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Epigenomics and Mechanisms Branch (EGM)

Publications

KEY RECENT PUBLICATIONS


  1. Talukdar FR, Soares Lima SC, Khoueiry R, Laskar RS, Cuenin C, Sorroche BP, et al. (2021). Genome-wide DNA methylation profiling of esophageal squamous cell carcinoma from global high-incidence regions identifies crucial genes and potential cancer markers. Cancer Res. canres.3445.2020. https://doi.org/10.1158/0008-5472.CAN-20-3445 PMID:33741694
  2. Halaburkova A, Cahais V, Novoloaca A, Araujo MGDS, Khoueiry R, Ghantous A, et al. (2020). Pan-cancer multi-omics analysis and orthogonal experimental assessment of epigenetic driver genes. Genome Res. 30(10):1517–32. https://doi.org/10.1101/gr.268292.120 PMID:32963031
  3. Pashayan N, Antoniou AC, Ivanus U, Esserman LJ, Easton DF, French D, et al. (2020). Publisher correction: Personalized early detection and prevention of breast cancer: ENVISION consensus statement. Nat Rev Clin Oncol. 17(11):716. https://doi.org/10.1038/s41571-020-0412-0 PMID:32601456
  4. Melki PN, Korenjak M, Zavadil J (2020). Experimental investigations of carcinogen-induced mutation spectra: innovation, challenges and future directions. Mutat Res. 853:503195. https://doi.org/10.1016/j.mrgentox.2020.503195 PMID:32522347
  5. Karabegović I, Portilla-Fernandez E, Li Y, Ma J, Maas SCE, Sun D, et al. (2021). Epigenome-wide association meta-analysis of DNA methylation with coffee and tea consumption. Nat Commun. https://doi.org/10.1038/s41467-021-22752-6 PMID:33990564
  6. Zhivagui M, Ng AWT, Ardin M, Churchwell MI, Pandey M, Renard C, et al. (2019). Experimental and pan-cancer genome analyses reveal widespread contribution of acrylamide exposure to carcinogenesis in humans. Genome Res. 29(4):521–31. https://doi.org/10.1101/gr.242453.118 PMID:30846532
  7. Chung FF, Herceg Z (2020). The promises and challenges of toxico-epigenomics: environmental chemicals and their impacts on the epigenome. Environ Health Perspect. 128(1):15001. https://doi.org/10.1289/EHP6104 PMID:31950866
  8. Küpers LK, Monnereau C, Sharp GC, Yousefi P, Salas LA, Ghantous A, et al. (2019). Meta-analysis of epigenome-wide association studies in neonates reveals widespread differential DNA methylation associated with birthweight. Nat Commun. 10(1):1893. https://doi.org/10.1038/s41467-019-09671-3 PMID:31015461
  9. Huang MN, Yu W, Teoh WW, Ardin M, Jusakul A, Ng AWT, et al. (2017). Genome-scale mutational signatures of aflatoxin in cells, mice, and human tumors. Genome Res. 27(9):1475–86. https://doi.org/10.1101/gr.220038.116 PMID:28739859
  10. Patil V, Cuenin C, Chung F, Aguilera JRR, Fernandez-Jimenez N, Romero-Garmendia I, et al. (2019). Human mitochondrial DNA is extensively methylated in a non-CpG context. Nucleic Acids Res. 47(19):10072–85. https://doi.org/10.1093/nar/gkz762 PMID:31665742
  11. Woo HD, Fernandez-Jimenez N, Ghantous A, Degli Esposti D, Cuenin C, Cahais V, et al. (2018). Genome-wide profiling of normal gastric mucosa identifies Helicobacter pylori– and cancer-associated DNA methylome changes. Int J Cancer. 143(3):597–609. https://doi.org/10.1002/ijc.31381 PMID:29574700
  12. Herceg Z, Ghantous A, Wild CP, Sklias A, Casati L, Duthie SJ, et al. (2018). Roadmap for investigating epigenome deregulation and environmental origins of cancer. Int J Cancer. 142(5):874–82. https://doi.org/10.1002/ijc.31014 PMID:28836271
  13. Huskova H, Ardin M, Weninger A, Vargova K, Barrin S, Villar S, et al. (2017). Modeling cancer driver events in vitro using barrier bypass-clonal expansion assays and massively parallel sequencing. Oncogene. 36(43):6041–8. https://doi.org/10.1038/onc.2017.215 PMID:28692054
  14. Degli Esposti D, Sklias A, Lima SC, Beghelli-de la Forest Divonne S, Cahais V, Fernandez-Jimenez N, et al. (2017). Unique DNA methylation signature in HPV-positive head and neck squamous cell carcinomas. Genome Med. 9(1):33. https://doi.org/10.1186/s13073-017-0419-z PMID:28381277
  15. Hollstein M, Alexandrov LB, Wild CP, Ardin M, Zavadil J (2017). Base changes in tumour DNA have the power to reveal the causes and evolution of cancer. Oncogene. 36(2):158–67. https://doi.org/10.1038/onc.2016.192 PMID:27270430
  16. Joubert BR, Felix JF, Yousefi P, Bakulski KM, Just AC, Breton C, et al. (2016). DNA methylation in newborns and maternal smoking in pregnancy: genome-wide consortium meta-analysis. Am J Hum Genet. 98(4):680–96. https://doi.org/10.1016/j.ajhg.2016.02.019 PMID:27040690
  17. Ambatipudi S, Cuenin C, Hernandez-Vargas H, Ghantous A, Le Calvez-Kelm F, Kaaks R, et al. (2016). Tobacco smoking-associated genome-wide DNA methylation changes in the EPIC study. Epigenomics. 8(5):599–618. https://doi.org/10.2217/epi-2016-0001 PMID:26864933
  18. Ardin M, Cahais V, Castells X, Bouaoun L, Byrnes G, Herceg Z, et al. (2016). MutSpec: a Galaxy toolbox for streamlined analyses of somatic mutation spectra in human and mouse cancer genomes. BMC Bioinformatics. 17(1):170. https://doi.org/10.1186/s12859-016-1011-z PMID:27091472
  19. Castells X, Karanović S, Ardin M, Tomić K, Xylinas E, Durand G, et al. (2015). Low-coverage exome sequencing screen in formalin-fixed paraffin-embedded tumors reveals evidence of exposure to carcinogenic aristolochic acid. Cancer Epidemiol Biomarkers Prev. 24(12):1873–81. https://doi.org/10.1158/1055-9965.EPI-15-0553 PMID:26383547
  20. Jelaković B, Castells X, Tomić K, Ardin M, Karanović S, Zavadil J (2015). Renal cell carcinomas of chronic kidney disease patients harbor the mutational signature of carcinogenic aristolochic acid. Int J Cancer. 136(12):2967–72. https://doi.org/10.1002/ijc.29338 PMID:25403517

 

Epigenomics and Mechanisms
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