Epigenome-wide association study of systemic effects of obesity susceptibility in human twins

References

• Payab M, Tayanloo-Beik A, Falahzadeh K, et al. Metabolomics prospect of obesity and metabolic syndrome; a systematic review. J Diabetes Metab Disord. 2022;21(1):889–18. doi: 10.1007/s40200-021-00917-w
   PubMed Web of Science ®Google Scholar
• King SE, Skinner MK. Epigenetic transgenerational inheritance of obesity susceptibility trends Endocrinol Metab. Trends Endocrinol Metab. 2020;31(7):478–494. doi: 10.1016/j.tem.2020.02.009
   PubMed Web of Science ®Google Scholar
• Qasim A, Turcotte M, de Souza RJ, et al. On the origin of obesity: identifying the biological, environmental and cultural drivers of genetic risk among human populations. Obes Rev. 2018;19(2):121–149. doi: 10.1111/obr.12625
   PubMed Web of Science ®Google Scholar
• Prasad M, Rajagopal P, Devarajan N, et al. A comprehensive review on high -fat diet-induced diabetes mellitus: an epigenetic view. J Nutr Biochem. 2022;107:109037. doi: 10.1016/j.jnutbio.2022.109037
   PubMed Web of Science ®Google Scholar
• Shioda K, Odajima J, Blumberg B, et al. Transgenerational transcriptomic and DNA methylome profiling of mouse fetal testicular germline and somatic cells after exposure of pregnant mothers to Tributyltin, a potent Obesogen. Metabolites. 2022;12(2):95. doi: 10.3390/metabo12020095
   PubMed Web of Science ®Google Scholar
• Panera N, Mandato C, Crudele A, et al. Genetics, epigenetics and transgenerational transmission of obesity in children. Front Endocrinol. 2022;13:1006008. doi: 10.3389/fendo.2022.1006008
   PubMed Web of Science ®Google Scholar
• Nuttman-Shwartz O. The long-term effects of living in a shared and continuous traumatic reality: the case of Israeli families on the border with gaza. Trauma Violence Abuse. 2023;24(3):1387–1404. doi: 10.1177/15248380211063467
   PubMed Web of Science ®Google Scholar
• Gonzalez-Rodriguez P, Fullgrabe J, Joseph B. The hunger strikes back: an epigenetic memory for autophagy. Cell Death Diff. 2023;30(6):1404–1415. doi: 10.1038/s41418-023-01159-4
   PubMed Web of Science ®Google Scholar
• Watkins SH, Iles-Caven Y, Pembrey M, et al. Grandmaternal smoking during pregnancy is associated with differential DNA methylation in peripheral blood of their grandchildren. Eur J Hum Genet. 2022;30(12):1373–1379. doi: 10.1038/s41431-022-01081-2
   PubMed Web of Science ®Google Scholar
• Richards Steed R, Bakian AV, Smith KR, et al. Evidence of transgenerational effects on autism spectrum disorder using multigenerational space-time cluster detection. Int J Health Geogr. 2022;21(1):13. doi: 10.1186/s12942-022-00313-4
   PubMed Web of Science ®Google Scholar
• Nilsson E, Sadler-Riggleman I, Skinner MK, et al. Environmentally induced epigenetic transgenerational inheritance of disease. Environ Epigenet. 2018;4(2):1–13, dvy016. doi: 10.1093/eep/dvy016
   Web of Science ®Google Scholar
• Ben Maamar M, Sadler-Riggleman I, Beck D, et al. Alterations in sperm DNA methylation, non-coding RNA expression, and histone retention mediate vinclozolin-induced epigenetic transgenerational inheritance of disease. Environ Epigenet. 2018;4(2):1–19, dvy010. doi: 10.1093/eep/dvy010
   Web of Science ®Google Scholar
• Skinner MK. Environmental epigenetic transgenerational inheritance and somatic epigenetic mitotic stability epigenetics: official. J DNA Methylation Society. 2011;6(7):838–842.
   Google Scholar
• Al-Mousawi J, Boskovic A. Transcriptional and epigenetic control of early life cell fate decisions. Curr Opin Oncol. 2022;34(2):148–154. doi: 10.1097/CCO.0000000000000814
   PubMed Web of Science ®Google Scholar
• Hoffman DJ, Powell TL, Barrett ES, et al. Developmental origins of metabolic diseases. Physiol Rev. 2021;101(3):739–795. doi: 10.1152/physrev.00002.2020
   PubMed Web of Science ®Google Scholar
• Skinner MK, Nilsson EE. Role of environmentally induced epigenetic transgenerational inheritance in evolutionary biology: unified evolution theory. Environ Epigenet. 2021;7(1):1–12. dvab012. doi: 10.1093/eep/dvab012.
   Web of Science ®Google Scholar
• Paugh JR, Nguyen T, Sasai A, et al. The efficacy of clinical tests to diagnose evaporative dry eye disease related to meibomian gland dysfunction. J Ophthalmol. 2022;2022:3889474. doi: 10.1155/2022/3889474
   PubMed Web of Science ®Google Scholar
• Anway MD, Cupp AS, Uzumcu M, et al. Epigenetic transgenerational actions of endocrine disruptors and male fertility. Science. 2005;308(5727):1466–1469. doi: 10.1126/science.1108190
   PubMed Web of Science ®Google Scholar
• Petronis A, Gottesman II, Kan P, et al. Monozygotic twins exhibit numerous epigenetic differences: clues to twin discordance? Schizophr Bull. 2003;29(1):169–178. doi: 10.1093/oxfordjournals.schbul.a006988
   PubMed Web of Science ®Google Scholar
• Craig G, Kenny H, Nilsson E, et al. Epigenome association study for DNA methylation biomarkers in buccal and monocyte cells for female rheumatoid arthritis scientific reports. Sci Rep. 2021;11(1):23789. doi: 10.1038/s41598-021-03170-6
   PubMed Web of Science ®Google Scholar
• Winchester P, Nilsson E, Beck D, et al. Preterm birth buccal cell epigenetic biomarkers to facilitate preventative medicine. Sci Rep. 2022;12(1):3361. doi: 10.1038/s41598-022-07262-9
   PubMed Web of Science ®Google Scholar
• Garrido N, Cruz F, Rivera Egea R, et al. Sperm DNA methylation epimutation biomarker for paternal offspring autism susceptibility. Clin Epigenetics. 2021;13(6):1–13. doi: 10.1186/s13148-020-00995-2
   PubMedGoogle Scholar
• Luján S, Caroppo E, Niederberger C, et al. Sperm DNA methylation epimutation biomarkers for male infertility and FSH therapeutic responsiveness. Sci Rep. 2019;9(1):16786. doi: 10.1038/s41598-019-52903-1
   PubMedGoogle Scholar
• Kaidesoja M, Aaltonen S, Bogl LH, et al. FinnTwin16: a longitudinal study from age 16 of a population-based Finnish twin cohort. Twin Res Hum Genet. 2019;22(6):530–539. doi: 10.1017/thg.2019.106
   PubMed Web of Science ®Google Scholar
• Birk RZ, Ermakov S, Livshits G. Common FSNP variants of fourteen bardet-biedl syndrome genes and adult body mass. Obesity (Silver Spring). 2013;21(8):1684–1689. doi: 10.1002/oby.20056
   PubMed Web of Science ®Google Scholar
• Young KL, Graff M, Fernandez-Rhodes L, et al. Genetics of obesity in diverse populations. Curr Diab Rep. 2018;18(12):145. doi: 10.1007/s11892-018-1107-0
   PubMed Web of Science ®Google Scholar
• Jovanovich S, Bogdan G, Belcinski R, et al. Developmental validation of a fully integrated sample-to-profile rapid human identification system for processing single-source reference buccal samples. Forensic Sci Int Genet. 2015;16:181–194. doi: 10.1016/j.fsigen.2014.12.004
   PubMed Web of Science ®Google Scholar
• Beck D, Ben Maamar M, Skinner MK. Genome-wide CpG density and DNA methylation analysis method (MeDIP, RRBS, and WGBS) comparisons epigenetics: official. J DNA Methylation Society. 2022;17(5):518–530. doi: 10.1080/15592294.2021.1924970
   Google Scholar
• Zhao W, Langfelder P, Fuller T, et al. Weighted gene coexpression network analysis: state of the art. J Biopharm Stat. 2010;20(2):281–300. doi: 10.1080/10543400903572753
   PubMed Web of Science ®Google Scholar
• Chuang YH, Paul KC, Bronstein JM, et al. Parkinson’s disease is associated with DNA methylation levels in human blood and saliva. Genome Med. 2017;9(1):76. doi: 10.1186/s13073-017-0466-5
   PubMedGoogle Scholar
• Mahmoud R, Kimonis V, Butler MG. Genetics of obesity in humans: a clinical review. Int J Mol Sci. 2022;23(19):11005. doi: 10.3390/ijms231911005
   PubMed Web of Science ®Google Scholar
• Das L, Gupta N, Dutta P, et al. Early initiation of temozolomide therapy may improve response in aggressive pituitary adenomas. Front Endocrinol. 2021;12:774686. doi: 10.3389/fendo.2021.774686
   PubMed Web of Science ®Google Scholar
• King SE, McBirney M, Beck D, et al. Sperm epimutation biomarkers of obesity and pathologies following DDT induced epigenetic transgenerational inheritance of disease. Environ Epigenet. 2019;5(2):1–15, dvz008. doi: 10.1093/eep/dvz008
   Web of Science ®Google Scholar
• Nilsson EE, Ben Maamar M, Skinner MK. Role of epigenetic transgenerational inheritance in generational toxicology. Environ Epigenet. 2022;8(1):dvac001 (1–9. doi: 10.1093/eep/dvac001
   Web of Science ®Google Scholar
• Duncan GE, Avery A, Ben Maamar M, et al. Epigenome-wide association study for physical activity and physiological parameters in discordant monozygotic twins. Sci Rep. 2022;12(1). doi: 10.1038/s41598-022-24642-3
   Web of Science ®Google Scholar
• Govender P, Ghai M, Okpeku M. Sex-specific DNA methylation: impact on human health and development. Mol Genet Genomics. 2022;297(6):1451–1466. doi: 10.1007/s00438-022-01935-w
   PubMed Web of Science ®Google Scholar
• Beck D, Nilsson EE, Ben Maamar M, et al. Environmental induced transgenerational inheritance impacts systems epigenetics in disease etiology. Sci Rep. 2022;12(1):5452. doi: 10.1038/s41598-022-09336-0
   PubMed Web of Science ®Google Scholar
• Eney AE, Tsang S, Delaney JA, et al. Cross-sectional association between soda consumption and body mass index in a community-based sample of twins. Nutr J. 2017;16(1):48. doi: 10.1186/s12937-017-0269-y
   PubMedGoogle Scholar
• Duncan GE, Avery AR, Strachan E, et al. The Washington state twin registry: 2019 update. Twin Res Hum Genet. 2019;22(6):788–793. doi: 10.1017/thg.2019.36
   PubMed Web of Science ®Google Scholar
• Andrews S FastQC: a quality control tool for high throughput sequence data. UK2010. Available from: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
   Google Scholar
• Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114–2120. doi: 10.1093/bioinformatics/btu170
   PubMed Web of Science ®Google Scholar
• Langmead B, Salzberg SL. Fast gapped-read alignment with bowtie 2. Nat Methods. 2012;9(4):357–359. doi: 10.1038/nmeth.1923
   PubMed Web of Science ®Google Scholar
• Li H, Handsaker B, Wysoker A, et al. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25(16):2078–2079. doi: 10.1093/bioinformatics/btp352
   PubMed Web of Science ®Google Scholar
• Lienhard M, Grimm C, Morkel M, et al. MEDIPS: genome-wide differential coverage analysis of sequencing data derived from DNA enrichment experiments. Bioinformatics. 2014;30(2):284–286. doi: 10.1093/bioinformatics/btt650
   PubMed Web of Science ®Google Scholar
• Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26(1):139–140. doi: 10.1093/bioinformatics/btp616
   PubMed Web of Science ®Google Scholar
• Kanehisa M, Goto S. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 2000;28(1):27–30. doi: 10.1093/nar/28.1.27
   PubMed Web of Science ®Google Scholar
• Kanehisa M, Goto S, Sato Y, et al. Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res. 2014;42(Database issue):D199–205. doi: 10.1093/nar/gkt1076
   PubMedGoogle Scholar
• Mi H, Muruganujan A, Casagrande JT, et al. Large-scale gene function analysis with the PANTHER classification system. Nat Protoc. 2013;8(8):1551–1566. doi: 10.1038/nprot.2013.092
   PubMed Web of Science ®Google Scholar
• Pinero J, Ramirez-Anguita JM, Sauch-Pitarch J, et al. The DisGeNET knowledge platform for disease genomics: 2019 update. Nucleic Acids Res. 2020;48(D1):D845–D55. doi: 10.1093/nar/gkz1021
   PubMed Web of Science ®Google Scholar
• Zhang B, Horvath S. A general framework for weighted gene co-expression network analysis. Stat Appl Genet Mol Biol. 2005;4(1):17. doi: 10.2202/1544-6115.1128
   Web of Science ®Google Scholar
• Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinf. 2008;9(1):559. doi: 10.1186/1471-2105-9-559
   PubMed Web of Science ®Google Scholar