Identifying Candidate Genes for Type 2 Diabetes Mellitus and Obesity Through Gene Expression Profiling in Multiple Tissues or Cells

Overview

Journal J Diabetes Res

Publisher Wiley

Specialty Endocrinology

Date 2014 Jan 24

PMID 24455749

Citations 31

Authors

Junhui Chen

Yuhuan Meng

Jinghui Zhou

Min Zhuo

Fei Ling

Yu Zhang

Hongli Du

Xiaoning Wang

Affiliations

Soon will be listed here.

Abstract

Type 2 Diabetes Mellitus (T2DM) and obesity have become increasingly prevalent in recent years. Recent studies have focused on identifying causal variations or candidate genes for obesity and T2DM via analysis of expression quantitative trait loci (eQTL) within a single tissue. T2DM and obesity are affected by comprehensive sets of genes in multiple tissues. In the current study, gene expression levels in multiple human tissues from GEO datasets were analyzed, and 21 candidate genes displaying high percentages of differential expression were filtered out. Specifically, DENND1B, LYN, MRPL30, POC1B, PRKCB, RP4-655J12.3, HIBADH, and TMBIM4 were identified from the T2DM-control study, and BCAT1, BMP2K, CSRNP2, MYNN, NCKAP5L, SAP30BP, SLC35B4, SP1, BAP1, GRB14, HSP90AB1, ITGA5, and TOMM5 were identified from the obesity-control study. The majority of these genes are known to be involved in T2DM and obesity. Therefore, analysis of gene expression in various tissues using GEO datasets may be an effective and feasible method to determine novel or causal genes associated with T2DM and obesity.

Citing Articles

Transcriptomics of Subcutaneous Tissue of Lipedema Identified Differentially Expressed Genes Involved in Adipogenesis, Inflammation, and Pain.

Streubel M, Baumgartner A, Meier-Vollrath I, Frambach Y, Brandenburger M, Kisch T Plast Reconstr Surg Glob Open. 2024; 12(11):e6288.

PMID: 39525887 PMC: 11548906. DOI: 10.1097/GOX.0000000000006288.

The effects of exercise on microRNA expression profiling in adipose tissue macrophages of mice.

Qin F, Huang W, Qu C, Zhao L, Du Y, Zhao T Front Immunol. 2024; 15:1412621.

PMID: 39224599 PMC: 11366585. DOI: 10.3389/fimmu.2024.1412621.

Bioinformatics analysis and validation of CSRNP1 as a key prognostic gene in non-small cell lung cancer.

Xu Z, Zhou H, Luo Y, Li N, Chen S Heliyon. 2024; 10(7):e28412.

PMID: 38560128 PMC: 10979096. DOI: 10.1016/j.heliyon.2024.e28412.

Diagnostic model based on key autophagy-related genes in intervertebral disc degeneration.

Wang Y, Wang Z, Tang Y, Chen Y, Fang C, Li Z BMC Musculoskelet Disord. 2023; 24(1):927.

PMID: 38041088 PMC: 10691083. DOI: 10.1186/s12891-023-06886-w.

Research progress on branched-chain amino acid aminotransferases.

Chen C, Naveed H, Chen K Front Genet. 2023; 14:1233669.

PMID: 38028625 PMC: 10658711. DOI: 10.3389/fgene.2023.1233669.

References

Kodama K, Horikoshi M, Toda K, Yamada S, Hara K, Irie J . Expression-based genome-wide association study links the receptor CD44 in adipose tissue with type 2 diabetes. Proc Natl Acad Sci U S A. 2012; 109(18):7049-54. PMC: 3344989. DOI: 10.1073/pnas.1114513109. View

Gubser C, Bergamaschi D, Hollinshead M, Lu X, van Kuppeveld F, Smith G . A new inhibitor of apoptosis from vaccinia virus and eukaryotes. PLoS Pathog. 2007; 3(2):e17. PMC: 1803007. DOI: 10.1371/journal.ppat.0030017. View

Keller L, Geimer S, Romijn E, Yates 3rd J, Zamora I, Marshall W . Molecular architecture of the centriole proteome: the conserved WD40 domain protein POC1 is required for centriole duplication and length control. Mol Biol Cell. 2008; 20(4):1150-66. PMC: 2642750. DOI: 10.1091/mbc.e08-06-0619. View

Cooney G, Lyons R, Crew A, Jensen T, Molero J, Mitchell C . Improved glucose homeostasis and enhanced insulin signalling in Grb14-deficient mice. EMBO J. 2004; 23(3):582-93. PMC: 1271812. DOI: 10.1038/sj.emboj.7600082. View

Voight B, Scott L, Steinthorsdottir V, Morris A, Dina C, Welch R . Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis. Nat Genet. 2010; 42(7):579-89. PMC: 3080658. DOI: 10.1038/ng.609. View

Cariou B, Capitaine N, Le Marcis V, Vega N, Bereziat V, Kergoat M . Increased adipose tissue expression of Grb14 in several models of insulin resistance. FASEB J. 2004; 18(9):965-7. DOI: 10.1096/fj.03-0824fje. View

Kang H, Yang X, Chen R, Zhang B, Corona E, Schadt E . Integration of disease-specific single nucleotide polymorphisms, expression quantitative trait loci and coexpression networks reveal novel candidate genes for type 2 diabetes. Diabetologia. 2012; 55(8):2205-13. PMC: 3390705. DOI: 10.1007/s00125-012-2568-3. View

Kahn B . Lilly lecture 1995. Glucose transport: pivotal step in insulin action. Diabetes. 1996; 45(11):1644-54. DOI: 10.2337/diab.45.11.1644. View

Dedoussis G, Kaliora A, Panagiotakos D . Genes, diet and type 2 diabetes mellitus: a review. Rev Diabet Stud. 2007; 4(1):13-24. PMC: 1892523. DOI: 10.1900/RDS.2007.4.13. View

10.

Wright D, Fick C, Olesen J, Craig B . Evidence for the involvement of a phospholipase C--protein kinase C signaling pathway in insulin stimulated glucose transport in skeletal muscle. Life Sci. 2003; 73(1):61-71. DOI: 10.1016/s0024-3205(03)00256-x. View

11.

Holt L, Lyons R, Ryan A, Beale S, Ward A, Cooney G . Dual ablation of Grb10 and Grb14 in mice reveals their combined role in regulation of insulin signaling and glucose homeostasis. Mol Endocrinol. 2009; 23(9):1406-14. PMC: 2737556. DOI: 10.1210/me.2008-0386. View

12.

Fox C, Heard-Costa N, Cupples L, Dupuis J, Vasan R, Atwood L . Genome-wide association to body mass index and waist circumference: the Framingham Heart Study 100K project. BMC Med Genet. 2007; 8 Suppl 1:S18. PMC: 1995618. DOI: 10.1186/1471-2350-8-S1-S18. View

13.

Stumvoll M, Goldstein B, van Haeften T . Type 2 diabetes: principles of pathogenesis and therapy. Lancet. 2005; 365(9467):1333-46. DOI: 10.1016/S0140-6736(05)61032-X. View

14.

Naukkarinen J, Surakka I, Pietilainen K, Rissanen A, Salomaa V, Ripatti S . Use of genome-wide expression data to mine the "Gray Zone" of GWA studies leads to novel candidate obesity genes. PLoS Genet. 2010; 6(6):e1000976. PMC: 2880558. DOI: 10.1371/journal.pgen.1000976. View

15.

Abbaszadegan H, von Sivers K, Jonsson U . Late displacement of Colles' fractures. Int Orthop. 1988; 12(3):197-9. DOI: 10.1007/BF00547163. View

16.

Urtasun R, Lopategi A, George J, Leung T, Lu Y, Wang X . Osteopontin, an oxidant stress sensitive cytokine, up-regulates collagen-I via integrin α(V)β(3) engagement and PI3K/pAkt/NFκB signaling. Hepatology. 2011; 55(2):594-608. PMC: 3561739. DOI: 10.1002/hep.24701. View

17.

Schleinitz D, Kloting N, Lindgren C, Breitfeld J, Dietrich A, Schon M . Fat depot-specific mRNA expression of novel loci associated with waist-hip ratio. Int J Obes (Lond). 2013; 38(1):120-5. PMC: 7116610. DOI: 10.1038/ijo.2013.56. View

18.

Muller G, Wied S, Frick W . Cross talk of pp125(FAK) and pp59(Lyn) non-receptor tyrosine kinases to insulin-mimetic signaling in adipocytes. Mol Cell Biol. 2000; 20(13):4708-23. PMC: 85892. DOI: 10.1128/MCB.20.13.4708-4723.2000. View

19.

Fromm-Dornieden C, von der Heyde S, Lytovchenko O, Salinas-Riester G, Brenig B, Beissbarth T . Novel polysome messages and changes in translational activity appear after induction of adipogenesis in 3T3-L1 cells. BMC Mol Biol. 2012; 13:9. PMC: 3347988. DOI: 10.1186/1471-2199-13-9. View

20.

Jensen D, Proctor M, Marquis S, Gardner H, Ha S, Chodosh L . BAP1: a novel ubiquitin hydrolase which binds to the BRCA1 RING finger and enhances BRCA1-mediated cell growth suppression. Oncogene. 1998; 16(9):1097-112. DOI: 10.1038/sj.onc.1201861. View