Human gut Microbiome, gene Expression and Colorectal Cancer: Assigning causal roles from a novel Mendelian randomization perspective.

Project Information

MECoCaM

Grant agreement ID: 796216

DOI

10.3030/796216

Project closed

EC signature date 5 April 2018

Start date 3 September 2018

End date 2 September 2020

Funded under

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Total cost

€ 158 121,60

EU contribution

€ 158 121,60

Coordinated by

FUNDACIO INSTITUT D'INVESTIGACIO BIOMEDICA DE BELLVITGE
Spain

Periodic Reporting for period 1 - MECoCaM (Human gut Microbiome, gene Expression and Colorectal Cancer: Assigning causal roles from a novel Mendelian randomization perspective.)

Reporting period: 2018-09-03 to 2020-09-02

Summary of the context and overall objectives of the project

Colorectal cancer (CRC) is the fourth leading cause of cancer-related deaths in the world and its burden is expected to increase by 60% to more than 1.1 million cancer deaths by 2030. Among CRC risk factors, the contribution of the microbial ecosystem in the gut (gut microbiome) to CRC is not well understood. Some correlations between a microbe and cancer stages have been observed, but only Fusobacterium has shown consistent evidence as risk factor. Additionally, the enrichment of a microbe at a tumour site does not directly assume causation. Rather, microbes may find a carcinogenic ambient as underused nutritional niche (reverse causation) or external exposures can be independently influencing both microbial and host cell proliferation (confounding).
In order to reveal causal associations between microbiota and CRC risk and its biological mechanism, in this project, we assessed the potential causal effect of microbiota on host colon gene expression and on CRC risk, using genetic instruments under a Mendelian randomization approach.
The results did not clarify the role of microbiota to CRC risk; however, their reflected the effect of the gut microbiota composition in the gene expression of a healthy colon tissue. This can be used as a reference dataset for microbiome-based therapies in colon diseases, such as CRC and inflammatory bowel diseases.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

Initially, using genetic instruments for gut microbiota from The Flemish Gut Flora Project (FGFP), we identified weak association between microbiome taxa and CRC risk, and we could not appraise the role of microbiota to CRC risk. This was done in collaboration with Prof. Nicholas Timpson from the School of Social and Community Medicine of the University of Bristol in UK.
Analysing 350 gut healthy tissue samples we identified 15,542 genes expressed in the gut that clustered in 22 modules of gene co-expression (correlated gene expression). Then, during the secondment performed at the APC Microbiome Institute at the University of Cork under the supervision of Prof. Paul O’Toole, we distinguished 245 different bacterial taxa, most of them clustered in 28 modules of co-abundance (correlated taxa), and 14 of these clusters influenced the gene expression of 17 modules of gene co-expression.
The methodology and results were disseminated in international conferences as poster or oral presentations for the scientific audience, and as videos at the IDIBELL Youtube channel for the general audience. Scientific publications will be ready by 2021.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

We described for first time the effect of the gut microbiota composition in the gene expression of a healthy colon tissue, and generated a reference dataset for microbiome-based therapies in colon diseases, such as CRC and inflammatory bowel diseases. These results are paving the way to guide a state-of-art multidisciplinary approach to the microbiome-based therapies, a research field with great success in the following decade.

Reddish and bluish colours represent that bacterial module increase or decrease, respectively.