. Psicobiología y Neurociencias, Fac. Psicología, Universidad Nacional Autónoma de México (UNAM), Mexico.
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Comprehensive omic characterization of breast cancer in Mexican-Hispanic women. Nat Commun 2021; 12:2245. [PMID: 33854067 PMCID: PMC8046804 DOI: 10.1038/s41467-021-22478-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 03/16/2021] [Indexed: 12/26/2022] Open
Abstract
Breast cancer is a heterogeneous pathology, but the genomic basis of its variability remains poorly understood in populations other than Caucasians. Here, through DNA and RNA portraits we explored the molecular features of breast cancers in a set of Hispanic-Mexican (HM) women and compared them to public multi-ancestry datasets. HM patients present an earlier onset of the disease, particularly in aggressive clinical subtypes, compared to non-Hispanic women. The age-related COSMIC signature 1 was more frequent in HM women than in those from other ancestries. We found the AKT1E17K hotspot mutation in 8% of the HM women and identify the AKT1/PIK3CA axis as a potentially druggable target. Also, HM luminal breast tumors present an enhanced immunogenic phenotype compared to Asiatic and Caucasian tumors. This study is an initial effort to include patients from Hispanic populations in the research of breast cancer etiology and biology to further understand breast cancer disparities. Cancers in different populations have been shown to be genetically distinct. Here, the authors sequence breast cancers from Mexican-Hispanic patients and find that these patients have a higher percentage of Akt1 mutations compared to Caucasian and Asian populations, suggesting these are clinically actionable.
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Does FMI Correlate Better than BMI with the Occurrence of Metabolic Changes in Obese Patients? Study Based on 2007 Consecutive Mexican Patients. Obes Surg 2021; 30:1324-1331. [PMID: 31820402 DOI: 10.1007/s11695-019-04289-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
BACKGROUND The body mass index (BMI) is the most commonly used anthropometric indicator. However, it does not discern among the different body components. The body fat content, expressed as fat mass index (FMI), is an accurate way to estimate adiposity. Since most metabolic diseases are associated with excess fat tissue, our aims were to comparatively analyze the frequency of associated metabolic abnormalities in patients with different obesity degrees based on BMI and FMI and to determine the best cut-off value of both indicators to predict metabolic abnormalities. METHODS From a cohort of 2007 patients, BMI and FMI were calculated using DXA. Individuals were classified into the different obesity degrees according to the reference ranges from the World Health Organization (WHO) and the National Health and Nutrition Examination Survey (NHANES). A comparative analysis between BMI, FMI, and their correlation to the presence of metabolic alterations was performed. RESULTS BMI underestimated the degree of obesity when compared with FMI. Spearman's rank-order correlation for both indexes resulted in very high coefficients (rho Spearman's = 0.857; p = 0.0001). The prevalence of metabolic alterations increased as BMI and FMI also increased. Despite the high positive statistical correlation between BMI and FMI, it was seen that some comorbidities were more specifically related to one particular index. CONCLUSIONS There were no significant differences between the BMI and the FMI for predicting the degree of obesity. Likewise, there were no significant differences between them for the prediction of metabolic alterations.
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Aguilar-Ordoñez I, Pérez-Villatoro F, García-Ortiz H, Barajas-Olmos F, Ballesteros-Villascán J, González-Buenfil R, Fresno C, Garcíarrubio A, Fernández-López JC, Tovar H, Hernández-Lemus E, Orozco L, Soberón X, Morett E. Whole genome variation in 27 Mexican indigenous populations, demographic and biomedical insights. PLoS One 2021; 16:e0249773. [PMID: 33831079 PMCID: PMC8031408 DOI: 10.1371/journal.pone.0249773] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 03/24/2021] [Indexed: 12/12/2022] Open
Abstract
There has been limited study of Native American whole genome diversity to date, which impairs effective implementation of personalized medicine and a detailed description of its demographic history. Here we report high coverage whole genome sequencing of 76 unrelated individuals, from 27 indigenous groups across Mexico, with more than 97% average Native American ancestry. On average, each individual has 3.26 million Single Nucleotide Variants and short indels, that together comprise a catalog of 9,737,152 variants, 44,118 of which are novel. We report 497 common Single Nucleotide Variants (with allele frequency > 5%) mapped to drug responses and 316,577 in enhancer or promoter elements; interestingly we found some of these enhancer variants in PPARG, a nuclear receptor involved in highly prevalent health problems in Mexican population, such as obesity, diabetes, and insulin resistance. By detecting signals of positive selection we report 24 enriched key pathways under selection, most of them related to immune mechanisms. No missense variants in ACE2, the receptor responsible for the entry of the SARS CoV-2 virus, were found in any individual. Population genomics and phylogenetic analyses demonstrated stratification in a Northern-Central-Southern axis, with major substructure in the Central region. The Seri, a northern group with the most genetic divergence in our study, showed a distinctive genomic context with the most novel variants, and the most population specific genotypes. Genome-wide analysis showed that the average haplotype blocks are longer in Native Mexicans than in other world populations. With this dataset we describe previously undetected population level variation in Native Mexicans, helping to reduce the gap in genomic data representation of such groups.
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Affiliation(s)
- Israel Aguilar-Ordoñez
- Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, México
- Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, México
| | - Fernando Pérez-Villatoro
- Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, México
- Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, México
- Winter Genomics, Mexico City, México
| | | | | | | | - Ram González-Buenfil
- Benemérita Universidad Autónoma de Puebla (BUAP), Puebla de Zaragoza, Puebla, México
| | - Cristobal Fresno
- Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, México
| | - Alejandro Garcíarrubio
- Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, México
| | | | - Hugo Tovar
- Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, México
| | | | - Lorena Orozco
- Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, México
| | - Xavier Soberón
- Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, México
- Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, México
| | - Enrique Morett
- Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, México
- * E-mail:
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Pérez-Rubio G, Falfán-Valencia R, Fernández-López JC, Ramírez-Venegas A, Hernández-Zenteno RDJ, Flores-Trujillo F, Silva-Zolezzi I. Genetic Factors Associated with COPD Depend on the Ancestral Caucasian/Amerindian Component in the Mexican Population. Diagnostics (Basel) 2021; 11:diagnostics11040599. [PMID: 33801584 PMCID: PMC8067148 DOI: 10.3390/diagnostics11040599] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/11/2021] [Accepted: 03/19/2021] [Indexed: 11/16/2022] Open
Abstract
Genetic variability influences the susceptibility to and severity of complex diseases; there is a lower risk of COPD in Hispanics than in non-Hispanic Caucasians. In this study, we included 830 Mexican-Mestizo subjects; 299 were patients with COPD secondary to tobacco smoking, and 531 were smokers without COPD. We employed a customized genotyping array of single nucleotide polymorphisms (SNPs). The population structure was evaluated by principal component analysis and allele association through a logistic regression model and haplotype identification. In this study, 118 individuals were identified with a high Caucasian component and 712 with a high Amerindian component. Independent of the ancestral contribution, two SNPs were associated with a reduced risk (p ≤ 0.01) of developing COPD in the CYP2A6 (rs4105144) and CYP2B6 (rs10426235) genes; however, a haplotype was associated with an increased risk of COPD (p = 0.007, OR = 2.47) in the CHRNA5-CHRNA3 loci among smokers with a high Caucasian component. In Mexican-Mestizo smokers, there are SNPs in genes that encode proteins responsible for the metabolism of nicotine associated with a lower risk of COPD; individuals with a high Caucasian component harboring a haplotype in the CHRNA5-CHRNA3 loci have a higher risk of suffering from COPD.
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Affiliation(s)
- Gloria Pérez-Rubio
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico;
- Correspondence: ; Tel.: +52-(55)-5487-1700 (ext. 5152)
| | - Ramcés Falfán-Valencia
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico;
| | | | - Alejandra Ramírez-Venegas
- Tobacco Smoking and COPD Research Department, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (A.R.-V.); (R.d.J.H.-Z.); (F.F.-T.)
| | - Rafael de Jesús Hernández-Zenteno
- Tobacco Smoking and COPD Research Department, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (A.R.-V.); (R.d.J.H.-Z.); (F.F.-T.)
| | - Fernando Flores-Trujillo
- Tobacco Smoking and COPD Research Department, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (A.R.-V.); (R.d.J.H.-Z.); (F.F.-T.)
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The genetics of recurrent hydatidiform moles in Mexico: further evidence of a strong founder effect for one mutation in NLRP7 and its widespread. J Assist Reprod Genet 2021; 38:1879-1886. [PMID: 33751332 DOI: 10.1007/s10815-021-02132-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 02/24/2021] [Indexed: 12/11/2022] Open
Abstract
PURPOSE To investigate the frequency of a founder mutation in NLRP7, L750V, in independent cohorts of Mexican patients with recurrent hydatidiform moles (RHMs). METHODS Mutation analysis was performed by Sanger sequencing on DNA from 44 unrelated Mexican patients with RHMs and seven molar tissues from seven additional unrelated patients. RESULTS L750V was present in homozygous or heterozygous state in 37 (86%) patients and was transmitted on the same haplotype to patients from different states of Mexico. We also identified a second founder mutation, c.2810+2T>G in eight (18.1%) patients, and a novel premature stop-codon mutation W653*. CONCLUSION Our data confirm the strong founder effect for L750V, which appears to be the most common mutation in NLRP7. We also report on six healthy live births to five patients with biallelic NLRP7 mutations, two from spontaneous conceptions and four from donated ovum and discuss our recommendations for DNA testing and genetic counseling.
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Ávila-Arcos MC, McManus KF, Sandoval K, Rodríguez-Rodríguez JE, Villa-Islas V, Martin AR, Luisi P, Peñaloza-Espinosa RI, Eng C, Huntsman S, Burchard EG, Gignoux CR, Bustamante CD, Moreno-Estrada A. Population History and Gene Divergence in Native Mexicans Inferred from 76 Human Exomes. Mol Biol Evol 2021; 37:994-1006. [PMID: 31848607 PMCID: PMC7086176 DOI: 10.1093/molbev/msz282] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Native American genetic variation remains underrepresented in most catalogs of human genome sequencing data. Previous genotyping efforts have revealed that Mexico’s Indigenous population is highly differentiated and substructured, thus potentially harboring higher proportions of private genetic variants of functional and biomedical relevance. Here we have targeted the coding fraction of the genome and characterized its full site frequency spectrum by sequencing 76 exomes from five Indigenous populations across Mexico. Using diffusion approximations, we modeled the demographic history of Indigenous populations from Mexico with northern and southern ethnic groups splitting 7.2 KYA and subsequently diverging locally 6.5 and 5.7 KYA, respectively. Selection scans for positive selection revealed BCL2L13 and KBTBD8 genes as potential candidates for adaptive evolution in Rarámuris and Triquis, respectively. BCL2L13 is highly expressed in skeletal muscle and could be related to physical endurance, a well-known phenotype of the northern Mexico Rarámuri. The KBTBD8 gene has been associated with idiopathic short stature and we found it to be highly differentiated in Triqui, a southern Indigenous group from Oaxaca whose height is extremely low compared to other Native populations.
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Affiliation(s)
- María C Ávila-Arcos
- International Laboratory for Human Genome Research (LIIGH), UNAM Juriquilla, Queretaro, Mexico.,Department of Genetics, Stanford University School of Medicine, Stanford, CA
| | - Kimberly F McManus
- Department of Biology, Stanford University, Stanford, CA.,Department of Biomedical Informatics, Stanford School of Medicine, Stanford, CA
| | - Karla Sandoval
- National Laboratory of Genomics for Biodiversity (LANGEBIO), UGA, CINVESTAV, Irapuato, Guanajuato 36821, Mexico
| | | | - Viridiana Villa-Islas
- International Laboratory for Human Genome Research (LIIGH), UNAM Juriquilla, Queretaro, Mexico
| | - Alicia R Martin
- Department of Genetics, Stanford University School of Medicine, Stanford, CA
| | - Pierre Luisi
- Centro de Investigación y Desarrollo en Inmunología y Enfermedades Infecciosas, Consejo Nacional de Investigaciones Científicas y Técnicas, Córdoba, Argentina.,Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Rosenda I Peñaloza-Espinosa
- Division of Biological and Health Sciences, Department of Biological Systems, Universidad Autónoma Metropolitana-Xochimilco, Mexico City, Mexico
| | - Celeste Eng
- Department Bioengineering & Therapeutic Sciences and Medicine, University of California San Francisco, San Francisco, CA
| | - Scott Huntsman
- Department Bioengineering & Therapeutic Sciences and Medicine, University of California San Francisco, San Francisco, CA
| | - Esteban G Burchard
- Department Bioengineering & Therapeutic Sciences and Medicine, University of California San Francisco, San Francisco, CA
| | - Christopher R Gignoux
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Denver, CO
| | - Carlos D Bustamante
- Department of Genetics, Stanford University School of Medicine, Stanford, CA
| | - Andrés Moreno-Estrada
- National Laboratory of Genomics for Biodiversity (LANGEBIO), UGA, CINVESTAV, Irapuato, Guanajuato 36821, Mexico
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Posadas-Sánchez R, Cardoso-Saldaña G, Fragoso JM, Vargas-Alarcón G. Interferon Regulatory Factor 5 ( IRF5) Gene Haplotypes Are Associated with Premature Coronary Artery Disease. Association of the IRF5 Polymorphisms with Cardiometabolic Parameters. The Genetics of Atherosclerotic Disease (GEA) Mexican Study. Biomolecules 2021; 11:biom11030443. [PMID: 33802675 PMCID: PMC8002496 DOI: 10.3390/biom11030443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/11/2021] [Accepted: 03/13/2021] [Indexed: 10/25/2022] Open
Abstract
Interferon regulatory factor 5 (IRF5) has an important role in the inflammatory process, a fundamental component of coronary artery disease (CAD). Thus, the objective of this study was to evaluate the association of IRF5 polymorphisms with the development of premature CAD (pCAD) and cardiometabolic parameters. IRF5 polymorphisms (rs1874330, rs3778754, rs3757386, rs3757385, rs3807134, rs3807135, and rs6968563) were determined in 1116 pCAD patients and 1003 controls. Polymorphism distribution was similar in patients and controls; however, the haplotype analysis showed five haplotypes with a different distribution. TGCGTCT (OR (odds ratio) = 1.248, p = 0005) and TCTGCCT (OR = 10.73, p < 0.0001) were associated with a high risk, whereas TCCGTCT (OR = 0.155, p < 0.0001), CGCTTTT (OR = 0.108, p < 0.0001), and TCCGCCT (OR = 0.014, p < 0.0001) were associated with a low risk of pCAD. Associations with aspartate aminotransferase, hypertriglyceridemia, magnesium deficiency, triglycerides/HDL-C index, LDL-C, and adiponectin levels were observed in pCAD patients. In controls, associations with hypoalphalipoproteinemia, non-HDL-C, apolipoprotein B, hyperuricemia, TNF-α, IL-6, IL-15, valvular calcification, and subclinical hypothyroidism were observed. In summary, five haplotypes were associated with pCAD, two with high risk and three with low risk. Some IRF5 polymorphisms were associated with cardiometabolic parameters in pCAD patients and control.
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Affiliation(s)
- Rosalinda Posadas-Sánchez
- Department of Endocrinology, Instituto Nacional de Cardiología Ignacio Chávez, 14080 Mexico City, Mexico; (R.P.-S.); (G.C.-S.)
| | - Guillermo Cardoso-Saldaña
- Department of Endocrinology, Instituto Nacional de Cardiología Ignacio Chávez, 14080 Mexico City, Mexico; (R.P.-S.); (G.C.-S.)
| | - José Manuel Fragoso
- Department of Molecular Biology, Instituto Nacional de Cardiología Ignacio Chávez, 14080 Mexico City, Mexico;
| | - Gilberto Vargas-Alarcón
- Department of Molecular Biology, Instituto Nacional de Cardiología Ignacio Chávez, 14080 Mexico City, Mexico;
- Correspondence: ; Tel.: +52-55-5573-2911 (ext. 20134)
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Differences in MTHFR and LRRK2 variant's association with sporadic Parkinson's disease in Mexican Mestizos correlated to Native American ancestry. NPJ Parkinsons Dis 2021; 7:13. [PMID: 33574311 PMCID: PMC7878860 DOI: 10.1038/s41531-021-00157-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 01/08/2021] [Indexed: 01/30/2023] Open
Abstract
Parkinson's disease (PD), a common neurodegenerative disorder, has a complex etiology where environmental and genetic factors intervene. While a number of genes and variants have been identified in recent decades as causative or protective agents of this condition, a limited number of studies have been conducted in mixed populations, such as Mexican Mestizos. The historical convergence of two founding groups and three ethnicities, and the increasing north-to-south gradient of Native American ancestry in Mexico resulted in a subpopulation structure with considerable genetic diversity. In this work, we investigate the influence of 21 known susceptibility variants for PD. Our case-control study, with a cohort of 311 Mexican Mestizo subjects, found a significant risk association for the variant rs1491942 in LRRK2. However, when stratification by ancestry was performed, a risk effect for MTHFR rs1801133 was observed only in the group with the highest percentage of European ancestry, and the PD risk effect for LRRK2 rs1491942 was significant in subjects with a higher ratio of Native American ancestry. Meta-analyses of these SNP revealed the effect of LRRK2 rs1491942 to be even more significant than previously described in populations of European descent. Although corroboration is necessary, our findings suggest that polymorphism rs1491942 may be useful as a risk marker of PD in Mexican Mestizos with greater Native American ancestry. The absence of associations with the remaining known risk factors is, in itself, a relevant finding and invites further research into the shared risk factors' role in the pathophysiological mechanisms of this neurodegenerative disorder.
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Ortiz-Cruz G, Aguayo-Gómez A, Luna-Muñoz L, Muñoz-Téllez LA, Mutchinick OM. Myelomeningocele genotype-phenotype correlation findings in cilia, HH, PCP, and WNT signaling pathways. Birth Defects Res 2021; 113:371-381. [PMID: 33470056 DOI: 10.1002/bdr2.1872] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/27/2020] [Accepted: 01/09/2021] [Indexed: 11/08/2022]
Abstract
BACKGROUND Myelomeningocele (MMC) is the most severe and frequent type of spina bifida. Its etiology remains poorly understood. The Hedgehog (Hh), Wnt, and planar cell polarity (PCP) signaling pathways are essential for normal tube closure, needing a structural-functional cilium for its adequate function. The present study aimed to investigate the impact of different gene variants (GV) from those pathways on MMC genotype-subphenotype correlations. METHODS The study comprised 500 MMC trios and 500 controls, from 16 Telethon centers of 16 Mexican states. Thirty-four GVs of 29 genes from cilia, Hh, PCP, and Wnt pathways, were analyzed, by an Illumina on design microarray. The total sample (T-MMC) was stratified in High-MMC (H-MMC) when thoracic and Low-MMC (L-MMC) when lumbar-sacral vertebrae affected. STATA/SE-12.1 and PLINK software were used for allelic association, TDT, and gene-gene interaction (GGI) analyses, considering p value <.01 as statistically significant differences (SSD). RESULTS Association analysis showed SSD for COBL-rs10230120, DVL2-rs2074216, PLCB4-rs6077510 GVs in T-MMC and L-MMC, and VANGL2-rs120886448 in T-MMC and H-MMC, and INVS-rs7024375 exclusively in L-MMC. TDT assay showed SSD preferential transmissions of C2CD3-rs826058 in H-MMC, and LRP5-rs3736228, and BBS2-rs1373 in L-MMC. Statistically significant GGI was observed in four in T-MMC, four completely different in L-MMC, and one in H-MMC. Interestingly, no one repeated in subphenotypes. CONCLUSIONS Our results support an association of GVs in Hh, Wnt, PCP, and cilia pathways, with MMC occurrence location, although further validation is needed. Furthermore, present results show a distinctive panel of gene-variants in H-MMC and LMMC subphenotypes, suggesting a feasible genotype-phenotype correlation.
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Affiliation(s)
- Gabriela Ortiz-Cruz
- Department of Genetics, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, México City, Mexico
| | - Adolfo Aguayo-Gómez
- Department of Genetics, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, México City, Mexico
| | - Leonora Luna-Muñoz
- Department of Genetics, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, México City, Mexico
| | - Luis A Muñoz-Téllez
- Department of Genetics, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, México City, Mexico
| | - Osvaldo M Mutchinick
- Department of Genetics, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, México City, Mexico
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Ponce-Gallegos MA, Ramos-Martínez E, García-Carmona A, Mejía M, Nava-Quiroz KJ, Pérez-Rubio G, Ambrocio-Ortiz E, González-Pérez MI, Buendía-Roldán I, Rojas-Serrano J, Falfán-Valencia R. Genetic Susceptibility to Antisynthetase Syndrome Associated With Single-Nucleotide Variants in the IL1B Gene That Lead Variation in IL-1β Serum Levels. Front Med (Lausanne) 2020; 7:547186. [PMID: 33330522 PMCID: PMC7732678 DOI: 10.3389/fmed.2020.547186] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 10/12/2020] [Indexed: 01/09/2023] Open
Abstract
The antisynthetase syndrome (ASSD) is an autoimmune disorder characterized by myositis, arthritis, mechanic's hands, fever, Raynaud phenomenon, and interstitial lung disease (ILD). We aimed to evaluate single-nucleotide polymorphisms in the interleukin 1B (IL1B) gene and their association between ILD with antisynthetase autoantibodies, as well as IL-1β serum levels. The most frequent antisynthetase autoantibody was anti-Jo1. The most frequent tomographic pattern was non-specific interstitial pneumonia, whereas in the anti-Jo1 subjects, it was organized pneumonia. Anti-Jo1 patients tend to have more significant arthritis, and Raynaud phenomenon have higher levels of creatinine phosphokinase. In the IL1B gene, the GG genotype and G allele of rs1143634 [odds ratio (OR) = 2.21 and OR = 2.60, respectively, p < 0.05] are associated with an increased risk, as well as with the dominant and recessive models (p < 0.05). This finding is maintained after logistic regression analysis adjusting for potential confounding variables (p < 0.05). Subjects with the rs16944/AG heterozygous genotype had higher serum levels of IL-1β compared to homozygous (p < 0.05). In conclusion, rs1143634 is associated with a higher risk of ASSD. Also, the GA genotype is associated with higher levels of IL-1β in ASSD patients.
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Affiliation(s)
| | - Espiridión Ramos-Martínez
- Unidad de Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Adriana García-Carmona
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas, Mexico City, Mexico
| | - Mayra Mejía
- Interstitial Lung Disease and Rheumatology Unit, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas, Mexico City, Mexico
| | - Karol J Nava-Quiroz
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas, Mexico City, Mexico
| | - Gloria Pérez-Rubio
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas, Mexico City, Mexico
| | - Enrique Ambrocio-Ortiz
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas, Mexico City, Mexico
| | - Montserrat I González-Pérez
- Interstitial Lung Disease and Rheumatology Unit, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas, Mexico City, Mexico
| | - Ivette Buendía-Roldán
- Translational Research Laboratory on Aging and Pulmonary Fibrosis, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas, Mexico City, Mexico
| | - Jorge Rojas-Serrano
- Interstitial Lung Disease and Rheumatology Unit, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas, Mexico City, Mexico
| | - Ramcés Falfán-Valencia
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas, Mexico City, Mexico
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Bioinformatics in Mexico: A diagnostic from the academic perspective and recommendations for a public policy. PLoS One 2020; 15:e0243531. [PMID: 33320879 PMCID: PMC7737905 DOI: 10.1371/journal.pone.0243531] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 11/24/2020] [Indexed: 11/19/2022] Open
Abstract
In this work, we present a diagnostic analysis of strengths, weaknesses, opportunities and threats (SWOT) of the current state of Bioinformatics in Mexico. We conducted semi-structured interviews among researchers and academics with key expertise in this field, identified by bibliometric analyses and qualitative sampling techniques. Additionally, an online survey was conducted reaching a higher number of respondents. Among the relevant findings of our study, the lack of specialized human resources and technological infrastructure stood out, along with deficiencies in the number and quality of academic programs, scarce public investment and a weak relationship between public and private institutions. However, there are great opportunities for developing a national Bioinformatics to support different economic sectors. In our opinion, this work could be useful to favor a comprehensive network among Mexican researchers, in order to lay the foundations of a national strategy towards a well designed public policy.
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Reynoso-Villalpando GL, Casillas-Muñoz FA, Padilla-Gutiérrez JR, Sevillano-Collantes C, Moreno-Ruiz I, Del Cañizo-Gómez FJ, Valdez-Haro A, Martínez-Fernández DE, Valle Y. The Genetic Variants -717T>C (rs2794521), 1444G>A (rs1130864), and 1846 C > T (rs1205) of CRP Gene, Their Haplotypes, and Their Association with Serum CRP Levels, Acute Coronary Syndrome, and Diabetes in Patients from Western Mexico. Metab Syndr Relat Disord 2020; 19:127-136. [PMID: 33296257 DOI: 10.1089/met.2020.0080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Background: C-reactive protein (CRP) is involved in inflammatory pathways that are associated with the onset and progression of type 2 diabetes mellitus (T2DM) as well as an increased risk of an acute coronary syndrome (ACS). This research aimed to evaluate the potential association of the genetic variants -717T>C, 1444G>A, and 1846 C > T of CRP gene on CRP levels, ACS, and T2DM in participants from Western Mexico. Methods: Six hundred three participants were studied: (1) control group (CG); (2) ACS participants classified as unstable angina (UA), myocardial infarction without ST-segment elevation (NSTEMI), and myocardial infarction with ST-segment elevation (STEMI); (3) T2DM Participants; and (4) ACS plus T2DM participants (ACS+T2DM). Genetic variants were genotyped using allelic discrimination with TaqMan® probes, and high-sensitivity CRP (hs-CRP) was measured by Turbidimetry. Results: TAC haplotype frequency was significantly higher in ACS+T2DM versus CG and versus ACS participants (odds ratio [OR] = 2.774, P = 0.017 and OR = 3.479, P = 0.020, respectively). hs-CRP levels were especially higher for ACS and for ACS+T2DM participants with respect to CG and T2DM (with P < 0.0001). We observed higher hs-CRP levels in NSTEMI and STEMI versus UA in ACS scenario (P = 0.001, P = 0.027, respectively) and for ACS+T2DM scenario (P = 0.0001, P = 0.002, respectively). Conclusion: hs-CRP level fluctuations are related to the presence of T2DM and the presence and severity of ACS. Very high levels (>10 mg/L) are a risk marker of cardiovascular complications. Our results demonstrate a possible relationship between TAC haplotype and an increased risk for T2DM and ACS.
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Affiliation(s)
- Gabriela Lizet Reynoso-Villalpando
- Departamento de Clínicas Médicas, Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud (CUCS), Universidad de Guadalajara (UdG), Colonia Independencia, Guadalajara, México.,Doctorado en Genética Humana, Centro Universitario de Ciencias de la Salud, Guadalajara, México
| | - Fidel Antonio Casillas-Muñoz
- Departamento de Clínicas Médicas, Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud (CUCS), Universidad de Guadalajara (UdG), Colonia Independencia, Guadalajara, México.,Doctorado en Genética Humana, Centro Universitario de Ciencias de la Salud, Guadalajara, México
| | - Jorge Ramón Padilla-Gutiérrez
- Departamento de Clínicas Médicas, Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud (CUCS), Universidad de Guadalajara (UdG), Colonia Independencia, Guadalajara, México
| | - Cristina Sevillano-Collantes
- Sección de Endocrinología y Nutrición, Hospital Universitario Infanta Leonor, Facultad de Medicina, Universidad Complutense, Madrid, España
| | - Inmaculada Moreno-Ruiz
- Sección de Endocrinología y Nutrición, Hospital Universitario Infanta Leonor, Facultad de Medicina, Universidad Complutense, Madrid, España
| | - Francisco Javier Del Cañizo-Gómez
- Sección de Endocrinología y Nutrición, Hospital Universitario Infanta Leonor, Facultad de Medicina, Universidad Complutense, Madrid, España
| | - Angélica Valdez-Haro
- Hospital Infantil del Estado de Sonora, Departamento de Enseñanza y Calidad, Hermosillo, Sonora, Mexico
| | | | - Yeminia Valle
- Departamento de Clínicas Médicas, Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud (CUCS), Universidad de Guadalajara (UdG), Colonia Independencia, Guadalajara, México
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