Multi-omic profiling reveals associations between the gut mucosal microbiome, the metabolome, and host DNA methylation associated gene expression in patients with colorectal cancer

Abstract

Background: The human gut microbiome plays a critical role in the carcinogenesis of colorectal cancer (CRC). However, a comprehensive analysis of the interaction between the host and microbiome is still lacking.

Results: We found correlations between the change in abundance of microbial taxa, butyrate-related colonic metabolites, and methylation-associated host gene expression in colonic tumour mucosa tissues compared with the adjacent normal mucosa tissues. The increase of genus Fusobacterium abundance was correlated with a decrease in the level of 4-hydroxybutyric acid (4-HB) and expression of immune-related peptidase inhibitor 16 (PI16), Fc Receptor Like A (FCRLA) and Lymphocyte Specific Protein 1 (LSP1). The decrease in the abundance of another potentially 4-HB-associated genus, Prevotella 2, was also found to be correlated with the down-regulated expression of metallothionein 1 M (MT1M). Additionally, the increase of glutamic acid-related family Halomonadaceae was correlated with the decreased expression of reelin (RELN). The decreased abundance of genus Paeniclostridium and genus Enterococcus were correlated with increased lactic acid level, and were also linked to the expression change of Phospholipase C Beta 1 (PLCB1) and Immunoglobulin Superfamily Member 9 (IGSF9) respectively. Interestingly, 4-HB, glutamic acid and lactic acid are all butyrate precursors, which may modify gene expression by epigenetic regulation such as DNA methylation.

Conclusions: Our study identified associations between previously reported CRC-related microbial taxa, butyrate-related metabolites and DNA methylation-associated gene expression in tumour and normal colonic mucosa tissues from CRC patients, which uncovered a possible mechanism of the role of microbiome in the carcinogenesis of CRC. In addition, these findings offer insight into potential new biomarkers, therapeutic and/or prevention strategies for CRC.

Background: Colorectal cancer (CRC) is the third most commonly diagnosed cancer and second leading cause of cancer death in both men and women globally, leading to an estimated 551,269 annual deaths worldwide [1]. Diet plays an important role in the initiation, promotion and progression of colon carcinogenesis [2]. Epidemiological surveys indicate that approximately 80% of CRC cases in Western countries are due to dietary factors [3].

The human intestine harbours a complex microbial community comprising more than 1014 microorganisms; it carries greater than 150 times the number of genes in the human genome [4]. Diet has been shown to have a dominant impact on the structure and composition of the gut microbiome, microbial generated metabolites and host metabolism [5, 6]. Many studies have demonstrated the effect of the gut microbiome on the pathogenesis of CRC, revealing potential pathogenic bacteria such as Fusobacterium as well as beneficial bacteria such as Lactobacillales [6,7,8].

Nevertheless, dietary factors have also been shown to induce epigenetic changes. The most extensively studied epigenetic mechanism is DNA methylation, which involves the transfer of methyl group to the cytosine of a CpG dinucleotide and is responsible for regulating the expression of genes related with critical pathological processes [9]. Carcinogenic gene silencing may occur due to aberrant gene-specific hypermethylation at the CpG rich region (CpG island) which is located in the promotors of the genes and interfere with transcription factor binding [10, 11].

One possible mechanism underlying the effects of diet and microbiome on CRC development is a potential interaction between the microbiome and the host, whereby the colonic metabolome is impacted, leading to a subsequent alteration in host epigenetic activity and host gene expression [12, 13]. Research on selected aspects of the microbiome, metabolome, host epigenome and host transcriptome have been carried out in human, animal and cell models [14]. For instance, the interaction between the microbiome and metabolome has been extensively studied, revealing various epigenome-modulation-related metabolites such as butyrate and folate [15, 16]. In addition, the contribution of commensal bacteria to epigenetic control in the host large intestine has been demonstrated by comparing conventional and germ-free mice [17]. Associations between the microbiome and differentially methylated genes have also been investigated in patients with ulcerative colitis [18]. The interplay between the microbiome, host transcripts related to adhesion molecules and fatty acid biosynthesis was strongly supported in one study of inflammatory bowel disease [19].

Despite the mounting evidence of a potential host-microbiome interaction, a comprehensive human study integrating all the aforementioned omics is still lacking. Thus, in this pilot study, we generated and analysed four types of omic data: the microbiome (16S rRNA sequencing; 36 pairs), the metabolome (untargeted GC/MS; 17 pairs), the host transcriptome (RNA-seq; 4 pairs) and the host epigenome (Infinium HumanMethylation850 BeadChip array; 4 pairs), as measured from paired tumour and adjacent normal colonic mucosa tissues samples obtained from CRC patients (details of the study design in Additional file 1: Figure S1).

Results: Comparison of microbial composition between tumour and adjacent normal tissues Non-metric multidimensional scaling (NMDS) analysis based on the unweighted UniFrac distance on operational taxonomic units (OTUs) revealed that the microbial community composition of the cancerous tissues could be clearly distinguished from the non-cancerous tissues, which was confirmed by analysis of similarities (Anosim) (p-value = 0.002; Fig. 1a).