Sequencing of the 16S rRNA gene of the gut microbiota in mice treated with a high fibre diet as a potential endogenous mechanism of radiosensitisation

Thesis

New non-toxic radiosensitisers are needed in the treatment of muscle-invasive bladder cancer because elderly patients are very vulnerable to chemotherapy-related toxicity of currently available radiosensitisers. Histone deacetylase (HDAC) inhibition is a promising mechanism of radiosensitisation. Tumour cells can accumulate butyrate which is produced by the gut microbiota via fibre fermentation to sufficient levels to cause HDAC inhibition, due to the Warburg effect. This has been seen when mice were treated with high-fibre diets. I hypothesise that the gut microbiota in mice fed a high fibre diet provide a sufficiently high systemic butyrate level for this to act as an endogenous mechanism of radiosensitisation. The specific aims are to examine the impact of the diet on the microbiome, and subsequently correlate diet-induced microbiome changes with tumour growth and response to radiation treatment.

RT112 xenografts were used in this study. 16S rRNA gene sequencing was performed on a MiSeq platform and metagenomic analysis was conducted using a QIIME2 platform.

The faecal (n=59) and caecal (n=59) microbiomes from mice were similar and they shared the 3 major taxa (> 80% abundance): Bacteroidales, Clostridiales and Verrucomicrobiales. Significantly higher abundance of Bacteroides acidifaciens (p < 0.001) existed in the gut microbiome of mice fed soluble high fibre (HF) for 2 weeks. Principal coordinate analysis showed a notable clustering effect within groups, indicating that diet indeed modified the faecal microbiome. Survival analysis by log-rank test showed soluble HF conferred survival benefits with delayed tumour growth after irradiation (n = 32, p = 0.045). Comparison of the gut microbiome of responders (n = 4) and non-responders (n = 4) to irradiation in the soluble HF group revealed higher abundance of B. acidifaciens in responding mice (p < 0.05). Predictive metagenomic profiling showed gut microbiota in responders to be enriched for carbohydrate metabolism. To investigate the correlation between specific bacterial taxa and tumour response to irradiation, all mice fed different diets (n = 32) were pooled together. Univariate linear regression revealed a statistically significant positive correlation between the survival time of mice and abundance of the B. acidifaciens (R2 = 0.528, P < 0.001).

In conclusion, high fibre diets sensitised RT112 xenografts to irradiation by modifying the gut microbiome and this phenotype was associated with higher relative abundance of B. acidifaciens. Therefore, B. acidifaciens could be a potential radiosensitiser in bladder cancer.

Authors: Then, CK

• Type of award: MSc by Research
• Level of award: Masters
• Awarding institution: University of Oxford