Assessment of Histone Tail Modifications and Transcriptional Profiling during Colon Cancer Progression: Effect of Chemoprotective Natural Compounds

During colon cancer development, epigenetic alterations contribute to the dysregulation of major cellular functions and signaling pathways. Recent evidence suggests that nutritionally chemoprotective components that influence cellular dynamics in the colonic epithelium can also directly affect their epigenetic landscape. We hypothesize that the chemoprotective nutritional bioactives found in fish oil and fermentable fiber can act as epigenetic modifiers and mechanistically counteract epigenetic distortions associated with colonic tumorigenesis. Fermentable fiber generates short-chain fatty acids (SCFA), e.g., butyrate, in the lumen of the colon that can serve as a chemoprotective histone deacetylase inhibitor and/or as an acetylation substrate for histone acetylases. In addition, n-3 polyunsaturated fatty acids (n-3 PUFAs) in fish oil can affect the chromatin landscape by acting as ligands for tumor suppressive nuclear receptors. In an effort to gain insight into the extensive dimension of post-translational modifications in histones (including H3K4me3 and H3K9ac) and elucidate the chemoprotective impact of dietary bioactive compounds on transcriptional control in a colon cancer preclinical model, we generated high-resolution genome-wide RNA (RNA-Seq) and “chromatin-state” (H3K4me3-seq and H3K9ac-seq) maps for intestinal (epithelial colonocytes) crypts in rats treated with a colon carcinogen and fed bioactive (i) fish oil (ii) butyrate (in the form of a fermentable fiber a rich source of SCFA), (iii) a combination of fish oil plus butyrate or (iv) control diets. Poor correlation was observed between differentially transcribed (DE) and enriched genes (DERs) at multiple epigenetic levels in fat x fiber dietary combinations and in the presence/absence of carcinogen. The genome-wide carcinogen (AOM) effects were most prevalent at the RNA (116 DE genes) and K4me3 (7678 DERs including 3792 genes) levels. Pathway analysis of the differentially transcribed genes after AOM exposure indicated a strong link to interferon-associated innate immune responses often associated with anti-microbial activity, while K4me3 DERs were strongly linked to colon tumorigenesis. However, these changes in K4me3 enrichment were not reflected at the transcriptional level during the early stages of cancer progression. Therefore, we propose that carcinogen-induced changes in genes with K4me3 DERs are harbingers of future transcriptional events, which drive malignant transformation of the colon cells. We also demonstrated that the combinatorial diet (fish oil + pectin) was synergistically chemoprotective, and uniquely affected epigenetic profiles in the intestinal epithelium, e.g., upregulating lipid catabolism and beta-oxidation associated genes. These genes were linked to activated ligand-dependent nuclear receptors associated with n-3 PUFAs and were also correlated with the inhibition of lipogenesis and a decreased concentration of cholesterol. Interestingly, only a subset of these genes was affected in animals fed fish oil without pectin, and there was a markedly enhanced effect of biological mechanisms associated with n-3 PUFAs in the combinatorial diet. In conclusion, we propose that the chemoprotective effects of the bioactive mediators of the combination fish oil + pectin diet during colon cancer progression are multifaceted and generate specific epigenetic modifications and transcriptional profiles. Our data contribute to the understanding of the regulatory action of chemoprotective bioactive compounds found in fish oil and readily fermentable fiber (n-3 PUFAs and SCFAs) in colonic crypts and provide mechanistic insight into current clinical and epidemiological findings