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Diego VP, Manusov EG, Mao X, Almeida M, Peralta JM, Curran JE, Mahaney MC, Göring H, Blangero J, Williams-Blangero S. Metabolic syndrome traits exhibit genotype-by-environment interaction in relation to socioeconomic status in the Mexican American family heart study. Front Genet 2024; 15:1240462. [PMID: 38495670 PMCID: PMC10940335 DOI: 10.3389/fgene.2024.1240462] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 02/08/2024] [Indexed: 03/19/2024] Open
Abstract
Background: Socioeconomic Status (SES) is a potent environmental determinant of health. To our knowledge, no assessment of genotype-environment interaction has been conducted to consider the joint effects of socioeconomic status and genetics on risk for metabolic disease. We analyzed data from the Mexican American Family Studies (MAFS) to evaluate the hypothesis that genotype-by-environment interaction (GxE) is an essential determinant of variation in risk factors for metabolic syndrome (MS). Methods: We employed a maximum likelihood estimation of the decomposition of variance components to detect GxE interaction. After excluding individuals with diabetes and individuals on medication for diabetes, hypertension, or dyslipidemia, we analyzed 12 MS risk factors: fasting glucose (FG), fasting insulin (FI), 2-h glucose (2G), 2-h insulin (2I), body mass index (BMI), waist circumference (WC), leptin (LP), high-density lipoprotein-cholesterol (HDL-C), triglycerides (TG), total serum cholesterol (TSC), systolic blood pressure (SBP), and diastolic blood pressure (DBP). Our SES variable used a combined score of Duncan's socioeconomic index and education years. Heterogeneity in the additive genetic variance across the SES continuum and a departure from unity in the genetic correlation coefficient were taken as evidence of GxE interaction. Hypothesis tests were conducted using standard likelihood ratio tests. Results: We found evidence of GxE for fasting glucose, 2-h glucose, 2-h insulin, BMI, and triglycerides. The genetic effects underlying the insulin/glucose metabolism component of MS are upregulated at the lower end of the SES spectrum. We also determined that the household variance for systolic blood pressure decreased with increasing SES. Conclusion: These results show a significant change in the GxE interaction underlying the major components of MS in response to changes in socioeconomic status. Further mRNA sequencing studies will identify genes and canonical gene pathways to support our molecular-level hypotheses.
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Affiliation(s)
- Vincent P. Diego
- South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX, United States
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Eron G. Manusov
- South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX, United States
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Xi Mao
- Department of Economics, University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Marcio Almeida
- South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX, United States
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Juan M. Peralta
- South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX, United States
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Joanne E. Curran
- South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX, United States
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Michael C. Mahaney
- South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX, United States
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Harald Göring
- South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX, United States
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - John Blangero
- South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX, United States
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Sarah Williams-Blangero
- South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX, United States
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX, United States
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Kumar S, Granados J, Aceves M, Peralta J, Leandro AC, Thomas J, Williams-Blangero S, Curran JE, Blangero J. Pre-Infection Innate Immunity Attenuates SARS-CoV-2 Infection and Viral Load in iPSC-Derived Alveolar Epithelial Type 2 Cells. Cells 2024; 13:369. [PMID: 38474333 PMCID: PMC10931100 DOI: 10.3390/cells13050369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 02/05/2024] [Accepted: 02/19/2024] [Indexed: 03/14/2024] Open
Abstract
A large portion of the heterogeneity in coronavirus disease 2019 (COVID-19) susceptibility and severity of illness (SOI) remains poorly understood. Recent evidence suggests that SARS-CoV-2 infection-associated damage to alveolar epithelial type 2 cells (AT2s) in the distal lung may directly contribute to disease severity and poor prognosis in COVID-19 patients. Our in vitro modeling of SARS-CoV-2 infection in induced pluripotent stem cell (iPSC)-derived AT2s from 10 different individuals showed interindividual variability in infection susceptibility and the postinfection cellular viral load. To understand the underlying mechanism of the AT2's capacity to regulate SARS-CoV-2 infection and cellular viral load, a genome-wide differential gene expression analysis between the mock and SARS-CoV-2 infection-challenged AT2s was performed. The 1393 genes, which were significantly (one-way ANOVA FDR-corrected p ≤ 0.05; FC abs ≥ 2.0) differentially expressed (DE), suggest significant upregulation of viral infection-related cellular innate immune response pathways (p-value ≤ 0.05; activation z-score ≥ 3.5), and significant downregulation of the cholesterol- and xenobiotic-related metabolic pathways (p-value ≤ 0.05; activation z-score ≤ -3.5). Whilst the effect of post-SARS-CoV-2 infection response on the infection susceptibility and postinfection viral load in AT2s is not clear, interestingly, pre-infection (mock-challenged) expression of 238 DE genes showed a high correlation with the postinfection SARS-CoV-2 viral load (FDR-corrected p-value ≤ 0.05 and r2-absolute ≥ 0.57). The 85 genes whose expression was negatively correlated with the viral load showed significant enrichment in viral recognition and cytokine-mediated innate immune GO biological processes (p-value range: 4.65 × 10-10 to 2.24 × 10-6). The 153 genes whose expression was positively correlated with the viral load showed significant enrichment in cholesterol homeostasis, extracellular matrix, and MAPK/ERK pathway-related GO biological processes (p-value range: 5.06 × 10-5 to 6.53 × 10-4). Overall, our results strongly suggest that AT2s' pre-infection innate immunity and metabolic state affect their susceptibility to SARS-CoV-2 infection and viral load.
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Affiliation(s)
- Satish Kumar
- Division of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, McAllen, TX 78504, USA; (J.G.); (M.A.); (J.T.)
| | - Jose Granados
- Division of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, McAllen, TX 78504, USA; (J.G.); (M.A.); (J.T.)
| | - Miriam Aceves
- Division of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, McAllen, TX 78504, USA; (J.G.); (M.A.); (J.T.)
| | - Juan Peralta
- Division of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA; (J.P.); (A.C.L.); (S.W.-B.); (J.E.C.); (J.B.)
| | - Ana C. Leandro
- Division of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA; (J.P.); (A.C.L.); (S.W.-B.); (J.E.C.); (J.B.)
| | - John Thomas
- Division of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, McAllen, TX 78504, USA; (J.G.); (M.A.); (J.T.)
| | - Sarah Williams-Blangero
- Division of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA; (J.P.); (A.C.L.); (S.W.-B.); (J.E.C.); (J.B.)
| | - Joanne E. Curran
- Division of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA; (J.P.); (A.C.L.); (S.W.-B.); (J.E.C.); (J.B.)
| | - John Blangero
- Division of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA; (J.P.); (A.C.L.); (S.W.-B.); (J.E.C.); (J.B.)
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Howard T, Almieda M, Diego V, Viel K, Luu B, Haack K, Raja R, Ameri A, Chitlur M, Rydz N, Lillicrap D, Watts R, Kessler C, Ramsey C, Dinh L, Kim B, Powell J, Peralta J, Bouls R, Abraham S, Shen YM, Murillo C, Mead H, Lehmann P, Fine E, Escobar M, Kumar S, Williams-Blangero S, Kasper C, Almasy L, Cole S, Blangero J, Konkle B. A Scan of Pleiotropic Immune Mediated Disease Genes Identifies Novel Determinants of Baseline FVIII Inhibitor Status in Hemophilia-A. Res Sq 2023:rs.3.rs-3371095. [PMID: 37886476 PMCID: PMC10602130 DOI: 10.21203/rs.3.rs-3371095/v1] [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] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Hemophilia-A (HA) is caused by heterogeneous loss-of-function factor (F)VIII gene (F8)-mutations and deficiencies in plasma-FVIII-activity that impair intrinsic-pathway-mediated coagulation-amplification. The standard-of-care for severe-HA-patients is regular infusions of therapeutic-FVIII-proteins (tFVIIIs) but ~30% develop neutralizing-tFVIII-antibodies called "FVIII-inhibitors (FEIs)" and become refractory. We used the PATH study and ImmunoChip to scan immune-mediated-disease (IMD)-genes for novel and/or replicated genomic-sequence-variations associated with baseline-FEI-status while accounting for non-independence of data due to genetic-relatedness and F8-mutational-heterogeneity. The baseline-FEI-status of 450 North American PATH subjects-206 with black-African-ancestry and 244 with white-European-ancestry-was the dependent variable. The F8-mutation-data and a genetic-relatedness matrix were incorporated into a binary linear-mixed model of genetic association with baseline-FEI-status. We adopted a gene-centric-association-strategy to scan, as candidates, pleiotropic-IMD-genes implicated in the development of either ³2 autoimmune-/autoinflammatory-disorders (AADs) or ³1 AAD and FEIs. Baseline-FEI-status was significantly associated with SNPs assigned to NOS2A (rs117382854; p=3.2E-6) and B3GNT2 (rs10176009; p=5.1E-6), which have functions in anti-microbial-/-tumoral-immunity. Among IMD-genes implicated in FEI-risk previously, we identified strong associations with CTLA4 assigned SNPs (p=2.2E-5). The F8-mutation-effect underlies ~15% of the total heritability for baseline-FEI-status. Additive genetic heritability and SNPs in IMD-genes account for >50% of the patient-specific variability in baseline-FEI-status. Race is a significant determinant independent of F8-mutation-effects and non-F8-genetics.
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Affiliation(s)
- Tom Howard
- University of Texas Rio Grande Valley School of Medicine
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Diego VP, Manusov EG, Mao X, Curran JE, Göring H, Almeida M, Mahaney MC, Peralta JM, Blangero J, Williams-Blangero S. Genotype-by-socioeconomic status interaction influences heart disease risk scores and carotid artery thickness in Mexican Americans: the predominant role of education in comparison to household income and socioeconomic index. Front Genet 2023; 14:1132110. [PMID: 37795246 PMCID: PMC10547145 DOI: 10.3389/fgene.2023.1132110] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 07/17/2023] [Indexed: 10/06/2023] Open
Abstract
Background: Socioeconomic status (SES) is a potent environmental determinant of health. To our knowledge, no assessment of genotype-environment interaction has been conducted to consider the joint effects of socioeconomic status and genetics on risk for cardiovascular disease (CVD). We analyzed Mexican American Family Studies (MAFS) data to evaluate the hypothesis that genotype-by-environment interaction (GxE) is an important determinant of variation in CVD risk factors. Methods: We employed a linear mixed model to investigate GxE in Mexican American extended families. We studied two proxies for CVD [Pooled Cohort Equation Risk Scores/Framingham Risk Scores (FRS/PCRS) and carotid artery intima-media thickness (CA-IMT)] in relation to socioeconomic status as determined by Duncan's Socioeconomic Index (SEI), years of education, and household income. Results: We calculated heritability for FRS/PCRS and carotid artery intima-media thickness. There was evidence of GxE due to additive genetic variance heterogeneity and genetic correlation for FRS, PCRS, and CA-IMT measures for education (environment) but not for household income or SEI. Conclusion: The genetic effects underlying CVD are dynamically modulated at the lower end of the SES spectrum. There is a significant change in the genetic architecture underlying the major components of CVD in response to changes in education.
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Affiliation(s)
- Vincent P. Diego
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX, United States
- School of Medicine, South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Eron G. Manusov
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX, United States
- School of Medicine, South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Xi Mao
- Department of Economics, University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Joanne E. Curran
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX, United States
- School of Medicine, South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Harald Göring
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX, United States
- School of Medicine, South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Marcio Almeida
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX, United States
- School of Medicine, South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Michael C. Mahaney
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX, United States
- School of Medicine, South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Juan M. Peralta
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX, United States
- School of Medicine, South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - John Blangero
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX, United States
- School of Medicine, South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Sarah Williams-Blangero
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX, United States
- School of Medicine, South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX, United States
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Manusov EG, Diego VP, Abrego E, Herklotz K, Almeida M, Mao X, Laston S, Blangero J, Williams-Blangero S. Gene-by-Environment Interaction in Non-Alcoholic Fatty Liver Disease and Depression: The Role of Hepatic Transaminases. Med Res Arch 2023; 11:10.18103/mra.v11i9.4408. [PMID: 38698891 PMCID: PMC11064892 DOI: 10.18103/mra.v11i9.4408] [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] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Non-alcoholic fatty liver disease (NAFLD) encompasses a range of liver conditions, from benign fatty accumulation to severe fibrosis. The global prevalence of NAFLD has risen to 25-30%, with variations across ethnic groups. NAFLD may advance to hepatocellular carcinoma, increases cardiovascular risk, is associated with chronic kidney disease, and is an independent metabolic disease risk factor. Assessment methods for liver health include liver biopsy, magnetic resonance imaging, ultrasound, and vibration-controlled transient elastography (VCTE by FibroScan). Hepatic transaminases are cost-effective and minimally invasive liver health assessment methods options. This study focuses on the interaction between genetic factors underlying the traits (hepatic transaminases and the FibroScan results) on the one hand and the environment (depression) on the other. We examined 525 individuals at risk for metabolic disorders. We utilized variance components models and likelihood-based statistical inference to examine potential GxE interactions in markers of NAFLD, including aspartate aminotransferase (AST), alanine aminotransferase (ALT), and the AST/ALT ratio, and Vibration-Controlled Transient Elastography (VCTE by FibroScan). We calculated the Fibroscan-AST (FAST) score (a score that identifies the risk of progressive non-alcoholic steatohepatitis (NASH) and screened for depression using the Beck Depression Inventory-II (BDI-II). We identified significant G × E interactions for AST/ALT ratio × BDI-II, but not AST, ALT, or the FAST score. Our findings support that genetic factors play a role in hepatic transaminases, especially the AST/ALT ratio, with depression influencing this relationship. These insights contribute to understanding the complex interplay of genetics, environment, and liver health, potentially guiding future personalized interventions.
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Affiliation(s)
- Eron G Manusov
- Department of Human Genetics, The University of Texas Rio Grande Valley, Brownsville, TX, United States
- South Texas Diabetes and Obesity Institute, The University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Vincent P Diego
- Department of Human Genetics, The University of Texas Rio Grande Valley, Brownsville, TX, United States
- South Texas Diabetes and Obesity Institute, The University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Edward Abrego
- The University of Texas Rio Grande Valley, School of Medicine, Edinburg Texas
| | - Kathryn Herklotz
- The University of Texas Rio Grande Valley, School of Medicine, Edinburg Texas
| | - Marcio Almeida
- Department of Human Genetics, The University of Texas Rio Grande Valley, Brownsville, TX, United States
- South Texas Diabetes and Obesity Institute, The University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Xi Mao
- Department of Economics, University of Texas Rio Grande Valley, Brownsville, TX 78520
| | - Sandra Laston
- Department of Human Genetics, The University of Texas Rio Grande Valley, Brownsville, TX, United States
- South Texas Diabetes and Obesity Institute, The University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - John Blangero
- Department of Human Genetics, The University of Texas Rio Grande Valley, Brownsville, TX, United States
- South Texas Diabetes and Obesity Institute, The University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Sarah Williams-Blangero
- Department of Human Genetics, The University of Texas Rio Grande Valley, Brownsville, TX, United States
- South Texas Diabetes and Obesity Institute, The University of Texas Rio Grande Valley, Brownsville, TX, United States
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Manusov E, Reininger B, Ulloa-Aguirre A, Williams-Blangero S. Editorial: The biology and management of chronic diseases in Mexican Americans. Front Med (Lausanne) 2022; 9:1095203. [PMID: 36582289 PMCID: PMC9793578 DOI: 10.3389/fmed.2022.1095203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 11/22/2022] [Indexed: 12/15/2022] Open
Affiliation(s)
- Eron Manusov
- Department of Human Genetics, University of Texas Rio Grande Valley-School of Medicine, Brownsville, TX, United States,*Correspondence: Eron Manusov
| | - Belinda Reininger
- University of Texas Health Science Center at Houston School of Public Health Brownsville Campus, Brownsville, TX, United States
| | - Alfredo Ulloa-Aguirre
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, National Autonomous University of Mexico, Mexico City, Mexico
| | - Sarah Williams-Blangero
- Department of Human Genetics, University of Texas Rio Grande Valley-School of Medicine, Brownsville, TX, United States
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Hardin AM, Knigge RP, Duren DL, Williams-Blangero S, Subedi J, Mahaney MC, Sherwood RJ. Genetic influences on dentognathic morphology in the Jirel population of Nepal. Anat Rec (Hoboken) 2022; 305:2137-2157. [PMID: 34981668 PMCID: PMC9250551 DOI: 10.1002/ar.24857] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/26/2021] [Accepted: 11/29/2021] [Indexed: 12/12/2022]
Abstract
Patterns of genetic variation and covariation impact the evolution of the craniofacial complex and contribute to clinically significant malocclusions in modern human populations. Previous quantitative genetic studies have estimated the heritabilities and genetic correlations of skeletal and dental traits in humans and nonhuman primates, but none have estimated these quantitative genetic parameters across the dentognathic complex. A large and powerful pedigree from the Jirel population of Nepal was leveraged to estimate heritabilities and genetic correlations in 62 maxillary and mandibular arch dimensions, incisor and canine lengths, and post-canine tooth crown areas (N ≥ 739). Quantitative genetic parameter estimation was performed using maximum likelihood-based variance decomposition. Residual heritability estimates were significant for all traits, ranging from 0.269 to 0.898. Genetic correlations were positive for all trait pairs. Principal components analyses of the phenotypic and genetic correlation matrices indicate an overall size effect across all measurements on the first principal component. Additional principal components demonstrate positive relationships between post-canine tooth crown areas and arch lengths and negative relationships between post-canine tooth crown areas and arch widths, and between arch lengths and arch widths. Based on these findings, morphological variation in the human dentognathic complex may be constrained by genetic relationships between dental dimensions and arch lengths, with weaker genetic correlations between these traits and arch widths allowing for variation in arch shape. The patterns identified are expected to have impacted the evolution of the dentognathic complex and its genetic architecture as well as the prevalence of dental crowding in modern human populations.
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Affiliation(s)
- Anna M. Hardin
- Biology Department, Western Oregon University
- Craniofacial Research Center, Department of Pathology and Anatomical Sciences, University of Missouri School of Medicine
- Department of Orthopaedic Surgery, University of Missouri School of Medicine
| | - Ryan P. Knigge
- Craniofacial Research Center, Department of Pathology and Anatomical Sciences, University of Missouri School of Medicine
- Department of Orthopaedic Surgery, University of Missouri School of Medicine
- Department of Integrative Biology and Physiology, University of Minnesota Medical School
| | - Dana L. Duren
- Craniofacial Research Center, Department of Pathology and Anatomical Sciences, University of Missouri School of Medicine
- Department of Orthopaedic Surgery, University of Missouri School of Medicine
| | - Sarah Williams-Blangero
- South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley
| | | | - Michael C. Mahaney
- South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley
| | - Richard J. Sherwood
- Craniofacial Research Center, Department of Pathology and Anatomical Sciences, University of Missouri School of Medicine
- Department of Orthopaedic Surgery, University of Missouri School of Medicine
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Manusov EG, Diego VP, Sheikh K, Laston S, Blangero J, Williams-Blangero S. Non-alcoholic Fatty Liver Disease and Depression: Evidence for Genotype × Environment Interaction in Mexican Americans. Front Psychiatry 2022; 13:936052. [PMID: 35845438 PMCID: PMC9283683 DOI: 10.3389/fpsyt.2022.936052] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 06/13/2022] [Indexed: 11/17/2022] Open
Abstract
This study examines the impact of G × E interaction effects on non-alcoholic fatty liver disease (NAFLD) among Mexican Americans in the Rio Grande Valley (RGV) of South Texas. We examined potential G × E interaction using variance components models and likelihood-based statistical inference in the phenotypic expression of NAFLD, including hepatic steatosis and hepatic fibrosis (identified using vibration controlled transient elastography and controlled attenuation parameter measured by the FibroScan Device). We screened for depression using the Beck Depression Inventory-II (BDI-II). We identified significant G × E interactions for hepatic fibrosis × BDI-II. These findings provide evidence that genetic factors interact with depression to influence the expression of hepatic fibrosis.
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Affiliation(s)
- Eron Grant Manusov
- Department of Human Genetics, The University of Texas Rio Grande Valley, Brownsville, TX, United States.,School of Medicine, South Texas Diabetes and Obesity Institute, The University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Vincent P Diego
- Department of Human Genetics, The University of Texas Rio Grande Valley, Brownsville, TX, United States.,School of Medicine, South Texas Diabetes and Obesity Institute, The University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Khalid Sheikh
- School of Medicine, The University of Texas Rio Grande Valley, Edinburg, TX, United States
| | - Sandra Laston
- Department of Human Genetics, The University of Texas Rio Grande Valley, Brownsville, TX, United States.,School of Medicine, South Texas Diabetes and Obesity Institute, The University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - John Blangero
- Department of Human Genetics, The University of Texas Rio Grande Valley, Brownsville, TX, United States.,School of Medicine, South Texas Diabetes and Obesity Institute, The University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Sarah Williams-Blangero
- Department of Human Genetics, The University of Texas Rio Grande Valley, Brownsville, TX, United States.,School of Medicine, South Texas Diabetes and Obesity Institute, The University of Texas Rio Grande Valley, Brownsville, TX, United States
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Kumar S, Curran JE, Williams-Blangero S, Blangero J. Efficient Generation of Functional Hepatocytes from Human Induced Pluripotent Stem Cells for Disease Modeling and Disease Gene Discovery. Methods Mol Biol 2022; 2549:85-101. [PMID: 33772461 DOI: 10.1007/7651_2021_375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
In vitro hepatocyte cell models are being used to study the pathogenesis of liver disease and in the discovery and preclinical stages of drug development. The culture of hepatic cell lines and primary hepatocytes as in vitro cell models has been carried out for several decades. However, hepatic cell lines (hepatic carcinoma generated or immortalized) have limited accuracy when recapitulating complex physiological functions of the liver. Additionally, primary hepatocytes sourced from human cadavers or medical biopsies are difficult to obtain due to sourcing limitations, particularly for large-scale population studies or in applications requiring large number of cells. Hepatocyte cultures differentiated from human embryonic stem cells (ESCs) and induced pluripotent stem cell (iPSCs) overcome in large part the limitations of traditional hepatocyte in vitro models. In this chapter, we described an efficient protocol routinely used in our laboratory to differentiate human iPSCs into functional hepatocyte cultures for in vitro modeling of liver function and disease. The protocol uses a three-stage differentiation strategy to generate functional hepatocytes from human iPSCs. The differentiated cells show characteristic hepatocyte morphology including flat and polygonal shape, distinct round nuclei, and presence of biliary canaliculi and they express hepatic markers alpha-fetoprotein (AFP), albumin (ALB), E-cadherin (CHD1), hepatocyte nuclear factor 4 alpha (HNF4α), and actin.
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Affiliation(s)
- Satish Kumar
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, McAllen, TX, 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, USA
| | - Sarah Williams-Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, McAllen, TX, USA
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, 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, USA
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10
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Manusov EG, Gomez De Ziegler C, Diego VP, Munoz-Monaco G, Williams-Blangero S. Frailty Index in the Colonias on the US-Mexico Border: A Special Report. Front Med (Lausanne) 2021; 8:650259. [PMID: 34485319 PMCID: PMC8416248 DOI: 10.3389/fmed.2021.650259] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 07/14/2021] [Indexed: 11/13/2022] Open
Abstract
Frailty is the age-related decline in well-being. The Frailty index (FI) measures the accumulation of health deficits and reflects biopsychosocial and cultural determinants of well-being. Frailty is measured as a static phenotype or as a Frailty Index comprising a ratio of suffered health deficits and total deficits. We report a Frailty Index calculated from routinely measured clinical variables gathered from residents of two Colonias (neighborhoods) in South Texas. A Colonia is a predominantly Hispanic, economically distressed, unincorporated neighborhood. We analyzed retrospective data from 894 patients that live in two Colonias located on the Texas-Mexico border. We calculated the FI with seven physiological variables, PHQ-9 score, and the 11 domain-specific Duke Profile scores, for a total of 19 possible health deficits. FI against age separately in males (n = 272) and females (n = 622) was regressed. Females had a significantly higher starting frailty, and males had a significantly greater change rate with age. FI against age for Cameron Park Colonia and Indian Hills Colonia was regressed. We calculated a significantly higher starting FI in Indian Hills and a significantly greater change rate in Cameron Park residents. Frailty's contributors are complex, especially in neighborhoods of poverty, immigration, low education level, and high prevalence of chronic disease. We report baseline Frailty Index data from two Colonias in South Texas and the clinical and research implications.
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Affiliation(s)
- Eron G Manusov
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Edinburg, TX, United States
| | - Carolina Gomez De Ziegler
- Knapp Family Medicine Residency Program, University of Texas Rio Grande Valley, Edinburg, TX, United States
| | - Vincent P Diego
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Edinburg, TX, United States
| | - Gerardo Munoz-Monaco
- Knapp Family Medicine Residency Program, University of Texas Rio Grande Valley, Edinburg, TX, United States
| | - Sarah Williams-Blangero
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Edinburg, TX, United States.,South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Edinburg, TX, United States
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11
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Blackburn NB, Meikle PJ, Peralta JM, Kumar S, Leandro AC, Bellinger MA, Giles C, Huynh K, Mahaney MC, Göring HHH, VandeBerg JL, Williams-Blangero S, Glahn DC, Duggirala R, Blangero J, Michael LF, Curran JE. Identifying the Lipidomic Effects of a Rare Loss-of-Function Deletion in ANGPTL3. Circ Genom Precis Med 2021; 14:e003232. [PMID: 33887960 DOI: 10.1161/circgen.120.003232] [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] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND The identification and understanding of therapeutic targets for atherosclerotic cardiovascular disease is of fundamental importance given its global health and economic burden. Inhibition of ANGPTL3 (angiopoietin-like 3) has demonstrated a cardioprotective effect, showing promise for atherosclerotic cardiovascular disease treatment, and is currently the focus of ongoing clinical trials. Here, we assessed the genetic basis of variation in ANGPTL3 levels in the San Antonio Family Heart Study. METHODS We assayed ANGPTL3 protein levels in ≈1000 Mexican Americans from extended pedigrees. By drawing upon existing plasma lipidome profiles and genomic data we conducted analyses to understand the genetic basis to variation in ANGPTL3 protein levels, and accordingly the correlation with the plasma lipidome. RESULTS In a variance components framework, we identified that variation in ANGPTL3 was significantly heritable (h2=0.33, P=1.31×10-16). To explore the genetic basis of this heritability, we conducted a genome-wide linkage scan and identified significant linkage (logarithm of odds =6.18) to a locus on chromosome 1 at 90 centimorgans, corresponding to the ANGPTL3 gene location. In the genomes of 23 individuals from a single pedigree, we identified a loss-of-function variant, rs398122988 (N121Kfs*2), in ANGPTL3, that was significantly associated with lower ANGPTL3 levels (β=-1.69 SD units, P=3.367×10-13), and accounted for the linkage signal at this locus. Given the known role of ANGPTL3 as an inhibitor of endothelial and lipoprotein lipase, we explored the association of ANGPTL3 protein levels and rs398122988 with the plasma lipidome and related phenotypes, identifying novel associations with phosphatidylinositols. CONCLUSIONS Variation in ANGPTL3 protein levels is heritable and under significant genetic control. Both ANGPTL3 levels and loss-of-function variants in ANGPTL3 have significant associations with the plasma lipidome. These findings further our understanding of ANGPTL3 as a therapeutic target for atherosclerotic cardiovascular disease.
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Affiliation(s)
- Nicholas B Blackburn
- South Texas Diabetes and Obesity Institute (N.B.B., J.M.P., S.K., A.C.L., M.C.M., H.H.H.G., J.L.V., S.W.-B., R.D., J.B., J.E.C.), School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX.,Department of Human Genetics (N.B.B., J.M.P., S.K., A.C.L., M.C.M., H.H.H.G., J.L.V., S.W.-B., R.D., J.B., J.E.C.), School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX.,Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia (N.B.B., J.M.P.)
| | - Peter J Meikle
- Baker Heart and Diabetes Institute, Melbourne, VIC, Australia (P.J.M., C.G., K.H.)
| | - Juan M Peralta
- South Texas Diabetes and Obesity Institute (N.B.B., J.M.P., S.K., A.C.L., M.C.M., H.H.H.G., J.L.V., S.W.-B., R.D., J.B., J.E.C.), School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX.,Department of Human Genetics (N.B.B., J.M.P., S.K., A.C.L., M.C.M., H.H.H.G., J.L.V., S.W.-B., R.D., J.B., J.E.C.), School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX.,Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia (N.B.B., J.M.P.)
| | - Satish Kumar
- South Texas Diabetes and Obesity Institute (N.B.B., J.M.P., S.K., A.C.L., M.C.M., H.H.H.G., J.L.V., S.W.-B., R.D., J.B., J.E.C.), School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX.,Department of Human Genetics (N.B.B., J.M.P., S.K., A.C.L., M.C.M., H.H.H.G., J.L.V., S.W.-B., R.D., J.B., J.E.C.), School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX
| | - Ana C Leandro
- South Texas Diabetes and Obesity Institute (N.B.B., J.M.P., S.K., A.C.L., M.C.M., H.H.H.G., J.L.V., S.W.-B., R.D., J.B., J.E.C.), School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX.,Department of Human Genetics (N.B.B., J.M.P., S.K., A.C.L., M.C.M., H.H.H.G., J.L.V., S.W.-B., R.D., J.B., J.E.C.), School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX
| | | | - Corey Giles
- Baker Heart and Diabetes Institute, Melbourne, VIC, Australia (P.J.M., C.G., K.H.)
| | - Kevin Huynh
- Baker Heart and Diabetes Institute, Melbourne, VIC, Australia (P.J.M., C.G., K.H.)
| | - Michael C Mahaney
- South Texas Diabetes and Obesity Institute (N.B.B., J.M.P., S.K., A.C.L., M.C.M., H.H.H.G., J.L.V., S.W.-B., R.D., J.B., J.E.C.), School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX.,Department of Human Genetics (N.B.B., J.M.P., S.K., A.C.L., M.C.M., H.H.H.G., J.L.V., S.W.-B., R.D., J.B., J.E.C.), School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX
| | - Harald H H Göring
- South Texas Diabetes and Obesity Institute (N.B.B., J.M.P., S.K., A.C.L., M.C.M., H.H.H.G., J.L.V., S.W.-B., R.D., J.B., J.E.C.), School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX.,Department of Human Genetics (N.B.B., J.M.P., S.K., A.C.L., M.C.M., H.H.H.G., J.L.V., S.W.-B., R.D., J.B., J.E.C.), School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX
| | - John L VandeBerg
- South Texas Diabetes and Obesity Institute (N.B.B., J.M.P., S.K., A.C.L., M.C.M., H.H.H.G., J.L.V., S.W.-B., R.D., J.B., J.E.C.), School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX.,Department of Human Genetics (N.B.B., J.M.P., S.K., A.C.L., M.C.M., H.H.H.G., J.L.V., S.W.-B., R.D., J.B., J.E.C.), School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX
| | - Sarah Williams-Blangero
- South Texas Diabetes and Obesity Institute (N.B.B., J.M.P., S.K., A.C.L., M.C.M., H.H.H.G., J.L.V., S.W.-B., R.D., J.B., J.E.C.), School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX.,Department of Human Genetics (N.B.B., J.M.P., S.K., A.C.L., M.C.M., H.H.H.G., J.L.V., S.W.-B., R.D., J.B., J.E.C.), School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX
| | - David C Glahn
- Department of Psychiatry, Boston Children's Hospital and Harvard Medical School, Boston, MA (D.C.G.).,Olin Neuropsychiatry Research Center, Institute of Living, Hartford Hospital, Hartford, CT (D.C.G.)
| | - Ravindranath Duggirala
- South Texas Diabetes and Obesity Institute (N.B.B., J.M.P., S.K., A.C.L., M.C.M., H.H.H.G., J.L.V., S.W.-B., R.D., J.B., J.E.C.), School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX.,Department of Human Genetics (N.B.B., J.M.P., S.K., A.C.L., M.C.M., H.H.H.G., J.L.V., S.W.-B., R.D., J.B., J.E.C.), School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX
| | - John Blangero
- South Texas Diabetes and Obesity Institute (N.B.B., J.M.P., S.K., A.C.L., M.C.M., H.H.H.G., J.L.V., S.W.-B., R.D., J.B., J.E.C.), School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX.,Department of Human Genetics (N.B.B., J.M.P., S.K., A.C.L., M.C.M., H.H.H.G., J.L.V., S.W.-B., R.D., J.B., J.E.C.), School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX
| | | | - Joanne E Curran
- South Texas Diabetes and Obesity Institute (N.B.B., J.M.P., S.K., A.C.L., M.C.M., H.H.H.G., J.L.V., S.W.-B., R.D., J.B., J.E.C.), School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX.,Department of Human Genetics (N.B.B., J.M.P., S.K., A.C.L., M.C.M., H.H.H.G., J.L.V., S.W.-B., R.D., J.B., J.E.C.), School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX
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12
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Kumar S, Curran JE, DeLeon E, Leandro AC, Howard TE, Lehman DM, Williams-Blangero S, Glahn DC, Blangero J. Role of miRNA-mRNA Interaction in Neural Stem Cell Differentiation of Induced Pluripotent Stem Cells. Int J Mol Sci 2020; 21:ijms21196980. [PMID: 32977388 PMCID: PMC7582477 DOI: 10.3390/ijms21196980] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 08/26/2020] [Revised: 09/17/2020] [Accepted: 09/21/2020] [Indexed: 11/16/2022] Open
Abstract
miRNA regulates the expression of protein coding genes and plays a regulatory role in human development and disease. The human iPSCs and their differentiated progenies provide a unique opportunity to identify these miRNA-mediated regulatory mechanisms. To identify miRNA-mRNA regulatory interactions in human nervous system development, well characterized NSCs were differentiated from six validated iPSC lines and analyzed for differentially expressed (DE) miRNome and transcriptome by RNA sequencing. Following the criteria, moderated t statistics, FDR-corrected p-value ≤ 0.05 and fold change-absolute (FC-abs) ≥2.0, 51 miRNAs and 4033 mRNAs were found to be significantly DE between iPSCs and NSCs. The miRNA target prediction analysis identified 513 interactions between 30 miRNA families (mapped to 51 DE miRNAs) and 456 DE mRNAs that were paradoxically oppositely expressed. These 513 interactions were highly enriched in nervous system development functions (154 mRNAs; FDR-adjusted p-value range: 8.06 × 10-15-1.44 × 10-4). Furthermore, we have shown that the upregulated miR-10a-5p, miR-30c-5p, miR23-3p, miR130a-3p and miR-17-5p miRNA families were predicted to down-regulate several genes associated with the differentiation of neurons, neurite outgrowth and synapse formation, suggesting their role in promoting the self-renewal of undifferentiated NSCs. This study also provides a comprehensive characterization of iPSC-generated NSCs as dorsal neuroepithelium, important for their potential use in in vitro modeling of human brain development and disease.
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Affiliation(s)
- Satish Kumar
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, McAllen, TX 78504, USA; (E.D.); (S.W.-B.)
- Correspondence:
| | - 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; (J.E.C.); (A.C.L.); (T.E.H.); (J.B.)
| | - Erica DeLeon
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, McAllen, TX 78504, USA; (E.D.); (S.W.-B.)
| | - Ana C. Leandro
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA; (J.E.C.); (A.C.L.); (T.E.H.); (J.B.)
| | - Tom E. Howard
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA; (J.E.C.); (A.C.L.); (T.E.H.); (J.B.)
| | - Donna M. Lehman
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA;
| | - Sarah Williams-Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, McAllen, TX 78504, USA; (E.D.); (S.W.-B.)
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA; (J.E.C.); (A.C.L.); (T.E.H.); (J.B.)
| | - David C. Glahn
- Department of Psychiatry, Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115, USA;
- Olin Neuropsychiatric Research Center, Institute of Living, Hartford, CT 06102, 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; (J.E.C.); (A.C.L.); (T.E.H.); (J.B.)
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13
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Diego VP, Luu BW, Hofmann M, Dinh LV, Almeida M, Powell JS, Rajalingam R, Peralta JM, Kumar S, Curran JE, Sauna ZE, Kellerman R, Park Y, Key NS, Escobar MA, Huynh H, Verhagen AM, Williams-Blangero S, Lehmann PV, Maraskovsky E, Blangero J, Howard TE. Quantitative HLA-class-II/factor VIII (FVIII) peptidomic variation in dendritic cells correlates with the immunogenic potential of therapeutic FVIII proteins in hemophilia A. J Thromb Haemost 2020; 18:201-216. [PMID: 31556206 DOI: 10.1111/jth.14647] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 09/23/2019] [Accepted: 09/23/2019] [Indexed: 01/19/2023]
Abstract
BACKGROUND Plasma-derived (pd) or recombinant (r) therapeutic factor VIII proteins (FVIIIs) are infused to arrest/prevent bleeding in patients with hemophilia A (PWHA). However, FVIIIs are neutralized if anti-FVIII-antibodies (inhibitors) develop. Accumulating evidence suggests that pdFVIIIs with von Willebrand factor (VWF) are less immunogenic than rFVIIIs and that distinct rFVIIIs are differentially immunogenic. Since inhibitor development is T-helper-cell-dependent, human leukocyte antigen (HLA)-class-II (HLAcII) molecules constitute an important early determinant. OBJECTIVES Use dendritic cell (DC)-protein processing/presentation assays with mass-spectrometric and peptide-proteomic analyses to quantify the DP-bound, DQ-bound, and DR-bound FVIII-derived peptides in individual HLAcII repertoires and compare the immunogenic potential of six distinct FVIIIs based on their measured peptide counts. PATIENTS/METHODS Monocyte-derived DCs from normal donors and/or PWHA were cultured with either: Mix-rFVIII, a VWF-free equimolar mixture of a full-length (FL)-rFVIII [Advate® (Takeda)] and four distinct B-domain-deleted (BDD)-rFVIIIs [Xyntha® (Pfizer), NovoEight® (Novo-Nordisk), Nuwiq® (Octapharma), and Afstyla® (CSL Behring GmBH)]; a pdFVIII + pdVWF [Beriate® (CSL Behring GmBH)]; Advate ± pdVWF; Afstyla ± pdVWF; and Xyntha + pdVWF. RESULTS We showed that (i) Beriate had a significantly lower immunogenic potential than Advate ± pdVWF, Afstyla - pdVWF, and Mix-rFVIII; (ii) distinct FVIIIs differed significantly in their immunogenic potential in that, in addition to (i), Afstyla + pdVWF had a significantly lower immunogenic potential than Beriate, while the immunogenic potential of Beriate was not significantly different from that of Xyntha + pdVWF; and (iii) rFVIIIs with pdVWF had significantly lower immunogenic potentials than the same rFVIIIs without pdVWF. CONCLUSIONS Our results provide HLAcII peptidomic level explanations for several important clinical observations/issues including the differential immunogenicity of distinct FVIIIs and the role of HLAcII genetics in inhibitor development.
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Affiliation(s)
- Vincent P Diego
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, Texas
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Brownsville, Texas
| | - Bernadette W Luu
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, Texas
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Brownsville, Texas
- Haplogenics Corporation, Brownsville, Texas
| | | | | | - Marcio Almeida
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, Texas
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Brownsville, Texas
| | | | - Raja Rajalingam
- Immunogenetics and Transplantation Laboratory, Department of Surgery, School of Medicine, University of California at San Francisco, California
| | - Juan M Peralta
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, Texas
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Brownsville, Texas
| | - Satish Kumar
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, Texas
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Brownsville, Texas
| | - Joanne E Curran
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, Texas
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Brownsville, Texas
| | - Zuben E Sauna
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapeutics, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland
| | - Roberta Kellerman
- Division of Hematology, Department of Medicine, University of North Carolina at Chapel Hill, North Carolina
| | - Yara Park
- Department of Laboratory Medicine and Pathology, University of North Carolina at Chapel Hill, North Carolina
| | - Nigel S Key
- Division of Hematology, Department of Medicine, University of North Carolina at Chapel Hill, North Carolina
- Department of Laboratory Medicine and Pathology, University of North Carolina at Chapel Hill, North Carolina
| | - Miguel A Escobar
- Division of Hematology, Department of Medicine, McGovern School of Medicine, University of Texas Health Sciences Center at Houston, Texas
| | - Huy Huynh
- CSL Limited Research, Bio21 Institute, Melbourne, Australia
| | | | - Sarah Williams-Blangero
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, Texas
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Brownsville, Texas
| | - Paul V Lehmann
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio
- Department of Neurology, Case Western Reserve University School of Medicine, Cleveland, Ohio
- Cellular Technology Ltd, Shaker Heights, Ohio
| | | | - John Blangero
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, Texas
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Brownsville, Texas
| | - Tom E Howard
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, Texas
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Brownsville, Texas
- Haplogenics Corporation, Brownsville, Texas
- Department of Pathology and Lab Medicine, VA Valley Coastal Bend Healthcare Center, Harlingen, Texas
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Qiu X, Sun N, McLaughlin SJ, Subedi J, Thapa SS, Shrestha MK, Johnson M, Williams-Blangero S. GENDER AND BELIEFS ABOUT SUCCESSFUL AGING IN EASTERN NEPAL. Innov Aging 2019. [PMCID: PMC6845916 DOI: 10.1093/geroni/igz038.3131] [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] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
Gender shapes opportunities and experiences over the life course, which may influence beliefs about what it means to age successfully. In Nepal, a developing nation in South Asia, women and girls have historically had fewer social and economic opportunities than their male counterparts. To understand how gender may shape beliefs about successful aging, adult members of the Jiri population in eastern Nepal were asked to rate the importance of health-related (e.g., longevity), psychological (e.g., satisfaction with life), and social (e.g., support of family and friends) elements of successful aging (n = 1479; 52.9% female; 49.0% age 18-39, 33.1% age 40 to 59, 17.8% age 60 and over). Each of the 13 elements was rated as very important by over two thirds of the sample. Few gender differences in beliefs were observed; however, results of logistic regression analysis indicate that the odds of Jiri women endorsing longevity (OR = 0.75, p = 0.02) and life satisfaction (OR = 0.65, p = 0.02) as very important to successful aging were significantly lower than for men, controlling for age, education, and presence of illness. While more similarities than differences in beliefs about successful aging were observed by gender, the extent to which socially-defined roles and expectations may be responsible for observed differences should be explored in future research.
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Affiliation(s)
- Xiao Qiu
- Miami University, Oxford, Ohio, United States
| | - Na Sun
- Miami University, Oxford, Ohio, United States
| | | | | | - Suman S Thapa
- Tilganga Institute of Ophthalmology, Kathmandu, Kathmandu, Nepal
| | | | - Matthew Johnson
- The University of Texas Rio Grande Valley, Brownsville, Texas, United States
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15
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Blackburn NB, Michael LF, Meikle PJ, Peralta JM, Mosior M, McAhren S, Bui HH, Bellinger MA, Giles C, Kumar S, Leandro AC, Almeida M, Weir JM, Mahaney MC, Dyer TD, Almasy L, VandeBerg JL, Williams-Blangero S, Glahn DC, Duggirala R, Kowala M, Blangero J, Curran JE. Rare DEGS1 variant significantly alters de novo ceramide synthesis pathway. J Lipid Res 2019; 60:1630-1639. [PMID: 31227640 PMCID: PMC6718439 DOI: 10.1194/jlr.p094433] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 06/13/2019] [Indexed: 02/06/2023] Open
Abstract
The de novo ceramide synthesis pathway is essential to human biology and health, but genetic influences remain unexplored. The core function of this pathway is the generation of biologically active ceramide from its precursor, dihydroceramide. Dihydroceramides have diverse, often protective, biological roles; conversely, increased ceramide levels are biomarkers of complex disease. To explore the genetics of the ceramide synthesis pathway, we searched for deleterious nonsynonymous variants in the genomes of 1,020 Mexican Americans from extended pedigrees. We identified a Hispanic ancestry-specific rare functional variant, L175Q, in delta 4-desaturase, sphingolipid 1 (DEGS1), a key enzyme in the pathway that converts dihydroceramide to ceramide. This amino acid change was significantly associated with large increases in plasma dihydroceramides. Indexes of DEGS1 enzymatic activity were dramatically reduced in heterozygotes. CRISPR/Cas9 genome editing of HepG2 cells confirmed that the L175Q variant results in a partial loss of function for the DEGS1 enzyme. Understanding the biological role of DEGS1 variants, such as L175Q, in ceramide synthesis may improve the understanding of metabolic-related disorders and spur ongoing research of drug targets along this pathway.
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Affiliation(s)
- Nicholas B Blackburn
- South Texas Diabetes and Obesity Institute University of Texas Rio Grande Valley School of Medicine, Brownsville, TX; Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX.
| | - Laura F Michael
- Lilly Research Laboratories,Eli Lilly and Company, Indianapolis, IN
| | - Peter J Meikle
- Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Juan M Peralta
- South Texas Diabetes and Obesity Institute University of Texas Rio Grande Valley School of Medicine, Brownsville, TX; Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX; Menzies Institute for Medical Research University of Tasmania, Hobart, TAS, Australia
| | - Marian Mosior
- Lilly Research Laboratories,Eli Lilly and Company, Indianapolis, IN
| | - Scott McAhren
- Lilly Research Laboratories,Eli Lilly and Company, Indianapolis, IN
| | - Hai H Bui
- Lilly Research Laboratories,Eli Lilly and Company, Indianapolis, IN
| | | | - Corey Giles
- Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Satish Kumar
- South Texas Diabetes and Obesity Institute University of Texas Rio Grande Valley School of Medicine, Brownsville, TX; Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX
| | - Ana C Leandro
- South Texas Diabetes and Obesity Institute University of Texas Rio Grande Valley School of Medicine, Brownsville, TX; Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX
| | - Marcio Almeida
- South Texas Diabetes and Obesity Institute University of Texas Rio Grande Valley School of Medicine, Brownsville, TX; Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX
| | | | - Michael C Mahaney
- South Texas Diabetes and Obesity Institute University of Texas Rio Grande Valley School of Medicine, Brownsville, TX; Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX
| | - Thomas D Dyer
- South Texas Diabetes and Obesity Institute University of Texas Rio Grande Valley School of Medicine, Brownsville, TX; Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX
| | - Laura Almasy
- Department of Biomedical and Health Informatics Children's Hospital of Philadelphia, Philadelphia, PA; Department of Human Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA
| | - John L VandeBerg
- South Texas Diabetes and Obesity Institute University of Texas Rio Grande Valley School of Medicine, Brownsville, TX; Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX
| | - Sarah Williams-Blangero
- South Texas Diabetes and Obesity Institute University of Texas Rio Grande Valley School of Medicine, Brownsville, TX; Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX
| | - David C Glahn
- Department of Psychiatry Boston Children's Hospital and Harvard Medical School, Boston, MA; Olin Neuropsychiatry Research Center Institute of Living, Hartford Hospital, Hartford, CT
| | - Ravindranath Duggirala
- South Texas Diabetes and Obesity Institute University of Texas Rio Grande Valley School of Medicine, Brownsville, TX; Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX
| | - Mark Kowala
- Lilly Research Laboratories,Eli Lilly and Company, Indianapolis, IN
| | - John Blangero
- South Texas Diabetes and Obesity Institute University of Texas Rio Grande Valley School of Medicine, Brownsville, TX; Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX
| | - Joanne E Curran
- South Texas Diabetes and Obesity Institute University of Texas Rio Grande Valley School of Medicine, Brownsville, TX; Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX.
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Manusov EG, Diego VP, Smith J, Garza JR, Lowdermilk J, Blangero J, Williams-Blangero S, Fernandez F. UniMóvil: A Mobile Health Clinic Providing Primary Care to the Colonias of the Rio Grande Valley, South Texas. Front Public Health 2019; 7:215. [PMID: 31497586 PMCID: PMC6712363 DOI: 10.3389/fpubh.2019.00215] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 07/18/2019] [Indexed: 11/13/2022] Open
Abstract
Background: We describe a mobile unit (UniMóvil) designed to improve poor healthcare access delivery to residents in two South Texas underserved Colonias. The interprofessional team measured seven clinical outcomes [obesity, diabetes, hypertension, hypertriglyceridemia, low high-density lipoprotein cholesterol (HDL-C) levels, and depression], and using the Duke Health Profile, assessed the health-related quality of life (HrQoL). Methods: The investigators used previously reported disease prevalence, an implementation model, and community needs-assessments to design an outreach healthcare delivery model. A retrospective review of the cohort provides data used to determine potential predictors of clinical variables, 11 domains of HrQOL, and inter/intra Colonia differences. Results: The average age of patients was 45 years-old and females represented 67% of the population served. Results include a high prevalence of obesity (55.5%), hypertension (39%), diabetes (32.5%), and depression (19%), gender differences, and inter-Colonia differences. A generalized linear mixed model analysis provided associations between clinical outcomes and predictors (age, sex, BMI, PHQ-9 score, HbA1c, blood pressure, serum cholesterol, low HDL, triglycerides, and HrQOL domains). The HrQol domain of low self-perceived health, relates to obesity, diabetes, low HDL, and depression. Depression predicted all 11 domains of the HrQol. Conclusion: The prevalence of diabetes, hypertension, obesity, and depression remains epidemic. Mobile clinics increase access and address highly prevalent illnesses in the Colonias. The data collected can be used to address chronic disease and quality of life, focus care, and direct research in high-need underserved areas.
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Affiliation(s)
- Eron G. Manusov
- Department of Family and Community Medicine, Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Harlingen, TX, United States
| | - Vincent P. Diego
- Department of Human Genetics, School of Medicine, South Texas Diabetes and Obesity Institute, The University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Jacob Smith
- University of Texas Rio Grande Valley School of Medicine, Edinburg, TX, United States
| | - Jesús R. Garza
- VIDAS [United Health Foundation], University of Texas Rio Grande Valley School of Medicine, Edinburg, TX, United States
| | - John Lowdermilk
- Human Development & School Services, University of Texas Rio Grande Valley, Edinburg, TX, United States
| | - John Blangero
- Department of Human Genetics, Genomics Computing Center, School of Medicine, South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Sarah Williams-Blangero
- Department of Human Genetics, School of Medicine, South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Francisco Fernandez
- Department of Psychiatry, School of Medicine, University of Texas Rio Grande Valley, Harlingen, TX, United States
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17
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Johnson MP, Keyho R, Blackburn NB, Laston S, Kumar S, Peralta J, Thapa SS, Towne B, Subedi J, Blangero J, Williams-Blangero S. Glycated Serum Protein Genetics and Pleiotropy with Cardiometabolic Risk Factors. J Diabetes Res 2019; 2019:2310235. [PMID: 31089471 PMCID: PMC6476113 DOI: 10.1155/2019/2310235] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 08/17/2018] [Revised: 12/20/2018] [Accepted: 01/12/2019] [Indexed: 01/08/2023] Open
Abstract
Measurements of fasting glucose (FG) or glycated hemoglobin A1c (HbA1c) are two clinically approved approaches commonly used to determine glycemia, both of which are influenced by genetic factors. Obtaining accurate measurements of FG or HbA1c is not without its challenges, though. Measuring glycated serum protein (GSP) offers an alternative approach for assessing glycemia. The aim of this study was to estimate the heritability of GSP and GSP expressed as a percentage of total serum albumin (%GA) using a variance component approach and localize genomic regions (QTLs) that harbor genes likely to influence GSP and %GA trait variation in a large extended multigenerational pedigree from Jiri, Nepal (n = 1,800). We also performed quantitative bivariate analyses to assess the relationship between GSP or %GA and several cardiometabolic traits. Additive genetic effects significantly influence variation in GSP and %GA levels (p values: 1.15 × 10-5 and 3.39 × 10-5, respectively). We localized a significant (LOD score = 3.18) and novel GSP QTL on chromosome 11q, which has been previously linked to type 2 diabetes. Two common (MAF > 0.4) SNPs within the chromosome 11 QTL were associated with GSP (adjusted pvalue < 5.87 × 10-5): an intronic variant (rs10790184) in the DSCAML1 gene and a 3'UTR variant (rs8258) in the CEP164 gene. Significant positive correlations were observed between GSP or %GA and blood pressure, and lipid traits (p values: 0.0062 to 1.78 × 10-9). A significant negative correlation was observed between %GA and HDL cholesterol (p = 1.12 × 10-5). GSP is influenced by genetic factors and can be used to assess glycemia and diabetes risk. Thus, GSP measurements can facilitate glycemic studies when accurate FG and/or HbA1c measurements are difficult to obtain. GSP can also be measured from frozen blood (serum) samples, which allows the prospect of retrospective glycemic studies using archived samples.
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Affiliation(s)
- Matthew P. Johnson
- South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Brownsville, Texas 78520, USA
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Brownsville, Texas 78520, USA
| | - Ryan Keyho
- The University of Texas at Austin, Austin, Texas 78705, USA
| | - Nicholas B. Blackburn
- South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Brownsville, Texas 78520, USA
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Brownsville, Texas 78520, USA
| | - Sandra Laston
- South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Brownsville, Texas 78520, USA
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Brownsville, Texas 78520, USA
| | - Satish Kumar
- South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Brownsville, Texas 78520, USA
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Brownsville, Texas 78520, USA
| | - Juan Peralta
- South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Brownsville, Texas 78520, USA
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Brownsville, Texas 78520, USA
- Menzies Institute for Medical Research, University of Tasmania, Hobart 7000, Australia
| | - Suman S. Thapa
- Tilganga Institute of Ophthalmology, Gaushala, Bagmati Bridge, P.O. Box 561, Kathmandu, Nepal
| | - Bradford Towne
- Department of Population Health and Public Health Sciences, Boonshoft School of Medicine, Wright State University, Kettering, Ohio 45435, USA
| | - Janardan Subedi
- Department of Sociology and Gerontology, College of Arts and Science, Miami University, Oxford, Ohio 45056, USA
| | - John Blangero
- South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Brownsville, Texas 78520, USA
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Brownsville, Texas 78520, USA
| | - Sarah Williams-Blangero
- South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Brownsville, Texas 78520, USA
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Brownsville, Texas 78520, USA
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18
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Howard TE, Diego VP, Hofmann M, Almeida M, Luu BW, Dinh LV, Rajalingam R, Escobar M, Curran J, Williams-Blangero S, Powell J, Blangero J, Maraskovsky E, Key NS, Sauna ZE. P059 Analysis of HLAcII peptidomes presented by dendritic cells (DCs) from healthy donors and hemophilia-A (HA) patients with or without factor VIII (FVIII) inhibitors after ex vivo administration of different therapeutic FVIII proteins (tFVIIIs). Hum Immunol 2018. [DOI: 10.1016/j.humimm.2018.07.117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Abstract
High-throughput platforms allow the characterization of thousands of previously known methylation sites. These platforms have great potential for investigating the epigenetic effects that are partially responsible for gene expression control. Methylation sites provide a bridge for the investigation of real-time environmental contributions on genomic events by the alteration of methylation status of those sites. Using the data provided by GAW20's organization committee, we calculated the heritability estimates of each cytosine-phosphate-guanine (CpG) island before and after the use of fenofibrate, a lipid-control drug. Surprisingly, we detected substantially high heritability estimates before drug usage. This somewhat unexpected high sample correlation was corrected by the use of principal components and the distributions of heritability estimates before and after fenofibrate treatment, which made the distributions comparable. The methylation sites located near a gene were collected and a genetic relationship matrix estimated to represent the overall correlation between samples. We implemented a random-effect association test to screen genes whose methylation patterns partially explain the observable high-density lipoprotein (HDL) heritability. Our leading association was observed for the TMEM52 gene that encodes a transmembrane protein, and is largely expressed in the liver, had not been previously associated with HDL until this manuscript. Using a variance component decomposition framework with the linear mixed model allows the integration of data from different sources, such as methylation, gene expression, metabolomics, and proteomics. The decomposition of the genetic variance component decomposition provides a flexible analytical approach for the challenges of this new omics era.
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Affiliation(s)
- Marcio Almeida
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, One West University Blvd., STDOI Modular Building #100, Brownsville, TX 78520 USA
| | - Juan Peralta
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, One West University Blvd., STDOI Modular Building #100, Brownsville, TX 78520 USA
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS Australia
| | - Jose Garcia
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, One West University Blvd., STDOI Modular Building #100, Brownsville, TX 78520 USA
| | - Vincent Diego
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, One West University Blvd., STDOI Modular Building #100, Brownsville, TX 78520 USA
| | - Harald Goring
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, One West University Blvd., STDOI Modular Building #100, Brownsville, TX 78520 USA
| | - Sarah Williams-Blangero
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, One West University Blvd., STDOI Modular Building #100, Brownsville, TX 78520 USA
| | - John Blangero
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, One West University Blvd., STDOI Modular Building #100, Brownsville, TX 78520 USA
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20
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Baek M, Kim M, Lim JS, Morales LD, Hernandez J, Mummidi S, Williams-Blangero S, Jang IS, Tsin AT, Kim DJ. Epidermal-specific deletion of TC-PTP promotes UVB-induced epidermal cell survival through the regulation of Flk-1/JNK signaling. Cell Death Dis 2018; 9:730. [PMID: 29955047 PMCID: PMC6023867 DOI: 10.1038/s41419-018-0781-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 05/24/2018] [Accepted: 06/04/2018] [Indexed: 01/27/2023]
Abstract
UVB exposure can contribute to the development of skin cancer by modulating protein tyrosine kinase (PTK) signaling. It has been suggested that UVB radiation increases the ligand-dependent activation of PTKs and induces PTP inactivation. Our recent studies have shown that T-cell protein tyrosine phosphatase (TC-PTP) attenuates skin carcinogenesis induced by chemical regimens, which indicates its critical role in the prevention of skin cancer. In the current work, we report that TC-PTP increases keratinocyte susceptibility to UVB-induced apoptosis via the downregulation of Flk-1/JNK signaling. We showed that loss of TC-PTP led to resistance to UVB-induced apoptosis in vivo epidermis. We established immortalized primary keratinocytes (IPKs) from epidermal-specific TC-PTP-deficient (K14Cre.Ptpn2fl/fl) mice. Immortalized TC-PTP-deficient keratinocytes (TC-PTP/KO IPKs) showed increased cell survival against UVB-induced apoptosis which was concomitant with a UVB-mediated increase in Flk-1 phosphorylation, especially on tyrosine residue 1173. Inhibition of Flk-1 by either its specific inhibitors or siRNA in TC-PTP/KO IPKs reversed this effect and significantly increased cell death after UVB irradiation in comparison with untreated TC-PTP/KO IPKs. Immunoprecipitation analysis using the TC-PTP substrate-trapping mutant TCPTP-D182A indicated that TC-PTP directly interacts with Flk-1 to dephosphorylate it and their interaction was stimulated by UVB. Following UVB-mediated Flk-1 activation, the level of JNK phosphorylation was also significantly increased in TC-PTP/KO IPKs compared to control IPKs. Similar to our results with Flk-1, treatment of TC-PTP/KO IPKs with the JNK inhibitor SP600125 significantly increased apoptosis after UVB irradiation, confirming that the effect of TC-PTP on UVB-mediated apoptosis is regulated by Flk-1/JNK signaling. Western blot analysis showed that both phosphorylated Flk-1 and phosphorylated JNK were significantly increased in the epidermis of TC-PTP-deficient mice compared to control mice following UVB. Our results suggest that TC-PTP plays a protective role against UVB-induced keratinocyte cell damage by promoting apoptosis via negative regulation of Flk-1/JNK survival signaling.
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Affiliation(s)
- Minwoo Baek
- Department of Biomedical Sciences, School of Medicine, University of Texas Rio Grande Valley, Edinburg, TX, USA.,College of Pharmacy, University of Minnesota, Duluth, MN, USA
| | - Mihwa Kim
- Department of Biomedical Sciences, School of Medicine, University of Texas Rio Grande Valley, Edinburg, TX, USA
| | - Jae Sung Lim
- Department of Biomedical Sciences, School of Medicine, University of Texas Rio Grande Valley, Edinburg, TX, USA
| | - Liza D Morales
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Edinburg, TX, USA.,South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Edinburg, TX, USA
| | - Joselin Hernandez
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Edinburg, TX, USA.,South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Edinburg, TX, USA
| | - Srinivas Mummidi
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Edinburg, TX, USA.,South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Edinburg, TX, USA
| | - Sarah Williams-Blangero
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Edinburg, TX, USA.,South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Edinburg, TX, USA
| | - Ik-Soon Jang
- Division of Bioconvergence Analysis, Korea Basic Science Institute, Daejeon, 305-333, Republic of Korea
| | - Andrew T Tsin
- Department of Biomedical Sciences, School of Medicine, University of Texas Rio Grande Valley, Edinburg, TX, USA
| | - Dae Joon Kim
- Department of Biomedical Sciences, School of Medicine, University of Texas Rio Grande Valley, Edinburg, TX, USA. .,Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Edinburg, TX, USA.
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21
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McLaughlin S, Subedi J, Thapa S, Shrestha M, Johnson M, Williams-Blangero S. PERSPECTIVES ON SUCCESSFUL AGING: INSIGHT FROM THE JIRELS IN EASTERN NEPAL. Innov Aging 2017. [DOI: 10.1093/geroni/igx004.4299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
| | | | - S.S. Thapa
- Tilganga Institute of Ophthalmology, Kathmandu, Nepal,
| | - M.K. Shrestha
- Tilganga Institute of Ophthalmology, Kathmandu, Nepal,
| | - M. Johnson
- The University of Texas Rio Grande Valley, Brownsville, Texas
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Abstract
Objective: This article attempts to document the prevalence of psychiatric disorders among elders in a rural village in Nepal. In addition, we investigate the relationship between psychiatric illness and functional disability to assess the impact of disorder on social functioning. Method: A semistructured interview checklist to diagnose six disorders was used ( N = 182). In addition, elders older than age 60 were examined to assess the functional impact of mental health conditions by measuring functional disability. Results: Eighteen percent of elders seem to have a diagnosable psychiatric disorder. Furthermore, in general these elders were also less likely to receive assistance with the disabilities they report, compared with those who do not experience a psychiatric disorder. Discussion: Documenting the extent of psychiatric disorder among elders in developing societies sensitizes health planners to the growing reality of aging in their societies and the need for expanded physical and psychiatric health care services.
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Affiliation(s)
- Sree Subedi
- Department of Sociology, Miami University, Oxford, OH, USA.
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23
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Mamtani M, Kulkarni H, Wong G, Weir JM, Barlow CK, Dyer TD, Almasy L, Mahaney MC, Comuzzie AG, Glahn DC, Magliano DJ, Zimmet P, Shaw J, Williams-Blangero S, Duggirala R, Blangero J, Meikle PJ, Curran JE. Lipidomic risk score independently and cost-effectively predicts risk of future type 2 diabetes: results from diverse cohorts. Lipids Health Dis 2016; 15:67. [PMID: 27044508 PMCID: PMC4820916 DOI: 10.1186/s12944-016-0234-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 03/24/2016] [Indexed: 12/12/2022] Open
Abstract
Background Detection of type 2 diabetes (T2D) is routinely based on the presence of dysglycemia. Although disturbed lipid metabolism is a hallmark of T2D, the potential of plasma lipidomics as a biomarker of future T2D is unknown. Our objective was to develop and validate a plasma lipidomic risk score (LRS) as a biomarker of future type 2 diabetes and to evaluate its cost-effectiveness for T2D screening. Methods Plasma LRS, based on significantly associated lipid species from an array of 319 lipid species, was developed in a cohort of initially T2D-free individuals from the San Antonio Family Heart Study (SAFHS). The LRS derived from SAFHS as well as its recalibrated version were validated in an independent cohort from Australia – the AusDiab cohort. The participants were T2D-free at baseline and followed for 9197 person-years in the SAFHS cohort (n = 771) and 5930 person-years in the AusDiab cohort (n = 644). Statistically and clinically improved T2D prediction was evaluated with established statistical parameters in both cohorts. Modeling studies were conducted to determine whether the use of LRS would be cost-effective for T2D screening. The main outcome measures included accuracy and incremental value of the LRS over routinely used clinical predictors of T2D risk; validation of these results in an independent cohort and cost-effectiveness of including LRS in screening/intervention programs for T2D. Results The LRS was based on plasma concentration of dihydroceramide 18:0, lysoalkylphosphatidylcholine 22:1 and triacyglycerol 16:0/18:0/18:1. The score predicted future T2D independently of prediabetes with an accuracy of 76 %. Even in the subset of initially euglycemic individuals, the LRS improved T2D prediction. In the AusDiab cohort, the LRS continued to predict T2D significantly and independently. When combined with risk-stratification methods currently used in clinical practice, the LRS significantly improved the model fit (p < 0.001), information content (p < 0.001), discrimination (p < 0.001) and reclassification (p < 0.001) in both cohorts. Modeling studies demonstrated that LRS-based risk-stratification combined with metformin supplementation for high-risk individuals was the most cost-effective strategy for T2D prevention. Conclusions Considering the novelty, incremental value and cost-effectiveness of LRS it should be used for risk-stratification of future T2D. Electronic supplementary material The online version of this article (doi:10.1186/s12944-016-0234-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Manju Mamtani
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, 78520, USA.
| | - Hemant Kulkarni
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, 78520, USA
| | - Gerard Wong
- Baker IDI Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Jacquelyn M Weir
- Baker IDI Heart and Diabetes Institute, Melbourne, VIC, Australia
| | | | - Thomas D Dyer
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, 78520, USA
| | - Laura Almasy
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, 78520, USA
| | - Michael C Mahaney
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, 78520, USA
| | - Anthony G Comuzzie
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - David C Glahn
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA.,Olin Neuropsychiatry Research Center, Institute of Living, Hartford Hospital, 200 Retreat Avenue, New Haven, CT, USA
| | | | - Paul Zimmet
- Baker IDI Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Jonathan Shaw
- Baker IDI Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Sarah Williams-Blangero
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, 78520, USA
| | - Ravindranath Duggirala
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, 78520, USA
| | - John Blangero
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, 78520, USA
| | - Peter J Meikle
- Baker IDI Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Joanne E Curran
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, 78520, USA
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24
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Kulkarni H, Mamtani M, Peralta J, Almeida M, Dyer TD, Goring HH, Johnson MP, Duggirala R, Mahaney MC, Olvera RL, Almasy L, Glahn DC, Williams-Blangero S, Curran JE, Blangero J. Soluble Forms of Intercellular and Vascular Cell Adhesion Molecules Independently Predict Progression to Type 2 Diabetes in Mexican American Families. PLoS One 2016; 11:e0151177. [PMID: 27007680 PMCID: PMC4805238 DOI: 10.1371/journal.pone.0151177] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 02/24/2016] [Indexed: 12/16/2022] Open
Abstract
Objective While the role of type 2 diabetes (T2D) in inducing endothelial dysfunction is fairly well-established the etiological role of endothelial dysfunction in the onset of T2D is still a matter of debate. In the light of conflicting evidence in this regard, we conducted a prospective study to determine the association of circulating levels of soluble intercellular adhesion molecule 1 (sICAM-1) and soluble vessel cell adhesion molecule 1 (sVCAM-1) with incident T2D. Methods Data from this study came from 1,269 Mexican Americans of whom 821 initially T2D-free individuals were longitudinally followed up in the San Antonio Family Heart Study. These individuals were followed for 9752.95 person-years for development of T2D. Prospective association of sICAM-1 and sVCAM-1 with incident T2D was studied using Kaplan-Meier survival plots and mixed effects Cox proportional hazards modeling to account for relatedness among study participants. Incremental value of adhesion molecule biomarkers was studied using integrated discrimination improvement (IDI) and net reclassification improvement (NRI) indexes. Results Decreasing median values for serum concentrations of sICAM-1 and sVCAM-1 were observed in the following groups in this order: individuals with T2D at baseline, individuals who developed T2D during follow-up, individuals with prediabetes at baseline and normal glucose tolerant (NGT) individuals who remained T2D-free during follow-up. Top quartiles for sICAM-1 and sVCAM-1 were strongly and significantly associated with homeostatic model of assessment—insulin resistance (HOMA-IR). Mixed effects Cox proportional hazards modeling revealed that after correcting for important clinical confounders, high sICAM-1 and sVCAM-1 concentrations were associated with 2.52 and 1.99 times faster progression to T2D as compared to low concentrations, respectively. Individuals with high concentrations for both sICAM-1 and sVCAM-1 progressed to T2D 3.42 times faster than those with low values for both sICAM-1 and sVCAM-1. The results were similar in women in reproductive age group and the remainder of the cohort. Inclusion of sICAM-1 and sVCAM-1 in predictive models significantly improved reclassification and discrimination. The majority of these results were seen even when the analyses were restricted to NGT individuals. Conclusion Serum concentrations of sICAM-1 and sVCAM-1 independently and additively predict future T2D and represent important candidate biomarkers of T2D.
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Affiliation(s)
- Hemant Kulkarni
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, United States of America
- * E-mail:
| | - Manju Mamtani
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, United States of America
| | - Juan Peralta
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, United States of America
| | - Marcio Almeida
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, United States of America
| | - Thomas D. Dyer
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, United States of America
| | - Harald H. Goring
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, United States of America
| | - Matthew P. Johnson
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, United States of America
| | - Ravindranath Duggirala
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, United States of America
| | - Michael C. Mahaney
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, United States of America
| | - Rene L. Olvera
- Department of Psychiatry, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States of America
| | - Laura Almasy
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, United States of America
| | - David C. Glahn
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, United States of America
- Olin Neuropsychiatric Research Center, Institute of Living, Hartford Hospital, Hartford, CT, United States of America
| | - Sarah Williams-Blangero
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, United States of America
| | - Joanne E. Curran
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, United States of America
| | - John Blangero
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, United States of America
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25
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Kulkarni H, Mamtani M, Peralta JM, Diego V, Dyer TD, Goring H, Almasy L, Mahaney MC, Williams-Blangero S, Duggirala R, Curran JE, Blangero J. Lack of Association between SLC30A8 Variants and Type 2 Diabetes in Mexican American Families. J Diabetes Res 2016; 2016:6463214. [PMID: 27896278 PMCID: PMC5118530 DOI: 10.1155/2016/6463214] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [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: 08/04/2016] [Accepted: 10/11/2016] [Indexed: 12/15/2022] Open
Abstract
SLC30A8 encodes zinc transporter 8 which is involved in packaging and release of insulin. Evidence for the association of SLC30A8 variants with type 2 diabetes (T2D) is inconclusive. We interrogated single nucleotide polymorphisms (SNPs) around SLC30A8 for association with T2D in high-risk, pedigreed individuals from extended Mexican American families. This study of 118 SNPs within 50 kb of the SLC30A8 locus tested the association with eight T2D-related traits at four levels: (i) each SNP using measured genotype approach (MGA); (ii) interaction of SNPs with age and sex; (iii) combinations of SNPs using Bayesian Quantitative Trait Nucleotide (BQTN) analyses; and (iv) entire gene locus using the gene burden test. Only one SNP (rs7817754) was significantly associated with incident T2D but a summary statistic based on all T2D-related traits identified 11 novel SNPs. Three SNPs and one SNP were weakly but interactively associated with age and sex, respectively. BQTN analyses could not demonstrate any informative combination of SNPs over MGA. Lastly, gene burden test results showed that at best the SLC30A8 locus could account for only 1-2% of the variability in T2D-related traits. Our results indicate a lack of association of the SLC30A8 SNPs with T2D in Mexican American families.
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Affiliation(s)
- Hemant Kulkarni
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX, USA
- *Hemant Kulkarni:
| | - Manju Mamtani
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Juan Manuel Peralta
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Vincent Diego
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Thomas D. Dyer
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Harald Goring
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Laura Almasy
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Michael C. Mahaney
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Sarah Williams-Blangero
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Ravindranath Duggirala
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Joanne E. Curran
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - John Blangero
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX, USA
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26
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Peters MJ, Joehanes R, Pilling LC, Schurmann C, Conneely KN, Powell J, Reinmaa E, Sutphin GL, Zhernakova A, Schramm K, Wilson YA, Kobes S, Tukiainen T, Ramos YF, Göring HHH, Fornage M, Liu Y, Gharib SA, Stranger BE, De Jager PL, Aviv A, Levy D, Murabito JM, Munson PJ, Huan T, Hofman A, Uitterlinden AG, Rivadeneira F, van Rooij J, Stolk L, Broer L, Verbiest MMPJ, Jhamai M, Arp P, Metspalu A, Tserel L, Milani L, Samani NJ, Peterson P, Kasela S, Codd V, Peters A, Ward-Caviness CK, Herder C, Waldenberger M, Roden M, Singmann P, Zeilinger S, Illig T, Homuth G, Grabe HJ, Völzke H, Steil L, Kocher T, Murray A, Melzer D, Yaghootkar H, Bandinelli S, Moses EK, Kent JW, Curran JE, Johnson MP, Williams-Blangero S, Westra HJ, McRae AF, Smith JA, Kardia SLR, Hovatta I, Perola M, Ripatti S, Salomaa V, Henders AK, Martin NG, Smith AK, Mehta D, Binder EB, Nylocks KM, Kennedy EM, Klengel T, Ding J, Suchy-Dicey AM, Enquobahrie DA, Brody J, Rotter JI, Chen YDI, Houwing-Duistermaat J, Kloppenburg M, Slagboom PE, Helmer Q, den Hollander W, Bean S, Raj T, Bakhshi N, Wang QP, Oyston LJ, Psaty BM, Tracy RP, Montgomery GW, Turner ST, Blangero J, Meulenbelt I, Ressler KJ, Yang J, Franke L, Kettunen J, Visscher PM, Neely GG, Korstanje R, Hanson RL, Prokisch H, Ferrucci L, Esko T, Teumer A, van Meurs JBJ, Johnson AD. The transcriptional landscape of age in human peripheral blood. Nat Commun 2015; 6:8570. [PMID: 26490707 PMCID: PMC4639797 DOI: 10.1038/ncomms9570] [Citation(s) in RCA: 407] [Impact Index Per Article: 45.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 09/07/2015] [Indexed: 02/08/2023] Open
Abstract
Disease incidences increase with age, but the molecular characteristics of ageing that lead to increased disease susceptibility remain inadequately understood. Here we perform a whole-blood gene expression meta-analysis in 14,983 individuals of European ancestry (including replication) and identify 1,497 genes that are differentially expressed with chronological age. The age-associated genes do not harbor more age-associated CpG-methylation sites than other genes, but are instead enriched for the presence of potentially functional CpG-methylation sites in enhancer and insulator regions that associate with both chronological age and gene expression levels. We further used the gene expression profiles to calculate the ‘transcriptomic age' of an individual, and show that differences between transcriptomic age and chronological age are associated with biological features linked to ageing, such as blood pressure, cholesterol levels, fasting glucose, and body mass index. The transcriptomic prediction model adds biological relevance and complements existing epigenetic prediction models, and can be used by others to calculate transcriptomic age in external cohorts. Ageing increases the risk of many diseases. Here the authors compare blood cell transcriptomes of over 14,000 individuals and identify a set of about 1,500 genes that are differently expressed with age, shedding light on transcriptional programs linked to the ageing process and age-associated diseases.
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Affiliation(s)
- Marjolein J Peters
- Department of Internal Medicine, Erasmus Medical Centre Rotterdam, Rotterdam 3000CA, The Netherlands
| | - Roby Joehanes
- The National Heart, Lung, and Blood Institute's and Boston University's Framingham Heart Study, Framingham, Massachusetts 01702, USA.,Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland 20817, USA
| | - Luke C Pilling
- Epidemiology and Public Health, University of Exeter Medical School, Exeter EX4 1DB, UK
| | - Claudia Schurmann
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald 17493, Germany.,The Charles Bronfman Institute for Personalized Medicine, Genetics of Obesity &Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York 10029, USA
| | - Karen N Conneely
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, Georgia 30301, USA
| | - Joseph Powell
- Centre for Neurogenetics and Statistical Genomics, Queensland Brain Institute, University of Queensland, St Lucia, Brisbane, Queensland 4000, Australia.,The Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4000, Australia
| | - Eva Reinmaa
- Estonian Genome Center, University of Tartu, Tartu 0794, Estonia
| | - George L Sutphin
- Nathan Shock Center of Excellence in the Basic Biology of Aging, The Jackson Laboratory, Bar Harbor, Maine 04609, USA
| | - Alexandra Zhernakova
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen 9700RB, The Netherlands
| | - Katharina Schramm
- Institute of Human Genetics, Helmholz Zentrum München - German Research Center for Environmental Health, Neuherberg 85764, Germany.,Institute of Human Genetics, Technical University Munich, Munich 85540, Germany
| | - Yana A Wilson
- Neuroscience Division, Garvan Institute of Medical Research, Australia and Charles Perkins Centre and School of Molecular Bioscience, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Sayuko Kobes
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health, Phoenix, Arizona 85001, USA
| | - Taru Tukiainen
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki 00131, Finland.,Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki 00131, Finland
| | | | - Yolande F Ramos
- Department of Molecular Epidemiology, Leiden University Medical Center, Leiden 2300RC, The Netherlands
| | - Harald H H Göring
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas 78201, USA
| | - Myriam Fornage
- Division of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, University of Texas Health Sciences, Center at Houston, Texas 77001, USA.,Institute of Molecular Medicine, University of Texas Health Sciences Center at Houston, Houston, Texas 77001, USA
| | - Yongmei Liu
- Department of Epidemiology and Prevention, Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina 27101, USA
| | - Sina A Gharib
- Computational Medicine Core, Center for Lung Biology, University of Washington, Seattle, Washington 98101, USA
| | - Barbara E Stranger
- Section of Genetic Medicine, Institute for Genomics and Systems Biology, University of Chicago, Chicago, Illinois 60290, USA
| | - Philip L De Jager
- Program in Translational NeuroPsychiatric Genomics, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02108, USA
| | - Abraham Aviv
- Center of Human Development and Aging, New Jersey Medical School, Newark 07101, USA
| | - Daniel Levy
- The National Heart, Lung, and Blood Institute's and Boston University's Framingham Heart Study, Framingham, Massachusetts 01702, USA.,Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland 20817, USA
| | - Joanne M Murabito
- The National Heart, Lung, and Blood Institute's and Boston University's Framingham Heart Study, Framingham, Massachusetts 01702, USA.,General Internal Medicine Section, Boston University, Boston, Massachusetts 02108, USA
| | - Peter J Munson
- The Mathematical and Statistical Computing Laboratory, Center for Information Technology, National Institutes of Health, Bethesda, Maryland 20817, USA
| | - Tianxiao Huan
- The National Heart, Lung, and Blood Institute's and Boston University's Framingham Heart Study, Framingham, Massachusetts 01702, USA.,Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland 20817, USA
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000CA, The Netherlands
| | - André G Uitterlinden
- Department of Internal Medicine, Erasmus Medical Centre Rotterdam, Rotterdam 3000CA, The Netherlands.,Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000CA, The Netherlands
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus Medical Centre Rotterdam, Rotterdam 3000CA, The Netherlands.,Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000CA, The Netherlands
| | - Jeroen van Rooij
- Department of Internal Medicine, Erasmus Medical Centre Rotterdam, Rotterdam 3000CA, The Netherlands
| | - Lisette Stolk
- Department of Internal Medicine, Erasmus Medical Centre Rotterdam, Rotterdam 3000CA, The Netherlands
| | - Linda Broer
- Department of Internal Medicine, Erasmus Medical Centre Rotterdam, Rotterdam 3000CA, The Netherlands
| | - Michael M P J Verbiest
- Department of Internal Medicine, Erasmus Medical Centre Rotterdam, Rotterdam 3000CA, The Netherlands
| | - Mila Jhamai
- Department of Internal Medicine, Erasmus Medical Centre Rotterdam, Rotterdam 3000CA, The Netherlands
| | - Pascal Arp
- Department of Internal Medicine, Erasmus Medical Centre Rotterdam, Rotterdam 3000CA, The Netherlands
| | - Andres Metspalu
- Estonian Genome Center, University of Tartu, Tartu 0794, Estonia
| | - Liina Tserel
- Molecular Pathology, Institute of Biomedicine, University of Tartu, Tartu 0794, Estonia
| | - Lili Milani
- Estonian Genome Center, University of Tartu, Tartu 0794, Estonia
| | - Nilesh J Samani
- Department of Cardiovascular Sciences, University of Leicester, Leicester LE1, UK.,National Institute for Health Research Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, Leicester LE1, UK
| | - Pärt Peterson
- Molecular Pathology, Institute of Biomedicine, University of Tartu, Tartu 0794, Estonia
| | - Silva Kasela
- Institute of Molecular and Cell Biology, Estonian Genome Center, University of Tartu, Tartu 0794, Estonia
| | - Veryan Codd
- Department of Cardiovascular Sciences, University of Leicester, Leicester LE1, UK.,National Institute for Health Research Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, Leicester LE1, UK
| | - Annette Peters
- Institute of Epidemiologie II, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg 85764, Germany.,Research Unit of Molecular Epidemiology, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Cavin K Ward-Caviness
- Institute of Epidemiologie II, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Christian Herder
- Institute of Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf 40593, Germany
| | - Melanie Waldenberger
- Institute of Epidemiologie II, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg 85764, Germany.,Research Unit of Molecular Epidemiology, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Michael Roden
- Institute of Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf 40593, Germany.,Division of Endocrinology and Diabetology, University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf 40593, Germany
| | - Paula Singmann
- Institute of Epidemiologie II, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg 85764, Germany.,Research Unit of Molecular Epidemiology, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Sonja Zeilinger
- Institute of Epidemiologie II, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg 85764, Germany.,Research Unit of Molecular Epidemiology, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Thomas Illig
- Hannover Unified Biobank, Hannover Medical School, Hannover 30519, Germany
| | - Georg Homuth
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald 17493, Germany
| | - Hans-Jörgen Grabe
- Department of Psychiatry and Psychotherapy, Helios Hospital Stralsund, University Medicine Greifswald, Greifswald 17489, Germany
| | - Henry Völzke
- Institute for Community Medicine, University Medicine Greifswald, Greifswald 17489, Germany
| | - Leif Steil
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald 17493, Germany
| | - Thomas Kocher
- Unit of Periodontology, Department of Restorative Dentistry, Periodontology and Endodontology, University Medicine Greifswald, Greifswald 17489, Germany
| | - Anna Murray
- Epidemiology and Public Health, University of Exeter Medical School, Exeter EX4 1DB, UK
| | - David Melzer
- Epidemiology and Public Health, University of Exeter Medical School, Exeter EX4 1DB, UK
| | - Hanieh Yaghootkar
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK
| | | | - Eric K Moses
- Centre for Genetic Origins of Health and Disease, The University of Western Australia, and Faculty of Health Sciences, Curtin University, Perth, Western Australia 9011, Australia
| | - Jack W Kent
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas 78201, USA
| | - Joanne E Curran
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas 78201, USA
| | - Matthew P Johnson
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas 78201, USA
| | | | - Harm-Jan Westra
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen 9700RB, The Netherlands.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge 02138, USA.,Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02108, USA.,Partners Center for Personalized Genetic Medicine, Boston, Massachusetts 02108, USA
| | - Allan F McRae
- The Queensland Brain Institute, University of Queensland, Brisbane, Queensland 4000, Australia.,University of Queensland Diamantina Institute, University of Queensland, Princess Alexandra Hospital, Brisbane, Queensland 4000, Australia
| | - Jennifer A Smith
- Department of Epidemiology, University of Michigan, Ann Arbor, Michigan 48103, USA
| | - Sharon L R Kardia
- Department of Epidemiology, University of Michigan, Ann Arbor, Michigan 48103, USA
| | - Iiris Hovatta
- Department of Biosciences, University of Helsinki, Helsinki 00100, Finland.,Department of Mental Health and Substance Abuse Services, National Institute for Health and Welfare, Helsinki 00100, Finland
| | - Markus Perola
- Estonian Genome Center, University of Tartu, Tartu 0794, Estonia.,Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki 00131, Finland.,Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki 00131, Finland
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki 00131, Finland.,Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki 00131, Finland.,Wellcome Trust Sanger Institute, Hinxton, Cambridge CB4, UK.,Department of Public Health, Hjelt Institute, University of Helsinki, Helsinki 00100, Finland
| | - Veikko Salomaa
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki 00131, Finland
| | - Anjali K Henders
- The Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4000, Australia
| | - Nicholas G Martin
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4000, Australia
| | - Alicia K Smith
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, Georgia 30301, USA
| | - Divya Mehta
- Max-Planck Institute of Psychiatry, Munich 80331, Germany
| | | | - K Maria Nylocks
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, Georgia 30301, USA
| | - Elizabeth M Kennedy
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, Georgia 30301, USA
| | | | - Jingzhong Ding
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina 27101, USA
| | - Astrid M Suchy-Dicey
- Department of Epidemiology, University of Washington, Seattle, Washington 98101, USA
| | - Daniel A Enquobahrie
- Department of Epidemiology, University of Washington, Seattle, Washington 98101, USA
| | - Jennifer Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, Washington 98101, USA
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, California 90501, USA
| | - Yii-Der I Chen
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, California 90501, USA
| | | | - Margreet Kloppenburg
- Department of Rheumatology, Leiden University Medical Center, Leiden 2300RC, The Netherlands.,Department of Clinical Epidemiology, Leiden University Medical Center, Leiden 2300RC, The Netherlands
| | - P Eline Slagboom
- Department of Molecular Epidemiology, Leiden University Medical Center, Leiden 2300RC, The Netherlands
| | - Quinta Helmer
- Department of Medical Statistics, Leiden University Medical Center, Leiden 2300RC, The Netherlands
| | - Wouter den Hollander
- Department of Molecular Epidemiology, Leiden University Medical Center, Leiden 2300RC, The Netherlands
| | - Shannon Bean
- Nathan Shock Center of Excellence in the Basic Biology of Aging, The Jackson Laboratory, Bar Harbor, Maine 04609, USA
| | - Towfique Raj
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02138, USA
| | - Noman Bakhshi
- Neuroscience Division, Garvan Institute of Medical Research, Australia and Charles Perkins Centre and School of Molecular Bioscience, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Qiao Ping Wang
- Neuroscience Division, Garvan Institute of Medical Research, Australia and Charles Perkins Centre and School of Molecular Bioscience, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Lisa J Oyston
- Neuroscience Division, Garvan Institute of Medical Research, Australia and Charles Perkins Centre and School of Molecular Bioscience, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, Washington 98195, USA.,Cardiovascular Health Research Unit, Department of Epidemiology, University of Washington, Seattle, Washington 98195, USA.,Cardiovascular Health Research Unit, Department of Health Services, University of Washington, Seattle, Washington 98195, USA.,Group Health Research Institute, Group Health Cooperative, Seattle, Washington 98195, USA
| | - Russell P Tracy
- Department of Pathology, University of Vermont College of Medicine, Colchester, Vermont 98195, USA
| | - Grant W Montgomery
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4000, Australia
| | - Stephen T Turner
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, Rochester, Minnesota 55901, USA
| | - John Blangero
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas 78201, USA
| | - Ingrid Meulenbelt
- Department of Molecular Epidemiology, Leiden University Medical Center, Leiden 2300RC, The Netherlands
| | - Kerry J Ressler
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, Georgia 30301, USA
| | - Jian Yang
- The Queensland Brain Institute, University of Queensland, Brisbane, Queensland 4000, Australia.,University of Queensland Diamantina Institute, University of Queensland, Princess Alexandra Hospital, Brisbane, Queensland 4000, Australia
| | - Lude Franke
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen 9700RB, The Netherlands
| | - Johannes Kettunen
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki 00131, Finland.,Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki 00131, Finland.,Computational Medicine, Institute of Health Sciences, Faculty of Medicine, University of Oulu, Oulu 90570, Finland
| | - Peter M Visscher
- The Queensland Brain Institute, University of Queensland, Brisbane, Queensland 4000, Australia.,University of Queensland Diamantina Institute, University of Queensland, Princess Alexandra Hospital, Brisbane, Queensland 4000, Australia
| | - G Gregory Neely
- Neuroscience Division, Garvan Institute of Medical Research, Australia and Charles Perkins Centre and School of Molecular Bioscience, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Ron Korstanje
- Nathan Shock Center of Excellence in the Basic Biology of Aging, The Jackson Laboratory, Bar Harbor, Maine 04609, USA
| | - Robert L Hanson
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health, Phoenix, Arizona 85001, USA
| | - Holger Prokisch
- Institute of Human Genetics, Helmholz Zentrum München - German Research Center for Environmental Health, Neuherberg 85764, Germany.,Institute of Human Genetics, Technical University Munich, Munich 85540, Germany
| | - Luigi Ferrucci
- Clinical Research Branch, National Institute on Aging, Baltimore, Maryland 21218, USA
| | - Tonu Esko
- Estonian Genome Center, University of Tartu, Tartu 0794, Estonia.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge 02138, USA.,Division of Endocrinology, Children's Hospital Boston, Boston, Massachusetts 02108, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02108, USA
| | - Alexander Teumer
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald 17493, Germany
| | - Joyce B J van Meurs
- Department of Internal Medicine, Erasmus Medical Centre Rotterdam, Rotterdam 3000CA, The Netherlands
| | - Andrew D Johnson
- The National Heart, Lung, and Blood Institute's and Boston University's Framingham Heart Study, Framingham, Massachusetts 01702, USA.,Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland 20817, USA
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Williams KD, Blangero J, Mahaney MC, Subedi J, Jha B, Williams-Blangero S, Towne B. Axial quantitative ultrasound assessment of pediatric bone quality in eastern Nepal. Osteoporos Int 2015; 26:2319-28. [PMID: 25862355 DOI: 10.1007/s00198-015-3115-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 03/18/2015] [Indexed: 12/29/2022]
Abstract
UNLABELLED This study presents quantitative ultrasonography (QUS) bone quality data for an underrepresented, south Asian pediatric population from Nepal. Data were collected as part of a longitudinal study of growth and development. This study offers normative data and documents the effect of stunting, wasting, and underweight on the bone properties measured by QUS. INTRODUCTION The purpose of this study was to (1) examine the bone quality of a rural, non-Western pediatric population using QUS, (2) explore variation in the trajectory of bone quality development between males and females, and (3) examine the impact of growth disruption(s) on bone quality. METHODS A cross-sectional study of 860 children and adolescents aged 5-18 years from the Jirel ethnic group in eastern Nepal was performed. The Sunlight Omnisense 7000P was used to assess bone quality of the distal 1/3 radius and midshaft tibia. WHO reference standards were used to assess growth disruptions of height, weight, and BMI. RESULTS QUS bone quality data for an underrepresented, non-Western pediatric population are presented for the radius and tibia. A sizable portion of the study participants were classified as stunted, wasted, and/or underweight. Despite this prevalence of growth disruption in the study sample, bone quality data conform to other documented populations with less growth disruption. Thus, this study offers normative data and documents the minimal effect of stunting, wasting, and underweight on the bone properties measured by QUS. CONCLUSIONS Non-Western pediatric populations are significantly underserved with regard to simple, non-invasive screening tools that may help identify developmental disorders and assess bone health. The children and adolescents examined here represent normal growth and development for an underrepresented south Asian population. While this work demonstrates that stunting, wasting, or underweight status at time of QUS assessment is not associated with poor bone quality, we do suggest that further study is needed to examine possible cumulative effects of persistent disruptions that may lead to compromised bone quality in later adolescence.
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Affiliation(s)
- K D Williams
- Department of Anthropology, Temple University, 1115 Polett Walk, 210 Gladfelter Hall, Philadelphia, PA, 19120, USA,
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Williams KD, Subedi J, Jha B, Blangero J, Williams-Blangero S, Towne B. Quantitative physical activity assessment of children and adolescents in a rural population from Eastern Nepal. Am J Hum Biol 2015; 28:129-37. [PMID: 26179444 DOI: 10.1002/ajhb.22762] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 04/27/2015] [Accepted: 06/16/2015] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVES We report cross-sectional, objectively measured physical activity data for 399 children and adolescents aged 6 to 18 years. We evaluated physical activity of children and adolescents, considered time spent in each activity intensity category, and explored the impact of growth disruption (stunting and wasting) on physical activity patterns. METHODS Participants wore an Actical (Mini-Mitter, Bend, OR) omnidirectional accelerometer for one week as part of their annual visit to the Jiri Growth Study. The percentage of time spent in standard activity intensities were computed using standard metabolic equivalents (METS) cutpoints and compared by chronological age, sex, and school versus non-school days. RESULTS Primary findings include (1) children are more active on non-school days and adolescents are more active during the school week; (2) Jirel children do not exhibit the reduction in physical activity that most Western populations experience during the transition from childhood to adolescence; and (3) Jirel children and adolescents routinely meet the suggested one hour/day MVPA threshold; (4) Stunting is prevalent and factors leading to this growth disruption may contribute to the amount of time in sedentary or light physical activity. CONCLUSIONS We report child and adolescent physical activity patterns from the Jirel population of eastern Nepal. In this rural context, children and adolescents are more active than populations reported from Western contexts. This key finding has important biomedical implications for the maintenance of healthy body composition, skeletal health, and other health traits.
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Affiliation(s)
- Kimberly D Williams
- Department of Anthropology, Temple University, Philadelphia, Pennsylvania.,Institute for Genomic and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania
| | - Janardan Subedi
- Department of Sociology and Gerontology, Miami University, Oxford, Ohio
| | - Bharat Jha
- Tribhuvan University Institute of Medicine, Kathmandu, Nepal
| | - John Blangero
- South Texas Diabetes and Obesity Institute, University of Texas Health Science Center Regional Academic Health Center, Harlingen, Texas
| | - Sarah Williams-Blangero
- South Texas Diabetes and Obesity Institute, University of Texas Health Science Center Regional Academic Health Center, Harlingen, Texas
| | - Bradford Towne
- Department of Community Health, Lifespan Health Research Center, Boonshoft School of Medicine, Wright State University, Dayton, Ohio
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Bellis C, Kulkarni H, Mamtani M, Kent JW, Wong G, Weir JM, Barlow CK, Diego V, Almeida M, Dyer TD, Göring HHH, Almasy L, Mahaney MC, Comuzzie AG, Williams-Blangero S, Meikle PJ, Blangero J, Curran JE. Human plasma lipidome is pleiotropically associated with cardiovascular risk factors and death. ACTA ACUST UNITED AC 2014; 7:854-863. [PMID: 25363705 DOI: 10.1161/circgenetics.114.000600] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
BACKGROUND Cardiovascular disease (CVD) is the most common cause of death in the United States and is associated with a high economic burden. Prevention of CVD focuses on controlling or improving the lipid profile of patients at risk. The human lipidome is made up of thousands of ubiquitous lipid species. By studying biologically simple canonical lipid species, we investigated whether the lipidome is genetically redundant and whether its genetic influences can provide clinically relevant clues of CVD risk. METHODS AND RESULTS We performed a genetic study of the human lipidome in 1212 individuals from 42 extended Mexican American families. High-throughput mass spectrometry enabled rapid capture of precise lipidomic profiles, providing 319 unique species. Using variance component-based heritability analyses and bivariate trait analyses, we detected significant genetic influences on each lipid assayed. Median heritability of the plasma lipid species was 0.37. Hierarchical clustering based on complex genetic correlation patterns identified 12 genetic clusters that characterized the plasma lipidome. These genetic clusters were differentially but consistently associated with risk factors of CVD, including central obesity, obesity, type 2 diabetes mellitus, raised serum triglycerides, and metabolic syndrome. Also, these clusters consistently predicted occurrence of cardiovascular deaths during follow-up. CONCLUSIONS The human plasma lipidome is heritable. Shared genetic influences reduce the dimensionality of the human lipidome into clusters that are associated with risk factors of CVD.
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Affiliation(s)
- Claire Bellis
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
| | - Hemant Kulkarni
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
| | - Manju Mamtani
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
| | - Jack W Kent
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
| | - Gerard Wong
- Baker IDI Heart and Diabetes Institute, Melbourne VIC, Australia
| | - Jacquelyn M Weir
- Baker IDI Heart and Diabetes Institute, Melbourne VIC, Australia
| | | | - Vincent Diego
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
| | - Marcio Almeida
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
| | - Thomas D Dyer
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
| | - Harald H H Göring
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
| | - Laura Almasy
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
| | - Michael C Mahaney
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
| | - Anthony G Comuzzie
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
| | - Sarah Williams-Blangero
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX.,Southwest National Primate Research Center, San Antonio, TX
| | - Peter J Meikle
- Baker IDI Heart and Diabetes Institute, Melbourne VIC, Australia
| | - John Blangero
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
| | - Joanne E Curran
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
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Williams KD, Blangero J, Subedi J, Jha B, Dyer T, VandeBerg JL, Towne B, Williams-Blangero S. Nonsyndromic brachydactyly type D and type E mapped to 7p15 in healthy children and adults from the Jirel ethnic group in eastern Nepal. Am J Hum Biol 2013; 25:743-50. [PMID: 24022874 PMCID: PMC3968259 DOI: 10.1002/ajhb.22441] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [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: 04/09/2013] [Revised: 07/14/2013] [Accepted: 07/15/2013] [Indexed: 11/06/2022] Open
Abstract
OBJECTIVES There is phenotypic overlap between Brachydactyly Type D (BDD) and Brachydactyly Type E (BDE) that suggests a possible common underlying etiology. We seek to understand the genetic underpinnings of, and relationship between, these skeletal anomalies. METHODS The Jirel ethnic group of eastern Nepal participates in various genetic epidemiologic studies, including those in which hand-wrist radiographs have been taken to examine skeletal development. Nearly 2,130 individuals (969 males; 1,161 females) were phenotyped for BDD/BDE. Of these, 1,722 individuals (773 males; 949 females) were genotyped for 371 STR markers spanning the autosomal genome. Variance components-based linkage analysis was used to conduct a genome-wide linkage scan for QTL influencing the BDD/BDE phenotype. RESULTS BDD was present in 3.55%, and BDE was present in 0.39%, of the study sample. Because of the phenotypic overlap between two traits, affecteds of either type were considered as affected by a single combined phenotype (BDD/BDE) having a prevalence of 3.94%. The additive genetic heritability of BDD/BDE was highly significant (h(2) ± SE = 0.89 ± 0.13; P = 1.7 × 10(-11) ). Significant linkage of BDD/BDE was found to markers on chromosome 7p21-7p14 (peak LOD score = 3.74 at 7p15 between markers D7S493 and D7S516). CONCLUSIONS Possible positional candidate genes in the one-lod support interval of this QTL include TWIST and the HOXA1-A13 cluster. This is the first study to report significant linkage results for BDD/BDE using a large extended pedigree, and the first to suggest that mutations in TWIST and/or the HOXA1-A13 cluster may contribute to these specific skeletal anomalies.
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Affiliation(s)
- Kimberly D. Williams
- Department of Anthropology, Temple University, Philadelphia, PA
- Department of Pediatrics, Temple University School of Medicine, Philadelphia, PA
| | - John Blangero
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
| | - Janardan Subedi
- Department of Sociology and Gerontology, Miami University, Oxford, OH
| | - Bharat Jha
- Tribhuvan University Institute of Medicine, Kathmandu, Nepal
| | - Thomas Dyer
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
| | - John L. VandeBerg
- Office of the Chief Scientific Officer, Texas Biomedical Research Institute, San Antonio, TX
- Southwest National Primate Research Center, San Antonio, TX 78227
| | - Bradford Towne
- Department of Community Health, Wright State University Boonshoft School of Medicine, Dayton, OH
- Department of Pediatrics, Wright State University Boonshoft School of Medicine, Dayton, OH
| | - Sarah Williams-Blangero
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
- Southwest National Primate Research Center, San Antonio, TX 78227
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Szabó CÁ, Knape KD, Leland MM, Cwikla DJ, Williams-Blangero S, Williams JT. Epidemiology and characterization of seizures in a pedigreed baboon colony. Comp Med 2012; 62:535-8. [PMID: 23561888 PMCID: PMC3527759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Revised: 04/14/2012] [Accepted: 06/11/2012] [Indexed: 06/02/2023]
Abstract
This study evaluated the incidence, prevalence, and clinical features of seizures in a pedigreed captive colony of baboons. The association of seizures with subspecies, age, sex, and various clinical features was assessed. Records for 1527 captive, pedigreed baboons were reviewed, and 3389 events were identified in 1098 baboons. Of these events, 1537 (45%) represented witnessed seizures, whereas the remaining 1852 presented with craniofacial trauma or episodic changes in behavior that were suggestive, but not diagnostic, of seizure activity. Seizures were generalized myoclonic or tonic-clonic, with two thirds of the events witnessed in the morning. Seizure onset occurred in adolescence (age, 5 y), with an average of 3 seizures in a lifetime. The incidence and prevalence of seizures were 2.5% and 26%, respectively, whereas the prevalence of recurrent seizures (that is, epilepsy) was 15%. Seizures were more prevalent in male baboons, which tended to present with earlier onset and more seizures over a lifetime than did female baboons. Seizures were equally distributed between the subspecies; age of onset and seizure recurrences did not differ significantly between subspecies. Clinical features including age of onset, characteristics, and diurnal presentation of seizures in baboons suggested similarities to juvenile myoclonic epilepsy in humans. Facial trauma may be useful marker for epilepsy in baboons, but its specificity should be characterized.
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Affiliation(s)
- C Ákos Szabó
- Department of Neurology and South Texas Comprehensive Epilepsy Center, San Antonio, TX, USA.
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32
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Kent JW, Göring HHH, Charlesworth JC, Drigalenko E, Diego VP, Curran JE, Johnson MP, Dyer TD, Cole SA, Jowett JBM, Mahaney MC, Comuzzie AG, Almasy L, Moses EK, Blangero J, Williams-Blangero S. Genotype×age interaction in human transcriptional ageing. Mech Ageing Dev 2012; 133:581-90. [PMID: 22871458 DOI: 10.1016/j.mad.2012.07.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Revised: 07/05/2012] [Accepted: 07/21/2012] [Indexed: 01/24/2023]
Abstract
Individual differences in biological ageing (i.e., the rate of physiological response to the passage of time) may be due in part to genotype-specific variation in gene action. However, the sources of heritable variation in human age-related gene expression profiles are largely unknown. We have profiled genome-wide expression in peripheral blood mononuclear cells from 1240 individuals in large families and found 4472 human autosomal transcripts, representing ~4349 genes, significantly correlated with age. We identified 623 transcripts that show genotype by age interaction in addition to a main effect of age, defining a large set of novel candidates for characterization of the mechanisms of differential biological ageing. We applied a novel SNP genotype × age interaction test to one of these candidates, the ubiquilin-like gene UBQLNL, and found evidence of joint cis-association and genotype by age interaction as well as trans-genotype by age interaction for UBQLNL expression. Both UBQLNL expression levels at recruitment and cis genotype are associated with longitudinal cancer risk in our study cohort.
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Affiliation(s)
- Jack W Kent
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX 78245, USA.
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Williams-Blangero S, Criscione CD, VandeBerg JL, Correa-Oliveira R, Williams KD, Subedi J, Kent JW, Williams J, Kumar S, Blangero J. Host genetics and population structure effects on parasitic disease. Philos Trans R Soc Lond B Biol Sci 2012; 367:887-94. [PMID: 22312056 PMCID: PMC3267115 DOI: 10.1098/rstb.2011.0296] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Host genetic factors exert significant influences on differential susceptibility to many infectious diseases. In addition, population structure of both host and parasite may influence disease distribution patterns. In this study, we assess the effects of population structure on infectious disease in two populations in which host genetic factors influencing susceptibility to parasitic disease have been extensively studied. The first population is the Jirel population of eastern Nepal that has been the subject of research on the determinants of differential susceptibility to soil-transmitted helminth infections. The second group is a Brazilian population residing in an area endemic for Trypanosoma cruzi infection that has been assessed for genetic influences on differential disease progression in Chagas disease. For measures of Ascaris worm burden, within-population host genetic effects are generally more important than host population structure factors in determining patterns of infectious disease. No significant influences of population structure on measures associated with progression of cardiac disease in individuals who were seropositive for T. cruzi infection were found.
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Pinkerton RC, Oriá RB, Kent JW, Kohli A, Abreu C, Bushen O, Lima AAM, Blangero J, Williams-Blangero S, Guerrant RL. Evidence for genetic susceptibility to developing early childhood diarrhea among shantytown children living in northeastern Brazil. Am J Trop Med Hyg 2011; 85:893-6. [PMID: 22049044 DOI: 10.4269/ajtmh.2011.11-0159] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
To explore the genetic components of susceptibility to early childhood diarrhea (ECD), we used a quantitative genetic approach to estimate the heritability of ECD among children from two Brazilian favelas. Shared environment was used to model common exposure to environmental factors. Genetic relatedness was determined from pedigree information collected by screening household participants (n = 3,267) from two geographically related favelas located in Fortaleza, Brazil. There were 277 children within these pedigrees for whom diarrheal episodes in the first two years of life were recorded. Data on environmental exposure and pedigree relationship were combined to quantitatively partition phenotypic variance in ECD into environmental and genetic components by using a variance components approach as implemented in Sequential Oligogenic Linkage Analysis Routines program. Heritability accounted for 54% of variance in ECD and proximity of residence effect accounted for 21% (P < 0.0001). These findings suggest a substantial genetic component to ECD susceptibility and the potential importance of future genetics studies.
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35
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Diego VP, Curran JE, Charlesworth J, Peralta JM, Voruganti VS, Cole SA, Dyer TD, Johnson MP, Moses EK, Göring HHH, Williams JT, Comuzzie AG, Almasy L, Blangero J, Williams-Blangero S. Systems genetics of the nuclear factor-κB signal transduction network. I. Detection of several quantitative trait loci potentially relevant to aging. Mech Ageing Dev 2011; 133:11-9. [PMID: 22155176 DOI: 10.1016/j.mad.2011.11.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2011] [Revised: 11/14/2011] [Accepted: 11/19/2011] [Indexed: 01/22/2023]
Abstract
A theory of aging holds that senescence is caused by a dysregulated nuclear factor kappa B (NF-κB) signal transduction network (STN). We adopted a systems genetics approach in our study of the NF-κB STN. Ingenuity Pathways Analysis (IPA) was used to identify gene/gene product interactions between NF-κB and the genes in our transcriptional profiling array. Principal components factor analysis (PCFA) was performed on a sub-network of 19 genes, including two initiators of the toll-like receptor (TLR) pathway, myeloid differentiation primary response gene (88) (MyD88) and TIR (Toll/interleukin-1 receptor)-domain-containing adapter-inducing interferon-β (TRIF). TLR pathways are either MyD88-dependent or TRIF-dependent. Therefore, we also performed PCFA on a subset excluding the MyD88 transcript, and on another subset excluding two TRIF transcripts. Using linkage analysis we found that each set gave rise to at least one factor with a logarithm of the odds (LOD) score greater than 3, two on chromosome 15 at 15q12 and 15q22.2, and another two on chromosome 17 at 17p13.3 and 17q25.3. We also found several suggestive signals (2<LOD score<3) at 1q32.1, 1q41, 2q34, 3q23, and 7p15.3. We are currently examining potential associations with single nucleotide polymorphisms within the 1-LOD intervals of our linkage signals.
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Affiliation(s)
- Vincent P Diego
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX 78245-0549, USA.
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Williams KD, Nahhas RW, Cottom CR, Lawrence S, Subedi J, Jha B, Czerwinski SA, Blangero J, Williams-Blangero S, Towne B. Evaluation of qualitative methods for phenotyping brachymesophalangia-V from radiographs of children. Am J Hum Biol 2011; 24:68-73. [PMID: 22131202 DOI: 10.1002/ajhb.22205] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2011] [Revised: 09/27/2011] [Accepted: 11/08/2011] [Indexed: 11/09/2022] Open
Abstract
OBJECTIVE Brachymesophalangia-V (BMP-V), the general term for a short and broad middle phalanx of the 5th digit, presents both alone and in a large number of complex brachydactylies and developmental disorders. Past anthropological and epidemiological studies of growth and development have examined the prevalence of BMP-V because small developmental disorders may signal more complex disruptions of skeletal growth and development. Historically, however, consensus on qualitative phenotype methodology has not been established. In large-scale, non-clinical studies such as the Fels Longitudinal Study and the Jiri Growth Study, quantitative assessment of the hand is not always the most efficient manner of screening for skeletal dysmorphologies. The current study evaluates qualitative phenotyping techniques for BMP-V used in past anthropological studies of growth and development to establish a useful and reliable screening method for large study samples. METHODS A total of 1,360 radiographs from Jiri Growth Study participants aged 3-18 years were evaluated. BMP-V was assessed using three methods: (1) subjective evaluation of length and width of the bone; (2) comparison with skeletal age-matched radiographs; and (3) subjective evaluation of the length of the middle 4th and 5th phalanges. RESULTS We found that the method that uses skeletal age-matched reference radiographs is the better tool for assessing BMP-V because it considers the shape, rather than solely the length and width of the bone, which can be difficult to judge accurately without measurement. This study highlights the complexity of phenotypic assessment of BMP-V and by extension other brachydactylies.
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Affiliation(s)
- Kimberly D Williams
- Department of Anthropology, Temple University, Philadelphia, Pennsylvania 19122, USA.
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Abstract
Genetic epidemiological approaches hold great promise for improving the understanding of the determinants of susceptibility to infection with Trypanosoma cruzi and the causes of differential disease outcome in T. cruzi-infected individuals. To date, a variety of approaches have been used to understand the role of genetic factors in Chagas disease. Quantitative genetic techniques have been used to estimate the heritabilities for seropositivity for T. cruzi infection and traits that are associated with disease progression in chronic T. cruzi infection. These studies have demonstrated that a significant proportion of the variation in seropositivity and a number of traits related to Chagas disease progression is attributable to genetic factors. Candidate gene studies have provided intriguing evidence for the roles of numerous individual genes in determining cardiac outcomes in chronically infected individuals. Recent results from a long-term study of Chagas disease in a rural area of Brazil have documented that over 60% of the variation in seropositivity status is attributable to genetic factors in that population. Additionally, there are significant genetic effects on a number of electrocardiographic measures and other Chagas disease-related traits. The application of genome-wide approaches will yield new evidence for the roles of specific genes in Chagas disease.
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Criscione CD, Anderson JD, Sudimack D, Subedi J, Upadhayay RP, Jha B, Williams KD, Williams-Blangero S, Anderson TJC. Landscape genetics reveals focal transmission of a human macroparasite. PLoS Negl Trop Dis 2010; 4:e665. [PMID: 20421919 PMCID: PMC2857643 DOI: 10.1371/journal.pntd.0000665] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [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: 11/25/2009] [Accepted: 03/10/2010] [Indexed: 01/06/2023] Open
Abstract
Macroparasite infections (e.g., helminths) remain a major human health concern. However, assessing transmission dynamics is problematic because the direct observation of macroparasite dispersal among hosts is not possible. We used a novel landscape genetics approach to examine transmission of the human roundworm Ascaris lumbricoides in a small human population in Jiri, Nepal. Unexpectedly, we found significant genetic structuring of parasites, indicating the presence of multiple transmission foci within a small sampling area (∼14 km2). We analyzed several epidemiological variables, and found that transmission is spatially autocorrelated around households and that transmission foci are stable over time despite extensive human movement. These results would not have been obtainable via a traditional epidemiological study based on worm counts alone. Our data refute the assumption that a single host population corresponds to a single parasite transmission unit, an assumption implicit in many classic models of macroparasite transmission. Newer models have shown that the metapopulation-like pattern observed in our data can adversely affect targeted control strategies aimed at community-wide impacts. Furthermore, the observed metapopulation structure and local mating patterns generate an excess of homozygotes that can accelerate the spread of recessive traits such as drug resistance. Our study illustrates how molecular analyses complement traditional epidemiological information in providing a better understanding of parasite transmission. Similar landscape genetic approaches in other macroparasite systems will be warranted if an accurate depiction of the transmission process is to be used to inform effective control strategies. Currently, knowledge of transmission patterns of human helminth parasites is based on traditional epidemiological data such as the number of parasites within hosts. Genetic markers can greatly facilitate our understanding of the transmission process because they provide an indirect means to infer dispersal. Here, we apply novel landscape genetics methods to examine the transmission dynamics of the world's most common human macroparasite, Ascaris lumbricoides. Specifically, we tested for both the presence of multiple transmission foci in a single human village in Nepal and the epidemiological factors associated with such infection foci. On this very local scale, we were surprised to find multiple transmission foci that were centered on households and that reinfections were occurring from the same foci. Thus, our study illustrates the utility of population genetics analyses in epidemiology. Furthermore, our study challenges current dogma by revealing fragmentation of transmission rather than homogeneous parasite mixing within a single human community. Thus, the results have important implications for drug resistance evolution and parasite control.
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Affiliation(s)
- Charles D Criscione
- Department of Biology, Texas A&M University, College Station, Texas, United States of America.
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Saranga SPJ, Prista A, Nhantumbo L, Beunen G, Rocha J, Williams-Blangero S, Maia JA. Heritabilities of somatotype components in a population from rural Mozambique. Am J Hum Biol 2008; 20:642-6. [DOI: 10.1002/ajhb.20733] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Williams-Blangero S, Vandeberg JL, Subedi J, Jha B, Dyer TD, Blangero J. Two quantitative trait loci influence whipworm (Trichuris trichiura) infection in a Nepalese population. J Infect Dis 2008; 197:1198-203. [PMID: 18462166 DOI: 10.1086/533493] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND Whipworm (Trichuris trichiura) infection is a soil-transmitted helminth infection that affects >1 billion people. It is a serious public health problem in many developing countries and can result in deficits in growth and cognitive development. In a follow-up study of significant heritability for whipworm infection, we conducted the first genome scan for quantitative trait loci (QTL) influencing the heritability of susceptibility to this important parasitic disease. METHODS Whipworm egg counts were determined for 1,253 members of the Jirel population of eastern Nepal. All individuals in the study sample belonged to a single pedigree including >26,000 pairs of relatives that are informative for genetic analysis. RESULTS Linkage analysis of genome scan data generated for the pedigree provided unambiguous evidence for 2 QTL influencing susceptibility to whipworm infection, one located on chromosome 9 (logarithm of the odds ratio [LOD] score, 3.35; genomewide P = .0138) and the other located on chromosome 18 (LOD score, 3.29; genomewide P = .0159). There was also suggestive evidence that 2 loci located on chromosomes 12 and 13 influenced whipworm infection. CONCLUSION The results of this first genome scan for T. trichiura egg counts provides new information on the determinants of genetic predisposition to whipworm infection.
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Affiliation(s)
- Sarah Williams-Blangero
- Department of Genetics, Southwest Foundation for Biomedical Research, San Antonio, Texas 78245-0549, USA.
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Williams KD, Blangero J, Cottom CR, Lawrence S, Choh AC, Czerwinski SA, Lee M, Duren DL, Sherwood RJ, Dyer TD, Jha B, Subedi J, Williams-Blangero S, Towne B. Heritability of brachydactyly type A3 in children, adolescents, and young adults from an endogamous population in eastern Nepal. Hum Biol 2008; 79:609-22. [PMID: 18494372 DOI: 10.1353/hub.2008.0016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Brachymesophalangia-V (BMP-V), a short and broad middle phalanx of the fifth digit, is the most common of all skeletal anomalies of the hand. When this feature appears alone, it is clinically known as brachydactyly type A3 (BDA3). A high prevalence of BDA3 has been observed among the children of the Jirel ethnic group in eastern Nepal. As part of the Jiri Growth Study, a hand-wrist radiograph is taken annually of each child to assess skeletal development. For this study the most recent radiographs of 1,357 Jirel children, adolescents, and young adults (676 boys, 681 girls), age 3-20 years, were examined for the presence or absence of BDA3, to report the prevalence and estimate the heritability of BDA3 in the Jirel population. The overall prevalence of BDA3 in this sample was 10.5% (12.9% of the males and 8.9% of the females were classified as BDA3 affected). The additive genetic heritability of BDA3 was statistically significant in this sample (h2 +/- SE = 0.87 +/- 0.16, p < 0.0001). This study is the first to estimate the prevalence and heritability of BDA3 in a large South Asian family-based sample.
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Affiliation(s)
- Kimberly D Williams
- Lifespan Health Research Center, Department of Community Health, Boonshoft School of Medicine, Wright State University, 3171 Research Blvd., Dayton, OH 45420-4014, USA
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Williams-Blangero S, Vandeberg JL, Subedi J, Jha B, Corrêa-Oliveira R, Blangero J. Localization of Multiple Quantitative Trait Loci Influencing Susceptibility to Infection withAscaris lumbricoides. J Infect Dis 2008; 197:66-71. [PMID: 18171287 DOI: 10.1086/524060] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Affiliation(s)
- Sarah Williams-Blangero
- Department of Genetics, Southwest Foundation for Biomedical Research, San Antonio, Texas 78245-0549, USA.
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Criscione CD, Anderson JD, Sudimack D, Peng W, Jha B, Williams-Blangero S, Anderson TJC. Disentangling hybridization and host colonization in parasitic roundworms of humans and pigs. Proc Biol Sci 2007; 274:2669-77. [PMID: 17725977 PMCID: PMC2279219 DOI: 10.1098/rspb.2007.0877] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Knowledge of cross-transmission and hybridization between parasites of humans and reservoir hosts is critical for understanding the evolution of the parasite and for implementing control programmes. There is now a consensus that populations of pig and human Ascaris (roundworms) show significant genetic subdivision. However, it is unclear whether this has resulted from a single or multiple host shift(s). Furthermore, previous molecular data have not been sufficient to determine whether sympatric populations of human and pig Ascaris can exchange genes. To disentangle patterns of host colonization and hybridization, we used 23 microsatellite loci to conduct Bayesian clustering analyses of individual worms collected from pigs and humans. We observed strong differentiation between populations which was primarily driven by geography, with secondary differentiation resulting from host affiliation within locations. This pattern is consistent with multiple host colonization events. However, there is low support for the short internal branches of the dendrograms. In part, the relationships among clusters may result from current hybridization among sympatric human and pig roundworms. Indeed, congruence in three Bayesian methods indicated that 4 and 7% of roundworms sampled from Guatemala and China, respectively, were hybrids. These results indicate that there is contemporary cross-transmission between populations of human and pig Ascaris.
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Affiliation(s)
- Charles D Criscione
- Department of Genetics, Southwest Foundation for Biomedical Research, PO Box 760549, San Antonio, TX 78245, USA.
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Williams-Blangero S, Magalhaes T, Rainwater E, Blangero J, Corrêa-Oliveira R, Vandeberg JL. Electrocardiographic characteristics in a population with high rates of seropositivity for Trypanosoma cruzi infection. Am J Trop Med Hyg 2007; 77:495-9. [PMID: 17827366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Abstract
This study was conducted in Posse, a rural community in Goiàs, Brazil. Persons were recruited into the study through house-to-house sampling of all houses in the sampled area. Blood samples were collected for seropositivity assessments for Trypanosoma cruzi and an electrocardiogram was assessed using a portable system. The results demonstrate significant differences between seropositive and seronegative persons for electrocardiographic (ECG)-derived traits. Seropositive persons had substantially longer QRS and QT intervals than seronegative persons. The PR interval was significantly different between seropositive and seronegative persons. Conduction abnormalities were observed more frequently in seropositive than seronegative persons. Right bundle branch block, an ECG abnormality typical of Chagas disease, was observed in 15% of seropositive persons compared with less than 1% of seronegative persons. Results indicate that T. cruzi infection and subsequent Chagas disease will continue to be major health problems for the foreseeable future in this typical rural area of Brazil.
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Affiliation(s)
- S Williams-Blangero
- Department of Genetics, Southwest Foundation for Biomedical Research, San Antonio, Texas, USA.
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Williams-Blangero S, Corrêa-Oliveira R, Blangero J, Magalhaes T, Rainwater E, VandeBerg JL. Electrocardiographic Characteristics in a Population with High Rates of Seropositivity for Trypanosoma cruzi Infection. Am J Trop Med Hyg 2007. [DOI: 10.4269/ajtmh.2007.77.495] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Criscione CD, Anderson JD, Raby K, Sudimack D, Subedi J, Rai DR, Upadhayay RP, Jha B, Williams-Blangero S, Anderson TJC. Microsatellite markers for the human nematode parasite Ascaris lumbricoides: development and assessment of utility. J Parasitol 2007; 93:704-8. [PMID: 17626368 DOI: 10.1645/ge-1058r.1] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
We describe 35 microsatellite markers from the human parasitic nematode Ascaris lumbricoides. We found 7 sex-linked markers and demonstrate that 26 autosomal loci can be scored reliably. These markers have high genetic variability and provide the tools to address multiple questions concerning the epidemiology, fine-scale genetic structure, host specificity, and mating systems of this parasite.
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Affiliation(s)
- Charles D Criscione
- Department of Genetics, Southwest Foundation for Biomedical Research, P.O. Box 760549, San Antonio, Texas 78245, USA.
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Araujo FF, Gomes JAS, Rocha MOC, Williams-Blangero S, Pinheiro VM, Morato MJF, Correa-Oliveira R. Potential role of CD4+CD25HIGH regulatory T cells in morbidity in Chagas disease. FRONT BIOSCI-LANDMRK 2007; 12:2797-806. [PMID: 17485260 DOI: 10.2741/2273] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Several immunoregulatory mechanisms are proposed to be effective both in human and experimental Trypanosoma cruzi infection. However, the role of CD4+CD25high T cells in Chagas disease has not yet been elucidated. These cells are critical for the regulation of immune response to infectious agents and in the control of autoimmune diseases. In this study, the presence of CD4+CD25high regulatory T cells in the whole blood of non-infected individuals (NI), and patients with the indeterminate (IND) and cardiac form (CARD) of Chagas disease was evaluated. To further characterize this population of regulatory cells, the co-expression of CTLA-4, CD62L, CD45RO, CD45RA, HLA-DR, CD40L, CD69, CD54, IL-10R and the intracellular molecules FOXP3 and IL-10 on the CD4+CD25high T lymphocytes was examined. FOXP3 was expressed by the majority of CD4+CD25high when compared with the other CD4+ T cells subsets in patients with Chagas disease. Patients with the IND form of the disease had a higher frequency of circulating regulatory CD4+CD25high T cells than patients with the CARD form. Moreover, there was an increase in CD4+CD25highFOXP3+ cells that were also IL-10+ in the IND group whereas, in the CARD group, there was an increase in the percentage of CD4+CD25high FOXP3+ cells that expressed CTLA-4. These data suggest that IL-10 produced by regulatory T cells is effective in controlling disease development in patients with the IND form. However, in individuals with the CARD form of the disease, the same regulatory mechanism, mediated by IL-10 and CTLA-4 expression is not sufficient to control the progression of the disease. The data suggest that CD4+CD25highFOXP3+ regulatory T cells in patients with Chagas disease might play a role in the immune response against T. cruzi infection although with distinct effects in patients with the IND and CARD forms of disease.
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Affiliation(s)
- Fernanda Fortes Araujo
- Laboratorio de Imunologia Celular e Molecular, Centro de Pesquisas Rene Rachou-FIOCRUZ, Belo Horizonte, Minas Gerais, Brazil
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Kunwar CB, Chapagain RH, Subba B, Shrestha M, Jha B, Subedi J, Blangero J, Williams-Blangero S, Towne B. Occurrence of soil-transmitted helminths in women at the Himalayan region of Nepal. Kathmandu Univ Med J (KUMJ) 2006; 4:444-447. [PMID: 18603951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
OBJECTIVE To find the occurrence pattern and prevalence of the soil transmitted helminths in women of child bearing age group. METHODS AND MATERIALS The study was conducted in Jiri , an area of Dolakha district at the altitude of 2100 meter from sea level. The faecal sample of 478 women of childbearing age (15 to 45 years) were taken randomly and examined for the ova of soil transmitted helianthus. RESULT The occurrence pattern was 53.0%, 20.0% and 2.7% for Hookworms, Ascaries lumbricoids and Trichuris Trichuria respectively. Both Ascaries and Hookworm prevalence rates noticeably increased with increasing age, with the highest infection rate between the age of 36-45 years while trichuris infection reached the highest in women of 15-25 years of age. CONCLUSION There is a high prevalence of hookworm and ascaries in women of childbearing age and necessary intervention is needed according to WHO guidelines.
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Affiliation(s)
- C B Kunwar
- Jiri Helminth Project/Jiri Growth Study, Jiri-9, Naya Bazaar, Dolakha, Nepal
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Abstract
Pedigree data are useful for a wealth of research purposes in human population biology and genetics. The collection of extended pedigrees represents the most powerful sampling design for quantitative genetic and linkage studies of both normal and disease-related quantitative traits. In this paper we outline an approach for collecting pedigree data in stable isolate populations. As an example, the pedigree for the Jirel population, which was obtained using the methods presented, is described. The Jirel pedigree contains 2,000 study participants and more than 62,000 pairwise relationships that are informative for genetic analysis. Once such pedigrees are genetically characterized by a genome scan for a given trait, they become an invaluable resource for future genetic studies of any quantitative trait.
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Affiliation(s)
- Sarah Williams-Blangero
- Department of Genetics, Southwest Foundation for Biomedical Research, San Antonio, TX 78245-0549, USA
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Cardoso GM, Morato MJF, Gomes JAS, Rocha MOC, Bonfim IP, Williams-Blangero S, VandeBerg JL, Reis MR, Magalhães EFL, Correa-Oliveira R. Comparative analysis of cell phenotypes in different severe clinical forms of Chagas' disease. FRONT BIOSCI-LANDMRK 2006; 11:1158-63. [PMID: 16146804 DOI: 10.2741/1870] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The understanding of the role of the immune response in the development of gastrointestinal and cardio-digestive (CD) forms of Chagas disease has received little attention. In this paper, the commitment of each leukocyte population of peripheral blood to the production of IFN-gamma, TNF-alpha, IL-12, IL-4, IL-5 and IL-10 was studied in patients with the CD form of Chagas disease. The data show that cells from patients with the CD form of the disease have distinct cytokine profiles when compared with the other clinical forms of Chagas disease and suggest that eosinophils are the major source of cytokine production in this clinical entity. The data presented in this paper demonstrate that patients with CD form can be distinguished from patients with gastrointestinal or cardiac forms of the disease by the distinct cytokine profile of peripheral blood cells.
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Affiliation(s)
- Glenda M Cardoso
- Laboratório de Imunologia Celular e Molecular, Centro de Pesquisas René Rachou-FIOCRUZ, Belo Horizonte, MG, Brazil
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