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Berumen J, Orozco L, Gallardo-Rincón H, Rivas F, Barrera E, Benuto RE, García-Ortiz H, Marin-Medina M, Juárez-Torres E, Alvarado-Silva A, Ramos-Martinez E, MartÍnez-Juárez LA, Lomelín-Gascón J, Montoya A, Ortega-Montiel J, Alvarez-Hernández DA, Larriva-Shad J, Tapia-Conyer R. Sex differences in the influence of type 2 diabetes (T2D)-related genes, parental history of T2D, and obesity on T2D development: a case-control study. Biol Sex Differ 2023; 14:39. [PMID: 37291636 DOI: 10.1186/s13293-023-00521-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 05/24/2023] [Indexed: 06/10/2023] Open
Abstract
BACKGROUND This study investigated the effect of sex and age at type 2 diabetes (T2D) diagnosis on the influence of T2D-related genes, parental history of T2D, and obesity on T2D development. METHODS In this case-control study, 1012 T2D cases and 1008 healthy subjects were selected from the Diabetes in Mexico Study database. Participants were stratified by sex and age at T2D diagnosis (early, ≤ 45 years; late, ≥ 46 years). Sixty-nine T2D-associated single nucleotide polymorphisms were explored and the percentage contribution (R2) of T2D-related genes, parental history of T2D, and obesity (body mass index [BMI] and waist-hip ratio [WHR]) on T2D development was calculated using univariate and multivariate logistic regression models. RESULTS T2D-related genes influenced T2D development most in males who were diagnosed early (R2 = 23.5%; females, R2 = 13.5%; males and females diagnosed late, R2 = 11.9% and R2 = 7.3%, respectively). With an early diagnosis, insulin production-related genes were more influential in males (76.0% of R2) while peripheral insulin resistance-associated genes were more influential in females (52.3% of R2). With a late diagnosis, insulin production-related genes from chromosome region 11p15.5 notably influenced males while peripheral insulin resistance and genes associated with inflammation and other processes notably influenced females. Influence of parental history was higher among those diagnosed early (males, 19.9%; females, 17.5%) versus late (males, 6.4%; females, 5,3%). Unilateral maternal T2D history was more influential than paternal T2D history. BMI influenced T2D development for all, while WHR exclusively influenced males. CONCLUSIONS The influence of T2D-related genes, maternal T2D history, and fat distribution on T2D development was greater in males than females.
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Affiliation(s)
- Jaime Berumen
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Cuauhtémoc, 06720, Ciudad de Mexico, México.
| | - Lorena Orozco
- Instituto Nacional de Medicina Genómica, Ciudad de Mexico, México
| | - Héctor Gallardo-Rincón
- Universidad of Guadalajara, Health Sciences University Center, Guadalajara, Jalisco, México.
- Fundación Carlos Slim, Lago Zurich 245, Presa Falcon Building (Floor 20), Col. Ampliacion Granada, Miguel Hidalgo, 11529, Mexico City, México.
| | - Fernando Rivas
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Cuauhtémoc, 06720, Ciudad de Mexico, México
| | - Elizabeth Barrera
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Cuauhtémoc, 06720, Ciudad de Mexico, México
| | | | | | | | | | | | - Espiridión Ramos-Martinez
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Cuauhtémoc, 06720, Ciudad de Mexico, México
| | - Luis Alberto MartÍnez-Juárez
- Fundación Carlos Slim, Lago Zurich 245, Presa Falcon Building (Floor 20), Col. Ampliacion Granada, Miguel Hidalgo, 11529, Mexico City, México
| | - Julieta Lomelín-Gascón
- Fundación Carlos Slim, Lago Zurich 245, Presa Falcon Building (Floor 20), Col. Ampliacion Granada, Miguel Hidalgo, 11529, Mexico City, México
| | - Alejandra Montoya
- Fundación Carlos Slim, Lago Zurich 245, Presa Falcon Building (Floor 20), Col. Ampliacion Granada, Miguel Hidalgo, 11529, Mexico City, México
| | - Janinne Ortega-Montiel
- Fundación Carlos Slim, Lago Zurich 245, Presa Falcon Building (Floor 20), Col. Ampliacion Granada, Miguel Hidalgo, 11529, Mexico City, México
| | - Diego-Abelardo Alvarez-Hernández
- Fundación Carlos Slim, Lago Zurich 245, Presa Falcon Building (Floor 20), Col. Ampliacion Granada, Miguel Hidalgo, 11529, Mexico City, México
| | - Jorge Larriva-Shad
- Instituto de Neurobiología, Universidad Nacional Autónoma de México, Juriquilla, Querétaro, México
| | - Roberto Tapia-Conyer
- Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de Mexico, México
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2
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Analysis of the different characteristics between omental preadipocytes and differentiated white adipocytes using bioinformatics methods. Adipocyte 2022; 11:227-238. [PMID: 35499169 PMCID: PMC9067510 DOI: 10.1080/21623945.2022.2063471] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Obesity is emerging as an epidemiological issue, being associated with the onset and progress of various metabolism-related disorders. Obesity is characterized by the white adipose expansion, which encounters white adipocyte hypertrophy and hyperplasia. White adipocyte hyperplasia is defined as adipogenesis with the increase in the number of the white adipocytes from the preadipocytes. Adipogenesis contributes to distributing excess triglycerides among the smaller newly formed adipocytes, reducing the number of hypertrophic adipocytes and secreting anti-inflammatory factor. Therefore, adipogenesis is emerging as a new therapeutic target for the treatment of obesity. In the present study, for a better understanding of the contribution of the alteration of the omental differentiated white adipocytes to the systemic metabolic disorders, we downloaded the mRNA expression profiles from GEO database GSE1657, 328 differentially expressed genes (DEGs) were screened between the undifferentiated preadipocytes (UNDIF) and omental differentiated white adipocytes (DIF). The contributions of the upregulated and downregulated DEGs to the system were performed via the Gene Ontology (GO) analysis, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and Protein-Protein Interaction (PPI) network, respectively. The potential contribution of the whole altered genes in the differentiated white adipocytes was explored with the performance of Gene Set Enrichment Analysis (GSEA), especially on the GO analysis, KEGG analysis, hallmark analysis, oncogenic analysis and related miRNA analysis. The output of the current study will shed light on the new targets for the treatment of obesity and obesity-related disorders.
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3
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Lv B, Yang X, An T, Wu Y, He Z, Li B, Wang Y, Tan F, Wang T, Zhu J, Hu Y, Liu X, Jiang G. Combined analysis of whole-exome sequencing and RNA sequencing in type 2 diabetes mellitus patients with thirst and fatigue. Diabetol Metab Syndr 2022; 14:111. [PMID: 35941691 PMCID: PMC9358875 DOI: 10.1186/s13098-022-00884-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 07/28/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The principal objective of this study was to gain a better understanding of the mechanisms of type 2 diabetes mellitus (T2DM) patients with fatigue (D-T2DM) through exome and transcriptome sequencing. METHODS After whole-exome sequencing on peripheral blood of 6 D-T2DM patients, the consensus mutations were screen out and analyzed by a series of bioinformatics analyses. Then, we combined whole-exome sequencing and transcriptome sequencing results to find the important genes that changed at both the DNA and RNA levels. RESULTS The results showed that a total of 265,393 mutation sites were found in D-T2DM patients compared with normal individuals, 235 of which were consensus mutations shared with D-T2DM patients. These genes significantly enriched in HIF-1 signaling pathway and sphingolipid signaling pathway. At the RNA level, a total of 375 genes were identified to be differentially expressed. After the DNA-RNA joint analysis, eight genes were screened that changed at both DNA and RNA levels. Among these genes, FUS and LMNA were related to carbohydrate metabolism, energy metabolism, and mitochondrial function. Subsequently, we predicted the herbs, including Qin Pi and Hei Zhi Ma, that might play a therapeutic role in D-T2DM through the SymMap database. CONCLUSION These findings have significant implications for understanding the mechanisms of D-T2DM and provide potential targets for D-T2DM diagnosis and treatment.
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Affiliation(s)
- Bohan Lv
- Traditional Chinese Medicine School, Beijing University of Chinese Medicine, Beijing, China
| | - Xiuyan Yang
- Traditional Chinese Medicine School, Beijing University of Chinese Medicine, Beijing, China
| | - Tian An
- Traditional Chinese Medicine School, Beijing University of Chinese Medicine, Beijing, China
| | - Yanxiang Wu
- Traditional Chinese Medicine School, Beijing University of Chinese Medicine, Beijing, China
| | - Zhongchen He
- Department of Endocrinology, Beijing He Ping li Hospital, Beijing, China
| | - Bowu Li
- Department of Endocrinology, Beijing He Ping li Hospital, Beijing, China
| | - Yijiao Wang
- Department of Endocrinology, Beijing He Ping li Hospital, Beijing, China
| | - Fang Tan
- Department of Endocrinology, Beijing He Ping li Hospital, Beijing, China
| | - Tingye Wang
- Traditional Chinese Medicine School, Beijing University of Chinese Medicine, Beijing, China
| | - Jiajian Zhu
- Traditional Chinese Medicine School, Beijing University of Chinese Medicine, Beijing, China
| | - Yuanyuan Hu
- Traditional Chinese Medicine School, Beijing University of Chinese Medicine, Beijing, China
| | - Xiaokun Liu
- Department of Cardiology, Gongren Hospital of Tangshan City, Tangshan, China
| | - Guangjian Jiang
- Traditional Chinese Medicine School, Beijing University of Chinese Medicine, Beijing, China
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4
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Potter JHT, Davies KTJ, Yohe LR, Sanchez MKR, Rengifo EM, Struebig M, Warren K, Tsagkogeorga G, Lim BK, dos Reis M, Dávalos LM, Rossiter SJ. Dietary Diversification and Specialization in Neotropical Bats Facilitated by Early Molecular Evolution. Mol Biol Evol 2021; 38:3864-3883. [PMID: 34426843 PMCID: PMC8382914 DOI: 10.1093/molbev/msab028] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Dietary adaptation is a major feature of phenotypic and ecological diversification, yet the genetic basis of dietary shifts is poorly understood. Among mammals, Neotropical leaf-nosed bats (family Phyllostomidae) show unmatched diversity in diet; from a putative insectivorous ancestor, phyllostomids have radiated to specialize on diverse food sources including blood, nectar, and fruit. To assess whether dietary diversification in this group was accompanied by molecular adaptations for changing metabolic demands, we sequenced 89 transcriptomes across 58 species and combined these with published data to compare ∼13,000 protein coding genes across 66 species. We tested for positive selection on focal lineages, including those inferred to have undergone dietary shifts. Unexpectedly, we found a broad signature of positive selection in the ancestral phyllostomid branch, spanning genes implicated in the metabolism of all major macronutrients, yet few positively selected genes at the inferred switch to plantivory. Branches corresponding to blood- and nectar-based diets showed selection in loci underpinning nitrogenous waste excretion and glycolysis, respectively. Intriguingly, patterns of selection in metabolism genes were mirrored by those in loci implicated in craniofacial remodeling, a trait previously linked to phyllostomid dietary specialization. Finally, we show that the null model of the widely-used branch-site test is likely to be misspecified, with the implication that the test is too conservative and probably under-reports true cases of positive selection. Our findings point to a complex picture of adaptive radiation, in which the evolution of new dietary specializations has been facilitated by early adaptations combined with the generation of new genetic variation.
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Affiliation(s)
- Joshua H T Potter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Kalina T J Davies
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Laurel R Yohe
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA
- Department of Earth and Planetary Science, Yale University, 210 Whitney Ave, New Haven, CT, USA
| | - Miluska K R Sanchez
- Escuela Profesional de Ciencias Biológicas, Universidad Nacional de Piura, Piura, Peru
| | - Edgardo M Rengifo
- Escola Superior de Agricultura ‘Luiz de Queiroz,’ Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, Brazil
- Centro de Investigación Biodiversidad Sostenible (BioS), Lima, Peru
| | - Monika Struebig
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Kim Warren
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Georgia Tsagkogeorga
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Burton K Lim
- Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada
| | - Mario dos Reis
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Liliana M Dávalos
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA
- Consortium for Inter-Disciplinary Environmental Research, Stony Brook University, Stony Brook, NY, USA
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
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5
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Yang K, Lu K, Wu Y, Yu J, Liu B, Zhao Y, Chen J, Zhou X. A network-based machine-learning framework to identify both functional modules and disease genes. Hum Genet 2021; 140:897-913. [PMID: 33409574 DOI: 10.1007/s00439-020-02253-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 12/22/2020] [Indexed: 01/20/2023]
Abstract
Disease gene identification is a critical step towards uncovering the molecular mechanisms of diseases and systematically investigating complex disease phenotypes. Despite considerable efforts to develop powerful computing methods, candidate gene identification remains a severe challenge owing to the connectivity of an incomplete interactome network, which hampers the discovery of true novel candidate genes. We developed a network-based machine-learning framework to identify both functional modules and disease candidate genes. In this framework, we designed a semi-supervised non-negative matrix factorization model to obtain the functional modules related to the diseases and genes. Of note, we proposed a disease gene-prioritizing method called MapGene that integrates the correlations from both functional modules and network closeness. Our framework identified a set of functional modules with highly functional homogeneity and close gene interactions. Experiments on a large-scale benchmark dataset showed that MapGene performs significantly better than the state-of-the-art algorithms. Further analysis demonstrates MapGene can effectively relieve the impact of the incompleteness of interactome networks and obtain highly reliable rankings of candidate genes. In addition, disease cases on Parkinson's disease and diabetes mellitus confirmed the generalization of MapGene for novel candidate gene identification. This work proposed, for the first time, an integrated computing framework to predict both functional modules and disease candidate genes. The methodology and results support that our framework has the potential to help discover underlying functional modules and reliable candidate genes in human disease.
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Affiliation(s)
- Kuo Yang
- School of Computer and Information Technology, Institute of Medical Intelligence, Beijing Jiaotong University, Beijing, 100044, China.,Institute for TCM-X, MOE Key Laboratory of Bioinformatics / Bioinformatics Division, BNRIST, Department of Automation, Tsinghua University, Beijing, 10084, China
| | - Kezhi Lu
- School of Computer and Information Technology, Institute of Medical Intelligence, Beijing Jiaotong University, Beijing, 100044, China.,imec-DistriNet, KU Leuven, Leuven, 3001, Belgium
| | - Yang Wu
- Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, China
| | - Jian Yu
- Beijing Key Laboratory of Traffic Data Analysis and Mining, School of Computer and Information Technology, Beijing Jiaotong University, Beijing, 100044, China
| | - Baoyan Liu
- Data Center of Traditional Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Yi Zhao
- Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, China
| | - Jianxin Chen
- Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Xuezhong Zhou
- School of Computer and Information Technology, Institute of Medical Intelligence, Beijing Jiaotong University, Beijing, 100044, China. .,Data Center of Traditional Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
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6
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Lalrohlui F, Zohmingthanga J, Hruaii V, Vanlallawma A, Senthil Kumar N. Whole exome sequencing identifies the novel putative gene variants related with type 2 diabetes in Mizo population, northeast India. Gene 2020; 769:145229. [PMID: 33059026 DOI: 10.1016/j.gene.2020.145229] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 09/30/2020] [Accepted: 10/07/2020] [Indexed: 11/30/2022]
Abstract
The contribution of genes towards T2D development varies among different population groups across the world. It has been reported that a number of loci involved in T2D susceptibility are common across certain population groups, but ethnicity specific variants are also observed. The population of Mizoram has an independent ethnic identity and there are no scientific records about the history of the Mizo people; which makes this ethnic group unique and interesting to study. The aim of the study focuses on the identification of the gene variants which may contribute to T2D susceptibility in Mizo-Mongloid ethnic tribe of North east India through whole exome sequencing. The variants like 328G > C (KRT18), 997G > T (CYP4A11), 2368 T > C (SLC4A3), 508G > A (SLC26A5), 1659C > T (KCNS1), 650C > A (ABCD1) 821A > T (YTHDC2), 931G > T (PINX1), 3280C > A (TNRC6A), 48C > A(TACO1), 6035A > T(LAMA1), 805C > A(ACP7) and 806A > G(ACP7) variants were not reported for any disease in the database and were found to be pathogenic in different insilico analysis softwares. The changes in protein stability upon mutation has been predicted where 35.71% increases the stability of the protein, while 64.28% of the variants decrease the stability of the protein. These findings present the population specific variants which might involve in the susceptibility to T2D in Mizo population. Further, in this study some gene variants have contribution as a possible diagnostic or prognostic marker for other diseases as well, which suggests the need for performing association analysis for different disease manifestations in Mizo population in the near future.
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Affiliation(s)
- Freda Lalrohlui
- Department of Biotechnology, Mizoram University, Aizawl 796004, Mizoram, India
| | | | - Vanlal Hruaii
- Department of Medicine, Zoram Medical College, Aizawl 796005, Mizoram, India
| | - Andrew Vanlallawma
- Department of Biotechnology, Mizoram University, Aizawl 796004, Mizoram, India
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7
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Casamayor A, Ariño J. Controlling Ser/Thr protein phosphatase PP1 activity and function through interaction with regulatory subunits. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 122:231-288. [PMID: 32951813 DOI: 10.1016/bs.apcsb.2020.06.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein phosphatase 1 is a major Ser/Thr protein phosphatase activity in eukaryotic cells. It is composed of a catalytic polypeptide (PP1C), with little substrate specificity, that interacts with a large variety of proteins of diverse structure (regulatory subunits). The diversity of holoenzymes that can be formed explain the multiplicity of cellular functions under the control of this phosphatase. In quite a few cases, regulatory subunits have an inhibitory role, downregulating the activity of the phosphatase. In this chapter we shall introduce PP1C and review the most relevant families of PP1C regulatory subunits, with particular emphasis in describing the structural basis for their interaction.
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Affiliation(s)
- Antonio Casamayor
- Institut de Biotecnologia i Biomedicina & Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola, del Vallès, Spain
| | - Joaquín Ariño
- Institut de Biotecnologia i Biomedicina & Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola, del Vallès, Spain
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8
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Gonzalez-Covarrubias V, Morales-Franco M, Cruz-Correa OF, Martínez-Hernández A, García-Ortíz H, Barajas-Olmos F, Genis-Mendoza AD, Martínez-Magaña JJ, Nicolini H, Orozco L, Soberón X. Variation in Actionable Pharmacogenetic Markers in Natives and Mestizos From Mexico. Front Pharmacol 2019; 10:1169. [PMID: 31649539 PMCID: PMC6796793 DOI: 10.3389/fphar.2019.01169] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 09/12/2019] [Indexed: 12/12/2022] Open
Abstract
The identification and characterization of pharmacogenetic variants in Latin American populations is still an ongoing endeavor. Here, we investigated SNVs on genes listed by the Pharmacogenomics Knowledge Base in 1284 Mestizos and 94 Natives from Mexico. Five institutional cohorts with NGS data were retrieved from different research projects at INMEGEN, sequencing files were filtered for 55 pharmacogenes present in all cohorts to identify novel and known variation. Bioinformatic tools VEP, PROVEAN, and FATHMM were used to assess, in silico, the functional impact of this variation. Next, we focused on 17 genes with actionable variants that have been clinically implemented. Allele frequencies were compared with major continental groups and differences discussed in the scope of a pharmacogenomic impact. We observed a wide genetic variability for known and novel SNVs, the largest variation was on UGT1A > ACE > COMT > ABCB1 and the lowest on APOE and NAT2. Although with allele frequencies around 1%, novel variation was observed in 16 of 17 PGKB genes. In Natives we identified 59 variants and 58 in Mestizos. Several genes did not show novel variation, on CYP2B6, CYP2D6, and CYP3A4 in Natives; and APOE, UGT1A, and VKORC1 in Mestizos. Similarities in allele frequency, comparing major continental groups for VIP pharmacogenes, hint towards a comparable PGx for drugs metabolized by UGT1A1, DPYD, ABCB1, CBR3, COMT, and TPMT; in contrast to variants on CYP3A5 and CYP2B6 for which significant MAF differences were identified. Our observations offer some discernment into the extent of pharmacogenetic variation registered up-to-date in Mexicans and contribute to quantitatively dissect actionable pharmacogenetic variants in Natives and Mestizos.
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Affiliation(s)
| | | | | | | | - Humberto García-Ortíz
- Immunogenomics and Metabolic Diseases Laboratory, INMEGEN, CDMX, Mexico City, Mexico
| | | | | | | | - Humberto Nicolini
- Genomics of Psychiatric and Neurodegenerative Diseases Laboratory, INMEGEN, Mexico City, Mexico
| | - Lorena Orozco
- Immunogenomics and Metabolic Diseases Laboratory, INMEGEN, CDMX, Mexico City, Mexico
| | - Xavier Soberón
- Pharmacogenomics Laboratory, INMEGEN, CDMX, Mexico City, Mexico
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9
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GWAS for Meat and Carcass Traits Using Imputed Sequence Level Genotypes in Pooled F2-Designs in Pigs. G3-GENES GENOMES GENETICS 2019; 9:2823-2834. [PMID: 31296617 PMCID: PMC6723123 DOI: 10.1534/g3.119.400452] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In order to gain insight into the genetic architecture of economically important traits in pigs and to derive suitable genetic markers to improve these traits in breeding programs, many studies have been conducted to map quantitative trait loci. Shortcomings of these studies were low mapping resolution, large confidence intervals for quantitative trait loci-positions and large linkage disequilibrium blocks. Here, we overcome these shortcomings by pooling four large F2 designs to produce smaller linkage disequilibrium blocks and by resequencing the founder generation at high coverage and the F1 generation at low coverage for subsequent imputation of the F2 generation to whole genome sequencing marker density. This lead to the discovery of more than 32 million variants, 8 million of which have not been previously reported. The pooling of the four F2 designs enabled us to perform a joint genome-wide association study, which lead to the identification of numerous significantly associated variant clusters on chromosomes 1, 2, 4, 7, 17 and 18 for the growth and carcass traits average daily gain, back fat thickness, meat fat ratio, and carcass length. We could not only confirm previously reported, but also discovered new quantitative trait loci. As a result, several new candidate genes are discussed, among them BMP2 (bone morphogenetic protein 2), which we recently discovered in a related study. Variant effect prediction revealed that 15 high impact variants for the traits back fat thickness, meat fat ratio and carcass length were among the statistically significantly associated variants.
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10
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Vidal EA, Moyano TC, Bustos BI, Pérez-Palma E, Moraga C, Riveras E, Montecinos A, Azócar L, Soto DC, Vidal M, Di Genova A, Puschel K, Nürnberg P, Buch S, Hampe J, Allende ML, Cambiazo V, González M, Hodar C, Montecino M, Muñoz-Espinoza C, Orellana A, Reyes-Jara A, Travisany D, Vizoso P, Moraga M, Eyheramendy S, Maass A, De Ferrari GV, Miquel JF, Gutiérrez RA. Whole Genome Sequence, Variant Discovery and Annotation in Mapuche-Huilliche Native South Americans. Sci Rep 2019; 9:2132. [PMID: 30765821 PMCID: PMC6376018 DOI: 10.1038/s41598-019-39391-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 01/23/2019] [Indexed: 12/15/2022] Open
Abstract
Whole human genome sequencing initiatives help us understand population history and the basis of genetic diseases. Current data mostly focuses on Old World populations, and the information of the genomic structure of Native Americans, especially those from the Southern Cone is scant. Here we present annotation and variant discovery from high-quality complete genome sequences of a cohort of 11 Mapuche-Huilliche individuals (HUI) from Southern Chile. We found approximately 3.1 × 106 single nucleotide variants (SNVs) per individual and identified 403,383 (6.9%) of novel SNVs events. Analyses of large-scale genomic events detected 680 copy number variants (CNVs) and 4,514 structural variants (SVs), including 398 and 1,910 novel events, respectively. Global ancestry composition of HUI genomes revealed that the cohort represents a sample from a marginally admixed population from the Southern Cone, whose main genetic component derives from Native American ancestors. Additionally, we found that HUI genomes contain variants in genes associated with 5 of the 6 leading causes of noncommunicable diseases in Chile, which may have an impact on the risk of prevalent diseases in Chilean and Amerindian populations. Our data represents a useful resource that can contribute to population-based studies and for the design of early diagnostics or prevention tools for Native and admixed Latin American populations.
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Affiliation(s)
- Elena A Vidal
- FONDAP Center for Genome Regulation, Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile.,Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Tomás C Moyano
- FONDAP Center for Genome Regulation, Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Bernabé I Bustos
- FONDAP Center for Genome Regulation, Santiago, Chile.,Centro de Investigaciones Biomédicas, Facultad de Ciencias Biológicas y Facultad de Medicina, Universidad Andres Bello, Santiago, Chile
| | - Eduardo Pérez-Palma
- FONDAP Center for Genome Regulation, Santiago, Chile.,Centro de Investigaciones Biomédicas, Facultad de Ciencias Biológicas y Facultad de Medicina, Universidad Andres Bello, Santiago, Chile
| | - Carol Moraga
- FONDAP Center for Genome Regulation, Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Eleodoro Riveras
- FONDAP Center for Genome Regulation, Santiago, Chile.,Departamento de Gastroenterología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alejandro Montecinos
- FONDAP Center for Genome Regulation, Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Lorena Azócar
- FONDAP Center for Genome Regulation, Santiago, Chile.,Departamento de Gastroenterología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Daniela C Soto
- FONDAP Center for Genome Regulation, Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Mabel Vidal
- FONDAP Center for Genome Regulation, Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alex Di Genova
- FONDAP Center for Genome Regulation, Santiago, Chile.,Laboratorio de Bioinformática y Matemática del Genoma (LBMG-Mathomics), Centro de Modelamiento Matemático, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Santiago, Chile
| | - Klaus Puschel
- Departamento de Medicina Familiar, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Peter Nürnberg
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Stephan Buch
- Medical Department I, University Hospital Dresden, TU Dresden, Germany
| | - Jochen Hampe
- Medical Department I, University Hospital Dresden, TU Dresden, Germany
| | - Miguel L Allende
- FONDAP Center for Genome Regulation, Santiago, Chile.,Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Verónica Cambiazo
- FONDAP Center for Genome Regulation, Santiago, Chile.,Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
| | - Mauricio González
- FONDAP Center for Genome Regulation, Santiago, Chile.,Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
| | - Christian Hodar
- FONDAP Center for Genome Regulation, Santiago, Chile.,Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
| | - Martín Montecino
- FONDAP Center for Genome Regulation, Santiago, Chile.,Centro de Investigaciones Biomédicas, Facultad de Ciencias Biológicas y Facultad de Medicina, Universidad Andres Bello, Santiago, Chile
| | - Claudia Muñoz-Espinoza
- FONDAP Center for Genome Regulation, Santiago, Chile.,Centro de Biotecnología Vegetal, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile
| | - Ariel Orellana
- FONDAP Center for Genome Regulation, Santiago, Chile.,Centro de Biotecnología Vegetal, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile
| | - Angélica Reyes-Jara
- FONDAP Center for Genome Regulation, Santiago, Chile.,Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
| | - Dante Travisany
- FONDAP Center for Genome Regulation, Santiago, Chile.,Laboratorio de Bioinformática y Matemática del Genoma (LBMG-Mathomics), Centro de Modelamiento Matemático, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Santiago, Chile
| | - Paula Vizoso
- FONDAP Center for Genome Regulation, Santiago, Chile.,Centro de Propagación y Conservación Vegetal (CEPROVEG), Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Mauricio Moraga
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile.,Departamento de Antropología, Facultad de Ciencias Sociales, Universidad de Chile, Santiago, Chile
| | - Susana Eyheramendy
- Departmento de Estadística, Facultad de Matemáticas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alejandro Maass
- FONDAP Center for Genome Regulation, Santiago, Chile.,Departamento de Medicina Familiar, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Giancarlo V De Ferrari
- FONDAP Center for Genome Regulation, Santiago, Chile. .,Centro de Investigaciones Biomédicas, Facultad de Ciencias Biológicas y Facultad de Medicina, Universidad Andres Bello, Santiago, Chile.
| | - Juan Francisco Miquel
- FONDAP Center for Genome Regulation, Santiago, Chile. .,Departamento de Gastroenterología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile.
| | - Rodrigo A Gutiérrez
- FONDAP Center for Genome Regulation, Santiago, Chile. .,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile.
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