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Wang X, Liu J, Wang Q, Chen Q. The transcriptomic and epigenetic alterations in type 2 diabetes mellitus patients of Chinese Tibetan and Han populations. Front Endocrinol (Lausanne) 2023; 14:1122047. [PMID: 36891054 PMCID: PMC9987421 DOI: 10.3389/fendo.2023.1122047] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 02/01/2023] [Indexed: 02/22/2023] Open
Abstract
BACKGROUND Due to the distinctive living environment, lifestyle, and diet, the Tibetan community in China has the lowest prevalence of T2DM and prediabetes among numerous ethnic groups, while Han community shows the highest statistic. In this study, we aim to conclude the clinical manifestations of both Tibetan and Han T2DM patients and their association with transcriptomic and epigenetic alterations. METHODS A cross-sectional study including 120 T2DM patients from Han and Tibetan ethnic groups were conducted between 2019 to 2021 at the Hospital of Chengdu University of Traditional Chinese Medicine. The various clinical features and laboratory tests were recorded and analyzed between the two groups. The genome-wide methylation pattern and RNA expression were determined by Reduced Representation Bisulfite Sequencing (RBBS) and Poly (A) RNA sequencing (RNA-seq) from leucocytes of peripheral blood samples in 6 Han and 6 Tibetan patients. GO analysis and KEGG analysis were conducted in differentially expressed genes and those with differentially methylated regions. RESULTS Compared to Han, Tibetan T2DM individuals intake more coarse grains, meat and yak butter, but less refined grains, vegetables and fruit. They also showed increased BMI, Hb, HbA1c, LDL, ALT, GGT and eGFR, and decreased level of BUN. Among the 12 patients in the exploratory cohort, we identified 5178 hypomethylated and 4787 hypermethylated regions involving 1613 genes in the Tibetan group. RNA-seq showed a total of 947 differentially expressed genes (DEGs) between the two groups, with 523 up-regulated and 424 down-regulated in Tibetan patients. By integrating DNA methylation and RNA expression data, we identified 112 DEGs with differentially methylated regions (overlapping genes) and 14 DEGs with promoter-related DMRs. The functional enrichment analysis demonstrated that the overlapping genes were primarily involved in metabolic pathways, PI3K-Akt signaling pathway, MAPK signaling pathway, pathways in cancer and Rap1 signaling pathway. CONCLUSION Our study demonstrates the clinical characteristics of T2DM differ subtly between various ethnic groups that may be related to epigenetic modifications, thus providing evidence and ideas for additional research on the genetic pattern of T2DM.
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Affiliation(s)
- Xian Wang
- School of Biological and Behavioral Sciences, Queen Mary University of London, London, United Kingdom
- Department of Endocrinology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Jie Liu
- Department of Endocrinology, Kunming Municipal Hospital of Traditional Chinese Medicine, Kumning, China
| | - Qiuhong Wang
- Department of Endocrinology, Guang’anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
- *Correspondence: Qiuhong Wang, ; Qiu Chen,
| | - Qiu Chen
- Department of Endocrinology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
- *Correspondence: Qiuhong Wang, ; Qiu Chen,
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Lee S, Kim SA, Hong J, Kim Y, Hong G, Baik S, Choi K, Lee MK, Lee KR. Identification of genetic variants related to metabolic syndrome by next-generation sequencing. Diabetol Metab Syndr 2022; 14:119. [PMID: 35999587 PMCID: PMC9396768 DOI: 10.1186/s13098-022-00893-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 08/12/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Metabolic syndrome (MetS) is a cluster of conditions associated with glucose intolerance, hypertension, abdominal obesity, dyslipidemia, and insulin resistance that increase the risk of cardiovascular diseases (CVD) and type 2 diabetes (T2D). Since MetS is known as a complex symptom with a high incidence of genetic factors, it is important to identify genetic variants for each clinical characteristic of MetS. METHODS We performed targeted next-generation sequencing (NGS) to identify genetic variants related to obesity, blood glucose, triacylglycerol (TG), and high-density lipoprotein (HDL)-cholesterol level, and hypertension in 48 subjects with MetS and in 48 healthy subjects. RESULTS NGS analysis revealed that 26 of 48 subjects (54.2%) with MetS had putative non-synonymous variants related to the clinical features of MetS. Of the subjects with MetS, 8 (16.7%) had variants in 4 genes (COL6A2, FTO, SPARC, and MTHFR) related to central obesity, 17 (35.4%) had variants in 6 genes (APOB, SLC2A2, LPA, ABCG5, ABCG8, and GCKR) related to hyperglycemia, 3 (6.3%) had variants in 4 genes (APOA1, APOC2, APOA4, and LMF1) related to hypertriglyceridemia, 8 (16.7%) had variants in 4 genes (ABCA1, CETP, SCARB1, and LDLR) related to low HDL-cholesterolemia, and 5 (10.4%) had variants in ADD1 related to hypertension. CONCLUSIONS Our findings may contribute to broadening the genetic spectrum of risk variants related to the development of MetS.
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Affiliation(s)
- Sanghoo Lee
- Center for Companion Biomarker, Seoul Clinical Laboratories Healthcare Inc., 23F, Bldg. A, Heungdeok IT Valley, 13 Heungdeok 1-ro, Giheung-gu, Yongin, Gyeonggi-do, 16954, Korea.
| | - Seol-A Kim
- Center for Companion Biomarker, Seoul Clinical Laboratories Healthcare Inc., 23F, Bldg. A, Heungdeok IT Valley, 13 Heungdeok 1-ro, Giheung-gu, Yongin, Gyeonggi-do, 16954, Korea
| | - Jeonghoon Hong
- Center for Companion Biomarker, Seoul Clinical Laboratories Healthcare Inc., 23F, Bldg. A, Heungdeok IT Valley, 13 Heungdeok 1-ro, Giheung-gu, Yongin, Gyeonggi-do, 16954, Korea
| | - Yejin Kim
- Center for Companion Biomarker, Seoul Clinical Laboratories Healthcare Inc., 23F, Bldg. A, Heungdeok IT Valley, 13 Heungdeok 1-ro, Giheung-gu, Yongin, Gyeonggi-do, 16954, Korea
| | - Gayeon Hong
- Center for Companion Biomarker, Seoul Clinical Laboratories Healthcare Inc., 23F, Bldg. A, Heungdeok IT Valley, 13 Heungdeok 1-ro, Giheung-gu, Yongin, Gyeonggi-do, 16954, Korea
| | - SaeYun Baik
- Central Laboratory, Seoul Clinical Laboratories Healthcare Inc., 23F, Bldg. A, Heungdeok IT Valley, 13 Heungdeok 1-ro, Giheung-gu, Yongin, Gyeonggi-do, 16954, Korea
| | - Kyeonghwan Choi
- HANARO Medical Foundation, 5F, 1 TOWER, GRAN SEOUL, 33 Jong-ro, Jongno-gu, Seoul, 03159, Korea
| | - Mi-Kyeong Lee
- Department of MyGenome, Seoul Clinical Laboratories, 28F, Bldg. A, Heungdeok IT Valley, 13 Heungdeok 1-ro, Giheung-gu, Yongin, Gyeonggi-do, 16954, Korea
| | - Kyoung-Ryul Lee
- Center for Companion Biomarker, Seoul Clinical Laboratories Healthcare Inc., 23F, Bldg. A, Heungdeok IT Valley, 13 Heungdeok 1-ro, Giheung-gu, Yongin, Gyeonggi-do, 16954, Korea.
- Central Laboratory, Seoul Clinical Laboratories Healthcare Inc., 23F, Bldg. A, Heungdeok IT Valley, 13 Heungdeok 1-ro, Giheung-gu, Yongin, Gyeonggi-do, 16954, Korea.
- HANARO Medical Foundation, 5F, 1 TOWER, GRAN SEOUL, 33 Jong-ro, Jongno-gu, Seoul, 03159, Korea.
- Department of MyGenome, Seoul Clinical Laboratories, 28F, Bldg. A, Heungdeok IT Valley, 13 Heungdeok 1-ro, Giheung-gu, Yongin, Gyeonggi-do, 16954, Korea.
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Association of APOB and LIPC polymorphisms with type 2 diabetes in Chinese Han population. Gene 2018; 672:150-155. [PMID: 29883758 DOI: 10.1016/j.gene.2018.06.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 05/19/2018] [Accepted: 06/04/2018] [Indexed: 02/06/2023]
Abstract
BACKGROUND Apolipoprotein B (APOB), and hepatic lipase (LIPC) genes have been shown to play a key role in lipid metabolism in type 2 diabetes (T2D). This study aimed to investigate the association of the three polymorphisms (rs679899 in APOB and rs6078 and rs6083 in LIPC) with T2D and related clinical quantitative traits. METHODS We conducted a case-control study in Chinese Han population, with a total of 929 T2D patients and 1044 healthy subjects in Chinese Han population. Polymorphisms were genotyped by MassARRAY Genotyping System. RESULTS The risk allele G of the polymorphism rs679899 was related to T2D (odds ratio (OR): 1.207, 95% confidence interval (CL): 1.006-1.448, P = 0.043) and the polymorphism rs679899 was associated with glutamyl transpeptidase (GGT) levels (P = 0.001). We also showed that the polymorphism rs6083 was associated with cholesterol (CHOL) levels (P = 0.012), triglyceride (TG) levels (P = 0.040), and low-density lipoprotein cholesterol (LDL) levels (P = 0.033). No significant difference in genotypic frequencies of rs6078 and rs6083 was observed between T2D patients and controls. CONCLUSION This study suggests that the APOB polymorphism rs679899 is associated with type 2 diabetes and GGT levels, while the LIPC polymorphism rs6083 may influence CHOL, TG, and LDL levels in Chinese Han population.
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Niu C, Luo Z, Yu L, Yang Y, Chen Y, Luo X, Lai F, Song Y. Associations of the APOB rs693 and rs17240441 polymorphisms with plasma APOB and lipid levels: a meta-analysis. Lipids Health Dis 2017; 16:166. [PMID: 28874158 PMCID: PMC5586014 DOI: 10.1186/s12944-017-0558-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 08/31/2017] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND The associations of the apolipoprotein B gene (APOB) rs693 and rs17240441 polymorphisms with plasma levels of APOB and lipids have been widely explored, but the results were inconclusive. This meta-analysis aimed to clarify the associations of the rs693 and rs17240441 polymorphisms with fasting APOB and lipid levels. METHODS Sixty-one studies (50,018 subjects) and 23 studies (8425 subjects) were respectively identified for the rs693 and rs17240441 polymorphisms by searching in PubMed, Google Scholar, Web of Science, Cochrane Library, Wanfang, VIP and CNKI databases. The following information was collected for each study: first author, age, gender, ethnicity, health condition, sample size, genotyping, lipid assay method, mean and standard deviation or standard error of APOB and lipid variables by genotypes. A dominant model was used for this meta-analysis. RESULTS The carriers of the rs693 variant allele (T) had higher levels of APOB [standardized mean difference (SMD) = 0.26, 95% confidence interval (CI) = 0.16-0.36, P < 0.01], triglycerides (TG) (SMD = 0.12, 95% CI = 0.05-0.20, P < 0.01), total cholesterol (TC) (SMD = 0.24, 95% CI = 0.17-0.30, P < 0.01) and low-density lipoprotein cholesterol (LDL-C) (SMD = 0.22, 95% CI = 0.14-0.30, P < 0.01), and lower levels of high-density lipoprotein cholesterol (HDL-C) (SMD = -0.06, 95% CI = -0.11-0.01, P = 0.01) than the non-carriers. The carriers of the rs17240441 deletion allele had higher levels of APOB (SMD = 0.13, 95% CI = 0.06-0.20, P < 0.01), TC (SMD = 0.17, 95% CI = 0.07-0.26, P < 0.01) and LDL-C (SMD = 0.15, 95% CI = 0.07-0.23, P < 0.01) than the non-carriers. CONCLUSIONS The rs693 polymorphism is significantly associated with higher levels of APOB, TG, TC and LDL-C, and lower levels of HDL-C. The rs17240441 polymorphism is significantly associated with higher levels of APOB, TC and LDL-C. Further studies are needed to elucidate the underlying mechanisms.
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Affiliation(s)
- Caiqin Niu
- Department of Traditional Chinese Medicine, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, People's Republic of China
| | - Zhi Luo
- Department of Cardiology, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, People's Republic of China
| | - Liuqin Yu
- Institute of Materia Medica, School of Pharmacy, North Sichuan Medical College, Nanchong, 637000, People's Republic of China
| | - Yang Yang
- School of Clinical Medicine, North Sichuan Medical College, Nanchong, 637000, People's Republic of China
| | - Yun Chen
- Department of Cardiology, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, People's Republic of China
| | - Xin Luo
- School of Clinical Medicine, North Sichuan Medical College, Nanchong, 637000, People's Republic of China
| | - Feiya Lai
- School of Clinical Medicine, North Sichuan Medical College, Nanchong, 637000, People's Republic of China
| | - Yongyan Song
- Department of Medical Biochemistry, School of Preclinical Medicine, North Sichuan Medical College, Nanchong, 637000, People's Republic of China.
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Hammoud A, Gastaldi M, Maillot M, Mercier CS, Defoort C, Lairon D, Planells R. APOB-516 T allele homozygous subjects are unresponsive to dietary changes in a three-month primary intervention study targeted to reduce fat intake. GENES AND NUTRITION 2009; 5:29-37. [PMID: 19841959 DOI: 10.1007/s12263-009-0155-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Accepted: 09/29/2009] [Indexed: 11/30/2022]
Abstract
Dietary guidelines aim to control fat intake and reduce cardiovascular risk but an important interindividual variability occurs among subjects. The objective was to investigate whether the response of lipid and glucose homeostasis parameters after a three-month diet aimed at reducing cardiovascular risk could be modulated by the -516C/T polymorphism in the apolipoprotein B gene (APOB). Middle-aged men (n = 69) and women (n = 100) with moderate cardiovascular disease risk were advised to reduce total energy and fat intakes and replace saturated dietary fat by monounsaturated and polyunsaturated fat. Subjects were genotyped for APOB-516C/T polymorphism. At the entry and at the end of the three-month period, fasting and postprandial plasma lipid analyses were performed. At entry, subjects homozygous for the APOB-516 T allele exhibited significantly lower fasting plasma concentrations of apolipoprotein B 48, triglycerides and triglyceride-rich lipoproteins-triglycerides compared to C carrier subjects. After the diet period, while C carrier subjects presented a clear improvement of most biological parameters, paradoxically T/T subjects did not modify them. In addition, the apoB 48 postprandial response after a standardized mixed test meal was not improved in T/T subjects after the three-month diet, contrary to C allele carriers. Even though their phenotype at entry does not show any significant increase of risk factors when compared to other groups, subjects homozygous for the APOB-516 T allele are unresponsive to a healthy diet that improves cardiovascular risk status in the whole population.
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Hu P, Qin YH, Jing CX, Lei FY, Chen P, Li MF. Association of polymorphisms at restriction enzyme recognition sites of apolipoprotein B and E gene with dyslipidemia in children undergoing primary nephrotic syndrome. Mol Biol Rep 2008; 36:1015-21. [PMID: 18512131 DOI: 10.1007/s11033-008-9275-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2008] [Accepted: 05/21/2008] [Indexed: 12/12/2022]
Abstract
BACKGROUND Dyslipidemia, a common complication, is very prevalent in children with primary nephrotic syndrome (PNS). Recent studies have shown that genetic basis may be involved in the onset of HLP secondary to PNS. ApoB and E have been identified as the important candidate genes for lipid abnormalities. OBJECTIVE To investigate the association of apolipoprotein B (apoB) and E (apoE) genetic polymorphisms (Xba I, EcoR I, Msp I, and Hha I) with parameters describing the serum lipid profiles in children undergoing PNS. METHODS Genomic DNA was extracted from 250 children diagnosed with PNS and 200 healthy controls with neither allergic nor renal disease. ApoB (Xba I, EcoR I, and Msp I) and apoE (Hha I) genotypes were determined by PCR-restriction fragment length polymorphism (RFLP) analysis. The fasting serum lipoprotein (a) [Lp(a)], total cholesterol (TC), triglyceride (TG), high density lipoprotein cholesterol (HDL-C), low density lipoprotein cholesterol (LDL-C), apolipoprotein A1 (apoA1), apoB, and total protein from a 24-h urine sample were measured. RESULTS No significant differences in genotypes and alleles frequencies were observed for the apoB Xba I, EcoR I, Msp I and the apoE Hha I restriction sites in PNS patients as compared to controls (P > 0.05). Patients and controls with X + allele exhibited significantly higher serum levels of Lp(a), TC, nonHDL-C, LDL-C, LDL-C/HDL-C ratio, and apoB than that with X- allele (P < 0.05), whereas for apoA1/B ratio the opposite was found (P < 0.01). E-/E- carriers had significantly higher Lp(a), TC, HDL-C, and apoA1 concentrations than did E+/E- or E+/E+ carriers in control group (P < 0.05). Healthy children carrying the rare EcoR I allele had higher mean Lp(a), TC, and HDL-C levels than homozygotes for E+ (P < 0.05). Higher Lp(a) serum concentrations were observed in patients with E- allele (P < 0.05). No significant differences in lipid parameters were determined for the apoB Msp I and apoE Hha I the polymorphisms study (P > 0.05). When genetic variations were compared with urinary protein excretion, the Xba I X- allele was more frequent in patients with elevated proteinuria (P < 0.01). CONCLUSION Presence of Xba I X+ allele and/or EcoR I E- at the apoB gene may be risk factors for lipid abnormalities secondary to childhood PNS.
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Affiliation(s)
- Peng Hu
- Department of Pediatrics, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
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Apolipoprotein B gene polymorphisms in patients from Serbia with ischemic cerebrovascular disease. ARCH BIOL SCI 2007. [DOI: 10.2298/abs0704303s] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The plasma concentration of apoB has recently been reported to be the best lipid predictor of coronary heart disease. The possible associations of genetic markers in the apolipoprotein B gene (XbaI, EcoRI, MspI, Ins/Del, and 4311 A/G polymorphisms) were evaluated in patients with ischemic cerebrovascular disease (ICVD) and controls of equivalent BMI. The odds ratio for ICVD in the X+X+ genotype was 2.22, 95% CI 1.24-3.96 (P<0.05), while that for ICVD in the Ins/Ins genotype was 2.82, 95% CI 1.57-5.06 (P<0.05). The patients had significantly higher frequency of the 4311A allele compared to the controls (P<0.01). Our results support the assumption that apoB gene polymorphisms may contribute to the extent of cerebrovascular disease risk.
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