Integration of the microbiome, metabolome and transcriptomics data identified novel metabolic pathway regulation in colorectal cancer

Vartika Bisht, Katrina Nash, Yuanwei Xu, Prasoon Agarwal, Sofie Bosch, Georgios V. Gkoutos, Animesh Acharjee

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Integrative multiomics data analysis provides a unique opportunity for the mechanistic understanding of colorectal cancer (CRC) in addition to the identification of potential novel therapeutic targets. In this study, we used public omics data sets to investigate potential associations between microbiome, metabolome, bulk transcriptomics and single cell RNA sequencing datasets. We identified multiple potential interactions, for example 5-aminovalerate interacting with Adlercreutzia; cholesteryl ester interacting with bacterial genera Staphylococcus, Blautia and Roseburia. Using public single cell and bulk RNA sequencing, we identified 17 overlapping genes involved in epithelial cell pathways, with particular significance of the oxidative phosphorylation pathway and the ACAT1 gene that indirectly regulates the esterification of cholesterol. These findings demonstrate that the integration of multiomics data sets from diverse populations can help us in untangling the colorectal cancer pathogenesis as well as postulate the disease pathology mechanisms and therapeutic targets.
Original languageEnglish
Article number5763
JournalInternational Journal of Molecular Sciences
Issue number11
Publication statusPublished - 28 May 2021

Bibliographical note

Funding Information:
This study was supported by the National Institute for Health Research (NIHR) Surgical Reconstruction and Microbiology Research Centre (SRMRC), Birmingham. GVG also acknowledges support from H2020-EINFRA (731075) and the National Science Foundation (IOS:1340112) as well as support from the NIHR Birmingham ECMC, the NIHR Birmingham Biomedical Research Centre and the MRC HDR UK. The views expressed in this publication are those of the authors and not necessarily those of the NHS, the National Institute for Health Research, the Medical Research Council or the Department of Health, UK. The funders provided the financial support to this research but had no role in the design of the study, analysis, interpretations of the data and in writing the manuscript.

Publisher Copyright:
© 2021 by the authors. Licensee MDPI, Basel, Switzerland.


  • microbiota
  • colorectal neoplasms
  • biomarkers
  • metabolomics
  • transcriptome
  • omics integration
  • Metabolomics
  • Microbiota
  • Transcriptome
  • Biomarkers
  • Omics integration
  • Colorectal neoplasms

ASJC Scopus subject areas

  • Molecular Biology
  • Spectroscopy
  • Catalysis
  • Inorganic Chemistry
  • Computer Science Applications
  • Physical and Theoretical Chemistry
  • Organic Chemistry


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