Altered Fecal Small RNA Profiles in Colorectal Cancer Reflect Gut Microbiome Composition in Stool Samples

Abstract

Dysbiotic configurations of the human gut microbiota have been linked to colorectal cancer (CRC). Human small noncoding RNAs are also implicated in CRC, and recent findings suggest that their release in the gut lumen contributes to shape the gut microbiota. Bacterial small RNAs (bsRNAs) may also play a role in carcinogenesis, but their role has been less extensively explored. Here, we performed small RNA and shotgun sequencing on 80 stool specimens from patients with CRC or with adenomas and from healthy subjects collected in a cross-sectional study to evaluate their combined use as a predictive tool for disease detection. We observed considerable overlap and a correlation between metagenomic and bsRNA quantitative taxonomic profiles obtained from the two approaches. We identified a combined predictive signature composed of 32 features from human and microbial small RNAs and DNA-based microbiome able to accurately classify CRC samples separately from healthy and adenoma samples (area under the curve [AUC] = 0.87). In the present study, we report evidence that host-microbiome dysbiosis in CRC can also be observed by examination of altered small RNA stool profiles. Integrated analyses of the microbiome and small RNAs in the human stool may provide insights for designing more-accurate tools for diagnostic purposes. IMPORTANCE The characteristics of microbial small RNA transcription are largely unknown, while it is of primary importance for a better identification of molecules with functional activities in the gut niche under both healthy and disease conditions. By performing combined analyses of metagenomic and small RNA sequencing (sRNA-Seq) data, we characterized both the human and microbial small RNA contents of stool samples from healthy individuals and from patients with colorectal carcinoma or adenoma. With the integrative analyses of metagenomic and sRNA-Seq data, we identified a human and microbial small RNA signature which can be used to improve diagnosis of the disease. Our analysis of human and gut microbiome small RNA expression is relevant to generation of the first hypotheses about the potential molecular interactions occurring in the gut of CRC patients, and it can be the basis for further mechanistic studies and clinical tests.

Dysbiosis in intestinal microbiome linked to fecal blood determined by direct hybridization

“…2 and in Supplementary Table 2, show that bacteria biodiversity between the two groups is greatly different. The information obtained is in agreement with those reported in a recently paper from Tarallo et al ( 2019 ).…”

“…In particular, bacteria belonging to Bacteroidetes phylum was recently reviewed for its role in metabolic disease, among which Prevotella assumes an important meaning (Johnson et al 2017 ). Likewise, Proteobacteria phylum such as Helicobacter pylori , Desulfovibrio vulgaris , Desulfovibrio fairfieldensis, Desulfovibrio desulfuricans , Escherichia fergusonii , and Haemophiilus parainfluenzae are higher in pathophysiological gut status according to our heat map results and previous studies (Tarallo et al 2019 ; Rizzatti et al 2017 ). Additionally, Libby et al (2019) pointed out a significant correlation for fecal blood presence and the increasing risk of dying from circulatory, respiratory and digestive diseases (excluding colorectal cancer) as well as neuropsychological, blood and endocrine disease (Walker 1990 ).…”

“…Of note, several inflammatory intestinal disorders are related to FOB which is not strictly related to colon cancer (Walker 1990 ; Libby et al 2018 ). In this scenario, we have designed in July 2017 the first custom panel “CDR_CNV_Bc_miCrobioTA22586” with 79 bacteria 16S rRNA target genes representative of gut health and impaired in gut inflammation status (Tarallo et al 2019 ). Alicyclobacillus acidophilus , Rhizobium radiobacter and Salinibacter ruber are not present in the human gut and were used as negative control of human microbiota bacteria 16S rRNA gene.…”

Interspecies Communication in Holobionts by Non-Coding RNA Exchange

“…Selected human and animal studies clearly showed the existence of communication axes between the intestine and other organs that are extended beyond the gut, and that contribute to the function and dysfunction of distant organ systems [125,126]. Gut microbiome dysbiosis has been correlated with several types of tumors, suggesting the direct connection between the microbiota and tumor proliferation [127,128].…”

Mast Cells, microRNAs and Others: The Role of Translational Research on Colorectal Cancer in the Forthcoming Era of Precision Medicine

“…Fecal miRNAs have been shown to correlate with tumor stage [ 76 , 77 ], probably because they are continuously released into the intestinal lumen by CRC cells and can be detected in stool samples [ 78 ]. Stool comes into direct contact with the intestinal lumen, providing a rationale for the use of miRNAs as biomarkers in CRC [ 79 ].…”