Human Colon Mucosal Biofilms and Murine Host Communicate via Altered mRNA and microRNA Expression during Cancer

Abstract

Disrupted interactions between host and intestinal bacteria are implicated in colorectal cancer (CRC) development. However, activities derived from these bacteria and their interplay with the host are unclear. Here, we examine this interplay by performing mouse and microbiota RNA sequencing on colon tissues and 16S and small RNA sequencing on stools from germfree (GF) and gnotobiotic ApcMinΔ850/+;Il10−/− mice associated with microbes from biofilm-positive human CRC tumor (BF+T) and biofilm-negative healthy (BF-bx) tissues. The bacteria in BF+T mice differentially expressed (DE) >2,900 genes, including genes related to bacterial secretion, virulence, and biofilms but affected only 62 host genes. Small RNA sequencing of stools from these cohorts revealed eight significant DE host microRNAs (miRNAs) based on biofilm status and several miRNAs that correlated with bacterial taxon abundances. Additionally, computational predictions suggest that some miRNAs preferentially target bacterial genes while others primarily target mouse genes. 16S rRNA sequencing of mice that were reassociated with mucosa-associated communities from the initial association revealed a set of 13 bacterial genera associated with cancer that were maintained regardless of whether the reassociation inoculums were initially obtained from murine proximal or distal colon tissues. Our findings suggest that complex interactions within bacterial communities affect host-derived miRNA, bacterial composition, and CRC development. IMPORTANCE Bacteria and bacterial biofilms have been implicated in colorectal cancer (CRC), but it is still unclear what genes these microbial communities express and how they influence the host. MicroRNAs regulate host gene expression and have been explored as potential biomarkers for CRC. An emerging area of research is the ability of microRNAs to impact growth and gene expression of members of the intestinal microbiota. This study examined the bacteria and bacterial transcriptome associated with microbes derived from biofilm-positive human cancers that promoted tumorigenesis in a murine model of CRC. The murine response to different microbial communities (derived from CRC patients or healthy people) was evaluated through RNA and microRNA sequencing. We identified a complex interplay between biofilm-associated bacteria and the host during CRC in mice. These findings may lead to the development of new biomarkers and therapeutics for identifying and treating biofilm-associated CRCs.

MicroRNAs Regulate Intestinal Immunity and Gut Microbiota for Gastrointestinal Health: A Comprehensive Review

“…Moreover, in a study based on the DSS-induced colitis mice model, miR-21 was mentioned as a factor for the pathogenicity of intestinal inflammatory diseases and colitis-associated colorectal cancer, primarily through stimulating IL-10 and prostaglandin E2, which further inhibit anti-tumor adaptive immunity [ 102 ]. While Fusobacterium nucleatum can significantly up-regulate the expression of miR-21 through TLR4/MYD88/NF-κB pathway and facilitate the progression of colitis-associated colorectal cancer [ 102 ], in CRC patients on the other side, intestinal microbiota can also influence the host gene expression of intestinal microRNAs, which contributes to protecting intestinal homeostasis and attenuating gut inflammation [ 103 , 104 ]. For example, two probiotic strains, Lactobacillus fermentum and Lactobacillus salivarius , can restore the down-regulated expressions of miR-155 and miR-223, which ameliorate microbiota dysbiosis, preserve the function of the mucosal barrier, and relieve the DSS-induced colitis in mice model [ 105 ].…”

Fecal microRNAs as Innovative Biomarkers of Intestinal Diseases and Effective Players in Host-Microbiome Interactions

“…Very recently Tomkovich and colleagues were able to unveil a complex interaction among tumorigenic bacterial community, deregulated host-derived miRNAs and CRC development. Germ-free Apc MinΔ850/+ ;Il10 -/- mice, representing a model for CRC, were transplanted with tumorigenic bacterial community isolated from biofilm-positive and –negative tissues from human CRC tumor and healthy mucosa, respectively, being biofilms a condition associated with adenomatous lesions and CRC progression [ 88 , 149 , 150 ]. By miRNA sequencing on stools, they found deregulated fecal miRNAs in Apc MinΔ850/+ ; Il10 -/- mice associated with tumorigenic bacterial community compared to mice associated with non-tumorigenic bacteria, as expected.…”

“…By miRNA sequencing on stools, they found deregulated fecal miRNAs in Apc MinΔ850/+ ; Il10 -/- mice associated with tumorigenic bacterial community compared to mice associated with non-tumorigenic bacteria, as expected. Moreover, the human homologous miRNAs (hsa-miR-21-5p, hsa-miR-142-5p, and hsa-miR- 146a-5p) were shown to be increased in CRC patients highlighting the impact of tumorigenic bacteria on host-derived miRNAs [ 150 ]. Interestingly, differentially regulated miRNAs (miR-2137, miR-5126, miR-6239, miR-6240 and miR-6538) were predicted to target bacterial genes, including genes regulating motility, secretion, outer membrane proteins, stress response, iron acquisition and carbohydrate utilization/transport.…”

“…Interestingly, differentially regulated miRNAs (miR-2137, miR-5126, miR-6239, miR-6240 and miR-6538) were predicted to target bacterial genes, including genes regulating motility, secretion, outer membrane proteins, stress response, iron acquisition and carbohydrate utilization/transport. Furthermore, they observed that several genes belonging to these functional categories were upregulated in Apc MinΔ850/+ ; Il10 -/- mice associated with tumorigenic bacterial community [ 150 ].…”

Does the Gut Microbiota Modulate Host Physiology through Polymicrobial Biofilms?

“…The same group also discovered that biofilm communities on the colon epithelium prepared from CRC patients and even healthy individuals were carcinogenic in murine CRC models ( Tomkovich et al , 2019 ). Moreover, biofilm-forming bacteria from CRC patients interacted with the host and altered host microRNA expression during the development of CRC in murine CRC models ( Tomkovich et al , 2020 ). One species of Fusobacterium , Fusobacterium nucleatum , is frequently detected in liver metastases of Fusobacterium -associated CRC ( Bullman et al , 2017 ).…”