1
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Schäfer A, Gralinski LE, Leist SR, Hampton BK, Mooney MA, Jensen KL, Graham RL, Agnihothram S, Jeng S, Chamberlin S, Bell TA, Scobey DT, Linnertz CL, VanBlargan LA, Thackray LB, Hock P, Miller DR, Shaw GD, Diamond MS, de Villena FPM, McWeeney SK, Heise MT, Menachery VD, Ferris MT, Baric RS. Genetic loci regulate Sarbecovirus pathogenesis: A comparison across mice and humans. Virus Res 2024; 344:199357. [PMID: 38508400 PMCID: PMC10981091 DOI: 10.1016/j.virusres.2024.199357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 02/15/2024] [Accepted: 03/16/2024] [Indexed: 03/22/2024]
Abstract
Coronavirus (CoV) cause considerable morbidity and mortality in humans and other mammals, as evidenced by the emergence of Severe Acute Respiratory CoV (SARS-CoV) in 2003, Middle East Respiratory CoV (MERS-CoV) in 2012, and SARS-CoV-2 in 2019. Although poorly characterized, natural genetic variation in human and other mammals modulate virus pathogenesis, as reflected by the spectrum of clinical outcomes ranging from asymptomatic infections to lethal disease. Using multiple human epidemic and zoonotic Sarbecoviruses, coupled with murine Collaborative Cross genetic reference populations, we identify several dozen quantitative trait loci that regulate SARS-like group-2B CoV pathogenesis and replication. Under a Chr4 QTL, we deleted a candidate interferon stimulated gene, Trim14 which resulted in enhanced SARS-CoV titers and clinical disease, suggesting an antiviral role during infection. Importantly, about 60 % of the murine QTL encode susceptibility genes identified as priority candidates from human genome-wide association studies (GWAS) studies after SARS-CoV-2 infection, suggesting that similar selective forces have targeted analogous genes and pathways to regulate Sarbecovirus disease across diverse mammalian hosts. These studies provide an experimental platform in rodents to investigate the molecular-genetic mechanisms by which potential cross mammalian susceptibility loci and genes regulate type-specific and cross-SARS-like group 2B CoV replication, immunity, and pathogenesis in rodent models. Our study also provides a paradigm for identifying susceptibility loci for other highly heterogeneous and virulent viruses that sporadically emerge from zoonotic reservoirs to plague human and animal populations.
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Affiliation(s)
- Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Lisa E Gralinski
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Sarah R Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Brea K Hampton
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michael A Mooney
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Division of Bioinformatics and Computational Biology, Oregon Health & Science University, Portland, OR, USA; Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA
| | - Kara L Jensen
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Rachel L Graham
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sudhakar Agnihothram
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sophia Jeng
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, OR, USA
| | - Steven Chamberlin
- Division of Bioinformatics and Computational Biology, Oregon Health & Science University, Portland, OR, USA; Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA
| | - Timothy A Bell
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - D Trevor Scobey
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Colton L Linnertz
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Laura A VanBlargan
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Larissa B Thackray
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Pablo Hock
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Darla R Miller
- 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
| | - Ginger D Shaw
- 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
| | - Michael S Diamond
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA; Department of Pathology & Immunology2, Washington University School of Medicine, St. Louis, MO, USA; Department of Molecular Microbiology3, Washington University School of Medicine, St. Louis, MO, 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
| | - Shannon K McWeeney
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Division of Bioinformatics and Computational Biology, Oregon Health & Science University, Portland, OR, USA; Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA; Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, OR, USA
| | - Mark T Heise
- Department of Genetics, 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; Rapidly Emerging Antiviral Drug Discovery Initiative, University of North Carolina, Chapel Hill NC, USA
| | - Vineet D Menachery
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston TX, USA; Department of Pathology and Center for Biodefense & Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX, USA
| | - Martin T Ferris
- Department of Genetics, 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; Rapidly Emerging Antiviral Drug Discovery Initiative, University of North Carolina, Chapel Hill NC, USA.
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2
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Dillard JA, Taft-Benz SA, Knight AC, Anderson EJ, Pressey KD, Parotti B, Martinez SA, Diaz JL, Sarkar S, Madden EA, De la Cruz G, Adams LE, Dinnon KH, Leist SR, Martinez DR, Schäfer A, Powers JM, Yount BL, Castillo IN, Morales NL, Burdick J, Evangelista MKD, Ralph LM, Pankow NC, Linnertz CL, Lakshmanane P, Montgomery SA, Ferris MT, Baric RS, Baxter VK, Heise MT. Adjuvant-dependent impact of inactivated SARS-CoV-2 vaccines during heterologous infection by a SARS-related coronavirus. Nat Commun 2024; 15:3738. [PMID: 38702297 PMCID: PMC11068739 DOI: 10.1038/s41467-024-47450-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 04/02/2024] [Indexed: 05/06/2024] Open
Abstract
Whole virus-based inactivated SARS-CoV-2 vaccines adjuvanted with aluminum hydroxide have been critical to the COVID-19 pandemic response. Although these vaccines are protective against homologous coronavirus infection, the emergence of novel variants and the presence of large zoonotic reservoirs harboring novel heterologous coronaviruses provide significant opportunities for vaccine breakthrough, which raises the risk of adverse outcomes like vaccine-associated enhanced respiratory disease. Here, we use a female mouse model of coronavirus disease to evaluate inactivated vaccine performance against either homologous challenge with SARS-CoV-2 or heterologous challenge with a bat-derived coronavirus that represents a potential emerging disease threat. We show that inactivated SARS-CoV-2 vaccines adjuvanted with aluminum hydroxide can cause enhanced respiratory disease during heterologous infection, while use of an alternative adjuvant does not drive disease and promotes heterologous viral clearance. In this work, we highlight the impact of adjuvant selection on inactivated vaccine safety and efficacy against heterologous coronavirus infection.
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Affiliation(s)
- Jacob A Dillard
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sharon A Taft-Benz
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Audrey C Knight
- Department of Pathology & Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Elizabeth J Anderson
- Division of Comparative Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Katia D Pressey
- Division of Comparative Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Breantié Parotti
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sabian A Martinez
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jennifer L Diaz
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sanjay Sarkar
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Emily A Madden
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Gabriela De la Cruz
- Pathology Services Core, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lily E Adams
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kenneth H Dinnon
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sarah R Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - David R Martinez
- 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
| | - John M Powers
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Boyd L Yount
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Izabella N Castillo
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Noah L Morales
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jane Burdick
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Lauren M Ralph
- Pathology Services Core, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Nicholas C Pankow
- Pathology Services Core, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Colton L Linnertz
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Premkumar Lakshmanane
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Stephanie A Montgomery
- Department of Pathology & Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Dallas Tissue Research, Farmers Branch, TX, USA
| | - Martin T Ferris
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ralph S Baric
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Victoria K Baxter
- Department of Pathology & Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Division of Comparative Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Texas Biomedical Research Institute, San Antonio, TX, USA.
| | - Mark T Heise
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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3
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Risemberg EL, Smeekens JM, Cruz Cisneros MC, Hampton BK, Hock P, Linnertz CL, Miller DR, Orgel K, Shaw GD, Manuel de Villena FP, Burks AW, Valdar W, Kulis MD, Ferris MT. A mutation in Themis contributes to anaphylaxis severity following oral peanut challenge in CC027 mice. J Allergy Clin Immunol 2024:S0091-6749(24)00411-1. [PMID: 38670234 DOI: 10.1016/j.jaci.2024.03.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 03/12/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024]
Abstract
BACKGROUND The development of peanut allergy is due to a combination of genetic and environmental factors, although specific genes have proven difficult to identify. Previously, we reported that peanut-sensitized CC027/GeniUnc (CC027) mice develop anaphylaxis upon oral challenge to peanut, unlike C3H/HeJ (C3H) mice. OBJECTIVE To determine the genetic basis of orally-induced anaphylaxis to peanut in CC027 mice. METHODS A genetic mapping population between CC027 and C3H mice was designed to identify the genetic factors that drive oral anaphylaxis. A total of 356 CC027xC3H backcrossed mice were generated, sensitized to peanut, then challenged to peanut by oral gavage. Anaphylaxis and peanut-specific IgE were quantified for all mice. T-cell phenotyping was conducted on CC027 and five additional CC strains. RESULTS Anaphylaxis to peanut was absent in 77% of backcrossed mice, with 19% showing moderate anaphylaxis, and 4% having severe anaphylaxis. A total of eight genetic loci were associated with variation in response to peanut challenge, six associated with anaphylaxis (temperature decrease) and two associated with peanut-specific IgE levels. There were two major loci that impacted multiple aspects of the severity of acute anaphylaxis, at which the CC027 allele was associated with worse outcome. At one of these loci, CC027 has a private genetic variant in the Themis (thymocyte-expressed molecule involved in selection) gene. Consistent with Themis' described functions, we found that CC027 have more immature T cells with fewer CD8+, CD4+, and CD4+CD25+CD127- regulatory T cells. CONCLUSION Our results demonstrate a key role for Themis in the orally-reactive CC027 mouse model of peanut allergy.
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Affiliation(s)
- Ellen L Risemberg
- Curriculum in Bioinformatics and Computational Biology, UNC Chapel Hill; Department of Genetics, UNC Chapel Hill
| | - Johanna M Smeekens
- Department of Pediatrics, Division of Allergy and Immunology, UNC Chapel Hill
| | - Marta C Cruz Cisneros
- Department of Genetics, UNC Chapel Hill; Curriculum in Genetics and Molecular Biology, UNC Chapel Hill
| | - Brea K Hampton
- Department of Genetics, UNC Chapel Hill; Curriculum in Genetics and Molecular Biology, UNC Chapel Hill
| | | | | | | | - Kelly Orgel
- Department of Pediatrics, Division of Allergy and Immunology, UNC Chapel Hill
| | - Ginger D Shaw
- Department of Genetics, UNC Chapel Hill; Lineberger Comprehensive Cancer Center, UNC Chapel Hill
| | | | - A Wesley Burks
- Department of Pediatrics, Division of Allergy and Immunology, UNC Chapel Hill
| | - William Valdar
- Department of Genetics, UNC Chapel Hill; Lineberger Comprehensive Cancer Center, UNC Chapel Hill
| | - Michael D Kulis
- Department of Pediatrics, Division of Allergy and Immunology, UNC Chapel Hill
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4
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Schäfer A, Marzi A, Furuyama W, Catanzaro NJ, Nguyen C, Haddock E, Feldmann F, Meade-White K, Thomas T, Hubbard ML, Gully KL, Leist SR, Hock P, Bell TA, De la Cruz GE, Midkiff BR, Martinez DR, Shaw GD, Miller DR, Vernon MJ, Graham RL, Cowley DO, Montgomery SA, Schughart K, de Villena FPM, Wilkerson GK, Ferris MT, Feldmann H, Baric RS. Mapping of susceptibility loci for Ebola virus pathogenesis in mice. Cell Rep 2024; 43:114127. [PMID: 38652660 DOI: 10.1016/j.celrep.2024.114127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 03/11/2024] [Accepted: 04/03/2024] [Indexed: 04/25/2024] Open
Abstract
Ebola virus (EBOV), a major global health concern, causes severe, often fatal EBOV disease (EVD) in humans. Host genetic variation plays a critical role, yet the identity of host susceptibility loci in mammals remains unknown. Using genetic reference populations, we generate an F2 mapping cohort to identify host susceptibility loci that regulate EVD. While disease-resistant mice display minimal pathogenesis, susceptible mice display severe liver pathology consistent with EVD-like disease and transcriptional signatures associated with inflammatory and liver metabolic processes. A significant quantitative trait locus (QTL) for virus RNA load in blood is identified in chromosome (chr)8, and a severe clinical disease and mortality QTL is mapped to chr7, which includes the Trim5 locus. Using knockout mice, we validate the Trim5 locus as one potential driver of liver failure and mortality after infection. The identification of susceptibility loci provides insight into molecular genetic mechanisms regulating EVD progression and severity, potentially informing therapeutics and vaccination strategies.
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Affiliation(s)
- Alexandra Schäfer
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA.
| | - Andrea Marzi
- Laboratory of Virology, Division of Intramural Research, NIAID, NIH, Hamilton, MT 59840, USA.
| | - Wakako Furuyama
- Laboratory of Virology, Division of Intramural Research, NIAID, NIH, Hamilton, MT 59840, USA
| | - Nicholas J Catanzaro
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Cameron Nguyen
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Elaine Haddock
- Laboratory of Virology, Division of Intramural Research, NIAID, NIH, Hamilton, MT 59840, USA
| | - Friederike Feldmann
- Rocky Mountain Veterinary Branch, Division of Intramural Research, NIAID, NIH, Hamilton, MT 59840, USA
| | - Kimberly Meade-White
- Laboratory of Virology, Division of Intramural Research, NIAID, NIH, Hamilton, MT 59840, USA
| | - Tina Thomas
- Rocky Mountain Veterinary Branch, Division of Intramural Research, NIAID, NIH, Hamilton, MT 59840, USA
| | - Miranda L Hubbard
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Kendra L Gully
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Sarah R Leist
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Pablo Hock
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Timothy A Bell
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Gabriela E De la Cruz
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Bentley R Midkiff
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - David R Martinez
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Ginger D Shaw
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Darla R Miller
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Michael J Vernon
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Rachel L Graham
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Dale O Cowley
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; Animal Models Core Facility, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Stephanie A Montgomery
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Klaus Schughart
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA; Institute of Virology, University of Muenster, 48149 Muenster, Germany
| | - Fernando Pardo Manuel de Villena
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Gregory K Wilkerson
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Martin T Ferris
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Heinz Feldmann
- Laboratory of Virology, Division of Intramural Research, NIAID, NIH, Hamilton, MT 59840, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA.
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5
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Diaz J, Sears J, Chang CK, Burdick J, Law I, Sanders W, Linnertz C, Sylvester P, Moorman N, Ferris MT, Heise MT. U-CAN-seq: A Universal Competition Assay by Nanopore Sequencing. Viruses 2024; 16:636. [PMID: 38675976 PMCID: PMC11054411 DOI: 10.3390/v16040636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/09/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
RNA viruses quickly evolve subtle genotypic changes that can have major impacts on viral fitness and host range, with potential consequences for human health. It is therefore important to understand the evolutionary fitness of novel viral variants relative to well-studied genotypes of epidemic viruses. Competition assays are an effective and rigorous system with which to assess the relative fitness of viral genotypes. However, it is challenging to quickly and cheaply distinguish and quantify fitness differences between very similar viral genotypes. Here, we describe a protocol for using reverse transcription PCR in combination with commercial nanopore sequencing services to perform competition assays on untagged RNA viruses. Our assay, called the Universal Competition Assay by Nanopore Sequencing (U-CAN-seq), is relatively cheap and highly sensitive. We used a well-studied N24A mutation in the chikungunya virus (CHIKV) nsp3 gene to confirm that we could detect a competitive disadvantage using U-CAN-seq. We also used this approach to show that mutations to the CHIKV 5' conserved sequence element that disrupt sequence but not structure did not affect the fitness of CHIKV. However, similar mutations to an adjacent CHIKV stem loop (SL3) did cause a fitness disadvantage compared to wild-type CHIKV, suggesting that structure-independent, primary sequence determinants in this loop play an important role in CHIKV biology. Our novel findings illustrate the utility of the U-CAN-seq competition assay.
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Affiliation(s)
- Jennifer Diaz
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA; (J.D.)
| | - John Sears
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA; (J.D.)
| | - Che-Kang Chang
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA; (J.D.)
| | - Jane Burdick
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Isabella Law
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Wes Sanders
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA; (J.D.)
| | - Colton Linnertz
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Paul Sylvester
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Nathaniel Moorman
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA; (J.D.)
- The Rapidly Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, NC 275114, USA
| | - Martin T. Ferris
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Mark T. Heise
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA; (J.D.)
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
- The Rapidly Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, NC 275114, USA
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6
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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7
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Blanchard MW, Sigmon JS, Brennan J, Ahulamibe C, Allen ME, Baric RS, Bell TA, Farrington J, Ciavatta D, Cruz Cisneros M, Drushal M, Ferris MT, Fry R, Gaines C, Gu B, Heise MT, Hodges RA, Kafri T, Lynch R, Magnuson T, Miller D, Murphy CEY, Nguyen DT, Noll KE, Proulx M, Sassetti C, Shaw GD, Simon JM, Smith C, Styblo M, Tarantino L, Woo J, Pardo Manuel de Villena F. The Updated Mouse Universal Genotyping Array Bioinformatic Pipeline Improves Genetic QC in Laboratory Mice. bioRxiv 2024:2024.02.29.582794. [PMID: 38464063 PMCID: PMC10925293 DOI: 10.1101/2024.02.29.582794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
The MiniMUGA genotyping array is a popular tool for genetic QC of laboratory mice and genotyping of samples from most types of experimental crosses involving laboratory strains, particularly for reduced complexity crosses. The content of the production version of the MiniMUGA array is fixed; however, there is the opportunity to improve array's performance and the associated report's usefulness by leveraging thousands of samples genotyped since the initial description of MiniMUGA in 2020. Here we report our efforts to update and improve marker annotation, increase the number and the reliability of the consensus genotypes for inbred strains and increase the number of constructs that can reliably be detected with MiniMUGA. In addition, we have implemented key changes in the informatics pipeline to identify and quantify the contribution of specific genetic backgrounds to the makeup of a given sample, remove arbitrary thresholds, include the Y Chromosome and mitochondrial genome in the ideogram, and improve robust detection of the presence of commercially available substrains based on diagnostic alleles. Finally, we have made changes to the layout of the report, to simplify the interpretation and completeness of the analysis and added a table summarizing the ideogram. We believe that these changes will be of general interest to the mouse research community and will be instrumental in our goal of improving the rigor and reproducibility of mouse-based biomedical research.
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Cruz Cisneros MC, Anderson EJ, Hampton BK, Parotti B, Sarkar S, Taft-Benz S, Bell TA, Blanchard M, Dillard JA, Dinnon KH, Hock P, Leist SR, Madden EA, Shaw GD, West A, Baric RS, Baxter VK, Pardo-Manuel de Villena F, Heise MT, Ferris MT. Host Genetic Variation Impacts SARS-CoV-2 Vaccination Response in the Diversity Outbred Mouse Population. Vaccines (Basel) 2024; 12:103. [PMID: 38276675 PMCID: PMC10821422 DOI: 10.3390/vaccines12010103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024] Open
Abstract
The COVID-19 pandemic led to the rapid and worldwide development of highly effective vaccines against SARS-CoV-2. However, there is significant individual-to-individual variation in vaccine efficacy due to factors including viral variants, host age, immune status, environmental and host genetic factors. Understanding those determinants driving this variation may inform the development of more broadly protective vaccine strategies. While host genetic factors are known to impact vaccine efficacy for respiratory pathogens such as influenza and tuberculosis, the impact of host genetic variation on vaccine efficacy against COVID-19 is not well understood. To model the impact of host genetic variation on SARS-CoV-2 vaccine efficacy, while controlling for the impact of non-genetic factors, we used the Diversity Outbred (DO) mouse model. We found that DO mice immunized against SARS-CoV-2 exhibited high levels of variation in vaccine-induced neutralizing antibody responses. While the majority of the vaccinated mice were protected from virus-induced disease, similar to human populations, we observed vaccine breakthrough in a subset of mice. Importantly, we found that this variation in neutralizing antibody, virus-induced disease, and viral titer is heritable, indicating that the DO serves as a useful model system for studying the contribution of genetic variation of both vaccines and disease outcomes.
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Affiliation(s)
- Marta C. Cruz Cisneros
- Genetics and Molecular Biology Curriculum, University of North Carolina, Chapel Hill, NC 27599, USA; (M.C.C.C.); (B.K.H.)
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; (B.P.); (S.S.); (S.T.-B.); (T.A.B.); (M.B.); (P.H.); (G.D.S.); (F.P.-M.d.V.); (M.T.H.)
| | - Elizabeth J. Anderson
- Division of Comparative Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; (E.J.A.); (V.K.B.)
| | - Brea K. Hampton
- Genetics and Molecular Biology Curriculum, University of North Carolina, Chapel Hill, NC 27599, USA; (M.C.C.C.); (B.K.H.)
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; (B.P.); (S.S.); (S.T.-B.); (T.A.B.); (M.B.); (P.H.); (G.D.S.); (F.P.-M.d.V.); (M.T.H.)
| | - Breantié Parotti
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; (B.P.); (S.S.); (S.T.-B.); (T.A.B.); (M.B.); (P.H.); (G.D.S.); (F.P.-M.d.V.); (M.T.H.)
| | - Sanjay Sarkar
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; (B.P.); (S.S.); (S.T.-B.); (T.A.B.); (M.B.); (P.H.); (G.D.S.); (F.P.-M.d.V.); (M.T.H.)
| | - Sharon Taft-Benz
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; (B.P.); (S.S.); (S.T.-B.); (T.A.B.); (M.B.); (P.H.); (G.D.S.); (F.P.-M.d.V.); (M.T.H.)
| | - Timothy A. Bell
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; (B.P.); (S.S.); (S.T.-B.); (T.A.B.); (M.B.); (P.H.); (G.D.S.); (F.P.-M.d.V.); (M.T.H.)
| | - Matthew Blanchard
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; (B.P.); (S.S.); (S.T.-B.); (T.A.B.); (M.B.); (P.H.); (G.D.S.); (F.P.-M.d.V.); (M.T.H.)
| | - Jacob A. Dillard
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599, USA; (J.A.D.); (E.A.M.); (R.S.B.)
| | - Kenneth H. Dinnon
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599, USA; (J.A.D.); (E.A.M.); (R.S.B.)
| | - Pablo Hock
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; (B.P.); (S.S.); (S.T.-B.); (T.A.B.); (M.B.); (P.H.); (G.D.S.); (F.P.-M.d.V.); (M.T.H.)
| | - Sarah R. Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (S.R.L.)
| | - Emily A. Madden
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599, USA; (J.A.D.); (E.A.M.); (R.S.B.)
| | - Ginger D. Shaw
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; (B.P.); (S.S.); (S.T.-B.); (T.A.B.); (M.B.); (P.H.); (G.D.S.); (F.P.-M.d.V.); (M.T.H.)
| | - Ande West
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (S.R.L.)
| | - Ralph S. Baric
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599, USA; (J.A.D.); (E.A.M.); (R.S.B.)
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (S.R.L.)
| | - Victoria K. Baxter
- Division of Comparative Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; (E.J.A.); (V.K.B.)
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Fernando Pardo-Manuel de Villena
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; (B.P.); (S.S.); (S.T.-B.); (T.A.B.); (M.B.); (P.H.); (G.D.S.); (F.P.-M.d.V.); (M.T.H.)
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Mark T. Heise
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; (B.P.); (S.S.); (S.T.-B.); (T.A.B.); (M.B.); (P.H.); (G.D.S.); (F.P.-M.d.V.); (M.T.H.)
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599, USA; (J.A.D.); (E.A.M.); (R.S.B.)
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Martin T. Ferris
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; (B.P.); (S.S.); (S.T.-B.); (T.A.B.); (M.B.); (P.H.); (G.D.S.); (F.P.-M.d.V.); (M.T.H.)
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9
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Brown AJ, Won JJ, Wolfisberg R, Fahnøe U, Catanzaro N, West A, Moreira FR, Nogueira Batista M, Ferris MT, Linnertz CL, Leist SR, Nguyen C, De la Cruz G, Midkiff BR, Xia Y, Evangelista MD, Montgomery SA, Billerbeck E, Bukh J, Scheel TK, Rice CM, Sheahan TP. Host genetic variation guides hepacivirus clearance, chronicity, and liver fibrosis in mice. Hepatology 2024; 79:183-197. [PMID: 37540195 PMCID: PMC10718216 DOI: 10.1097/hep.0000000000000547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 06/14/2023] [Indexed: 08/05/2023]
Abstract
BACKGROUND AIMS Human genetic variation is thought to guide the outcome of HCV infection, but model systems within which to dissect these host genetic mechanisms are limited. Norway rat hepacivirus, closely related to HCV, causes chronic liver infection in rats but causes acute self-limiting hepatitis in typical strains of laboratory mice, which resolves in 2 weeks. The Collaborative Cross (CC) is a robust mouse genetics resource comprised of a panel of recombinant inbred strains, which model the complexity of the human genome and provide a system within which to understand diseases driven by complex allelic variation. APPROACH RESULTS We infected a panel of CC strains with Norway rat hepacivirus and identified several that failed to clear the virus after 4 weeks. Strains displayed an array of virologic phenotypes ranging from delayed clearance (CC046) to chronicity (CC071, CC080) with viremia for at least 10 months. Body weight loss, hepatocyte infection frequency, viral evolution, T-cell recruitment to the liver, liver inflammation, and the capacity to develop liver fibrosis varied among infected CC strains. CONCLUSIONS These models recapitulate many aspects of HCV infection in humans and demonstrate that host genetic variation affects a multitude of viruses and host phenotypes. These models can be used to better understand the molecular mechanisms that drive hepacivirus clearance and chronicity, the virus and host interactions that promote chronic disease manifestations like liver fibrosis, therapeutic and vaccine performance, and how these factors are affected by host genetic variation.
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Affiliation(s)
- Ariane J. Brown
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - John J. Won
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Raphael Wolfisberg
- Department of Infectious Diseases, Copenhagen Hepatitis C Program (CO-HEP), Copenhagen University Hospital, Hvidovre and Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Ulrik Fahnøe
- Department of Infectious Diseases, Copenhagen Hepatitis C Program (CO-HEP), Copenhagen University Hospital, Hvidovre and Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Nicholas Catanzaro
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ande West
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Fernando R. Moreira
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Mariana Nogueira Batista
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, USA
| | - Martin T. Ferris
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Colton L. Linnertz
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sarah R. Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Cameron Nguyen
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Gabriela De la Cruz
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Bentley R. Midkiff
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Yongjuan Xia
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Mia D. Evangelista
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Stephanie A. Montgomery
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
- Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Eva Billerbeck
- Department of Medicine and Department of Microbiology and Immunology, Division of Hepatology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Jens Bukh
- Department of Infectious Diseases, Copenhagen Hepatitis C Program (CO-HEP), Copenhagen University Hospital, Hvidovre and Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Troels K.H. Scheel
- Department of Infectious Diseases, Copenhagen Hepatitis C Program (CO-HEP), Copenhagen University Hospital, Hvidovre and Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, USA
| | - Charles M. Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, USA
| | - Timothy P. Sheahan
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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10
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Tibbs TN, Donoghue LJ, Buzzelli AA, Misumi I, DeMonia M, Ferris MT, Kelada SN, Whitmire JK. Mice with FVB-derived sequence on chromosome 17 succumb to disseminated virus infection due to aberrant NK cell and T cell responses. iScience 2023; 26:108348. [PMID: 38026197 PMCID: PMC10665959 DOI: 10.1016/j.isci.2023.108348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 09/19/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Zoonotic arenavirus infections can result in viral hemorrhagic disease, characterized by platelet loss, petechia, and multi-organ injury. The mechanisms governing these outcomes are likely impacted by virus strain and infection dose, as well as an individual's genetic background and immune constitution. To better understand the processes leading to severe pathogenesis, we compared two strains of inbred mice, C57BL/6J (B6) and FVB/NJ (FVB), that have diametrically opposed outcomes during disseminated lymphocytic choriomeningitis virus (LCMV) infection. Infection caused minimal pathogenesis in B6 mice, whereas FVB mice developed acute hepatitis and perished due, in part, to aberrant NK cell and T cell responses. Susceptible mice showed an outgrowth of cytolytic CD4+ T cells and loss of Treg cells. B6 congenic mice with the FVB allele at a 25Mb locus on chromosome 17 recapitulated FVB pathogenesis upon infection. A locus containing a limited number of variants in immune-related genes greatly impacts survival during infection.
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Affiliation(s)
- Taylor N. Tibbs
- Department of Microbiology and Immunology, UNC-Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Lauren J. Donoghue
- Department of Genetics, UNC-Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Ashlyn A. Buzzelli
- Department of Genetics, UNC-Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Ichiro Misumi
- Department of Genetics, UNC-Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Maggie DeMonia
- Department of Genetics, UNC-Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Martin T. Ferris
- Department of Genetics, UNC-Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Samir N.P. Kelada
- Department of Genetics, UNC-Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Jason K. Whitmire
- Department of Microbiology and Immunology, UNC-Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
- Department of Genetics, UNC-Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, UNC-Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
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11
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Faber JE, Zhang H, Xenakis JG, Bell TA, Hock P, Pardo-Manuel de Villena F, Ferris MT, Rzechorzek W. Large differences in collateral blood vessel abundance among individuals arise from multiple genetic variants. J Cereb Blood Flow Metab 2023; 43:1983-2004. [PMID: 37572089 PMCID: PMC10676139 DOI: 10.1177/0271678x231194956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/14/2023]
Abstract
Collateral blood flow varies greatly among humans for reasons that remain unclear, resulting in significant differences in ischemic tissue damage. A similarly large variation has also been found in mice that is caused by genetic background-dependent differences in the extent of collateral formation, termed collaterogenesis-a unique angiogenic process that occurs during development and determines collateral number and diameter in the adult. Previous studies have identified several quantitative trait loci (QTL) linked to this variation. However, understanding has been hampered by the use of closely related inbred strains that do not model the wide genetic variation present in the "outbred" human population. The Collaborative Cross (CC) multiparent mouse genetic reference panel was developed to address this limitation. Herein we measured the number and average diameter of cerebral collaterals in 60 CC strains, their 8 founder strains, 8 F1 crosses of CC strains selected for abundant versus sparse collaterals, and 2 intercross populations created from the latter. Collateral number evidenced 47-fold variation among the 60 CC strains, with 14% having poor, 25% poor-to-intermediate, 47% intermediate-to-good, and 13% good collateral abundance, that was associated with large differences in post-stroke infarct volume. Collateral number in skeletal muscle and intestine of selected high- and low-collateral strains evidenced the same relative abundance as in brain. Genome-wide mapping demonstrated that collateral abundance is a highly polymorphic trait. Subsequent analysis identified: 6 novel QTL circumscribing 28 high-priority candidate genes harboring putative loss-of-function polymorphisms (SNPs) associated with low collateral number; 335 predicted-deleterious SNPs present in their human orthologs; and 32 genes associated with vascular development but lacking protein coding variants. Six additional suggestive QTL (LOD > 4.5) were also identified in CC-wide QTL mapping. This study provides a comprehensive set of candidate genes for future investigations aimed at identifying signaling proteins within the collaterogenesis pathway whose variants potentially underlie genetic-dependent collateral insufficiency in brain and other tissues.
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Affiliation(s)
- James E Faber
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC, USA
- Curriculum in Neuroscience, University of North Carolina, Chapel Hill, NC, USA
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC, USA
| | - Hua Zhang
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC, USA
| | - James G Xenakis
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Timothy A Bell
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Pablo Hock
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Fernando Pardo-Manuel de Villena
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- Carolina Institute for Developmental Disabilities, University of North Carolina, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Martin T Ferris
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Wojciech Rzechorzek
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC, USA
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12
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Risemberg EL, Smeekens JM, Cisneros MCC, Hampton BK, Hock P, Linnertz CL, Miller DR, Orgel K, Shaw GD, de Villena FPM, Burks AW, Valdar W, Kulis MD, Ferris MT. A mutation in Themis contributes to peanut-induced oral anaphylaxis in CC027 mice. bioRxiv 2023:2023.09.13.557467. [PMID: 37745496 PMCID: PMC10515941 DOI: 10.1101/2023.09.13.557467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Background The development of peanut allergy is due to a combination of genetic and environmental factors, although specific genes have proven difficult to identify. Previously, we reported that peanut-sensitized CC027/GeniUnc (CC027) mice develop anaphylaxis upon oral challenge to peanut, unlike C3H/HeJ (C3H) mice. Objective To determine the genetic basis of orally-induced anaphylaxis to peanut in CC027 mice. Methods A genetic mapping population between CC027 and C3H mice was designed to identify the genetic factors that drive oral anaphylaxis. A total of 356 CC027xC3H backcrossed mice were generated, sensitized to peanut, then challenged to peanut by oral gavage. Anaphylaxis and peanut-specific IgE were quantified for all mice. T-cell phenotyping was conducted on CC027 and five additional CC strains. Results Anaphylaxis to peanut was absent in 77% of backcrossed mice, with 19% showing moderate anaphylaxis, and 4% having severe anaphylaxis. A total of eight genetic loci were associated with variation in response to peanut challenge, six associated with anaphylaxis (temperature decrease) and two associated with peanut-specific IgE levels. There were two major loci that impacted multiple aspects of the severity of acute anaphylaxis, at which the CC027 allele was associated with worse outcome. At one of these loci, CC027 has a private genetic variant in the Themis (thymocyte-expressed molecule involved in selection) gene. Consistent with Themis' described functions, we found that CC027 have more immature T cells with fewer CD8+, CD4+, and CD4+CD25+CD127- regulatory T cells. Conclusion Our results demonstrate a key role for Themis in the orally-reactive CC027 mouse model of peanut allergy.
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Affiliation(s)
- Ellen L. Risemberg
- Curriculum in Bioinformatics and Computational Biology, UNC Chapel Hill
- Department of Genetics, UNC Chapel Hill
| | - Johanna M. Smeekens
- Department of Pediatrics, Division of Allergy and Immunology, UNC Chapel Hill
| | - Marta C. Cruz Cisneros
- Department of Genetics, UNC Chapel Hill
- Curriculum in Genetics and Molecular Biology, UNC Chapel Hill
| | - Brea K. Hampton
- Department of Genetics, UNC Chapel Hill
- Curriculum in Genetics and Molecular Biology, UNC Chapel Hill
| | | | | | | | - Kelly Orgel
- Department of Pediatrics, Division of Allergy and Immunology, UNC Chapel Hill
| | - Ginger D. Shaw
- Department of Genetics, UNC Chapel Hill
- Lineberger Comprehensive Cancer Center, UNC Chapel Hill
| | | | - A. Wesley Burks
- Department of Pediatrics, Division of Allergy and Immunology, UNC Chapel Hill
| | - William Valdar
- Department of Genetics, UNC Chapel Hill
- Lineberger Comprehensive Cancer Center, UNC Chapel Hill
| | - Michael D. Kulis
- Department of Pediatrics, Division of Allergy and Immunology, UNC Chapel Hill
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13
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Lai R, Gong DN, Williams T, Ogunsola AF, Cavallo K, Lindestam Arlehamn CS, Acolatse S, Beamer GL, Ferris MT, Sassetti CM, Lauffenburger DA, Behar SM. Host genetic background is a barrier to broadly effective vaccine-mediated protection against tuberculosis. J Clin Invest 2023; 133:e167762. [PMID: 37200108 PMCID: PMC10313364 DOI: 10.1172/jci167762] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 05/11/2023] [Indexed: 05/20/2023] Open
Abstract
Heterogeneity in human immune responses is difficult to model in standard laboratory mice. To understand how host variation affects Bacillus Calmette Guerin-induced (BCG-induced) immunity against Mycobacterium tuberculosis, we studied 24 unique collaborative cross (CC) mouse strains, which differ primarily in the genes and alleles they inherit from founder strains. The CC strains were vaccinated with or without BCG and challenged with aerosolized M. tuberculosis. Since BCG protects only half of the CC strains tested, we concluded that host genetics has a major influence on BCG-induced immunity against M. tuberculosis infection, making it an important barrier to vaccine-mediated protection. Importantly, BCG efficacy is dissociable from inherent susceptibility to tuberculosis (TB). T cell immunity was extensively characterized to identify components associated with protection that were stimulated by BCG and recalled after M. tuberculosis infection. Although considerable diversity is observed, BCG has little impact on the composition of T cells in the lung after infection. Instead, variability is largely shaped by host genetics. BCG-elicited protection against TB correlated with changes in immune function. Thus, CC mice can be used to define correlates of protection and to identify vaccine strategies that protect a larger fraction of genetically diverse individuals instead of optimizing protection for a single genotype.
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Affiliation(s)
- Rocky Lai
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Diana N. Gong
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Travis Williams
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Abiola F. Ogunsola
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Kelly Cavallo
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | | | - Sarah Acolatse
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | - Martin T. Ferris
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Christopher M. Sassetti
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Douglas A. Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Samuel M. Behar
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
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Ahuja SK, Manoharan MS, Lee GC, McKinnon LR, Meunier JA, Steri M, Harper N, Fiorillo E, Smith AM, Restrepo MI, Branum AP, Bottomley MJ, Orrù V, Jimenez F, Carrillo A, Pandranki L, Winter CA, Winter LA, Gaitan AA, Moreira AG, Walter EA, Silvestri G, King CL, Zheng YT, Zheng HY, Kimani J, Blake Ball T, Plummer FA, Fowke KR, Harden PN, Wood KJ, Ferris MT, Lund JM, Heise MT, Garrett N, Canady KR, Abdool Karim SS, Little SJ, Gianella S, Smith DM, Letendre S, Richman DD, Cucca F, Trinh H, Sanchez-Reilly S, Hecht JM, Cadena Zuluaga JA, Anzueto A, Pugh JA, Agan BK, Root-Bernstein R, Clark RA, Okulicz JF, He W. Immune resilience despite inflammatory stress promotes longevity and favorable health outcomes including resistance to infection. Nat Commun 2023; 14:3286. [PMID: 37311745 PMCID: PMC10264401 DOI: 10.1038/s41467-023-38238-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 04/17/2023] [Indexed: 06/15/2023] Open
Abstract
Some people remain healthier throughout life than others but the underlying reasons are poorly understood. Here we hypothesize this advantage is attributable in part to optimal immune resilience (IR), defined as the capacity to preserve and/or rapidly restore immune functions that promote disease resistance (immunocompetence) and control inflammation in infectious diseases as well as other causes of inflammatory stress. We gauge IR levels with two distinct peripheral blood metrics that quantify the balance between (i) CD8+ and CD4+ T-cell levels and (ii) gene expression signatures tracking longevity-associated immunocompetence and mortality-associated inflammation. Profiles of IR metrics in ~48,500 individuals collectively indicate that some persons resist degradation of IR both during aging and when challenged with varied inflammatory stressors. With this resistance, preservation of optimal IR tracked (i) a lower risk of HIV acquisition, AIDS development, symptomatic influenza infection, and recurrent skin cancer; (ii) survival during COVID-19 and sepsis; and (iii) longevity. IR degradation is potentially reversible by decreasing inflammatory stress. Overall, we show that optimal IR is a trait observed across the age spectrum, more common in females, and aligned with a specific immunocompetence-inflammation balance linked to favorable immunity-dependent health outcomes. IR metrics and mechanisms have utility both as biomarkers for measuring immune health and for improving health outcomes.
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Affiliation(s)
- Sunil K Ahuja
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA.
- Department of Microbiology, Immunology & Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA.
- South Texas Veterans Health Care System, San Antonio, TX, 78229, USA.
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA.
| | - Muthu Saravanan Manoharan
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Grace C Lee
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- Pharmacotherapy Education and Research Center, School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
- College of Pharmacy, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Lyle R McKinnon
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, 4001, South Africa
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Justin A Meunier
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- The Foundation for Advancing Veterans' Health Research, San Antonio, TX, 78229, USA
| | - Maristella Steri
- Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, Monserrato, 09042, Italy
| | - Nathan Harper
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- The Foundation for Advancing Veterans' Health Research, San Antonio, TX, 78229, USA
| | - Edoardo Fiorillo
- Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, Monserrato, 09042, Italy
| | - Alisha M Smith
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- Department of Microbiology, Immunology & Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
- The Foundation for Advancing Veterans' Health Research, San Antonio, TX, 78229, USA
| | - Marcos I Restrepo
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Anne P Branum
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- The Foundation for Advancing Veterans' Health Research, San Antonio, TX, 78229, USA
| | - Matthew J Bottomley
- Transplantation Research Immunology Group, Nuffield Department of Surgical Sciences, University of Oxford, Oxford, OX1 2JD, UK
- Oxford Kidney Unit, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 7LE, UK
| | - Valeria Orrù
- Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, Monserrato, 09042, Italy
| | - Fabio Jimenez
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- The Foundation for Advancing Veterans' Health Research, San Antonio, TX, 78229, USA
| | - Andrew Carrillo
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- The Foundation for Advancing Veterans' Health Research, San Antonio, TX, 78229, USA
| | - Lavanya Pandranki
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Caitlyn A Winter
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
- The Foundation for Advancing Veterans' Health Research, San Antonio, TX, 78229, USA
- Department of Pediatrics, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Lauryn A Winter
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
- The Foundation for Advancing Veterans' Health Research, San Antonio, TX, 78229, USA
- Department of Pediatrics, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Alvaro A Gaitan
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- The Foundation for Advancing Veterans' Health Research, San Antonio, TX, 78229, USA
| | - Alvaro G Moreira
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- Department of Pediatrics, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Elizabeth A Walter
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Guido Silvestri
- Department of Pathology, Emory University School of Medicine & Emory National Primate Research Center, Atlanta, GA, 30322, USA
| | - Christopher L King
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Yong-Tang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- National Resource Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650107, China
| | - Hong-Yi Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- National Resource Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650107, China
| | - Joshua Kimani
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - T Blake Ball
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Francis A Plummer
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Keith R Fowke
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Paul N Harden
- Oxford Kidney Unit, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 7LE, UK
| | - Kathryn J Wood
- Transplantation Research Immunology Group, Nuffield Department of Surgical Sciences, University of Oxford, Oxford, OX1 2JD, UK
| | - Martin T Ferris
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, 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
| | - Mark T Heise
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Nigel Garrett
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Kristen R Canady
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
| | - Salim S Abdool Karim
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, 4001, South Africa
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, 10032, USA
| | - Susan J Little
- Department of Medicine, University of California, La Jolla, CA, 92093, USA
- San Diego Center for AIDS Research, University of California San Diego, La Jolla, CA, 92093, USA
| | - Sara Gianella
- Department of Medicine, University of California, La Jolla, CA, 92093, USA
- San Diego Center for AIDS Research, University of California San Diego, La Jolla, CA, 92093, USA
| | - Davey M Smith
- Department of Medicine, University of California, La Jolla, CA, 92093, USA
- San Diego Center for AIDS Research, University of California San Diego, La Jolla, CA, 92093, USA
- Veterans Affairs San Diego Healthcare System, San Diego, CA, 92161, USA
| | - Scott Letendre
- Department of Medicine, University of California, La Jolla, CA, 92093, USA
| | - Douglas D Richman
- San Diego Center for AIDS Research, University of California San Diego, La Jolla, CA, 92093, USA
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, Monserrato, 09042, Italy
- Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, 07100, Italy
| | - Hanh Trinh
- South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
| | - Sandra Sanchez-Reilly
- South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Joan M Hecht
- South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- The Foundation for Advancing Veterans' Health Research, San Antonio, TX, 78229, USA
| | - Jose A Cadena Zuluaga
- South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Antonio Anzueto
- South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Jacqueline A Pugh
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Brian K Agan
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | | | - Robert A Clark
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- Department of Microbiology, Immunology & Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
- South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
- The Foundation for Advancing Veterans' Health Research, San Antonio, TX, 78229, USA
| | - Jason F Okulicz
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
- Department of Medicine, Infectious Diseases Service, Brooke Army Medical Center, San Antonio, TX, 78234, USA
| | - Weijing He
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- The Foundation for Advancing Veterans' Health Research, San Antonio, TX, 78229, USA
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15
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Jasperse BA, Mattocks MD, Noll KE, Ferris MT, Heise MT, Lazear HM. Neuroinvasive Flavivirus Pathogenesis Is Restricted by Host Genetic Factors in Collaborative Cross Mice, Independently of Oas1b. J Virol 2023:e0071523. [PMID: 37310228 PMCID: PMC10373552 DOI: 10.1128/jvi.00715-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023] Open
Abstract
Powassan virus (POWV) is an emerging tick-borne flavivirus that causes neuroinvasive diseases, including encephalitis, meningitis, and paralysis. Similar to other neuroinvasive flaviviruses, such as West Nile virus (WNV) and Japanese encephalitis virus (JEV), POWV disease presentation is heterogeneous, and the factors influencing disease outcome are not fully understood. We used Collaborative Cross (CC) mice to assess the impact of host genetic factors on POWV pathogenesis. We infected a panel of Oas1b-null CC lines with POWV and observed a range of susceptibility, indicating that host factors other than the well-characterized flavivirus restriction factor Oas1b modulate POWV pathogenesis in CC mice. Among the Oas1b-null CC lines, we identified multiple highly susceptible lines (0% survival), including CC071 and CC015, and two resistant lines, CC045 and CC057 (>75% survival). The susceptibility phenotypes generally were concordant among neuroinvasive flaviviruses, although we did identify one line, CC006, that was specifically resistant to JEV, suggesting that both pan-flavivirus and virus-specific mechanisms contribute to susceptibility phenotypes in CC mice. We found that POWV replication was restricted in bone marrow-derived macrophages from CC045 and CC057 mice, suggesting that resistance could result from cell-intrinsic restriction of viral replication. Although serum viral loads at 2 days postinfection were equivalent between resistant and susceptible CC lines, clearance of POWV from the serum was significantly enhanced in CC045 mice. Furthermore, CC045 mice had significantly lower viral loads in the brain at 7 days postinfection than did CC071 mice, suggesting that reduced central nervous system (CNS) infection contributes to the resistant phenotype of CC045 mice. IMPORTANCE Neuroinvasive flaviviruses, such as WNV, JEV, and POWV, are transmitted to humans by mosquitoes or ticks and can cause neurologic diseases, such as encephalitis, meningitis, and paralysis, and they can result in death or long-term sequelae. Although potentially severe, neuroinvasive disease is a rare outcome of flavivirus infection. The factors that determine whether someone develops severe disease after a flavivirus infection are not fully understood, but host genetic differences in polymorphic antiviral response genes likely contribute to the outcome of infection. We evaluated a panel of genetically diverse mice and identified lines with distinct outcomes following infection with POWV. We found that resistance to POWV pathogenesis corresponded to reduced viral replication in macrophages, more rapid clearance of virus in peripheral tissues, and reduced viral infection in the brain. These susceptible and resistant mouse lines will provide a system for investigating the pathogenic mechanisms of POWV and identifying polymorphic host genes that contribute to resistance.
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Affiliation(s)
- Brittany A Jasperse
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Melissa D Mattocks
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Kelsey E Noll
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Martin T Ferris
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Mark T Heise
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Helen M Lazear
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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16
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Faber JE, Zhang H, Xenakis JG, Bell TA, Hock P, de Villena FPM, Ferris MT, Rzechorzek W. Large differences in collateral blood vessel abundance among individuals arise from multiple genetic variants. bioRxiv 2023:2023.05.28.542633. [PMID: 37398475 PMCID: PMC10312463 DOI: 10.1101/2023.05.28.542633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Collateral blood flow varies greatly among humans for reasons that remain unclear, resulting in significant differences in ischemic tissue damage. A similarly large variation has also been found in mice that is caused by genetic background-dependent differences in the extent of collateral formation, termed collaterogenesis-a unique angiogenic process that occurs during development and determines collateral number and diameter in the adult. Previous studies have identified several quantitative trait loci (QTL) linked to this variation. However, understanding has been hampered by the use of closely related inbred strains that do not model the wide genetic variation present in the "outbred" human population. The Collaborative Cross (CC) multiparent mouse genetic reference panel was developed to address this limitation. Herein we measured the number and average diameter of cerebral collaterals in 60 CC strains, their 8 founder strains, 8 F1 crosses of CC strains selected for abundant versus sparse collaterals, and 2 intercross populations created from the latter. Collateral number evidenced 47-fold variation among the 60 CC strains, with 14% having poor, 25% poor-to-intermediate, 47% intermediate-to-good, and 13% good collateral abundance, that was associated with large differences in post-stroke infarct volume. Genome-wide mapping demonstrated that collateral abundance is a highly polymorphic trait. Subsequent analysis identified: 6 novel QTL circumscribing 28 high-priority candidate genes harboring putative loss-of-function polymorphisms (SNPs) associated with low collateral number; 335 predicted-deleterious SNPs present in their human orthologs; and 32 genes associated with vascular development but lacking protein coding variants. This study provides a comprehensive set of candidate genes for future investigations aimed at identifying signaling proteins within the collaterogenesis pathway whose variants potentially underlie genetic-dependent collateral insufficiency in brain and other tissues.
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17
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Arkatkar T, Davé VA, Cruz Talavera I, Graham JB, Swarts JL, Hughes SM, Bell TA, Hock P, Farrington J, Shaw GD, Kirby AC, Fialkow M, Huang ML, Jerome KR, Ferris MT, Hladik F, Schiffer JT, Prlic M, Lund JM. Memory T cells possess an innate-like function in local protection from mucosal infection. J Clin Invest 2023; 133:162800. [PMID: 36951943 PMCID: PMC10178838 DOI: 10.1172/jci162800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 03/22/2023] [Indexed: 03/24/2023] Open
Abstract
Mucosal infections pose a significant global health burden. Antigen-specific tissue resident T cells are critical to maintaining barrier immunity. Previous studies in the context of systemic infection suggest that memory CD8 T cells may also provide innate-like protection against antigenically unrelated pathogens independent of TCR engagement. Whether "bystander T cell activation" is also an important defense mechanism in the mucosa is poorly understood. Here, we investigated if innate-like memory CD8 T cells could protect against a model mucosal virus infection, herpes simplex virus 2 (HSV-2). We found that immunization with an irrelevant antigen delayed disease progression from lethal HSV-2 challenge, suggesting that memory CD8 T cells may mediate protection despite the lack of antigen-specificity. Upon HSV-2 infection, we observed an early infiltration, rather than substantial local proliferation, of antigen-non-specific CD8 T cells, which became bystander-activated only within the infected mucosal tissue. Critically, we show that bystander-activated CD8 T cells are sufficient to reduce early viral burden after HSV-2 infection. Finally, local cytokine cues within the tissue microenvironment after infection were sufficient for bystander activation of mucosal tissue memory CD8 T cells from mice and humans. Altogether, our findings suggest that local bystander-activation of CD8 memory T cells contribute a fast and effective innate-like response to infection in mucosal tissue.
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Affiliation(s)
- Tanvi Arkatkar
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, United States of America
| | - Veronica A Davé
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, United States of America
| | - Irene Cruz Talavera
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, United States of America
| | - Jessica B Graham
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, United States of America
| | - Jessica L Swarts
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, United States of America
| | - Sean M Hughes
- Department of Obstetrics and Gynecology, University of Washington, Seattle, United States of America
| | - Timothy A Bell
- Department of Genetics, University of North Carolina, Chapel Hill, United States of America
| | - Pablo Hock
- Department of Genetics, University of North Carolina, Chapel Hill, United States of America
| | - Joe Farrington
- Department of Genetics, University of North Carolina, Chapel Hill, United States of America
| | - Ginger D Shaw
- Department of Genetics, University of North Carolina, Chapel Hill, United States of America
| | - Anna C Kirby
- Department of Obstetrics and Gynecology, University of Washington, Seattle, United States of America
| | - Michael Fialkow
- Department of Obstetrics and Gynecology, University of Washington, Seattle, United States of America
| | - Meei-Li Huang
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, United States of America
| | - Keith R Jerome
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, United States of America
| | - Martin T Ferris
- Department of Genetics, University of North Carolina, Chapel Hill, United States of America
| | - Florian Hladik
- Department of Obstetrics and Gynecology, University of Washington, Seattle, United States of America
| | - Joshua T Schiffer
- Fred Hutchinson Cancer Research Center, Seattle, United States of America
| | - Martin Prlic
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, United States of America
| | - Jennifer M Lund
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, United States of America
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18
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Zhang T, Keele GR, Gyuricza IG, Vincent M, Brunton C, Bell TA, Hock P, Shaw GD, Munger SC, de Villena FPM, Ferris MT, Paulo JA, Gygi SP, Churchill GA. Multi-omics analysis identifies drivers of protein phosphorylation. Genome Biol 2023; 24:52. [PMID: 36944993 PMCID: PMC10031968 DOI: 10.1186/s13059-023-02892-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 03/09/2023] [Indexed: 03/23/2023] Open
Abstract
BACKGROUND Phosphorylation of proteins is a key step in the regulation of many cellular processes including activation of enzymes and signaling cascades. The abundance of a phosphorylated peptide (phosphopeptide) is determined by the abundance of its parent protein and the proportion of target sites that are phosphorylated. RESULTS We quantified phosphopeptides, proteins, and transcripts in heart, liver, and kidney tissue samples of mice from 58 strains of the Collaborative Cross strain panel. We mapped ~700 phosphorylation quantitative trait loci (phQTL) across the three tissues and applied genetic mediation analysis to identify causal drivers of phosphorylation. We identified kinases, phosphatases, cytokines, and other factors, including both known and potentially novel interactions between target proteins and genes that regulate site-specific phosphorylation. Our analysis highlights multiple targets of pyruvate dehydrogenase kinase 1 (PDK1), a regulator of mitochondrial function that shows reduced activity in the NZO/HILtJ mouse, a polygenic model of obesity and type 2 diabetes. CONCLUSIONS Together, this integrative multi-omics analysis in genetically diverse CC strains provides a powerful tool to identify regulators of protein phosphorylation. The data generated in this study provides a resource for further exploration.
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Affiliation(s)
- Tian Zhang
- Harvard Medical School, Boston, MA, 02115, USA
| | | | | | | | | | - Timothy A Bell
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Pablo Hock
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Ginger D Shaw
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | | | - Fernando Pardo-Manuel de Villena
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Martin T Ferris
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
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19
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Snouwaert JN, Jania LA, Nguyen T, Martinez DR, Schäfer A, Catanzaro NJ, Gully KL, Baric RS, Heise M, Ferris MT, Anderson E, Pressey K, Dillard JA, Taft-Benz S, Baxter VK, Ting JPY, Koller BH. Human ACE2 expression, a major tropism determinant for SARS-CoV-2, is regulated by upstream and intragenic elements. PLoS Pathog 2023; 19:e1011168. [PMID: 36812267 PMCID: PMC9987828 DOI: 10.1371/journal.ppat.1011168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 03/06/2023] [Accepted: 01/30/2023] [Indexed: 02/24/2023] Open
Abstract
Angiotensin-converting enzyme 2 (ACE2), part of the renin-angiotensin system (RAS), serves as an entry point for SARS-CoV-2, leading to viral proliferation in permissive cell types. Using mouse lines in which the Ace2 locus has been humanized by syntenic replacement, we show that regulation of basal and interferon induced ACE2 expression, relative expression levels of different ACE2 transcripts, and sexual dimorphism in ACE2 expression are unique to each species, differ between tissues, and are determined by both intragenic and upstream promoter elements. Our results indicate that the higher levels of expression of ACE2 observed in the lungs of mice relative to humans may reflect the fact that the mouse promoter drives expression of ACE2 in populous airway club cells while the human promoter drives expression in alveolar type 2 (AT2) cells. In contrast to transgenic mice in which human ACE2 is expressed in ciliated cells under the control of the human FOXJ1 promoter, mice expressing ACE2 in club cells under the control of the endogenous Ace2 promoter show a robust immune response after infection with SARS-CoV-2, leading to rapid clearance of the virus. This supports a model in which differential expression of ACE2 determines which cell types in the lung are infected, and this in turn modulates the host response and outcome of COVID-19.
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Affiliation(s)
- John N. Snouwaert
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Leigh A. Jania
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Trang Nguyen
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - David R. Martinez
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Alexandra Schäfer
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Nicholas J. Catanzaro
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Kendra L. Gully
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Ralph S. Baric
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Mark Heise
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Martin T. Ferris
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Elizabeth Anderson
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Katia Pressey
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jacob A. Dillard
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Sharon Taft-Benz
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Victoria K. Baxter
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jenny P-Y Ting
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Center for Translational Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Beverly H. Koller
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
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20
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Steinbach EC, Smeekens JM, Roy S, Toyonaga T, Cornaby C, Perini L, Berglind A, Kulis MD, Kim EH, Ferris MT, Furey TS, Burks AW, Sheikh SZ. Intestinal epithelial cell barrier dysfunction and elevated Angiopoietin-like 4 identified in orally susceptible peanut allergy model. Clin Exp Allergy 2023; 53:210-215. [PMID: 36336910 PMCID: PMC9976618 DOI: 10.1111/cea.14248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 09/20/2022] [Accepted: 09/25/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Erin C. Steinbach
- Division of Rheumatology, Allergy, and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
- Center for Gastrointestinal Biology and Disease, Division of Gastroenterology and Hepatology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
- Division of Allergy and Immunology, Department of Pediatrics, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Johanna M. Smeekens
- Division of Allergy and Immunology, Department of Pediatrics, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Satyaki Roy
- Center for Gastrointestinal Biology and Disease, Division of Gastroenterology and Hepatology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
- Department of Genetics, Curriculum in Bioinformatics and Computational Biology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Takahiko Toyonaga
- Center for Gastrointestinal Biology and Disease, Division of Gastroenterology and Hepatology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Caleb Cornaby
- Department of Pathology and Lab Medicine, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Layna Perini
- Center for Gastrointestinal Biology and Disease, Division of Gastroenterology and Hepatology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ana Berglind
- Center for Gastrointestinal Biology and Disease, Division of Gastroenterology and Hepatology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
- Department of Genetics, Curriculum in Bioinformatics and Computational Biology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Michael D. Kulis
- Division of Allergy and Immunology, Department of Pediatrics, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Edwin H. Kim
- Division of Allergy and Immunology, Department of Pediatrics, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Martin T. Ferris
- Department of Genetics, Curriculum in Bioinformatics and Computational Biology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Terrence S. Furey
- Center for Gastrointestinal Biology and Disease, Division of Gastroenterology and Hepatology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
- Department of Genetics, Curriculum in Bioinformatics and Computational Biology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - A. Wesley Burks
- Division of Allergy and Immunology, Department of Pediatrics, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Shehzad Z. Sheikh
- Center for Gastrointestinal Biology and Disease, Division of Gastroenterology and Hepatology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
- Department of Genetics, Curriculum in Bioinformatics and Computational Biology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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21
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Hampton BK, Plante KS, Whitmore AC, Linnertz CL, Madden EA, Noll KE, Boyson SP, Parotti B, Xenakis JG, Bell TA, Hock P, Shaw GD, de Villena FPM, Ferris MT, Heise MT. Forward genetic screen of homeostatic antibody levels in the Collaborative Cross identifies MBD1 as a novel regulator of B cell homeostasis. PLoS Genet 2022; 18:e1010548. [PMID: 36574452 PMCID: PMC9829176 DOI: 10.1371/journal.pgen.1010548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 01/09/2023] [Accepted: 11/28/2022] [Indexed: 12/28/2022] Open
Abstract
Variation in immune homeostasis, the state in which the immune system is maintained in the absence of stimulation, is highly variable across populations. This variation is attributed to both genetic and environmental factors. However, the identity and function of specific regulators have been difficult to identify in humans. We evaluated homeostatic antibody levels in the serum of the Collaborative Cross (CC) mouse genetic reference population. We found heritable variation in all antibody isotypes and subtypes measured. We identified 4 quantitative trait loci (QTL) associated with 3 IgG subtypes: IgG1, IgG2b, and IgG2c. While 3 of these QTL map to genome regions of known immunological significance (major histocompatibility and immunoglobulin heavy chain locus), Qih1 (associated with variation in IgG1) mapped to a novel locus on Chromosome 18. We further associated this locus with B cell proportions in the spleen and identify Methyl-CpG binding domain protein 1 under this locus as a novel regulator of homeostatic IgG1 levels in the serum and marginal zone B cells (MZB) in the spleen, consistent with a role in MZB differentiation to antibody secreting cells.
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Affiliation(s)
- Brea K. Hampton
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Kenneth S. Plante
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Alan C. Whitmore
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Colton L. Linnertz
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Emily A. Madden
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Kelsey E. Noll
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Samuel P. Boyson
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Breantie Parotti
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - James G. Xenakis
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Timothy A. Bell
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Pablo Hock
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Ginger D. Shaw
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Fernando Pardo-Manuel de Villena
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Martin T. Ferris
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Mark T. Heise
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
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22
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Beierle JA, Yao EJ, Goldstein SI, Lynch WB, Scotellaro JL, Shah AA, Sena KD, Wong AL, Linnertz CL, Averin O, Moody DE, Reilly CA, Peltz G, Emili A, Ferris MT, Bryant CD. Zhx2 Is a Candidate Gene Underlying Oxymorphone Metabolite Brain Concentration Associated with State-Dependent Oxycodone Reward. J Pharmacol Exp Ther 2022; 382:167-180. [PMID: 35688478 PMCID: PMC9341249 DOI: 10.1124/jpet.122.001217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 05/16/2022] [Indexed: 11/22/2022] Open
Abstract
Understanding the pharmacogenomics of opioid metabolism and behavior is vital to therapeutic success, as mutations can dramatically alter therapeutic efficacy and addiction liability. We found robust, sex-dependent BALB/c substrain differences in oxycodone behaviors and whole brain concentration of oxycodone metabolites. BALB/cJ females showed robust state-dependent oxycodone reward learning as measured via conditioned place preference when compared with the closely related BALB/cByJ substrain. Accordingly, BALB/cJ females also showed a robust increase in brain concentration of the inactive metabolite noroxycodone and the active metabolite oxymorphone compared with BALB/cByJ mice. Oxymorphone is a highly potent, full agonist at the mu opioid receptor that could enhance drug-induced interoception and state-dependent oxycodone reward learning. Quantitative trait locus (QTL) mapping in a BALB/c F2 reduced complexity cross revealed one major QTL on chromosome 15 underlying brain oxymorphone concentration that explained 32% of the female variance. BALB/cJ and BALB/cByJ differ by fewer than 10,000 variants, which can greatly facilitate candidate gene/variant identification. Hippocampal and striatal cis-expression QTL (eQTL) and exon-level eQTL analysis identified Zhx2, a candidate gene coding for a transcriptional repressor with a private BALB/cJ retroviral insertion that reduces Zhx2 expression and sex-dependent dysregulation of cytochrome P450 enzymes. Whole brain proteomics corroborated the Zhx2 eQTL and identified upregulated CYP2D11 that could increase brain oxymorphone in BALB/cJ females. To summarize, Zhx2 is a highly promising candidate gene underlying brain oxycodone metabolite levels. Future studies will validate Zhx2 and its site of action using reciprocal gene editing and tissue-specific viral manipulations in BALB/c substrains. SIGNIFICANCE STATEMENT: Our findings show that genetic variation can result in sex-specific alterations in whole brain concentration of a bioactive opioid metabolite after oxycodone administration, reinforcing the need for sex as a biological factor in pharmacogenomic studies. The cooccurrence of female-specific increased oxymorphone and state-dependent reward learning suggests that this minor yet potent and efficacious metabolite of oxycodone could increase opioid interoception and drug-cue associative learning of opioid reward, which has implications for cue-induced relapse of drug-seeking behavior and for precision pharmacogenetics.
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Affiliation(s)
- Jacob A Beierle
- Ph.D. Program in Biomolecular Pharmacology (J.A.B., S.I.G.), Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry (J.A.B., E.J.Y., W.B.L., J.L.S., A.A.S., K.D.S., A.L.W., C.D.B.), Department of Biology and Biochemistry, Center for Network Systems Biology (S.I.G., A.E.), and Graduate Program in Neuroscience (W.B.L), Boston University School of Medicine, Boston, Massachusetts; Transformative Training Program in Addiction Science (TTPAS) (J.A.B., W.B.L.) and Undergraduate Research Opportunity Program (J.L.S., K.D.S.), Boston University, Boston, Massachusetts; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (C.L.L., M.T.F.); Department of Pharmacology and Toxicity, Center for Human Toxicology, University of Utah, Salt Lake City, Utah (O.A., D.E.M., C.A.R.); and Department of Anesthesiology, Pain, and Preoperative Medicine Stanford University School of Medicine, Stanford, California (G.P.)
| | - Emily J Yao
- Ph.D. Program in Biomolecular Pharmacology (J.A.B., S.I.G.), Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry (J.A.B., E.J.Y., W.B.L., J.L.S., A.A.S., K.D.S., A.L.W., C.D.B.), Department of Biology and Biochemistry, Center for Network Systems Biology (S.I.G., A.E.), and Graduate Program in Neuroscience (W.B.L), Boston University School of Medicine, Boston, Massachusetts; Transformative Training Program in Addiction Science (TTPAS) (J.A.B., W.B.L.) and Undergraduate Research Opportunity Program (J.L.S., K.D.S.), Boston University, Boston, Massachusetts; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (C.L.L., M.T.F.); Department of Pharmacology and Toxicity, Center for Human Toxicology, University of Utah, Salt Lake City, Utah (O.A., D.E.M., C.A.R.); and Department of Anesthesiology, Pain, and Preoperative Medicine Stanford University School of Medicine, Stanford, California (G.P.)
| | - Stanley I Goldstein
- Ph.D. Program in Biomolecular Pharmacology (J.A.B., S.I.G.), Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry (J.A.B., E.J.Y., W.B.L., J.L.S., A.A.S., K.D.S., A.L.W., C.D.B.), Department of Biology and Biochemistry, Center for Network Systems Biology (S.I.G., A.E.), and Graduate Program in Neuroscience (W.B.L), Boston University School of Medicine, Boston, Massachusetts; Transformative Training Program in Addiction Science (TTPAS) (J.A.B., W.B.L.) and Undergraduate Research Opportunity Program (J.L.S., K.D.S.), Boston University, Boston, Massachusetts; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (C.L.L., M.T.F.); Department of Pharmacology and Toxicity, Center for Human Toxicology, University of Utah, Salt Lake City, Utah (O.A., D.E.M., C.A.R.); and Department of Anesthesiology, Pain, and Preoperative Medicine Stanford University School of Medicine, Stanford, California (G.P.)
| | - William B Lynch
- Ph.D. Program in Biomolecular Pharmacology (J.A.B., S.I.G.), Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry (J.A.B., E.J.Y., W.B.L., J.L.S., A.A.S., K.D.S., A.L.W., C.D.B.), Department of Biology and Biochemistry, Center for Network Systems Biology (S.I.G., A.E.), and Graduate Program in Neuroscience (W.B.L), Boston University School of Medicine, Boston, Massachusetts; Transformative Training Program in Addiction Science (TTPAS) (J.A.B., W.B.L.) and Undergraduate Research Opportunity Program (J.L.S., K.D.S.), Boston University, Boston, Massachusetts; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (C.L.L., M.T.F.); Department of Pharmacology and Toxicity, Center for Human Toxicology, University of Utah, Salt Lake City, Utah (O.A., D.E.M., C.A.R.); and Department of Anesthesiology, Pain, and Preoperative Medicine Stanford University School of Medicine, Stanford, California (G.P.)
| | - Julia L Scotellaro
- Ph.D. Program in Biomolecular Pharmacology (J.A.B., S.I.G.), Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry (J.A.B., E.J.Y., W.B.L., J.L.S., A.A.S., K.D.S., A.L.W., C.D.B.), Department of Biology and Biochemistry, Center for Network Systems Biology (S.I.G., A.E.), and Graduate Program in Neuroscience (W.B.L), Boston University School of Medicine, Boston, Massachusetts; Transformative Training Program in Addiction Science (TTPAS) (J.A.B., W.B.L.) and Undergraduate Research Opportunity Program (J.L.S., K.D.S.), Boston University, Boston, Massachusetts; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (C.L.L., M.T.F.); Department of Pharmacology and Toxicity, Center for Human Toxicology, University of Utah, Salt Lake City, Utah (O.A., D.E.M., C.A.R.); and Department of Anesthesiology, Pain, and Preoperative Medicine Stanford University School of Medicine, Stanford, California (G.P.)
| | - Anyaa A Shah
- Ph.D. Program in Biomolecular Pharmacology (J.A.B., S.I.G.), Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry (J.A.B., E.J.Y., W.B.L., J.L.S., A.A.S., K.D.S., A.L.W., C.D.B.), Department of Biology and Biochemistry, Center for Network Systems Biology (S.I.G., A.E.), and Graduate Program in Neuroscience (W.B.L), Boston University School of Medicine, Boston, Massachusetts; Transformative Training Program in Addiction Science (TTPAS) (J.A.B., W.B.L.) and Undergraduate Research Opportunity Program (J.L.S., K.D.S.), Boston University, Boston, Massachusetts; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (C.L.L., M.T.F.); Department of Pharmacology and Toxicity, Center for Human Toxicology, University of Utah, Salt Lake City, Utah (O.A., D.E.M., C.A.R.); and Department of Anesthesiology, Pain, and Preoperative Medicine Stanford University School of Medicine, Stanford, California (G.P.)
| | - Katherine D Sena
- Ph.D. Program in Biomolecular Pharmacology (J.A.B., S.I.G.), Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry (J.A.B., E.J.Y., W.B.L., J.L.S., A.A.S., K.D.S., A.L.W., C.D.B.), Department of Biology and Biochemistry, Center for Network Systems Biology (S.I.G., A.E.), and Graduate Program in Neuroscience (W.B.L), Boston University School of Medicine, Boston, Massachusetts; Transformative Training Program in Addiction Science (TTPAS) (J.A.B., W.B.L.) and Undergraduate Research Opportunity Program (J.L.S., K.D.S.), Boston University, Boston, Massachusetts; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (C.L.L., M.T.F.); Department of Pharmacology and Toxicity, Center for Human Toxicology, University of Utah, Salt Lake City, Utah (O.A., D.E.M., C.A.R.); and Department of Anesthesiology, Pain, and Preoperative Medicine Stanford University School of Medicine, Stanford, California (G.P.)
| | - Alyssa L Wong
- Ph.D. Program in Biomolecular Pharmacology (J.A.B., S.I.G.), Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry (J.A.B., E.J.Y., W.B.L., J.L.S., A.A.S., K.D.S., A.L.W., C.D.B.), Department of Biology and Biochemistry, Center for Network Systems Biology (S.I.G., A.E.), and Graduate Program in Neuroscience (W.B.L), Boston University School of Medicine, Boston, Massachusetts; Transformative Training Program in Addiction Science (TTPAS) (J.A.B., W.B.L.) and Undergraduate Research Opportunity Program (J.L.S., K.D.S.), Boston University, Boston, Massachusetts; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (C.L.L., M.T.F.); Department of Pharmacology and Toxicity, Center for Human Toxicology, University of Utah, Salt Lake City, Utah (O.A., D.E.M., C.A.R.); and Department of Anesthesiology, Pain, and Preoperative Medicine Stanford University School of Medicine, Stanford, California (G.P.)
| | - Colton L Linnertz
- Ph.D. Program in Biomolecular Pharmacology (J.A.B., S.I.G.), Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry (J.A.B., E.J.Y., W.B.L., J.L.S., A.A.S., K.D.S., A.L.W., C.D.B.), Department of Biology and Biochemistry, Center for Network Systems Biology (S.I.G., A.E.), and Graduate Program in Neuroscience (W.B.L), Boston University School of Medicine, Boston, Massachusetts; Transformative Training Program in Addiction Science (TTPAS) (J.A.B., W.B.L.) and Undergraduate Research Opportunity Program (J.L.S., K.D.S.), Boston University, Boston, Massachusetts; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (C.L.L., M.T.F.); Department of Pharmacology and Toxicity, Center for Human Toxicology, University of Utah, Salt Lake City, Utah (O.A., D.E.M., C.A.R.); and Department of Anesthesiology, Pain, and Preoperative Medicine Stanford University School of Medicine, Stanford, California (G.P.)
| | - Olga Averin
- Ph.D. Program in Biomolecular Pharmacology (J.A.B., S.I.G.), Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry (J.A.B., E.J.Y., W.B.L., J.L.S., A.A.S., K.D.S., A.L.W., C.D.B.), Department of Biology and Biochemistry, Center for Network Systems Biology (S.I.G., A.E.), and Graduate Program in Neuroscience (W.B.L), Boston University School of Medicine, Boston, Massachusetts; Transformative Training Program in Addiction Science (TTPAS) (J.A.B., W.B.L.) and Undergraduate Research Opportunity Program (J.L.S., K.D.S.), Boston University, Boston, Massachusetts; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (C.L.L., M.T.F.); Department of Pharmacology and Toxicity, Center for Human Toxicology, University of Utah, Salt Lake City, Utah (O.A., D.E.M., C.A.R.); and Department of Anesthesiology, Pain, and Preoperative Medicine Stanford University School of Medicine, Stanford, California (G.P.)
| | - David E Moody
- Ph.D. Program in Biomolecular Pharmacology (J.A.B., S.I.G.), Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry (J.A.B., E.J.Y., W.B.L., J.L.S., A.A.S., K.D.S., A.L.W., C.D.B.), Department of Biology and Biochemistry, Center for Network Systems Biology (S.I.G., A.E.), and Graduate Program in Neuroscience (W.B.L), Boston University School of Medicine, Boston, Massachusetts; Transformative Training Program in Addiction Science (TTPAS) (J.A.B., W.B.L.) and Undergraduate Research Opportunity Program (J.L.S., K.D.S.), Boston University, Boston, Massachusetts; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (C.L.L., M.T.F.); Department of Pharmacology and Toxicity, Center for Human Toxicology, University of Utah, Salt Lake City, Utah (O.A., D.E.M., C.A.R.); and Department of Anesthesiology, Pain, and Preoperative Medicine Stanford University School of Medicine, Stanford, California (G.P.)
| | - Christopher A Reilly
- Ph.D. Program in Biomolecular Pharmacology (J.A.B., S.I.G.), Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry (J.A.B., E.J.Y., W.B.L., J.L.S., A.A.S., K.D.S., A.L.W., C.D.B.), Department of Biology and Biochemistry, Center for Network Systems Biology (S.I.G., A.E.), and Graduate Program in Neuroscience (W.B.L), Boston University School of Medicine, Boston, Massachusetts; Transformative Training Program in Addiction Science (TTPAS) (J.A.B., W.B.L.) and Undergraduate Research Opportunity Program (J.L.S., K.D.S.), Boston University, Boston, Massachusetts; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (C.L.L., M.T.F.); Department of Pharmacology and Toxicity, Center for Human Toxicology, University of Utah, Salt Lake City, Utah (O.A., D.E.M., C.A.R.); and Department of Anesthesiology, Pain, and Preoperative Medicine Stanford University School of Medicine, Stanford, California (G.P.)
| | - Gary Peltz
- Ph.D. Program in Biomolecular Pharmacology (J.A.B., S.I.G.), Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry (J.A.B., E.J.Y., W.B.L., J.L.S., A.A.S., K.D.S., A.L.W., C.D.B.), Department of Biology and Biochemistry, Center for Network Systems Biology (S.I.G., A.E.), and Graduate Program in Neuroscience (W.B.L), Boston University School of Medicine, Boston, Massachusetts; Transformative Training Program in Addiction Science (TTPAS) (J.A.B., W.B.L.) and Undergraduate Research Opportunity Program (J.L.S., K.D.S.), Boston University, Boston, Massachusetts; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (C.L.L., M.T.F.); Department of Pharmacology and Toxicity, Center for Human Toxicology, University of Utah, Salt Lake City, Utah (O.A., D.E.M., C.A.R.); and Department of Anesthesiology, Pain, and Preoperative Medicine Stanford University School of Medicine, Stanford, California (G.P.)
| | - Andrew Emili
- Ph.D. Program in Biomolecular Pharmacology (J.A.B., S.I.G.), Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry (J.A.B., E.J.Y., W.B.L., J.L.S., A.A.S., K.D.S., A.L.W., C.D.B.), Department of Biology and Biochemistry, Center for Network Systems Biology (S.I.G., A.E.), and Graduate Program in Neuroscience (W.B.L), Boston University School of Medicine, Boston, Massachusetts; Transformative Training Program in Addiction Science (TTPAS) (J.A.B., W.B.L.) and Undergraduate Research Opportunity Program (J.L.S., K.D.S.), Boston University, Boston, Massachusetts; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (C.L.L., M.T.F.); Department of Pharmacology and Toxicity, Center for Human Toxicology, University of Utah, Salt Lake City, Utah (O.A., D.E.M., C.A.R.); and Department of Anesthesiology, Pain, and Preoperative Medicine Stanford University School of Medicine, Stanford, California (G.P.)
| | - Martin T Ferris
- Ph.D. Program in Biomolecular Pharmacology (J.A.B., S.I.G.), Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry (J.A.B., E.J.Y., W.B.L., J.L.S., A.A.S., K.D.S., A.L.W., C.D.B.), Department of Biology and Biochemistry, Center for Network Systems Biology (S.I.G., A.E.), and Graduate Program in Neuroscience (W.B.L), Boston University School of Medicine, Boston, Massachusetts; Transformative Training Program in Addiction Science (TTPAS) (J.A.B., W.B.L.) and Undergraduate Research Opportunity Program (J.L.S., K.D.S.), Boston University, Boston, Massachusetts; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (C.L.L., M.T.F.); Department of Pharmacology and Toxicity, Center for Human Toxicology, University of Utah, Salt Lake City, Utah (O.A., D.E.M., C.A.R.); and Department of Anesthesiology, Pain, and Preoperative Medicine Stanford University School of Medicine, Stanford, California (G.P.)
| | - Camron D Bryant
- Ph.D. Program in Biomolecular Pharmacology (J.A.B., S.I.G.), Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry (J.A.B., E.J.Y., W.B.L., J.L.S., A.A.S., K.D.S., A.L.W., C.D.B.), Department of Biology and Biochemistry, Center for Network Systems Biology (S.I.G., A.E.), and Graduate Program in Neuroscience (W.B.L), Boston University School of Medicine, Boston, Massachusetts; Transformative Training Program in Addiction Science (TTPAS) (J.A.B., W.B.L.) and Undergraduate Research Opportunity Program (J.L.S., K.D.S.), Boston University, Boston, Massachusetts; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (C.L.L., M.T.F.); Department of Pharmacology and Toxicity, Center for Human Toxicology, University of Utah, Salt Lake City, Utah (O.A., D.E.M., C.A.R.); and Department of Anesthesiology, Pain, and Preoperative Medicine Stanford University School of Medicine, Stanford, California (G.P.)
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23
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Cartwright HN, Barbeau DJ, Doyle JD, Klein E, Heise MT, Ferris MT, McElroy AK. Genetic diversity of collaborative cross mice enables identification of novel rift valley fever virus encephalitis model. PLoS Pathog 2022; 18:e1010649. [PMID: 35834486 PMCID: PMC9282606 DOI: 10.1371/journal.ppat.1010649] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 06/07/2022] [Indexed: 11/18/2022] Open
Abstract
Rift Valley fever (RVF) is an arboviral disease of humans and livestock responsible for severe economic and human health impacts. In humans, RVF spans a variety of clinical manifestations, ranging from an acute flu-like illness to severe forms of disease, including late-onset encephalitis. The large variations in human RVF disease are inadequately represented by current murine models, which overwhelmingly die of early-onset hepatitis. Existing mouse models of RVF encephalitis are either immunosuppressed, display an inconsistent phenotype, or develop encephalitis only when challenged via intranasal or aerosol exposure. In this study, the genetically defined recombinant inbred mouse resource known as the Collaborative Cross (CC) was used to identify mice with additional RVF disease phenotypes when challenged via a peripheral foot-pad route to mimic mosquito-bite exposure. Wild-type Rift Valley fever virus (RVFV) challenge of 20 CC strains revealed three distinct disease phenotypes: early-onset hepatitis, mixed phenotype, and late-onset encephalitis. Strain CC057/Unc, with the most divergent phenotype, which died of late-onset encephalitis at a median of 11 days post-infection, is the first mouse strain to develop consistent encephalitis following peripheral challenge. CC057/Unc mice were directly compared to C57BL/6 mice, which uniformly succumb to hepatitis within 2–4 days of infection. Encephalitic disease in CC057/Unc mice was characterized by high viral RNA loads in brain tissue, accompanied by clearance of viral RNA from the periphery, low ALT levels, lymphopenia, and neutrophilia. In contrast, C57BL/6 mice succumbed from hepatitis at 3 days post-infection with high viral RNA loads in the liver, viremia, high ALT levels, lymphopenia, and thrombocytopenia. The identification of a strain of CC mice as an RVFV encephalitis model will allow for future investigation into the pathogenesis and treatment of RVF encephalitic disease and indicates that genetic background makes a major contribution to RVF disease variation.
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Affiliation(s)
- Haley N. Cartwright
- University of Pittsburgh, School of Medicine, Department of Pediatrics, Division of Pediatric Infectious Disease, and Center for Vaccine Research, Pittsburgh, Pennsylvania, United States of America
| | - Dominique J. Barbeau
- University of Pittsburgh, School of Medicine, Department of Pediatrics, Division of Pediatric Infectious Disease, and Center for Vaccine Research, Pittsburgh, Pennsylvania, United States of America
| | - Joshua D. Doyle
- University of Pittsburgh, School of Medicine, Department of Pediatrics, Division of Pediatric Infectious Disease, and Center for Vaccine Research, Pittsburgh, Pennsylvania, United States of America
| | - Ed Klein
- University of Pittsburgh, Division of Laboratory Animal Resources, Pittsburgh, Pennsylvania, United States of America
| | - Mark T. Heise
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Martin T. Ferris
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Anita K. McElroy
- University of Pittsburgh, School of Medicine, Department of Pediatrics, Division of Pediatric Infectious Disease, and Center for Vaccine Research, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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24
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Schäfer A, Leist SR, Gralinski LE, Martinez DR, Winkler ES, Okuda K, Hawkins PE, Gully KL, Graham RL, Scobey DT, Bell TA, Hock P, Shaw GD, Loome JF, Madden EA, Anderson E, Baxter VK, Taft-Benz SA, Zweigart MR, May SR, Dong S, Clark M, Miller DR, Lynch RM, Heise MT, Tisch R, Boucher RC, Pardo Manuel de Villena F, Montgomery SA, Diamond MS, Ferris MT, Baric RS. A Multitrait Locus Regulates Sarbecovirus Pathogenesis. bioRxiv 2022. [PMID: 35677067 DOI: 10.1101/2022.06.01.494461] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Infectious diseases have shaped the human population genetic structure, and genetic variation influences the susceptibility to many viral diseases. However, a variety of challenges have made the implementation of traditional human Genome-wide Association Studies (GWAS) approaches to study these infectious outcomes challenging. In contrast, mouse models of infectious diseases provide an experimental control and precision, which facilitates analyses and mechanistic studies of the role of genetic variation on infection. Here we use a genetic mapping cross between two distinct Collaborative Cross mouse strains with respect to SARS-CoV disease outcomes. We find several loci control differential disease outcome for a variety of traits in the context of SARS-CoV infection. Importantly, we identify a locus on mouse Chromosome 9 that shows conserved synteny with a human GWAS locus for SARS-CoV-2 severe disease. We follow-up and confirm a role for this locus, and identify two candidate genes, CCR9 and CXCR6 that both play a key role in regulating the severity of SARS-CoV, SARS-CoV-2 and a distantly related bat sarbecovirus disease outcomes. As such we provide a template for using experimental mouse crosses to identify and characterize multitrait loci that regulate pathogenic infectious outcomes across species.
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25
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Beierle JA, Yao EJ, Goldstein SI, Scotellaro JL, Sena KD, Averin O, Moody DE, Reilly CA, Emili A, Peltz G, Ferris MT, Bryant CD. A reduced complexity cross between BALB/c substrains identifies Zhx2 as a candidate gene underlying oxycodone metabolite brain concentration and state‐dependent learning of opioid reward. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.r4573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Emily J. Yao
- PharmacologyBoston University School of MedicineBostonMA
| | | | | | | | - Olga Averin
- Pharmacology and ToxicologyUniversity of UtahSalt Lake CityUT
| | - David E. Moody
- Pharmacology and ToxicologyUniversity of UtahSalt Lake CityUT
| | | | - Andrew Emili
- Biology and BiochemistryBoston University School of MedicineBostonMA
| | - Gary Peltz
- Anesthesiology, Perioperative, and Pain MedicineStanford University School of MedicineStanfordCA
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26
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Gaines CH, Schoenrock SA, Farrington J, Lee DF, Aponte-Collazo LJ, Shaw GD, Miller DR, Ferris MT, Pardo-Manuel de Villena F, Tarantino LM. Cocaine-Induced Locomotor Activation Differs Across Inbred Mouse Substrains. Front Psychiatry 2022; 13:800245. [PMID: 35599758 PMCID: PMC9120424 DOI: 10.3389/fpsyt.2022.800245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 03/22/2022] [Indexed: 11/13/2022] Open
Abstract
Cocaine use disorders (CUD) are devastating for affected individuals and impose a significant societal burden, but there are currently no FDA-approved therapies. The development of novel and effective treatments has been hindered by substantial gaps in our knowledge about the etiology of these disorders. The risk for developing a CUD is influenced by genetics, the environment and complex interactions between the two. Identifying specific genes and environmental risk factors that increase CUD risk would provide an avenue for the development of novel treatments. Rodent models of addiction-relevant behaviors have been a valuable tool for studying the genetics of behavioral responses to drugs of abuse. Traditional genetic mapping using genetically and phenotypically divergent inbred mice has been successful in identifying numerous chromosomal regions that influence addiction-relevant behaviors, but these strategies rarely result in identification of the causal gene or genetic variant. To overcome this challenge, reduced complexity crosses (RCC) between closely related inbred mouse strains have been proposed as a method for rapidly identifying and validating functional variants. The RCC approach is dependent on identifying phenotypic differences between substrains. To date, however, the study of addiction-relevant behaviors has been limited to very few sets of substrains, mostly comprising the C57BL/6 lineage. The present study expands upon the current literature to assess cocaine-induced locomotor activation in 20 inbred mouse substrains representing six inbred strain lineages (A/J, BALB/c, FVB/N, C3H/He, DBA/2 and NOD) that were either bred in-house or supplied directly by a commercial vendor. To our knowledge, we are the first to identify significant differences in cocaine-induced locomotor response in several of these inbred substrains. The identification of substrain differences allows for the initiation of RCC populations to more rapidly identify specific genetic variants associated with acute cocaine response. The observation of behavioral profiles that differ between mice generated in-house and those that are vendor-supplied also presents an opportunity to investigate the influence of environmental factors on cocaine-induced locomotor activity.
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Affiliation(s)
- Christiann H. Gaines
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Neuroscience Curriculum, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Sarah A. Schoenrock
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Joseph Farrington
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - David F. Lee
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Pharmacology Curriculum, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Lucas J. Aponte-Collazo
- Pharmacology Curriculum, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Ginger D. Shaw
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Darla R. Miller
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Martin T. Ferris
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Fernando Pardo-Manuel de Villena
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Lisa M. Tarantino
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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27
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Cruz Cisneros MC, Parotti B, Noll K, Bell TA, Hock P, Heise MT, Ferris MT. Genetic analysis of differential responses to adjuvanted influenza vaccination. The Journal of Immunology 2022. [DOI: 10.4049/jimmunol.208.supp.64.08] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Abstract
Each year the seasonal influenza vaccine is administered to protect individuals from infection, but vaccination often shows variable efficacy against influenza infections. While the inclusion of adjuvants can boost vaccine efficacy, individuals also vary in their response to adjuvants, and understanding the basis of this variation would provide insights into adjuvant mechanisms and advance vaccine development. Host genetics contribute to variation in vaccine response, but the specific genetic factors that impact immune responses to adjuvanted vaccination are not well understood. To better understand how the genetic background of individuals can modify vaccine and adjuvant-induced immune responses, we screened a set of Collaborative Cross (CC) mouse strains with immunization via inactivated influenza with or without alum. Across these genetically diverse CC strains, we observed wide variation in levels of influenza specific antibodies and isotypes (e.g., IgG1, IgG2). We further focused on two strains, CC002 and CC072, that had contrasting antibody responses to vaccine + alum. To understand the genetic factors driving these responses, we generated an F2 population to map quantitative trait loci (qtl) driving the differences between CC002 and CC072 in vaccine responses. Among the F2 population, variation across antibody levels were observed in mice vaccinated with the vaccine with and without alum that reflected the variation in the parent strains. QTL were mapped for variation in antibody levels for mice vaccinated without alum, further supporting a role for host genetics in regulating vaccine responses. Future analysis will focus on analyzing specific host factors modulating antibody responses to adjuvanted vaccination.
Supported by grants from NIH (U19 AI100625, 5T32 GM007092, 1T32 GM135128, 5R25 GM055336-19) and Burroughs Wellcome Fund GDEP to MCC.
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Affiliation(s)
| | - Breantié Parotti
- 2Department of Genetics, University of North Carolina at Chapel Hill
| | - Kelsey Noll
- 3Microbiology, University of North Carolina at Chapel Hill
| | - Timothy A Bell
- 2Department of Genetics, University of North Carolina at Chapel Hill
| | - Pablo Hock
- 2Department of Genetics, University of North Carolina at Chapel Hill
| | - Mark T Heise
- 2Department of Genetics, University of North Carolina at Chapel Hill
| | - Martin T Ferris
- 2Department of Genetics, University of North Carolina at Chapel Hill
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28
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Smith CM, Baker RE, Proulx MK, Mishra BB, Long JE, Park SW, Lee HN, Kiritsy MC, Bellerose MM, Olive AJ, Murphy KC, Papavinasasundaram K, Boehm FJ, Reames CJ, Meade RK, Hampton BK, Linnertz CL, Shaw GD, Hock P, Bell TA, Ehrt S, Schnappinger D, Pardo-Manuel de Villena F, Ferris MT, Ioerger TR, Sassetti CM. Host-pathogen genetic interactions underlie tuberculosis susceptibility in genetically diverse mice. eLife 2022; 11:74419. [PMID: 35112666 PMCID: PMC8846590 DOI: 10.7554/elife.74419] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 01/27/2022] [Indexed: 11/21/2022] Open
Abstract
The outcome of an encounter with Mycobacterium tuberculosis (Mtb) depends on the pathogen’s ability to adapt to the variable immune pressures exerted by the host. Understanding this interplay has proven difficult, largely because experimentally tractable animal models do not recapitulate the heterogeneity of tuberculosis disease. We leveraged the genetically diverse Collaborative Cross (CC) mouse panel in conjunction with a library of Mtb mutants to create a resource for associating bacterial genetic requirements with host genetics and immunity. We report that CC strains vary dramatically in their susceptibility to infection and produce qualitatively distinct immune states. Global analysis of Mtb transposon mutant fitness (TnSeq) across the CC panel revealed that many virulence pathways are only required in specific host microenvironments, identifying a large fraction of the pathogen’s genome that has been maintained to ensure fitness in a diverse population. Both immunological and bacterial traits can be associated with genetic variants distributed across the mouse genome, making the CC a unique population for identifying specific host-pathogen genetic interactions that influence pathogenesis.
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Affiliation(s)
- Clare M Smith
- Department of Molecular Genetics and Microbiology, Duke University, Durham, United States
| | - Richard E Baker
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Megan K Proulx
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Bibhuti B Mishra
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Jarukit E Long
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Sae Woong Park
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, United States
| | - Ha-Na Lee
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, United States
| | - Michael C Kiritsy
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Michelle M Bellerose
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Andrew J Olive
- Microbiology and Molecular Genetics, Michigan State University, East Lansing, United States
| | - Kenan C Murphy
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Kadamba Papavinasasundaram
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Frederick J Boehm
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Charlotte J Reames
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Rachel K Meade
- Department of Molecular Genetics and Microbiology, Duke University, Durham, United States
| | - Brea K Hampton
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Colton L Linnertz
- Department of Genetics, University of North Carolina at Chapel Hill, Morrisville, United States
| | - Ginger D Shaw
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Pablo Hock
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Timothy A Bell
- Department of Genetics,, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Sabine Ehrt
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, United States
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, United States
| | | | - Martin T Ferris
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Thomas R Ioerger
- Department of Computer Science and Engineering, Texas A&M University, College Station, United States
| | - Christopher M Sassetti
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
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29
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Beierle JA, Yao EJ, Goldstein SI, Scotellaro JL, Sena KD, Linnertz CA, Willits AB, Kader L, Young EE, Peltz G, Emili A, Ferris MT, Bryant CD. Genetic basis of thermal nociceptive sensitivity and brain weight in a BALB/c reduced complexity cross. Mol Pain 2022; 18:17448069221079540. [PMID: 35088629 PMCID: PMC8891926 DOI: 10.1177/17448069221079540] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 01/20/2022] [Indexed: 11/30/2022] Open
Abstract
Thermal nociception involves the transmission of temperature-related noxious information from the periphery to the CNS and is a heritable trait that could predict transition to persistent pain. Rodent forward genetics complement human studies by controlling genetic complexity and environmental factors, analysis of end point tissue, and validation of variants on appropriate genetic backgrounds. Reduced complexity crosses between nearly identical inbred substrains with robust trait differences can greatly facilitate unbiased discovery of novel genes and variants. We found BALB/cByJ mice showed enhanced sensitivity on the 53.5°C hot plate and mechanical stimulation in the von Frey test compared to BALB/cJ mice and replicated decreased gross brain weight in BALB/cByJ versus BALB/cJ. We then identified a quantitative trait locus (QTL) on chromosome 13 for hot plate sensitivity (LOD = 10.7; p < 0.001; peak = 56 Mb) and a QTL for brain weight on chromosome 5 (LOD = 8.7; p < 0.001). Expression QTL mapping of brain tissues identified H2afy (56.07 Mb) as the top transcript with the strongest association at the hot plate locus (FDR = 0.0002) and spliceome analysis identified differential exon usage within H2afy associated with the same locus. Whole brain proteomics further supported decreased H2AFY expression could underlie enhanced hot plate sensitivity, and identified ACADS as a candidate for reduced brain weight. To summarize, a BALB/c reduced complexity cross combined with multiple-omics approaches facilitated identification of candidate genes underlying thermal nociception and brain weight. These substrains provide a powerful, reciprocal platform for future validation of candidate variants.
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Affiliation(s)
- Jacob A Beierle
- Program in Biomolecular Pharmacology, Boston University School of Medicine, Boston, MA, USA
- Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry, Boston University School of Medicine, Boston, MA, USA
| | - Emily J Yao
- Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry, Boston University School of Medicine, Boston, MA, USA
| | - Stanley I Goldstein
- Program in Biomolecular Pharmacology, Boston University School of Medicine, Boston, MA, USA
- Department of Biology and Biochemistry, Center for Network Systems Biology, Boston University School of Medicine, Boston, MA, USA
| | - Julia L Scotellaro
- Department of Biology and Biochemistry, Center for Network Systems Biology, Boston University School of Medicine, Boston, MA, USA
- Undergraduate Research Opportunity Program, Boston University, Boston, MA, USA
| | - Katherine D Sena
- Department of Biology and Biochemistry, Center for Network Systems Biology, Boston University School of Medicine, Boston, MA, USA
- Undergraduate Research Opportunity Program, Boston University, Boston, MA, USA
| | - Colton A Linnertz
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Adam B Willits
- Neuroscience Program, University of Kansas Medical Center, Kansas City, KS, USA
| | - Leena Kader
- Neuroscience Program, University of Kansas Medical Center, Kansas City, KS, USA
| | - Erin E Young
- Department of Anesthesiology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Gary Peltz
- Department of Anesthesiology, Pain, and Preoperative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Andrew Emili
- Department of Biology and Biochemistry, Center for Network Systems Biology, Boston University School of Medicine, Boston, MA, USA
| | - Martin T Ferris
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Camron D Bryant
- Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry, Boston University School of Medicine, Boston, MA, USA
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30
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Fay EJ, Balla KM, Roach SN, Shepherd FK, Putri DS, Wiggen TD, Goldstein SA, Pierson MJ, Ferris MT, Thefaine CE, Tucker A, Salnikov M, Cortez V, Compton SR, Kotenko SV, Hunter RC, Masopust D, Elde NC, Langlois RA. Natural rodent model of viral transmission reveals biological features of virus population dynamics. J Exp Med 2021; 219:212940. [PMID: 34958350 PMCID: PMC8713297 DOI: 10.1084/jem.20211220] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 11/05/2021] [Accepted: 12/08/2021] [Indexed: 12/21/2022] Open
Abstract
Emerging viruses threaten global health, but few experimental models can characterize the virus and host factors necessary for within- and cross-species transmission. Here, we leverage a model whereby pet store mice or rats-which harbor natural rodent pathogens-are cohoused with laboratory mice. This "dirty" mouse model offers a platform for studying acute transmission of viruses between and within hosts via natural mechanisms. We identified numerous viruses and other microbial species that transmit to cohoused mice, including prospective new members of the Coronaviridae, Astroviridae, Picornaviridae, and Narnaviridae families, and uncovered pathogen interactions that promote or prevent virus transmission. We also evaluated transmission dynamics of murine astroviruses during transmission and spread within a new host. Finally, by cohousing our laboratory mice with the bedding of pet store rats, we identified cross-species transmission of a rat astrovirus. Overall, this model system allows for the analysis of transmission of natural rodent viruses and is a platform to further characterize barriers to zoonosis.
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Affiliation(s)
- Elizabeth J. Fay
- Biochemistry, Molecular Biology and Biophysics Graduate Program, University of Minnesota, Minneapolis, MN,Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN,Center for Immunology, University of Minnesota, Minneapolis, MN
| | - Keir M. Balla
- Department of Human Genetics, University of Utah, Salt Lake City, UT
| | - Shanley N. Roach
- Biochemistry, Molecular Biology and Biophysics Graduate Program, University of Minnesota, Minneapolis, MN,Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN
| | - Frances K. Shepherd
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN
| | - Dira S. Putri
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN,Microbiology, Immunology and Cancer Biology Graduate Program, University of Minnesota, Minneapolis, MN
| | - Talia D. Wiggen
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN
| | | | - Mark J. Pierson
- Center for Immunology, University of Minnesota, Minneapolis, MN
| | - Martin T. Ferris
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Claire E. Thefaine
- Microbiology, Immunology and Cancer Biology Graduate Program, University of Minnesota, Minneapolis, MN
| | - Andrew Tucker
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN
| | - Mark Salnikov
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN
| | - Valerie Cortez
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA
| | - Susan R. Compton
- Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT
| | - Sergei V. Kotenko
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ
| | - Ryan C. Hunter
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN
| | - David Masopust
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN,Center for Immunology, University of Minnesota, Minneapolis, MN
| | - Nels C. Elde
- Department of Human Genetics, University of Utah, Salt Lake City, UT
| | - Ryan A. Langlois
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN,Center for Immunology, University of Minnesota, Minneapolis, MN,Correspondence to Ryan A. Langlois:
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31
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Keele GR, Zhang T, Pham DT, Vincent M, Bell TA, Hock P, Shaw GD, Paulo JA, Munger SC, Pardo-Manuel de Villena F, Ferris MT, Gygi SP, Churchill GA. Regulation of protein abundance in genetically diverse mouse populations. Cell Genom 2021; 1:100003. [PMID: 36212994 PMCID: PMC9536773 DOI: 10.1016/j.xgen.2021.100003] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 04/01/2021] [Accepted: 05/10/2021] [Indexed: 12/12/2022]
Abstract
Genetically diverse mouse populations are powerful tools for characterizing the regulation of the proteome and its relationship to whole-organism phenotypes. We used mass spectrometry to profile and quantify the abundance of 6,798 proteins in liver tissue from mice of both sexes across 58 Collaborative Cross (CC) inbred strains. We previously collected liver proteomics data from the related Diversity Outbred (DO) mice and their founder strains. We show concordance across the proteomics datasets despite being generated from separate experiments, allowing comparative analysis. We map protein abundance quantitative trait loci (pQTLs), identifying 1,087 local and 285 distal in the CC mice and 1,706 local and 414 distal in the DO mice. We find that regulatory effects on individual proteins are conserved across the mouse populations, in particular for local genetic variation and sex differences. In comparison, proteins that form complexes are often co-regulated, displaying varying genetic architectures, and overall show lower heritability and map fewer pQTLs. We have made this resource publicly available to enable quantitative analyses of the regulation of the proteome.
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Affiliation(s)
| | - Tian Zhang
- Harvard Medical School, Boston, MA 02115, USA
| | - Duy T. Pham
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | | | - Timothy A. Bell
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Pablo Hock
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Ginger D. Shaw
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | | | | | - Fernando Pardo-Manuel de Villena
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Martin T. Ferris
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
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32
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Schäfer A, Gralinski LE, Leist SR, Winkler ES, Hampton BK, Mooney MA, Jensen KL, Graham RL, Agnihothram S, Jeng S, Chamberlin S, Bell TA, Scobey DT, VanBlargan LA, Thackray LB, Hock P, Miller DR, Shaw GD, de Villena FPM, McWeeney SK, Montgomery SA, Diamond MS, Heise MT, Menachery VD, Ferris MT, Baric RS. Common Mechanism of SARS-CoV and SARS-CoV-2 Pathogenesis across Species. bioRxiv 2021:2021.05.14.444205. [PMID: 34013261 PMCID: PMC8132217 DOI: 10.1101/2021.05.14.444205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Sarbecovirus (CoV) infections, including Severe Acute Respiratory CoV (SARS-CoV) and SARS-CoV-2, are considerable human threats. Human GWAS studies have recently identified loci associated with variation in SARS-CoV-2 susceptibility. However, genetically tractable models that reproduce human CoV disease outcomes are needed to mechanistically evaluate genetic determinants of CoV susceptibility. We used the Collaborative Cross (CC) and human GWAS datasets to elucidate host susceptibility loci that regulate CoV infections and to identify host quantitative trait loci that modulate severe CoV and pan-CoV disease outcomes including a major disease regulating loci including CCR9. CCR9 ablation resulted in enhanced titer, weight loss, respiratory dysfunction, mortality, and inflammation, providing mechanistic support in mitigating protection from severe SARS-CoV-2 pathogenesis across species. This study represents a comprehensive analysis of susceptibility loci for an entire genus of human pathogens conducted, identifies a large collection of susceptibility loci and candidate genes that regulate multiple aspects type-specific and cross-CoV pathogenesis, and also validates the paradigm of using the CC platform to identify common cross-species susceptibility loci and genes for newly emerging and pre-epidemic viruses.
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33
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Hampton BK, Jensen KL, Whitmore AC, Gralinski LE, Leist SR, Linnertz CL, Maurizio P, Menachery VD, Morrison CR, Noll KE, Plante KS, Shäfer A, Shaw GD, West A, de Villena FPM, Baric RS, Heise MT, Ferris MT. Genetic regulation of immune homeostatic lung leukocyte populations influences respiratory virus induced disease in collaborative cross mice. The Journal of Immunology 2021. [DOI: 10.4049/jimmunol.206.supp.24.05] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Abstract
Immune homeostasis is the state that the immune system maintains in the absence of insult. Perturbation of immune homeostasis can impact autoimmunity/allergy and adversely affect infectious responses. To date, much of the analysis of immune homeostasis has focused on systemic immunity, but it is also likely to be important in an organ specific manner. Since the lungs are a major site of environmental exposure and infection, we used the Collaborative Cross (CC) mouse genetic reference population to study the genetic regulation of the breadth of baseline immune cell populations in the lung and identify loci regulating these cells at homeostasis. We found that all 54 immune cell phenotypes measured showed strong genetic variation in cell type abundances. We identified 28 quantitative trait loci associated with variation in 24 immune cell populations or the relationship between cell populations. Further, we identified significant associations between 20 of these loci and responses to either influenza A virus (IAV) or Severe acute respiratory syndrome associated coronavirus (SARS-CoV) disease in the same strains of mice. Notably, a locus mapped for variation in Ly6C+ monocyte abundance was associated with SARS-CoV weight loss, as well as titer at days 2 and 4 post-infection. This locus is also associated with influenza-induced disease, as measured by weight loss post-infection. Our analysis highlights the strong genetic control of immune homeostasis, and the key role that immune homeostasis plays in contributing to downstream infectious responses. In particular, our analysis suggests that the abundance of a variety of lung leukocyte populations prior to infection could serve as predictors of immune responses to respiratory viruses.
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Affiliation(s)
| | - Kara L Jensen
- 2Epidemiology, Univ. of North Carolina at Chapel Hill
| | | | | | - Sarah R Leist
- 2Epidemiology, Univ. of North Carolina at Chapel Hill
| | | | | | | | | | | | | | | | | | - Ande West
- 2Epidemiology, Univ. of North Carolina at Chapel Hill
| | | | - Ralph S Baric
- 2Epidemiology, Univ. of North Carolina at Chapel Hill
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34
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Graham JB, Swarts JL, Edwards KR, Voss KM, Green R, Jeng S, Miller DR, Mooney MA, McWeeney SK, Ferris MT, Pardo-Manuel de Villena F, Gale M, Lund JM. Correlation of Regulatory T Cell Numbers with Disease Tolerance upon Virus Infection. Immunohorizons 2021; 5:157-169. [PMID: 33893179 PMCID: PMC8281504 DOI: 10.4049/immunohorizons.2100009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 02/19/2021] [Indexed: 11/19/2022] Open
Abstract
The goal of a successful immune response is to clear the pathogen while sparing host tissues from damage associated with pathogen replication and active immunity. Regulatory T cells (Treg) have been implicated in maintaining this balance as they contribute both to the organization of immune responses as well as restriction of inflammation and immune activation to limit immunopathology. To determine if Treg abundance prior to pathogen encounter can be used to predict the success of an antiviral immune response, we used genetically diverse mice from the collaborative cross infected with West Nile virus (WNV). We identified collaborative cross lines with extreme Treg abundance at steady state, either high or low, and used mice with these extreme phenotypes to demonstrate that baseline Treg quantity predicted the magnitude of the CD8 T cell response to WNV infection, although higher numbers of baseline Tregs were associated with reduced CD8 T cell functionality in terms of TNF and granzyme B expression. Finally, we found that abundance of CD44+ Tregs in the spleen at steady state was correlated with an increased early viral load within the spleen without an association with clinical disease. Thus, we propose that Tregs participate in disease tolerance in the context of WNV infection by tuning an appropriately focused and balanced immune response to control the virus while at the same time minimizing immunopathology and clinical disease. We hypothesize that Tregs limit the antiviral CD8 T cell function to curb immunopathology at the expense of early viral control as an overall host survival strategy.
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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
| | - Kristina R Edwards
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Kathleen M Voss
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington School of Medicine, Seattle, WA
| | - Richard Green
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington School of Medicine, Seattle, WA
| | - Sophia Jeng
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR.,OHSU Knight Cancer Institute, Oregon Health & Science University, Portland, OR
| | - Darla R Miller
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Michael A Mooney
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR.,OHSU Knight Cancer Institute, Oregon Health & Science University, Portland, OR
| | - Shannon K McWeeney
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR.,OHSU Knight Cancer Institute, Oregon Health & Science University, Portland, OR.,Oregon Clinical and Translational Research Institute, 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; and
| | - Michael Gale
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR
| | - 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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35
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Smeekens JM, Johnson-Weaver BT, Hinton AL, Azcarate-Peril MA, Moran TP, Immormino RM, Kesselring JR, Steinbach EC, Orgel KA, Staats HF, Burks AW, Mucha PJ, Ferris MT, Kulis MD. Fecal IgA, Antigen Absorption, and Gut Microbiome Composition Are Associated With Food Antigen Sensitization in Genetically Susceptible Mice. Front Immunol 2021; 11:599637. [PMID: 33542716 PMCID: PMC7850988 DOI: 10.3389/fimmu.2020.599637] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 11/25/2020] [Indexed: 01/04/2023] Open
Abstract
Food allergy is a potentially fatal disease affecting 8% of children and has become increasingly common in the past two decades. Despite the prevalence and severe nature of the disease, the mechanisms underlying sensitization remain to be further elucidated. The Collaborative Cross is a genetically diverse panel of inbred mice that were specifically developed to study the influence of genetics on complex diseases. Using this panel of mouse strains, we previously demonstrated CC027/GeniUnc mice, but not C3H/HeJ mice, develop peanut allergy after oral exposure to peanut in the absence of a Th2-skewing adjuvant. Here, we investigated factors associated with sensitization in CC027/GeniUnc mice following oral exposure to peanut, walnut, milk, or egg. CC027/GeniUnc mice mounted antigen-specific IgE responses to peanut, walnut and egg, but not milk, while C3H/HeJ mice were not sensitized to any antigen. Naïve CC027/GeniUnc mice had markedly lower total fecal IgA compared to C3H/HeJ, which was accompanied by stark differences in gut microbiome composition. Sensitized CC027/GeniUnc mice had significantly fewer CD3+ T cells but higher numbers of CXCR5+ B cells and T follicular helper cells in the mesenteric lymph nodes compared to C3H/HeJ mice, which is consistent with their relative immunoglobulin production. After oral challenge to the corresponding food, peanut- and walnut-sensitized CC027/GeniUnc mice experienced anaphylaxis, whereas mice exposed to milk and egg did not. Ara h 2 was detected in serum collected post-challenge from peanut-sensitized mice, indicating increased absorption of this allergen, while Bos d 5 and Gal d 2 were not detected in mice exposed to milk and egg, respectively. Machine learning on the change in gut microbiome composition as a result of food protein exposure identified a unique signature in CC027/GeniUnc mice that experienced anaphylaxis, including the depletion of Akkermansia. Overall, these results demonstrate several factors associated with enteral sensitization in CC027/GeniUnc mice, including diminished total fecal IgA, increased allergen absorption and altered gut microbiome composition. Furthermore, peanuts and tree nuts may have inherent properties distinct from milk and eggs that contribute to allergy.
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Affiliation(s)
- Johanna M. Smeekens
- Department of Pediatrics, Division of Rheumatology, Allergy and Immunology, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
- UNC Food Allergy Initiative, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | | | - Andrew L. Hinton
- UNC Food Allergy Initiative, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC, United States
| | - M. Andrea Azcarate-Peril
- Department of Medicine, Division of Gastroenterology and Hepatology, University of North Carolina, Chapel Hill, NC, United States
- UNC Microbiome Core, Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, NC, United States
| | - Timothy P. Moran
- Department of Pediatrics, Division of Rheumatology, Allergy and Immunology, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - Robert M. Immormino
- Department of Pediatrics, Division of Rheumatology, Allergy and Immunology, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - Janelle R. Kesselring
- Department of Pediatrics, Division of Rheumatology, Allergy and Immunology, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
- UNC Food Allergy Initiative, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - Erin C. Steinbach
- Department of Pediatrics, Division of Rheumatology, Allergy and Immunology, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - Kelly A. Orgel
- Department of Pediatrics, Division of Rheumatology, Allergy and Immunology, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
- UNC Food Allergy Initiative, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - Herman F. Staats
- Department of Pathology, Duke University School of Medicine, Durham, NC, United States
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
- Department of Immunology, Duke University School of Medicine, Durham, NC, United States
| | - A. Wesley Burks
- Department of Pediatrics, Division of Rheumatology, Allergy and Immunology, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
- UNC Food Allergy Initiative, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - Peter J. Mucha
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC, United States
- Department of Mathematics and Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, United States
| | - Martin T. Ferris
- Department of Genetics, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - Michael D. Kulis
- Department of Pediatrics, Division of Rheumatology, Allergy and Immunology, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
- UNC Food Allergy Initiative, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
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36
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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: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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37
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Sigmon JS, Blanchard MW, Baric RS, Bell TA, Brennan J, Brockmann GA, Burks AW, Calabrese JM, Caron KM, Cheney RE, Ciavatta D, Conlon F, Darr DB, Faber J, Franklin C, Gershon TR, Gralinski L, Gu B, Gaines CH, Hagan RS, Heimsath EG, Heise MT, Hock P, Ideraabdullah F, Jennette JC, Kafri T, Kashfeen A, Kulis M, Kumar V, Linnertz C, Livraghi-Butrico A, Lloyd KCK, Lutz C, Lynch RM, Magnuson T, Matsushima GK, McMullan R, Miller DR, Mohlke KL, Moy SS, Murphy CEY, Najarian M, O'Brien L, Palmer AA, Philpot BD, Randell SH, Reinholdt L, Ren Y, Rockwood S, Rogala AR, Saraswatula A, Sassetti CM, Schisler JC, Schoenrock SA, Shaw GD, Shorter JR, Smith CM, St Pierre CL, Tarantino LM, Threadgill DW, Valdar W, Vilen BJ, Wardwell K, Whitmire JK, Williams L, Zylka MJ, Ferris MT, McMillan L, Manuel de Villena FP. Content and Performance of the MiniMUGA Genotyping Array: A New Tool To Improve Rigor and Reproducibility in Mouse Research. Genetics 2020; 216:905-930. [PMID: 33067325 PMCID: PMC7768238 DOI: 10.1534/genetics.120.303596] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 10/06/2020] [Indexed: 12/14/2022] Open
Abstract
The laboratory mouse is the most widely used animal model for biomedical research, due in part to its well-annotated genome, wealth of genetic resources, and the ability to precisely manipulate its genome. Despite the importance of genetics for mouse research, genetic quality control (QC) is not standardized, in part due to the lack of cost-effective, informative, and robust platforms. Genotyping arrays are standard tools for mouse research and remain an attractive alternative even in the era of high-throughput whole-genome sequencing. Here, we describe the content and performance of a new iteration of the Mouse Universal Genotyping Array (MUGA), MiniMUGA, an array-based genetic QC platform with over 11,000 probes. In addition to robust discrimination between most classical and wild-derived laboratory strains, MiniMUGA was designed to contain features not available in other platforms: (1) chromosomal sex determination, (2) discrimination between substrains from multiple commercial vendors, (3) diagnostic SNPs for popular laboratory strains, (4) detection of constructs used in genetically engineered mice, and (5) an easy-to-interpret report summarizing these results. In-depth annotation of all probes should facilitate custom analyses by individual researchers. To determine the performance of MiniMUGA, we genotyped 6899 samples from a wide variety of genetic backgrounds. The performance of MiniMUGA compares favorably with three previous iterations of the MUGA family of arrays, both in discrimination capabilities and robustness. We have generated publicly available consensus genotypes for 241 inbred strains including classical, wild-derived, and recombinant inbred lines. Here, we also report the detection of a substantial number of XO and XXY individuals across a variety of sample types, new markers that expand the utility of reduced complexity crosses to genetic backgrounds other than C57BL/6, and the robust detection of 17 genetic constructs. We provide preliminary evidence that the array can be used to identify both partial sex chromosome duplication and mosaicism, and that diagnostic SNPs can be used to determine how long inbred mice have been bred independently from the relevant main stock. We conclude that MiniMUGA is a valuable platform for genetic QC, and an important new tool to increase the rigor and reproducibility of mouse research.
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Affiliation(s)
- John Sebastian Sigmon
- Department of Computer Science, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Matthew W Blanchard
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
- Mutant Mouse Resource and Research Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Ralph S Baric
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Timothy A Bell
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Jennifer Brennan
- Mutant Mouse Resource and Research Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | | | - A Wesley Burks
- Department of Pediatrics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - J Mauro Calabrese
- Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Kathleen M Caron
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Richard E Cheney
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Dominic Ciavatta
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Frank Conlon
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - David B Darr
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - James Faber
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Craig Franklin
- Department of Veterinary Pathobiology, University of Missouri, Columbia, Missouri 65211
| | - Timothy R Gershon
- Department of Neurology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Lisa Gralinski
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Bin Gu
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Christiann H Gaines
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Robert S Hagan
- Division of Pulmonary Diseases and Critical Care Medicine, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Ernest G Heimsath
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Mark T Heise
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Pablo Hock
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Folami Ideraabdullah
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
- Department of Nutrition, Gillings School of Public Health, University of North Carolina, Chapel Hill, North Carolina 27599
| | - J Charles Jennette
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Tal Kafri
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina 27599
- Gene Therapy Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Anwica Kashfeen
- Department of Computer Science, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Mike Kulis
- Department of Pediatrics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Vivek Kumar
- The Jackson Laboratory, Bar Harbor, Maine 04609
| | - Colton Linnertz
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Alessandra Livraghi-Butrico
- Marsico Lung Institute/UNC Cystic Fibrosis Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - K C Kent Lloyd
- Department of Surgery, University of California Davis, Davis, California 95616
- School of Medicine, University of California Davis, California 95616
- Mouse Biology Program, University of California Davis, California 95616
| | | | - Rachel M Lynch
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Terry Magnuson
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
- Mutant Mouse Resource and Research Center, University of North Carolina, Chapel Hill, North Carolina 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Glenn K Matsushima
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina 27599
- UNC Neuroscience Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Rachel McMullan
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Darla R Miller
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Sheryl S Moy
- Department of Psychiatry, University of North Carolina, Chapel Hill, North Carolina 27599
- Carolina Institute for Developmental Disabilities, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Caroline E Y Murphy
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Maya Najarian
- Department of Computer Science, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Lori O'Brien
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599
| | | | - Benjamin D Philpot
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599
- Marsico Lung Institute/UNC Cystic Fibrosis Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Scott H Randell
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599
| | | | - Yuyu Ren
- University of California San Diego, La Jolla, California 92093
| | | | - Allison R Rogala
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, North Carolina 27599
- Division of Comparative Medicine, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Avani Saraswatula
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Christopher M Sassetti
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts 01655
| | - Jonathan C Schisler
- Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Sarah A Schoenrock
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Ginger D Shaw
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - John R Shorter
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Clare M Smith
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts 01655
| | | | - Lisa M Tarantino
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599
| | - David W Threadgill
- University of California San Diego, La Jolla, California 92093
- Department of Biochemistry and Biophysics, Texas A&M University, Texas 77843
| | - William Valdar
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Barbara J Vilen
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina 27599
| | | | - Jason K Whitmire
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Lucy Williams
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Mark J Zylka
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Martin T Ferris
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Leonard McMillan
- Department of Computer Science, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Fernando Pardo Manuel de Villena
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
- Mutant Mouse Resource and Research Center, University of North Carolina, Chapel Hill, North Carolina 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
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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 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] [What about the content of this article? (0)] [Affiliation(s)] [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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39
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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40
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Hampton BK, Jensen K, Whitmore AC, Morrison CR, Plante KS, Leist SR, Gralinski LE, Menachery VD, Schäfer A, de Villena FPM, Baric RS, Heise MT, Ferris MT. Genetic regulation of immune homeostatic lung leukocyte populations. The Journal of Immunology 2020. [DOI: 10.4049/jimmunol.204.supp.235.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
Immune homeostasis is the state where the immune system maintains stability in the absence of insult. Much of the analysis of immune homeostasis has focused on systemic immunity, but it is also likely to be important in an organ specific manner. There is evidence that homeostatic immunity can affect subsequent responses to infection or vaccination. Since the lungs are a major site of infection, we used the Collaborative Cross (CC) mouse genetic reference population to study the genetic regulation of the breadth of baseline immune cell populations in the lung and identify loci regulating these cells at the steady state. We found that all immune cell populations measured showed strong genetic (i.e. strain-specific) variation in cell type abundances. We identified 12 quantitative trait loci (QTL) associated with variation in 12 immune cell populations or the relationships between cell populations. Given the role of various immune cells in the lungs during respiratory virus pathogenesis, we asked whether any of the mapped QTL correlated with influenza A virus (IAV) or Severe acute respiratory syndrome associated coronavirus (SARS-CoV) disease following infection in the same strains of mice. Notably, a locus we mapped for baseline abundance of CD8+ T cells in the lungs was associated with peak weight loss following IAV infection. Additionally, a locus mapped for variation in Ly6C+ monocyte/macrophage abundance was associated with SARS-CoV titer at days 2 and 4 post-infection. These data suggest that abundance of lung leukocyte populations prior to infection could serve as predictors of immune responses to respiratory viruses.
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Affiliation(s)
- Brea K Hampton
- 1Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Kara Jensen
- 2University of North Carolina, Gillings School of Public Health
| | - Alan C. Whitmore
- 3Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Clayton R. Morrison
- 3Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Kenneth S. Plante
- 3Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Sarah R. Leist
- 2University of North Carolina, Gillings School of Public Health
| | | | | | | | | | - Ralph S. Baric
- 2University of North Carolina, Gillings School of Public Health
| | - Mark T. Heise
- 3Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
- 4Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Martin T. Ferris
- 3Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
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41
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Noll KE, Whitmore AC, West A, McCarthy MK, Morrison CR, Plante KS, Hampton BK, Kollmus H, Pilzner C, Leist SR, Gralinski LE, Menachery VD, Schäfer A, Miller D, Shaw G, Mooney M, McWeeney S, Pardo-Manuel de Villena F, Schughart K, Morrison TE, Baric RS, Ferris MT, Heise MT. Complex Genetic Architecture Underlies Regulation of Influenza-A-Virus-Specific Antibody Responses in the Collaborative Cross. Cell Rep 2020; 31:107587. [PMID: 32348764 PMCID: PMC7195006 DOI: 10.1016/j.celrep.2020.107587] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 02/20/2020] [Accepted: 04/08/2020] [Indexed: 02/07/2023] Open
Abstract
Host genetic factors play a fundamental role in regulating humoral immunity to viral infection, including influenza A virus (IAV). Here, we utilize the Collaborative Cross (CC), a mouse genetic reference population, to study genetic regulation of variation in antibody response following IAV infection. CC mice show significant heritable variation in the magnitude, kinetics, and composition of IAV-specific antibody response. We map 23 genetic loci associated with this variation. Analysis of a subset of these loci finds that they broadly affect the antibody response to IAV as well as other viruses. Candidate genes are identified based on predicted variant consequences and haplotype-specific expression patterns, and several show overlap with genes identified in human mapping studies. These findings demonstrate that the host antibody response to IAV infection is under complex genetic control and highlight the utility of the CC in modeling and identifying genetic factors with translational relevance to human health and disease.
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Affiliation(s)
- Kelsey E Noll
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alan C Whitmore
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ande West
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Mary K McCarthy
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, USA
| | | | - Kenneth S Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Brea K Hampton
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Heike Kollmus
- Department of Infection Genetics, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Carolin Pilzner
- Department of Infection Genetics, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Sarah R Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Infection Genetics, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Lisa E Gralinski
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Vineet D Menachery
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Darla Miller
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ginger Shaw
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michael Mooney
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR, USA; OHSU Knight Cancer Center Institute, Oregon Health and Science University, Portland, OR, USA
| | - Shannon McWeeney
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR, USA; OHSU Knight Cancer Center Institute, Oregon Health and Science University, Portland, OR, USA; Oregon Clinical and Translational Research Institute, Oregon Health and Science University, Portland, OR, 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, Chapel Hill, NC, USA
| | - Klaus Schughart
- Department of Infection Genetics, Helmholtz Centre for Infection Research, Braunschweig, Germany; University of Veterinary Medicine Hannover, Hannover, Germany; Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Thomas E Morrison
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Ralph S Baric
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Martin T Ferris
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Mark T Heise
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA.
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Shorter JR, Najarian ML, Bell TA, Blanchard M, Ferris MT, Hock P, Kashfeen A, Kirchoff KE, Linnertz CL, Sigmon JS, Miller DR, McMillan L, Pardo-Manuel de Villena F. Whole Genome Sequencing and Progress Toward Full Inbreeding of the Mouse Collaborative Cross Population. G3 (Bethesda) 2019; 9:1303-1311. [PMID: 30858237 PMCID: PMC6505143 DOI: 10.1534/g3.119.400039] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 03/08/2019] [Indexed: 12/20/2022]
Abstract
Two key features of recombinant inbred panels are well-characterized genomes and reproducibility. Here we report on the sequenced genomes of six additional Collaborative Cross (CC) strains and on inbreeding progress of 72 CC strains. We have previously reported on the sequences of 69 CC strains that were publicly available, bringing the total of CC strains with whole genome sequence up to 75. The sequencing of these six CC strains updates the efforts toward inbreeding undertaken by the UNC Systems Genetics Core. The timing reflects our competing mandates to release to the public as many CC strains as possible while achieving an acceptable level of inbreeding. The new six strains have a higher than average founder contribution from non-domesticus strains than the previously released CC strains. Five of the six strains also have high residual heterozygosity (>14%), which may be related to non-domesticus founder contributions. Finally, we report on updated estimates on residual heterozygosity across the entire CC population using a novel, simple and cost effective genotyping platform on three mice from each strain. We observe a reduction in residual heterozygosity across all previously released CC strains. We discuss the optimal use of different genetic resources available for the CC population.
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Affiliation(s)
| | | | - Timothy A Bell
- Department of Genetics
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
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43
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Menachery VD, McAnarney ET, Ferris MT. Age-dependent Susceptibility To Virus Infection Is Governed by Host Genetics. The Journal of Immunology 2019. [DOI: 10.4049/jimmunol.202.supp.197.9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
While improved sanitation and medical care have reduced the burden of infectious disease, it remains the 4th leading cause of death in the elderly. Coupled with the expansion of the aged population over the next two decades, understanding the interplay between infection and the senescent host is critical. Both the microbiome and host genetics have been predicted to play critical roles in aging immunity. In this work, we explore the role of each in age-dependent susceptibility to virus infection. Severe acute respiratory syndrome coronavirus (SARS-CoV), the first outbreak virus of the 21st century, produces increased disease in aged patients as compared to the young. Importantly, age-dependent susceptibility is observed in mouse models of SARS-CoV infection. Our results indicate that despite microbiome variation between young and aged animals, limiting these differences had only a marginal effect on disease in the aged following infection. In contrast, age-dependent susceptibility was not fully conserved across genetically diverse Collaborative Cross (CC) mice. We found that while the majority of CC lines maintained increased disease as they aged, several lines showed no distinction between young and aged animals. In one CC line, we found that aged mice were more resistant to SARS-CoV infection than their younger equivalent. Notably, age-dependent susceptibility was not simply associated with higher viral loads driving augmented disease. Instead, the results suggest that host factors including tissue and inflammation responses govern disease in the senescent host. Together, the work highlights the importance of genetic elements in driving age-dependent disease following infection.
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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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45
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Ferris MT, Hood DW. Host genetic regulation of immune-based and infectious diseases : Introduction to mammalian genome special issue: genetics of infectious disease. Mamm Genome 2019; 29:365-366. [PMID: 30171339 PMCID: PMC7088047 DOI: 10.1007/s00335-018-9779-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Martin T Ferris
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA.
| | - Derek W Hood
- Mammalian Genetics Unit, MRC Harwell Institute, Harwell Campus, Oxfordshire, OX11 0RD, UK
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Orgel K, Smeekens JM, Ye P, Fotsch L, Guo R, Miller DR, Pardo-Manuel de Villena F, Burks AW, Ferris MT, Kulis MD. Genetic diversity between mouse strains allows identification of the CC027/GeniUnc strain as an orally reactive model of peanut allergy. J Allergy Clin Immunol 2018; 143:1027-1037.e7. [PMID: 30342892 PMCID: PMC7252586 DOI: 10.1016/j.jaci.2018.10.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 09/17/2018] [Accepted: 10/01/2018] [Indexed: 02/08/2023]
Abstract
BACKGROUND Improved animal models are needed to understand the genetic and environmental factors that contribute to food allergy. OBJECTIVE We sought to assess food allergy phenotypes in a genetically diverse collection of mice. METHODS We selected 16 Collaborative Cross (CC) mouse strains, as well as the classic inbred C57BL/6J, C3H/HeJ, and BALB/cJ strains, for screening. Female mice were sensitized to peanut intragastrically with or without cholera toxin and then challenged with peanut by means of oral gavage or intraperitoneal injection and assessed for anaphylaxis. Peanut-specific immunoglobulins, T-cell cytokines, regulatory T cells, mast cells, and basophils were quantified. RESULTS Eleven of the 16 CC strains had allergic reactions to intraperitoneal peanut challenge, whereas only CC027/GeniUnc mice reproducibly experienced severe symptoms after oral food challenge (OFC). CC027/GeniUnc, C3H/HeJ, and C57BL/6J mice all mounted a TH2 response against peanut, leading to production of IL-4 and IgE, but only the CC027/GeniUnc mice reacted to OFC. Orally induced anaphylaxis in CC027/GeniUnc mice was correlated with serum levels of Ara h 2 in circulation but not with allergen-specific IgE or mucosal mast cell protease 1 levels, indicating systemic allergen absorption is important for anaphylaxis through the gastrointestinal tract. Furthermore, CC027/GeniUnc, but not C3H/HeJ or BALB/cJ, mice can be sensitized in the absence of cholera toxin and react on OFC to peanut. CONCLUSIONS We have identified and characterized CC027/GeniUnc mice as a strain that is genetically susceptible to peanut allergy and prone to severe reactions after OFC. More broadly, these findings demonstrate the untapped potential of the CC population in developing novel models for allergy research.
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Affiliation(s)
- Kelly Orgel
- Department of Pediatrics, University of North Carolina School of Medicine, Chapel Hill, NC; University of North Carolina Food Allergy Initiative, Chapel Hill, NC
| | - Johanna M Smeekens
- Department of Pediatrics, University of North Carolina School of Medicine, Chapel Hill, NC; University of North Carolina Food Allergy Initiative, Chapel Hill, NC
| | - Ping Ye
- Department of Pediatrics, University of North Carolina School of Medicine, Chapel Hill, NC; University of North Carolina Food Allergy Initiative, Chapel Hill, NC
| | - Lauren Fotsch
- Department of Pediatrics, University of North Carolina School of Medicine, Chapel Hill, NC; University of North Carolina Food Allergy Initiative, Chapel Hill, NC
| | - Rishu Guo
- Department of Pediatrics, University of North Carolina School of Medicine, Chapel Hill, NC; University of North Carolina Food Allergy Initiative, Chapel Hill, NC
| | - Darla R Miller
- Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, NC
| | - Fernando Pardo-Manuel de Villena
- Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, NC; Lineberger Comprehensive Cancer Center, Chapel Hill, NC
| | - A Wesley Burks
- Department of Pediatrics, University of North Carolina School of Medicine, Chapel Hill, NC; University of North Carolina Food Allergy Initiative, Chapel Hill, NC
| | - Martin T Ferris
- Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, NC.
| | - Michael D Kulis
- Department of Pediatrics, University of North Carolina School of Medicine, Chapel Hill, NC; University of North Carolina Food Allergy Initiative, Chapel Hill, NC.
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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: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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McMullan RC, Ferris MT, Bell TA, Menachery VD, Baric RS, Hua K, Pomp D, Smith‐Ryan AE, de Villena FP. CC002/Unc females are mouse models of exercise-induced paradoxical fat response. Physiol Rep 2018; 6:e13716. [PMID: 29924460 PMCID: PMC6009762 DOI: 10.14814/phy2.13716] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 05/03/2018] [Indexed: 12/13/2022] Open
Abstract
Exercise results in beneficial health outcomes and protects against a variety of chronic diseases. However, U.S. exercise guidelines recommend identical exercise programs for everyone, despite individual variation in responses to these programs, including paradoxical fat gain. Experimental models of exercise-induced paradoxical outcomes may enable the dissection of underlying physiological mechanisms as well as the evaluation of potential interventions. Whereas several studies have identified individual mice exhibiting paradoxical fat gain following exercise, no systematic effort has been conducted to identify and characterize models of paradoxical response. Strains from the Collaborative Cross (CC) genetic reference population were used due to its high levels of genetic variation, its reproducible nature, and the observation that the CC is a rich source of novel disease models, to assess the impact genetic background has on exercise responses. We identified the strain CC002/Unc as an exercise-induced paradoxical fat response model in a controlled voluntary exercise study across multiple ages in female mice. We also found sex and genetic differences were consistent with this pattern in a study of forced exercise programs. These results provide a novel model for studies to determine the mechanisms behind paradoxical metabolic responses to exercise, and enable development of more rational personalized exercise recommendations based on factors such as age, sex, and genetic background.
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Affiliation(s)
- Rachel C. McMullan
- Department of GeneticsSchool of MedicineUniversity of North Carolina at Chapel HillChapel HillNorth Carolina
- Genetics and Molecular Biology CurriculumSchool of MedicineUniversity of North Carolina at Chapel HillChapel HillNorth Carolina
- Lineberger Comprehensive Cancer CenterUniversity of North Carolina at Chapel HillChapel HillNorth Carolina
| | - Martin T. Ferris
- Department of GeneticsSchool of MedicineUniversity of North Carolina at Chapel HillChapel HillNorth Carolina
| | - Timothy A. Bell
- Department of GeneticsSchool of MedicineUniversity of North Carolina at Chapel HillChapel HillNorth Carolina
- Lineberger Comprehensive Cancer CenterUniversity of North Carolina at Chapel HillChapel HillNorth Carolina
| | - Vineet D. Menachery
- Department of EpidemiologyGillings School of Global Public HealthUniversity of North Carolina at Chapel HillChapel HillNorth Carolina
| | - Ralph S. Baric
- Department of EpidemiologyGillings School of Global Public HealthUniversity of North Carolina at Chapel HillChapel HillNorth Carolina
| | - Kunjie Hua
- Department of GeneticsSchool of MedicineUniversity of North Carolina at Chapel HillChapel HillNorth Carolina
| | - Daniel Pomp
- Department of GeneticsSchool of MedicineUniversity of North Carolina at Chapel HillChapel HillNorth Carolina
| | - Abbie E. Smith‐Ryan
- Department of Exercise and Sport ScienceCollege of Arts and SciencesUniversity of North Carolina at Chapel HillChapel HillNorth Carolina
| | - Fernando Pardo‐Manuel de Villena
- Department of GeneticsSchool of MedicineUniversity of North Carolina at Chapel HillChapel HillNorth Carolina
- Lineberger Comprehensive Cancer CenterUniversity of North Carolina at Chapel HillChapel HillNorth Carolina
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Hampton BK, Noll KE, Whitmore AC, Plante KS, Ferris MT, Heise MT. Methyl-CpG binding domain protein-1 polymorphisms impact immune homeostatic levels of IgG. The Journal of Immunology 2018. [DOI: 10.4049/jimmunol.200.supp.48.19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Host immunity plays a key role in protection against infection, however, there is significant individual-to-individual variation in the induction and quality of immune response that is driven in part by genetic factors. A growing body of evidence suggests that variation in immune status prior to specific insult may influence subsequent response to vaccination or pathogen challenge. Therefore, understanding the variation in immune status prior to specific insult is necessary for assessing variability in immune response to vaccination or pathogen challenge. The Collaborative Cross (CC) mouse population is a genetically diverse population that was designed to mimic the genetic and phenotypic diversity that is observed in humans and allows us to investigate mechanistically the contribution of genetics to complex phenotypes. Consequently, we asked whether there was variation in antibody levels in 57 CC strains prior to pathogen challenge and if that variation was associated with specific genetic factors. To assess this, we measured antibody levels for IgM, total IgG, IgG1, IgG2a, IgG2b, and IgG2c by ELISA and mapped quantitative trait loci (QTL) associated with variation in antibody concentrations. We observed substantial variation in all antibody isotypes measured. We also identified a suggestive (p=0.1) QTL on chromosome 18. Allele effects show that the C57Bl/6J allele at the locus of interest is linked to higher levels of total IgG. Subsequent analysis of genes under the QTL identified Methyl-CpG binding domain protein-1 (Mbd1) as the most promising candidate gene associated with total IgG variation. Ongoing studies are evaluating the role of Mbd1 in the regulation of total IgG production.
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Smeekens J, Orgel K, Ferris MT, Miller D, Burks AW, Pardo-Manuel de Villena F, Kulis MD. Intragastric sensitization to peanut in the absence of a Th2-skewing adjuvant in mice genetically predisposed to food allergy. J Allergy Clin Immunol 2018. [DOI: 10.1016/j.jaci.2017.12.472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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