An intergrative genomic pipeline to target the NCOR1 cistrome with precision
Van Den Berg, Patrick Robert
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In an effort to completely annotate the human epigenome, the Encyclopedia of DNA Elements (ENCODE) has generated thousands of epigenomic datasets in hundreds of different cell lines. These datasets are freely available for one's own analysis, but integration of multiple datasets often poses a problem. We are interested in Nuclear Receptor Corepressor 1 (NCOR1), a gene that forms complexes in the order of mega Dalton with repressive proteins like Histone Deacetylase 3 (HDAC3). We constructed a pipeline in R which integrates NCOR1 ChIP-seq, FAIRE-seq, H3K9Me3 ChIP-seq, methyl-seq and RNA-seq datasets from ENCODE from the Chronic Myelogenous Leukemia (CML) cell line K562. We identified 1899 genes that have proximal NCOR1 binding, which we have summated as the NCOR1 cistrome, and 44 NCOR1 sub-cistromes depending on the epigenetic context. Integration of the NCOR1 cistrome with gene expression data revealed that NCOR1 is positively associated with highly expressed genes, but a poor predictor of its expression. Part of the bioinformatics pipeline utilizes publicly available drug sensitivity data to discover drugs potentially reliant on NCOR1 activity. This method was adapted from the CellMiner tool which is based on the NCI-60 drug database. From this analysis we identified three clinically utilized tyrosine kinase inhibitors (TKIs), imatinib, nilotinib and dasatinib, to be potentially amenable by NCOR1 modulation. These TKIs target the BCR-ABL fusion gene and have made a big impact on CML survival rates in the past decade, but because in some cases the CML becomes resistant to treatment the complete effect of TKIs are of high interest. Using GEO data sets we confirmed that NCOR1 is also bound to genes that are differentially expressed by TKI treatment. We made a K562 NCOR1 shRNA knockdown cell line to investigate NCOR1's role in TKI biology in vitro. Initial results show that NCOR1 knockdown alters the sensitivity of the three TKIs in K562 and the drug induced erythroid differentiation. The data we generated suggest that targeting NCOR1 together with BCR-ABL could have an additive effect and could be beneficial to CML therapy.