Differential methylation patterns from clusters associated with glucose metabolism: evidence from a Shanghai twin study

References

• American Diabetes Association . Diagnosis and classification of diabetes mellitus. Diabetes Care36(Suppl. 1), S67–S74 (2013).
   PubMed Web of Science ®Google Scholar
• Tabak AG , HerderC, RathmannW, BrunnerEJ, KivimakiM. Prediabetes: a high-risk state for diabetes development. Lancet379(9833), 2279–2290 (2012).
   PubMed Web of Science ®Google Scholar
• Tabak AG , JokelaM, AkbaralyTN, BrunnerEJ, KivimakiM, WitteDR. Trajectories of glycaemia, insulin sensitivity, and insulin secretion before diagnosis of type 2 diabetes: an analysis from the Whitehall II study. Lancet373(9682), 2215–2221 (2009).
   PubMed Web of Science ®Google Scholar
• Wang L , PengW, ZhaoZ et al. Prevalence and treatment of diabetes in China, 2013–2018. JAMA326(24), 2498–2506 (2021).
   PubMed Web of Science ®Google Scholar
• Sun H , SaeediP, KarurangaS et al. IDF Diabetes Atlas: global, regional and country-level diabetes prevalence estimates for 2021 and projections for 2045. Diabetes Res. Clin. Pract.183, 109119 (2022).
   PubMed Web of Science ®Google Scholar
• Trerotola M , RelliV, SimeoneP, AlbertiS. Epigenetic inheritance and the missing heritability. Hum. Genomics9(1), 17 (2015).
   PubMedGoogle Scholar
• Chen R , XiaL, TuK et al. Longitudinal personal DNA methylome dynamics in a human with a chronic condition. Nat. Med.24(12), 1930–1939 (2018).
   PubMed Web of Science ®Google Scholar
• Hong X , WuZ, CaoW et al. Longitudinal association of DNA methylation with type 2 diabetes and glycemic traits: a 5-year cross-lagged twin study. Diabetes71(12), 2804–2817 (2022).
   PubMed Web of Science ®Google Scholar
• Kriebel J , HerderC, RathmannW et al. Association between DNA methylation in whole blood and measures of glucose metabolism: KORA F4 study. PLOS ONE11(3), e152314 (2016).
   PubMed Web of Science ®Google Scholar
• Liu J , Carnero-MontoroE, van DongenJ et al. An integrative cross-omics analysis of DNA methylation sites of glucose and insulin homeostasis. Nat. Commun.10(1), 2581 (2019).
   PubMedGoogle Scholar
• Wang Z , PengH, GaoW et al. Blood DNA methylation markers associated with type 2 diabetes, fasting glucose, and HbA1c levels: an epigenome-wide association study in 316 adult twin pairs. Genomics113(6), 4206–4213 (2021).
   PubMed Web of Science ®Google Scholar
• Tan Q , ChristiansenL, ThomassenM, KruseTA, ChristensenK. Twins for epigenetic studies of human aging and development. Ageing Res. Rev.12(1), 182–187 (2013).
   PubMed Web of Science ®Google Scholar
• Nilsson E , VavakovaM, PerfilyevA et al. Differential DNA methylation and expression of miRNAs in adipose tissue from twin pairs discordant for type 2 diabetes. Diabetes70(10), 2402–2418 (2021).
   PubMed Web of Science ®Google Scholar
• Gao W , CaoW, LvJ et al. The Chinese National Twin Registry: a ‘gold mine’ for scientific research. J. Intern. Med.286(3), 299–308 (2019).
   PubMed Web of Science ®Google Scholar
• Ainsworth BE , HaskellWL, HerrmannSD et al. 2011 Compendium of Physical Activities: a second update of codes and MET values. Med. Sci. Sports Exerc.43(8), 1575–1581 (2011).
   PubMed Web of Science ®Google Scholar
• Manichaikul A , MychaleckyjJC, RichSS, DalyK, SaleM, ChenWM. Robust relationship inference in genome-wide association studies. Bioinformatics26(22), 2867–2873 (2010).
   PubMed Web of Science ®Google Scholar
• Purcell S , NealeB, Todd-BrownK et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet.81(3), 559–575 (2007).
   PubMed Web of Science ®Google Scholar
• Aryee MJ , JaffeAE, Corrada-BravoH et al. Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays. Bioinformatics30(10), 1363–1369 (2014).
   PubMed Web of Science ®Google Scholar
• Gu Z . Illuminahumanmethylationepicv2manifest (2023). https://github.com/jokergoo/IlluminaHumanMethylationEPICv2manifest
   Google Scholar
• Gu Z . Illuminahumanmethylationepicv2anno.20a1.hg38 (2023). https://github.com/jokergoo/IlluminaHumanMethylationEPICv2anno.20a1.hg38
   Google Scholar
• Chen YA , LemireM, ChoufaniS et al. Discovery of cross-reactive probes and polymorphic CpGs in the Illumina Infinium HumanMethylation450 microarray. Epigenetics8(2), 203–209 (2013).
   PubMed Web of Science ®Google Scholar
• Fortin JP , LabbeA, LemireM et al. Functional normalization of 450k methylation array data improves replication in large cancer studies. Genome Biol.15(12), 503 (2014).
   PubMed Web of Science ®Google Scholar
• Salas LA , KoestlerDC, ButlerRA et al. An optimized library for reference-based deconvolution of whole-blood biospecimens assayed using the Illumina HumanMethylationEPIC BeadArray. Genome Biol.19(1), 64 (2018).
   PubMed Web of Science ®Google Scholar
• Johnson WE , LiC, RabinovicA. Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics8(1), 118–127 (2007).
   PubMed Web of Science ®Google Scholar
• Benjamini Y , HochbergY. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc.: Ser. B (Methodol.)57(1), 289–300 (1995).
   Google Scholar
• Mohammadnejad A , SoerensenM, BaumbachJ et al. Novel DNA methylation marker discovery by assumption-free genome-wide association analysis of cognitive function in twins. Aging Cell20(2), e13293 (2021).
   PubMed Web of Science ®Google Scholar
• Spindel ON , WorldC, BerkBC. Thioredoxin interacting protein: redox dependent and independent regulatory mechanisms. Antioxid. Redox Signal.16(6), 587–596 (2012).
   PubMed Web of Science ®Google Scholar
• Li X , ShaoX, BazzanoLA et al. Blood DNA methylation at TXNIP and glycemic changes in response to weight-loss diet interventions: the POUNDS lost trial. Int. J. Obes. (Lond.)46(6), 1122–1127 (2022).
   PubMed Web of Science ®Google Scholar
• Volkmar M , DedeurwaerderS, CunhaDA et al. DNA methylation profiling identifies epigenetic dysregulation in pancreatic islets from type 2 diabetic patients. EMBO J.31(6), 1405–1426 (2012).
   PubMed Web of Science ®Google Scholar
• Chambers JC , LohM, LehneB et al. Epigenome-wide association of DNA methylation markers in peripheral blood from Indian Asians and Europeans with incident type 2 diabetes: a nested case-control study. Lancet Diabetes Endocrinol.3(7), 526–534 (2015).
   PubMed Web of Science ®Google Scholar
• Juvinao-Quintero DL , MarioniRE, Ochoa-RosalesC et al. DNA methylation of blood cells is associated with prevalent type 2 diabetes in a meta-analysis of four European cohorts. Clin. Epigenetics13(1), 40 (2021).
   PubMed Web of Science ®Google Scholar
• Xu G , ChenJ, JingG, ShalevA. Thioredoxin-interacting protein regulates insulin transcription through microRNA-204. Nat. Med.19(9), 1141–1146 (2013).
   PubMed Web of Science ®Google Scholar
• Chen J , SaxenaG, MungrueIN, LusisAJ, ShalevA. Thioredoxin-interacting protein: a critical link between glucose toxicity and beta-cell apoptosis. Diabetes57(4), 938–944 (2008).
   PubMed Web of Science ®Google Scholar
• Parikh H , CarlssonE, ChutkowWA et al. TXNIP regulates peripheral glucose metabolism in humans. PLOS Med.4(5), e158 (2007).
   PubMed Web of Science ®Google Scholar
• Yoshihara E . TXNIP/TBP-2: a master regulator for glucose homeostasis. Antioxidants (Basel)9(8), 765 (2020).
   PubMedGoogle Scholar
• Lea RA , AquinoEM, BentonMC, HauptLM, SutherlandHG, GriffithsLR. Current understanding of DNA methylation and age-related disease. OBM Genetics2(2), 16 (2018).
   Google Scholar
• Halleck MS , SchlegelRA, WilliamsonPL. Reanalysis of ATP11B, a type IV P-type ATPase. J. Biol. Chem.277(12), 9736–9740 (2002).
   PubMed Web of Science ®Google Scholar
• Tholen LE , BosC, JansenP et al. Bifunctional protein PCBD2 operates as a co-factor for hepatocyte nuclear factor 1beta and modulates gene transcription. FASEB J.35(4), e21366 (2021).
   PubMed Web of Science ®Google Scholar
• Mahajan A , GoMJ, ZhangW et al. Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility. Nat. Genet.46(3), 234–244 (2014).
   PubMed Web of Science ®Google Scholar
• Tang T , HuangX, ZhangG et al. Oncolytic peptide LTX-315 induces anti-pancreatic cancer immunity by targeting the ATP11B-PD-L1 axis. J. Immunother. Cancer10(3), e004129 (2022).
   PubMed Web of Science ®Google Scholar
• Smith NL , ChenMH, DehghanA et al. Novel associations of multiple genetic loci with plasma levels of factor VII, factor VIII, and von Willebrand factor: the CHARGE (Cohorts for Heart and Aging Research in Genome Epidemiology) Consortium. Circulation121(12), 1382–1392 (2010).
   PubMed Web of Science ®Google Scholar
• Lautier C , ElMS, RenardE et al. Complex haplotypes of IRS2 gene are associated with severe obesity and reveal heterogeneity in the effect of Gly1057Asp mutation. Hum. Genet.113(1), 34–43 (2003).
   PubMed Web of Science ®Google Scholar
• Zhong J , JermusykA, WuL et al. A transcriptome-wide association study identifies novel candidate susceptibility genes for pancreatic cancer. J. Natl Cancer Inst.112(10), 1003–1012 (2020).
   PubMedGoogle Scholar
• Panatta E , ButeraA, MammarellaE et al. Metabolic regulation by p53 prevents R-loop-associated genomic instability. Cell Rep.41(5), 111568 (2022).
   PubMed Web of Science ®Google Scholar
• Meabon JS , LeeA, MeekerKD et al. Differential expression of the glutamate transporter GLT-1 in pancreas. J. Histochem. Cytochem.60(2), 139–151 (2012).
   PubMed Web of Science ®Google Scholar
• Choi JH , YeeSW, RamirezAH et al. A common 5′-UTR variant in MATE2-K is associated with poor response to metformin. Clin. Pharmacol. Ther.90(5), 674–684 (2011).
   PubMed Web of Science ®Google Scholar
• Christensen MM , Brasch-AndersenC, GreenH et al. The pharmacogenetics of metformin and its impact on plasma metformin steady-state levels and glycosylated hemoglobin A1c. Pharmacogenet. Genomics21(12), 837–850 (2011).
   PubMed Web of Science ®Google Scholar
• Willemsen G , WardKJ, BellCG et al. The concordance and heritability of type 2 diabetes in 34,166 twin pairs from international twin registers: the Discordant Twin (DISCOTWIN) Consortium. Twin Res. Hum. Genet.18(6), 762–771 (2015).
   PubMed Web of Science ®Google Scholar
• Feng J , ZhuZ, WuF. Progress of application of the twin method in diabetes factorial studies. Shanghai J. Prev. Med.35(1), 70–77 (2023).
   Google Scholar
• Li W , ChristiansenL, HjelmborgJ, BaumbachJ, TanQ. On the power of epigenome-wide association studies using a disease-discordant twin design. Bioinformatics34(23), 4073–4078 (2018).
   PubMed Web of Science ®Google Scholar
• Salas LA , ZhangZ, KoestlerDC et al. Enhanced cell deconvolution of peripheral blood using DNA methylation for high-resolution immune profiling. Nat. Commun.13(1), 761 (2022).
   PubMed Web of Science ®Google Scholar