Intestinal bacteria and colorectal cancer: etiology and treatment

Abstract

The etiology of colorectal cancer (CRC) is influenced by bacterial communities that colonize the gastrointestinal tract. These microorganisms derive essential nutrients from indigestible dietary or host-derived compounds and activate molecular signaling pathways necessary for normal tissue and immune function. Associative and mechanistic studies have identified bacterial species whose presence may increase CRC risk, including notable examples such as Fusobacterium nucleatum, Enterotoxigenic Bacteroides fragilis, and pks⁺ E. coli. In recent years this work has expanded in scope to include aspects of host mutational status, intra-tumoral microbial heterogeneity, transient infection, and the cumulative influence of multiple carcinogenic bacteria after sequential or co-colonization. In this review, we will provide an updated overview of how host-bacteria interactions influence CRC development, how this knowledge may be utilized to diagnose or prevent CRC, and how the gut microbiome influences CRC treatment efficacy.

Keywords: Colorectal cancer; genotoxin; immunotherapy; inflammation; microbiome; probiotics.

Figure 1.

Carcinogenic mechanisms of intestinal bacteria. a) pks⁺ Escherichia coli produce a genotoxin known as colibactin, that induces interstrand crosslinks in host cells resulting in a defined mutational signature detected in colorectal cancer (CRC) genomes. The right panel shows several microbial genotoxins with nonspecific DNA degrading activity, including the cytolethal distending toxin (CDT) found in the human enteric pathogen Campylobacter jejuni, UshA in the murine bacteria Citrobacter rodentium, and indolimines isolated from a commenstal strain of Morganella morganii obtained from patients with inflammatory bowel disease. b) Enterotoxigenic bacteroides fragilis (ETBF) secretes a toxin known as the bacteroides fragilis toxin (BFT), that degrades E-cadherin promoting nuclear translocation of β-Catenin and the activation of proliferative signaling pathways to promote tumor formation. Fusobacterium nucleatum produces a membrane-bound Fusobacterium adhesin A (FadA) protein that binds to E-cadherin to upregulate expression of the Annexin A1/β-Catenin complex to activate proliferative signaling pathways. AvrA is a virulence factor produced by Salmonella spp. promoting epithelial adherence and persistent colonization in the gastrointestinal tract, while simultaneously activating AKT serine/threonine kinase 1 (AKT)-mediated β-Catenin phosphorylation, facilitating nuclear translocation and the activation of signaling pathways to promote proliferation and cell survival. Peptostreptococcus anaerobius are selectively enriched in CRC tissue, facilitated in part by the binding of an outer membrane protein putative cell wall binding repeat 2 (PCWBR2) to α2/β1 integrins overexpressed in cancer cells. This interaction promotes phosphoinositide 3-kinase (P13K) and AKT phosphorylation to promote cell proliferation. c) A superoxide producing strain (OG1RF) of the human pathogen Enterococcus faecalis causes chromosomal instability after infection in cell lines and intestinal ligation models, resulting from the production of reactive oxygen species (ROS). Alternatively, OG1RF infected macrophages elicit similar effects in human cell lines. On the right, infection with ETBF upregulates expression of a spermine oxidase that generates ROS and DNA damage in colonic epithelial cells. d) F. nucleatum produces short-chain fatty acids (SCFA) that bind to Free Fatty Acid Receptor 2 (Ffar2) receptors on T helper 17 (Th17) macrophages or an undetermined intermediate dendritic cell to stimulate interleukin 17 (IL-17) production. The human pathogens Enterotoxigenic Bacteroides fragilis (ETBF) and Clostridioides difficile (C. difficile) secrete toxins (the Bacteroides fragilis toxin, BFT, and Clostridioides difficile toxin B, TcdB, respectively) that promote signal transducer and activator of transcription 3 (STAT3) phosphorylation and the recruitment of IL-17 producing Th17 cells. In both cases, these microbes promote IL-17 mediated inflammation that contributes to neoplastic transformation. e) ETBF infection promotes hypermethylation in Apc^Min/+BRAF^V600ELgr5^Cre mice, resulting in the formation of proximal tumors and activation of IFNγ gene signatures. F. nucleatum infection downregulates methyltransferase 3 (METTL3) expression in a Yes1 associated transcriptional regulator (YAP)-dependent manner to inhibit m⁶A RNA methylation, altering mRNA translation to promote cancer metastasis.

Figure 2.

Multi-omics microbiome-based diagnostic methods. Microbiome-based diagnostic models typically utilize three primary technologies derived from patient fecal samples: 1) 16s amplicon or metagenomic sequencing to determine microbial taxa, 2) Liquid chromatography-mass spectrometry (LC-MS) metabolomics/proteomics to identify microbially derived metabolites, and 3) High-performance liquid chromatography (HP-LC) profiling of amino stool amino acid profiles. A fourth and more recently proposed approach amplifies circulating microbial DNA from patient blood or plasma samples, followed by stringent computational filtering. In all methods, marker selection is conducted using machine learning models to identify discriminating markers correlating with tumor stage, and accuracy can be improved by integrating one or more of these datasets.

Figure 3.

Lactic acid bacteria inhibit colorectal cancer tumorigenesis. Colorectal cancer (CRC) is characterized by a reduction in lactic acid bacteria (LAB). In a murine model of adenomatous polyposis coli/tumor protein 53/Kirsten rat sarcoma viral oncogene homolog (APC/p53/KRAS) mutant CRC, host metabolites directly inhibit Lactobacillus reuteri (L. reuteri) growth and the production of the microbial metabolite reuterin, that inhibits protein translation and generates cytotoxic reactive oxygen species in CRC cells to restrict cell growth. Streptococcus thermophilus (S. thermophilus) secretes the enzyme β-Galactosidase that produces galactose, that inhibits oxidative phosphorylation and Warburg metabolism in CRC cells. Various LAB inhibit tumor growth through a variety of indeterminate mechanisms, and the CRC-associated depletion of these species can be offset by increased abundance of galactose, dietary fibers, or the presence of other probiotic species. Finally, LAB may ferment dietary components such as Cudrania triscuspidata (C. tricuspidata) to produce antioxidants that restrict tumor growth.

Figure 4.

The impact of intestinal bacteria on colorectal cancer treatment. a) In mice harboring a commensal microbiota, neutrophils and macrophages invade tumors and produce reactive oxygen species (ROS), enhancing the tumor-killing effect of oxaliplatin. In mice administered antibiotics, the number of infiltrating immune cells and ROS-mediated cytotoxicity is reduced. In the presence of commensal bacteria (such as Escherichia coli Nissle 1917) harboring the long form of a cytidine deaminse (CDD_L), gemcitabine levels are reduced after degradation by this bacterial enzyme, resulting in a reduced therapeutic response. Similarly, infection with Fusobacterium nucleatum confers resistance to oxaliplatin and 5-Fu by downregulating miRNAs that suppress autophagy and survival signaling. b) Several bacterial species have been linked to enhanced immunotherapy response in murine models of CRC or MC-38 xenografts. The species Bifidobacterium longum produces a metabolite inosine, which activates tumor-infiltrating T cells and exacerbates tumor killing after anti-CTLA4 treatment. Enterococcus spp. harboring the secreted antigen A (sagA) gene generate high levels of muramyl dipeptide (MDP) that activates nucleotide-binding oligomerization domain-containing protein 2 (NOD2) signaling pathways in colonic epithelial cells that drives immune recruitment and synergizes with anti-CTLA4 treatment. In a murine model of CpG island methylator phenotype (CIMP) CRC, infection with Enterotoxigenic Bacteroides fragilis promotes the recruitment of interferon gamma (IFNγ)-producing CD8⁺ T cells to enhance anti-PD-1 efficacy. Lactobacillus delbrueckii subsp. bulgaricus exopolysaccharides (EPS-R1) promote the activation of CCR6⁺CD8⁺ T cells in intestinal Peyer’s patches, as well as the number of IFNγ producing CD8⁺ tumor infiltrating cells, promoting the efficacy of anti-PD-1 and anti-CTLA4 treatment. Conversely, pks⁺ E. coli can migrate to mesenteric lymph nodes (MLN) and reduce systemic levels of CD3⁺ and CD8⁺ T cells, as well as the number of these cells observed in invasive tumor margins and reduces anti-PD-1 treatment efficacy.