Chemical perturbations impacting histone acetylation regulate colorectal cancer differentiation

Histone acetylation governs broad gene expression programs in normal tissue and disease states. By applying a small chemical compound library targeting epigenetic regulators to a dual endogenous reporter system, we found that inhibiting histone deacetylase (HDAC) 1/2 initiates colorectal cancer (CRC) differentiation. Inhibiting the enzymatic pocket of HDAC1/2 induced differentiation and reduced proliferation across in vitro and in vivo models. On-target HDAC1/2 inhibition was validated using biochemical, chemical, and genetic approaches. A survey of histone posttranslational modifications from HDAC1/2 selective inhibition nominated acetylation of specific H3 and H4 lysine (K) residues as potential regulators of differentiation. Genome-wide profiles of these histone acetylation marks indicated that gains in histone 3 lysine 27 acetylation (H3K27ac) most strongly correlated to opening of chromatin and upregulation of genes associated with differentiation upon HDAC1/2 inhibition. Blocking acetylation of H3K27 by degrading its writer EP300 rescued the differentiation phenotype induced by HDAC1/2 inhibition in a patient-derived CRC model by single cell RNA-sequencing among other readouts. These results highlight the importance of specific chemically targetable histone modifications in governing cancer cell states and implicate precision targeting of H3K27ac as a potential therapeutic approach for CRC. To define the mechanism(s) by which MRK60 promotes CRC differentiation, we started with the analysis of gene expression profiles from CRC cells treated with MRK60.