Mapping adipose and muscle tissue expression quantitative trait loci in African Americans to identify genes for type 2 diabetes and obesity

Satria P. Sajuthi, Neeraj K. Sharma, Jeff W. Chou, Nicholette D. Palmer, David R. McWilliams, John Beal, Mary E. Comeau, Lijun Ma, Jorge Calles-Escandon, Jamehl Demons, Samantha Rogers, Kristina Cherry, Lata Menon, Ethel Kouba, Donna Davis, Marcie Burris, Sara J. Byerly, Maggie C Y Ng, Nisa Maruthur, Sanjay R. PatelLawrence F. Bielak, Leslie A. Lange, Xiuqing Guo, Michèle M. Sale, Kei Hang K Chan, Keri L. Monda, Gary K. Chen, Kira Taylor, Cameron Palmer, Todd L. Edwards, Kari E. North, Christopher A. Haiman, Donald W. Bowden, Barry I. Freedman, Carl D. Langefeld, Swapan K. Das

Research output: Contribution to journalArticle

Abstract

Relative to European Americans, type 2 diabetes (T2D) is more prevalent in African Americans (AAs). Genetic variation may modulate transcript abundance in insulin-responsive tissues and contribute to risk; yet, published studies identifying expression quantitative trait loci (eQTLs) in African ancestry populations are restricted to blood cells. This study aims to develop a map of genetically regulated transcripts expressed in tissues important for glucose homeostasis in AAs, critical for identifying the genetic etiology of T2D and related traits. Quantitative measures of adipose and muscle gene expression, and genotypic data were integrated in 260 non-diabetic AAs to identify expression regulatory variants. Their roles in genetic susceptibility to T2D, and related metabolic phenotypes, were evaluated by mining GWAS datasets. eQTL analysis identified 1971 and 2078 cis-eGenes in adipose and muscle, respectively. Cis-eQTLs for 885 transcripts including top cis-eGenes CHURC1, USMG5, and ERAP2 were identified in both tissues. 62.1 % of top cis-eSNPs were within ±50 kb of transcription start sites and cis-eGenes were enriched for mitochondrial transcripts. Mining GWAS databases revealed association of cis-eSNPs for more than 50 genes with T2D (e.g. PIK3C2A, RBMS1, UFSP1), gluco-metabolic phenotypes (e.g. INPP5E, SNX17, ERAP2, FN3KRP), and obesity (e.g. POMC, CPEB4). Integration of GWAS meta-analysis data from AA cohorts revealed the most significant association for cis-eSNPs of ATP5SL and MCCC1 genes, with T2D and BMI, respectively. This study developed the first comprehensive map of adipose and muscle tissue eQTLs in AAs (publically accessible at https://mdsetaa.phs.wakehealth.edu) and identified genetically regulated transcripts for delineating genetic causes of T2D, and related metabolic phenotypes.

Original languageEnglish (US)
Pages (from-to)1-12
Number of pages12
JournalHuman Genetics
DOIs
StateAccepted/In press - May 19 2016

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Quantitative Trait Loci
African Americans
Type 2 Diabetes Mellitus
Adipose Tissue
Obesity
Muscles
Genome-Wide Association Study
Genes
Phenotype
Pro-Opiomelanocortin
Transcription Initiation Site
Genetic Predisposition to Disease
Meta-Analysis
Blood Cells
Homeostasis
Databases
Insulin
Gene Expression
Glucose
Population

ASJC Scopus subject areas

  • Genetics(clinical)
  • Genetics

Cite this

Sajuthi, S. P., Sharma, N. K., Chou, J. W., Palmer, N. D., McWilliams, D. R., Beal, J., ... Das, S. K. (Accepted/In press). Mapping adipose and muscle tissue expression quantitative trait loci in African Americans to identify genes for type 2 diabetes and obesity. Human Genetics, 1-12. https://doi.org/10.1007/s00439-016-1680-8

Mapping adipose and muscle tissue expression quantitative trait loci in African Americans to identify genes for type 2 diabetes and obesity. / Sajuthi, Satria P.; Sharma, Neeraj K.; Chou, Jeff W.; Palmer, Nicholette D.; McWilliams, David R.; Beal, John; Comeau, Mary E.; Ma, Lijun; Calles-Escandon, Jorge; Demons, Jamehl; Rogers, Samantha; Cherry, Kristina; Menon, Lata; Kouba, Ethel; Davis, Donna; Burris, Marcie; Byerly, Sara J.; Ng, Maggie C Y; Maruthur, Nisa; Patel, Sanjay R.; Bielak, Lawrence F.; Lange, Leslie A.; Guo, Xiuqing; Sale, Michèle M.; Chan, Kei Hang K; Monda, Keri L.; Chen, Gary K.; Taylor, Kira; Palmer, Cameron; Edwards, Todd L.; North, Kari E.; Haiman, Christopher A.; Bowden, Donald W.; Freedman, Barry I.; Langefeld, Carl D.; Das, Swapan K.

In: Human Genetics, 19.05.2016, p. 1-12.

Research output: Contribution to journalArticle

Sajuthi, SP, Sharma, NK, Chou, JW, Palmer, ND, McWilliams, DR, Beal, J, Comeau, ME, Ma, L, Calles-Escandon, J, Demons, J, Rogers, S, Cherry, K, Menon, L, Kouba, E, Davis, D, Burris, M, Byerly, SJ, Ng, MCY, Maruthur, N, Patel, SR, Bielak, LF, Lange, LA, Guo, X, Sale, MM, Chan, KHK, Monda, KL, Chen, GK, Taylor, K, Palmer, C, Edwards, TL, North, KE, Haiman, CA, Bowden, DW, Freedman, BI, Langefeld, CD & Das, SK 2016, 'Mapping adipose and muscle tissue expression quantitative trait loci in African Americans to identify genes for type 2 diabetes and obesity', Human Genetics, pp. 1-12. https://doi.org/10.1007/s00439-016-1680-8
Sajuthi, Satria P. ; Sharma, Neeraj K. ; Chou, Jeff W. ; Palmer, Nicholette D. ; McWilliams, David R. ; Beal, John ; Comeau, Mary E. ; Ma, Lijun ; Calles-Escandon, Jorge ; Demons, Jamehl ; Rogers, Samantha ; Cherry, Kristina ; Menon, Lata ; Kouba, Ethel ; Davis, Donna ; Burris, Marcie ; Byerly, Sara J. ; Ng, Maggie C Y ; Maruthur, Nisa ; Patel, Sanjay R. ; Bielak, Lawrence F. ; Lange, Leslie A. ; Guo, Xiuqing ; Sale, Michèle M. ; Chan, Kei Hang K ; Monda, Keri L. ; Chen, Gary K. ; Taylor, Kira ; Palmer, Cameron ; Edwards, Todd L. ; North, Kari E. ; Haiman, Christopher A. ; Bowden, Donald W. ; Freedman, Barry I. ; Langefeld, Carl D. ; Das, Swapan K. / Mapping adipose and muscle tissue expression quantitative trait loci in African Americans to identify genes for type 2 diabetes and obesity. In: Human Genetics. 2016 ; pp. 1-12.
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abstract = "Relative to European Americans, type 2 diabetes (T2D) is more prevalent in African Americans (AAs). Genetic variation may modulate transcript abundance in insulin-responsive tissues and contribute to risk; yet, published studies identifying expression quantitative trait loci (eQTLs) in African ancestry populations are restricted to blood cells. This study aims to develop a map of genetically regulated transcripts expressed in tissues important for glucose homeostasis in AAs, critical for identifying the genetic etiology of T2D and related traits. Quantitative measures of adipose and muscle gene expression, and genotypic data were integrated in 260 non-diabetic AAs to identify expression regulatory variants. Their roles in genetic susceptibility to T2D, and related metabolic phenotypes, were evaluated by mining GWAS datasets. eQTL analysis identified 1971 and 2078 cis-eGenes in adipose and muscle, respectively. Cis-eQTLs for 885 transcripts including top cis-eGenes CHURC1, USMG5, and ERAP2 were identified in both tissues. 62.1 {\%} of top cis-eSNPs were within ±50 kb of transcription start sites and cis-eGenes were enriched for mitochondrial transcripts. Mining GWAS databases revealed association of cis-eSNPs for more than 50 genes with T2D (e.g. PIK3C2A, RBMS1, UFSP1), gluco-metabolic phenotypes (e.g. INPP5E, SNX17, ERAP2, FN3KRP), and obesity (e.g. POMC, CPEB4). Integration of GWAS meta-analysis data from AA cohorts revealed the most significant association for cis-eSNPs of ATP5SL and MCCC1 genes, with T2D and BMI, respectively. This study developed the first comprehensive map of adipose and muscle tissue eQTLs in AAs (publically accessible at https://mdsetaa.phs.wakehealth.edu) and identified genetically regulated transcripts for delineating genetic causes of T2D, and related metabolic phenotypes.",
author = "Sajuthi, {Satria P.} and Sharma, {Neeraj K.} and Chou, {Jeff W.} and Palmer, {Nicholette D.} and McWilliams, {David R.} and John Beal and Comeau, {Mary E.} and Lijun Ma and Jorge Calles-Escandon and Jamehl Demons and Samantha Rogers and Kristina Cherry and Lata Menon and Ethel Kouba and Donna Davis and Marcie Burris and Byerly, {Sara J.} and Ng, {Maggie C Y} and Nisa Maruthur and Patel, {Sanjay R.} and Bielak, {Lawrence F.} and Lange, {Leslie A.} and Xiuqing Guo and Sale, {Mich{\`e}le M.} and Chan, {Kei Hang K} and Monda, {Keri L.} and Chen, {Gary K.} and Kira Taylor and Cameron Palmer and Edwards, {Todd L.} and North, {Kari E.} and Haiman, {Christopher A.} and Bowden, {Donald W.} and Freedman, {Barry I.} and Langefeld, {Carl D.} and Das, {Swapan K.}",
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AU - Sajuthi, Satria P.

AU - Sharma, Neeraj K.

AU - Chou, Jeff W.

AU - Palmer, Nicholette D.

AU - McWilliams, David R.

AU - Beal, John

AU - Comeau, Mary E.

AU - Ma, Lijun

AU - Calles-Escandon, Jorge

AU - Demons, Jamehl

AU - Rogers, Samantha

AU - Cherry, Kristina

AU - Menon, Lata

AU - Kouba, Ethel

AU - Davis, Donna

AU - Burris, Marcie

AU - Byerly, Sara J.

AU - Ng, Maggie C Y

AU - Maruthur, Nisa

AU - Patel, Sanjay R.

AU - Bielak, Lawrence F.

AU - Lange, Leslie A.

AU - Guo, Xiuqing

AU - Sale, Michèle M.

AU - Chan, Kei Hang K

AU - Monda, Keri L.

AU - Chen, Gary K.

AU - Taylor, Kira

AU - Palmer, Cameron

AU - Edwards, Todd L.

AU - North, Kari E.

AU - Haiman, Christopher A.

AU - Bowden, Donald W.

AU - Freedman, Barry I.

AU - Langefeld, Carl D.

AU - Das, Swapan K.

PY - 2016/5/19

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