Genetic and microbial determinants of azoxymethane-induced colorectal tumor susceptibility in Collaborative Cross mice and their implication in human cancer

ABSTRACT

The insights into interactions between host genetics and gut microbiome (GM) in colorectal tumor susceptibility (CTS) remains lacking. We used Collaborative Cross mouse population model to identify genetic and microbial determinants of Azoxymethane-induced CTS. We identified 4417 CTS-associated single nucleotide polymorphisms (SNPs) containing 334 genes that were transcriptionally altered in human colorectal cancers (CRCs) and consistently clustered independent human CRC cohorts into two subgroups with different prognosis. We discovered a set of genera in early-life associated with CTS and defined a 16-genus signature that accurately predicted CTS, the majority of which were correlated with human CRCs. We identified 547 SNPs associated with abundances of these genera. Mediation analysis revealed GM as mediators partially exerting the effect of SNP UNC3869242 within Duox2 on CTS. Intestine cell-specific depletion of Duox2 altered GM composition and contribution of Duox2 depletion to CTS was significantly influenced by GM. Our findings provide potential novel targets for personalized CRC prevention and treatment.

KEYWORDS:

• Colorectal tumor susceptibility
• azoxymethane
• genome-wide association study
• gut microbiome
• conditional knockout mouse
• DUOX2

Acknowledgments

We thank staff at the LBNL Animal Facility for maintenance of Collaborative Cross mice.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Author contribution

JHM, AMS and YY conceptualized and designed the study. DL, CZ, MY, LH, NZ, AMS and JHM performed animal experiments, quantified colon tumor development in mice, and collected fecal and tissues. SEC performed 16 sRNA sequencing. DL, CZ and HC performed formal analysis including bioinformatics and statistical analyses. HC, DWT, AMS, JHM and YY were involved in critical review of the data and interpretation of results. DL, CZ, HC and JHM created the manuscript figures and Supplemental materials. DL and CZ drafted the manuscript. All authors edited, reviewed, revised, and approved the manuscript text. JHM, CZ and YY acquired funding for the study.

Consent for publication

The authors consent to publish this work.

Data availability statement

Mouse gut microbiome 16S rRNA gene sequencing data and RNA-Seq data from Doux2 knockout mice are are available in the National Center for Biotechnology Information (NCBI) BioProject Repository (https://www.ncbi.nlm.nih.gov/bioproject) under the BioProject “PRJNA802804”. Mouse gut microbiome 16S rRNA gene sequencing data from CC mouse cohort is available on OSF (https://osf.io/jbt5g/).³⁰ The mouse data has been included in Supplemental Table S1. The numeric counts table at genus level and corresponding taxonomic classifications have all been included as Supplemental Table S5.

Ethics approval and consent to participate

All animal experiments were approved by the Institutional Animal Welfare and Research Committee at Lawrence Berkeley National Laboratory or the Institutional Animal Care and Bioethical Committee of Zhejiang University.

Supplementary material

Supplemental data for this article can be accessed online at https://doi.org/10.1080/19490976.2024.2341647

Correction Statement

This article has been corrected with minor changes. These changes do not impact the academic content of the article.

Additional information

Funding

This study was partly supported by the Lawrence Berkeley National Laboratory Directed Research and Development (LDRD) program to JHM and the U.S.-China Program for Biomedical Collaborative Research NIEHS (R01ES031322) to AMS. Lawrence Berkeley National Laboratory (LBNL) is a multi-program national laboratory operated by the University of California for the DOE under contract DE AC02-05CH11231. Additional support was provided by the Foundation from the Health Bureau of Zhejiang Province [2022RC172] to CZ and by the Provincial Key R&D Program of Zhejiang Province [2021C03125] to YY.