1
|
Chong EA, Kumashie KG, Chong ER, Fabrizio J, Gupta A, Svoboda J, Barta SK, Walsh KM, Napier EB, Lundberg RK, Nasta SD, Gerson JN, Landsburg DJ, Gonzalez J, Gaano A, Weirick ME, McAllister CM, Awofolaju M, John GN, Kammerman SC, Novaceck J, Pajarillo R, Lundgreen KA, Tanenbaum N, Gouma S, Drapeau EM, Adamski S, D'Andrea K, Pattekar A, Hicks A, Korte S, Sharma H, Herring S, Williams JC, Hamilton JT, Bates P, Hensley SE, Prak ETL, Greenplate AR, Wherry EJ, Schuster SJ, Ruella M, Vella LA. Immunologic predictors of vaccine responsiveness in patients with lymphoma and CLL. J Infect Dis 2024:jiae106. [PMID: 38437622 DOI: 10.1093/infdis/jiae106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 02/13/2024] [Accepted: 02/26/2024] [Indexed: 03/06/2024] Open
Abstract
Patients with B-cell lymphomas have altered cellular components of vaccine responses due to malignancy and therapy, and the optimal timing of vaccination relative to therapy remains unknown. SARS-CoV-2 vaccines created an opportunity for new insights in vaccine timing because patients were challenged with a novel antigen across multiple phases of treatment. We studied serologic mRNA vaccine response in retrospective and prospective cohorts with lymphoma and CLL, paired with clinical and research immune parameters. Reduced serologic response was observed more frequently during active therapies, but non-response was also common within observation and post-treatment groups. Total IgA and IgM correlated with successful vaccine response. In individuals treated with CART-19, non-response was associated with reduced B and T follicular helper cells. Predictors of vaccine response varied by disease and therapeutic group, and therefore further studies of immune health during and after cancer therapies are needed to allow individualized vaccine timing.
Collapse
Affiliation(s)
- Elise A Chong
- The Richard Berman Family Innovations Center in CLL and Lymphomas, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Division of Hematology/Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kingsley Gideon Kumashie
- Division of Infectious Diseases, Department of Pediatrics, Children's Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Emeline R Chong
- The Richard Berman Family Innovations Center in CLL and Lymphomas, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Joseph Fabrizio
- The Richard Berman Family Innovations Center in CLL and Lymphomas, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Aditi Gupta
- Division of Hematology/Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jakub Svoboda
- The Richard Berman Family Innovations Center in CLL and Lymphomas, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Division of Hematology/Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Stefan K Barta
- The Richard Berman Family Innovations Center in CLL and Lymphomas, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Division of Hematology/Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kristy M Walsh
- The Richard Berman Family Innovations Center in CLL and Lymphomas, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ellen B Napier
- The Richard Berman Family Innovations Center in CLL and Lymphomas, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rachel K Lundberg
- The Richard Berman Family Innovations Center in CLL and Lymphomas, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sunita D Nasta
- The Richard Berman Family Innovations Center in CLL and Lymphomas, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Division of Hematology/Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James N Gerson
- The Richard Berman Family Innovations Center in CLL and Lymphomas, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Division of Hematology/Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Daniel J Landsburg
- The Richard Berman Family Innovations Center in CLL and Lymphomas, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Division of Hematology/Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Joyce Gonzalez
- Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Andrew Gaano
- Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Madison E Weirick
- Department of Microbiology, University of Pennsylvania, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Christopher M McAllister
- Department of Microbiology, University of Pennsylvania, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Moses Awofolaju
- Department of Microbiology, University of Pennsylvania, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Gavin N John
- Division of Infectious Diseases, Department of Pediatrics, Children's Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Shane C Kammerman
- Division of Infectious Diseases, Department of Pediatrics, Children's Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Josef Novaceck
- Division of Infectious Diseases, Department of Pediatrics, Children's Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Raymone Pajarillo
- Center for Cellular Immunotherapies, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kendall A Lundgreen
- Department of Microbiology, University of Pennsylvania, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Nicole Tanenbaum
- Department of Microbiology, University of Pennsylvania, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Sigrid Gouma
- Department of Microbiology, University of Pennsylvania, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Elizabeth M Drapeau
- Department of Microbiology, University of Pennsylvania, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Sharon Adamski
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kurt D'Andrea
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Ajinkya Pattekar
- Center for Cellular Immunotherapies, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Amanda Hicks
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Scott Korte
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Harsh Sharma
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Sarah Herring
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Justine C Williams
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jacob T Hamilton
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Paul Bates
- Department of Microbiology, University of Pennsylvania, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Scott E Hensley
- Department of Microbiology, University of Pennsylvania, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Eline T Luning Prak
- Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Allison R Greenplate
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - E John Wherry
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Stephen J Schuster
- The Richard Berman Family Innovations Center in CLL and Lymphomas, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Division of Hematology/Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Marco Ruella
- The Richard Berman Family Innovations Center in CLL and Lymphomas, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Division of Hematology/Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA
- Center for Cellular Immunotherapies, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Laura A Vella
- Division of Infectious Diseases, Department of Pediatrics, Children's Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| |
Collapse
|
2
|
Narasaraju T, Neeli I, Criswell SL, Krishnappa A, Meng W, Silva V, Bila G, Vovk V, Serhiy Z, Bowlin GL, Meyer N, Luning Prak ET, Radic M, Bilyy R. Neutrophil Activity and Extracellular Matrix Degradation: Drivers of Lung Tissue Destruction in Fatal COVID-19 Cases and Implications for Long COVID. Biomolecules 2024; 14:236. [PMID: 38397474 PMCID: PMC10886497 DOI: 10.3390/biom14020236] [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: 01/03/2024] [Revised: 02/04/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
Pulmonary fibrosis, severe alveolitis, and the inability to restore alveolar epithelial architecture are primary causes of respiratory failure in fatal COVID-19 cases. However, the factors contributing to abnormal fibrosis in critically ill COVID-19 patients remain unclear. This study analyzed the histopathology of lung specimens from eight COVID-19 and six non-COVID-19 postmortems. We assessed the distribution and changes in extracellular matrix (ECM) proteins, including elastin and collagen, in lung alveoli through morphometric analyses. Our findings reveal the significant degradation of elastin fibers along the thin alveolar walls of the lung parenchyma, a process that precedes the onset of interstitial collagen deposition and widespread intra-alveolar fibrosis. Lungs with collapsed alveoli and organized fibrotic regions showed extensive fragmentation of elastin fibers, accompanied by alveolar epithelial cell death. Immunoblotting of lung autopsy tissue extracts confirmed elastin degradation. Importantly, we found that the loss of elastin was strongly correlated with the induction of neutrophil elastase (NE), a potent protease that degrades ECM. This study affirms the critical role of neutrophils and neutrophil enzymes in the pathogenesis of COVID-19. Consistently, we observed increased staining for peptidyl arginine deiminase, a marker for neutrophil extracellular trap release, and myeloperoxidase, an enzyme-generating reactive oxygen radical, indicating active neutrophil involvement in lung pathology. These findings place neutrophils and elastin degradation at the center of impaired alveolar function and argue that elastolysis and alveolitis trigger abnormal ECM repair and fibrosis in fatal COVID-19 cases. Importantly, this study has implications for severe COVID-19 complications, including long COVID and other chronic inflammatory and fibrotic disorders.
Collapse
Affiliation(s)
- Teluguakula Narasaraju
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA or (T.N.); (I.N.); (V.S.)
- Department of Microbiology, Adichunchanagiri Institute of Medical Sciences, Center for Research and Innovation, Adichunchanagiri University, Mandya 571448, India
| | - Indira Neeli
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA or (T.N.); (I.N.); (V.S.)
| | - Sheila L. Criswell
- Department of Diagnostic and Health Sciences, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Amita Krishnappa
- Department of Pathology, Adichunchanagiri Institute of Medical Sciences, Adichunchanagiri University, Mandya 571448, India;
| | - Wenzhao Meng
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (W.M.); (E.T.L.P.)
| | - Vasuki Silva
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA or (T.N.); (I.N.); (V.S.)
| | - Galyna Bila
- Department of Histology, Cytology, Histology & Embryology, Danylo Halytsky Lviv National Medical University, 79010 Lviv, Ukraine; (G.B.); (R.B.)
| | - Volodymyr Vovk
- Department of Pathological Anatomy and Forensic Medicine, Danylo Halytsky Lviv National Medical University, 79010 Lviv, Ukraine;
- Lviv Regional Pathological Anatomy Office, CU ENT (Pulmonology Lviv Regional Diagnostic Center), 79000 Lviv, Ukraine;
| | - Zolotukhin Serhiy
- Lviv Regional Pathological Anatomy Office, CU ENT (Pulmonology Lviv Regional Diagnostic Center), 79000 Lviv, Ukraine;
| | - Gary L. Bowlin
- Department of Biomedical Engineering, University of Memphis, Memphis, TN 38152, USA;
| | - Nuala Meyer
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA;
- Pulmonary, Allergy, and Critical Care Medicine and Center for Translational Lung Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Eline T. Luning Prak
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (W.M.); (E.T.L.P.)
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA;
| | - Marko Radic
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA or (T.N.); (I.N.); (V.S.)
| | - Rostyslav Bilyy
- Department of Histology, Cytology, Histology & Embryology, Danylo Halytsky Lviv National Medical University, 79010 Lviv, Ukraine; (G.B.); (R.B.)
| |
Collapse
|
3
|
Horvath S, Schreiber CA, Luning Prak ET. Rh Sensitization and Induced Abortion-Reply. JAMA 2024; 331:445-446. [PMID: 38319335 DOI: 10.1001/jama.2023.25017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Affiliation(s)
- Sarah Horvath
- Department of Obstetrics and Gynecology, Penn State University College of Medicine, Hershey, Pennsylvania
| | - Courtney A Schreiber
- Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Eline T Luning Prak
- Human Immunology Core, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| |
Collapse
|
4
|
Fu J, Hsiao T, Waffarn E, Meng W, Long KD, Frangaj K, Jones R, Gorur A, Shtewe A, Li M, Muntnich CB, Rogers K, Jiao W, Velasco M, Matsumoto R, Kubota M, Wells S, Danzl N, Ravella S, Iuga A, Vasilescu ER, Griesemer A, Weiner J, Farber DL, Luning Prak ET, Martinez M, Kato T, Hershberg U, Sykes M. Dynamic establishment and maintenance of the human intestinal B cell population and repertoire following transplantation. medRxiv 2023:2023.11.15.23298517. [PMID: 38014202 PMCID: PMC10680888 DOI: 10.1101/2023.11.15.23298517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
It is unknown how intestinal B cell populations and B cell receptor (BCR) repertoires are established and maintained over time in humans. Following intestinal transplantation (ITx), surveillance ileal mucosal biopsies provide a unique opportunity to map the dynamic establishment of gut lymphocyte populations. Using polychromatic flow cytometry that includes HLA allele group-specific mAbs distinguishing donor from recipient cells along with high throughput BCR sequencing, we tracked the establishment of recipient B cell populations and BCR repertoire in the allograft mucosa of ITx recipients. We confirm the early presence of naïve donor B cells in the circulation and, for the first time, document the establishment of recipient B cell populations, including B resident memory cells, in the intestinal allograft mucosa. Recipient B cell repopulation of the allograft was most rapid in infant (<1 year old)-derived allografts and, unlike T cell repopulation, did not correlate with rejection rates. While recipient memory B cell populations were increased in graft mucosa compared to circulation, naïve recipient B cells remained detectable in the graft mucosa for years. Comparisons of peripheral and intra-mucosal B cell repertoires in the absence of rejection revealed increased BCR mutation rates and clonal expansion in graft mucosa compared to circulating B cells, but these parameters did not increase markedly after the first year post-transplant. Furthermore, clonal mixing between the allograft mucosa and the circulation was significantly greater in ITx recipients, even years after transplantation, than in healthy control adults. Collectively, our data demonstrate intestinal mucosal B cell repertoire establishment from a circulating pool, a process that continues for years without evidence of establishment of a stable mucosal B cell repertoire.
Collapse
Affiliation(s)
- Jianing Fu
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, USA
| | - Thomas Hsiao
- Department of Human Biology, University of Haifa, Haifa, Israel
| | - Elizabeth Waffarn
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, USA
| | - Wenzhao Meng
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Katherine D Long
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, USA
| | - Kristjana Frangaj
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, USA
| | - Rebecca Jones
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, USA
| | - Alaka Gorur
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, USA
| | - Areen Shtewe
- Department of Human Biology, University of Haifa, Haifa, Israel
| | - Muyang Li
- Department of Pathology, Columbia University, New York, NY, USA
| | - Constanza Bay Muntnich
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, USA
| | - Kortney Rogers
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, USA
| | - Wenyu Jiao
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, USA
| | - Monica Velasco
- Department of Pediatrics, Columbia University, New York, NY, USA
| | - Rei Matsumoto
- Department of Microbiology and Immunology, Columbia University, New York, NY, USA
| | - Masaru Kubota
- Department of Microbiology and Immunology, Columbia University, New York, NY, USA
| | - Steven Wells
- Department of Microbiology and Immunology, Columbia University, New York, NY, USA
| | - Nichole Danzl
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, USA
| | - Shilpa Ravella
- Division of Digestive and Liver Diseases, Department of Medicine, Columbia University, New York, NY, USA
| | - Alina Iuga
- Department of Pathology, Columbia University, New York, NY, USA
| | | | - Adam Griesemer
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, USA
- Department of Surgery, Columbia University, New York, NY, USA
| | - Joshua Weiner
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, USA
- Department of Surgery, Columbia University, New York, NY, USA
| | - Donna L Farber
- Department of Microbiology and Immunology, Columbia University, New York, NY, USA
- Department of Surgery, Columbia University, New York, NY, USA
| | - Eline T Luning Prak
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Tomoaki Kato
- Department of Surgery, Columbia University, New York, NY, USA
| | - Uri Hershberg
- Department of Human Biology, University of Haifa, Haifa, Israel
| | - Megan Sykes
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, USA
- Department of Microbiology and Immunology, Columbia University, New York, NY, USA
- Department of Surgery, Columbia University, New York, NY, USA
| |
Collapse
|
5
|
Horvath S, Huang ZY, Koelper NC, Martinez C, Tsao PY, Zhao L, Goldberg AB, Hannum C, Putt ME, Luning Prak ET, Schreiber CA. Induced Abortion and the Risk of Rh Sensitization. JAMA 2023; 330:1167-1174. [PMID: 37750879 PMCID: PMC10524155 DOI: 10.1001/jama.2023.16953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 08/14/2023] [Indexed: 09/27/2023]
Abstract
Importance While population-level data suggest Rh immunoglobulin is unnecessary before 12 weeks' gestation, clinical evidence is limited. Thus, guidelines vary, creating confusion surrounding risks and benefits of Rh testing and treatment. As abortion care in traditional clinical settings becomes harder to access, many people are choosing to self-manage and need to know if ancillary blood type testing is necessary. Objective To determine how frequently maternal exposure to fetal red blood cells (fRBCs) exceeds the most conservative published threshold for Rh sensitization in induced first-trimester abortion. Design, Setting, and Participants Multicenter, observational, prospective cohort study using high-throughput flow cytometry to detect circulating fRBCs in paired maternal blood samples before and after induced first-trimester abortion (medication or procedural). Individuals undergoing induced first-trimester abortion before 12 weeks 0 days' gestation were included. Paired blood samples were available from 506 participants who underwent either medical (n = 319 [63.0%]) or procedural (n = 187 [37.0%]) abortion. Exposure Induced first-trimester abortion. Main Outcomes and Measures The primary outcome was the proportion of participants with fRBC counts above the sensitization threshold (125 fRBCs/5 million total RBCs) after induced first-trimester abortion. Results Among the 506 participants, the mean (SD) age was 27.4 (5.5) years, 313 (61.9%) were Black, and 123 (24.3%) were White. Three of the 506 participants had elevated fRBC counts at baseline; 1 of these patients had an elevated fRBC count following the abortion (0.2% [95% CI, 0%-0.93%]). No other participants had elevated fRBC counts above the sensitization threshold after induced first-trimester abortion. The median change from baseline was 0 fRBCs, with upper 95th and 99th percentiles of 24 and 35.6 fRBCs, respectively. Although there was a strong association between the preabortion and postabortion fRBC counts, no other baseline characteristic was significantly associated with postabortion fRBC count. Conclusions and Relevance Induced first-trimester abortion is not a risk factor for Rh sensitization, indicating that Rh testing and treatment are unnecessary before 12 weeks' gestation. This evidence may be used to inform international guidelines for Rh immunoglobulin administration following first-trimester induced abortion.
Collapse
Affiliation(s)
- Sarah Horvath
- Department of Obstetrics and Gynecology, Penn State University College of Medicine, Hershey, Pennsylvania
| | - Zhen-Yu Huang
- Human Immunology Core, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Nathanael C. Koelper
- Pregnancy Early Access Center (PEACE), Division of Family Planning, Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Christian Martinez
- Human Immunology Core, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Patricia Y. Tsao
- Human Immunology Core, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Ling Zhao
- Human Immunology Core, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia
- Cleveland Clinic BioRepository, Cleveland Clinic, Cleveland, Ohio
| | - Alisa B. Goldberg
- Division of Family Planning, Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women’s Hospital, Boston, Massachusetts
- Planned Parenthood League of Massachusetts, Boston
| | | | - Mary E. Putt
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Eline T. Luning Prak
- Human Immunology Core, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Courtney A. Schreiber
- Pregnancy Early Access Center (PEACE), Division of Family Planning, Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| |
Collapse
|
6
|
Rybkina K, Bell JN, Bradley MC, Wohlbold T, Scafuro M, Meng W, Korenberg RC, Davis-Porada J, Anderson BR, Weller RJ, Milner JD, Moscona A, Porotto M, Luning Prak ET, Pethe K, Connors TJ, Farber DL. SARS-CoV-2 infection and recovery in children: Distinct T cell responses in MIS-C compared to COVID-19. J Exp Med 2023; 220:e20221518. [PMID: 37133746 PMCID: PMC10163842 DOI: 10.1084/jem.20221518] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 09/01/2022] [Revised: 02/09/2023] [Accepted: 04/07/2023] [Indexed: 05/04/2023] Open
Abstract
SARS-CoV-2 infection for most children results in mild or minimal symptoms, though in rare cases severe disease can develop, including a multisystem inflammatory syndrome (MIS-C) with myocarditis. Here, we present longitudinal profiling of immune responses during acute disease and following recovery in children who developed MIS-C, relative to children who experienced more typical symptoms of COVID-19. T cells in acute MIS-C exhibited transient signatures of activation, inflammation, and tissue residency which correlated with cardiac disease severity, while T cells in acute COVID-19 upregulated markers of follicular helper T cells for promoting antibody production. The resultant memory immune response in recovery showed increased frequencies of virus-specific memory T cells with pro-inflammatory functions in children with prior MIS-C compared to COVID-19 while both cohorts generated comparable antibody responses. Together our results reveal distinct effector and memory T cell responses in pediatric SARS-CoV-2 infection delineated by clinical syndrome, and a potential role for tissue-derived T cells in the immune pathology of systemic disease.
Collapse
Affiliation(s)
- Ksenia Rybkina
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Joseph N. Bell
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Marissa C. Bradley
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Teddy Wohlbold
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Marika Scafuro
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Wenzhao Meng
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rebecca C. Korenberg
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Julia Davis-Porada
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Brett R. Anderson
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Rachel J. Weller
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Joshua D. Milner
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Anne Moscona
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Matteo Porotto
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Eline T. Luning Prak
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kalpana Pethe
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Thomas J. Connors
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Donna L. Farber
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Surgery, Columbia Irving University Medical Center, New York, NY, USA
| |
Collapse
|
7
|
Matsumoto R, Gray J, Rybkina K, Oppenheimer H, Levy L, Friedman LM, Khamaisi M, Meng W, Rosenfeld AM, Guyer RS, Bradley MC, Chen D, Atkinson MA, Brusko TM, Brusko M, Connors TJ, Luning Prak ET, Hershberg U, Sims PA, Hertz T, Farber DL. Induction of bronchus-associated lymphoid tissue is an early life adaptation for promoting human B cell immunity. Nat Immunol 2023; 24:1370-1381. [PMID: 37460638 PMCID: PMC10529876 DOI: 10.1038/s41590-023-01557-3] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 06/09/2023] [Indexed: 07/20/2023]
Abstract
Infants and young children are more susceptible to common respiratory pathogens than adults but can fare better against novel pathogens like severe acute respiratory syndrome coronavirus 2. The mechanisms by which infants and young children mount effective immune responses to respiratory pathogens are unknown. Through investigation of lungs and lung-associated lymph nodes from infant and pediatric organ donors aged 0-13 years, we show that bronchus-associated lymphoid tissue (BALT), containing B cell follicles, CD4+ T cells and functionally active germinal centers, develop during infancy. BALT structures are prevalent around lung airways during the first 3 years of life, and their numbers decline through childhood coincident with the accumulation of memory T cells. Single-cell profiling and repertoire analysis reveals that early life lung B cells undergo differentiation, somatic hypermutation and immunoglobulin class switching and exhibit a more activated profile than lymph node B cells. Moreover, B cells in the lung and lung-associated lymph nodes generate biased antibody responses to multiple respiratory pathogens compared to circulating antibodies, which are mostly specific for vaccine antigens in the early years of life. Together, our findings provide evidence for BALT as an early life adaptation for mobilizing localized immune protection to the diverse respiratory challenges during this formative life stage.
Collapse
Affiliation(s)
- Rei Matsumoto
- Department of Surgery, Columbia University Irving Medical Center, New York, NY, USA
| | - Joshua Gray
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Ksenia Rybkina
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Hanna Oppenheimer
- Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, Be'er-Sheva, Israel
- The National Institute for Biotechnology in the Negev, Ben-Gurion University of Negev, Be'er-Sheva, Israel
| | - Lior Levy
- Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, Be'er-Sheva, Israel
- The National Institute for Biotechnology in the Negev, Ben-Gurion University of Negev, Be'er-Sheva, Israel
| | - Lilach M Friedman
- Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, Be'er-Sheva, Israel
- The National Institute for Biotechnology in the Negev, Ben-Gurion University of Negev, Be'er-Sheva, Israel
| | | | - Wenzhao Meng
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Aaron M Rosenfeld
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rebecca S Guyer
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Marissa C Bradley
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - David Chen
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Mark A Atkinson
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida Diabetes Institute, Gainesville, FL, USA
| | - Todd M Brusko
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida Diabetes Institute, Gainesville, FL, USA
| | - Maigan Brusko
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida Diabetes Institute, Gainesville, FL, USA
| | - Thomas J Connors
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Eline T Luning Prak
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Uri Hershberg
- Department of Human Biology, University of Haifa, Haifa, Israel
| | - Peter A Sims
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, USA
| | - Tomer Hertz
- Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, Be'er-Sheva, Israel
- The National Institute for Biotechnology in the Negev, Ben-Gurion University of Negev, Be'er-Sheva, Israel
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Donna L Farber
- Department of Surgery, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA.
| |
Collapse
|
8
|
Fike AJ, Chodisetti SB, Wright NE, Bricker KN, Domeier PP, Maienschein-Cline M, Rosenfeld AM, Luckenbill SA, Weber JL, Choi NM, Luning Prak ET, Mandal M, Clark MR, Rahman ZSM. STAT3 signaling in B cells controls germinal center zone organization and recycling. Cell Rep 2023; 42:112512. [PMID: 37200190 PMCID: PMC10311431 DOI: 10.1016/j.celrep.2023.112512] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 03/05/2023] [Accepted: 05/01/2023] [Indexed: 05/20/2023] Open
Abstract
Germinal centers (GCs), sites of antibody affinity maturation, are organized into dark (DZ) and light (LZ) zones. Here, we show a B cell-intrinsic role for signal transducer and activator of transcription 3 (STAT3) in GC DZ and LZ organization. Altered zonal organization of STAT3-deficient GCs dampens development of long-lived plasma cells (LL-PCs) but increases memory B cells (MBCs). In an abundant antigenic environment, achieved here by prime-boost immunization, STAT3 is not required for GC initiation, maintenance, or proliferation but is important for sustaining GC zonal organization by regulating GC B cell recycling. Th cell-derived signals drive STAT3 tyrosine 705 and serine 727 phosphorylation in LZ B cells, regulating their recycling into the DZ. RNA sequencing (RNA-seq) and chromatin immunoprecipitation sequencing (ChIP-seq) analyses identified STAT3 regulated genes that are critical for LZ cell recycling and transiting through DZ proliferation and differentiation phases. Thus, STAT3 signaling in B cells controls GC zone organization and recycling, and GC egress of PCs, but negatively regulates MBC output.
Collapse
Affiliation(s)
- Adam J Fike
- Department of Microbiology and Immunology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Sathi Babu Chodisetti
- Department of Microbiology and Immunology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Nathaniel E Wright
- Department of Medicine, Section of Rheumatology and Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, IL 60637, USA
| | - Kristen N Bricker
- Department of Microbiology and Immunology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Phillip P Domeier
- Center for Fundamental Immunology, Benaroya Research Institute, Seattle, WA 98101, USA
| | | | - Aaron M Rosenfeld
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sara A Luckenbill
- Department of Microbiology and Immunology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Julia L Weber
- Department of Microbiology and Immunology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Nicholas M Choi
- Department of Microbiology and Immunology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Eline T Luning Prak
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Malay Mandal
- Department of Medicine, Section of Rheumatology and Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, IL 60637, USA
| | - Marcus R Clark
- Department of Medicine, Section of Rheumatology and Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, IL 60637, USA
| | - Ziaur S M Rahman
- Department of Microbiology and Immunology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA.
| |
Collapse
|
9
|
Skarke C, Lordan R, Barekat K, Naik A, Mathew D, Ohtani T, Greenplate AR, Grant GR, Lahens NF, Gouma S, Troisi E, Sengupta A, Weljie AM, Meng W, Luning Prak ET, Lundgreen K, Bates P, Meng H, FitzGerald GA. Modulation of the immune response to SARS-CoV-2 vaccination by NSAIDs. J Pharmacol Exp Ther 2023:jpet.122.001415. [PMID: 37105582 PMCID: PMC10353078 DOI: 10.1124/jpet.122.001415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 01/13/2023] [Accepted: 02/09/2023] [Indexed: 04/29/2023] Open
Abstract
Evidence is scarce to guide the use of nonsteroidal anti-inflammatory drugs (NSAIDs) to mitigate SARS-CoV-2 vaccine related adverse effects, given the possibility of blunting the desired immune response. In this pilot study, we deeply phenotyped a small number of volunteers who did or did not take NSAIDs concomitant with SARS-CoV-2 immunizations to seek initial information on the immune response. A SARS-CoV-2 vaccine specific RBD-IgG antibody response and efficacy in the evoked neutralization titers were evident irrespective of concomitant NSAID consumption. Given the sample size, only a large and consistent signal of immunomodulation would have been detectable, and this was not apparent. However, the information gathered may inform the design of a definitive clinical trial. Here, we report a series of divergent omics signals that invite additional hypotheses testing. Significance Statement A SARS-CoV-2 vaccine specific immune response was evident irrespective of concomitant NSAID consumption in a clinical pilot study of small sample size.
Collapse
Affiliation(s)
- Carsten Skarke
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, United States
| | - Ronan Lordan
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, United States
| | - Kayla Barekat
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, United States
| | - Amruta Naik
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, United States
| | - Divij Mathew
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, United States
| | - Takuya Ohtani
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, United States
| | - Allison R Greenplate
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, United States
| | - Gregory R Grant
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, United States
| | - Nicholas F Lahens
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, United States
| | - Sigrid Gouma
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, United States
| | - Elizabeth Troisi
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, United States
| | - Arjun Sengupta
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, United States
| | - Aalim M Weljie
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, United States
| | - Wenzhao Meng
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, United States
| | - Eline T Luning Prak
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, United States
| | - Kendall Lundgreen
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, United States
| | - Paul Bates
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, United States
| | - Hu Meng
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, United States
| | - Garret A FitzGerald
- Center for Experimental Therapeutics, University of Pennsylvania, United States
| |
Collapse
|
10
|
Feng A, Yang EY, Moore AR, Dhingra S, Chang SE, Yin X, Pi R, Mack EK, Völkel S, Geßner R, Gündisch M, Neubauer A, Renz H, Tsiodras S, Fragkou PC, Asuni AA, Levitt JE, Wilson JG, Leong M, Lumb JH, Mao R, Pinedo K, Roque J, Richards CM, Stabile M, Swaminathan G, Salagianni ML, Triantafyllia V, Bertrams W, Blish CA, Carette JE, Frankovich J, Meffre E, Nadeau KC, Singh U, Wang TT, Luning Prak ET, Herold S, Andreakos E, Schmeck B, Skevaki C, Rogers AJ, Utz PJ. Autoantibodies are highly prevalent in non-SARS-CoV-2 respiratory infections and critical illness. JCI Insight 2023; 8:e163150. [PMID: 36752204 PMCID: PMC9977421 DOI: 10.1172/jci.insight.163150] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 12/14/2022] [Indexed: 02/09/2023] Open
Abstract
The widespread presence of autoantibodies in acute infection with SARS-CoV-2 is increasingly recognized, but the prevalence of autoantibodies in non-SARS-CoV-2 infections and critical illness has not yet been reported. We profiled IgG autoantibodies in 267 patients from 5 independent cohorts with non-SARS-CoV-2 viral, bacterial, and noninfectious critical illness. Serum samples were screened using Luminex arrays that included 58 cytokines and 55 autoantigens, many of which are associated with connective tissue diseases (CTDs). Samples positive for anti-cytokine antibodies were tested for receptor blocking activity using cell-based functional assays. Anti-cytokine antibodies were identified in > 50% of patients across all 5 acutely ill cohorts. In critically ill patients, anti-cytokine antibodies were far more common in infected versus uninfected patients. In cell-based functional assays, 11 of 39 samples positive for select anti-cytokine antibodies displayed receptor blocking activity against surface receptors for Type I IFN, GM-CSF, and IL-6. Autoantibodies against CTD-associated autoantigens were also commonly observed, including newly detected antibodies that emerged in longitudinal samples. These findings demonstrate that anti-cytokine and autoantibodies are common across different viral and nonviral infections and range in severity of illness.
Collapse
Affiliation(s)
- Allan Feng
- Department of Medicine, Division of Immunology and Rheumatology
- Institute for Immunity, Transplantation and Infection
| | - Emily Y. Yang
- Department of Medicine, Division of Immunology and Rheumatology
- Institute for Immunity, Transplantation and Infection
| | - Andrew Reese Moore
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, and
| | - Shaurya Dhingra
- Department of Medicine, Division of Immunology and Rheumatology
- Institute for Immunity, Transplantation and Infection
| | - Sarah Esther Chang
- Department of Medicine, Division of Immunology and Rheumatology
- Institute for Immunity, Transplantation and Infection
| | - Xihui Yin
- Department of Medicine, Division of Immunology and Rheumatology
- Institute for Immunity, Transplantation and Infection
| | - Ruoxi Pi
- Department of Medicine, Division of Infectious Diseases, Stanford University School of Medicine, Stanford, California, USA
| | - Elisabeth K.M. Mack
- Department of Hematology, Oncology, Immunology, Philipps University Marburg, Marburg, Germany
| | - Sara Völkel
- Institute of Laboratory Medicine, Universities of Giessen and Marburg Lung Center (UGMLC), Philipps University Marburg, German Center for Lung Research (DZL), Marburg, Germany
| | - Reinhard Geßner
- Institute of Laboratory Medicine, Universities of Giessen and Marburg Lung Center (UGMLC), Philipps University Marburg, German Center for Lung Research (DZL), Marburg, Germany
| | - Margrit Gündisch
- Institute of Laboratory Medicine, Universities of Giessen and Marburg Lung Center (UGMLC), Philipps University Marburg, German Center for Lung Research (DZL), Marburg, Germany
| | - Andreas Neubauer
- Department of Hematology, Oncology, Immunology, Philipps University Marburg, Marburg, Germany
| | - Harald Renz
- Institute of Laboratory Medicine, Universities of Giessen and Marburg Lung Center (UGMLC), Philipps University Marburg, German Center for Lung Research (DZL), Marburg, Germany
| | - Sotirios Tsiodras
- 4th Department of Internal Medicine, Medical School, National and Kapodistrian University of Athens, Attikon University Hospital, Athens, Greece
| | - Paraskevi C. Fragkou
- 4th Department of Internal Medicine, Medical School, National and Kapodistrian University of Athens, Attikon University Hospital, Athens, Greece
- European Society of Clinical Microbiology and Infectious Diseases (ESCMID), Study Group for Respiratory Viruses (ESGREV), Basel, Switzerland
| | - Adijat A. Asuni
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, and
| | - Joseph E. Levitt
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, and
| | | | - Michelle Leong
- Department of Medicine, Division of Infectious Diseases, Stanford University School of Medicine, Stanford, California, USA
| | - Jennifer H. Lumb
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Rong Mao
- Department of Medicine, Division of Immunology and Rheumatology
- Institute for Immunity, Transplantation and Infection
| | - Kassandra Pinedo
- Department of Medicine, Division of Infectious Diseases, Stanford University School of Medicine, Stanford, California, USA
| | - Jonasel Roque
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, and
| | - Christopher M. Richards
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Mikayla Stabile
- Department of Medicine, Division of Infectious Diseases, Stanford University School of Medicine, Stanford, California, USA
| | - Gayathri Swaminathan
- Department of Medicine, Division of Immunology and Rheumatology
- Institute for Immunity, Transplantation and Infection
| | - Maria L. Salagianni
- Laboratory of Immunobiology, Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Vasiliki Triantafyllia
- Laboratory of Immunobiology, Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Wilhelm Bertrams
- Institute for Lung Research, UGMLC, Philipps University Marburg, Marburg, Germany
| | - Catherine A. Blish
- Institute for Immunity, Transplantation and Infection
- Department of Medicine, Division of Infectious Diseases, Stanford University School of Medicine, Stanford, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Jan E. Carette
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Jennifer Frankovich
- Department of Pediatrics, Division of Allergy, Immunology, Rheumatology, Stanford University School of Medicine, Stanford, California, USA
| | - Eric Meffre
- Department of Immunobiology, Yale University, New Haven, Connecticut, USA
| | - Kari Christine Nadeau
- Institute for Immunity, Transplantation and Infection
- Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, California, USA
| | - Upinder Singh
- Institute for Immunity, Transplantation and Infection
- Department of Medicine, Division of Infectious Diseases, Stanford University School of Medicine, Stanford, California, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Taia T. Wang
- Institute for Immunity, Transplantation and Infection
- Department of Medicine, Division of Infectious Diseases, Stanford University School of Medicine, Stanford, California, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Eline T. Luning Prak
- Department of Pathology and Laboratory Medicine and
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Susanne Herold
- Department of Internal Medicine V, Infectious Diseases and Infection Control, UKGM, Justus Liebig University, and Institute for Lung Health (ILH), Giessen, Germany
- DZL and UGMLC, Giessen, Germany
| | - Evangelos Andreakos
- Laboratory of Immunobiology, Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Bernd Schmeck
- Institute for Lung Research, UGMLC, Philipps University Marburg, Marburg, Germany
- Department of Medicine, Pulmonary and Critical Care Medicine, University Medical Center Marburg, Marburg, Germany
- DZL, German Center for Infection Research (DZIF), Center for Synthetic Microbiology (SYNMIKRO), Philipps University of Marburg, Marburg, Germany
| | - Chrysanthi Skevaki
- Institute of Laboratory Medicine, Universities of Giessen and Marburg Lung Center (UGMLC), Philipps University Marburg, German Center for Lung Research (DZL), Marburg, Germany
| | - Angela J. Rogers
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, and
| | - Paul J. Utz
- Department of Medicine, Division of Immunology and Rheumatology
- Institute for Immunity, Transplantation and Infection
| |
Collapse
|
11
|
Greiff V, Luning Prak ET, O'Donnell T, Finotello F, Reddy ST, Walczak A, Mora T. What are the current driving questions in immune repertoire research? Cell Syst 2022; 13:683-686. [PMID: 36137509 DOI: 10.1016/j.cels.2022.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
|
12
|
Alameh MG, Tombácz I, Bettini E, Lederer K, Sittplangkoon C, Wilmore JR, Gaudette BT, Soliman OY, Pine M, Hicks P, Manzoni TB, Knox JJ, Johnson JL, Laczkó D, Muramatsu H, Davis B, Meng W, Rosenfeld AM, Strohmeier S, Lin PJC, Mui BL, Tam YK, Karikó K, Jacquet A, Krammer F, Bates P, Cancro MP, Weissman D, Luning Prak ET, Allman D, Locci M, Pardi N. Lipid nanoparticles enhance the efficacy of mRNA and protein subunit vaccines by inducing robust T follicular helper cell and humoral responses. Immunity 2022; 55:1136-1138. [PMID: 35704995 PMCID: PMC9195404 DOI: 10.1016/j.immuni.2022.05.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
13
|
Caron DP, Poon MM, Wang Z, Meng W, Lam N, Szabo PA, Wells SB, Thapa P, Dogra P, Lee B, Kubota M, Matsumoto R, Rahman A, Luning Prak ET, Sims P, Shen Y, Farber DL. Human T cells in barrier sites exhibit site-specific characteristics and clonal compartmentalization. The Journal of Immunology 2022. [DOI: 10.4049/jimmunol.208.supp.57.11] [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: 01/04/2023]
Abstract
Abstract
The skin, gut, and lung are critical physical and immune barriers that protect from pathogen entry. Within these sites, T cell memory is largely maintained by populations of tissue resident memory T cells (TRMs), capable of rapid protective responses. The degree of interconnection between these TRMs from various sites of residence is poorly understood, particularly in humans. Here, we analyze how tissue specificity affects transcriptional heterogeneity and the T cell receptor (TCR) repertoire across 9 tissue sites within individual donors, including barrier sites (skin, gut, and lung) and associated lymph nodes, as well as blood and lymphoid organs (blood, bone marrow, spleen). Cytometry by time-of-flight (CyTOF) and single cell RNA sequencing reveal phenotypic and transcriptomic features unique to skin or gut T cells, which are distinct from T cells in lymphoid sites or blood. These results were reflected in both bulk sequencing of TRBV gene rearrangement and single cell TCR sequencing, where skin and gut T cells exhibited site-specific clonal expansions that were not present in other sites. Conversely, lung T cells showed clonal overlap and transcriptional similarity to T cells in lymphoid and blood rich sites. Site-specific expansions were mediated by TRMs, while clones disseminated across tissues exhibit large clonal expansions and a CD8 terminal effector (TEMRA) phenotype. Together, these results reveal that TRMs in barrier sites are maintained in situ, while memory T cells in the lung, blood-rich and lymphoid sites are more interconnected. Blood T cells are not representative of barrier T cell clonal space. These results have important implications for monitoring and promoting barrier immunity through site-specific targeting.
Supported by grants from NIH (P01 AI106697)
Collapse
Affiliation(s)
| | | | | | | | - Nora Lam
- 1Columbia University Medical Center
| | | | | | | | | | - Brian Lee
- 3Icahn School of Medicine at Mount Sinai
| | | | | | | | | | | | | | | |
Collapse
|
14
|
Luning Prak ET, Brooks T, Makhoul W, Beer JC, Zhao L, Girelli T, Skarke C, Sheline YI. No increase in inflammation in late-life major depression screened to exclude physical illness. Transl Psychiatry 2022; 12:118. [PMID: 35332134 PMCID: PMC8948274 DOI: 10.1038/s41398-022-01883-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/18/2022] [Accepted: 03/02/2022] [Indexed: 12/12/2022] Open
Abstract
Depression is a common and debilitating disorder in the elderly. Late-life depression (LLD) has been associated with inflammation and elevated levels of proinflammatory cytokines including interleukin (IL)-1β, tumor necrosis factor-alpha, and IL-6, but often depressed individuals have comorbid medical conditions that are associated with immune dysregulation. To determine whether depression has an association with inflammation independent of medical illness, 1120 adults were screened to identify individuals who had clinically significant depression but not medical conditions associated with systemic inflammation. In total, 66 patients with LLD screened to exclude medical conditions associated with inflammation were studied in detail along with 26 age-matched controls (HC). At baseline, circulating cytokines were low and similar in LLD and HC individuals. Furthermore, cytokines did not change significantly after treatment with either an antidepressant (escitalopram 20 mg/day) or an antidepressant plus a COX-2 inhibitor or placebo, even though depression scores improved in the non-placebo treatment arms. An analysis of cerebrospinal fluid in a subset of individuals for IL-1β using an ultrasensitive digital enzyme-linked immunosorbent assay revealed low levels in both LLD and HC at baseline. Our results indicate that depression by itself does not result in systemic or intrathecal elevations in cytokines and that celecoxib does not appear to have an adjunctive antidepressant role in older patients who do not have medical reasons for having inflammation. The negative finding for increased inflammation and the lack of a treatment effect for celecoxib in this carefully screened depressed population taken together with multiple positive results for inflammation in previous studies that did not screen out physical illness support a precision medicine approach to the treatment of depression that takes the medical causes for inflammation into account.
Collapse
Affiliation(s)
- Eline T. Luning Prak
- grid.25879.310000 0004 1936 8972Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA ,grid.25879.310000 0004 1936 8972Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - Thomas Brooks
- grid.25879.310000 0004 1936 8972Center for Neuromodulation in Depression and Stress (CNDS), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA ,grid.25879.310000 0004 1936 8972Institute for Translational Medicine and Therapeutics (ITMAT), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - Walid Makhoul
- grid.25879.310000 0004 1936 8972Center for Neuromodulation in Depression and Stress (CNDS), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - Joanne C. Beer
- grid.25879.310000 0004 1936 8972Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA USA
| | - Ling Zhao
- grid.25879.310000 0004 1936 8972Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA ,grid.25879.310000 0004 1936 8972Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - Tommaso Girelli
- grid.25879.310000 0004 1936 8972Center for Neuromodulation in Depression and Stress (CNDS), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - Carsten Skarke
- grid.25879.310000 0004 1936 8972Institute for Translational Medicine and Therapeutics (ITMAT), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA ,grid.25879.310000 0004 1936 8972Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - Yvette I. Sheline
- grid.25879.310000 0004 1936 8972Center for Neuromodulation in Depression and Stress (CNDS), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA ,grid.25879.310000 0004 1936 8972Departments of Psychiatry, Radiology, Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| |
Collapse
|
15
|
Pero SC, Rosenfeld AM, Shukla GS, Mei L, Sun Y, Meng W, Fournier DJ, Harlow SP, Robinson MK, Krag DN, Luning Prak ET, Harman BC. Diversification and shared features of tumor‐binding antibody repertoires in tumor, sentinel lymph node and blood of three patients with breast cancer. Clin Transl Immunology 2022. [DOI: 10.1002/cti2.1409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- Stephanie C Pero
- Department of Surgery & University of Vermont Cancer Center University of Vermont Larner College of Medicine Burlington VT USA
| | - Aaron M Rosenfeld
- Department of Pathology and Lab Medicine, Perelman School of Medicine University of Pennsylvania Philadelphia PA USA
| | - Girja S Shukla
- Department of Surgery & University of Vermont Cancer Center University of Vermont Larner College of Medicine Burlington VT USA
| | - Linda Mei
- Department of Surgery & University of Vermont Cancer Center University of Vermont Larner College of Medicine Burlington VT USA
| | - Yujing Sun
- Department of Surgery & University of Vermont Cancer Center University of Vermont Larner College of Medicine Burlington VT USA
| | - Wenzhao Meng
- Department of Pathology and Lab Medicine, Perelman School of Medicine University of Pennsylvania Philadelphia PA USA
| | - David J Fournier
- Department of Surgery & University of Vermont Cancer Center University of Vermont Larner College of Medicine Burlington VT USA
| | - Seth P Harlow
- Department of Surgery & University of Vermont Cancer Center University of Vermont Larner College of Medicine Burlington VT USA
| | | | - David N Krag
- Department of Surgery & University of Vermont Cancer Center University of Vermont Larner College of Medicine Burlington VT USA
| | - Eline T Luning Prak
- Department of Pathology and Lab Medicine, Perelman School of Medicine University of Pennsylvania Philadelphia PA USA
| | | |
Collapse
|
16
|
Marquez S, Babrak L, Greiff V, Hoehn KB, Lees WD, Luning Prak ET, Miho E, Rosenfeld AM, Schramm CA, Stervbo U. Adaptive Immune Receptor Repertoire (AIRR) Community Guide to Repertoire Analysis. Methods Mol Biol 2022; 2453:297-316. [PMID: 35622333 PMCID: PMC9761518 DOI: 10.1007/978-1-0716-2115-8_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Adaptive immune receptor repertoires (AIRRs) are rich with information that can be mined for insights into the workings of the immune system. Gene usage, CDR3 properties, clonal lineage structure, and sequence diversity are all capable of revealing the dynamic immune response to perturbation by disease, vaccination, or other interventions. Here we focus on a conceptual introduction to the many aspects of repertoire analysis and orient the reader toward the uses and advantages of each. Along the way, we note some of the many software tools that have been developed for these investigations and link the ideas discussed to chapters on methods provided elsewhere in this volume.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Chaim A Schramm
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Ulrik Stervbo
- Center for Translational Medicine, Immunology, and Transplantation, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Herne, Germany. .,Immundiagnostik, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Herne, Germany.
| | | |
Collapse
|
17
|
Wilmore JR, Gaudette BT, Gómez Atria D, Rosenthal RL, Reiser SK, Meng W, Rosenfeld AM, Luning Prak ET, Allman D. IgA Plasma Cells Are Long-Lived Residents of Gut and Bone Marrow That Express Isotype- and Tissue-Specific Gene Expression Patterns. Front Immunol 2021; 12:791095. [PMID: 35003110 PMCID: PMC8739487 DOI: 10.3389/fimmu.2021.791095] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 12/06/2021] [Indexed: 12/12/2022] Open
Abstract
Antibody secreting plasma cells are made in response to a variety of pathogenic and commensal microbes. While all plasma cells express a core gene transcription program that allows them to secrete large quantities of immunoglobulin, unique transcriptional profiles are linked to plasma cells expressing different antibody isotypes. IgA expressing plasma cells are generally thought of as short-lived in mucosal tissues and they have been understudied in systemic sites like the bone marrow. We find that IgA+ plasma cells in both the small intestine lamina propria and the bone marrow are long-lived and transcriptionally related compared to IgG and IgM expressing bone marrow plasma cells. IgA+ plasma cells show signs of shared clonality between the gut and bone marrow, but they do not recirculate at a significant rate and are found within bone marrow plasma cells niches. These data suggest that systemic and mucosal IgA+ plasma cells are from a common source, but they do not migrate between tissues. However, comparison of the plasma cells from the small intestine lamina propria to the bone marrow demonstrate a tissue specific gene transcription program. Understanding how these tissue specific gene networks are regulated in plasma cells could lead to increased understanding of the induction of mucosal versus systemic antibody responses and improve vaccine design.
Collapse
Affiliation(s)
- Joel R. Wilmore
- The Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
- Department of Microbiology and Immunology, State University of New York (SUNY) Upstate Medical University, Syracuse, NY, United States
| | - Brian T. Gaudette
- The Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
| | - Daniela Gómez Atria
- The Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
| | - Rebecca L. Rosenthal
- The Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
| | - Sarah Kim Reiser
- The Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
| | - Wenzhao Meng
- The Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
| | - Aaron M. Rosenfeld
- The Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
| | - Eline T. Luning Prak
- The Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
| | - David Allman
- The Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
| |
Collapse
|
18
|
Bar KJ, Shaw PA, Choi GH, Aqui N, Fesnak A, Yang JB, Soto-Calderon H, Grajales L, Starr J, Andronov M, Mastellone M, Amonu C, Feret G, DeMarshall M, Buchanan M, Caturla M, Gordon J, Wanicur A, Monroy MA, Mampe F, Lindemuth E, Gouma S, Mullin AM, Barilla H, Pronina A, Irwin L, Thomas R, Eichinger RA, Demuth F, Luning Prak ET, Pascual JL, Short WR, Elovitz MA, Baron J, Meyer NJ, Degnan KO, Frank I, Hensley SE, Siegel DL, Tebas P. A randomized controlled study of convalescent plasma for individuals hospitalized with COVID-19 pneumonia. J Clin Invest 2021; 131:e155114. [PMID: 34788233 PMCID: PMC8670841 DOI: 10.1172/jci155114] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 11/01/2021] [Indexed: 11/17/2022] Open
Abstract
BackgroundAntibody-based strategies for COVID-19 have shown promise in prevention and treatment of early disease. COVID-19 convalescent plasma (CCP) has been widely used but results from randomized trials supporting its benefit in hospitalized patients with pneumonia are limited. Here, we assess the efficacy of CCP in severely ill, hospitalized adults with COVID-19 pneumonia.MethodsWe performed a randomized control trial (PennCCP2), with 80 adults hospitalized with COVID-19 pneumonia, comparing up to 2 units of locally sourced CCP plus standard care versus standard care alone. The primary efficacy endpoint was comparison of a clinical severity score. Key secondary outcomes include 14- and 28-day mortality, 14- and 28-day maximum 8-point WHO ordinal score (WHO8) score, duration of supplemental oxygenation or mechanical ventilation, respiratory SARS-CoV-2 RNA, and anti-SARS-CoV-2 antibodies.ResultsEighty hospitalized adults with confirmed COVID-19 pneumonia were enrolled at median day 6 of symptoms and day 1 of hospitalization; 60% were anti-SARS-CoV-2 antibody seronegative. Participants had a median of 3 comorbidities, including risk factors for severe COVID-19 and immunosuppression. CCP treatment was safe and conferred significant benefit by clinical severity score (median [MED] and interquartile range [IQR] 10 [5.5-30] vs. 7 [2.75-12.25], P = 0.037) and 28-day mortality (n = 10, 26% vs. n = 2, 5%; P = 0.013). All other prespecified outcome measures showed weak evidence toward benefit of CCP.ConclusionTwo units of locally sourced CCP administered early in hospitalization to majority seronegative participants conferred a significant benefit in clinical severity score and 28-day mortality. Results suggest CCP may benefit select populations, especially those with comorbidities who are treated early.Trial RegistrationClinicalTrials.gov NCT04397757.FundingUniversity of Pennsylvania.
Collapse
Affiliation(s)
- Katharine J. Bar
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Pamela A. Shaw
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Kaiser Permanente Washington Health Research Group, Seattle, Washington, USA
| | - Grace H. Choi
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Nicole Aqui
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Andrew Fesnak
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jasper B. Yang
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Kaiser Permanente Washington Health Research Group, Seattle, Washington, USA
| | | | - Lizette Grajales
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Julie Starr
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Michelle Andronov
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Miranda Mastellone
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Chigozie Amonu
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Geoff Feret
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Maureen DeMarshall
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Marie Buchanan
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Maria Caturla
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - James Gordon
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Alan Wanicur
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - M. Alexandra Monroy
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Felicity Mampe
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Emily Lindemuth
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Sigrid Gouma
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Anne M. Mullin
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Holly Barilla
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Anastasiya Pronina
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Leah Irwin
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Raeann Thomas
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Risa A. Eichinger
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Faye Demuth
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Eline T. Luning Prak
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jose L. Pascual
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - William R. Short
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Michal A. Elovitz
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jillian Baron
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Nuala J. Meyer
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kathleen O. Degnan
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ian Frank
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Scott E. Hensley
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Donald L. Siegel
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Pablo Tebas
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| |
Collapse
|
19
|
Alameh MG, Tombácz I, Bettini E, Lederer K, Sittplangkoon C, Wilmore JR, Gaudette BT, Soliman OY, Pine M, Hicks P, Manzoni TB, Knox JJ, Johnson JL, Laczkó D, Muramatsu H, Davis B, Meng W, Rosenfeld AM, Strohmeier S, Lin PJC, Mui BL, Tam YK, Karikó K, Jacquet A, Krammer F, Bates P, Cancro MP, Weissman D, Luning Prak ET, Allman D, Locci M, Pardi N. Lipid nanoparticles enhance the efficacy of mRNA and protein subunit vaccines by inducing robust T follicular helper cell and humoral responses. Immunity 2021; 54:2877-2892.e7. [PMID: 34852217 PMCID: PMC8566475 DOI: 10.1016/j.immuni.2021.11.001] [Citation(s) in RCA: 212] [Impact Index Per Article: 70.7] [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: 01/24/2021] [Revised: 07/29/2021] [Accepted: 10/29/2021] [Indexed: 12/15/2022]
Abstract
Adjuvants are critical for improving the quality and magnitude of adaptive immune responses to vaccination. Lipid nanoparticle (LNP)-encapsulated nucleoside-modified mRNA vaccines have shown great efficacy against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), but the mechanism of action of this vaccine platform is not well-characterized. Using influenza virus and SARS-CoV-2 mRNA and protein subunit vaccines, we demonstrated that our LNP formulation has intrinsic adjuvant activity that promotes induction of strong T follicular helper cell, germinal center B cell, long-lived plasma cell, and memory B cell responses that are associated with durable and protective antibodies in mice. Comparative experiments demonstrated that this LNP formulation outperformed a widely used MF59-like adjuvant, AddaVax. The adjuvant activity of the LNP relies on the ionizable lipid component and on IL-6 cytokine induction but not on MyD88- or MAVS-dependent sensing of LNPs. Our study identified LNPs as a versatile adjuvant that enhances the efficacy of traditional and next-generation vaccine platforms.
Collapse
Affiliation(s)
| | - István Tombácz
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Emily Bettini
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Katlyn Lederer
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Chutamath Sittplangkoon
- Center of Excellence in Vaccine Research and Development, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Joel R Wilmore
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Brian T Gaudette
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ousamah Y Soliman
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew Pine
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Philip Hicks
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Tomaz B Manzoni
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - James J Knox
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - John L Johnson
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Dorottya Laczkó
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hiromi Muramatsu
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Benjamin Davis
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Wenzhao Meng
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Aaron M Rosenfeld
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Shirin Strohmeier
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | | | - Ying K Tam
- Acuitas Therapeutics, Vancouver, BC, Canada
| | - Katalin Karikó
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA; BioNTech RNA Pharmaceuticals, Mainz, Germany
| | - Alain Jacquet
- Center of Excellence in Vaccine Research and Development, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Paul Bates
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael P Cancro
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Drew Weissman
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Eline T Luning Prak
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - David Allman
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Michela Locci
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Norbert Pardi
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
20
|
Goel RR, Painter MM, Apostolidis SA, Mathew D, Meng W, Rosenfeld AM, Lundgreen KA, Reynaldi A, Khoury DS, Pattekar A, Gouma S, Kuri-Cervantes L, Hicks P, Dysinger S, Hicks A, Sharma H, Herring S, Korte S, Baxter AE, Oldridge DA, Giles JR, Weirick ME, McAllister CM, Awofolaju M, Tanenbaum N, Drapeau EM, Dougherty J, Long S, D’Andrea K, Hamilton JT, McLaughlin M, Williams JC, Adamski S, Kuthuru O, Frank I, Betts MR, Vella LA, Grifoni A, Weiskopf D, Sette A, Hensley SE, Davenport MP, Bates P, Luning Prak ET, Greenplate AR, Wherry EJ. mRNA vaccines induce durable immune memory to SARS-CoV-2 and variants of concern. Science 2021; 374:abm0829. [PMID: 34648302 PMCID: PMC9284784 DOI: 10.1126/science.abm0829] [Citation(s) in RCA: 490] [Impact Index Per Article: 163.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 10/10/2021] [Indexed: 12/13/2022]
Abstract
The durability of immune memory after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) messenger RNA (mRNA) vaccination remains unclear. In this study, we longitudinally profiled vaccine responses in SARS-CoV-2–naïve and –recovered individuals for 6 months after vaccination. Antibodies declined from peak levels but remained detectable in most subjects at 6 months. By contrast, mRNA vaccines generated functional memory B cells that increased from 3 to 6 months postvaccination, with the majority of these cells cross-binding the Alpha, Beta, and Delta variants. mRNA vaccination further induced antigen-specific CD4+ and CD8+ T cells, and early CD4+ T cell responses correlated with long-term humoral immunity. Recall responses to vaccination in individuals with preexisting immunity primarily increased antibody levels without substantially altering antibody decay rates. Together, these findings demonstrate robust cellular immune memory to SARS-CoV-2 and its variants for at least 6 months after mRNA vaccination.
Collapse
Affiliation(s)
- Rishi R. Goel
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Mark M. Painter
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Sokratis A. Apostolidis
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Division of Rheumatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Divij Mathew
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Wenzhao Meng
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Aaron M. Rosenfeld
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Kendall A. Lundgreen
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Arnold Reynaldi
- Kirby Institute, University of New South Wales, Sydney, NSW, Australia
| | - David S. Khoury
- Kirby Institute, University of New South Wales, Sydney, NSW, Australia
| | - Ajinkya Pattekar
- Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Sigrid Gouma
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Leticia Kuri-Cervantes
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Philip Hicks
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Sarah Dysinger
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Amanda Hicks
- Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Harsh Sharma
- Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Sarah Herring
- Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Scott Korte
- Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Amy E. Baxter
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Derek A. Oldridge
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Josephine R. Giles
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Madison E. Weirick
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Christopher M. McAllister
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Moses Awofolaju
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Nicole Tanenbaum
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Elizabeth M. Drapeau
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Jeanette Dougherty
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Sherea Long
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Kurt D’Andrea
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Jacob T. Hamilton
- Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Maura McLaughlin
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Justine C. Williams
- Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Sharon Adamski
- Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Oliva Kuthuru
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - The UPenn COVID Processing Unit‡
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Division of Rheumatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Kirby Institute, University of New South Wales, Sydney, NSW, Australia
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Division of Infectious Disease, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Division of Infectious Disease, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California San Diego (UCSD), La Jolla, CA, USA
| | - Ian Frank
- Division of Infectious Disease, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Michael R. Betts
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Laura A. Vella
- Division of Infectious Disease, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, USA
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California San Diego (UCSD), La Jolla, CA, USA
| | - Scott E. Hensley
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | | | - Paul Bates
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Eline T. Luning Prak
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Allison R. Greenplate
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - E. John Wherry
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| |
Collapse
|
21
|
Awasthi S, Knox JJ, Desmond A, Alameh MG, Gaudette BT, Lubinski JM, Naughton A, Hook LM, Egan KP, Tam YK, Pardi N, Allman D, Luning Prak ET, Cancro MP, Weissman D, Cohen GH, Friedman HM. Trivalent nucleoside-modified mRNA vaccine yields durable memory B cell protection against genital herpes in preclinical models. J Clin Invest 2021; 131:e152310. [PMID: 34618692 PMCID: PMC8631595 DOI: 10.1172/jci152310] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 10/05/2021] [Indexed: 11/17/2022] Open
Abstract
Nucleoside-modified mRNA vaccines have gained global attention because of COVID-19. We evaluated a similar vaccine approach for preventing a chronic, latent genital infection rather than an acute respiratory infection. We used animal models to compare an HSV-2 trivalent nucleoside-modified mRNA vaccine with the same antigens prepared as proteins, with an emphasis on antigen-specific memory B cell responses and immune correlates of protection. In guinea pigs, serum neutralizing-antibody titers were higher at 1 month and declined far less by 8 months in mRNA- compared with protein-immunized animals. Both vaccines protected against death and genital lesions when infected 1 month after immunization; however, protection was more durable in the mRNA group compared with the protein group when infected after 8 months, an interval representing greater than 15% of the animal's lifespan. Serum and vaginal neutralizing-antibody titers correlated with protection against infection, as measured by genital lesions and vaginal virus titers 2 days after infection. In mice, the mRNA vaccine generated more antigen-specific memory B cells than the protein vaccine at early times after immunization that persisted for up to 1 year. High neutralizing titers and robust B cell immune memory likely explain the more durable protection by the HSV-2 mRNA vaccine.
Collapse
Affiliation(s)
- Sita Awasthi
- Infectious Disease Division, Department of Medicine and
| | - James J. Knox
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Angela Desmond
- Infectious Disease Division, Department of Medicine and
- Infectious Disease Division, Department of Pediatrics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | - Brian T. Gaudette
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | | | | | - Kevin P. Egan
- Infectious Disease Division, Department of Medicine and
| | - Ying K. Tam
- Acuitas Therapeutics Inc., Vancouver, British Columbia, Canada
| | - Norbert Pardi
- Infectious Disease Division, Department of Medicine and
| | - David Allman
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Eline T. Luning Prak
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Michael P. Cancro
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Drew Weissman
- Infectious Disease Division, Department of Medicine and
| | - Gary H. Cohen
- Department of Basic and Translational Sciences, School of Dental Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | |
Collapse
|
22
|
Poon MML, Byington E, Meng W, Kubota M, Matsumoto R, Grifoni A, Weiskopf D, Dogra P, Lam N, Szabo PA, Ural BB, Wells SB, Rosenfeld AM, Brusko MA, Brusko TM, Connors TJ, Sette A, Sims PA, Luning Prak ET, Shen Y, Farber DL. Heterogeneity of human anti-viral immunity shaped by virus, tissue, age, and sex. Cell Rep 2021; 37:110071. [PMID: 34852222 PMCID: PMC8719595 DOI: 10.1016/j.celrep.2021.110071] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [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: 06/25/2021] [Revised: 10/21/2021] [Accepted: 11/05/2021] [Indexed: 12/14/2022] Open
Abstract
The persistence of anti-viral immunity is essential for protection and exhibits profound heterogeneity across individuals. Here, we elucidate the factors that shape maintenance and function of anti-viral T cell immunity in the body by comprehensive profiling of virus-specific T cells across blood, lymphoid organs, and mucosal tissues of organ donors. We use flow cytometry, T cell receptor sequencing, single-cell transcriptomics, and cytokine analysis to profile virus-specific CD8+ T cells recognizing the ubiquitous pathogens influenza and cytomegalovirus. Our results reveal that virus specificity determines overall magnitude, tissue distribution, differentiation, and clonal repertoire of virus-specific T cells. Age and sex influence T cell differentiation and dissemination in tissues, while T cell tissue residence and functionality are highly correlated with the site. Together, our results demonstrate how the covariates of virus, tissue, age, and sex impact the anti-viral immune response, which is important for targeting, monitoring, and predicting immune responses to existing and emerging viruses.
Collapse
Affiliation(s)
- Maya M L Poon
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA; Medical Scientist Training Program, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Eve Byington
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Wenzhao Meng
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Masaru Kubota
- Department of Surgery, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Rei Matsumoto
- Department of Surgery, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Alba Grifoni
- Center of Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Daniela Weiskopf
- Center of Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Pranay Dogra
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Nora Lam
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Peter A Szabo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Basak Burcu Ural
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Steven B Wells
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Aaron M Rosenfeld
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Maigan A Brusko
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Todd M Brusko
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Thomas J Connors
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Alessandro Sette
- Center of Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Peter A Sims
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Eline T Luning Prak
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yufeng Shen
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Donna L Farber
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Surgery, Columbia University Irving Medical Center, New York, NY 10032, USA.
| |
Collapse
|
23
|
Apostolidis SA, Kakara M, Painter MM, Goel RR, Mathew D, Lenzi K, Rezk A, Patterson KR, Espinoza DA, Kadri JC, Markowitz DM, E Markowitz C, Mexhitaj I, Jacobs D, Babb A, Betts MR, Prak ETL, Weiskopf D, Grifoni A, Lundgreen KA, Gouma S, Sette A, Bates P, Hensley SE, Greenplate AR, Wherry EJ, Li R, Bar-Or A. Cellular and humoral immune responses following SARS-CoV-2 mRNA vaccination in patients with multiple sclerosis on anti-CD20 therapy. Nat Med 2021; 27:1990-2001. [PMID: 34522051 PMCID: PMC8604727 DOI: 10.1038/s41591-021-01507-2] [Citation(s) in RCA: 320] [Impact Index Per Article: 106.7] [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: 06/22/2021] [Accepted: 08/16/2021] [Indexed: 02/08/2023]
Abstract
SARS-CoV-2 messenger RNA vaccination in healthy individuals generates immune protection against COVID-19. However, little is known about SARS-CoV-2 mRNA vaccine-induced responses in immunosuppressed patients. We investigated induction of antigen-specific antibody, B cell and T cell responses longitudinally in patients with multiple sclerosis (MS) on anti-CD20 antibody monotherapy (n = 20) compared with healthy controls (n = 10) after BNT162b2 or mRNA-1273 mRNA vaccination. Treatment with anti-CD20 monoclonal antibody (aCD20) significantly reduced spike-specific and receptor-binding domain (RBD)-specific antibody and memory B cell responses in most patients, an effect ameliorated with longer duration from last aCD20 treatment and extent of B cell reconstitution. By contrast, all patients with MS treated with aCD20 generated antigen-specific CD4 and CD8 T cell responses after vaccination. Treatment with aCD20 skewed responses, compromising circulating follicular helper T (TFH) cell responses and augmenting CD8 T cell induction, while preserving type 1 helper T (TH1) cell priming. Patients with MS treated with aCD20 lacking anti-RBD IgG had the most severe defect in circulating TFH responses and more robust CD8 T cell responses. These data define the nature of the SARS-CoV-2 vaccine-induced immune landscape in aCD20-treated patients and provide insights into coordinated mRNA vaccine-induced immune responses in humans. Our findings have implications for clinical decision-making and public health policy for immunosuppressed patients including those treated with aCD20.
Collapse
Grants
- U19AI082630 U.S. Department of Health & Human Services | NIH | Office of Extramural Research, National Institutes of Health (OER)
- T32 AR076951 NIAMS NIH HHS
- AI082630 U.S. Department of Health & Human Services | NIH | Office of Extramural Research, National Institutes of Health (OER)
- R21 AI142638 NIAID NIH HHS
- AI108545 U.S. Department of Health & Human Services | NIH | Office of Extramural Research, National Institutes of Health (OER)
- R01 AI152236 NIAID NIH HHS
- 75N9301900065 U.S. Department of Health & Human Services | NIH | Office of Extramural Research, National Institutes of Health (OER)
- AI149680 U.S. Department of Health & Human Services | NIH | Office of Extramural Research, National Institutes of Health (OER)
- T32 CA009140 NCI NIH HHS
- R01 AI118694 NIAID NIH HHS
- U19 AI082630 NIAID NIH HHS
- AI152236 U.S. Department of Health & Human Services | NIH | Office of Extramural Research, National Institutes of Health (OER)
- P30-AI0450080 U.S. Department of Health & Human Services | NIH | Office of Extramural Research, National Institutes of Health (OER)
- T32 AR076951-01 U.S. Department of Health & Human Services | NIH | National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS)
- R01 AI105343 NIAID NIH HHS
- AI105343 U.S. Department of Health & Human Services | NIH | Office of Extramural Research, National Institutes of Health (OER)
- R01 AI155577 NIAID NIH HHS
- UM1 AI144288 NIAID NIH HHS
- U19 AI149680 NIAID NIH HHS
- AI155577 U.S. Department of Health & Human Services | NIH | Office of Extramural Research, National Institutes of Health (OER)
- SI-2011-37160 National Multiple Sclerosis Society (National MS Society)
- UC4 DK112217 NIDDK NIH HHS
- P01 AI108545 NIAID NIH HHS
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)
- Penn | Perelman School of Medicine, University of Pennsylvania (Perelman School of Medicine at the University of Pennsylvania)
Collapse
Affiliation(s)
- Sokratis A Apostolidis
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Division of Rheumatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Mihir Kakara
- Center for Neuroinflammation and Experimental Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Mark M Painter
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Rishi R Goel
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Divij Mathew
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Kerry Lenzi
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Ayman Rezk
- Center for Neuroinflammation and Experimental Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Kristina R Patterson
- Center for Neuroinflammation and Experimental Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Diego A Espinoza
- Center for Neuroinflammation and Experimental Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Immunology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jessy C Kadri
- Center for Neuroinflammation and Experimental Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Daniel M Markowitz
- Center for Neuroinflammation and Experimental Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Clyde E Markowitz
- Center for Neuroinflammation and Experimental Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Ina Mexhitaj
- Center for Neuroinflammation and Experimental Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Dina Jacobs
- Center for Neuroinflammation and Experimental Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Allison Babb
- Center for Neuroinflammation and Experimental Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Michael R Betts
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Eline T Luning Prak
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Kendall A Lundgreen
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Penn Center for Research on Coronavirus and Other Emerging Pathogens, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Sigrid Gouma
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California San Diego, La Jolla, CA, USA
| | - Paul Bates
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Penn Center for Research on Coronavirus and Other Emerging Pathogens, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Scott E Hensley
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Allison R Greenplate
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - E John Wherry
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
| | - Rui Li
- Center for Neuroinflammation and Experimental Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
| | - Amit Bar-Or
- Center for Neuroinflammation and Experimental Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
| |
Collapse
|
24
|
Chang SE, Feng A, Meng W, Apostolidis SA, Mack E, Artandi M, Barman L, Bennett K, Chakraborty S, Chang I, Cheung P, Chinthrajah S, Dhingra S, Do E, Finck A, Gaano A, Geßner R, Giannini HM, Gonzalez J, Greib S, Gündisch M, Hsu AR, Kuo A, Manohar M, Mao R, Neeli I, Neubauer A, Oniyide O, Powell AE, Puri R, Renz H, Schapiro J, Weidenbacher PA, Wittman R, Ahuja N, Chung HR, Jagannathan P, James JA, Kim PS, Meyer NJ, Nadeau KC, Radic M, Robinson WH, Singh U, Wang TT, Wherry EJ, Skevaki C, Luning Prak ET, Utz PJ. New-onset IgG autoantibodies in hospitalized patients with COVID-19. Nat Commun 2021; 12:5417. [PMID: 34521836 PMCID: PMC8440763 DOI: 10.1038/s41467-021-25509-3] [Citation(s) in RCA: 214] [Impact Index Per Article: 71.3] [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: 02/02/2021] [Accepted: 08/09/2021] [Indexed: 02/08/2023] Open
Abstract
COVID-19 is associated with a wide range of clinical manifestations, including autoimmune features and autoantibody production. Here we develop three protein arrays to measure IgG autoantibodies associated with connective tissue diseases, anti-cytokine antibodies, and anti-viral antibody responses in serum from 147 hospitalized COVID-19 patients. Autoantibodies are identified in approximately 50% of patients but in less than 15% of healthy controls. When present, autoantibodies largely target autoantigens associated with rare disorders such as myositis, systemic sclerosis and overlap syndromes. A subset of autoantibodies targeting traditional autoantigens or cytokines develop de novo following SARS-CoV-2 infection. Autoantibodies track with longitudinal development of IgG antibodies recognizing SARS-CoV-2 structural proteins and a subset of non-structural proteins, but not proteins from influenza, seasonal coronaviruses or other pathogenic viruses. We conclude that SARS-CoV-2 causes development of new-onset IgG autoantibodies in a significant proportion of hospitalized COVID-19 patients and are positively correlated with immune responses to SARS-CoV-2 proteins.
Collapse
Affiliation(s)
- Sarah Esther Chang
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Allan Feng
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Wenzhao Meng
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sokratis A Apostolidis
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Elisabeth Mack
- Department of Hematology, Oncology, Immunology, Philipps University Marburg, Marburg, Germany
| | - Maja Artandi
- Department of Medicine, Division of Primary Care and Population Health, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Stanford CROWN Clinic, Stanford University School of Medicine, Stanford, CA, USA
| | - Linda Barman
- Department of Medicine, Division of Primary Care and Population Health, Stanford University School of Medicine, Stanford, CA, USA
| | - Kate Bennett
- Molecular Pathology and Imaging Core, Department of Medicine, Gastroenterology Division, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Saborni Chakraborty
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Iris Chang
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, CA, USA
| | - Peggie Cheung
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Sharon Chinthrajah
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, CA, USA
| | - Shaurya Dhingra
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Evan Do
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, CA, USA
| | - Amanda Finck
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrew Gaano
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Reinhard Geßner
- Institute of Laboratory Medicine, Philipps University Marburg, Marburg, Germany
| | - Heather M Giannini
- Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Joyce Gonzalez
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sarah Greib
- Institute of Laboratory Medicine, Philipps University Marburg, Marburg, Germany
| | - Margrit Gündisch
- Institute of Laboratory Medicine, Philipps University Marburg, Marburg, Germany
| | - Alex Ren Hsu
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Alex Kuo
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Monali Manohar
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Rong Mao
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Indira Neeli
- Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Andreas Neubauer
- Department of Hematology, Oncology, Immunology, Philipps University Marburg, Marburg, Germany
| | - Oluwatosin Oniyide
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Abigail E Powell
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- ChEM-H, Stanford University, Stanford, USA
| | - Rajan Puri
- Department of Medicine, Division of Primary Care and Population Health, Stanford University School of Medicine, Stanford, CA, USA
| | - Harald Renz
- Institute of Laboratory Medicine, Philipps University Marburg, Marburg, Germany
- Member of the Universities of Giessen and Marburg Lung Center (UGMLC), and the German Center for Lung Research (DZL), Giessen, Germany
| | - Jeffrey Schapiro
- TPMG Regional Reference Laboratory, Kaiser Permanente Northern California, Berkeley, CA, USA
| | - Payton A Weidenbacher
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- ChEM-H, Stanford University, Stanford, USA
| | - Richard Wittman
- Department of Medicine, Division of Primary Care and Population Health, Stanford University School of Medicine, Stanford, CA, USA
| | - Neera Ahuja
- Department of Medicine, Division of Hospital Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Ho-Ryun Chung
- Institute for Medical Bioinformatics and Biostatistics, Philipps University Marburg, Marburg, Germany
| | - Prasanna Jagannathan
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Judith A James
- Arthritis & Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Peter S Kim
- Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Nuala J Meyer
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kari C Nadeau
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, CA, USA
| | - Marko Radic
- Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - William H Robinson
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- VA Palo Alto Health Care System, Palo Alto, CA, USA
| | - Upinder Singh
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Taia T Wang
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - E John Wherry
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Chrysanthi Skevaki
- Institute of Laboratory Medicine, Philipps University Marburg, Marburg, Germany.
- Member of the Universities of Giessen and Marburg Lung Center (UGMLC), and the German Center for Lung Research (DZL), Giessen, Germany.
| | - Eline T Luning Prak
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Paul J Utz
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA.
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA.
| |
Collapse
|
25
|
Agarwal D, Luning Prak ET, Bharani T, Everly M, Migone TS, Cancro M, Allman D, Choe I, Kearns JD, Trofe-Clark J, Naji A, Kamoun M. BLyS neutralization results in selective anti-HLA alloantibody depletion without successful desensitization. Transpl Immunol 2021; 69:101465. [PMID: 34506905 DOI: 10.1016/j.trim.2021.101465] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 08/21/2021] [Revised: 09/05/2021] [Accepted: 09/05/2021] [Indexed: 11/15/2022]
Abstract
Pre-existing anti-HLA allo-antibodies (allo-Abs) are a major barrier to successful kidney transplantation, resulting in an elevated risk for antibody-mediated rejection (AMR) and eventual graft loss. The cytokine B lymphocyte stimulator (BLyS) promotes B cell maturation and plasma cell survival; consequently, anti-BLyS therapy represents a potential therapeutic opportunity in diminishing pre-existing allo-Abs. Here we report that in our 1-year pilot trial, BLyS neutralization failed to reduce total anti-HLA allo-Ab levels in highly sensitized candidates awaiting kidney transplant in a clinically meaningful way. Additionally, we performed a post hoc analysis using sera from trial candidates which revealed selective depletion of anti-HLA class I and class II Abs in response to belimumab treatment, restricted to certain allele specificities and IgG subclasses. Altogether, we observed that BLyS blockade only results in selective depletion of anti-HLA Abs recognizing a few discrete HLA allele specificities.
Collapse
Affiliation(s)
- Divyansh Agarwal
- Department of Surgery, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Surgery, Division of Transplantation, Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Eline T Luning Prak
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Tina Bharani
- Department of General Surgery, Thomas Jefferson University Hospital, Philadelphia, PA 19107, USA
| | | | - Thi-Sau Migone
- Iconic Therapeutics, Shoreline Court, South San Francisco, CA 94080, USA
| | - Michael Cancro
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - David Allman
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Insuk Choe
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jane D Kearns
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jennifer Trofe-Clark
- Department of Pharmacy Services, Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA.; Department of Medicine, Division of Renal, Electrolyte and Hypertension, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ali Naji
- Department of Surgery, Division of Transplantation, Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Malek Kamoun
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| |
Collapse
|
26
|
Goel RR, Painter MM, Apostolidis SA, Mathew D, Meng W, Rosenfeld AM, Lundgreen KA, Reynaldi A, Khoury DS, Pattekar A, Gouma S, Kuri-Cervantes L, Hicks P, Dysinger S, Hicks A, Sharma H, Herring S, Korte S, Baxter AE, Oldridge DA, Giles JR, Weirick ME, McAllister CM, Awofolaju M, Tanenbaum N, Drapeau EM, Dougherty J, Long S, D’Andrea K, Hamilton JT, McLaughlin M, Williams JC, Adamski S, Kuthuru O, Frank I, Betts MR, Vella LA, Grifoni A, Weiskopf D, Sette A, Hensley SE, Davenport MP, Bates P, Luning Prak ET, Greenplate AR, Wherry EJ. mRNA Vaccination Induces Durable Immune Memory to SARS-CoV-2 with Continued Evolution to Variants of Concern. bioRxiv 2021:2021.08.23.457229. [PMID: 34462751 PMCID: PMC8404899 DOI: 10.1101/2021.08.23.457229] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [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: 01/19/2023]
Abstract
SARS-CoV-2 mRNA vaccines have shown remarkable efficacy, especially in preventing severe illness and hospitalization. However, the emergence of several variants of concern and reports of declining antibody levels have raised uncertainty about the durability of immune memory following vaccination. In this study, we longitudinally profiled both antibody and cellular immune responses in SARS-CoV-2 naïve and recovered individuals from pre-vaccine baseline to 6 months post-mRNA vaccination. Antibody and neutralizing titers decayed from peak levels but remained detectable in all subjects at 6 months post-vaccination. Functional memory B cell responses, including those specific for the receptor binding domain (RBD) of the Alpha (B.1.1.7), Beta (B.1.351), and Delta (B.1.617.2) variants, were also efficiently generated by mRNA vaccination and continued to increase in frequency between 3 and 6 months post-vaccination. Notably, most memory B cells induced by mRNA vaccines were capable of cross-binding variants of concern, and B cell receptor sequencing revealed significantly more hypermutation in these RBD variant-binding clones compared to clones that exclusively bound wild-type RBD. Moreover, the percent of variant cross-binding memory B cells was higher in vaccinees than individuals who recovered from mild COVID-19. mRNA vaccination also generated antigen-specific CD8+ T cells and durable memory CD4+ T cells in most individuals, with early CD4+ T cell responses correlating with humoral immunity at later timepoints. These findings demonstrate robust, multi-component humoral and cellular immune memory to SARS-CoV-2 and current variants of concern for at least 6 months after mRNA vaccination. Finally, we observed that boosting of pre-existing immunity with mRNA vaccination in SARS-CoV-2 recovered individuals primarily increased antibody responses in the short-term without significantly altering antibody decay rates or long-term B and T cell memory. Together, this study provides insights into the generation and evolution of vaccine-induced immunity to SARS-CoV-2, including variants of concern, and has implications for future booster strategies.
Collapse
Affiliation(s)
- Rishi R. Goel
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USAs
| | - Mark M. Painter
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USAs
| | - Sokratis A. Apostolidis
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USAs
- Division of Rheumatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Divij Mathew
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USAs
| | - Wenzhao Meng
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Aaron M. Rosenfeld
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Kendall A. Lundgreen
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Arnold Reynaldi
- Kirby Institute, University of New South Wales, Sydney, Australia
| | - David S. Khoury
- Kirby Institute, University of New South Wales, Sydney, Australia
| | - Ajinkya Pattekar
- Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USAs
| | - Sigrid Gouma
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Leticia Kuri-Cervantes
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Philip Hicks
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Sarah Dysinger
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Amanda Hicks
- Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USAs
| | - Harsh Sharma
- Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USAs
| | - Sarah Herring
- Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USAs
| | - Scott Korte
- Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USAs
| | - Amy E. Baxter
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Derek A. Oldridge
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Josephine R. Giles
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Madison E. Weirick
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Christopher M. McAllister
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Moses Awofolaju
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Nicole Tanenbaum
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Elizabeth M. Drapeau
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Jeanette Dougherty
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Sherea Long
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Kurt D’Andrea
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Jacob T. Hamilton
- Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USAs
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Maura McLaughlin
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Justine C. Williams
- Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USAs
| | - Sharon Adamski
- Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USAs
| | - Oliva Kuthuru
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | | | - Ian Frank
- Division of Infectious Disease, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Michael R. Betts
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Laura A. Vella
- Division of Infectious Disease, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, USA
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, USA
| | - Scott E. Hensley
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | | | - Paul Bates
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Eline T. Luning Prak
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Allison R. Greenplate
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USAs
| | - E. John Wherry
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USAs
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| |
Collapse
|
27
|
Japp AS, Meng W, Rosenfeld AM, Perry DJ, Thirawatananond P, Bacher RL, Liu C, Gardner JS, Atkinson MA, Kaestner KH, Brusko TM, Naji A, Luning Prak ET, Betts MR. TCR +/BCR + dual-expressing cells and their associated public BCR clonotype are not enriched in type 1 diabetes. Cell 2021; 184:827-839.e14. [PMID: 33545036 DOI: 10.1016/j.cell.2020.11.035] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 06/30/2020] [Accepted: 11/19/2020] [Indexed: 12/20/2022]
Abstract
Ahmed and colleagues recently described a novel hybrid lymphocyte expressing both a B and T cell receptor, termed double expresser (DE) cells. DE cells in blood of type 1 diabetes (T1D) subjects were present at increased numbers and enriched for a public B cell clonotype. Here, we attempted to reproduce these findings. While we could identify DE cells by flow cytometry, we found no association between DE cell frequency and T1D status. We were unable to identify the reported public B cell clone, or any similar clone, in bulk B cells or sorted DE cells from T1D subjects or controls. We also did not observe increased usage of the public clone VH or DH genes in B cells or in sorted DE cells. Taken together, our findings suggest that DE cells and their alleged public clonotype are not enriched in T1D. This Matters Arising paper is in response to Ahmed et al. (2019), published in Cell. See also the response by Ahmed et al. (2021), published in this issue.
Collapse
Affiliation(s)
- Alberto Sada Japp
- Department of Microbiology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA; Institute for Immunology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Wenzhao Meng
- Institute for Immunology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Aaron M Rosenfeld
- Institute for Immunology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Daniel J Perry
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida Diabetes Institute, College of Medicine, Gainesville, FL 32610, USA
| | - Puchong Thirawatananond
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida Diabetes Institute, College of Medicine, Gainesville, FL 32610, USA
| | - Rhonda L Bacher
- Department of Biostatistics, University of Florida, College of Medicine, Gainesville, FL 32610, USA
| | - Chengyang Liu
- Institute for Immunology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Surgery, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jay S Gardner
- Department of Microbiology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA; Institute for Immunology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | -
- The Human Pancreas Analysis Program, Perelman School of Medicine, Philadelphia, PA 19104
| | - Mark A Atkinson
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida Diabetes Institute, College of Medicine, Gainesville, FL 32610, USA
| | - Klaus H Kaestner
- Department of Genetics and Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104
| | - Todd M Brusko
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida Diabetes Institute, College of Medicine, Gainesville, FL 32610, USA
| | - Ali Naji
- Institute for Immunology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Surgery, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Eline T Luning Prak
- Institute for Immunology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA.
| | - Michael R Betts
- Department of Microbiology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA; Institute for Immunology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA.
| |
Collapse
|
28
|
Ricker E, Manni M, Flores-Castro D, Jenkins D, Gupta S, Rivera-Correa J, Meng W, Rosenfeld AM, Pannellini T, Bachu M, Chinenov Y, Sculco PK, Jessberger R, Prak ETL, Pernis AB. Altered function and differentiation of age-associated B cells contribute to the female bias in lupus mice. Nat Commun 2021; 12:4813. [PMID: 34376664 PMCID: PMC8355159 DOI: 10.1038/s41467-021-25102-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [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: 10/15/2020] [Accepted: 07/15/2021] [Indexed: 12/11/2022] Open
Abstract
Differences in immune responses to viruses and autoimmune diseases such as systemic lupus erythematosus (SLE) can show sexual dimorphism. Age-associated B cells (ABC) are a population of CD11c+T-bet+ B cells critical for antiviral responses and autoimmune disorders. Absence of DEF6 and SWAP-70, two homologous guanine exchange factors, in double-knock-out (DKO) mice leads to a lupus-like syndrome in females marked by accumulation of ABCs. Here we demonstrate that DKO ABCs show sex-specific differences in cell number, upregulation of an ISG signature, and further differentiation. DKO ABCs undergo oligoclonal expansion and differentiate into both CD11c+ and CD11c- effector B cell populations with pathogenic and pro-inflammatory function as demonstrated by BCR sequencing and fate-mapping experiments. Tlr7 duplication in DKO males overrides the sex-bias and further augments the dissemination and pathogenicity of ABCs, resulting in severe pulmonary inflammation and early mortality. Thus, sexual dimorphism shapes the expansion, function and differentiation of ABCs that accompanies TLR7-driven immunopathogenesis.
Collapse
Affiliation(s)
- Edd Ricker
- Autoimmunity and Inflammation Program, Hospital for Special Surgery, New York, NY, USA
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Michela Manni
- Autoimmunity and Inflammation Program, Hospital for Special Surgery, New York, NY, USA
| | - Danny Flores-Castro
- Autoimmunity and Inflammation Program, Hospital for Special Surgery, New York, NY, USA
| | - Daniel Jenkins
- Autoimmunity and Inflammation Program, Hospital for Special Surgery, New York, NY, USA
| | - Sanjay Gupta
- Autoimmunity and Inflammation Program, Hospital for Special Surgery, New York, NY, USA
| | - Juan Rivera-Correa
- Autoimmunity and Inflammation Program, Hospital for Special Surgery, New York, NY, USA
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Wenzhao Meng
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, Philadelphia, PA, USA
| | - Aaron M Rosenfeld
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, Philadelphia, PA, USA
| | - Tania Pannellini
- Research Division and Precision Medicine Laboratory, Hospital for Special Surgery, New York, NY, USA
| | - Mahesh Bachu
- Arthritis and Tissue Degeneration Program, Hospital for Special Surgery, New York, NY, USA
| | - Yurii Chinenov
- David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, USA
| | - Peter K Sculco
- Department of Orthopedic Surgery, Hospital for Special Surgery, New York, NY, USA
| | - Rolf Jessberger
- Institute of Physiological Chemistry, Technische Universitat, Dresden, Germany
| | - Eline T Luning Prak
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, Philadelphia, PA, USA
| | - Alessandra B Pernis
- Autoimmunity and Inflammation Program, Hospital for Special Surgery, New York, NY, USA.
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA.
- David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, USA.
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
| |
Collapse
|
29
|
de Mattos Barbosa MG, Lefferts AR, Huynh D, Liu H, Zhang Y, Fu B, Barnes J, Samaniego M, Bram RJ, Geha R, Shikanov A, Luning Prak ET, Farkash EA, Platt JL, Cascalho M. TNFRSF13B genotypes control immune-mediated pathology by regulating the functions of innate B cells. JCI Insight 2021; 6:e150483. [PMID: 34283811 PMCID: PMC8492324 DOI: 10.1172/jci.insight.150483] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 04/14/2021] [Accepted: 07/14/2021] [Indexed: 11/20/2022] Open
Abstract
Host genes define the severity of inflammation and immunity but specific loci doing so are unknown. Here we show that TNF receptor superfamily member 13B (TNFRSF13B) variants, which enhance defense against certain pathogens, also control immune-mediated injury of transplants, by regulating innate B cells’ functions. Analysis of TNFRSF13B in human kidney transplant recipients revealed that 33% of those with antibody-mediated rejection (AMR) but fewer than 6% of those with stable graft function had TNFRSF13B missense mutations. To explore mechanisms underlying aggressive immune responses, we investigated alloimmunity and rejection in mice. Cardiac allografts in Tnfrsf13b-mutant mice underwent early and severe AMR. The dominance and precocity of AMR in Tnfrsf13b-deficient mice were not caused by increased alloantibodies. Rather, Tnfrsf13b mutations decreased “natural” IgM and compromised complement regulation, leading to complement deposition in allografted hearts and autogenous kidneys. Thus, WT TNFRSF13B and Tnfrsf13b support innate B cell functions that limit complement-associated inflammation; in contrast, common variants of these genes intensify inflammatory responses that help clear microbial infections but allow inadvertent tissue injury to ensue. The wide variation in inflammatory reactions associated with TNFRSF13B diversity suggests polymorphisms could underlie variation in host defense and explosive inflammatory responses that sometimes enhance morbidity associated with immune responses.
Collapse
Affiliation(s)
| | - Adam R Lefferts
- Department of Surgery, University of Michigan, Ann Arbor, United States of America
| | - Daniel Huynh
- Department of Surgery, University of Michigan, Ann Arbor, United States of America
| | - Hui Liu
- Department of Surgery, University of Michigan, Ann Arbor, United States of America
| | - Yu Zhang
- Department of Surgery, University of Michigan, Ann Arbor, United States of America
| | - Beverly Fu
- Department of Surgery, University of Michigan, Ann Arbor, United States of America
| | - Jenna Barnes
- Department of Pathology, University of Michigan, Ann Arbor, United States of America
| | - Milagros Samaniego
- Department of Medicine, University of Michigan, Ann Arbor, United States of America
| | - Richard J Bram
- Department of Pediatric and Adolescent Medicine, Mayo Clinic/Foundation, Rochester, United States of America
| | - Raif Geha
- Division of Immunology, Department of Pediatrics, Harvard Medical School, Boston, United States of America
| | - Ariella Shikanov
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, United States of America
| | - Eline T Luning Prak
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, United States of America
| | - Evan A Farkash
- Department of Pathology, University of Michigan, Ann Arbor, United States of America
| | - Jeffrey L Platt
- Transplantation Biology, University of Michigan, Ann Arbor, United States of America
| | - Marilia Cascalho
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, United States of America
| |
Collapse
|
30
|
Miron M, Meng W, Rosenfeld AM, Dvorkin S, Poon MML, Lam N, Kumar BV, Louzoun Y, Luning Prak ET, Farber DL. Maintenance of the human memory T cell repertoire by subset and tissue site. Genome Med 2021; 13:100. [PMID: 34127056 PMCID: PMC8204429 DOI: 10.1186/s13073-021-00918-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 06/01/2021] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Immune-mediated protection is mediated by T cells expressing pathogen-specific T cell antigen receptors (TCR) that are maintained at diverse sites of infection as tissue-resident memory T cells (TRM) or that disseminate as circulating effector-memory (TEM), central memory (TCM), or terminal effector (TEMRA) subsets in blood and tissues. The relationship between circulating and tissue resident T cell subsets in humans remains elusive, and is important for promoting site-specific protective immunity. METHODS We analyzed the TCR repertoire of the major memory CD4+ and CD8+T cell subsets (TEM, TCM, TEMRA, and TRM) isolated from blood and/or lymphoid organs (spleen, lymph nodes, bone marrow) and lungs of nine organ donors, and blood of three living individuals spanning five decades of life. High-throughput sequencing of the variable (V) portion of individual TCR genes for each subset, tissue, and individual were analyzed for clonal diversity, expansion and overlap between lineage, T cell subsets, and anatomic sites. TCR repertoires were further analyzed for TRBV gene usage and CDR3 edit distance. RESULTS Across blood, lymphoid organs, and lungs, human memory, and effector CD8+T cells exhibit greater clonal expansion and distinct TRBV usage compared to CD4+T cell subsets. Extensive sharing of clones between tissues was observed for CD8+T cells; large clones specific to TEMRA cells were present in all sites, while TEM cells contained clones shared between sites and with TRM. For CD4+T cells, TEM clones exhibited the most sharing between sites, followed by TRM, while TCM clones were diverse with minimal sharing between sites and subsets. Within sites, TRM clones exhibited tissue-specific expansions, and maintained clonal diversity with age, compared to age-associated clonal expansions in circulating memory subsets. Edit distance analysis revealed tissue-specific biases in clonal similarity. CONCLUSIONS Our results show that the human memory T cell repertoire comprises clones which persist across sites and subsets, along with clones that are more restricted to certain subsets and/or tissue sites. We also provide evidence that the tissue plays a key role in maintaining memory T cells over age, bolstering the rationale for site-specific targeting of memory reservoirs in vaccines and immunotherapies.
Collapse
Affiliation(s)
- Michelle Miron
- grid.21729.3f0000000419368729Department of Microbiology and Immunology, Columbia University, New York, NY USA ,grid.21729.3f0000000419368729Columbia Center for Translational Immunology, Columbia University, New York, NY USA
| | - Wenzhao Meng
- grid.25879.310000 0004 1936 8972Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - Aaron M. Rosenfeld
- grid.25879.310000 0004 1936 8972Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - Shirit Dvorkin
- grid.22098.310000 0004 1937 0503Department of Mathematics, Bar Ilan University, Ramat Gan, Israel
| | - Maya Meimei Li Poon
- grid.21729.3f0000000419368729Department of Microbiology and Immunology, Columbia University, New York, NY USA
| | - Nora Lam
- grid.21729.3f0000000419368729Department of Microbiology and Immunology, Columbia University, New York, NY USA ,grid.21729.3f0000000419368729Department of Pathology and Cell Biology, Columbia University, New York, NY USA
| | - Brahma V. Kumar
- grid.21729.3f0000000419368729Columbia Center for Translational Immunology, Columbia University, New York, NY USA
| | - Yoram Louzoun
- grid.22098.310000 0004 1937 0503Department of Mathematics, Bar Ilan University, Ramat Gan, Israel
| | - Eline T. Luning Prak
- grid.25879.310000 0004 1936 8972Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - Donna L. Farber
- grid.21729.3f0000000419368729Department of Microbiology and Immunology, Columbia University, New York, NY USA ,grid.21729.3f0000000419368729Department of Surgery, Columbia University, New York, NY USA
| |
Collapse
|
31
|
Trück J, Eugster A, Barennes P, Tipton CM, Luning Prak ET, Bagnara D, Soto C, Sherkow JS, Payne AS, Lefranc MP, Farmer A, Bostick M, Mariotti-Ferrandiz E. Biological controls for standardization and interpretation of adaptive immune receptor repertoire profiling. eLife 2021; 10:66274. [PMID: 34037521 PMCID: PMC8154019 DOI: 10.7554/elife.66274] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 05/15/2021] [Indexed: 12/15/2022] Open
Abstract
Use of adaptive immune receptor repertoire sequencing (AIRR-seq) has become widespread, providing new insights into the immune system with potential broad clinical and diagnostic applications. However, like many high-throughput technologies, it comes with several problems, and the AIRR Community was established to understand and help solve them. We, the AIRR Community’s Biological Resources Working Group, have surveyed scientists about the need for standards and controls in generating and annotating AIRR-seq data. Here, we review the current status of AIRR-seq, provide the results of our survey, and based on them, offer recommendations for developing AIRR-seq standards and controls, including future work.
Collapse
Affiliation(s)
- Johannes Trück
- University Children's Hospital and the Children's Research Center, University of Zurich, Zurich, Switzerland
| | - Anne Eugster
- CRTD Center for Regenerative Therapies Dresden, Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Pierre Barennes
- Sorbonne Université U959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France.,AP-HP Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi), Paris, France
| | - Christopher M Tipton
- Lowance Center for Human Immunology, Emory University School of Medicine, Atlanta, United States
| | - Eline T Luning Prak
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Davide Bagnara
- University of Genoa, Department of Experimental Medicine, Genoa, Italy
| | - Cinque Soto
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, United States.,Department of Pediatrics, Vanderbilt University Medical Center, Nashville, United States
| | - Jacob S Sherkow
- College of Law, University of Illinois, Champaign, United States.,Center for Advanced Studies in Biomedical Innovation Law, University of Copenhagen Faculty of Law, Copenhagen, Denmark.,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States
| | - Aimee S Payne
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Marie-Paule Lefranc
- IMGT, The International ImMunoGeneTics Information System (IMGT), Laboratoire d'ImmunoGénétique Moléculaire (LIGM), Institut de Génétique Humaine (IGH), CNRS, University of Montpellier, Montpellier, France.,Laboratoire d'ImmunoGénétique Moléculaire (LIGM) CNRS, University of Montpellier, Montpellier, France.,Institut de Génétique Humaine (IGH), CNRS, University of Montpellier, Montpellier, France
| | | | | | | | | |
Collapse
|
32
|
de Mattos Barbosa MG, Liu H, Huynh D, Shelley G, Keller ET, Emmer BT, Sherman E, Ginsburg D, Kennedy AA, Tai AW, Wobus C, Mirabeli C, Lanigan TM, Samaniego M, Meng W, Rosenfeld AM, Prak ETL, Platt JL, Cascalho M. IgV somatic mutation of human anti-SARS-CoV-2 monoclonal antibodies governs neutralization and breadth of reactivity. JCI Insight 2021; 6:147386. [PMID: 33769311 PMCID: PMC8262290 DOI: 10.1172/jci.insight.147386] [Citation(s) in RCA: 10] [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: 01/04/2021] [Accepted: 03/24/2021] [Indexed: 12/24/2022] Open
Abstract
Abs that neutralize SARS-CoV-2 are thought to provide the most immediate and effective treatment for those severely afflicted by this virus. Because coronavirus potentially diversifies by mutation, broadly neutralizing Abs are especially sought. Here, we report a possibly novel approach to rapid generation of potent broadly neutralizing human anti-SARS-CoV-2 Abs. We isolated SARS-CoV-2 spike protein-specific memory B cells by panning from the blood of convalescent subjects after infection with SARS-CoV-2 and sequenced and expressed Ig genes from individual B cells as human mAbs. All of 43 human mAbs generated in this way neutralized SARS-CoV-2. Eighteen of the forty-three human mAbs exhibited half-maximal inhibitory concentrations (IC50) of 6.7 × 10-12 M to 6.7 × 10-15 M for spike-pseudotyped virus. Seven of the human mAbs also neutralized (with IC50 < 6.7 × 10-12 M) viruses pseudotyped with mutant spike proteins (including receptor-binding domain mutants and the S1 C-terminal D614G mutant). Neutralization of the Wuhan Hu-1 founder strain and of some variants decreased when coding sequences were reverted to germline, suggesting that potency of neutralization was acquired by somatic hypermutation and selection of B cells. These results indicate that infection with SARS-CoV-2 evokes high-affinity B cell responses, some products of which are broadly neutralizing and others highly strain specific. We also identify variants that would potentially resist immunity evoked by infection with the Wuhan Hu-1 founder strain or by vaccines developed with products of that strain, suggesting evolutionary courses that SARS-CoV-2 could take.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Emily Sherman
- Department of Internal Medicine
- Life Sciences Institute
| | - David Ginsburg
- Department of Internal Medicine
- Life Sciences Institute
- Departments of Human Genetics and Pediatrics and Howard Hughes Medical Institute
| | | | | | | | | | - Thomas M. Lanigan
- Department of Internal Medicine
- Vector Core, Biomedical Research Core Facilities, University of Michigan, Ann Arbor, Michigan, USA
| | - Milagros Samaniego
- Department of Medicine, Henry Ford Health Systems, Detroit, Michigan, USA
| | - Wenzhao Meng
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Aaron M. Rosenfeld
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Eline T. Luning Prak
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jeffrey L. Platt
- Department of Surgery
- Department of Microbiology and Immunology, and
| | - Marilia Cascalho
- Department of Surgery
- Department of Microbiology and Immunology, and
| |
Collapse
|
33
|
Nelson ND, Meng W, Rosenfeld AM, Bullman S, Sekhar Pedamallu C, Nomburg JL, Wertheim GB, Paessler ME, Pinkus G, Hornick JL, Meyerson M, Luning Prak ET, Pillai V. Characterization of Plasmacytoid Dendritic Cells, Microbial Sequences, and Identification of a Candidate Public T-Cell Clone in Kikuchi-Fujimoto Disease. Pediatr Dev Pathol 2021; 24:193-205. [PMID: 33530869 DOI: 10.1177/1093526620987961] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
OBJECTIVES Kikuchi-Fujimoto disease (KFD) is a self-limited lymphadenitis of unclear etiology. We aimed to further characterize this disease in pediatric patients, including evaluation of the CD123 immunohistochemical (IHC) staining and investigation of potential immunologic and infectious causes. METHODS Seventeen KFD cases and 12 controls were retrospectively identified, and the histologic and clinical features were evaluated. CD123 IHC staining was quantified by digital image analysis. Next generation sequencing was employed for comparative microbial analysis via RNAseq (5 KFD cases) and to evaluate the immune repertoire (9 KFD cases). RESULTS In cases of lymphadenitis with necrosis, >0.85% CD123+ cells by IHC was found to be six times more likely in cases with a final diagnosis of KFD (sensitivity 75%, specificity 87.5%). RNAseq based comparative microbial analysis did not detect novel or known pathogen sequences in KFD. A shared complementarity determining region 3 (CDR3) sequence and use of the same T-cell receptor beta variable region family was identified in KFD LNs but not controls, and was not identified in available databases. CONCLUSIONS Digital quantification of CD123 IHC can distinguish KFD from other necrotizing lymphadenitides. The presence of a unique shared CDR3 sequence suggests that a shared antigen underlies KFD pathogenesis.
Collapse
Affiliation(s)
- Nya D Nelson
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Wenzhao Meng
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Aaron M Rosenfeld
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Susan Bullman
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts.,Department of Medical Oncology and Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Chandra Sekhar Pedamallu
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts.,Department of Medical Oncology and Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jason L Nomburg
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts.,Department of Medical Oncology and Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Gerald B Wertheim
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Michele E Paessler
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Geraldine Pinkus
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jason L Hornick
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Matthew Meyerson
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts.,Department of Medical Oncology and Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Eline T Luning Prak
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Vinodh Pillai
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| |
Collapse
|
34
|
Poon MM, Byington E, Meng W, Dogra P, Lam N, Szabo PA, Ural B, Grifoni A, Weiskopf D, Kubota M, Matsumoto R, Sette A, Shen Y, Prak ETL, Farber DL. Tissue localization and virus specificity shape the maintenance and function of human virus-specific memory T cells recognizing HCMV and influenza A. The Journal of Immunology 2021. [DOI: 10.4049/jimmunol.206.supp.103.18] [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
Generation and maintenance of memory T cells within tissue sites of infection is critical for long-term antiviral protection. Current knowledge of human antiviral responses is largely derived from studies sampling peripheral blood. Yet, little is known about human tissue-localized antiviral immunity. Utilizing our human donor tissue resource established in collaboration with LiveOnNY, we investigated how tissue, virus, and age shape T cell maintenance across diverse tissues and their function when presented with antigens derived from human cytomegalovirus (HCMV) or influenza A virus (flu). Using flow cytometry, we show that virus-specific CD8 T cells are maintained in diverse tissues with subset differentiation and distribution shaped by virus specificity and age. Compared to T cells recognizing HCMV, flu-specific T cells display higher levels of residency markers—CD69 and CD103—particularly in adult compared to pediatric donors. In contrast, HCMV-specific T cells are maintained in greater abundance as terminally-differentiated effector T cells. Sequencing of the T cell receptor CDR3b chain reveals that, while both HCMV- and flu-specific T cells demonstrate clonal overlap across multiple tissues, HCMV-specific T cells display greater clonality and less diversity. When presented with viral antigens, HCMV- and flu-specific T cells are polyfunctional. Additionally, single-cell transcriptome profiling reveals tissue localization is the primary determinant of antigen-driven responses. Together, these studies demonstrate the dynamics of T cell differentiation and maintenance throughout the human body, which is primarily driven by virus specificity, and the role of tissue localization in shaping antiviral response.
Collapse
Affiliation(s)
| | | | | | | | - Nora Lam
- 1Columbia University Medical Center
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Fu J, Zuber J, Shonts B, Obradovic A, Wang Z, Frangaj K, Meng W, Rosenfeld AM, Waffarn EE, Liou P, Lau SP, Savage TM, Yang S, Rogers K, Danzl NM, Ravella S, Satwani P, Iuga A, Ho SH, Griesemer A, Shen Y, Prak ETL, Martinez M, Kato T, Sykes M. Lymphohematopoietic graft-versus-host responses promote mixed chimerism in patients receiving intestinal transplantation. J Clin Invest 2021; 131:141698. [PMID: 33630757 DOI: 10.1172/jci141698] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [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: 06/25/2020] [Accepted: 02/23/2021] [Indexed: 12/22/2022] Open
Abstract
In humans receiving intestinal transplantation (ITx), long-term multilineage blood chimerism often develops. Donor T cell macrochimerism (≥4%) frequently occurs without graft-versus-host disease (GVHD) and is associated with reduced rejection. Here we demonstrate that patients with macrochimerism had high graft-versus-host (GvH) to host-versus-graft (HvG) T cell clonal ratios in their allografts. These GvH clones entered the circulation, where their peak levels were associated with declines in HvG clones early after transplant, suggesting that GvH reactions may contribute to chimerism and control HvG responses without causing GVHD. Consistently, donor-derived T cells, including GvH clones, and CD34+ hematopoietic stem and progenitor cells (HSPCs) were simultaneously detected in the recipients' BM more than 100 days after transplant. Individual GvH clones appeared in ileal mucosa or PBMCs before detection in recipient BM, consistent with an intestinal mucosal origin, where donor GvH-reactive T cells expanded early upon entry of recipient APCs into the graft. These results, combined with cytotoxic single-cell transcriptional profiles of donor T cells in recipient BM, suggest that tissue-resident GvH-reactive donor T cells migrated into the recipient circulation and BM, where they destroyed recipient hematopoietic cells through cytolytic effector functions and promoted engraftment of graft-derived HSPCs that maintain chimerism. These mechanisms suggest an approach to achieving intestinal allograft tolerance.
Collapse
Affiliation(s)
- Jianing Fu
- Columbia Center for Translational Immunology, Department of Medicine and
| | - Julien Zuber
- Columbia Center for Translational Immunology, Department of Medicine and
| | - Brittany Shonts
- Columbia Center for Translational Immunology, Department of Medicine and
| | | | - Zicheng Wang
- Center for Computational Biology and Bioinformatics, Department of Systems Biology, Columbia University, New York, New York, USA
| | - Kristjana Frangaj
- Columbia Center for Translational Immunology, Department of Medicine and
| | - Wenzhao Meng
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Aaron M Rosenfeld
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | | | - Sai-Ping Lau
- Columbia Center for Translational Immunology, Department of Medicine and
| | - Thomas M Savage
- Columbia Center for Translational Immunology, Department of Medicine and
| | - Suxiao Yang
- Columbia Center for Translational Immunology, Department of Medicine and
| | - Kortney Rogers
- Columbia Center for Translational Immunology, Department of Medicine and
| | - Nichole M Danzl
- Columbia Center for Translational Immunology, Department of Medicine and
| | - Shilpa Ravella
- Division of Digestive and Liver Diseases, Department of Medicine
| | | | - Alina Iuga
- Department of Pathology and Cell Biology, and
| | - Siu-Hong Ho
- Columbia Center for Translational Immunology, Department of Medicine and
| | - Adam Griesemer
- Columbia Center for Translational Immunology, Department of Medicine and.,Department of Surgery
| | - Yufeng Shen
- Center for Computational Biology and Bioinformatics, Department of Systems Biology, Columbia University, New York, New York, USA
| | - Eline T Luning Prak
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | | | - Megan Sykes
- Columbia Center for Translational Immunology, Department of Medicine and.,Department of Surgery.,Department of Microbiology and Immunology, Columbia University, New York, New York, USA
| |
Collapse
|
36
|
Goel RR, Apostolidis SA, Painter MM, Mathew D, Pattekar A, Kuthuru O, Gouma S, Hicks P, Meng W, Rosenfeld AM, Dysinger S, Lundgreen KA, Kuri-Cervantes L, Adamski S, Hicks A, Korte S, Oldridge DA, Baxter AE, Giles JR, Weirick ME, McAllister CM, Dougherty J, Long S, D'Andrea K, Hamilton JT, Betts MR, Luning Prak ET, Bates P, Hensley SE, Greenplate AR, Wherry EJ. Distinct antibody and memory B cell responses in SARS-CoV-2 naïve and recovered individuals following mRNA vaccination. Sci Immunol 2021; 6:eabi6950. [PMID: 33858945 PMCID: PMC8158969 DOI: 10.1126/sciimmunol.abi6950] [Citation(s) in RCA: 422] [Impact Index Per Article: 140.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 04/12/2021] [Indexed: 12/12/2022]
Abstract
Novel mRNA vaccines for SARS-CoV-2 have been authorized for emergency use. Despite their efficacy in clinical trials, data on mRNA vaccine-induced immune responses are mostly limited to serological analyses. Here, we interrogated antibody and antigen-specific memory B cells over time in 33 SARS-CoV-2 naïve and 11 SARS-CoV-2 recovered subjects. SARS-CoV-2 naïve individuals required both vaccine doses for optimal increases in antibodies, particularly for neutralizing titers against the B.1.351 variant. Memory B cells specific for full-length spike protein and the spike receptor binding domain (RBD) were also efficiently primed by mRNA vaccination and detectable in all SARS-CoV-2 naive subjects after the second vaccine dose, though the memory B cell response declined slightly with age. In SARS-CoV-2 recovered individuals, antibody and memory B cell responses were significantly boosted after the first vaccine dose; however, there was no increase in circulating antibodies, neutralizing titers, or antigen-specific memory B cells after the second dose. This robust boosting after the first vaccine dose strongly correlated with levels of pre-existing memory B cells in recovered individuals, identifying a key role for memory B cells in mounting recall responses to SARS-CoV-2 antigens. Together, our data demonstrated robust serological and cellular priming by mRNA vaccines and revealed distinct responses based on prior SARS-CoV-2 exposure, whereby COVID-19 recovered subjects may only require a single vaccine dose to achieve peak antibody and memory B cell responses. These findings also highlight the utility of defining cellular responses in addition to serologies and may inform SARS-CoV-2 vaccine distribution in a resource-limited setting.
Collapse
Affiliation(s)
- Rishi R Goel
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Immune Health™, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Sokratis A Apostolidis
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Immune Health™, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Division of Rheumatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Mark M Painter
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Immune Health™, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Divij Mathew
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Immune Health™, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Ajinkya Pattekar
- Immune Health™, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Oliva Kuthuru
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Sigrid Gouma
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Philip Hicks
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Wenzhao Meng
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Aaron M Rosenfeld
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Sarah Dysinger
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Kendall A Lundgreen
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Leticia Kuri-Cervantes
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Sharon Adamski
- Immune Health™, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Amanda Hicks
- Immune Health™, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Scott Korte
- Immune Health™, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Derek A Oldridge
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Amy E Baxter
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Josephine R Giles
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Madison E Weirick
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Christopher M McAllister
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Jeanette Dougherty
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Sherea Long
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Kurt D'Andrea
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Jacob T Hamilton
- Immune Health™, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Michael R Betts
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Eline T Luning Prak
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Paul Bates
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Scott E Hensley
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Allison R Greenplate
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Immune Health™, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - E John Wherry
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Immune Health™, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| |
Collapse
|
37
|
Abstract
It is increasingly clear that an extraordinarily diverse range of clinically important conditions—including infections, vaccinations, autoimmune diseases, transplants, transfusion reactions, aging, and cancers—leave telltale signatures in the millions of V(D)J-rearranged antibody and T cell receptor [TR per the Human Genome Organization (HUGO) nomenclature but more commonly known as TCR] genes collectively expressed by a person’s B cells (antibodies) and T cells. We refer to these as the immunome. Because of its diversity and complexity, the immunome provides singular opportunities for advancing personalized medicine by serving as the substrate for a highly multiplexed, near-universal blood test. Here we discuss some of these opportunities, the current state of immunome-based diagnostics, and highlight some of the challenges involved. We conclude with a call to clinicians, researchers, and others to join efforts with the Adaptive Immune Receptor Repertoire Community (AIRR-C) to realize the diagnostic potential of the immunome.
Collapse
Affiliation(s)
- Ramy A Arnaout
- Department of Pathology and Division of Clinical Informatics, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, United States.,Department of Pathology, Harvard Medical School, Boston, MA, United States
| | - Eline T Luning Prak
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Nicholas Schwab
- Department of Neurology and Institute of Translational Neurology, University of Muenster, Muenster, Germany
| | - Florian Rubelt
- Roche Sequencing Solutions, Pleasanton, CA, United States
| | | |
Collapse
|
38
|
Goel RR, Apostolidis SA, Painter MM, Mathew D, Pattekar A, Kuthuru O, Gouma S, Kuri-Cervantes L, Meng W, Adamski S, Baxter AE, Giles JR, Weirick ME, McAllister CM, Hicks A, Korte S, Dougherty J, Long S, D’Andrea K, Hamilton JT, Prak ETL, Betts MR, Bates P, Hensley SE, Greenplate AR, Wherry EJ. Longitudinal Analysis Reveals Distinct Antibody and Memory B Cell Responses in SARS-CoV2 Naïve and Recovered Individuals Following mRNA Vaccination. medRxiv 2021:2021.03.03.21252872. [PMID: 33688691 PMCID: PMC7941668 DOI: 10.1101/2021.03.03.21252872] [Citation(s) in RCA: 15] [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: 06/12/2023]
Abstract
Novel mRNA vaccines for SARS-CoV2 have been authorized for emergency use and are currently being administered to millions of individuals worldwide. Despite their efficacy in clinical trials, there is limited data on vaccine-induced immune responses in individuals with a prior SARS-CoV2 infection compared to SARS-CoV2 naïve subjects. Moreover, how mRNA vaccines impact the development of antibodies as well as memory B cells in COVID-19 experienced versus COVID-19 naïve subjects remains poorly understood. In this study, we evaluated antibody responses and antigen-specific memory B cell responses over time in 33 SARS-CoV2 naïve and 11 SARS-CoV2 recovered subjects. mRNA vaccination induced significant antibody and memory B cell responses against full-length SARS-CoV2 spike protein and the spike receptor binding domain (RBD). SARS-CoV2 naïve individuals benefitted from both doses of mRNA vaccine with additional increases in antibodies and memory B cells following booster immunization. In contrast, SARS-CoV2 recovered individuals had a significant immune response after the first dose with no increase in circulating antibodies or antigen-specific memory B cells after the second dose. Moreover, the magnitude of the memory B cell response induced by vaccination was lower in older individuals, revealing an age-dependence to mRNA vaccine-induced B cell memory. Side effects also tended to associate with post-boost antibody levels, but not with post-boost memory B cells, suggesting that side effect severity may be a surrogate of short-term antibody responses. The frequency of pre-vaccine antigen-specific memory B cells in SARS-CoV2 recovered individuals strongly correlated with post-vaccine antibody levels, supporting a key role for memory B cells in humoral recall responses to SARS-CoV2. This observation may have relevance for future booster vaccines and for responses to viral variants that partially escape pre-existing antibodies and require new humoral responses to be generated from memory B cells. Finally, post-boost antibody levels were not correlated with post-boost memory responses in SARS-CoV2 naïve individuals, indicating that short-term antibody levels and memory B cells are complementary immunological endpoints that should be examined in tandem when evaluating vaccine response. Together, our data provide evidence of both serological response and immunological memory following mRNA vaccination that is distinct based on prior SARS-CoV2 exposure. These findings may inform vaccine distribution in a resource-limited setting.
Collapse
Affiliation(s)
- Rishi R. Goel
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Immune Health™, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Sokratis A. Apostolidis
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Immune Health™, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Division of Rheumatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Mark M. Painter
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Immune Health™, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Divij Mathew
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Immune Health™, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Ajinkya Pattekar
- Immune Health™, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Oliva Kuthuru
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Sigrid Gouma
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Leticia Kuri-Cervantes
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Wenzhao Meng
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Sharon Adamski
- Immune Health™, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Amy E. Baxter
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Josephine R. Giles
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Madison E. Weirick
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Christopher M. McAllister
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Amanda Hicks
- Immune Health™, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Scott Korte
- Immune Health™, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Jeanette Dougherty
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Sherea Long
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Kurt D’Andrea
- Immune Health™, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Jacob T. Hamilton
- Immune Health™, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Eline T Luning Prak
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Michael R. Betts
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Paul Bates
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Scott E. Hensley
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Allison R. Greenplate
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Immune Health™, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - E. John Wherry
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Immune Health™, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| |
Collapse
|
39
|
Chang SE, Feng A, Meng W, Apostolidis SA, Mack E, Artandi M, Barman L, Bennett K, Chakraborty S, Chang I, Cheung P, Chinthrajah S, Dhingra S, Do E, Finck A, Gaano A, Geßner R, Giannini HM, Gonzalez J, Greib S, Gündisch M, Hsu AR, Kuo A, Manohar M, Mao R, Neeli I, Neubauer A, Oniyide O, Powell AE, Puri R, Renz H, Schapiro JM, Weidenbacher PA, Wittman R, Ahuja N, Chung HR, Jagannathan P, James J, Kim PS, Meyer NJ, Nadeau K, Radic M, Robinson WH, Singh U, Wang TT, Wherry EJ, Skevaki C, Prak ETL, Utz PJ. New-Onset IgG Autoantibodies in Hospitalized Patients with COVID-19. medRxiv 2021. [PMID: 33532787 DOI: 10.1101/2021.01.27.21250559] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Coronavirus Disease 2019 (COVID-19), caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), is associated with a wide range of clinical manifestations, including autoimmune features and autoantibody production. We developed three different protein arrays to measure hallmark IgG autoantibodies associated with Connective Tissue Diseases (CTDs), Anti-Cytokine Antibodies (ACA), and anti-viral antibody responses in 147 hospitalized COVID-19 patients in three different centers. Autoantibodies were identified in approximately 50% of patients, but in <15% of healthy controls. When present, autoantibodies largely targeted autoantigens associated with rare disorders such as myositis, systemic sclerosis and CTD overlap syndromes. Anti-nuclear antibodies (ANA) were observed in ∼25% of patients. Patients with autoantibodies tended to demonstrate one or a few specificities whereas ACA were even more prevalent, and patients often had antibodies to multiple cytokines. Rare patients were identified with IgG antibodies against angiotensin converting enzyme-2 (ACE-2). A subset of autoantibodies and ACA developed de novo following SARS-CoV-2 infection while others were transient. Autoantibodies tracked with longitudinal development of IgG antibodies that recognized SARS-CoV-2 structural proteins such as S1, S2, M, N and a subset of non-structural proteins, but not proteins from influenza, seasonal coronaviruses or other pathogenic viruses. COVID-19 patients with one or more autoantibodies tended to have higher levels of antibodies against SARS-CoV-2 Nonstructural Protein 1 (NSP1) and Methyltransferase (ME). We conclude that SARS-CoV-2 causes development of new-onset IgG autoantibodies in a significant proportion of hospitalized COVID-19 patients and are positively correlated with immune responses to SARS-CoV-2 proteins.
Collapse
|
40
|
Weisel NM, Weisel FJ, Farber DL, Borghesi LA, Shen Y, Ma W, Luning Prak ET, Shlomchik MJ. Comprehensive analyses of B-cell compartments across the human body reveal novel subsets and a gut-resident memory phenotype. Blood 2020; 136:2774-2785. [PMID: 32750113 PMCID: PMC7731793 DOI: 10.1182/blood.2019002782] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 06/22/2020] [Indexed: 11/20/2022] Open
Abstract
Although human B cells have been extensively studied, most reports have used peripheral blood as a source. Here, we used a unique tissue resource derived from healthy organ donors to deeply characterize human B-cell compartments across multiple tissues and donors. These datasets revealed that B cells in the blood are not in homeostasis with compartments in other tissues. We found striking donor-to-donor variability in the frequencies and isotype of CD27+ memory B cells (MBCs). A comprehensive antibody-based screen revealed markers of MBC and allowed identification of novel MBC subsets with distinct functions defined according to surface expression of CD69 and CD45RB. We defined a tissue-resident MBC phenotype that was predominant in the gut but absent in blood. RNA-sequencing of MBC subsets from multiple tissues revealed a tissue-resident MBC gene signature as well as gut- and spleen-specific signatures. Overall, these studies provide novel insights into the nature and function of human B-cell compartments across multiple tissues.
Collapse
Affiliation(s)
- Nadine M Weisel
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Florian J Weisel
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Donna L Farber
- Columbia Center for Translational Immunology
- Department of Microbiology and Immunology
- Department of Surgery, and
| | - Lisa A Borghesi
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Yufeng Shen
- Department of Systems Biology, Columbia University Medical Center, New York, NY; and
| | - Wenji Ma
- Department of Systems Biology, Columbia University Medical Center, New York, NY; and
| | - Eline T Luning Prak
- Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Mark J Shlomchik
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| |
Collapse
|
41
|
Abstract
In this issue of Cell Host & Microbe, Nielsen and colleagues sequence antibody repertoires of patients with severe COVID-19 to reveal potentially convergent features on the background of a larger, polyclonal response. Their findings suggest that, as databases improve, it may be possible to monitor virus-specific B cells after infection or vaccination using antibody sequencing.
Collapse
Affiliation(s)
- Wenzhao Meng
- Perelman School of Medicine, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Aaron M Rosenfeld
- Perelman School of Medicine, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Eline T Luning Prak
- Perelman School of Medicine, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology University of Pennsylvania, Philadelphia, PA 19104, USA.
| |
Collapse
|
42
|
Kuri-Cervantes L, Pampena MB, Meng W, Rosenfeld AM, Ittner CAG, Weisman AR, Agyekum RS, Mathew D, Baxter AE, Vella LA, Kuthuru O, Apostolidis SA, Bershaw L, Dougherty J, Greenplate AR, Pattekar A, Kim J, Han N, Gouma S, Weirick ME, Arevalo CP, Bolton MJ, Goodwin EC, Anderson EM, Hensley SE, Jones TK, Mangalmurti NS, Luning Prak ET, Wherry EJ, Meyer NJ, Betts MR. Comprehensive mapping of immune perturbations associated with severe COVID-19. Sci Immunol 2020; 5:eabd7114. [PMID: 32669287 PMCID: PMC7402634 DOI: 10.1126/sciimmunol.abd7114] [Citation(s) in RCA: 555] [Impact Index Per Article: 138.8] [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: 07/07/2020] [Accepted: 07/10/2020] [Indexed: 01/08/2023]
Abstract
Although critical illness has been associated with SARS-CoV-2-induced hyperinflammation, the immune correlates of severe COVID-19 remain unclear. Here, we comprehensively analyzed peripheral blood immune perturbations in 42 SARS-CoV-2 infected and recovered individuals. We identified extensive induction and activation of multiple immune lineages, including T cell activation, oligoclonal plasmablast expansion, and Fc and trafficking receptor modulation on innate lymphocytes and granulocytes, that distinguished severe COVID-19 cases from healthy donors or SARS-CoV-2-recovered or moderate severity patients. We found the neutrophil to lymphocyte ratio to be a prognostic biomarker of disease severity and organ failure. Our findings demonstrate broad innate and adaptive leukocyte perturbations that distinguish dysregulated host responses in severe SARS-CoV-2 infection and warrant therapeutic investigation.
Collapse
Affiliation(s)
- Leticia Kuri-Cervantes
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - M Betina Pampena
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wenzhao Meng
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, Philadelphia, PA19104, USA
| | - Aaron M Rosenfeld
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, Philadelphia, PA19104, USA
| | - Caroline A G Ittner
- Division of Pulmonary, Allergy and Critical Care, Center for Translational Lung Biology, Lung Biology Institute, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Ariel R Weisman
- Division of Pulmonary, Allergy and Critical Care, Center for Translational Lung Biology, Lung Biology Institute, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Roseline S Agyekum
- Division of Pulmonary, Allergy and Critical Care, Center for Translational Lung Biology, Lung Biology Institute, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Divij Mathew
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Amy E Baxter
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Laura A Vella
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Division of Infectious Diseases, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Oliva Kuthuru
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Sokratis A Apostolidis
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Division of Rheumatology, Department of Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - Luanne Bershaw
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jeanette Dougherty
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Allison R Greenplate
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Ajinkya Pattekar
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Division of Gastroenterology, Department of Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - Justin Kim
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Nicholas Han
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Sigrid Gouma
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Madison E Weirick
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Claudia P Arevalo
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Marcus J Bolton
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Eileen C Goodwin
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Elizabeth M Anderson
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Scott E Hensley
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Tiffanie K Jones
- Division of Pulmonary, Allergy and Critical Care, Center for Translational Lung Biology, Lung Biology Institute, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Nilam S Mangalmurti
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Division of Pulmonary, Allergy and Critical Care, Center for Translational Lung Biology, Lung Biology Institute, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Eline T Luning Prak
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, Philadelphia, PA19104, USA
| | - E John Wherry
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Parker Institute for Cancer Immunotherapy at the University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - Nuala J Meyer
- Division of Pulmonary, Allergy and Critical Care, Center for Translational Lung Biology, Lung Biology Institute, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Michael R Betts
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| |
Collapse
|
43
|
Horvath S, Tsao P, Huang ZY, Zhao L, Du Y, Sammel MD, Prak ETL, Schreiber CA. The concentration of fetal red blood cells in first-trimester pregnant women undergoing uterine aspiration is below the calculated threshold for Rh sensitization. Contraception 2020; 102:1-6. [PMID: 32135125 PMCID: PMC7272297 DOI: 10.1016/j.contraception.2020.02.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 08/11/2019] [Revised: 02/24/2020] [Accepted: 02/24/2020] [Indexed: 12/22/2022]
Abstract
OBJECTIVES To calculate the minimum fetal red blood cell concentration required to cause maternal Rh sensitization; validate the use of a flow cytometry protocol below that concentration; preliminarily assess the concentrations of fetal red blood cells in pregnant women before and after uterine aspiration. STUDY DESIGN Using pre-existing literature, we calculated the lowest concentration of fetal red blood cells found to cause sensitization within adult female circulation. We validated a two-color flow cytometry protocol using fluorescently labeled antibodies to Hemoglobin F (expressed by fetal red blood cells and adult F cells) and Carbonic Anhydrase (expressed in red blood cells during the third trimester and postnatally) by titrating second trimester cord blood into non-pregnant adult blood. We applied this flow cytometry protocol in a prospective cohort study of 42 pregnant women at 5-12 weeks gestational age undergoing uterine aspiration for induced or spontaneous abortion. RESULTS The calculated threshold for causing Rh sensitization was 250 fetal red blood cells per 10 million total red blood cells. We showed a linear relationship between observed and expected fetal red blood cell fractions in titrated samples. Fetal red blood cell counts were more reliable when samples acquired by flow cytometry contained at least 1 million red blood cells. All 37 subjects with evaluable paired samples demonstrated fetal red blood cell concentrations below the calculated threshold for Rh sensitization both pre- and post-procedure. The fetal RBC concentrations increased from a mean of 4.5 (median 0, range 0-57) fetal RBCS pre- to a mean of 8.6 (median 2, range 0-32) fetal RBCs post- per 10 million total RBCs (p < 0.001). CONCLUSIONS Flow cytometry was capable of separately quantifying fetal red blood cells and maternal F cells to very dilute concentrations. Fetal red blood cell exposure in the first trimester was well below the calculated threshold for maternal Rh sensitization in our cohort. Larger studies are warranted to confirm our pilot study findings, fill this evidence gap and inform universal guidelines for administering Rh immunoglobulin after first trimester uterine aspiration. IMPLICATIONS Fetal red blood cell exposure following first trimester uterine aspiration is well below the calculated threshold for maternal Rh sensitization in our cohort.
Collapse
Affiliation(s)
- Sarah Horvath
- Division of Family Planning, Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States.
| | - Patricia Tsao
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States.
| | - Zhen-Yu Huang
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States.
| | - Ling Zhao
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States.
| | - Yangzhu Du
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States.
| | - Mary D Sammel
- Center for Clinical Epidemiology and Biostatistics, Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States.
| | - Eline T Luning Prak
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States.
| | - Courtney A Schreiber
- Division of Family Planning, Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States.
| |
Collapse
|
44
|
Kuri-Cervantes L, Pampena MB, Meng W, Rosenfeld AM, Ittner CAG, Weisman AR, Agyekum R, Mathew D, Baxter AE, Vella L, Kuthuru O, Apostolidis S, Bershaw L, Dougherty J, Greenplate AR, Pattekar A, Kim J, Han N, Gouma S, Weirick ME, Arevalo CP, Bolton MJ, Goodwin EC, Anderson EM, Hensley SE, Jones TK, Mangalmurti NS, Luning Prak ET, Wherry EJ, Meyer NJ, Betts MR. Immunologic perturbations in severe COVID-19/SARS-CoV-2 infection. bioRxiv 2020:2020.05.18.101717. [PMID: 32511394 PMCID: PMC7263541 DOI: 10.1101/2020.05.18.101717] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Although critical illness has been associated with SARS-CoV-2-induced hyperinflammation, the immune correlates of severe COVID-19 remain unclear. Here, we comprehensively analyzed peripheral blood immune perturbations in 42 SARS-CoV-2 infected and recovered individuals. We identified broad changes in neutrophils, NK cells, and monocytes during severe COVID-19, suggesting excessive mobilization of innate lineages. We found marked activation within T and B cells, highly oligoclonal B cell populations, profound plasmablast expansion, and SARS-CoV-2-specific antibodies in many, but not all, severe COVID-19 cases. Despite this heterogeneity, we found selective clustering of severe COVID-19 cases through unbiased analysis of the aggregated immunological phenotypes. Our findings demonstrate broad immune perturbations spanning both innate and adaptive leukocytes that distinguish dysregulated host responses in severe SARS-CoV-2 infection and warrant therapeutic investigation. One Sentence Summary Broad immune perturbations in severe COVID-19.
Collapse
|
45
|
Poon MM, Meng W, Dogra P, Lam N, Szabo PA, Grifoni A, Tian Y, Kubota M, Matsumoto R, Sette A, Prak ETL, Farber DL. Human influenza A-specific memory T cells reside within multiple tissues and elicit a tissue-specific antiviral response when presented with viral antigens. The Journal of Immunology 2020. [DOI: 10.4049/jimmunol.204.supp.93.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Generation of memory T cells specific for conserved viral epitopes provides heterosubtypic protection to influenza infection. Previous mouse studies have shown that tissue-resident memory T cells (TRM) are critical for optimal protection. However, knowledge of human antiviral response is largely derived from blood. With our unique human donor tissue resource established in collaboration with LiveOnNY, we investigate the maintenance of influenza-specific T cells across diverse tissue sites and their response when presented with viral antigens. Using multimer staining and flow cytometry, we show that influenza-specific CD8 T cells are maintained in the lung tissue site of infection, as well as in blood, bone marrow, multiple lymph nodes, and small intestines. Compared to T cells recognizing persistent cytomegalovirus infection, influenza-specific T cells display higher levels of canonical residency markers—CD69 and CD103. Additionally, deep sequencing of the T cell receptor CDR3b repertoire reveals that influenza-specific T cells isolated from human tissue donors without active infection are clonally expanded and display a high degree of clonal overlap across tissue sites. When presented with viral antigens, influenza-specific T cells in all sites are polyfunctional and rapidly respond through cytokine production. Together, these studies reveal the dynamics of immune memory maintenance and antiviral response across tissues in the human body in response to influenza A virus.
Collapse
Affiliation(s)
| | | | | | - Nora Lam
- 1Columbia University Medical Center
| | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Poon MML, Meng W, Dogra P, Lam N, Szabo PA, Kubota M, Matsumoto R, Rahman A, Luning Prak ET, Farber DL. Human T cell immunity in barrier sites is phenotypically distinct but clonally connected to other sites. The Journal of Immunology 2020. [DOI: 10.4049/jimmunol.204.supp.235.7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
The gut, lung, and skin are physical and immunological barriers that serve as the first line of defense against pathogens and foreign substances. Due to sampling limitations, previous studies have been limited to studying human barrier sites in isolation and often in the context of specific diseases. Our donor tissue resource established in collaboration with LiveOnNY offers a unique opportunity to examine human barrier T cell immunity as a network and elucidate how barrier sites are connected to each other and to lymphoid sites (lymph nodes, bone marrow, spleen). Here, using cytometry by time-of-flight (CyTOF) and T cell receptor (TCR) CDR3b sequencing, we investigate the unique defining characteristics and connectivity of T cells in barrier tissue – gut, lung, and skin – to lymphoid sites and blood. Through high-dimensional marker analysis by CyTOF, our results show that T cell subset composition and phenotype across 8 different sites comprise 33 clusters that are highly conserved between donors of different ages (22–70 yrs). Skin and gut T cells are distinct from each other and from lung, lymphoid sites, and blood, while lung T cells share features with lymphoid sites and blood. TCR repertoire analysis shows that, though majority of gut and skin T cell clones are unique to the tissue, expanded clones within these barrier sites share clonal overlap with other barrier and lymphoid sites. Moreover, T cells in the lung exhibit increased sharing with lymphoid sites and blood. Together, these results reveal how human T cells are compartmentalized in the skin and gut through site-specific adaptations while demonstrating that gut, lung, and skin barrier T cells are connected through shared specificities in a network of immune protection across the body.
Collapse
Affiliation(s)
| | | | | | - Nora Lam
- 1Columbia University Medical Center
| | | | | | | | | | | | | |
Collapse
|
47
|
Johnson JL, Rosenthal RL, Knox JJ, Myles A, Naradikian MS, Madej J, Kostiv M, Rosenfeld AM, Meng W, Christensen SR, Hensley SE, Yewdell J, Canaday DH, Zhu J, McDermott AB, Dori Y, Itkin M, Wherry EJ, Pardi N, Weissman D, Naji A, Prak ETL, Betts MR, Cancro MP. The Transcription Factor T-bet Resolves Memory B Cell Subsets with Distinct Tissue Distributions and Antibody Specificities in Mice and Humans. Immunity 2020; 52:842-855.e6. [PMID: 32353250 DOI: 10.1016/j.immuni.2020.03.020] [Citation(s) in RCA: 121] [Impact Index Per Article: 30.3] [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: 10/08/2018] [Revised: 01/28/2020] [Accepted: 03/27/2020] [Indexed: 12/11/2022]
Abstract
B cell subsets expressing the transcription factor T-bet are associated with humoral immune responses and autoimmunity. Here, we examined the anatomic distribution, clonal relationships, and functional properties of T-bet+ and T-bet- memory B cells (MBCs) in the context of the influenza-specific immune response. In mice, both T-bet- and T-bet+ hemagglutinin (HA)-specific B cells arose in germinal centers, acquired memory B cell markers, and persisted indefinitely. Lineage tracing and IgH repertoire analyses revealed minimal interconversion between T-bet- and T-bet+ MBCs, and parabionts showed differential tissue residency and recirculation properties. T-bet+ MBCs could be subdivided into recirculating T-betlo MBCs and spleen-resident T-bethi MBCs. Human MBCs displayed similar features. Conditional gene deletion studies revealed that T-bet expression in B cells was required for nearly all HA stalk-specific IgG2c antibodies and for durable neutralizing titers to influenza. Thus, T-bet expression distinguishes MBC subsets that have profoundly different homing, residency, and functional properties, and mediate distinct aspects of humoral immune memory.
Collapse
Affiliation(s)
- John L Johnson
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rebecca L Rosenthal
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James J Knox
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Arpita Myles
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Joanna Madej
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mariya Kostiv
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Aaron M Rosenfeld
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wenzhao Meng
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Scott E Hensley
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jonathan Yewdell
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - David H Canaday
- Division of Infectious Disease, Case Western Reserve University School of Medicine, and Cleveland VA Hospital, Cleveland, OH 45106, USA
| | - Jinfang Zhu
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Adrian B McDermott
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yoav Dori
- Center for Lymphatic Imaging and Intervention, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Max Itkin
- Division of Interventional Radiology, Department of Radiology, Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - E John Wherry
- Institute for Immunology, Parker Institute for Cancer Immunotherapy at University of Pennsylvania, and Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, 19104, USA
| | - Norbert Pardi
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Drew Weissman
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ali Naji
- Department of Surgery, Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Eline T Luning Prak
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael R Betts
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael P Cancro
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| |
Collapse
|
48
|
Belman JP, Meng W, Wang HY, Li J, Strauser HT, Rosenfeld AM, Zhang Q, Prak ETL, Wasik M. Dramatic increase in gene mutational burden after transformation of follicular lymphoma into TdT + B-lymphoblastic leukemia/lymphoma. Cold Spring Harb Mol Case Stud 2019; 6:mcs.a004614. [PMID: 31776129 PMCID: PMC6996523 DOI: 10.1101/mcs.a004614] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 07/25/2019] [Accepted: 10/16/2019] [Indexed: 12/17/2022] Open
Abstract
Transformation of follicular lymphoma (FL) into B-lymphoblastic leukemia/lymphoma (B-ALL/LBL) is rare and results in greatly increased aggressiveness of clinical course. Here we present extensive molecular analysis of this unusual transformation, including immunoglobulin (Ig) gene rearrangement studies, cytogenetic analysis, and whole-exome sequencing (WES) of the patient's FL, B-ALL/LBL, and normal cells. Although FL showed marked somatic hypermutation (SHM) of the Ig genes, SHM appeared to be even more extensive in B-ALL/LBL. Cytogenetically, at least three translocations were identified in the B-ALL/LBL involving the BCL2, BCL6, and MYC genes; two of these, the BCL6 and BCL2 gene rearrangements, were already seen at the FL stage. WES identified 751 single-nucleotide variants with high allelic burden in the patient's cells, with the vast majority (575) present exclusively at the B-ALL/LBL stage. Of note, a TAF3 gene mutation was shared by normal, FL, and B-ALL/LBL tissue. A KMT2D nonsense mutation was identified in both FL and B-ALL/LBL and therefore may have contributed directly to lymphomagenesis. Mutations in KDM6A, SMARCA4, CBX1, and JMY were specific to the B-ALL/LBL stage, possibly contributing to the B-ALL/LBL transformation. Functionally, these identified mutations may lead to dysregulation of DNA repair, transcription, and cell differentiation. Thus, these genetic changes, together with the identified chromosomal translocations, may have contributed to lymphoma development and progression. Our findings may improve the mechanistic understanding of the FL-B-ALL/LBL transformation and may have therapeutic implications for this aggressive disease.
Collapse
Affiliation(s)
- Jonathan P Belman
- Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Wenzhao Meng
- Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Hong Yi Wang
- Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Jie Li
- Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
| | - Honore T Strauser
- Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Aaron M Rosenfeld
- Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Qian Zhang
- Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Eline T Luning Prak
- Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Mariusz Wasik
- Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| |
Collapse
|
49
|
Rubelt F, Busse CE, Bukhari SAC, Bürckert JP, Mariotti-Ferrandiz E, Cowell LG, Watson CT, Marthandan N, Faison WJ, Hershberg U, Laserson U, Corrie BD, Davis MM, Peters B, Lefranc MP, Scott JK, Breden F, Luning Prak ET, Kleinstein SH. Adaptive Immune Receptor Repertoire Community recommendations for sharing immune-repertoire sequencing data. Nat Immunol 2019; 18:1274-1278. [PMID: 29144493 DOI: 10.1038/ni.3873] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Florian Rubelt
- Department of Microbiology and Immunology and Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, California, USA
| | - Christian E Busse
- Division of B Cell Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Jean-Philippe Bürckert
- Department of Infection and Immunity, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Encarnita Mariotti-Ferrandiz
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France
| | - Lindsay G Cowell
- Department of Clinical Sciences, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, Kentucky, USA
| | - Nishanth Marthandan
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - William J Faison
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Uri Hershberg
- School of Biomedical Engineering, Science & Health Systems, and Department of Microbiology and Immunology, College of Medicine, Drexel University, Philadelphia, Pennsylvania, USA
| | - Uri Laserson
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Brian D Corrie
- iReceptor, Simon Fraser University, Burnaby, British Columbia, Canada.,Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Mark M Davis
- Department of Microbiology and Immunology and Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, California, USA.,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, USA
| | - Bjoern Peters
- La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
| | - Marie-Paule Lefranc
- IMGT, the international ImMunoGeneTics information system, LIGM, Institut de Génétique Humaine IGH, CNRS, University of Montpellier, Montpellier, France
| | - Jamie K Scott
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada.,iReceptor, Simon Fraser University, Burnaby, British Columbia, Canada.,Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Felix Breden
- iReceptor, Simon Fraser University, Burnaby, British Columbia, Canada.,Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | | | - Eline T Luning Prak
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Steven H Kleinstein
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, USA.,Department of Immunobiology, Yale School of Medicine, and Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA
| |
Collapse
|
50
|
Rosenfeld AM, Meng W, Luning Prak ET, Hershberg U. ImmuneDB, a Novel Tool for the Analysis, Storage, and Dissemination of Immune Repertoire Sequencing Data. Front Immunol 2018; 9:2107. [PMID: 30298069 PMCID: PMC6161679 DOI: 10.3389/fimmu.2018.02107] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [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: 07/13/2018] [Accepted: 08/28/2018] [Indexed: 11/16/2022] Open
Abstract
ImmuneDB is a system for storing and analyzing high-throughput immune receptor sequencing data. Unlike most existing tools, which utilize flat-files, ImmuneDB stores data in a well-structured MySQL database, enabling efficient data queries. It can take raw sequencing data as input and annotate receptor gene usage, infer clonotypes, aggregate results, and run common downstream analyses such as calculating selection pressure and constructing clonal lineages. Alternatively, pre-annotated data can be imported and analyzed data can be exported in a variety of common Adaptive Immune Receptor Repertoire (AIRR) file formats. To validate ImmuneDB, we compare its results to those of another pipeline, MiXCR. We show that the biological conclusions drawn would be similar with either tool, while ImmuneDB provides the additional benefits of integrating other common tools and storing data in a database. ImmuneDB is freely available on GitHub at https://github.com/arosenfeld/immunedb, on PyPi at https://pypi.org/project/ImmuneDB, and a Docker container is provided at https://hub.docker.com/r/arosenfeld/immunedb. Full documentation is available at http://immunedb.com.
Collapse
Affiliation(s)
- Aaron M Rosenfeld
- School of Biomedical Engineering Science and Health Systems, Drexel University, Philadelphia, PA, United States
| | - Wenzhao Meng
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Eline T Luning Prak
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Uri Hershberg
- School of Biomedical Engineering Science and Health Systems, Drexel University, Philadelphia, PA, United States.,Department of Microbiology and Immunology, College of Medicine, Drexel University, Philadelphia, PA, United States.,Department of Human Biology, Faculty of Sciences, University of Haifa, Haifa, Israel
| |
Collapse
|