Changes in the Abundances of Cervical and Rectal Mycobiota during Chemoradiotherapy in Cervical Cancer

Abstract

Globally, cervical cancer is the fourth most frequent cancer in women. The local and gut microbiomes of cervical cancer patients primarily consist of bacteria, viruses, and fungi. Bacterial composition has been previously associated with response to chemoradiotherapy (CRT) and patient outcome. Recently, our group has demonstrated that the HPV virome dynamically shifts during treatment and was associated with treatment response. Although connections between fungi and cervicovaginal health have been established, little is known about the fungal microbiome during treatment of cervical cancer. In this study, we sought to explore changes in fungal distribution throughout CRT for a cohort of cervical cancer patients. This study includes 57 patients diagnosed with cervical cancer at a single institution with samples collected throughout CRT timepoints: baseline, week 1, week 3, and week 5. 170 swab specimens were included in this analysis: 138 cervical swabs from 56 patients and 32 rectal swabs from 9 patients. Whole genome sequencing data was obtained from the swabs using the Illumina HiSeqX platform (2 × 150bp). Fungal reads were log transformed to reduce variability and skewness and normalized to the total library size resulting in log normalized fungal reads per million (RPM). Bacterial reads were normalized with the same methodology. Timepoint analysis was performed using Wilcoxon signed rank tests or Friedman tests (with Dunn's multiple comparisons test) when comparing two or more time points, respectively. All swab samples contained reads mapped to fungi. Of the 3.70 × 109 total reads across all sequenced samples, 19.2% did not map specifically to the human genome: 91.8% of these non-human reads could not be mapped to an individual microbial genome. Of the remaining 8.2% of non-human reads that mapped to a specific microbial genome (1.6% of total), 97.4% were classified as bacterial (1.5% of total), 0.71% as virus (0.011% of total), and 0.44% as fungal (0.0069% of total). Comparison of fungal RPM in the cervical and rectal microbiome revealed a significant decrease during treatment from baseline to week 5 (cervical, P = 0.0002; rectal, P = 0.0273). Distribution of bacterial reads exhibited similar trends as decreases were observed between baseline and week 5 for both cervical (P = 0.0116) and rectal (P = 0.0195) samples. Fungi to bacteria distribution ratios in the rectal microbiome revealed significant differences when comparing across all timepoints (P = 0.0041), baseline vs. week 1 (P = 0.0028), baseline vs. week 3 (P = 0.0389), and baseline vs. week 5 (P = 0.0113) with all three later timepoints higher relative to baseline. The distributions of cervical and gut fungal reads and their relationship to the bacteriome shift during CRT. Further investigation into characterizing fungi and their relationship with other microbiota will be valuable to understanding its potential associations with cervical cancer and treatment response.