Integrated analysis of intestinal microbiota and host gene expression in colorectal cancer patients
Open Access
- 22 September 2022
- journal article
- research article
- Published by Microbiology Society in Journal of Medical Microbiology
- Vol. 71 (9), 001596
- https://doi.org/10.1099/jmm.0.001596
Abstract
Introduction. Colorectal cancer (CRC) is one of the most common cancers and poses heavy burden on global health. The relationship between mucosal microbiome composition and colorectal gene expression are rarely studied. In this study, we integrated transcriptome data with microbiome data to investigate the relationship between them in colorectal cancer patients. Gap statement. Previous studies have identified the contribution of gut microbiota and DEGs to the pathogenesis of CRC, but the relationship between mucosal microbiome composition and colorectal gene expression are rarely studied. Aim. In this study, we integrated transcriptome data with microbiome data to investigate the relationship between mucosal microbiome composition and colorectal gene expression. Methodology. First, three independent CRC gene expression profiles (GSE184093, GSE156355 and GSE146587) from Gene Expression Omnibus (GEO) were used to identify differentially expressed genes (DEGs). Second, another dataset (GSE163366) was used to analyse gut mucosal microbiome differential abundance. GO (Gene Ontology) function and KEGG (Kyoto Encyclopaedia of Genes and Genomes) pathway enrichment analyses of the DEGs were performed. Protein-protein interactions (PPIs) of the DEGs were constructed. The Spearman correlation analysis was computed between host DEGs and gut microbiome abundance data. Results. A total of 1036 upregulated DEGs and 1194 downregulated DEGs between noncancerous tissues and cancerous tissues were identified based on the analysis. One significant module with a score 37.65 was selected out via MCODE including 41 upregulated DEGs, which are were mostly enriched in two pathways, including microtubule binding and tubulin binding. In particular, significant negative correlations are prevalent between Fusobacterium and the 41 DEGs with the correlation ranging between −0.54 and −0.35, and there commonly exist significant positive correlations between Blautia and the 41 DEGs with the correlation ranging between 0.42 and 0.54, indicating that Fusobacterium and Blautia are two of the most important microbes interacting with the gene regulation. Conclusion. Our results demonstrate significant correlation between some gut microbes and DEGs, providing a comprehensive bioinformatics analysis of them for future investigation into the molecular mechanisms and biomarkers.Keywords
Funding Information
- National Natural Science Foundation of China (81871317)
- Military Medical Innovation Project (18CXZ025)
This publication has 40 references indexed in Scilit:
- Inferring Correlation Networks from Genomic Survey DataPLoS Computational Biology, 2012
- Human chromokinesins promote chromosome congression and spindle microtubule dynamics during mitosisThe Journal of cell biology, 2012
- Human Intestinal Lumen and Mucosa-Associated Microbiota in Patients with Colorectal CancerPLOS ONE, 2012
- clusterProfiler: an R Package for Comparing Biological Themes Among Gene ClustersOMICS: A Journal of Integrative Biology, 2012
- Gut bacteria in health and disease: a survey on the interface between intestinal microbiology and colorectal cancerBiological Reviews, 2012
- Cantharidin induces G2/M phase arrest and apoptosis in human colorectal cancer colo 205 cells through inhibition of CDK1 activity and caspase-dependent signaling pathwaysInternational Journal of Oncology, 2011
- Systematic enrichment analysis of gene expression profiling studies identifies consensus pathways implicated in colorectal cancer developmentJournal of Carcinogenesis, 2011
- Gene expression profiling in colorectal cancer using microarray technologies: Results and perspectivesCancer Treatment Reviews, 2009
- The Innate Immune Receptor Nod1 Protects the Intestine from Inflammation-Induced TumorigenesisCancer Research, 2008
- Strategies for discovering novel cancer biomarkers through utilization of emerging technologiesNature Clinical Practice Oncology, 2008