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Martínez-Hernández A, Mendoza-Caamal EC, Mendiola-Vidal NG, Barajas-Olmos F, Villafan-Bernal JR, Jiménez-Ruiz JL, Monge-Cazares T, García-Ortiz H, Cubas CC, Centeno-Cruz F, Alaez-Verson C, Ortega-Torres S, Luna-Castañeda ADC, Baca V, Lezana JL, Orozco L. CFTR pathogenic variants spectrum in a cohort of Mexican patients with cystic fibrosis. Heliyon 2024; 10:e28984. [PMID: 38601560 PMCID: PMC11004572 DOI: 10.1016/j.heliyon.2024.e28984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 03/27/2024] [Accepted: 03/27/2024] [Indexed: 04/12/2024] Open
Abstract
Background Molecular diagnosis of cystic fibrosis (CF) is challenging in Mexico due to the population's high genetic heterogeneity. To date, 46 pathogenic variants (PVs) have been reported, yielding a detection rate of 77%. We updated the spectrum and frequency of PVs responsible for this disease in mexican patients. Methods We extracted genomic DNA from peripheral blood lymphocytes obtained from 297 CF patients and their parents. First, we analyzed the five most frequent PVs in the Mexican population using PCR-mediated site-directed mutagenesis. In patients with at least one identified allele, CFTR sequencing was performed using next-generation sequencing tools and multiplex ligation-dependent probe amplification. For variants not previously classified as pathogenic, we used a combination of in silico prediction, CFTR modeling, and clinical characteristics to determine a genotype-phenotype correlation. Results We identified 95 PVs, increasing the detection rate to 87.04%. The most frequent variants were p.(PheF508del) (42.7%), followed by p.(Gly542*) (5.6%), p.(Ser945Leu) (2.9%), p.(Trp1204*) and p.(Ser549Asn) (2.5%), and CFTRdel25-26 and p.(Asn386Ilefs*3) (2.3%). The remaining variants had frequencies of <2.0%, and some were exclusive to one family. We identified 10 novel PVs localized in different exons (frequency range: 0.1-0.8%), all of which produced structural changes, deletions, or duplications in different domains of the protein, resulting in dysfunctional ion flow. The use of different in silico software and American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) criteria allowed us to assume that all of these PVs were pathogenic, causing a severe phenotype. Conclusions In a highly heterogeneous population, combinations of different tools are needed to identify the variants responsible for CF and enable the establishment of appropriate strategies for CF diagnosis, prevention, and treatment.
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Affiliation(s)
- Angélica Martínez-Hernández
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genomica, SS, Tlalpan, 14610, Mexico City, Mexico
| | - Elvia C. Mendoza-Caamal
- Clinical Area, Instituto Nacional de Medicina Genómica, SS, Tlalpan, 14610, CDMX, Mexico City, Mexico
| | - Namibia G. Mendiola-Vidal
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genomica, SS, Tlalpan, 14610, Mexico City, Mexico
- Maestría en Ciencias Médicas. PMDCMOS. Sede: HGGEA, UNAM. Coyoacan, 04510, Mexico City, Mexico
| | - Francisco Barajas-Olmos
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genomica, SS, Tlalpan, 14610, Mexico City, Mexico
| | - José Rafael Villafan-Bernal
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genomica, SS, Tlalpan, 14610, Mexico City, Mexico
- Investigador por Mexico, Consejo Nacional de Humanidades, Ciencia y Tecnología (CONAHCYT), Benito Juarez, 03940, Mexico City, Mexico
| | - Juan Luis Jiménez-Ruiz
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genomica, SS, Tlalpan, 14610, Mexico City, Mexico
| | - Tulia Monge-Cazares
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genomica, SS, Tlalpan, 14610, Mexico City, Mexico
| | - Humberto García-Ortiz
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genomica, SS, Tlalpan, 14610, Mexico City, Mexico
| | - Cecilia Contreras- Cubas
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genomica, SS, Tlalpan, 14610, Mexico City, Mexico
| | - Federico Centeno-Cruz
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genomica, SS, Tlalpan, 14610, Mexico City, Mexico
| | - Carmen Alaez-Verson
- Genomic Diagnostic Laboratory, Instituto Nacional de Medicina Genomica, SS, Tlalpan, 14610, CDMX, Mexico City, Mexico
| | - Soraya Ortega-Torres
- Curso de Alta Especialidad en Medicina Genómica, Instituto Nacional de Medicina Genomica, Facultad de Medicina, Universidad Nacional Autonoma de Mexico, Coyoacan, 04510, Mexico City, Mexico
| | | | - Vicente Baca
- Rheumatology Department, Hospital de Pediatría, CMN Siglo XXI IMSS, Cuauhtemoc, 06720, Mexico City, Mexico
| | - José Luis Lezana
- Cystic Fibrosis Clinic and Pulmonary Physiology Laboratory. Hospital Infantil de Mexico Federico Gómez, SS, Cuauhtemoc, 06720, Mexico City, Mexico
- Asociacion Mexicana de Fibrosis Quistica, A.C. Benito Juarez, 03700, Mexico City, Mexico
| | - Lorena Orozco
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genomica, SS, Tlalpan, 14610, Mexico City, Mexico
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Morales-Marín ME, Castro Martínez XH, Centeno Cruz F, Barajas-Olmos F, Náfate López O, Gómez Cotero AG, Orozco L, Nicolini Sánchez H. Differential DNA Methylation from Autistic Children Enriches Evidence for Genes Associated with ASD and New Candidate Genes. Brain Sci 2023; 13:1420. [PMID: 37891789 PMCID: PMC10605446 DOI: 10.3390/brainsci13101420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/13/2023] [Accepted: 09/20/2023] [Indexed: 10/29/2023] Open
Abstract
The etiology of Autism Spectrum Disorders (ASD) is a result of the interaction between genes and the environment. The study of epigenetic factors that affect gene expression, such as DNA methylation, has become an important area of research in ASD. In recent years, there has been an increasing body of evidence pointing to epigenetic mechanisms that influence brain development, as in the case of ASD, when gene methylation dysregulation is present. Our analysis revealed 853 differentially methylated CpG in ASD patients, affecting 509 genes across the genome. Enrichment analysis showed five related diseases, including autistic disorder and mental disorders, which are particularly significant. In this work, we identified 64 genes that were previously reported in the SFARI gene database, classified according to their impact index. Additionally, we identified new genes that have not been previously reported as candidates with differences in the methylation patterns of Mexican children with ASD.
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Affiliation(s)
- Mirna Edith Morales-Marín
- Laboratorio de Genómica de Enfermedades Psiquiátricas y Neurodegenerativas, Instituto Nacional de Medicina Genómica, Mexico City 14610, Mexico; (X.H.C.M.); (H.N.S.)
| | - Xochitl Helga Castro Martínez
- Laboratorio de Genómica de Enfermedades Psiquiátricas y Neurodegenerativas, Instituto Nacional de Medicina Genómica, Mexico City 14610, Mexico; (X.H.C.M.); (H.N.S.)
| | - Federico Centeno Cruz
- Laboratorio de Inmunogenómica y Enfermedades Metabólicas, Instituto Nacional de Medicina Genómica, Mexico City 14610, Mexico; (F.C.C.); (F.B.-O.); (L.O.)
| | - Francisco Barajas-Olmos
- Laboratorio de Inmunogenómica y Enfermedades Metabólicas, Instituto Nacional de Medicina Genómica, Mexico City 14610, Mexico; (F.C.C.); (F.B.-O.); (L.O.)
| | - Omar Náfate López
- Hospital de Especialidades Pediátricas, Tuxtla Gutiérrez 29045, Mexico;
| | - Amalia Guadalupe Gómez Cotero
- Centro de Investigación en Ciencias de la Salud, Unidad Santo Tomás, Instituto Politécnico Nacional, Mexico City 07738, Mexico;
| | - Lorena Orozco
- Laboratorio de Inmunogenómica y Enfermedades Metabólicas, Instituto Nacional de Medicina Genómica, Mexico City 14610, Mexico; (F.C.C.); (F.B.-O.); (L.O.)
| | - Humberto Nicolini Sánchez
- Laboratorio de Genómica de Enfermedades Psiquiátricas y Neurodegenerativas, Instituto Nacional de Medicina Genómica, Mexico City 14610, Mexico; (X.H.C.M.); (H.N.S.)
- Grupo Médico Carracci, Mexico City 03740, Mexico
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Sánchez EC, Barajas-Olmos F, Baca P, Zerrweck C, Guilbert L, Martínez-Hernández A, Centeno F, Orozco L. DNA Methylation Remodeling after Bariatric Surgery Correlates with Clinical Parameters. Adv Biol (Weinh) 2023; 7:e2300001. [PMID: 37144655 DOI: 10.1002/adbi.202300001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 03/27/2023] [Indexed: 05/06/2023]
Abstract
The altered functions of adipose tissue are one of the main issues in obesity. Bariatric surgery is associated with improvement of obesity associated comorbidities. Here DNA methylation remodeling in adipose tissue after bariatric surgery is examined. After six months postoperative, DNA methylation shows changes in 1155 CpG sites, 66 of these sites correlate with body mass index. Some sites also show correlation with LDL-C, HDL-C, total cholesterol, and triglycerides. CpG sites are located in genes that have not previously been linked to obesity or metabolic diseases. GNAS complex locus is one of those that presented CpG site with the greatest changes after surgery, and the most significant correlation with BMI and lipid profiles. These results show that epigenetic regulation may be involved in the alteration of adipose tissue functions in obesity.
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Affiliation(s)
- Ernesto Carlos Sánchez
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genómica, SS, Periférico Sur 4809, Mexico City, Tlalpan, 14610, Mexico
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Cto. de los Posgrados, Ciudad Universitaria, Mexico City, Coyoacán, 04510, Mexico
| | - Francisco Barajas-Olmos
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genómica, SS, Periférico Sur 4809, Mexico City, Tlalpan, 14610, Mexico
| | - Paulina Baca
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genómica, SS, Periférico Sur 4809, Mexico City, Tlalpan, 14610, Mexico
| | - Carlos Zerrweck
- Facultad de Medicina, Alta especialidad en Cirugía Bariatrica, UNAM, Escolar 411A, Copilco Universidad, Mexico City, Coyoacán, 04360, Mexico
| | - Lizbeth Guilbert
- Clínica Integral de Obesidad, Hospital General Tláhuac, Secretaría de Salud de la CDMX, Av. La turba 655, Mexico City, Tláhuac, 13278, Mexico
| | - Angélica Martínez-Hernández
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genómica, SS, Periférico Sur 4809, Mexico City, Tlalpan, 14610, Mexico
| | - Federico Centeno
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genómica, SS, Periférico Sur 4809, Mexico City, Tlalpan, 14610, Mexico
| | - Lorena Orozco
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genómica, SS, Periférico Sur 4809, Mexico City, Tlalpan, 14610, Mexico
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Anaya-Morua W, Villafan-Bernal JR, Ramírez-Moreno E, García-Ortiz H, Martínez-Portilla RJ, Contreras-Cubas C, Martínez-Hernández A, Centeno-Cruz F, Pedroza-Montoya FE, Orozco L, Barajas-Olmos F. Total Antioxidant Capacity in Obese and Non-Obese Subjects and Its Association with Anthropo-Metabolic Markers: Systematic Review and Meta-Analysis. Antioxidants (Basel) 2023; 12:1512. [PMID: 37627507 PMCID: PMC10451178 DOI: 10.3390/antiox12081512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 07/26/2023] [Accepted: 07/26/2023] [Indexed: 08/27/2023] Open
Abstract
The total antioxidant capacity (TAC) has been related to the development of and complications associated with chronic diseases, but its importance during obesity is not entirely clear. We conducted a systematic review and meta-analysis to clarify whether there are differences or similarities in the TAC between subjects with obesity (SO) and subjects with normal weight (NW). Following the recommendations of PRISMA and Cochrane, we performed a systematic search in the PubMed, Scopus, Web of Science, Cochrane, and PROSPERO databases, identifying 1607 studies. Among these, 22 studies were included in the final analysis, comprising 3937 subjects (1665 SO and 2272 NW) in whom serum TAC was measured, and from these 19,201 subjects, the correlation of serum TAC with anthropo-metabolic parameters was also estimated. The Newcastle-Ottawa method was used for the evaluation of the risk of bias. Using a random-effect model (REM), TAC was reduced in SO independently of age (SMD, -0.86; 95% CI -1.38 to -0.34; p = 0.0012), whereas malondialdehyde (SMD, 1.50; 95% CI 0.60 to 2.41), oxidative stress index (SMD, 1.0; 95% CI 0.16 to 1.84), and total oxidant status (SMD, 0.80; 0.22 to 1.37) were increased. There were seven significant pooled correlations of TAC with anthropometric and metabolic parameters: weight (r = -0.17), hip circumference (r= -0.11), visceral adipose index (r = 0.29), triglycerides (r = 0.25), aspartate aminotransferase (r = 0.41), alanine aminotransferase (r = 0.38), and uric acid (r = 0.53). Our results confirm a decrease in TAC and an increase in markers of oxidative stress in SO and underpin the importance of these serum biomarkers in obesity.
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Affiliation(s)
- Wendoline Anaya-Morua
- Academic Area of Medicine, Interdisciplinary Research Center, Institute of Health Sciences, Autonomous University of the State of Hidalgo, Pachuca 42160, Mexico;
| | - José Rafael Villafan-Bernal
- Investigador por México, Consejo Nacional de Humanidades, Ciencia y Tecnología (CONAHCYT), Mexico City 03940, Mexico;
- Iberoamerican Research Network in Obstetrics, Gynecology and Translational Medicine, Mexico City 42160, Mexico; (R.J.M.-P.); (F.E.P.-M.)
- Immunogenomics and Metabolic Diseases Laboratory, Instituto Nacional de Medicina Genómica, SS, Mexico City 14610, Mexico; (H.G.-O.); (C.C.-C.); (A.M.-H.); (F.C.-C.)
| | - Esther Ramírez-Moreno
- Academic Area of Nutrition, Interdisciplinary Research Center, Institute of Health Sciences, Autonomous University of the State of Hidalgo, Pachuca 42184, Mexico;
| | - Humberto García-Ortiz
- Immunogenomics and Metabolic Diseases Laboratory, Instituto Nacional de Medicina Genómica, SS, Mexico City 14610, Mexico; (H.G.-O.); (C.C.-C.); (A.M.-H.); (F.C.-C.)
| | - Raigam Jafet Martínez-Portilla
- Iberoamerican Research Network in Obstetrics, Gynecology and Translational Medicine, Mexico City 42160, Mexico; (R.J.M.-P.); (F.E.P.-M.)
- Clinical Research Branch, Evidence-Based Medicine Department, National Institute of Perinatology, Mexico City 11000, Mexico
| | - Cecilia Contreras-Cubas
- Immunogenomics and Metabolic Diseases Laboratory, Instituto Nacional de Medicina Genómica, SS, Mexico City 14610, Mexico; (H.G.-O.); (C.C.-C.); (A.M.-H.); (F.C.-C.)
| | - Angélica Martínez-Hernández
- Immunogenomics and Metabolic Diseases Laboratory, Instituto Nacional de Medicina Genómica, SS, Mexico City 14610, Mexico; (H.G.-O.); (C.C.-C.); (A.M.-H.); (F.C.-C.)
| | - Federico Centeno-Cruz
- Immunogenomics and Metabolic Diseases Laboratory, Instituto Nacional de Medicina Genómica, SS, Mexico City 14610, Mexico; (H.G.-O.); (C.C.-C.); (A.M.-H.); (F.C.-C.)
| | - Florencia Estefana Pedroza-Montoya
- Iberoamerican Research Network in Obstetrics, Gynecology and Translational Medicine, Mexico City 42160, Mexico; (R.J.M.-P.); (F.E.P.-M.)
| | - Lorena Orozco
- Immunogenomics and Metabolic Diseases Laboratory, Instituto Nacional de Medicina Genómica, SS, Mexico City 14610, Mexico; (H.G.-O.); (C.C.-C.); (A.M.-H.); (F.C.-C.)
| | - Francisco Barajas-Olmos
- Immunogenomics and Metabolic Diseases Laboratory, Instituto Nacional de Medicina Genómica, SS, Mexico City 14610, Mexico; (H.G.-O.); (C.C.-C.); (A.M.-H.); (F.C.-C.)
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5
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Rivera-Paredez B, Hidalgo-Bravo A, León-Reyes G, Barajas-Olmos F, Martínez-Hernández A, Orozco L, Denova-Gutiérrez E, Salmerón J, Velázquez-Cruz R. The role of single nucleotide variant rs3819817 of the Histidine Ammonia-Lyase gene and 25-Hydroxyvitamin D on bone mineral density, adiposity markers, and skin pigmentation, in Mexican population. J Endocrinol Invest 2023:10.1007/s40618-023-02051-1. [PMID: 36862244 DOI: 10.1007/s40618-023-02051-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 02/24/2023] [Indexed: 03/03/2023]
Abstract
PURPOSE Vitamin D (VD) deficiency and osteoporosis have become a global public health problem. A variant in the Histidine Ammonia-Lyase (HAL) gene has been associated with VD levels and bone mineral density (BMD). However, whether this variant has an influence on VD levels and BMD in Mexican adults remain unclear. METHODS This cross-sectional analysis included 1,905 adults participating in the Health Worker Cohort Study and 164 indigenous postmenopausal women from the Metabolic Analysis in an Indigenous Sample (MAIS) cohort. The rs3819817 variant was genotyped by TaqMan probe assay. Total 25 hydroxyvitamin D levels were measured by DiaSorin Liaison. BMD at the different sites was assessed through dual-energy X-ray absorptiometry. Linear and logistic regression models were performed to evaluate the associations of interest. RESULTS The prevalence of VD deficiency was 41%, showing differences between sexes. Obesity and skin pigmentation were associated with lower levels of VD in males and females. rs3819817-T allele was associated with low levels of 25-hydroxyvitamin D, VD deficiency, and hip and femoral neck BMD values (g/cm2). We found two interactions with VD levels, one between adiposity and rs3819817-T allele (P = 0.017) and another between skin pigmentation and rs3819817-T allele (P = 0.019). In indigenous postmenopausal women, we observed higher VD levels in the southern region compared to the northern region (P < 0.001); however, we did not observe differences by genotype. CONCLUSION Our findings confirm that the genetic variant rs3819817 has an essential function in VD levels and BMD and suggests a role in skin pigmentation in the Mexican population.
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Affiliation(s)
- B Rivera-Paredez
- Centro de Investigación en Políticas, Población y Salud de la Facultad de Medicina de la Universidad Nacional Autónoma de México (UNAM), Mexico City, México
| | - A Hidalgo-Bravo
- Departamento de Genética, Instituto Nacional de Rehabilitación, Mexico City, México
| | - G León-Reyes
- Laboratorio de Genómica del Metabolismo Óseo, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, México
| | - F Barajas-Olmos
- Laboratorio de Inmunogenómica y Enfermedades Metabólicas, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, México
| | - A Martínez-Hernández
- Laboratorio de Inmunogenómica y Enfermedades Metabólicas, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, México
| | - L Orozco
- Laboratorio de Inmunogenómica y Enfermedades Metabólicas, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, México
| | - E Denova-Gutiérrez
- Centro de Investigación en Nutrición y Salud, Instituto Nacional de Salud Pública (INSP), Cuernavaca, Morelos, México
| | - J Salmerón
- Centro de Investigación en Políticas, Población y Salud de la Facultad de Medicina de la Universidad Nacional Autónoma de México (UNAM), Mexico City, México
| | - R Velázquez-Cruz
- Laboratorio de Genómica del Metabolismo Óseo, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, México.
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García-Ortiz H, Barajas-Olmos F, Flores-Huacuja M, Morales-Rivera MI, Martínez-Hernández A, Baca V, Contreras-Cubas C, Orozco L. Ancestry-dependent genetic structure of the Xq28 risk haplotype in the Mexican population and its association with childhood-onset systemic lupus erythematosus. Front Med (Lausanne) 2023; 9:1044856. [PMID: 36714151 PMCID: PMC9877425 DOI: 10.3389/fmed.2022.1044856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 12/27/2022] [Indexed: 01/15/2023] Open
Abstract
Objective Here we aimed to investigate the association of the Xq28 risk haplotype (H1) with susceptibility to childhood-onset systemic lupus erythematosus (SLE), and to compare its frequency and genetic structure in the Mexican population with those in other continental populations. Methods We genotyped 15 single-nucleotide variants (SNVs) that form the H1 haplotype, using TaqMan real-time PCR. The association analysis [case-control and transmission disequilibrium test (TDT)] included 376 cases and 400 adult controls, all of whom were mestizos (MEZ). To identify risk alleles in Mexican Indigenous individuals, SNVs were imputed from whole-exome sequencing data of 1,074 individuals. The allelic frequencies determined in MEZ and Indigenous individuals were compared with those of the continental populations from the 1,000 Genomes database phase 3. Linkage disequilibrium (LD) analysis of risk alleles was performed on all populations. Interleukin-1 receptor associated kinase 1 (IRAK1) and methyl CpG binding protein 2 (MECP2) mRNA levels were determined using real-time PCR. Results Case-control analysis revealed genetic association with childhood-onset SLE for all 15 SNVs (OR = 1.49-1.75; p = 0.0095 to 1.81 × 10-4) and for the Xq28 risk haplotype (OR = 1.97, p = 4 × 10-6). Comparing with individuals of European ancestry (0.14-0.16), the frequencies of the risk alleles were significantly higher in the MEZ individuals (0.55-0.68) and even higher in Indigenous individuals (0.57-0.83). LD analysis indicated a differential haplotype structure within the Indigenous groups, which was inherited to the MEZ population as a result of genetic admixture. Individuals homozygous for the Xq28 risk haplotype exhibited decreased levels of both MECP2A and B transcripts. Conclusion We found that the H1 risk haplotype differs in its conformation in the Mexican population. This difference could be attributed to positive selection within the Indigenous population, with its inheritance now having an autoimmune health impact in both the Mexican Indigenous and MEZ populations.
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Affiliation(s)
- Humberto García-Ortiz
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, SS, Mexico City, Mexico
| | - Francisco Barajas-Olmos
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, SS, Mexico City, Mexico
| | - Marlen Flores-Huacuja
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, SS, Mexico City, Mexico
| | - Monserrat I. Morales-Rivera
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, SS, Mexico City, Mexico
| | - Angélica Martínez-Hernández
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, SS, Mexico City, Mexico
| | - Vicente Baca
- Department of Rheumatology, Hospital de Pediatría, CMN Siglo XXI IMSS, Mexico City, Mexico
| | - Cecilia Contreras-Cubas
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, SS, Mexico City, Mexico,*Correspondence: Cecilia Contreras-Cubas,
| | - Lorena Orozco
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, SS, Mexico City, Mexico,Lorena Orozco,
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García-Ortiz H, Barajas-Olmos F, Contreras-Cubas C, Reynolds AW, Flores-Huacuja M, Snow M, Ramos-Madrigal J, Mendoza-Caamal E, Baca P, López-Escobar TA, Bolnick DA, Flores-Martínez SE, Ortiz-Lopez R, Kostic AD, Villafan-Bernal JR, Galaviz-Hernández C, Centeno-Cruz F, García-Zapién AG, Monge-Cázares T, Lazalde-Ramos BP, Loeza-Becerra F, Abrahantes-Pérez MDC, Rangel-Villalobos H, Sosa-Macías M, Rojas-Martínez A, Martínez-Hernández A, Orozco L. Unraveling Signatures of Local Adaptation among Indigenous Groups from Mexico. Genes (Basel) 2022; 13:genes13122251. [PMID: 36553518 PMCID: PMC9778281 DOI: 10.3390/genes13122251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 11/05/2022] [Accepted: 11/15/2022] [Indexed: 12/03/2022] Open
Abstract
Few studies have addressed how selective pressures have shaped the genetic structure of the current Native American populations, and they have mostly limited their inferences to admixed Latin American populations. Here, we searched for local adaptation signals, based on integrated haplotype scores and population branch statistics, in 325 Mexican Indigenous individuals with at least 99% Native American ancestry from five previously defined geographical regions. Although each region exhibited its own local adaptation profile, only PPARG and AJAP1, both negative regulators of the Wnt/β catenin signaling pathway, showed significant adaptation signals in all the tested regions. Several signals were found, mainly in the genes related to the metabolic processes and immune response. A pathway enrichment analysis revealed the overrepresentation of selected genes related to several biological phenotypes/conditions, such as the immune response and metabolic pathways, in agreement with previous studies, suggesting that immunological and metabolic pressures are major drivers of human adaptation. Genes related to the gut microbiome measurements were overrepresented in all the regions, highlighting the importance of studying how humans have coevolved with the microbial communities that colonize them. Our results provide a further explanation of the human evolutionary history in response to environmental pressures in this region.
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Affiliation(s)
- Humberto García-Ortiz
- Instituto Nacional de Medicina Genómica, Tlalpan, Mexico City 14610, Mexico
- Correspondence:
| | | | | | | | | | - Meradeth Snow
- Department of Anthropology, University of Montana, Missoula, MT 59812, USA
| | - Jazmín Ramos-Madrigal
- Section for Evolutionary Genomics, The GLOBE Institute, The University of Copenhagen, Øster Farimagsgade 5A, 1352 Copenhagen, Denmark
| | | | - Paulina Baca
- Instituto Nacional de Medicina Genómica, Tlalpan, Mexico City 14610, Mexico
| | | | - Deborah A. Bolnick
- Department of Anthropology and Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269-3003, USA
| | - Silvia Esperanza Flores-Martínez
- División de Medicina Molecular, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social (IMSS), Guadalajara 44340, Mexico
| | - Rocio Ortiz-Lopez
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud and Insitute for Obesity Research, Monterrey 64700, Mexico
- Centro de Investigacion y Desarrollo en Ciencias de la Salud, Universidad Autonoma de Nuevo Leon, Monterrey 64460, Mexico
| | | | | | | | | | - Alejandra Guadalupe García-Zapién
- Departamento de Farmacobiología, Centro Universitario de Ciencias Exactas e Ingenierías, Universidad de Guadalajara, Guadalajara 44430, Mexico
| | | | | | | | | | - Héctor Rangel-Villalobos
- Instituto de Investigación en Genética Molecular, Universidad de Guadalajara Ocotlán, Ocotlán 44100, Mexico
| | | | - Augusto Rojas-Martínez
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud and Insitute for Obesity Research, Monterrey 64700, Mexico
- Centro de Investigacion y Desarrollo en Ciencias de la Salud, Universidad Autonoma de Nuevo Leon, Monterrey 64460, Mexico
| | | | - Lorena Orozco
- Instituto Nacional de Medicina Genómica, Tlalpan, Mexico City 14610, Mexico
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8
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Askapuli A, Vilar M, Garcia-Ortiz H, Zhabagin M, Sabitov Z, Akilzhanova A, Ramanculov E, Schamiloglu U, Martinez-Hernandez A, Contreras-Cubas C, Barajas-Olmos F, Schurr TG, Zhumadilov Z, Flores-Huacuja M, Orozco L, Hawks J, Saitou N. Kazak mitochondrial genomes provide insights into the human population history of Central Eurasia. PLoS One 2022; 17:e0277771. [PMID: 36445929 PMCID: PMC9707748 DOI: 10.1371/journal.pone.0277771] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 11/03/2022] [Indexed: 11/30/2022] Open
Abstract
As a historical nomadic group in Central Asia, Kazaks have mainly inhabited the steppe zone from the Altay Mountains in the East to the Caspian Sea in the West. Fine scale characterization of the genetic profile and population structure of Kazaks would be invaluable for understanding their population history and modeling prehistoric human expansions across the Eurasian steppes. With this mind, we characterized the maternal lineages of 200 Kazaks from Jetisuu at mitochondrial genome level. Our results reveal that Jetisuu Kazaks have unique mtDNA haplotypes including those belonging to the basal branches of both West Eurasian (R0, H, HV) and East Eurasian (A, B, C, D) lineages. The great diversity observed in their maternal lineages may reflect pivotal geographic location of Kazaks in Eurasia and implies a complex history for this population. Comparative analyses of mitochondrial genomes of human populations in Central Eurasia reveal a common maternal genetic ancestry for Turko-Mongolian speakers and their expansion being responsible for the presence of East Eurasian maternal lineages in Central Eurasia. Our analyses further indicate maternal genetic affinity between the Sherpas from the Tibetan Plateau with the Turko-Mongolian speakers.
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Affiliation(s)
- Ayken Askapuli
- School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
- National Center for Biotechnology, Astana, Kazakhstan
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Miguel Vilar
- The Genographic Project, National Geographic Society, Washington, DC, United States of America
- Department of Anthropology, University of Maryland, College Park, Maryland, United States of America
| | - Humberto Garcia-Ortiz
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Maxat Zhabagin
- School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
- National Center for Biotechnology, Astana, Kazakhstan
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | | | - Ainur Akilzhanova
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | - Erlan Ramanculov
- School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
- National Center for Biotechnology, Astana, Kazakhstan
| | - Uli Schamiloglu
- School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
| | - Angelica Martinez-Hernandez
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Cecilia Contreras-Cubas
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Francisco Barajas-Olmos
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Theodore G. Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Zhaxybay Zhumadilov
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
- School of Medicine, Nazarbayev University, Astana, Kazakhstan
| | - Marlen Flores-Huacuja
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Lorena Orozco
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - John Hawks
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Anthropology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Naruya Saitou
- Population Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
- Advanced Medical Research Center, Faculty of Medicine, University of the Ryukyus, Okinawa Ken, Japan
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9
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Jiménez-Morales JM, Hernández-Cuenca YE, Reyes-Abrahantes A, Ruiz-García H, Barajas-Olmos F, García-Ortiz H, Orozco L, Quiñones-Hinojosa A, Reyes-González J, Del Carmen Abrahantes-Pérez M. MicroRNA delivery systems in glioma therapy and perspectives: A systematic review. J Control Release 2022; 349:712-730. [PMID: 35905783 DOI: 10.1016/j.jconrel.2022.07.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 07/21/2022] [Accepted: 07/21/2022] [Indexed: 11/29/2022]
Abstract
Gliomas are the deadliest of all primary brain tumors, and they constitute a serious global health problem. MicroRNAs (miRNAs) are gene expression regulators associated with glioma pathogenesis. Thus, miRNAs represent potential therapeutic agents for treating gliomas. However, miRNAs have not been established as part of the regular clinical armamentarium. This systemic review evaluates current molecular and pre-clinical studies with the aim of defining the most appealing supramolecular platform for administering therapeutic miRNA to patients with gliomas. An integrated analysis suggested that cationic lipid nanoparticles, functionalized with octa-arginine peptides, represent a potentially specific, practical, non-invasive intervention for treating gliomas. This supramolecular platform allows loading both hydrophilic (miRNA) and hydrophobic (anti-tumor drugs, like temozolomide) molecules. This systemic review is the first to describe miRNA delivery systems targeted to gliomas that integrate several types of molecules as active ingredients. Further experimental validation is warranted to confirm the practical value of miRNA delivery systems.
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Affiliation(s)
- José Marcos Jiménez-Morales
- Precision Translational Oncology Laboratory, National Institute of Genomic Medicine (INMEGEN), 14610 Mexico City, Mexico
| | - Yanet Elisa Hernández-Cuenca
- Precision Translational Oncology Laboratory, National Institute of Genomic Medicine (INMEGEN), 14610 Mexico City, Mexico
| | - Ander Reyes-Abrahantes
- Precision Translational Oncology Laboratory, National Institute of Genomic Medicine (INMEGEN), 14610 Mexico City, Mexico
| | - Henry Ruiz-García
- Department of Neurosurgery, Mayo Clinic, Jacksonville, United States; Brain Tumor Stem Cell Research Laboratory, Mayo Clinic, Jacksonville, United States
| | - Francisco Barajas-Olmos
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine (INMEGEN), 14610 Mexico City, Mexico
| | - Humberto García-Ortiz
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine (INMEGEN), 14610 Mexico City, Mexico
| | - Lorena Orozco
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine (INMEGEN), 14610 Mexico City, Mexico
| | - Alfredo Quiñones-Hinojosa
- Department of Neurosurgery, Mayo Clinic, Jacksonville, United States; Brain Tumor Stem Cell Research Laboratory, Mayo Clinic, Jacksonville, United States
| | - Jesús Reyes-González
- Precision Translational Oncology Laboratory, National Institute of Genomic Medicine (INMEGEN), 14610 Mexico City, Mexico.
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10
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Reyes-González J, Barajas-Olmos F, García-Ortiz H, Magraner-Pardo L, Pons T, Moreno S, Aguirre-Cruz L, Reyes-Abrahantes A, Martínez-Hernández A, Contreras-Cubas C, Barrios-Payan J, Ruiz-Garcia H, Hernandez-Pando R, Quiñones-Hinojosa A, Orozco L, Abrahantes-Pérez MDC. Brain radiotoxicity-related 15CAcBRT gene expression signature predicts survival prognosis of glioblastoma patients. Neuro Oncol 2022; 25:303-314. [PMID: 35802478 PMCID: PMC9925695 DOI: 10.1093/neuonc/noac171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Glioblastoma is the most common and devastating primary brain cancer. Radiotherapy is standard of care; however, it is associated with brain radiation toxicity (BRT). This study used a multi-omics approach to determine whether BRT-related genes (RGs) harbor survival prognostic value and whether their encoded proteins represent novel therapeutic targets for glioblastoma. METHODS RGs were identified through analysis of single-nucleotide variants associated with BRT (R-SNVs). Functional relationships between RGs were established using Protein-Protein Interaction networks. The influence of RGs and their functional groups on glioblastoma prognosis was evaluated using clinical samples from the Glioblastoma Bio-Discovery Portal database and validated using the Chinese Glioma Genome Atlas dataset. The identification of clusters of radiotoxic and putative pathogenic variants in proteins encoded by RGs was achieved by computational 3D structural analysis. RESULTS We identified the BRT-related 15CAcBRT molecular signature with prognostic value in glioblastoma, by analysis of the COMT and APOE protein functional groups. Its external validation confirmed clinical relevance independent of age, MGMT promoter methylation status, and IDH mutation status. Interestingly, the genes IL6, APOE, and MAOB documented significant gene expression levels alteration, useful for drug repositioning. Biological networks associated with 15CAcBRT signature involved pathways relevant to cancer and neurodegenerative diseases. Analysis of 3D clusters of radiotoxic and putative pathogenic variants in proteins coded by RGs unveiled potential novel therapeutic targets in neuro-oncology. CONCLUSIONS 15CAcBRT is a BRT-related molecular signature with prognostic significance for glioblastoma patients and represents a hub for drug repositioning and development of novel therapies.
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Affiliation(s)
| | | | - Humberto García-Ortiz
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | | | - Tirso Pons
- Department of Immunology and Oncology, National Center for Biotechnology, Spanish National Research Council (CNB-CSIC), Madrid, Spain
| | - Sergio Moreno
- Radioneurosurgery Unit, National Institute of Neurology and Neurosurgery;Mexico City, Mexico
| | - Lucinda Aguirre-Cruz
- Neuroendocrinology Laboratory, National Institute of Neurology and Neurosurgery; Mexico City, Mexico
| | - Andy Reyes-Abrahantes
- Precision Translational Oncology Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Angélica Martínez-Hernández
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Cecilia Contreras-Cubas
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Jorge Barrios-Payan
- Department of Pathology, National Institute of Medical Sciences and Nutrition Salvador Zubiran, Mexico City, Mexico
| | - Henry Ruiz-Garcia
- Department of Neurosurgery and Brain Tumor Stem Cell Research Laboratory, Mayo Clinic, Jacksonville, Florida,USA
| | - Rogelio Hernandez-Pando
- Department of Pathology, National Institute of Medical Sciences and Nutrition Salvador Zubiran, Mexico City, Mexico
| | - Alfredo Quiñones-Hinojosa
- Department of Neurosurgery and Brain Tumor Stem Cell Research Laboratory, Mayo Clinic, Jacksonville, Florida,USA
| | - Lorena Orozco
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - María del Carmen Abrahantes-Pérez
- Corresponding Author: María del Carmen Abrahantes-Pérez, PhD, Precision Translational Oncology Laboratory, National Institute of Genomic Medicine, Periférico Sur 4809, Tlalpan, Mexico City C.P. 14610, Mexico ()
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11
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Contreras-Cubas C, Barajas-Olmos F, Frayre-Martínez MI, Siordia-Reyes G, Guízar-Sánchez CC, García-Ortiz H, Orozco L, Baca V. Dysferlinopathy misdiagnosed with juvenile polymyositis in the pre-symptomatic stage of hyperCKemia: a case report and literature review. BMC Med Genomics 2022; 15:139. [PMID: 35725460 PMCID: PMC9208210 DOI: 10.1186/s12920-022-01284-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 06/10/2022] [Indexed: 12/05/2022] Open
Abstract
Background Dysferlinopathy encompasses a group of rare muscular dystrophies caused by recessive mutations in the DYSF gene. The phenotype ranges from asymptomatic elevated serum creatine kinase (hyperCKemia) to selective and progressive involvement of the proximal and/or distal muscles of the limbs. Bohan and Peter criteria are the most widely used for the diagnosis of polymyositis, but they have limitations and can misclassify muscular dystrophies with inflammation as polymyositis. Most dysferlinopathy patients have muscle biopsies with inflammation and thus are vulnerable to misdiagnosis with polymyositis and inappropriate treatment with steroids and immunosuppressors.
Case presentation We describe a 14 years-old male patient who was referred for assessment of asymptomatic hyperCKemia (26,372 IU/L). An X-linked dystrophinopathy initially was ruled out by direct genetic testing. Juvenile polymyositis was considered based on muscle biopsy, creatine kinase levels, and electromyography changes. Corticosteroid treatment triggered proximal lower limb muscular weakness, and no full muscular strength recovery was observed after corticosteroid withdrawal. Based on these observations, a limb-girdle muscular dystrophy (LGMD) was suspected, and LGMDR2 was confirmed by whole exome sequencing. Conclusion We report a dysferlinopathy patient who was misdiagnosed with juvenile polymyositis and explore in a literature review how common such misdiagnoses are. With diagnosis based only on routine clinicopathological examinations, distinguishing an inflammatory myopathy from dysferlinopathy is quite difficult. We suggest that before establishing a diagnosis of “definite” or “probable” juvenile polymyositis, according to Bohan and Peter or current ACR/EULAR criteria, a muscular dystrophy must first be ruled out.
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Affiliation(s)
- Cecilia Contreras-Cubas
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, SS, Mexico City, Mexico
| | - Francisco Barajas-Olmos
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, SS, Mexico City, Mexico
| | | | | | - Claudia C Guízar-Sánchez
- Department of Physical Medicine and Rehabilitation, Hospital de Pediatría, CMN Siglo XXI IMSS, Mexico City, Mexico
| | - Humberto García-Ortiz
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, SS, Mexico City, Mexico
| | - Lorena Orozco
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, SS, Mexico City, Mexico
| | - Vicente Baca
- Department of Rheumatology, Hospital de Pediatría, CMN Siglo XXI IMSS, Mexico City, Mexico.
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12
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Aguilar-Ordoñez I, Pérez-Villatoro F, García-Ortiz H, Barajas-Olmos F, Ballesteros-Villascán J, Fresno C, Garcíarrubio A, Fernández-López JC, Tovar H, Hernández-Lemus E, Orozco L, Soberón X, Morett E. Correction: Whole genome variation in 27 Mexican indigenous populations, demographic and biomedical insights. PLoS One 2022; 17:e0269217. [PMID: 35613137 PMCID: PMC9132332 DOI: 10.1371/journal.pone.0269217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
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13
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Jurado-Camacho PA, Cid-Soto MA, Barajas-Olmos F, García-Ortíz H, Baca-Peynado P, Martínez-Hernández A, Centeno-Cruz F, Contreras-Cubas C, González-Villalpando ME, Saldaña-Álvarez Y, Salas-Martinez G, Mendoza-Caamal EC, González-Villalpando C, Córdova EJ, Orozco L. Exome Sequencing Data Analysis and a Case-Control Study in Mexican Population Reveals Lipid Trait Associations of New and Known Genetic Variants in Dyslipidemia-Associated Loci. Front Genet 2022; 13:807381. [PMID: 35669185 PMCID: PMC9164108 DOI: 10.3389/fgene.2022.807381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Plasma lipid levels are a major risk factor for cardiovascular diseases. Although international efforts have identified a group of loci associated with the risk of dyslipidemia, Latin American populations have been underrepresented in these studies.Objective: To know the genetic variation occurring in lipid-related loci in the Mexican population and its association with dyslipidemia.Methods: We searched for single-nucleotide variants in 177 lipid candidate genes using previously published exome sequencing data from 2838 Mexican individuals belonging to three different cohorts. With the extracted variants, we performed a case-control study. Logistic regression and quantitative trait analyses were implemented in PLINK software. We used an LD pruning using a 50-kb sliding window size, a 5-kb window step size and a r2 threshold of 0.1.Results: Among the 34251 biallelic variants identified in our sample population, 33% showed low frequency. For case-control study, we selected 2521 variants based on a minor allele frequency ≥1% in all datasets. We found 19 variants in 9 genes significantly associated with at least one lipid trait, with the most significant associations found in the APOA1/C3/A4/A5-ZPR1-BUD13 gene cluster on chromosome 11. Notably, all 11 variants associated with hypertriglyceridemia were within this cluster; whereas variants associated with hypercholesterolemia were located at chromosome 2 and 19, and for low high density lipoprotein cholesterol were in chromosomes 9, 11, and 19. No significant associated variants were found for low density lipoprotein. We found several novel variants associated with different lipemic traits: rs3825041 in BUD13 with hypertriglyceridemia, rs7252453 in CILP2 with decreased risk to hypercholesterolemia and rs11076176 in CETP with increased risk to low high density lipoprotein cholesterol.Conclusions: We identified novel variants in lipid-regulation candidate genes in the Mexican population, an underrepresented population in genomic studies, demonstrating the necessity of more genomic studies on multi-ethnic populations to gain a deeper understanding of the genetic structure of the lipemic traits.
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Affiliation(s)
- Pedro A. Jurado-Camacho
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
- Posgraduate in Biomedical Sciences, National Autonomous University of Mexico, Mexico City, Mexico
| | - Miguel A. Cid-Soto
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Francisco Barajas-Olmos
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Humberto García-Ortíz
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Paulina Baca-Peynado
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
- Posgraduate in Biomedical Sciences, National Autonomous University of Mexico, Mexico City, Mexico
| | - Angélica Martínez-Hernández
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Federico Centeno-Cruz
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Cecilia Contreras-Cubas
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - María Elena González-Villalpando
- Centro de Estudios en Diabetes, Unidad de Investigación en Diabetes y Riesgo Cardiovascular, Centro de Investigación en Salud Poblacional, Instituto Nacional de Salud Pública, Mexico City, Mexico
| | - Yolanda Saldaña-Álvarez
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Guadalupe Salas-Martinez
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | | | - Clicerio González-Villalpando
- Centro de Estudios en Diabetes, Unidad de Investigación en Diabetes y Riesgo Cardiovascular, Centro de Investigación en Salud Poblacional, Instituto Nacional de Salud Pública, Mexico City, Mexico
| | - Emilio J. Córdova
- Oncogenomics Consortium Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
- *Correspondence: Emilio J. Córdova, ; Lorena Orozco,
| | - Lorena Orozco
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
- *Correspondence: Emilio J. Córdova, ; Lorena Orozco,
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14
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Hindy G, Dornbos P, Chaffin MD, Liu DJ, Wang M, Selvaraj MS, Zhang D, Park J, Aguilar-Salinas CA, Antonacci-Fulton L, Ardissino D, Arnett DK, Aslibekyan S, Atzmon G, Ballantyne CM, Barajas-Olmos F, Barzilai N, Becker LC, Bielak LF, Bis JC, Blangero J, Boerwinkle E, Bonnycastle LL, Bottinger E, Bowden DW, Bown MJ, Brody JA, Broome JG, Burtt NP, Cade BE, Centeno-Cruz F, Chan E, Chang YC, Chen YDI, Cheng CY, Choi WJ, Chowdhury R, Contreras-Cubas C, Córdova EJ, Correa A, Cupples LA, Curran JE, Danesh J, de Vries PS, DeFronzo RA, Doddapaneni H, Duggirala R, Dutcher SK, Ellinor PT, Emery LS, Florez JC, Fornage M, Freedman BI, Fuster V, Garay-Sevilla ME, García-Ortiz H, Germer S, Gibbs RA, Gieger C, Glaser B, Gonzalez C, Gonzalez-Villalpando ME, Graff M, Graham SE, Grarup N, Groop LC, Guo X, Gupta N, Han S, Hanis CL, Hansen T, He J, Heard-Costa NL, Hung YJ, Hwang MY, Irvin MR, Islas-Andrade S, Jarvik GP, Kang HM, Kardia SLR, Kelly T, Kenny EE, Khan AT, Kim BJ, Kim RW, Kim YJ, Koistinen HA, Kooperberg C, Kuusisto J, Kwak SH, Laakso M, Lange LA, Lee J, Lee J, Lee S, Lehman DM, Lemaitre RN, Linneberg A, Liu J, Loos RJF, Lubitz SA, Lyssenko V, Ma RCW, Martin LW, Martínez-Hernández A, Mathias RA, McGarvey ST, McPherson R, Meigs JB, Meitinger T, Melander O, Mendoza-Caamal E, Metcalf GA, Mi X, Mohlke KL, Montasser ME, Moon JY, Moreno-Macías H, Morrison AC, Muzny DM, Nelson SC, Nilsson PM, O'Connell JR, Orho-Melander M, Orozco L, Palmer CNA, Palmer ND, Park CJ, Park KS, Pedersen O, Peralta JM, Peyser PA, Post WS, Preuss M, Psaty BM, Qi Q, Rao DC, Redline S, Reiner AP, Revilla-Monsalve C, Rich SS, Samani N, Schunkert H, Schurmann C, Seo D, Seo JS, Sim X, Sladek R, Small KS, So WY, Stilp AM, Tai ES, Tam CHT, Taylor KD, Teo YY, Thameem F, Tomlinson B, Tsai MY, Tuomi T, Tuomilehto J, Tusié-Luna T, Udler MS, van Dam RM, Vasan RS, Viaud Martinez KA, Wang FF, Wang X, Watkins H, Weeks DE, Wilson JG, Witte DR, Wong TY, Yanek LR, Kathiresan S, Rader DJ, Rotter JI, Boehnke M, McCarthy MI, Willer CJ, Natarajan P, Flannick JA, Khera AV, Peloso GM. Rare coding variants in 35 genes associate with circulating lipid levels-A multi-ancestry analysis of 170,000 exomes. Am J Hum Genet 2022; 109:81-96. [PMID: 34932938 PMCID: PMC8764201 DOI: 10.1016/j.ajhg.2021.11.021] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/21/2021] [Indexed: 01/14/2023] Open
Abstract
Large-scale gene sequencing studies for complex traits have the potential to identify causal genes with therapeutic implications. We performed gene-based association testing of blood lipid levels with rare (minor allele frequency < 1%) predicted damaging coding variation by using sequence data from >170,000 individuals from multiple ancestries: 97,493 European, 30,025 South Asian, 16,507 African, 16,440 Hispanic/Latino, 10,420 East Asian, and 1,182 Samoan. We identified 35 genes associated with circulating lipid levels; some of these genes have not been previously associated with lipid levels when using rare coding variation from population-based samples. We prioritize 32 genes in array-based genome-wide association study (GWAS) loci based on aggregations of rare coding variants; three (EVI5, SH2B3, and PLIN1) had no prior association of rare coding variants with lipid levels. Most of our associated genes showed evidence of association among multiple ancestries. Finally, we observed an enrichment of gene-based associations for low-density lipoprotein cholesterol drug target genes and for genes closest to GWAS index single-nucleotide polymorphisms (SNPs). Our results demonstrate that gene-based associations can be beneficial for drug target development and provide evidence that the gene closest to the array-based GWAS index SNP is often the functional gene for blood lipid levels.
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Affiliation(s)
- George Hindy
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Clinical Sciences, Lund University, Malmö, Sweden; Department of Population Medicine, Qatar University College of Medicine, QU Health, Doha, Qatar
| | - Peter Dornbos
- Programs in Metabolism and Medical & Population Genetics, Broad Institute, Cambridge, MA 02142, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Mark D Chaffin
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Dajiang J Liu
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA 17033, USA
| | - Minxian Wang
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Margaret Sunitha Selvaraj
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - David Zhang
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Joseph Park
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Lucinda Antonacci-Fulton
- Department of Genetics, Washington University in St. Louis, St. Louis, MO 63110, USA; The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Diego Ardissino
- ASTC: Associazione per lo Studio Della Trombosi in Cardiologia, Pavia, Italy; Azienda Ospedaliero-Universitaria di Parma, Parma, Italy; Universitˆ, degli Studi di Parma, Parma, Italy
| | - Donna K Arnett
- Dean's Office, College of Public Health, University of Kentucky, Lexington, KY 40536, USA
| | - Stella Aslibekyan
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Gil Atzmon
- Departments of Medicine and Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA; University of Haifa, Faculty of Natural Science, Haifa, Israel
| | - Christie M Ballantyne
- Houston Methodist Debakey Heart and Vascular Center, Houston, TX 77030, USA; Section of Cardiovascular Research, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Nir Barzilai
- Departments of Medicine and Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Lewis C Becker
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Lawrence F Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 49109, USA
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101, USA
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lori L Bonnycastle
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Erwin Bottinger
- Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Digital Health Center, Hasso Plattner Institute, University of Potsdam, Potsdam, Germany
| | - Donald W Bowden
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Matthew J Bown
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK; NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101, USA
| | - Jai G Broome
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Noël P Burtt
- Programs in Metabolism and Medical & Population Genetics, Broad Institute, Cambridge, MA 02142, USA
| | - Brian E Cade
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Division of Sleep Medicine, Harvard Medical School, Boston, MA 02115, USA
| | | | - Edmund Chan
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Singapore
| | - Yi-Cheng Chang
- Institute of Biomedical Sciences, Academia Sinica, Taiwan
| | - Yii-Der I Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Ching-Yu Cheng
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Singapore; Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore; Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
| | - Won Jung Choi
- Psomagen, Inc. (formerly Macrogen USA), 1330 Piccard Drive Ste 103, Rockville, MD 20850, USA
| | - Rajiv Chowdhury
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK; Centre for Non-Communicable Disease Research, Bangladesh
| | | | | | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - L Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA; NHLBI Framingham Heart Study, Framingham, MA 01702, USA
| | - Joanne E Curran
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA
| | - John Danesh
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK; The National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics at the University of Cambridge, Cambridge, UK
| | - Paul S de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Ralph A DeFronzo
- Department of Medicine, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ravindranath Duggirala
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA
| | - Susan K Dutcher
- Department of Genetics, Washington University in St. Louis, St. Louis, MO 63110, USA; The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Patrick T Ellinor
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA 02114, USA; Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Leslie S Emery
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Jose C Florez
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Diabetes Research Center (Diabetes Unit), Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Myriam Fornage
- Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 770030, USA
| | - Barry I Freedman
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Valentin Fuster
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
| | - Ma Eugenia Garay-Sevilla
- Department of Medical Science, Division of Health Science, University of Guanajuato, Guanajuanto, Mexico
| | | | | | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; German Center for Diabetes Research, Neuherberg, Germany
| | - Benjamin Glaser
- Endocrinology and Metabolism Service, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Clicerio Gonzalez
- Unidad de Diabetes y Riesgo Cardiovascular, Instituto Nacional de Salud Pœblica, Cuernavaca, Morelos, Mexico
| | | | - Mariaelisa Graff
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Sarah E Graham
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Niels Grarup
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Leif C Groop
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University Diabetes Centre, Malmö, Sweden; Finnish Institute for Molecular Genetics, University of Helsinki, Helsinki, Finland
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Namrata Gupta
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Sohee Han
- Division of Genome Science, Department of Precision Medicine, Chungcheongbuk-do, Republic of Korea
| | - Craig L Hanis
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Jiang He
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA 70112, USA; Tulane University Translational Science Institute, New Orleans, LA 70112, USA
| | - Nancy L Heard-Costa
- NHLBI Framingham Heart Study, Framingham, MA 01702, USA; Department of Neurology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Yi-Jen Hung
- Division of Endocrine and Metabolism, Tri-Service General Hospital Songshan Branch, Taipei, Taiwan
| | - Mi Yeong Hwang
- Division of Genome Science, Department of Precision Medicine, Chungcheongbuk-do, Republic of Korea
| | - Marguerite R Irvin
- Department of Epidemiology, School of Public Health, UAB, Birmingham, AL 35294, USA
| | - Sergio Islas-Andrade
- Dirección de Investigación, Hospital General de México "Dr. Eduardo Liceaga," Secretaría de Salud, Mexico City, Mexico
| | - Gail P Jarvik
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington Medical Center, Seattle, WA 98195, USA
| | - Hyun Min Kang
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 49109, USA
| | - Tanika Kelly
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA 70112, USA
| | - Eimear E Kenny
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alyna T Khan
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Bong-Jo Kim
- Division of Genome Science, Department of Precision Medicine, Chungcheongbuk-do, Republic of Korea
| | - Ryan W Kim
- Psomagen, Inc. (formerly Macrogen USA), 1330 Piccard Drive Ste 103, Rockville, MD 20850, USA
| | - Young Jin Kim
- Division of Genome Science, Department of Precision Medicine, Chungcheongbuk-do, Republic of Korea
| | - Heikki A Koistinen
- Department of Public Health Solutions, Finnish Institute for Health and Welfare, Helsinki, Finland; Minerva Foundation Institute for Medical Research, Helsinki, Finland; University of Helsinki and Department of Medicine, Helsinki University Central Hospital, Helsinki, Finland
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98103, USA
| | - Johanna Kuusisto
- Institute of Clinical Medicine, University of Eastern Finland, and Kuopio University Hospital, Kuopio, Finland
| | - Soo Heon Kwak
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Markku Laakso
- Institute of Clinical Medicine, University of Eastern Finland, and Kuopio University Hospital, Kuopio, Finland
| | - Leslie A Lange
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Jiwon Lee
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Juyoung Lee
- Division of Genome Science, Department of Precision Medicine, Chungcheongbuk-do, Republic of Korea
| | - Seonwook Lee
- Psomagen, Inc. (formerly Macrogen USA), 1330 Piccard Drive Ste 103, Rockville, MD 20850, USA
| | - Donna M Lehman
- Department of Medicine, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Rozenn N Lemaitre
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101, USA
| | - Allan Linneberg
- Center for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, The Capital Region, Copenhagen, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jianjun Liu
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Singapore; Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
| | - Ruth J F Loos
- Charles R. Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Steven A Lubitz
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA 02114, USA; Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Valeriya Lyssenko
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University Diabetes Centre, Malmö, Sweden; University of Bergen, Bergen, Norway
| | - Ronald C W Ma
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China; Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong, China; Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Lisa Warsinger Martin
- Division of Cardiology, Department of Medicine, George Washington University, Washington, DC 20037, USA
| | | | - Rasika A Mathias
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Stephen T McGarvey
- Department of Epidemiology and International Health Institute, Brown University School of Public Health, Providence, RI 02912, USA
| | - Ruth McPherson
- Ruddy Canadian Cardiovascuar Genetics Centre, University of Ottawa Heart Institute, Ottawa, ON, Canada
| | - James B Meigs
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; General Medicine Division, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Thomas Meitinger
- Deutsches Forschungszentrum fŸr Herz-Kreislauferkrankungen, Partner Site Munich Heart Alliance, Munich, Germany; Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Olle Melander
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University Diabetes Centre, Malmö, Sweden; Department of Emergency and Internal Medicine, SkŒne University Hospital, Malmö, Sweden
| | | | - Ginger A Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xuenan Mi
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA 70112, USA
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27514, USA
| | - May E Montasser
- University of Maryland School of Medicine, Division of Endocrinology, Diabetes and Nutrition and Program for Personalized and Genomic Medicine, Baltimore, MD 21201, USA
| | - Jee-Young Moon
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | | | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sarah C Nelson
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Peter M Nilsson
- Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Jeffrey R O'Connell
- University of Maryland School of Medicine, Division of Endocrinology, Diabetes and Nutrition and Program for Personalized and Genomic Medicine, Baltimore, MD 21201, USA
| | | | - Lorena Orozco
- Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Colin N A Palmer
- Pat Macpherson Centre for Pharmacogenetics and Pharmacogenomics, Division of Population Health and Genomics, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Nicholette D Palmer
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Cheol Joo Park
- Psomagen, Inc. (formerly Macrogen USA), 1330 Piccard Drive Ste 103, Rockville, MD 20850, USA
| | - Kyong Soo Park
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea; Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea; Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Republic of Korea
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Juan M Peralta
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 49109, USA
| | - Wendy S Post
- Division of Cardiology, Department of Medicine, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Michael Preuss
- Charles R. Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101, USA; Department of Epidemiology, University of Washington, Seattle, WA 98101, USA; Department of Health Services, University of Washington, Seattle, WA 98101, USA
| | - Qibin Qi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - D C Rao
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Susan Redline
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Division of Sleep Medicine, Harvard Medical School, Boston, MA 02115, USA
| | | | | | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Nilesh Samani
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK; NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Heribert Schunkert
- Deutsches Herzzentrum München, Technische UniversitŠt München, Deutsches Zentrum fŸr Herz-Kreislauf-Forschung, München, Germany
| | - Claudia Schurmann
- Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Digital Health Center, Hasso Plattner Institute, University of Potsdam, Potsdam, Germany; Charles R. Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Daekwan Seo
- Psomagen, Inc. (formerly Macrogen USA), 1330 Piccard Drive Ste 103, Rockville, MD 20850, USA
| | - Jeong-Sun Seo
- Psomagen, Inc. (formerly Macrogen USA), 1330 Piccard Drive Ste 103, Rockville, MD 20850, USA
| | - Xueling Sim
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore
| | - Rob Sladek
- Department of Human Genetics, McGill University, Montreal, QC, Canada; Division of Endocrinology and Metabolism, Department of Medicine, McGill University, Montreal, QC, Canada; McGill University and Génome Québec Innovation Centre, Montreal, QC, Canada
| | - Kerrin S Small
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Wing Yee So
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China; Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong, China; Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Adrienne M Stilp
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - E Shyong Tai
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Singapore; Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore; Duke-NUS Medical School Singapore, Singapore
| | - Claudia H T Tam
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China; Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong, China; Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Yik Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore; Department of Statistics and Applied Probability, National University of Singapore, Singapore; Life Sciences Institute, National University of Singapore, Singapore
| | - Farook Thameem
- Department of Biochemistry, Faculty of Medicine, Health Science Center, Kuwait University, Safat, Kuwait
| | - Brian Tomlinson
- Faculty of Medicine, Macau University of Science & Technology, Macau, China
| | - Michael Y Tsai
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Tiinamaija Tuomi
- Department of Endocrinology, Abdominal Centre, Helsinki University Hospital, Helsinki, Finland; Folkhälsan Research Centre, Helsinki, Finland; Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland
| | - Jaakko Tuomilehto
- Public Health Promotion Unit, Finnish Institute for Health and Welfare, Helsinki, Finland; Department of Public Health, University of Helsinki, Helsinki, Finland; Diabetes Research Group, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Teresa Tusié-Luna
- Instituto Nacional de Ciencias Medicas y Nutricion, Mexico City, Mexico; Departamento de Medicina Genómica y Toxicología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México/ Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Miriam S Udler
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Diabetes Research Center (Diabetes Unit), Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Rob M van Dam
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore; Department of Nutrition, Harvard School of Public Health, Boston, MA 02115, USA
| | - Ramachandran S Vasan
- NHLBI Framingham Heart Study, Framingham, MA 01702, USA; Departments of Medicine & Epidemiology, Boston University Schools of Medicine & Public Health, Boston, MA 02118, USA
| | | | - Fei Fei Wang
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Xuzhi Wang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
| | - Hugh Watkins
- Cardiovascular Medicine, Radcliffe Department of Medicine and the Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Daniel E Weeks
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA; Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - James G Wilson
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Daniel R Witte
- Department of Public Health, Aarhus University, Aarhus, Denmark; Steno Diabetes Center Aarhus, Aarhus, Denmark
| | - Tien-Yin Wong
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Singapore; Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore; Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
| | - Lisa R Yanek
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Sekar Kathiresan
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Verve Therapeutics, Cambridge, MA 02139, USA
| | - Daniel J Rader
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Mark I McCarthy
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK; Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Cristen J Willer
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Pradeep Natarajan
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA 02114, USA; Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Jason A Flannick
- Programs in Metabolism and Medical & Population Genetics, Broad Institute, Cambridge, MA 02142, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Amit V Khera
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Gina M Peloso
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA.
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15
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Mirzaeicheshmeh E, Zerrweck C, Centeno-Cruz F, Baca-Peynado P, Martinez-Hernandez A, García-Ortiz H, Contreras-Cubas C, Salas-Martínez MG, Saldaña-Alvarez Y, Mendoza-Caamal EC, Barajas-Olmos F, Orozco L. Alterations of DNA methylation during adipogenesis differentiation of mesenchymal stem cells isolated from adipose tissue of patients with obesity is associated with type 2 diabetes. Adipocyte 2021; 10:493-504. [PMID: 34699309 PMCID: PMC8555535 DOI: 10.1080/21623945.2021.1978157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 09/01/2021] [Accepted: 09/03/2021] [Indexed: 11/22/2022] Open
Abstract
Adipogenesis regulation is crucial for mature adipocyte function. In obesity, a major driver of type 2 diabetes (T2D), this process is disrupted and remains poorly characterized. Here we identified altered DNA methylation profiles in diabetic obese patients, during three adipocytes differentiation stages. We isolated mesenchymal cells from visceral adipose tissue of obese patients with and without T2D to analyse DNA methylation profiles at 0, 3, and 18 days of ex vivo differentiation and documented their impact on gene expression. Methylation and gene expression were analysed with EPIC and Clarion S arrays, respectively. Patients with T2D had epigenetic alterations in all the analysed stages, and these were mainly observed in genes important in adipogenesis, insulin resistance, cell death programming, and immune effector processes. Importantly, at 3 days, we found six-fold more methylated CpG alterations than in the other stages. This is the first study to document epigenetic markers that persist through all three adipogenesis stages and their impact on gene expression, which could be a cellular metabolic memory involved in T2D. Our data provided evidence that, throughout the adipogenesis process, alterations occur in methylation that might impact mature adipocyte function, cause tissue malfunction, and potentially, lead to the development of T2D.
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Affiliation(s)
- Elaheh Mirzaeicheshmeh
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional De Medicina Genómica, Ss, Mexico City, Mexico
| | - Carlos Zerrweck
- Clínica de Obesidad del Hospital General Tláhuac, SSA, Mexico City, Mexico
- Facultad De Medicina, Alta Especialidad En Cirugía Bariatrica, Unam, Mexico City, Mexico
| | - Federico Centeno-Cruz
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional De Medicina Genómica, Ss, Mexico City, Mexico
| | - Paulina Baca-Peynado
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional De Medicina Genómica, Ss, Mexico City, Mexico
| | - Angélica Martinez-Hernandez
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional De Medicina Genómica, Ss, Mexico City, Mexico
| | - Humberto García-Ortiz
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional De Medicina Genómica, Ss, Mexico City, Mexico
| | - Cecilia Contreras-Cubas
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional De Medicina Genómica, Ss, Mexico City, Mexico
| | | | - Yolanda Saldaña-Alvarez
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional De Medicina Genómica, Ss, Mexico City, Mexico
| | | | - Francisco Barajas-Olmos
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional De Medicina Genómica, Ss, Mexico City, Mexico
| | - Lorena Orozco
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional De Medicina Genómica, Ss, Mexico City, Mexico
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16
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Morales-Rivera MI, Alemón-Medina R, Martínez-Hernández A, Gómez-Garduño J, Mirzaeicheshmeh E, Altamirano-Bustamante NF, Ilizaliturri-Flores I, Mendoza-Caamal EC, Pérez-Guillé MG, García-Álvarez R, Contreras-Cubas C, Centeno-Cruz F, Revilla-Monsalve C, García-Ortiz H, Barajas-Olmos F, Orozco L. The L125F MATE1 variant enriched in populations of Amerindian origin is associated with increased plasma levels of metformin and lactate. Biomed Pharmacother 2021; 142:112009. [PMID: 34388523 DOI: 10.1016/j.biopha.2021.112009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 07/26/2021] [Accepted: 08/02/2021] [Indexed: 11/28/2022] Open
Abstract
Genetic factors that affect variability in metformin response have been poorly studied in the Latin American population, despite its being the initial drug therapy for type 2 diabetes, one of the most prevalent diseases in that region. Metformin pharmacokinetics is carried out by members of the membrane transporters superfamily (SLCs), being the multidrug and toxin extrusion protein 1 (MATE1), one of the most studied. Some genetic variants in MATE1 have been associated with reduced in vitro metformin transport. They include rs77474263 p.[L125F], a variant present at a frequency of 13.8% in Latin Americans, but rare worldwide (less than 1%). Using exome sequence data and TaqMan genotyping, we revealed that the Mexican population has the highest frequency of this variant: 16% in Mestizos and 27% in Amerindians, suggesting a possible Amerindian origin. To elucidate the metformin pharmacogenetics, a children cohort was genotyped, allowing us to describe, for the first time, a MATE1 rs77474263 TT homozygous individual. An additive effect of the L125F variant was observed on blood metformin accumulation, revealing the highest metformin and lactate serum levels in the TT homozygote, and intermediate metformin values in the heterozygotes. Moreover, a molecular dynamics analysis suggested that the genetic variant effect on metformin efflux could be due to a decreased protein permeability. We conclude that pharmacogenetics could be useful in enhancing metformin pharmacovigilance in populations having a high frequency of the risk genotype, especially considering that these populations also have a higher susceptibility to the diseases for which metformin is the first-choice drug.
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Affiliation(s)
- Monserrat I Morales-Rivera
- Immunogenomics and Metabolic Diseases Laboratory, Instituto Nacional de Medicina Genómica, SS, CDMX, Mexico; Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, CDMX, Mexico
| | | | | | | | - Elaheh Mirzaeicheshmeh
- Immunogenomics and Metabolic Diseases Laboratory, Instituto Nacional de Medicina Genómica, SS, CDMX, Mexico
| | | | | | - Elvia C Mendoza-Caamal
- Immunogenomics and Metabolic Diseases Laboratory, Instituto Nacional de Medicina Genómica, SS, CDMX, Mexico
| | | | | | - Cecilia Contreras-Cubas
- Immunogenomics and Metabolic Diseases Laboratory, Instituto Nacional de Medicina Genómica, SS, CDMX, Mexico
| | - Federico Centeno-Cruz
- Immunogenomics and Metabolic Diseases Laboratory, Instituto Nacional de Medicina Genómica, SS, CDMX, Mexico
| | - Cristina Revilla-Monsalve
- Medical Research Unit in Metabolic Diseases, UMAE Hospital de Cardiología, Centro Médico Nacional Siglo XXI, IMSS, CDMX, Mexico
| | - Humberto García-Ortiz
- Immunogenomics and Metabolic Diseases Laboratory, Instituto Nacional de Medicina Genómica, SS, CDMX, Mexico
| | - Francisco Barajas-Olmos
- Immunogenomics and Metabolic Diseases Laboratory, Instituto Nacional de Medicina Genómica, SS, CDMX, Mexico
| | - Lorena Orozco
- Immunogenomics and Metabolic Diseases Laboratory, Instituto Nacional de Medicina Genómica, SS, CDMX, Mexico.
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17
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Mendoza-Caamal EC, Barajas-Olmos F, Mirzaeicheshmeh E, Ilizaliturri-Flores I, Aguilar-Salinas CA, Gómez-Velasco DV, Cicerón-Arellano I, Reséndiz-Rodríguez A, Martínez-Hernández A, Contreras-Cubas C, Islas-Andrade S, Zerrweck C, García-Ortiz H, Orozco L. Two novel variants in DYRK1B causative of AOMS3: expanding the clinical spectrum. Orphanet J Rare Dis 2021; 16:291. [PMID: 34193236 PMCID: PMC8247206 DOI: 10.1186/s13023-021-01924-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 06/20/2021] [Indexed: 12/28/2022] Open
Abstract
Background We investigated pathogenic DYRK1B variants causative of abdominal obesity-metabolic syndrome 3 (AOMS3) in a group of patients originally diagnosed with type 2 diabetes. All DYRK1B exons were analyzed in a sample of 509 unrelated adults with type 2 diabetes and 459 controls, all belonging to the DMS1 SIGMA-cohort (ExAC). We performed in silico analysis on missense variants using Variant Effect Predictor software. To evaluate co-segregation, predicted pathogenic variants were genotyped in other family members. We performed molecular dynamics analysis for the co-segregating variants. Results After filtering, Mendelian genotypes were confirmed in two probands bearing two novel variants, p.Arg252His and p.Lys68Gln. Both variants co-segregated with the AOMS3 phenotype in classic dominant autosomal inheritance with full penetrance. In silico analysis revealed impairment of the DYRK1B protein function by both variants. For the first time, we describe age-dependent variable expressivity of this entity, with central obesity and insulin resistance apparent in childhood; morbid obesity, severe hypertriglyceridemia, and labile type 2 diabetes appearing before 40 years of age; and hypertension emerging in the fifth decade of life. We also report the two youngest individuals suffering from AOMS3. Conclusions Monogenic forms of metabolic diseases could be misdiagnosed and should be suspected in families with several affected members and early-onset metabolic phenotypes that are difficult to control. Early diagnostic strategies and medical interventions, even before symptoms or complications appear, could be useful. Supplementary Information The online version contains supplementary material available at 10.1186/s13023-021-01924-z.
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Affiliation(s)
| | - Francisco Barajas-Olmos
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, SS. Periférico Sur 4809, Colonia Arenal Tepepan, Alcaldía Tlalpan, C.P. 14610, Mexico City, Mexico
| | - Elaheh Mirzaeicheshmeh
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, SS. Periférico Sur 4809, Colonia Arenal Tepepan, Alcaldía Tlalpan, C.P. 14610, Mexico City, Mexico
| | | | - Carlos A Aguilar-Salinas
- Metabolic Diseases Research Unit, National Institute of Medical Science and Nutrition Salvador Zubirán, Mexico City, Mexico.,Department of Endocrinology and Metabolism, National Institute of Medical Science and Nutrition Salvador Zubirán, Mexico City, Mexico.,Direction of Nutrition, National Institute of Medical Science and Nutrition Salvador Zubirán, Mexico City, Mexico.,School of Medicine and Health Sciences, Monterrey Institute of Technology, Mexico City, Mexico
| | - Donaji V Gómez-Velasco
- Metabolic Diseases Research Unit, National Institute of Medical Science and Nutrition Salvador Zubirán, Mexico City, Mexico.,Department of Endocrinology and Metabolism, National Institute of Medical Science and Nutrition Salvador Zubirán, Mexico City, Mexico.,Direction of Nutrition, National Institute of Medical Science and Nutrition Salvador Zubirán, Mexico City, Mexico.,School of Medicine and Health Sciences, Monterrey Institute of Technology, Mexico City, Mexico
| | | | | | - Angélica Martínez-Hernández
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, SS. Periférico Sur 4809, Colonia Arenal Tepepan, Alcaldía Tlalpan, C.P. 14610, Mexico City, Mexico
| | - Cecilia Contreras-Cubas
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, SS. Periférico Sur 4809, Colonia Arenal Tepepan, Alcaldía Tlalpan, C.P. 14610, Mexico City, Mexico
| | - Sergio Islas-Andrade
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, SS. Periférico Sur 4809, Colonia Arenal Tepepan, Alcaldía Tlalpan, C.P. 14610, Mexico City, Mexico
| | - Carlos Zerrweck
- Integral Clinic of Surgery for Obesity and Metabolic Diseases, General Hospital Tláhuac, SS, Mexico City, Mexico
| | - Humberto García-Ortiz
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, SS. Periférico Sur 4809, Colonia Arenal Tepepan, Alcaldía Tlalpan, C.P. 14610, Mexico City, Mexico
| | - Lorena Orozco
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, SS. Periférico Sur 4809, Colonia Arenal Tepepan, Alcaldía Tlalpan, C.P. 14610, Mexico City, Mexico.
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18
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Goodrich JK, Singer-Berk M, Son R, Sveden A, Wood J, England E, Cole JB, Weisburd B, Watts N, Caulkins L, Dornbos P, Koesterer R, Zappala Z, Zhang H, Maloney KA, Dahl A, Aguilar-Salinas CA, Atzmon G, Barajas-Olmos F, Barzilai N, Blangero J, Boerwinkle E, Bonnycastle LL, Bottinger E, Bowden DW, Centeno-Cruz F, Chambers JC, Chami N, Chan E, Chan J, Cheng CY, Cho YS, Contreras-Cubas C, Córdova E, Correa A, DeFronzo RA, Duggirala R, Dupuis J, Garay-Sevilla ME, García-Ortiz H, Gieger C, Glaser B, González-Villalpando C, Gonzalez ME, Grarup N, Groop L, Gross M, Haiman C, Han S, Hanis CL, Hansen T, Heard-Costa NL, Henderson BE, Hernandez JMM, Hwang MY, Islas-Andrade S, Jørgensen ME, Kang HM, Kim BJ, Kim YJ, Koistinen HA, Kooner JS, Kuusisto J, Kwak SH, Laakso M, Lange L, Lee JY, Lee J, Lehman DM, Linneberg A, Liu J, Loos RJF, Lyssenko V, Ma RCW, Martínez-Hernández A, Meigs JB, Meitinger T, Mendoza-Caamal E, Mohlke KL, Morris AD, Morrison AC, Ng MCY, Nilsson PM, O'Donnell CJ, Orozco L, Palmer CNA, Park KS, Post WS, Pedersen O, Preuss M, Psaty BM, Reiner AP, Revilla-Monsalve C, Rich SS, Rotter JI, Saleheen D, Schurmann C, Sim X, Sladek R, Small KS, So WY, Spector TD, Strauch K, Strom TM, Tai ES, Tam CHT, Teo YY, Thameem F, Tomlinson B, Tracy RP, Tuomi T, Tuomilehto J, Tusié-Luna T, van Dam RM, Vasan RS, Wilson JG, Witte DR, Wong TY, Burtt NP, Zaitlen N, McCarthy MI, Boehnke M, Pollin TI, Flannick J, Mercader JM, O'Donnell-Luria A, Baxter S, Florez JC, MacArthur DG, Udler MS. Determinants of penetrance and variable expressivity in monogenic metabolic conditions across 77,184 exomes. Nat Commun 2021; 12:3505. [PMID: 34108472 PMCID: PMC8190084 DOI: 10.1038/s41467-021-23556-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 04/27/2021] [Indexed: 11/16/2022] Open
Abstract
Hundreds of thousands of genetic variants have been reported to cause severe monogenic diseases, but the probability that a variant carrier develops the disease (termed penetrance) is unknown for virtually all of them. Additionally, the clinical utility of common polygenetic variation remains uncertain. Using exome sequencing from 77,184 adult individuals (38,618 multi-ancestral individuals from a type 2 diabetes case-control study and 38,566 participants from the UK Biobank, for whom genotype array data were also available), we apply clinical standard-of-care gene variant curation for eight monogenic metabolic conditions. Rare variants causing monogenic diabetes and dyslipidemias display effect sizes significantly larger than the top 1% of the corresponding polygenic scores. Nevertheless, penetrance estimates for monogenic variant carriers average 60% or lower for most conditions. We assess epidemiologic and genetic factors contributing to risk prediction in monogenic variant carriers, demonstrating that inclusion of polygenic variation significantly improves biomarker estimation for two monogenic dyslipidemias.
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Affiliation(s)
- Julia K Goodrich
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Moriel Singer-Berk
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rachel Son
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Abigail Sveden
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jordan Wood
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eleina England
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joanne B Cole
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ben Weisburd
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nick Watts
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lizz Caulkins
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Peter Dornbos
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ryan Koesterer
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Zachary Zappala
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Haichen Zhang
- School of Medicine, University of Maryland Baltimore, Baltimore, MD, USA
| | - Kristin A Maloney
- School of Medicine, University of Maryland Baltimore, Baltimore, MD, USA
| | - Andy Dahl
- Department of Neurology, UCLA, Los Angeles, CA, USA
| | | | - Gil Atzmon
- Department of Medicine, Albert Einstein College of Medicine, New York, NY, USA
- Faculty of Natural Science, University of Haifa, Haifa, Israel
- Department of Genetics, Albert Einstein College of Medicine, New York, NY, USA
| | | | - Nir Barzilai
- Department of Medicine, Albert Einstein College of Medicine, New York, NY, USA
- Department of Genetics, Albert Einstein College of Medicine, New York, NY, USA
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville and Edinburg, TX, USA
| | - Eric Boerwinkle
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Lori L Bonnycastle
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Erwin Bottinger
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Donald W Bowden
- Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | | | - John C Chambers
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Nathalie Chami
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute, Ichan School of Medicine at Mount Sinai, New York, NY, USA
| | - Edmund Chan
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Juliana Chan
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
- Chinese University of Hong Kong-Shanghai Jiao Tong University Joint Research Centre in Diabetes Genomics and Precision Medicine, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Ching-Yu Cheng
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Yoon Shin Cho
- Department of Biomedical Science, Hallym University, Chuncheon, South Korea
| | | | - Emilio Córdova
- Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Ralph A DeFronzo
- Department of Medicine, University of Texas Health San Antonio (aka University of Texas Health Science Center at San Antonio), San Antonio, TX, USA
| | - Ravindranath Duggirala
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville and Edinburg, TX, USA
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Ma Eugenia Garay-Sevilla
- Department of Medical Science, División of Health Science, University of Guanjuato. Campus León. León, Guanjuato, Mexico
| | | | - Christian Gieger
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Benjamin Glaser
- Endocrinology and Metabolism Service, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Clicerio González-Villalpando
- Unidad de Investigacion en Diabetes y Riesgo Cardiovascular, Instituto Nacional de Salud Publica, Cuernavaca, Mexico
| | | | - Niels Grarup
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Leif Groop
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University Diabetes Centre, Malmö, Sweden
- Institute for Molecular Genetics Finland, University of Helsinki, Helsinki, Finland
| | - Myron Gross
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Christopher Haiman
- Department of Preventive Medicine, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Sohee Han
- Division of Genome Research, Center for Genome Science, National Institute of Health, Chungcheongbuk-do, South Korea
| | - Craig L Hanis
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nancy L Heard-Costa
- Boston University and National Heart Lung and Blood Institute's Framingham Heart Study, Framingham, MA, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
| | - Brian E Henderson
- Department of Preventive Medicine, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Juan Manuel Malacara Hernandez
- Department of Medical Science, División of Health Science, University of Guanjuato. Campus León. León, Guanjuato, Mexico
| | - Mi Yeong Hwang
- Division of Genome Research, Center for Genome Science, National Institute of Health, Chungcheongbuk-do, South Korea
| | | | - Marit E Jørgensen
- Steno Diabetes Center Copenhagen, Gentofte, Denmark
- National Institute of Public Health, University of Southern Denmark, Copenhagen, Denmark
- Greenland Centre for Health Research, University of Greenland, Nuuk, Greenland
| | - Hyun Min Kang
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Bong-Jo Kim
- Division of Genome Research, Center for Genome Science, National Institute of Health, Chungcheongbuk-do, South Korea
| | - Young Jin Kim
- Division of Genome Research, Center for Genome Science, National Institute of Health, Chungcheongbuk-do, South Korea
| | - Heikki A Koistinen
- Department of Public Health Solutions, Finnish Institute for Health and Welfare, Helsinki, Finland
- University of Helsinki and Department of Medicine, Helsinki University Central Hospital, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Jaspal Singh Kooner
- Department of Cardiology, Ealing Hospital, London North West Healthcare NHS Trust, London, UK
- MRC-PHE Centre for Environment and Health, Imperial College London, London, UK
- Imperial College Healthcare NHS Trust, Imperial College London, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Johanna Kuusisto
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Soo-Heon Kwak
- Department of Internal Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Leslie Lange
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Jong-Young Lee
- Oneomics Soonchunhyang Mirae Medical Center, Bucheon-si Gyeonggi-do, Republic of Korea
| | - Juyoung Lee
- Division of Genome Research, Center for Genome Science, National Institute of Health, Chungcheongbuk-do, South Korea
| | - Donna M Lehman
- Department of Medicine, University of Texas Health San Antonio (aka University of Texas Health Science Center at San Antonio), San Antonio, TX, USA
| | - Allan Linneberg
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Center for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, Copenhagen, Denmark
- Department of Clinical Experimental Research, Rigshospitalet, Copenhagen, Denmark
| | - Jianjun Liu
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute, Ichan School of Medicine at Mount Sinai, New York, NY, USA
| | - Valeriya Lyssenko
- Centro de Estudios en Diabetes, Mexico City, Mexico
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Ronald C W Ma
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
- Chinese University of Hong Kong-Shanghai Jiao Tong University Joint Research Centre in Diabetes Genomics and Precision Medicine, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | | | - James B Meigs
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Thomas Meitinger
- Institute of Human Genetics, Technical University of Munich, Munich, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | | | - Karen L Mohlke
- Department of Genetics, University of North Carolina Chapel Hill, Chapel Hill, NC, USA
| | - Andrew D Morris
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Biostatistics, University of Liverpool, Liverpool, UK
| | - Alanna C Morrison
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Maggie C Y Ng
- Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Peter M Nilsson
- Department of Clinical Sciences, Medicine, Lund University, Malmö, Sweden
| | - Christopher J O'Donnell
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Section of Cardiology, Department of Medicine, VA Boston Healthcare, Boston, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
- Intramural Administration Management Branch, National Heart Lung and Blood Institute, NIH, Framingham, MA, USA
| | - Lorena Orozco
- Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Colin N A Palmer
- Pat Macpherson Centre for Pharmacogenetics and Pharmacogenomics, University of Dundee, Dundee, UK
| | - Kyong Soo Park
- Department of Internal Medicine, Seoul National University Hospital, Seoul, South Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, South Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, South Korea
| | - Wendy S Post
- Division of Cardiology, Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Michael Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Services, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Research Institute, Seattle, WA, USA
| | | | | | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation (formerly Los Angeles Biomedical Research Institute) at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Danish Saleheen
- Division of Translational Medicine and Human Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, PA, USA
- Center for Non-Communicable Diseases, Karachi, Pakistan
| | - Claudia Schurmann
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Digital Health Center, Hasso Plattner Institute, University of Potsdam, Prof.-Dr.-Helmert-Str. 2-3, Potsdam, Germany
- Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, USA
| | - Xueling Sim
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Rob Sladek
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Division of Endocrinology and Metabolism, Department of Medicine, McGill University, Montreal, QC, Canada
- McGill University and Génome Québec Innovation Centre, Montreal, QC, Canada
| | - Kerrin S Small
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Wing Yee So
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
- Chinese University of Hong Kong-Shanghai Jiao Tong University Joint Research Centre in Diabetes Genomics and Precision Medicine, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong, China
| | - Timothy D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum Munchen, German Research Center for Environmental Health, Neuherberg, Germany
- Institute for Medical Informatics Biometry and Epidemiology, Ludwig-Maximilians University, Munich, Germany
| | - Tim M Strom
- Institute of Human Genetics, Technical University of Munich, Munich, Germany
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - E Shyong Tai
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Claudia H T Tam
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
- Chinese University of Hong Kong-Shanghai Jiao Tong University Joint Research Centre in Diabetes Genomics and Precision Medicine, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong, China
| | - Yik Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
- Life Sciences Institute, National University of Singapore, Singapore, Singapore
- Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore
| | - Farook Thameem
- Department of Biochemistry, Faculty of Medicine, Health Science Center, Kuwait University, Safat, Kuwait
| | - Brian Tomlinson
- Faculty of Medicine, Macau University of Science & Technology, Macau, China
| | - Russell P Tracy
- Department of Pathology and Laboratory Medicine, The Robert Larner M.D. College of Medicine, University of Vermont, Burlington, VT, USA
- Department of Biochemistry, The Robert Larner M.D. College of Medicine, University of Vermont, Burlington, VT, USA
| | - Tiinamaija Tuomi
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University Diabetes Centre, Malmö, Sweden
- Institute for Molecular Genetics Finland, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Centre, Helsinki, Finland
- Department of Endocrinology, Abdominal Centre, Helsinki University Hospital, Helsinki, Finland
- Research Programs Unit, Clinical and Molecular Medicine, University of Helsinki, Helsinki, Finland
| | - Jaakko Tuomilehto
- Public Health Promotion Unit, Finnish Institute for Health and Welfare, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Saudi Diabetes Research Group, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of International Health, National School of Public Health, Instituto de Salud Carlos III, Madrid, Spain
| | - Teresa Tusié-Luna
- Unidad de Biología Molecular y Medicina Genómica, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
- Departamento de Medicina Genómica y Toxiología Ambiental, Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Rob M van Dam
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
- Department of Nutrition, Harvard School of Public Health, Boston, MA, USA
| | - Ramachandran S Vasan
- Boston University and National Heart Lung and Blood Institute's Framingham Heart Study, Framingham, MA, USA
- Preventive Medicine & Epidemiology, and Cardiovascular Medicine, Medicine, Boston University School of Medicine, and Epidemiology, Boston University School of Public health, Boston, MA, USA
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, USA
| | - Daniel R Witte
- Department of Public Health, Aarhus University, Aarhus, Denmark
- Danish Diabetes Academy, Odense, Denmark
| | - Tien-Yin Wong
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Noël P Burtt
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Noah Zaitlen
- Department of Neurology, UCLA, Los Angeles, CA, USA
| | - Mark I McCarthy
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Genentech, South San Francisco, CA, USA
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Toni I Pollin
- School of Medicine, University of Maryland Baltimore, Baltimore, MD, USA
| | - Jason Flannick
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Josep M Mercader
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Anne O'Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Samantha Baxter
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jose C Florez
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Daniel G MacArthur
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Centre for Population Genomics, Garvan Institute of Medical Research, UNSW Sydney, Sydney, NSW, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Miriam S Udler
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
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19
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Wibowo MC, Yang Z, Borry M, Hübner A, Huang KD, Tierney BT, Zimmerman S, Barajas-Olmos F, Contreras-Cubas C, García-Ortiz H, Martínez-Hernández A, Luber JM, Kirstahler P, Blohm T, Smiley FE, Arnold R, Ballal SA, Pamp SJ, Russ J, Maixner F, Rota-Stabelli O, Segata N, Reinhard K, Orozco L, Warinner C, Snow M, LeBlanc S, Kostic AD. Reconstruction of ancient microbial genomes from the human gut. Nature 2021; 594:234-239. [PMID: 33981035 PMCID: PMC8189908 DOI: 10.1038/s41586-021-03532-0] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 04/12/2021] [Indexed: 12/26/2022]
Abstract
Loss of gut microbial diversity1–6 in industrial populations is associated with chronic diseases7, underscoring the importance of studying our ancestral gut microbiome. However, relatively little is known about the composition of pre-industrial gut microbiomes. Here we performed a large-scale de novo assembly of microbial genomes from palaeofaeces. From eight authenticated human palaeofaeces samples (1,000–2,000 years old) with well-preserved DNA from southwestern USA and Mexico, we reconstructed 498 medium- and high-quality microbial genomes. Among the 181 genomes with the strongest evidence of being ancient and of human gut origin, 39% represent previously undescribed species-level genome bins. Tip dating suggests an approximate diversification timeline for the key human symbiont Methanobrevibacter smithii. In comparison to 789 present-day human gut microbiome samples from eight countries, the palaeofaeces samples are more similar to non-industrialized than industrialized human gut microbiomes. Functional profiling of the palaeofaeces samples reveals a markedly lower abundance of antibiotic-resistance and mucin-degrading genes, as well as enrichment of mobile genetic elements relative to industrial gut microbiomes. This study facilitates the discovery and characterization of previously undescribed gut microorganisms from ancient microbiomes and the investigation of the evolutionary history of the human gut microbiota through genome reconstruction from palaeofaeces. Ancient microbiomes from palaeofaeces are more similar to non-industrialized than industrialized human gut microbiomes regardless of geography, but 39% of their de novo reconstructed genomes represent previously undescribed microbial species.
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Affiliation(s)
- Marsha C Wibowo
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Zhen Yang
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, USA.,Department of Combinatorics and Optimization, University of Waterloo, Waterloo, Ontario, Canada
| | - Maxime Borry
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Alexander Hübner
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Kun D Huang
- CIBIO Department, University of Trento, Trento, Italy.,Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Braden T Tierney
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Samuel Zimmerman
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Francisco Barajas-Olmos
- Immunogenomics and Metabolic Diseases Laboratory, Secretaría de Salud, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Cecilia Contreras-Cubas
- Immunogenomics and Metabolic Diseases Laboratory, Secretaría de Salud, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Humberto García-Ortiz
- Immunogenomics and Metabolic Diseases Laboratory, Secretaría de Salud, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Angélica Martínez-Hernández
- Immunogenomics and Metabolic Diseases Laboratory, Secretaría de Salud, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Jacob M Luber
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, USA.,Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Philipp Kirstahler
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Tre Blohm
- Department of Anthropology, University of Montana, Missoula, MT, USA
| | - Francis E Smiley
- Department of Anthropology, Northern Arizona University, Flagstaff, AZ, USA
| | - Richard Arnold
- Pahrump Paiute Tribe and Consolidated Group of Tribes and Organizations, Pahrump, NV, USA
| | - Sonia A Ballal
- Department of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA
| | - Sünje Johanna Pamp
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Julia Russ
- Morrison Microscopy Core Research Facility, Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Frank Maixner
- Institute for Mummy Studies, EURAC Research, Bolzano, Italy
| | - Omar Rota-Stabelli
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy.,Center Agriculture Food Environment (C3A), University of Trento, Trento, Italy
| | - Nicola Segata
- CIBIO Department, University of Trento, Trento, Italy
| | - Karl Reinhard
- School of Natural Resources, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Lorena Orozco
- Immunogenomics and Metabolic Diseases Laboratory, Secretaría de Salud, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.,Department of Anthropology, Harvard University, Cambridge, MA, USA.,Faculty of Biological Sciences, Friedrich-Schiller University, Jena, Germany
| | - Meradeth Snow
- Department of Anthropology, University of Montana, Missoula, MT, USA
| | - Steven LeBlanc
- Peabody Museum of Archaeology and Ethnology, Harvard University, Cambridge, MA, USA
| | - Aleksandar D Kostic
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA. .,Department of Microbiology, Harvard Medical School, Boston, MA, USA.
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20
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Aguilar-Ordoñez I, Pérez-Villatoro F, García-Ortiz H, Barajas-Olmos F, Ballesteros-Villascán J, González-Buenfil R, Fresno C, Garcíarrubio A, Fernández-López JC, Tovar H, Hernández-Lemus E, Orozco L, Soberón X, Morett E. Whole genome variation in 27 Mexican indigenous populations, demographic and biomedical insights. PLoS One 2021; 16:e0249773. [PMID: 33831079 PMCID: PMC8031408 DOI: 10.1371/journal.pone.0249773] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 03/24/2021] [Indexed: 12/12/2022] Open
Abstract
There has been limited study of Native American whole genome diversity to date, which impairs effective implementation of personalized medicine and a detailed description of its demographic history. Here we report high coverage whole genome sequencing of 76 unrelated individuals, from 27 indigenous groups across Mexico, with more than 97% average Native American ancestry. On average, each individual has 3.26 million Single Nucleotide Variants and short indels, that together comprise a catalog of 9,737,152 variants, 44,118 of which are novel. We report 497 common Single Nucleotide Variants (with allele frequency > 5%) mapped to drug responses and 316,577 in enhancer or promoter elements; interestingly we found some of these enhancer variants in PPARG, a nuclear receptor involved in highly prevalent health problems in Mexican population, such as obesity, diabetes, and insulin resistance. By detecting signals of positive selection we report 24 enriched key pathways under selection, most of them related to immune mechanisms. No missense variants in ACE2, the receptor responsible for the entry of the SARS CoV-2 virus, were found in any individual. Population genomics and phylogenetic analyses demonstrated stratification in a Northern-Central-Southern axis, with major substructure in the Central region. The Seri, a northern group with the most genetic divergence in our study, showed a distinctive genomic context with the most novel variants, and the most population specific genotypes. Genome-wide analysis showed that the average haplotype blocks are longer in Native Mexicans than in other world populations. With this dataset we describe previously undetected population level variation in Native Mexicans, helping to reduce the gap in genomic data representation of such groups.
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Affiliation(s)
- Israel Aguilar-Ordoñez
- Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, México
- Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, México
| | - Fernando Pérez-Villatoro
- Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, México
- Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, México
- Winter Genomics, Mexico City, México
| | | | | | | | - Ram González-Buenfil
- Benemérita Universidad Autónoma de Puebla (BUAP), Puebla de Zaragoza, Puebla, México
| | - Cristobal Fresno
- Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, México
| | - Alejandro Garcíarrubio
- Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, México
| | | | - Hugo Tovar
- Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, México
| | | | - Lorena Orozco
- Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, México
| | - Xavier Soberón
- Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, México
- Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, México
| | - Enrique Morett
- Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, México
- * E-mail:
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21
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Escalante-Araiza F, Barajas-Olmos F, Martínez-Hernández A, Huerta-Ávila E, Peschard VG, Rodríguez-Ayala E, Bastarrachea RA, Orozco L. MON-708 Characterizing DNA Methylation Signatures in Adipose Tissue from Metabolic Impaired Asymptomatic Individuals. J Endocr Soc 2020. [PMCID: PMC7208964 DOI: 10.1210/jendso/bvaa046.924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Obesity remains as a global epidemic characterized by progressive metabolic dysregulation in glucose homeostasis. Along with a genetic association in the development of T2D, epigenetic regulation has been suggested as a significant contributor in altered gene expression. Recent studies have described DNA methylation changes in insulin-sensitive tissues involved in T2D pathogenesis, however epigenetic dynamics on early stages to metabolic alterations is still unclear. We investigated potential DNA methylation signatures in 34 asymptomatic individuals from the GEMM family study. We compared differentially methylated CpG sites (DMC: B value>0 and delta Beta >|10%|; Infinium EPIC array) from subcutaneous adipose tissue (SCAT) in different groups of individuals according to BMI (kg/m2) and HbA1c (%) levels as follow: Group A Control (C): n=9, 22.0±1.9 kg/m2, 4.8±0.3%; Group B Overweight (OW) with normal HbA1c: n=6, 27.8±1.6 kg/m2, 5±0.2%; Group C Obese (OB) with normal HbA1c: n=6, 34.6±4.2 kg/m2, 5.2±0.2%; Group D Prediabetes (PD): n=7, 31.1±5.7 kg/m2, 5.9±0.2% and Group E T2D: n=6, 30.6±7.3 kg/m2, 7.2±0.9%. We found 43 overlapping genes with shared pathways in all groups, mainly those related to metabolism and adipogenesis. We also documented particular altered methylated genes, in each group (OW: 386, OB:1005, PD:76 and T2D:189). Pathway enrichment analysis in OB and T2D was mainly related to glucose metabolism, while in OW and PD was NOTCH signaling. All groups displayed a consistent hypermethylation in RARA, ESR1 and NCOR2, well known genes involved in lipid metabolism. Additionally, we describe for the first time, a progression toward hypomethylation in ARHGAP15 and MTAP, related with an impaired metabolic status. Otherwise, analysis of overlapping CpG sites revealed a consistently hypermethylated state in OW (86.42%), OB (86.48%) and PD (51.72%), in contrast with the hypomethylation state (56.3%) observed in the T2D group, previously observed elsewhere (1). In conclusion, comparison of methylation in SCAT obtained from OW, OB, PD and T2D individuals, display potential pathways and DMC signatures specific in each group. Common novel overlapping genes in global DNA methylation profiles of SCAT, were also observed. Reference: (1) Barajas-Olmos et al., BMC Med Genet. 2018 Feb 21;19(1):1-8. Nothing to Disclose: FE, FB, AM, EH, GEMM, ER, RB, LO.
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Affiliation(s)
- Fabiola Escalante-Araiza
- Immunogenomics and Metabolic Diseases Laboratory, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
| | - Francisco Barajas-Olmos
- Immunogenomics and Metabolic Diseases Laboratory, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
| | - Angélica Martínez-Hernández
- Immunogenomics and Metabolic Diseases Laboratory, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
| | - Eira Huerta-Ávila
- Immunogenomics and Metabolic Diseases Laboratory, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
| | | | | | - Raul A Bastarrachea
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Lorena Orozco
- Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
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22
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Mendoza-Caamal EC, Barajas-Olmos F, García-Ortiz H, Cicerón-Arellano I, Martínez-Hernández A, Córdova EJ, Esparza-Aguilar M, Contreras-Cubas C, Centeno-Cruz F, Cid-Soto M, Morales-Marín ME, Reséndiz-Rodríguez A, Jiménez-Ruiz JL, Salas-Martínez MG, Saldaña-Alvarez Y, Mirzaeicheshmeh E, Rojas-Martínez MR, Orozco L. Metabolic syndrome in indigenous communities in Mexico: a descriptive and cross-sectional study. BMC Public Health 2020; 20:339. [PMID: 32183766 PMCID: PMC7076922 DOI: 10.1186/s12889-020-8378-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 02/20/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND An Amerindian genetic background could play an important role in susceptibility to metabolic diseases, which have alarmingly increased in recent decades. Mexico has one of the highest prevalences of metabolic disease worldwide. The purpose of this study was to determine the prevalence of metabolic syndrome and its components in a population with high Amerindian ancestry. METHODS We performed a descriptive, quantitative, and analytical cross-sectional study of 2596 adult indigenous volunteers from 60 different ethnic groups. Metabolic syndrome and its components were evaluated using the American Heart Association/National Heart, Lung, and Blood Institute Scientific Statement criteria. RESULTS The overall prevalence of metabolic syndrome in the indigenous Mexican population was 50.3%. Although females had a higher prevalence than males (55.6% vs. 38.2%), the males presented with combinations of metabolic syndrome components that confer a higher risk of cardiovascular disease. The most frequent metabolic syndrome component in both genders was low HDL-cholesterol levels (75.8%). Central obesity was the second most frequent component in females (61%), though it had a low prevalence in males (16.5%). The overall prevalence of elevated blood pressure was 42.7% and was higher in males than females (48.8 vs. 40%). We found no gender differences in the overall prevalence of elevated triglycerides (56.7%) or fasting glucose (27.9%). CONCLUSIONS We documented that individuals with Amerindian ancestry have a high prevalence of metabolic syndrome. Health policies are needed to control the development of metabolic disorders in a population with high genetic risk.
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Affiliation(s)
- Elvia Cristina Mendoza-Caamal
- Clinical Area, Instituto Nacional de Medicina Genómica, SS, Periférico Sur 4809, Colonia Arenal Tepepan, Delegación Tlalpan, C.P. 14610, Ciudad de México, Mexico
| | - Francisco Barajas-Olmos
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genómica, SS, Periférico Sur 4809, Colonia Arenal Tepepan, Delegación Tlalpan, C.P. 14610, Ciudad de México, Mexico
| | - Humberto García-Ortiz
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genómica, SS, Periférico Sur 4809, Colonia Arenal Tepepan, Delegación Tlalpan, C.P. 14610, Ciudad de México, Mexico
| | - Isabel Cicerón-Arellano
- Clinical Area, Instituto Nacional de Medicina Genómica, SS, Periférico Sur 4809, Colonia Arenal Tepepan, Delegación Tlalpan, C.P. 14610, Ciudad de México, Mexico
| | - Angélica Martínez-Hernández
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genómica, SS, Periférico Sur 4809, Colonia Arenal Tepepan, Delegación Tlalpan, C.P. 14610, Ciudad de México, Mexico
| | - Emilio J Córdova
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genómica, SS, Periférico Sur 4809, Colonia Arenal Tepepan, Delegación Tlalpan, C.P. 14610, Ciudad de México, Mexico
| | - Marcelino Esparza-Aguilar
- Epidemiology Research Department, Instituto Nacional de Pediatría, Insurgentes Sur 3700, Letra C, Colonia Insurgentes Cuicuilco, Delegación Coyoacán, C.P. 04530, Ciudad de México, Mexico
| | - Cecilia Contreras-Cubas
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genómica, SS, Periférico Sur 4809, Colonia Arenal Tepepan, Delegación Tlalpan, C.P. 14610, Ciudad de México, Mexico
| | - Federico Centeno-Cruz
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genómica, SS, Periférico Sur 4809, Colonia Arenal Tepepan, Delegación Tlalpan, C.P. 14610, Ciudad de México, Mexico
| | - Miguel Cid-Soto
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genómica, SS, Periférico Sur 4809, Colonia Arenal Tepepan, Delegación Tlalpan, C.P. 14610, Ciudad de México, Mexico
| | - Mirna Edith Morales-Marín
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genómica, SS, Periférico Sur 4809, Colonia Arenal Tepepan, Delegación Tlalpan, C.P. 14610, Ciudad de México, Mexico
| | - Adriana Reséndiz-Rodríguez
- Clinical Area, Instituto Nacional de Medicina Genómica, SS, Periférico Sur 4809, Colonia Arenal Tepepan, Delegación Tlalpan, C.P. 14610, Ciudad de México, Mexico
| | - Juan Luis Jiménez-Ruiz
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genómica, SS, Periférico Sur 4809, Colonia Arenal Tepepan, Delegación Tlalpan, C.P. 14610, Ciudad de México, Mexico
| | - María Guadalupe Salas-Martínez
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genómica, SS, Periférico Sur 4809, Colonia Arenal Tepepan, Delegación Tlalpan, C.P. 14610, Ciudad de México, Mexico
| | - Yolanda Saldaña-Alvarez
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genómica, SS, Periférico Sur 4809, Colonia Arenal Tepepan, Delegación Tlalpan, C.P. 14610, Ciudad de México, Mexico
| | - Elaheh Mirzaeicheshmeh
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genómica, SS, Periférico Sur 4809, Colonia Arenal Tepepan, Delegación Tlalpan, C.P. 14610, Ciudad de México, Mexico
| | - María Rosalba Rojas-Martínez
- Public Health Research Center, Instituto Nacional de Salud Pública, 7a Cerrada de Fray Pedro de Gante 50, Colonia Sección XVI, Delegación Tlalpan, C.P. 14080, Ciudad de México, Mexico
| | - Lorena Orozco
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genómica, SS, Periférico Sur 4809, Colonia Arenal Tepepan, Delegación Tlalpan, C.P. 14610, Ciudad de México, Mexico.
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23
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Gonzalez-Covarrubias V, Morales-Franco M, Cruz-Correa OF, Martínez-Hernández A, García-Ortíz H, Barajas-Olmos F, Genis-Mendoza AD, Martínez-Magaña JJ, Nicolini H, Orozco L, Soberón X. Variation in Actionable Pharmacogenetic Markers in Natives and Mestizos From Mexico. Front Pharmacol 2019; 10:1169. [PMID: 31649539 PMCID: PMC6796793 DOI: 10.3389/fphar.2019.01169] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 09/12/2019] [Indexed: 12/12/2022] Open
Abstract
The identification and characterization of pharmacogenetic variants in Latin American populations is still an ongoing endeavor. Here, we investigated SNVs on genes listed by the Pharmacogenomics Knowledge Base in 1284 Mestizos and 94 Natives from Mexico. Five institutional cohorts with NGS data were retrieved from different research projects at INMEGEN, sequencing files were filtered for 55 pharmacogenes present in all cohorts to identify novel and known variation. Bioinformatic tools VEP, PROVEAN, and FATHMM were used to assess, in silico, the functional impact of this variation. Next, we focused on 17 genes with actionable variants that have been clinically implemented. Allele frequencies were compared with major continental groups and differences discussed in the scope of a pharmacogenomic impact. We observed a wide genetic variability for known and novel SNVs, the largest variation was on UGT1A > ACE > COMT > ABCB1 and the lowest on APOE and NAT2. Although with allele frequencies around 1%, novel variation was observed in 16 of 17 PGKB genes. In Natives we identified 59 variants and 58 in Mestizos. Several genes did not show novel variation, on CYP2B6, CYP2D6, and CYP3A4 in Natives; and APOE, UGT1A, and VKORC1 in Mestizos. Similarities in allele frequency, comparing major continental groups for VIP pharmacogenes, hint towards a comparable PGx for drugs metabolized by UGT1A1, DPYD, ABCB1, CBR3, COMT, and TPMT; in contrast to variants on CYP3A5 and CYP2B6 for which significant MAF differences were identified. Our observations offer some discernment into the extent of pharmacogenetic variation registered up-to-date in Mexicans and contribute to quantitatively dissect actionable pharmacogenetic variants in Natives and Mestizos.
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Affiliation(s)
| | | | | | | | - Humberto García-Ortíz
- Immunogenomics and Metabolic Diseases Laboratory, INMEGEN, CDMX, Mexico City, Mexico
| | | | | | | | - Humberto Nicolini
- Genomics of Psychiatric and Neurodegenerative Diseases Laboratory, INMEGEN, Mexico City, Mexico
| | - Lorena Orozco
- Immunogenomics and Metabolic Diseases Laboratory, INMEGEN, CDMX, Mexico City, Mexico
| | - Xavier Soberón
- Pharmacogenomics Laboratory, INMEGEN, CDMX, Mexico City, Mexico
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24
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Flannick J, Mercader JM, Fuchsberger C, Udler MS, Mahajan A, Wessel J, Teslovich TM, Caulkins L, Koesterer R, Barajas-Olmos F, Blackwell TW, Boerwinkle E, Brody JA, Centeno-Cruz F, Chen L, Chen S, Contreras-Cubas C, Córdova E, Correa A, Cortes M, DeFronzo RA, Dolan L, Drews KL, Elliott A, Floyd JS, Gabriel S, Garay-Sevilla ME, García-Ortiz H, Gross M, Han S, Heard-Costa NL, Jackson AU, Jørgensen ME, Kang HM, Kelsey M, Kim BJ, Koistinen HA, Kuusisto J, Leader JB, Linneberg A, Liu CT, Liu J, Lyssenko V, Manning AK, Marcketta A, Malacara-Hernandez JM, Martínez-Hernández A, Matsuo K, Mayer-Davis E, Mendoza-Caamal E, Mohlke KL, Morrison AC, Ndungu A, Ng MCY, O'Dushlaine C, Payne AJ, Pihoker C, Post WS, Preuss M, Psaty BM, Vasan RS, Rayner NW, Reiner AP, Revilla-Monsalve C, Robertson NR, Santoro N, Schurmann C, So WY, Soberón X, Stringham HM, Strom TM, Tam CHT, Thameem F, Tomlinson B, Torres JM, Tracy RP, van Dam RM, Vujkovic M, Wang S, Welch RP, Witte DR, Wong TY, Atzmon G, Barzilai N, Blangero J, Bonnycastle LL, Bowden DW, Chambers JC, Chan E, Cheng CY, Cho YS, Collins FS, de Vries PS, Duggirala R, Glaser B, Gonzalez C, Gonzalez ME, Groop L, Kooner JS, Kwak SH, Laakso M, Lehman DM, Nilsson P, Spector TD, Tai ES, Tuomi T, Tuomilehto J, Wilson JG, Aguilar-Salinas CA, Bottinger E, Burke B, Carey DJ, Chan JCN, Dupuis J, Frossard P, Heckbert SR, Hwang MY, Kim YJ, Kirchner HL, Lee JY, Lee J, Loos RJF, Ma RCW, Morris AD, O'Donnell CJ, Palmer CNA, Pankow J, Park KS, Rasheed A, Saleheen D, Sim X, Small KS, Teo YY, Haiman C, Hanis CL, Henderson BE, Orozco L, Tusié-Luna T, Dewey FE, Baras A, Gieger C, Meitinger T, Strauch K, Lange L, Grarup N, Hansen T, Pedersen O, Zeitler P, Dabelea D, Abecasis G, Bell GI, Cox NJ, Seielstad M, Sladek R, Meigs JB, Rich SS, Rotter JI, Altshuler D, Burtt NP, Scott LJ, Morris AP, Florez JC, McCarthy MI, Boehnke M. Exome sequencing of 20,791 cases of type 2 diabetes and 24,440 controls. Nature 2019; 570:71-76. [PMID: 31118516 PMCID: PMC6699738 DOI: 10.1038/s41586-019-1231-2] [Citation(s) in RCA: 181] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 04/23/2019] [Indexed: 02/08/2023]
Abstract
Protein-coding genetic variants that strongly affect disease risk can yield relevant clues to disease pathogenesis. Here we report exome-sequencing analyses of 20,791 individuals with type 2 diabetes (T2D) and 24,440 non-diabetic control participants from 5 ancestries. We identify gene-level associations of rare variants (with minor allele frequencies of less than 0.5%) in 4 genes at exome-wide significance, including a series of more than 30 SLC30A8 alleles that conveys protection against T2D, and in 12 gene sets, including those corresponding to T2D drug targets (P = 6.1 × 10-3) and candidate genes from knockout mice (P = 5.2 × 10-3). Within our study, the strongest T2D gene-level signals for rare variants explain at most 25% of the heritability of the strongest common single-variant signals, and the gene-level effect sizes of the rare variants that we observed in established T2D drug targets will require 75,000-185,000 sequenced cases to achieve exome-wide significance. We propose a method to interpret these modest rare-variant associations and to incorporate these associations into future target or gene prioritization efforts.
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Affiliation(s)
- Jason Flannick
- Program in Metabolism, Broad Institute, Cambridge, MA, USA.
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
- Program in Medical & Population Genetics, Broad Institute, Cambridge, MA, USA.
| | - Josep M Mercader
- Program in Metabolism, Broad Institute, Cambridge, MA, USA
- Program in Medical & Population Genetics, Broad Institute, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Diabetes Research Center (Diabetes Unit), Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Christian Fuchsberger
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
- Institute for Biomedicine, Eurac Research, Bolzano, Italy
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Miriam S Udler
- Program in Metabolism, Broad Institute, Cambridge, MA, USA
- Program in Medical & Population Genetics, Broad Institute, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Diabetes Research Center (Diabetes Unit), Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Anubha Mahajan
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Jennifer Wessel
- Department of Epidemiology, Fairbanks School of Public Health, Indiana University, Indianapolis, IN, USA
- Department of Medicine, School of Medicine, Indiana University, Indianapolis, IN, USA
- Diabetes Translational Research Center, Indiana University, Indianapolis, IN, USA
| | - Tanya M Teslovich
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Lizz Caulkins
- Program in Metabolism, Broad Institute, Cambridge, MA, USA
- Program in Medical & Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Ryan Koesterer
- Program in Metabolism, Broad Institute, Cambridge, MA, USA
- Program in Medical & Population Genetics, Broad Institute, Cambridge, MA, USA
| | | | - Thomas W Blackwell
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer A Brody
- Cardiovascular Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | | | - Ling Chen
- Diabetes Research Center (Diabetes Unit), Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Siying Chen
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | | | - Emilio Córdova
- Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Maria Cortes
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ralph A DeFronzo
- Department of Medicine, University of Texas Health Science Center, San Antonio, TX, USA
| | - Lawrence Dolan
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kimberly L Drews
- Biostatistics Center, George Washington University, Rockville, MD, USA
| | - Amanda Elliott
- Program in Metabolism, Broad Institute, Cambridge, MA, USA
- Program in Medical & Population Genetics, Broad Institute, Cambridge, MA, USA
- Diabetes Research Center (Diabetes Unit), Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - James S Floyd
- Department of Medicine and Epidemiology, University of Washington, Seattle, WA, USA
| | | | - Maria Eugenia Garay-Sevilla
- Department of Medicine, The University of Chicago, Chicago, IL, USA
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA
| | | | - Myron Gross
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Sohee Han
- Division of Genome Research, Center for Genome Science, National Institute of Health, Chungcheongbuk-do, South Korea
| | - Nancy L Heard-Costa
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
- National Heart Lung and Blood Institute's Framingham Heart Study, Framingham, MA, USA
| | - Anne U Jackson
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Marit E Jørgensen
- Steno Diabetes Center Copenhagen, Gentofte, Denmark
- National Institute of Public Health, University of Southern Denmark, Copenhagen, Denmark
- Greenland Centre for Health Research, University of Greenland, Nuuk, Greenland
| | - Hyun Min Kang
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Megan Kelsey
- Biostatistics Center, George Washington University, Rockville, MD, USA
| | - Bong-Jo Kim
- Division of Genome Research, Center for Genome Science, National Institute of Health, Chungcheongbuk-do, South Korea
| | - Heikki A Koistinen
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
- University of Helsinki and Department of Medicine, Helsinki University Central Hospital, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Johanna Kuusisto
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
- Department of Medicin, Kuopio University Hospital, Kuopio, Finland
| | | | - Allan Linneberg
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Center for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, Copenhagen, Denmark
- Department of Clinical Experimental Research, Rigshospitalet, Copenhagen, Denmark
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Jianjun Liu
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Valeriya Lyssenko
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University Diabetes Centre, Malmö, Sweden
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Alisa K Manning
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Harvard University, Boston, MA, USA
| | - Anthony Marcketta
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Juan Manuel Malacara-Hernandez
- Department of Medicine, The University of Chicago, Chicago, IL, USA
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA
| | | | - Karen Matsuo
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | | | | | - Karen L Mohlke
- Department of Genetics, University of North Carolina Chapel Hill, Chapel Hill, NC, USA
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Anne Ndungu
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Maggie C Y Ng
- Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Colm O'Dushlaine
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Anthony J Payne
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Wendy S Post
- Division of Cardiology, Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Michael Preuss
- Charles R. Bronfman Institute of Personalized Medicine, Mount Sinai School of Medicine, New York, NY, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Health Services, University of Washington, Seattle, WA, USA
| | - Ramachandran S Vasan
- National Heart Lung and Blood Institute's Framingham Heart Study, Framingham, MA, USA
- Preventive Medicine & Epidemiology, Medicine, Boston University School of Medicine, Boston, MA, USA
| | - N William Rayner
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | | | | | - Neil R Robertson
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Nicola Santoro
- Department of Pediatrics, Yale University, New Haven, CT, USA
| | - Claudia Schurmann
- Charles R. Bronfman Institute of Personalized Medicine, Mount Sinai School of Medicine, New York, NY, USA
| | - Wing Yee So
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong, China
| | - Xavier Soberón
- Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Heather M Stringham
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Tim M Strom
- Institute of Human Genetics, Technische Universität München, Munich, Germany
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Claudia H T Tam
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong, China
| | - Farook Thameem
- Health Science Center, Department of Biochemistry, Faculty of Medicine, Kuwait University, Safat, Kuwait
| | - Brian Tomlinson
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Jason M Torres
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Russell P Tracy
- Department of Pathology and Laboratory Medicine, The Robert Larner M.D. College of Medicine, University of Vermont, Burlington, VT, USA
- Department of Biochemistry, The Robert Larner M.D. College of Medicine, University of Vermont, Burlington, VT, USA
| | - Rob M van Dam
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- Department of Nutrition, Harvard School of Public Health, Boston, MA, USA
| | - Marijana Vujkovic
- Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Shuai Wang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Ryan P Welch
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Daniel R Witte
- Department of Public Health, Aarhus University, Aarhus, Denmark
- Danish Diabetes Academy, Odense, Denmark
| | - Tien-Yin Wong
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Duke-NUS Medical School Singapore, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Singapore, Singapore
| | - Gil Atzmon
- Department of Medicine, Albert Einstein College of Medicine, New York, NY, USA
- Faculty of Natural Science, University of Haifa, Haifa, Israel
- Department of Genetics, Albert Einstein College of Medicine, New York, NY, USA
| | - Nir Barzilai
- Department of Medicine, Albert Einstein College of Medicine, New York, NY, USA
- Department of Genetics, Albert Einstein College of Medicine, New York, NY, USA
| | - John Blangero
- Department of Human Genetics, University of Texas Rio Grande Valley, Edinburg, TX, USA
- South Texas Diabetes and Obesity Institute, Brownsville, TX, USA
| | - Lori L Bonnycastle
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Donald W Bowden
- Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - John C Chambers
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Department of Cardiology, Ealing Hospital NHS Trust, Southall, UK
- Imperial College Healthcare NHS Trust, Imperial College London, London, UK
| | - Edmund Chan
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Singapore, Singapore
| | - Ching-Yu Cheng
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
| | - Yoon Shin Cho
- Department of Biomedical Science, Hallym University, Chuncheon, South Korea
| | - Francis S Collins
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Paul S de Vries
- Human Genetics Center, Department of Epidemiology Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Ravindranath Duggirala
- Department of Human Genetics, University of Texas Rio Grande Valley, Edinburg, TX, USA
- South Texas Diabetes and Obesity Institute, Brownsville, TX, USA
| | - Benjamin Glaser
- Endocrinology and Metabolism Service, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Clicerio Gonzalez
- Unidad de Diabetes y Riesgo Cardiovascular, Instituto Nacional de Salud Pública, Cuernavaca, Mexico
| | | | - Leif Groop
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University Diabetes Centre, Malmö, Sweden
- Institute for Molecular Genetics Finland, University of Helsinki, Helsinki, Finland
| | - Jaspal Singh Kooner
- National Heart and Lung Institute, Cardiovascular Sciences, Imperial College London, London, UK
| | - Soo Heon Kwak
- Department of Internal Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
- Department of Medicin, Kuopio University Hospital, Kuopio, Finland
| | - Donna M Lehman
- Department of Medicine, University of Texas Health Science Center, San Antonio, TX, USA
| | - Peter Nilsson
- Department of Clinical Sciences, Medicine, Lund University, Malmö, Sweden
| | - Timothy D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - E Shyong Tai
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- Duke-NUS Medical School Singapore, Singapore, Singapore
| | - Tiinamaija Tuomi
- Institute for Molecular Genetics Finland, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Centre, Helsinki, Finland
- Department of Endocrinology, Abdominal Centre, Helsinki University Hospital, Helsinki, Finland
- Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland
| | - Jaakko Tuomilehto
- Diabetes Prevention Unit, National Institute for Health and Welfare, Helsinki, Finland
- Center for Vascular Prevention, Danube University Krems, Krems, Austria
- Diabetes Research Group, King Abdulaziz University, Jeddah, Saudi Arabia
- Instituto de Investigacion Sanitaria del Hospital Universario LaPaz (IdiPAZ), University Hospital LaPaz, Autonomous University of Madrid, Madrid, Spain
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, USA
| | | | - Erwin Bottinger
- Charles R. Bronfman Institute of Personalized Medicine, Mount Sinai School of Medicine, New York, NY, USA
| | - Brian Burke
- Biostatistics Center, George Washington University, Rockville, MD, USA
| | | | - Juliana C N Chan
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong, China
| | - Josée Dupuis
- National Heart Lung and Blood Institute's Framingham Heart Study, Framingham, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | | | - Susan R Heckbert
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Mi Yeong Hwang
- Division of Genome Research, Center for Genome Science, National Institute of Health, Chungcheongbuk-do, South Korea
| | - Young Jin Kim
- Division of Genome Research, Center for Genome Science, National Institute of Health, Chungcheongbuk-do, South Korea
| | | | - Jong-Young Lee
- Department of Business Data Convergence, Chungbuk National University, Gyeonggi-do, South Korea
| | - Juyoung Lee
- Division of Genome Research, Center for Genome Science, National Institute of Health, Chungcheongbuk-do, South Korea
| | - Ruth J F Loos
- Charles R. Bronfman Institute of Personalized Medicine, Mount Sinai School of Medicine, New York, NY, USA
- The Mindich Child Health and Development Insititute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ronald C W Ma
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong, China
| | - Andrew D Morris
- Clinical Research Centre, Centre for Molecular Medicine, Ninewells Hospital and Medical School, Dundee, UK
| | - Christopher J O'Donnell
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Section of Cardiology, Department of Medicine, VA Boston Healthcare, Boston, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
- Intramural Administration Management Branch, National Heart Lung and Blood Institute, NIH, Framingham, MA, USA
| | - Colin N A Palmer
- Pat Macpherson Centre for Pharmacogenetics and Pharmacogenomics, Medical Research Institute, Ninewells Hospital and Medical School, Dundee, UK
| | - James Pankow
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, MN, USA
| | - Kyong Soo Park
- National Heart and Lung Institute, Cardiovascular Sciences, Imperial College London, London, UK
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, South Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Asif Rasheed
- Center for Non-Communicable Diseases, Karachi, Pakistan
| | - Danish Saleheen
- Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, PA, USA
- Center for Non-Communicable Diseases, Karachi, Pakistan
| | - Xueling Sim
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Kerrin S Small
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Yik Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- Life Sciences Institute, National University of Singapore, Singapore, Singapore
- Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore
| | - Christopher Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Craig L Hanis
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Brian E Henderson
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Lorena Orozco
- Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Teresa Tusié-Luna
- Instituto Nacional de Ciencias Medicas y Nutricion, Mexico City, Mexico
- Instituto de Investigaciones Biomédicas, Departamento de Medicina Genómica y Toxicología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Frederick E Dewey
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Aris Baras
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Technische Universität München, Munich, Germany
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Deutsches Forschungszentrum für Herz-Kreislauferkrankungen (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Konstantin Strauch
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Medical Informatics, Biometry and Epidemiology, Chair of Genetic Epidemiology, Ludwig-Maximilians-Universität, Neuherberg, Germany
| | - Leslie Lange
- Department of Medicine, University of Colorado Denver, Aurora, CO, USA
| | - Niels Grarup
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Philip Zeitler
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Dana Dabelea
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO, USA
| | - Goncalo Abecasis
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Graeme I Bell
- Department of Medicine, The University of Chicago, Chicago, IL, USA
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA
| | - Nancy J Cox
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA
| | - Mark Seielstad
- Department of Laboratory Medicine & Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
- Blood Systems Research Institute, San Francisco, CA, USA
| | - Rob Sladek
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Division of Endocrinology and Metabolism, Department of Medicine, McGill University, Montreal, Quebec, Canada
- McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | - James B Meigs
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Steve S Rich
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Jerome I Rotter
- Department of Pediatrics, Los Angeles BioMedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
- Department of Medicine, Los Angeles BioMedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
- Institute for Translational Genomics and Population Sciences, Los Angeles BioMedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - David Altshuler
- Program in Metabolism, Broad Institute, Cambridge, MA, USA
- Program in Medical & Population Genetics, Broad Institute, Cambridge, MA, USA
- Diabetes Research Center (Diabetes Unit), Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Noël P Burtt
- Program in Metabolism, Broad Institute, Cambridge, MA, USA
- Program in Medical & Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Laura J Scott
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Andrew P Morris
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Biostatistics, University of Liverpool, Liverpool, UK
| | - Jose C Florez
- Program in Metabolism, Broad Institute, Cambridge, MA, USA
- Program in Medical & Population Genetics, Broad Institute, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Diabetes Research Center (Diabetes Unit), Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Mark I McCarthy
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Oxford NIHR Biomedical Research Centre, Oxford University Hospitals Trust, Oxford, UK
| | - Michael Boehnke
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
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Martínez-Hernández A, Larrosa J, Barajas-Olmos F, García-Ortíz H, Mendoza-Caamal EC, Contreras-Cubas C, Mirzaeicheshmeh E, Lezana JL, Orozco L. Next-generation sequencing for identifying a novel/de novo pathogenic variant in a Mexican patient with cystic fibrosis: a case report. BMC Med Genomics 2019; 12:68. [PMID: 31118044 PMCID: PMC6532186 DOI: 10.1186/s12920-019-0528-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 05/13/2019] [Indexed: 01/18/2023] Open
Abstract
Background Mexico is among the countries showing the highest heterogeneity of CFTR variants. However, no de novo variants have previously been reported in Mexican patients with cystic fibrosis (CF). Case presentation Here, we report the first case of a novel/de novo variant in a Mexican patient with CF. Our patient was an 8-year-old male who had exhibited the clinical onset of CF at one month of age, with steatorrhea, malabsorption, poor weight gain, anemia, and recurrent respiratory tract infections. Complete sequencing of the CFTR gene by next generation sequencing (NGS) revealed two different variants in trans, including the previously reported CF-causing variant c.3266G > A (p.Trp1089*, W1089*), that was inherited from the mother, and the novel/de novo CFTR variant c.1762G > T (p.Glu588*). Conclusion Our results demonstrate the efficiency of targeted NGS for making a rapid and precise diagnosis in patients with clinically suspected CF. This method can enable the provision of accurate genetic counselling, and improve our understanding of the molecular basis of genetic diseases.
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Affiliation(s)
- Angélica Martínez-Hernández
- Laboratorio de Inmunogenómica y enfermedades metabólicas, Instituto Nacional de Medicina Genómica,SS, Periférico Sur No. 4809, Arenal Tepepan,Tlalpan, 14610. CDMX, Mexico City, Mexico
| | - Julieta Larrosa
- Laboratorio de Inmunogenómica y enfermedades metabólicas, Instituto Nacional de Medicina Genómica, SS, CDMX, Mexico y Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, CDMX, Mexico City, Mexico
| | - Francisco Barajas-Olmos
- Laboratorio de Inmunogenómica y enfermedades metabólicas, Instituto Nacional de Medicina Genómica,SS, Periférico Sur No. 4809, Arenal Tepepan,Tlalpan, 14610. CDMX, Mexico City, Mexico
| | - Humberto García-Ortíz
- Laboratorio de Inmunogenómica y enfermedades metabólicas, Instituto Nacional de Medicina Genómica,SS, Periférico Sur No. 4809, Arenal Tepepan,Tlalpan, 14610. CDMX, Mexico City, Mexico
| | | | - Cecilia Contreras-Cubas
- Laboratorio de Inmunogenómica y enfermedades metabólicas, Instituto Nacional de Medicina Genómica,SS, Periférico Sur No. 4809, Arenal Tepepan,Tlalpan, 14610. CDMX, Mexico City, Mexico
| | - Elaheh Mirzaeicheshmeh
- Laboratorio de Inmunogenómica y enfermedades metabólicas, Instituto Nacional de Medicina Genómica,SS, Periférico Sur No. 4809, Arenal Tepepan,Tlalpan, 14610. CDMX, Mexico City, Mexico
| | - José Luis Lezana
- Clinica de Fibrosis Quística y Laboratorio de Fisiologia Pulmonar Hospital Infantil de México Federico Gómez. Asociación Mexicana de Fibrosis Quística, A. C, CDMX, Mexico City, Mexico
| | - Lorena Orozco
- Laboratorio de Inmunogenómica y enfermedades metabólicas, Instituto Nacional de Medicina Genómica,SS, Periférico Sur No. 4809, Arenal Tepepan,Tlalpan, 14610. CDMX, Mexico City, Mexico.
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26
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Reynolds AW, Mata-Míguez J, Miró-Herrans A, Briggs-Cloud M, Sylestine A, Barajas-Olmos F, Garcia-Ortiz H, Rzhetskaya M, Orozco L, Raff JA, Hayes MG, Bolnick DA. Comparing signals of natural selection between three Indigenous North American populations. Proc Natl Acad Sci U S A 2019; 116:9312-9317. [PMID: 30988184 PMCID: PMC6511053 DOI: 10.1073/pnas.1819467116] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
While many studies have highlighted human adaptations to diverse environments worldwide, genomic studies of natural selection in Indigenous populations in the Americas have been absent from this literature until very recently. Since humans first entered the Americas some 20,000 years ago, they have settled in many new environments across the continent. This diversity of environments has placed variable selective pressures on the populations living in each region, but the effects of these pressures have not been extensively studied to date. To help fill this gap, we collected genome-wide data from three Indigenous North American populations from different geographic regions of the continent (Alaska, southeastern United States, and central Mexico). We identified signals of natural selection in each population and compared signals across populations to explore the differences in selective pressures among the three regions sampled. We find evidence of adaptation to cold and high-latitude environments in Alaska, while in the southeastern United States and central Mexico, pathogenic environments seem to have created important selective pressures. This study lays the foundation for additional functional and phenotypic work on possible adaptations to varied environments during the history of population diversification in the Americas.
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Affiliation(s)
- Austin W Reynolds
- Department of Anthropology, University of California, Davis, CA 95616;
| | - Jaime Mata-Míguez
- Department of Anthropology, The University of Texas at Austin, Austin, TX 78712
| | - Aida Miró-Herrans
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611
| | - Marcus Briggs-Cloud
- Maskoke, Gainesville, FL 32611
- School of Natural Resources and Environment, University of Florida, Gainesville, FL 32611
| | | | | | | | - Margarita Rzhetskaya
- Division of Endocrinology, Metabolism, and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Lorena Orozco
- National Institute of Genomic Medicine, Delegación Tlalpan, 14610 México
| | - Jennifer A Raff
- Department of Anthropology, University of Kansas, Lawrence, KS 66045-7556
| | - M Geoffrey Hayes
- Division of Endocrinology, Metabolism, and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
- Department of Anthropology, Northwestern University, Evanston, IL 60208
| | - Deborah A Bolnick
- Department of Anthropology, University of Connecticut, Storrs, CT 06269-1176
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269-1176
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27
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Mercader JM, Liao RG, Bell AD, Dymek Z, Estrada K, Tukiainen T, Huerta-Chagoya A, Moreno-Macías H, Jablonski KA, Hanson RL, Walford GA, Moran I, Chen L, Agarwala V, Ordoñez-Sánchez ML, Rodríguez-Guillen R, Rodríguez-Torres M, Segura-Kato Y, García-Ortiz H, Centeno-Cruz F, Barajas-Olmos F, Caulkins L, Puppala S, Fontanillas P, Williams AL, Bonàs-Guarch S, Hartl C, Ripke S, Tooley K, Lane J, Zerrweck C, Martínez-Hernández A, Córdova EJ, Mendoza-Caamal E, Contreras-Cubas C, González-Villalpando ME, Cruz-Bautista I, Muñoz-Hernández L, Gómez-Velasco D, Alvirde U, Henderson BE, Wilkens LR, Le Marchand L, Arellano-Campos O, Riba L, Harden M, Gabriel S, Abboud HE, Cortes ML, Revilla-Monsalve C, Islas-Andrade S, Soberon X, Curran JE, Jenkinson CP, DeFronzo RA, Lehman DM, Hanis CL, Bell GI, Boehnke M, Blangero J, Duggirala R, Saxena R, MacArthur D, Ferrer J, McCarroll SA, Torrents D, Knowler WC, Baier LJ, Burtt N, González-Villalpando C, Haiman CA, Aguilar-Salinas CA, Tusié-Luna T, Flannick J, Jacobs SBR, Orozco L, Altshuler D, Florez JC. A Loss-of-Function Splice Acceptor Variant in IGF2 Is Protective for Type 2 Diabetes. Diabetes 2017; 66:2903-2914. [PMID: 28838971 PMCID: PMC5652606 DOI: 10.2337/db17-0187] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 08/13/2017] [Indexed: 12/12/2022]
Abstract
Type 2 diabetes (T2D) affects more than 415 million people worldwide, and its costs to the health care system continue to rise. To identify common or rare genetic variation with potential therapeutic implications for T2D, we analyzed and replicated genome-wide protein coding variation in a total of 8,227 individuals with T2D and 12,966 individuals without T2D of Latino descent. We identified a novel genetic variant in the IGF2 gene associated with ∼20% reduced risk for T2D. This variant, which has an allele frequency of 17% in the Mexican population but is rare in Europe, prevents splicing between IGF2 exons 1 and 2. We show in vitro and in human liver and adipose tissue that the variant is associated with a specific, allele-dosage-dependent reduction in the expression of IGF2 isoform 2. In individuals who do not carry the protective allele, expression of IGF2 isoform 2 in adipose is positively correlated with both incidence of T2D and increased plasma glycated hemoglobin in individuals without T2D, providing support that the protective effects are mediated by reductions in IGF2 isoform 2. Broad phenotypic examination of carriers of the protective variant revealed no association with other disease states or impaired reproductive health. These findings suggest that reducing IGF2 isoform 2 expression in relevant tissues has potential as a new therapeutic strategy for T2D, even beyond the Latin American population, with no major adverse effects on health or reproduction.
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Affiliation(s)
- Josep M Mercader
- Broad Metabolism Program and Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Barcelona Supercomputing Center, Joint BSC-CRG-IRB Research Programme in Computational Biology, Barcelona, Spain
| | - Rachel G Liao
- Broad Metabolism Program and Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - Avery D Bell
- Department of Genetics, Harvard Medical School, Boston, MA
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - Zachary Dymek
- Broad Metabolism Program and Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - Karol Estrada
- Broad Metabolism Program and Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Taru Tukiainen
- Department of Genetics, Harvard Medical School, Boston, MA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA
| | - Alicia Huerta-Chagoya
- Consejo Nacional de Ciencia y Tecnología (CONACYT), Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Hortensia Moreno-Macías
- Unidad de Biología Molecular y Medicina Genómica, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México/Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
- Universidad Autónoma Metropolitana, Mexico City, Mexico
| | | | - Robert L Hanson
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, AZ
| | - Geoffrey A Walford
- Broad Metabolism Program and Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Ignasi Moran
- Department of Medicine, Imperial College London, London, U.K
| | - Ling Chen
- Broad Metabolism Program and Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
| | - Vineeta Agarwala
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - María Luisa Ordoñez-Sánchez
- Consejo Nacional de Ciencia y Tecnología (CONACYT), Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Rosario Rodríguez-Guillen
- Consejo Nacional de Ciencia y Tecnología (CONACYT), Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Maribel Rodríguez-Torres
- Consejo Nacional de Ciencia y Tecnología (CONACYT), Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Yayoi Segura-Kato
- Consejo Nacional de Ciencia y Tecnología (CONACYT), Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | | | | | | | - Lizz Caulkins
- Broad Metabolism Program and Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - Sobha Puppala
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
| | - Pierre Fontanillas
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - Amy L Williams
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY
| | - Sílvia Bonàs-Guarch
- Barcelona Supercomputing Center, Joint BSC-CRG-IRB Research Programme in Computational Biology, Barcelona, Spain
| | - Chris Hartl
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - Stephan Ripke
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA
- Department of Psychiatry and Psychotherapy, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | | | - Katherine Tooley
- Department of Genetics, Harvard Medical School, Boston, MA
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - Jacqueline Lane
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Carlos Zerrweck
- Clínica Integral de Cirugía para la Obesidad y Enfermedades Metabólicas, Hospital General Tláhuac, Mexico City, Mexico
| | | | | | | | | | - María E González-Villalpando
- Centro de Estudios en Diabetes, Unidad de Investigacion en Diabetes y Riesgo Cardiovascular, Centro de Investigacion en Salud Poblacional, Instituto Nacional de Salud Pública, Mexico City, Mexico
| | - Ivette Cruz-Bautista
- Departamento de Endocrinología y Metabolismo, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Liliana Muñoz-Hernández
- Departamento de Endocrinología y Metabolismo, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Donaji Gómez-Velasco
- Departamento de Endocrinología y Metabolismo, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Ulises Alvirde
- Departamento de Endocrinología y Metabolismo, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Brian E Henderson
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Lynne R Wilkens
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI
| | - Loic Le Marchand
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI
| | - Olimpia Arellano-Campos
- Departamento de Endocrinología y Metabolismo, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Laura Riba
- Departamento de Endocrinología y Metabolismo, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Maegan Harden
- The Genomics Platform, Broad Institute, Cambridge, MA
| | | | | | | | - Hanna E Abboud
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX
| | | | - Cristina Revilla-Monsalve
- Unidad de Investigación Médica en Enfermedades Metabólicas, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Sergio Islas-Andrade
- Unidad de Investigación Médica en Enfermedades Metabólicas, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Xavier Soberon
- Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Joanne E Curran
- South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX
| | - Christopher P Jenkinson
- South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Edinburg, TX
| | - Ralph A DeFronzo
- Division of Diabetes, Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX
| | - Donna M Lehman
- Departments of Medicine and Cellular & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX
| | - Craig L Hanis
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX
| | - Graeme I Bell
- Department of Medicine, The University of Chicago, Chicago, IL
- Department of Human Genetics, The University of Chicago, Chicago, IL
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI
| | - John Blangero
- South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX
| | - Ravindranath Duggirala
- South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Edinburg, TX
| | - Richa Saxena
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Daniel MacArthur
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Jorge Ferrer
- Department of Medicine, Imperial College London, London, U.K
- Genomic Programming of Beta Cells and Diabetes, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- CIBERDEM, Barcelona, Spain
| | - Steven A McCarroll
- Department of Genetics, Harvard Medical School, Boston, MA
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - David Torrents
- Barcelona Supercomputing Center, Joint BSC-CRG-IRB Research Programme in Computational Biology, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - William C Knowler
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, AZ
| | - Leslie J Baier
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, AZ
| | - Noel Burtt
- Broad Metabolism Program and Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - Clicerio González-Villalpando
- Centro de Estudios en Diabetes, Unidad de Investigacion en Diabetes y Riesgo Cardiovascular, Centro de Investigacion en Salud Poblacional, Instituto Nacional de Salud Pública, Mexico City, Mexico
| | | | - Carlos A Aguilar-Salinas
- Departamento de Endocrinología y Metabolismo, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Teresa Tusié-Luna
- Unidad de Biología Molecular y Medicina Genómica, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México/Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Jason Flannick
- Broad Metabolism Program and Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Department of Molecular Biology, Harvard Medical School, Boston, MA
| | - Suzanne B R Jacobs
- Broad Metabolism Program and Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
| | - Lorena Orozco
- Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - David Altshuler
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Department of Genetics, Harvard Medical School, Boston, MA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Department of Medicine, Harvard Medical School, Boston, MA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Department of Molecular Biology, Harvard Medical School, Boston, MA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA
| | - Jose C Florez
- Broad Metabolism Program and Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
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28
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Contreras-Cubas C, Sánchez-Hernández BE, García-Ortiz H, Martínez-Hernández A, Barajas-Olmos F, Cid M, Mendoza-Caamal EC, Centeno-Cruz F, Ortiz-Cruz G, Jiménez-López JC, Córdova EJ, Salas-Bautista EG, Saldaña-Alvarez Y, Fernández-López JC, Mutchinick OM, Orozco L. Heterogenous Distribution of MTHFR Gene Variants among Mestizos and Diverse Amerindian Groups from Mexico. PLoS One 2016; 11:e0163248. [PMID: 27649570 PMCID: PMC5029802 DOI: 10.1371/journal.pone.0163248] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 09/05/2016] [Indexed: 11/18/2022] Open
Abstract
Methylenetetrahydrofolate reductase (MTHFR) is a key enzyme in folate metabolism. Folate deficiency has been related to several conditions, including neural tube defects (NTDs) and cardiovascular diseases. Hence, MTHFR genetic variants have been studied worldwide, particularly the C677T and A1298C. We genotyped the C677T and A1298C MTHFR polymorphisms in Mexican Amerindians (MAs), from the largest sample included in a genetic study (n = 2026, from 62 ethnic groups), and in a geographically-matched Mexican Mestizo population (MEZ, n = 638). The 677T allele was most frequent in Mexican individuals, particularly in MAs. The frequency of this allele in both MAs and MEZs was clearly enriched in the South region of the country, followed by the Central East and South East regions. In contrast, the frequency of the 1298C risk allele in Mexicans was one of the lowest in the world. Both in MAs and MEZs the variants 677T and 1298C displayed opposite allele frequency gradients from southern to northern Mexico. Our findings suggest that in Mestizos the 677T allele was derived from Amerindians while the 1298C allele was a European contribution. Some subgroups showed an allele frequency distribution that highlighted their genetic diversity. Notably, the distribution of the frequency of the 677T allele was consistent with that of the high incidence of NTDs reported in MEZ.
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Affiliation(s)
- Cecilia Contreras-Cubas
- Inmunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genómica, SS, Mexico City, Mexico
| | - Beatríz E. Sánchez-Hernández
- Genetic Department, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, SS, Mexico City, Mexico
| | - Humberto García-Ortiz
- Inmunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genómica, SS, Mexico City, Mexico
| | - Angélica Martínez-Hernández
- Inmunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genómica, SS, Mexico City, Mexico
| | - Francisco Barajas-Olmos
- Inmunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genómica, SS, Mexico City, Mexico
| | - Miguel Cid
- Inmunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genómica, SS, Mexico City, Mexico
| | - Elvia C. Mendoza-Caamal
- Inmunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genómica, SS, Mexico City, Mexico
| | - Federico Centeno-Cruz
- Inmunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genómica, SS, Mexico City, Mexico
| | - Gabriela Ortiz-Cruz
- Genetic Department, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, SS, Mexico City, Mexico
| | - José Concepción Jiménez-López
- Physic Anthropology Direction, Instituto Nacional de Antropología e Historia, Museo Nacional de Antropología, Mexico City, Mexico
| | - Emilio J. Córdova
- Inmunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genómica, SS, Mexico City, Mexico
| | - Eva Gabriela Salas-Bautista
- Physic Anthropology Direction, Instituto Nacional de Antropología e Historia, Museo Nacional de Antropología, Mexico City, Mexico
| | - Yolanda Saldaña-Alvarez
- Inmunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genómica, SS, Mexico City, Mexico
| | | | - Osvaldo M. Mutchinick
- Genetic Department, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, SS, Mexico City, Mexico
| | - Lorena Orozco
- Inmunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genómica, SS, Mexico City, Mexico
- * E-mail:
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Larqué C, Velasco M, Barajas-Olmos F, García-Delgado N, Chávez-Maldonado JP, García-Morales J, Orozco L, Hiriart M. Transcriptome landmarks of the functional maturity of rat beta-cells, from lactation to adulthood. J Mol Endocrinol 2016; 57:45-59. [PMID: 27220619 DOI: 10.1530/jme-16-0052] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 05/24/2016] [Indexed: 12/22/2022]
Abstract
Research on the postnatal development of pancreatic beta-cells has become an important subject in recent years. Understanding the mechanisms that govern beta-cell postnatal maturation could bring new opportunities to therapeutic approaches for diabetes. The weaning period consists of a critical postnatal window for structural and physiologic maturation of rat beta-cells. To investigate transcriptome changes involved in the maturation of beta-cells neighboring this period, we performed microarray analysis in fluorescence-activated cell-sorted (FACS) beta-cell-enriched populations. Our results showed a variety of gene sets including those involved in the integration of metabolism, modulation of electrical activity, and regulation of the cell cycle that play important roles in the maturation process. These observations were validated using reverse hemolytic plaque assay, electrophysiological recordings, and flow cytometry analysis. Moreover, we suggest some unexplored pathways such as sphingolipid metabolism, insulin-vesicle trafficking, regulation of transcription/transduction by miRNA-30, trafficking proteins, and cell cycle proteins that could play important roles in the process mentioned above for further investigation.
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Affiliation(s)
- Carlos Larqué
- Department of Neurodevelopment and PhysiologyNeuroscience Division, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Myrian Velasco
- Department of Neurodevelopment and PhysiologyNeuroscience Division, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Francisco Barajas-Olmos
- Immunogenomics and Metabolic Disease LaboratoryInstituto Nacional de Medicina Genómica, SS, Mexico City, Mexico
| | - Neyvis García-Delgado
- Department of Neurodevelopment and PhysiologyNeuroscience Division, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Juan Pablo Chávez-Maldonado
- Department of Neurodevelopment and PhysiologyNeuroscience Division, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Jazmín García-Morales
- Department of Neurodevelopment and PhysiologyNeuroscience Division, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Lorena Orozco
- Immunogenomics and Metabolic Disease LaboratoryInstituto Nacional de Medicina Genómica, SS, Mexico City, Mexico
| | - Marcia Hiriart
- Department of Neurodevelopment and PhysiologyNeuroscience Division, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
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