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Rodrigues LM, Maistro S, Katayama MLH, Rocha VM, Lopez RVM, Lopes EFDT, Gonçalves FT, Fridman C, Serio PADMP, Barros LRC, Leite LAS, Segatelli V, Estevez-Diz MDP, Guindalini RSC, Ribeiro Junior U, Folgueira MAAK. Prevalence of germline variants in Brazilian pancreatic carcinoma patients. Sci Rep 2024; 14:21083. [PMID: 39256447 PMCID: PMC11387492 DOI: 10.1038/s41598-024-71884-4] [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: 05/06/2024] [Accepted: 09/02/2024] [Indexed: 09/12/2024] Open
Abstract
We evaluated the prevalence of pathogenic/likely pathogenic germline variants (PGV) in Brazilian pancreatic adenocarcinoma (PC) patients, that represent a multiethnic population, in a cross-sectional study. We included 192 PC patients unselected for family history of cancer. We evaluated a panel of 113 cancer genes, through genomic DNA sequencing and 46 ancestry-informative markers, through multiplex PCR. The median age was 61 years; 63.5% of the patients presented disease clinical stages III or IV; 8.3% reported personal history of cancer; 4.7% and 16.1% reported first-degree relatives with PC or breast and/or prostate cancer, respectively. Although the main ancestry was European, there was considerable genetic composition admixture. Twelve patients (6.25%) were PGV carriers in PC predisposition genes (ATM, BRCA1, BRCA2, CDKN2A, MSH2, PALB2) and another 25 (13.0%) were PGV carriers in genes with a limited association or not previously associated with PC (ACD, BLM, BRIP1, CHEK2, ERCC4, FANCA, FANCE, FANCM, GALNT12, MITF, MRE11, MUTYH, POLE, RAD51B, RAD51C, RECQL4, SDHA, TERF2IP). The most frequently affected genes were CHEK2, ATM and FANC. In tumor samples from PGV carriers in ACD, BRIP1, MRE11, POLE, SDHA, TERF2IP, which were examined through exome sequencing, the main single base substitutions (SBS) mutational signature was SBS1+5+18, probably associated with age, tobacco smoking and reactive oxygen species. SBS3 associated with homologous repair deficiency was also represented, but on a lower scale. There was no difference in the frequency of PGV carriers between: (a) patients with or without first-degree relatives with cancer; and (b) patients with admixed ancestry versus those with predominantly European ancestry. Furthermore, there was no difference in overall survival between PGV carriers and non-carriers. Therefore, genetic testing should be offered to all Brazilian pancreatic cancer patients, regardless of their ancestry. Genes with limited or previously unrecognized associations with pancreatic cancer should be further investigated to clarify their role in cancer risk.
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Affiliation(s)
- Lívia Munhoz Rodrigues
- Departamento de Radiologia e Oncologia, Comprehensive Center for Precision Oncology - C2PO, Centro de Investigação Translacional em Oncologia (CTO), Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, FMUSP, Av. Dr. Arnaldo 251, 8º. Andar, sala 69, Sao Paulo, SP, 01246-000, Brazil
| | - Simone Maistro
- Departamento de Radiologia e Oncologia, Comprehensive Center for Precision Oncology - C2PO, Centro de Investigação Translacional em Oncologia (CTO), Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, FMUSP, Av. Dr. Arnaldo 251, 8º. Andar, sala 69, Sao Paulo, SP, 01246-000, Brazil
| | - Maria Lucia Hirata Katayama
- Departamento de Radiologia e Oncologia, Comprehensive Center for Precision Oncology - C2PO, Centro de Investigação Translacional em Oncologia (CTO), Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, FMUSP, Av. Dr. Arnaldo 251, 8º. Andar, sala 69, Sao Paulo, SP, 01246-000, Brazil
| | - Vinícius Marques Rocha
- Departamento de Radiologia e Oncologia, Comprehensive Center for Precision Oncology - C2PO, Centro de Investigação Translacional em Oncologia (CTO), Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, FMUSP, Av. Dr. Arnaldo 251, 8º. Andar, sala 69, Sao Paulo, SP, 01246-000, Brazil
| | - Rossana Veronica Mendoza Lopez
- Departamento de Radiologia e Oncologia, Comprehensive Center for Precision Oncology - C2PO, Centro de Investigação Translacional em Oncologia (CTO), Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, FMUSP, Av. Dr. Arnaldo 251, 8º. Andar, sala 69, Sao Paulo, SP, 01246-000, Brazil
| | - Edia Filomena di Tullio Lopes
- Registro Hospitalar de Cancer, Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, FMUSP, São Paulo, SP, Brazil
| | - Fernanda Toledo Gonçalves
- Departamento de Medicina Legal, Bioetica, Medicina do Trabalho e Medicina Física e Reabilitação, Faculdade de Medicina, Universidade de Sao Paulo, FMUSP, Sao Paulo, SP, Brazil
| | - Cintia Fridman
- Departamento de Medicina Legal, Bioetica, Medicina do Trabalho e Medicina Física e Reabilitação, Faculdade de Medicina, Universidade de Sao Paulo, FMUSP, Sao Paulo, SP, Brazil
| | | | - Luciana Rodrigues Carvalho Barros
- Departamento de Radiologia e Oncologia, Comprehensive Center for Precision Oncology - C2PO, Centro de Investigação Translacional em Oncologia (CTO), Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, FMUSP, Av. Dr. Arnaldo 251, 8º. Andar, sala 69, Sao Paulo, SP, 01246-000, Brazil
| | - Luiz Antonio Senna Leite
- Departamento de Radiologia e Oncologia, Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, FMUSP, Sao Paulo, SP, Brazil
| | - Vanderlei Segatelli
- Departamento de Patologia Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, FMUSP, Sao Paulo, SP, Brazil
| | - Maria Del Pilar Estevez-Diz
- Departamento de Radiologia e Oncologia, Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, FMUSP, Sao Paulo, SP, Brazil
| | | | - Ulysses Ribeiro Junior
- Division of Digestive Surgery, Department of Gastroenterology, Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo FMUSP, Sao Paulo, SP, Brazil
| | - Maria Aparecida Azevedo Koike Folgueira
- Departamento de Radiologia e Oncologia, Comprehensive Center for Precision Oncology - C2PO, Centro de Investigação Translacional em Oncologia (CTO), Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, FMUSP, Av. Dr. Arnaldo 251, 8º. Andar, sala 69, Sao Paulo, SP, 01246-000, Brazil.
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Boleti APDA, Jacobowski AC, Monteiro-Alfredo T, Pereira APR, Oliva MLV, Maria DA, Macedo MLR. Cutaneous Melanoma: An Overview of Physiological and Therapeutic Aspects and Biotechnological Use of Serine Protease Inhibitors. Molecules 2024; 29:3891. [PMID: 39202970 PMCID: PMC11357276 DOI: 10.3390/molecules29163891] [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: 07/04/2024] [Revised: 08/11/2024] [Accepted: 08/14/2024] [Indexed: 09/03/2024] Open
Abstract
BACKGROUND Metastatic melanoma stands out as the most lethal form of skin cancer because of its high propensity to spread and its remarkable resistance to treatment methods. METHODS In this review article, we address the incidence of melanoma worldwide and its staging phases. We thoroughly investigate the different melanomas and their associated risk factors. In addition, we underscore the principal therapeutic goals and pharmacological methods that are currently used in the treatment of melanoma. RESULTS The implementation of targeted therapies has contributed to improving the approach to patients. However, because of the emergence of resistance early in treatment, overall survival and progression-free periods continue to be limited. CONCLUSIONS We provide new insights into plant serine protease inhibitor therapeutics, supporting high-throughput drug screening soon, and seeking a complementary approach to explain crucial mechanisms associated with melanoma.
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Affiliation(s)
- Ana Paula De Araújo Boleti
- Laboratory of Protein Purification and Their Biological Functions, Food Technology and Public Health Unit, Federal University of Mato Grosso do Sul (UFMS), Campo Grande 79070-900, MS, Brazil; (A.P.D.A.B.); (A.C.J.); (T.M.-A.); (A.P.R.P.)
| | - Ana Cristina Jacobowski
- Laboratory of Protein Purification and Their Biological Functions, Food Technology and Public Health Unit, Federal University of Mato Grosso do Sul (UFMS), Campo Grande 79070-900, MS, Brazil; (A.P.D.A.B.); (A.C.J.); (T.M.-A.); (A.P.R.P.)
| | - Tamaeh Monteiro-Alfredo
- Laboratory of Protein Purification and Their Biological Functions, Food Technology and Public Health Unit, Federal University of Mato Grosso do Sul (UFMS), Campo Grande 79070-900, MS, Brazil; (A.P.D.A.B.); (A.C.J.); (T.M.-A.); (A.P.R.P.)
| | - Ana Paula Ramos Pereira
- Laboratory of Protein Purification and Their Biological Functions, Food Technology and Public Health Unit, Federal University of Mato Grosso do Sul (UFMS), Campo Grande 79070-900, MS, Brazil; (A.P.D.A.B.); (A.C.J.); (T.M.-A.); (A.P.R.P.)
| | - Maria Luiza Vilela Oliva
- Departamento de Bioquímica, Universidade Federal de São Paulo (UNIFESP), São Paulo 04023-062, SP, Brazil;
| | - Durvanei Augusto Maria
- Divisão de Ciências Fisiológicas e Químicas, Serviço de Bioquímica, Instituto Butantan, São Paulo 05585-000, SP, Brazil;
| | - Maria Lígia Rodrigues Macedo
- Laboratory of Protein Purification and Their Biological Functions, Food Technology and Public Health Unit, Federal University of Mato Grosso do Sul (UFMS), Campo Grande 79070-900, MS, Brazil; (A.P.D.A.B.); (A.C.J.); (T.M.-A.); (A.P.R.P.)
- Department of Pharmaceutical Sciences, Food, and Nutrition, Federal University of Mato Grosso do Sul, Campo Grande 79070-900, MS, Brazil
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Ruíz-Patiño A, Rojas L, Zuluaga J, Arrieta O, Corrales L, Martín C, Franco S, Raez L, Rolfo C, Sánchez N, Cardona AF. Genomic ancestry and cancer among Latin Americans. Clin Transl Oncol 2024; 26:1856-1871. [PMID: 38581481 PMCID: PMC11249489 DOI: 10.1007/s12094-024-03415-6] [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: 09/23/2023] [Accepted: 02/20/2024] [Indexed: 04/08/2024]
Abstract
Latin American populations, characterized by intricate admixture patterns resulting from the intermingling of ancestries from European, Native American (NA) Asian, and African ancestries which result in a vast and complex genetic landscape, harboring unique combinations of novel variants. This genetic diversity not only poses challenges in traditional population genetics methods but also opens avenues for a deeper understanding of its implications in health. In cancer, the interplay between genetic ancestry, lifestyle factors, and healthcare disparities adds a layer of complexity to the varying incidence and mortality rates observed across different Latin American subpopulations. This complex interdependence has been unveiled through numerous studies, whether conducted on Latin American patients residing on the continent or abroad, revealing discernible differences in germline composition that influence divergent disease phenotypes such as higher incidence of Luminal B and Her2 breast tumors, EGFR and KRAS mutated lung adenocarcinomas in addition to an enrichment in BRCA1/2 pathogenic variants and a higher than expected prevalence of variants in colorectal cancer associated genes such as APC and MLH1. In prostate cancer novel risk variants have also been solely identified in Latin American populations. Due to the complexity of genetic divergence, inputs from each individual ancestry seem to carry independent contributions that interplay in the development of these complex disease phenotypes. By understanding these unique population characteristics, genomic ancestries hold a promising avenue for tailoring prognostic assessments and optimizing responses to oncological interventions.
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Affiliation(s)
- Alejandro Ruíz-Patiño
- Clinical Genetics, Luis Carlos Sarmiento Angulo Cancer Treatment and Research Center (CTIC), Bogotá, Colombia
- Foundation for Clinical and Applied Cancer Research - FICMAC, Bogotá, Colombia
- GIGA/TERA Research Group, CTIC/Universidad El Bosque, Bogotá, Colombia
| | - Leonardo Rojas
- GIGA/TERA Research Group, CTIC/Universidad El Bosque, Bogotá, Colombia
- Thoracic Oncology Unit, Luis Carlos Sarmiento Angulo Cancer Treatment and Research Center (CTIC), Bogotá, Colombia
| | - Jairo Zuluaga
- GIGA/TERA Research Group, CTIC/Universidad El Bosque, Bogotá, Colombia
- Thoracic Oncology Unit, Luis Carlos Sarmiento Angulo Cancer Treatment and Research Center (CTIC), Bogotá, Colombia
| | - Oscar Arrieta
- Instituto Nacional de Cancerología -INCaN, Mexico City, Mexico
| | - Luis Corrales
- Thoracic Oncology Unit, Centro de Investigación y Manejo del Cáncer (CIMCA), San José, Costa Rica
| | - Claudio Martín
- Thoracic Oncology Unit, Instituto Alexander Fleming, Buenos Aires, Argentina
| | - Sandra Franco
- GIGA/TERA Research Group, CTIC/Universidad El Bosque, Bogotá, Colombia
- Breast Cancer Unit, Luis Carlos Sarmiento Angulo Cancer Treatment and Research Center (CTIC), Bogotá, Colombia
| | - Luis Raez
- Oncology Department, Memorial Cancer Institute (MCI), Memorial Healthcare System, Miami, FL, USA
| | - Christian Rolfo
- Center for Thoracic Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Natalia Sánchez
- GIGA/TERA Research Group, CTIC/Universidad El Bosque, Bogotá, Colombia
- Institute of Research, Science and Education, Luis Carlos Sarmiento Angulo Cancer Treatment and Research Center (CTIC), Bogotá, Colombia
| | - Andrés Felipe Cardona
- GIGA/TERA Research Group, CTIC/Universidad El Bosque, Bogotá, Colombia.
- Thoracic Oncology Unit, Luis Carlos Sarmiento Angulo Cancer Treatment and Research Center (CTIC), Bogotá, Colombia.
- Institute of Research, Science and Education, Luis Carlos Sarmiento Angulo Cancer Treatment and Research Center (CTIC), Bogotá, Colombia.
- Direction of Research and Education, Luis Carlos Sarmiento Angulo Cancer Treatment and Research Center (CTIC), Cra. 14 #169-49, Bogotá, Colombia.
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Pereira JL, de Souza CA, Neyra JEM, Leite JMRS, Cerqueira A, Mingroni-Netto RC, Soler JMP, Rogero MM, Sarti FM, Fisberg RM. Genetic Ancestry and Self-Reported "Skin Color/Race" in the Urban Admixed Population of São Paulo City, Brazil. Genes (Basel) 2024; 15:917. [PMID: 39062696 PMCID: PMC11276533 DOI: 10.3390/genes15070917] [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: 06/17/2024] [Revised: 07/08/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
Epidemiological studies frequently classify groups based on phenotypes like self-reported skin color/race, which inaccurately represent genetic ancestry and may lead to misclassification, particularly among individuals of multiracial backgrounds. This study aimed to characterize both global and local genome-wide genetic ancestries and to assess their relationship with self-reported skin color/race in an admixed population of Sao Paulo city. We analyzed 226,346 single-nucleotide polymorphisms from 841 individuals participating in the population-based ISA-Nutrition study. Our findings confirmed the admixed nature of the population, demonstrating substantial European, significant Sub-Saharan African, and minor Native American ancestries, irrespective of skin color. A correlation was observed between global genetic ancestry and self-reported color-race, which was more evident in the extreme proportions of African and European ancestries. Individuals with higher African ancestry tended to identify as Black, those with higher European ancestry tended to identify as White, and individuals with higher Native American ancestry were more likely to self-identify as Mixed, a group with diverse ancestral compositions. However, at the individual level, this correlation was notably weak, and no deviations were observed for specific regions throughout the individual's genome. Our findings emphasize the significance of accurately defining and thoroughly analyzing race and ancestry, especially within admixed populations.
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Affiliation(s)
- Jaqueline L. Pereira
- Department of Nutrition, School of Public Health, University of São Paulo, São Paulo 01246-904, Brazil; (J.L.P.); (J.M.R.S.L.); (M.M.R.)
| | - Camila A. de Souza
- Department of Statistics, Institute of Mathematics and Statistics, University of São Paulo, São Paulo 05508-090, Brazil; (C.A.d.S.); (J.E.M.N.); (J.M.P.S.)
| | - Jennyfer E. M. Neyra
- Department of Statistics, Institute of Mathematics and Statistics, University of São Paulo, São Paulo 05508-090, Brazil; (C.A.d.S.); (J.E.M.N.); (J.M.P.S.)
| | - Jean M. R. S. Leite
- Department of Nutrition, School of Public Health, University of São Paulo, São Paulo 01246-904, Brazil; (J.L.P.); (J.M.R.S.L.); (M.M.R.)
| | - Andressa Cerqueira
- Department of Statistics, Federal University of Sao Carlos, São Carlos 13565-905, Brazil;
| | - Regina C. Mingroni-Netto
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo 05508-090, Brazil;
| | - Julia M. P. Soler
- Department of Statistics, Institute of Mathematics and Statistics, University of São Paulo, São Paulo 05508-090, Brazil; (C.A.d.S.); (J.E.M.N.); (J.M.P.S.)
| | - Marcelo M. Rogero
- Department of Nutrition, School of Public Health, University of São Paulo, São Paulo 01246-904, Brazil; (J.L.P.); (J.M.R.S.L.); (M.M.R.)
| | - Flavia M. Sarti
- School of Arts, Sciences and Humanities, University of Sao Paulo, São Paulo 03828-000, Brazil;
| | - Regina M. Fisberg
- Department of Nutrition, School of Public Health, University of São Paulo, São Paulo 01246-904, Brazil; (J.L.P.); (J.M.R.S.L.); (M.M.R.)
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Llibre‐Guerra JJ, Jiang M, Acosta I, Sosa AL, Acosta D, Jimenez‐Velasquez IZ, Guerra M, Salas A, Rodriguez Salgado AM, Llibre‐Guerra JC, Sánchez ND, Prina M, Renton A, Albanese E, Yokoyama JS, Llibre Rodriguez JJ. Social determinants of health but not global genetic ancestry predict dementia prevalence in Latin America. Alzheimers Dement 2024; 20:4828-4840. [PMID: 38837526 PMCID: PMC11247688 DOI: 10.1002/alz.14041] [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: 03/04/2024] [Revised: 05/08/2024] [Accepted: 05/09/2024] [Indexed: 06/07/2024]
Abstract
INTRODUCTION Leveraging the nonmonolithic structure of Latin America, which represents a large variability in social determinants of health (SDoH) and high levels of genetic admixture, we aim to evaluate the relative contributions of SDoH and genetic ancestry in predicting dementia prevalence in Latin American populations. METHODS Community-dwelling participants aged 65 and older (N = 3808) from Cuba, Dominican Republic, Mexico, and Peru completed the 10/66 protocol assessments. Dementia was diagnosed using the cross-culturally validated 10/66 algorithm. Multivariate linear regression models adjusted for SDoH were used in the main analysis. This study used cross-sectional data from the 1066 population-based study. RESULTS Individuals with higher proportions of Native American (>70%) and African American (>70%) ancestry were more likely to exhibit factors contributing to worse SDoH, such as lower educational levels (p < 0.001), lower socioeconomic status (p < 0.001), and higher frequency of vascular risk factors (p < 0.001). After adjusting for measures of SDoH, there was no association between ancestry proportion and dementia probability, and ancestry proportions no longer significantly accounted for the variance in cognitive performance (African predominant p = 0.31 [-0.19, 0.59] and Native predominant p = 0.74 [-0.24, 0.33]). DISCUSSION The findings suggest that social and environmental factors play a more crucial role than genetic ancestry in predicting dementia prevalence in Latin American populations. This underscores the need for public health strategies and policies that address these social determinants to effectively reduce dementia risk in these communities. HIGHLIGHTS Countries in Latin America express a large variability in social determinants of health and levels of admixture. After adjustment for downstream societal factors linked to SDoH, genetic ancestry shows no link to dementia. Population ancestry profiles alone do not influence cognitive performance. SDoH are key drivers of racial disparities in dementia and cognitive performance.
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Affiliation(s)
- Jorge J. Llibre‐Guerra
- Department of NeurologyWashington University School of Medicine in St. LouisSt LouisMissouriUSA
| | - Miao Jiang
- Institute of Public HealthFaculty of Biomedical SciencesUniversità della Svizzera italianaLuganoSwitzerland
| | - Isaac Acosta
- Laboratory of the DementiasNational Institute of Neurology and NeurosurgeryMexico CityMexico
- National Autonomous University of MexicoMexico CityMexico
| | - Ana Luisa Sosa
- Laboratory of the DementiasNational Institute of Neurology and NeurosurgeryMexico CityMexico
- National Autonomous University of MexicoMexico CityMexico
| | - Daisy Acosta
- Internal Medicine DepartmentUniversidad Nacional Pedro Henriquez Ureña (UNPHU), Geriatric SectionSanto DomingoDominican Republic
| | - Ivonne Z. Jimenez‐Velasquez
- Internal Medicine DepartmentGeriatrics Program, School of MedicineMedical Sciences CampusUniversity of Puerto RicoSan JuanPuerto RicoUSA
| | - Mariella Guerra
- Instituto de la Memoria Depresion y Enfermedades de Riesgo IMEDERLimaPerú
| | - Aquiles Salas
- Medicine DepartmentCaracas University Hospital, Faculty of Medicine, Universidad Central de VenezuelaCaracasVenezuela
| | | | | | - Nedelys Díaz Sánchez
- Dementia Research Unit, Facultad de Medicina Finlay‐AlbarranMedical University of HavanaHavanaCuba
| | - Matthew Prina
- Population Health Sciences InstituteFaculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Alan Renton
- Department of NeuroscienceIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Emiliano Albanese
- Institute of Public HealthFaculty of Biomedical SciencesUniversità della Svizzera italianaLuganoSwitzerland
| | - Jennifer S. Yokoyama
- Department of NeurologyUCSF Weill Institute for Neurosciences, University of California, San FranciscoSan FranciscoCaliforniaUSA
- Department of Radiology and Biomedical ImagingUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
| | - Juan J. Llibre Rodriguez
- Dementia Research Unit, Facultad de Medicina Finlay‐AlbarranMedical University of HavanaHavanaCuba
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Ferreira LL, Gonçalves ABR, Adiala IJB, Loiola S, Dias A, Azulay RS, Silva DA, Gomes MB. A pilot study of mitochondrial genomic ancestry in admixed Brazilian patients with type 1 diabetes. Diabetol Metab Syndr 2024; 16:130. [PMID: 38879575 PMCID: PMC11179274 DOI: 10.1186/s13098-024-01342-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 05/01/2024] [Indexed: 06/19/2024] Open
Abstract
Interactions between multiple genes and environmental factors could be related to the pathogenesis of type 1 diabetes (T1D). The Brazilian population results from different historical miscegenation events, resulting in a highly diverse genetic pool. This study aimed to analyze the mtDNA of patients with T1D and to investigate whether there is a relationship between maternal ancestry, self-reported color and the presence of T1D. The mtDNA control region of 204 patients with T1D residing in three geographic regions of Brazil was sequenced following the International Society for Forensic Genetics (ISFG) recommendations. We obtained a frequency of Native American matrilineal origin (43.6%), African origin (38.2%), and European origin (18.1%). For self-declared color, 42.6% of the patients with diabetes reported that they were White, 50.9% were Brown, and 5.4% were Black. Finally, when we compared the self-declaration data with maternal ancestral origin, we found that for the self-declared White group, there was a greater percentage of haplogroups of Native American origin (50.6%); for the self-declared Black group, there was a greater percentage of African haplogroups (90.9%); and for the Brown group, there was a similar percentage of Native American and African haplogroups (42.3% and 45.2%, respectively). The Brazilian population with diabetic has a maternal heritage of more than 80% Native American and African origin, corroborating the country's colonization history.
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Affiliation(s)
- Lívia Leite Ferreira
- DNA Diagnostic Laboratory, IBRAG, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | - Silvia Loiola
- DNA Diagnostic Laboratory, IBRAG, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alessandra Dias
- Forensic Science and Technology Laboratory, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rossana Sousa Azulay
- Service of Endocrinology, University Hospital of the Federal University of Maranhão, São Luís, Brazil
| | - Dayse Aparecida Silva
- DNA Diagnostic Laboratory, IBRAG, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marília Brito Gomes
- Department of Internal Medicine, Diabetes Unit, Rio de Janeiro State University (UERJ), Boulevard 28 Setembro 77, Rio de Janeiro, Rio de Janeiro, Brazil.
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Lopes GDS, Guimarães L, Nascimento E, Freitas DQ, Rebello I, Medrado AP, Coletta RD, Reis SRA. Root Curvature in Non-Syndromic Oral Clefts: A Case-Control Study in a Brazilian Population. Cleft Palate Craniofac J 2024; 61:740-747. [PMID: 36475900 DOI: 10.1177/10556656221143299] [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] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVE This study assesses the degree of root curvature in patients with non-syndromic cleft lip and/or palate (NSCL/P). DESIGN Retrospective. Case-control study. SETTING Root curvature was assessed in lower premolars and molars in 800 panoramic radiographs: 400 from patients with cleft and 400 from healthy control individuals. Root curvature was classified according to its angulation, as well as its apical, medial, or coronal localization. RESULTS The frequency of mild curvature in the NSCL/P group compared to the control group was higher in premolars especially in the left second premolar in cleft palate (OR: 6.91; 95% CI: 3.23-14.77; P < .0001). The frequency of moderate curvature in molars was significantly higher in the cleft group, with the highest risk in the right first molar in the cleft lip group (OR: 2.74; 95% CI: 1.67-4.52; P < .0001). Inclination was more frequently observed in the apical third of the root in the group with cleft, whereas for the control group, the curvature was more frequent in the medial third. In patients with cleft, the OR of curvature in the apical third was significant in premolars (left lower second premolar: Cleft lip, OR: 1.91; 95% CI: 1.04-3.52; P = .03; right lower second premolar: Cleft lip, OR: 1.91, 95% CI: 1.04-3.50; P = .03, cleft lip and palate, OR: 1.75; 95% CI: 1.12-2.73; P = .01). CONCLUSION The results of the current study indicate differences in root curvature in patients with non-syndromic cleft lip and/or palate, which should be considered during the dental treatment planning of patients.
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Affiliation(s)
| | - Laís Guimarães
- Bahiana School of Medicine and Public Health, Salvador, Brazil
| | | | - Deborah Q Freitas
- Piracicaba Dental School, University of Campinas, Piracicaba, Brazil
| | | | - Alena P Medrado
- Bahiana School of Medicine and Public Health, Salvador, Brazil
| | - Ricardo D Coletta
- Piracicaba Dental School, University of Campinas, Piracicaba, Brazil
| | - Silvia R A Reis
- Bahiana School of Medicine and Public Health, Salvador, Brazil
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8
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Suarez-Kurtz G, Struchiner CJ. Pharmacogenomic implications of the differential distribution of CYP3A5 metabolic phenotypes among Latin American populations. Pharmacogenomics 2024; 25:187-195. [PMID: 38506326 DOI: 10.2217/pgs-2024-0009] [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: 01/11/2024] [Accepted: 02/28/2024] [Indexed: 03/21/2024] Open
Abstract
This study shows that the distribution of CYP3A5 alleles (*1, *3, *6 and *7) and genotype-predicted CYP3A5 phenotypes vary significantly across Latin American cohorts (Brazilians and the One Thousand Genomes Admixed American superpopulation), as well as among subcohorts comprising individuals with the highest proportions of Native, European or sub-Saharan African ancestry. Differences in biogeographical ancestry across the study groups are the likely explanation for these results. The differential distribution of CYP3A5 phenotypes has major pharmacogenomic implications, affecting the proportion of individuals carrying high risk CYP3A5 phenotypes for the immunosuppressant tacrolimus and the number of patients that would need to be genotyped to prevent acute rejection in kidney transplant recipients under tacrolimus treatment.
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Affiliation(s)
- Guilherme Suarez-Kurtz
- Divisão de Pesquisa Clínica e Desenvolvimento Tecnológico, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
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9
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Lara LDS, Coletta RD, Assis Machado R, Querino Rocha de Oliveira L, Martelli Júnior H, de Almeida Reis SR, Scariot R, Evaristo Ricci Volpato L. Exploring the role of the WNT5A rs566926 polymorphism and its interactions in non-syndromic orofacial cleft: a multicenter study in Brazil. J Appl Oral Sci 2024; 32:e20230353. [PMID: 38359266 PMCID: PMC11018296 DOI: 10.1590/1678-7757-2023-0353] [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: 10/21/2023] [Accepted: 01/04/2024] [Indexed: 02/17/2024] Open
Abstract
BACKGROUND Associations between the WNT5A rs566926 variant and non-syndromic orofacial cleft (NSOC) have been reported in different populations. OBJECTIVE This study aimed to investigate the role of the rs566926 single nucleotide polymorphism (SNP) in WNT5A and its interactions with SNPs in BMP4, FGFR1, GREM1, MMP2, and WNT3 in the occurrence of NSOC in a Brazilian population. METHODOLOGY A case-control genetic association study was carried out involving participants from four regions of Brazil, totaling 801 patients with non-syndromic cleft lip with or without cleft palate (NSCL±P), 273 patients with cleft palate only (NSCPO), and 881 health volunteers without any congenital condition (control). Applying TaqMan allelic discrimination assays, we evaluated WNT5A rs566926 in an ancestry-structured multiple logistic regression analysis, considering sex and genomic ancestry as covariates. Interactions between rs566926 and variants in genes involved in the WNT5A signaling pathway (BMP4, FGFR1, GREM1, MMP2, and WNT3) were also explored. RESULTS WNT5A rs566926 was significantly associated with an increased risk of NSCL±P, particularly due to a strong association with non-syndromic cleft lip only (NSCLO), in which the C allele increased the risk by 32% (OR: 1.32, 95% CI: 1.04-1.67, p=0.01). According to the proportions of European and African genomic ancestry, the association of rs566926 reached significant levels only in patients with European ancestry. Multiple interactions were detected between WNT5A rs566926 and BMP4 rs2071047, GREM1 rs16969681 and rs16969862, and FGFR1 rs7829058. CONCLUSION The WNT5A rs566926 polymorphism was associated with NSCL±P, particularly in individuals with NSCLO and high European ancestry. Epistatic interactions involving WNT5A rs566926 and variants in BMP4, GREM1, and FGFR1 may contribute to the risk of NSCL±P in the Brazilian population.
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Affiliation(s)
- Lorraynne Dos Santos Lara
- Universidade de Cuiabá, Programa de Pós-Graduação em Ciências Odontológicas Integradas, Faculdade de Odontologia de Cuiabá, Cuiabá, MT, Brasil
| | - Ricardo D Coletta
- Universidade Estadual de Campinas, Departamento de Diagnóstico Oral e Programa de Pós-Graduação em Biologia Buco-Dental, Faculdade de Odontologia de Piracicaba, Piracicaba, SP, Brasil
| | - Renato Assis Machado
- Universidade Estadual de Campinas, Faculdade de Odontologia de Piracicaba, Programa de Pós-Graduação em Biologia Buco-Dental, Piracicaba, SP, Brasil
| | - Lilianny Querino Rocha de Oliveira
- Universidade Estadual de Campinas, Faculdade de Odontologia de Piracicaba, Programa de Pós-Graduação em Biologia Buco-Dental, Piracicaba, SP, Brasil
| | - Hercílio Martelli Júnior
- Universidade Estadual de Montes Claros, Departamento de Odontologia, Clínica de Estomatologia, Montes Claros, MG, Brasil, e
| | | | - Rafaela Scariot
- Universidade Federal do Paraná, setor de Ciências da Saúde, Departamento de Estomatologia, Disciplina de Cirurgia Bucomaxilofacial, Curitiba, PR, Brasil
| | - Luiz Evaristo Ricci Volpato
- Universidade de Cuiabá, Programa de Pós-Graduação em Ciências Odontológicas Integradas, Faculdade de Odontologia de Cuiabá, Cuiabá, MT, Brasil
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10
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Perini JA, Basta PC, Suarez-Kurtz G. NUDT15 and TPMT polymorphisms in three distinct native populations of the Brazilian Amazon. Front Pharmacol 2024; 15:1359570. [PMID: 38379902 PMCID: PMC10876798 DOI: 10.3389/fphar.2024.1359570] [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: 12/21/2023] [Accepted: 01/18/2024] [Indexed: 02/22/2024] Open
Abstract
This is the first report of the distribution of TPMT and NUDT15 single nucleotide polymorphisms and metabolic phenotypes associated with cytotoxicity of thiopurine drugs, in indigenous groups of Brazilian Amazon: Munduruku, Paiter-Suruí and Yanomami. The minor allele frequency (MAF) of NUDT15 rs116855232 did not differ significantly across the groups; TPMT rs1800462 was absent, while rs1800460 and rs1142345 were in strong linkage disequilibrium, and 10- and 30-fold more common in Paiter-Suruí. Indeed, the MAFs in Paiter-Surui (0.193 and 0.188) are the largest report globally. The distribution of combined NUDT15/TPMT metabolic phenotypes differed significantly (p < 0.0001) and largely (Cramér´s V = 0.37) across cohorts. This has important pharmacogenetic implications: the Clinical Pharmacogenetics Implementation Consortium recommendations to reduce or consider reduction of thiopurine dose applies to 4.4% Yanomami, 5.6% Munduruku, versus 41% Paiter-Suruí. The proportion of Paiter-Suruí at risk of thiopurine intolerance is 3- to 4-fold higher than any other population worldwide.
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Affiliation(s)
- Jamila Alessandra Perini
- Laboratório de Pesquisa de Ciências Farmacêuticas (LAPESF), Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Paulo Cesar Basta
- Departamento de Endemias Samuel Pessoa, Escola Nacional de Saúde Pública, Fundação Oswaldo Cruz (ENSP/Fiocruz), Rio de Janeiro, Brazil
| | - Guilherme Suarez-Kurtz
- Divisão de Pesquisa Clínica e Desenvolvimento Tecnológico, Coordenação de Pesquisa, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
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11
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Trevisano RG, Matias H, de Jesus Teani T, Silvino VO, Ferreira CP, Dos Santos MAP, Braga PLG, Almeida SS. The frequency of the ACE I/D polymorphism in South America: a systematic review and meta-analysis. Mol Cell Biochem 2024:10.1007/s11010-023-04923-9. [PMID: 38310174 DOI: 10.1007/s11010-023-04923-9] [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: 08/02/2023] [Accepted: 12/26/2023] [Indexed: 02/05/2024]
Abstract
Angiotensin-converting enzyme (ACE) is a key component of the renin-angiotensin system and plays an important role in homeostasis and maintenance of blood pressure. However, little is known about allele and genotypic frequencies, as well as phenotypic characteristics associated with ACE polymorphism genotypes in South American populations. This study aimed to verify the allelic predominance and genotype frequency of ACE I/D polymorphism in South America and its association with the main diseases and related conditions. We conducted a systematic review considering studies published in the last 25 years available in PubMed, Scielo, LILACS, LIPECS, Coleciona SUS, CUMED, BINACIS, IBECS, and MEDLINE databases, resulting in the inclusion of 121 studies. Quality of the studies was assessed according to the Strengthening the Reporting of Genetic Association (STREGA) guidelines. We mapped the frequency of the ACE I/D polymorphism in South American populations. 8,856 (32.1%) subjects were DD, 13,050 were ID (47.4%), and 5,644 were II (20.5%) carriers. The main associated conditions included systemic arterial hypertension and other cardiovascular conditions, cardiorespiratory or respiratory characteristics, physical activity level, kidney conditions, aging-related diseases, as well as different types of cancers and metabolic conditions. 61.1% of the studies found no significant association between the respective conditions investigated and the ACE I/D polymorphism. Considering DD genotype or D allele, 21.5% of the studies observed negative and 4.9% positive outcomes. Regarding ID genotype, 4.1% of the studies identified negative and 0.8% positive outcomes, and for II genotype or I allele, 4.1% of the results had negative and 10.7% positive associations.
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Affiliation(s)
- Rebeca Gonçalves Trevisano
- Department of Obstetrician, Escola Paulista de Medicina, Universidade Federal de São Paulo (UNIFESP), São Paulo, SP, Brazil
| | - Helen Matias
- Department of Obstetrician, Escola Paulista de Medicina, Universidade Federal de São Paulo (UNIFESP), São Paulo, SP, Brazil
| | | | - Valmir Oliveira Silvino
- Department of Biophysics and Physiology, Nucleus of Study in Physiology Applied to Performance and Health (NEFADS), Federal University of Piaui, Teresina, Brazil
- Rede Nordeste de Biotecnologia (RENORBIO) post-graduation program, Teresina, Brazil
| | - Cirley Pinheiro Ferreira
- Department of Biophysics and Physiology, Nucleus of Study in Physiology Applied to Performance and Health (NEFADS), Federal University of Piaui, Teresina, Brazil
- Rede Nordeste de Biotecnologia (RENORBIO) post-graduation program, Teresina, Brazil
| | - Marcos Antonio Pereira Dos Santos
- Department of Biophysics and Physiology, Nucleus of Study in Physiology Applied to Performance and Health (NEFADS), Federal University of Piaui, Teresina, Brazil
- Rede Nordeste de Biotecnologia (RENORBIO) post-graduation program, Teresina, Brazil
| | | | - Sandro Soares Almeida
- Department of Obstetrician, Escola Paulista de Medicina, Universidade Federal de São Paulo (UNIFESP), São Paulo, SP, Brazil.
- Hospital Israelita Albert Einstein, São Paulo, SP, Brazil.
- Universidade Ibirapuera, São Paulo, SP, Brazil.
- Faculdade Anhanguera de Guarulhos, Guarulhos, SP, Brazil.
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12
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Schauren JDS, de Oliveira AH, Consiglio CR, Monticielo OA, Xavier RM, Nunes NS, Ellwanger JH, Chies JAB. CCR5 promoter region polymorphisms in systemic lupus erythematosus. Int J Immunogenet 2024; 51:20-31. [PMID: 37984413 DOI: 10.1111/iji.12646] [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: 09/19/2023] [Revised: 10/26/2023] [Accepted: 11/09/2023] [Indexed: 11/22/2023]
Abstract
This study investigated the impacts of CCR5 promoter region polymorphisms on the development of systemic lupus erythematosus (SLE) by comparing CCR5 genotypes and haplotypes from SLE patients with ethnically matched controls. A total of 382 SLE patients (289 European-derived and 93 African-derived) and 375 controls (243 European-derived and 132 African-derived) were genotyped for the CCR2-64I G > A (rs1799864), CCR5-59353 C > T (rs1799988), CCR5-59356 C > T (rs41469351), CCR5-59402 A > G (rs1800023) and CCR5-59653 C > T (rs1800024) polymorphisms through polymerase chain reaction-restriction fragment length polymorphism and direct sequencing. Previous data from CCR5Δ32 analysis was included in the study to infer the CCR5 haplotypes and as a possible confounding factor in the binary logistic regression. European-derived patients showed a higher frequency of CCR5 wild-type genotype (conversely, a reduced frequency of Δ32 allele) and a reduced frequency of the HHG*2 haplotype compared to controls; both factors significantly affecting disease risk [p = .003 (OR 3.5, 95%CI 1.6-7.5) and 2.0% vs. 7.2% (residual p = 2.9E - 5), respectively]. Additionally, the HHA/HHB, HHC and HHG*2 haplotype frequencies differed between African-derived patients and controls [10% vs. 20.5% (residual p = .003), 29.4% vs. 17.4% (residual p = .003) and 3.9% vs. 0.8% (residual p = .023), respectively]. Considering the clinical manifestations of the disease, the CCR5Δ32 presence was confirmed as a susceptibility factor to class IV nephritis in the African-derived group and when all patients were grouped for comparison [pcorrected = .012 (OR 3.0; 95%CI 3.0-333.3) and pcorrected = .0006 (OR 6.8; 95%CI 1.9-24.8), respectively]. In conclusion, this study indicates that CCR5 promoter polymorphisms are important disease modifiers in SLE. Present data reinforces the CCR5Δ32 polymorphism as a protective factor for the development of the disease in European-derived patients and as a susceptibility factor for class IV nephritis in African-derived patients. Furthermore, we also described a reduced frequency of HHA/HHB and an increased frequency of HHC and HHG*2 haplotypes in African-derived patients, which could modify the CCR5 protein expression in specific cell subsets.
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Affiliation(s)
- Juliana da Silveira Schauren
- Laboratory of Immunobiology and Immunogenetics, Department of Genetics, Postgraduate Program in Genetics and Molecular Biology (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Amanda Henrique de Oliveira
- Laboratory of Immunobiology and Immunogenetics, Department of Genetics, Postgraduate Program in Genetics and Molecular Biology (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
- Postgraduate Program in Gastroenterology and Hepatology Sciences, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Camila Rosat Consiglio
- Laboratory of Immunobiology and Immunogenetics, Department of Genetics, Postgraduate Program in Genetics and Molecular Biology (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Odirlei André Monticielo
- Division of Rheumatology, Department of Internal Medicine, Hospital de Clínicas de Porto Alegre (HCPA), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Ricardo Machado Xavier
- Division of Rheumatology, Department of Internal Medicine, Hospital de Clínicas de Porto Alegre (HCPA), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Natália Schneider Nunes
- Postgraduate Program in Gastroenterology and Hepatology Sciences, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Joel Henrique Ellwanger
- Laboratory of Immunobiology and Immunogenetics, Department of Genetics, Postgraduate Program in Genetics and Molecular Biology (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - José Artur Bogo Chies
- Laboratory of Immunobiology and Immunogenetics, Department of Genetics, Postgraduate Program in Genetics and Molecular Biology (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
- Postgraduate Program in Gastroenterology and Hepatology Sciences, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
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13
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Lopes ARDO, Silva EML, Nascimento MMDS, Silva MC, Magalhães CP, Cerqueira GS. DSP2 for sex determination of miscegenated contemporary hip bones. Anat Histol Embryol 2024; 53:e12979. [PMID: 37792903 DOI: 10.1111/ahe.12979] [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: 07/18/2023] [Revised: 08/25/2023] [Accepted: 09/17/2023] [Indexed: 10/06/2023]
Abstract
The bones of the human pelvis are used in sexual diagnosis generating a high level of accuracy for this type of identification. Morphological and/or morphometric methods are used in the identification of sex. Sexual dimorphism may be affected by ethnic differences in the population. One of the methods for determining sex using hip bone is the 'Diagnose Sexuelle Probabiliste (DSP)' or Probabilistic Sexual Diagnosis (DSP) method. The method presents a new version (Probabilistic Sexual Diagnosis v.2-DSP2) more advisable to be used because it has a more up-to-date database. The objective of this study is to investigate the applicability of the DSP2 method in a population in the Northeast region of Brazil. We used 128 hip bones, 50 female and 78 males, aged between 17 and 101 years, belonging to the Laboratory of Human Identification and Forensic Osteology of the University Federal Government of Pernambuco. The research was conducted between 2019 and 2020 and approved by the Research Ethics Committee of the Federal University of Pernambuco no. 43228015.0.0000.5208. The probability equal to or greater than 0.95 was used as the limit for the determination of sex, and the results were compared with the actual sex of each bone. In the Brazilian collection study, it was observed that the percentage of sex estimation provided by the DSP2 tool using all reference samples was 71.09%, and accuracy was 64.06%. In the analysis of the gender estimate, 82.0% and 78% were obtained for females and males, respectively. Regarding accuracy, it was 64.10% and 55.13% for females and males, respectively. In the contemporary osteological collection of the Northeast region of Brazil, which presents immigrant peoples, we obtained a high index of assertiveness in the DSP2 method. The study concluded that the DSP2 method is important for determining the sex of human skeletons in a miscegenated population.
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Affiliation(s)
- Allyson Rodrigo de Oliveira Lopes
- Laboratory of Human Identification and Forensic Osteology - LIHOF, Federal University of Pernambuco, Academic Center of Vitória de Santo Antão - CAV/UFPE, Vitória de Santo Antão, Brazil
- Morphofunctional Sciences, Federal University of Ceará - UFC, Fortaleza, Brazil
| | - Ellen Mayara Lima Silva
- Laboratory of Human Identification and Forensic Osteology - LIHOF, Federal University of Pernambuco, Academic Center of Vitória de Santo Antão - CAV/UFPE, Vitória de Santo Antão, Brazil
| | - Marcela Martins da Silva Nascimento
- Laboratory of Human Identification and Forensic Osteology - LIHOF, Federal University of Pernambuco, Academic Center of Vitória de Santo Antão - CAV/UFPE, Vitória de Santo Antão, Brazil
| | - Melina Calmon Silva
- National Center for Dissemination of Forensic Sciences, National Institute of Criminalistics/Federal Police, Brasília, Brazil
| | - Carolina Peixoto Magalhães
- Laboratory of Human Identification and Forensic Osteology - LIHOF, Federal University of Pernambuco, Academic Center of Vitória de Santo Antão - CAV/UFPE, Vitória de Santo Antão, Brazil
- Laboratory of Human Identification and Forensic Osteology - LIHOF, Federal University of Pernambuco - UFPE, Recife, Brazil
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Suarez-Kurtz G. The c.415C>T polymorphism in NUDT15 is more frequent than the polymorphisms in TPMT in Chilean patients who use thiopurine drugs. Pharmacogenet Genomics 2023; 33:217-218. [PMID: 37767624 DOI: 10.1097/fpc.0000000000000508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2023]
Affiliation(s)
- Guilherme Suarez-Kurtz
- Divisão de Pesquisa Clínica e Desenvolvimento Tecnológico, Instituto Nacional de Câncer, Rio de Janeiro-RJ, Brazil
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15
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Basgalupp SP, Altmann V, Vairo FPE, Schwartz IVD, Siebert M. GBA1 variants in Brazilian Gaucher disease patients. Mol Genet Metab Rep 2023; 37:101006. [PMID: 38053927 PMCID: PMC10694776 DOI: 10.1016/j.ymgmr.2023.101006] [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: 04/30/2023] [Revised: 08/29/2023] [Accepted: 08/30/2023] [Indexed: 12/07/2023] Open
Abstract
Gaucher disease (GD) is an autosomal recessive lysosomal disorder caused by pathogenic variants in GBA1 which result in the deficient activity of glucocerebrosidase (GCase). There are few data on the genetic characterization of Brazilian GD patients. This study aimed at characterizing the genotype of 72 unrelated Brazilian GD patients (type I = 63, type II = 4, type III = 5; male = 31). Forty patients were from South Brazil (SB), and 32 were from other regions of Brazil (Others). The exons and exon/intron junctions of GBA1 were analyzed by Sanger sequencing in 8 patients, or by massive parallel sequencing followed by Sanger of exons 9 and 10 in 64 patients. In total, 31 pathogenic variants were identified. The most frequent allele found was N370S (p.(Asn409Ser)) (41.0%), and the most frequent genotype was N370S/RecNciI p.[Asn409Ser];[Leu483Pro;Ala495Pro;Val499=](23.6%). Three variants (N370S - in exon 9, and RecNciI and L444P (p.(Leu483Pro), in exon 10) correspond to 76.3% of total alleles in SB and 59.4% in Others. Two novel variants were described: c.326del(p.(Gln109Argfs*9)) and c.690G>A (p.(?)). Although sequencing all the exons of GBA1 is the gold-standard method for the genetic analysis of GD patients, a step analysis can be proposed for Brazilian patients, starting with analysis of exons 9 and 10. The N370S allele is the most frequently associated with GD in Brazil.
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Affiliation(s)
- Suelen Porto Basgalupp
- Hospital Moinhos de Vento, Porto Alegre, RS, Brazil
- Basic Research and Advanced Investigations in Neurosciences Laboratory, Experimental Research Center, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, RS, Brazil
| | - Vivian Altmann
- Basic Research and Advanced Investigations in Neurosciences Laboratory, Experimental Research Center, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, RS, Brazil
| | - Filippo Pinto e Vairo
- Department of Clinical Genomics and Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Ida Vanessa Doederlein Schwartz
- Basic Research and Advanced Investigations in Neurosciences Laboratory, Experimental Research Center, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, RS, Brazil
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, RS, Brazil
- Department of Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Marina Siebert
- Basic Research and Advanced Investigations in Neurosciences Laboratory, Experimental Research Center, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, RS, Brazil
- Postgraduate Program in Sciences of Gastroenterology and Hepatology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
- Unit of Laboratorial Research, Experimental Research Center, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, RS, Brazil
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16
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Al-Shuhaib MBS, Hashim HO. Mastering DNA chromatogram analysis in Sanger sequencing for reliable clinical analysis. J Genet Eng Biotechnol 2023; 21:115. [PMID: 37955813 PMCID: PMC10643650 DOI: 10.1186/s43141-023-00587-6] [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: 10/04/2023] [Accepted: 11/06/2023] [Indexed: 11/14/2023]
Abstract
BACKGROUND Sanger dideoxy sequencing is vital in clinical analysis due to its accuracy, ability to analyze genetic markers like SNPs and STRs, capability to generate reliable DNA profiles, and its role in resolving complex clinical cases. The precision and robustness of Sanger sequencing contribute significantly to the scientific basis of clinical investigations. Though the reading of chromatograms seems to be a routine step, many errors conducted in PCR may lead to consequent limitations in the readings of AGCT peaks. These errors are possibly associated with improper DNA amplification and its subsequent interpretation of DNA sequencing files, such as noisy peaks, artifacts, and confusion between double-peak technical errors, heterozygosity, and double infection potentials. Thus, it is not feasible to read nucleic acid sequences without giving serious attention to these technical problems. To ensure the accuracy of DNA sequencing outcomes, it is also imperative to detect and rectify technical challenges that may lead to misinterpretation of the DNA sequence, resulting in errors and incongruities in subsequent analyses. SHORT CONCLUSION This overview sheds light on prominent technical concerns that can emerge prior to and during the interpretation of DNA chromatograms in Sanger sequencing, along with offering strategies to address them effectively. The significance of identifying and tackling these technical limitations during the chromatogram analysis is underscored in this review. Recognizing these concerns can aid in enhancing the quality of downstream analyses for Sanger sequencing results, which holds notable improvement in accuracy, reliability, and ability to provide crucial genetic information in clinical analysis.
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Affiliation(s)
- Mohammed Baqur S Al-Shuhaib
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim 8, Babil, 51001, Iraq.
| | - Hayder O Hashim
- Department of Clinical Laboratory Sciences, College of Pharmacy, University of Babylon, Babil, 51001, Iraq
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Zambrano AK, Cadena-Ullauri S, Guevara-Ramírez P, Paz-Cruz E, Tamayo-Trujillo R, Ruiz-Pozo VA, Doménech N, Ibarra-Rodríguez AA, Gaviria A. The Autosomal Short Tandem Repeat Polymorphisms Are Potentially Associated with Cardiovascular Disease Predisposition in the Latin American Population: A Mini Review. BIOMED RESEARCH INTERNATIONAL 2023; 2023:6152905. [PMID: 38027043 PMCID: PMC10651335 DOI: 10.1155/2023/6152905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 10/02/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023]
Abstract
According to the World Health Organization, cardiovascular diseases (CVDs) are the leading cause of death worldwide across nearly all ethnic groups. Inherited cardiac conditions comprise a wide spectrum of diseases that affect the heart, including abnormal structural features and functional impairments. In Latin America, CVDs are the leading cause of death within the region. Factors such as population aging, unhealthy diet, obesity, smoking, and a sedentary lifestyle have increased the risk of CVD. The Latin American population is characterized by its diverse ethnic composition with varying percentages of each ancestral component (African, European, and Native American ancestry). Short tandem repeats (STRs) are DNA sequences with 2-6 base pair repetitions and constitute ~3% of the human genome. Importantly, significant allele frequency variations exist between different populations. While studies have described that STRs are in noncoding regions of the DNA, increasing evidence suggests that simple sequence repeat variations may be critical for proper gene activity and regulation. Furthermore, several STRs have been identified as potential disease predisposition markers. The present review is aimed at comparing and describing the frequencies of autosomal STR polymorphisms potentially associated with cardiovascular disease predisposition in Latin America compared with other populations.
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Affiliation(s)
- Ana Karina Zambrano
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | - Santiago Cadena-Ullauri
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | - Patricia Guevara-Ramírez
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | - Elius Paz-Cruz
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | - Rafael Tamayo-Trujillo
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | - Viviana A. Ruiz-Pozo
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | - Nieves Doménech
- Instituto de Investigación Biomédica de A Coruña (INIBIC)-CIBERCV, Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, Universidad da Coruña (UDC), La Coruña, Spain
| | | | - Aníbal Gaviria
- Laboratorio de Genética Molecular, Centros Médicos Especializados Cruz Roja Ecuatoriana, Quito, Ecuador
- Hemocentro Nacional, Cruz Roja Ecuatoriana, Quito, Ecuador
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18
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Cardoso JV, Machado DE, da Silva MC, de Mello MP, Berardo PT, Medeiros R, Perini JA. Influence of interleukin-8 polymorphism on endometriosis-related pelvic pain. Hum Immunol 2023; 84:561-566. [PMID: 37468423 DOI: 10.1016/j.humimm.2023.07.004] [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: 01/27/2023] [Revised: 05/26/2023] [Accepted: 07/11/2023] [Indexed: 07/21/2023]
Abstract
Endometriosis presents a pro-inflammatory microenvironment influenced by cytokines, such as interleukin (IL)-8, which expression may be influenced by genetic polymorphisms. Therefore, we aimed to investigate the role of interleukin (IL)-8 rs4073 polymorphism in endometriosis' development and its related symptoms. A case-control study was conducted with 207 women with endometriosis and 193 healthy controls. Polymorphism was genotyped using a TaqMan validated assay. Associations were evaluated by binary logistic regression, using odds ratios (OR) and 95 % confidence intervals (CI), and P ≤ 0.05 was considered significant. Cases were younger (36 ± 6.8 versus 39 ± 8.4) and had lower body mass index (26.5 ± 5.3 versus 35.7 ± 6.3 Kg/m2) than controls (P < 0.001). Higher prevalence of symptoms and infertility was observed in cases, compared to controls (P < 0.001). Minor allele frequencies of IL-8 rs4073 (T) were 42.3 % and 39.9 % for cases and controls, respectively, and no associations were found between IL and 8 rs4073 polymorphism and endometriosis' prevalence or staging. However, the polymorphism was associated with chronic pelvic pain among cases (OR = 0.54; 95 %CI = 0.29-0.98). The IL-8 rs4073A > T polymorphism may contribute to lower IL-8 expression and, consequently, decrease endometriosis-related pelvic pain. These findings can support the early diagnosis of endometriosis' painful symptoms, preventing its complications, and allowing an individualized treatment.
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Affiliation(s)
- Jéssica Vilarinho Cardoso
- Laboratório de Pesquisa de Ciências Farmacêuticas (LAPESF), Universidade do Estado do Rio de Janeiro (UERJ), RJ, Brazil
| | - Daniel Escorsim Machado
- Laboratório de Pesquisa de Ciências Farmacêuticas (LAPESF), Universidade do Estado do Rio de Janeiro (UERJ), RJ, Brazil
| | - Mayara Calixto da Silva
- Laboratório de Pesquisa de Ciências Farmacêuticas (LAPESF), Universidade do Estado do Rio de Janeiro (UERJ), RJ, Brazil
| | - Matheus Pereira de Mello
- Laboratório de Pesquisa de Ciências Farmacêuticas (LAPESF), Universidade do Estado do Rio de Janeiro (UERJ), RJ, Brazil
| | - Plinio Tostes Berardo
- Serviço de Ginecologia, Hospital Federal dos Servidores do Estado (HFSE), Rio de Janeiro, Brazil
| | - Rui Medeiros
- Grupo de Oncologia Molecular e Patologia Viral, Centro de Investigação do Instituto Português de Oncologia do Porto (IPO Porto)/Dep. Patologia e Medicina Laboratorial, Patologia Clínica SV/ (Rede de Investigação em Saúde)/Porto, Centro Abrangente de Oncologia, Porto, Portugal
| | - Jamila Alessandra Perini
- Laboratório de Pesquisa de Ciências Farmacêuticas (LAPESF), Universidade do Estado do Rio de Janeiro (UERJ), RJ, Brazil.
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May GB, de Souza BR, Gueuvoghlanian-Silva BY, Dos Reis EC, Mostardeiro SR, Boabaid May PP, Mateo EC, Vietta GG, Hoss GW. Distribution of pharmacogene allele and phenotype frequencies in Brazilian psychiatric patients. Pharmacogenomics 2023; 24:747-760. [PMID: 37846556 DOI: 10.2217/pgs-2023-0075] [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] [Indexed: 10/18/2023] Open
Abstract
Purpose: This work was designed to identify the pharmacogenetic profile of Brazilian psychiatric patients receiving psychoactive drug treatment according to ethnicity. Methods: Based on the GnTech® database, this cross-sectional study analyzed data from self-reported sociodemographic and genetic results from the next-generation sequencing panel composed of 26 pharmacogenes from 359 psychotropic drug users. Results: Variant frequencies of multiple pharmacogenes presented differences between ethnicities (CYP3A5, CYP2D6, CYP1A2, CYP2B6, CYP3A4, UGT1A4, UGT2B15, ABCB1 rs1045642, ADRA2A rs1800544, COMT rs4680, GRIK4 rs1954787, GSK3B rs334558, GSK3B rs6438552, HTR1A rs6295, HTR2A rs7997012, HTR2C rs1414334, MTHFR rs1801131, OPRM1 rs1799971 and 5-HTTLPR), endorsing the necessity of individual-level analyses in drug treatment. Conclusion: A discussion of pharmacogenomic test implementation in psychiatric clinical practice is needed to improve treatment choices, especially in Brazil, a multiethnic country.
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Affiliation(s)
| | | | | | | | - Sofia Rech Mostardeiro
- Universidade do Sul de Santa Catarina (UNISUL)-Campus Pedra Branca, Palhoça, SC, 88137-270, Brazil
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Macedo JMB, Silva AL, Pinto AC, Landeira LFL, Portari EA, Santos-Rebouças CB, Klumb EM. TP53 and p21 (CDKN1A) polymorphisms and the risk of systemic lupus erythematosus. Adv Rheumatol 2023; 63:43. [PMID: 37605254 DOI: 10.1186/s42358-023-00320-4] [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: 03/08/2023] [Accepted: 08/03/2023] [Indexed: 08/23/2023] Open
Abstract
BACKGROUND The p53 and p21 proteins are important regulators of cell cycle and apoptosis and may contribute to autoimmune diseases, such as systemic lupus erythematosus (SLE). As genetic polymorphisms may cause changes in protein levels and functions, we investigated associations of TP53 and p21 (CDKN1A) polymorphisms (p53 72 G > C-rs1042522; p53 PIN3-rs17878362; p21 31 C > A-rs1801270; p21 70 C > T-rs1059234) with the development of systemic lupus erythematosus (SLE) in a Southeastern Brazilian population. METHODS Genotyping of 353 female volunteers (cases, n = 145; controls, n = 208) was performed by polymerase chain reaction, restriction fragment length polymorphism and/or DNA sequencing. Associations between TP53 and p21 polymorphisms and SLE susceptibility and clinical manifestations of SLE patients were assessed by logistic regression analysis. RESULTS Protective effect was observed for the genotype combinations p53 PIN3 A1/A1-p21 31 C/A, in the total study population (OR 0.45), and p53 PIN3 A1/A2-p21 31 C/C, in non-white women (OR 0.28). In Whites, p53 72 C-containing (OR 3.06) and p53 PIN3 A2-containing (OR 6.93) genotypes were associated with SLE risk, and higher OR value was observed for the combined genotype p53 72 G/C-p53 PIN3 A1/A2 (OR 9.00). Further, p53 PIN3 A1/A2 genotype was associated with serositis (OR 2.82), while p53 PIN3 A2/A2 and p53 72 C/C genotypes were associated with neurological disorders (OR 4.69 and OR 3.34, respectively). CONCLUSIONS Our findings showed that the TP53 and p21 polymorphisms included in this study may have potential to emerge as SLE susceptibility markers for specific groups of patients. Significant interactions of the TP53 polymorphisms with serositis and neurological disorders were also observed in SLE patients.
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Affiliation(s)
| | - Amanda Lima Silva
- Department of Biochemistry, State University of Rio de Janeiro - UERJ, Rio de Janeiro, Brazil
| | - Amanda Chaves Pinto
- Department of Biochemistry, State University of Rio de Janeiro - UERJ, Rio de Janeiro, Brazil
| | | | - Elyzabeth Avvad Portari
- Department of Pathological Anatomy, State University of Rio de Janeiro - UERJ, Rio de Janeiro, Brazil
- Department of Pathology, Fernandes Figueira Institute - FIOCRUZ, Rio de Janeiro, Brazil
| | | | - Evandro Mendes Klumb
- Department of Rheumatology, Pedro Ernesto University Hospital, State University of Rio de Janeiro - UERJ, Boulevard 28 de Setembro, 87, Vila Isabel, Rio de Janeiro, RJ, CEP 20551-030, Brazil.
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Suarez-Kurtz G. Pharmacogenomic implications of the differential distribution of CYP2C9 metabolic phenotypes among Latin American populations. Front Pharmacol 2023; 14:1246765. [PMID: 37693910 PMCID: PMC10488705 DOI: 10.3389/fphar.2023.1246765] [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: 07/03/2023] [Accepted: 08/01/2023] [Indexed: 09/12/2023] Open
Abstract
The CYP2C9 gene encodes the major drug metabolism enzyme CYP2C9. This gene is highly polymorphic, and no-function (CYP2C9*3) plus decreased function (CYP2C9*2, *5, *8 and *11) star alleles (haplotypes) are commonly used to predict CYP2C9 metabolic phenotypes. This study explores the pharmacogenomic implications of the differential distribution of genotype-predicted CYP2C9 phenotypes across Latin American populations. Data from 1,404 individuals from the South American countries Brazil, Colombia and Peru, from Puerto Rico in the Caribbean and from persons with Mexican ancestry living in North America were analysed. The results showed that the distribution of CYP2C9 alleles and diplotypes, and diplotype-predicted CYP2C9 phenotypes vary significantly across the distinct country cohorts, as well as among self-identified White, Brown and Black Brazilians. Differences in average proportions of biogeographical ancestry across the study groups, especially Native American and African ancestry, are the likely explanation for these results. The differential distribution of genotype-predicted CYP2C9 phenotypes has potentially clinically-relevant pharmacogenomic implications, through its influence on the proportion of individuals at high risk for adverse response to medications that are CYP2C9 substrates, the proportion on individuals with CPIC therapeutic recommendations for dosing and choice of nonsteroidal antinflammatory drugs (NSAIDs) and the number of individuals that need to be genotyped in order to prevent adverse effects of NSAIDs. Collectively, these findings are likely to impact the perceived benefits, cost-effectiveness and clinical adoption of pharmacogenomic screening for drugs that are predominantly metabolized by CYP2C9.
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Stolf CS, Taiete T, Nascimento PAD, Paz HES, Sallum EA, Ruiz KGS, Casati MZ, Casarin RCV. Association of rs142548867 (EEFSEC) and periodontitis Grade C in a young Brazilian population. J Appl Oral Sci 2023; 31:e20230058. [PMID: 37466550 PMCID: PMC10356128 DOI: 10.1590/1678-7757-2023-0058] [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: 02/17/2023] [Accepted: 06/12/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND Periodontitis Stage III-IV, Grade C (PerioC) is a severe form of Periodontitis. The individual genetic background has been shown to be an important etiopathogenic factor for the development of this disease in young, systemically healthy, and non-smokers patients. Recently, after exome sequencing of families with a history of the disease, PerioC was associated with three single nucleotide variations (SNVs) - rs142548867 (EEFSEC), rs574301770 (ZNF136), and rs72821893 (KRT25) - which were classified as deleterious or possibly harmful by prediction algorithms. OBJECTIVE Seeking to validate these findings in a cohort evaluation, this study aims to characterize the allele and genotypic frequency of the SNVs rs142548867, rs574301770, and rs72821893 in the Brazilian population with PerioC and who were periodontally healthy (PH). METHODOLOGY Thus, epithelial oral cells from 200 PerioC and 196 PH patients were harvested at three distinct centers at the Brazilian Southern region, their DNA were extracted, and the SNVs rs142548867, rs574301770, rs72821893 were genotyped using 5'-nuclease allelic discrimination assay. Differences in allele and genotype frequencies were analyzed using Fisher's Exact Test. Only the SNV rs142548867 (C > T) was associated with PerioC. RESULTS The CT genotype was detected more frequently in patients with PerioC when compared with PH subjects (6% and 0.5% respectively), being significantly associated with PerioC (odds ratio 11.76, p=0.02). CONCLUSION rs142548867 represents a potential risk for the occurrence of this disease in the Brazilian population.
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Affiliation(s)
- Camila Schmidt Stolf
- Universidade Estadual de Campinas - UNICAMP, Faculdade de Odontologia de Piracicaba, Departamento de Prótese e Periodontia, Piracicaba, SP, Brasil
| | - Tiago Taiete
- Universidade de Araras, Departamento de Odontologia, Araras, SP, Brasil
| | - Paloma A do Nascimento
- Universidade Estadual de Campinas - UNICAMP, Faculdade de Odontologia de Piracicaba, Departamento de Prótese e Periodontia, Piracicaba, SP, Brasil
| | - Hélvis E S Paz
- Universidade Estadual de Campinas - UNICAMP, Faculdade de Odontologia de Piracicaba, Departamento de Prótese e Periodontia, Piracicaba, SP, Brasil
| | - Enílson Antônio Sallum
- Universidade Estadual de Campinas - UNICAMP, Faculdade de Odontologia de Piracicaba, Departamento de Prótese e Periodontia, Piracicaba, SP, Brasil
| | - Karina Gonzalez Silvério Ruiz
- Universidade Estadual de Campinas - UNICAMP, Faculdade de Odontologia de Piracicaba, Departamento de Prótese e Periodontia, Piracicaba, SP, Brasil
| | - Márcio Zaffalon Casati
- Universidade Estadual de Campinas - UNICAMP, Faculdade de Odontologia de Piracicaba, Departamento de Prótese e Periodontia, Piracicaba, SP, Brasil
- Universidade Paulista, Departamento de Periodontia, São Paulo, SP, Brasil
| | - Renato Corrêa Viana Casarin
- Universidade Estadual de Campinas - UNICAMP, Faculdade de Odontologia de Piracicaba, Departamento de Prótese e Periodontia, Piracicaba, SP, Brasil
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Soares SDS, Aquino JR, Petrolli F, de Oliveira TB, Almeida S, Fiegenbaum M. Frequencies of genetic variants of the Rh, Kell, Duffy, Kidd, MNS and Diego systems of northwest Rio Grande do Sul, Brazil. Hematol Transfus Cell Ther 2023; 45:317-323. [PMID: 35715379 PMCID: PMC10499560 DOI: 10.1016/j.htct.2022.05.004] [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: 12/22/2021] [Revised: 04/01/2022] [Accepted: 05/04/2022] [Indexed: 11/28/2022] Open
Abstract
INTRODUCTION To date, 340 antigen-organized 43 blood group systems are recognized, being ABO, Rh, Kell, Duffy, Kidd, MNS and Diego the most clinically relevant. The aim of this study was to assess the distribution of alleles and genotypes of the blood group systems Rh, Kell, Duffy, Kidd, MNS and Diego in 810 blood donors registered in the hemotherapy unit in northwest Rio Grande do Sul, Brazil METHODS: We evaluated the genetic variability of blood groups Rh (c.676G>C and c.307C>T), Kell (c.578C>T), Kidd (c.838A>G), Duffy (c.125A>G and c.1-67T>C), Diego (c.2561C>T) and MNS (c.143T>C) in 810 volunteer blood donors of Rio Grande do Sul, southern Brazil. The genetic profiling was performed through allelic discrimination assays using hydrolysis probes (TaqMan®) real-time PCR system. RESULTS The most frequent blood group genotypes found in our study population were: RHC*Cc (51.5%), RHC*ee (70.1%), FY*A/FY*B (49.3%), GATA -67T/T (93.5%), KEL*2/KEL*2 (93.4%), JK*A/JK*B (53.2%) and DI*02/DI*02 (95.4%). Some statistical differences were observed on comparing the population of this study with populations from other states in Brazil, mainly with population of Minas Gerais, Bahia and Paraná, which showed some differences from the population of Porto Alegre, which was more similar to those of Santa Catarina and São Paulo CONCLUSION: The frequency of red blood cell polymorphisms in our study is different from that of blood donors in other regions of Brazil. The results showed the importance of extended genotyping in adequate blood screening and the existence of rare genotypes in Brazilian regular blood donors.
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Affiliation(s)
- Scheila da Silva Soares
- Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil
| | | | - Francini Petrolli
- Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil
| | | | - Silvana Almeida
- Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil
| | - Marilu Fiegenbaum
- Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil.
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Carnauba RA, Sarti FM, Hassimotto NMA, Lajolo FM. Bioactive Compounds Intake of the Brazilian Population According to Geographic Region. PLANTS (BASEL, SWITZERLAND) 2023; 12:2414. [PMID: 37446975 DOI: 10.3390/plants12132414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/15/2023] [Accepted: 06/17/2023] [Indexed: 07/15/2023]
Abstract
Studies have been conducted in order to estimate bioactive compound consumption across populations, with substantial disparities according to the origin of the cohort examined. In this sense, Brazil is a continental country with marked differences in food plant availability across geographic regions. We aimed to estimate the bioactive compound intake according to Brazilian geographic region, as well as to determine the major contributors. Data were obtained from the National Dietary Survey 2017-2018, a cross-sectional population-based study including data on the individual food intake of 46,164 subjects aged ≥10 years. The consumption of polyphenols (total and classes) was significantly higher in the South compared with other regions (p = 0.0001). Total carotenoid intake was higher in the Midwest, followed by the Southeast (p = 0.0001). Tea was the main supplier of total polyphenol intake in the South, whereas coffee contributed the most to total polyphenol intake in other Brazilian regions. Açaí, caja juice, mango and corn were important suppliers of carotenoid intake in the North and Northeast. Bioactive compound intake presented variations according to Brazilian region, and individuals living in the South, Midwest and Southeast may experience higher bioactive-dense diets. We highlight the potential of many food plants for sustained explorations to the development of marketable products, possibly increasing the bioactive compound intake.
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Affiliation(s)
- Renata A Carnauba
- Department of Food Science and Experimental Nutrition, School of Pharmaceutical Sciences, University of São Paulo, São Paulo 05508-220, Brazil
- Food Research Center, CEPID-FAPESP (Research Innovation and Dissemination Centers, São Paulo Research Foundation), São Paulo 05508-020, Brazil
| | - Flavia M Sarti
- Center for Research in Complex Systems Modeling, School of Arts, Sciences and Humanities, University of São Paulo, São Paulo 05508-220, Brazil
| | - Neuza M A Hassimotto
- Department of Food Science and Experimental Nutrition, School of Pharmaceutical Sciences, University of São Paulo, São Paulo 05508-220, Brazil
- Food Research Center, CEPID-FAPESP (Research Innovation and Dissemination Centers, São Paulo Research Foundation), São Paulo 05508-020, Brazil
| | - Franco M Lajolo
- Department of Food Science and Experimental Nutrition, School of Pharmaceutical Sciences, University of São Paulo, São Paulo 05508-220, Brazil
- Food Research Center, CEPID-FAPESP (Research Innovation and Dissemination Centers, São Paulo Research Foundation), São Paulo 05508-020, Brazil
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25
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Bertholim-Nasciben L, Scliar MO, Debortoli G, Thiruvahindrapuram B, Scherer SW, Duarte YAO, Zatz M, Suarez-Kurtz G, Parra EJ, Naslavsky MS. Characterization of pharmacogenomic variants in a Brazilian admixed cohort of elderly individuals based on whole-genome sequencing data. Front Pharmacol 2023; 14:1178715. [PMID: 37234706 PMCID: PMC10206227 DOI: 10.3389/fphar.2023.1178715] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 04/10/2023] [Indexed: 05/28/2023] Open
Abstract
Introduction: Research in the field of pharmacogenomics (PGx) aims to identify genetic variants that modulate response to drugs, through alterations in their pharmacokinetics (PK) or pharmacodynamics (PD). The distribution of PGx variants differs considerably among populations, and whole-genome sequencing (WGS) plays a major role as a comprehensive approach to detect both common and rare variants. This study evaluated the frequency of PGx markers in the context of the Brazilian population, using data from a population-based admixed cohort from Sao Paulo, Brazil, which includes variants from WGS of 1,171 unrelated, elderly individuals. Methods: The Stargazer tool was used to call star alleles and structural variants (SVs) from 38 pharmacogenes. Clinically relevant variants were investigated, and the predicted drug response phenotype was analyzed in combination with the medication record to assess individuals potentially at high-risk of gene-drug interaction. Results: In total, 352 unique star alleles or haplotypes were observed, of which 255 and 199 had a frequency < 0.05 and < 0.01, respectively. For star alleles with frequency > 5% (n = 97), decreased, loss-of-function and unknown function accounted for 13.4%, 8.2% and 27.8% of alleles or haplotypes, respectively. Structural variants (SVs) were identified in 35 genes for at least one individual, and occurred with frequencies >5% for CYP2D6, CYP2A6, GSTM1, and UGT2B17. Overall 98.0% of the individuals carried at least one high risk genotype-predicted phenotype in pharmacogenes with PharmGKB level of evidence 1A for drug interaction. The Electronic Health Record (EHR) Priority Result Notation and the cohort medication registry were combined to assess high-risk gene-drug interactions. In general, 42.0% of the cohort used at least one PharmGKB evidence level 1A drug, and 18.9% of individuals who used PharmGKB evidence level 1A drugs had a genotype-predicted phenotype of high-risk gene-drug interaction. Conclusion: This study described the applicability of next-generation sequencing (NGS) techniques for translating PGx variants into clinically relevant phenotypes on a large scale in the Brazilian population and explores the feasibility of systematic adoption of PGx testing in Brazil.
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Affiliation(s)
- Luciana Bertholim-Nasciben
- School of Public Health, University of São Paulo, São Paulo, Brazil
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Marilia O. Scliar
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Guilherme Debortoli
- Department of Anthropology, University of Toronto at Mississauga, Mississauga, ON, Canada
| | | | - Stephen W. Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Yeda A. O. Duarte
- Medical-Surgical Nursing Department, School of Nursing, University of São Paulo, São Paulo, Brazil
| | - Mayana Zatz
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Guilherme Suarez-Kurtz
- Divisão de Pesquisa Clínica e Desenvolvimento Tecnológico, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Esteban J. Parra
- Department of Anthropology, University of Toronto at Mississauga, Mississauga, ON, Canada
| | - Michel S. Naslavsky
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
- Hospital Israelita Albert Einstein, São Paulo, Brazil
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Suarez-Kurtz G, Fernandes VC, Elias ABR. Implementation of DPYD Genotyping in Admixed American Populations: Brazil as a Model Case. Clin Pharmacol Ther 2023. [PMID: 37161547 DOI: 10.1002/cpt.2921] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 03/21/2023] [Indexed: 05/11/2023]
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Lana-Peixoto MA, Talim NC, Callegaro D, Marques VD, Damasceno A, Becker J, Gonçalves MVM, Sato H. Neuromyelitis optica spectrum disorders with a benign course. Analysis of 544 patients. Mult Scler Relat Disord 2023; 75:104730. [PMID: 37156036 DOI: 10.1016/j.msard.2023.104730] [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: 02/02/2023] [Revised: 03/16/2023] [Accepted: 04/23/2023] [Indexed: 05/10/2023]
Abstract
BACKGROUND Neuromyelitis optica spectrum disorders (NMOSD) most commonly cause severe disability which is related to disease attacks. However, some patients retain good neurological function for a long time after disease onset. OBJECTIVES To determine the frequency, demographic and the clinical features of good outcome NMOSD, and analyze their predictive factors. METHODS We selected patients who met the 2015 International Panel for NMOSD diagnostic criteria from seven MS Centers. Assessed data included age at disease onset, sex, race, number of attacks within the first and three years from onset, annualized relapsing rate (ARR), total number of attacks, aquaporin-IgG serum status, presence of cerebrospinal fluid (CSF)-specific oligoclonal bands (OCB) and the Expanded Disability Status Scale (EDSS) score at the last follow-up visit. NMOSD was classified as non-benign if patients developed sustained EDSS score >3.0 during the disease course, or benign if patients had EDSS score ≤3.0 after ≥15 years from disease onset. Patients with EDSS <3.0 and disease duration shorter than 15 years were not qualified for classification. We compared the demographic and clinical characteristics of benign and non-benign NMOSD. Logistic regression analysis identified predictive factors of outcome. RESULTS There were 16 patients with benign NMOSD (3% of the entire cohort; 4.2% of those qualified for classification; and 4.1% of those who tested positive for aquaporin 4-IgG), and 362 (67.7%) with non-benign NMOSD, whereas 157 (29.3%) did not qualify for classification. All patients with benign NMOSD were female, 75% were Caucasian, 75% tested positive for AQP4-IgG, and 28.6% had CSF-specific OCB. Regression analysis showed that female sex, pediatric onset, and optic neuritis, area postrema syndrome, and brainstem symptoms at disease onset, as well as fewer relapses in the first year and three years from onset, and CSF-specific OCB were more commonly found in benign NMOSD, but the difference did not reach statistical significance. Conversely, non-Caucasian race (OR: 0.29, 95% CI: 0.07-0.99; p = 0.038), myelitis at disease presentation (OR: 0.07, 95% CI: 0.01-0.52; p <0.001), and high ARR (OR: 0.07, 95% CI: 0.01-0.67; p = 0.011) were negative risk factors for benign NMOSD. CONCLUSION Benign NMOSD is very rare and occurs more frequently in Caucasians, patients with low ARR, and those who do not have myelitis at disease onset.
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Affiliation(s)
| | - Natália C Talim
- Federal University of Minas Gerais Medical School, Belo Horizonte, MG, Brazil
| | | | | | | | - Jefferson Becker
- Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | | | - Henry Sato
- Neurological Institute of Curitiba, Curitiba, PR, Brazil
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Resende GG, Saad CGS, de Oliveira DCM, de Sousa Bueno Filho JS, Sampaio-Barros PD, de Medeiros Pinheiro M. HLA-B27 positivity in a large miscegenated population of 5,389,143 healthy blood marrow donors in Brazil. Adv Rheumatol 2023; 63:16. [PMID: 37081582 DOI: 10.1186/s42358-023-00302-6] [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: 02/15/2023] [Accepted: 04/13/2023] [Indexed: 04/22/2023] Open
Abstract
BACKGROUND The prevalence of HLA-B27 gene positivity in healthy Caucasian communities varies between 8 and 14%. However, there is a lack of information in countries with a high rate of miscegenation, such as Brazil. AIM To estimate the frequency of HLA-B27 in the Brazilian general population using a large national registry database. METHODS This is a cross-sectional ecological study using the Brazilian Registry of Volunteer Bone Marrow Donors (REDOME) database on HLA-B27 allelic frequency and proportion of positives of healthy donors (18-60 years old). Data were analyzed according to sex, age, race (by self-reported skin color recommended by the Brazilian Institute of Geography and Statistics - IBGE), and geographic region of residence. RESULTS From 1994 to 2022, a total of 5,389,143 healthy bone marrow donors were included. The overall positivity for HLA-B27 was 4.35% (CI 95% 4.32-4.37%), regardless of sex and age (57.2% were women, mean age was 41.7yo). However, there was a difference between races: 4.85% in Whites; 2.92% in Blacks; 3.76% in Pardos (Browns i.e. mixed races); 3.95% in Amarelos (Yellows i.e. Asian Brazilians); and 3.18% in Indigenous. There was also a difference regarding geographic region of residence (North: 3.62%; Northeast: 3.63%; Southeast: 4.29%; Midwest: 4.5% and 5.25% in South). The homozygosity rate for the HLA-B27 was 1.32% of all the positives and only 0.06% in the general population. CONCLUSIONS Our findings provide the first Brazilian national prevalence for HLA-B27 in 4.35%. There is a gradient gene positivity from North to South, suggesting that the genetic background related to the miscegenation due to colonization, slavery, and some later waves of immigration together with internal migratory flows, could explain our findings.
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Affiliation(s)
- Gustavo Gomes Resende
- Hospital das Clínicas - Universidade Federal de Minas Gerais (HC-UFMG), Al. Álvaro Celso 175 / 2º floor, Belo Horizonte, MG, Brasil.
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da Costa Vieira RA, Sant'Anna D, Laus AC, Bacchi CE, Silva RJC, de Oliveira-Junior I, da Silva VD, Pereira R, Reis RM. Genetic Ancestry of 1127 Brazilian Breast Cancer Patients and Its Correlation With Molecular Subtype and Geographic Region. Clin Breast Cancer 2023:S1526-8209(23)00086-1. [PMID: 37183096 DOI: 10.1016/j.clbc.2023.04.001] [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: 01/03/2022] [Revised: 03/25/2023] [Accepted: 04/09/2023] [Indexed: 05/16/2023]
Abstract
PURPOSE Breast cancer molecular subtypes show significant differences in different ethnic groups in the United States, but no study has evaluated genetic ancestry in breast cancer in Brazilian women. METHODS Breast cancer patients from distinct parts of Brazil were evaluated. Molecular subtypes were determined by immunohistochemistry. Genetic ancestry was evaluated using a panel of 46 AIMs (ancestry informative markers), which classified genetic ancestry as European, African, Asian, and Amerindian. PCR products were subjected to capillary electrophoresis and analyzed using GeneMapper 4.0 software. Ancestry was evaluated with Structure v.2.3.3 software. Ancestry was tested for correlations with geographic region and molecular subtype. The chi-square test and ANOVA with Bonferroni adjustment were applied. RESULTS Genetic ancestry and clinical data were evaluated in 1127 patients. Higher rates of self-reported white ethnicity, European ancestry, and HER-2- luminal tumors were identified in the South region, which may influence age at diagnosis and result in a higher rate of early tumors. Conversely, higher rates of African ancestry in the North and Northeast regions, self-reported nonwhite ethnicity, HER-2+ tumors, and triple-negative tumors were noted. Triple-negative and HER-2+ tumors were associated with higher advanced and metastatic disease rates at diagnosis, with triple-negative tumors being more frequent in young women. CONCLUSION Differences in genetic ancestry, self-reported ethnicity, and molecular subtype were found between Brazilian demographic regions. Knowledge of these features may contribute to a better understanding of age at diagnosis and the molecular distribution of breast cancer in Brazil.
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Affiliation(s)
- René Aloisio da Costa Vieira
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP, Brazil; Postgraduate Program in Oncology, Barretos Cancer Hospital, Barretos, SP, Brazil; Postgraduate Program in Tocogynecology, Botucatu School of Medicine, Botucatu, SP, Brazil.
| | - Débora Sant'Anna
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP, Brazil
| | - Ana Carolina Laus
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP, Brazil
| | | | | | - Idam de Oliveira-Junior
- Postgraduate Program in Oncology, Barretos Cancer Hospital, Barretos, SP, Brazil; Postgraduate Program in Tocogynecology, Botucatu School of Medicine, Botucatu, SP, Brazil
| | - Vinicius Duval da Silva
- Postgraduate Program in Oncology, Barretos Cancer Hospital, Barretos, SP, Brazil; Bacchi Laboratory, Botucatu, SP, Brazil; Department of Pathology, Barretos Cancer Hospital, Barretos, SP, Brazil
| | | | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP, Brazil; Postgraduate Program in Oncology, Barretos Cancer Hospital, Barretos, SP, Brazil; Life and Health Sciences Research Institute (ICVS), Medical School, University of Minho, Braga, Portugal; ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
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30
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Gumes-Felix HM, Ramalho RJR, Melo EV, Matos DM, Menezes NV, Oliveira CRP, Campos VC, Santos EG, da S Marques D, Vaz Dos Santos B, de Andrade BMR, Aguiar-Oliveira MH. Predictive factors for the diagnosis of permanent congenital hypothyroidism and its temporal changes in Sergipe, Brazil - A real-life retrospective study. ARCHIVES OF ENDOCRINOLOGY AND METABOLISM 2023; 67:189-196. [PMID: 36651708 PMCID: PMC10689040 DOI: 10.20945/2359-3997000000579] [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: 05/23/2022] [Accepted: 10/03/2022] [Indexed: 01/19/2023]
Abstract
Objective Congenital hypothyroidism (CH) can be permanent (PCH) or transient (TCH). While the importance of thyroxine in myelination of the brain is undisputed, the benefits to neurodevelopmental outcomes of TCH treatment are controversial. Our objectives were to determine predictive factors for PCH and verify its prevalence changes over time. Subjects and methods A total of 165 children were evaluated at 3 years of age to verify the diagnosis of PCH. 130 were submitted to a two-step cluster analysis, with the aim of grouping them into homogeneous clusters. The mean incidence of PCH and TCH was calculated from 2004 to 2010 and 2011 to 2015. Results Sixty-six children were diagnosed with PCH, and 99 were diagnosed with TCH. Eighty-one percent of PCH children and all TCH children with thyroid imaging had glands in situ. Eighty children (61.5%) were in Cluster 1, 8 children (6.2%) were in Cluster 2 and 42 children (32.3%) were in Cluster 3. No children had PCH in Cluster 1, while 87.5% of children in Cluster 2 and all children in Cluster 3 had PCH. The most important predictor for PCH was the initial serum TSH, which was marginally higher in importance than the blood spot TSH, followed by the initial serum free T4. The mean incidence of PCH (odds ratio: 1.95, 95% CI 1.36 to 2.95, p < 0.0001) and TCH (odds ratio 1.33, 95%, CI 1.02 to 1.77, p = 0,038) increased over time. Conclusion The most important PCH predictors are the initial serum TSH and the blood spot TSH. The mean incidence of both PCH and TCH in our series increased.
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Affiliation(s)
- Hérika M Gumes-Felix
- Divisão de Endocrinologia, Programa de Pós-graduação em Ciências da Saúde, Universidade Federal de Sergipe, Aracaju, SE, Brasil
| | - Roberto J R Ramalho
- Departamento de Medicina, Universidade Federal de Sergipe, Aracaju, SE, Brasil
| | - Enaldo V Melo
- Departamento de Medicina, Universidade Federal de Sergipe, Aracaju, SE, Brasil
| | - Diana M Matos
- Divisão de Endocrinologia, Programa de Pós-graduação em Ciências da Saúde, Universidade Federal de Sergipe, Aracaju, SE, Brasil
| | - Nelmo V Menezes
- Departamento de Medicina, Universidade Federal de Sergipe, Aracaju, SE, Brasil
| | - Carla R P Oliveira
- Divisão de Endocrinologia, Programa de Pós-graduação em Ciências da Saúde, Universidade Federal de Sergipe, Aracaju, SE, Brasil
| | - Viviane C Campos
- Divisão de Endocrinologia, Programa de Pós-graduação em Ciências da Saúde, Universidade Federal de Sergipe, Aracaju, SE, Brasil
| | - Elenilde G Santos
- Divisão de Endocrinologia, Programa de Pós-graduação em Ciências da Saúde, Universidade Federal de Sergipe, Aracaju, SE, Brasil
| | | | | | - Bruna M R de Andrade
- Departamento de Fonoaudiologia, Programa de Pós-graduação em Ciências da Saúde, Universidade Federal de Sergipe, Aracaju, SE, Brasil
| | - Manuel H Aguiar-Oliveira
- Divisão de Endocrinologia, Programa de Pós-graduação em Ciências da Saúde, Universidade Federal de Sergipe, Aracaju, SE, Brasil,
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Lima ÉRG, Queiroz MAF, Lima SS, Machado LFA, Cayres-Vallinoto IMV, Vallinoto ACR, Figueiredo FADPL, Guerreiro JF, Guimarães Ishak MDO, Ishak R. CCR5∆32 and SDF1 3'A: Gene Variants, Expression and Influence on Biological Markers for the Clinical Progression to AIDS among HIV-1 Virus Controllers in a Mixed Population of the Amazon Region of Brazil. Int J Mol Sci 2023; 24:ijms24054958. [PMID: 36902388 PMCID: PMC10003039 DOI: 10.3390/ijms24054958] [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: 12/30/2022] [Revised: 01/24/2023] [Accepted: 01/26/2023] [Indexed: 03/08/2023] Open
Abstract
CCR5Δ32 and SDF1-3'A polymorphisms were investigated in a cohort of viremia controllers, without the use of therapy, along with their influence on CD4+ T lymphocytes (TLs), CD8+ TLs, and plasma viral load (VL). The samples were analyzed from 32 HIV-1-infected individuals classified as viremia controllers 1 and 2 and viremia non-controllers, from both sexes, mostly heterosexuals, paired with 300 individuals from a control group. CCR5∆32 polymorphism was identified by PCR amplification of a fragment of 189 bp for the wild-type allele and 157 bp for the allele with the ∆32 deletion. SDF1-3'A polymorphism was identified by PCR, followed by enzymatic digestion (restriction fragment length polymorphism) with the Msp I enzyme. The relative quantification of gene expression was performed by real-time PCR. The distribution of allele and genotype frequencies did not show significant differences between the groups. The gene expression of CCR5 and SDF1 was not different between the profiles of AIDS progression. There was no significant correlation between the progression markers (CD4+ TL/CD8+ TL and VL) and the CCR5∆32 polymorphism carrier status. The 3'A allele variant was associated with a marked loss of CD4+ TLs and a higher plasma VL. Neither CCR5∆32 nor SDF1-3'A was associated with viremia control or the controlling phenotype.
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Affiliation(s)
- Érica Ribeiro Gomes Lima
- Virus Laboratory, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil
| | - Maria Alice Freitas Queiroz
- Virus Laboratory, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil
- Correspondence: ; Tel.: +55-91-98864-4259
| | - Sandra Souza Lima
- Virus Laboratory, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil
| | | | | | | | | | - João Farias Guerreiro
- Human and Medical Genetics Laboratory, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil
| | | | - Ricardo Ishak
- Virus Laboratory, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil
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Joerin-Luque IA, Sukow NM, Bucco ID, Tessaro JG, Lopes CVG, Barbosa AAL, Beltrame MH. Ancestry, diversity, and genetics of health-related traits in African-derived communities (quilombos) from Brazil. Funct Integr Genomics 2023; 23:74. [PMID: 36867305 PMCID: PMC9982798 DOI: 10.1007/s10142-023-00999-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/22/2023] [Accepted: 02/23/2023] [Indexed: 03/04/2023]
Abstract
Brazilian quilombos are communities formed by enslaved Africans and their descendants all over the country during slavery and shortly after its abolition. Quilombos harbor a great fraction of the largely unknown genetic diversity of the African diaspora in Brazil. Thus, genetic studies in quilombos have the potential to provide important insights not only into the African roots of the Brazilian population but also into the genetic bases of complex traits and human adaptation to diverse environments. This review summarizes the main results of genetic studies performed on quilombos so far. Here, we analyzed the patterns of African, Amerindian, European, and subcontinental ancestry (within Africa) of quilombos from the five different geographic regions of Brazil. In addition, uniparental markers (from the mtDNA and the Y chromosome) studies are analyzed together to reveal demographic processes and sex-biased admixture that occurred during the formation of these unique populations. Lastly, the prevalence of known malaria-adaptive African mutations and other African-specific variants discovered in quilombos, as well as the genetic bases of health-related traits, are discussed here, together with their implication for the health of populations of African descent.
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Affiliation(s)
- Iriel A Joerin-Luque
- Programa de Pós-Graduação Em Genética, Laboratório de Genética Molecular Humana, Departamento de Genética, Universidade Federal Do Paraná (UFPR), Centro Politécnico, Jardim das Américas, Curitiba, Paraná, 81531-980, Brazil.
| | - Natalie Mary Sukow
- Programa de Pós-Graduação Em Genética, Laboratório de Genética Molecular Humana, Departamento de Genética, Universidade Federal Do Paraná (UFPR), Centro Politécnico, Jardim das Américas, Curitiba, Paraná, 81531-980, Brazil
| | - Isabela Dall'Oglio Bucco
- Laboratório de Genética Molecular Humana, Departamento de Genética, Universidade Federal Do Paraná (UFPR), Centro Politécnico, Jardim das Américas, Curitiba, Paraná, 81531-980, Brazil
| | - Joana Gehlen Tessaro
- Laboratório de Genética Molecular Humana, Departamento de Genética, Universidade Federal Do Paraná (UFPR), Centro Politécnico, Jardim das Américas, Curitiba, Paraná, 81531-980, Brazil
| | | | - Ana Angélica Leal Barbosa
- Laboratório de Biologia E Genética Humana, Departamento de Ciências Biológicas, Universidade Estadual Do Sudoeste da Bahia (UESB), Campus de Jequié, Bahia, Brazil
| | - Marcia H Beltrame
- Programa de Pós-Graduação Em Genética, Laboratório de Genética Molecular Humana, Departamento de Genética, Universidade Federal Do Paraná (UFPR), Centro Politécnico, Jardim das Américas, Curitiba, Paraná, 81531-980, Brazil
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Felkl AB, Avila E, Gastaldo AZ, Lindholz CG, Dorn M, Alho CS. Ancestry resolution of South Brazilians by forensic 165 ancestry-informative SNPs panel. Forensic Sci Int Genet 2023; 64:102838. [PMID: 36736201 DOI: 10.1016/j.fsigen.2023.102838] [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: 08/24/2022] [Revised: 01/15/2023] [Accepted: 01/22/2023] [Indexed: 01/24/2023]
Abstract
Forensic DNA phenotyping (FDP) includes biogeographic ancestry (BGA) inference and externally visible characteristics (EVCs) prediction directly from an evidential DNA sample as alternatives to provide valuable intelligence when conventional DNA profiling fails to achieve identification. In this context, the application of Massively Parallel Sequencing (MPS) methodologies, which enables simultaneous typing of multiple samples and hundreds of forensic markers, has been gradually implemented in forensic genetic casework. The Precision ID Ancestry Panel (Thermo Fisher Scientific, Waltham, USA) is a forensic multiplex assay consisting of 165 autosomal SNPs designed to provide biogeographic ancestry information. In this work, a sample of 250 individuals from Rio Grande do Sul (RS) State, southern Brazil, apportioned into four main population groups (African-, European-, Amerindian-, and Admixed-derived Gauchos), was evaluated with this panel, to assess the feasibility of this approach in a highly heterogeneous population. Forensic descriptive parameters estimated for each population group revealed that this panel has enough polymorphic and informative SNPs to be used as a supplementary instrument in forensic individual identification and kinship testing regardless of ethnicity. No statistically significant deviation from Hardy-Weinberg equilibrium was observed after Bonferroni correction. However, seven loci pairs displayed linkage disequilibrium in pairwise LD testing (p < 3.70 × 10-6). Interpopulation comparisons by FST analysis, MDS plot, and STRUCTURE analysis among the four RS population groups apart and along with 89 reference worldwide populations demonstrated that Admixed- and African-derived Gauchos present the highest levels of admixture and population stratification, whereas European- and Amerindian-derived exhibit a more homogeneous genetic conformation.
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Affiliation(s)
- Aline Brugnera Felkl
- Forensic Genetics Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, RS, Brazil; National Institute of Science and Technology - Forensic Science, Porto Alegre, RS, Brazil.
| | - Eduardo Avila
- Forensic Genetics Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, RS, Brazil; Technical Scientific Section, Federal Police Department in Rio Grande do Sul State, Porto Alegre, RS, Brazil; National Institute of Science and Technology - Forensic Science, Porto Alegre, RS, Brazil
| | - André Zoratto Gastaldo
- Forensic Genetics Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, RS, Brazil; National Institute of Science and Technology - Forensic Science, Porto Alegre, RS, Brazil
| | - Catieli Gobetti Lindholz
- Forensic Genetics Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Márcio Dorn
- Forensic Genetics Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, RS, Brazil; National Institute of Science and Technology - Forensic Science, Porto Alegre, RS, Brazil; Institute of Informatics, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Clarice Sampaio Alho
- Forensic Genetics Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, RS, Brazil; National Institute of Science and Technology - Forensic Science, Porto Alegre, RS, Brazil
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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: 9] [Impact Index Per Article: 9.0] [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
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Laczynski CMM, Machado Filho CDS, Miot HA, Christofolini DM, Rodart IF, Criado PR. Prevalence of filaggrin gene polymorphisms (exon-3) in patients with atopic dermatitis in a multiracial Brazilian population. An Bras Dermatol 2023; 98:236-239. [PMID: 36669978 PMCID: PMC9984714 DOI: 10.1016/j.abd.2022.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/11/2022] [Accepted: 04/23/2022] [Indexed: 01/20/2023] Open
Affiliation(s)
| | | | - Hélio Amante Miot
- Department of Dermatology, Faculty of Medicine, Universidade Estadual Paulista, Botucatu, SP, Brazil
| | | | | | - Paulo Ricardo Criado
- Discipline of Dermatology, Centro Universitário Faculdade de Medicina do ABC, Santo André, SP, Brazil
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Quirino MG, Neto QADL, Zacarias JMV, Góis KS, Maria Sell A, Visentainer JEL. Low-cost molecular methodology for blood group antigens identification and genotyping contribution to transfusion efficacy in multiple transfused patients. Expert Rev Mol Diagn 2022; 22:1-9. [PMID: 36333936 DOI: 10.1080/14737159.2022.2144236] [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: 07/13/2022] [Accepted: 11/02/2022] [Indexed: 11/07/2022]
Abstract
BACKGROUND Blood transfusions usually result in the production of alloantibodies, complicating subsequent transfusions. Many blood group systems, in addition to ABO and Rh, can lead to the production of irregular antibodies in multiple transfused patients. OBJECTIVES The aim of this work was to standardize a molecular biology methodology for identified some alleles of KEL, FY, JK and DI blood group system; the transfusion efficacy of chronically transfused patients with phenotype-matched blood was also evaluated. METHODS A PCR-SSP was developed and validated using Sanger sequencing. The genotype and frequencies of 141 multiple transfused patients treated at blood banks of Maringá were compared with the blood donor's population to assess the availability of compatible blood bags. The clinical history of 29 patients on a phenotype-compatible transfusion regimen was followed to assess pre- and post-genotyping alloimmunization. RESULTS The PCR-SSP was effective in identifying the genotypes under study. Significant differences were observed in genotype and allele frequencies for FY and JK. Compatible bags were identified for all patients. Most patients (93.1%) did not develop new alloantibodies after erythrocyte genotyping. CONCLUSION Erythrocyte genotyping proved to be important both in the search for positive blood bags for rare alleles and in the prevention of alloimmunization.
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Affiliation(s)
| | - Quirino Alves de Lima Neto
- Department of Clinical Analysis and Biomedicine, Maringá State University, Maringá, Brazil
- Department of Basic Health Sciences, State University of Maringá, Maringá, Brazil
| | - Joana Maira Valentini Zacarias
- Department of Clinical Analysis and Biomedicine, Maringá State University, Maringá, Brazil
- Department of Basic Health Sciences, State University of Maringá, Maringá, Brazil
| | - Kelly Silvério Góis
- Department of Clinical Analysis and Biomedicine, Maringá State University, Maringá, Brazil
| | - Ana Maria Sell
- Department of Clinical Analysis and Biomedicine, Maringá State University, Maringá, Brazil
| | - Jeane Eliete Laguila Visentainer
- Department of Clinical Analysis and Biomedicine, Maringá State University, Maringá, Brazil
- Department of Basic Health Sciences, State University of Maringá, Maringá, Brazil
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da Luz Moreira A, de Campos Lobato LF, de Lima Moreira JP, Luiz RR, Elia C, Fiocchi C, de Souza HSP. Geosocial Features and Loss of Biodiversity Underlie Variable Rates of Inflammatory Bowel Disease in a Large Developing Country: A Population-Based Study. Inflamm Bowel Dis 2022; 28:1696-1708. [PMID: 35089325 DOI: 10.1093/ibd/izab346] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND The epidemiology of inflammatory bowel disease (IBD) in developing countries may uncover etiopathogenic factors. We investigated IBD prevalence in Brazil by investigating its geographic, spatial, and temporal distribution, and attempted to identify factors associated with its recent increase. METHODS A drug prescription database was queried longitudinally to identify patients and verify population distribution and density, race, urbanicity, sanitation, and Human Development Index. Prevalence was calculated using the number of IBD patients and the population estimated during the same decade. Data were matched to indices using linear regression analyses. RESULTS We identified 162 894 IBD patients, 59% with ulcerative colitis (UC) and 41% with Crohn's disease (CD). The overall prevalence of IBD was 80 per 100 000, with 46 per 100 000 for UC and 36 per 100 000 for CD. Estimated rates adjusted to total population showed that IBD more than triplicated from 2008 to 2017. The distribution of IBD demonstrated a South-to-North gradient that generally followed population apportionment. However, marked regional differences and disease clusters were identified that did not fit with conventionally accepted IBD epidemiological associations, revealing that the rise of IBD was variable. In some areas, loss of biodiversity was associated with high IBD prevalence. CONCLUSIONS When distribution is considered in the context of IBD prevalence, marked regional differences become evident. Despite a background of Westernization, hotspots of IBD are recognized that are not explained by population density, urbanicity, sanitation, or other indices but apparently are explained by biodiversity loss. Thus, the rise of IBD in developing countries is not uniform, but rather is one that varies depending on yet unexplored factors like geoecological conditions.
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Affiliation(s)
- Andre da Luz Moreira
- D'Or Institute for Research and Education, Rio de Janeiro, Brazil.,Inflammatory Bowel Disease Center, NYU Langone Health, NYU Grossman School of Medicine, New York, NY, USA
| | | | | | - Ronir Raggio Luiz
- Institute of Collective Health Studies, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Celeste Elia
- D'Or Institute for Research and Education, Rio de Janeiro, Brazil
| | - Claudio Fiocchi
- Department of Immunity & Inflammation, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Heitor Siffert Pereira de Souza
- D'Or Institute for Research and Education, Rio de Janeiro, Brazil.,Department of Clinical Medicine, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
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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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da Silva Lawisch GK, Biolchi V, Kaufmann G, Nicolai G, Capitaneo E, Rosembach TR, Zang J, Brum IS, Chies JAB. The role of FASL, BCL-2 and BAX polymorphisms in brazilian patients with prostate cancer and benign prostatic hyperplasia. Mol Biol Rep 2022; 49:9445-9451. [DOI: 10.1007/s11033-022-07805-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 06/22/2022] [Accepted: 07/15/2022] [Indexed: 11/30/2022]
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Sampaio B, Dos Santos Silva AM, de Sá Paiva Leitão Júnior S, de Souza Liberal AT, da Cruz HLA, de Queiroz Balbino V. Allelic frequencies distribution and forensic parameters of 23 autosomal short tandem repeats in the population of the State of Pernambuco, Brazil. Leg Med (Tokyo) 2022; 59:102112. [PMID: 35839577 DOI: 10.1016/j.legalmed.2022.102112] [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: 02/11/2022] [Revised: 05/30/2022] [Accepted: 07/01/2022] [Indexed: 10/31/2022]
Abstract
Located in the Northeast Region, the Pernambuco State is one of the 27 federative units of Brazil. Here, we determined populational data for 23 short tandem repeat (STR) markers - CSF1PO, FGA, TH01, TPOX, vWA, D1S1656, D2S1338, D2S441, D3S1358, D5S818, D7S820, D8S1179, D10S1248, D12S391, D13S317, D16S539, D18S51, D19S433, D21S11, D22S1045, PENTA D, PENTA E and SE33 - of the Pernambuco population. The sample consisted of 767 healthy, adult, unrelated individuals (437 males, 330 females) born and resident in the State of Pernambuco. STRs were amplified using three multiplex kits, according to the availability: PowerPlex® Fusion 6C System (Promega Corporation), PowerPlex® Fusion System (Promega Corporation) and GlobalFiler™ Express (Thermo Fisher Scientific). Allelic frequencies, forensic parameters and Hardy-Weinberg equilibrium determinations were estimated for all the 23 loci. No deviations from the Hardy-Weinberg equilibrium were observed for any of the markers, after Bonferroni correction. We observed that the most and less informative markers were SE33 and TPOX, respectively. The combined power of discrimination (CPD) was 0.99999999999999999999999999999, and the combined power of exclusion (CPE) was 0.99999999997. The cumulative typical paternity index was 37,919,301,869.3021. Interpopulation analyses (Nei's genetic distance) based on the expanded CODIS core loci was performed between the Pernambuco sample and other global populations. Pernambuco was the closest Brazilian population to African group and stayed distant from the Native American group. This work contributed to show that a panel of 23 autosomal STR loci is very informative, being able for forensic applications related in this population.
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Affiliation(s)
- Bruno Sampaio
- Laboratory of Bioinformatics and Evolutionary Biology, Department of Genetics, Federal University of Pernambuco, Recife, Pernambuco (PE), Brazil.
| | - Abigail Marcelino Dos Santos Silva
- Laboratory of Bioinformatics and Evolutionary Biology, Department of Genetics, Federal University of Pernambuco, Recife, Pernambuco (PE), Brazil
| | - Sérgio de Sá Paiva Leitão Júnior
- Laboratory of Bioinformatics and Evolutionary Biology, Department of Genetics, Federal University of Pernambuco, Recife, Pernambuco (PE), Brazil
| | - Anna Theresa de Souza Liberal
- Laboratory of Bioinformatics and Evolutionary Biology, Department of Genetics, Federal University of Pernambuco, Recife, Pernambuco (PE), Brazil
| | - Heidi Lacerda Alves da Cruz
- Laboratory of Bioinformatics and Evolutionary Biology, Department of Genetics, Federal University of Pernambuco, Recife, Pernambuco (PE), Brazil
| | - Valdir de Queiroz Balbino
- Laboratory of Bioinformatics and Evolutionary Biology, Department of Genetics, Federal University of Pernambuco, Recife, Pernambuco (PE), Brazil
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da Cruz PRS, Ananina G, Secolin R, Gil-da-Silva-Lopes VL, Lima CSP, de França PHC, Donatti A, Lourenço GJ, de Araujo TK, Simioni M, Lopes-Cendes I, Costa FF, de Melo MB. Demographic history differences between Hispanics and Brazilians imprint haplotype features. G3 GENES|GENOMES|GENETICS 2022; 12:6576632. [PMID: 35511163 PMCID: PMC9258545 DOI: 10.1093/g3journal/jkac111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 04/27/2022] [Indexed: 11/24/2022]
Abstract
Admixture is known to greatly impact the genetic landscape of a population and, while genetic variation underlying human phenotypes has been shown to differ among populations, studies on admixed subjects are still scarce. Latin American populations are the result of complex demographic history, such as 2 or 3-way admixing events, bottlenecks and/or expansions, and adaptive events unique to the American continent. To explore the impact of these events on the genetic structure of Latino populations, we evaluated the following haplotype features: linkage disequilibrium, shared identity by descent segments, runs of homozygosity, and extended haplotype homozygosity (integrated haplotype score) in Latinos represented in the 1000 Genome Project along with array data from 171 Brazilians sampled in the South and Southeast regions of Brazil. We found that linkage disequilibrium decay relates to the amount of American and African ancestry. The extent of identity by descent sharing positively correlates with historical effective population sizes, which we found to be steady or growing, except for Puerto Ricans and Colombians. Long runs of homozygosity, a particular instance of autozygosity, was only enriched in Peruvians and Native Americans. We used simulations to account for random sampling and linkage disequilibrium to filter positive selection indexes and found 244 unique markers under selection, 26 of which are common to 2 or more populations. Some markers exhibiting positive selection signals had estimated time to the most recent common ancestor consistent with human adaptation to the American continent. In conclusion, Latino populations present highly divergent haplotype characteristics that impact genetic architecture and underlie complex phenotypes.
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Affiliation(s)
- Pedro Rodrigues Sousa da Cruz
- Laboratory of Human Genetics, Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas—UNICAMP , Campinas, SP 13083-875, Brazil
| | - Galina Ananina
- Laboratory of Human Genetics, Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas—UNICAMP , Campinas, SP 13083-875, Brazil
| | - Rodrigo Secolin
- Department of Medical Genetics and Genomic Medicine, School of Medical Sciences, University of Campinas—UNICAMP , Campinas, SP 13083-887, Brazil
- The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN) , Campinas, SP 13083-887, Brazil
| | - Vera Lúcia Gil-da-Silva-Lopes
- Department of Medical Genetics and Genomic Medicine, School of Medical Sciences, University of Campinas—UNICAMP , Campinas, SP 13083-887, Brazil
| | - Carmen Silvia Passos Lima
- Clinical Oncology Service, Department of Internal Medicine, School of Medical Sciences, University of Campinas—UNICAMP , Campinas, SP 13083-887, Brazil
| | | | - Amanda Donatti
- Department of Medical Genetics and Genomic Medicine, School of Medical Sciences, University of Campinas—UNICAMP , Campinas, SP 13083-887, Brazil
- The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN) , Campinas, SP 13083-887, Brazil
| | - Gustavo Jacob Lourenço
- Laboratory of Cancer Genetics, School of Medical Sciences, University of Campinas—UNICAMP , Campinas, SP 13083-887, Brazil
| | - Tânia Kawasaki de Araujo
- Department of Medical Genetics and Genomic Medicine, School of Medical Sciences, University of Campinas—UNICAMP , Campinas, SP 13083-887, Brazil
| | - Milena Simioni
- Department of Medical Genetics and Genomic Medicine, School of Medical Sciences, University of Campinas—UNICAMP , Campinas, SP 13083-887, Brazil
| | - Iscia Lopes-Cendes
- Department of Medical Genetics and Genomic Medicine, School of Medical Sciences, University of Campinas—UNICAMP , Campinas, SP 13083-887, Brazil
- The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN) , Campinas, SP 13083-887, Brazil
| | - Fernando Ferreira Costa
- Hematology and Hemotherapy Center, University of Campinas—UNICAMP, Campinas, SP, 13083-878 , Brazil
| | - Mônica Barbosa de Melo
- Laboratory of Human Genetics, Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas—UNICAMP , Campinas, SP 13083-875, Brazil
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Kim T, Yoon S, Shin DE, Lee SC, Oh J, Lee SY, Kim DK, Kim S, Jung B, Kim M, Lee S. Incidence and Survival Rates of Cutaneous Melanoma in South Korea Using Nationwide Health Insurance Claims Data. Cancer Res Treat 2022; 54:937-949. [PMID: 34607396 PMCID: PMC9296926 DOI: 10.4143/crt.2021.871] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 09/25/2021] [Indexed: 11/21/2022] Open
Abstract
PURPOSE Melanoma incidence is rising worldwide along with the associated personal and socioeconomic health expenditures. We investigated the incidence and survival-rate patterns of melanoma in South Korea using nationwide data. MATERIALS AND METHODS This retrospective cohort study included patients with melanoma between 2004 and 2017, based on National Health Insurance (NHI) claims data in South Korea. The incidence, prevalence, and survival rate were analyzed along with baseline demographic characteristics. We collected solar irradiation dose (SID) and healthcare ranking score (HRS) according to the administrative district from the Korea Meteorological Administration and Korea Health Promotion Institute. The incidence and survival rates were assessed using Pearson's correlation, the Kaplan-Meier estimation, multiple linear regression, and multiple logistic regression methods. RESULTS Twenty-five thousand, five hundred ninety-one patients with melanoma were diagnosed during the study period. The age-standardized incidence of melanoma steadily increased from 2004 to 2017 from 2.6 to 3.0/100,000/yr. The incidence of melanoma increased with significantly higher income (p < 0.05). The prevalence followed a similar pattern as the incidence. According to multivariate analysis, HRS significantly influenced the incidence of melanoma in high sun-exposed sites (p < 0.001). There was no significant change in annual mortality. Women had a higher 5-year survival rate than men (78.4% vs. 72.8%). Mortality by the administrative district was highly correlated with HRS. CONCLUSION The incidence of melanoma is increasing in South Korea. A low HRS is associated with both higher incidence and mortality. The findings of this study could be utilized as a guideline for treating melanoma patients.
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Affiliation(s)
- TaeHo Kim
- Department of Orthopaedic Surgery, CHA Bundang Medical Center, CHA University, Seongnam,
Korea
| | - Siyeong Yoon
- Department of Orthopaedic Surgery, CHA Bundang Medical Center, CHA University, Seongnam,
Korea
| | - Dong-Eun Shin
- Department of Orthopaedic Surgery, CHA Bundang Medical Center, CHA University, Seongnam,
Korea
| | - Sang Cheol Lee
- Department of Orthopaedic Surgery, CHA Bundang Medical Center, CHA University, Seongnam,
Korea
| | - Jisu Oh
- Department of Internal Medicine Yongin Severance Hospital, Yonsei University College of Medicine, Yongin,
Korea
| | - So-Young Lee
- Department of Internal Medicine, CHA Bundang Medical Center CHA University, Seongnam,
Korea
| | - Do Kyung Kim
- CHA Graduate School of Medicine, Seongnam,
Korea
| | - Segi Kim
- Department of Orthopaedic Surgery, CHA Bundang Medical Center, CHA University, Seongnam,
Korea
| | - Bosung Jung
- Department of Orthopaedic Surgery, CHA Bundang Medical Center, CHA University, Seongnam,
Korea
| | - Minsup Kim
- inCerebro Drug Discovery Institute, inCerebro Co., Ltd., Seoul,
Korea
| | - Soonchul Lee
- Department of Orthopaedic Surgery, CHA Bundang Medical Center, CHA University, Seongnam,
Korea
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Ossa Gomez CA, Achatz MI, Hurtado M, Sanabria-Salas MC, Sullcahuaman Y, Chávarri-Guerra Y, Dutil J, Nielsen SM, Esplin ED, Michalski ST, Bristow SL, Hatchell KE, Nussbaum RL, Pineda-Alvarez DE, Ashton-Prolla P. Germline Pathogenic Variant Prevalence Among Latin American and US Hispanic Individuals Undergoing Testing for Hereditary Breast and Ovarian Cancer: A Cross-Sectional Study. JCO Glob Oncol 2022; 8:e2200104. [PMID: 35867948 PMCID: PMC9812461 DOI: 10.1200/go.22.00104] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/13/2022] [Accepted: 06/15/2022] [Indexed: 01/07/2023] Open
Abstract
PURPOSE To report on pathogenic germline variants detected among individuals undergoing genetic testing for hereditary breast and/or ovarian cancer (HBOC) from Latin America and compare them with self-reported Hispanic individuals from the United States. METHODS In this cross-sectional study, unrelated individuals with a personal/family history suggestive of HBOC who received clinician-ordered germline multigene sequencing were grouped according to the location of the ordering physician: group A, Mexico, Central America, and the Caribbean; group B, South America; and group C, United States with individuals who self-reported Hispanic ethnicity. Relatives who underwent cascade testing were analyzed separately. RESULTS Among 24,075 unrelated probands across all regions, most were female (94.9%) and reported a personal history suggestive of HBOC (range, 65.0%-80.6%); the mean age at testing was 49.1 ± 13.1 years. The average number of genes analyzed per patient was highest in group A (A 63 ± 28, B 56 ± 29, and C 40 ± 28). Between 9.1% and 18.7% of patients had pathogenic germline variants in HBOC genes (highest yield in group A), with the majority associated with high HBOC risk. Compared with US Hispanics individuals the overall yield was significantly higher in both Latin American regions (A v C P = 1.64×10-9, B v C P < 2.2×10-16). Rates of variants of uncertain significance were similar across all three regions (33.7%-42.6%). Cascade testing uptake was low in all regions (A 6.6%, B 4.5%, and C 1.9%). CONCLUSION This study highlights the importance of multigene panel testing in Latin American individuals with newly diagnosed or history of HBOC, who can benefit from medical management changes including targeted therapies, eligibility to clinical trials, risk-reducing surgeries, surveillance and prevention of secondary malignancy, and genetic counseling and subsequent cascade testing of at-risk relatives.
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Affiliation(s)
| | - Maria Isabel Achatz
- Department of Oncology, Hospital Sírio-Libanês, Brasília, Distrito Federal, Brazil
| | - Mabel Hurtado
- Instituto Oncológico, Fundación Arturo López Pérez, Santiago, Chile
| | | | - Yasser Sullcahuaman
- Universidad Peruana de Ciencias Aplicadas, Lima, Peru
- Instituto de Investigación Genomica, Lima, Peru
| | - Yanin Chávarri-Guerra
- Department of Hemato-Oncology, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Julie Dutil
- Cancer Biology Division, Ponce Research Institute, Ponce Health Sciences University, Pone, Puerto Rico
| | | | | | | | | | | | | | | | - Patricia Ashton-Prolla
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Serviço de Genética Médica e Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
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HLA Genotypes and Type 1 Diabetes and Its Relationship to Reported Race/Skin Color in Their Relatives: A Brazilian Multicenter Study. Genes (Basel) 2022; 13:genes13060972. [PMID: 35741734 PMCID: PMC9223352 DOI: 10.3390/genes13060972] [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] [Received: 05/03/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 11/18/2022] Open
Abstract
We aimed to investigate the relationship between HLA alleles in patients with type 1 diabetes from an admixed population and the reported race/skin color of their relatives. This cross-sectional, multicenter study was conducted in public clinics in nine Brazilian cities and included 662 patients with type 1 diabetes and their relatives. Demographic data for patients and information on the race/skin color and birthplace of their relatives were obtained. Typing of the HLA-DRB1, -DQA1, and -DQB1 genes was performed. Most studied patients reported having a White relative (95.17%), and the most frequently observed allele among them was DRB1*03:01. Increased odds of presenting this allele were found only in those patients who reported having all White relatives. Considering that most of the patients reported having a White relative and that the most frequent observed allele was DRB1*03:01 (probably a European-derived allele), regardless of the race/skin color of their relatives, we conclude that the type 1 diabetes genotype comes probably from European, Caucasian ethnicity. However, future studies with other ancestry markers are needed to fill the knowledge gap regarding the genetic origin of the type 1 diabetes genotype in admixed populations such as the Brazilian.
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de Azevedo GBL, Perini JA, Araújo Junior AEP, Moliterno LAM, Andrande RM, Guimarães JAM, Defino HLA. Association of FBN1 polymorphism with susceptibility of adolescent idiopathic scoliosis: a case-control study. BMC Musculoskelet Disord 2022; 23:430. [PMID: 35526034 PMCID: PMC9077855 DOI: 10.1186/s12891-022-05370-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 04/21/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Fibrillin-1 (FBN1) is an extracellular matrix glycoprotein essential to the structural component of microfibrils and FBN1 gene polymorphisms can be associated with adolescent idiopathic scoliosis (AIS) susceptibility. This study aimed to evaluate the potential role of the FBN1 rs12916536 polymorphism in AIS development or severity and the variation in Cobb angle in relation to patient's characteristics. METHODS DNA from 563 subjects (185 AIS patients and 378 controls) were genotyped using a validated TaqMan allelic discrimination assay. A multivariate logistic regression model evaluated the association between polymorphism and AIS, using the adjusted odds ratios (OR) with their respective 95% confidence intervals (95% CI). A linear regression analysis evaluated the variation in Cobb angle according to the patient's age and body mass index (BMI). RESULTS Among the AIS group there was a predominance of females (12:1), low or normal BMI (90%), 58% had a Cobb angle greater than 45° and 74% were skeletally mature. Age was a risk factor (4-fold) for curve progression higher than BMI (P < 0.001). The allelic frequency of the rs12916536 G > A polymorphism was 40% in controls and 31% in AIS cases; and this difference was statistically significant (P = 0.004). FBN1 rs12916536 GA + AA genotypes were associated with a lower risk of AIS susceptibility (OR = 0.58 and 95% CI = 0.35-0.98), after adjustment for age, sex and BMI. However, no significant differences were detected in polymorphism distribution with the severity of the disease (Cobb < 45° or ≥ 45°). CONCLUSION Age was a risk factor for progression of the scoliotic curve and FBN1 rs12916536 polymorphism a protective factor for AIS susceptibility.
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Affiliation(s)
- Gustavo Borges Laurindo de Azevedo
- Spine Surgery Center, National Institute of Traumatology and Orthopaedics (INTO), Rio de Janeiro, RJ, Brazil.,Departments of Orthopaedic and Anesthesiology, Ribeirão Preto Medical School, University of São Paulo, de São Paulo, Brazil
| | - Jamila Alessandra Perini
- Research Division, National Institute of Traumatology and Orthopaedics (INTO), Avenida Brasil, 500, Rio de Janeiro, RJ, zip code 20940-070, Brazil. .,Research Laboratory of Pharmaceutical Sciences (LAPESF), State University of Rio de Janeiro (UERJ), Rio de Janeiro, RJ, Brazil.
| | - Antônio Eulálio Pedrosa Araújo Junior
- Spine Surgery Center, National Institute of Traumatology and Orthopaedics (INTO), Rio de Janeiro, RJ, Brazil.,Departments of Orthopaedic and Anesthesiology, Ribeirão Preto Medical School, University of São Paulo, de São Paulo, Brazil
| | - Luis Antonio Medeiros Moliterno
- Spine Surgery Center, National Institute of Traumatology and Orthopaedics (INTO), Rio de Janeiro, RJ, Brazil.,Departments of Orthopaedic and Anesthesiology, Ribeirão Preto Medical School, University of São Paulo, de São Paulo, Brazil
| | - Rodrigo Mantelatto Andrande
- Departments of Orthopaedic and Anesthesiology, Ribeirão Preto Medical School, University of São Paulo, de São Paulo, Brazil
| | - João Antonio Matheus Guimarães
- Research Division, National Institute of Traumatology and Orthopaedics (INTO), Avenida Brasil, 500, Rio de Janeiro, RJ, zip code 20940-070, Brazil
| | - Helton Luiz Aparecido Defino
- Departments of Orthopaedic and Anesthesiology, Ribeirão Preto Medical School, University of São Paulo, de São Paulo, Brazil
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Ximenez JP, Elias ABR, Nardotto GHB, Barroso PF, Bollela VR, Lanchote VL, Suarez-Kurtz G. Pharmacogenetic predictors of variability in efavirenz pharmacokinetics in an admixed Brazilian HIV cohort. Br J Clin Pharmacol 2022; 88:4585-4594. [PMID: 35514050 DOI: 10.1111/bcp.15387] [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: 02/25/2022] [Revised: 04/25/2022] [Accepted: 04/27/2022] [Indexed: 11/24/2022] Open
Abstract
AIMS To investigate the influence of pharmacogenetic polymorphisms on efavirenz (EFV) exposure and metabolism in HIV-infected Brazilians under treatment with EFV-containing antiretroviral (ART) regimens. METHODS HIV-positive adults (n=82) on stable ART regimens containing 600 mg EFV once daily for at least 6 months were recruited at two university hospitals. Blood samples collected at mid-dose interval were used to quantify the plasma concentrations of EFV (denoted [EFV]), its major metabolite 8-OH-EFV ([8-OH-EFV]) and [8-OH-EFV]/[EFV] metabolic ratio, and to genotype single nucleotide polymorphisms (SNPs) in CYP2B6 (rs3745274, c.516G>T; rs28399499, c.983T>C) and ABCB1 (rs3842, c.4036G>A). CYP2B6 metabolic phenotypes were inferred from the CYP2B6 diplotypes. Linear regression modeling was applied to identify sociodemographic, clinical and pharmacogenetic predictors of [EFV] and [8-OH-EFV]/[EFV] metabolic ratio. RESULTS Wide (50-fold) interindividual variation in [EFV], [8-OH-EFV] and [8-OH-EFV]/[EFV] was observed; 69.5% of participants had [EFV] within the nominal therapeutic range (1000-4000 ng/ml), while 19.5%, and 11.0% had [EFV] below and above this range, respectively. Multiple regression modeling retained only CYP2B6 metabolic phenotypes or the combined rs3745274 and rs28399499 genotypes, as significant predictors of [EFV] and [8-OH-EFV]/[EFV]. CONCLUSION EFV exposure and disposition varied widely among HIV-infected Brazilians under stable treatment with EFV-containing ART regimens. About one-tenth of the participants had [EFV] exceeding nominal supratherapeutic concentration (4000 ng/mL), but reported tolerance to the ARV regimens, while one fifth of participants had nominal subtherapeutic [EFV] (<1000 ng/ml) but adequate virological response. Genotype for the two CYP2B6 SNPs studied explained 48% of variation in [EFV] and 35% of variation in [8-OH-EFV]/[EFV].
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Affiliation(s)
- João Paulo Ximenez
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | | | | | - Paulo Feijó Barroso
- Hospital Universitário Clementino Fraga Filho, Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Valdes Roberto Bollela
- Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Vera Lucia Lanchote
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
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Bernardes JGB, Fernandes MR, Rodrigues JCG, Vinagre LWMS, Pastana LF, Dobbin EAF, Medeiros JAG, Dias Junior LB, Bernardes GM, Bernardes IMM, Santos NPCD, Demachki S, Burbano RMR. Association of Androgenic Regulation and MicroRNAs in Acinar Adenocarcinoma of Prostate. Genes (Basel) 2022; 13:genes13040622. [PMID: 35456428 PMCID: PMC9030213 DOI: 10.3390/genes13040622] [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: 02/14/2022] [Revised: 03/11/2022] [Accepted: 03/12/2022] [Indexed: 12/13/2022] Open
Abstract
Background: Prostate cancer represents 3.8% of cancer deaths worldwide. For most prostate cancer cells to grow, androgens need to bind to a cellular protein called the androgen receptor (AR). This study aims to demonstrate the expression of five microRNAs (miRs) and its influence on the AR formation in patients from the northern region of Brazil. Material and Methods: Eighty-four tissue samples were investigated, including nodular prostatic hyperplasia (NPH) and acinar prostatic adenocarcinoma (CaP). Five miRs (27a-3p, 124, 130a, 488-3p, and 506) were quantified using the TaqMan® Real Time PCR method and AR was measured using Western blotting. Results: Levels of miRs 124, 130a, 488-3p, and 506 were higher in NPH samples. Conversely, in the CaP cases, higher levels of miR 27a-3p and AR were observed. Conclusion: In the future, these microRNAs may be tested as markers of CaP at the serum level. The relative expression of AR was 20% higher in patients with prostate cancer, which suggests its potential as a biomarker for prostate malignancy.
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Affiliation(s)
- Julio Guilherme Balieiro Bernardes
- Instituto de Ciências da Saúde, Universidade Federal do Pará, Belém 66050-160, Brazil; (J.G.B.B.); (L.B.D.J.); (I.M.M.B.)
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém 66073-005, Brazil; (J.C.G.R.); (L.W.M.S.V.); (L.F.P.); (E.A.F.D.); (J.A.G.M.); (N.P.C.D.S.); (S.D.); (R.M.R.B.)
| | - Marianne Rodrigues Fernandes
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém 66073-005, Brazil; (J.C.G.R.); (L.W.M.S.V.); (L.F.P.); (E.A.F.D.); (J.A.G.M.); (N.P.C.D.S.); (S.D.); (R.M.R.B.)
- Hospital Ophir Loyola, Belém 66063-240, Brazil
- Correspondence:
| | - Juliana Carla Gomes Rodrigues
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém 66073-005, Brazil; (J.C.G.R.); (L.W.M.S.V.); (L.F.P.); (E.A.F.D.); (J.A.G.M.); (N.P.C.D.S.); (S.D.); (R.M.R.B.)
| | - Lui Wallacy Morikawa Souza Vinagre
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém 66073-005, Brazil; (J.C.G.R.); (L.W.M.S.V.); (L.F.P.); (E.A.F.D.); (J.A.G.M.); (N.P.C.D.S.); (S.D.); (R.M.R.B.)
| | - Lucas Favacho Pastana
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém 66073-005, Brazil; (J.C.G.R.); (L.W.M.S.V.); (L.F.P.); (E.A.F.D.); (J.A.G.M.); (N.P.C.D.S.); (S.D.); (R.M.R.B.)
| | - Elizabeth Ayres Fragoso Dobbin
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém 66073-005, Brazil; (J.C.G.R.); (L.W.M.S.V.); (L.F.P.); (E.A.F.D.); (J.A.G.M.); (N.P.C.D.S.); (S.D.); (R.M.R.B.)
| | - Jéssyca Amanda Gomes Medeiros
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém 66073-005, Brazil; (J.C.G.R.); (L.W.M.S.V.); (L.F.P.); (E.A.F.D.); (J.A.G.M.); (N.P.C.D.S.); (S.D.); (R.M.R.B.)
| | - Leonidas Braga Dias Junior
- Instituto de Ciências da Saúde, Universidade Federal do Pará, Belém 66050-160, Brazil; (J.G.B.B.); (L.B.D.J.); (I.M.M.B.)
| | | | | | - Ney Pereira Carneiro Dos Santos
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém 66073-005, Brazil; (J.C.G.R.); (L.W.M.S.V.); (L.F.P.); (E.A.F.D.); (J.A.G.M.); (N.P.C.D.S.); (S.D.); (R.M.R.B.)
| | - Samia Demachki
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém 66073-005, Brazil; (J.C.G.R.); (L.W.M.S.V.); (L.F.P.); (E.A.F.D.); (J.A.G.M.); (N.P.C.D.S.); (S.D.); (R.M.R.B.)
| | - Rommel Mario Rodriguez Burbano
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém 66073-005, Brazil; (J.C.G.R.); (L.W.M.S.V.); (L.F.P.); (E.A.F.D.); (J.A.G.M.); (N.P.C.D.S.); (S.D.); (R.M.R.B.)
- Hospital Ophir Loyola, Belém 66063-240, Brazil
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Assessment of NKG2C copy number variation in HIV-1 infection susceptibility, and considerations about the potential role of lacking receptors and virus infection. J Hum Genet 2022; 67:475-479. [PMID: 35314764 PMCID: PMC8938163 DOI: 10.1038/s10038-022-01029-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 02/16/2022] [Accepted: 02/28/2022] [Indexed: 12/02/2022]
Abstract
Human Immunodeficiency Virus (HIV) infection dynamics is strongly influenced by the host genetic background. NKG2C is an activating receptor expressed mainly on Natural Killer (NK) cells, and a polymorphism of copy number variation in the gene coding for this molecule has been pointed as a potential factor involved in HIV infection susceptibility. We evaluated the impact of the NKG2C deletion on HIV-1 susceptibility, with or without HBV/HCV co-infection, in a total of 780 individuals, including 385 HIV-infected patients and 395 healthy blood donors. NKG2C deletion genotyping was performed by standard PCR. To our knowledge, this is the first study to access the impact of complete NKG2C deletion among HIV-infected Brazilian individuals. The frequency of NKG2C deletion (range: 19–22%) was similar in cases and controls. No association of NKG2C deletion with HIV-1 susceptibility or influence on clinical features, HBV or HCV co-infection was observed in the evaluated population. Our findings suggest that NKG2C deletion, and the consequent absence of this receptor expression, does not directly impact HIV susceptibility, HBV/HCV-co-infection in the studied population, suggesting that other signaling pathways might be triggered and perform similar functions in cell activity in the absence of this specific receptor, preventing the development of disadvantageous phenotypes. Larger cohorts and studies involving protein expression are necessary to confirm our findings.
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Li J, Feng D, He S, Yang H, Su Z, Ye H. Association of MTHFR 677C > T gene polymorphism with neonatal defects: a meta-analysis of 81444 subjects. J OBSTET GYNAECOL 2022; 42:1811-1822. [PMID: 35282788 DOI: 10.1080/01443615.2022.2039908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Juan Li
- Department of Clinical Laboratory, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Danqin Feng
- Department of Clinical Laboratory, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Shiwei He
- School of Public Health, Xiamen University, Xiamen, China
| | - Hua Yang
- Department of Obstetrics, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Zhiying Su
- Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Huiming Ye
- Department of Clinical Laboratory, Women and Children’s Hospital, School of Medicine, and Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen, China
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Araki MVR, Silva YCO, Rodrigues TAR, Bajano FF, de Souza BB, Costa FF, Costa VP, de Melo MB, de Vasconcellos JPC. Association of ABCA1 (rs2472493) and GAS7 (rs9913911) gene variants with primary open-angle glaucoma in a Brazilian population. Mol Vis 2022; 28:1-10. [PMID: 35400990 PMCID: PMC8942454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 02/20/2022] [Indexed: 11/11/2022] Open
Abstract
Purpose Glaucoma is the world's leading cause of irreversible blindness, with primary open-angle glaucoma (POAG) being the most prevalent subtype. In recent years, there have been advances in knowledge about the genetics involved in POAG, but genetic studies in admixed populations, such as Brazilians, are still rare. This study aimed to evaluate the association of single nucleotide variants (SNV) of the ABCA1 (rs2472493) and GAS7 (rs9913911) genes with POAG in a sample of the Brazilian population. Furthermore, the study aimed to evaluate the relationship between these SNVs and the need for surgical intervention in glaucoma control. Methods A cross-sectional association study with 1,009 subjects (505 patients with POAG and 504 controls) was performed. Participants underwent a comprehensive ocular examination, including the need for surgical procedures for intraocular pressure control. Genotyping of SNVs was performed using the TaqMan genotyping assay. Results SNV rs9913911 of GAS7 was found to be associated with POAG in the presence of the risk allele A (p = 0.0004) and the AA genotype (p = 0.002). There was no association between SNV rs2472493 of ABCA1 for either the allele risk or genotypes. However, the combination of these variants showed an additive effect on the risk for POAG: ABCA1(GG) + GAS7(AA; p = 0.02), ABCA1(GG) + GAS7(AG; p = 0.003), and ABCA1(AG) + GAS7(AG; p = 0.004). Also, POAG patients carrying the AA genotype of the GAS7 gene required antiglaucomatous surgery more frequently than those without the AA genotype (p = 0.01). Conclusions In a Brazilian population sample, there was an association identified between SNV rs9913911 (GAS7) and the risk of POAG, and an additive effect was found when GAS7 was combined with SNV rs2472493 (ABCA1). There was an association between SNV rs9913911 (GAS7) and the risk for antiglaucomatous surgery.
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Affiliation(s)
- Manoel Vinicius Rocha Araki
- Department of Ophthalmology, Faculty of Medical Sciences, University of Campinas – UNICAMP, Campinas – SP, Brazil
| | - Yuri Carvalho Oiamore Silva
- Laboratory of Human Genetics, Center for Molecular Biology and Genetic Engineering, University of Campinas – UNICAMP, Campinas – SP, Brazil
| | - Thiago Adalton Rosa Rodrigues
- Laboratory of Human Genetics, Center for Molecular Biology and Genetic Engineering, University of Campinas – UNICAMP, Campinas – SP, Brazil
| | - Flavia Fialho Bajano
- Laboratory of Human Genetics, Center for Molecular Biology and Genetic Engineering, University of Campinas – UNICAMP, Campinas – SP, Brazil
| | - Bruno Batista de Souza
- Laboratory of Human Genetics, Center for Molecular Biology and Genetic Engineering, University of Campinas – UNICAMP, Campinas – SP, Brazil
| | | | - Vital Paulino Costa
- Department of Ophthalmology, Faculty of Medical Sciences, University of Campinas – UNICAMP, Campinas – SP, Brazil
| | - Mônica Barbosa de Melo
- Laboratory of Human Genetics, Center for Molecular Biology and Genetic Engineering, University of Campinas – UNICAMP, Campinas – SP, Brazil
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