BRAFV600E mutation impinges on gut microbial markers defining novel biomarkers for serrated colorectal cancer effective therapies

Abstract

Background Colorectal cancer (CRC) harboring BRAFV600E mutation exhibits low response to conventional therapy and poorest prognosis. Due to the emerging correlation between gut microbiota and CRC carcinogenesis, we investigated in serrated BRAFV600E cases the existence of a peculiar fecal microbial fingerprint and specific bacterial markers, which might represent a tool for the development of more effective clinical strategies. Methods By injecting human CRC stem-like cells isolated from BRAFV600E patients in immunocompromised mice, we described a new xenogeneic model of this subtype of CRC. By performing bacterial 16S rRNA sequencing, the fecal microbiota profile was then investigated either in CRC-carrying mice or in a cohort of human CRC subjects. The microbial communities’ functional profile was also predicted. Data were compared with Mann-Whitney U, Welch’s t-test for unequal variances and Kruskal-Wallis test with Benjamini–Hochberg false discovery rate (FDR) correction, extracted as potential BRAF class biomarkers and selected as model features. The obtained mean test prediction scores were subjected to Receiver Operating characteristic (ROC) analysis. To discriminate the BRAF status, a Random Forest classifier (RF) was employed. Results A specific microbial signature distinctive for BRAF status emerged, being the BRAF-mutated cases closer to healthy controls than BRAF wild-type counterpart. In agreement, a considerable score of correlation was also pointed out between bacteria abundance from BRAF-mutated cases and the level of markers distinctive of BRAFV600E pathway, including those involved in inflammation, innate immune response and epithelial-mesenchymal transition. We provide evidence that two candidate bacterial markers, Prevotella enoeca and Ruthenibacterium lactatiformans, more abundant in BRAFV600E and BRAF wild-type subjects respectively, emerged as single factors with the best performance in distinguishing BRAF status (AUROC = 0.72 and 0.74, respectively, 95% confidence interval). Furthermore, the combination of the 10 differentially represented microorganisms between the two groups improved performance in discriminating serrated CRC driven by BRAF mutation from BRAF wild-type CRC cases (AUROC = 0.85, 95% confidence interval, 0.69–1.01). Conclusion Overall, our results suggest that BRAFV600E mutation itself drives a distinctive gut microbiota signature and provide predictive CRC-associated bacterial biomarkers able to discriminate BRAF status in CRC patients and, thus, useful to devise non-invasive patient-selective diagnostic strategies and patient-tailored optimized therapies.

Gut microbiome: New biomarkers in early screening of colorectal cancer

“… 19 In addition, two studies indicated that the fecal microbiome has the potential to predict the presence of mutations in BRAF and KRAS genes, the latter being closely associated with targeted therapies. 20 , 21 The above studies suggest that the fecal microbiome may potentially identify high‐risk groups carrying mutations in CRC‐related genes, providing a reference for the selection of the optimal treatment for CRC patients.…”

Alterations in the Gut Microbiota and Their Metabolites in Colorectal Cancer: Recent Progress and Future Prospects

“…BRAF mutation is linked to DNA methylation in serrated polyps and CRC. A previous study has discovered that the BRAFV600E mutation causes a unique gut microbiome signature (Prevotella enoeca and Ruthenibacterium lactatiformans) (48). And, Fusobacterium nucleatum positive was significantly related to MSI-high status and CIMP (49).…”

The gut microbiome and melanoma: A review

“…23 A study by Trivieri et al has found that BRAF-mutated colorectal cancer cases harbouring the V600E mutation have a distinct microbiota profile, implicating the presence of a bidirectional tumor-microbiotatumor relationship. 24 The authors suggest that the mutation itself drives a distinct gut microbiota blueprint and this can be used as a novel biomarker for patient-tailored diagnostic strategies and therapies. 24 Despite research taking a promising direction with regards to colorectal cancer, this has not yet been replicated in melanoma patients and as a result a potential link between gut microbiota and BRAF mutations has not yet been exploited.…”

“…A study by Trivieri et al has found that BRAF‐mutated colorectal cancer cases harbouring the V600E mutation have a distinct microbiota profile, implicating the presence of a bidirectional tumor‐microbiota‐tumor relationship 24 . The authors suggest that the mutation itself drives a distinct gut microbiota blueprint and this can be used as a novel biomarker for patient‐tailored diagnostic strategies and therapies 24 …”