For some time, researchers around the world have been investigating the importance of the gut microbiome - the collection of bacteria, viruses, and fungi in our body - and its role in cancer.
In a recent publication in Nature, a team of researchers at Fred Hutch reported that a specific subtype of Fusobacterium nucleatum (Fn), a bacterium commonly found in the mouth, has the genetic potential to travel to the gut and grow within colorectal cancer (CRC) tumors.
“The enrichment of Fusobacterium nucleatum, a bacterium typically found in the human oral cavity, with colorectal tumors, was discovered over a decade ago,” said Dr. Martha Zepeda Rivera, a staff scientist at Fred Hutch and the lead author of the study. “Since then, this association has been reproduced in studies around the globe.” While Fn has been identified as an emerging cancer-associated bacterium, its subtypes contributing to CRC have not yet been identified. “It was unknown whether all F. nucleatum subtypes present in the mouth contribute to colorectal cancer (CRC),” Zepeda Rivera added.
Fn is rarely detected in the lower gastrointestinal tract (GI) of healthy individuals, and yet it is enriched in CRC tumors. This indicates that Fn must travel from the oral cavity to the lower GI tract and find its home within CRC tumors. Now, you may be asking, which Fn subtypes are present in CRC tumors? Zepeda Rivera and colleagues isolated and sequenced Fn strains isolated from patient CRC tumor tissue and Fn strains isolated from the oral cavity of healthy individuals as a control group. They found that the Fn subspecies animalis (Fna) is enriched in the CRC tumors. Zepeda Rivera and colleagues investigated even deeper to identify the subtypes -clades- of Fn within the Fnasubspecies. Two clades were found: Fna clade 1 (Fna C1) and Fna clade 2 (Fna C2). However, only Fna C2 was enriched in CRC tumors compared with Fna C1. "Although both Fna clades are present in the oral cavity with non-significant differences, only Fna C2 is significantly associated with the CRC niche,” the authors stated. “Our work parsed the considerable genomic and physiological diversity within the F. nucleatum species and identified the particular clade, which we call Fna C2, that is enriched in CRC tumors. This is important because it allows the field to focus on this highly virulent subtype for mechanistic studies to inform diagnostic and therapeutic efforts,” Zepeda Rivera commented.
Once Fna C2 was found enriched in the CRC tumors, Zepeda Rivera aimed to understand what was so special about this clade that allows it to colonize the CRC tumors compared to the other clades. Different analyses revealed genetic differences between Fna C1 and Fna C2. For example, factors required for cell invasion were present in Fna C2 but not in Fna C1. Moreover, “Fna C1 and Fna C2 had similar core genome sizes, although Fna C2 had a larger accessory genome, suggesting that Fna C2 strains harbor additional genetic factors that may be beneficial during colonization of CRC tumors.” Additional analysis of the Fna C2 accessory genes showed differences in metabolic potential. These findings showed that “the pathoadaptation of Fna C2 to the CRC niche is multifactorial, and in addition to canonical Fnvirulence factors is potentially facilitated by enhanced metabolic capabilities.” To test if metabolic processes are important for Fna C2 enrichment in CRC, Zepeda Rivera focused on Fna C2 genes involved in ethanolamine and 1,2-propanediol metabolism which are absent in Fna C1. RNA sequencing analysis revealed that exposure to these metabolites - ethanolamine and 1,2-propanediol- induced expression of these utilization operons and importantly upregulated the expression of virulent factors required for colonization of Fna C2.
The enhanced metabolic potential of Fna C2 as compared to Fna C1 were validated in a CRC mouse model. Metabolite analysis of the intestinal tissue revealed that metabolites involved in oxidative stress, inflammation, and tumor progression were enriched in Fna C2-treated mice, compared to both Fna C1-treated and control mice. These results demonstrated the “ability of Fna C2, but not Fna C1, to metabolically affect the intestinal milieu towards pro-oncogenic conditions.” In line with these observations, the number of intestinal adenomas was higher in mice that received Fna C2 compared with Fna C1 or control. In comparison, the Fna C1 intestinal metabolite profile overlapped with control, and no significant differences were observed in the number of intestinal adenomas between Fna C1-treated or control mice.
Lastly, Zepeda Rivera validated the enrichment of Fna C2 in human CRC cohorts. Once again, it was found that only Fna C2 was highly expressed in CRC tumor tissue as compared with normal adjacent tissue. Overall, Zepeda Rivera’s work demonstrated “the increased virulence and tumorigenic potential of Fna C2 compared to Fna C1.” In addition, these findings suggest that targeting Fna C2 could be a potential strategy for CRC diagnosis and treatment.
Now, Zepeda Rivera is working on “further characterizing Fna C2 to increase our understanding of how it travels from the oral cavity to tumor tissues, and whether this subgroup is also dominant in other cancer types associated with F. nucleatum presence.” So, stay tuned!
The spotlighted research was funded by the National Institute of Dental and Craniofacial Research of the National Institutes of Health, the National Cancer Institute, the W.M. Keck Research Foundation, the Washington Research Foundation Postdoctoral Fellowship, and the Bio & Medical Technology Development Program of the National Research Foundation funded by the Korean government.
Fred Hutch/University of Washington/Seattle Children's Cancer Consortium members Drs. Chris Johnston and Susan Bullman contributed to this work.
Zepeda-Rivera M, Minot SS, Bouzek H, Wu H, Blanco-Míguez A, Manghi P, Jones DS, LaCourse KD, Wu Y, McMahon EF, Park SN, Lim YK, Kempchinsky AG, Willis AD, Cotton SL, Yost SC, Sicinska E, Kook JK, Dewhirst FE, Segata N, Bullman S, Johnston CD. A distinct Fusobacterium nucleatum clade dominates the colorectal cancer niche. Nature. 2024.