AIM: To provide characteristics of major genomic correlates in CpG island methylator phenotype-high (CIMP-H) subgroups in relation to corresponding non-CIMP-H subgroups by use of phenotypic, DNA methylation and RNAseq data. MATERIALS & METHODS: Twenty-three datasets generated by The Cancer Genome Atlas project encompassing over 7200 unique samples were analyzed. We identified 23 CIMP-H clusters by use of unsupervised clustering. RESULTS & CONCLUSION: More than 90% of CIMP-H clusters were significantly associated with accelerated epigenetic mitotic clock, demethylation of enhancer sites, backbone and repetitive sequences. Pronounced epigenetic drift observed in majority of CIMP-H subgroups may be related to increased cell division rate, which leads to expansion of DNA methylation errors. This may explain pan-cancer mechanism of establishing CIMP-H in majority of tissue types.
AIM: To provide characteristics of major genomic correlates in CpG island methylator phenotype-high (CIMP-H) subgroups in relation to corresponding non-CIMP-H subgroups by use of phenotypic, DNA methylation and RNAseq data. MATERIALS & METHODS: Twenty-three datasets generated by The Cancer Genome Atlas project encompassing over 7200 unique samples were analyzed. We identified 23 CIMP-H clusters by use of unsupervised clustering. RESULTS & CONCLUSION: More than 90% of CIMP-H clusters were significantly associated with accelerated epigenetic mitotic clock, demethylation of enhancer sites, backbone and repetitive sequences. Pronounced epigenetic drift observed in majority of CIMP-H subgroups may be related to increased cell division rate, which leads to expansion of DNA methylation errors. This may explain pan-cancer mechanism of establishing CIMP-H in majority of tissue types.
Authors: Michael Scherer; Petr V Nazarov; Reka Toth; Shashwat Sahay; Tony Kaoma; Valentin Maurer; Nikita Vedeneev; Christoph Plass; Thomas Lengauer; Jörn Walter; Pavlo Lutsik Journal: Nat Protoc Date: 2020-09-25 Impact factor: 13.491
Authors: Huang Kie Kyon; Arnoud Boot; Nisha Padmanabhan; Kevin Lim; Supriya Srivastava; Shuwen Chen; Zhiyuan Wu; Hyung-Ok Lee; Vineeth T Mukundan; Charlene Chan; Yarn Kit Chan; Ong Xuewen; Jason J Pitt; Zul Fazreen Adam Isa; Manjie Xing; Ming Hui Lee; Angie Lay Keng Tan; Shamaine Ho Wei Ting; Micah A Luftig; Dennis Kappei; Warren D Kruger; Jinsong Bian; Ying Swan Ho; Ming Teh; Steve George Rozen; Patrick Tan Journal: Genome Biol Date: 2021-06-01 Impact factor: 13.583