Discovery and validation of pan cancer epigenetic biomarkers

2019 Fiscal Year Annual Research Report

• Project/Area Number: 17K18366
• Research Institution: Institute of Physical and Chemical Research
• Principal Investigator: カチコフスキー ボグミル 国立研究開発法人理化学研究所, 生命医科学研究センター, 研究員 (50648136)
• Project Period (FY): 2017-04-01 – 2020-03-31
• Keywords: cancer / genome / epi-genome / transcriptome

Outline of Annual Research Achievements

First, we performed integrative analyses of gene expression and DNA methylation in lung cancer cell lines and clinical tumors. We observed that multiple copies of the REP522 DNA repeat family are epigenetically activated in lung cancer by DNA hypomethylation and histone modification typical to active promoters. The activated REP522 repeat elements act as bi-directional promoters for cancer-specific lncRNAs, e.g. RP1-90G24.10, AL022344.4, and PCAT7 (Horie, M., Kaczkowski, B.*, et al., Molecular Cancer Research 2017, *co-corresponding author). In the second step, I performed the pan-cancer analyses using RNA-Seq data from 21 tumor types profiled by The Cancer Genome Atlas (TCGA) and found that activation of REP522 promoters occurs at varying frequency across 21 cancer types (Kaczkowski B.*, et. al. 2018, Poster at Human Genomics meeting 2018, 12(Suppl 1):9).
To further elucidate the impact of hypomethylation on gene expression, we performed a series of epigenetic perturbations in normal epithelial cells (MCF10A). We tested 4 conditions, where the cells were treated with: 1) DAC (DNA demethylating agent), 2) TSA (Histone Deacetylase inhibitor), 3) DAC and TSA combination, and 4) DMSO control. The cells were then profiled by CAGE 5’start RNA sequencing and DNA methylation array that covers ~830 thousand methylation sites across the genome. Additionally, in FY2019, we performed single-cell gene expression profiling using the single-cell implementation of CAGE (C1-CAGE). The generated data allows us to study how aberrations of the epigenome affect the gene expression.