J Bacteriol Virol.  2019 Dec;49(4):162-175. 10.4167/jbv.2019.49.4.162.

Analysis of Intestinal Mucosal Microbiome Changes before and after Chemoradiation in Locally Advanced Rectal Cancer Patients

• Seo I
• Bae SU
• Kim S
• Jeong WK
• Baek SK

• KMID: 2468023
• DOI: http://doi.org/10.4167/jbv.2019.49.4.162

Abstract

PURPOSE
Dysbiosis of gut microbiota has been reported to participate in the pathogenesis of colorectal cancer, but changes in microbiota due to radiotherapy have not been studied. In this study, we tried to elucidate the changes in the microbiome in rectal cancer after chemoradiotherapy using RNA sequencing analysis.
MATERIALS AND METHODS
We included 11 pairs of human rectal cancer tissues before and after irradiation between August 2016 and December 2017 and performed RNA sequencing analysis. Mapped reads to human reference genomes were used for pair-wise transcriptome comparisons, and unmapped (non-human) reads were then mapped to bacterial marker genes using PathSeq.
RESULTS
At microbiome level, interindividual variability of mucosal microbiota was greater than the change in microbial composition during radiotherapy. This indicates that rapid homeostatic recovery of the mucosal microbial composition takes place short after radiotherapy. At single microbe level, Prevotella and Fusobacterium, which were identified as important causative microbes of the initiation and progression of rectal cancer were decreased by radiotherapy. Moreover, changes in Prevotella were associated with changes in the human transcriptome of rectal cancer. We also found that there was a gene cluster that increased and decreased in association with changes in microbial composition by chemoradiation.
CONCLUSION
This study revealed changes in tumor-associated microbial community by irradiation in rectal cancer. These findings can be used to develop a new treatment strategy of neoadjuvant therapy for locally advanced rectal cancer by overcoming radio-resistance or facilitating radio-sensitivity.

Keyword

Microbiome; Rectal cancer; Radiotherapy

MeSH Terms

Chemoradiotherapy
Colorectal Neoplasms
Dysbiosis
Fusobacterium
Gastrointestinal Microbiome
Genes, vif
Genome
Humans
Microbiota*
Neoadjuvant Therapy
Prevotella
Radiotherapy
Rectal Neoplasms*
Sequence Analysis, RNA
Transcriptome

Figure

• 

  Figure 1 Microbial composition before and after chemoradiation in rectal cancer patients. The relative abundance of OTU is shown for each taxonomic rank. The paired bar plots on the right show the microbial composition before and after chemoradiation in the same patients. The numbers on the bar plot represent the patient identification numbers. The skyline plots on the left show the bar plot in ascending order based on the most abundant OTU. The y-axis of both charts indicates the relative abundance (%). “PRE” and “PRERT” represent samples before chemoradiation therapy. “POST” and “POSTRT” represent samples after chemoradiation therapy. OTUs that differ in ANCOM analysis are marked with an asterisk and the W-statistics are shown in parentheses. (A) Phylum (B) Class (C) Order and (D) Family.

• 

  Figure 2 Principal component analysis of the microbiota before and after chemoradiation in rectal cancer patients. The numbers represent the patient identification numbers. “PRERT” and “POSTRT” represent samples before and after chemoradiation therapy, respectively. (A) Phylum (B) Class (C) Order (D) Family.

• 

  Figure 3 Changes in the abundance of Prevotellaceae family after chemoradiation and concomitant changes in the human transcriptome. (A) Box plot shows the relative abundance of Prevotellaceae before and after chemoradiotherapy. “PRERT” and “POSTRT” represent samples before and after chemoradiation therapy, respectively. (B) Bubble chart shows the functional annotation of host gene expression highly correlated with changes in relative abundance of Prevotellaceae before and after chemoradiotherapy. Gene-Enrichment and Functional Annotation Analysis was performed using DAVID. The y-axis represents the functional term defined in GOTERM_MF_DIRECT. The numbers in parentheses are the identification numbers of the Gene Ontology. Fold enrichment, ratio of the number of genes involved the function term to the total number of inputs genes, and p-value are represented by x-axis, bubble size, and bubble color, respectively.

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