1
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Keller MD, Schattgen SA, Chandrakasan S, Allen EK, Jensen-Wachspress MA, Lazarski CA, Qayed M, Lang H, Hanley PJ, Tanna J, Pai SY, Parikh S, Berger SI, Gottschalk S, Pulsipher MA, Thomas PG, Bollard CM. Secondary bone marrow graft loss after third-party virus-specific T cell infusion: Case report of a rare complication. Nat Commun 2024; 15:2749. [PMID: 38553461 PMCID: PMC10980733 DOI: 10.1038/s41467-024-47056-3] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 12/20/2023] [Indexed: 04/02/2024] Open
Abstract
Virus-specific T cells (VST) from partially-HLA matched donors have been effective for treatment of refractory viral infections in immunocompromised patients in prior studies with a good safety profile, but rare adverse events have been described. Here we describe a unique and severe adverse event of VST therapy in an infant with severe combined immunodeficiency, who receives, as part of a clinical trial (NCT03475212), third party VSTs for treating cytomegalovirus viremia following bone marrow transplantation. At one-month post-VST infusion, rejection of graft and reversal of chimerism is observed, as is an expansion of T cells exclusively from the VST donor. Single-cell gene expression and T cell receptor profiling demonstrate a narrow repertoire of predominantly activated CD4+ T cells in the recipient at the time of rejection, with the repertoire overlapping more with that of peripheral blood from VST donor than the infused VST product. This case thus demonstrates a rare but serious side effect of VST therapy.
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Affiliation(s)
- Michael D Keller
- Center for Cancer and Immunology Research, Children's National Hospital, Washington, DC, USA
- Division of Allergy and Immunology, Children's National Hospital, Washington, DC, USA
- GW Cancer Center, George Washington University, Washington, DC, USA
| | - Stefan A Schattgen
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | | | - E Kaitlynn Allen
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Christopher A Lazarski
- Center for Cancer and Immunology Research, Children's National Hospital, Washington, DC, USA
| | - Muna Qayed
- Aflac Cancer and Blood Disorders Center, Children's Hospital of Atlanta, Atlanta, GA, USA
| | - Haili Lang
- Center for Cancer and Immunology Research, Children's National Hospital, Washington, DC, USA
| | - Patrick J Hanley
- Center for Cancer and Immunology Research, Children's National Hospital, Washington, DC, USA
- GW Cancer Center, George Washington University, Washington, DC, USA
- Division of Blood and Marrow Transplantation, Children's National Hospital, Washington, DC, USA
| | - Jay Tanna
- Center for Cancer and Immunology Research, Children's National Hospital, Washington, DC, USA
- Division of Blood and Marrow Transplantation, Children's National Hospital, Washington, DC, USA
| | - Sung-Yun Pai
- Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Suhag Parikh
- Aflac Cancer and Blood Disorders Center, Children's Hospital of Atlanta, Atlanta, GA, USA
| | - Seth I Berger
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, USA
| | - Stephen Gottschalk
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Michael A Pulsipher
- Division of Pediatric Hematology/Oncology, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Paul G Thomas
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Catherine M Bollard
- Center for Cancer and Immunology Research, Children's National Hospital, Washington, DC, USA.
- GW Cancer Center, George Washington University, Washington, DC, USA.
- Division of Blood and Marrow Transplantation, Children's National Hospital, Washington, DC, USA.
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2
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Kirk AM, Crawford JC, Chou CH, Guy C, Pandey K, Kozlik T, Shah RK, Chung S, Nguyen P, Zhang X, Wang J, Bell M, Mettelman RC, Allen EK, Pogorelyy MV, Kim H, Minervina AA, Awad W, Bajracharya R, White T, Long D, Gordon B, Morrison M, Glazer ES, Murphy AJ, Jiang Y, Fitzpatrick EA, Yarchoan M, Sethupathy P, Croft NP, Purcell AW, Federico SM, Stewart E, Gottschalk S, Zamora AE, DeRenzo C, Strome SE, Thomas PG. DNAJB1-PRKACA fusion neoantigens elicit rare endogenous T cell responses that potentiate cell therapy for fibrolamellar carcinoma. Cell Rep Med 2024; 5:101469. [PMID: 38508137 PMCID: PMC10983114 DOI: 10.1016/j.xcrm.2024.101469] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 11/29/2023] [Accepted: 02/20/2024] [Indexed: 03/22/2024]
Abstract
Fibrolamellar carcinoma (FLC) is a liver tumor with a high mortality burden and few treatment options. A promising therapeutic vulnerability in FLC is its driver mutation, a conserved DNAJB1-PRKACA gene fusion that could be an ideal target neoantigen for immunotherapy. In this study, we aim to define endogenous CD8 T cell responses to this fusion in FLC patients and evaluate fusion-specific T cell receptors (TCRs) for use in cellular immunotherapies. We observe that fusion-specific CD8 T cells are rare and that FLC patient TCR repertoires lack large clusters of related TCR sequences characteristic of potent antigen-specific responses, potentially explaining why endogenous immune responses are insufficient to clear FLC tumors. Nevertheless, we define two functional fusion-specific TCRs, one of which has strong anti-tumor activity in vivo. Together, our results provide insights into the fragmented nature of neoantigen-specific repertoires in humans and indicate routes for clinical development of successful immunotherapies for FLC.
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Affiliation(s)
- Allison M Kirk
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jeremy Chase Crawford
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ching-Heng Chou
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Cliff Guy
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Kirti Pandey
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Tanya Kozlik
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Ravi K Shah
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Shanzou Chung
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Phuong Nguyen
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Xiaoyu Zhang
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Jin Wang
- Department of Microbiology, Immunology, and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Matthew Bell
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Robert C Mettelman
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - E Kaitlynn Allen
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Mikhail V Pogorelyy
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Hyunjin Kim
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Anastasia A Minervina
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Walid Awad
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Resha Bajracharya
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Toni White
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Donald Long
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14850, USA
| | - Brittney Gordon
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Michelle Morrison
- Center for Cancer Research, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Evan S Glazer
- Center for Cancer Research, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN 38163, USA; Department of Surgery, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Andrew J Murphy
- Department of Surgery, The University of Tennessee Health Science Center, Memphis, TN 38163, USA; Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Yixing Jiang
- Department of Medical Oncology, Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Elizabeth A Fitzpatrick
- Department of Microbiology, Immunology, and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Mark Yarchoan
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Praveen Sethupathy
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14850, USA
| | - Nathan P Croft
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Anthony W Purcell
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Sara M Federico
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Elizabeth Stewart
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Stephen Gottschalk
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Anthony E Zamora
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Christopher DeRenzo
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Scott E Strome
- College of Medicine, The University of Tennessee Health Science Center, Memphis, TN 38163, USA.
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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3
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Kim M, Cheng WA, Congrave-Wilson Z, Marentes Ruiz CJ, Turner L, Mendieta S, Jumarang J, Del Valle J, Lee Y, Fabrizio T, Allen EK, Thomas PG, Webby R, Gordon A, Pannaraj PS. Comparisons of Pediatric and Adult SARS-CoV-2-Specific Antibodies up to 6 Months after Infection, Vaccination, or Hybrid Immunity. J Pediatric Infect Dis Soc 2024; 13:91-99. [PMID: 38016076 PMCID: PMC10824260 DOI: 10.1093/jpids/piad107] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 05/31/2023] [Accepted: 11/27/2023] [Indexed: 11/30/2023]
Abstract
BACKGROUND Characterization of longitudinal SARS-CoV-2-specific antibody responses in children following infection and vaccination is needed to inform SARS-CoV-2 vaccine policy decisions for children, which may differ from adults. METHODS We enrolled individuals at the time of SARS-CoV-2 infection or vaccination for longitudinal serological testing and compared SARS-CoV-2-spike-specific IgG and neutralization activity in children and adults stratified by infection and vaccination status using enzyme-linked immunosorbent and virus neutralization assays. RESULTS Between June 2020 and December 2022, we collected sera from 669 participants aged 40 days to 55 years, including 330 unvaccinated individuals with laboratory-confirmed SARS-CoV-2 infection, 180 vaccinated SARS-CoV-2-naïve individuals, and 159 vaccinated previously infected individuals. Half (n = 330, 49.3%) were children. SARS-CoV-2-specific IgG and neutralization activity in children < 12 years old in response to infection persisted at higher levels than those of adults through at least 6 months (spike-specific IgG levels, 2.05 [95% CI: 1.4-3.1] times higher than adults; neutralizing activity, median 88.8 vs 75.2%, respectively, p = .04). In addition, all pediatric participants had significantly higher IgG levels compared with adults at 6 months following infection or vaccination, regardless of prior infection status. Vaccine-induced SARS-CoV-2-specific IgG responses in previously infected individuals persisted at higher levels than those from infection alone at 6 months (median AUC, children 5-11 years old, 9115 vs 368; adolescents 3613 vs 475; adults 1956 vs 263, all p < .001). CONCLUSIONS These data demonstrate the robust and persistent immunologic response of SARS-CoV-2 vaccination in children and emphasize the benefit of vaccination after SARS-CoV-2 infection.
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Affiliation(s)
- Minjun Kim
- Division of Infectious Diseases, Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Wesley A Cheng
- Division of Infectious Diseases, Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Zion Congrave-Wilson
- Division of Infectious Diseases, Children’s Hospital Los Angeles, Los Angeles, CA, USA
| | | | - Lauren Turner
- Division of Infectious Diseases, Children’s Hospital Los Angeles, Los Angeles, CA, USA
| | - Shirley Mendieta
- Division of Infectious Diseases, Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Jaycee Jumarang
- Division of Infectious Diseases, Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Jennifer Del Valle
- Division of Infectious Diseases, Children’s Hospital Los Angeles, Los Angeles, CA, USA
| | - Yesun Lee
- Division of Infectious Diseases, Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Thomas Fabrizio
- Department of Infectious Diseases, St Jude Children’s Research Hospital, Memphis, TN, USA
| | - E Kaitlynn Allen
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Paul G Thomas
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Richard Webby
- Department of Infectious Diseases, St Jude Children’s Research Hospital, Memphis, TN, USA
| | - Aubree Gordon
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Pia S Pannaraj
- Division of Infectious Diseases, Department of Pediatrics, University of California San Diego, San Diego, CA, USA
- Division of Infectious Diseases, Rady Children’s Hospital, San Diego, CA, USA
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4
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Mettelman RC, Souquette A, Van de Velde LA, Vegesana K, Allen EK, Kackos CM, Trifkovic S, DeBeauchamp J, Wilson TL, St James DG, Menon SS, Wood T, Jelley L, Webby RJ, Huang QS, Thomas PG. Baseline innate and T cell populations are correlates of protection against symptomatic influenza virus infection independent of serology. Nat Immunol 2023; 24:1511-1526. [PMID: 37592015 PMCID: PMC10566627 DOI: 10.1038/s41590-023-01590-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [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: 12/16/2022] [Accepted: 07/13/2023] [Indexed: 08/19/2023]
Abstract
Evidence suggests that innate and adaptive cellular responses mediate resistance to the influenza virus and confer protection after vaccination. However, few studies have resolved the contribution of cellular responses within the context of preexisting antibody titers. Here, we measured the peripheral immune profiles of 206 vaccinated or unvaccinated adults to determine how baseline variations in the cellular and humoral immune compartments contribute independently or synergistically to the risk of developing symptomatic influenza. Protection correlated with diverse and polyfunctional CD4+ and CD8+ T, circulating T follicular helper, T helper type 17, myeloid dendritic and CD16+ natural killer (NK) cell subsets. Conversely, increased susceptibility was predominantly attributed to nonspecific inflammatory populations, including γδ T cells and activated CD16- NK cells, as well as TNFα+ single-cytokine-producing CD8+ T cells. Multivariate and predictive modeling indicated that cellular subsets (1) work synergistically with humoral immunity to confer protection, (2) improve model performance over demographic and serologic factors alone and (3) comprise the most important predictive covariates. Together, these results demonstrate that preinfection peripheral cell composition improves the prediction of symptomatic influenza susceptibility over vaccination, demographics or serology alone.
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Affiliation(s)
- Robert C Mettelman
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Aisha Souquette
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Lee-Ann Van de Velde
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kasi Vegesana
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - E Kaitlynn Allen
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Christina M Kackos
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Sanja Trifkovic
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jennifer DeBeauchamp
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Taylor L Wilson
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Microbiology, Immunology and Biochemistry, College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Deryn G St James
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Microbiology, Immunology and Biochemistry, College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Smrithi S Menon
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Timothy Wood
- Institute of Environmental Science and Research Limited (ESR), Wallaceville Science Centre, Upper Hutt, New Zealand
| | - Lauren Jelley
- Institute of Environmental Science and Research Limited (ESR), Wallaceville Science Centre, Upper Hutt, New Zealand
| | - Richard J Webby
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - Q Sue Huang
- Institute of Environmental Science and Research Limited (ESR), Wallaceville Science Centre, Upper Hutt, New Zealand.
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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5
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Flerlage T, Crawford JC, Allen EK, Severns D, Tan S, Surman S, Ridout G, Novak T, Randolph A, West AN, Thomas PG. Single cell transcriptomics identifies distinct profiles in pediatric acute respiratory distress syndrome. Nat Commun 2023; 14:3870. [PMID: 37391405 PMCID: PMC10313703 DOI: 10.1038/s41467-023-39593-0] [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: 08/24/2022] [Accepted: 06/21/2023] [Indexed: 07/02/2023] Open
Abstract
Acute respiratory distress syndrome (ARDS), termed pediatric ARDS (pARDS) in children, is a severe form of acute respiratory failure (ARF). Pathologic immune responses are implicated in pARDS pathogenesis. Here, we present a description of microbial sequencing and single cell gene expression in tracheal aspirates (TAs) obtained longitudinally from infants with ARF. We show reduced interferon stimulated gene (ISG) expression, altered mononuclear phagocyte (MNP) transcriptional programs, and progressive airway neutrophilia associated with unique transcriptional profiles in patients with moderate to severe pARDS compared to those with no or mild pARDS. We additionally show that an innate immune cell product, Folate Receptor 3 (FOLR3), is enriched in moderate or severe pARDS. Our findings demonstrate distinct inflammatory responses in pARDS that are dependent upon etiology and severity and specifically implicate reduced ISG expression, altered macrophage repair-associated transcriptional programs, and accumulation of aged neutrophils in the pathogenesis of moderate to severe pARDS caused by RSV.
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Affiliation(s)
- Tim Flerlage
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
- Division of Pediatric Critical Care Medicine, Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN, USA
| | | | - E Kaitlynn Allen
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Danielle Severns
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Shaoyuan Tan
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Sherri Surman
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Granger Ridout
- Hartwell Center for Biotechnology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Tanya Novak
- Department of Anesthesiology, Critical Care, and Pain Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Anaesthesia, Harvard Medical School, Boston, MA, USA
| | - Adrienne Randolph
- Department of Anesthesiology, Critical Care, and Pain Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Anaesthesia, Harvard Medical School, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Alina N West
- Division of Pediatric Critical Care Medicine, Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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6
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Habel JR, Chua BY, Kedzierski L, Selva KJ, Damelang T, Haycroft ER, Nguyen TH, Koay HF, Nicholson S, McQuilten HA, Jia X, Allen LF, Hensen L, Zhang W, van de Sandt CE, Neil JA, Pragastis K, Lau JS, Jumarang J, Allen EK, Amanant F, Krammer F, Wragg KM, Juno JA, Wheatley AK, Tan HX, Pell G, Walker S, Audsley J, Reynaldi A, Thevarajan I, Denholm JT, Subbarao K, Davenport MP, Hogarth PM, Godfrey DI, Cheng AC, Tong SY, Bond K, Williamson DA, McMahon JH, Thomas PG, Pannaraj PS, James F, Holmes NE, Smibert OC, Trubiano JA, Gordon CL, Chung AW, Whitehead CL, Kent SJ, Lappas M, Rowntree LC, Kedzierska K. Immune profiling of SARS-CoV-2 infection during pregnancy reveals NK cell and γδ T cell perturbations. JCI Insight 2023; 8:167157. [PMID: 37036008 PMCID: PMC10132165 DOI: 10.1172/jci.insight.167157] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 11/14/2022] [Accepted: 02/15/2023] [Indexed: 04/11/2023] Open
Abstract
Pregnancy poses a greater risk for severe COVID-19; however, underlying immunological changes associated with SARS-CoV-2 during pregnancy are poorly understood. We defined immune responses to SARS-CoV-2 in unvaccinated pregnant and nonpregnant women with acute and convalescent COVID-19, quantifying 217 immunological parameters. Humoral responses to SARS-CoV-2 were similar in pregnant and nonpregnant women, although our systems serology approach revealed distinct antibody and FcγR profiles between pregnant and nonpregnant women. Cellular analyses demonstrated marked differences in NK cell and unconventional T cell activation dynamics in pregnant women. Healthy pregnant women displayed preactivated NK cells and γδ T cells when compared with healthy nonpregnant women, which remained unchanged during acute and convalescent COVID-19. Conversely, nonpregnant women had prototypical activation of NK and γδ T cells. Activation of CD4+ and CD8+ T cells and T follicular helper cells was similar in SARS-CoV-2-infected pregnant and nonpregnant women, while antibody-secreting B cells were increased in pregnant women during acute COVID-19. Elevated levels of IL-8, IL-10, and IL-18 were found in pregnant women in their healthy state, and these cytokine levels remained elevated during acute and convalescent COVID-19. Collectively, we demonstrate perturbations in NK cell and γδ T cell activation in unvaccinated pregnant women with COVID-19, which may impact disease progression and severity during pregnancy.
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Affiliation(s)
- Jennifer R Habel
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Brendon Y Chua
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo, Japan
| | - Lukasz Kedzierski
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, Victoria, Australia
| | - Kevin J Selva
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Timon Damelang
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Ebene R Haycroft
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Thi Ho Nguyen
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Hui-Fern Koay
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Suellen Nicholson
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Hayley A McQuilten
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Xiaoxiao Jia
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Lilith F Allen
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Luca Hensen
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Wuji Zhang
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Carolien E van de Sandt
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Jessica A Neil
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Katherine Pragastis
- Department of Infectious Diseases, Alfred Health, Monash University, Melbourne, Victoria, Australia
| | - Jillian Sy Lau
- Department of Infectious Diseases, Alfred Health, Monash University, Melbourne, Victoria, Australia
- Department of Infectious Diseases, Eastern Health, Box Hill, Victoria, Australia
| | - Jaycee Jumarang
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, California, USA
| | - E Kaitlynn Allen
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Fatima Amanant
- Department of Microbiology, and
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Kathleen M Wragg
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Jennifer A Juno
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Adam K Wheatley
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of Melbourne, Melbourne, Victoria, Australia
| | - Hyon-Xhi Tan
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Gabrielle Pell
- Mercy Perinatal Research Centre, Mercy Hospital for Women, Heidelberg, Victoria, Australia
| | - Susan Walker
- Mercy Perinatal Research Centre, Mercy Hospital for Women, Heidelberg, Victoria, Australia
| | - Jennifer Audsley
- Department of Infectious Diseases, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Arnold Reynaldi
- Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Irani Thevarajan
- Department of Infectious Diseases, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Victorian Infectious Diseases Service, Royal Melbourne Hospital, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Justin T Denholm
- Department of Infectious Diseases, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Victorian Infectious Diseases Service, Royal Melbourne Hospital, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Kanta Subbarao
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- WHO Collaborating Centre for Reference and Research on Influenza, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Miles P Davenport
- Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - P Mark Hogarth
- Immune Therapies Laboratory, Burnet Institute, Melbourne, Victoria, Australia
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Department of Clinical Pathology, University of Melbourne, Parkville, Victoria, Australia
| | - Dale I Godfrey
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Allen C Cheng
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
- Infection Prevention and Healthcare Epidemiology Unit, Alfred Health, and Monash Infectious Diseases, Monash Health, Melbourne, Victoria, Australia
| | - Steven Yc Tong
- Victorian Infectious Diseases Service, Royal Melbourne Hospital, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Katherine Bond
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Microbiology, Royal Melbourne Hospital, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Deborah A Williamson
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Microbiology, Royal Melbourne Hospital, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - James H McMahon
- Department of Infectious Diseases, Alfred Health, Monash University, Melbourne, Victoria, Australia
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Pia S Pannaraj
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, California, USA
- Departments of Pediatrics, Molecular Microbiology and Immunology, Keck School of Medicine, UCLA, Los Angeles, California, USA
| | - Fiona James
- Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia
| | - Natasha E Holmes
- Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia
- Department of Critical Care, University of Melbourne, Parkville, Victoria, Australia
- Data Analytics Research and Evaluation Centre, Austin Health, University of Melbourne, Heidelberg, Victoria, Australia
- Centre for Antibiotic Allergy and Research, Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia
| | - Olivia C Smibert
- Departments of Pediatrics, Molecular Microbiology and Immunology, Keck School of Medicine, UCLA, Los Angeles, California, USA
- Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia
- Centre for Antibiotic Allergy and Research, Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia
- Department of Infectious Diseases, and
- National Centre for Infections in Cancer, Peter McCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Jason A Trubiano
- Centre for Antibiotic Allergy and Research, Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia
- Department of Infectious Diseases, and
- National Centre for Infections in Cancer, Peter McCallum Cancer Centre, Melbourne, Victoria, Australia
- Department of Medicine (Austin Health), University of Melbourne, Heidelberg, Victoria, Australia
| | - Claire L Gordon
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia
| | - Amy W Chung
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Clare L Whitehead
- Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, Victoria, Australia
- Pregnancy Research Centre, Royal Women's Hospital, Parkville, Victoria, Australia
| | - Stephen J Kent
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of Melbourne, Melbourne, Victoria, Australia
- Melbourne Sexual Health Centre, Infectious Diseases Department, Alfred Health, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Martha Lappas
- Obstetrics, Nutrition and Endocrinology Group, Department of Obstetrics and Gynaecology, University of Melbourne, Victoria, Australia
| | - Louise C Rowntree
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo, Japan
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7
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Souquette A, Allen EK, Oshansky CM, Tang L, Wong SS, Jeevan T, Shi L, Pounds S, Elias G, Kuan G, Balmaseda A, Zapata R, Shaw-Saliba K, Damme PV, Tendeloo VV, Dib JC, Ogunjimi B, Webby R, Schultz-Cherry S, Pekosz A, Rothman R, Gordon A, Thomas PG. Integrated Drivers of Basal and Acute Immunity in Diverse Human Populations. bioRxiv 2023:2023.03.25.534227. [PMID: 36993205 PMCID: PMC10055315 DOI: 10.1101/2023.03.25.534227] [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: 06/19/2023]
Abstract
Prior studies have identified genetic, infectious, and biological associations with immune competence and disease severity; however, there have been few integrative analyses of these factors and study populations are often limited in demographic diversity. Utilizing samples from 1,705 individuals in 5 countries, we examined putative determinants of immunity, including: single nucleotide polymorphisms, ancestry informative markers, herpesvirus status, age, and sex. In healthy subjects, we found significant differences in cytokine levels, leukocyte phenotypes, and gene expression. Transcriptional responses also varied by cohort, and the most significant determinant was ancestry. In influenza infected subjects, we found two disease severity immunophenotypes, largely driven by age. Additionally, cytokine regression models show each determinant differentially contributes to acute immune variation, with unique and interactive, location-specific herpesvirus effects. These results provide novel insight into the scope of immune heterogeneity across diverse populations, the integrative effects of factors which drive it, and the consequences for illness outcomes.
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8
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Hijano DR, Gu Z, de Cardenas JB, Zhu H, Suganda S, Glasgow HL, Darji H, Tang L, Fabrizio TP, Allison KJ, Allen EK, Gaur AH, Wolf J, Thomas PG, Webby RJ, Hayden RT. Prediction of Symptomatic SARS-CoV-2 infection by Quantitative Digital PCR Normalized to International Units. Open Forum Infect Dis 2022; 9:ofac490. [PMID: 36221269 PMCID: PMC9494499 DOI: 10.1093/ofid/ofac490] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 09/17/2022] [Indexed: 11/14/2022] Open
Abstract
Although numerous studies have evaluated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection using cycle threshold (Ct) values as a surrogate of viral ribonucleic acid (RNA) load, few studies have used standardized, quantitative methods. We validated a quantitative SARS-CoV-2 digital polymerase chain reaction assay normalized to World Health Organization International Units and correlated viral RNA load with symptoms and disease severity.
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Affiliation(s)
- Diego R Hijano
- Department of Infectious Diseases, St. Jude Children’s Research Hospital , Memphis, TN , USA
| | - Zhengming Gu
- Department of Pathology, St. Jude Children’s Research Hospital , Memphis, TN , USA
| | | | - Haiqing Zhu
- Department of Pathology, St. Jude Children’s Research Hospital , Memphis, TN , USA
| | - Sri Suganda
- Department of Pathology, St. Jude Children’s Research Hospital , Memphis, TN , USA
| | - Heather L Glasgow
- Department of Pathology, St. Jude Children’s Research Hospital , Memphis, TN , USA
| | - Himani Darji
- Department of Biostatistics, St. Jude Children’s Research Hospital , Memphis, TN , USA
| | - Li Tang
- Department of Biostatistics, St. Jude Children’s Research Hospital , Memphis, TN , USA
| | - Thomas P Fabrizio
- Department of Infectious Diseases, St. Jude Children’s Research Hospital , Memphis, TN , USA
| | - Kim J Allison
- Department of Infectious Diseases, St. Jude Children’s Research Hospital , Memphis, TN , USA
| | - E Kaitlynn Allen
- Department of Immunology, St. Jude Children’s Research Hospital , Memphis, TN , USA
| | - Aditya H Gaur
- Department of Infectious Diseases, St. Jude Children’s Research Hospital , Memphis, TN , USA
| | - Joshua Wolf
- Department of Infectious Diseases, St. Jude Children’s Research Hospital , Memphis, TN , USA
| | - Paul G Thomas
- Department of Immunology, St. Jude Children’s Research Hospital , Memphis, TN , USA
| | - Richard J Webby
- Department of Infectious Diseases, St. Jude Children’s Research Hospital , Memphis, TN , USA
| | - Randall T Hayden
- Department of Pathology, St. Jude Children’s Research Hospital , Memphis, TN , USA
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9
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Tang L, Cherry S, Tuomanen EI, Kirkpatrick Roubidoux E, Lin CY, Allison KJ, Gowen A, Freiden P, Allen EK, Su Y, Gaur AH, Estepp JH, McGargill MA, Krammer F, Thomas PG, Schultz-Cherry S, Wolf J. Host Predictors of Broadly Cross-Reactive Antibodies Against Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants of Concern Differ Between Infection and Vaccination. Clin Infect Dis 2022; 75:e705-e714. [PMID: 34891165 PMCID: PMC8689782 DOI: 10.1093/cid/ciab996] [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: 08/22/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Following severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection or vaccination there is significant variability between individuals in protective antibody levels against SARS-CoV-2, and within individuals against different virus variants. However, host demographic or clinical characteristics that predict variability in cross-reactive antibody levels are not well-described. These data could inform clinicians, researchers, and policymakers on the populations most likely to require vaccine booster shots. METHODS In an institutional review board-approved prospective observational cohort study of staff at St. Jude Children's Research Hospital, we identified participants with plasma samples collected after SARS-CoV-2 infection, after mRNA vaccination, and after vaccination following infection, and quantitated immunoglobulin G (IgG) levels by enzyme-linked immunosorbent assay to the spike receptor binding domain (RBD) from 5 important SARS-CoV-2 variants (Wuhan Hu-1, B.1.1.7, B.1.351, P.1, and B.1.617.2). We used regression models to identify factors that contributed to cross-reactive IgG against 1 or multiple viral variants. RESULTS Following infection, a minority of the cohort generated cross-reactive antibodies, IgG antibodies that bound all tested variants. Those who did had increased disease severity, poor metabolic health, and were of a particular ancestry. Vaccination increased the levels of cross-reactive IgG levels in all populations, including immunocompromised, elderly, and persons with poor metabolic health. Younger people with a healthy weight mounted the highest responses. CONCLUSIONS Our findings provide important new information on individual antibody responses to infection/vaccination that could inform clinicians on populations that may require follow-on immunization.
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Affiliation(s)
- Li Tang
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Sean Cherry
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Elaine I Tuomanen
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | | | - Chun Yang Lin
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Kim J Allison
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Ashleigh Gowen
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Pamela Freiden
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - E Kaitlynn Allen
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Yin Su
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Aditya H Gaur
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Jeremie H Estepp
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
- Department of Global Pediatric Medicine, St. Jude Children’s Research Hospital, Memphis, Tennessee, USAand
| | - Maureen A McGargill
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Paul G Thomas
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Stacey Schultz-Cherry
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Joshua Wolf
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
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10
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Rowntree LC, Nguyen THO, Kedzierski L, Neeland MR, Petersen J, Crawford JC, Allen LF, Clemens EB, Chua B, McQuilten HA, Minervina AA, Pogorelyy MV, Chaurasia P, Tan HX, Wheatley AK, Jia X, Amanat F, Krammer F, Allen EK, Sonda S, Flanagan KL, Jumarang J, Pannaraj PS, Licciardi PV, Kent SJ, Bond KA, Williamson DA, Rossjohn J, Thomas PG, Tosif S, Crawford NW, van de Sandt CE, Kedzierska K. SARS-CoV-2-specific T cell memory with common TCRαβ motifs is established in unvaccinated children who seroconvert after infection. Immunity 2022; 55:1299-1315.e4. [PMID: 35750048 PMCID: PMC9174177 DOI: 10.1016/j.immuni.2022.06.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [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: 10/29/2021] [Revised: 03/31/2022] [Accepted: 06/01/2022] [Indexed: 11/05/2022]
Abstract
As the establishment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific T cell memory in children remains largely unexplored, we recruited convalescent COVID-19 children and adults to define their circulating memory SARS-CoV-2-specific CD4+ and CD8+ T cells prior to vaccination. We analyzed epitope-specific T cells directly ex vivo using seven HLA class I and class II tetramers presenting SARS-CoV-2 epitopes, together with Spike-specific B cells. Unvaccinated children who seroconverted had comparable Spike-specific but lower ORF1a- and N-specific memory T cell responses compared with adults. This agreed with our TCR sequencing data showing reduced clonal expansion in children. A strong stem cell memory phenotype and common T cell receptor motifs were detected within tetramer-specific T cells in seroconverted children. Conversely, children who did not seroconvert had tetramer-specific T cells of predominantly naive phenotypes and diverse TCRαβ repertoires. Our study demonstrates the generation of SARS-CoV-2-specific T cell memory with common TCRαβ motifs in unvaccinated seroconverted children after their first virus encounter.
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Affiliation(s)
- Louise C Rowntree
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Thi H O Nguyen
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Lukasz Kedzierski
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Melanie R Neeland
- Infection and Immunity, Murdoch Children's Research Institute, Melbourne, VIC 3000, Australia; Department of Paediatrics, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Jan Petersen
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Jeremy Chase Crawford
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Lilith F Allen
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - E Bridie Clemens
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Brendon Chua
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Hayley A McQuilten
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Anastasia A Minervina
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Mikhail V Pogorelyy
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Priyanka Chaurasia
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Hyon-Xhi Tan
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Adam K Wheatley
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Xiaoxiao Jia
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Fatima Amanat
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Center for Vaccine Research and Pandemic Preparedness (C-VARPP), Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - E Kaitlynn Allen
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Sabrina Sonda
- School of Health Sciences and School of Medicine, University of Tasmania, Launceston, TAS 7248, Australia
| | - Katie L Flanagan
- School of Health Sciences and School of Medicine, University of Tasmania, Launceston, TAS 7248, Australia; Department of Immunology and Pathology, Monash University, Commercial Road, Melbourne, VIC 3004, Australia; School of Health and Biomedical Science, RMIT University, Melbourne, VIC 3000, Australia; Tasmanian Vaccine Trial Centre, Clifford Craig Foundation, Launceston General Hospital, Launceston, TAS 7250, Australia
| | - Jaycee Jumarang
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, CA 90027, USA
| | - Pia S Pannaraj
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, CA 90027, USA; Departments of Pediatrics and Molecular Microbiology and Immunology, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90089, USA
| | - Paul V Licciardi
- Infection and Immunity, Murdoch Children's Research Institute, Melbourne, VIC 3000, Australia; Department of Paediatrics, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Stephen J Kent
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of Melbourne, Melbourne, VIC 3000, Australia; Melbourne Sexual Health Centre, Infectious Diseases Department, Alfred Health, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia
| | - Katherine A Bond
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Department of Microbiology, Royal Melbourne Hospital, Melbourne, VIC 3000, Australia
| | - Deborah A Williamson
- Department of Infectious Diseases, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Victorian Infectious Diseases Reference Laboratory at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3000, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, UK
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Shidan Tosif
- Infection and Immunity, Murdoch Children's Research Institute, Melbourne, VIC 3000, Australia; Department of Paediatrics, The University of Melbourne, Melbourne, VIC 3000, Australia; Department of General Medicine, Royal Children's Hospital Melbourne, Melbourne, VIC 3000, Australia
| | - Nigel W Crawford
- Infection and Immunity, Murdoch Children's Research Institute, Melbourne, VIC 3000, Australia; Department of Paediatrics, The University of Melbourne, Melbourne, VIC 3000, Australia; Department of General Medicine, Royal Children's Hospital Melbourne, Melbourne, VIC 3000, Australia; Royal Children's Hospital Melbourne, Immunisation Service, Melbourne, VIC 3000, Australia
| | - Carolien E van de Sandt
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia.
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11
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Wilson TL, Kim H, Chou CH, Langfitt D, Mettelman RC, Minervina AA, Allen EK, Metais JY, Pogorelyy MV, Riberdy JM, Velasquez MP, Kottapalli P, Trivedi S, Olsen SR, Lockey T, Willis C, Meagher MM, Triplett BM, Talleur AC, Gottschalk S, Crawford JC, Thomas PG. Common trajectories of highly effective CD19-specific CAR T cells identified by endogenous T cell receptor lineages. Cancer Discov 2022; 12:2098-2119. [DOI: 10.1158/2159-8290.cd-21-1508] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 05/18/2022] [Accepted: 06/27/2022] [Indexed: 11/16/2022]
Abstract
Abstract
Current chimeric antigen receptor-modified (CAR) T cell products are evaluated in bulk, without assessing functional heterogeneity. We therefore generated a comprehensive single-cell gene expression and T cell receptor (TCR) sequencing dataset using pre- and post-infusion CD19-CAR T cells from blood and bone marrow samples of pediatric patients with B cell acute lymphoblastic leukemia (B-ALL). We identified cytotoxic post-infusion cells with identical TCRs to a subset of pre-infusion CAR T cells. These effector precursor cells exhibited a unique transcriptional profile compared to other pre-infusion cells, corresponding to an unexpected surface phenotype (TIGIT+, CD62Llo, CD27-). Upon stimulation, these cells showed functional superiority and decreased expression of the exhaustion-associated transcription factor, TOX. Collectively, these results demonstrate diverse effector potentials within pre-infusion CAR T cell products, which can be exploited for therapeutic applications. Furthermore, we provide an integrative experimental and analytical framework for elucidating the mechanisms underlying effector development in CAR T cell products.
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Affiliation(s)
- Taylor L. Wilson
- St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Hyunjin Kim
- St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Ching-Heng Chou
- St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Deanna Langfitt
- St. Jude Children's Research Hospital, TN, TN, United States
| | | | | | | | - Jean-Yves Metais
- St. Jude Children's Research Hospital, Memphis, TN, United States
| | | | | | | | | | - Sanchit Trivedi
- St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Scott R. Olsen
- St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Timothy Lockey
- St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Catherine Willis
- St. Jude Children's Research Hospital, Memphis, TN, United States
| | | | | | - Aimee C. Talleur
- St. Jude Children's Research Hospital, Memphis, TN, United States
| | | | | | - Paul G. Thomas
- St. Jude Children's Research Hospital, Memphis, TN, United States
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12
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Kirk AM, Chou CH, Crawford JC, Awad W, Allen EK, Zhang X, Zamora AE, Strome SE, Thomas PG. Abstract 1383: Characterization of CD8 T cell responses to DNAJB1-PRKACA fusion neoantigens in fibrolamellar carcinoma. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-1383] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Fibrolamellar carcinoma (FLC) is a rare liver malignancy that has no known cure. Novel therapies for FLC are urgently needed to improve patient outcomes. The key genetic event in FLC tumorigenesis is a highly conserved gene fusion between the first exon of DNAJB1 and the last nine exons of PRKACA. This fusion gene is present in all FLC tumors, and more than 90% of patients express fusion proteins with identical amino acid sequences. Genetic mutations like this gene fusion can serve as important therapeutic vulnerabilities, in part because they may be processed and presented on the surface of tumor cells as neoantigens that can activate an anti-tumor T cell response. The purpose of our study was to test the hypothesis that DNAJB1-PRKACA fusion neoantigens could elicit T cell responses against FLC and serve as targets for novel immunotherapies. Spatial transcriptomic analyses of human FLC tumor samples indicated that CD8+ T cells could infiltrate these tumors, but often expressed markers of dysfunction and exhaustion, such as TOX. Nevertheless, we successfully expanded tumor-infiltrating T cells from FLC ex vivo and used intracellular cytokine staining (ICS) to identify a subset of FLC patient T cells that produced IFNγ and TNFα in response to stimulation with a fusion neoantigen. We used both peptide-MHC tetramer staining and functional response after stimulation to identify T cells in FLC patients and healthy donors that recognize fusion neoantigens. We then determined the paired T cell receptor (TCR) sequences using single-cell sequencing and expressed the TCRs in primary human T cells to test their potential utility in TCR-engineered immunotherapies. We validated the specificity and functionality of these TCRs using peptide-MHC tetramer staining, ICS, and in vitro cytotoxicity assays on the xCelligence and Berkeley Lights Lightning platforms. Primary T cells expressing fusion-specific TCRs bound to their cognate peptide-MHC tetramer, produced multiple cytokines in response to stimulation with their cognate fusion peptide, and specifically killed fusion-presenting target cells in vitro. Ongoing experiments will test whether T cells expressing these fusion-specific TCRs can control growth of fusion-presenting tumors in vivo. Collectively, these studies have defined the first reported fusion-specific T cell response in FLC, as well as fusion-specific TCRs that hold promise for use in adoptive T cell therapies. Our spatial transcriptomic analyses have also begun to illuminate the immune microenvironment in FLC and will inform future efforts to develop immunotherapies for this disease.
Citation Format: Allison M. Kirk, Ching-Heng Chou, Jeremy Chase Crawford, Walid Awad, E. Kaitlynn Allen, Xiaoyu Zhang, Anthony E. Zamora, Scott E. Strome, Paul G. Thomas. Characterization of CD8 T cell responses to DNAJB1-PRKACA fusion neoantigens in fibrolamellar carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1383.
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Affiliation(s)
| | | | | | - Walid Awad
- 1St. Jude Children's Research Hospital, Memphis, TN
| | | | - Xiaoyu Zhang
- 2University of Maryland School of Medicine, Baltimore, MD
| | | | - Scott E. Strome
- 4University of Tennessee Health Sciences Center, Memphis, TN
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13
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Mettelman RC, Allen EK, Thomas PG. Mucosal immune responses to infection and vaccination in the respiratory tract. Immunity 2022; 55:749-780. [PMID: 35545027 PMCID: PMC9087965 DOI: 10.1016/j.immuni.2022.04.013] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [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: 03/14/2022] [Revised: 04/12/2022] [Accepted: 04/15/2022] [Indexed: 01/25/2023]
Abstract
The lungs are constantly exposed to inhaled debris, allergens, pollutants, commensal or pathogenic microorganisms, and respiratory viruses. As a result, innate and adaptive immune responses in the respiratory tract are tightly regulated and are in continual flux between states of enhanced pathogen clearance, immune-modulation, and tissue repair. New single-cell-sequencing techniques are expanding our knowledge of airway cellular complexity and the nuanced connections between structural and immune cell compartments. Understanding these varied interactions is critical in treatment of human pulmonary disease and infections and in next-generation vaccine design. Here, we review the innate and adaptive immune responses in the lung and airways following infection and vaccination, with particular focus on influenza virus and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The ongoing SARS-CoV-2 pandemic has put pulmonary research firmly into the global spotlight, challenging previously held notions of respiratory immunity and helping identify new populations at high risk for respiratory distress.
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Affiliation(s)
- Robert C Mettelman
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - E Kaitlynn Allen
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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14
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Kirk AM, Chou CH, Awad W, Crawford JC, Allen EK, Zhang X, Zamora AE, Strome SE, Thomas PG. CD8 T cell responses to conserved DNAJB1-PRKACA fusion neoantigens in fibrolamellar carcinoma. The Journal of Immunology 2022. [DOI: 10.4049/jimmunol.208.supp.121.06] [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
Fibrolamellar carcinoma (FLC) is an often-lethal liver malignancy of adolescents and young adults. No systemic therapies are currently approved for FLC, so novel treatments are needed to improve patient outcomes. A promising therapeutic vulnerability in FLC is a highly-conserved gene fusion between DNAJB1 and PRKACA. The resultant fusion protein is identical in more than 90% of patients, making it a potentially ideal neoantigen target for T cell-based immunotherapy. The goal of our study was to test if DNAJB1-PRKACA neoantigens could elicit T cell responses and serve as targets for immunotherapy. Spatial transcriptomic analyses of FLC tumor tissue indicated that CD8 T cells could infiltrate FLC tumors, but expressed exhaustion markers such as TOX. Nevertheless, we expanded T cells from an FLC patient tumor ex vivo and detected T cells that produced IFNγ and TNFα in response to stimulation with a fusion neoantigen. We then used functional response after peptide stimulation or peptide-MHC tetramer staining to identify fusion-specific T cell receptors (TCRs) in both FLC patients and healthy donors. We expressed these TCRs in primary human T cells and found that cells expressing fusion-specific TCRs bound to their cognate tetramer and produced IFNγ, TNFα, and IL-2 in response to stimulation with their cognate peptide. TCR-expressing cells also specifically killed target cells presenting their cognate fusion peptide in vitro. Ongoing experiments will test if cells expressing these TCRs can control growth of fusion-expressing tumors in vivo. Together, these studies have defined the first reported fusion-specific T cell response in an FLC patient, as well as fusion-specific TCRs that hold promise for development in adoptive T cell therapies.
Supported by grants from NIH (R01 AI136514, F31 CA254423) and The Mark Foundation for Cancer Research (Aspire Award)
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Affiliation(s)
- Allison M Kirk
- 1Department of Immunology, St. Jude Children’s Research Hospital
| | - Ching-Heng Chou
- 1Department of Immunology, St. Jude Children’s Research Hospital
| | - Walid Awad
- 1Department of Immunology, St. Jude Children’s Research Hospital
| | | | - E Kaitlynn Allen
- 1Department of Immunology, St. Jude Children’s Research Hospital
| | - Xiaoyu Zhang
- 2Department of Otorhinolaryngology/Head & Neck Surgery, University of Maryland School of Medicine
| | | | - Scott E Strome
- 4College of Medicine, University of Tennessee Health Science Center
| | - Paul G Thomas
- 1Department of Immunology, St. Jude Children’s Research Hospital
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15
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Minervina AA, Pogorelyy MV, Kirk AM, Crawford JC, Allen EK, Chou CH, Mettelman RC, Allison KJ, Lin CY, Brice DC, Zhu X, Vegesana K, Wu G, Trivedi S, Kottapalli P, Darnell D, McNeely S, Olsen SR, Schultz-Cherry S, Estepp JH, McGargill MA, Wolf J, Thomas PG. SARS-CoV-2 antigen exposure history shapes phenotypes and specificity of memory CD8 + T cells. Nat Immunol 2022; 23:781-790. [PMID: 35383307 PMCID: PMC9106845 DOI: 10.1038/s41590-022-01184-4] [Citation(s) in RCA: 83] [Impact Index Per Article: 41.5] [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: 12/14/2021] [Accepted: 03/11/2022] [Indexed: 12/12/2022]
Abstract
Although mRNA vaccine efficacy against severe coronavirus disease 2019 remains high, variant emergence has prompted booster immunizations. However, the effects of repeated exposures to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antigens on memory T cells are poorly understood. Here, we utilize major histocompatibility complex multimers with single-cell RNA sequencing to profile SARS-CoV-2-responsive T cells ex vivo from humans with one, two or three antigen exposures, including vaccination, primary infection and breakthrough infection. Exposure order determined the distribution between spike-specific and non-spike-specific responses, with vaccination after infection leading to expansion of spike-specific T cells and differentiation to CCR7-CD45RA+ effectors. In contrast, individuals after breakthrough infection mount vigorous non-spike-specific responses. Analysis of over 4,000 epitope-specific T cell antigen receptor (TCR) sequences demonstrates that all exposures elicit diverse repertoires characterized by shared TCR motifs, confirmed by monoclonal TCR characterization, with no evidence for repertoire narrowing from repeated exposure. Our findings suggest that breakthrough infections diversify the T cell memory repertoire and current vaccination protocols continue to expand and differentiate spike-specific memory.
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Affiliation(s)
| | - Mikhail V Pogorelyy
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Allison M Kirk
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - E Kaitlynn Allen
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ching-Heng Chou
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Robert C Mettelman
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kim J Allison
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Chun-Yang Lin
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - David C Brice
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Xun Zhu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kasi Vegesana
- Information Services, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Gang Wu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Sanchit Trivedi
- Hartwell Center for Bioinformatics & Biotechnology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Pratibha Kottapalli
- Hartwell Center for Bioinformatics & Biotechnology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Daniel Darnell
- Hartwell Center for Bioinformatics & Biotechnology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Suzanne McNeely
- Hartwell Center for Bioinformatics & Biotechnology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Scott R Olsen
- Hartwell Center for Bioinformatics & Biotechnology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Stacey Schultz-Cherry
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jeremie H Estepp
- Department of Global Pediatric Medicine, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Maureen A McGargill
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Joshua Wolf
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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16
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Crawford JC, Wilson TL, Kim H, Chou CH, Langfitt D, Allen EK, Metais JY, Pogorelyy M, Kottapalli P, Trivedi S, Olsen S, Lockey T, Willis C, Meagher MM, Triplett B, Talleur AC, Gottschalk S, Thomas PG. Common trajectories of highly effective CD19-specific CAR T cells identified by endogenous T cell receptor lineages. The Journal of Immunology 2022. [DOI: 10.4049/jimmunol.208.supp.120.15] [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
Current chimeric antigen receptor-modified (CAR) T cell therapy products are evaluated in bulk, without assessment of the possible heterogeneity in effector potential between cells. Conceivably, only a subset of the pre-infusion product differentiates into optimal effectors. We generated a comprehensive single-cell gene expression and T cell receptor (TCR) sequencing dataset using both pre- and post-infusion CD19-CAR T cells from peripheral blood and bone marrow of pediatric patients with B cell acute lymphoblastic leukemia (B-ALL). We identified potent effector post-infusion cells with identical TCRs to a subset of pre-infusion CAR T cells. Effector precursor CAR T cells exhibited a unique transcriptional profile compared to other pre-infusion cells, and the number of effector precursor cells infused correlated with peak CAR T cell expansion. Additionally, we identified an unexpected cell surface phenotype (TIGIT+, CD62Llo, CD27−), conventionally associated with inhibiting effective T cell responses, that we used to successfully enrich for subsequent effector potential. Collectively, these results demonstrate that highly diverse effector potentials are present among cells in pre-infusion cell products, which can be exploited for diagnostic and therapeutic applications. Furthermore, we provide an integrative experimental and analytical framework for elucidating the biological mechanisms underlying effector development in other CAR T cell therapy products.
This work was supported by the National Institutes of Health (NIH)/National Cancer Institute grant P30CA021765, NIH grants U01AI150747 and R01AI136514 (PGT), the American Society of Transplantation and Cellular Therapy (AT), the American Society of Hematology (AT), the Key for a Cure Foundation (PGT), the Mark Foundation ASPIRE Award (PGT), and the American Lebanese Syrian Associated Charities (SG, PGT). Part of the laboratory studies were performed by the Center for Translational Immunology and Immunotherapy (CeTI2), which is supported by SJCRH. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH.
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Affiliation(s)
| | | | - Hyunjin Kim
- 1Department of Immunology, St. Jude Children’s Research Hospital
| | - Ching-Heng Chou
- 1Department of Immunology, St. Jude Children’s Research Hospital
| | - Deanna Langfitt
- 2Department of Bone Marrow Transplantation & Cellular Therapy, St. Jude Children’s Research Hospital
| | - E Kaitlynn Allen
- 1Department of Immunology, St. Jude Children’s Research Hospital
| | - Jean-Yves Metais
- 2Department of Bone Marrow Transplantation & Cellular Therapy, St. Jude Children’s Research Hospital
| | | | - Pratibha Kottapalli
- 3Hartwell Center for Bioinformatics & Biotechnology, St. Jude Children’s Research Hospital
| | - Sanchit Trivedi
- 3Hartwell Center for Bioinformatics & Biotechnology, St. Jude Children’s Research Hospital
| | - Scott Olsen
- 3Hartwell Center for Bioinformatics & Biotechnology, St. Jude Children’s Research Hospital
| | - Timothy Lockey
- 4Children’s GMP, LLC, St. Jude Children’s Research Hospital
| | | | | | - Brandon Triplett
- 2Department of Bone Marrow Transplantation & Cellular Therapy, St. Jude Children’s Research Hospital
| | - Aimee C Talleur
- 2Department of Bone Marrow Transplantation & Cellular Therapy, St. Jude Children’s Research Hospital
| | - Stephen Gottschalk
- 2Department of Bone Marrow Transplantation & Cellular Therapy, St. Jude Children’s Research Hospital
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17
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Clark BL, Flerlage T, Schattgen SA, Allen EK, Boyd DF, Crawford JC, Thomas PG. Identifying distinct T cell subsets in the context of pediatric ARDS. The Journal of Immunology 2022. [DOI: 10.4049/jimmunol.208.supp.125.11] [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
Acute respiratory distress syndrome (ARDS) is a condition defined by sudden respiratory failure caused by severe lung injury, with disease etiology that can differ across pediatric and adult patients. While T lymphocytes have been implicated in ARDS, the role of T cell subsets in pediatric ARDS (pARDS) is not fully understood. In this study, we sought to characterize the potential role of T cells in pARDS caused by viral lower respiratory tract infection (LRTI). To do this, we performed single cell RNA-Seq on tracheal aspirate samples from three categories of mechanically ventilated pediatric patients: 1) LRTI patients with pARDS, 2) LRTI patients without pARDS, and 3) ventilated patients without underlying LRTI or pARDS. All LRTI patients were diagnosed with respiratory viral infections, 70 percent of which were respiratory syncytial virus (RSV). Within the T lymphocytes, we identified populations of CD8+ T cells, CD4+ regulatory T cells, and γδ T cells that each expressed unique gene signatures with distinct distribution across disease states. We compared these data to T cell subsets within healthy lung tissue at multiple ages, and within the periphery of healthy adults. These analyses identified age, location, and disease-specific differences within T cell subsets, highlighting the unique role of T cells in pARDS.
Supported by grants from NIH (R01 AI54470, R01 AI121832)
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Affiliation(s)
| | - Tim Flerlage
- 2Infectious Diseases, St. Jude Children’s Research Hospital
| | | | | | - David F Boyd
- 1Immunology, St. Jude Children’s Research Hospital
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18
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Minervina A, Pogorelyy M, Kirk AM, Chou CH, Allen EK, Crawford JC, McGargill MA, Thomas PG. Epitope-specific T cell response to SARS-CoV-2 infection and vaccination. The Journal of Immunology 2022. [DOI: 10.4049/jimmunol.208.supp.125.41] [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
SARS-CoV-2 mRNA vaccines are effective for COVID-19 prevention, eliciting both robust antibody responses in naive individuals and boosting antibody levels in convalescent donors. However, the effect of repeated antigen exposures, such as vaccination following infection or breakthrough infections, on the magnitude, repertoire, and phenotype of pre-existing memory T cells, is still poorly understood. Thus, we compared epitope-specific CD8 T cells elicited after SARS-CoV-2 infection, vaccination of both naive and recovered individuals, and breakthrough infection cases. We used pools of 18 DNA-barcoded MHC-class I multimers, combined with scRNAseq and scTCRseq, to characterize T cell responses as defined by magnitude, specificity, T cell receptor (TCR) repertoire, and gene expression profile to both spike-derived and non-spike derived epitopes. In-depth analysis of over 4000 unique epitope-specific TCR sequences demonstrates that both vaccination and infection, including breakthrough cases, elicit identical repertoires as measured by dominant TCR motifs and repertoire diversity, indicating that BNT162b2 vaccination largely recapitulates spike-specific T cell repertoire generation by infection. Importantly, in COVID-19-recovered individuals receiving the vaccine, pre-existing spike-specific memory cells showed both clonal expansion and a phenotypic shift towards more differentiated CCR7-CD45RA+ effector cells, demonstrating the potency of this vaccine to recall spike-specific CD8 memory T cells. Importantly, in breakthrough infections, we observed a high proportion of T cells targeting non-spike epitopes, showing that new immune memory could be formed during SARS-CoV-2 infection after vaccination.
The work was funded by 75N93019C00052, HHSN272201400006C, 3U01AI144616-02S1, R01AI136514
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19
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Russell ML, Souquette A, Levine DM, Schattgen SA, Allen EK, Kuan G, Simon N, Balmaseda A, Gordon A, Thomas PG, Matsen FA, Bradley P. Combining genotypes and T cell receptor distributions to infer genetic loci determining V(D)J recombination probabilities. eLife 2022; 11:73475. [PMID: 35315770 PMCID: PMC8940181 DOI: 10.7554/elife.73475] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 01/17/2022] [Indexed: 12/12/2022] Open
Abstract
Every T cell receptor (TCR) repertoire is shaped by a complex probabilistic tangle of genetically determined biases and immune exposures. T cells combine a random V(D)J recombination process with a selection process to generate highly diverse and functional TCRs. The extent to which an individual’s genetic background is associated with their resulting TCR repertoire diversity has yet to be fully explored. Using a previously published repertoire sequencing dataset paired with high-resolution genome-wide genotyping from a large human cohort, we infer specific genetic loci associated with V(D)J recombination probabilities using genome-wide association inference. We show that V(D)J gene usage profiles are associated with variation in the TCRB locus and, specifically for the functional TCR repertoire, variation in the major histocompatibility complex locus. Further, we identify specific variations in the genes encoding the Artemis protein and the TdT protein to be associated with biasing junctional nucleotide deletion and N-insertion, respectively. These results refine our understanding of genetically-determined TCR repertoire biases by confirming and extending previous studies on the genetic determinants of V(D)J gene usage and providing the first examples of trans genetic variants which are associated with modifying junctional diversity. Together, these insights lay the groundwork for further explorations into how immune responses vary between individuals.
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Affiliation(s)
- Magdalena L Russell
- Computational Biology Program, Fred Hutch Cancer Research Center
- Molecular and Cellular Biology Program, University of Washington
| | - Aisha Souquette
- Department of Immunology, St. Jude Children’s Research Hospital
- Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center
| | | | | | | | - Guillermina Kuan
- Centro Nacional de Diagnóstico y Referencia, Ministry of Health
- Sustainable Sciences Institute
| | - Noah Simon
- Department of Biostatistics, University of Washington
| | - Angel Balmaseda
- Centro Nacional de Diagnóstico y Referencia, Ministry of Health
- Sustainable Sciences Institute
| | | | - Paul G Thomas
- Department of Immunology, St. Jude Children’s Research Hospital
| | - Frederick A Matsen
- Computational Biology Program, Fred Hutch Cancer Research Center
- Department of Genome Sciences, University of Washington
- Department of Statistics, University of Washington
- Howard Hughes Medical Institute
| | - Philip Bradley
- Computational Biology Program, Fred Hutch Cancer Research Center
- Institute for Protein Design, Department of Biochemistry, University of Washington
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20
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Minervina AA, Pogorelyy MV, Kirk AM, Crawford JC, Allen EK, Chou CH, Mettelman RC, Allison KJ, Lin CY, Brice DC, Zhu X, Vegesana K, Wu G, Trivedi S, Kottapalli P, Darnell D, McNeely S, Olsen SR, Schultz-Cherry S, Estepp JH, McGargill MA, Wolf J, Thomas PG. SARS-CoV-2 antigen exposure history shapes phenotypes and specificity of memory CD8 T cells. medRxiv 2022:2021.07.12.21260227. [PMID: 34341799 PMCID: PMC8328067 DOI: 10.1101/2021.07.12.21260227] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Although mRNA vaccine efficacy against severe COVID-19 remains high, variant emergence and breakthrough infections have changed vaccine policy to include booster immunizations. However, the effect of diverse and repeated antigen exposures on SARS-CoV-2 memory T cells is poorly understood. Here, we utilize DNA-barcoded MHC-multimers combined with scRNAseq and scTCRseq to capture the ex vivo profile of SARS-CoV-2-responsive T cells within a cohort of individuals with one, two, or three antigen exposures, including vaccination, primary infection, and breakthrough infection. We found that the order of exposure determined the relative distribution between spike- and non-spike-specific responses, with vaccination after infection leading to further expansion of spike-specific T cells and differentiation to a CCR7-CD45RA+ effector phenotype. In contrast, individuals experiencing a breakthrough infection mount vigorous non-spike-specific responses. In-depth analysis of over 4,000 epitope-specific T cell receptor sequences demonstrates that all types of exposures elicit diverse repertoires characterized by shared, dominant TCR motifs, with no evidence for repertoire narrowing from repeated exposure. Our findings suggest that breakthrough infections diversify the T cell memory repertoire and that current vaccination protocols continue to expand and differentiate spike-specific memory responses.
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Affiliation(s)
| | - Mikhail V. Pogorelyy
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN USA
| | - Allison M. Kirk
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN USA
| | | | - E. Kaitlynn Allen
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN USA
| | - Ching-Heng Chou
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN USA
| | - Robert C. Mettelman
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN USA
| | - Kim J. Allison
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN USA
| | - Chun-Yang Lin
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN USA
| | - David C. Brice
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN USA
| | - Xun Zhu
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN USA
| | - Kasi Vegesana
- Information Services, St. Jude Children’s Research Hospital, Memphis, TN USA
| | - Gang Wu
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN USA
| | - Sanchit Trivedi
- Hartwell Center for Bioinformatics & Biotechnology, St. Jude Children’s Research Hospital, Memphis, TN USA
| | - Pratibha Kottapalli
- Hartwell Center for Bioinformatics & Biotechnology, St. Jude Children’s Research Hospital, Memphis, TN USA
| | - Daniel Darnell
- Hartwell Center for Bioinformatics & Biotechnology, St. Jude Children’s Research Hospital, Memphis, TN USA
| | - Suzanne McNeely
- Hartwell Center for Bioinformatics & Biotechnology, St. Jude Children’s Research Hospital, Memphis, TN USA
| | - Scott R. Olsen
- Hartwell Center for Bioinformatics & Biotechnology, St. Jude Children’s Research Hospital, Memphis, TN USA
| | - Stacey Schultz-Cherry
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN USA
| | - Jeremie H. Estepp
- Department of Global Pediatric Medicine, St. Jude Children’s Research Hospital, Memphis, TN USA
| | | | - Maureen A. McGargill
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN USA
| | - Joshua Wolf
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN USA
| | - Paul G. Thomas
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN USA
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21
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Lin CY, Wolf J, Brice DC, Sun Y, Locke M, Cherry S, Castellaw AH, Wehenkel M, Crawford JC, Zarnitsyna VI, Duque D, Allison KJ, Allen EK, Brown SA, Mandarano AH, Estepp JH, Taylor C, Molina-Paris C, Schultz-Cherry S, Tang L, Thomas PG, McGargill MA. Pre-existing humoral immunity to human common cold coronaviruses negatively impacts the protective SARS-CoV-2 antibody response. Cell Host Microbe 2022; 30:83-96.e4. [PMID: 34965382 PMCID: PMC8648673 DOI: 10.1016/j.chom.2021.12.005] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [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: 08/25/2021] [Revised: 11/05/2021] [Accepted: 11/30/2021] [Indexed: 11/03/2022]
Abstract
SARS-CoV-2 infection causes diverse outcomes ranging from asymptomatic infection to respiratory distress and death. A major unresolved question is whether prior immunity to endemic, human common cold coronaviruses (hCCCoVs) impacts susceptibility to SARS-CoV-2 infection or immunity following infection and vaccination. Therefore, we analyzed samples from the same individuals before and after SARS-CoV-2 infection or vaccination. We found hCCCoV antibody levels increase after SARS-CoV-2 exposure, demonstrating cross-reactivity. However, a case-control study indicates that baseline hCCCoV antibody levels are not associated with protection against SARS-CoV-2 infection. Rather, higher magnitudes of pre-existing betacoronavirus antibodies correlate with more SARS-CoV-2 antibodies following infection, an indicator of greater disease severity. Additionally, immunization with hCCCoV spike proteins before SARS-CoV-2 immunization impedes the generation of SARS-CoV-2-neutralizing antibodies in mice. Together, these data suggest that pre-existing hCCCoV antibodies hinder SARS-CoV-2 antibody-based immunity following infection and provide insight on how pre-existing coronavirus immunity impacts SARS-CoV-2 infection, which is critical considering emerging variants.
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Affiliation(s)
- Chun-Yang Lin
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA; Integrated Biomedical Sciences Program, University of Tennessee Health Science, Memphis, TN, USA
| | - Joshua Wolf
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - David C Brice
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yilun Sun
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Sean Cherry
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ashley H Castellaw
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Marie Wehenkel
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Veronika I Zarnitsyna
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Daniel Duque
- School of Mathematics, University of Leeds, Leeds, UK
| | - Kim J Allison
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - E Kaitlynn Allen
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Scott A Brown
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Jeremie H Estepp
- Department of Global Pediatric Medicine, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Carmen Molina-Paris
- School of Mathematics, University of Leeds, Leeds, UK; T-6, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Stacey Schultz-Cherry
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Li Tang
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Maureen A McGargill
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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22
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Wilson T, Kim H, Crawford J, Chou CH, Langfitt D, Kaitlynn Allen E, Lockey T, Meagher M, Talleur A, Gottschalk S, Thomas P. 152 Common trajectories of highly effective anti-CD19 chimeric antigen receptor-modified T cells identified by endogenous T cell receptor lineages. J Immunother Cancer 2021. [DOI: 10.1136/jitc-2021-sitc2021.152] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
BackgroundChimeric antigen receptor modified (CAR) T cells have revolutionized the treatment of blood cancers, though some patients still show a poor response in either CAR expansion, effector response, or persistence.1 In this study, we determined the features of pre-infusion CAR-transduced T cells that generated optimally functional responses after infusion.MethodsUsing both the pre-infusion product and PBMCs isolated at weeks 1–4, 8, and 3-months post-infusion from 15 patients undergoing experimental anti-CD19 CAR T cell treatment for refractory or relapsed B-ALL, we generated a comprehensive single cell gene expression and T cell receptor (TCR) sequencing dataset on over 180,000 CAR T cells (figure 1).ResultsAs expected, pre-infusion CAR T cells tend to highly express genes associated with proliferation, while post-infusion CARs show signs of either cytotoxic effector differentiation or dysfunctional terminal differentiation. Sequencing of the endogenous TCR, at the single cell level, allows us to track the trajectories of clonally and transcriptionally related cells (figure 2). Post-infusion cells with significant cytotoxic effector function share TCRs with a statistically defined subset of CARs in the pre-infusion sample (figure 3). Using a machine learning approach, we found that potent effector precursor CAR T cells have a specific transcriptional profile distinct from the other pre-infusion CAR T cells, including markers of early effector function such as increased EOMES, GNLY, GZMH, GZMK, KLRD1, and IFNγ. Formalizing this signature, we have developed a robust classifier that can predict with 82.8% accuracy whether a CAR T is likely to become a favorable effector based on its pre-infusion profile (figure 4). This prediction model can be used to evaluate the extent to which a patient‘s generated CAR product will be able to mount a robust response after encountering its target. Additionally, there are a number of genes, as a part of this signature, that are expressed on the cell surface and can be utilized as a method to differentiate the effector precursor pre-infusion CAR T cells from other pre-infusion CARs, including CD52, CD74, CD86, and LAG3, among others.Abstract 152 Figure 1Clustering of 184, 791 CAR-transduced T cells based on gene expressionAbstract 152 Figure 2Alluvial plot depicting CAR T cell lineage tracing using the endogenous T cell receptorAbstract 152 Figure 3Visualization of CAR T cell clusters with arrows indicating the shared TCRs between pre-infusion and post-infusion cellsAbstract 152 Figure 4Machine learning classifier of pre-infusion, early effector CAR T cell phenotypeConclusionsOur findings suggest a therapeutic approach that enriches these cells prior to infusion resulting in superior per cell CAR effector activity.ReferenceXu X, Huang S, Xiao X, Sun Q, Liang X, Chen S, et al. Challenges and Clinical Strategies of CAR T-cell Therapy for Acute Lymphoblastic Leukemia: Overview and Developments. Front Immunol 2020;11:569117.Ethics ApprovalThis study was approved by St. Jude Children’s Research Hospital’s Institutional Review Board (IRB); IRB number Pro00007661. All patients consented to the use of materials for the research study.
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23
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Schultz-Cherry S, McGargill MA, Thomas PG, Estepp JH, Gaur AH, Allen EK, Allison KJ, Tang L, Webby RJ, Cherry SD, Lin CY, Fabrizio T, Tuomanen EI, Wolf J. Cross-reactive Antibody Response to mRNA SARS-CoV-2 Vaccine After Recent COVID-19-Specific Monoclonal Antibody Therapy. Open Forum Infect Dis 2021; 8:ofab420. [PMID: 34557558 PMCID: PMC8454518 DOI: 10.1093/ofid/ofab420] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 08/06/2021] [Indexed: 11/14/2022] Open
Abstract
The efficacy of coronavirus disease 2019 (COVID-19) vaccines administered after COVID-19-specific monoclonal antibody is unknown, and “antibody interference” might hinder immune responses leading to vaccine failure. In an institutional review board–approved prospective study, we found that an individual who received mRNA COVID-19 vaccination <40 days after COVID-19-specific monoclonal antibody therapy for symptomatic COVID-19 had similar postvaccine antibody responses to SARS-CoV-2 receptor binding domain (RBD) for 4 important SARS-CoV-2 variants (B.1, B.1.1.7, B.1.351, and P.1) as other participants who were also vaccinated following COVID-19. Vaccination against COVID-19 shortly after COVID-19-specific monoclonal antibody can boost and expand antibody protection, questioning the need to delay vaccination in this setting.
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Affiliation(s)
- Stacey Schultz-Cherry
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Maureen A McGargill
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jeremie H Estepp
- Department of Global Pediatric Medicine, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Aditya H Gaur
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - E Kaitlynn Allen
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Kim J Allison
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Li Tang
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Richard J Webby
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Sean D Cherry
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Chun-Yang Lin
- Department of Global Pediatric Medicine, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Thomas Fabrizio
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Elaine I Tuomanen
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Joshua Wolf
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.,Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee, USA
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24
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Van de Velde LA, Allen EK, Crawford JC, Wilson TL, Guy CS, Russier M, Zeitler L, Bahrami A, Finkelstein D, Pelletier S, Schultz-Cherry S, Thomas PG, Murray PJ. Neuroblastoma Formation Requires Unconventional CD4 T Cells and Arginase-1-Dependent Myeloid Cells. Cancer Res 2021; 81:5047-5059. [PMID: 34301764 PMCID: PMC8488023 DOI: 10.1158/0008-5472.can-21-0691] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/29/2021] [Accepted: 07/22/2021] [Indexed: 01/07/2023]
Abstract
Immune cells regulate tumor growth by mirroring their function as tissue repair organizers in normal tissues. To understand the different facets of immune-tumor collaboration through genetics, spatial transcriptomics, and immunologic manipulation with noninvasive, longitudinal imaging, we generated a penetrant double oncogene-driven autochthonous model of neuroblastoma. Spatial transcriptomic analysis showed that CD4+ and myeloid populations colocalized within the tumor parenchyma, while CD8+ T cells and B cells were peripherally dispersed. Depletion of CD4+ T cells or CCR2+ macrophages, but not B cells, CD8+ T cells, or natural killer (NK) cells, prevented tumor formation. Tumor CD4+ T cells displayed unconventional phenotypes and were clonotypically diverse and antigen independent. Within the myeloid fraction, tumor growth required myeloid cells expressing arginase-1. Overall, these results demonstrate how arginine-metabolizing myeloid cells conspire with pathogenic CD4+ T cells to create permissive conditions for tumor formation, suggesting that these protumorigenic pathways could be disabled by targeting myeloid arginine metabolism. SIGNIFICANCE: A new model of human neuroblastoma provides ways to track tumor formation and expansion in living animals, allowing identification of CD4+ T-cell and macrophage functions required for oncogenesis.
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Affiliation(s)
- Lee-Ann Van de Velde
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee.,Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - E. Kaitlynn Allen
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | | | - Taylor L. Wilson
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Clifford S. Guy
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Marion Russier
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Leonie Zeitler
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Armita Bahrami
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - David Finkelstein
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Stephane Pelletier
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Stacey Schultz-Cherry
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Paul G. Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee.,Corresponding Authors: Peter J. Murray, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried 82152, Germany. Phone: 49-89-8578-2428; E-mail: ; and Paul G. Thomas, Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105. Phone: 901-595-6507; E-mail:
| | - Peter J. Murray
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee.,Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee.,Max Planck Institute of Biochemistry, Martinsried, Germany.,Institute of Molecular Immunology and Experimental Oncology, Klinikum rechts der Isar, Technical University of Munich, München, Germany.,Corresponding Authors: Peter J. Murray, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried 82152, Germany. Phone: 49-89-8578-2428; E-mail: ; and Paul G. Thomas, Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105. Phone: 901-595-6507; E-mail:
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25
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Mettelman RC, Souquette A, Van de Velde LA, Allen EK, Wood T, Krammer F, Petrie JG, Martin ET, Monto AS, Huang QS, Thomas PG. Defining cellular correlates of protection and vaccine failure to influenza across two human cohorts. The Journal of Immunology 2021. [DOI: 10.4049/jimmunol.206.supp.103.37] [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
Influenza viruses are endemic viral pathogens causing mild to severe respiratory illness in humans. Immunologic protection against influenza is determined by immune correlates of protection– factors associated with reduced infection or severe disease. While antibodies specific to viral surface proteins are known correlates, waning seasonal vaccine efficacy and reported infection of patients despite elevated antibody titers suggest that humoral responses alone do not provide complete protective immunity. Indeed, evidence points to a larger role for cell-mediated immunity (CMI; innate cells and antigen-specific T cells) in conferring protection. CMI correlates, which act independently from humoral responses, have yet to be identified. Here, we analyzed samples from adult human subjects across two influenza infection and vaccination cohorts to identify distinct CMI correlates of protection to influenza. We profiled CMI responses using high-dimension flow cytometry from PBMCs collected pre- and post-exposure to influenza infection or vaccination. Statistical comparison of cell frequency and infection status identified candidate CMI correlates, which were validated using logistic regression accounting for vaccination, demographic (age, sex, BMI), and serologic (antibody) covariates. We identified 9 individual and 6 cell clusters across myeloid and lymphoid compartments associated with protection. The strongest correlations were observed in Th17, cTfh, and subsets of NK and dendritic cells. Further, AUROC models identified 3 baseline CMI infection classifiers. Lastly, our study identified correlates of vaccine failure– pre-exposure CMI profiles correlated with positive infection status despite vaccination.
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Affiliation(s)
- Robert C Mettelman
- 1Department of Immunology, St Jude Children’s Research Hospital, Memphis
| | - Aisha Souquette
- 1Department of Immunology, St Jude Children’s Research Hospital, Memphis
| | | | - E. Kaitlynn Allen
- 1Department of Immunology, St Jude Children’s Research Hospital, Memphis
| | - Timothy Wood
- 2Institute for Environmental Science and Research, National Centre for Biosecurity and Infectious Disease, Wallaceville, Upper Hutt, New Zealand
| | - Florian Krammer
- 3Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York City, NY
| | - Joshua G Petrie
- 4Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI
| | - Emily T Martin
- 4Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI
| | - Arnold S Monto
- 4Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI
| | - Q. Sue Huang
- 2Institute for Environmental Science and Research, National Centre for Biosecurity and Infectious Disease, Wallaceville, Upper Hutt, New Zealand
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26
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Tanaka ML, Marentes Ruiz CJ, Malhotra S, Turner L, Peralta A, Lee Y, Jumarang J, Perez SE, Navarro J, Dien Bard J, Gordon A, Allen EK, Thomas PG, Pannaraj PS. SARS-CoV-2 Transmission Dynamics in Households With Children, Los Angeles, California. Front Pediatr 2021; 9:752993. [PMID: 35071125 PMCID: PMC8767010 DOI: 10.3389/fped.2021.752993] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 11/30/2021] [Indexed: 12/23/2022] Open
Abstract
Objectives: Studies of household transmission of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) focused on households with children are limited. We investigated household secondary attack rate (SAR), transmission dynamics, and contributing factors in households with children. Materials and Methods: In this prospective case-ascertained study in Los Angeles County, California, all households members were enrolled if ≥1 member tested positive for SARS-CoV-2 by polymerase chain reaction (PCR). Nasopharyngeal PCRs, serology, and symptom data were obtained over multiple visits. Results: A total of 489 individuals in 105 households were enrolled from June to December 2020. The majority (77.3%) reported a household annual income of <$50,000, and most (92.9%) were of Hispanic/Latinx ethnicity. Children <18 years old accounted for 46.9% index cases, of whom 45.3% were asymptomatic. Household index cases were predominantly children during low community transmission and adults during the high community transmission period (χ2 = 7.647, p = 0.0036. The mean household SAR was 77.0% (95% CI: 69.4-84.6%). Child and adult index cases both efficiently transmitted SARS-CoV-2 within households [81.9%, (95% CI: 72.1-91.9%) vs. 72.4% (95% CI: 59.8-85.1%), p = 0.23]. Household income and pets were significantly associated with higher SAR in the multivariable analysis of household factors (p = 0.0013 and 0.004, respectively). Conclusions: The SAR in households with children in an urban setting with a large ethnic minority population is much higher than previously described. Children play important roles as index cases. SAR was disproportionately impacted by household income. Vaccination and public health efforts need special focus on children and vulnerable communities to help mitigate SARS-CoV-2 spread.
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Affiliation(s)
- Melissa Lucero Tanaka
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, CA, United States
| | | | - Sanchi Malhotra
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, CA, United States
| | - Lauren Turner
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, CA, United States
| | - Ariana Peralta
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, CA, United States
| | - Yesun Lee
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, CA, United States
| | - Jaycee Jumarang
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, CA, United States
| | - Stephanie E Perez
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, CA, United States
| | - Jocelyn Navarro
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, CA, United States
| | - Jennifer Dien Bard
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Aubree Gordon
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, United States
| | - E Kaitlynn Allen
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Pia S Pannaraj
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, CA, United States.,Department of Pediatrics and Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
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27
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Boyd DF, Allen EK, Randolph AG, Guo XZJ, Weng Y, Sanders CJ, Bajracharya R, Lee NK, Guy CS, Vogel P, Guan W, Li Y, Liu X, Novak T, Newhams MM, Fabrizio TP, Wohlgemuth N, Mourani PM, Wight TN, Schultz-Cherry S, Cormier SA, Shaw-Saliba K, Pekosz A, Rothman RE, Chen KF, Yang Z, Webby RJ, Zhong N, Crawford JC, Thomas PG. Publisher Correction: Exuberant fibroblast activity compromises lung function via ADAMTS4. Nature 2020; 588:E5. [PMID: 33208953 DOI: 10.1038/s41586-020-2987-0] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- David F Boyd
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - E Kaitlynn Allen
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Adrienne G Randolph
- Boston Children's Hospital, Department of Anesthesiology, Critical Care and Pain Medicine, Boston, MA, USA.,Department of Anesthesia, Harvard Medical School, Boston, MA, USA
| | - Xi-Zhi J Guo
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Yunceng Weng
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Catherine J Sanders
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Resha Bajracharya
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Natalie K Lee
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Clifford S Guy
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Peter Vogel
- Veterinary Pathology Core, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Wenda Guan
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yimin Li
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiaoqing Liu
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Tanya Novak
- Boston Children's Hospital, Department of Anesthesiology, Critical Care and Pain Medicine, Boston, MA, USA.,Department of Anesthesia, Harvard Medical School, Boston, MA, USA
| | - Margaret M Newhams
- Boston Children's Hospital, Department of Anesthesiology, Critical Care and Pain Medicine, Boston, MA, USA
| | - Thomas P Fabrizio
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Nicholas Wohlgemuth
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Peter M Mourani
- Section of Critical Care Medicine, Department of Pediatrics, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO, USA
| | | | - Thomas N Wight
- Matrix Biology Program, Benaroya Research Institute, Seattle, WA, USA
| | - Stacey Schultz-Cherry
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Stephania A Cormier
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA.,Pennington Biomedical Research Center, Baton Rouge, LA, USA
| | - Kathryn Shaw-Saliba
- Department of Emergency Medicine and Medicine, Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Andrew Pekosz
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Richard E Rothman
- Department of Emergency Medicine and Medicine, Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kuan-Fu Chen
- Department of Emergency Medicine of Chang Gung Memorial Hospital at Keelung, Keelung City, Taiwan.,Clinical Informatics and Medical Statistics Research Center of Chang Gung University, Taoyuan, Taiwan
| | - Zifeng Yang
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Richard J Webby
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Nanshan Zhong
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | | | - Paul G Thomas
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA.
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28
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Flerlage T, Souquette A, Allen EK, Brahm T, Crawford JC, Tang L, Sun Y, Maron G, Wolf J, Triplett B, Thomas PG. Nasal Wash Cytokines during Respiratory Viral Infection in Pediatric Allogeneic Hematopoietic Cell-Transplant Recipients. Am J Respir Cell Mol Biol 2020; 63:349-361. [PMID: 32551899 DOI: 10.1165/rcmb.2020-0014oc] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Allogeneic hematopoietic cell-transplant (alloHCT) recipients are at increased risk of complications from viral respiratory-tract infections (vRTIs). We measured cytokine concentrations in nasal washes (NWs) from pediatric alloHCT recipients to better understand their local response to vRTI. Forty-one immunologic analytes were measured in 70 NWs, collected during and after vRTI, from 15 alloHCT recipients (median age, 11 yr) with 19 episodes of vRTI. These were compared with NW cytokine concentrations from an independent group of otherwise healthy patients. AlloHCT recipients are able to produce a local response to vRTI and produce IFN-α2 and IL-12p40 in significant quantities above an uninfected baseline early in infection. Compared with otherwise healthy comparator-group patients, alloHCT recipients have higher NW concentrations of IL-4 when challenged with vRTI. Further study of these immunologic analytes as well as of type 1 versus type 2 balance in the respiratory mucosa in the context of vRTI during immune reconstitution may be of future research interest in this vulnerable patient population.
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Affiliation(s)
- Tim Flerlage
- Department of Infectious Diseases.,Division of Pediatric Critical Care Medicine and
| | | | | | | | | | - Li Tang
- Department of Biostatistics, and
| | | | | | - Joshua Wolf
- Department of Infectious Diseases.,Department of Pediatrics, Health Science Center, University of Tennessee, Memphis, Tennessee
| | - Brandon Triplett
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, Tennessee; and
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29
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Zamora AE, Crawford JC, Allen EK, Guo XZJ, Bakke J, Carter RA, Abdelsamed HA, Moustaki A, Li Y, Chang TC, Awad W, Dallas MH, Mullighan CG, Downing JR, Geiger TL, Chen T, Green DR, Youngblood BA, Zhang J, Thomas PG. Pediatric patients with acute lymphoblastic leukemia generate abundant and functional neoantigen-specific CD8 + T cell responses. Sci Transl Med 2020; 11:11/498/eaat8549. [PMID: 31243155 DOI: 10.1126/scitranslmed.aat8549] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 11/16/2018] [Accepted: 05/06/2019] [Indexed: 12/12/2022]
Abstract
Cancer arises from the accumulation of genetic alterations, which can lead to the production of mutant proteins not expressed by normal cells. These mutant proteins can be processed and presented on the cell surface by major histocompatibility complex molecules as neoepitopes, allowing CD8+ T cells to mount responses against them. For solid tumors, only an average 2% of neoepitopes predicted by algorithms have detectable endogenous antitumor T cell responses. This suggests that low mutation burden tumors, which include many pediatric tumors, are poorly immunogenic. Here, we report that pediatric patients with acute lymphoblastic leukemia (ALL) have tumor-associated neoepitope-specific CD8+ T cells, responding to 86% of tested neoantigens and recognizing 68% of the tested neoepitopes. These responses include a public neoantigen from the ETV6-RUNX1 fusion that is targeted in seven of nine tested patients. We characterized phenotypic and transcriptional profiles of CD8+ tumor-infiltrating lymphocytes (TILs) at the single-cell level and found a heterogeneous population that included highly functional effectors. Moreover, we observed immunodominance hierarchies among the CD8+ TILs restricted to one or two putative neoepitopes. Our results indicate that robust antitumor immune responses are induced in pediatric ALL despite their low mutation burdens and emphasize the importance of immunodominance in shaping cellular immune responses. Furthermore, these data suggest that pediatric cancers may be amenable to immunotherapies aimed at enhancing immune recognition of tumor-specific neoantigens.
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Affiliation(s)
- Anthony E Zamora
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jeremy Chase Crawford
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - E Kaitlynn Allen
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Xi-Zhi J Guo
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.,Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Jesse Bakke
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.,Department of Foundational Sciences, College of Medicine, Central Michigan University, Mount Pleasant, MI 48858, USA
| | - Robert A Carter
- Department of Computational Biology and Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Hossam A Abdelsamed
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ardiana Moustaki
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Yongjin Li
- Department of Computational Biology and Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ti-Cheng Chang
- Department of Computational Biology and Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Walid Awad
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Mari H Dallas
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - James R Downing
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Terrence L Geiger
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Douglas R Green
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Benjamin A Youngblood
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jinghui Zhang
- Department of Computational Biology and Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA. .,Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN 38163, USA
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Loh L, Gherardin NA, Sant S, Grzelak L, Crawford JC, Bird NL, Koay HF, van de Sandt CE, Moreira ML, Lappas M, Allen EK, Crowe J, Loudovaris T, Flanagan KL, Quinn KM, Rossjohn J, Thomas PG, Eckle SBG, McCluskey J, Godfrey DI, Kedzierska K. Human Mucosal-Associated Invariant T Cells in Older Individuals Display Expanded TCRαβ Clonotypes with Potent Antimicrobial Responses. J Immunol 2020; 204:1119-1133. [PMID: 31988181 DOI: 10.4049/jimmunol.1900774] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 12/16/2019] [Indexed: 12/20/2022]
Abstract
Mucosal-associated invariant T (MAIT) cells are important for immune responses against microbial infections. Although known to undergo marked numerical changes with age in humans, our understanding of how MAIT cells are altered during different phases across the human life span is largely unknown. Although also abundant in the tissues, our study focuses on MAIT cell analyses in blood. Across the human life span, we show that naive-like MAIT cells in umbilical cord blood switch to a central/effector memory-like profile that is sustained into older age. Whereas low-grade levels of plasma cytokine/chemokine were apparent in older donors (>65 y old), surprisingly, they did not correlate with the ex vivo MAIT hyperinflammatory cytokine profile observed in older adults. Removal of MAIT cells from older individuals and an aged environment resulted in the reversal of the baseline effector molecule profile comparable with MAIT cells from younger adults. An upregulated basal inflammatory profile accounted for reduced Escherichia coli-specific responses in aged MAIT cells compared with their young adult counterparts when fold change in expression levels of GzmB, CD107a, IFN-γ, and TNF was examined. However, the magnitude of antimicrobial MR1-dependent activation remained as potent and polyfunctional as with younger adults. Paired TCRαβ analyses of MAIT cells revealed large clonal expansions in older adults and tissues that rivalled, remarkably, the TCRαβ repertoire diversity of virus-specific CD8+ T cells. These data suggest that MAIT cells in older individuals, although associated with large clonal TCRαβ expansions and increased baseline inflammatory potential, demonstrate plasticity and provide potent antimicrobial immunity.
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Affiliation(s)
- Liyen Loh
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia;
| | - Nicholas A Gherardin
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, The University of Melbourne, Parkville, Victoria 3052, Australia
| | - Sneha Sant
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Ludivine Grzelak
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia
| | | | - Nicola L Bird
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Hui-Fern Koay
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, The University of Melbourne, Parkville, Victoria 3052, Australia
| | - Carolien E van de Sandt
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia.,Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam University Medical Centers, University of Amsterdam, 1066CX Amsterdam, the Netherlands
| | - Marcela L Moreira
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Martha Lappas
- Obstetrics, Nutrition and Endocrinology Group, Department of Obstetrics and Gynaecology, The University of Melbourne, Mercy Hospital for Women, Heidelberg, Victoria 3084, Australia
| | - E Kaitlynn Allen
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Jane Crowe
- Deepdene Surgery, Deepdene, Victoria 3103, Australia
| | - Thomas Loudovaris
- Immunology and Diabetes Unit, St. Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia
| | - Katie L Flanagan
- Launceston General Hospital, Launceston, Tasmania 7250, Australia.,University of Tasmania, Launceston, Tasmania 7250, Australia.,Department of Immunology and Pathology, Monash University, Melbourne, Victoria 3004, Australia.,School of Health and Biomedical Science, Royal Melbourne Institute of Technology University, Bundoora, Victoria 3083, Australia
| | - Kylie M Quinn
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia; and.,Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Sidonia B G Eckle
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia
| | - James McCluskey
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Dale I Godfrey
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, The University of Melbourne, Parkville, Victoria 3052, Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia;
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31
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Koutsakos M, Illing PT, Nguyen THO, Mifsud NA, Crawford JC, Rizzetto S, Eltahla AA, Clemens EB, Sant S, Chua BY, Wong CY, Allen EK, Teng D, Dash P, Boyd DF, Grzelak L, Zeng W, Hurt AC, Barr I, Rockman S, Jackson DC, Kotsimbos TC, Cheng AC, Richards M, Westall GP, Loudovaris T, Mannering SI, Elliott M, Tangye SG, Wakim LM, Rossjohn J, Vijaykrishna D, Luciani F, Thomas PG, Gras S, Purcell AW, Kedzierska K. Human CD8 + T cell cross-reactivity across influenza A, B and C viruses. Nat Immunol 2019; 20:613-625. [PMID: 30778243 DOI: 10.1038/s41590-019-0320-6] [Citation(s) in RCA: 150] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 01/10/2019] [Indexed: 12/18/2022]
Abstract
Influenza A, B and C viruses (IAV, IBV and ICV, respectively) circulate globally and infect humans, with IAV and IBV causing the most severe disease. CD8+ T cells confer cross-protection against IAV strains, however the responses of CD8+ T cells to IBV and ICV are understudied. We investigated the breadth of CD8+ T cell cross-recognition and provide evidence of CD8+ T cell cross-reactivity across IAV, IBV and ICV. We identified immunodominant CD8+ T cell epitopes from IBVs that were protective in mice and found memory CD8+ T cells directed against universal and influenza-virus-type-specific epitopes in the blood and lungs of healthy humans. Lung-derived CD8+ T cells displayed tissue-resident memory phenotypes. Notably, CD38+Ki67+CD8+ effector T cells directed against novel epitopes were readily detected in IAV- or IBV-infected pediatric and adult subjects. Our study introduces a new paradigm whereby CD8+ T cells confer unprecedented cross-reactivity across all influenza viruses, a key finding for the design of universal vaccines.
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Affiliation(s)
- Marios Koutsakos
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Patricia T Illing
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Thi H O Nguyen
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Nicole A Mifsud
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | | | - Simone Rizzetto
- School of Medical Sciences and The Kirby Institute, UNSW, Sydney, New South Wales, Australia
| | - Auda A Eltahla
- School of Medical Sciences and The Kirby Institute, UNSW, Sydney, New South Wales, Australia
| | - E Bridie Clemens
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Sneha Sant
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Brendon Y Chua
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Chinn Yi Wong
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - E Kaitlynn Allen
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Don Teng
- Infection and Immunity Program & Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Pradyot Dash
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - David F Boyd
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Ludivine Grzelak
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- Biology Department, École Normale Supérieure Paris-Saclay, Université Paris-Saclay, Cachan, France
| | - Weiguang Zeng
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Aeron C Hurt
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- World Health Organization (WHO) Collaborating Centre for Reference and Research on Influenza, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Ian Barr
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- World Health Organization (WHO) Collaborating Centre for Reference and Research on Influenza, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- School of Applied Biomedical Sciences, Federation University, Churchill, Victoria, Australia
| | - Steve Rockman
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- Seqirus, Parkville, Victoria, Australia
| | - David C Jackson
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Tom C Kotsimbos
- Department of Allergy, Immunology and Respiratory Medicine, The Alfred Hospital, Melbourne, Victoria, Australia
- Department of Medicine, Monash University, Central Clinical School, The Alfred Hospital, Melbourne, Victoria, Australia
| | - Allen C Cheng
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
- Infection Prevention and Healthcare Epidemiology Unit, Alfred Health, Melbourne, Victoria, Australia
| | - Michael Richards
- Victorian Infectious Diseases Service, The Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Glen P Westall
- Lung Transplant Unit, Alfred Hospital, Melbourne, Victoria, Australia
| | - Thomas Loudovaris
- Immunology and Diabetes Unit, St Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia
| | | | - Michael Elliott
- Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
- Chris O'Brien Lifehouse Cancer Centre, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - Stuart G Tangye
- Immunology Division, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- St. Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Linda M Wakim
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Dhanasekaran Vijaykrishna
- Infection and Immunity Program & Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Fabio Luciani
- School of Medical Sciences and The Kirby Institute, UNSW, Sydney, New South Wales, Australia
| | - Paul G Thomas
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Stephanie Gras
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| | - Anthony W Purcell
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia.
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Guo XZJ, Dash P, Crawford JC, Allen EK, Zamora AE, Boyd DF, Duan S, Bajracharya R, Awad WA, Apiwattanakul N, Vogel P, Kanneganti TD, Thomas PG. Lung γδ T Cells Mediate Protective Responses during Neonatal Influenza Infection that Are Associated with Type 2 Immunity. Immunity 2018; 49:531-544.e6. [PMID: 30170813 DOI: 10.1016/j.immuni.2018.07.011] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [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: 07/12/2017] [Revised: 04/25/2018] [Accepted: 07/20/2018] [Indexed: 12/25/2022]
Abstract
Compared to adults, infants suffer higher rates of hospitalization, severe clinical complications, and mortality due to influenza infection. We found that γδ T cells protected neonatal mice against mortality during influenza infection. γδ T cell deficiency did not alter viral clearance or interferon-γ production. Instead, neonatal influenza infection induced the accumulation of interleukin-17A (IL-17A)-producing γδ T cells, which was associated with IL-33 production by lung epithelial cells. Neonates lacking IL-17A-expressing γδ T cells or Il33 had higher mortality upon influenza infection. γδ T cells and IL-33 promoted lung infiltration of group 2 innate lymphoid cells and regulatory T cells, resulting in increased amphiregulin secretion and tissue repair. In influenza-infected children, IL-17A, IL-33, and amphiregulin expression were correlated, and increased IL-17A levels in nasal aspirates were associated with better clinical outcomes. Our results indicate that γδ T cells are required in influenza-infected neonates to initiate protective immunity and mediate lung homeostasis.
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Affiliation(s)
- Xi-Zhi J Guo
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Pradyot Dash
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jeremy Chase Crawford
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - E Kaitlynn Allen
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Anthony E Zamora
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - David F Boyd
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Susu Duan
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Resha Bajracharya
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Walid A Awad
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Nopporn Apiwattanakul
- Division of Infectious Diseases, Department of Pediatrics Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Peter Vogel
- Veterinary Pathology Core, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | | | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
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Santos-Cortez RLP, Chiong CM, Reyes-Quintos MRT, Tantoco MLC, Wang X, Acharya A, Abbe I, Giese AP, Smith JD, Allen EK, Li B, Cutiongco-de la Paz EM, Garcia MC, Llanes EGD, Labra PJ, Gloria-Cruz TLI, Chan AL, Wang GT, Daly KA, Shendure J, Bamshad MJ, Nickerson DA, Patel JA, Riazuddin S, Sale MM, Chonmaitree T, Ahmed ZM, Abes GT, Leal SM. Rare A2ML1 variants confer susceptibility to otitis media. Nat Genet 2015; 47:917-20. [PMID: 26121085 PMCID: PMC4528370 DOI: 10.1038/ng.3347] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [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: 02/15/2015] [Accepted: 06/03/2015] [Indexed: 11/15/2022]
Abstract
A duplication variant within the middle ear-specific gene A2ML1 cosegregates with otitis media in an indigenous Filipino pedigree (LOD score = 7.5 at reduced penetrance) and lies within a founder haplotype that is also shared by 3 otitis-prone European-American and Hispanic-American children but is absent in non-otitis-prone children and >62,000 next-generation sequences. We identified seven additional A2ML1 variants in six otitis-prone children. Collectively, our studies support a role for A2ML1 in the pathophysiology of otitis media.
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Affiliation(s)
- Regie Lyn P. Santos-Cortez
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Charlotte M. Chiong
- Philippine National Ear Institute, University of the Philippines Manila – National Institutes of Health, Manila, Philippines
- Department of Otorhinolaryngology, University of the Philippines College of Medicine – Philippine General Hospital, Manila, Philippines
| | - Ma. Rina T. Reyes-Quintos
- Philippine National Ear Institute, University of the Philippines Manila – National Institutes of Health, Manila, Philippines
- Department of Otorhinolaryngology, University of the Philippines College of Medicine – Philippine General Hospital, Manila, Philippines
| | - Ma. Leah C. Tantoco
- Philippine National Ear Institute, University of the Philippines Manila – National Institutes of Health, Manila, Philippines
| | - Xin Wang
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Anushree Acharya
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Izoduwa Abbe
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Arnaud P. Giese
- Department of Otorhinolaryngology Head & Neck Surgery, School of Medicine, University of Maryland, Baltimore, Maryland, USA
| | - Joshua D. Smith
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - E. Kaitlynn Allen
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, Virginia, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, USA
| | - Biao Li
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Eva Maria Cutiongco-de la Paz
- Institute of Human Genetics, University of the Philippines Manila – National Institutes of Health, Manila, Philippines
- Department of Pediatrics, University of the Philippines College of Medicine – Philippine General Hospital, Manila, Philippines
| | - Marieflor Cristy Garcia
- Department of Otorhinolaryngology, University of the Philippines College of Medicine – Philippine General Hospital, Manila, Philippines
| | - Erasmo Gonzalo D.V. Llanes
- Philippine National Ear Institute, University of the Philippines Manila – National Institutes of Health, Manila, Philippines
- Department of Otorhinolaryngology, University of the Philippines College of Medicine – Philippine General Hospital, Manila, Philippines
| | - Patrick John Labra
- Department of Otorhinolaryngology, University of the Philippines College of Medicine – Philippine General Hospital, Manila, Philippines
| | - Teresa Luisa I. Gloria-Cruz
- Philippine National Ear Institute, University of the Philippines Manila – National Institutes of Health, Manila, Philippines
- Department of Otorhinolaryngology, University of the Philippines College of Medicine – Philippine General Hospital, Manila, Philippines
| | - Abner L. Chan
- Philippine National Ear Institute, University of the Philippines Manila – National Institutes of Health, Manila, Philippines
- Department of Otorhinolaryngology, University of the Philippines College of Medicine – Philippine General Hospital, Manila, Philippines
| | - Gao T. Wang
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Kathleen A. Daly
- Department of Otolaryngology, Head and Neck Surgery, University of Minnesota, Minneapolis, Minnesota, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Michael J. Bamshad
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Deborah A. Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Janak A. Patel
- Division of Pediatric Infectious Disease and Immunology, Department of Pediatrics, University of Texas Medical Branch, Galveston, Texas, USA
| | - Saima Riazuddin
- Department of Otorhinolaryngology Head & Neck Surgery, School of Medicine, University of Maryland, Baltimore, Maryland, USA
| | - Michele M. Sale
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, Virginia, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia, USA
| | | | - Tasnee Chonmaitree
- Division of Pediatric Infectious Disease and Immunology, Department of Pediatrics, University of Texas Medical Branch, Galveston, Texas, USA
| | - Zubair M. Ahmed
- Department of Otorhinolaryngology Head & Neck Surgery, School of Medicine, University of Maryland, Baltimore, Maryland, USA
| | - Generoso T. Abes
- Philippine National Ear Institute, University of the Philippines Manila – National Institutes of Health, Manila, Philippines
- Department of Otorhinolaryngology, University of the Philippines College of Medicine – Philippine General Hospital, Manila, Philippines
| | - Suzanne M. Leal
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
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34
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Affiliation(s)
- E Kaitlynn Allen
- 1 Department of Immunology St. Jude Children's Research Hospital Memphis, Tennessee
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35
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Abstract
Otitis media (OM) is the most common disease in children in the United States, with about $5 billion spent each year in direct and indirect costs. OM is the number one reason for pediatric antibiotic usage and surgery, although treatment options are limited. Numerous studies have established the high heritability of OM and a genetic contribution to OM pathogenesis. Candidate gene studies have highlighted the roles of inflammation, mucin secretion, and pathogen recognition, but this approach is unable to identify novel pathways to target for treatment or screening purposes. Here, we review the current literature on agnostic approaches to discover novel genes and pathways involved in OM pathogenesis.
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Affiliation(s)
- E Kaitlynn Allen
- Center for Public Health Genomics, University of Virginia, PO Box 800717, Charlottesville, VA, 22908, USA
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36
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Allen EK, Koeppel AF, Hendley JO, Turner SD, Winther B, Sale MM. Characterization of the nasopharyngeal microbiota in health and during rhinovirus challenge. Microbiome 2014; 2:22. [PMID: 25028608 PMCID: PMC4098959 DOI: 10.1186/2049-2618-2-22] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 05/28/2014] [Indexed: 05/05/2023]
Abstract
BACKGROUND The bacterial communities of the nasopharynx play an important role in upper respiratory tract infections (URTIs). Our study represents the first survey of the nasopharynx during a known, controlled viral challenge. We aimed to gain a better understanding of the composition and dynamics of the nasopharyngeal microbiome during viral infection. METHODS Rhinovirus illnesses were induced by self-inoculation using the finger to nose or eye natural transmission route in ten otherwise healthy young adults. Nasal lavage fluid samples (NLF) samples were collected at specific time points before, during, and following experimental rhinovirus inoculation. Bacterial DNA from each sample (N = 97 from 10 subjects) was subjected to 16S rRNA sequencing by amplifying the V1-V2 hypervariable region followed by sequencing using the 454-FLX platform. RESULTS This survey of the nasopharyngeal microbiota revealed a highly complex microbial ecosystem. Taxonomic composition varied widely between subjects and between time points of the same subject. We also observed significantly higher diversity in not infected individuals compared to infected individuals. Two genera - Neisseria and Propionibacterium - differed significantly between infected and not infected individuals. Certain phyla, including Firmicutes, Actinobacteria, and Proteobacteria, were detected in all samples. CONCLUSIONS Our results reveal the complex and diverse nature of the nasopharyngeal microbiota in both healthy and viral-challenged adults. Although some phyla were common to all samples, differences in levels of diversity and selected phyla were detected between infected and uninfected participants. Deeper, species-level metagenomic sequencing in a larger sample is warranted.
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Affiliation(s)
- E Kaitlynn Allen
- Center for Public Health Genomics, University of Virginia, PO Box 800717, Charlottesville, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, USA
| | - Alex F Koeppel
- Bioinformatics Core Facility, University of Virginia, Charlottesville, USA
| | - J Owen Hendley
- Department of Pediatrics, University of Virginia, Charlottesville, USA
| | - Stephen D Turner
- Bioinformatics Core Facility, University of Virginia, Charlottesville, USA
| | - Birgit Winther
- Department of Otolaryngology, University of Virginia, Charlottesville, USA
| | - Michèle M Sale
- Center for Public Health Genomics, University of Virginia, PO Box 800717, Charlottesville, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, USA
- Department of Medicine, University of Virginia, Charlottesville, USA
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37
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Allen EK, Pitkäranta A, Mäki M, Hendley JO, Laakso S, Sale MM, Winther B. Bacteria in the nose of young adults during wellness and rhinovirus colds: detection by culture and microarray methods in 100 nasal lavage specimens. Int Forum Allergy Rhinol 2013; 3:731-9. [PMID: 23801660 DOI: 10.1002/alr.21191] [Citation(s) in RCA: 14] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 04/22/2013] [Accepted: 05/10/2013] [Indexed: 11/07/2022]
Abstract
BACKGROUND Patients with viral respiratory infections/viral rhinitis/common colds are often treated with antibiotic; however, there is little information on whether or how bacterial microbiota in the nose and nasopharynx might influence the course of viral illnesses. METHODS To initiate investigation of possible interaction between viral respiratory illness and microbiota of the nose/nasopharynx, we used microarray technology to examine 100 nasal lavage fluid (NLF) samples for bacterial species and recorded the bacterial titer of culturable bacteria. Rhinovirus illnesses were induced by self-inoculation using the "finger to nose or eye natural transmission route" in 10 otherwise healthy young adults. NLF samples were collected during wellness and at specific time points following experimental rhinovirus inoculation. RESULTS The rhinovirus infection rate was 70%. There were no consistent changes in the prevalence of different bacterial species determined by microarray and bacterial titer by culture methods during rhinovirus infection. The bacterial profile in NLF samples showed high variability between volunteers but low variability in multiple NLFs obtained before and following infection from the same volunteer. Streptococcus epidermidis/coagulase-negative staphylococcus (CNS) were identified in all 10 subjects. One or more bacterial sinus/otitis pathogens were identified by microarray in 6 of the 10 volunteers. The microarray identified a few bacteria not included in traditional bacterial cultures. CONCLUSION Our pilot study showed that each of the 10 volunteers had a unique bacterial profile in the nose by microarray analysis and that bacterial load did not change during experimental rhinovirus colds. Larger scale studies are warranted.
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Affiliation(s)
- E Kaitlynn Allen
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA; Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA
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Chen WM, Allen EK, Mychaleckyj JC, Chen F, Hou X, Rich SS, Daly KA, Sale MM. Significant linkage at chromosome 19q for otitis media with effusion and/or recurrent otitis media (COME/ROM). BMC Med Genet 2011; 12:124. [PMID: 21943191 PMCID: PMC3191346 DOI: 10.1186/1471-2350-12-124] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Accepted: 09/26/2011] [Indexed: 01/22/2023]
Abstract
Background In previous analyses, we identified a region of chromosome 19 as harboring a susceptibility locus for chronic otitis media with effusion and/or recurrent otitis media (COME/ROM). Our aim was to further localize the linkage signal and ultimately identify the causative variant or variants. We followed up our previous linkage scan with dense SNP genotyping across in a 5 Mb region. A total of 607 individuals from 139 families, including 159 affected sib pairs and 62 second-degree affected relative pairs, were genotyped at 1,091 SNPs. We carried out a nonparametric linkage analysis, modeling marker-to-marker linkage disequilibrium. Results The maximum log of the odds (LOD) score increased to 3.75 (P = 1.6 × 10-5) at position 63.4 Mb, with a LOD-1 support interval between 61.6 Mb and 63.8 Mb, providing significant evidence of linkage between this region and COME/ROM. The support interval contains over 90 known genes, including several genes involved in the inflammasome protein complex, a key regulator of the innate immune response to harmful exogenous or endogenous stimuli. Parametric linkage analysis suggests that for a sib of an affected individual, the recurrence risk of COME/ROM due to this linkage region is twice the recurrence risk in the population. We examined potential associations between the SNPs genotyped in this region and COME/ROM, however none provided evidence for association. Conclusion This study has refined the 19q region of linkage with COME/ROM, and association results suggest that the linkage signal may be due to rare variants.
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Affiliation(s)
- Wei-Min Chen
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
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