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Gatti DM, Tyler AL, Mahoney JM, Churchill GA, Yener B, Koyuncu D, Gurcan MN, Niazi M, Tavolara T, Gower AC, Dayao D, McGlone E, Ginese ML, Specht A, Alsharaydeh A, Tessier PA, Kurtz SL, Elkins K, Kramnik I, Beamer G. Systems genetics uncover new loci containing functional gene candidates in Mycobacterium tuberculosis-infected Diversity Outbred mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.21.572738. [PMID: 38187647 PMCID: PMC10769337 DOI: 10.1101/2023.12.21.572738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Mycobacterium tuberculosis, the bacillus that causes tuberculosis (TB), infects 2 billion people across the globe, and results in 8-9 million new TB cases and 1-1.5 million deaths each year. Most patients have no known genetic basis that predisposes them to disease. We investigated the complex genetic basis of pulmonary TB by modelling human genetic diversity with the Diversity Outbred mouse population. When infected with M. tuberculosis, one-third develop early onset, rapidly progressive, necrotizing granulomas and succumb within 60 days. The remaining develop non-necrotizing granulomas and survive longer than 60 days. Genetic mapping using clinical indicators of disease, granuloma histopathological features, and immune response traits identified five new loci on mouse chromosomes 1, 2, 4, 16 and three previously identified loci on chromosomes 3 and 17. Quantitative trait loci (QTLs) on chromosomes 1, 16, and 17, associated with multiple correlated traits and had similar patterns of allele effects, suggesting these QTLs contain important genetic regulators of responses to M. tuberculosis. To narrow the list of candidate genes in QTLs, we used a machine learning strategy that integrated gene expression signatures from lungs of M. tuberculosis-infected Diversity Outbred mice with gene interaction networks, generating functional scores. The scores were then used to rank candidates for each mapped trait in each locus, resulting in 11 candidates: Ncf2, Fam20b, S100a8, S100a9, Itgb5, Fstl1, Zbtb20, Ddr1, Ier3, Vegfa, and Zfp318. Importantly, all 11 candidates have roles in infection, inflammation, cell migration, extracellular matrix remodeling, or intracellular signaling. Further, all candidates contain single nucleotide polymorphisms (SNPs), and some but not all SNPs were predicted to have deleterious consequences on protein functions. Multiple methods were used for validation including (i) a statistical method that showed Diversity Outbred mice carrying PWH/PhJ alleles on chromosome 17 QTL have shorter survival; (ii) quantification of S100A8 protein levels, confirming predicted allele effects; and (iii) infection of C57BL/6 mice deficient for the S100a8 gene. Overall, this work demonstrates that systems genetics using Diversity Outbred mice can identify new (and known) QTLs and new functionally relevant gene candidates that may be major regulators of granuloma necrosis and acute inflammation in pulmonary TB.
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Affiliation(s)
- D M Gatti
- The Jackson Laboratory, Bar Harbor, ME
| | - A L Tyler
- The Jackson Laboratory, Bar Harbor, ME
| | | | | | - B Yener
- Rensselaer Polytechnic Institute, Troy, NY
| | - D Koyuncu
- Rensselaer Polytechnic Institute, Troy, NY
| | - M N Gurcan
- Wake Forest University School of Medicine, Winston Salem, NC
| | - Mkk Niazi
- Wake Forest University School of Medicine, Winston Salem, NC
| | - T Tavolara
- Wake Forest University School of Medicine, Winston Salem, NC
| | - A C Gower
- Clinical and Translational Science Institute, Boston University, Boston, MA
| | - D Dayao
- Tufts University Cummings School of Veterinary Medicine, North Grafton, MA
| | - E McGlone
- Tufts University Cummings School of Veterinary Medicine, North Grafton, MA
| | - M L Ginese
- Tufts University Cummings School of Veterinary Medicine, North Grafton, MA
| | - A Specht
- Tufts University Cummings School of Veterinary Medicine, North Grafton, MA
| | - A Alsharaydeh
- Texas Biomedical Research Institute, San Antonio, TX
| | - P A Tessier
- Department of Microbiology and Immunology, Laval University School of Medicine, Quebec, Canada
| | - S L Kurtz
- Center for Biologics, Food and Drug Administration, Bethesda, MD
| | - K Elkins
- Center for Biologics, Food and Drug Administration, Bethesda, MD
| | - I Kramnik
- NIEDL, Boston University, Boston, MA
| | - G Beamer
- Texas Biomedical Research Institute, San Antonio, TX
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