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Comparative gene expression profile and DNA methylation status in diabetic patients of Kazak and Han people.

ABSTRACT: We attempted to investigate the mechanism and susceptibility genes for diabetes in Han and Kazak ethnic individuals.The abdominal omental adipose tissues were obtained from diabetic cases and healthy controls. The gene expression and methylation data were produced for Kazak and Han individuals, respectively, and analyzed by bioinformatics analysis.We obtained 921 differentially expressed genes (DEGs) in Han group and 1772 in Kazak group. DEGs in Han group were significantly related with type 2 diabetes mellitus, and biosynthesis of amino acids, while the DEGs specific to Kazak patients were significantly enriched in metabolism-related pathways such as carbon metabolism, propanoate metabolism, and 2-oxocarboxylic acid metabolism. Major facilitator superfamily domain containing 1 (MFSD1) was found to be a methylation associated gene at hypermethylation site of cg16289538 in Han group. Rho guanine nucleotide exchange factor 1 (ARHGEF1) was the susceptible gene corresponding to the methylation sites of cg18800192 and cg00759295 in Kazak group. ARHGEF1 was also a node in protein-protein interaction network and significantly enriched in hsa04270: vascular smooth muscle contraction pathways.The molecular mechanism of diabetes may be different in Han and Kazak patients. MFSD1 and ARHGEF1 may be the diabetes susceptible genes.

SUBMITTER: Wang C

PROVIDER: S-EPMC6133596 | biostudies-literature | 2018 Sep

REPOSITORIES: biostudies-literature

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Comparative gene expression profile and DNA methylation status in diabetic patients of Kazak and Han people.

Wang Cuizhe C Ha Xiaodan X Li Wei W Xu Peng P Zhang Zhiwei Z Wang Tingting T Li Jun J Wang Yan Y Li Siyuan S Xie Jianxin J Zhang Jun J

Medicine 20180901 36

We attempted to investigate the mechanism and susceptibility genes for diabetes in Han and Kazak ethnic individuals.The abdominal omental adipose tissues were obtained from diabetic cases and healthy controls. The gene expression and methylation data were produced for Kazak and Han individuals, respectively, and analyzed by bioinformatics analysis.We obtained 921 differentially expressed genes (DEGs) in Han group and 1772 in Kazak group. DEGs in Han group were significantly related with type 2 d ...[more]

PMID: 30200077

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Project description:ObjectiveThe objective of this study was to compare the DNA methylation profile in the longissimus dorsi muscle between Small Tailed Han and Dorper×Small Tailed Han crossbred sheep which were known to exhibit significant difference in meat-production.MethodsSix samples (three in each group) were subjected to the methylated DNA immunoprecipitation sequencing (MeDIP-seq) and subsequent bioinformatics analyses to detect differentially methylated regions (DMRs) between the two groups.Results23.08 Gb clean data from six samples were generated and 808 DMRs were identified in gene body or their neighboring up/downstream regions. Compared with Small Tailed Han sheep, we observed a tendency toward a global loss of DNA methylation in these DMRs in the crossbred group. Gene ontology enrichment analysis found several gene sets which were hypo-methylated in gene-body region, including nucleoside binding, motor activity, phospholipid binding and cell junction. Numerous genes were found to be differentially methylated between the two groups with several genes significantly differentially methylated, including transforming growth factor beta 3 (TGFB3), acyl-CoA synthetase long chain family member 1 (ACSL1), ryanodine receptor 1 (RYR1), acyl-CoA oxidase 2 (ACOX2), peroxisome proliferator activated receptor-gamma2 (PPARG2), netrin 1 (NTN1), ras and rab interactor 2 (RIN2), microtubule associated protein RP/EB family member 1 (MAPRE1), ADAM metallopeptidase with thrombospondin type 1 motif 2 (ADAMTS2), myomesin 1 (MYOM1), zinc finger, DHHC type containing 13 (ZDHHC13), and SH3 and PX domains 2B (SH3PXD2B). The real-time quantitative polymerase chain reaction validation showed that the 12 genes are differentially expressed between the two groups.ConclusionIn the current study, a tendency to a global loss of DNA methylation in these DMRs in the crossbred group was found. Twelve genes, TGFB3, ACSL1, RYR1, ACOX2, PPARG2, NTN1, RIN2, MAPRE1, ADAMTS2, MYOM1, ZDHHC13, and SH3PXD2B, were found to be differentially methylated between the two groups by gene ontology enrichment analysis. There are differences in the expression of 12 genes, of which ACSL1, RIN2, and ADAMTS2 have a negative correlation with methylation levels and the data suggest that DNA methylation levels in DMRs of the 3 genes may have an influence on the expression. These results will serve as a valuable resource for DNA methylation investigations on screening candidate genes which might be related to meat production in sheep.

Dataset Information

Comparative gene expression profile and DNA methylation status in diabetic patients of Kazak and Han people.

Publications

Comparative gene expression profile and DNA methylation status in diabetic patients of Kazak and Han people.

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