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Mallory M, Munt JE, Narowski TM, Castillo I, Cuadra E, Pisanic N, Fields P, Powers JM, Dickson A, Harris R, Wargowsky R, Moran S, Allabban A, Raphel K, McCaffrey TA, Brien JD, Heaney CD, Lafleur JE, Baric RS, Premkumar L. COVID-19 point-of-care tests can identify low-antibody individuals: In-depth immunoanalysis of boosting benefits in a healthy cohort. SCIENCE ADVANCES 2024; 10:eadi1379. [PMID: 38865463 PMCID: PMC11168476 DOI: 10.1126/sciadv.adi1379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 05/08/2024] [Indexed: 06/14/2024]
Abstract
The recommended COVID-19 booster vaccine uptake is low. At-home lateral flow assay (LFA) antigen tests are widely accepted for detecting infection during the pandemic. Here, we present the feasibility and potential benefits of using LFA-based antibody tests as a means for individuals to detect inadequate immunity and make informed decisions about COVID-19 booster immunization. In a health care provider cohort, we investigated the changes in the breadth and depth of humoral and T cell immune responses following mRNA vaccination and boosting in LFA-positive and LFA-negative antibody groups. We show that negative LFA antibody tests closely reflect the lack of functional humoral immunity observed in a battery of sophisticated immune assays, while positive results do not necessarily reflect adequate immunity. After booster vaccination, both groups gain depth and breadth of systemic antibodies against evolving SARS-CoV-2 and related viruses. Our findings show that LFA-based antibody tests can alert individuals about inadequate immunity against COVID-19, thereby increasing booster shots and promoting herd immunity.
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Affiliation(s)
- Michael Mallory
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
- Department of Epidemiology, UNC Chapel Hill School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jennifer E. Munt
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
- Department of Epidemiology, UNC Chapel Hill School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Tara M. Narowski
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Izabella Castillo
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Edwing Cuadra
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Nora Pisanic
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | - John M. Powers
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
- Department of Epidemiology, UNC Chapel Hill School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alexandria Dickson
- Department of Molecular Microbiology and Immunology, Saint Louis University, Saint Louis, MO, USA
| | - Rohan Harris
- Department Emergency Medicine, George Washington University School of Medicine, Washington, DC, USA
| | - Richard Wargowsky
- Department of Medicine, Division of Genomic Medicine, The George Washington University Medical Center, Washington, DC, USA
| | - Seamus Moran
- Department Emergency Medicine, George Washington University School of Medicine, Washington, DC, USA
| | - Ahmed Allabban
- Department Emergency Medicine, George Washington University School of Medicine, Washington, DC, USA
| | - Kristin Raphel
- Department Emergency Medicine, George Washington University School of Medicine, Washington, DC, USA
| | - Timothy A. McCaffrey
- Department of Medicine, Division of Genomic Medicine, The George Washington University Medical Center, Washington, DC, USA
| | - James D. Brien
- Department of Molecular Microbiology and Immunology, Saint Louis University, Saint Louis, MO, USA
| | - Christopher D. Heaney
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of International Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - John E. Lafleur
- Department Emergency Medicine, George Washington University School of Medicine, Washington, DC, USA
| | - Ralph S. Baric
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
- Department of Epidemiology, UNC Chapel Hill School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lakshmanane Premkumar
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
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2
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Chandraker A, Regmi A, Gohh R, Sharma A, Woodle ES, Ansari MJ, Nair V, Chen LX, Alhamad T, Norman S, Cibrik D, Singh M, Alper A, Jain D, Zaky Z, Knechtle S, Sharfuddin A, Gupta G, Lonze BE, Young JAH, Adey D, Faravardeh A, Dadhania DM, Rossi AP, Florescu D, Cardarelli F, Ma J, Gilmore S, Vasileiou S, Jindra PT, Wojciechowski D. Posoleucel in Kidney Transplant Recipients with BK Viremia: Multicenter, Randomized, Double-Blind, Placebo-Controlled Phase 2 Trial. J Am Soc Nephrol 2024; 35:618-629. [PMID: 38470444 PMCID: PMC11149047 DOI: 10.1681/asn.0000000000000329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 03/05/2024] [Indexed: 03/13/2024] Open
Abstract
Key Points Posoleucel was generally safe, well tolerated, and associated with a greater reduction of BK viremia compared with placebo. BK viremia reduction occurred coincident with an increase in the circulating frequency of BK virus–specific T cells in posoleucel recipients. The presence and persistence of posoleucel was confirmed by T-cell receptor variable β sequencing. Background Kidney transplant recipients with BK virus infection are at risk of developing BK virus–associated nephropathy, allograft rejection, and subsequent graft loss. There are no approved treatments for BK virus infection. Posoleucel is an off-the-shelf, allogeneic, multivirus-specific T-cell investigational therapy targeting BK virus, as well as five other opportunistic viruses: adenovirus, cytomegalovirus, Epstein–Barr virus, human herpesvirus 6, and John Cunningham virus. Methods In this phase 2, double-blind study, kidney transplant recipients with BK viremia were randomized 1:1:1 to receive posoleucel weekly for 3 weeks and then every 14 days (bi-weekly dosing) or every 28 days (monthly dosing) or placebo for 12 weeks. Participants were followed for 12 weeks after completing treatment. The primary objective was safety; the secondary objective was plasma BK viral load reduction. Results Sixty-one participants were randomized and dosed. Baseline characteristics were similar across groups. No deaths, graft-versus-host disease, or cytokine release syndrome occurred. The proportion of patients who had adverse events (AEs) judged by the investigators to be treatment-related was slightly lower in recipients of posoleucel: 20% (4 of 20 patients) and 18% (4 of 22) in those infused on a bi-weekly and monthly schedule, respectively, and 26% (5 of 19) in placebo recipients. None of the grade 3–4 AEs or serious AEs in any group were deemed treatment-related. No deaths, graft-versus-host disease, or cytokine release syndrome occurred. Three participants had allograft rejection, but none were deemed treatment-related by investigators. In posoleucel recipients, BK viremia reduction was associated with an increase in the circulating frequency of BK virus–specific T cells, and the presence and persistence of posoleucel was confirmed by T-cell receptor sequencing. Conclusions Posoleucel was generally safe, well tolerated, and associated with a larger reduction of BK viremia compared with placebo. Limitations of this study include the relatively short duration of follow-up and lack of power to detect significant differences in clinical outcomes. Clinical Trial registry name and registration number: Study of Posoleucel (Formerly Known as ALVR105; Viralym-M) in Kidney Transplant Patients With BK Viremia, NCT04605484 .
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Affiliation(s)
- Anil Chandraker
- Division of Renal Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Division of Renal Medicine, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts
| | - Anil Regmi
- Inova Transplant Center, Falls Church, Virginia
| | | | - Akhil Sharma
- University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | | | | | - Vinay Nair
- Northwell Health, New Hyde Park, New York
| | - Ling-Xin Chen
- University of California Davis, Sacramento, California
| | - Tarek Alhamad
- Washington University School of Medicine at St. Louis, St. Louis, Missouri
| | | | | | | | | | | | | | | | - Asif Sharfuddin
- Indiana University School of Medicine, Indianapolis, Indiana
| | - Gaurav Gupta
- Virginia Commonwealth University, Richmond, Virginia
| | | | | | - Deborah Adey
- University of California, San Francisco, California
| | - Arman Faravardeh
- SHARP Kidney and Pancreas Transplant Center, San Diego, California
| | | | | | | | | | - Julie Ma
- AlloVir, Inc., Waltham, Massachusetts
| | | | - Spyridoula Vasileiou
- AlloVir, Inc., Waltham, Massachusetts
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, Texas
| | - Peter T. Jindra
- Immune Evaluation Laboratory, Baylor College of Medicine, Houston, Texas
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3
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Yarchoan M, Gane EJ, Marron TU, Perales-Linares R, Yan J, Cooch N, Shu DH, Fertig EJ, Kagohara LT, Bartha G, Northcott J, Lyle J, Rochestie S, Peters J, Connor JT, Jaffee EM, Csiki I, Weiner DB, Perales-Puchalt A, Sardesai NY. Personalized neoantigen vaccine and pembrolizumab in advanced hepatocellular carcinoma: a phase 1/2 trial. Nat Med 2024; 30:1044-1053. [PMID: 38584166 PMCID: PMC11031401 DOI: 10.1038/s41591-024-02894-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 03/01/2024] [Indexed: 04/09/2024]
Abstract
Programmed cell death protein 1 (PD-1) inhibitors have modest efficacy as a monotherapy in hepatocellular carcinoma (HCC). A personalized therapeutic cancer vaccine (PTCV) may enhance responses to PD-1 inhibitors through the induction of tumor-specific immunity. We present results from a single-arm, open-label, phase 1/2 study of a DNA plasmid PTCV (GNOS-PV02) encoding up to 40 neoantigens coadministered with plasmid-encoded interleukin-12 plus pembrolizumab in patients with advanced HCC previously treated with a multityrosine kinase inhibitor. Safety and immunogenicity were assessed as primary endpoints, and treatment efficacy and feasibility were evaluated as secondary endpoints. The most common treatment-related adverse events were injection-site reactions, observed in 15 of 36 (41.6%) patients. No dose-limiting toxicities or treatment-related grade ≥3 events were observed. The objective response rate (modified intention-to-treat) per Response Evaluation Criteria in Solid Tumors 1.1 was 30.6% (11 of 36 patients), with 8.3% (3 of 36) of patients achieving a complete response. Clinical responses were associated with the number of neoantigens encoded in the vaccine. Neoantigen-specific T cell responses were confirmed in 19 of 22 (86.4%) evaluable patients by enzyme-linked immunosorbent spot assays. Multiparametric cellular profiling revealed active, proliferative and cytolytic vaccine-specific CD4+ and CD8+ effector T cells. T cell receptor β-chain (TCRβ) bulk sequencing results demonstrated vaccination-enriched T cell clone expansion and tumor infiltration. Single-cell analysis revealed posttreatment T cell clonal expansion of cytotoxic T cell phenotypes. TCR complementarity-determining region cloning of expanded T cell clones in the tumors following vaccination confirmed reactivity against vaccine-encoded neoantigens. Our results support the PTCV's mechanism of action based on the induction of antitumor T cells and show that a PTCV plus pembrolizumab has clinical activity in advanced HCC. ClinicalTrials.gov identifier: NCT04251117 .
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Affiliation(s)
- Mark Yarchoan
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Edward J Gane
- New Zealand Liver Transplant Unit, University of Auckland, Auckland, New Zealand
| | - Thomas U Marron
- Early Phase Trials Unit, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Jian Yan
- Geneos Therapeutics, Philadelphia, PA, USA
| | - Neil Cooch
- Geneos Therapeutics, Philadelphia, PA, USA
| | - Daniel H Shu
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Elana J Fertig
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Applied Mathematics and Statistics, Johns Hopkins University Whiting School of Engineering, Baltimore, MD, USA
| | - Luciane T Kagohara
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | | | | | | | | | - Jason T Connor
- ConfluenceStat, Cooper City, FL, USA
- University of Central Florida College of Medicine, Orlando, FL, USA
| | - Elizabeth M Jaffee
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - David B Weiner
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, USA
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Tatsi EB, Filippatos F, Bello T, Syriopoulou V, Michos A. Comparative Study of T-Cell Repertoires after COVID-19 Immunization with Homologous or Heterologous Vaccine Booster. Pathogens 2024; 13:284. [PMID: 38668239 PMCID: PMC11054887 DOI: 10.3390/pathogens13040284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/12/2024] [Accepted: 03/25/2024] [Indexed: 04/29/2024] Open
Abstract
Sequencing of the T-cell repertoire is an innovative method to assess the cellular responses after immunization. The purpose of this study was to compare T-cell repertoires after COVID-19 immunization with homologous (HOB) and heterologous (HEB) boosting. The study included 20 participants with a median age of 27.5 (IQR:23) years, who were vaccinated with one dose of the Ad26.COV2.S vaccine and were boosted with either Ad26.COV2.S (n = 10) or BNT162b2 (n = 10) vaccine. Analysis of the T-cell receptor beta locus (TCRβ) sequencing one month after the booster dose identified that the HEB compared to the HOB group exhibited a higher number of both total and COVID-19-related functional T-cell rearrangements [mean of total productive rearrangements (TPRs): 63151.8 (SD ± 18441.5) vs. 34915.4 (SD ± 11121.6), p = 0.001 and COVID-19-TPRs: 522.5 (SD ± 178.0) vs. 298.3 (SD ± 101.1), p = 0.003]. A comparison between the HOB and HEB groups detected no statistically significant differences regarding T-cell Simpson clonality [0.021 (IQR:0.014) vs. 0.019 (IQR:0.007)], richness [8734.5 (IQR:973.3) vs. 8724 (IQR:383.7)] and T-cell fraction [0.19 (IQR:0.08) vs. 0.18 (IQR:0.08)]. HEB also exhibited a substantially elevated humoral immune response one month after the booster dose compared to HOB [median antibody titer (IQR): 10115.0 U/mL (6993.0) vs. 1781.0 U/mL (1314.0), p = 0.001]. T-cell repertoire sequencing indicated that HEB had increased SARS-CoV-2-related T-cell rearrangements, which was in accordance with higher humoral responses and possibly conferring longer protection. Data from the present study indicate that the administration of different COVID-19 vaccines as a booster may provide better protection.
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Affiliation(s)
- Elizabeth-Barbara Tatsi
- Infectious Diseases and Chemotherapy Research Laboratory, First Department of Pediatrics, Medical School, “Aghia Sophia” Children’s Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece; (E.-B.T.); (F.F.)
| | - Filippos Filippatos
- Infectious Diseases and Chemotherapy Research Laboratory, First Department of Pediatrics, Medical School, “Aghia Sophia” Children’s Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece; (E.-B.T.); (F.F.)
| | - Thomas Bello
- Adaptive Biotechnologies, Seattle 98109, WA, USA;
| | - Vasiliki Syriopoulou
- Infectious Diseases and Chemotherapy Research Laboratory, First Department of Pediatrics, Medical School, “Aghia Sophia” Children’s Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece; (E.-B.T.); (F.F.)
| | - Athanasios Michos
- Infectious Diseases and Chemotherapy Research Laboratory, First Department of Pediatrics, Medical School, “Aghia Sophia” Children’s Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece; (E.-B.T.); (F.F.)
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5
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Kallionpää RA, Peltonen S, Le KM, Martikkala E, Jääskeläinen M, Fazeli E, Riihilä P, Haapaniemi P, Rokka A, Salmi M, Leivo I, Peltonen J. Characterization of Immune Cell Populations of Cutaneous Neurofibromas in Neurofibromatosis 1. J Transl Med 2024; 104:100285. [PMID: 37949359 DOI: 10.1016/j.labinv.2023.100285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 10/20/2023] [Accepted: 11/03/2023] [Indexed: 11/12/2023] Open
Abstract
Cutaneous neurofibromas (cNFs) are characteristic of neurofibromatosis 1 (NF1), yet their immune microenvironment is incompletely known. A total of 61 cNFs from 10 patients with NF1 were immunolabeled for different types of T cells and macrophages, and the cell densities were correlated with clinical characteristics. Eight cNFs and their overlying skin were analyzed for T cell receptor CDR domain sequences, and mass spectrometry of 15 cNFs and the overlying skin was performed to study immune-related processes. Intratumoral T cells were detected in all cNFs. Tumors from individuals younger than the median age of the study participants (33 years), growing tumors, and tumors smaller than the data set median showed increased T cell density. Most samples displayed intratumoral or peritumoral aggregations of CD3-positive cells. T cell receptor sequencing demonstrated that the skin and cNFs host distinct T cell populations, whereas no dominant cNF-specific T cell clones were detected. Unique T cell clones were fewer in cNFs than in skin, and mass spectrometry suggested lower expression of proteins related to T cell-mediated immunity in cNFs than in skin. CD163-positive cells, suggestive of M2 macrophages, were abundant in cNFs. Human cNFs have substantial T cell and macrophage populations that may be tumor-specific.
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Affiliation(s)
- Roope A Kallionpää
- Institute of Biomedicine, University of Turku, Turku, Finland; FICAN West Cancer Centre, University of Turku and Turku University Hospital, Turku, Finland
| | - Sirkku Peltonen
- Department of Dermatology and Venereology, University of Turku, Turku, Finland; Department of Dermatology, Turku University Hospital, Turku, Finland; Department of Dermatology and Venereology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Department of Dermatology and Venereology, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Dermatology and Allergology, University of Helsinki, Helsinki, Finland; Skin and Allergy Hospital, Helsinki University Hospital, Helsinki, Finland
| | - Kim My Le
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Eija Martikkala
- Institute of Biomedicine, University of Turku, Turku, Finland
| | | | - Elnaz Fazeli
- Institute of Biomedicine, University of Turku, Turku, Finland; Biomedicum Imaging Unit, Faculty of Medicine and HiLIFE, University of Helsinki, Helsinki, Finland
| | - Pilvi Riihilä
- Department of Dermatology and Venereology, University of Turku, Turku, Finland; Department of Dermatology, Turku University Hospital, Turku, Finland; FICAN West Cancer Research Laboratory, University of Turku and Turku University Hospital, Turku, Finland
| | - Pekka Haapaniemi
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Anne Rokka
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Marko Salmi
- Institute of Biomedicine, University of Turku, Turku, Finland; MediCity Research Laboratory, and InFLAMES Research Flagship Center, University of Turku, Turku, Finland
| | - Ilmo Leivo
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Juha Peltonen
- Institute of Biomedicine, University of Turku, Turku, Finland; FICAN West Cancer Centre, University of Turku and Turku University Hospital, Turku, Finland.
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6
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Ford ES, Mayer-Blackwell K, Jing L, Laing KJ, Sholukh AM, St Germain R, Bossard EL, Xie H, Pulliam TH, Jani S, Selke S, Burrow CJ, McClurkan CL, Wald A, Greninger AL, Holbrook MR, Eaton B, Eudy E, Murphy M, Postnikova E, Robins HS, Elyanow R, Gittelman RM, Ecsedi M, Wilcox E, Chapuis AG, Fiore-Gartland A, Koelle DM. Repeated mRNA vaccination sequentially boosts SARS-CoV-2-specific CD8 + T cells in persons with previous COVID-19. Nat Immunol 2024; 25:166-177. [PMID: 38057617 PMCID: PMC10981451 DOI: 10.1038/s41590-023-01692-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 10/27/2023] [Indexed: 12/08/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) hybrid immunity is more protective than vaccination or previous infection alone. To investigate the kinetics of spike-reactive T (TS) cells from SARS-CoV-2 infection through messenger RNA vaccination in persons with hybrid immunity, we identified the T cell receptor (TCR) sequences of thousands of index TS cells and tracked their frequency in bulk TCRβ repertoires sampled longitudinally from the peripheral blood of persons who had recovered from coronavirus disease 2019 (COVID-19). Vaccinations led to large expansions in memory TS cell clonotypes, most of which were CD8+ T cells, while also eliciting diverse TS cell clonotypes not observed before vaccination. TCR sequence similarity clustering identified public CD8+ and CD4+ TCR motifs associated with spike (S) specificity. Synthesis of longitudinal bulk ex vivo single-chain TCRβ repertoires and paired-chain TCRɑβ sequences from droplet sequencing of TS cells provides a roadmap for the rapid assessment of T cell responses to vaccines and emerging pathogens.
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Affiliation(s)
- Emily S Ford
- Department of Medicine, University of Washington, Seattle, WA, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | | | - Lichen Jing
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Kerry J Laing
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Anton M Sholukh
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Russell St Germain
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Emily L Bossard
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Hong Xie
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Thomas H Pulliam
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Saumya Jani
- Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Stacy Selke
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | | | | | - Anna Wald
- Department of Medicine, University of Washington, Seattle, WA, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Alexander L Greninger
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Michael R Holbrook
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Brett Eaton
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Elizabeth Eudy
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Michael Murphy
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Elena Postnikova
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | | | | | - Rachel M Gittelman
- Adaptive Biotechnologies, Seattle, WA, USA
- Guardant Health, Redwood City, CA, USA
| | - Matyas Ecsedi
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Takeda Oncology, Cambridge, MA, USA
| | - Elise Wilcox
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Aude G Chapuis
- Department of Medicine, University of Washington, Seattle, WA, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Andrew Fiore-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - David M Koelle
- Department of Medicine, University of Washington, Seattle, WA, USA.
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.
- Department of Global Health, University of Washington, Seattle, WA, USA.
- Department of Translational Research, Benaroya Research Institute, Seattle, WA, USA.
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7
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Onyango TB, Zhou F, Bredholt G, Brokstad KA, Lartey S, Mohn KGI, Özgümüs T, Kittang BR, Linchausen DW, Shafiani S, Elyanow R, Blomberg B, Langeland N, Cox RJ. SARS-CoV-2 specific immune responses in overweight and obese COVID-19 patients. Front Immunol 2023; 14:1287388. [PMID: 38022529 PMCID: PMC10653322 DOI: 10.3389/fimmu.2023.1287388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 10/05/2023] [Indexed: 12/01/2023] Open
Abstract
Obesity is a known risk factor for severe respiratory tract infections. In this prospective study, we assessed the impact of being obese or overweight on longitudinal SARS-CoV-2 humoral and cellular responses up to 18 months after infection. 274 patients provided blood samples at regular time intervals up to 18 months including obese (BMI ≥30, n=32), overweight (BMI 25-29.9, n=103) and normal body weight (BMI 18.5-24.9, n=134) SARS-CoV-2 patients. We determined SARS-CoV-2 spike-specific IgG, IgA, IgM levels by ELISA and neutralising antibody titres by neutralisation assay. RBD- and spike-specific memory B cells were investigated by ELISpot, spike- and non-spike-specific IFN-γ, IL-2 and IFN-γ/IL-2 secreting T cells by FluoroSpot and T cell receptor (TCR) sequencing was performed. Higher BMI correlated with increased COVID-19 severity. Humoral and cellular responses were stronger in overweight and obese patients than normal weight patients and associated with higher spike-specific IgG binding titres relative to neutralising antibody titres. Linear regression models demonstrated that BMI, age and COVID-19 severity correlated independently with higher SARS-CoV-2 immune responses. We found an increased proportion of unique SARS-CoV-2 specific T cell clonotypes after infection in overweight and obese patients. COVID-19 vaccination boosted humoral and cellular responses irrespective of BMI, although stronger immune boosting was observed in normal weight patients. Overall, our results highlight more severe disease and an over-reactivity of the immune system in overweight and obese patients after SARS-CoV-2 infection, underscoring the importance of recognizing overweight/obese individuals as a risk group for prioritisation for COVID-19 vaccination.
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Affiliation(s)
| | - Fan Zhou
- Influenza Centre, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Geir Bredholt
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Karl A. Brokstad
- Influenza Centre, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Safety, Chemistry and Biomedical Laboratory Sciences, Western Norway University of Applied Sciences, Bergen, Norway
| | - Sarah Lartey
- Influenza Centre, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Kristin G.-I. Mohn
- Influenza Centre, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Türküler Özgümüs
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | | | | | | | | | - Bjørn Blomberg
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
- National Advisory Unit for Tropical Infectious Diseases, Haukeland University Hospital, Bergen, Norway
| | - Nina Langeland
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
- National Advisory Unit for Tropical Infectious Diseases, Haukeland University Hospital, Bergen, Norway
| | - Rebecca Jane Cox
- Influenza Centre, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
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Miller D, Romero R, Myers L, Xu Y, Arenas-Hernandez M, Galaz J, Soto C, Done B, Quiroz A, Awonuga AO, Bryant DR, Tarca AL, Gomez-Lopez N. Immunosequencing and Profiling of T Cells at the Maternal-Fetal Interface of Women with Preterm Labor and Chronic Chorioamnionitis. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 211:1082-1098. [PMID: 37647360 PMCID: PMC10528178 DOI: 10.4049/jimmunol.2300201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/31/2023] [Indexed: 09/01/2023]
Abstract
T cells are implicated in the pathophysiology of preterm labor and birth, the leading cause of neonatal morbidity and mortality worldwide. Specifically, maternal decidual T cells infiltrate the chorioamniotic membranes in chronic chorioamnionitis (CCA), a placental lesion considered to reflect maternal anti-fetal rejection, leading to preterm labor and birth. However, the phenotype and TCR repertoire of decidual T cells in women with preterm labor and CCA have not been investigated. In this study, we used phenotyping, TCR sequencing, and functional assays to elucidate the molecular characteristics and Ag specificity of T cells infiltrating the chorioamniotic membranes in women with CCA who underwent term or preterm labor. Phenotyping indicated distinct enrichment of human decidual effector memory T cell subsets in cases of preterm labor with CCA without altered regulatory T cell proportions. TCR sequencing revealed that the T cell repertoire of CCA is characterized by increased TCR richness and decreased clonal expansion in women with preterm labor. We identified 15 clones associated with CCA and compared these against established TCR databases, reporting that infiltrating T cells may possess specificity for maternal and fetal Ags, but not common viral Ags. Functional assays demonstrated that choriodecidual T cells can respond to maternal and fetal Ags. Collectively, our findings provide, to our knowledge, novel insight into the complex processes underlying chronic placental inflammation and further support a role for effector T cells in the mechanisms of disease for preterm labor and birth. Moreover, this work further strengthens the contribution of adaptive immunity to the syndromic nature of preterm labor and birth.
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Affiliation(s)
- Derek Miller
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, US Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, 48201, and Bethesda, MD, 20892 USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Roberto Romero
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, US Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, 48201, and Bethesda, MD, 20892 USA
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, 48201, USA
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, 48201, USA
| | - Luke Myers
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Yi Xu
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, US Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, 48201, and Bethesda, MD, 20892 USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Marcia Arenas-Hernandez
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, US Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, 48201, and Bethesda, MD, 20892 USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Jose Galaz
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, US Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, 48201, and Bethesda, MD, 20892 USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, 48201, USA
- Division of Obstetrics and Gynecology, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, 8330024, Chile
| | - Cinque Soto
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Bogdan Done
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, US Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, 48201, and Bethesda, MD, 20892 USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Angelica Quiroz
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Awoniyi O. Awonuga
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - David R. Bryant
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Adi L. Tarca
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, US Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, 48201, and Bethesda, MD, 20892 USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, 48201, USA
- Department of Computer Science, Wayne State University College of Engineering, Detroit, MI, 48201, USA
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Nardhy Gomez-Lopez
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, US Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, 48201, and Bethesda, MD, 20892 USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, 48201, USA
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI, 48201, USA
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, 48201, USA
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9
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Carbone ML, Capone A, Guercio M, Reddel S, Silvestris DA, Lulli D, Ramondino C, Peluso D, Quintarelli C, Volpe E, Failla CM. Insight into immune profile associated with vitiligo onset and anti-tumoral response in melanoma patients receiving anti-PD-1 immunotherapy. Front Immunol 2023; 14:1197630. [PMID: 37680638 PMCID: PMC10482109 DOI: 10.3389/fimmu.2023.1197630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 08/04/2023] [Indexed: 09/09/2023] Open
Abstract
Introduction Immunotherapy with checkpoint inhibitors is an efficient treatment for metastatic melanoma. Development of vitiligo upon immunotherapy represents a specific immune-related adverse event (irAE) diagnosed in 15% of patients and associated with a positive clinical response. Therefore, a detailed characterization of immune cells during vitiligo onset in melanoma patients would give insight into the immune mechanisms mediating both the irAE and the anti-tumor response. Methods To better understand these aspects, we analyzed T cell subsets from peripheral blood of metastatic melanoma patients undergoing treatment with anti-programmed cell death protein (PD)-1 antibodies. To deeply characterize the antitumoral T cell response concomitant to vitiligo onset, we analyzed T cell content in skin biopsies collected from melanoma patients who developed vitiligo. Moreover, to further characterize T cells in vitiligo skin lesion of melanoma patients, we sequenced T cell receptor (TCR) of cells derived from biopsies of vitiligo and primary melanoma of the same patient. Results and discussion Stratification of patients for developing or not developing vitiligo during anti-PD-1 therapy revealed an association between blood reduction of CD8-mucosal associated invariant T (MAIT), T helper (h) 17, natural killer (NK) CD56bright, and T regulatory (T-reg) cells and vitiligo onset. Consistently with the observed blood reduction of Th17 cells in melanoma patients developing vitiligo during immunotherapy, we found high amount of IL-17A expressing cells in the vitiligo skin biopsy, suggesting a possible migration of Th17 cells from the blood into the autoimmune lesion. Interestingly, except for a few cases, we found different TCR sequences between vitiligo and primary melanoma lesions. In contrast, shared TCR sequences were identified between vitiligo and metastatic tissues of the same patient. These data indicate that T cell response against normal melanocytes, which is involved in vitiligo onset, is not typically mediated by reactivation of specific T cell clones infiltrating primary melanoma but may be elicited by T cell clones targeting metastatic tissues. Altogether, our data indicate that anti-PD-1 therapy induces a de novo immune response, stimulated by the presence of metastatic cells, and composed of different T cell subtypes, which may trigger the development of vitiligo and the response against metastatic tumor.
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Affiliation(s)
- Maria Luigia Carbone
- Laboratory of Experimental Immunology, Istituto Dermopatico dell’Immacolata (IDI)-IRCCS, Rome, Italy
| | - Alessia Capone
- Laboratory of Molecular Neuroimmunology, Santa Lucia Foundation-IRCCS, Rome, Italy
| | - Marika Guercio
- Department of Oncology-Hematology, and Cell and Gene Therapy, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
| | - Sofia Reddel
- Department of Oncology-Hematology, and Cell and Gene Therapy, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
| | | | - Daniela Lulli
- Laboratory of Experimental Immunology, Istituto Dermopatico dell’Immacolata (IDI)-IRCCS, Rome, Italy
| | - Carmela Ramondino
- Laboratory of Experimental Immunology, Istituto Dermopatico dell’Immacolata (IDI)-IRCCS, Rome, Italy
| | - Daniele Peluso
- Department of Biology, University “Tor Vergata”, Rome, Italy
| | - Concetta Quintarelli
- Department of Oncology-Hematology, and Cell and Gene Therapy, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
- Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Elisabetta Volpe
- Laboratory of Molecular Neuroimmunology, Santa Lucia Foundation-IRCCS, Rome, Italy
| | - Cristina Maria Failla
- Laboratory of Experimental Immunology, Istituto Dermopatico dell’Immacolata (IDI)-IRCCS, Rome, Italy
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10
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Tsimberidou AM, Guenther K, Andersson BS, Mendrzyk R, Alpert A, Wagner C, Nowak A, Aslan K, Satelli A, Richter F, Kuttruff-Coqui S, Schoor O, Fritsche J, Coughlin Z, Mohamed AS, Sieger K, Norris B, Ort R, Beck J, Vo HH, Hoffgaard F, Ruh M, Backert L, Wistuba II, Fuhrmann D, Ibrahim NK, Morris VK, Kee BK, Halperin DM, Nogueras-Gonzalez GM, Kebriaei P, Shpall EJ, Vining D, Hwu P, Singh H, Reinhardt C, Britten CM, Hilf N, Weinschenk T, Maurer D, Walter S. Feasibility and Safety of Personalized, Multi-Target, Adoptive Cell Therapy (IMA101): First-in-Human Clinical Trial in Patients with Advanced Metastatic Cancer. Cancer Immunol Res 2023; 11:925-945. [PMID: 37172100 PMCID: PMC10330623 DOI: 10.1158/2326-6066.cir-22-0444] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 12/15/2022] [Accepted: 05/11/2023] [Indexed: 05/14/2023]
Abstract
IMA101 is an actively personalized, multi-targeted adoptive cell therapy (ACT), whereby autologous T cells are directed against multiple novel defined peptide-HLA (pHLA) cancer targets. HLA-A*02:01-positive patients with relapsed/refractory solid tumors expressing ≥1 of 8 predefined targets underwent leukapheresis. Endogenous T cells specific for up to 4 targets were primed and expanded in vitro. Patients received lymphodepletion (fludarabine, cyclophosphamide), followed by T-cell infusion and low-dose IL2 (Cohort 1). Patients in Cohort 2 received atezolizumab for up to 1 year (NCT02876510). Overall, 214 patients were screened, 15 received lymphodepletion (13 women, 2 men; median age, 44 years), and 14 were treated with T-cell products. IMA101 treatment was feasible and well tolerated. The most common adverse events were cytokine release syndrome (Grade 1, n = 6; Grade 2, n = 4) and expected cytopenias. No patient died during the first 100 days after T-cell therapy. No neurotoxicity was observed. No objective responses were noted. Prolonged disease stabilization was noted in three patients lasting for 13.7, 12.9, and 7.3 months. High frequencies of target-specific T cells (up to 78.7% of CD8+ cells) were detected in the blood of treated patients, persisted for >1 year, and were detectable in posttreatment tumor tissue. Individual T-cell receptors (TCR) contained in T-cell products exhibited broad variation in TCR avidity, with the majority being low avidity. High-avidity TCRs were identified in some patients' products. This study demonstrates the feasibility and tolerability of an actively personalized ACT directed to multiple defined pHLA cancer targets. Results warrant further evaluation of multi-target ACT approaches using potent high-avidity TCRs. See related Spotlight by Uslu and June, p. 865.
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Affiliation(s)
- Apostolia M Tsimberidou
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Borje S Andersson
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | | | | | - Anna Nowak
- Immatics Biotechnologies GmbH, Tuebingen, Germany
| | - Katrin Aslan
- Immatics Biotechnologies GmbH, Tuebingen, Germany
| | | | | | | | | | | | | | | | | | - Becky Norris
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rita Ort
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jennifer Beck
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Henry Hiep Vo
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Manuel Ruh
- Immatics Biotechnologies GmbH, Tuebingen, Germany
| | | | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Nuhad K Ibrahim
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Van Karlyle Morris
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Texas
| | - Bryan K Kee
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Texas
| | - Daniel M Halperin
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Texas
| | | | - Partow Kebriaei
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Elizabeth J Shpall
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - David Vining
- Department of Abdominal Imaging, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Patrick Hwu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | | | | | - Norbert Hilf
- Immatics Biotechnologies GmbH, Tuebingen, Germany
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11
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Rojas LA, Sethna Z, Soares KC, Olcese C, Pang N, Patterson E, Lihm J, Ceglia N, Guasp P, Chu A, Yu R, Chandra AK, Waters T, Ruan J, Amisaki M, Zebboudj A, Odgerel Z, Payne G, Derhovanessian E, Müller F, Rhee I, Yadav M, Dobrin A, Sadelain M, Łuksza M, Cohen N, Tang L, Basturk O, Gönen M, Katz S, Do RK, Epstein AS, Momtaz P, Park W, Sugarman R, Varghese AM, Won E, Desai A, Wei AC, D'Angelica MI, Kingham TP, Mellman I, Merghoub T, Wolchok JD, Sahin U, Türeci Ö, Greenbaum BD, Jarnagin WR, Drebin J, O'Reilly EM, Balachandran VP. Personalized RNA neoantigen vaccines stimulate T cells in pancreatic cancer. Nature 2023; 618:144-150. [PMID: 37165196 PMCID: PMC10171177 DOI: 10.1038/s41586-023-06063-y] [Citation(s) in RCA: 245] [Impact Index Per Article: 245.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 04/06/2023] [Indexed: 05/12/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is lethal in 88% of patients1, yet harbours mutation-derived T cell neoantigens that are suitable for vaccines 2,3. Here in a phase I trial of adjuvant autogene cevumeran, an individualized neoantigen vaccine based on uridine mRNA-lipoplex nanoparticles, we synthesized mRNA neoantigen vaccines in real time from surgically resected PDAC tumours. After surgery, we sequentially administered atezolizumab (an anti-PD-L1 immunotherapy), autogene cevumeran (a maximum of 20 neoantigens per patient) and a modified version of a four-drug chemotherapy regimen (mFOLFIRINOX, comprising folinic acid, fluorouracil, irinotecan and oxaliplatin). The end points included vaccine-induced neoantigen-specific T cells by high-threshold assays, 18-month recurrence-free survival and oncologic feasibility. We treated 16 patients with atezolizumab and autogene cevumeran, then 15 patients with mFOLFIRINOX. Autogene cevumeran was administered within 3 days of benchmarked times, was tolerable and induced de novo high-magnitude neoantigen-specific T cells in 8 out of 16 patients, with half targeting more than one vaccine neoantigen. Using a new mathematical strategy to track T cell clones (CloneTrack) and functional assays, we found that vaccine-expanded T cells comprised up to 10% of all blood T cells, re-expanded with a vaccine booster and included long-lived polyfunctional neoantigen-specific effector CD8+ T cells. At 18-month median follow-up, patients with vaccine-expanded T cells (responders) had a longer median recurrence-free survival (not reached) compared with patients without vaccine-expanded T cells (non-responders; 13.4 months, P = 0.003). Differences in the immune fitness of the patients did not confound this correlation, as responders and non-responders mounted equivalent immunity to a concurrent unrelated mRNA vaccine against SARS-CoV-2. Thus, adjuvant atezolizumab, autogene cevumeran and mFOLFIRINOX induces substantial T cell activity that may correlate with delayed PDAC recurrence.
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Affiliation(s)
- Luis A Rojas
- Immuno-Oncology Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zachary Sethna
- Immuno-Oncology Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kevin C Soares
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Cristina Olcese
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nan Pang
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Erin Patterson
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jayon Lihm
- Computational Oncology Service, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nicholas Ceglia
- Computational Oncology Service, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pablo Guasp
- Immuno-Oncology Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexander Chu
- Computational Oncology Service, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rebecca Yu
- Immuno-Oncology Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Adrienne Kaya Chandra
- Immuno-Oncology Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Theresa Waters
- Immuno-Oncology Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jennifer Ruan
- Immuno-Oncology Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Masataka Amisaki
- Immuno-Oncology Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Abderezak Zebboudj
- Immuno-Oncology Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zagaa Odgerel
- Immuno-Oncology Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - George Payne
- Immuno-Oncology Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | - Ina Rhee
- Genentech, San Francisco, CA, USA
| | | | - Anton Dobrin
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michel Sadelain
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marta Łuksza
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Noah Cohen
- Department of Surgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Laura Tang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Olca Basturk
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mithat Gönen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Seth Katz
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Richard Kinh Do
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrew S Epstein
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Parisa Momtaz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wungki Park
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ryan Sugarman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anna M Varghese
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elizabeth Won
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Avni Desai
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alice C Wei
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael I D'Angelica
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - T Peter Kingham
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Taha Merghoub
- Meyer Cancer Center, Weill Cornell Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Jedd D Wolchok
- Meyer Cancer Center, Weill Cornell Medicine, Weill Cornell Medical College, New York, NY, USA
| | | | - Özlem Türeci
- BioNTech, Mainz, Germany
- HI-TRON, Helmholtz Institute for Translational Oncology, Mainz, Germany
| | - Benjamin D Greenbaum
- Computational Oncology Service, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, Weill Cornell Medical College, New York, NY, USA.
| | - William R Jarnagin
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jeffrey Drebin
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eileen M O'Reilly
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Vinod P Balachandran
- Immuno-Oncology Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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12
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Pagliuca S, Gurnari C, Hercus C, Hergalant S, Hong S, Dhuyser A, D'Aveni M, Aarnink A, Rubio MT, Feugier P, Ferraro F, Carraway HE, Sobecks R, Hamilton BK, Majhail NS, Visconte V, Maciejewski JP. Leukemia relapse via genetic immune escape after allogeneic hematopoietic cell transplantation. Nat Commun 2023; 14:3153. [PMID: 37258544 PMCID: PMC10232425 DOI: 10.1038/s41467-023-38113-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 04/13/2023] [Indexed: 06/02/2023] Open
Abstract
Graft-versus-leukemia (GvL) reactions are responsible for the effectiveness of allogeneic hematopoietic cell transplantation as a treatment modality for myeloid neoplasia, whereby donor T- effector cells recognize leukemia neoantigens. However, a substantial fraction of patients experiences relapses because of the failure of the immunological responses to control leukemic outgrowth. Here, through a broad immunogenetic study, we demonstrate that germline and somatic reduction of human leucocyte antigen (HLA) heterogeneity enhances the risk of leukemic recurrence. We show that preexistent germline-encoded low evolutionary divergence of class II HLA genotypes constitutes an independent factor associated with disease relapse and that acquisition of clonal somatic defects in HLA alleles may lead to escape from GvL control. Both class I and II HLA genes are targeted by somatic mutations as clonal selection factors potentially impairing cellular immune responses and response to immunomodulatory strategies. These findings define key molecular modes of post-transplant leukemia escape contributing to relapse.
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Affiliation(s)
- Simona Pagliuca
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Hematology, CHRU de Nancy, Vandœuvre-lès-Nancy, France
- CNRS UMR 7365, IMoPA, Biopole of University of Lorraine, Vandœuvre-lès-Nancy, France
| | - Carmelo Gurnari
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Biomedicine and Prevention, PhD in Immunology, Molecular Medicine and Applied Biotechnology, University of Rome Tor Vergata, Rome, Italy
| | - Colin Hercus
- Novocraft Technologies Sdn Bhd, Kuala Lumpur, Malaysia
| | - Sébastien Hergalant
- Inserm UMR-S 1256 Nutrition-Genetics-Environmental Risk Exposure, University of Lorraine, 54500, Vandœuvre-lès-Nancy, France
| | - Sanghee Hong
- Division of Hematologic Malignancies and Cellular Therapy, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Adele Dhuyser
- CNRS UMR 7365, IMoPA, Biopole of University of Lorraine, Vandœuvre-lès-Nancy, France
- Histocompatibility Department, CHRU de Nancy, Vandœuvre-lès-Nancy, France
| | - Maud D'Aveni
- Department of Hematology, CHRU de Nancy, Vandœuvre-lès-Nancy, France
- CNRS UMR 7365, IMoPA, Biopole of University of Lorraine, Vandœuvre-lès-Nancy, France
| | - Alice Aarnink
- CNRS UMR 7365, IMoPA, Biopole of University of Lorraine, Vandœuvre-lès-Nancy, France
- Histocompatibility Department, CHRU de Nancy, Vandœuvre-lès-Nancy, France
| | - Marie Thérèse Rubio
- Department of Hematology, CHRU de Nancy, Vandœuvre-lès-Nancy, France
- CNRS UMR 7365, IMoPA, Biopole of University of Lorraine, Vandœuvre-lès-Nancy, France
| | - Pierre Feugier
- Department of Hematology, CHRU de Nancy, Vandœuvre-lès-Nancy, France
| | - Francesca Ferraro
- Division of Oncology, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Hetty E Carraway
- Leukemia Program, Hematology Department, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Ronald Sobecks
- Blood and Marrow Transplant Program, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Betty K Hamilton
- Blood and Marrow Transplant Program, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Navneet S Majhail
- Sarah Cannon Transplant and Cellular Therapy Network, Nashville, TN, USA
| | - Valeria Visconte
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Jaroslaw P Maciejewski
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA.
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13
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Pagliuca S, Gurnari C, Hercus C, Hergalant S, Hong S, Dhuyser A, D'Aveni M, Aarnink A, Rubio MT, Feugier P, Ferraro F, Carraway HE, Sobecks R, Hamilton BK, Majhail NS, Visconte V, Maciejewski JP. Leukemia relapse via genetic immune escape after allogeneic hematopoietic cell transplantation. RESEARCH SQUARE 2023:rs.3.rs-2773498. [PMID: 37066269 PMCID: PMC10104200 DOI: 10.21203/rs.3.rs-2773498/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Graft-versus-leukemia (GvL) reactions are responsible for the effectiveness of allogeneic hematopoietic cell transplantation as a treatment modality for myeloid neoplasia, whereby donor T- effector cells recognize leukemia neoantigens. However, a substantial fraction of patients experience relapses because of the failure of the immunological responses to control leukemic outgrowth. Here, through a broad immunogenetic study, we demonstrate that germline and somatic reduction of human leucocyte antigen (HLA) heterogeneity enhances the risk of leukemic recurrence. We show that preexistent germline-encoded low evolutionary divergence of class II HLA genotypes constitutes an independent factor associated with disease relapse and that acquisition of clonal somatic defects in HLA alleles may lead to escape from GvL control. Both class I and II HLA genes are targeted by somatic mutations as clonal selection factors potentially impairing cellular immune reactions and response to immunomodulatory strategies. These findings define key molecular modes of post-transplant leukemia escape contributing to relapse.
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14
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Mallory M, Munt JE, Narowski TM, Castillo I, Cuadra E, Pisanic N, Fields P, Powers JM, Dickson A, Harris R, Wargowsky R, Moran S, Allabban A, Raphel K, McCaffrey TA, Brien JD, Heaney CD, Lafleur JE, Baric RS, Premkumar L. Longitudinal Analysis of Humoral and Cellular Immune Response Following SARS-CoV-2 Vaccination Supports Utilizing Point-Of-Care Tests to Enhance COVID-19 Booster Uptake. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.04.03.23287498. [PMID: 37066219 PMCID: PMC10104219 DOI: 10.1101/2023.04.03.23287498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Individuals with weaker neutralizing responses show reduced protection with SARS-CoV-2 variants. Booster vaccines are recommended for vaccinated individuals, but the uptake is low. We present the feasibility of utilizing point-of-care tests (POCT) to support evidence-based decision-making around COVID-19 booster vaccinations. Using infectious virus neutralization, ACE2 blocking, spike binding, and TCR sequencing assays, we investigated the dynamics of changes in the breadth and depth of blood and salivary antibodies as well as T-cell clonal response following mRNA vaccination in a cohort of healthcare providers. We evaluated the accuracy of two POCTs utilizing either blood or saliva to identify those in whom humoral immunity was inadequate. >4 months after two doses of mRNA vaccine, SARS-CoV-2 binding and neutralizing Abs (nAbs) and T-cell clones declined 40-80%, and 2/3rd lacked Omicron nAbs. After the third mRNA booster, binding and neutralizing Abs increased overall in the systemic compartment; notably, individuals with previously weak nAbs gained sharply. The third dose failed to stimulate secretory IgA, but salivary IgG closely tracked systemic IgG levels. Vaccine boosting increased Ab breadth against a divergent bat sarbecovirus, SHC014, although the TCR-beta sequence breadth was unchanged. Post 3rd booster dose, Ab avidity increased for the Wuhan and Delta strains, while avidity against Omicron and SHC014 increased to levels seen for Wuhan after the second dose. Negative results on POCTs strongly correlated with a lack of functional humoral immunity. The third booster dose helps vaccinees gain depth and breadth of systemic Abs against evolving SARS-CoV-2 and related viruses. Our findings show that POCTs are useful and easy-to-access tools to inform inadequate humoral immunity accurately. POCTs designed to match the circulating variants can help individuals with booster vaccine decisions and could serve as a population-level screening platform to preserve herd immunity. One Sentence Summary SARS-CoV-2 point-of-care antibody tests are valuable and easy-to-access tools to inform inadequate humoral immunity and to support informed decision-making regarding the current and future booster vaccination.
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15
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Ruan R, Li L, Li X, Huang C, Zhang Z, Zhong H, Zeng S, Shi Q, Xia Y, Zeng Q, Wen Q, Chen J, Dai X, Xiong J, Xiang X, Lei W, Deng J. Unleashing the potential of combining FGFR inhibitor and immune checkpoint blockade for FGF/FGFR signaling in tumor microenvironment. Mol Cancer 2023; 22:60. [PMID: 36966334 PMCID: PMC10039534 DOI: 10.1186/s12943-023-01761-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 03/14/2023] [Indexed: 03/27/2023] Open
Abstract
BACKGROUND Fibroblast growth factors (FGFs) and their receptors (FGFRs) play a crucial role in cell fate and angiogenesis, with dysregulation of the signaling axis driving tumorigenesis. Therefore, many studies have targeted FGF/FGFR signaling for cancer therapy and several FGFR inhibitors have promising results in different tumors but treatment efficiency may still be improved. The clinical use of immune checkpoint blockade (ICB) has resulted in sustained remission for patients. MAIN: Although there is limited data linking FGFR inhibitors and immunotherapy, preclinical research suggest that FGF/FGFR signaling is involved in regulating the tumor microenvironment (TME) including immune cells, vasculogenesis, and epithelial-mesenchymal transition (EMT). This raises the possibility that ICB in combination with FGFR-tyrosine kinase inhibitors (FGFR-TKIs) may be feasible for treatment option for patients with dysregulated FGF/FGFR signaling. CONCLUSION Here, we review the role of FGF/FGFR signaling in TME regulation and the potential mechanisms of FGFR-TKI in combination with ICB. In addition, we review clinical data surrounding ICB alone or in combination with FGFR-TKI for the treatment of FGFR-dysregulated tumors, highlighting that FGFR inhibitors may sensitize the response to ICB by impacting various stages of the "cancer-immune cycle".
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Affiliation(s)
- Ruiwen Ruan
- Department of Oncology, First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, 330006, China
- Jiangxi Key Laboratory for lndividualized Cancer Therapy, 17 YongwaiStreet, Donghu District, Nanchang, Jiangxi, 330006, China
| | - Li Li
- Department of Oncology, First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, 330006, China
- Jiangxi Key Laboratory for lndividualized Cancer Therapy, 17 YongwaiStreet, Donghu District, Nanchang, Jiangxi, 330006, China
| | - Xuan Li
- Department of Oncology, First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, 330006, China
- Jiangxi Key Laboratory for lndividualized Cancer Therapy, 17 YongwaiStreet, Donghu District, Nanchang, Jiangxi, 330006, China
| | - Chunye Huang
- Department of Oncology, First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, 330006, China
- Jiangxi Key Laboratory for lndividualized Cancer Therapy, 17 YongwaiStreet, Donghu District, Nanchang, Jiangxi, 330006, China
| | - Zhanmin Zhang
- Department of Oncology, First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, 330006, China
- Jiangxi Key Laboratory for lndividualized Cancer Therapy, 17 YongwaiStreet, Donghu District, Nanchang, Jiangxi, 330006, China
| | - Hongguang Zhong
- Department of Oncology, First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, 330006, China
- Jiangxi Key Laboratory for lndividualized Cancer Therapy, 17 YongwaiStreet, Donghu District, Nanchang, Jiangxi, 330006, China
| | - Shaocheng Zeng
- Department of Oncology, First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, 330006, China
- Jiangxi Key Laboratory for lndividualized Cancer Therapy, 17 YongwaiStreet, Donghu District, Nanchang, Jiangxi, 330006, China
| | - Qianqian Shi
- Department of Oncology, First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, 330006, China
- Jiangxi Key Laboratory for lndividualized Cancer Therapy, 17 YongwaiStreet, Donghu District, Nanchang, Jiangxi, 330006, China
| | - Yang Xia
- Department of Oncology, First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, 330006, China
- Jiangxi Key Laboratory for lndividualized Cancer Therapy, 17 YongwaiStreet, Donghu District, Nanchang, Jiangxi, 330006, China
| | - Qinru Zeng
- Department of Oncology, First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, 330006, China
- Jiangxi Key Laboratory for lndividualized Cancer Therapy, 17 YongwaiStreet, Donghu District, Nanchang, Jiangxi, 330006, China
| | - Qin Wen
- Department of Oncology, First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, 330006, China
- Jiangxi Key Laboratory for lndividualized Cancer Therapy, 17 YongwaiStreet, Donghu District, Nanchang, Jiangxi, 330006, China
| | - Jingyi Chen
- Department of Oncology, First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, 330006, China
- Jiangxi Key Laboratory for lndividualized Cancer Therapy, 17 YongwaiStreet, Donghu District, Nanchang, Jiangxi, 330006, China
| | - Xiaofeng Dai
- Department of Oncology, First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, 330006, China
- Jiangxi Key Laboratory for lndividualized Cancer Therapy, 17 YongwaiStreet, Donghu District, Nanchang, Jiangxi, 330006, China
| | - Jianping Xiong
- Department of Oncology, First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, 330006, China
- Jiangxi Key Laboratory for lndividualized Cancer Therapy, 17 YongwaiStreet, Donghu District, Nanchang, Jiangxi, 330006, China
| | - Xiaojun Xiang
- Department of Oncology, First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, 330006, China.
- Jiangxi Key Laboratory for lndividualized Cancer Therapy, 17 YongwaiStreet, Donghu District, Nanchang, Jiangxi, 330006, China.
| | - Wan Lei
- Department of Oncology, First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, 330006, China.
- Jiangxi Key Laboratory for lndividualized Cancer Therapy, 17 YongwaiStreet, Donghu District, Nanchang, Jiangxi, 330006, China.
| | - Jun Deng
- Department of Oncology, First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, 330006, China.
- Jiangxi Key Laboratory for lndividualized Cancer Therapy, 17 YongwaiStreet, Donghu District, Nanchang, Jiangxi, 330006, China.
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16
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Lozano-Ojalvo D, Tyler SR, Aranda CJ, Wang J, Sicherer S, Sampson HA, Wood RA, Burks AW, Jones SM, Leung DYM, de Lafaille MC, Berin MC. Allergen recognition by specific effector Th2 cells enables IL-2-dependent activation of regulatory T-cell responses in humans. Allergy 2023; 78:697-713. [PMID: 36089900 PMCID: PMC10111618 DOI: 10.1111/all.15512] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 08/11/2022] [Accepted: 08/28/2022] [Indexed: 11/29/2022]
Abstract
Type 2 allergen-specific T cells are essential for the induction and maintenance of allergies to foods, and Tregs specific for these allergens are assumed to be involved in their resolution. However, it has not been convincingly demonstrated whether allergen-specific Treg responses are responsible for the generation of oral tolerance in humans. We observed that sustained food allergen exposure in the form of oral immunotherapy resulted in increased frequency of Tregs only in individuals with lasting clinical tolerance. We sought to identify regulatory components of the CD4+ T-cell response to food allergens by studying their functional activation over time in vitro and in vivo. Two subsets of Tregs expressing CD137 or CD25/OX40 were identified with a delayed kinetics of activation compared with clonally enriched pathogenic effector Th2 cells. Treg activation was dependent on IL-2 derived from effector T cells. In vivo exposure to peanut in the form of an oral food challenge of allergic subjects induced a delayed and persistent activation of Tregs after initiation of the allergen-specific Th2 response. The novel finding of our work is that a sustained wave of Treg activation is induced by the release of IL-2 from Th2 effector cells, with the implication that therapeutic administration of IL-2 could improve current OIT approaches.
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Affiliation(s)
- Daniel Lozano-Ojalvo
- Icahn School of Medicine at Mount Sinai, Jaffe Food Allergy Institute, New York, New York, USA
- Icahn School of Medicine at Mount Sinai, Precision Immunology Institute, New York, New York, USA
| | - Scott R Tyler
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Carlos J Aranda
- Icahn School of Medicine at Mount Sinai, Jaffe Food Allergy Institute, New York, New York, USA
- Icahn School of Medicine at Mount Sinai, Precision Immunology Institute, New York, New York, USA
| | - Julie Wang
- Icahn School of Medicine at Mount Sinai, Jaffe Food Allergy Institute, New York, New York, USA
| | - Scott Sicherer
- Icahn School of Medicine at Mount Sinai, Jaffe Food Allergy Institute, New York, New York, USA
| | - Hugh A Sampson
- Icahn School of Medicine at Mount Sinai, Jaffe Food Allergy Institute, New York, New York, USA
- Icahn School of Medicine at Mount Sinai, Precision Immunology Institute, New York, New York, USA
| | - Robert A Wood
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - A Wesley Burks
- Department of Medicine and Pediatrics, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Stacie M Jones
- Department of Pediatrics, University of Arkansas for Medical Sciences and Arkansas Children’s Hospital, Little Rock, Arkansas, USA
| | - Donald Y M Leung
- Department of Pediatrics, National Jewish Health, Denver, Colorado, USA
| | - Maria Curotto de Lafaille
- Icahn School of Medicine at Mount Sinai, Jaffe Food Allergy Institute, New York, New York, USA
- Icahn School of Medicine at Mount Sinai, Precision Immunology Institute, New York, New York, USA
| | - M Cecilia Berin
- Icahn School of Medicine at Mount Sinai, Jaffe Food Allergy Institute, New York, New York, USA
- Icahn School of Medicine at Mount Sinai, Precision Immunology Institute, New York, New York, USA
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17
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Azeem MI, Nooka AK, Shanmugasundaram U, Cheedarla N, Potdar S, Manalo RJ, Moreno A, Switchenko JM, Cheedarla S, Doxie DB, Radzievski R, Ellis ML, Manning KE, Wali B, Valanparambil RM, Maples KT, Baymon E, Kaufman JL, Hofmeister CC, Joseph NS, Lonial S, Roback JD, Sette A, Ahmed R, Suthar MS, Neish AS, Dhodapkar MV, Dhodapkar KM. Impaired SARS-CoV-2 Variant Neutralization and CD8+ T-cell Responses Following 3 Doses of mRNA Vaccines in Myeloma: Correlation with Breakthrough Infections. Blood Cancer Discov 2023; 4:106-117. [PMID: 36511813 PMCID: PMC9975771 DOI: 10.1158/2643-3230.bcd-22-0173] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/23/2022] [Accepted: 12/06/2022] [Indexed: 12/15/2022] Open
Abstract
Patients with multiple myeloma (MM) mount suboptimal neutralizing antibodies (nAb) following 2 doses of SARS-CoV-2 mRNA vaccines. Currently, circulating SARS-CoV-2 variants of concern (VOC) carry the risk of breakthrough infections. We evaluated immune recognition of current VOC including BA.1, BA.2, and BA.5 in 331 racially representative patients with MM following 2 or 3 doses of mRNA vaccines. The third dose increased nAbs against WA1 in 82%, but against BA variants in only 33% to 44% of patients. Vaccine-induced nAbs correlated with receptor-binding domain (RBD)-specific class-switched memory B cells. Vaccine-induced spike-specific T cells were detected in patients without seroconversion and cross-recognized variant-specific peptides but were predominantly CD4+ T cells. Detailed clinical/immunophenotypic analysis identified features correlating with nAb/B/T-cell responses. Patients who developed breakthrough infections following 3 vaccine doses had lower live-virus nAbs, including against VOC. Patients with MM remain susceptible to SARS-CoV-2 variants following 3 vaccine doses and should be prioritized for emerging approaches to elicit variant-nAb and CD8+ T cells. SIGNIFICANCE Three doses of SARS-CoV-2 mRNA vaccines fail to yield detectable VOC nAbs in nearly 60% and spike-specific CD8+ T cells in >80% of myeloma patients. Patients who develop breakthrough infections following vaccination have low levels of live-virus nAb. This article is highlighted in the In This Issue feature, p. 101.
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Affiliation(s)
- Maryam I. Azeem
- Department of Hematology/Medical Oncology, Emory University, Atlanta, Georgia
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Emory University, Atlanta, Georgia
| | - Ajay K. Nooka
- Department of Hematology/Medical Oncology, Emory University, Atlanta, Georgia
- Winship Cancer Institute, Atlanta, Georgia
| | | | | | - Sayalee Potdar
- Department of Hematology/Medical Oncology, Emory University, Atlanta, Georgia
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Emory University, Atlanta, Georgia
| | - Renee Julia Manalo
- Department of Hematology/Medical Oncology, Emory University, Atlanta, Georgia
| | - Alberto Moreno
- Emory Vaccine Center, Emory University, Atlanta, Georgia
- Emory National Primate Research Center, Atlanta, Georgia
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia
| | | | | | | | | | - Madison Leigh Ellis
- Emory Vaccine Center, Emory University, Atlanta, Georgia
- Emory National Primate Research Center, Atlanta, Georgia
| | - Kelly E. Manning
- Emory Vaccine Center, Emory University, Atlanta, Georgia
- Emory National Primate Research Center, Atlanta, Georgia
| | - Bushra Wali
- Emory Vaccine Center, Emory University, Atlanta, Georgia
- Emory National Primate Research Center, Atlanta, Georgia
| | | | | | | | - Jonathan L. Kaufman
- Department of Hematology/Medical Oncology, Emory University, Atlanta, Georgia
- Winship Cancer Institute, Atlanta, Georgia
| | - Craig C. Hofmeister
- Department of Hematology/Medical Oncology, Emory University, Atlanta, Georgia
- Winship Cancer Institute, Atlanta, Georgia
| | - Nisha S. Joseph
- Department of Hematology/Medical Oncology, Emory University, Atlanta, Georgia
- Winship Cancer Institute, Atlanta, Georgia
| | - Sagar Lonial
- Department of Hematology/Medical Oncology, Emory University, Atlanta, Georgia
- Winship Cancer Institute, Atlanta, Georgia
| | - John D. Roback
- Winship Cancer Institute, Atlanta, Georgia
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia
| | | | - Rafi Ahmed
- Winship Cancer Institute, Atlanta, Georgia
- Emory Vaccine Center, Emory University, Atlanta, Georgia
- Department of Microbiology and Immunology, Emory University, Atlanta, Georgia
| | - Mehul S. Suthar
- Emory Vaccine Center, Emory University, Atlanta, Georgia
- Emory National Primate Research Center, Atlanta, Georgia
- Department of Microbiology and Immunology, Emory University, Atlanta, Georgia
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia
| | - Andrew S. Neish
- Winship Cancer Institute, Atlanta, Georgia
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia
| | - Madhav V. Dhodapkar
- Department of Hematology/Medical Oncology, Emory University, Atlanta, Georgia
- Winship Cancer Institute, Atlanta, Georgia
| | - Kavita M. Dhodapkar
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Emory University, Atlanta, Georgia
- Winship Cancer Institute, Atlanta, Georgia
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia
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18
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Malle L, Patel RS, Martin-Fernandez M, Stewart OJ, Philippot Q, Buta S, Richardson A, Barcessat V, Taft J, Bastard P, Samuels J, Mircher C, Rebillat AS, Maillebouis L, Vilaire-Meunier M, Tuballes K, Rosenberg BR, Trachtman R, Casanova JL, Notarangelo LD, Gnjatic S, Bush D, Bogunovic D. Autoimmunity in Down's syndrome via cytokines, CD4 T cells and CD11c + B cells. Nature 2023; 615:305-314. [PMID: 36813963 PMCID: PMC9945839 DOI: 10.1038/s41586-023-05736-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 01/17/2023] [Indexed: 02/24/2023]
Abstract
Down's syndrome (DS) presents with a constellation of cardiac, neurocognitive and growth impairments. Individuals with DS are also prone to severe infections and autoimmunity including thyroiditis, type 1 diabetes, coeliac disease and alopecia areata1,2. Here, to investigate the mechanisms underlying autoimmune susceptibility, we mapped the soluble and cellular immune landscape of individuals with DS. We found a persistent elevation of up to 22 cytokines at steady state (at levels often exceeding those in patients with acute infection) and detected basal cellular activation: chronic IL-6 signalling in CD4 T cells and a high proportion of plasmablasts and CD11c+TbethighCD21low B cells (Tbet is also known as TBX21). This subset is known to be autoimmune-prone and displayed even greater autoreactive features in DS including receptors with fewer non-reference nucleotides and higher IGHV4-34 utilization. In vitro, incubation of naive B cells in the plasma of individuals with DS or with IL-6-activated T cells resulted in increased plasmablast differentiation compared with control plasma or unstimulated T cells, respectively. Finally, we detected 365 auto-antibodies in the plasma of individuals with DS, which targeted the gastrointestinal tract, the pancreas, the thyroid, the central nervous system, and the immune system itself. Together, these data point to an autoimmunity-prone state in DS, in which a steady-state cytokinopathy, hyperactivated CD4 T cells and ongoing B cell activation all contribute to a breach in immune tolerance. Our findings also open therapeutic paths, as we demonstrate that T cell activation is resolved not only with broad immunosuppressants such as Jak inhibitors, but also with the more tailored approach of IL-6 inhibition.
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Affiliation(s)
- Louise Malle
- Center for Inborn Errors of Immunity, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Roosheel S Patel
- Center for Inborn Errors of Immunity, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marta Martin-Fernandez
- Center for Inborn Errors of Immunity, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - O Jay Stewart
- Center for Inborn Errors of Immunity, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Quentin Philippot
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
| | - Sofija Buta
- Center for Inborn Errors of Immunity, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ashley Richardson
- Center for Inborn Errors of Immunity, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vanessa Barcessat
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Justin Taft
- Center for Inborn Errors of Immunity, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Paul Bastard
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Pediatric Hematology-Immunology and Rheumatology Unit, Necker Hospital for Sick Children, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Julie Samuels
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | | | | | | | - Kevin Tuballes
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Brad R Rosenberg
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rebecca Trachtman
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Department of Pediatrics, Necker Hospital for Sick Children, Paris, France
- Howard Hughes Medical Institute, New York, NY, USA
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sacha Gnjatic
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Douglas Bush
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dusan Bogunovic
- Center for Inborn Errors of Immunity, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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19
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Chen R, Li J, Fujimoto J, Hong L, Hu X, Quek K, Tang M, Mitra A, Behrens C, Chow CW, Jiang P, Little LD, Gumbs C, Song X, Zhang J, Tan D, Heymach JV, Wistuba I, Futreal PA, Gibbons DL, Byers LA, Zhang J, Reuben A. Immunogenomic intertumor heterogeneity across primary and metastatic sites in a patient with lung adenocarcinoma. J Exp Clin Cancer Res 2022; 41:172. [PMID: 35546239 PMCID: PMC9092788 DOI: 10.1186/s13046-022-02361-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 04/10/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Lung cancer is the leading cause of cancer death, partially owing to its extensive heterogeneity. The analysis of intertumor heterogeneity has been limited by an inability to concurrently obtain tissue from synchronous metastases unaltered by multiple prior lines of therapy.
Methods
In order to study the relationship between genomic, epigenomic and T cell repertoire heterogeneity in a rare autopsy case from a 32-year-old female never-smoker with left lung primary late-stage lung adenocarcinoma (LUAD), we did whole-exome sequencing (WES), DNA methylation and T cell receptor (TCR) sequencing to characterize the immunogenomic landscape of one primary and 19 synchronous metastatic tumors.
Results
We observed heterogeneous mutation, methylation, and T cell patterns across distinct metastases. Only TP53 mutation was detected in all tumors suggesting an early event while other cancer gene mutations were later events which may have followed subclonal diversification. A set of prevalent T cell clonotypes were completely excluded from left-side thoracic tumors indicating distinct T cell repertoire profiles between left-side and non left-side thoracic tumors. Though a limited number of predicted neoantigens were shared, these were associated with homology of the T cell repertoire across metastases. Lastly, ratio of methylated neoantigen coding mutations was negatively associated with T-cell density, richness and clonality, suggesting neoantigen methylation may partially drive immunosuppression.
Conclusions
Our study demonstrates heterogeneous genomic and T cell profiles across synchronous metastases and how restriction of unique T cell clonotypes within an individual may differentially shape the genomic and epigenomic landscapes of synchronous lung metastases.
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20
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Takahashi H, Kühtreiber WM, Keefe RC, Lee AH, Aristarkhova A, Dias HF, Ng N, Nelson KJ, Bien S, Scheffey D, Faustman DL. BCG vaccinations drive epigenetic changes to the human T cell receptor: Restored expression in type 1 diabetes. SCIENCE ADVANCES 2022; 8:eabq7240. [PMID: 36383663 PMCID: PMC9668301 DOI: 10.1126/sciadv.abq7240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 09/27/2022] [Indexed: 06/16/2023]
Abstract
The BCG (Bacille Calmette-Guérin) vaccine, introduced 100 years ago for tuberculosis prevention, has emerging therapeutic off-target benefits for autoimmunity. In randomized controlled trials, BCG vaccinations were shown to gradually improve two autoimmune conditions, type 1 diabetes (T1D) and multiple sclerosis. Here, we investigate the mechanisms behind the autoimmune benefits and test the hypothesis that this microbe synergy could be due to an impact on the host T cell receptor (TCR) and TCR signal strength. We show a quantitative TCR defect in T1D subjects consisting of a marked reduction in receptor density on T cells due to hypermethylation of TCR-related genes. BCG corrects this defect gradually over 3 years by demethylating hypermethylated sites on members of the TCR gene family. The TCR sequence is not modified through recombination, ruling out a qualitative defect. These findings support an underlying density defect in the TCR affecting TCR signal strength in T1D.
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Affiliation(s)
- Hiroyuki Takahashi
- Immunobiology Department, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02129, USA
| | - Willem M. Kühtreiber
- Immunobiology Department, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02129, USA
| | - Ryan C. Keefe
- Immunobiology Department, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02129, USA
| | - Amanda H. Lee
- Immunobiology Department, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02129, USA
| | - Anna Aristarkhova
- Immunobiology Department, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02129, USA
| | - Hans F. Dias
- Immunobiology Department, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02129, USA
| | - Nathan Ng
- Immunobiology Department, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02129, USA
| | - Kacie J. Nelson
- Immunobiology Department, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02129, USA
| | | | | | - Denise L. Faustman
- Immunobiology Department, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02129, USA
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21
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Sigdel TK, Fields PA, Liberto J, Damm I, Kerwin M, Hood J, Towfighi P, Sirota M, Robins HS, Sarwal MM. Perturbations of the T-cell immune repertoire in kidney transplant rejection. Front Immunol 2022; 13:1012042. [PMID: 36466928 PMCID: PMC9709472 DOI: 10.3389/fimmu.2022.1012042] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 10/26/2022] [Indexed: 01/06/2024] Open
Abstract
In this cross-sectional and longitudinal analysis of mapping the T-cell repertoire in kidney transplant recipients, we have investigated and validated T-cell clonality, immune repertoire chronology at rejection, and contemporaneous allograft biopsy quantitative tissue injury, to better understand the pathobiology of acute T-cell fraction, T-cell repertoire and antibody-mediated kidney transplant rejection. To follow the dynamic evolution of T-cell repertoire changes before and after engraftment and during biopsy-confirmed acute rejection, we sequenced 323 peripheral blood samples from 200 unique kidney transplant recipients, with (n=100) and without (n=100) biopsy-confirmed acute rejection. We report that patients who develop acute allograft rejection, have lower (p=0.01) T-cell fraction even before transplantation, followed by its rise after transplantation and at the time of acute rejection accompanied by high TCR repertoire turnover (p=0.004). Acute rejection episodes occurring after the first 6 months post-transplantation, and those with a component of antibody-mediated rejection, had the highest turnover; p=0.0016) of their T-cell repertoire. In conclusion, we validated that detecting repertoire changes in kidney transplantation correlates with post-transplant rejection episodes suggesting that T-cell receptor sequencing may provide recipient pre-transplant and post-transplant predictors of rejection risk.
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Affiliation(s)
- Tara K. Sigdel
- Department of Surgery, Division of Multi Organ Transplantation, University of California, San Francisco, San Francisco, CA, United States
| | | | - Juliane Liberto
- Department of Surgery, Division of Multi Organ Transplantation, University of California, San Francisco, San Francisco, CA, United States
| | - Izabella Damm
- Department of Surgery, Division of Multi Organ Transplantation, University of California, San Francisco, San Francisco, CA, United States
| | - Maggie Kerwin
- Department of Surgery, Division of Multi Organ Transplantation, University of California, San Francisco, San Francisco, CA, United States
| | - Jill Hood
- Adaptive Biotechnologies, Seattle, WA, United States
| | - Parhom Towfighi
- Department of Surgery, Division of Multi Organ Transplantation, University of California, San Francisco, San Francisco, CA, United States
| | - Marina Sirota
- Department of Surgery, Division of Multi Organ Transplantation, University of California, San Francisco, San Francisco, CA, United States
| | | | - Minnie M. Sarwal
- Department of Surgery, Division of Multi Organ Transplantation, University of California, San Francisco, San Francisco, CA, United States
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22
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Ford ES, Mayer-Blackwell K, Jing L, Sholukh AM, St Germain R, Bossard EL, Xie H, Pulliam TH, Jani S, Selke S, Burrow CJ, McClurkan CL, Wald A, Holbrook MR, Eaton B, Eudy E, Murphy M, Postnikova E, Robins HS, Elyanow R, Gittelman RM, Ecsedi M, Wilcox E, Chapuis AG, Fiore-Gartland A, Koelle DM. CD8 + T cell clonotypes from prior SARS-CoV-2 infection predominate during the cellular immune response to mRNA vaccination. RESEARCH SQUARE 2022:rs.3.rs-2146712. [PMID: 36263073 PMCID: PMC9580387 DOI: 10.21203/rs.3.rs-2146712/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Almost three years into the SARS-CoV-2 pandemic, hybrid immunity is highly prevalent worldwide and more protective than vaccination or prior infection alone. Given emerging resistance of variant strains to neutralizing antibodies (nAb), it is likely that T cells contribute to this protection. To understand how sequential SARS-CoV-2 infection and mRNA-vectored SARS-CoV-2 spike (S) vaccines affect T cell clonotype-level expansion kinetics, we identified and cross-referenced TCR sequences from thousands of S-reactive single cells against deeply sequenced peripheral blood TCR repertoires longitudinally collected from persons during COVID-19 convalescence through booster vaccination. Successive vaccinations recalled memory T cells and elicited antigen-specific T cell clonotypes not detected after infection. Vaccine-related recruitment of novel clonotypes and the expansion of S-specific clones were most strongly observed for CD8+ T cells. Severe COVID-19 illness was associated with a more diverse CD4+ T cell response to SARS-CoV-2 both prior to and after mRNA vaccination, suggesting imprinting of CD4+ T cells by severe infection. TCR sequence similarity search algorithms revealed myriad public TCR clusters correlating with human leukocyte antigen (HLA) alleles. Selected TCRs from distinct clusters functionally recognized S in the predicted HLA context, with fine viral peptide requirements differing between TCRs. Most subjects tested had S-specific T cells in the nasal mucosa after a 3rd mRNA vaccine dose. The blood and nasal T cell responses to vaccination revealed by clonal tracking were more heterogeneous than nAb boosts. Analysis of bulk and single cell TCR sequences reveals T cell kinetics and diversity at the clonotype level, without requiring prior knowledge of T cell epitopes or HLA restriction, providing a roadmap for rapid assessment of T cell responses to emerging pathogens.
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23
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Akhave N, Zhang J, Bayley E, Frank M, Chiou SH, Behrens C, Chen R, Hu X, Parra ER, Lee WC, Swisher S, Solis L, Weissferdt A, Moran C, Kalhor N, Zhang J, Scheet P, Vaporciyan AA, Sepesi B, Gibbons DL, Heymach JV, Lee JJ, Wistuba II, Andrew Futreal P, Zhang J, Fujimoto J, Reuben A. Immunogenomic profiling of lung adenocarcinoma reveals poorly differentiated tumors are associated with an immunogenic tumor microenvironment. Lung Cancer 2022; 172:19-28. [PMID: 35973335 DOI: 10.1016/j.lungcan.2022.08.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 08/05/2022] [Accepted: 08/06/2022] [Indexed: 10/15/2022]
Abstract
OBJECTIVES Pathologists have routinely observed distinct histologic patterns of growth in early-stage lung adenocarcinoma (LUAD), which have been suggested to be associated with prognosis. Herein, we investigated the relationship between LUAD patterns of growth, as defined by the updated international association for the study of lung cancer (IASLC) grading criteria, and differences in the tumor immune microenvironment to identify predictors of response to immunotherapy. METHODS 174 resected stage I-III LUAD tumors were classified by histologic pattern of growth (i.e. solid, micropapillary, acinar, papillary, and lepidic) and then grouped as well differentiated, moderately differentiated, and poorly differentiated. Comprehensive multiplatform analysis including whole exome sequencing, gene expression profiling, immunohistochemistry, CIBERSORT, and T-cell receptor sequencing was performed and groups were compared for differences in genomic drivers, immune cell infiltrate, clonality, and survival. Finally, multivariate analysis was performed adjusting for pathologic stage and smoking status. RESULTS Poorly differentiated tumors demonstrated a strong association with smoking relative to moderately differentiated or well differentiated tumors. However, unlike in prior reports, poorly differentiated tumors were not associated with a worse survival after curative-intent resection. Genomic analysis revealed that poorly differentiated tumors are associated with high tumor mutation burden but showed no association with oncogenic drivers. Immune analyses revealed that poorly differentiated tumors are associated with increased T-cell clonality, expression of PD-L1, and infiltration by cytotoxic CD8 T-cells, activated CD4 T-cells, and pro-inflammatory (M1) macrophages. Finally, multivariate analysis controlling for stage and smoking status confirmed independence of immune differences between IASLC grade groups. CONCLUSIONS Poorly differentiated tumors, as defined by the updated IASLC grading criteria, are associated with a distinct immunogenic tumor microenvironment that predicts for therapeutic response to immune agents, including checkpoint inhibitors, and should be included in the clinical trial design of immunotherapy studies in early-stage lung adenocarcinoma.
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Affiliation(s)
- Neal Akhave
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA
| | - Jiexin Zhang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA
| | - Erin Bayley
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA
| | - Meredith Frank
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA
| | - Shin-Heng Chiou
- Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, 195 Little Albany St, New Brunswick, NJ 08901, USA
| | - Carmen Behrens
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA; Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA
| | - Runzhe Chen
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA
| | - Xin Hu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA
| | - Edwin Roger Parra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA
| | - Won-Chul Lee
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA
| | - Stephen Swisher
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA
| | - Luisa Solis
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA
| | - Annikka Weissferdt
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA; Department of Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA
| | - Cesar Moran
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA; Department of Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA
| | - Neda Kalhor
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA; Department of Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA
| | - Paul Scheet
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA; Department of Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA
| | - Ara A Vaporciyan
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA
| | - Boris Sepesi
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA
| | - Don L Gibbons
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA
| | - John V Heymach
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA
| | - Jack J Lee
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA
| | - Ignacio I Wistuba
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA; Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA
| | - P Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA
| | - Jianjun Zhang
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA.
| | - Junya Fujimoto
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA.
| | - Alexandre Reuben
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA.
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24
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Elyanow R, Snyder TM, Dalai SC, Gittelman RM, Boonyaratanakornkit J, Wald A, Selke S, Wener MH, Morishima C, Greninger AL, Gale M, Hsiang TY, Jing L, Holbrook MR, Kaplan IM, Zahid HJ, May DH, Carlson JM, Baldo L, Manley T, Robins HS, Koelle DM. T cell receptor sequencing identifies prior SARS-CoV-2 infection and correlates with neutralizing antibodies and disease severity. JCI Insight 2022; 7:e150070. [PMID: 35439166 PMCID: PMC9220924 DOI: 10.1172/jci.insight.150070] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 04/15/2022] [Indexed: 11/17/2022] Open
Abstract
BACKGROUNDMeasuring the immune response to SARS-CoV-2 enables assessment of past infection and protective immunity. SARS-CoV-2 infection induces humoral and T cell responses, but these responses vary with disease severity and individual characteristics.METHODSA T cell receptor (TCR) immunosequencing assay was conducted using small-volume blood samples from 302 individuals recovered from COVID-19. Correlations between the magnitude of the T cell response and neutralizing antibody (nAb) titers or indicators of disease severity were evaluated. Sensitivity of T cell testing was assessed and compared with serologic testing.RESULTSSARS-CoV-2-specific T cell responses were significantly correlated with nAb titers and clinical indicators of disease severity, including hospitalization, fever, and difficulty breathing. Despite modest declines in depth and breadth of T cell responses during convalescence, high sensitivity was observed until at least 6 months after infection, with overall sensitivity ~5% greater than serology tests for identifying prior SARS-CoV-2 infection. Improved performance of T cell testing was most apparent in recovered, nonhospitalized individuals sampled > 150 days after initial illness, suggesting greater sensitivity than serology at later time points and in individuals with less severe disease. T cell testing identified SARS-CoV-2 infection in 68% (55 of 81) of samples with undetectable nAb titers (<1:40) and in 37% (13 of 35) of samples classified as negative by 3 antibody assays.CONCLUSIONThese results support TCR-based testing as a scalable, reliable measure of past SARS-CoV-2 infection with clinical value beyond serology.TRIAL REGISTRATIONSpecimens were accrued under trial NCT04338360 accessible at clinicaltrials.gov.FUNDINGThis work was funded by Adaptive Biotechnologies, Frederick National Laboratory for Cancer Research, NIAID, Fred Hutchinson Joel Meyers Endowment, Fast Grants, and American Society for Transplantation and Cell Therapy.
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Affiliation(s)
| | | | - Sudeb C. Dalai
- Adaptive Biotechnologies, Seattle, Washington, USA
- Stanford University School of Medicine, Stanford, California, USA
| | | | - Jim Boonyaratanakornkit
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Anna Wald
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Epidemiology
- Department of Laboratory Medicine and Pathology
| | - Stacy Selke
- Department of Laboratory Medicine and Pathology
| | - Mark H. Wener
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology
| | | | | | - Michael Gale
- Department of Immunology
- Department of Microbiology, and
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | | | - Lichen Jing
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Michael R. Holbrook
- National Institute of Allergy and Infectious Diseases (NIAID) Integrated Research Facility, Frederick, Maryland, USA
| | | | | | - Damon H. May
- Adaptive Biotechnologies, Seattle, Washington, USA
| | | | - Lance Baldo
- Adaptive Biotechnologies, Seattle, Washington, USA
| | | | | | - David M. Koelle
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Benaroya Research Institute, Seattle, Washington, USA
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25
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Gittelman RM, Lavezzo E, Snyder TM, Zahid HJ, Carty CL, Elyanow R, Dalai S, Kirsch I, Baldo L, Manuto L, Franchin E, Del Vecchio C, Pacenti M, Boldrin C, Cattai M, Saluzzo F, Padoan A, Plebani M, Simeoni F, Bordini J, Lorè NI, Lazarević D, Cirillo DM, Ghia P, Toppo S, Carlson JM, Robins HS, Crisanti A, Tonon G. Longitudinal analysis of T cell receptor repertoires reveals shared patterns of antigen-specific response to SARS-CoV-2 infection. JCI Insight 2022; 7:e151849. [PMID: 35439174 PMCID: PMC9220833 DOI: 10.1172/jci.insight.151849] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 04/13/2022] [Indexed: 11/22/2022] Open
Abstract
T cells play a prominent role in orchestrating the immune response to viral diseases, but their role in the clinical presentation and subsequent immunity to SARS-CoV-2 infection remains poorly understood. As part of a population-based survey of the municipality of Vo', Italy, conducted after the initial SARS-CoV-2 outbreak, we sampled the T cell receptor (TCR) repertoires of the population 2 months after the initial PCR survey and followed up positive cases 9 and 15 months later. At 2 months, we found that 97.0% (98 of 101) of cases had elevated levels of TCRs associated with SARS-CoV-2. T cell frequency (depth) was increased in individuals with more severe disease. Both depth and diversity (breadth) of the TCR repertoire were positively associated with neutralizing antibody titers, driven mostly by CD4+ T cells directed against spike protein. At the later time points, detection of these TCRs remained high, with 90.7% (78 of 96) and 86.2% (25 of 29) of individuals having detectable signal at 9 and 15 months, respectively. Forty-three individuals were vaccinated by month 15 and showed a significant increase in TCRs directed against spike protein. Taken together, these results demonstrate the central role of T cells in mounting an immune defense against SARS-CoV-2 that persists out to 15 months.
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Affiliation(s)
| | - Enrico Lavezzo
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | | | | | | | | | - Sudeb Dalai
- Adaptive Biotechnologies, Seattle, Washington, USA
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Ilan Kirsch
- Adaptive Biotechnologies, Seattle, Washington, USA
| | - Lance Baldo
- Adaptive Biotechnologies, Seattle, Washington, USA
| | - Laura Manuto
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Elisa Franchin
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | | | - Monia Pacenti
- Azienda Ospedale Padova, Microbiology and Virology Unit, Padua, Italy
| | - Caterina Boldrin
- Azienda Ospedale Padova, Microbiology and Virology Unit, Padua, Italy
| | - Margherita Cattai
- Azienda Ospedale Padova, Microbiology and Virology Unit, Padua, Italy
| | - Francesca Saluzzo
- Division of Immunology, Transplantation and Infectious Disease, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Andrea Padoan
- Department of Medicine, University of Padova, Padua, Italy
| | - Mario Plebani
- Department of Medicine, University of Padova, Padua, Italy
| | | | - Jessica Bordini
- Division of Experimental Oncology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Nicola I. Lorè
- Division of Immunology, Transplantation and Infectious Disease, IRCCS Ospedale San Raffaele, Milan, Italy
| | | | - Daniela M. Cirillo
- Division of Immunology, Transplantation and Infectious Disease, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Paolo Ghia
- Division of Experimental Oncology, IRCCS Ospedale San Raffaele, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Stefano Toppo
- Department of Molecular Medicine, University of Padova, Padua, Italy
- CRIBI Biotech Center, University of Padova, Padua, Italy
| | | | | | - Andrea Crisanti
- Department of Molecular Medicine, University of Padova, Padua, Italy
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Giovanni Tonon
- Center for Omics Sciences and
- Division of Experimental Oncology, IRCCS Ospedale San Raffaele, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
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26
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Yaddanapudi K, Stamp BF, Subrahmanyam PB, Smolenkov A, Waigel SJ, Gosain R, Egger ME, Martin RC, Buscaglia R, Maecker HT, McMasters KM, Chesney JA. Single-Cell Immune Mapping of Melanoma Sentinel Lymph Nodes Reveals an Actionable Immunotolerant Microenvironment. Clin Cancer Res 2022; 28:2069-2081. [PMID: 35046061 PMCID: PMC9840851 DOI: 10.1158/1078-0432.ccr-21-0664] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 05/16/2021] [Accepted: 01/14/2022] [Indexed: 01/17/2023]
Abstract
PURPOSE Improving our understanding of the immunologic response to cancer cells within the sentinel lymph nodes (SLN) of primary tumors is expected to identify new approaches to stimulate clinically meaningful cancer immunity. EXPERIMENTAL DESIGN We used mass cytometry by time-of-flight (CyTOF), flow cytometry, and T-cell receptor immunosequencing to conduct simultaneous single-cell analyses of immune cells in the SLNs of patients with melanoma. RESULTS We found increased effector-memory αβ T cells, TCR clonality, and γδ T cells selectively in the melanoma-bearing SLNs relative to non-melanoma-bearing SLNs, consistent with possible activation of an antitumor immune response. However, we also observed a markedly immunotolerant environment in the melanoma-bearing SLNs indicated by reduced and impaired NK cells and increased levels of CD8+CD57+PD-1+ cells, which are known to display low melanoma killing capabilities. Other changes observed in melanoma-bearing SLNs when compared with non-melanoma-bearing SLNs include (i) reduced CD8+CD69+ T cell/T regulatory cell ratio, (ii) high PD-1 expression on CD4+ and CD8+ T cells, and (iii) high CTLA-4 expression on γδ T cells. CONCLUSIONS Our data suggest that these immunologic changes compromise antimelanoma immunity and contribute to a high relapse rate. We propose the development of clinical trials to test the neo-adjuvant administration of anti-PD-1 antibodies prior to SLN resection in patients with stage III melanoma. See related commentary by Lund, p. 1996.
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Affiliation(s)
- Kavitha Yaddanapudi
- Immuno-Oncology Group, James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA,Department of Surgery, Division of Immunotherapy, University of Louisville, Louisville, KY, USA,Department of Microbiology/Immunology, University of Louisville, Louisville, KY, USA
| | - Bryce F. Stamp
- Immuno-Oncology Group, James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA,Department of Surgery, Division of Immunotherapy, University of Louisville, Louisville, KY, USA
| | - Priyanka B. Subrahmanyam
- Institute for Immunity, Transplantation and Infection, Stanford School of Medicine, Stanford, CA, USA
| | - Andrei Smolenkov
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA
| | - Sabine J. Waigel
- Department of Medicine, University of Louisville, Louisville, KY, USA
| | - Rahul Gosain
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA
| | - Michael E. Egger
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA,Department of Surgery, Division of Surgical Oncology, University of Louisville, Louisville, KY, USA
| | - Robert C.G. Martin
- Department of Surgery, Division of Surgical Oncology, University of Louisville, Louisville, KY, USA,Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, USA
| | - Robert Buscaglia
- Department of Mathematics and Statistics, Northern Arizona University, Arizona, USA
| | - Holden T. Maecker
- Institute for Immunity, Transplantation and Infection, Stanford School of Medicine, Stanford, CA, USA
| | - Kelly M. McMasters
- Department of Surgery, Division of Surgical Oncology, University of Louisville, Louisville, KY, USA,Correspondence to: Jason A. Chesney, MD, PhD, Kelly M. McMasters, MD, PhD, University of Louisville, Clinical and Translational Research Building, Louisville, KY 40202, ,
| | - Jason A. Chesney
- Immuno-Oncology Group, James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA,Department of Medicine, University of Louisville, Louisville, KY, USA,Department of Surgery, Division of Immunotherapy, University of Louisville, Louisville, KY, USA,Correspondence to: Jason A. Chesney, MD, PhD, Kelly M. McMasters, MD, PhD, University of Louisville, Clinical and Translational Research Building, Louisville, KY 40202, ,
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27
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Kim JK, Chen CT, Keshinro A, Khan A, Firat C, Vanderbilt C, Segal N, Stadler Z, Shia J, Balachandran VP, Weiser MR. Intratumoral T-cell repertoires in DNA mismatch repair-proficient and -deficient colon tumors containing high or low numbers of tumor-infiltrating lymphocytes. Oncoimmunology 2022; 11:2054757. [PMID: 35481287 PMCID: PMC9037499 DOI: 10.1080/2162402x.2022.2054757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Colon tumors with deficient DNA mismatch repair (dMMR) are generally infiltrated by T cells more densely than tumors with proficient mismatch repair (pMMR). However, high numbers of tumor-infiltrating lymphocytes (TILs) are found in select pMMR tumors, and low numbers of TILs are seen in select dMMR tumors. In this study, we compared T-cell repertoires in 20 pMMR and 27 dMMR colon tumors with high and low TIL counts. We found that T cells in dMMR tumors are more clonal and their repertoire is less rich compared with T cells in pMMR tumors. In the dMMR group, T cells in TIL-high tumors were more clonal and their repertoire was less rich compared with T cells in TIL-low tumors, but in the pMMR group, T-cell diversity in TIL-high tumors was comparable to T-cell diversity in TIL-low tumors. These findings suggest that T cells clonally expand in dMMR tumors, possibly in response to MMR deficiency-induced tumor neoantigens.
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Affiliation(s)
- Jin K. Kim
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Chin-Tung Chen
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ajaratu Keshinro
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Asama Khan
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Canan Firat
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Chad Vanderbilt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Neil Segal
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Zsofia Stadler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jinru Shia
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Vinod P. Balachandran
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Martin R. Weiser
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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28
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Chun B, Pucilowska J, Chang S, Kim I, Nikitin B, Koguchi Y, Redmond WL, Bernard B, Rajamanickam V, Polaske N, Fields PA, Conrad V, Schmidt M, Urba WJ, Conlin AK, McArthur HL, Page DB. Changes in T-cell subsets and clonal repertoire during chemoimmunotherapy with pembrolizumab and paclitaxel or capecitabine for metastatic triple-negative breast cancer. J Immunother Cancer 2022; 10:jitc-2021-004033. [PMID: 35086949 PMCID: PMC8796261 DOI: 10.1136/jitc-2021-004033] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Chemoimmunotherapy is a standard treatment for triple-negative breast cancer (TNBC), however, the impacts of different chemotherapies on T-cell populations, which could correlate with clinical activity, are not known. Quantifying T-cell populations with flow cytometry and T-cell receptor (TCR) immunosequencing may improve our understanding of how chemoimmunotherapy affects T-cell subsets, and to what extent clonal shifts occur during treatment. TCR immunosequencing of intratumoral T cells may facilitate the identification and monitoring of putatively tumor-reactive T-cell clones within the blood. METHODS Blood and tumor biopsies were collected from patients with metastatic TNBC enrolled in a phase Ib clinical trial of first or second-line pembrolizumab with paclitaxel or capecitabine. Using identical biospecimen processing protocols, blood samples from a cohort of patients treated for early-stage breast cancer were obtained for comparison. Treatment-related immunological changes in peripheral blood and intratumoral T cells were characterized using flow cytometry and TCR immunosequencing. Clonal proliferation rates of T cells were compared based on intratumoral enrichment. RESULTS When combined with pembrolizumab, paclitaxel and capecitabine resulted in similar time-dependent lymphodepletions across measured peripheral T-cell subsets. Their effects were more modest than that observed following curative-intent dose-dense anthracycline and cyclophosphamide (ddAC) (average fold-change in CD3+ cells, capecitabine: -0.42, paclitaxel: -0.56, ddAC: -1.21). No differences in T-cell clonality or richness were observed following capecitabine or paclitaxel-based treatments. Regression modeling identified differences in the emergence of novel T-cell clones that were not detected at baseline (odds compared with ddAC, capecitabine: 0.292, paclitaxel: 0.652). Pembrolizumab with paclitaxel or capecitabine expanded T-cell clones within tumors; however, these clones did not always expand within the blood. Proliferation rates within the blood were similar between clones that were enriched and those that were not enriched within tumors. CONCLUSION Chemoimmunotherapy for metastatic TNBC with pembrolizumab and capecitabine or paclitaxel resulted in similar peripheral T-cell subset lymphodepletion without altering T-cell clonal diversity. Regression modeling methods are applicable in immune monitoring studies, such as this to identify the odds of novel T-cell clones emerging during treatment, and proliferation rates of tumor-enriched T-cell clones.
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Affiliation(s)
- Brie Chun
- Earle A Chiles Research Institute, Providence Cancer Institute, Portland, Oregon, USA
| | - Joanna Pucilowska
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA
| | - ShuChing Chang
- Medical Data Research Center, Providence St Joseph Health, Portland, Oregon, USA
| | - Isaac Kim
- Earle A Chiles Research Institute, Providence Cancer Institute, Portland, Oregon, USA
| | - Benjamin Nikitin
- Earle A Chiles Research Institute, Providence Cancer Institute, Portland, Oregon, USA
| | - Yoshinobu Koguchi
- Earle A Chiles Research Institute, Providence Cancer Institute, Portland, Oregon, USA
| | - William L Redmond
- Earle A Chiles Research Institute, Providence Cancer Institute, Portland, Oregon, USA
| | - Brady Bernard
- Earle A Chiles Research Institute, Providence Cancer Institute, Portland, Oregon, USA.,Computational Immuno-Oncology and Bioinformatics Core, Earle A. Chiles Research Institute, Portland, Oregon, USA
| | - Venkatesh Rajamanickam
- Earle A Chiles Research Institute, Providence Cancer Institute, Portland, Oregon, USA.,Computational Immuno-Oncology and Bioinformatics Core, Earle A. Chiles Research Institute, Portland, Oregon, USA
| | | | - Paul A Fields
- Adaptive Biotechnologies Corp, Seattle, Washington, USA
| | - Valerie Conrad
- Earle A Chiles Research Institute, Providence Cancer Institute, Portland, Oregon, USA
| | - Mark Schmidt
- Earle A Chiles Research Institute, Providence Cancer Institute, Portland, Oregon, USA
| | - Walter J Urba
- Earle A Chiles Research Institute, Providence Cancer Institute, Portland, Oregon, USA
| | - Alison K Conlin
- Earle A Chiles Research Institute, Providence Cancer Institute, Portland, Oregon, USA
| | - Heather L McArthur
- Department of Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - David B Page
- Earle A Chiles Research Institute, Providence Cancer Institute, Portland, Oregon, USA
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29
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Dave H, Terpilowski M, Mai M, Toner K, Grant M, Stanojevic M, Lazarski C, Shibli A, Bien SA, Maglo P, Hoq F, Schore R, Glenn M, Hu B, Hanley PJ, Ambinder R, Bollard CM. Tumor-associated antigen-specific T cells with nivolumab are safe and persist in vivo in relapsed/refractory Hodgkin lymphoma. Blood Adv 2022; 6:473-485. [PMID: 34495306 PMCID: PMC8791594 DOI: 10.1182/bloodadvances.2021005343] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 07/25/2021] [Indexed: 11/20/2022] Open
Abstract
Hodgkin lymphoma (HL) Reed Sternberg cells express tumor-associated antigens (TAA) that are potential targets for cellular therapies. We recently demonstrated that TAA-specific T cells (TAA-Ts) targeting WT1, PRAME, and Survivin were safe and associated with prolonged time to progression in solid tumors. Hence, we evaluated whether TAA-Ts when given alone or with nivolumab were safe and could elicit antitumor effects in vivo in patients with relapsed/refractory (r/r) HL. Ten patients were infused with TAA-Ts (8 autologous and 2 allogeneic) for active HL (n = 8) or as adjuvant therapy after hematopoietic stem cell transplant (n = 2). Six patients received nivolumab priming before TAA-Ts and continued until disease progression or unacceptable toxicity. All 10 products recognized 1 or more TAAs and were polyfunctional. Patients were monitored for safety for 6 weeks after the TAA-Ts and for response until disease progression. The infusions were safe with no clear dose-limiting toxicities. Patients receiving TAA-Ts as adjuvant therapy remain in continued remission at 3+ years. Of the 8 patients with active disease, 1 patient had a complete response and 7 had stable disease at 3 months, 3 of whom remain with stable disease at 1 year. Antigen spreading and long-term persistence of TAA-Ts in vivo were observed in responding patients. Nivolumab priming impacted TAA-T recognition and persistence. In conclusion, treatment of patients with r/r HL with TAA-Ts alone or in combination with nivolumab was safe and produced promising results. This trial was registered at www.clinicaltrials.gov as #NCT022039303 and #NCT03843294.
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Affiliation(s)
- Hema Dave
- Center for Cancer and Immunology Research, Children’s National Hospital, Washington, DC
- Department of Pediatrics, George Washington School of Medicine and Health Sciences, Washington, DC
| | - Madeline Terpilowski
- Center for Cancer and Immunology Research, Children’s National Hospital, Washington, DC
| | - Mimi Mai
- Center for Cancer and Immunology Research, Children’s National Hospital, Washington, DC
| | - Keri Toner
- Center for Cancer and Immunology Research, Children’s National Hospital, Washington, DC
- Department of Pediatrics, George Washington School of Medicine and Health Sciences, Washington, DC
| | - Melanie Grant
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | - Maja Stanojevic
- Center for Cancer and Immunology Research, Children’s National Hospital, Washington, DC
| | - Christopher Lazarski
- Center for Cancer and Immunology Research, Children’s National Hospital, Washington, DC
| | - Abeer Shibli
- Center for Cancer and Immunology Research, Children’s National Hospital, Washington, DC
| | | | - Philip Maglo
- Center for Cancer and Immunology Research, Children’s National Hospital, Washington, DC
| | - Fahmida Hoq
- Center for Cancer and Immunology Research, Children’s National Hospital, Washington, DC
- Department of Pediatrics, George Washington School of Medicine and Health Sciences, Washington, DC
| | - Reuven Schore
- Center for Cancer and Immunology Research, Children’s National Hospital, Washington, DC
- Department of Pediatrics, George Washington School of Medicine and Health Sciences, Washington, DC
| | - Martha Glenn
- Division of Hematology and Hematologic Malignancies, Huntsman Cancer Institute/University of Utah, Salt Lake City, UT; and
| | - Boyu Hu
- Division of Hematology and Hematologic Malignancies, Huntsman Cancer Institute/University of Utah, Salt Lake City, UT; and
| | - Patrick J. Hanley
- Center for Cancer and Immunology Research, Children’s National Hospital, Washington, DC
- Department of Pediatrics, George Washington School of Medicine and Health Sciences, Washington, DC
| | | | - Catherine M. Bollard
- Center for Cancer and Immunology Research, Children’s National Hospital, Washington, DC
- Department of Pediatrics, George Washington School of Medicine and Health Sciences, Washington, DC
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30
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Pagliuca S, Gurnari C, Awada H, Kishtagari A, Kongkiatkamon S, Terkawi L, Zawit M, Guan Y, LaFramboise T, Jha BK, Patel BJ, Hamilton BK, Majhail NS, Lundgren S, Mustjoki S, Saunthararajah Y, Visconte V, Chan TA, Yang CY, Lenz TL, Maciejewski JP. The similarity of class II HLA genotypes defines patterns of autoreactivity in idiopathic bone marrow failure disorders. Blood 2021; 138:2781-2798. [PMID: 34748628 PMCID: PMC8718627 DOI: 10.1182/blood.2021012900] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 10/18/2021] [Indexed: 01/01/2023] Open
Abstract
Idiopathic aplastic anemia (IAA) is a rare autoimmune bone marrow failure (BMF) disorder initiated by a human leukocyte antigen (HLA)-restricted T-cell response to unknown antigens. As in other autoimmune disorders, the predilection for certain HLA profiles seems to represent an etiologic factor; however, the structure-function patterns involved in the self-presentation in this disease remain unclear. Herein, we analyzed the molecular landscape of HLA complexes of a cohort of 300 IAA patients and almost 3000 healthy and disease controls by deeply dissecting their genotypic configurations, functional divergence, self-antigen binding capabilities, and T-cell receptor (TCR) repertoire specificities. Specifically, analysis of the evolutionary divergence of HLA genotypes (HED) showed that IAA patients carried class II HLA molecules whose antigen-binding sites were characterized by a high level of structural homology, only partially explained by specific risk allele profiles. This pattern implies reduced HLA binding capabilities, confirmed by binding analysis of hematopoietic stem cell (HSC)-derived self-peptides. IAA phenotype was associated with the enrichment in a few amino acids at specific positions within the peptide-binding groove of DRB1 molecules, affecting the interface HLA-antigen-TCR β and potentially constituting the basis of T-cell dysfunction and autoreactivity. When analyzing associations with clinical outcomes, low HED was associated with risk of malignant progression and worse survival, underlying reduced tumor surveillance in clearing potential neoantigens derived from mechanisms of clonal hematopoiesis. Our data shed light on the immunogenetic risk associated with IAA etiology and clonal evolution and on general pathophysiological mechanisms potentially involved in other autoimmune disorders.
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Affiliation(s)
- Simona Pagliuca
- Translational Hematology and Oncology Research Department, Cleveland Clinic, Cleveland, OH
- University of Paris, Paris, France
| | - Carmelo Gurnari
- Translational Hematology and Oncology Research Department, Cleveland Clinic, Cleveland, OH
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Hassan Awada
- Translational Hematology and Oncology Research Department, Cleveland Clinic, Cleveland, OH
| | - Ashwin Kishtagari
- Translational Hematology and Oncology Research Department, Cleveland Clinic, Cleveland, OH
| | - Sunisa Kongkiatkamon
- Translational Hematology and Oncology Research Department, Cleveland Clinic, Cleveland, OH
| | - Laila Terkawi
- Translational Hematology and Oncology Research Department, Cleveland Clinic, Cleveland, OH
| | - Misam Zawit
- Translational Hematology and Oncology Research Department, Cleveland Clinic, Cleveland, OH
| | - Yihong Guan
- Translational Hematology and Oncology Research Department, Cleveland Clinic, Cleveland, OH
| | - Thomas LaFramboise
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH
| | - Babal K Jha
- Translational Hematology and Oncology Research Department, Cleveland Clinic, Cleveland, OH
| | - Bhumika J Patel
- Leukemia Program, Department of Hematology and Oncology, Cleveland Clinic, Cleveland, OH
| | - Betty K Hamilton
- Blood and Marrow Transplant Program, Department of Hematology and Oncology, Cleveland Clinic, Cleveland, OH
| | - Navneet S Majhail
- Blood and Marrow Transplant Program, Department of Hematology and Oncology, Cleveland Clinic, Cleveland, OH
| | - Sofie Lundgren
- Hematology Research Unit Helsinki, University of Helsinki-Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
| | - Satu Mustjoki
- Hematology Research Unit Helsinki, University of Helsinki-Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- ICAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Yogen Saunthararajah
- Translational Hematology and Oncology Research Department, Cleveland Clinic, Cleveland, OH
| | - Valeria Visconte
- Translational Hematology and Oncology Research Department, Cleveland Clinic, Cleveland, OH
| | - Timothy A Chan
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, OH
| | - Chao-Yie Yang
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN
| | - Tobias L Lenz
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany; and
- Research Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, Hamburg, Germany
| | - Jaroslaw P Maciejewski
- Translational Hematology and Oncology Research Department, Cleveland Clinic, Cleveland, OH
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31
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Swanson PA, Padilla M, Hoyland W, McGlinchey K, Fields PA, Bibi S, Faust SN, McDermott AB, Lambe T, Pollard AJ, Durham NM, Kelly EJ. AZD1222/ChAdOx1 nCoV-19 vaccination induces a polyfunctional spike protein-specific T H1 response with a diverse TCR repertoire. Sci Transl Med 2021; 13:eabj7211. [PMID: 34591596 PMCID: PMC9924073 DOI: 10.1126/scitranslmed.abj7211] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/20/2021] [Accepted: 09/27/2021] [Indexed: 12/14/2022]
Abstract
AZD1222 (ChAdOx1 nCoV-19), a replication-deficient simian adenovirus–vectored vaccine, has demonstrated safety, efficacy, and immunogenicity against coronavirus disease 2019 in clinical trials and real-world studies. We characterized CD4+ and CD8+ T cell responses induced by AZD1222 vaccination in peripheral blood mononuclear cells from 296 unique vaccine recipients aged 18 to 85 years who enrolled in the phase 2/3 COV002 trial. Total spike protein–specific CD4+ T cell helper type 1 (TH1) and CD8+ T cell responses were increased in AZD1222-vaccinated adults of all ages after two doses of AZD1222. CD4+ TH2 responses after AZD1222 vaccination were not detected. Furthermore, AZD1222-specific TH1 and CD8+ T cells both displayed a high degree of polyfunctionality in all adult age groups. T cell receptor β (TCRβ) sequences from vaccinated participants mapped against TCR sequences known to react to SARS-CoV-2 revealed substantial breadth and depth across the SARS-CoV-2 spike protein for both AZD1222-induced CD4+ and CD8+ T cell responses. Overall, AZD1222 vaccination induced a polyfunctional TH1-dominated T cell response, with broad CD4+ and CD8+ T cell coverage across the SARS-CoV-2 spike protein.
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Affiliation(s)
- Phillip A. Swanson
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Marcelino Padilla
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wesley Hoyland
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kelly McGlinchey
- Discovery, Research and Early Development, Oncology R&D, AstraZeneca, Gaithersburg, MD 20878, USA
| | | | - Sagida Bibi
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and NIHR Oxford Biomedical Research Centre, Oxford OX4 6PG, UK
| | - Saul N. Faust
- NIHR Southampton Clinical Research Facility and Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, and Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO16 6YD, UK
| | - Adrian B. McDermott
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Teresa Lambe
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK
| | - Andrew J. Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and NIHR Oxford Biomedical Research Centre, Oxford OX4 6PG, UK
| | - Nicholas M. Durham
- Translational Medicine, Oncology R&D, AstraZeneca, Gaithersburg, MD 20878, USA
| | - Elizabeth J. Kelly
- Translational Medicine, Microbial Sciences, Biopharmaceuticals R&D, AstraZeneca, Gaithersburg, MD 20878, USA
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32
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Chen M, Chen R, Jin Y, Li J, Hu X, Zhang J, Fujimoto J, Hubert SM, Gay CM, Zhu B, Tian Y, McGranahan N, Lee WC, George J, Hu X, Chen Y, Wu M, Behrens C, Chow CW, Pham HHN, Fukuoka J, Wu J, Parra ER, Little LD, Gumbs C, Song X, Wu CJ, Diao L, Wang Q, Cardnell R, Zhang J, Wang J, Le X, Gibbons DL, Heymach JV, Jack Lee J, William WN, Cheng C, Glisson B, Wistuba I, Andrew Futreal P, Thomas RK, Reuben A, Byers LA, Zhang J. Cold and heterogeneous T cell repertoire is associated with copy number aberrations and loss of immune genes in small-cell lung cancer. Nat Commun 2021; 12:6655. [PMID: 34789716 PMCID: PMC8599854 DOI: 10.1038/s41467-021-26821-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 10/25/2021] [Indexed: 02/03/2023] Open
Abstract
Small-cell lung cancer (SCLC) is speculated to harbor complex genomic intratumor heterogeneity (ITH) associated with high recurrence rate and suboptimal response to immunotherapy. Here, using multi-region whole exome/T cell receptor (TCR) sequencing as well as immunohistochemistry, we reveal a rather homogeneous mutational landscape but extremely cold and heterogeneous TCR repertoire in limited-stage SCLC tumors (LS-SCLCs). Compared to localized non-small cell lung cancers, LS-SCLCs have similar predicted neoantigen burden and genomic ITH, but significantly colder and more heterogeneous TCR repertoire associated with higher chromosomal copy number aberration (CNA) burden. Furthermore, copy number loss of IFN-γ pathway genes is frequently observed and positively correlates with CNA burden. Higher mutational burden, higher T cell infiltration and positive PD-L1 expression are associated with longer overall survival (OS), while higher CNA burden is associated with shorter OS in patients with LS-SCLC.
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Affiliation(s)
- Ming Chen
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510060, China. .,The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang, 310022, China. .,Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China. .,Zhejiang Key Laboratory of Radiation Oncology, Hangzhou, Zhejiang, 310022, China.
| | - Runzhe Chen
- grid.12981.330000 0001 2360 039XDepartment of Radiation Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510060 China ,grid.240145.60000 0001 2291 4776Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA ,grid.240145.60000 0001 2291 4776Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Ying Jin
- grid.410726.60000 0004 1797 8419The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang 310022 China ,grid.9227.e0000000119573309Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022 China ,Zhejiang Key Laboratory of Radiation Oncology, Hangzhou, Zhejiang 310022 China
| | - Jun Li
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Xin Hu
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Jiexin Zhang
- grid.240145.60000 0001 2291 4776Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Junya Fujimoto
- grid.240145.60000 0001 2291 4776Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Shawna M. Hubert
- grid.240145.60000 0001 2291 4776Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA ,grid.240145.60000 0001 2291 4776Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Carl M. Gay
- grid.240145.60000 0001 2291 4776Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Bo Zhu
- grid.240145.60000 0001 2291 4776Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA ,grid.240145.60000 0001 2291 4776Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Yanhua Tian
- grid.240145.60000 0001 2291 4776Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA ,grid.240145.60000 0001 2291 4776Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Nicholas McGranahan
- grid.11485.390000 0004 0422 0975Cancer Research United Kingdom-University College London Lung Cancer Centre of Excellence, London, WC1E6BT UK
| | - Won-Chul Lee
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Julie George
- grid.6190.e0000 0000 8580 3777Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, 50931 Germany ,grid.411097.a0000 0000 8852 305XDepartment of Otorhinolaryngology, Head and Neck Surgery, University Hospital Cologne, 50937 Cologne, Germany
| | - Xiao Hu
- grid.410726.60000 0004 1797 8419The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang 310022 China ,grid.9227.e0000000119573309Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022 China ,Zhejiang Key Laboratory of Radiation Oncology, Hangzhou, Zhejiang 310022 China
| | - Yamei Chen
- grid.410726.60000 0004 1797 8419The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang 310022 China ,grid.9227.e0000000119573309Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022 China ,Zhejiang Key Laboratory of Radiation Oncology, Hangzhou, Zhejiang 310022 China
| | - Meijuan Wu
- grid.410726.60000 0004 1797 8419The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang 310022 China ,grid.9227.e0000000119573309Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022 China ,Zhejiang Key Laboratory of Radiation Oncology, Hangzhou, Zhejiang 310022 China
| | - Carmen Behrens
- grid.240145.60000 0001 2291 4776Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Chi-Wan Chow
- grid.240145.60000 0001 2291 4776Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Hoa H. N. Pham
- grid.174567.60000 0000 8902 2273Department of Pathology, Nagasaki University Graduate school of Biomedical Sciences, Nagasaki, Japan
| | - Junya Fukuoka
- grid.174567.60000 0000 8902 2273Department of Pathology, Nagasaki University Graduate school of Biomedical Sciences, Nagasaki, Japan
| | - Jia Wu
- grid.240145.60000 0001 2291 4776Department of Image Physics, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Edwin Roger Parra
- grid.240145.60000 0001 2291 4776Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Latasha D. Little
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Curtis Gumbs
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Xingzhi Song
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Chang-Jiun Wu
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Lixia Diao
- grid.240145.60000 0001 2291 4776Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Qi Wang
- grid.240145.60000 0001 2291 4776Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Robert Cardnell
- grid.240145.60000 0001 2291 4776Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Jianhua Zhang
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Jing Wang
- grid.240145.60000 0001 2291 4776Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Xiuning Le
- grid.240145.60000 0001 2291 4776Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Don L. Gibbons
- grid.240145.60000 0001 2291 4776Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - John V. Heymach
- grid.240145.60000 0001 2291 4776Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - J. Jack Lee
- grid.240145.60000 0001 2291 4776Department of Biostatistics, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - William N. William
- grid.240145.60000 0001 2291 4776Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Chao Cheng
- grid.39382.330000 0001 2160 926XInstitute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas 77030 USA
| | - Bonnie Glisson
- grid.240145.60000 0001 2291 4776Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Ignacio Wistuba
- grid.240145.60000 0001 2291 4776Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - P. Andrew Futreal
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Roman K. Thomas
- grid.6190.e0000 0000 8580 3777Department of Translational Genomics, Medical Faculty, University of Cologne, Cologne, 50931 Germany ,grid.411097.a0000 0000 8852 305XDepartment of Pathology, Medical Faculty, University Hospital Cologne, Cologne, 50931 Germany ,grid.7497.d0000 0004 0492 0584DKFZ, German Cancer Research Center and German Cancer Consortium (DKTK), Heidelberg, 69115 Germany
| | - Alexandre Reuben
- Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas, 77030, USA.
| | - Lauren A. Byers
- grid.240145.60000 0001 2291 4776Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Jianjun Zhang
- Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas, 77030, USA. .,Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas, 77030, USA.
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33
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Talebian F, Yu J, Lynch K, Liu JQ, Carson WE, Bai XF. CD200 Blockade Modulates Tumor Immune Microenvironment but Fails to Show Efficacy in Inhibiting Tumor Growth in a Murine Model of Melanoma. Front Cell Dev Biol 2021; 9:739816. [PMID: 34692697 PMCID: PMC8531493 DOI: 10.3389/fcell.2021.739816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 09/20/2021] [Indexed: 01/14/2023] Open
Abstract
CD200-CD200R pathway regulates immune responses and has been implicated in the pathogenesis of a number of cancer types. CD200 blockade is considered a strategy for immunotherapy of CD200-positive cancers such as melanoma. Thus, it is critical to understand the potential impacts of CD200 blockade in a more human relevant tumor model. In this study, we evaluated these issues using the CD200+ Yumm1.7 mouse melanoma model. Yumm1.7 cells bear Braf/Pten mutations resembling human melanoma. We found that Yumm1.7 tumors grow significantly faster in CD200R–/– mice compared to wild type mice. Analysis of tumor immune microenvironment (TIME) revealed that tumors from CD200R–/– or anti-CD200 treated mice had downregulated immune cell contents and reduced TCR clonality compared to tumors from untreated wild type mice. T cells also showed impaired effector functions, as reflected by reduced numbers of IFN-γ+ and TNF-α+ T cells. Mechanistically, we found upregulation of the CCL8 gene in CD200R–/– tumors. In vitro co-culture experiments using Yumm1.7 tumor cells with bone marrow derived macrophages (BMDM) from WT and CD200R–/– mice confirmed upregulation of macrophage CCL8 in the absence of CD200-CD200R interaction. Finally, we found that anti-CD200 therapy failed to show efficacy either alone or in combination with checkpoint inhibitors such as anti-PD-1 or anti-CTLA4 in inhibiting Yumm1.7 tumor growth. Given that CD200R-deficiency or anti-CD200 treatment leads to reduced T cell responses in TME, using blockade of CD200 as an immunotherapy for cancers such as melanoma should be practiced with caution.
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Affiliation(s)
- Fatemeh Talebian
- Department of Pathology, College of Medicine, The Ohio State University, Columbus, OH, United States
| | - Jianyu Yu
- Department of Pathology, College of Medicine, The Ohio State University, Columbus, OH, United States
| | - Kimberly Lynch
- Department of Pathology, College of Medicine, The Ohio State University, Columbus, OH, United States
| | - Jin-Qing Liu
- Department of Pathology, College of Medicine, The Ohio State University, Columbus, OH, United States
| | - William E Carson
- Division of Surgical Oncology, Department of Surgery, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, United States.,Comprehensive Cancer Center, Institute for Immuno-Oncology, The Ohio State University, Columbus, OH, United States
| | - Xue-Feng Bai
- Department of Pathology, College of Medicine, The Ohio State University, Columbus, OH, United States.,Comprehensive Cancer Center, Institute for Immuno-Oncology, The Ohio State University, Columbus, OH, United States
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34
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Hou X, Wang G, Fan W, Chen X, Mo C, Wang Y, Gong W, Wen X, Chen H, He D, Mo L, Jiang S, Ou M, Guo H, Liu H. T-cell receptor repertoires as potential diagnostic markers for patients with COVID-19. Int J Infect Dis 2021; 113:308-317. [PMID: 34688948 PMCID: PMC8530772 DOI: 10.1016/j.ijid.2021.10.033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 09/25/2021] [Accepted: 10/15/2021] [Indexed: 12/23/2022] Open
Abstract
Objective Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is an ongoing global health emergency. T-cell receptors (TCRs) are crucial mediators of antiviral adaptive immunity. This study sought to comprehensively characterize the TCR repertoire changes in patients with COVID-19. Methods A large sample size multi-center randomized controlled trial was implemented to study the features of the TCR repertoire and identify COVID-19 disease-related TCR sequences. Results It was found that some T-cell receptor beta chain (TCRβ) features differed markedly between COVID-19 patients and healthy controls, including decreased repertoire diversity, longer complementarity-determining region 3 (CDR3) length, skewed utilization of the TCRβ variable gene/joining gene (TRBV/J), and a high degree of TCRβ sharing in COVID-19 patients. Moreover, this analysis showed that TCR repertoire diversity declines with aging, which may be a cause of the higher infection and mortality rates in elderly patients. Importantly, a set of TCRβ clones that can distinguish COVID-19 patients from healthy controls with high accuracy was identified. Notably, this diagnostic model demonstrates 100% specificity and 82.68% sensitivity at 0–3 days post diagnosis. Conclusions This study lays the foundation for immunodiagnosis and the development of medicines and vaccines for COVID-19 patients.
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Affiliation(s)
- Xianliang Hou
- Central Laboratory, Guangxi Health Commission Key Laboratory of Glucose and Lipid Metabolism Disorders, the Second Affiliated Hospital of Guilin Medical University, Guilin, 541199, China
| | - Guangyu Wang
- College of Laboratory Medicine, Guilin Medical University, Guilin, 541199, China
| | - Wentao Fan
- Guangzhou Huayin Health Medical Group Co., Ltd, Guangzhou, China
| | - Xiaoyan Chen
- Department of State Owned Assets Management, Affiliated Hospital of Guilin Medical University, Guilin, 541001, China
| | - Chune Mo
- Central Laboratory, Guangxi Health Commission Key Laboratory of Glucose and Lipid Metabolism Disorders, the Second Affiliated Hospital of Guilin Medical University, Guilin, 541199, China
| | - Yongsi Wang
- Guangzhou Huayin Health Medical Group Co., Ltd, Guangzhou, China
| | - Weiwei Gong
- Central Laboratory, Guangxi Health Commission Key Laboratory of Glucose and Lipid Metabolism Disorders, the Second Affiliated Hospital of Guilin Medical University, Guilin, 541199, China
| | - Xuyan Wen
- Department of Pathology, Affiliated Hospital of Guilin Medical University, Guilin, 541001, China
| | - Hui Chen
- Guangzhou Huayin Health Medical Group Co., Ltd, Guangzhou, China
| | - Dan He
- Guangzhou Huayin Health Medical Group Co., Ltd, Guangzhou, China
| | - Lijun Mo
- Clinical Laboratory, the Second Affiliated Hospital of Guilin Medical University, Guilin, 541199, China
| | - Shaofeng Jiang
- Guangxi Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Guilin, Guangxi, 541199, China
| | - Minglin Ou
- Central Laboratory, Guangxi Health Commission Key Laboratory of Glucose and Lipid Metabolism Disorders, the Second Affiliated Hospital of Guilin Medical University, Guilin, 541199, China
| | - Haonan Guo
- Department of Clinical Laboratory, The Affiliated Hospital of Guilin Medical University, Guilin, Guangxi, 541001, China.
| | - Hongbo Liu
- Department of Laboratory Medicine, the Second Affiliated Hospital of Guilin Medical University, Guilin, 541199, China.
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35
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Biavati L, Huff CA, Ferguson A, Sidorski A, Stevens MA, Rudraraju L, Zucchinetti C, Ali SA, Imus P, Gocke CB, Gittelman RM, Johnson S, Sanders C, Vignali M, Gandhi A, Ye X, Noonan KA, Borrello I. An Allogeneic Multiple Myeloma GM-CSF-Secreting Vaccine with Lenalidomide Induces Long-term Immunity and Durable Clinical Responses in Patients in Near Complete Remission. Clin Cancer Res 2021; 27:6696-6708. [PMID: 34667029 DOI: 10.1158/1078-0432.ccr-21-1916] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 07/29/2021] [Accepted: 09/24/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE This proof-of-principle clinical trial evaluated whether an allogeneic multiple myeloma GM-CSF-secreting vaccine (MM-GVAX) in combination with lenalidomide could deepen the clinical response in patients with multiple myeloma in sustained near complete remission (nCR). PATIENTS AND METHODS Fifteen patients on lenalidomide were treated with MM-GVAX and pneumococcal conjugate vaccine (PCV; Prevnar) at 1, 2, 3, and 6 months. RESULTS Eight patients (53.3%) achieved a true CR. With a median follow-up of 5 years, the median progression-free survival had not been reached, and the median overall survival was 7.8 years from enrollment. MM-GVAX induced clonal T-cell expansion and measurable cytokine responses that persisted up to 7 years in all patients. At baseline, a higher minimal residual disease was predictive of early relapse. After vaccination, a lack of both CD27-DNAM1-CD8+ T cells and antigen-presenting cells was associated with disease progression. CONCLUSIONS MM-GVAX, along with lenalidomide, effectively primed durable immunity and resulted in long-term disease control, as suggested by the reappearance of a detectable, fluctuating M-spike without meeting the criteria for clinical relapse. For patients in a nCR, MM-GVAX administration was safe and resulted in prolonged clinical responses.
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Affiliation(s)
- Luca Biavati
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Carol Ann Huff
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Anna Ferguson
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Amy Sidorski
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - M Amanda Stevens
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Lakshmi Rudraraju
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Cristina Zucchinetti
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Syed Abbas Ali
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Philip Imus
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Christian B Gocke
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | | | | | | | | | | | - Xiaobu Ye
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Kimberly A Noonan
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Ivan Borrello
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland.
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36
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Schroeder BA, LaFranzo NA, LaFleur BJ, Gittelman RM, Vignali M, Zhang S, Flanagan KC, Rytlewski J, Riolobos L, Schulte BC, Kim TS, Chen E, Smythe KS, Wagner MJ, Mantilla JG, Campbell JS, Pierce RH, Jones RL, Cranmer LD, Pollack SM. CD4+ T cell and M2 macrophage infiltration predict dedifferentiated liposarcoma patient outcomes. J Immunother Cancer 2021; 9:jitc-2021-002812. [PMID: 34465597 PMCID: PMC8413967 DOI: 10.1136/jitc-2021-002812] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/26/2021] [Indexed: 01/13/2023] Open
Abstract
Background Dedifferentiated liposarcoma (DDLPS) is one of the most common soft tissue sarcoma subtypes and is devastating in the advanced/metastatic stage. Despite the observation of clinical responses to PD-1 inhibitors, little is known about the immune microenvironment in relation to patient prognosis. Methods We performed a retrospective study of 61 patients with DDLPS. We completed deep sequencing of the T-cell receptor (TCR) β-chain and RNA sequencing for predictive modeling, evaluating both immune markers and tumor escape genes. Hierarchical clustering and recursive partitioning were employed to elucidate relationships of cellular infiltrates within the tumor microenvironment, while an immune score for single markers was created as a predictive tool. Results Although many DDLPS samples had low TCR clonality, high TCR clonality combined with low T-cell fraction predicted lower 3-year overall survival (p=0.05). Higher levels of CD14+ monocytes (p=0.02) inversely correlated with 3-year recurrence-free survival (RFS), while CD4+ T-cell infiltration (p=0.05) was associated with a higher RFS. Genes associated with longer RFS included PD-1 (p=0.003), ICOS (p=0.006), BTLA (p=0.033), and CTLA4 (p=0.02). In a composite immune score, CD4+ T cells had the strongest positive predictive value, while CD14+ monocytes and M2 macrophages had the strongest negative predictive values. Conclusions Immune cell infiltration predicts clinical outcome in DDLPS, with CD4+ cells associated with better outcomes; CD14+ cells and M2 macrophages are associated with worse outcomes. Future checkpoint inhibitor studies in DDLPS should incorporate immunosequencing and gene expression profiling techniques that can generate immune landscape profiles.
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Affiliation(s)
- Brett A Schroeder
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | | | | | | | - Shihong Zhang
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | | | - Laura Riolobos
- UW Medicine Cancer Vaccine Institute, University of Washington, Seattle, Washington, USA
| | - Brian C Schulte
- Division of Oncology, Northwestern University Department of Medicine, Chicago, Illinois, USA
| | - Teresa S Kim
- Department of Surgery, University of Washington, Seattle, Washington, USA
| | - Eleanor Chen
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Kimberly S Smythe
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Michael J Wagner
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Division of Oncology, University of Washington, Seattle, Washington, USA
| | - Jose G Mantilla
- Pathology, University of Washington Medical Center, Seattle, Washington, USA
| | | | - Robert H Pierce
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Robin L Jones
- Sarcoma, Royal Marsden Hospital NHS Trust, London, UK
| | - Lee D Cranmer
- Seattle Cancer Care Alliance, Seattle, Washington, USA
| | - Seth M Pollack
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA .,Division of Oncology, Northwestern University, Chicago, Illinois, USA
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37
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Swanson PA, Padilla M, Hoyland W, McGlinchey K, Fields PA, Bibi S, Faust SN, McDermott AB, Lambe T, Pollard AJ, Durham NM, Kelly EJ. T-cell mediated immunity after AZD1222 vaccination: A polyfunctional spike-specific Th1 response with a diverse TCR repertoire. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021. [PMID: 34189538 DOI: 10.1101/2021.06.17.21259027] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
AZD1222 (ChAdOx1 nCoV-19), a replication-deficient simian adenovirus-vectored vaccine, has demonstrated safety, efficacy, and immunogenicity against coronavirus disease 2019 (COVID-19) in clinical trials and real-world studies. We characterized CD4+ and CD8+ T-cell responses induced by AZD1222 vaccination in peripheral blood mononuclear cells (PBMCs) from 280 unique vaccine recipients aged 18-85 years who enrolled in the phase 2/3 COV002 trial. Total spike-specific CD4+ T cell helper type 1 (Th1) and CD8+ T-cell responses were significantly increased in AZD1222-vaccinated adults of all ages following two doses of AZD1222. CD4+ Th2 responses following AZD1222 vaccination were not detected. Furthermore, AZD1222-specific Th1 and CD8+ T cells both displayed a high degree of polyfunctionality in all adult age groups. T-cell receptor (TCR) β sequences from vaccinated participants mapped against TCR sequences known to react to SARS-CoV-2 revealed substantial breadth and depth across the SARS-CoV-2 spike protein for the AZD1222-induced CD4+ and CD8+ T-cell responses. Overall, AZD1222 vaccination induced a robust, polyfunctional Th1-dominated T-cell response, with broad CD4+ and CD8+ T-cell coverage across the SARS-CoV-2 spike protein. One Sentence Summary Polyfunctional CD4+ and CD8+ T-cell responses are elicited against the SARS-CoV-2 spike protein following vaccination with AZD1222.
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38
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Pagliuca S, Gurnari C, Hong S, Zhao R, Kongkiatkamon S, Terkawi L, Zawit M, Guan Y, Awada H, Kishtagari A, Kerr CM, LaFramboise T, Patel BJ, Jha BK, Carraway HE, Visconte V, Majhail NS, Hamilton BK, Maciejewski JP. Clinical and basic implications of dynamic T cell receptor clonotyping in hematopoietic cell transplantation. JCI Insight 2021; 6:e149080. [PMID: 34236054 PMCID: PMC8410023 DOI: 10.1172/jci.insight.149080] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 05/26/2021] [Indexed: 12/02/2022] Open
Abstract
TCR repertoire diversification constitutes a foundation for successful immune reconstitution after allogeneic hematopoietic cell transplantation (allo-HCT). Deep TCR Vβ sequencing of 135 serial specimens from a cohort of 35 allo-HCT recipients/donors was performed to dissect posttransplant TCR architecture and dynamics. Paired analysis of clonotypic repertoires showed a minimal overlap with donor expansions. Rarefied and hyperexpanded clonotypic patterns were hallmarks of T cell reconstitution and influenced clinical outcomes. Donor and pretransplant TCR diversity as well as divergence of class I human leukocyte antigen genotypes were major predictors of recipient TCR repertoire recovery. Complementary determining region 3–based specificity spectrum analysis indicated a predominant expansion of pathogen- and tumor-associated clonotypes in the late post–allo-HCT phase, while autoreactive clones were more expanded in the case of graft-versus-host disease occurrence. These findings shed light on post–allo-HCT adaptive immune reconstitution processes and possibly help in tracking alloreactive responses.
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Affiliation(s)
- Simona Pagliuca
- Translational Hematology and Oncology Research Program, Department of Hematology and Oncology, Cleveland Clinic, Cleveland, Ohio, USA.,University of Paris, Paris, France
| | - Carmelo Gurnari
- Translational Hematology and Oncology Research Program, Department of Hematology and Oncology, Cleveland Clinic, Cleveland, Ohio, USA.,Department of Biomedicine and Prevention, School of Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
| | - Sanghee Hong
- Blood and Marrow Transplant Program, Department of Hematology and Oncology and
| | - Ran Zhao
- Department of Quantitative Health Sciences, Cleveland Clinic, Cleveland, Ohio, USA
| | - Sunisa Kongkiatkamon
- Translational Hematology and Oncology Research Program, Department of Hematology and Oncology, Cleveland Clinic, Cleveland, Ohio, USA
| | - Laila Terkawi
- Translational Hematology and Oncology Research Program, Department of Hematology and Oncology, Cleveland Clinic, Cleveland, Ohio, USA
| | - Misam Zawit
- Translational Hematology and Oncology Research Program, Department of Hematology and Oncology, Cleveland Clinic, Cleveland, Ohio, USA
| | - Yihong Guan
- Translational Hematology and Oncology Research Program, Department of Hematology and Oncology, Cleveland Clinic, Cleveland, Ohio, USA
| | - Hassan Awada
- Translational Hematology and Oncology Research Program, Department of Hematology and Oncology, Cleveland Clinic, Cleveland, Ohio, USA
| | - Ashwin Kishtagari
- Translational Hematology and Oncology Research Program, Department of Hematology and Oncology, Cleveland Clinic, Cleveland, Ohio, USA
| | - Cassandra M Kerr
- Translational Hematology and Oncology Research Program, Department of Hematology and Oncology, Cleveland Clinic, Cleveland, Ohio, USA
| | - Thomas LaFramboise
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Bhumika J Patel
- Leukemia and Myeloid Disorders Program, Department of Hematology and Oncology, Cleveland Clinic, Cleveland, Ohio, USA
| | - Babal K Jha
- Translational Hematology and Oncology Research Program, Department of Hematology and Oncology, Cleveland Clinic, Cleveland, Ohio, USA
| | - Hetty E Carraway
- Blood and Marrow Transplant Program, Department of Hematology and Oncology and
| | - Valeria Visconte
- Translational Hematology and Oncology Research Program, Department of Hematology and Oncology, Cleveland Clinic, Cleveland, Ohio, USA
| | - Navneet S Majhail
- Blood and Marrow Transplant Program, Department of Hematology and Oncology and
| | - Betty K Hamilton
- Blood and Marrow Transplant Program, Department of Hematology and Oncology and
| | - Jaroslaw P Maciejewski
- Translational Hematology and Oncology Research Program, Department of Hematology and Oncology, Cleveland Clinic, Cleveland, Ohio, USA
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Kim BJ, Ahn JH, Youn DH, Jeon JP. Profiling of T Cell Receptor β-Chain Complimentary Determining Regions 3 Repertoire in Subarachnoid Hemorrhage Patients Using High-Throughput Sequencing. J Korean Neurosurg Soc 2021; 64:505-513. [PMID: 34185982 PMCID: PMC8273768 DOI: 10.3340/jkns.2020.0214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/07/2020] [Indexed: 12/01/2022] Open
Abstract
Objective The adaptive immune response following subarachnoid hemorrhage (SAH) is not well understood. We evaluated and compared the T cell receptor (TCR) immune repertoire of good-grade and poor-grade SAH patients to elucidate the T cell immunology after ictus.
Methods Peripheral blood from six SAH patients was collected at two different times, admission and at the 7-day follow-up. Composition and variation of the TCR β-chain (TCRB) complimentary determining regions (CDR) 3 repertoire was examined using high-throughput sequencing; the analysis was based on sampling time and disease severity (good vs. poor-grade SAH).
Results Clonality at admission and follow-up were 0.059 (0.037–0.038) and 0.027 (0.014–0.082) (median, 25th–75th percentile). Poor-grade SAH (0.025 [0.011–0.038]) was associated with significantly lower clonality than good-grade SAH (0.095 [0.079–0.101]). Poor-grade SAH patients had higher diversity scores than good-grade SAH patients. CDR length was shorter in good-grade SAH vs. poor-grade SAH. Differences in clonotype distribution were more prominent in TCRBV gene segments than TCRBJ segments. TCRBV19-01/TCRBJ02-04 and TCRBV28-01/TCRBJ02-04 were the most increased and the most decreased V-J pairs in the 7-day follow-up compared to admission in good-grade SAH. The most increased and decreased V-J pairs in poor-grade SAH patients were TCRBV28-01/TCRBJ02-06 and TCRBV30-01/TCRBJ02-04, respectively.
Conclusion The TCRB repertoire is dynamic in nature following SAH. TCRB repertoire may facilitate our understanding of adaptive immune response according to SAH severity.
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Affiliation(s)
- Bong Jun Kim
- Institute of New Frontier Stroke Research, Hallym University College of Medicine, Chuncheon, Korea
| | - Jun Hyong Ahn
- Department of Neurosurgery, Hallym University College of Medicine, Chuncheon, Korea
| | - Dong Hyuk Youn
- Institute of New Frontier Stroke Research, Hallym University College of Medicine, Chuncheon, Korea
| | - Jin Pyeong Jeon
- Institute of New Frontier Stroke Research, Hallym University College of Medicine, Chuncheon, Korea.,Department of Neurosurgery, Hallym University College of Medicine, Chuncheon, Korea.,Genetic and Research Inc., Chuncheon, Korea
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40
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Pre-transplant T-cell Clonality: An Observational Study of a Biomarker for Prediction of Sepsis in Liver Transplant Recipients. Ann Surg 2021; 274:411-418. [PMID: 34132702 DOI: 10.1097/sla.0000000000004998] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
OBJECTIVE This study investigated the ability of pre-transplant T-cell clonality to predict sepsis after liver transplant (LT). SUMMARY BACKGROUND DATA Sepsis is a leading cause of death in LT recipients. Currently, no biomarkers predict sepsis before clinical symptom manifestation. METHODS Between December 2013 and March 2018, our institution performed 478 LTs. After exclusions (eg, patients with marginal donor livers, autoimmune disorders, nonabdominal multi-organ, and liver retransplantations), 180 consecutive LT were enrolled. T-cell characterization was assessed within 48 hours before LT (immunoSEQ Assay, Adaptive Biotechnologies, Seattle, WA). Sepsis-2 and Sepsis-3 cases, defined by presence of acute infection plus ≥2 SIRS criteria, or clinical documentation of sepsis, were identified by chart review. Receiver-operating characteristic analyses determined optimal T-cell repertoire clonality for predicting post-LT sepsis. Kaplan-Meier and Cox proportional hazard modeling assessed outcome-associated prognostic variables. RESULTS Patients with baseline T-cell repertoire clonality ≥0.072 were 3.82 (1.25, 11.40; P = 0.02), and 2.40 (1.00, 5.75; P = 0.049) times more likely to develop sepsis 3 and 12 months post-LT, respectively, when compared to recipients with lower (<0.072) clonality. T-cell repertoire clonality was the only predictor of sepsis 3 months post-LT in multivariate analysis (C-Statistic, 0.75). Adequate treatment resulted in equivalent survival rates between both groups: (93.4% vs 96.2%, respectively, P = 0.41) at 12 months post-LT. CONCLUSIONS T-cell repertoire clonality is a novel biomarker predictor of sepsis before development of clinical symptoms. Early sepsis monitoring and management may reduce post-LT mortality. These findings have implications for developing sepsis-prevention protocols in transplantation and potentially other populations.
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Zhang X, Luo M, Dastagir SR, Nixon M, Khamhoung A, Schmidt A, Lee A, Subbiah N, McLaughlin DC, Moore CL, Gribble M, Bayhi N, Amin V, Pepi R, Pawar S, Lyford TJ, Soman V, Mellen J, Carpenter CL, Turka LA, Wickham TJ, Chen TF. Engineered red blood cells as an off-the-shelf allogeneic anti-tumor therapeutic. Nat Commun 2021; 12:2637. [PMID: 33976146 PMCID: PMC8113241 DOI: 10.1038/s41467-021-22898-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 03/31/2021] [Indexed: 02/03/2023] Open
Abstract
Checkpoint inhibitors and T-cell therapies have highlighted the critical role of T cells in anti-cancer immunity. However, limitations associated with these treatments drive the need for alternative approaches. Here, we engineer red blood cells into artificial antigen-presenting cells (aAPCs) presenting a peptide bound to the major histocompatibility complex I, the costimulatory ligand 4-1BBL, and interleukin (IL)-12. This leads to robust, antigen-specific T-cell expansion, memory formation, additional immune activation, tumor control, and antigen spreading in tumor models in vivo. The presence of 4-1BBL and IL-12 induces minimal toxicities due to restriction to the vasculature and spleen. The allogeneic aAPC, RTX-321, comprised of human leukocyte antigen-A*02:01 presenting the human papilloma virus (HPV) peptide HPV16 E711-19, 4-1BBL, and IL-12 on the surface, activates HPV-specific T cells and promotes effector function in vitro. Thus, RTX-321 is a potential 'off-the-shelf' in vivo cellular immunotherapy for treating HPV + cancers, including cervical and head/neck cancers.
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Affiliation(s)
- Xuqing Zhang
- grid.507501.60000 0004 6022 070XRubius Therapeutics, Inc., Cambridge, MA USA
| | - Mengyao Luo
- grid.507501.60000 0004 6022 070XRubius Therapeutics, Inc., Cambridge, MA USA
| | - Shamael R. Dastagir
- grid.507501.60000 0004 6022 070XRubius Therapeutics, Inc., Cambridge, MA USA
| | - Mellissa Nixon
- grid.507501.60000 0004 6022 070XRubius Therapeutics, Inc., Cambridge, MA USA
| | - Annie Khamhoung
- grid.507501.60000 0004 6022 070XRubius Therapeutics, Inc., Cambridge, MA USA
| | - Andrea Schmidt
- grid.507501.60000 0004 6022 070XRubius Therapeutics, Inc., Cambridge, MA USA
| | - Albert Lee
- grid.507501.60000 0004 6022 070XRubius Therapeutics, Inc., Cambridge, MA USA
| | - Naren Subbiah
- grid.507501.60000 0004 6022 070XRubius Therapeutics, Inc., Cambridge, MA USA
| | | | | | - Mary Gribble
- grid.507501.60000 0004 6022 070XRubius Therapeutics, Inc., Cambridge, MA USA
| | - Nicholas Bayhi
- grid.507501.60000 0004 6022 070XRubius Therapeutics, Inc., Cambridge, MA USA
| | - Viral Amin
- grid.507501.60000 0004 6022 070XRubius Therapeutics, Inc., Cambridge, MA USA
| | - Ryan Pepi
- grid.507501.60000 0004 6022 070XRubius Therapeutics, Inc., Cambridge, MA USA
| | - Sneha Pawar
- grid.507501.60000 0004 6022 070XRubius Therapeutics, Inc., Cambridge, MA USA
| | - Timothy J. Lyford
- grid.507501.60000 0004 6022 070XRubius Therapeutics, Inc., Cambridge, MA USA
| | - Vikram Soman
- grid.507501.60000 0004 6022 070XRubius Therapeutics, Inc., Cambridge, MA USA
| | - Jennifer Mellen
- grid.507501.60000 0004 6022 070XRubius Therapeutics, Inc., Cambridge, MA USA
| | | | - Laurence A. Turka
- grid.507501.60000 0004 6022 070XRubius Therapeutics, Inc., Cambridge, MA USA
| | - Thomas J. Wickham
- grid.507501.60000 0004 6022 070XRubius Therapeutics, Inc., Cambridge, MA USA
| | - Tiffany F. Chen
- grid.507501.60000 0004 6022 070XRubius Therapeutics, Inc., Cambridge, MA USA
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Soto C, Bombardi RG, Kozhevnikov M, Sinkovits RS, Chen EC, Branchizio A, Kose N, Day SB, Pilkinton M, Gujral M, Mallal S, Crowe JE. High Frequency of Shared Clonotypes in Human T Cell Receptor Repertoires. Cell Rep 2021; 32:107882. [PMID: 32668251 PMCID: PMC7433715 DOI: 10.1016/j.celrep.2020.107882] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 04/18/2020] [Accepted: 06/16/2020] [Indexed: 01/30/2023] Open
Abstract
The collection of T cell receptors (TCRs) generated by somatic recombination is large but unknown. We generate large TCR repertoire datasets as a resource to facilitate detailed studies of the role of TCR clonotypes and repertoires in health and disease. We estimate the size of individual human recombined and expressed TCRs by sequence analysis and determine the extent of sharing between individual repertoires. Our experiments reveal that each blood sample contains between 5 million and 21 million TCR clonotypes. Three individuals share 8% of TCRβ- or 11% of TCRα-chain clonotypes. Sorting by T cell phenotypes in four individuals shows that 5% of naive CD4+ and 3.5% of naive CD8+ subsets share their TCRβ clonotypes, whereas memory CD4+ and CD8+ subsets share 2.3% and 0.4% of their clonotypes, respectively. We identify the sequences of these shared TCR clonotypes that are of interest for studies of human T cell biology. Soto et al. examine the extent to which five healthy adults share their T cell receptor (TCR) repertoire. Using sequencing and bioinformatics, they show a high prevalence of shared clonotypes even considering different T cell phenotypes. Possible functions for some clonotypes are inferred based on homology with TCRs in GenBank.
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Affiliation(s)
- Cinque Soto
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Robin G Bombardi
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Morgan Kozhevnikov
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Robert S Sinkovits
- San Diego Supercomputer Center, University of California, San Diego, San Diego, CA 92093, USA
| | - Elaine C Chen
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37212, USA
| | - Andre Branchizio
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Nurgun Kose
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Samuel B Day
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Mark Pilkinton
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Madhusudan Gujral
- San Diego Supercomputer Center, University of California, San Diego, San Diego, CA 92093, USA
| | - Simon Mallal
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37212, USA; Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - James E Crowe
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37212, USA.
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Elyanow R, Snyder TM, Dalai SC, Gittelman RM, Boonyaratanakornkit J, Wald A, Selke S, Wener MH, Morishima C, Greninger AL, Holbrook MR, Kaplan IM, Zahid HJ, Carlson JM, Baldo L, Manley T, Robins HS, Koelle DM. T-cell receptor sequencing identifies prior SARS-CoV-2 infection and correlates with neutralizing antibody titers and disease severity. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.03.19.21251426. [PMID: 33791723 PMCID: PMC8010755 DOI: 10.1101/2021.03.19.21251426] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Measuring the adaptive immune response to SARS-CoV-2 can enable the assessment of past infection as well as protective immunity and the risk of reinfection. While neutralizing antibody (nAb) titers are one measure of protection, such assays are challenging to perform at a large scale and the longevity of the SARS-CoV-2 nAb response is not fully understood. Here, we apply a T-cell receptor (TCR) sequencing assay that can be performed on a small volume standard blood sample to assess the adaptive T-cell response to SARS-CoV-2 infection. Samples were collected from a cohort of 302 individuals recovered from COVID-19 up to 6 months after infection. Previously published findings in this cohort showed that two commercially available SARS-CoV-2 serologic assays correlate well with nAb testing. We demonstrate that the magnitude of the SARS-CoV-2-specific T-cell response strongly correlates with nAb titer, as well as clinical indicators of disease severity including hospitalization, fever, or difficulty breathing. While the depth and breadth of the T-cell response declines during convalescence, the T-cell signal remains well above background with high sensitivity up to at least 6 months following initial infection. Compared to serology tests detecting binding antibodies to SARS-CoV-2 spike and nucleoprotein, the overall sensitivity of the TCR-based assay across the entire cohort and all timepoints was approximately 5% greater for identifying prior SARS-CoV-2 infection. Notably, the improved performance of T-cell testing compared to serology was most apparent in recovered individuals who were not hospitalized and were sampled beyond 150 days of their initial illness, suggesting that antibody testing may have reduced sensitivity in individuals who experienced less severe COVID-19 illness and at later timepoints. Finally, T-cell testing was able to identify SARS-CoV-2 infection in 68% (55/81) of convalescent samples having nAb titers below the lower limit of detection, as well as 37% (13/35) of samples testing negative by all three antibody assays. These results demonstrate the utility of a TCR-based assay as a scalable, reliable measure of past SARS-CoV-2 infection across a spectrum of disease severity. Additionally, the TCR repertoire may be useful as a surrogate for protective immunity with additive clinical value beyond serologic or nAb testing methods.
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Affiliation(s)
| | | | - Sudeb C. Dalai
- Adaptive Biotechnologies, Seattle, Washington, USA
- Stanford University School of Medicine, Stanford, California, USA
| | | | - Jim Boonyaratanakornkit
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Anna Wald
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Stacy Selke
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Mark H. Wener
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Chihiro Morishima
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Alex L. Greninger
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Michael R. Holbrook
- National Institute of Allergy and Infectious Diseases Integrated Research Facility, Frederick, Maryland, USA
| | | | | | | | - Lance Baldo
- Adaptive Biotechnologies, Seattle, Washington, USA
| | | | | | - David M. Koelle
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Benaroya Research Institute, Seattle, Washington, USA
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Dimopoulos M, Bringhen S, Anttila P, Capra M, Cavo M, Cole C, Gasparetto C, Hungria V, Jenner M, Vorobyev V, Ruiz EY, Yin JY, Saleem R, Hellet M, Macé S, Paiva B, Vij R. Isatuximab as monotherapy and combined with dexamethasone in patients with relapsed/refractory multiple myeloma. Blood 2021; 137:1154-1165. [PMID: 33080623 PMCID: PMC7933767 DOI: 10.1182/blood.2020008209] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 09/18/2020] [Indexed: 01/09/2023] Open
Abstract
This phase 2 study evaluated isatuximab as monotherapy or combined with dexamethasone in relapsed/refractory multiple myeloma (RRMM). Patients had RRMM refractory to an immunomodulatory drug (IMiD) and a proteasome inhibitor (PI) or had received ≥3 prior lines of therapy incorporating an IMiD and PI. Patients received isatuximab either as monotherapy (20 mg/kg on days 1, 8, 15, and 22 [once weekly] of cycle 1 followed by 20 mg/kg on days 1 and 15 of subsequent cycles; Isa group) or in combination with dexamethasone (40 mg/d [20 mg/d in patients aged ≥75 years] once weekly; Isa-dex group). Treated patients (N = 164) had received a median of 4 (range, 2-10) prior treatment lines. Patients received a median of 5 (1-24) and 7 (1-22) treatment cycles; at data cutoff, 13 (11.9%) of 109 and 15 (27.3%) of 55 patients remained on treatment in the Isa and Isa-dex arms, respectively. Overall response rate (primary efficacy end point) was 23.9% in the Isa arm and 43.6% in the Isa-dex arm (odds ratio, 0.405; 95% confidence interval, 0.192-0.859; P = .008). Median progression-free survival and overall survival were 4.9 and 18.9 months for Isa, and 10.2 and 17.3 months for Isa-dex. Infusion reactions (mostly grade 1/2) and hematologic abnormalities were the most common adverse events. There was a similar incidence of grade 3 or higher infections in both groups (22.0% and 21.8%). In conclusion, addition of dexamethasone to isatuximab increased response rates and survival outcomes with no detrimental effect on safety. This trial was registered at www.clinicaltrials.gov as #NCT01084252.
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Affiliation(s)
- Meletios Dimopoulos
- Department of Clinical Therapeutics, National and Kapodistrian University of Athens, Athens, Greece
| | - Sara Bringhen
- Myeloma Unit, Division of Hematology, University of Torino, Azienda Ospedaliero-Universitaria Città della Salute e della Scienza di Torino, Torino, Italy
| | - Pekka Anttila
- Division of Hematology, Comprehensive Cancer Center, Helsinki University and Helsinki University Hospital, Helsinki, Finland
| | | | - Michele Cavo
- "Seràgnoli" Institute of Hematology, Sant'Orsola-Malpighi University Hospital, Bologna, Italy
| | - Craig Cole
- Division of Hematology and Oncology, University of Michigan Comprehensive Cancer Center, Ann Arbor, MI
| | - Cristina Gasparetto
- Hematologic Malignancies and Cellular Therapy, Duke University Medical Center, Durham, NC
| | - Vania Hungria
- Department of Hematology, Clínica São Germano, São Paulo, Brazil
| | - Matthew Jenner
- Department of Haematology, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
| | | | | | | | | | | | | | - Bruno Paiva
- Clinica Universidad de Navarra, Centro de Investigación Médica Aplicada (CIMA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), CIBER-ONC number CB16/12/00369, Pamplona, Spain; and
| | - Ravi Vij
- Division of Medical Oncology, Washington University, St. Louis, MO
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Xydia M, Rahbari R, Ruggiero E, Macaulay I, Tarabichi M, Lohmayer R, Wilkening S, Michels T, Brown D, Vanuytven S, Mastitskaya S, Laidlaw S, Grabe N, Pritsch M, Fronza R, Hexel K, Schmitt S, Müller-Steinhardt M, Halama N, Domschke C, Schmidt M, von Kalle C, Schütz F, Voet T, Beckhove P. Common clonal origin of conventional T cells and induced regulatory T cells in breast cancer patients. Nat Commun 2021; 12:1119. [PMID: 33602930 PMCID: PMC7893042 DOI: 10.1038/s41467-021-21297-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 12/11/2020] [Indexed: 02/06/2023] Open
Abstract
Regulatory CD4+ T cells (Treg) prevent tumor clearance by conventional T cells (Tconv) comprising a major obstacle of cancer immune-surveillance. Hitherto, the mechanisms of Treg repertoire formation in human cancers remain largely unclear. Here, we analyze Treg clonal origin in breast cancer patients using T-Cell Receptor and single-cell transcriptome sequencing. While Treg in peripheral blood and breast tumors are clonally distinct, Tconv clones, including tumor-antigen reactive effectors (Teff), are detected in both compartments. Tumor-infiltrating CD4+ cells accumulate into distinct transcriptome clusters, including early activated Tconv, uncommitted Teff, Th1 Teff, suppressive Treg and pro-tumorigenic Treg. Trajectory analysis suggests early activated Tconv differentiation either into Th1 Teff or into suppressive and pro-tumorigenic Treg. Importantly, Tconv, activated Tconv and Treg share highly-expanded clones contributing up to 65% of intratumoral Treg. Here we show that Treg in human breast cancer may considerably stem from antigen-experienced Tconv converting into secondary induced Treg through intratumoral activation.
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Affiliation(s)
- Maria Xydia
- RCI Regensburg Centre for Interventional Immunology, University and Department of Hematology/Oncology, University Medical Centre of Regensburg, Regensburg, Germany.
- Translational Immunology Department, German Cancer Research Centre, Heidelberg, Germany.
| | - Raheleh Rahbari
- The Cancer, Ageing and Somatic Mutation Program, Wellcome Sanger Institute, Hinxton, UK
| | - Eliana Ruggiero
- Translational Oncology Department, National Centre for Tumor Diseases and German Cancer Research Centre, Heidelberg, Germany
| | - Iain Macaulay
- The Cancer, Ageing and Somatic Mutation Program, Wellcome Sanger Institute, Hinxton, UK
- Technical Development, Earlham Institute, Norwich, UK
| | - Maxime Tarabichi
- The Cancer, Ageing and Somatic Mutation Program, Wellcome Sanger Institute, Hinxton, UK
- The Francis Crick Institute, London, UK
| | - Robert Lohmayer
- RCI Regensburg Centre for Interventional Immunology, University and Department of Hematology/Oncology, University Medical Centre of Regensburg, Regensburg, Germany
- Institute for Theoretical Physics, University of Regensburg, Regensburg, Germany
| | - Stefan Wilkening
- Translational Oncology Department, National Centre for Tumor Diseases and German Cancer Research Centre, Heidelberg, Germany
| | - Tillmann Michels
- RCI Regensburg Centre for Interventional Immunology, University and Department of Hematology/Oncology, University Medical Centre of Regensburg, Regensburg, Germany
| | - Daniel Brown
- Department of Human Genetics, University of Leuven, KU Leuven, Leuven, Belgium
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | - Sebastiaan Vanuytven
- The Francis Crick Institute, London, UK
- Department of Human Genetics, University of Leuven, KU Leuven, Leuven, Belgium
| | - Svetlana Mastitskaya
- Medical Oncology Department, National Centre for Tumor Diseases, Heidelberg, Germany
- Centre for Cardiovascular and Metabolic Neuroscience, Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK
| | - Sean Laidlaw
- The Cancer, Ageing and Somatic Mutation Program, Wellcome Sanger Institute, Hinxton, UK
| | - Niels Grabe
- Medical Oncology Department, National Centre for Tumor Diseases, Heidelberg, Germany
- Hamamatsu Tissue Imaging and Analysis Centre, BIOQUANT, University of Heidelberg, Heidelberg, Germany
| | - Maria Pritsch
- Translational Immunology Department, German Cancer Research Centre, Heidelberg, Germany
| | - Raffaele Fronza
- Translational Oncology Department, National Centre for Tumor Diseases and German Cancer Research Centre, Heidelberg, Germany
| | - Klaus Hexel
- Flow Cytometry Core Facility, German Cancer Research Centre, Heidelberg, Germany
| | - Steffen Schmitt
- Flow Cytometry Core Facility, German Cancer Research Centre, Heidelberg, Germany
| | - Michael Müller-Steinhardt
- German Red Cross (DRK Blood Donation Service in Baden-Württemberg-Hessen) and Institute for Transfusion Medicine and Immunology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Niels Halama
- Medical Oncology Department, National Centre for Tumor Diseases, Heidelberg, Germany
- Hamamatsu Tissue Imaging and Analysis Centre, BIOQUANT, University of Heidelberg, Heidelberg, Germany
| | - Christoph Domschke
- Department of Gynecology and Obstetrics, University Hospital of Heidelberg, Heidelberg, Germany
| | - Manfred Schmidt
- Translational Oncology Department, National Centre for Tumor Diseases and German Cancer Research Centre, Heidelberg, Germany
| | - Christof von Kalle
- Translational Oncology Department, National Centre for Tumor Diseases and German Cancer Research Centre, Heidelberg, Germany
- Clinical Study Centre, Charité/BIH, Berlin, Germany
| | - Florian Schütz
- Department of Gynecology and Obstetrics, University Hospital of Heidelberg, Heidelberg, Germany
| | - Thierry Voet
- The Cancer, Ageing and Somatic Mutation Program, Wellcome Sanger Institute, Hinxton, UK
- Department of Human Genetics, University of Leuven, KU Leuven, Leuven, Belgium
| | - Philipp Beckhove
- RCI Regensburg Centre for Interventional Immunology, University and Department of Hematology/Oncology, University Medical Centre of Regensburg, Regensburg, Germany.
- Translational Immunology Department, German Cancer Research Centre, Heidelberg, Germany.
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Yiu HH, Schoettle LN, Garcia-Neuer M, Blattman JN, Johnson PLF. Selection influences naive CD8+ TCR-β repertoire sharing. Immunology 2021; 162:464-475. [PMID: 33345304 DOI: 10.1111/imm.13299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 11/22/2020] [Accepted: 11/29/2020] [Indexed: 11/28/2022] Open
Abstract
Within each individual, the adaptive immune system generates a repertoire of cells expressing receptors capable of recognizing diverse potential pathogens. The theoretical diversity of the T-cell receptor (TCR) repertoire exceeds the actual size of the T-cell population in an individual by several orders of magnitude - making the observation of identical TCRs in different individuals extremely improbable if all receptors were equally likely. Despite this disparity between the theoretical and the realized diversity of the repertoire, these 'public' receptor sequences have been identified in autoimmune, cancer and pathogen interaction contexts. Biased generation processes explain the presence of public TCRs in the naive repertoire, but do not adequately explain the different abundances of these public TCRs. We investigate and characterize the distribution of genomic TCR-β sequences of naive CD8+ T cells from three genetically identical mice, comparing non-productive (non-functional sequences) and productive sequences. We find public TCR-β sequences at higher abundances compared with unshared sequences in the productive, but not in the non-productive, repertoire. We show that neutral processes such as recombination biases, codon degeneracy and generation probability do not fully account for these differences, and conclude that thymic or peripheral selection plays an important role in increasing the abundances of public TCR-β sequences.
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Affiliation(s)
- Hao H Yiu
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Louis N Schoettle
- School of Life Sciences, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Marlene Garcia-Neuer
- School of Life Sciences, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Joseph N Blattman
- School of Life Sciences, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
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47
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A phase 1/2 trial of an immune-modulatory vaccine against IDO/PD-L1 in combination with nivolumab in metastatic melanoma. Nat Med 2021; 27:2212-2223. [PMID: 34887574 PMCID: PMC8904254 DOI: 10.1038/s41591-021-01544-x] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 09/20/2021] [Indexed: 02/06/2023]
Abstract
Anti-programmed death (PD)-1 (aPD1) therapy is an effective treatment for metastatic melanoma (MM); however, over 50% of patients progress due to resistance. We tested a first-in-class immune-modulatory vaccine (IO102/IO103) against indoleamine 2,3-dioxygenase (IDO) and PD ligand 1 (PD-L1), targeting immunosuppressive cells and tumor cells expressing IDO and/or PD-L1 (IDO/PD-L1), combined with nivolumab. Thirty aPD1 therapy-naive patients with MM were treated in a phase 1/2 study ( https://clinicaltrials.gov/ , NCT03047928). The primary endpoint was feasibility and safety; the systemic toxicity profile was comparable to that of nivolumab monotherapy. Secondary endpoints were efficacy and immunogenicity; an objective response rate (ORR) of 80% (confidence interval (CI), 62.7-90.5%) was reached, with 43% (CI, 27.4-60.8%) complete responses. After a median follow-up of 22.9 months, the median progression-free survival (PFS) was 26 months (CI, 15.4-69 months). Median overall survival (OS) was not reached. Vaccine-specific responses assessed in vitro were detected in the blood of >93% of patients during vaccination. Vaccine-reactive T cells comprised CD4+ and CD8+ T cells with activity against IDO- and PD-L1-expressing cancer and immune cells. T cell influx of peripherally expanded T cells into tumor sites was observed in responding patients, and general enrichment of IDO- and PD-L1-specific clones after treatment was documented. These clinical efficacy and favorable safety data support further validation in a larger randomized trial to confirm the clinical potential of this immunomodulating approach.
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48
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Martini JF, Plimack ER, Choueiri TK, McDermott DF, Puzanov I, Fishman MN, Cho DC, Vaishampayan U, Rosbrook B, Fernandez KC, Tarazi JC, George S, Atkins MB. Angiogenic and Immune-Related Biomarkers and Outcomes Following Axitinib/Pembrolizumab Treatment in Patients with Advanced Renal Cell Carcinoma. Clin Cancer Res 2020; 26:5598-5608. [PMID: 32816890 DOI: 10.1158/1078-0432.ccr-20-1408] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/03/2020] [Accepted: 08/14/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE Combined axitinib/pembrolizumab is approved for advanced renal cell carcinoma (aRCC). This exploratory analysis examined associations between angiogenic and immune-related biomarkers and outcomes following axitinib/pembrolizumab treatment. PATIENTS AND METHODS Prospectively defined retrospective correlative exploratory analyses tested biospecimens from 52 treatment-naïve patients receiving axitinib and pembrolizumab (starting doses 5 mg twice daily and 2 mg/kg respectively, every 3 weeks). Tumor tissue, serum, and whole blood samples were collected at baseline, at cycle 2 day 1 (C2D1), and end of treatment (EOT) for blood-based samples. Clinical outcomes were objective response rate (ORR) and progression-free survival (PFS). RESULTS Higher baseline tumor levels of CD8 showed a trend toward longer PFS (HR 0.4; P = 0.091). Higher baseline serum levels of CXCL10 (P = 0.0197) and CEACAM1 (P = 0.085) showed a trend toward better ORR and longer PFS, respectively. Patients for whom IL6 was not detected at baseline had longer PFS versus patients for whom it was detected (HR 0.4; P = 0.028). At C2D1 and/or EOT, mainly immune-related biomarkers showed any association with better outcomes. The genes CA9 (P = 0.084), HIF1A (P = 0.064), and IFNG (P = 0.073) showed trending associations with ORR, and AKT3 (P = 0.0145), DDX58 (P = 0.0726), GZMA (P = 0.0666), LCN2 (NGAL; P = 0.0267), and PTPN11 (P = 0.0287) with PFS. CONCLUSIONS With combined axitinib/pembrolizumab treatment in patients with aRCC, mostly immune-related biomarkers are associated with better treatment outcomes. This exploratory analysis has identified some candidate biomarkers to consider in future prospective testing.
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MESH Headings
- Adult
- Aged
- Antibodies, Monoclonal, Humanized/administration & dosage
- Antibodies, Monoclonal, Humanized/adverse effects
- Antigens, Neoplasm/blood
- Axitinib/administration & dosage
- Axitinib/adverse effects
- Biomarkers, Tumor/blood
- Biomarkers, Tumor/genetics
- Carbonic Anhydrase IX/blood
- Carcinoma, Renal Cell/blood
- Carcinoma, Renal Cell/drug therapy
- Carcinoma, Renal Cell/genetics
- Carcinoma, Renal Cell/pathology
- DEAD Box Protein 58/blood
- Dose-Response Relationship, Drug
- Female
- Granzymes/blood
- Humans
- Hypoxia-Inducible Factor 1, alpha Subunit/blood
- Interferon-gamma/blood
- Lipocalin-2/blood
- Male
- Middle Aged
- Neoplasm Staging
- Neovascularization, Pathologic/blood
- Neovascularization, Pathologic/drug therapy
- Neovascularization, Pathologic/genetics
- Neovascularization, Pathologic/pathology
- Progression-Free Survival
- Protein Tyrosine Phosphatase, Non-Receptor Type 11/blood
- Receptors, Immunologic/blood
- Treatment Outcome
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Affiliation(s)
| | | | | | | | - Igor Puzanov
- Vanderbilt University Medical Center, Nashville, Tennessee
- Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | | | - Daniel C Cho
- Perlmutter Cancer Center at NYU Langone Medical Center, New York, New York
| | - Ulka Vaishampayan
- Karmanos Cancer Institute, Wayne State University, Detroit, Michigan
| | - Bradley Rosbrook
- Pfizer Global Product Development-Oncology, San Diego, California
| | | | - Jamal C Tarazi
- Pfizer Global Product Development-Oncology, San Diego, California
| | - Saby George
- Roswell Park Comprehensive Cancer Center, Buffalo, New York
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49
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Snyder TM, Gittelman RM, Klinger M, May DH, Osborne EJ, Taniguchi R, Zahid HJ, Kaplan IM, Dines JN, Noakes MT, Pandya R, Chen X, Elasady S, Svejnoha E, Ebert P, Pesesky MW, De Almeida P, O'Donnell H, DeGottardi Q, Keitany G, Lu J, Vong A, Elyanow R, Fields P, Greissl J, Baldo L, Semprini S, Cerchione C, Nicolini F, Mazza M, Delmonte OM, Dobbs K, Laguna-Goya R, Carreño-Tarragona G, Barrio S, Imberti L, Sottini A, Quiros-Roldan E, Rossi C, Biondi A, Bettini LR, D'Angio M, Bonfanti P, Tompkins MF, Alba C, Dalgard C, Sambri V, Martinelli G, Goldman JD, Heath JR, Su HC, Notarangelo LD, Paz-Artal E, Martinez-Lopez J, Carlson JM, Robins HS. Magnitude and Dynamics of the T-Cell Response to SARS-CoV-2 Infection at Both Individual and Population Levels. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020:2020.07.31.20165647. [PMID: 32793919 PMCID: PMC7418734 DOI: 10.1101/2020.07.31.20165647] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
T cells are involved in the early identification and clearance of viral infections and also support the development of antibodies by B cells. This central role for T cells makes them a desirable target for assessing the immune response to SARS-CoV-2 infection. Here, we combined two high-throughput immune profiling methods to create a quantitative picture of the T-cell response to SARS-CoV-2. First, at the individual level, we deeply characterized 3 acutely infected and 58 recovered COVID-19 subjects by experimentally mapping their CD8 T-cell response through antigen stimulation to 545 Human Leukocyte Antigen (HLA) class I presented viral peptides (class II data in a forthcoming study). Then, at the population level, we performed T-cell repertoire sequencing on 1,815 samples (from 1,521 COVID-19 subjects) as well as 3,500 controls to identify shared "public" T-cell receptors (TCRs) associated with SARS-CoV-2 infection from both CD8 and CD4 T cells. Collectively, our data reveal that CD8 T-cell responses are often driven by a few immunodominant, HLA-restricted epitopes. As expected, the T-cell response to SARS-CoV-2 peaks about one to two weeks after infection and is detectable for at least several months after recovery. As an application of these data, we trained a classifier to diagnose SARS-CoV-2 infection based solely on TCR sequencing from blood samples, and observed, at 99.8% specificity, high early sensitivity soon after diagnosis (Day 3-7 = 85.1% [95% CI = 79.9-89.7]; Day 8-14 = 94.8% [90.7-98.4]) as well as lasting sensitivity after recovery (Day 29+/convalescent = 95.4% [92.1-98.3]). These results demonstrate an approach to reliably assess the adaptive immune response both soon after viral antigenic exposure (before antibodies are typically detectable) as well as at later time points. This blood-based molecular approach to characterizing the cellular immune response has applications in clinical diagnostics as well as in vaccine development and monitoring.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Allen Vong
- Adaptive Biotechnologies, Seattle, WA, USA
| | | | | | | | | | - Simona Semprini
- Unit of Microbiology - The Great Romagna Hub Laboratory, Pievesestina ITALY and DIMES, University of Bologna, Bologna, Italy
| | - Claudio Cerchione
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Fabio Nicolini
- Immunotherapy, Cell Therapy and Biobank (ITCB), Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, FC, Italy
| | - Massimiliano Mazza
- Immunotherapy, Cell Therapy and Biobank (ITCB), Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, FC, Italy
| | - Ottavia M Delmonte
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kerry Dobbs
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Rocio Laguna-Goya
- Department of Immunology, Hospital 12 de Octubre, i+12, CNIO, Complutense University, Madrid, Spain
| | | | - Santiago Barrio
- Hematology Department, Hospital 12 de Octubre, i+12, CNIO, Complutense University, Madrid, Spain
| | - Luisa Imberti
- Laboratorio CREA, Department of Infectious and Tropical Diseases, and Medical Officer, ASST Spedali Civili di Brescia and University of Brescia, Brescia, Italy
| | - Alessandra Sottini
- Laboratorio CREA, Department of Infectious and Tropical Diseases, and Medical Officer, ASST Spedali Civili di Brescia and University of Brescia, Brescia, Italy
| | - Eugenia Quiros-Roldan
- Laboratorio CREA, Department of Infectious and Tropical Diseases, and Medical Officer, ASST Spedali Civili di Brescia and University of Brescia, Brescia, Italy
| | - Camillo Rossi
- Laboratorio CREA, Department of Infectious and Tropical Diseases, and Medical Officer, ASST Spedali Civili di Brescia and University of Brescia, Brescia, Italy
| | - Andrea Biondi
- Department of Pediatrics and Centro Tettamanti-European Reference Network PaedCan, EuroBloodNet, MetabERN-University of Milano-Bicocca-Fondazione MBBM-Ospedale San Gerardo, Monza, IT
| | - Laura Rachele Bettini
- Department of Pediatrics and Centro Tettamanti-European Reference Network PaedCan, EuroBloodNet, MetabERN-University of Milano-Bicocca-Fondazione MBBM-Ospedale San Gerardo, Monza, IT
| | - Mariella D'Angio
- Department of Pediatrics and Centro Tettamanti-European Reference Network PaedCan, EuroBloodNet, MetabERN-University of Milano-Bicocca-Fondazione MBBM-Ospedale San Gerardo, Monza, IT
| | - Paolo Bonfanti
- Department of Infectious Diseases, University of Milano-Bicocca-Ospedale San Gerardo, Monza, IT
| | - Miranda F Tompkins
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Camille Alba
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Clifton Dalgard
- Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Vittorio Sambri
- Unit of Microbiology - The Great Romagna Hub Laboratory, Pievesestina ITALY and DIMES, University of Bologna, Bologna, Italy
| | - Giovanni Martinelli
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Jason D Goldman
- Swedish Medical Center, Seattle, WA, USA, and Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA
| | | | - Helen C Su
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Luigi D Notarangelo
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Estela Paz-Artal
- Department of Immunology, Hospital 12 de Octubre, i+12, CNIO, Complutense University, Madrid, Spain
| | - Joaquin Martinez-Lopez
- Hematology Department, Hospital 12 de Octubre, i+12, CNIO, Complutense University, Madrid, Spain
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50
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Ramien C, Yusko EC, Engler JB, Gamradt S, Patas K, Schweingruber N, Willing A, Rosenkranz SC, Diemert A, Harrison A, Vignali M, Sanders C, Robins HS, Tolosa E, Heesen C, Arck PC, Scheffold A, Chan K, Emerson RO, Friese MA, Gold SM. T Cell Repertoire Dynamics during Pregnancy in Multiple Sclerosis. Cell Rep 2020; 29:810-815.e4. [PMID: 31644905 DOI: 10.1016/j.celrep.2019.09.025] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/10/2019] [Accepted: 09/06/2019] [Indexed: 02/08/2023] Open
Abstract
Identifying T cell clones associated with human autoimmunity has remained challenging. Intriguingly, many autoimmune diseases, including multiple sclerosis (MS), show strongly diminished activity during pregnancy, providing a unique research paradigm to explore dynamics of immune repertoire changes during active and inactive disease. Here, we characterize immunomodulation at the single-clone level by sequencing the T cell repertoire in healthy women and female MS patients over the course of pregnancy. Clonality is significantly reduced from the first to third trimester in MS patients, indicating that the T cell repertoire becomes less dominated by expanded clones. However, only a few T cell clones are substantially modulated during pregnancy in each patient. Moreover, relapse-associated T cell clones identified in an individual patient contract during pregnancy and expand during a postpartum relapse. Our data provide evidence that profiling the T cell repertoire during pregnancy could serve as a tool to discover and track "private" T cell clones associated with disease activity in autoimmunity.
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Affiliation(s)
- Caren Ramien
- Institut für Neuroimmunologie und Multiple Sklerose (INIMS), Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Erik C Yusko
- Adaptive Biotechnologies Corp., 1551 Eastlake Ave. E., Seattle, WA 98102, USA
| | - Jan Broder Engler
- Institut für Neuroimmunologie und Multiple Sklerose (INIMS), Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Stefanie Gamradt
- Charité - Universitätsmedizin Berlin, Klinik für Psychiatrie und Medizinische Klinik m.S. Psychosomatik, Campus Benjamin Franklin, Hindenburgdamm 30, 12203 Berlin, Germany
| | - Kostas Patas
- Institut für Neuroimmunologie und Multiple Sklerose (INIMS), Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany; Laboratory for Biopathology and Immunology, Eginition University Hospital, 72-74 Vasilissis Sophias Ave., 11528 Athens, Greece
| | - Nils Schweingruber
- Institut für Neuroimmunologie und Multiple Sklerose (INIMS), Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany; Klinik für Neurologie, Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Anne Willing
- Institut für Neuroimmunologie und Multiple Sklerose (INIMS), Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Sina Cathérine Rosenkranz
- Institut für Neuroimmunologie und Multiple Sklerose (INIMS), Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany; Klinik für Neurologie, Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Anke Diemert
- Klinik für Geburtshilfe und Pränatalmedizin, Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Anja Harrison
- Institut für Neuroimmunologie und Multiple Sklerose (INIMS), Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany; Department of Psychology, University of Central Lancashire, Preston, PR1 2HE Lancashire, UK
| | - Marissa Vignali
- Adaptive Biotechnologies Corp., 1551 Eastlake Ave. E., Seattle, WA 98102, USA
| | - Catherine Sanders
- Adaptive Biotechnologies Corp., 1551 Eastlake Ave. E., Seattle, WA 98102, USA
| | - Harlan S Robins
- Adaptive Biotechnologies Corp., 1551 Eastlake Ave. E., Seattle, WA 98102, USA; Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109-1024, USA
| | - Eva Tolosa
- Institut für Immunologie, Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Christoph Heesen
- Institut für Neuroimmunologie und Multiple Sklerose (INIMS), Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany; Klinik für Neurologie, Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Petra C Arck
- Labor für Experimentelle Feto-Maternale Medizin, Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Alexander Scheffold
- Institut für Immunologie, Universitätsklinikum Schleswig-Holstein, Arnold Heller Str. 3, 24105 Kiel, Germany
| | - Kenneth Chan
- Adaptive Biotechnologies Corp., 1551 Eastlake Ave. E., Seattle, WA 98102, USA
| | - Ryan O Emerson
- Adaptive Biotechnologies Corp., 1551 Eastlake Ave. E., Seattle, WA 98102, USA
| | - Manuel A Friese
- Institut für Neuroimmunologie und Multiple Sklerose (INIMS), Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Stefan M Gold
- Institut für Neuroimmunologie und Multiple Sklerose (INIMS), Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany; Charité - Universitätsmedizin Berlin, Klinik für Psychiatrie und Medizinische Klinik m.S. Psychosomatik, Campus Benjamin Franklin, Hindenburgdamm 30, 12203 Berlin, Germany.
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