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Graham JB, Swarts JL, Leist SR, Schäfer A, Bell TA, Hock P, Farrington J, Shaw GD, Ferris MT, Pardo-Manuel de Villena F, Baric RS, Lund JM. Unique immune profiles in collaborative cross mice linked to survival and viral clearance upon infection. iScience 2024; 27:109103. [PMID: 38361611 PMCID: PMC10867580 DOI: 10.1016/j.isci.2024.109103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/18/2023] [Accepted: 01/30/2024] [Indexed: 02/17/2024] Open
Abstract
The response to infection is generally heterogeneous and diverse, with some individuals remaining asymptomatic while others present with severe disease or a diverse range of symptoms. Here, we address the role of host genetics on immune phenotypes and clinical outcomes following viral infection by studying genetically diverse mice from the Collaborative Cross (CC), allowing for use of a small animal model with controlled genetic diversity while maintaining genetic replicates. We demonstrate variation by deeply profiling a broad range of innate and adaptive immune cell phenotypes at steady-state in 63 genetically distinct CC mouse strains and link baseline immune signatures with virologic and clinical disease outcomes following infection of mice with herpes simplex virus 2 (HSV-2) or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This work serves as a resource for CC strain selection based on steady-state immune phenotypes or disease presentation upon viral infection, and further, points to possible pre-infection immune correlates of survival and early viral clearance upon infection.
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Affiliation(s)
- Jessica B. Graham
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Jessica L. Swarts
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Sarah R. Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Timothy A. Bell
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Pablo Hock
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Joe Farrington
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ginger D. Shaw
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Martin T. Ferris
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Fernando Pardo-Manuel de Villena
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ralph S. Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jennifer M. Lund
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Global Health, University of Washington, Seattle, WA, USA
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2
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Abu-Toamih-Atamni HJ, Lone IM, Binenbaum I, Mott R, Pilalis E, Chatziioannou A, Iraqi FA. Mapping novel QTL and fine mapping of previously identified QTL associated with glucose tolerance using the collaborative cross mice. Mamm Genome 2024; 35:31-55. [PMID: 37978084 DOI: 10.1007/s00335-023-10025-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 10/08/2023] [Indexed: 11/19/2023]
Abstract
A chronic metabolic illness, type 2 diabetes (T2D) is a polygenic and multifactorial complicated disease. With an estimated 463 million persons aged 20 to 79 having diabetes, the number is expected to rise to 700 million by 2045, creating a significant worldwide health burden. Polygenic variants of diabetes are influenced by environmental variables. T2D is regarded as a silent illness that can advance for years before being diagnosed. Finding genetic markers for T2D and metabolic syndrome in groups with similar environmental exposure is therefore essential to understanding the mechanism of such complex characteristic illnesses. So herein, we demonstrated the exclusive use of the collaborative cross (CC) mouse reference population to identify novel quantitative trait loci (QTL) and, subsequently, suggested genes associated with host glucose tolerance in response to a high-fat diet. In this study, we used 539 mice from 60 different CC lines. The diabetogenic effect in response to high-fat dietary challenge was measured by the three-hour intraperitoneal glucose tolerance test (IPGTT) test after 12 weeks of dietary challenge. Data analysis was performed using a statistical software package IBM SPSS Statistic 23. Afterward, blood glucose concentration at the specific and between different time points during the IPGTT assay and the total area under the curve (AUC0-180) of the glucose clearance was computed and utilized as a marker for the presence and severity of diabetes. The observed AUC0-180 averages for males and females were 51,267.5 and 36,537.5 mg/dL, respectively, representing a 1.4-fold difference in favor of females with lower AUC0-180 indicating adequate glucose clearance. The AUC0-180 mean differences between the sexes within each specific CC line varied widely within the CC population. A total of 46 QTL associated with the different studied phenotypes, designated as T2DSL and its number, for Type 2 Diabetes Specific Locus and its number, were identified during our study, among which 19 QTL were not previously mapped. The genomic interval of the remaining 27 QTL previously reported, were fine mapped in our study. The genomic positions of 40 of the mapped QTL overlapped (clustered) on 11 different peaks or close genomic positions, while the remaining 6 QTL were unique. Further, our study showed a complex pattern of haplotype effects of the founders, with the wild-derived strains (mainly PWK) playing a significant role in the increase of AUC values.
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Affiliation(s)
- Hanifa J Abu-Toamih-Atamni
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel-Aviv University, Ramat Aviv, 69978, Tel-Aviv, Israel
| | - Iqbal M Lone
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel-Aviv University, Ramat Aviv, 69978, Tel-Aviv, Israel
| | - Ilona Binenbaum
- Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, Soranou Ephessiou Str, 11527, Athens, Greece
- Division of Pediatric Hematology-Oncology, First Department of Pediatrics, National and Kapodistrian University of Athens, Athens, Greece
| | - Richard Mott
- Department of Genetics, University College of London, London, UK
| | | | - Aristotelis Chatziioannou
- Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, Soranou Ephessiou Str, 11527, Athens, Greece
- e-NIOS Applications PC, 196 Syggrou Ave., 17671, Kallithea, Greece
| | - Fuad A Iraqi
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel-Aviv University, Ramat Aviv, 69978, Tel-Aviv, Israel.
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3
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Rathnasinghe R, Jangra S, Ye C, Cupic A, Singh G, Martínez-Romero C, Mulder LCF, Kehrer T, Yildiz S, Choi A, Yeung ST, Mena I, Gillespie V, De Vrieze J, Aslam S, Stadlbauer D, Meekins DA, McDowell CD, Balaraman V, Corley MJ, Richt JA, De Geest BG, Miorin L, Krammer F, Martinez-Sobrido L, Simon V, García-Sastre A, Schotsaert M. Characterization of SARS-CoV-2 Spike mutations important for infection of mice and escape from human immune sera. Nat Commun 2022; 13:3921. [PMID: 35798721 PMCID: PMC9261898 DOI: 10.1038/s41467-022-30763-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 05/13/2022] [Indexed: 12/25/2022] Open
Abstract
Due to differences in human and murine angiotensin converting enzyme 2 (ACE-2) receptor, initially available SARS-CoV-2 isolates could not infect mice. Here we show that serial passaging of USA-WA1/2020 strain in mouse lungs results in "mouse-adapted" SARS-CoV-2 (MA-SARS-CoV-2) with mutations in S, M, and N genes, and a twelve-nucleotide insertion in the S gene. MA-SARS-CoV-2 infection causes mild disease, with more pronounced morbidity depending on genetic background and in aged and obese mice. Two mutations in the S gene associated with mouse adaptation (N501Y, H655Y) are present in SARS-CoV-2 variants of concern (VoCs). N501Y in the receptor binding domain of viruses of the B.1.1.7, B.1.351, P.1 and B.1.1.529 lineages (Alpha, Beta, Gamma and Omicron variants) is associated with high transmissibility and allows VoCs to infect wild type mice. We further show that S protein mutations of MA-SARS-CoV-2 do not affect neutralization efficiency by human convalescent and post vaccination sera.
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Affiliation(s)
- Raveen Rathnasinghe
- grid.59734.3c0000 0001 0670 2351Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, New York, NY USA ,grid.476726.6Present Address: Seqirus, Cambridge, MT USA
| | - Sonia Jangra
- grid.59734.3c0000 0001 0670 2351Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, New York, NY USA
| | - Chengjin Ye
- grid.250889.e0000 0001 2215 0219Texas Biomedical Research Institute, San Antonio, TX USA
| | - Anastasija Cupic
- grid.59734.3c0000 0001 0670 2351Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, New York, NY USA
| | - Gagandeep Singh
- grid.59734.3c0000 0001 0670 2351Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, New York, NY USA
| | - Carles Martínez-Romero
- grid.59734.3c0000 0001 0670 2351Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, New York, NY USA
| | - Lubbertus C. F. Mulder
- grid.59734.3c0000 0001 0670 2351Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, New York, NY USA
| | - Thomas Kehrer
- grid.59734.3c0000 0001 0670 2351Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, New York, NY USA
| | - Soner Yildiz
- grid.59734.3c0000 0001 0670 2351Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, New York, NY USA
| | - Angela Choi
- grid.59734.3c0000 0001 0670 2351Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, New York, NY USA ,grid.479574.c0000 0004 1791 3172Present Address: Moderna Therapeutics, Cambridge, MT USA
| | - Stephen T. Yeung
- grid.5386.8000000041936877XDivision of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, NY USA
| | - Ignacio Mena
- grid.59734.3c0000 0001 0670 2351Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, New York, NY USA
| | - Virginia Gillespie
- grid.59734.3c0000 0001 0670 2351Center for Comparative Medicine and Surgery, Icahn School of Medicine at Mount Sinai New York, New York, NY USA
| | - Jana De Vrieze
- grid.5342.00000 0001 2069 7798Department of Pharmaceutics, Ghent University, Ghent, Belgium
| | - Sadaf Aslam
- grid.59734.3c0000 0001 0670 2351Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, New York, NY USA
| | - Daniel Stadlbauer
- grid.59734.3c0000 0001 0670 2351Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, New York, NY USA ,grid.479574.c0000 0004 1791 3172Present Address: Moderna Therapeutics, Cambridge, MT USA
| | - David A. Meekins
- grid.36567.310000 0001 0737 1259Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS USA
| | - Chester D. McDowell
- grid.36567.310000 0001 0737 1259Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS USA
| | - Velmurugan Balaraman
- grid.36567.310000 0001 0737 1259Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS USA
| | - Michael J. Corley
- grid.5386.8000000041936877XDivision of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, NY USA
| | - Juergen A. Richt
- grid.36567.310000 0001 0737 1259Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS USA
| | - Bruno G. De Geest
- grid.5342.00000 0001 2069 7798Department of Pharmaceutics, Ghent University, Ghent, Belgium
| | - Lisa Miorin
- grid.59734.3c0000 0001 0670 2351Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, New York, NY USA
| | | | - Florian Krammer
- grid.59734.3c0000 0001 0670 2351Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, New York, NY USA
| | - Luis Martinez-Sobrido
- grid.250889.e0000 0001 2215 0219Texas Biomedical Research Institute, San Antonio, TX USA
| | - Viviana Simon
- grid.59734.3c0000 0001 0670 2351Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai New York, New York, NY USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, New York, NY, USA. .,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, New York, NY, USA. .,Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai New York, New York, NY, USA. .,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai New York, New York, NY, USA.
| | - Michael Schotsaert
- Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, New York, NY, USA. .,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, New York, NY, USA.
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4
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Metabolomic Analysis of Diverse Mice Reveals Hepatic Arginase-1 as Source of Plasma Arginase in Plasmodium chabaudi Infection. mBio 2021; 12:e0242421. [PMID: 34607466 PMCID: PMC8546868 DOI: 10.1128/mbio.02424-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Infections disrupt host metabolism, but the factors that dictate the nature and magnitude of metabolic change are incompletely characterized. To determine how host metabolism changes in relation to disease severity in murine malaria, we performed plasma metabolomics on eight Plasmodium chabaudi-infected mouse strains with diverse disease phenotypes. We identified plasma metabolic biomarkers for both the nature and severity of different malarial pathologies. A subset of metabolic changes, including plasma arginine depletion, match the plasma metabolomes of human malaria patients, suggesting new connections between pathology and metabolism in human malaria. In our malarial mice, liver damage, which releases hepatic arginase-1 (Arg1) into circulation, correlated with plasma arginine depletion. We confirmed that hepatic Arg1 was the primary source of increased plasma arginase activity in our model, which motivates further investigation of liver damage in human malaria patients. More broadly, our approach shows how leveraging phenotypic diversity can identify and validate relationships between metabolism and the pathophysiology of infectious disease. IMPORTANCE Malaria is a severe and sometimes fatal infectious disease endemic to tropical and subtropical regions. Effective vaccines against malaria-causing Plasmodium parasites remain elusive, and malaria treatments often fail to prevent severe disease. Small molecules that target host metabolism have recently emerged as candidates for therapeutics in malaria and other diseases. However, our limited understanding of how metabolites affect pathophysiology limits our ability to develop new metabolite therapies. By providing a rich data set of metabolite-pathology correlations and by validating one of those correlations, our work is an important step toward harnessing metabolism to mitigate disease. Specifically, we showed that liver damage in P. chabaudi-infected mice releases hepatic arginase-1 into circulation, where it may deplete plasma arginine, a candidate malaria therapeutic that mitigates vascular stress. Our data suggest that liver damage may confound efforts to increase levels of arginine in human malaria patients.
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5
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Martin MD, Sompallae R, Winborn CS, Harty JT, Badovinac VP. Diverse CD8 T Cell Responses to Viral Infection Revealed by the Collaborative Cross. Cell Rep 2021; 31:107508. [PMID: 32294433 PMCID: PMC7212788 DOI: 10.1016/j.celrep.2020.03.072] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 01/31/2020] [Accepted: 03/20/2020] [Indexed: 12/24/2022] Open
Abstract
Enhanced host protection against re-infection requires generation of memory T cells of sufficient quantity and functional quality. Unlike well-studied inbred mice, T cell responses of diverse size and quality are generated following infection of humans and outbred mice. Thus, additional models are needed that accurately reflect variation in immune outcomes in genetically diverse populations and to uncover underlying genetic causes. The Collaborative Cross (CC), a large recombinant inbred panel of mice, is an ideal model in this pursuit for the high degree of genetic variation present, because it allows for assessment of genetic factors underlying unique phenotypes. Here, we advance the utility of the CC as a tool to analyze the immune response to viral infection. We describe variability in resting immune cell composition and adaptive immune responses generated among CC strains following systemic virus infection and reveal quantitative trait loci responsible for generation of CD62L+ memory CD8 T cells. Martin et al. advance the use of the Collaborative Cross (CC) for studying adaptive immune responses. They demonstrate that the CC better models variation in T cell responses seen in outbred mice and humans and that it can uncover genes linked to generation of qualitatively distinct memory cells following infection.
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Affiliation(s)
- Matthew D Martin
- Department of Pathology, University of Iowa, Iowa City, IA 52242, USA
| | | | | | - John T Harty
- Department of Pathology, University of Iowa, Iowa City, IA 52242, USA; Interdisciplinary Graduate Program in Immunology, University of Iowa, Iowa City, IA 52242, USA; Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242, USA
| | - Vladimir P Badovinac
- Department of Pathology, University of Iowa, Iowa City, IA 52242, USA; Interdisciplinary Graduate Program in Immunology, University of Iowa, Iowa City, IA 52242, USA; Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242, USA.
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6
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Graham JB, Swarts JL, Leist SR, Schäfer A, Menachery VD, Gralinski LE, Jeng S, Miller DR, Mooney MA, McWeeney SK, Ferris MT, Pardo-Manuel de Villena F, Heise MT, Baric RS, Lund JM. Baseline T cell immune phenotypes predict virologic and disease control upon SARS-CoV infection in Collaborative Cross mice. PLoS Pathog 2021; 17:e1009287. [PMID: 33513210 PMCID: PMC7875398 DOI: 10.1371/journal.ppat.1009287] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 02/10/2021] [Accepted: 01/05/2021] [Indexed: 12/25/2022] Open
Abstract
The COVID-19 pandemic has revealed that infection with SARS-CoV-2 can result in a wide range of clinical outcomes in humans. An incomplete understanding of immune correlates of protection represents a major barrier to the design of vaccines and therapeutic approaches to prevent infection or limit disease. This deficit is largely due to the lack of prospectively collected, pre-infection samples from individuals that go on to become infected with SARS-CoV-2. Here, we utilized data from genetically diverse Collaborative Cross (CC) mice infected with SARS-CoV to determine whether baseline T cell signatures are associated with a lack of viral control and severe disease upon infection. SARS-CoV infection of CC mice results in a variety of viral load trajectories and disease outcomes. Overall, a dysregulated, pro-inflammatory signature of circulating T cells at baseline was associated with severe disease upon infection. Our study serves as proof of concept that circulating T cell signatures at baseline can predict clinical and virologic outcomes upon SARS-CoV infection. Identification of basal immune predictors in humans could allow for identification of individuals at highest risk of severe clinical and virologic outcomes upon infection, who may thus most benefit from available clinical interventions to restrict infection and disease.
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Affiliation(s)
- Jessica B. Graham
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, Unites States of America
| | - Jessica L. Swarts
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, Unites States of America
| | - Sarah R. Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, Unites States of America
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, Unites States of America
| | - Vineet D. Menachery
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, Unites States of America
- Department of Microbiology and Immunology, University of Texas Medical Center, Galveston, Texas, Unites States of America
| | - Lisa E. Gralinski
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, Unites States of America
| | - Sophia Jeng
- OHSU Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, Unites States of America
- Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, Oregon, Unites States of America
| | - Darla R. Miller
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, Unites States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, Unites States of America
| | - Michael A. Mooney
- Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, Oregon, Unites States of America
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, Oregon, Unites States of America
| | - Shannon K. McWeeney
- OHSU Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, Unites States of America
- Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, Oregon, Unites States of America
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, Oregon, Unites States of America
| | - Martin T. Ferris
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, Unites States of America
| | - Fernando Pardo-Manuel de Villena
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, Unites States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, Unites States of America
| | - Mark T. Heise
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, Unites States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, Unites States of America
| | - Ralph S. Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, Unites States of America
| | - Jennifer M. Lund
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, Unites States of America
- Department of Global Health, University of Washington, Seattle, Wasington, Unites States of America
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7
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Griffin LE, Essenmacher L, Racine KC, Iglesias-Carres L, Tessem JS, Smith SM, Neilson AP. Diet-induced obesity in genetically diverse collaborative cross mouse founder strains reveals diverse phenotype response and amelioration by quercetin treatment in 129S1/SvImJ, PWK/EiJ, CAST/PhJ, and WSB/EiJ mice. J Nutr Biochem 2021; 87:108521. [PMID: 33039581 DOI: 10.1016/j.jnutbio.2020.108521] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 09/17/2020] [Accepted: 09/30/2020] [Indexed: 12/13/2022]
Abstract
Significant evidence suggests protective effects of flavonoids against obesity in animal models, but these often do not translate to humans. One explanation for this disconnect is use of a few mouse strains (notably C57BL/6 J) in obesity studies. Obesity is a multifactorial disease. The underlying causes are not fully replicated by the high-fat C57BL/6 J model, despite phenotypic similarities. Furthermore, the impact of genetic factors on the activities of flavonoids is unknown. This study was designed to explore how diverse mouse strains respond to diet-induced obesity when fed a representative flavonoid. A subset of Collaborative Cross founder strains (males and females) were placed on dietary treatments (low-fat, high-fat, high-fat with quercetin, high-fat with quercetin and antibiotics) longitudinally. Diverse responses were observed across strains and sexes. Quercetin appeared to moderately blunt weight gain in male C57 and both sexes of 129S1/SvImJ mice, and slightly increased weight gain in female C57 mice. Surprisingly, quercetin dramatically blunted weight gain in male, but not female, PWK/PhJ mice. For female mice, quercetin blunted weight gain (relative to the high-fat phase) in CAST/PhJ, PWK/EiJ and WSB/EiJ mice compared to C57. Antibiotics did not generally result in loss of protective effects of quercetin. This highlights complex interactions between genetic factors, sex, obesity stimuli, and flavonoid intake, and the need to move away from single inbred mouse models to enhance translatability to diverse humans. These data justify use of genetically diverse Collaborative Cross and Diversity Outbred models which are emerging as invaluable tools in the field of personalized nutrition.
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Affiliation(s)
- Laura E Griffin
- Department of Food, Bioprocessing and Nutrition Sciences, Plants for Human Health Institute, North Carolina State University, Kannapolis, North Carolina, USA
| | - Lauren Essenmacher
- Department of Food Science and Technology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Kathryn C Racine
- Department of Food, Bioprocessing and Nutrition Sciences, Plants for Human Health Institute, North Carolina State University, Kannapolis, North Carolina, USA
| | - Lisard Iglesias-Carres
- Department of Food, Bioprocessing and Nutrition Sciences, Plants for Human Health Institute, North Carolina State University, Kannapolis, North Carolina, USA
| | - Jeffery S Tessem
- Department of Nutrition, Dietetics, and Food Science, Brigham Young University, Provo, Utah, USA
| | - Susan M Smith
- Department of Nutrition, Nutrition Research Institute, The University of North Carolina at Chapel Hill, Kannapolis, North Carolina, USA
| | - Andrew P Neilson
- Department of Food, Bioprocessing and Nutrition Sciences, Plants for Human Health Institute, North Carolina State University, Kannapolis, North Carolina, USA.
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8
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Forbester JL, Humphreys IR. Genetic influences on viral-induced cytokine responses in the lung. Mucosal Immunol 2021; 14:14-25. [PMID: 33184476 PMCID: PMC7658619 DOI: 10.1038/s41385-020-00355-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 10/14/2020] [Accepted: 10/20/2020] [Indexed: 02/06/2023]
Abstract
Infection with respiratory viruses such as influenza, respiratory syncytial virus and coronavirus provides a difficult immunological challenge for the host, where a balance must be established between controlling viral replication and limiting damage to the delicate lung structure. Although the genetic architecture of host responses to respiratory viral infections is not yet understood, it is clear there is underlying heritability that influences pathogenesis. Immune control of virus replication is essential in respiratory infections, but overt activation can enhance inflammation and disease severity. Cytokines initiate antiviral immune responses but are implicated in viral pathogenesis. Here, we discuss how host genetic variation may influence cytokine responses to respiratory viral infections and, based on our current understanding of the role that cytokines play in viral pathogenesis, how this may influence disease severity. We also discuss how induced pluripotent stem cells may be utilised to probe the mechanistic implications of allelic variation in genes in virus-induced inflammatory responses. Ultimately, this could help to design better immune modulators, stratify high risk patients and tailor anti-inflammatory treatments, potentially expanding the ability to treat respiratory virus outbreaks in the future.
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Affiliation(s)
- Jessica L Forbester
- Division of Infection and Immunity/Systems Immunity University Research Institute, Cardiff University, Henry Wellcome Building, Heath Park, Cardiff, CF14 4XN, UK.
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DS, UK.
| | - Ian R Humphreys
- Division of Infection and Immunity/Systems Immunity University Research Institute, Cardiff University, Henry Wellcome Building, Heath Park, Cardiff, CF14 4XN, UK
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9
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Graham JB, Swarts JL, Leist SR, Schäfer A, Menachery VD, Gralinski LE, Jeng S, Miller DR, Mooney MA, McWeeney SK, Ferris MT, de Villena FPM, Heise MT, Baric RS, Lund JM. Baseline T cell immune phenotypes predict virologic and disease control upon SARS-CoV infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.09.21.306837. [PMID: 32995791 PMCID: PMC7523117 DOI: 10.1101/2020.09.21.306837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The COVID-19 pandemic has revealed that infection with SARS-CoV-2 can result in a wide range of clinical outcomes in humans, from asymptomatic or mild disease to severe disease that can require mechanical ventilation. An incomplete understanding of immune correlates of protection represents a major barrier to the design of vaccines and therapeutic approaches to prevent infection or limit disease. This deficit is largely due to the lack of prospectively collected, pre-infection samples from indiviuals that go on to become infected with SARS-CoV-2. Here, we utilized data from a screen of genetically diverse mice from the Collaborative Cross (CC) infected with SARS-CoV to determine whether circulating baseline T cell signatures are associated with a lack of viral control and severe disease upon infection. SARS-CoV infection of CC mice results in a variety of viral load trajectories and disease outcomes. Further, early control of virus in the lung correlates with an increased abundance of activated CD4 and CD8 T cells and regulatory T cells prior to infections across strains. A basal propensity of T cells to express IFNg and IL17 over TNFa also correlated with early viral control. Overall, a dysregulated, pro-inflammatory signature of circulating T cells at baseline was associated with severe disease upon infection. While future studies of human samples prior to infection with SARS-CoV-2 are required, our studies in mice with SARS-CoV serve as proof of concept that circulating T cell signatures at baseline can predict clinical and virologic outcomes upon SARS-CoV infection. Identification of basal immune predictors in humans could allow for identification of individuals at highest risk of severe clinical and virologic outcomes upon infection, who may thus most benefit from available clinical interventions to restrict infection and disease. SUMMARY We used a screen of genetically diverse mice from the Collaborative Cross infected with mouse-adapted SARS-CoV in combination with comprehensive pre-infection immunophenotyping to identify baseline circulating immune correlates of severe virologic and clinical outcomes upon SARS-CoV infection.
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Affiliation(s)
- Jessica B. Graham
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Jessica L. Swarts
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Sarah R. Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Vineet D. Menachery
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Microbiology and Immunology, University of Texas Medical Center, Galveston, TX
| | - Lisa E. Gralinski
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Sophia Jeng
- OHSU Knight Cancer Institute, Oregon Health & Science University, Portland, OR
- Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, OR
| | - Darla R. Miller
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Michael A. Mooney
- Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, OR
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR
| | - Shannon K. McWeeney
- OHSU Knight Cancer Institute, Oregon Health & Science University, Portland, OR
- Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, OR
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR
| | - Martin T. Ferris
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Fernando Pardo-Manuel de Villena
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Mark T. Heise
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Ralph S. Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Jennifer M. Lund
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
- Department of Global Health, University of Washington, Seattle, WA
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10
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Graham JB, Swarts JL, Menachery VD, Gralinski LE, Schäfer A, Plante KS, Morrison CR, Voss KM, Green R, Choonoo G, Jeng S, Miller DR, Mooney MA, McWeeney SK, Ferris MT, Pardo-Manuel de Villena F, Gale M, Heise MT, Baric RS, Lund JM. Immune Predictors of Mortality After Ribonucleic Acid Virus Infection. J Infect Dis 2020; 221:882-889. [PMID: 31621854 PMCID: PMC7107456 DOI: 10.1093/infdis/jiz531] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 10/11/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Virus infections result in a range of clinical outcomes for the host, from asymptomatic to severe or even lethal disease. Despite global efforts to prevent and treat virus infections to limit morbidity and mortality, the continued emergence and re-emergence of new outbreaks as well as common infections such as influenza persist as a health threat. Challenges to the prevention of severe disease after virus infection include both a paucity of protective vaccines as well as the early identification of individuals with the highest risk that may require supportive treatment. METHODS We completed a screen of mice from the Collaborative Cross (CC) that we infected with influenza, severe acute respiratory syndrome-coronavirus, and West Nile virus. RESULTS The CC mice exhibited a range of disease manifestations upon infections, and we used this natural variation to identify strains with mortality after infection and strains exhibiting no mortality. We then used comprehensive preinfection immunophenotyping to identify global baseline immune correlates of protection from mortality to virus infection. CONCLUSIONS These data suggest that immune phenotypes might be leveraged to identify humans at highest risk of adverse clinical outcomes upon infection, who may most benefit from intensive clinical interventions, in addition to providing insight for rational vaccine design.
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Affiliation(s)
- Jessica B Graham
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Jessica L Swarts
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Vineet D Menachery
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Department of Microbiology and Immunology, University of Texas Medical Center, Galveston, Texas, USA
| | - Lisa E Gralinski
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Kenneth S Plante
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Clayton R Morrison
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Kathleen M Voss
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Richard Green
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Gabrielle Choonoo
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, Oregon, USA
| | - Sophia Jeng
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, Oregon, USA
| | - Darla R Miller
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Michael A Mooney
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, Oregon, USA.,OHSU Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA
| | - Shannon K McWeeney
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, Oregon, USA.,OHSU Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA.,Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, Oregon, USA
| | - Martin T Ferris
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Fernando Pardo-Manuel de Villena
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Michael Gale
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Mark T Heise
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jennifer M Lund
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Global Health, University of Washington, Seattle, Washington, USA
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11
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Genetic Diversity of Collaborative Cross Mice Controls Viral Replication, Clinical Severity, and Brain Pathology Induced by Zika Virus Infection, Independently of Oas1b. J Virol 2020; 94:JVI.01034-19. [PMID: 31694939 DOI: 10.1128/jvi.01034-19] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 11/03/2019] [Indexed: 12/11/2022] Open
Abstract
The explosive spread of Zika virus (ZIKV) has been associated with major variations in severe disease and congenital afflictions among infected populations, suggesting an influence of host genes. We investigated how genome-wide variants could impact susceptibility to ZIKV infection in mice. We first describe that the susceptibility of Ifnar1-knockout mice is largely influenced by their genetic background. We then show that Collaborative Cross (CC) mice, which exhibit a broad genetic diversity, in which the type I interferon receptor (IFNAR) was blocked by an anti-IFNAR antibody expressed phenotypes ranging from complete resistance to severe symptoms and death, with large variations in the peak and the rate of decrease in the plasma viral load, in the brain viral load, in brain histopathology, and in the viral replication rate in infected cells. The differences in susceptibility to ZIKV between CC strains correlated with the differences in susceptibility to dengue and West Nile viruses between the strains. We identified highly susceptible and resistant mouse strains as new models to investigate the mechanisms of human ZIKV disease and other flavivirus infections. Genetic analyses revealed that phenotypic variations are driven by multiple genes with small effects, reflecting the complexity of ZIKV disease susceptibility in the human population. Notably, our results rule out the possibility of a role of the Oas1b gene in the susceptibility to ZIKV. Altogether, the findings of this study emphasize the role of host genes in the pathogeny of ZIKV infection and lay the foundation for further genetic and mechanistic studies.IMPORTANCE In recent outbreaks, ZIKV has infected millions of people and induced rare but potentially severe complications, including Guillain-Barré syndrome and encephalitis in adults. While several viral sequence variants were proposed to enhance the pathogenicity of ZIKV, the influence of host genetic variants in mediating the clinical heterogeneity remains mostly unexplored. We addressed this question using a mouse panel which models the genetic diversity of the human population and a ZIKV strain from a recent clinical isolate. Through a combination of in vitro and in vivo approaches, we demonstrate that multiple host genetic variants determine viral replication in infected cells and the clinical severity, the kinetics of blood viral load, and brain pathology in mice. We describe new mouse models expressing high degrees of susceptibility or resistance to ZIKV and to other flaviviruses. These models will facilitate the identification and mechanistic characterization of host genes that influence ZIKV pathogenesis.
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12
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Noll KE, Ferris MT, Heise MT. The Collaborative Cross: A Systems Genetics Resource for Studying Host-Pathogen Interactions. Cell Host Microbe 2019; 25:484-498. [PMID: 30974083 PMCID: PMC6494101 DOI: 10.1016/j.chom.2019.03.009] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Host genetic variation has a major impact on infectious disease susceptibility. The study of pathogen resistance genes, largely aided by mouse models, has significantly advanced our understanding of infectious disease pathogenesis. The Collaborative Cross (CC), a newly developed multi-parental mouse genetic reference population, serves as a tractable model system to study how pathogens interact with genetically diverse populations. In this review, we summarize progress utilizing the CC as a platform to develop improved models of pathogen-induced disease and to map polymorphic host response loci associated with variation in susceptibility to pathogens.
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Affiliation(s)
- Kelsey E Noll
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Martin T Ferris
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Mark T Heise
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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13
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Leist SR, Baric RS. Giving the Genes a Shuffle: Using Natural Variation to Understand Host Genetic Contributions to Viral Infections. Trends Genet 2018; 34:777-789. [PMID: 30131185 PMCID: PMC7114642 DOI: 10.1016/j.tig.2018.07.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 07/15/2018] [Accepted: 07/19/2018] [Indexed: 01/01/2023]
Abstract
The laboratory mouse has proved an invaluable model to identify host factors that regulate the progression and outcome of virus-induced disease. The paradigm is to use single-gene knockouts in inbred mouse strains or genetic mapping studies using biparental mouse populations. However, genetic variation among these mouse strains is limited compared with the diversity seen in human populations. To address this disconnect, a multiparental mouse population has been developed to specifically dissect the multigenetic regulation of complex disease traits. The Collaborative Cross (CC) population of recombinant inbred mouse strains is a well-suited systems-genetics tool to identify susceptibility alleles that control viral and microbial infection outcomes and immune responses and to test the promise of personalized medicine.
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Affiliation(s)
- Sarah R Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; https://sph.unc.edu/adv_profile/ralph-s-baric-phd/
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14
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Abu Toamih Atamni H, Nashef A, Iraqi FA. The Collaborative Cross mouse model for dissecting genetic susceptibility to infectious diseases. Mamm Genome 2018; 29:471-487. [PMID: 30143822 DOI: 10.1007/s00335-018-9768-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 08/02/2018] [Indexed: 12/18/2022]
Abstract
Infectious diseases, also known as communicable diseases, refer to a full range of maladies caused by pathogen invasion to the host body. Host response towards an infectious pathogen varies between individuals, and can be defined by responses from asymptomatic to lethal. Host response to infectious pathogens is considered as a complex trait controlled by gene-gene (host-pathogen) and gene-environment interactions, leading to the extensive phenotypic variations between individuals. With the advancement of the human genome mapping approaches and tools, various genome-wide association studies (GWAS) were performed, aimed at mapping the genetic basis underlying host susceptibility towards infectious pathogens. In parallel, immense efforts were invested in enhancing the genetic mapping resolution and gene-cloning efficacy, using advanced mouse models including advanced intercross lines; outbred populations; consomic, congenic; and recombinant inbred lines. Notwithstanding the evident advances achieved using these mouse models, the genetic diversity was low and quantitative trait loci (QTL) mapping resolution was inadequate. Consequently, the Collaborative Cross (CC) mouse model was established by full-reciprocal mating of eight divergent founder strains of mice (A/J, C57BL/6J, 129S1/SvImJ, NOD/LtJ, NZO/HiLtJ, CAST/Ei, PWK/PhJ, and WSB/EiJ) generating a next-generation mouse genetic reference population (CC lines). Presently, the CC mouse model population comprises a set of about 200 recombinant inbred CC lines exhibiting a unique high genetic diversity and which are accessible for multidisciplinary studies. The CC mouse model efficacy was validated by various studies in our lab and others, accomplishing high-resolution (< 1 MB) QTL genomic mapping for a variety of complex traits, using about 50 CC lines (3-4 mice per line). Herein, we present a number of studies demonstrating the power of the CC mouse model, which has been utilized in our lab for mapping the genetic basis of host susceptibility to various infectious pathogens. These include Aspergillus fumigatus, Klebsiella pneumoniae, Porphyromonas gingivalis and Fusobacterium nucleatum (causing oral mixed infection), Pseudomonas aeruginosa, and the bacterial toxins Lipopolysaccharide and Lipoteichoic acid.
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Affiliation(s)
- Hanifa Abu Toamih Atamni
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Tel Aviv, 69978, Israel
| | - Aysar Nashef
- Department of Prosthodontics, Dental school, The Hebrew University, Hadassah Jerusalem, Israel.,Department of Cranio-maxillofacial Surgery, Poria Medical Centre, The Azrieli School of Medicine, Bar Ilan University, Safed, Israel
| | - Fuad A Iraqi
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Tel Aviv, 69978, Israel.
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15
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Graham JB, Swarts JL, Mooney M, Choonoo G, Jeng S, Miller DR, Ferris MT, McWeeney S, Lund JM. Extensive Homeostatic T Cell Phenotypic Variation within the Collaborative Cross. Cell Rep 2018; 21:2313-2325. [PMID: 29166619 PMCID: PMC5728448 DOI: 10.1016/j.celrep.2017.10.093] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 07/14/2017] [Accepted: 10/25/2017] [Indexed: 12/11/2022] Open
Abstract
The Collaborative Cross (CC) is a panel of reproducible recombinant inbred mouse strains with high levels of standing genetic variation, affording an unprecedented opportunity to perform experiments in a small animal model containing controlled genetic diversity while allowing for genetic replicates. Here, we advance the utility of this unique mouse resource for immunology research because it allows for both examination and genetic dissection of mechanisms behind adaptive immune states in mice with distinct and defined genetic makeups. This approach is based on quantitative trait locus mapping: identifying genetically variant genome regions associated with phenotypic variance in traits of interest. Furthermore, the CC can be utilized for mouse model development; distinct strains have unique immunophenotypes and immune properties, making them suitable for research on particular diseases and infections. Here, we describe variations in cellular immune phenotypes across F1 crosses of CC strains and reveal quantitative trait loci responsible for several immune phenotypes. The Collaborative Cross models the phenotypic diversity observed in human immunity QTL mapping in the CC reveals candidate genes linked to T cell phenotypes
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Affiliation(s)
- Jessica B Graham
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jessica L Swarts
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Michael Mooney
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR 97239, USA; OHSU Knight Cancer Center Institute, Oregon Health and Science University, Portland, OR 97239, USA
| | - Gabrielle Choonoo
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR 97239, USA; OHSU Knight Cancer Center Institute, Oregon Health and Science University, Portland, OR 97239, USA
| | - Sophia Jeng
- Oregon Clinical and Translational Research Institute, Oregon Health and Science University, Portland, OR 97239, USA
| | - Darla R Miller
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Martin T Ferris
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Shannon McWeeney
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR 97239, USA; OHSU Knight Cancer Center Institute, Oregon Health and Science University, Portland, OR 97239, USA; Oregon Clinical and Translational Research Institute, Oregon Health and Science University, Portland, OR 97239, USA
| | - Jennifer M Lund
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Global Health, University of Washington, Seattle, WA 98195, USA.
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16
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Stacey HD, Barjesteh N, Mapletoft JP, Miller MS. "Gnothi Seauton": Leveraging the Host Response to Improve Influenza Virus Vaccine Efficacy. Vaccines (Basel) 2018; 6:vaccines6020023. [PMID: 29649134 PMCID: PMC6027147 DOI: 10.3390/vaccines6020023] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 04/09/2018] [Accepted: 04/10/2018] [Indexed: 02/07/2023] Open
Abstract
Vaccination against the seasonal influenza virus is the best way to prevent infection. Nevertheless, vaccine efficacy remains far from optimal especially in high-risk populations such as the elderly. Recent technological advancements have facilitated rapid and precise identification of the B and T cell epitopes that are targets for protective responses. While these discoveries have undoubtedly brought the field closer to "universal" influenza virus vaccines, choosing the correct antigen is only one piece of the equation. Achieving efficacy and durability requires a detailed understanding of the diverse host factors and pathways that are required for attaining optimal responses. Sequencing technologies, systems biology, and immunological studies have recently advanced our understanding of the diverse aspects of the host response required for vaccine efficacy. In this paper, we review the critical role of the host response in determining efficacious responses and discuss the gaps in knowledge that will need to be addressed if the field is to be successful in developing new and more effective influenza virus vaccines.
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Affiliation(s)
- Hannah D Stacey
- Michael G. DeGroote Institute for Infectious Diseases Research, McMaster Immunology Research Centre, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada.
| | - Neda Barjesteh
- Michael G. DeGroote Institute for Infectious Diseases Research, McMaster Immunology Research Centre, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada.
| | - Jonathan P Mapletoft
- Michael G. DeGroote Institute for Infectious Diseases Research, McMaster Immunology Research Centre, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada.
| | - Matthew S Miller
- Michael G. DeGroote Institute for Infectious Diseases Research, McMaster Immunology Research Centre, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada.
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17
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Influenza Pathogenesis in Genetically Defined Resistant and Susceptible Murine Strains
. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2017; 90:471-479. [PMID: 28955185 PMCID: PMC5612189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
The murine infection model is a cornerstone for influenza virus research and includes aspects such as disease pathogenesis, immunobiology, and vaccine and antiviral drug development. One compelling feature of the murine model is the availability of inbred mouse strains, each with a unique genetic makeup and potential for variable responses to influenza infection. Using highly controlled infection studies, the response to influenza virus infection is classified on a spectrum from susceptible to resistant, reflecting severe morbidity and high mortality, to limited or no morbidity and no mortality. Although there have been a variety of studies establishing disparate pathogenesis amongst various murine strains, thus far, there is no consensus regarding the determinants of the outcome of infection. The goal of this review is to explore and discuss the differences in pathogenesis, as well as the innate and adaptive immune responses to influenza infection that have been described in susceptible and resistant mouse strains. Understanding how host genetics influences the response to influenza infection provides valuable insight into the variable responses seen in vaccine or drug efficacy studies, as well as indicates possible mechanisms contributing to increased disease severity in humans infected with influenza virus with no known risk factors.
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18
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Suwanmanee T, Ferris MT, Hu P, Gui T, Montgomery SA, Pardo-Manuel de Villena F, Kafri T. Toward Personalized Gene Therapy: Characterizing the Host Genetic Control of Lentiviral-Vector-Mediated Hepatic Gene Delivery. Mol Ther Methods Clin Dev 2017; 5:83-92. [PMID: 28480308 PMCID: PMC5415322 DOI: 10.1016/j.omtm.2017.03.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 03/30/2017] [Indexed: 12/21/2022]
Abstract
The success of lentiviral vectors in curing fatal genetic and acquired diseases has opened a new era in human gene therapy. However, variability in the efficacy and safety of this therapeutic approach has been reported in human patients. Consequently, lentiviral-vector-based gene therapy is limited to incurable human diseases, with little understanding of the underlying causes of adverse effects and poor efficacy. To assess the role that host genetic variation has on efficacy of gene therapy, we characterized lentiviral-vector gene therapy within a set of 12 collaborative cross mouse strains. Lentiviral vectors carrying the firefly luciferase cDNA under the control of a liver-specific promoter were administered to female mice, with total-body and hepatic luciferase expression periodically monitored through 41 weeks post-vector administration. Vector copy number per diploid genome in mouse liver and spleen was determined at the end of this study. We identified major strain-specific contributions to overall success of transduction, vector biodistribution, maximum luciferase expression, and the kinetics of luciferase expression throughout the study. Our results highlight the importance of genetic variation on gene-therapeutic efficacy; provide new models with which to more rigorously assess gene therapy approaches; and suggest that redesigning preclinical studies of gene-therapy methodologies might be appropriate.
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Affiliation(s)
- Thipparat Suwanmanee
- Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Martin T. Ferris
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Peirong Hu
- Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Tong Gui
- Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Stephanie A. Montgomery
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Fernando Pardo-Manuel de Villena
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Tal Kafri
- Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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19
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Zhan L, Tang J, Sun M, Qin C. Animal Models for Tuberculosis in Translational and Precision Medicine. Front Microbiol 2017; 8:717. [PMID: 28522990 PMCID: PMC5415616 DOI: 10.3389/fmicb.2017.00717] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 04/06/2017] [Indexed: 12/12/2022] Open
Abstract
Tuberculosis (TB) is a health threat to the global population. Anti-TB drugs and vaccines are key approaches for TB prevention and control. TB animal models are basic tools for developing biomarkers of diagnosis, drugs for therapy, vaccines for prevention and researching pathogenic mechanisms for identification of targets; thus, they serve as the cornerstone of comparative medicine, translational medicine, and precision medicine. In this review, we discuss the current use of TB animal models and their problems, as well as offering perspectives on the future of these models.
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Affiliation(s)
- Lingjun Zhan
- Key Laboratory of Human Disease Comparative Medicine, Ministry of HealthBeijing, China.,Institution of Laboratory Animal Sciences, Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing, China.,Beijing Key Laboratory for Animal Models of Emerging and Reemerging InfectiousBeijing, China.,Beijing Engineering Research Center for Experimental Animal Models of Human Critical DiseasesBeijing, China.,Key Laboratory of Human Diseases Animal Model, State Administration of Traditional Chinese MedicineBeijing, China
| | - Jun Tang
- Key Laboratory of Human Disease Comparative Medicine, Ministry of HealthBeijing, China.,Institution of Laboratory Animal Sciences, Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing, China.,Beijing Key Laboratory for Animal Models of Emerging and Reemerging InfectiousBeijing, China.,Beijing Engineering Research Center for Experimental Animal Models of Human Critical DiseasesBeijing, China.,Key Laboratory of Human Diseases Animal Model, State Administration of Traditional Chinese MedicineBeijing, China
| | - Mengmeng Sun
- Key Laboratory of Human Disease Comparative Medicine, Ministry of HealthBeijing, China.,Institution of Laboratory Animal Sciences, Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing, China.,Beijing Key Laboratory for Animal Models of Emerging and Reemerging InfectiousBeijing, China.,Beijing Engineering Research Center for Experimental Animal Models of Human Critical DiseasesBeijing, China.,Key Laboratory of Human Diseases Animal Model, State Administration of Traditional Chinese MedicineBeijing, China
| | - Chuan Qin
- Key Laboratory of Human Disease Comparative Medicine, Ministry of HealthBeijing, China.,Institution of Laboratory Animal Sciences, Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing, China.,Beijing Key Laboratory for Animal Models of Emerging and Reemerging InfectiousBeijing, China.,Beijing Engineering Research Center for Experimental Animal Models of Human Critical DiseasesBeijing, China.,Key Laboratory of Human Diseases Animal Model, State Administration of Traditional Chinese MedicineBeijing, China
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