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Li D, Zhong C, Yang M, He L, Chang H, Zhu N, Celniker SE, Threadgill DW, Snijders AM, Mao JH, Yuan Y. Genetic and microbial determinants of azoxymethane-induced colorectal tumor susceptibility in Collaborative Cross mice and their implication in human cancer. Gut Microbes 2024; 16:2341647. [PMID: 38659246 PMCID: PMC11057575 DOI: 10.1080/19490976.2024.2341647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 04/08/2024] [Indexed: 04/26/2024] Open
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.
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Affiliation(s)
- Dan Li
- Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Hangzhou, ZJ, China
- Department of Medical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, ZJ, China
| | - Chenhan Zhong
- Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Hangzhou, ZJ, China
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mengyuan Yang
- Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Hangzhou, ZJ, China
| | - Li He
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Hematology, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Hang Chang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ning Zhu
- Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Hangzhou, ZJ, China
| | - Susan E Celniker
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David W Threadgill
- Texas A&M Institute for Genome Sciences and Society, Texas A&M University, College Station, TX, USA
- Department of Molecular and Cellular Medicine and Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX, USA
| | - Antoine M Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ying Yuan
- Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Hangzhou, ZJ, China
- Zhejiang Provincial Clinical Research Center for CANCER, Hangzhou, ZJ, China
- Cancer Center, Zhejiang University, Hangzhou, ZJ, China
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Quan L, Demant P. Clustering of colon, lung, and other cancer susceptibility genes with protein tyrosine phosphatases and protein kinases in multiple short genomic regions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.07.566108. [PMID: 37986945 PMCID: PMC10659278 DOI: 10.1101/2023.11.07.566108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Interactions of large gene families are poorly understood. We found that human, mouse, and rat colon and lung cancer susceptibility genes, presently considered as separate gene families, were frequently pairwise linked. The orthologous mouse map positions of 142 of 159 early discovered colon and lung cancer susceptibility genes formed 41 genomic clusters conserved >70 million years. These linked gene pairs concordantly affected both tumors and their majority was linked with two other gene families - protein tyrosine phosphatases and cancer driver protein kinases. 25% of both protein tyrosine phosphatases and protein kinases mapped <1 cM from a colon or lung cancer susceptibility gene, and 50% in <3 cM. Similar linkage was detected with most other human susceptibility genes that controlled 29 different cancer types. This concentration of tumor susceptibility genes with protein tyrosine phosphatases and driver protein kinases in multiple relatively short genomic regions suggests their possible functional diversity.
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Borrego A, Jensen JR, Cabrera WHK, Massa S, Ribeiro OG, Starobinas N, De Franco M, Eto SF, Manenti G, Dragani TA, Ibañez OM. Mapping of novel loci involved in lung and colon tumor susceptibility by the use of genetically selected mouse strains. Genes Immun 2021; 23:23-32. [PMID: 34966170 PMCID: PMC8866122 DOI: 10.1038/s41435-021-00159-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 11/29/2021] [Accepted: 12/13/2021] [Indexed: 11/29/2022]
Abstract
Two non-inbred mouse lines, phenotypically selected for maximal (AIRmin) and minimal (AIRmax) acute inflammatory response, show differential susceptibility/resistance to the development of several chemically-induced tumor types. An intercross pedigree of these mice was generated and treated with the chemical carcinogen dimethylhydrazine, which induces lung and intestinal tumors. Genome wide high-density genotyping with the Restriction Site-Associated DNA genotyping (2B-RAD) technique was used to map genetic loci modulating individual genetic susceptibility to both lung and intestinal cancer. Our results evidence new common quantitative trait loci (QTL) for those phenotypes and provide an improved understanding of the relationship between genomic variation and individual genetic predisposition to tumorigenesis in different organs.
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Affiliation(s)
- Andrea Borrego
- Laboratory of Immunogenetics, Instituto Butantan, São Paulo, Brazil
| | | | | | - Solange Massa
- Laboratory of Immunogenetics, Instituto Butantan, São Paulo, Brazil
| | | | - Nancy Starobinas
- Laboratory of Immunogenetics, Instituto Butantan, São Paulo, Brazil
| | | | - Silas Fernandes Eto
- Laboratory of Development and Innovation, Instituto Butantan, São Paulo, Brazil
| | - Giacomo Manenti
- Genetic Epidemiology and Pharmacogenomics Unit Fondazione IRCCS, Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Tommaso Antonio Dragani
- Genetic Epidemiology and Pharmacogenomics Unit Fondazione IRCCS, Istituto Nazionale dei Tumori di Milano, Milan, Italy.
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Mantilla Rojas C, McGill MP, Salvador AC, Bautz D, Threadgill DW. Epithelial-specific ERBB3 deletion results in a genetic background-dependent increase in intestinal and colon polyps that is mediated by EGFR. PLoS Genet 2021; 17:e1009931. [PMID: 34843459 PMCID: PMC8659709 DOI: 10.1371/journal.pgen.1009931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 12/09/2021] [Accepted: 11/05/2021] [Indexed: 11/18/2022] Open
Abstract
ERBB3 has gained attention as a potential therapeutic target to treat colorectal and other types of cancers. To confirm a previous study showing intestinal polyps are dependent upon ERBB3, we generated an intestinal epithelia-specific ERBB3 deletion in C57BL/6-ApcMin/+ mice. Contrary to the previous report showing a significant reduction in intestinal polyps with ablation of ERBB3 on a B6;129 mixed genetic background, we observed a significant increase in polyp number with ablation of ERBB3 on C57BL/6J compared to control littermates. We confirmed the genetic background dependency of ERBB3 by also analyzing polyp development on B6129 hybrid and B6;129 advanced intercross mixed genetic backgrounds, which showed that ERBB3 deficiency only reduced polyp number on the mixed background as previously reported. Increased polyp number with ablation of ERBB3 was also observed in C57BL/6J mice treated with azoxymethane showing the effect is model independent. Polyps forming in absence of ERBB3 were generally smaller than those forming in control mice, albeit the effect was greatest in genetic backgrounds with reduced polyp numbers. The mechanism for differential polyp number in the absence of ERBB3 was through altered proliferation. Backgrounds with increased polyp number with loss of ERBB3 showed an increase in cell proliferation even in non-tumor epithelia, while backgrounds showing reduced polyp number with loss of ERBB3 showed reduced cellular proliferation. Increase polyp number caused by loss of ERBB3 was mediated by increased epidermal growth factor receptor (EGFR) expression, which was confirmed by deletion of Egfr. Taken together, this study raises substantial implications on the use of ERBB3 inhibitors against colorectal cancer. The prediction is that some patients may have increased progression with ERBB3 inhibitor therapy, which is consistent with observations reported for ERBB3 inhibitor clinical trials.
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Affiliation(s)
- Carolina Mantilla Rojas
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, Texas, United States of America.,Department of Molecular and Cellular Medicine, Texas A&M University, College Station, Texas, United States of America
| | - Michael P McGill
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, Texas, United States of America.,Department of Molecular and Cellular Medicine, Texas A&M University, College Station, Texas, United States of America
| | - Anna C Salvador
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, Texas, United States of America.,Department of Nutrition, Texas A&M University, College Station, Texas, United States of America
| | - David Bautz
- Department of Genetics, North Carolina State University, Raleigh, North Carolina, United States of America
| | - David W Threadgill
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, Texas, United States of America.,Department of Molecular and Cellular Medicine, Texas A&M University, College Station, Texas, United States of America.,Department of Nutrition, Texas A&M University, College Station, Texas, United States of America.,Department of Biochemistry & Biophysics and Department of Nutrition, Texas A&M University, College Station, Texas, United States of America
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