1
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Schmit SL, Tsai YY, Bonner JD, Sanz-Pamplona R, Joshi AD, Ugai T, Lindsey SS, Melas M, McDonnell KJ, Idos GE, Walker CP, Qu C, Kast WM, Da Silva DM, Glickman JN, Chan AT, Giannakis M, Nowak JA, Rennert HS, Robins HS, Ogino S, Greenson JK, Moreno V, Rennert G, Gruber SB. Germline genetic regulation of the colorectal tumor immune microenvironment. BMC Genomics 2024; 25:409. [PMID: 38664626 PMCID: PMC11046907 DOI: 10.1186/s12864-024-10295-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
OBJECTIVE To evaluate the contribution of germline genetics to regulating the briskness and diversity of T cell responses in CRC, we conducted a genome-wide association study to examine the associations between germline genetic variation and quantitative measures of T cell landscapes in 2,876 colorectal tumors from participants in the Molecular Epidemiology of Colorectal Cancer Study (MECC). METHODS Germline DNA samples were genotyped and imputed using genome-wide arrays. Tumor DNA samples were extracted from paraffin blocks, and T cell receptor clonality and abundance were quantified by immunoSEQ (Adaptive Biotechnologies, Seattle, WA). Tumor infiltrating lymphocytes per high powered field (TILs/hpf) were scored by a gastrointestinal pathologist. Regression models were used to evaluate the associations between each variant and the three T-cell features, adjusting for sex, age, genotyping platform, and global ancestry. Three independent datasets were used for replication. RESULTS We identified a SNP (rs4918567) near RBM20 associated with clonality at a genome-wide significant threshold of 5 × 10- 8, with a consistent direction of association in both discovery and replication datasets. Expression quantitative trait (eQTL) analyses and in silico functional annotation for these loci provided insights into potential functional roles, including a statistically significant eQTL between the T allele at rs4918567 and higher expression of ADRA2A (P = 0.012) in healthy colon mucosa. CONCLUSIONS Our study suggests that germline genetic variation is associated with the quantity and diversity of adaptive immune responses in CRC. Further studies are warranted to replicate these findings in additional samples and to investigate functional genomic mechanisms.
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Affiliation(s)
- Stephanie L Schmit
- Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH, USA.
- Population and Cancer Prevention Program, Case Comprehensive Cancer Center, Cleveland, OH, USA.
| | - Ya-Yu Tsai
- Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Joseph D Bonner
- Center for Precision Medicine, City of Hope National Medical Center, Duarte, CA, USA
| | - Rebeca Sanz-Pamplona
- Catalan Institute of Oncology (ICO), Hospitalet de Llobregat, Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Barcelona, Spain
| | - Amit D Joshi
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Tomotaka Ugai
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Sidney S Lindsey
- Center for Precision Medicine, City of Hope National Medical Center, Duarte, CA, USA
| | - Marilena Melas
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Kevin J McDonnell
- Center for Precision Medicine, City of Hope National Medical Center, Duarte, CA, USA
| | - Gregory E Idos
- Center for Precision Medicine, City of Hope National Medical Center, Duarte, CA, USA
| | - Christopher P Walker
- Center for Precision Medicine, City of Hope National Medical Center, Duarte, CA, USA
| | - Chenxu Qu
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - W Martin Kast
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Diane M Da Silva
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | | | - Andrew T Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Marios Giannakis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jonathan A Nowak
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Hedy S Rennert
- B. Rappaport Faculty of Medicine, Technion and the Association for Promotion of Research in Precision Medicine (APRPM), Haifa, Israel
| | | | - Shuji Ogino
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Tokyo Medical and Dental University (Institute of Science Tokyo), Tokyo, Japan
| | - Joel K Greenson
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Victor Moreno
- Catalan Institute of Oncology (ICO), Hospitalet de Llobregat, Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Barcelona, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Gad Rennert
- B. Rappaport Faculty of Medicine, Technion and the Association for Promotion of Research in Precision Medicine (APRPM), Haifa, Israel
| | - Stephen B Gruber
- Center for Precision Medicine, City of Hope National Medical Center, Duarte, CA, USA.
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2
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [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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3
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Keitany GJ, Rubin BER, Garrett ME, Musa A, Tracy J, Liang Y, Ebert P, Moore AJ, Guan J, Eggers E, Lescano N, Brown R, Carbo A, Al-Asadi H, Ching T, Day A, Harris R, Linkem C, Popov D, Wilkins C, Li L, Wang J, Liu C, Chen L, Dines JN, Atyeo C, Alter G, Baldo L, Sherwood A, Howie B, Klinger M, Yusko E, Robins HS, Benzeno S, Gilbert AE. Multimodal, broadly neutralizing antibodies against SARS-CoV-2 identified by high-throughput native pairing of BCRs from bulk B cells. Cell Chem Biol 2023; 30:1377-1389.e8. [PMID: 37586370 PMCID: PMC10659930 DOI: 10.1016/j.chembiol.2023.07.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 04/25/2023] [Accepted: 07/23/2023] [Indexed: 08/18/2023]
Abstract
TruAB Discovery is an approach that integrates cellular immunology, high-throughput immunosequencing, bioinformatics, and computational biology in order to discover naturally occurring human antibodies for prophylactic or therapeutic use. We adapted our previously described pairSEQ technology to pair B cell receptor heavy and light chains of SARS-CoV-2 spike protein-binding antibodies derived from enriched antigen-specific memory B cells and bulk antibody-secreting cells. We identified approximately 60,000 productive, in-frame, paired antibody sequences, from which 2,093 antibodies were selected for functional evaluation based on abundance, isotype and patterns of somatic hypermutation. The exceptionally diverse antibodies included RBD-binders with broad neutralizing activity against SARS-CoV-2 variants, and S2-binders with broad specificity against betacoronaviruses and the ability to block membrane fusion. A subset of these RBD- and S2-binding antibodies demonstrated robust protection against challenge in hamster and mouse models. This high-throughput approach can accelerate discovery of diverse, multifunctional antibodies against any target of interest.
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Affiliation(s)
| | | | | | - Andrea Musa
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | - Jeff Tracy
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | - Yu Liang
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | - Peter Ebert
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | | | | | - Erica Eggers
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | | | - Ryan Brown
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | - Adria Carbo
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | | | | | - Austin Day
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | | | | | | | | | - Lianqu Li
- GenScript ProBio Biotech, Nanjing, Jiangsu Province, China
| | - Jiao Wang
- GenScript ProBio Biotech, Nanjing, Jiangsu Province, China
| | - Chuanxin Liu
- GenScript ProBio Biotech, Nanjing, Jiangsu Province, China
| | - Li Chen
- GenScript ProBio Biotech, Nanjing, Jiangsu Province, China
| | | | - Caroline Atyeo
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Lance Baldo
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | | | - Bryan Howie
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | - Mark Klinger
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | - Erik Yusko
- Adaptive Biotechnologies, Seattle, WA 98109, USA
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4
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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: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [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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5
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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. Res Sq 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] [What about the content of this article? (0)] [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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6
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Hoyos D, Zappasodi R, Schulze I, Sethna Z, de Andrade KC, Bajorin DF, Bandlamudi C, Callahan MK, Funt SA, Hadrup SR, Holm JS, Rosenberg JE, Shah SP, Vázquez-García I, Weigelt B, Wu M, Zamarin D, Campitelli LF, Osborne EJ, Klinger M, Robins HS, Khincha PP, Savage SA, Balachandran VP, Wolchok JD, Hellmann MD, Merghoub T, Levine AJ, Łuksza M, Greenbaum BD. Author Correction: Fundamental immune-oncogenicity trade-offs define driver mutation fitness. Nature 2022; 606:E5. [PMID: 35641605 PMCID: PMC9200628 DOI: 10.1038/s41586-022-04879-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- David Hoyos
- Computational Oncology, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Roberta Zappasodi
- Swim Across America Laboratory and Ludwig Collaborative, Immunology Program, Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Department of Medicine, Weill Cornell Medical College, New York, NY, USA. .,Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA.
| | - Isabell Schulze
- Swim Across America Laboratory and Ludwig Collaborative, Immunology Program, Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zachary Sethna
- Computational Oncology, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kelvin César de Andrade
- Division of Cancer Epidemiology and Genetics, Clinical Genetics Branch, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Dean F Bajorin
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chaitanya Bandlamudi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Margaret K Callahan
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Samuel A Funt
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sine R Hadrup
- Experimental and Translational Immunology, Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Jeppe S Holm
- Experimental and Translational Immunology, Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Jonathan E Rosenberg
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sohrab P Shah
- Computational Oncology, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Physiology, Biophysics & Systems Biology, Weill Cornell Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Ignacio Vázquez-García
- Computational Oncology, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michelle Wu
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dmitriy Zamarin
- Swim Across America Laboratory and Ludwig Collaborative, Immunology Program, Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Weill Cornell Medical College, New York, NY, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | | | | | - Payal P Khincha
- Division of Cancer Epidemiology and Genetics, Clinical Genetics Branch, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Sharon A Savage
- Division of Cancer Epidemiology and Genetics, Clinical Genetics Branch, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Vinod P Balachandran
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA.,Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, 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
| | - Jedd D Wolchok
- Swim Across America Laboratory and Ludwig Collaborative, Immunology Program, Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Weill Cornell Medical College, New York, NY, USA.,Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Matthew D Hellmann
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA.,Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Taha Merghoub
- Swim Across America Laboratory and Ludwig Collaborative, Immunology Program, Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Department of Medicine, Weill Cornell Medical College, New York, NY, USA. .,Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Arnold J Levine
- Simons Center for Systems Biology, Institute for Advanced Study, Princeton, NJ, USA
| | - Marta Łuksza
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Benjamin D Greenbaum
- Computational Oncology, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Physiology, Biophysics & Systems Biology, Weill Cornell Medicine, Weill Cornell Medical College, New York, NY, USA.
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7
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Hoyos D, Zappasodi R, Schulze I, Sethna Z, de Andrade KC, Bajorin DF, Bandlamudi C, Callahan MK, Funt SA, Hadrup SR, Holm JS, Rosenberg JE, Shah SP, Vázquez-García I, Weigelt B, Wu M, Zamarin D, Campitelli LF, Osborne EJ, Klinger M, Robins HS, Khincha PP, Savage SA, Balachandran VP, Wolchok JD, Hellmann MD, Merghoub T, Levine AJ, Łuksza M, Greenbaum BD. Fundamental immune-oncogenicity trade-offs define driver mutation fitness. Nature 2022; 606:172-179. [PMID: 35545680 PMCID: PMC9159948 DOI: 10.1038/s41586-022-04696-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 03/28/2022] [Indexed: 12/29/2022]
Abstract
Missense driver mutations in cancer are concentrated in a few hotspots1. Various mechanisms have been proposed to explain this skew, including biased mutational processes2, phenotypic differences3-6 and immunoediting of neoantigens7,8; however, to our knowledge, no existing model weighs the relative contribution of these features to tumour evolution. We propose a unified theoretical 'free fitness' framework that parsimoniously integrates multimodal genomic, epigenetic, transcriptomic and proteomic data into a biophysical model of the rate-limiting processes underlying the fitness advantage conferred on cancer cells by driver gene mutations. Focusing on TP53, the most mutated gene in cancer1, we present an inference of mutant p53 concentration and demonstrate that TP53 hotspot mutations optimally solve an evolutionary trade-off between oncogenic potential and neoantigen immunogenicity. Our model anticipates patient survival in The Cancer Genome Atlas and patients with lung cancer treated with immunotherapy as well as the age of tumour onset in germline carriers of TP53 variants. The predicted differential immunogenicity between hotspot mutations was validated experimentally in patients with cancer and in a unique large dataset of healthy individuals. Our data indicate that immune selective pressure on TP53 mutations has a smaller role in non-cancerous lesions than in tumours, suggesting that targeted immunotherapy may offer an early prophylactic opportunity for the former. Determining the relative contribution of immunogenicity and oncogenic function to the selective advantage of hotspot mutations thus has important implications for both precision immunotherapies and our understanding of tumour evolution.
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Affiliation(s)
- David Hoyos
- Computational Oncology, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Roberta Zappasodi
- Swim Across America Laboratory and Ludwig Collaborative, Immunology Program, Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA.
- Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA.
| | - Isabell Schulze
- Swim Across America Laboratory and Ludwig Collaborative, Immunology Program, Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zachary Sethna
- Computational Oncology, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kelvin César de Andrade
- Division of Cancer Epidemiology and Genetics, Clinical Genetics Branch, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Dean F Bajorin
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chaitanya Bandlamudi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Margaret K Callahan
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Samuel A Funt
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sine R Hadrup
- Experimental and Translational Immunology, Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Jeppe S Holm
- Experimental and Translational Immunology, Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Jonathan E Rosenberg
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sohrab P Shah
- Computational Oncology, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Physiology, Biophysics & Systems Biology, Weill Cornell Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Ignacio Vázquez-García
- Computational Oncology, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michelle Wu
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dmitriy Zamarin
- Swim Across America Laboratory and Ludwig Collaborative, Immunology Program, Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | | | | | - Payal P Khincha
- Division of Cancer Epidemiology and Genetics, Clinical Genetics Branch, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Sharon A Savage
- Division of Cancer Epidemiology and Genetics, Clinical Genetics Branch, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Vinod P Balachandran
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, 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
| | - Jedd D Wolchok
- Swim Across America Laboratory and Ludwig Collaborative, Immunology Program, Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Matthew D Hellmann
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Taha Merghoub
- Swim Across America Laboratory and Ludwig Collaborative, Immunology Program, Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA.
- Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Arnold J Levine
- Simons Center for Systems Biology, Institute for Advanced Study, Princeton, NJ, USA
| | - Marta Łuksza
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Benjamin D Greenbaum
- Computational Oncology, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Physiology, Biophysics & Systems Biology, Weill Cornell Medicine, Weill Cornell Medical College, New York, NY, USA.
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8
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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9
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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10
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Dalai SC, Greissl J, Pesesky M, Rebman AW, Soloski MJ, Horn EJ, Dines JN, Gittelman RM, Snyder TM, Emerson RO, Meeds E, Manley T, Kaplan IM, Baldo L, Carlson JM, Robins HS, Aucott J. LB17. Immunosequencing of the T-Cell Receptor Repertoire Reveals Signatures Specific for Diagnosis and Characterization of Early Lyme Disease. Open Forum Infect Dis 2021. [PMCID: PMC8644055 DOI: 10.1093/ofid/ofab466.1653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Background Changing climate and demographic trends have led to recent increases in the incidence of tick-borne illnesses. Early diagnosis of Lyme disease (LD) is critical for initiation of antibiotics to mitigate symptoms and prevent late manifestations. In patients not presenting with a typical erythema migrans rash, 2-tiered serologic testing is recommended to support a diagnosis of LD. However, 2-tiered testing is limited by ambiguity in interpretation and low sensitivity in early disease, highlighting an unmet clinical need for alternative diagnostic approaches. We identified a clinical signal for early LD based on evaluation of the T-cell response to B. burgdorferi infection. Methods We immunosequenced T-cell receptor (TCR) repertoires in blood samples from 3 independent cohorts of patients with laboratory-confirmed or clinically diagnosed early LD and endemic/non-endemic controls to identify 251 public, LD-associated TCRs. These TCRs were used to train a classifier that identified early LD with 99% specificity. Classifier sensitivity was evaluated in 211 LD cases and 2631 endemic controls and compared to that of standard 2-tiered testing (STTT). Biologic specificity was assessed by correlating TCR assay scores with clinical measures and by mapping the antigen specificity of Lyme-associated TCRs to B. burgdorferi antigens. Figure 1. LD-associated TCRs distinguish cases (orange) from controls (blue) in training cohorts. (A) Logistic-growth curve used to define a scoring function. (B) Positive-call threshold (99th percentile in endemic controls). ![]()
Results In early LD, TCR testing demonstrated a 1.9-fold increase in sensitivity compared to STTT (56% vs 30%), with a 3.1-fold increase ≤4 days from the onset of symptoms (44% vs 14%). TCR positivity predicted subsequent seroconversion in 37% of initially STTT-negative patients, suggesting the T-cell response is detectable before the humoral response. While positivity for both tests declined following treatment, greater declines in posttreatment sensitivity were observed for STTT compared to TCR testing. Higher TCR scores were associated with measures of disease severity, including abnormal liver function tests, disseminated rash, and number of symptoms. A subset of LD-associated TCRs mapped to B. burgdorferi antigens, demonstrating the high specificity of a TCR immunosequencing approach. ![]()
Figure 2. Validation of the TCR classifier in the JHU cohort and other holdout endemic controls. Distribution of model scores (A) and assay sensitivity (B). Model scores (C) and ROC (D) curves by serostatus. ![]()
Figure 3. Clinical correlates of TCR scoring. (A) Liver function test; (B) lymphocyte count, (C) rash presentation, (D) number of symptoms. ![]()
Conclusion T-cell-based testing has potential clinical utility as a sensitive and specific diagnostic for early LD, particularly in the initial days of illness. Disclosures Sudeb C. Dalai, MD, PhD, Adaptive Biotechnologies (Employee, Shareholder) Julia Greissl, PhD, Microsoft (Employee, Shareholder) Mitch Pesesky, PhD, Adaptive Biotechnologies (Employee, Shareholder) Allison W. Rebman, MPH, Global Lyme Alliance (Research Grant or Support)Steven and Alexandra Cohen Foundation (Research Grant or Support) Mark J. Soloski, PhD, NIH grant P30 AR070254 (Grant/Research Support)Steven and Alexandra Cohen Foundation (Research Grant or Support) Elizabeth J. Horn, PhD, Adaptive Biotechnologies (Research Grant or Support)Bay Area Lyme Foundation (Research Grant or Support)Lyme Disease Biobank (Employee)Steven and Alexandra Cohen Foundation (Research Grant or Support) Jennifer N. Dines, MD, Adaptive Biotechnologies (Employee, Shareholder) Rachel M. Gittelman, PhD, Adaptive Biotechnologies (Employee, Shareholder) Thomas M. Snyder, PhD, Adaptive Biotechnologies (Employee, Shareholder) Ryan O. Emerson, PhD, Adaptive Biotechnologies (Other Financial or Material Support, Employment with Adaptive Biotechnologies during the time of this study) Edward Meeds, PhD, Microsoft (Employee, Shareholder) Thomas Manley, MD, Adaptive Biotechnologies (Other Financial or Material Support, Declares employment with Adaptive Biotechnologies during the time of this study) Ian M. Kaplan, PhD, Adaptive Biotechnologies (Employee, Shareholder) Lance Baldo, MD, Adaptive Biotechnologies (Employee, Shareholder, Leadership Interest) Jonathan M. Carlson, PhD, Microsoft (Employee, Shareholder) Harlan S. Robins, PhD, Adaptive Biotechnologies (Board Member, Employee, Shareholder) John Aucott, MD, Adaptive Biotechnologies (Advisor or Review Panel member)Bay Area Lyme Foundation (Other Financial or Material Support, Scientific Advisory Board member)Department of Health and Human Services (Other Financial or Material Support, Past Chair, 2018, HHS Tick-borne Disease Working Group, Office of HIV/AIDS and Infectious Disease Policy, Office of the Assistant Secretary of Health)Expert testimony (Other Financial or Material Support, Expert testimony)Global Lyme Alliance (Research Grant or Support)Pfizer (Consultant)Steven and Alexandra Cohen Foundation (Research Grant or Support)Tarsus Pharmaceuticals (Consultant)
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Affiliation(s)
- Sudeb C Dalai
- Adaptive Biotechnologies and Stanford University School of Medicine, Seattle, WA
| | | | | | - Allison W Rebman
- Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Mark J Soloski
- Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | | | | | | | | | | | | | | | - Lance Baldo
- Adaptive Biotechnologies, Seattle, Washington
| | | | | | - John Aucott
- Johns Hopkins University School of Medicine, Baltimore, Maryland
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11
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Snyder TM, Gittelman RM, Klinger M, May DH, Osborne EJ, Taniguchi R, Jabran Zahid H, Elyanow R, Dalai SC, Kaplan IM, Dines JN, Noakes MT, Pandya R, 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. 126. Magnitude and Dynamics of the T-Cell Response to SARS-CoV-2 Infection and Vaccination. Open Forum Infect Dis 2021. [PMCID: PMC8690367 DOI: 10.1093/ofid/ofab466.126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Background T cells are central to the early identification and clearance of viral infections and support antibody generation by B cells, making them desirable for assessing the immune response to SARS-CoV-2 infection and vaccines. We combined 2 high-throughput immune profiling methods to create a quantitative picture of the SARS-CoV-2 T-cell response that is highly sensitive, durable, diagnostic, and discriminatory between natural infection and vaccination. Methods We deeply characterized 116 convalescent COVID-19 subjects by experimentally mapping CD8 and CD4 T-cell responses via antigen stimulation to 545 Human Leukocyte Antigen (HLA) class I and 284 class II viral peptides. We also performed T-cell receptor (TCR) repertoire sequencing on 1815 samples from 1521 PCR-confirmed SARS-CoV-2 cases and 3500 controls to identify shared public TCRs from SARS-CoV-2-associated CD8 and CD4 T cells. Combining these approaches with additional samples from vaccinated individuals, we characterized the response to natural infection as well as vaccination by separating responses to spike protein from other viral targets. Results We find that T-cell responses are often driven by a few immunodominant, HLA-restricted epitopes. As expected, the SARS-CoV-2 T-cell response peaks about 1-2 weeks after infection and is detectable at least several months after recovery. Applying these data, we trained a classifier to diagnose past SARS-CoV-2 infection based solely on TCR sequencing from blood samples and observed, at 99.8% specificity, high sensitivity soon after diagnosis (Day 3–7 = 85.1%; Day 8–14 = 94.8%) that persists after recovery (Day 29+/convalescent = 95.4%). Finally, by evaluating TCRs binding epitopes targeting all non-spike SARS-CoV-2 proteins, we were able to separate natural infection from vaccination with > 99% specificity. Conclusion TCR repertoire sequencing from whole blood reliably measures the adaptive immune response to SARS-CoV-2 soon after viral antigenic exposure (before antibodies are typically detectable) as well as at later time points, and distinguishes post-infection vs. vaccine immune responses with high specificity. This approach to characterizing the cellular immune response has applications in clinical diagnostics as well as vaccine development and monitoring. Disclosures Thomas M. Snyder, PhD, Adaptive Biotechnologies (Employee, Shareholder) Rachel M. Gittelman, PhD, Adaptive Biotechnologies (Employee, Shareholder) Mark Klinger, PhD, Adaptive Biotechnologies (Employee, Shareholder) Damon H. May, PhD, Adaptive Biotechnologies (Employee, Shareholder) Edward J. Osborne, PhD, Adaptive Biotechnologies (Employee, Shareholder) Ruth Taniguchi, PhD, Adaptive Biotechnologies (Employee, Shareholder) H. Jabran Zahid, PhD, Microsoft Research (Employee, Shareholder) Rebecca Elyanow, PhD, Adaptive Biotechnologies (Employee, Shareholder) Sudeb C. Dalai, MD, PhD, Adaptive Biotechnologies (Employee, Shareholder) Ian M. Kaplan, PhD, Adaptive Biotechnologies (Employee, Shareholder) Jennifer N. Dines, MD, Adaptive Biotechnologies (Employee, Shareholder) Matthew T. Noakes, PhD, Adaptive Biotechnologies (Employee, Shareholder) Ravi Pandya, PhD, Microsoft Research (Employee, Shareholder) Lance Baldo, MD, Adaptive Biotechnologies (Employee, Shareholder, Leadership Interest) James R. Heath, PhD, Merck (Research Grant or Support, Funding (from BARDA) for the ISB INCOV project, but had no role in planning the research or in writing the paper.) Joaquin Martinez-Lopez, MD, PhD, Adaptive Biotechnologies (Consultant) Jonathan M. Carlson, PhD, Microsoft Research (Employee, Shareholder) Harlan S. Robins, PhD, Adaptive Biotechnologies (Board Member, Employee, Shareholder)
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Affiliation(s)
| | | | | | - Damon H May
- Adaptive Biotechnologies, Seattle, Washington
| | | | | | | | | | - Sudeb C Dalai
- Adaptive Biotechnologies and Stanford University School of Medicine, Seattle, Washington
| | | | | | | | | | - Lance Baldo
- Adaptive Biotechnologies, Seattle, Washington
| | - Simona Semprini
- Unit of Microbiology - The Great Romagna Hub Laboratory, Pievesestina ITALY and DIMES, University of Bologna, Bologna, Emilia-Romagna, Italy
| | - Claudio Cerchione
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Medola, Lombardia, Italy
| | - Fabio Nicolini
- Immunotherapy, Cell Therapy and Biobank (ITCB), Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Medola, Lombardia, Italy
| | - Massimiliano Mazza
- Immunotherapy, Cell Therapy and Biobank (ITCB), Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Medola, Lombardia, 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, Maryland
| | - Kerry Dobbs
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Rocio Laguna-Goya
- Department of Immunology, Hospital 12de Octubre, i+12, Madrid, Madrid, Spain
| | | | - Santiago Barrio
- Hematology Department, Hospital 12de Octubre, i+12, CNIO, Complutense University, Madrid, 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, Lombardia, Italy
| | - Alessandra Sottini
- Laboratorio CREA, Department of Infectious and Tropical Diseases, and Medical Officer, ASST Spedali Civili di Brescia and University of Brescia, Brescia, Lombardia, 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, Lombardia, Italy
| | - Camillo Rossi
- Department of Pediatrics and Centro Tettamanti-European Reference Network PaedCan, EuroBloodNet, MetabERN-University of Milano-Bicocca-Fondazione MBBM-Ospedale San Gerardo, Monza, Lombardia, Italy
| | - Andrea Biondi
- Hematology Department, Hospital 12de Octubre, i+12, CNIO, Complutense University, Madrid, Madrid, Spain
| | - 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, Lombardia, Italy
| | - 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, Lombardia, Italy
| | - Paolo Bonfanti
- Department of Infectious Diseases, University of Milano-Bicocca-Ospedale San Gerardo, Monza, Lombardia, Italy
| | - Miranda F Tompkins
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, Maryland
| | - Camille Alba
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, Maryland
| | - Clifton Dalgard
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, Maryland
| | - Vittorio Sambri
- Unit of Microbiology - The Great Romagna Hub Laboratory, Pievesestina ITALY and DIMES, University of Bologna, Bologna, Emilia-Romagna, Italy
| | - Giovanni Martinelli
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Medola, Lombardia, Italy
| | - Jason D Goldman
- Swedish Medical Center, Seattle, WA, USA, and Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington
| | - James R Heath
- Institute for Systems Biology, Seattle, WA, USA, Seattle, Washington
| | - 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, Maryland
| | - Luigi D Notarangelo
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Estela Paz-Artal
- Department of Immunology, Hospital 12de Octubre, i+12, Madrid, Madrid, Spain
| | - Joaquin Martinez-Lopez
- Hematology Department, Hospital 12de Octubre, i+12, CNIO, Complutense University, Madrid, Madrid, Spain
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12
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Johnson SA, Seale SL, Gittelman RM, Rytlewski JA, Robins HS, Fields PA. Impact of HLA type, age and chronic viral infection on peripheral T-cell receptor sharing between unrelated individuals. PLoS One 2021; 16:e0249484. [PMID: 34460826 PMCID: PMC8405014 DOI: 10.1371/journal.pone.0249484] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 07/29/2021] [Indexed: 11/19/2022] Open
Abstract
The human adaptive immune system must generate extraordinary diversity to be able to respond to all possible pathogens. The T-cell repertoire derives this high diversity through somatic recombination of the T-cell receptor (TCR) locus, a random process that results in repertoires that are largely private to each individual. However, factors such as thymic selection and T-cell proliferation upon antigen exposure can affect TCR sharing among individuals. By immunosequencing the TCRβ variable region of 426 healthy individuals, we find that, on average, fewer than 1% of TCRβ clones are shared between individuals, consistent with largely private TCRβ repertoires. However, we detect a significant correlation between increased HLA allele sharing and increased number of shared TCRβ clones, with each additional shared HLA allele contributing to an increase in ~0.01% of the total shared TCRβ clones, supporting a key role for HLA type in shaping the immune repertoire. Surprisingly, we find that shared antigen exposure to CMV leads to fewer shared TCRβ clones, even after controlling for HLA, indicative of a largely private response to major viral antigenic exposure. Consistent with this hypothesis, we find that increased age is correlated with decreased overall TCRβ clone sharing, indicating that the pattern of private TCRβ clonal expansion is a general feature of the T-cell response to other infectious antigens as well. However, increased age also correlates with increased sharing among the lowest frequency clones, consistent with decreased repertoire diversity in older individuals. Together, all of these factors contribute to shaping the TCRβ repertoire, and understanding their interplay has important implications for the use of T cells for therapeutics and diagnostics.
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Affiliation(s)
- Sarah A. Johnson
- Adaptive Biotechnologies, Seattle, Washington, United States of America
| | - Spencer L. Seale
- Adaptive Biotechnologies, Seattle, Washington, United States of America
| | | | | | - Harlan S. Robins
- Adaptive Biotechnologies, Seattle, Washington, United States of America
| | - Paul A. Fields
- Adaptive Biotechnologies, Seattle, Washington, United States of America
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13
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Gruber SB, Bonner JD, Lindsey SS, Tsai YY, Sanz-Pamplona R, Alonso MH, Melas M, Rennert HS, McDonnell KJ, Idos GE, Walker CP, Kast WM, Da Silva D, Robins HS, Greenson JK, Moreno V, Schmit SL, Rennert G. Abstract 2737: Clinical and epidemiologic predictors of clonal immune responses in colorectal cancer. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-2737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The quantity and quality of immune responses in colorectal cancers (CRC) are widely variable and have important clinical, therapeutic, and prognostic implications. We studied clinical and epidemiologic factors that might influence T-cell quantity and clonality within colorectal adenocarcinomas to better understand the drivers of diverse immune responses. Incident cases of CRC from the Molecular Epidemiology of Colorectal Cancer Study (MECC) were interviewed, and 6,006 cases had complete epidemiologic data. Archived tumor blocks were retrieved from 3,865 (64.4%) cases, and all were reviewed by a single expert pathologist who quantified TILS/hpf. Sufficient tissue for macrodissection and measurement of TCR abundance and clonality using the immunoSEQ assay (Adaptive Biotechnologies) was available and completed for 2,750 cases. Logistic regression, negative binomial regression and linear regression models were used to evaluate potential associations between clinical and epidemiologic variables for: TILS/hpf, TCR abundance, and T-cell clonality. The stage distribution was representative of cancer incidence in the population, and the MSI-H phenotype was observed in 14.2% of cases. Clinical, pathologic, and epidemiologic variables including aspirin, alcohol, diet, hormone use, physical activity, smoking, and statins were assessed in relation to immune measures. Among other findings, >5 years of statins (p<0.001) and daily aspirin (p=0.037) were each strongly associated with T-cell clonality. Our study suggests that important parameters of the adaptive immune response may be mediated by modifiable factors. Mechanisms regulating immune responses in CRC may have implications for chemoprevention as well as immunotherapy.
Citation Format: Stephen B. Gruber, Joseph D. Bonner, Sidney S. Lindsey, Ya-Yu Tsai, Rebeca Sanz-Pamplona, M. Henar Alonso, Marilena Melas, Hedy S. Rennert, Kevin J. McDonnell, Gregory E. Idos, Christopher P. Walker, W. Martin Kast, Diane Da Silva, Harlan S. Robins, Joel K. Greenson, Victor Moreno, Stephanie L. Schmit, Gad Rennert. Clinical and epidemiologic predictors of clonal immune responses in colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2737.
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Affiliation(s)
- Stephen B. Gruber
- 1City of Hope National Medical Center and Beckman Research Institute, Duarte, CA
| | - Joseph D. Bonner
- 1City of Hope National Medical Center and Beckman Research Institute, Duarte, CA
| | - Sidney S. Lindsey
- 1City of Hope National Medical Center and Beckman Research Institute, Duarte, CA
| | - Ya-Yu Tsai
- 2Cleveland Clinic Foundation, Cleveland, OH, Cleveland, OH
| | - Rebeca Sanz-Pamplona
- 3Catalan Institute of Oncology (ICO), Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL) and CIBERESP, L'Hospitalet de Llobregat, Barcelona, Spain
| | - M. Henar Alonso
- 3Catalan Institute of Oncology (ICO), Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL) and CIBERESP, L'Hospitalet de Llobregat, Barcelona, Spain
| | | | - Hedy S. Rennert
- 5Carmel Medical Center and Faculty of Medicine, Technion-Israel Institute of Technology, Clalit National Cancer Control Center, Haifa, Israel
| | - Kevin J. McDonnell
- 1City of Hope National Medical Center and Beckman Research Institute, Duarte, CA
| | - Gregory E. Idos
- 1City of Hope National Medical Center and Beckman Research Institute, Duarte, CA
| | | | - W. Martin Kast
- 6Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Diane Da Silva
- 6Keck School of Medicine, University of Southern California, Los Angeles, CA
| | | | | | - Victor Moreno
- 3Catalan Institute of Oncology (ICO), Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL) and CIBERESP, L'Hospitalet de Llobregat, Barcelona, Spain
| | | | - Gad Rennert
- 5Carmel Medical Center and Faculty of Medicine, Technion-Israel Institute of Technology, Clalit National Cancer Control Center, Haifa, Israel
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14
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Schmit SL, Tsai YY, Bonner J, Sanz-Pamplona R, Joshi AD, Lindsey SS, Melas M, McDonnell KJ, Idos GE, Walker CP, Kast WM, Da Silva D, Ugai T, Rennert HS, Robins HS, Greenson JK, Ogino S, Moreno V, Rennert G, Gruber SB. Abstract 824: Germline genetic regulation of the adaptive immune response in colorectal cancer. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Adaptive immune responses in the tumor microenvironment of colorectal cancer (CRC) play an important role in prognosis. However, the contributions of germline genetic variations to the strength and diversity of T cell responses in CRC are unclear. We conducted a genome-wide association study to examine the relationships between germline genetic variants and measures of the T cell repertoire in colorectal tumors. Germline DNA samples from 5,581 CRC cases recruited into the Molecular Epidemiology of Colorectal Cancer Study (MECC) were genotyped in batches using four different platforms. Genotype data were imputed to the Haplotype Reference Consortium panel separately by genotyping platform. Tumor DNA samples were extracted from paraffin blocks, and tumor infiltrating lymphocytes per high powered field (TILs/hpf) were quantified by a single gastrointestinal pathologist. TCR abundance and clonality within individual CRCs were measured using the immunoSEQ assay (Adaptive Biotechnologies). Appropriate quality control steps and data transformations were applied to fit downstream statistical modeling assumptions. After standard quality control on both imputed genotypes and transformed immune metrics, 2,876 (TILs/hpf) and 2,395 (TCR abundance and clonality) cases with approximately 9 million imputed genetic variants were included in the discovery phase. Logistic or linear regression models were used to evaluate the associations between allelic dosage of each variant and each immune-related outcome, adjusting for sex, age at diagnosis, genotyping platform, and principal components for global ancestry. Three independent datasets were available to replicate our findings using similar quality control measures and regression models: Colonomics (N=96; TILs/hpf, TCR abundance, clonality), the CRC Genetics Study (N=162; TCR abundance, clonality), and the Harvard Cohorts (N=505; TILs/hpf; in progress). The discovery phase identified 5 independent genetic variants associated with TILs/hpf, 15 associated with TCR abundance, and 19 associated with clonality at p<5X10E-06. Replication analyses as well as expression quantitative trait analyses and in silico functional annotation are underway for the loci of interest. Our study suggests that germline genetic variation is associated with the quantity and quality of adaptive immune responses in CRC.
Citation Format: Stephanie L. Schmit, Ya-Yu Tsai, Joseph Bonner, Rebeca Sanz-Pamplona, Amit D. Joshi, Sidney S. Lindsey, Marilena Melas, Kevin J. McDonnell, Gregory E. Idos, Christopher P. Walker, W. Martin Kast, Diane Da Silva, Tomotaka Ugai, Hedy S. Rennert, Harlan S. Robins, Joel K. Greenson, Shuji Ogino, Victor Moreno, Gad Rennert, Stephen B. Gruber. Germline genetic regulation of the adaptive immune response in colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 824.
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Affiliation(s)
| | | | | | | | - Amit D. Joshi
- 4Massachusetts General Hospital and Harvard Medical School; Harvard T.H. Chan School of Public Health, Boston, MA
| | | | | | | | | | | | - W. Martin Kast
- 6University of Southern California; Norris Comprehensive Cancer Center, Los Angeles, CA
| | | | - Tomotaka Ugai
- 8Brigham and Women's Hospital and Harvard Medical School; Harvard T.H. Chan School of Public Health, Boston, MA
| | - Hedy S. Rennert
- 9Clalit Health Services National Cancer Control Center, Haifa, Israel
| | | | | | - Shuji Ogino
- 12Brigham and Women's Hospital and Harvard Medical School; Harvard T.H. Chan School of Public Health; Dana-Farber Cancer Institute, Boston, MA
| | | | - Gad Rennert
- 9Clalit Health Services National Cancer Control Center, Haifa, Israel
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15
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Bonner J, Schmit SL, Lindsey SS, Tsai YY, Sanz-Pamplona R, Alonso MH, Melas M, Rennert HS, McDonnell KJ, Idos G, Walker CP, Kast WM, Da Silva D, Robins HS, Greenson JK, Moreno V, Rennert G, Gruber SB. Abstract 835: T-cell abundance, clonality and disease specific survival in colorectal cancer. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Immune responses to colorectal cancer (CRC) are important prognostic factors as measured by either tumor infiltrating lymphocytes per high powered field or the presence of Crohn's like lymphoid reaction. New technologies to quantify specific features of immune responses include immunoSeq (Adaptive Biotechnologies), which accurately quantifies T-cell receptor (TCR) abundance and T-cell receptor clonality. Here we measured the independent contributions of TCR abundance and TCR clonality to 5-year CRC-specific survival in the Molecular Epidemiology of Colorectal Cancer (MECC) study. The MECC study consented, interviewed, and followed 6,006 incident cases of CRC diagnosed between March 31, 1998 and July 1, 2017 (median follow-up time = 6.9 years). Archived paraffin blocks were retrieved, and 2,750 cases had sufficient tissue and adequate DNA extraction to perform the immunoSeq assay. Analyses were restricted to 1,625 samples with more than 100 T-cells to permit accurate quantification of TCR abundance and TCR clonality as measured by Simpson Clonality Index. TCR abundance was log2 transformed for analyses, and Simpson Clonality Index was log2-transformed and z-scale normalized separately by assay version. In unadjusted models, dichotomized log2 transformed TCR abundance (Hazard Ratio (HR) = 0.57, 95% confidence interval (CI) 0.47-0.71, p=9.77E-08) and dichotomized TCR clonality (HR = 0.77, 95% CI 0.63-0.94, p=0.01) were each statistically significantly associated with 5-year CRC-specific survival. In a model with adjustment for age, sex, microsatellite instability, stage and assay version, both dichotomized log2 transformed TCR abundance (HR = 0.61, 95% CI, 0.49-0.75, p=3.03E-06), and dichotomized TCR clonality (HR = 0.81, 95% CI, 0.66-0.99, p=0.048) were associated with improved 5-year disease-specific survival.
Conclusion: TCR abundance and TCR clonality are independent prognostic indicators in CRC.
Citation Format: Joseph Bonner, Sephanie L. Schmit, Sidney S. Lindsey, Ya-Yu Tsai, Rebeca Sanz-Pamplona, M. Henar Alonso, Marilena Melas, Hedy S. Rennert, Kevin J. McDonnell, Gregory Idos, Christopher P. Walker, W. Martin Kast, Diane Da Silva, Harlan S. Robins, Joel K. Greenson, Victor Moreno, Gad Rennert, Stephen B. Gruber. T-cell abundance, clonality and disease specific survival in colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 835.
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Affiliation(s)
| | | | | | - Ya-Yu Tsai
- 2Cleveland Clinic Foundation, Cleveland, OH
| | | | | | | | | | | | | | | | | | | | | | | | | | - Gad Rennert
- 5Technion-Israel Institute of Technology, Haifa, Israel
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16
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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 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] [What about the content of this article? (0)] [Affiliation(s)] [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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17
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Milano F, Emerson RO, Salit R, Guthrie KA, Thur LA, Dahlberg A, Robins HS, Delaney C. Impact of T Cell Repertoire Diversity on Mortality Following Cord Blood Transplantation. Front Oncol 2020; 10:583349. [PMID: 33163411 PMCID: PMC7582952 DOI: 10.3389/fonc.2020.583349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 09/21/2020] [Indexed: 11/13/2022] Open
Abstract
Introduction Cord blood transplantation (CBT) recipients are at increased risk of mortality due to delayed immune recovery (IR). Prior studies in CBT patients have shown that recovery of absolute lymphocyte count is predictive of survival after transplant. However, there are no data on the association of T-cell receptor (TCR) and clinical outcomes after CBT. Here we retrospectively performed TCR beta chain sequencing on peripheral blood (PB) samples of 34 CBT patients. Methods All patients received a total body irradiation based conditioning regimen and cyclosporine and MMF were used for graft versus host disease (GvHD) prophylaxis. PB was collected pretransplant on days 28, 56, 80, 180, and 1-year posttransplant for retrospective analysis of IR utilizing high-throughput sequencing of TCRβ rearrangements from genomic DNA extracted from PB mononuclear cells. To test the association between TCR repertoire diversity and patient outcomes, we conducted a permutation test on median TCR repertoire diversity for patients who died within the first year posttransplant versus those who survived. Results Median age was 27 (range 1–58 years) and most of the patients (n = 27) had acute leukemias. There were 15 deaths occurring between 34 to 335 days after transplant. Seven deaths were due to relapse. Rapid turnover of T cell clones was observed at each time point, with TCR repertoires stabilizing by 1-year posttransplant. TCR diversity values at day 100 for patients who died between 100 and 365 days posttransplant were significantly lower than those of the surviving patients (p = 0.01). Conclusions Using a fast high-throughput TCR sequencing assay we have demonstrated that high TCR diversity is associated with better patient outcomes following CBT. Importantly, this assay is easily performed on posttransplant PB samples, even as early as day 28 posttransplant, making it an excellent candidate for early identification of patients at high risk of death.
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Affiliation(s)
- F Milano
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States.,Department of Medicine, University of Washington School of Medicine, Seattle, WA, United States
| | - R O Emerson
- Adaptive Biotechnologies, Seattle, WA, United States
| | - R Salit
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States.,Department of Medicine, University of Washington School of Medicine, Seattle, WA, United States
| | - K A Guthrie
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - L A Thur
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - A Dahlberg
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States.,Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, United States
| | - H S Robins
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States.,Adaptive Biotechnologies, Seattle, WA, United States
| | - C Delaney
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States.,Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, United States
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18
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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 2020:2020.07.31.20165647. [PMID: 32793919 PMCID: PMC7418734 DOI: 10.1101/2020.07.31.20165647] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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19
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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20
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Sanz-Pamplona R, Melas M, Maoz A, Schmit SL, Rennert H, Lejbkowicz F, Greenson JK, Sanjuan X, Lopez-Zambrano M, Alonso MH, Qu C, McDonnell KJ, Idos GE, Vignali M, Emerson R, Fields P, Guinó E, Santos C, Salazar R, Robins HS, Rennert G, Gruber SB, Moreno V. Lymphocytic infiltration in stage II microsatellite stable colorectal tumors: A retrospective prognosis biomarker analysis. PLoS Med 2020; 17:e1003292. [PMID: 32970670 PMCID: PMC7514069 DOI: 10.1371/journal.pmed.1003292] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 08/14/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Identifying stage II patients with colorectal cancer (CRC) at higher risk of progression is a clinical priority in order to optimize the advantages of adjuvant chemotherapy while avoiding unnecessary toxicity. Recently, the intensity and the quality of the host immune response in the tumor microenvironment have been reported to have an important role in tumorigenesis and an inverse association with tumor progression. This association is well established in microsatellite instable CRC. In this work, we aim to assess the usefulness of measures of T-cell infiltration as prognostic biomarkers in 640 stage II, CRC tumors, 582 of them confirmed microsatellite stable. METHODS AND FINDINGS We measured both the quantity and clonality index of T cells by means of T-cell receptor (TCR) immunosequencing in a discovery dataset (95 patients with colon cancer diagnosed at stage II and microsatellite stable, median age 67, 30% women) and replicated the results in 3 additional series of stage II patients from 2 countries. Series 1 and 2 were recruited in Barcelona, Spain and included 112 fresh frozen (FF, median age 69, 44% women) and 163 formalin-fixed paraffin-embedded (FFPE, median age 67, 39% women) samples, respectively. Series 3 included 270 FFPE samples from patients recruited in Haifa, Northern Israel, as part of a large case-control study of CRC (median age 73, 46% women). Median follow-up time was 81.1 months. Cox regression models were fitted to evaluate the prognostic value of T-cell abundance and Simpson clonality of TCR variants adjusting by sex, age, tumor location, and stage (IIA and IIB). In the discovery dataset, higher TCR abundance was associated with better prognosis (hazard ratio [HR] for ≥Q1 = 0.25, 95% CI 0.10-0.63, P = 0.003). A functional analysis of gene expression on these tumors revealed enrichment in pathways related to immune response. Higher values of clonality index (lower diversity) were not associated with worse disease-free survival, though the HR for ≥Q3 was 2.32 (95% CI 0.90-5.97, P = 0.08). These results were replicated in an independent FF dataset (TCR abundance: HR = 0.30, 95% CI 0.12-0.72, P = 0.007; clonality: HR = 3.32, 95% CI 1.38-7.94, P = 0.007). Also, the association with prognosis was tested in 2 independent FFPE datasets. The same association was observed with TCR abundance (HR = 0.41, 95% CI 0.18-0.93, P = 0.03 and HR = 0.56, 95% CI 0.31-1, P = 0.042, respectively, for each FFPE dataset). However, the clonality index was associated with prognosis only in the FFPE dataset from Israel (HR = 2.45, 95% CI 1.39-4.32, P = 0.002). Finally, a combined analysis combining all microsatellite stable (MSS) samples demonstrated a clear prognosis value both for TCR abundance (HR = 0.39, 95% CI 0.26-0.57, P = 1.3e-06) and the clonality index (HR = 2.13, 95% CI 1.44-3.15, P = 0.0002). These associations were also observed when variables were considered continuous in the models (HR per log2 of TCR abundance = 0.85, 95% CI 0.78-0.93, P = 0.0002; HR per log2 or clonality index = 1.16, 95% CI 1.03-1.31, P = 0.016). LIMITATIONS This is a retrospective study, and samples had been preserved with different methods. Validation series lack complete information about microsatellite instability (MSI) status and pathology assessment. The Molecular Epidemiology of Colorectal Cancer (MECC) study had information about overall survival instead of progression-free survival. CONCLUSION Results from this study demonstrate that tumor lymphocytes, assessed by TCR repertoire quantification based on a sequencing method, are an independent prognostic factor in microsatellite stable stage II CRC.
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Affiliation(s)
- Rebeca Sanz-Pamplona
- Catalan Institute of Oncology (ICO), Hospitalet de Llobregat, Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Spain
| | - Marilena Melas
- Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - Asaf Maoz
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Stephanie L. Schmit
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America
| | - Hedy Rennert
- Carmel Medical Center, and Technion, Haifa, Israel
| | | | - Joel K. Greenson
- University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Xavier Sanjuan
- University Hospital Bellvitge (HUB-IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Maria Lopez-Zambrano
- University Hospital Bellvitge (HUB-IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - M. Henar Alonso
- Catalan Institute of Oncology (ICO), Hospitalet de Llobregat, Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Chenxu Qu
- City of Hope National Medical Center, Duarte, California, United States of America
| | - Kevin J. McDonnell
- City of Hope National Medical Center, Duarte, California, United States of America
| | - Gregory E. Idos
- City of Hope National Medical Center, Duarte, California, United States of America
| | - Marissa Vignali
- Adaptive Biotechnologies, Seattle, Washington, United States of America
| | - Ryan Emerson
- Adaptive Biotechnologies, Seattle, Washington, United States of America
| | - Paul Fields
- Adaptive Biotechnologies, Seattle, Washington, United States of America
| | - Elisabet Guinó
- Catalan Institute of Oncology (ICO), Hospitalet de Llobregat, Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Spain
| | - Cristina Santos
- Catalan Institute of Oncology (ICO), Hospitalet de Llobregat, Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Consortium for Biomedical Research in Oncology (CIBERONC), Spain
| | - Ramon Salazar
- Catalan Institute of Oncology (ICO), Hospitalet de Llobregat, Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Consortium for Biomedical Research in Oncology (CIBERONC), Spain
| | - Harlan S. Robins
- Adaptive Biotechnologies, Seattle, Washington, United States of America
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * E-mail: (VM); (SBG); (GR); (HSR)
| | - Gad Rennert
- Carmel Medical Center, and Technion, Haifa, Israel
- * E-mail: (VM); (SBG); (GR); (HSR)
| | - Stephen B. Gruber
- City of Hope National Medical Center, Duarte, California, United States of America
- * E-mail: (VM); (SBG); (GR); (HSR)
| | - Victor Moreno
- Catalan Institute of Oncology (ICO), Hospitalet de Llobregat, Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
- * E-mail: (VM); (SBG); (GR); (HSR)
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21
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Nolan S, Vignali M, Klinger M, Dines JN, Kaplan IM, Svejnoha E, Craft T, Boland K, Pesesky M, Gittelman RM, Snyder TM, Gooley CJ, Semprini S, Cerchione C, Mazza M, Delmonte OM, Dobbs K, Carreño-Tarragona G, Barrio S, Sambri V, Martinelli G, Goldman JD, Heath JR, Notarangelo LD, Carlson JM, Martinez-Lopez J, Robins HS. A large-scale database of T-cell receptor beta (TCRβ) sequences and binding associations from natural and synthetic exposure to SARS-CoV-2. Res Sq 2020:rs.3.rs-51964. [PMID: 32793896 PMCID: PMC7418738 DOI: 10.21203/rs.3.rs-51964/v1] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
We describe the establishment and current content of the ImmuneCODE™ database, which includes hundreds of millions of T-cell Receptor (TCR) sequences from over 1,400 subjects exposed to or infected with the SARS-CoV-2 virus, as well as over 135,000 high-confidence SARS-CoV-2-specific TCRs. This database is made freely available, and the data contained in it can be downloaded and analyzed online or offline to assist with the global efforts to understand the immune response to the SARS-CoV-2 virus and develop new interventions.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Ottavia M Delmonte
- National Institute of Allergy and Infectious Diseases, National Institutes of Health
| | - Kerry Dobbs
- National Institute of Allergy and Infectious Diseases, National Institutes of Health
| | | | | | | | | | - Jason D Goldman
- Swedish Medical Center, Seattle, WA, USA and Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA
| | | | - Luigi D Notarangelo
- National Institute of Allergy and Infectious Diseases, National Institutes of Health
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22
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Chu ND, Bi HS, Emerson RO, Sherwood AM, Birnbaum ME, Robins HS, Alm EJ. Longitudinal immunosequencing in healthy people reveals persistent T cell receptors rich in highly public receptors. BMC Immunol 2019; 20:19. [PMID: 31226930 PMCID: PMC6588944 DOI: 10.1186/s12865-019-0300-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 06/06/2019] [Indexed: 11/18/2022] Open
Abstract
Background The adaptive immune system maintains a diversity of T cells capable of recognizing a broad array of antigens. Each T cell’s specificity for antigens is determined by its T cell receptors (TCRs), which together across all T cells form a repertoire of millions of unique receptors in each individual. Although many studies have examined how TCR repertoires change in response to disease or drugs, few have explored the temporal dynamics of the TCR repertoire in healthy individuals. Results Here we report immunosequencing of TCR β chains (TCRβ) from the blood of three healthy individuals at eight time points over one year. TCRβ repertoires of all peripheral-blood T cells and sorted memory T cells clustered clearly by individual, systematically demonstrating that TCRβ repertoires are specific to individuals across time. This individuality was absent from TCRβs from naive T cells, suggesting that the differences resulted from an individual’s antigen exposure history, not genetic background. Many characteristics of the TCRβ repertoire (e.g., diversity, clonality) were stable across time, although we found evidence of T cell expansion dynamics even within healthy individuals. We further identified a subset of “persistent” TCRβs present across all time points. These receptors were rich in clonal and highly public receptors and may play a key role in immune system maintenance. Conclusions Our results highlight the importance of longitudinal sampling of the immune system, providing a much-needed baseline for TCRβ dynamics in healthy individuals. Such a baseline will improve interpretation of changes in the TCRβ repertoire during disease or treatment. Electronic supplementary material The online version of this article (10.1186/s12865-019-0300-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nathaniel D Chu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA, USA.,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Haixin Sarah Bi
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA.,Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | | | - Michael E Birnbaum
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Harlan S Robins
- Adaptive Biotechnologies, Seattle, WA, USA.,Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Eric J Alm
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Broad Institute, Cambridge, MA, 02139, USA.
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23
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Lindau P, Mukherjee R, Gutschow MV, Vignali M, Warren EH, Riddell SR, Makar KW, Turtle CJ, Robins HS. Cytomegalovirus Exposure in the Elderly Does Not Reduce CD8 T Cell Repertoire Diversity. J Immunol 2018; 202:476-483. [PMID: 30541882 PMCID: PMC6321841 DOI: 10.4049/jimmunol.1800217] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 11/04/2018] [Indexed: 01/10/2023]
Abstract
With age, the immune system becomes less effective, causing increased susceptibility to infection. Chronic CMV infection further impairs immune function and is associated with increased mortality in the elderly. CMV exposure elicits massive CD8+ T cell clonal expansions and diminishes the cytotoxic T cell response to subsequent infections, leading to the hypothesis that to maintain homeostasis, T cell clones are expelled from the repertoire, reducing T cell repertoire diversity and diminishing the ability to combat new infections. However, in humans, the impact of CMV infection on the structure and diversity of the underlying T cell repertoire remains uncharacterized. Using TCR β-chain immunosequencing, we observed that the proportion of the peripheral blood T cell repertoire composed of the most numerous 0.1% of clones is larger in the CMV seropositive and gradually increases with age. We found that the T cell repertoire in the elderly grows to accommodate CMV-driven clonal expansions while preserving its underlying diversity and clonal structure. Our observations suggest that the maintenance of large CMV-reactive T cell clones throughout life does not compromise the underlying repertoire. Alternatively, we propose that the diminished immunity in elderly individuals with CMV is due to alterations in cellular function rather than a reduction in CD8+ T cell repertoire diversity.
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Affiliation(s)
- Paul Lindau
- Molecular and Cellular Biology Graduate Program, University of Washington School of Medicine, Seattle, WA 98195; .,Herbold Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | - Rithun Mukherjee
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA 98101
| | - Miriam V Gutschow
- Herbold Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | | | - Edus H Warren
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109.,Department of Medicine, University of Washington, Seattle, WA 98195; and
| | - Stanley R Riddell
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109.,Department of Medicine, University of Washington, Seattle, WA 98195; and
| | - Karen W Makar
- Bill and Melinda Gates Foundation, Seattle, WA 98109
| | - Cameron J Turtle
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109.,Department of Medicine, University of Washington, Seattle, WA 98195; and
| | - Harlan S Robins
- Herbold Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109; .,Adaptive Biotechnologies, Seattle, WA 98102
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24
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Hopkins AC, Yarchoan M, Durham JN, Yusko EC, Rytlewski JA, Robins HS, Laheru DA, Le DT, Lutz ER, Jaffee EM. T cell receptor repertoire features associated with survival in immunotherapy-treated pancreatic ductal adenocarcinoma. JCI Insight 2018; 3:122092. [PMID: 29997287 PMCID: PMC6124515 DOI: 10.1172/jci.insight.122092] [Citation(s) in RCA: 159] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 05/31/2018] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Immune checkpoint inhibitors provide significant clinical benefit to a subset of patients, but novel prognostic markers are needed to predict which patients will respond. This study was initiated to determine if features of patient T cell repertoires could provide insights into the mechanisms of immunotherapy, while also predicting outcomes. METHODS We examined T cell receptor (TCR) repertoires in peripheral blood of 25 metastatic pancreatic cancer patients treated with ipilimumab with or without GVAX (a pancreatic cancer vaccine), as well as peripheral blood and tumor biopsies from 32 patients treated with GVAX and mesothelin-expressing Listeria monocytogenes with or without nivolumab. Statistics from these repertoires were then tested for their association with clinical response and treatment group. RESULTS We demonstrate that, first, the majority of patients receiving these treatments experience a net diversification of their peripheral TCR repertoires. Second, patients receiving ipilimumab experienced larger changes in their repertoires, especially in combination with GVAX. Finally, both a low baseline clonality and a high number of expanded clones following treatment were associated with significantly longer survival in patients who received ipilimumab but not in patients receiving nivolumab. CONCLUSIONS We show that these therapies have measurably different effects on the peripheral repertoire, consistent with their mechanisms of action, and demonstrate the potential for TCR repertoire profiling to serve as a biomarker of clinical response in pancreatic cancer patients receiving immunotherapy. In addition, our results suggest testing sequential administration of anti-CTLA-4 and anti-PD-1 antibodies to achieve optimal therapeutic benefit. TRIAL REGISTRATION Samples used in this study were collected from the NCT00836407 and NCT02243371 clinical trials. FUNDING Research supported by a Stand Up To Cancer Lustgarten Foundation Pancreatic Cancer Convergence Dream Team Translational Research grant (SU2C-AACR-DT14-14). Stand Up To Cancer is a program of the Entertainment Industry Foundation administered by the American Association for Cancer Research (AACR). Additional clinical trial funding was provided by AACR-Pancreatic Cancer Action Network Research Acceleration Network grant (14-90-25-LE), NCI SPORE in GI Cancer (CA062924), Quick-Trials for Novel Cancer Therapies: Exploratory Grants (R21CA126058-01A2), and the US Food and Drug Administration (R01FD004819). Research collaboration and financial support were provided by Adaptive Biotechnologies.
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Affiliation(s)
- Alexander C. Hopkins
- Johns Hopkins University, Sidney Kimmel Cancer Center, Skip Viragh Center for Pancreas Cancer, The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Baltimore, Maryland, USA
| | - Mark Yarchoan
- Johns Hopkins University, Sidney Kimmel Cancer Center, Skip Viragh Center for Pancreas Cancer, The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Baltimore, Maryland, USA
| | - Jennifer N. Durham
- Johns Hopkins University, Sidney Kimmel Cancer Center, Skip Viragh Center for Pancreas Cancer, The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Baltimore, Maryland, USA
| | | | | | | | - Daniel A. Laheru
- Johns Hopkins University, Sidney Kimmel Cancer Center, Skip Viragh Center for Pancreas Cancer, The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Baltimore, Maryland, USA
| | - Dung T. Le
- Johns Hopkins University, Sidney Kimmel Cancer Center, Skip Viragh Center for Pancreas Cancer, The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Baltimore, Maryland, USA
| | - Eric R. Lutz
- Johns Hopkins University, Sidney Kimmel Cancer Center, Skip Viragh Center for Pancreas Cancer, The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Baltimore, Maryland, USA
| | - Elizabeth M. Jaffee
- Johns Hopkins University, Sidney Kimmel Cancer Center, Skip Viragh Center for Pancreas Cancer, The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Baltimore, Maryland, USA
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25
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DeWitt WS, Yu KKQ, Wilburn DB, Sherwood A, Vignali M, Day CL, Scriba TJ, Robins HS, Swanson WJ, Emerson RO, Bradley PH, Seshadri C. A Diverse Lipid Antigen-Specific TCR Repertoire Is Clonally Expanded during Active Tuberculosis. J Immunol 2018; 201:888-896. [PMID: 29914888 DOI: 10.4049/jimmunol.1800186] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 05/21/2018] [Indexed: 01/06/2023]
Abstract
Human T cells that recognize lipid Ags presented by highly conserved CD1 proteins often express semi-invariant TCRs, but the true diversity of lipid Ag-specific TCRs remains unknown. We use CD1b tetramers and high-throughput immunosequencing to analyze thousands of TCRs from ex vivo-sorted or in vitro-expanded T cells specific for the mycobacterial lipid Ag, glucose monomycolate. Our results reveal a surprisingly diverse repertoire resulting from editing of germline-encoded gene rearrangements analogous to MHC-restricted TCRs. We used a distance-based metric (TCRDist) to show how this diverse TCR repertoire builds upon previously reported conserved motifs by including subject-specific TCRs. In a South African cohort, we show that TCRDist can identify clonal expansion of diverse glucose monomycolate-specific TCRs and accurately distinguish patients with active tuberculosis from control subjects. These data suggest that similar mechanisms govern the selection and expansion of peptide and lipid Ag-specific T cells despite the nonpolymorphic nature of CD1.
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Affiliation(s)
- William S DeWitt
- Adaptive Biotechnologies, Seattle, WA 98102.,Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109.,Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Krystle K Q Yu
- Department of Medicine, University of Washington, Seattle, WA 98195
| | - Damien B Wilburn
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | | | | | - Cheryl L Day
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322.,Emory Vaccine Center, Atlanta, GA 30329
| | - Thomas J Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa.,Division of Immunology, Department of Pathology, University of Cape Town, Cape Town 7925, South Africa
| | - Harlan S Robins
- Adaptive Biotechnologies, Seattle, WA 98102.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | - Willie J Swanson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | | | - Philip H Bradley
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109; and.,Institute for Protein Design, University of Washington, Seattle, WA 98195
| | - Chetan Seshadri
- Department of Medicine, University of Washington, Seattle, WA 98195;
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26
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Rudqvist NP, Pilones KA, Lhuillier C, Wennerberg E, Sidhom JW, Emerson RO, Robins HS, Schneck J, Formenti SC, Demaria S. Radiotherapy and CTLA-4 Blockade Shape the TCR Repertoire of Tumor-Infiltrating T Cells. Cancer Immunol Res 2017; 6:139-150. [PMID: 29180535 DOI: 10.1158/2326-6066.cir-17-0134] [Citation(s) in RCA: 148] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Revised: 09/06/2017] [Accepted: 11/13/2017] [Indexed: 01/05/2023]
Abstract
Immune checkpoint inhibitors activate T cells to reject tumors. Unique tumor mutations are key T-cell targets, but a comprehensive understanding of the nature of a successful antitumor T-cell response is lacking. To investigate the T-cell receptor (TCR) repertoire associated with treatment success versus failure, we used a well-characterized mouse carcinoma that is rejected by CD8 T cells in mice treated with radiotherapy (RT) and anti-CTLA-4 in combination, but not as monotherapy, and comprehensively analyzed tumor-infiltrating lymphocytes (TILs) by high-throughput sequencing of the TCRΒ CDR3 region. The combined treatment increased TIL density and CD8/CD4 ratio. Assessment of the frequency of T-cell clones indicated that anti-CTLA-4 resulted in fewer clones and a more oligoclonal repertoire compared with untreated tumors. In contrast, RT increased the CD8/CD4 ratio and broadened the TCR repertoire, and when used in combination with anti-CTLA-4, these selected T-cell clones proliferated. Hierarchical clustering of CDR3 sequences showed a treatment-specific clustering of TCRs that were shared by different mice. Abundant clonotypes were commonly shared between animals and yet treatment-specific. Analysis of amino-acid sequence similarities revealed a significant increase in the number and richness of dominant CDR3 motifs in tumors treated with RT + anti-CTLA-4 compared with control. The repertoire of TCRs reactive with a single tumor antigen recognized by CD8+ T cells was heterogeneous but highly clonal, irrespective of treatment. Overall, data support a model whereby a diverse TCR repertoire is required to achieve tumor rejection and may underlie the synergy between RT and CTLA-4 blockade. Cancer Immunol Res; 6(2); 139-50. ©2017 AACR.
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Affiliation(s)
| | - Karsten A Pilones
- Department of Radiation Oncology, Weill Cornell Medicine, New York, New York
| | - Claire Lhuillier
- Department of Radiation Oncology, Weill Cornell Medicine, New York, New York
| | - Erik Wennerberg
- Department of Radiation Oncology, Weill Cornell Medicine, New York, New York
| | - John-William Sidhom
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Harlan S Robins
- Adaptive Biotechnologies, Seattle, Washington.,Public Health Sciences Division, Fred Hutchinson Cancer Research, Seattle, Washington
| | - Jonathan Schneck
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Silvia C Formenti
- Department of Radiation Oncology, Weill Cornell Medicine, New York, New York
| | - Sandra Demaria
- Department of Radiation Oncology, Weill Cornell Medicine, New York, New York. .,Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
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27
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Stevanović S, Pasetto A, Helman SR, Gartner JJ, Prickett TD, Howie B, Robins HS, Robbins PF, Klebanoff CA, Rosenberg SA, Hinrichs CS. Landscape of immunogenic tumor antigens in successful immunotherapy of virally induced epithelial cancer. Science 2017; 356:200-205. [PMID: 28408606 DOI: 10.1126/science.aak9510] [Citation(s) in RCA: 282] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 03/16/2017] [Indexed: 12/11/2022]
Abstract
Immunotherapy has clinical activity in certain virally associated cancers. However, the tumor antigens targeted in successful treatments remain poorly defined. We used a personalized immunogenomic approach to elucidate the global landscape of antitumor T cell responses in complete regression of human papillomavirus-associated metastatic cervical cancer after tumor-infiltrating adoptive T cell therapy. Remarkably, immunodominant T cell reactivities were directed against mutated neoantigens or a cancer germline antigen, rather than canonical viral antigens. T cells targeting viral tumor antigens did not display preferential in vivo expansion. Both viral and nonviral tumor antigen-specific T cells resided predominantly in the programmed cell death 1 (PD-1)-expressing T cell compartment, which suggests that PD-1 blockade may unleash diverse antitumor T cell reactivities. These findings suggest a new paradigm of targeting nonviral antigens in immunotherapy of virally associated cancers.
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Affiliation(s)
- Sanja Stevanović
- Experimental Transplantation and Immunology Branch, National Cancer Institute, Bethesda, MD 20892, USA.
| | - Anna Pasetto
- Surgery Branch, National Cancer Institute, Bethesda, MD 20892, USA
| | - Sarah R Helman
- Experimental Transplantation and Immunology Branch, National Cancer Institute, Bethesda, MD 20892, USA
| | - Jared J Gartner
- Surgery Branch, National Cancer Institute, Bethesda, MD 20892, USA
| | - Todd D Prickett
- Surgery Branch, National Cancer Institute, Bethesda, MD 20892, USA
| | - Bryan Howie
- Adaptive Biotechnologies, Seattle, WA 98102, USA
| | - Harlan S Robins
- Adaptive Biotechnologies, Seattle, WA 98102, USA.,Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Paul F Robbins
- Surgery Branch, National Cancer Institute, Bethesda, MD 20892, USA
| | - Christopher A Klebanoff
- Center for Cell Engineering and Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Parker Institute for Cancer Immunotherapy, New York, NY 10065, USA
| | | | - Christian S Hinrichs
- Experimental Transplantation and Immunology Branch, National Cancer Institute, Bethesda, MD 20892, USA.
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28
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Matos TR, O'Malley JT, Lowry EL, Hamm D, Kirsch IR, Robins HS, Kupper TS, Krueger JG, Clark RA. Clinically resolved psoriatic lesions contain psoriasis-specific IL-17-producing αβ T cell clones. J Clin Invest 2017; 127:4031-4041. [PMID: 28945199 DOI: 10.1172/jci93396] [Citation(s) in RCA: 178] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 08/02/2017] [Indexed: 01/15/2023] Open
Abstract
In psoriasis, an IL-17-mediated inflammatory skin disease, skin lesions resolve with therapy, but often recur in the same locations when therapy is discontinued. We propose that residual T cell populations in resolved psoriatic lesions represent the pathogenic T cells of origin in this disease. Utilizing high-throughput screening (HTS) of the T cell receptor (TCR) and immunostaining, we found that clinically resolved psoriatic lesions contained oligoclonal populations of T cells that produced IL-17A in both resolved and active psoriatic lesions. Putative pathogenic clones preferentially utilized particular Vβ and Vα subfamilies. We identified 15 TCRβ and 4 TCRα antigen receptor sequences shared between psoriasis patients and not observed in healthy controls or other inflammatory skin conditions. To address the relative roles of αβ versus γδ T cells in psoriasis, we carried out TCR/δ HTS. These studies demonstrated that the majority of T cells in psoriasis and healthy skin are αβ T cells. γδ T cells made up 1% of T cells in active psoriasis, less than 1% in resolved psoriatic lesions, and less than 2% in healthy skin. All of the 70 most frequent putative pathogenic T cell clones were αβ T cells. In summary, IL-17-producing αβ T cell clones with psoriasis-specific antigen receptors exist in clinically resolved psoriatic skin lesions. These cells likely represent the disease-initiating pathogenic T cells in psoriasis, suggesting that lasting control of this disease will require suppression of these resident T cell populations.
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Affiliation(s)
- Tiago R Matos
- Department of Dermatology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Instituto de Medicina Molecular, Faculty of Medicine, University of Lisbon, Lisbon, Portugal.,Academic Medical Center, Department of Dermatology, University of Amsterdam, Amsterdam, The Netherlands
| | - John T O'Malley
- Department of Dermatology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Elizabeth L Lowry
- Department of Dermatology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - David Hamm
- Adaptive Biotechnologies, Seattle, Washington, USA
| | | | | | - Thomas S Kupper
- Department of Dermatology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - James G Krueger
- Department of Dermatology, Rockefeller University, New York, New York, USA
| | - Rachael A Clark
- Department of Dermatology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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29
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Dovedi SJ, Cheadle EJ, Popple AL, Poon E, Morrow M, Stewart R, Yusko EC, Sanders CM, Vignali M, Emerson RO, Robins HS, Wilkinson RW, Honeychurch J, Illidge TM. Fractionated Radiation Therapy Stimulates Antitumor Immunity Mediated by Both Resident and Infiltrating Polyclonal T-cell Populations when Combined with PD-1 Blockade. Clin Cancer Res 2017; 23:5514-5526. [PMID: 28533222 DOI: 10.1158/1078-0432.ccr-16-1673] [Citation(s) in RCA: 245] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 11/17/2016] [Accepted: 05/16/2017] [Indexed: 12/18/2022]
Abstract
Purpose: Radiotherapy is a highly effective anticancer treatment forming part of the standard of care for the majority of patients, but local and distal disease recurrence remains a major cause of mortality. Radiotherapy is known to enhance tumor immunogenicity; however, the contribution and mechanisms of radiotherapy-induced immune responses are unknown.Experimental Design: The impact of low-dose fractionated radiotherapy (5 × 2 Gy) alone and in combination with αPD-1 mAb on the tumor microenvironment was evaluated by flow cytometry and next-generation sequencing of the T-cell receptor (TCR) repertoire. A dual-tumor model was used, with fractionated radiotherapy delivered to a single tumor site to enable evaluation of the local and systemic response to treatment and ability to induce abscopal responses outside the radiation field.Results: We show that fractionated radiotherapy leads to T-cell infiltration at the irradiated site; however, the TCR landscape remains dominated by polyclonal expansion of preexisting T-cell clones. Adaptive resistance via the PD-1/PD-L1 pathway restricts the generation of systemic anticancer immunity following radiotherapy, which can be overcome through combination with αPD-1 mAb leading to improved local and distal tumor control. Moreover, we show that effective clearance of tumor following combination therapy is dependent on both T cells resident in the tumor at the time of radiotherapy and infiltrating T cells.Conclusions: These data provide evidence that radiotherapy can enhance T-cell trafficking to locally treated tumor sites and augment preexisting anticancer T-cell responses with the capacity to mediate regression of out-of-field tumor lesions when delivered in combination with αPD-1 mAb therapy. Clin Cancer Res; 23(18); 5514-26. ©2017 AACR.
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MESH Headings
- Animals
- Antineoplastic Agents, Hormonal/pharmacology
- Cell Line, Tumor
- Combined Modality Therapy
- Cytokines/metabolism
- Disease Models, Animal
- Humans
- Lymphocytes, Tumor-Infiltrating/drug effects
- Lymphocytes, Tumor-Infiltrating/immunology
- Lymphocytes, Tumor-Infiltrating/metabolism
- Lymphocytes, Tumor-Infiltrating/radiation effects
- Mice
- Neoplasms/immunology
- Neoplasms/metabolism
- Neoplasms/pathology
- Neoplasms/therapy
- Programmed Cell Death 1 Receptor/antagonists & inhibitors
- Programmed Cell Death 1 Receptor/metabolism
- Radiotherapy
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
- Survival Rate
- T-Lymphocyte Subsets/drug effects
- T-Lymphocyte Subsets/immunology
- T-Lymphocyte Subsets/metabolism
- T-Lymphocyte Subsets/radiation effects
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Simon J Dovedi
- Targeted Therapy Group, Division of Molecular and Clinical Cancer Sciences, Manchester Cancer Research Centre, Christie Hospital, Manchester Academic Health Sciences Centre, United Kingdom.
- MedImmune Ltd., Granta Park, Cambridge, United Kingdom
| | - Eleanor J Cheadle
- Targeted Therapy Group, Division of Molecular and Clinical Cancer Sciences, Manchester Cancer Research Centre, Christie Hospital, Manchester Academic Health Sciences Centre, United Kingdom
| | - Amy L Popple
- Targeted Therapy Group, Division of Molecular and Clinical Cancer Sciences, Manchester Cancer Research Centre, Christie Hospital, Manchester Academic Health Sciences Centre, United Kingdom
| | - Edmund Poon
- MedImmune Ltd., Granta Park, Cambridge, United Kingdom
| | | | - Ross Stewart
- MedImmune Ltd., Granta Park, Cambridge, United Kingdom
| | | | | | | | | | | | | | - Jamie Honeychurch
- Targeted Therapy Group, Division of Molecular and Clinical Cancer Sciences, Manchester Cancer Research Centre, Christie Hospital, Manchester Academic Health Sciences Centre, United Kingdom
| | - Timothy M Illidge
- Targeted Therapy Group, Division of Molecular and Clinical Cancer Sciences, Manchester Cancer Research Centre, Christie Hospital, Manchester Academic Health Sciences Centre, United Kingdom.
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30
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Faham M, Carlton V, Moorhead M, Zheng J, Klinger M, Pepin F, Asbury T, Vignali M, Emerson RO, Robins HS, Ireland J, Baechler-Gillespie E, Inman RD. Discovery of T Cell Receptor β Motifs Specific to HLA-B27-Positive Ankylosing Spondylitis by Deep Repertoire Sequence Analysis. Arthritis Rheumatol 2017; 69:774-784. [PMID: 28002888 DOI: 10.1002/art.40028] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 12/13/2016] [Indexed: 12/14/2022]
Abstract
OBJECTIVE Ankylosing spondylitis (AS), a chronic inflammatory disorder, has a notable association with HLA-B27. One hypothesis suggests that a common antigen that binds to HLA-B27 is important for AS disease pathogenesis. This study was undertaken to determine sequences and motifs that are shared among HLA-B27-positive AS patients, using T cell repertoire next-generation sequencing. METHODS To identify motifs enriched among B27-positive AS patients, we performed T cell receptor β (TCRβ) repertoire sequencing on samples from 191 B27-positive AS patients, 43 B27-negative AS patients, and 227 controls, and we obtained >77 million TCRβ clonotype sequences. First, we assessed whether any of 50 previously published sequences were enriched in B27-positive AS patients. We then used training and test cohorts to identify discovered motifs that were enriched in B27-positive AS patients versus controls. RESULTS Six previously published and 11 discovered motifs were enriched in the B27-positive AS samples as compared to controls. After combining motifs related by sequence, we identified a total of 15 independent motifs. Both the full set of 15 motifs and a set of 6 published motifs were enriched in the B27-positive AS patients as compared to B27-positive healthy individuals (P = 0.049 and P = 0.001, respectively). Using an independent cohort, we validated that at least some of these motifs were associated with AS, and not simply with B27-positive status. CONCLUSION We identified TCRβ motifs that are enriched in B27-positive AS patients as compared to B27-positive healthy controls. This suggests that a common antigen, presented by HLA-B27 and detected by CD8+ T cells, may be associated with AS disease pathogenesis.
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Affiliation(s)
- Malek Faham
- Adaptive Biotechnologies Corporation, South San Francisco, California, and Adaptive Biotechnologies Corporation, Seattle, Washington
| | - Victoria Carlton
- Adaptive Biotechnologies Corporation, South San Francisco, California, and Adaptive Biotechnologies Corporation, Seattle, Washington
| | - Martin Moorhead
- Adaptive Biotechnologies Corporation, South San Francisco, California, and Adaptive Biotechnologies Corporation, Seattle, Washington
| | - Jianbiao Zheng
- Adaptive Biotechnologies Corporation, South San Francisco, California, and Adaptive Biotechnologies Corporation, Seattle, Washington
| | - Mark Klinger
- Adaptive Biotechnologies Corporation, South San Francisco, California, and Adaptive Biotechnologies Corporation, Seattle, Washington
| | - Francois Pepin
- Adaptive Biotechnologies Corporation, South San Francisco, California, and Adaptive Biotechnologies Corporation, Seattle, Washington
| | - Thomas Asbury
- Adaptive Biotechnologies Corporation, South San Francisco, California, and Adaptive Biotechnologies Corporation, Seattle, Washington
| | - Marissa Vignali
- Adaptive Biotechnologies Corporation, South San Francisco, California, and Adaptive Biotechnologies Corporation, Seattle, Washington
| | - Ryan O Emerson
- Adaptive Biotechnologies Corporation, South San Francisco, California, and Adaptive Biotechnologies Corporation, Seattle, Washington
| | - Harlan S Robins
- Adaptive Biotechnologies Corporation, South San Francisco, California, and Adaptive Biotechnologies Corporation and Fred Hutchinson Cancer Research Center, Seattle, Washington
| | | | | | - Robert D Inman
- Toronto Western Hospital, University of Toronto, Toronto, Ontario, Canada
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31
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Heit A, Schmitz F, Gerdts S, Flach B, Moore MS, Perkins JA, Robins HS, Aderem A, Spearman P, Tomaras GD, De Rosa SC, McElrath MJ. Vaccination establishes clonal relatives of germinal center T cells in the blood of humans. J Exp Med 2017. [PMID: 28637884 PMCID: PMC5502430 DOI: 10.1084/jem.20161794] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Heit et al. describe that in humans, circulating memory T follicular helper cells (cTfh) have a clonal relationship to germinal center Tfh (GCTfh) cells. Upon vaccination, such memory cTfh respond with clonal expansion, activation, and simultaneous expression of a GCTfh-like phenotype. Germinal center T follicular helper cells (GCTfh) in lymphatic tissue are critical for B cell differentiation and protective antibody induction, but whether GCTfh establish clonal derivatives as circulating memory T cells is less understood. Here, we used markers expressed on GCTfh, CXCR5, PD1, and ICOS, to identify potential circulating CXCR5+CD4+ Tfh-like cells (cTfh) in humans, and investigated their functional phenotypes, diversity, and ontogeny in paired donor blood and tonsils, and in blood after vaccination. Based on T cell receptor repertoire analysis, we found that PD-1–expressing cTfh and tonsillar GCTfh cells were clonally related. Furthermore, an activated, antigen-specific PD1+ICOS+ cTfh subset clonally expanded after booster immunization whose frequencies correlated with vaccine-specific serum IgG; these phenotypically resembled GCTfh, and were clonally related to a resting PD1+ICOS− CD4+ memory T cell subset. Thus, we postulate that vaccination establishes clonal relatives of GCTfh within the circulating memory CD4+CXCR5+PD1+ T cell pool that expand upon reencounter of their cognate antigen.
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Affiliation(s)
- Antje Heit
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | - Sarah Gerdts
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Britta Flach
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Miranda S Moore
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Jonathan A Perkins
- Department of Otolaryngology, University of Washington, Seattle, WA.,Seattle Children's Hospital Research Institute, Seattle, WA
| | - Harlan S Robins
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA.,Adaptive Biotechnologies Corporation, Seattle, WA
| | - Alan Aderem
- Center for Infectious Disease Research, Seattle, WA
| | - Paul Spearman
- Pediatric Infectious Diseases, Cincinnati Children's Hospital, Cincinnati, OH
| | | | - Stephen C De Rosa
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA.,Department of Laboratory Medicine, University of Washington, Seattle, WA
| | - M Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA.,Department of Laboratory Medicine, University of Washington, Seattle, WA.,Department of Medicine, University of Washington, Seattle, WA.,Department of Global Health, University of Washington, Seattle, WA
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32
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Snyder A, Nathanson T, Funt SA, Ahuja A, Buros Novik J, Hellmann MD, Chang E, Aksoy BA, Al-Ahmadie H, Yusko E, Vignali M, Benzeno S, Boyd M, Moran M, Iyer G, Robins HS, Mardis ER, Merghoub T, Hammerbacher J, Rosenberg JE, Bajorin DF. Contribution of systemic and somatic factors to clinical response and resistance to PD-L1 blockade in urothelial cancer: An exploratory multi-omic analysis. PLoS Med 2017; 14:e1002309. [PMID: 28552987 PMCID: PMC5446110 DOI: 10.1371/journal.pmed.1002309] [Citation(s) in RCA: 218] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 04/26/2017] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Inhibition of programmed death-ligand 1 (PD-L1) with atezolizumab can induce durable clinical benefit (DCB) in patients with metastatic urothelial cancers, including complete remissions in patients with chemotherapy refractory disease. Although mutation load and PD-L1 immune cell (IC) staining have been associated with response, they lack sufficient sensitivity and specificity for clinical use. Thus, there is a need to evaluate the peripheral blood immune environment and to conduct detailed analyses of mutation load, predicted neoantigens, and immune cellular infiltration in tumors to enhance our understanding of the biologic underpinnings of response and resistance. METHODS AND FINDINGS The goals of this study were to (1) evaluate the association of mutation load and predicted neoantigen load with therapeutic benefit and (2) determine whether intratumoral and peripheral blood T cell receptor (TCR) clonality inform clinical outcomes in urothelial carcinoma treated with atezolizumab. We hypothesized that an elevated mutation load in combination with T cell clonal dominance among intratumoral lymphocytes prior to treatment or among peripheral T cells after treatment would be associated with effective tumor control upon treatment with anti-PD-L1 therapy. We performed whole exome sequencing (WES), RNA sequencing (RNA-seq), and T cell receptor sequencing (TCR-seq) of pretreatment tumor samples as well as TCR-seq of matched, serially collected peripheral blood, collected before and after treatment with atezolizumab. These parameters were assessed for correlation with DCB (defined as progression-free survival [PFS] >6 months), PFS, and overall survival (OS), both alone and in the context of clinical and intratumoral parameters known to be predictive of survival in this disease state. Patients with DCB displayed a higher proportion of tumor-infiltrating T lymphocytes (TIL) (n = 24, Mann-Whitney p = 0.047). Pretreatment peripheral blood TCR clonality below the median was associated with improved PFS (n = 29, log-rank p = 0.048) and OS (n = 29, log-rank p = 0.011). Patients with DCB also demonstrated more substantial expansion of tumor-associated TCR clones in the peripheral blood 3 weeks after starting treatment (n = 22, Mann-Whitney p = 0.022). The combination of high pretreatment peripheral blood TCR clonality with elevated PD-L1 IC staining in tumor tissue was strongly associated with poor clinical outcomes (n = 10, hazard ratio (HR) (mean) = 89.88, HR (median) = 23.41, 95% CI [2.43, 506.94], p(HR > 1) = 0.0014). Marked variations in mutation loads were seen with different somatic variant calling methodologies, which, in turn, impacted associations with clinical outcomes. Missense mutation load, predicted neoantigen load, and expressed neoantigen load did not demonstrate significant association with DCB (n = 25, Mann-Whitney p = 0.22, n = 25, Mann-Whitney p = 0.55, and n = 25, Mann-Whitney p = 0.29, respectively). Instead, we found evidence of time-varying effects of somatic mutation load on PFS in this cohort (n = 25, p = 0.044). A limitation of our study is its small sample size (n = 29), a subset of the patients treated on IMvigor 210 (NCT02108652). Given the number of exploratory analyses performed, we intend for these results to be hypothesis-generating. CONCLUSIONS These results demonstrate the complex nature of immune response to checkpoint blockade and the compelling need for greater interrogation and data integration of both host and tumor factors. Incorporating these variables in prospective studies will facilitate identification and treatment of resistant patients.
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Affiliation(s)
- Alexandra Snyder
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- Department of Medicine, Weill Cornell Medical College, New York, New York, United States of America
- * E-mail:
| | - Tavi Nathanson
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Samuel A. Funt
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- Department of Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Arun Ahuja
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Jacqueline Buros Novik
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Matthew D. Hellmann
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- Department of Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Eliza Chang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Bulent Arman Aksoy
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Hikmat Al-Ahmadie
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Erik Yusko
- Adaptive Biotechnologies, Seattle, Washington, United States of America
| | - Marissa Vignali
- Adaptive Biotechnologies, Seattle, Washington, United States of America
| | - Sharon Benzeno
- Adaptive Biotechnologies, Seattle, Washington, United States of America
| | - Mariel Boyd
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Meredith Moran
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Gopa Iyer
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- Department of Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Harlan S. Robins
- Adaptive Biotechnologies, Seattle, Washington, United States of America
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Elaine R. Mardis
- Department of Pediatrics, Institute for Genomic Medicine, The Research Institute at Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, Ohio, United States of America
| | - Taha Merghoub
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Jeff Hammerbacher
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Jonathan E. Rosenberg
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Dean F. Bajorin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- Department of Medicine, Weill Cornell Medical College, New York, New York, United States of America
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Seay HR, Yusko E, Rothweiler SJ, Zhang L, Posgai AL, Campbell-Thompson M, Vignali M, Emerson RO, Kaddis JS, Ko D, Nakayama M, Smith MJ, Cambier JC, Pugliese A, Atkinson MA, Robins HS, Brusko TM. Tissue distribution and clonal diversity of the T and B cell repertoire in type 1 diabetes. JCI Insight 2016; 1:e88242. [PMID: 27942583 DOI: 10.1172/jci.insight.88242] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The adaptive immune repertoire plays a critical role in type 1 diabetes (T1D) pathogenesis. However, efforts to characterize B cell and T cell receptor (TCR) profiles in T1D subjects have been largely limited to peripheral blood sampling and restricted to known antigens. To address this, we collected pancreatic draining lymph nodes (pLN), "irrelevant" nonpancreatic draining lymph nodes, peripheral blood mononuclear cells (PBMC), and splenocytes from T1D subjects (n = 18) and control donors (n = 9) as well as pancreatic islets from 1 T1D patient; from these tissues, we collected purified CD4+ conventional T cells (Tconv), CD4+ Treg, CD8+ T cells, and B cells. By conducting high-throughput immunosequencing of the TCR β chain (TRB) and B cell receptor (BCR) immunoglobulin heavy chain (IGH) on these samples, we sought to analyze the molecular signature of the lymphocyte populations within these tissues and of T1D. Ultimately, we observed a highly tissue-restricted CD4+ repertoire, while up to 24% of CD8+ clones were shared among tissues. We surveyed our data set for previously described proinsulin- and glutamic acid decarboxylase 65-reactive (GAD65-reactive) receptors, and interestingly, we observed a TRB with homology to a known GAD65-reactive TCR (clone GAD4.13) present in 7 T1D donors (38.9%), representing >25% of all productive TRB within Tconv isolated from the pLN of 1 T1D subject. These data demonstrate diverse receptor signatures at the nucleotide level and enriched autoreactive clones at the amino acid level, supporting the utility of coupling immunosequencing data with knowledge of characterized autoreactive receptors.
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Affiliation(s)
- Howard R Seay
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida Diabetes Institute, Gainesville, Florida, USA
| | - Erik Yusko
- Adaptive Biotechnologies Corporation, Seattle, Washington, USA
| | - Stephanie J Rothweiler
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida Diabetes Institute, Gainesville, Florida, USA
| | - Lin Zhang
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida Diabetes Institute, Gainesville, Florida, USA
| | - Amanda L Posgai
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida Diabetes Institute, Gainesville, Florida, USA
| | - Martha Campbell-Thompson
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida Diabetes Institute, Gainesville, Florida, USA
| | - Marissa Vignali
- Adaptive Biotechnologies Corporation, Seattle, Washington, USA
| | - Ryan O Emerson
- Adaptive Biotechnologies Corporation, Seattle, Washington, USA
| | - John S Kaddis
- Department of Information Sciences, City of Hope National Medical Center, Duarte, California, USA
| | - Dave Ko
- Department of Information Sciences, City of Hope National Medical Center, Duarte, California, USA
| | | | - Mia J Smith
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - John C Cambier
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Alberto Pugliese
- Diabetes Research Institute and Departments of Medicine, Microbiology, and Immunology, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Mark A Atkinson
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida Diabetes Institute, Gainesville, Florida, USA
| | - Harlan S Robins
- Adaptive Biotechnologies Corporation, Seattle, Washington, USA.,Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Todd M Brusko
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida Diabetes Institute, Gainesville, Florida, USA
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Kirsch IR, Watanabe R, O'Malley JT, Williamson DW, Scott LL, Elco CP, Teague JE, Gehad A, Lowry EL, LeBoeuf NR, Krueger JG, Robins HS, Kupper TS, Clark RA. TCR sequencing facilitates diagnosis and identifies mature T cells as the cell of origin in CTCL. Sci Transl Med 2016; 7:308ra158. [PMID: 26446955 DOI: 10.1126/scitranslmed.aaa9122] [Citation(s) in RCA: 142] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Early diagnosis of cutaneous T cell lymphoma (CTCL) is difficult and takes on average 6 years after presentation, in part because the clinical appearance and histopathology of CTCL can resemble that of benign inflammatory skin diseases. Detection of a malignant T cell clone is critical in making the diagnosis of CTCL, but the T cell receptor γ (TCRγ) polymerase chain reaction (PCR) analysis in current clinical use detects clones in only a subset of patients. High-throughput TCR sequencing (HTS) detected T cell clones in 46 of 46 CTCL patients, was more sensitive and specific than TCRγ PCR, and successfully discriminated CTCL from benign inflammatory diseases. HTS also accurately assessed responses to therapy and facilitated diagnosis of disease recurrence. In patients with new skin lesions and no involvement of blood by flow cytometry, HTS demonstrated hematogenous spread of small numbers of malignant T cells. Analysis of CTCL TCRγ genes demonstrated that CTCL is a malignancy derived from mature T cells. There was a maximal T cell density in skin in benign inflammatory diseases that was exceeded in CTCL, suggesting that a niche of finite size may exist for benign T cells in skin. Last, immunostaining demonstrated that the malignant T cell clones in mycosis fungoides and leukemic CTCL localized to different anatomic compartments in the skin. In summary, HTS accurately diagnosed CTCL in all stages, discriminated CTCL from benign inflammatory skin diseases, and provided insights into the cell of origin and location of malignant CTCL cells in skin.
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Affiliation(s)
| | - Rei Watanabe
- Department of Dermatology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - John T O'Malley
- Department of Dermatology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Laura-Louise Scott
- Department of Dermatology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Christopher P Elco
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jessica E Teague
- Department of Dermatology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Ahmed Gehad
- Department of Dermatology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Elizabeth L Lowry
- Department of Dermatology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Nicole R LeBoeuf
- Department of Dermatology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Dana-Farber/Brigham and Women's Cancer Center, Boston, MA, USA
| | - James G Krueger
- Department of Dermatology, Rockefeller University, New York, NY, USA
| | | | - Thomas S Kupper
- Department of Dermatology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Dana-Farber/Brigham and Women's Cancer Center, Boston, MA, USA
| | - Rachael A Clark
- Department of Dermatology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Dana-Farber/Brigham and Women's Cancer Center, Boston, MA, USA
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DeWitt WS, Lindau P, Snyder TM, Sherwood AM, Vignali M, Carlson CS, Greenberg PD, Duerkopp N, Emerson RO, Robins HS. A Public Database of Memory and Naive B-Cell Receptor Sequences. PLoS One 2016; 11:e0160853. [PMID: 27513338 PMCID: PMC4981401 DOI: 10.1371/journal.pone.0160853] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 07/26/2016] [Indexed: 11/25/2022] Open
Abstract
The vast diversity of B-cell receptors (BCR) and secreted antibodies enables the recognition of, and response to, a wide range of epitopes, but this diversity has also limited our understanding of humoral immunity. We present a public database of more than 37 million unique BCR sequences from three healthy adult donors that is many fold deeper than any existing resource, together with a set of online tools designed to facilitate the visualization and analysis of the annotated data. We estimate the clonal diversity of the naive and memory B-cell repertoires of healthy individuals, and provide a set of examples that illustrate the utility of the database, including several views of the basic properties of immunoglobulin heavy chain sequences, such as rearrangement length, subunit usage, and somatic hypermutation positions and dynamics.
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Affiliation(s)
| | - Paul Lindau
- Fred Hutchinson Cancer Research Center, Seattle, United States of America
- University of Washington, Seattle, United States of America
| | | | | | | | | | | | - Natalie Duerkopp
- Fred Hutchinson Cancer Research Center, Seattle, United States of America
| | | | - Harlan S. Robins
- Adaptive Biotechnologies, Seattle, United States of America
- Fred Hutchinson Cancer Research Center, Seattle, United States of America
- * E-mail:
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Subudhi SK, Aparicio A, Gao J, Zurita-Saavedra A, Araujo JC, Logothetis CJ, Brinda KR, Allison JP, Vence L, Emerson RO, Yusko E, Vignali M, Robins HS, Sun J, Sharma P. Abstract 1402: Exploratory biomarkers that predict for clinical outcomes in a Phase II trial with ipilimumab plus finite androgen deprivation therapy for metastatic non-castrate prostate cancer. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-1402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Androgen deprivation therapy (ADT) is a standard treatment that, although not curative, often induces dramatic responses in patients with advanced prostate cancer by inducing tumor cell death, which may provoke antigen release to initiate T cell responses. Ipilimumab blocks the inhibitory immune checkpoint, CTLA-4, which enhances T cell responses and induces both clinical benefit and unique toxicities in a subset of patients with advanced cancer. We designed a clinical study combining ipilimumab with finite ADT in men with metastatic prostate cancer to estimate therapeutic efficacy, determine safety, and identify predictive biomarkers for clinical outcomes.
Methods: We screened 30 patients and enrolled 27 patients between July, 2011 and June, 2013 for an open-labelled, single-center, Phase II study of ipilimumab plus finite ADT as first-line therapy for metastatic non-castrate prostate cancer. Eligible patients had histological confirmation of prostate carcinoma and radiographic documentation of metastatic disease. ADT was given for a finite duration of eight months with concurrent ipilimumab (10 mg/kg) for up to four doses, each given four-weeks apart. The primary endpoint was the proportion of patients with undetectable PSA (≤0.2 ng/mL) at seven months post-treatment initiation with ADT. In addition, we performed comprehensive immune monitoring of the peripheral blood using multi-parametric flow cytometry and next-generation sequencing of T cell receptors.
Findings: All 27 of the enrolled patients were evaluable for safety and toxicity, and 24 of these patients were evaluable for therapeutic effectiveness. Ten of the 24 (42%) patients achieved the primary endpoint of undetectable PSA levels at seven months post-treatment initiation. The median time to PSA progression was 10.0 (IQR 5.9-13.3) months from treatment initiation, and one (4%) of the 24 patients continues to have a PSA response that is ongoing for 40.7 months. The trial was closed as prespecified due to grade 3 toxicities that occurred in 12 (44%) of 27 patients. The most common grade 3 adverse events were transaminitis, colitis/diarrhea, and hypophysitis. Immunological biomarkers were identified that potentially predict for clinical benefit and grade 3 toxicities in this small study. No grade 4 or 5 toxicities were observed.
Interpretation: Although the combination of 10 mg/kg ipilimumab plus finite ADT led to toxicities that met a prespecified endpoint for closure of the trial, our current knowledge and experience about combination therapies and dose of ipilimumab leads us to postulate that additional clinical trials evaluating ipilimumab at 3 mg/kg plus ADT is warranted. In addition, we identified candidate immunological biomarkers that need to be further tested as predictive markers of clinical benefit and grade 3 toxicities.
Citation Format: Sumit K. Subudhi, Ana Aparicio, Jianjun Gao, Amado Zurita-Saavedra, John C. Araujo, Christopher J. Logothetis, Korivi R. Brinda, Jim P. Allison, Luis Vence, Ryan O. Emerson, Erik Yusko, Marissa Vignali, Harlan S. Robins, Jingjing Sun, Padmanee Sharma. Exploratory biomarkers that predict for clinical outcomes in a Phase II trial with ipilimumab plus finite androgen deprivation therapy for metastatic non-castrate prostate cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1402.
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Affiliation(s)
| | - Ana Aparicio
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jianjun Gao
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - John C. Araujo
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | - Jim P. Allison
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Luis Vence
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Erik Yusko
- 2Adapative Biotechnologies Corporation, TX
| | | | | | - Jingjing Sun
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Padmanee Sharma
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
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Howie B, Sherwood AM, Berkebile AD, Berka J, Emerson RO, Williamson DW, Kirsch I, Vignali M, Rieder MJ, Carlson CS, Robins HS. High-throughput pairing of T cell receptor α and β sequences. Sci Transl Med 2016; 7:301ra131. [PMID: 26290413 DOI: 10.1126/scitranslmed.aac5624] [Citation(s) in RCA: 164] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The T cell receptor (TCR) protein is a heterodimer composed of an α chain and a β chain. TCR genes undergo somatic DNA rearrangements to generate the diversity of T cell binding specificities needed for effective immunity. Recently, high-throughput immunosequencing methods have been developed to profile the TCR α (TCRA) and TCR β (TCRB) repertoires. However, these methods cannot determine which TCRA and TCRB chains combine to form a specific TCR, which is essential for many functional and therapeutic applications. We describe and validate a method called pairSEQ, which can leverage the diversity of TCR sequences to accurately pair hundreds of thousands of TCRA and TCRB sequences in a single experiment. Our TCR pairing method uses standard laboratory consumables and equipment without the need for single-cell technologies. We show that pairSEQ can be applied to T cells from both blood and solid tissues, such as tumors.
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Affiliation(s)
- Bryan Howie
- Adaptive Biotechnologies, Seattle, WA 98102, USA
| | | | | | - Jan Berka
- Adaptive Biotechnologies, Seattle, WA 98102, USA
| | | | | | - Ilan Kirsch
- Adaptive Biotechnologies, Seattle, WA 98102, USA
| | | | | | | | - Harlan S Robins
- Adaptive Biotechnologies, Seattle, WA 98102, USA. Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
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DeWitt W, Emerson RO, Vignali M, House S, Desmarais C, Rieder MJ, Carlson CS, Gravley J, Hansen JA, Robins HS. Immunosequencing reveals diagnostic signatures of pathogen infection and HLA type in the T-cell Receptor Repertoire. The Journal of Immunology 2016. [DOI: 10.4049/jimmunol.196.supp.148.11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
We analyzed the T-cell response to CMV by sequencing rearranged TCRs in 528 subjects (240 CMV+ and 288 CMV−). We assessed concordance between ~80 million unique TCRs and CMV serostatus, looking for significant associations. We identified 104 CMV-associated TCRs at FDR ≈ 0.20. Training a binary classifier on these features, we predict CMV serostatus in a cross-validation procedure with a diagnostic odds ratio of 17 on the same cohort. A second independent cohort of 120 subjects with known CMV serostatus yielded a diagnostic odds ratio of 31.
Next, we studied the HLA-restriction of each CMV-associated TCR by assessing enrichment of particular HLA types among subjects that carry each CMV-associated TCR. Of 104 CMV-associated TCRs, 41 were HLA-restricted at p ≤ 10−3, and none of these were significantly associated with multiple alleles in any locus.
We find concordance between our data and previously-reported CMV-specific TCRs: most previously-reported CMV-specific TCRs are present in our data, however only 5 CMV-associated TCRs have been previously reported. Of these, four were significantly HLA-restricted in these data, and agreed with previous findings.
We investigated the association of TCRs with each HLA allele present in the cohort, with significant results for several higher frequency alleles. Cross validation with binary classifier training resulted in high accuracy prediction for these alleles, indicating that HLA type can be inferred from immunosequencing data.
We demonstrate the validity of association studies using immunosequencing for detection and HLA-association of public T-cell responses to infection, and report that assessing the presence of associated T-cell responses can serve as a powerful diagnostic classifier.
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Kanakry CG, Coffey DG, Towlerton AMH, Vulic A, Storer BE, Chou J, Yeung CCS, Gocke CD, Robins HS, O'Donnell PV, Luznik L, Warren EH. Origin and evolution of the T cell repertoire after posttransplantation cyclophosphamide. JCI Insight 2016; 1. [PMID: 27213183 DOI: 10.1172/jci.insight.86252] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Posttransplantation cyclophosphamide (PTCy) effectively prevents graft-versus-host disease (GVHD), but its immunologic impact is poorly understood. We assessed lymphocyte reconstitution via flow cytometry (n = 74) and antigen receptor sequencing (n = 35) in recipients of myeloablative, HLA-matched allogeneic BM transplantation using PTCy. Recovering T cells were primarily phenotypically effector memory with lower T cell receptor β (TRB) repertoire diversity than input donor repertoires. Recovering B cells were predominantly naive with immunoglobulin heavy chain locus (IGH) repertoire diversity similar to donors. Numerical T cell reconstitution and TRB diversity were strongly associated with recipient cytomegalovirus seropositivity. Global similarity between input donor and recipient posttransplant repertoires was uniformly low at 1-2 months after transplant but increased over the balance of the first posttransplant year. Blood TRB repertoires at ≥3 months after transplant were often dominated by clones present in the donor blood/marrow memory CD8+ compartment. Limited overlap was observed between the TRB repertoires of T cells infiltrating the skin or gastrointestinal tract versus the blood. Although public TRB sequences associated with herpesvirus- or alloantigen-specific CD8+ T cells were detected in some patients, posttransplant TRB and IGH repertoires were unique to each individual. These data define the immune dynamics occurring after PTCy and establish a benchmark against which immune recovery after other transplantation approaches can be compared.
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Affiliation(s)
- Christopher G Kanakry
- Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - David G Coffey
- Clinical Research Division, Fred Hutchinson Cancer Research Center (FHCRC), Seattle, Washington, USA; Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Andrea M H Towlerton
- Clinical Research Division, Fred Hutchinson Cancer Research Center (FHCRC), Seattle, Washington, USA
| | - Ante Vulic
- Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Barry E Storer
- Clinical Research Division, Fred Hutchinson Cancer Research Center (FHCRC), Seattle, Washington, USA
| | - Jeffrey Chou
- Clinical Research Division, Fred Hutchinson Cancer Research Center (FHCRC), Seattle, Washington, USA; Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Cecilia C S Yeung
- Clinical Research Division, Fred Hutchinson Cancer Research Center (FHCRC), Seattle, Washington, USA; Department of Pathology, University of Washington, Seattle, Washington, USA
| | - Christopher D Gocke
- Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Harlan S Robins
- Public Health Sciences Division, FHCRC, Seattle, Washington, USA
| | - Paul V O'Donnell
- Clinical Research Division, Fred Hutchinson Cancer Research Center (FHCRC), Seattle, Washington, USA; Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Leo Luznik
- Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Edus H Warren
- Clinical Research Division, Fred Hutchinson Cancer Research Center (FHCRC), Seattle, Washington, USA; Department of Medicine, University of Washington, Seattle, Washington, USA
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Hsu M, Sedighim S, Wang T, Antonios JP, Everson RG, Tucker AM, Du L, Emerson R, Yusko E, Sanders C, Robins HS, Yong WH, Davidson TB, Li G, Liau LM, Prins RM. TCR Sequencing Can Identify and Track Glioma-Infiltrating T Cells after DC Vaccination. Cancer Immunol Res 2016; 4:412-418. [PMID: 26968205 DOI: 10.1158/2326-6066.cir-15-0240] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Accepted: 01/29/2016] [Indexed: 01/21/2023]
Abstract
Although immunotherapeutic strategies are emerging as adjunctive treatments for cancer, sensitive methods of monitoring the immune response after treatment remain to be established. We used a novel next-generation sequencing approach to determine whether quantitative assessments of tumor-infiltrating lymphocyte (TIL) content and the degree of overlap of T-cell receptor (TCR) sequences in brain tumors and peripheral blood were predictors of immune response and overall survival in glioblastoma patients treated with autologous tumor lysate-pulsed dendritic cell immunotherapy. A statistically significant correlation was found between a higher estimated TIL content and increased time to progression and overall survival. In addition, we were able to assess the proportion of shared TCR sequences between tumor and peripheral blood at time points before and after therapy, and found the level of TCR overlap to correlate with survival outcomes. Higher degrees of overlap, or the development of an increased overlap following immunotherapy, was correlated with improved clinical outcome, and may provide insights into the successful, antigen-specific immune response. Cancer Immunol Res; 4(5); 412-8. ©2016 AACR.
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Affiliation(s)
- Melody Hsu
- Department of Neurosurgery, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Department of Pediatrics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Shaina Sedighim
- Department of Neurosurgery, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Tina Wang
- Department of Neurosurgery, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Department of Medicine (Hematology/Oncology), David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Joseph P Antonios
- Department of Neurosurgery, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,The Medical Scientist Training Program, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Richard G Everson
- Department of Neurosurgery, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Alexander M Tucker
- Department of Neurosurgery, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Lin Du
- Department of Biostatistics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | | | - Erik Yusko
- Adaptive Biotechnologies, Seattle, WA, USA
| | | | - Harlan S Robins
- Adaptive Biotechnologies, Seattle, WA, USA.,Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - William H Yong
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Tom B Davidson
- Department of Neurosurgery, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Department of Pediatrics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Gang Li
- Department of Biostatistics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Linda M Liau
- Department of Neurosurgery, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Robert M Prins
- Department of Neurosurgery, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
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42
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Dean J, Emerson RO, Vignali M, Sherwood AM, Rieder MJ, Carlson CS, Robins HS. Annotation of pseudogenic gene segments by massively parallel sequencing of rearranged lymphocyte receptor loci. Genome Med 2015; 7:123. [PMID: 26596423 PMCID: PMC4657264 DOI: 10.1186/s13073-015-0238-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 11/05/2015] [Indexed: 11/10/2022] Open
Abstract
Background The adaptive immune system generates a remarkable range of antigen-specific T-cell receptors (TCRs), allowing the recognition of a diverse set of antigens. Most of this diversity is encoded in the complementarity determining region 3 (CDR3) of the β chain of the αβ TCR, which is generated by somatic recombination of noncontiguous variable (V), diversity (D), and joining (J) gene segments. Deletion and non-templated insertion of nucleotides at the D-J and V-DJ junctions further increases diversity. Many of these gene segments are annotated as non-functional owing to defects in their primary sequence, the absence of motifs necessary for rearrangement, or chromosomal locations outside the TCR locus. Methods We sought to utilize a novel method, based on high-throughput sequencing of rearranged TCR genes in a large cohort of individuals, to evaluate the use of functional and non-functional alleles. We amplified and sequenced genomic DNA from the peripheral blood of 587 healthy volunteers using a multiplexed polymerase chain reaction assay that targets the variable region of the rearranged TCRβ locus, and we determined the presence and the proportion of productive rearrangements for each TCRβ V gene segment in each individual. We then used this information to annotate the functional status of TCRβ V gene segments in this cohort. Results For most TCRβ V gene segments, our method agrees with previously reported functional annotations. However, we identified novel non-functional alleles for several gene segments, some of which were used exclusively in our cohort to the detriment of reported functional alleles. We also saw that some gene segments reported to have both functional and non-functional alleles consistently behaved in our cohort as either functional or non-functional, suggesting that some reported alleles were not present in the population studied. Conclusions In this proof-of-principle study, we used high-throughput sequencing of the TCRβ locus of a large cohort of healthy volunteers to evaluate the use of functional and non-functional alleles of individual TCRβ V gene segments. With some modifications, our method has the potential to be extended to gene segments in the α, γ, and δ TCR loci, as well as the genes encoding for B-cell receptor chains. Electronic supplementary material The online version of this article (doi:10.1186/s13073-015-0238-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jared Dean
- Adaptive Biotechnologies, Seattle, WA, USA.
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43
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Gregory MT, Bertout JA, Ericson NG, Taylor SD, Mukherjee R, Robins HS, Drescher CW, Bielas JH. Targeted single molecule mutation detection with massively parallel sequencing. Nucleic Acids Res 2015; 44:e22. [PMID: 26384417 PMCID: PMC4756847 DOI: 10.1093/nar/gkv915] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 09/02/2015] [Indexed: 11/14/2022] Open
Abstract
Next-generation sequencing (NGS) technologies have transformed genomic research and have the potential to revolutionize clinical medicine. However, the background error rates of sequencing instruments and limitations in targeted read coverage have precluded the detection of rare DNA sequence variants by NGS. Here we describe a method, termed CypherSeq, which combines double-stranded barcoding error correction and rolling circle amplification (RCA)-based target enrichment to vastly improve NGS-based rare variant detection. The CypherSeq methodology involves the ligation of sample DNA into circular vectors, which contain double-stranded barcodes for computational error correction and adapters for library preparation and sequencing. CypherSeq is capable of detecting rare mutations genome-wide as well as those within specific target genes via RCA-based enrichment. We demonstrate that CypherSeq is capable of correcting errors incurred during library preparation and sequencing to reproducibly detect mutations down to a frequency of 2.4 × 10−7 per base pair, and report the frequency and spectra of spontaneous and ethyl methanesulfonate-induced mutations across the Saccharomycescerevisiae genome.
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Affiliation(s)
- Mark T Gregory
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jessica A Bertout
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Nolan G Ericson
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Sean D Taylor
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Rithun Mukherjee
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Harlan S Robins
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Charles W Drescher
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jason H Bielas
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA Department of Pathology, University of Washington, Seattle, WA 98195, USA
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44
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Šulc M, Marín RM, Robins HS, Vaníček J. PACCMIT/PACCMIT-CDS: identifying microRNA targets in 3' UTRs and coding sequences. Nucleic Acids Res 2015; 43:W474-9. [PMID: 25948580 PMCID: PMC4489287 DOI: 10.1093/nar/gkv457] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 04/24/2015] [Indexed: 11/14/2022] Open
Abstract
The purpose of the proposed web server, publicly available at http://paccmit.epfl.ch, is to provide a user-friendly interface to two algorithms for predicting messenger RNA (mRNA) molecules regulated by microRNAs: (i) PACCMIT (Prediction of ACcessible and/or Conserved MIcroRNA Targets), which identifies primarily mRNA transcripts targeted in their 3′ untranslated regions (3′ UTRs), and (ii) PACCMIT-CDS, designed to find mRNAs targeted within their coding sequences (CDSs). While PACCMIT belongs among the accurate algorithms for predicting conserved microRNA targets in the 3′ UTRs, the main contribution of the web server is 2-fold: PACCMIT provides an accurate tool for predicting targets also of weakly conserved or non-conserved microRNAs, whereas PACCMIT-CDS addresses the lack of similar portals adapted specifically for targets in CDS. The web server asks the user for microRNAs and mRNAs to be analyzed, accesses the precomputed P-values for all microRNA–mRNA pairs from a database for all mRNAs and microRNAs in a given species, ranks the predicted microRNA–mRNA pairs, evaluates their significance according to the false discovery rate and finally displays the predictions in a tabular form. The results are also available for download in several standard formats.
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Affiliation(s)
- Miroslav Šulc
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Ray M Marín
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Harlan S Robins
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jiří Vaníček
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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45
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Maldonado L, Teague JE, Morrow MP, Jotova I, Wu TC, Wang C, Desmarais C, Boyer JD, Tycko B, Robins HS, Clark RA, Trimble CL. Intramuscular therapeutic vaccination targeting HPV16 induces T cell responses that localize in mucosal lesions. Sci Transl Med 2014; 6:221ra13. [PMID: 24477000 DOI: 10.1126/scitranslmed.3007323] [Citation(s) in RCA: 166] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
About 25% of high-grade cervical intraepithelial neoplasias (CIN2/3) caused by human papillomavirus serotype 16 (HPV16) undergo complete spontaneous regression. However, to date, therapeutic vaccination strategies for HPV disease have yielded limited success when measured by their ability to induce robust peripheral blood T cell responses to vaccine antigen. We report marked immunologic changes in the target lesion microenvironment after intramuscular therapeutic vaccination targeting HPV16 E6/E7 antigens, in subjects with CIN2/3 who had modest detectable responses in circulating T lymphocytes. Histologic and molecular changes, including markedly (average threefold) increased intensity of CD8(+) T cell infiltrates in both the stromal and epithelial compartments, suggest an effector response to vaccination. Postvaccination cervical tissue immune infiltrates included organized tertiary lymphoid-like structures in the stroma subjacent to residual intraepithelial lesions and, unlike infiltrates in unvaccinated lesions, showed evidence of proliferation induced by recognition of cognate antigen. At a molecular level, these histologic changes in the stroma were characterized by increased expression of genes associated with immune activation (CXCR3) and effector function (Tbet and IFNβ), and were also associated with an immunologic signature in the overlying dysplastic epithelium. High-throughput T cell receptor sequencing of unmanipulated specimens identified clonal expansions in the tissue that were not readily detectable in peripheral blood. Together, these findings indicate that peripheral therapeutic vaccination to HPV antigens can induce a robust tissue-localized effector immune response, and that analyses of immune responses at sites of antigen are likely to be much more informative than analyses of cells that remain in the circulation.
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Affiliation(s)
- Leonel Maldonado
- Department of Gynecology and Obstetrics, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA
| | - Jessica E Teague
- Harvard Skin Disease Research Center and the Department of Dermatology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Matthew P Morrow
- Inovio Pharmaceuticals Inc., 1787 Sentry Parkway West, Building 18, Suite 400, Blue Bell, PA 19422, USA
| | - Iveta Jotova
- Department of Pathology and Cell Biology and Institute for Cancer Genetics, Columbia University Medical Center, New York, NY 10025, USA
| | - T C Wu
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA
| | - Chenguang Wang
- Oncology Biostatistics, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA
| | - Cindy Desmarais
- Adaptive Biotechnologies, 1551 Eastlake Avenue, Seattle, WA 98102, USA
| | - Jean D Boyer
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Benjamin Tycko
- Department of Pathology and Cell Biology and Institute for Cancer Genetics, Columbia University Medical Center, New York, NY 10025, USA
| | - Harlan S Robins
- Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Rachael A Clark
- Harvard Skin Disease Research Center and the Department of Dermatology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Cornelia L Trimble
- Department of Gynecology and Obstetrics, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA.,Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA.,Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA
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46
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Robins HS, Ericson NG, Guenthoer J, O'Briant KC, Tewari M, Drescher CW, Bielas JH. Digital genomic quantification of tumor-infiltrating lymphocytes. Sci Transl Med 2014; 5:214ra169. [PMID: 24307693 DOI: 10.1126/scitranslmed.3007247] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Infiltrating T lymphocytes are frequently found in malignant tumors and are suggestive of a host cancer immune response. Multiple independent studies have documented that the presence and quantity of tumor-infiltrating lymphocytes (TILs) are strongly correlated with increased survival. However, because of methodological factors, the exact effect of TILs on prognosis has remained enigmatic, and inclusion of TILs in standard prognostic panels has been limited. For example, some reports enumerate all CD3(+) cells, some count only cytotoxic CD8(+) T cells, and the criteria used to score tumors as TIL-positive or TIL-negative are inconsistent among studies. To address this limitation, we introduce a robust digital DNA-based assay, termed QuanTILfy, to count TILs and assess T cell clonality in tissue samples, including tumors. We demonstrate the clonal specificity of this approach by the diagnosis of T cell acute lymphoblastic leukemia and the accurate, sensitive, and highly reproducible measurement of TILs in primary and metastatic ovarian cancer. Our experiments demonstrate an association between higher TIL counts and improved survival among women with ovarian cancer, and are consistent with previous observations that the immune response against ovarian cancer is a meaningful and independent prognostic factor. Surprisingly, the TIL repertoire is diverse for all tumors in the study with no notable oligoclonal expansions. Furthermore, because variability in the measurement and characterization of TILs has limited their clinical utility as biomarkers, these results highlight the significant translational potential of a robust, standardizable DNA-based assay to assess TILs in a variety of cancer types.
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Affiliation(s)
- Harlan S Robins
- Herbold Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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47
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Emerson RO, Sherwood AM, Rieder MJ, Guenthoer J, Williamson DW, Carlson CS, Drescher CW, Tewari M, Bielas JH, Robins HS. High-throughput sequencing of T-cell receptors reveals a homogeneous repertoire of tumour-infiltrating lymphocytes in ovarian cancer. J Pathol 2014; 231:433-440. [PMID: 24027095 DOI: 10.1002/path.4260] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 08/20/2013] [Accepted: 09/06/2013] [Indexed: 12/20/2022]
Abstract
The cellular adaptive immune system mounts a response to many solid tumours mediated by tumour-infiltrating T lymphocytes (TILs). Basic measurements of these TILs, including total count, show promise as prognostic markers for a variety of cancers, including ovarian and colorectal. In addition, recent therapeutic advances are thought to exploit this immune response to effectively fight melanoma, with promising studies showing efficacy in additional cancers. However, many of the basic properties of TILs are poorly understood, including specificity, clonality, and spatial heterogeneity of the T-cell response. We utilize deep sequencing of rearranged T-cell receptor beta (TCRB) genes to characterize the basic properties of TILs in ovarian carcinoma. Due to somatic rearrangement during T-cell development, the TCR beta chain sequence serves as a molecular tag for each T-cell clone. Using these sequence tags, we assess similarities and differences between infiltrating T cells in discretely sampled sections of large tumours and compare to T cells from peripheral blood. Within the limits of sensitivity of our assay, the TIL repertoires show strong similarity throughout each tumour and are distinct from the circulating T-cell repertoire. We conclude that the cellular adaptive immune response within ovarian carcinomas is spatially homogeneous and distinct from the T-cell compartment of peripheral blood.
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Affiliation(s)
| | | | | | | | | | | | - Charles W Drescher
- Fred Hutchinson Cancer Research Center, Seattle, WA.,University of Washington School of Medicine, Seattle, WA
| | - Muneesh Tewari
- Fred Hutchinson Cancer Research Center, Seattle, WA.,University of Washington School of Medicine, Seattle, WA
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48
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Gerlinger M, Quezada SA, Peggs KS, Furness AJS, Fisher R, Marafioti T, Shende VH, McGranahan N, Rowan AJ, Hazell S, Hamm D, Robins HS, Pickering L, Gore M, Nicol DL, Larkin J, Swanton C. Ultra-deep T cell receptor sequencing reveals the complexity and intratumour heterogeneity of T cell clones in renal cell carcinomas. J Pathol 2014; 231:424-32. [PMID: 24122851 PMCID: PMC4241038 DOI: 10.1002/path.4284] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 09/24/2013] [Accepted: 09/25/2013] [Indexed: 12/31/2022]
Abstract
The recognition of cancer cells by T cells can impact upon prognosis and be exploited for immunotherapeutic approaches. This recognition depends on the specific interaction between antigens displayed on the surface of cancer cells and the T cell receptor (TCR), which is generated by somatic rearrangements of TCR α- and β-chains (TCRb). Our aim was to assess whether ultra-deep sequencing of the rearranged TCRb in DNA extracted from unfractionated clear cell renal cell carcinoma (ccRCC) samples can provide insights into the clonality and heterogeneity of intratumoural T cells in ccRCCs, a tumour type that can display extensive genetic intratumour heterogeneity (ITH). For this purpose, DNA was extracted from two to four tumour regions from each of four primary ccRCCs and was analysed by ultra-deep TCR sequencing. In parallel, tumour infiltration by CD4, CD8 and Foxp3 regulatory T cells was evaluated by immunohistochemistry and correlated with TCR-sequencing data. A polyclonal T cell repertoire with 367-16 289 (median 2394) unique TCRb sequences was identified per tumour region. The frequencies of the 100 most abundant T cell clones/tumour were poorly correlated between most regions (Pearson correlation coefficient, -0.218 to 0.465). 3-93% of these T cell clones were not detectable across all regions. Thus, the clonal composition of T cell populations can be heterogeneous across different regions of the same ccRCC. T cell ITH was higher in tumours pretreated with an mTOR inhibitor, which could suggest that therapy can influence adaptive tumour immunity. These data show that ultra-deep TCR-sequencing technology can be applied directly to DNA extracted from unfractionated tumour samples, allowing novel insights into the clonality of T cell populations in cancers. These were polyclonal and displayed ITH in ccRCC. TCRb sequencing may shed light on mechanisms of cancer immunity and the efficacy of immunotherapy approaches.
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Affiliation(s)
- Marco Gerlinger
- Cancer Research UK, London Research Institute, UK; Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, London, UK
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49
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Abstract
Diversity of T cell receptor (TCR) genes is primarily generated by nucleotide insertions upon rearrangement from their germ line-encoded V, D and J segments. Nucleotide insertions at V-D and D-J junctions are random, but some small subsets of these insertions are exceptional, in that one to three base pairs inversely repeat the sequence of the germline DNA. These short complementary palindromic sequences are called P nucleotides. We apply the ImmunoSeq deep-sequencing assay to the third complementarity determining region (CDR3) of the β chain of T cell receptors, and use the resulting data to study P nucleotides in the repertoire of naïve and memory CD8+ and CD4+ T cells. We estimate P nucleotide distributions in a cross section of healthy adults and different T cell subtypes. We show that P nucleotide frequency in all T cell subtypes ranges from 1% to 2%, and that the distribution is highly biased with respect to the coding end of the gene segment. Classification of observed palindromic sequences into P nucleotides using a maximum conditional probability model shows that single base P nucleotides are very rare in VDJ recombination; P nucleotides are primarily two bases long. To explore the role of P nucleotides in thymic selection, we compare P nucleotides in productive and non-productive sequences of CD8+ naïve T cells. The naïve CD8+ T cell clones with P nucleotides are more highly expanded.
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Affiliation(s)
| | - Harlan S. Robins
- Programs in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * E-mail:
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50
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Larimore K, McCormick MW, Robins HS, Greenberg PD. Shaping of Human Germline IgH Repertoires Revealed by Deep Sequencing. J I 2012; 189:3221-30. [DOI: 10.4049/jimmunol.1201303] [Citation(s) in RCA: 133] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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