دورية أكاديمية
أعرض في EDS

Integrating muti-omics data to identify tissue-specific DNA methylation biomarkers for cancer risk.

التفاصيل البيبلوغرافية
العنوان: Integrating muti-omics data to identify tissue-specific DNA methylation biomarkers for cancer risk.
المؤلفون: Yang Y; Center for Public Health Genomics, Department of Public Health Sciences, UVA Comprehensive Cancer Center, School of Medicine, University of Virginia, Charlottesville, VA, USA. vta8we@virginia.edu., Chen Y; Institute of Respiratory Health, Frontiers Science Center for Disease‑Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China., Xu S; Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA., Guo X; Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA., Jia G; Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA., Ping J; Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA., Shu X; Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA., Zhao T; Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA., Yuan F; Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA., Wang G; Institute of Respiratory Health, Frontiers Science Center for Disease‑Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China., Xie Y; Institute of Respiratory Health, Frontiers Science Center for Disease‑Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China., Ci H; Institute of Respiratory Health, Frontiers Science Center for Disease‑Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China., Liu H; Institute of Respiratory Health, Frontiers Science Center for Disease‑Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China., Qi Y; Institute of Respiratory Health, Frontiers Science Center for Disease‑Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China., Liu Y; Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, WA, USA., Liu D; Institute of Respiratory Health, Frontiers Science Center for Disease‑Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China., Li W; Institute of Respiratory Health, Frontiers Science Center for Disease‑Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China., Ye F; Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA., Shu XO; Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA., Zheng W; Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA., Li L; Department of Family Medicine, UVA Comprehensive Cancer Center, School of Medicine, University of Virginia, Charlottesville, VA, USA., Cai Q; Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA. qiuyin.cai@vumc.org., Long J; Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA. jirong.long@vumc.org.
المصدر: Nature communications [Nat Commun] 2024 Jul 18; Vol. 15 (1), pp. 6071. Date of Electronic Publication: 2024 Jul 18.
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101528555 Publication Model: Electronic Cited Medium: Internet ISSN: 2041-1723 (Electronic) Linking ISSN: 20411723 NLM ISO Abbreviation: Nat Commun Subsets: MEDLINE
أسماء مطبوعة: Original Publication: [London] : Nature Pub. Group
مواضيع طبية MeSH: DNA Methylation* , Genome-Wide Association Study* , CpG Islands*/genetics , Neoplasms*/genetics , Biomarkers, Tumor*/genetics , Organ Specificity*/genetics, Humans ; Male ; Female ; Genetic Predisposition to Disease ; Gene Expression Regulation, Neoplastic ; Epigenesis, Genetic ; Neoplasms, Germ Cell and Embryonal ; Testicular Neoplasms
مستخلص: The relationship between tissue-specific DNA methylation and cancer risk remains inadequately elucidated. Leveraging resources from the Genotype-Tissue Expression consortium, here we develop genetic models to predict DNA methylation at CpG sites across the genome for seven tissues and apply these models to genome-wide association study data of corresponding cancers, namely breast, colorectal, renal cell, lung, ovarian, prostate, and testicular germ cell cancers. At Bonferroni-corrected P < 0.05, we identify 4248 CpGs that are significantly associated with cancer risk, of which 95.4% (4052) are specific to a particular cancer type. Notably, 92 CpGs within 55 putative novel loci retain significant associations with cancer risk after conditioning on proximal signals identified by genome-wide association studies. Integrative multi-omics analyses reveal 854 CpG-gene-cancer trios, suggesting that DNA methylation at 309 distinct CpGs might influence cancer risk through regulating the expression of 205 unique cis-genes. These findings substantially advance our understanding of the interplay between genetics, epigenetics, and gene expression in cancer etiology.
(© 2024. The Author(s).)
References: Nat Genet. 2016 Mar;48(3):245-52. (PMID: 26854917)
Trends Genet. 2021 Nov;37(11):1012-1027. (PMID: 34120771)
Nat Commun. 2018 May 8;9(1):1825. (PMID: 29739930)
Cancer Epidemiol Biomarkers Prev. 2021 Nov;30(11):2079-2087. (PMID: 34497089)
Nat Genet. 2012 Mar 18;44(4):369-75, S1-3. (PMID: 22426310)
PLoS Genet. 2014 May 15;10(5):e1004383. (PMID: 24830394)
Am J Hum Genet. 2023 Jun 1;110(6):950-962. (PMID: 37164006)
Nat Commun. 2023 Jun 20;14(1):3671. (PMID: 37340002)
Nature. 2023 Jan;613(7944):508-518. (PMID: 36653562)
Bioinformatics. 2010 Sep 1;26(17):2190-1. (PMID: 20616382)
Nat Genet. 2017 Dec;49(12):1779-1784. (PMID: 29083409)
Nature. 2017 Nov 2;551(7678):92-94. (PMID: 29059683)
Nat Genet. 2022 Aug;54(8):1167-1177. (PMID: 35915169)
Nat Genet. 2023 Jan;55(1):112-122. (PMID: 36510025)
Nat Genet. 2017 May;49(5):680-691. (PMID: 28346442)
JAMA. 2016 Jan 5;315(1):68-76. (PMID: 26746459)
Nat Genet. 2023 Jan;55(1):89-99. (PMID: 36539618)
Nat Rev Mol Cell Biol. 2019 Oct;20(10):590-607. (PMID: 31399642)
Nat Commun. 2021 Jul 23;12(1):4487. (PMID: 34301922)
Nat Genet. 2022 Jul;54(7):950-962. (PMID: 35710981)
Nat Genet. 2021 Jan;53(1):65-75. (PMID: 33398198)
Cancer Res. 2019 Feb 1;79(3):505-517. (PMID: 30559148)
Gynecol Oncol. 2019 May;153(2):343-355. (PMID: 30898391)
Science. 2020 Sep 11;369(6509):1318-1330. (PMID: 32913098)
Nucleic Acids Res. 2019 Jul 2;47(W1):W556-W560. (PMID: 31114875)
Int J Cancer. 2024 Mar 1;154(5):807-815. (PMID: 37846649)
Nat Protoc. 2012 Feb 16;7(3):500-7. (PMID: 22343431)
J Natl Cancer Inst. 2015 Aug 29;107(11):. (PMID: 26319099)
Nat Genet. 2017 Jul;49(7):1126-1132. (PMID: 28604730)
Cell. 2018 Apr 5;173(2):400-416.e11. (PMID: 29625055)
Nature. 2018 Oct;562(7726):203-209. (PMID: 30305743)
Nat Genet. 2020 Nov;52(11):1239-1246. (PMID: 33020666)
Nat Genet. 2012 Dec;44(12):1330-5. (PMID: 23143601)
Nat Genet. 2021 Sep;53(9):1311-1321. (PMID: 34493871)
Am J Hum Genet. 2022 Dec 1;109(12):2185-2195. (PMID: 36356581)
Nat Commun. 2024 Jul 18;15(1):6071. (PMID: 39025880)
Nat Genet. 2019 Mar;51(3):568-576. (PMID: 30804563)
J Natl Cancer Inst. 2020 Mar 1;112(3):295-304. (PMID: 31143935)
Nat Commun. 2020 Aug 6;11(1):3905. (PMID: 32764609)
Nat Genet. 2015 Sep;47(9):1091-8. (PMID: 26258848)
Bioinformatics. 2017 Feb 15;33(4):558-560. (PMID: 28035024)
Genome Biol. 2021 Jan 26;22(1):49. (PMID: 33499903)
Nat Genet. 2023 Dec;55(12):2065-2074. (PMID: 37945903)
Bioinformatics. 2017 Dec 15;33(24):3982-3984. (PMID: 28961746)
Genome Biol. 2022 Oct 11;23(1):210. (PMID: 36221136)
Nucleic Acids Res. 2023 Jan 6;51(D1):D1179-D1187. (PMID: 36243959)
Nat Commun. 2017 Jun 09;8:15724. (PMID: 28598434)
معلومات مُعتمدة: R01 CA247987 United States CA NCI NIH HHS; R01CA247987 U.S. Department of Health & Human Services | National Institutes of Health (NIH); R01CA249863 U.S. Department of Health & Human Services | National Institutes of Health (NIH); R00CA248822 U.S. Department of Health & Human Services | National Institutes of Health (NIH); R01 CA249863 United States CA NCI NIH HHS; R00 CA248822 United States CA NCI NIH HHS
المشرفين على المادة: 0 (Biomarkers, Tumor)
SCR Disease Name: Testicular Germ Cell Tumor
تواريخ الأحداث: Date Created: 20240718 Date Completed: 20240718 Latest Revision: 20240721
رمز التحديث: 20240721
مُعرف محوري في PubMed: PMC11258330
DOI: 10.1038/s41467-024-50404-y
PMID: 39025880
قاعدة البيانات: MEDLINE
الوصف
تدمد:2041-1723
DOI:10.1038/s41467-024-50404-y