Global gene expression profile of coronary artery disease in Asian Indians
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE42148 | GEO | 2012/11/09
SECONDARY ACCESSION(S): PRJNA179208
REPOSITORIES: GEO
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Project description:Global gene expression profile of whole blood in patients with coronary artery disease (CAD) showed significant upregulation of 343 genes and down regulation of 151 genes as compared to controls (p<0.05). There was predominant differential regulation of inflammatory and immune response genes as well as early growth response genes in our dataset. Of the ten candidate genes selected for validation by real time PCR in an independent cohort, CXCL1, EGR3, IL8, PTGS2 and CD69 genes were up regulated and IFNG and FASLG down regulated in cases relative to controls. We selected 13 patients with angiographically confirmed coronary artery disease (CAD) between ages 40 - 55 years and 11 population-based asymptomatic controls with normal ECG and matched for age, gendre and common risk factors such as diabetes and hypertension to that of the cases. Global gene expression profiling was performed on the Agilent microarray platform.
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Project description:BACKGROUND:Asian Indians display a high prevalence of diseases linked to changes in diet and environment that have arisen as their lifestyle has become more westernized. Using 1200 genome-wide polymorphisms in 432 individuals from 15 Indian language groups, we have recently shown that: (i) Indians constitute a distinct population-genetic cluster, and (ii) despite the geographic and linguistic diversity of the groups they exhibit a relatively low level of genetic heterogeneity. RESULTS:We investigated the prevalence of common polymorphisms that have been associated with diseases, such as atherosclerosis (ALOX5), hypertension (CYP3A5, AGT, GNB3), diabetes (CAPN10, TCF7L2, PTPN22), prostate cancer (DG8S737, rs1447295), Hirschsprung disease (RET), and age-related macular degeneration (CFH, LOC387715). In addition, we examined polymorphisms associated with skin pigmentation (SLC24A5) and with the ability to taste phenylthiocarbamide (TAS2R38). All polymorphisms were studied in a cohort of 576 India-born Asian Indians sampled in the United States. This sample consisted of individuals whose mother tongue is one of 14 of the 22 "official" languages recognized in India as well as individuals whose mother tongue is Parsi, a cultural group that has resided in India for over 1000 years. Analysis of the data revealed that allele frequency differences between the different Indian language groups were small, and interestingly the variant alleles of ALOX5 g.8322G>A and g.50778G>A, and PTPN22 g.36677C>T were present only in a subset of the Indian language groups. Furthermore, a latitudinal cline was identified both for the allele frequencies of the SNPs associated with hypertension (CYP3A5, AGT, GNB3), as well as for those associated with the ability to taste phenylthiocarbamide (TAS2R38). CONCLUSION:Although caution is warranted due to the fact that this US-sampled Indian cohort may not represent a random sample from India, our results will hopefully assist in the design of future studies that investigate the genetic causes of these diseases in India. Our results also support the inclusion of the Indian population in disease-related genetic studies, as it exhibits unique genotype as well as phenotype characteristics that may yield new insights into the underlying causes of common diseases that are not available in other populations.
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Project description:GWAS to identify risk genes for type 2 diabetes in Asian Indians
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Project description:To examine ?-cell function across a spectrum of glycemia among Asian Indians, a population experiencing type 2 diabetes development at young ages despite low BMI.One-thousand two-hundred sixty-four individuals without known diabetes in the Diabetes Community Lifestyle Improvement Program in Chennai, India, had a 75-g oral glucose tolerance test, with glucose and insulin measured at 0, 30, and 120 min. Type 2 diabetes, isolated impaired fasting glucose (iIFG), isolated impaired glucose tolerance (iIGT), combined impaired fasting glucose and impaired glucose tolerance, and normal glucose tolerance (NGT) were defined by American Diabetes Association guidelines. Measures included insulin resistance and sensitivity (homeostasis model assessment of insulin resistance [HOMA-IR], modified Matsuda Index, 1/fasting insulin) and ?-cell function (oral disposition index = [? insulin0-30/? glucose 0-30] × [1/fasting insulin]).Mean age was 44.2 years (SD, 9.3) and BMI 27.4 kg/m(2) (SD, 3.8); 341 individuals had NGT, 672 had iIFG, IGT, or IFG plus IGT, and 251 had diabetes. Patterns of insulin resistance or sensitivity were similar across glycemic categories. With mild dysglycemia, the absolute differences in age- and sex-adjusted oral disposition index (NGT vs. iIFG, 38%; NGT vs. iIGT, 32%) were greater than the differences in HOMA-IR (NGT vs. iIFG, 25%; NGT vs. iIGT, 23%; each P < 0.0001). Compared with NGT and adjusted for age, sex, BMI, waist circumference, and family history, the odds of mild dysglycemia were more significant per SD of oral disposition index (iIFG: odds ratio [OR], 0.36; 95% CI, 0.23-0.55; iIGT: OR, 0.37; 95% CI, 0.24-0.56) than per SD of HOMA-IR (iIFG: OR, 1.69; 95% CI, 1.23-2.33; iIGT: OR, 1.53; 95% CI, 1.11-2.11).Asian Indians with mild dysglycemia have reduced ?-cell function, regardless of age, adiposity, insulin sensitivity, or family history. Strategies in diabetes prevention should minimize loss of ?-cell function.
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