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Fert I, Douguet L, Vesin B, Moncoq F, Noirat A, Authié P, Ciret S, Le Chevalier F, Blanc C, Vitrenko Y, Charneau P, Majlessi L, Anna F. T-cell immunity induced and reshaped by an anti-HPV immuno-oncotherapeutic lentiviral vector. NPJ Vaccines 2024; 9:102. [PMID: 38858404 PMCID: PMC11164992 DOI: 10.1038/s41541-024-00894-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 05/23/2024] [Indexed: 06/12/2024] Open
Abstract
We recently developed an immuno-oncotherapy against human papillomavirus (HPV)-induced tumors based on a lentiviral vector encoding the Early E6 and E7 oncoproteins of HPV16 and HPV18 genotypes, namely "Lenti-HPV-07". The robust and long-lasting anti-tumor efficacy of Lenti-HPV-07 is dependent on CD8+ T-cell induction and remodeling of the tumor microenvironment. Here, we first established that anti-vector immunity induced by Lenti-HPV-07 prime has no impact on the efficacy of a homologous boost to amplify anti-HPV T-cell immunity. To longitudinally monitor the evolution of the T-cell repertoire generated after the prime, homologous or heterologous boost with Lenti-HPV-07, we tracked T-cell clonotypes by deep sequencing of T-Cell Receptor (TCR) variable β and α chain mRNA, applied to whole peripheral blood cells (PBL) and a T cell population specific of an immunodominant E7HPV16 epitope. We observed a hyper-expansion of clonotypes post prime, accompanied by increased frequencies of HPV-07-specific T cells. Additionally, there was a notable diversification of clonotypes post boost in whole PBL, but not in the E7HPV16-specific T cells. We then demonstrated that the effector functions of such Lenti-HPV-07-induced T cells synergize with anti-checkpoint inhibitory treatments by systemic administration of anti-TIM3 or anti-NKG2A monoclonal antibodies. While Lenti-HPV-07 is about to enter a Phase I/IIa clinical trial, these results will help better elucidate its mode of action in immunotherapy against established HPV-mediated malignancies.
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Affiliation(s)
- Ingrid Fert
- Pasteur-TheraVectys Joint Lab, Institut Pasteur, Université de Paris, Virology Department, 28 Rue du Dr. Roux, F-75015, Paris, France
| | - Laëtitia Douguet
- Pasteur-TheraVectys Joint Lab, Institut Pasteur, Université de Paris, Virology Department, 28 Rue du Dr. Roux, F-75015, Paris, France
| | - Benjamin Vesin
- Pasteur-TheraVectys Joint Lab, Institut Pasteur, Université de Paris, Virology Department, 28 Rue du Dr. Roux, F-75015, Paris, France
| | - Fanny Moncoq
- Pasteur-TheraVectys Joint Lab, Institut Pasteur, Université de Paris, Virology Department, 28 Rue du Dr. Roux, F-75015, Paris, France
| | - Amandine Noirat
- Pasteur-TheraVectys Joint Lab, Institut Pasteur, Université de Paris, Virology Department, 28 Rue du Dr. Roux, F-75015, Paris, France
| | - Pierre Authié
- Pasteur-TheraVectys Joint Lab, Institut Pasteur, Université de Paris, Virology Department, 28 Rue du Dr. Roux, F-75015, Paris, France
| | - Sylvain Ciret
- Pasteur-TheraVectys Joint Lab, Institut Pasteur, Université de Paris, Virology Department, 28 Rue du Dr. Roux, F-75015, Paris, France
| | - Fabien Le Chevalier
- Pasteur-TheraVectys Joint Lab, Institut Pasteur, Université de Paris, Virology Department, 28 Rue du Dr. Roux, F-75015, Paris, France
| | - Catherine Blanc
- Pasteur-TheraVectys Joint Lab, Institut Pasteur, Université de Paris, Virology Department, 28 Rue du Dr. Roux, F-75015, Paris, France
| | - Yakov Vitrenko
- Institut Pasteur, Université Paris Cité, Biomics Technology Platform, F-75015, Paris, France
| | - Pierre Charneau
- Pasteur-TheraVectys Joint Lab, Institut Pasteur, Université de Paris, Virology Department, 28 Rue du Dr. Roux, F-75015, Paris, France
| | - Laleh Majlessi
- Pasteur-TheraVectys Joint Lab, Institut Pasteur, Université de Paris, Virology Department, 28 Rue du Dr. Roux, F-75015, Paris, France.
| | - François Anna
- Pasteur-TheraVectys Joint Lab, Institut Pasteur, Université de Paris, Virology Department, 28 Rue du Dr. Roux, F-75015, Paris, France.
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Pavlova AV, Zvyagin IV, Shugay M. Detecting T-cell clonal expansions and quantifying clone survival using deep profiling of immune repertoires. Front Immunol 2024; 15:1321603. [PMID: 38633256 PMCID: PMC11021634 DOI: 10.3389/fimmu.2024.1321603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 03/12/2024] [Indexed: 04/19/2024] Open
Abstract
An individual's T-cell repertoire constantly changes under the influence of external and internal factors. Cells that do not receive a stimulatory signal die, while those that encounter and recognize a pathogen or receive a co-stimulatory signal divide, resulting in clonal expansions. T-cell clones can be traced by monitoring the presence of their unique T-cell receptor (TCR) sequence, which is assembled de novo through a process known as V(D)J rearrangement. Tracking T cells can provide valuable insights into the survival of cells after hematopoietic stem cell transplantation (HSCT) or cancer treatment response and can indicate the induction of protective immunity by vaccination. In this study, we report a bioinformatic method for quantifying the T-cell repertoire dynamics from TCR sequencing data. We demonstrate its utility by measuring the T-cell repertoire stability in healthy donors, by quantifying the effect of donor lymphocyte infusion (DLI), and by tracking the fate of the different T-cell subsets in HSCT patients and the expansion of pathogen-specific clones in vaccinated individuals.
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Affiliation(s)
- Anastasia V. Pavlova
- Institute of Translational Medicine, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Ivan V. Zvyagin
- Institute of Translational Medicine, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Dmitriy Rogachev National Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Mikhail Shugay
- Institute of Translational Medicine, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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3
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Clark EA, Talatala ER, Ye W, Davis RJ, Collins SL, Hillel AT, Ramirez-Solano M, Sheng Q, Wanjalla CN, Mallal SA, Gelbard A. Characterizing the T Cell Repertoire in the Proximal Airway in Health and Disease. Laryngoscope 2024; 134:1757-1764. [PMID: 37787469 PMCID: PMC10947968 DOI: 10.1002/lary.31088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 09/14/2023] [Accepted: 09/19/2023] [Indexed: 10/04/2023]
Abstract
OBJECTIVES Recent translational scientific efforts in subglottic stenosis (SGS) support a disease model where epithelial alterations facilitate microbiome displacement, dysregulated immune activation, and localized fibrosis. Given the observed immune cell infiltrate in SGS, we sought to test the hypothesis that SGS cases possessed a low diversity (highly clonal) adaptive immune response when compared with healthy controls. METHODS Single cell RNA sequencing (scRNA-seq) of subglottic mucosal scar in iSGS (n = 24), iLTS (n = 8), and healthy controls (n = 7) was performed. T cell receptor (TCR) sequences were extracted, analyzed, and used to construct repertoire structure, compare diversity, interrogate overlap, and define antigenic targets using the Immunarch bioinformatics pipeline. RESULTS The proximal airway mucosa in health and disease are equally diverse via Hill framework quantitation (iSGS vs. iLTS vs. Control, p > 0.05). Repertoires do not significantly overlap between individuals (Morisita <0.02). Among iSGS patients, clonality of the TCR repertoire is driven by CD8+ T cells, and iSGS patients possess numerous TCRs targeting viral and intercellular pathogens. High frequency clonotypes do not map to known targets in public datasets. CONCLUSION SGS cases do not possess a lower diversity adaptive immune infiltrate when compared with healthy controls. Interestingly, the TCR repertoire in both health and disease contains a restricted number of high frequency clonotypes that do not significantly overlap between individuals. The target of the high frequency clonotypes in health and disease remain unresolved. LEVEL OF EVIDENCE NA Laryngoscope, 134:1757-1764, 2024.
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Affiliation(s)
- Evan A. Clark
- Department of Otolaryngology-Head & Neck Surgery, Vanderbilt University Medical Center, Nashville, TN
| | - Edward R.R. Talatala
- Department of Otolaryngology-Head & Neck Surgery, Vanderbilt University Medical Center, Nashville, TN
| | - Wenda Ye
- Department of Otolaryngology-Head & Neck Surgery, Vanderbilt University Medical Center, Nashville, TN
| | - Ruth J. Davis
- Department of Otolaryngology-Head & Neck Surgery, Vanderbilt University Medical Center, Nashville, TN
| | - Samuel L. Collins
- Department of Otolaryngology-Head & Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Alexander T. Hillel
- Department of Otolaryngology-Head & Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD
| | | | - Quanhu Sheng
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN
| | - Celestine N. Wanjalla
- Department of Medicine, Division of Infectious Disease, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Simon A. Mallal
- Department of Medicine, Division of Infectious Disease, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Alexander Gelbard
- Department of Otolaryngology-Head & Neck Surgery, Vanderbilt University Medical Center, Nashville, TN
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4
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Ford ES, Mayer-Blackwell K, Jing L, Laing KJ, Sholukh AM, St Germain R, Bossard EL, Xie H, Pulliam TH, Jani S, Selke S, Burrow CJ, McClurkan CL, Wald A, Greninger AL, Holbrook MR, Eaton B, Eudy E, Murphy M, Postnikova E, Robins HS, Elyanow R, Gittelman RM, Ecsedi M, Wilcox E, Chapuis AG, Fiore-Gartland A, Koelle DM. Repeated mRNA vaccination sequentially boosts SARS-CoV-2-specific CD8 + T cells in persons with previous COVID-19. Nat Immunol 2024; 25:166-177. [PMID: 38057617 PMCID: PMC10981451 DOI: 10.1038/s41590-023-01692-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 10/27/2023] [Indexed: 12/08/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) hybrid immunity is more protective than vaccination or previous infection alone. To investigate the kinetics of spike-reactive T (TS) cells from SARS-CoV-2 infection through messenger RNA vaccination in persons with hybrid immunity, we identified the T cell receptor (TCR) sequences of thousands of index TS cells and tracked their frequency in bulk TCRβ repertoires sampled longitudinally from the peripheral blood of persons who had recovered from coronavirus disease 2019 (COVID-19). Vaccinations led to large expansions in memory TS cell clonotypes, most of which were CD8+ T cells, while also eliciting diverse TS cell clonotypes not observed before vaccination. TCR sequence similarity clustering identified public CD8+ and CD4+ TCR motifs associated with spike (S) specificity. Synthesis of longitudinal bulk ex vivo single-chain TCRβ repertoires and paired-chain TCRɑβ sequences from droplet sequencing of TS cells provides a roadmap for the rapid assessment of T cell responses to vaccines and emerging pathogens.
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Affiliation(s)
- Emily S Ford
- Department of Medicine, University of Washington, Seattle, WA, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | | | - Lichen Jing
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Kerry J Laing
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Anton M Sholukh
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Russell St Germain
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Emily L Bossard
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Hong Xie
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Thomas H Pulliam
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Saumya Jani
- Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Stacy Selke
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | | | | | - Anna Wald
- Department of Medicine, University of Washington, Seattle, WA, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Alexander L Greninger
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Michael R Holbrook
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Brett Eaton
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Elizabeth Eudy
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Michael Murphy
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Elena Postnikova
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | | | | | - Rachel M Gittelman
- Adaptive Biotechnologies, Seattle, WA, USA
- Guardant Health, Redwood City, CA, USA
| | - Matyas Ecsedi
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Takeda Oncology, Cambridge, MA, USA
| | - Elise Wilcox
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Aude G Chapuis
- Department of Medicine, University of Washington, Seattle, WA, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Andrew Fiore-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - David M Koelle
- Department of Medicine, University of Washington, Seattle, WA, USA.
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.
- Department of Global Health, University of Washington, Seattle, WA, USA.
- Department of Translational Research, Benaroya Research Institute, Seattle, WA, USA.
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5
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Quan Z, Qi A, Ma S, Li Y, Chen H, Yu X, Dong T, Li K, Qiu Y. Altered T-cell receptor β repertoire in adults with SARS CoV-2 inactivated vaccine of BBIBP-CorV. Mol Immunol 2023; 162:54-63. [PMID: 37647774 DOI: 10.1016/j.molimm.2023.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 08/03/2023] [Accepted: 08/20/2023] [Indexed: 09/01/2023]
Abstract
OBJECTIVE Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the prolonged and widespread epidemic of coronavirus disease 2019 (COVID-19). The inactivated BBIBP-CorV vaccine has shown safety, efficacy and immunogenicity against COVID-19 in in-vitro studies and clinical trials. However, the characteristics changes of the TCRβ repertoire in patients receiving BBIBP-CorV remain unclear. METHODS TCRβ repertoire difference were analyzed between 54 uninfected subjects who received a third dose of the enhanced BBIBP-CorV vaccine and the 16 healthy donors who did not receive the vaccine and 44 COVID-19 patients with different courses of disease (asymptomatic, symptomatic and convalescent). Furthermore, antibody response, anti-inflammatory and pro-inflammatory cytokines also were examined. RESULTS We found that the third dose inactivated coronavirus vaccine induced widespread changes including the increased TCRβ repertoire diversity, a much shorter CDR3 length and high usage of V-J genes segments. Meanwhile, the vaccine-responding clones were also predicted. The results of the antibody response showed that 90.7 % of the vaccinated individuals were positive for NAb seroconversion and 88.9 % for IgG antibody about 60 days after the third dose. The concentration of IL-2 increased significantly compared to baseline inoculation. CONCLUSION Altered TCRβ repertoire in adults with SARS CoV-2 inactivated vaccine of BBIBP-CorV clarified the specific immunity induced by inactivated vaccines. Our research provides insights into the adaptive immune response induced by the new inactivated SARS-CoV-2 vaccine and strengthens the development of immunotherapy.
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Affiliation(s)
- Zhihui Quan
- Guangzhou Huayin Medical Laboratory Center Co., Ltd, Guangzhou, China; Translational Medicine Institute of Guangzhou Huayin Health Medical Group Co., Ltd, Guangzhou, China
| | - Aihong Qi
- Guangzhou Huayin Medical Laboratory Center Co., Ltd, Guangzhou, China
| | - Shuwen Ma
- Guangzhou Huayin Medical Laboratory Center Co., Ltd, Guangzhou, China
| | - Yanling Li
- Guangzhou Huayin Medical Laboratory Center Co., Ltd, Guangzhou, China; Guangzhou Huayin Health Medical Group Co., Ltd, Guangzhou, China
| | - Hui Chen
- Guangzhou Huayin Medical Laboratory Center Co., Ltd, Guangzhou, China; Guangzhou Huayin Health Medical Group Co., Ltd, Guangzhou, China
| | - Xue Yu
- Guangzhou Huayin Medical Laboratory Center Co., Ltd, Guangzhou, China; Translational Medicine Institute of Guangzhou Huayin Health Medical Group Co., Ltd, Guangzhou, China
| | - Tingyan Dong
- Guangzhou Huayin Medical Laboratory Center Co., Ltd, Guangzhou, China; Guangzhou Huayin Health Medical Group Co., Ltd, Guangzhou, China.
| | - Kui Li
- Guangzhou Huayin Medical Laboratory Center Co., Ltd, Guangzhou, China; Translational Medicine Institute of Guangzhou Huayin Health Medical Group Co., Ltd, Guangzhou, China.
| | - Yurong Qiu
- Guangzhou Huayin Medical Laboratory Center Co., Ltd, Guangzhou, China; Guangzhou Huayin Health Medical Group Co., Ltd, Guangzhou, China.
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Boughter CT, Meier-Schellersheim M. An integrated approach to the characterization of immune repertoires using AIMS: An Automated Immune Molecule Separator. PLoS Comput Biol 2023; 19:e1011577. [PMID: 37862356 PMCID: PMC10619816 DOI: 10.1371/journal.pcbi.1011577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 11/01/2023] [Accepted: 10/06/2023] [Indexed: 10/22/2023] Open
Abstract
The adaptive immune system employs an array of receptors designed to respond with high specificity to pathogens or molecular aberrations faced by the host organism. Binding of these receptors to molecular fragments-collectively referred to as antigens-initiates immune responses. These antigenic targets are recognized in their native state on the surfaces of pathogens by antibodies, whereas T cell receptors (TCR) recognize processed antigens as short peptides, presented on major histocompatibility complex (MHC) molecules. Recent research has led to a wealth of immune repertoire data that are key to interrogating the nature of these molecular interactions. However, existing tools for the analysis of these large datasets typically focus on molecular sets of a single type, forcing researchers to separately analyze strongly coupled sequences of interacting molecules. Here, we introduce a software package for the integrated analysis of immune repertoire data, capable of identifying distinct biophysical differences in isolated TCR, MHC, peptide, antibody, and antigen sequence data. This integrated analytical approach allows for direct comparisons across immune repertoire subsets and provides a starting point for the identification of key interaction hotspots in complementary receptor-antigen pairs. The software (AIMS-Automated Immune Molecule Separator) is freely available as an open access package in GUI or command-line form.
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Affiliation(s)
- Christopher T. Boughter
- Computational Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Martin Meier-Schellersheim
- Computational Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
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7
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Mayer-Blackwell K, Ryu H, Codd AS, Parks KR, MacMillan HR, Cohen KW, Stewart TL, Seese A, Lemos MP, De Rosa SC, Czartoski JL, Moodie Z, Nguyen LT, McGuire DJ, Ahmed R, Fiore-Gartland A, McElrath MJ, Newell EW. mRNA vaccination boosts S-specific T cell memory and promotes expansion of CD45RA int T EMRA-like CD8 + T cells in COVID-19 recovered individuals. Cell Rep Med 2023; 4:101149. [PMID: 37552991 PMCID: PMC10439252 DOI: 10.1016/j.xcrm.2023.101149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 06/01/2023] [Accepted: 07/17/2023] [Indexed: 08/10/2023]
Abstract
SARS-CoV-2 infection and mRNA vaccination both elicit spike (S)-specific T cell responses. To analyze how T cell memory from prior infection influences T cell responses to vaccination, we evaluated functional T cell responses in naive and previously infected vaccine recipients. Pre-vaccine S-specific responses are predictive of subsequent CD8+ T cell vaccine-response magnitudes. Comparing baseline with post-vaccination TCRβ repertoires, we observed large clonotypic expansions correlated with the frequency of spike-specific T cells. Epitope mapping the largest CD8+ T cell responses confirms that an HLA-A∗03:01 epitope was highly immunodominant. Peptide-MHC tetramer staining together with mass cytometry and single-cell sequencing permit detailed phenotyping and clonotypic tracking of these S-specific CD8+ T cells. Our results demonstrate that infection-induced S-specific CD8+ T cell memory plays a significant role in shaping the magnitude and clonal composition of the circulating T cell repertoire after vaccination, with mRNA vaccination promoting CD8+ memory T cells to a TEMRA-like phenotype.
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Affiliation(s)
- Koshlan Mayer-Blackwell
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Heeju Ryu
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Amy S Codd
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - K Rachael Parks
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Hugh R MacMillan
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Kristen W Cohen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Terri L Stewart
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Aaron Seese
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Maria P Lemos
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Stephen C De Rosa
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Julie L Czartoski
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Zoe Moodie
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Long T Nguyen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Donald J McGuire
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30329, USA; Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Rafi Ahmed
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30329, USA; Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Andrew Fiore-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - M Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.
| | - Evan W Newell
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.
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8
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Myronov A, Mazzocco G, Król P, Plewczynski D. BERTrand-peptide:TCR binding prediction using Bidirectional Encoder Representations from Transformers augmented with random TCR pairing. Bioinformatics 2023; 39:btad468. [PMID: 37535685 PMCID: PMC10444968 DOI: 10.1093/bioinformatics/btad468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 06/28/2023] [Accepted: 08/01/2023] [Indexed: 08/05/2023] Open
Abstract
MOTIVATION The advent of T-cell receptor (TCR) sequencing experiments allowed for a significant increase in the amount of peptide:TCR binding data available and a number of machine-learning models appeared in recent years. High-quality prediction models for a fixed epitope sequence are feasible, provided enough known binding TCR sequences are available. However, their performance drops significantly for previously unseen peptides. RESULTS We prepare the dataset of known peptide:TCR binders and augment it with negative decoys created using healthy donors' T-cell repertoires. We employ deep learning methods commonly applied in Natural Language Processing to train part a peptide:TCR binding model with a degree of cross-peptide generalization (0.69 AUROC). We demonstrate that BERTrand outperforms the published methods when evaluated on peptide sequences not used during model training. AVAILABILITY AND IMPLEMENTATION The datasets and the code for model training are available at https://github.com/SFGLab/bertrand.
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Affiliation(s)
- Alexander Myronov
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
- Ardigen, Krakow, Poland
| | | | | | - Dariusz Plewczynski
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
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9
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Tereshchenko V, Shevyrev D, Fisher M, Bulygin A, Khantakova J, Sennikov S. TCR Sequencing in Mouse Models of Allorecognition Unveils the Features of Directly and Indirectly Activated Clonotypes. Int J Mol Sci 2023; 24:12075. [PMID: 37569450 PMCID: PMC10418307 DOI: 10.3390/ijms241512075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/26/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023] Open
Abstract
Allorecognition is known to involve a large number of lymphocytes carrying diverse T-cell receptor repertoire. Thus, one way to understand allorecognition and rejection mechanisms is via high-throughput sequencing of T-cell receptors. In this study, in order to explore and systematize the properties of the alloreactive T-cell receptor repertoire, we modeled direct and indirect allorecognition pathways using material from inbred mice in vitro and in vivo. Decoding of the obtained T-cell receptor genes using high-throughput sequencing revealed some features of the alloreactive repertoires. Thus, alloreactive T-cell receptor repertoires were characterized by specific V-gene usage patterns, changes in CDR3 loop length, and some amino acid occurrence probabilities in the CDR3 loop. Particularly pronounced changes were observed for directly alloreactive clonotypes. We also revealed a clustering of directly and indirectly alloreactive clonotypes by their ability to bind a single antigen; amino acid patterns of the CDR3 loop of alloreactive clonotypes; and the presence in alloreactive repertoires of clonotypes also associated with infectious, autoimmune, and tumor diseases. The obtained results were determined by the modeling of the simplified allorecognition reaction in inbred mice in which stimulation was performed with a single MHCII molecule. We suppose that the decomposition of the diverse alloreactive TCR repertoire observed in humans with transplants into such simple reactions will help to find alloreactive repertoire features; e.g., a dominant clonotype or V-gene usage pattern, which may be targeted to correct the entire rejection reaction in patients. In this work, we propose several technical ways for such decomposition analysis, including separate modeling of the indirect alloreaction pathway and clustering of alloreactive clonotypes according to their ability to bind a single antigen, among others.
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Affiliation(s)
- Valeriy Tereshchenko
- Laboratory of Molecular Immunology, Research Institute of Fundamental and Clinical Immunology, 630099 Novosibirsk, Russia
- Resource Center for Cellular Technologies and Immunology, Sirius University of Science and Technology, 354340 Sochi, Russia
| | - Daniil Shevyrev
- Resource Center for Cellular Technologies and Immunology, Sirius University of Science and Technology, 354340 Sochi, Russia
| | - Marina Fisher
- Laboratory of Molecular Immunology, Research Institute of Fundamental and Clinical Immunology, 630099 Novosibirsk, Russia
| | - Aleksei Bulygin
- Laboratory of Molecular Immunology, Research Institute of Fundamental and Clinical Immunology, 630099 Novosibirsk, Russia
| | - Julia Khantakova
- Laboratory of Molecular Immunology, Research Institute of Fundamental and Clinical Immunology, 630099 Novosibirsk, Russia
| | - Sergey Sennikov
- Laboratory of Molecular Immunology, Research Institute of Fundamental and Clinical Immunology, 630099 Novosibirsk, Russia
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10
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Bujak J, Kłęk S, Balawejder M, Kociniak A, Wilkus K, Szatanek R, Orzeszko Z, Welanyk J, Torbicz G, Jęckowski M, Kucharczyk T, Wohadlo Ł, Borys M, Stadnik H, Wysocki M, Kayser M, Słomka ME, Kosmowska A, Horbacka K, Gach T, Markowska B, Kowalczyk T, Karoń J, Karczewski M, Szura M, Sanecka-Duin A, Blum A. Creating an Innovative Artificial Intelligence-Based Technology (TCRact) for Designing and Optimizing T Cell Receptors for Use in Cancer Immunotherapies: Protocol for an Observational Trial. JMIR Res Protoc 2023; 12:e45872. [PMID: 37440307 PMCID: PMC10375398 DOI: 10.2196/45872] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 06/01/2023] [Accepted: 06/02/2023] [Indexed: 07/14/2023] Open
Abstract
BACKGROUND Cancer continues to be the leading cause of mortality in high-income countries, necessitating the development of more precise and effective treatment modalities. Immunotherapy, specifically adoptive cell transfer of T cell receptor (TCR)-engineered T cells (TCR-T therapy), has shown promise in engaging the immune system for cancer treatment. One of the biggest challenges in the development of TCR-T therapies is the proper prediction of the pairing between TCRs and peptide-human leukocyte antigen (pHLAs). Modern computational immunology, using artificial intelligence (AI)-based platforms, provides the means to optimize the speed and accuracy of TCR screening and discovery. OBJECTIVE This study proposes an observational clinical trial protocol to collect patient samples and generate a database of pHLA:TCR sequences to aid the development of an AI-based platform for efficient selection of specific TCRs. METHODS The multicenter observational study, involving 8 participating hospitals, aims to enroll patients diagnosed with stage II, III, or IV colorectal cancer adenocarcinoma. RESULTS Patient recruitment has recently been completed, with 100 participants enrolled. Primary tumor tissue and peripheral blood samples have been obtained, and peripheral blood mononuclear cells have been isolated and cryopreserved. Nucleic acid extraction (DNA and RNA) has been performed in 86 cases. Additionally, 57 samples underwent whole exome sequencing to determine the presence of somatic mutations and RNA sequencing for gene expression profiling. CONCLUSIONS The results of this study may have a significant impact on the treatment of patients with colorectal cancer. The comprehensive database of pHLA:TCR sequences generated through this observational clinical trial will facilitate the development of the AI-based platform for TCR selection. The results obtained thus far demonstrate successful patient recruitment and sample collection, laying the foundation for further analysis and the development of an innovative tool to expedite and enhance TCR selection for precision cancer treatments. TRIAL REGISTRATION ClinicalTrials.gov NCT04994093; https://clinicaltrials.gov/ct2/show/NCT04994093. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID) DERR1-10.2196/45872.
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Affiliation(s)
- Joanna Bujak
- Ardigen SA, Cracow, Poland
- Department of Physics and Biophysics, Institute of Biology, Warsaw University of Life Sciences, Warszawa, Poland
| | - Stanisław Kłęk
- Surgical Oncology Clinic, Maria Sklodowska-Curie National Research Institute of Oncology, Cracow, Poland
| | | | | | | | | | - Zofia Orzeszko
- Department of General and Oncological Surgery, Brothers Hospitallers Hospital, Cracow, Poland
| | - Joanna Welanyk
- Surgical Oncology Clinic, Maria Sklodowska-Curie National Research Institute of Oncology, Cracow, Poland
| | - Grzegorz Torbicz
- Department of General Surgery and Surgical Oncology, Ludwik Rydygier Memorial Hospital, Cracow, Poland
| | - Mateusz Jęckowski
- Colon Cancer Unit, Department of Oncological Surgery, Voivodeship Multi-Specialist Center for Oncology and Traumatology, Lodz, Poland
| | - Tomasz Kucharczyk
- Holy Cross Cancer Center Clinic of Clinical Oncology, Cracow, Poland
| | - Łukasz Wohadlo
- Department of General Surgery, Andrzej Frycz Modrzewski Krakow University, Cracow, Poland
| | - Maciej Borys
- Department of General Surgery and Surgical Oncology, Ludwik Rydygier Memorial Hospital, Cracow, Poland
| | - Honorata Stadnik
- Department of General and Transplant Surgery, Poznan University of Medical Sciences, University Hospital, Poznan, Poland
| | - Michał Wysocki
- Department of General Surgery and Surgical Oncology, Ludwik Rydygier Memorial Hospital, Cracow, Poland
| | - Magdalena Kayser
- General and Colorectal Surgery Department, J Struś Multispecialist Municipal Hospital, Poznan, Poland
| | - Marta Ewa Słomka
- Colon Cancer Unit, Department of Oncological Surgery, Voivodeship Multi-Specialist Center for Oncology and Traumatology, Lodz, Poland
| | - Anna Kosmowska
- General and Colorectal Surgery Department, J Struś Multispecialist Municipal Hospital, Poznan, Poland
| | - Karolina Horbacka
- General and Colorectal Surgery Department, J Struś Multispecialist Municipal Hospital, Poznan, Poland
| | - Tomasz Gach
- Surgical Clinic Institute of Physiotherapy, Faculty of Health Sciences, Jagiellonian University Medical College, Cracow, Poland
| | - Beata Markowska
- Surgical Clinic Institute of Physiotherapy, Faculty of Health Sciences, Jagiellonian University Medical College, Cracow, Poland
| | - Tomasz Kowalczyk
- Department of General Surgery, Andrzej Frycz Modrzewski Krakow University, Cracow, Poland
| | - Jacek Karoń
- General and Colorectal Surgery Department, J Struś Multispecialist Municipal Hospital, Poznan, Poland
| | - Marek Karczewski
- Department of General and Transplant Surgery, Poznan University of Medical Sciences, University Hospital, Poznan, Poland
| | - Mirosław Szura
- Surgical Clinic Institute of Physiotherapy, Faculty of Health Sciences, Jagiellonian University Medical College, Cracow, Poland
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11
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de Greef PC, Lanfermeijer J, Hendriks M, Cevirgel A, Vos M, Borghans JAM, van Baarle D, de Boer RJ. On the feasibility of using TCR sequencing to follow a vaccination response - lessons learned. Front Immunol 2023; 14:1210168. [PMID: 37520553 PMCID: PMC10374308 DOI: 10.3389/fimmu.2023.1210168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 06/26/2023] [Indexed: 08/01/2023] Open
Abstract
T cells recognize pathogens by their highly specific T-cell receptor (TCR), which can bind small fragments of an antigen presented on the Major Histocompatibility Complex (MHC). Antigens that are provided through vaccination cause specific T cells to respond by expanding and forming specific memory to combat a future infection. Quantification of this T-cell response could improve vaccine monitoring or identify individuals with a reduced ability to respond to a vaccination. In this proof-of-concept study we use longitudinal sequencing of the TCRβ repertoire to quantify the response in the CD4+ memory T-cell pool upon pneumococcal conjugate vaccination. This comes with several challenges owing to the enormous size and diversity of the T-cell pool, the limited frequency of vaccine-specific TCRs in the total repertoire, and the variation in sample size and quality. We defined quantitative requirements to classify T-cell expansions and identified critical parameters that aid in reliable analysis of the data. In the context of pneumococcal conjugate vaccination, we were able to detect robust T-cell expansions in a minority of the donors, which suggests that the T-cell response against the conjugate in the pneumococcal vaccine is small and/or very broad. These results indicate that there is still a long way to go before TCR sequencing can be reliably used as a personal biomarker for vaccine-induced protection. Nevertheless, this study highlights the importance of having multiple samples containing sufficient T-cell numbers, which will support future studies that characterize T-cell responses using longitudinal TCR sequencing.
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Affiliation(s)
- Peter C. de Greef
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands
| | - Josien Lanfermeijer
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Marion Hendriks
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Alper Cevirgel
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Martijn Vos
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - José A. M. Borghans
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Debbie van Baarle
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Rob J. de Boer
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands
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12
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Milighetti M, Peng Y, Tan C, Mark M, Nageswaran G, Byrne S, Ronel T, Peacock T, Mayer A, Chandran A, Rosenheim J, Whelan M, Yao X, Liu G, Felce SL, Dong T, Mentzer AJ, Knight JC, Balloux F, Greenstein E, Reich-Zeliger S, Pade C, Gibbons JM, Semper A, Brooks T, Otter A, Altmann DM, Boyton RJ, Maini MK, McKnight A, Manisty C, Treibel TA, Moon JC, Noursadeghi M, Chain B. Large clones of pre-existing T cells drive early immunity against SARS-COV-2 and LCMV infection. iScience 2023; 26:106937. [PMID: 37275518 PMCID: PMC10201888 DOI: 10.1016/j.isci.2023.106937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/14/2023] [Accepted: 05/17/2023] [Indexed: 06/07/2023] Open
Abstract
T cell responses precede antibody and may provide early control of infection. We analyzed the clonal basis of this rapid response following SARS-COV-2 infection. We applied T cell receptor (TCR) sequencing to define the trajectories of individual T cell clones immediately. In SARS-COV-2 PCR+ individuals, a wave of TCRs strongly but transiently expand, frequently peaking the same week as the first positive PCR test. These expanding TCR CDR3s were enriched for sequences functionally annotated as SARS-COV-2 specific. Epitopes recognized by the expanding TCRs were highly conserved between SARS-COV-2 strains but not with circulating human coronaviruses. Many expanding CDR3s were present at high frequency in pre-pandemic repertoires. Early response TCRs specific for lymphocytic choriomeningitis virus epitopes were also found at high frequency in the preinfection naive repertoire. High-frequency naive precursors may allow the T cell response to respond rapidly during the crucial early phases of acute viral infection.
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Affiliation(s)
- Martina Milighetti
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Yanchun Peng
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Cedric Tan
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Michal Mark
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Gayathri Nageswaran
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Suzanne Byrne
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Tahel Ronel
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Tom Peacock
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Andreas Mayer
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Aneesh Chandran
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Joshua Rosenheim
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Matthew Whelan
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Xuan Yao
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Guihai Liu
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Suet Ling Felce
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Tao Dong
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | | | - Julian C Knight
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Francois Balloux
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Erez Greenstein
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Shlomit Reich-Zeliger
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Corinna Pade
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London E1 4NS, UK
| | - Joseph M Gibbons
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London E1 4NS, UK
| | - Amanda Semper
- UK Health Security Agency, Porton Down, Salisbury SP4 0JG, UK
| | - Tim Brooks
- UK Health Security Agency, Porton Down, Salisbury SP4 0JG, UK
| | - Ashley Otter
- UK Health Security Agency, Porton Down, Salisbury SP4 0JG, UK
| | - Daniel M Altmann
- Department of Immunology and Inflammation, Imperial College London, London SW7 2BX, UK
| | - Rosemary J Boyton
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK
- Lung Division, Royal Brompton Hospital, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Mala K Maini
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Aine McKnight
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London E1 4NS, UK
| | - Charlotte Manisty
- Institute of Cardiovascular Sciences, University College London, London WC1E 6BT, UK
| | - Thomas A Treibel
- Institute of Cardiovascular Sciences, University College London, London WC1E 6BT, UK
| | - James C Moon
- Institute of Cardiovascular Sciences, University College London, London WC1E 6BT, UK
| | - Mahdad Noursadeghi
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Benny Chain
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
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13
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Qi T, Vincent BG, Cao Y. A multispecies framework for modeling adaptive immunity and immunotherapy in cancer. PLoS Comput Biol 2023; 19:e1010976. [PMID: 37083574 PMCID: PMC10155959 DOI: 10.1371/journal.pcbi.1010976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 05/03/2023] [Accepted: 02/24/2023] [Indexed: 04/22/2023] Open
Abstract
Predator-prey theory is commonly used to describe tumor growth in the presence of selective pressure from the adaptive immune system. These interactions are mediated by the tumor immunopeptidome (what the tumor "shows" the body) and the T-cell receptor (TCR) repertoire (how well the body "sees" cancer cells). The tumor immunopeptidome comprises neoantigens which can be gained and lost throughout tumorigenesis and treatment. Heterogeneity in the immunopeptidome is predictive of poor response to immunotherapy in some tumor types, suggesting that the TCR repertoire is unable to support a fully polyclonal response against every neoantigen. Importantly, while tumor and T-cell populations are known to compete with each other for intratumoral resources, whether between-lineage competition among peripheral T cells influences the TCR repertoire is unknown and difficult to interrogate experimentally. Computational models may offer a way to investigate these phenomena and deepen our understanding of the tumor-immune axis. Here, we construct a predator-prey-like model and calibrate it to preclinical and clinical data to describe tumor growth and immunopeptidome diversification. Simultaneously, we model the expansion of antigen-specific T-cell lineages and their consumption of both lineage-specific antigenic resources and lineage-agnostic, shared resources. This predator-prey-like framework accurately described clinically observed immunopeptidomes; recapitulated response-associated effects of immunotherapy, including immunoediting; and allowed exploration of treatment of tumors with varying growth and mutation rates.
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Affiliation(s)
- Timothy Qi
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Benjamin G. Vincent
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Division of Hematology/Oncology, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Yanguang Cao
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
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14
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Gao Y, Bergman I. Anti-tumor memory CD4 and CD8 T-cells quantified by bulk T-cell receptor (TCR) clonal analysis. Front Immunol 2023; 14:1137054. [PMID: 37033929 PMCID: PMC10076582 DOI: 10.3389/fimmu.2023.1137054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 03/13/2023] [Indexed: 04/11/2023] Open
Abstract
Simple, reliable methods to detect anti-tumor memory T-cells are necessary to develop a clinical tumor vaccination program. A mouse model of curative viral onco-immunotherapy found that peritoneal tumor challenge following cure identified an oligoclonal anti-tumor memory CD4 and CD8 T-cell response. Clonotypes differed among the challenged animals but were congruent in blood, spleen and peritoneal cells (PC) of the same animal. Adoptive transfer demonstrated that the high-frequency responding T-cells were tumor specific. Tetramer analysis confirmed that clonotype frequency determined by T-cell receptor (TCR)- chain (TRB) analysis closely approximated cell clone frequency. The mean frequency of resting anti-tumor memory CD4 T-cells in unchallenged spleen was 0.028% and of memory CD8 T-cells was 0.11% which was not high enough to distinguish them from background. Stimulation produced a mean ~10-fold increase in splenic and 100-fold increase in peritoneal anti-tumor memory T-cell clonotypes. This methodology can be developed to use blood and tissue sampling to rapidly quantify the effectiveness of a tumor vaccine or any vaccine generating therapeutic T-cells.
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Affiliation(s)
- Yanhua Gao
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Ira Bergman
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- Department of Neurology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
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15
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Gao Y, Gao Y, Fan Y, Zhu C, Wei Z, Zhou C, Chuai G, Chen Q, Zhang H, Liu Q. Pan-Peptide Meta Learning for T-cell receptor–antigen binding recognition. NAT MACH INTELL 2023. [DOI: 10.1038/s42256-023-00619-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
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16
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Von Niederhäusern V, Ghraichy M, Trück J. Applicability of T cell receptor repertoire sequencing analysis to unbalanced clinical samples - comparing the T cell receptor repertoire of GATA2 deficient patients and healthy controls. Swiss Med Wkly 2023; 153:40046. [PMID: 36800891 DOI: 10.57187/smw.2023.40046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Indexed: 02/11/2023] Open
Abstract
T cell receptor repertoire sequencing (TCRseq) has become one of the major omic tools to study the immune system in health and disease. Multiple commercial solutions are currently available, greatly facilitating the implementation of this complex method into translational studies. However, the flexibility of these methods to react to suboptimal sample material is still limited. In a clinical research context, limited sample availability and/or unbalanced sample material can negatively impact the feasibility and quality of such analyses. We sequenced the T cell receptor repertoires of three healthy controls and four patients with GATA2 deficiency using a commercially available TCRseq kit and thereby (1) assessed the impact of suboptimal sample quality and (2) implemented a subsampling strategy to react to biased sample input quantity. Applying these strategies, we did not find significant differences in the global T cell receptor repertoire characteristics such as V and J gene usage, CDR3 junction length and repertoire diversity of GATA2-deficient patients compared with healthy control samples. Our results prove the adaptability of this TCRseq protocol to the analysis of unbalanced sample material and provide encouraging evidence for use of this method in future studies despite suboptimal patient samples.
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Affiliation(s)
- Valentin Von Niederhäusern
- Division of Immunology and Children's Research Center, University Children's Hospital, University of Zurich (UZH), Zurich, Switzerland
| | - Marie Ghraichy
- Division of Immunology and Children's Research Center, University Children's Hospital, University of Zurich (UZH), Zurich, Switzerland
| | - Johannes Trück
- Division of Immunology and Children's Research Center, University Children's Hospital, University of Zurich (UZH), Zurich, Switzerland
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17
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Ritacco C, Köse MC, Courtois J, Canti L, Beguin C, Dubois S, Vandenhove B, Servais S, Caers J, Beguin Y, Ehx G, Baron F. Post-transplant cyclophosphamide prevents xenogeneic graft-versus-host disease while depleting proliferating regulatory T cells. iScience 2023; 26:106085. [PMID: 36843851 PMCID: PMC9947306 DOI: 10.1016/j.isci.2023.106085] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/12/2022] [Accepted: 01/25/2023] [Indexed: 02/02/2023] Open
Abstract
Graft-versus-host disease (GVHD) remains a serious limitation of allogeneic hematopoietic cell transplantation (allo-HCT). While post-transplant administration of cyclophosphamide (PTCy) is increasingly used as GVHD prophylaxis, its precise mechanisms of action and its impact on graft-versus-leukemia effects have remained debated. Here, we studied the mechanisms of xenogeneic GVHD (xGVHD) prevention by PTCy in different humanized mouse models. We observed that PTCy attenuated xGVHD. Using flow cytometry and single-cell RNA-sequencing, we demonstrated that PTCy depleted proliferative CD8+ and conventional CD4+ T cells but also proliferative regulatory T cells (Treg). Further, T-cell receptor β variable region sequencing (TCRVB) analyses demonstrated that highly xenoreactive T-cell clones were depleted by PTCy. Although Treg frequencies were significantly higher in PTCy-treated than in control mice on day 21, xGVHD attenuation by PTCy was not abrogated by Treg depletion. Finally, we observed that PTCy did not abrogate graft-versus-leukemia effects.
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Affiliation(s)
- Caroline Ritacco
- Hematology Research Unit, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA)-I³, University of Liège, Liège 4000, Belgium
| | - Murat Cem Köse
- Hematology Research Unit, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA)-I³, University of Liège, Liège 4000, Belgium
| | - Justine Courtois
- Hematology Research Unit, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA)-I³, University of Liège, Liège 4000, Belgium
| | - Lorenzo Canti
- Hematology Research Unit, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA)-I³, University of Liège, Liège 4000, Belgium
| | - Charline Beguin
- Hematology Research Unit, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA)-I³, University of Liège, Liège 4000, Belgium
| | - Sophie Dubois
- Hematology Research Unit, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA)-I³, University of Liège, Liège 4000, Belgium
| | - Benoît Vandenhove
- Hematology Research Unit, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA)-I³, University of Liège, Liège 4000, Belgium
| | - Sophie Servais
- Hematology Research Unit, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA)-I³, University of Liège, Liège 4000, Belgium,Department of Medicine, Division of Hematology, CHU of Liège, Liège 4000, Belgium
| | - Jo Caers
- Hematology Research Unit, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA)-I³, University of Liège, Liège 4000, Belgium,Department of Medicine, Division of Hematology, CHU of Liège, Liège 4000, Belgium
| | - Yves Beguin
- Hematology Research Unit, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA)-I³, University of Liège, Liège 4000, Belgium,Department of Medicine, Division of Hematology, CHU of Liège, Liège 4000, Belgium
| | - Grégory Ehx
- Hematology Research Unit, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA)-I³, University of Liège, Liège 4000, Belgium,Corresponding author
| | - Frédéric Baron
- Hematology Research Unit, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA)-I³, University of Liège, Liège 4000, Belgium,Department of Medicine, Division of Hematology, CHU of Liège, Liège 4000, Belgium,Corresponding author
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18
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Inferring the T cell repertoire dynamics of healthy individuals. Proc Natl Acad Sci U S A 2023; 120:e2207516120. [PMID: 36669107 PMCID: PMC9942919 DOI: 10.1073/pnas.2207516120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The adaptive immune system is a diverse ecosystem that responds to pathogens by selecting cells with specific receptors. While clonal expansion in response to particular immune challenges has been extensively studied, we do not know the neutral dynamics that drive the immune system in the absence of strong stimuli. Here, we learn the parameters that underlie the clonal dynamics of the T cell repertoire in healthy individuals of different ages, by applying Bayesian inference to longitudinal immune repertoire sequencing (RepSeq) data. Quantifying the experimental noise accurately for a given RepSeq technique allows us to disentangle real changes in clonal frequencies from noise. We find that the data are consistent with clone sizes following a geometric Brownian motion and show that its predicted steady state is in quantitative agreement with the observed power-law behavior of the clone-size distribution. The inferred turnover time scale of the repertoire increases with patient age and depends on the clone size in some individuals.
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19
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Smirnova AO, Miroshnichenkova AM, Olshanskaya YV, Maschan MA, Lebedev YB, Chudakov DM, Mamedov IZ, Komkov A. The use of non-functional clonotypes as a natural calibrator for quantitative bias correction in adaptive immune receptor repertoire profiling. eLife 2023; 12:69157. [PMID: 36692004 PMCID: PMC9901932 DOI: 10.7554/elife.69157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 01/22/2023] [Indexed: 01/25/2023] Open
Abstract
High-throughput sequencing of adaptive immune receptor repertoires is a valuable tool for receiving insights in adaptive immunity studies. Several powerful TCR/BCR repertoire reconstruction and analysis methods have been developed in the past decade. However, detecting and correcting the discrepancy between real and experimentally observed lymphocyte clone frequencies are still challenging. Here, we discovered a hallmark anomaly in the ratio between read count and clone count-based frequencies of non-functional clonotypes in multiplex PCR-based immune repertoires. Calculating this anomaly, we formulated a quantitative measure of V- and J-genes frequency bias driven by multiplex PCR during library preparation called Over Amplification Rate (OAR). Based on the OAR concept, we developed an original software for multiplex PCR-specific bias evaluation and correction named iROAR: immune Repertoire Over Amplification Removal (https://github.com/smiranast/iROAR). The iROAR algorithm was successfully tested on previously published TCR repertoires obtained using both 5' RACE (Rapid Amplification of cDNA Ends)-based and multiplex PCR-based approaches and compared with a biological spike-in-based method for PCR bias evaluation. The developed approach can increase the accuracy and consistency of repertoires reconstructed by different methods making them more applicable for comparative analysis.
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Affiliation(s)
- Anastasia O Smirnova
- Skolkovo Institute of Science and TechnologyMoscowRussian Federation
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
| | - Anna M Miroshnichenkova
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and ImmunologyMoscowRussian Federation
| | - Yulia V Olshanskaya
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and ImmunologyMoscowRussian Federation
| | - Michael A Maschan
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and ImmunologyMoscowRussian Federation
| | - Yuri B Lebedev
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
- Pirogov Russian National Research Medical UniversityMoscowRussian Federation
| | - Dmitriy M Chudakov
- Skolkovo Institute of Science and TechnologyMoscowRussian Federation
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
- Pirogov Russian National Research Medical UniversityMoscowRussian Federation
- Abu Dhabi Stem Cells CenterAbu DhabiUnited Arab Emirates
| | - Ilgar Z Mamedov
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
- Pirogov Russian National Research Medical UniversityMoscowRussian Federation
| | - Alexander Komkov
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and ImmunologyMoscowRussian Federation
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20
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Distinguishing between monozygotic twins' blood samples through immune repertoire sequencing. Forensic Sci Int Genet 2023; 64:102828. [PMID: 36682099 DOI: 10.1016/j.fsigen.2023.102828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/30/2022] [Accepted: 01/06/2023] [Indexed: 01/09/2023]
Abstract
Monozygotic (MZ) twins with highly similar genomic DNA sequences can not be distinguished by conventional forensic DNA testing. The immune repertoire (IR) reflects an individual's immune history, which is unique between individuals, has been applied to individualized treatment in precision medicine. However, the application of IR in forensic genetics has not been reported to date. In this study, the diversity in the complementary determining region 3 (CDR3) of both the T-cell receptor β chain (TCRβ) and B-cell receptor heavy chain (also known as immunoglobulin heavy chain, IGH) in four pairs of MZ twins were analyzed. The results showed that the amino acid sequences length distribution frequency of TCRβ CDR3 had 4-10 differences, and the nucleic acid sequences length distribution frequency of TCRβ CDR3 had 2-7 differences between MZ twins. The shared difference of four pairs of MZ twins focused on the length distribution frequency of 34 bp nucleotide sequences in TCRβ. By analyzing the usage frequency of V and J genes in TCRβ and IGH CDR3 DNA sequence rearrangements, we also found that there were biases between each pair of MZ twins, and the usage frequency of TRBJ2-3 showed common differences between each pair of MZ twins. Furthermore, each pair of MZ twins had its own unique V-J genes combination mode in TCRβ and IGH CDR3 DNA sequences. This study, for the first time, suggested that IR can be used as a potential biological marker to distinguish MZ twins.
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21
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Valkiers S, Gielis S, Van Deuren VML, Laukens K, Meysman P. Clustering and Annotation of T Cell Receptor Repertoires. Methods Mol Biol 2023; 2673:33-51. [PMID: 37258905 DOI: 10.1007/978-1-0716-3239-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Immunological protection against a wide variety of pathogens is largely mediated by the diverse and dynamic T cell receptor (TCR) repertoire, a crucial component of the adaptive immune system. An encounter with infectious agents stimulates specific T cells to initiate a direct immune response to combat intruders. Hence, the TCR repertoire may conceal crucial information regarding current and past infections and might assist in the development and monitoring of vaccines. To unlock its knowledge, we describe a computational workflow involving both supervised and unsupervised machine learning techniques to analyze and annotate full TCR repertoire data. The method is explained using data from a published yellow fever virus (YFV) vaccination study in healthy individuals. The TCR repertoire of one individual is studied before and 2 weeks after vaccination, using an efficient clustering method and identification of YFV-specific TCRs.
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Affiliation(s)
- Sebastiaan Valkiers
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium
| | - Sofie Gielis
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium
| | - Vincent M L Van Deuren
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium
| | - Kris Laukens
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium
| | - Pieter Meysman
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium.
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium.
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22
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Safra M, Werner L, Peres A, Polak P, Salamon N, Schvimer M, Weiss B, Barshack I, Shouval DS, Yaari G. A somatic hypermutation-based machine learning model stratifies individuals with Crohn's disease and controls. Genome Res 2023; 33:71-79. [PMID: 36526432 PMCID: PMC9977146 DOI: 10.1101/gr.276683.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022]
Abstract
Crohn's disease (CD) is a chronic relapsing-remitting inflammatory disorder of the gastrointestinal tract that is characterized by altered innate and adaptive immune function. Although massively parallel sequencing studies of the T cell receptor repertoire identified oligoclonal expansion of unique clones, much less is known about the B cell receptor (BCR) repertoire in CD. Here, we present a novel BCR repertoire sequencing data set from ileal biopsies from pediatric patients with CD and controls, and identify CD-specific somatic hypermutation (SHM) patterns, revealed by a machine learning (ML) algorithm trained on BCR repertoire sequences. Moreover, ML classification of a different data set from blood samples of adults with CD versus controls identified that V gene usage, clusters, or mutation frequencies yielded excellent results in classifying the disease (F1 > 90%). In summary, we show that an ML algorithm enables the classification of CD based on unique BCR repertoire features with high accuracy.
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Affiliation(s)
- Modi Safra
- The Alexander Kofkin Faculty of Engineering, Bar Ilan University, 5290002, Ramat Gan, Israel;,Bar Ilan Institute of Nanotechnology and Advanced Materials, Bar Ilan University, 5290002, Ramat Gan, Israel
| | - Lael Werner
- Institute of Gastroenterology, Nutrition and Liver Diseases, Schneider Children's Medical Center of Israel, Petah Tikva 4920235, Israel;,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Ayelet Peres
- The Alexander Kofkin Faculty of Engineering, Bar Ilan University, 5290002, Ramat Gan, Israel;,Bar Ilan Institute of Nanotechnology and Advanced Materials, Bar Ilan University, 5290002, Ramat Gan, Israel
| | - Pazit Polak
- The Alexander Kofkin Faculty of Engineering, Bar Ilan University, 5290002, Ramat Gan, Israel;,Bar Ilan Institute of Nanotechnology and Advanced Materials, Bar Ilan University, 5290002, Ramat Gan, Israel
| | - Naomi Salamon
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan 5262100, Israel
| | - Michael Schvimer
- Institute of Pathology, Sheba Medical Center, Ramat Gan 5262100, Israel
| | - Batia Weiss
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel;,Pediatric Gastroenterology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan 5262100, Israel
| | - Iris Barshack
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel;,Institute of Pathology, Sheba Medical Center, Ramat Gan 5262100, Israel
| | - Dror S. Shouval
- Institute of Gastroenterology, Nutrition and Liver Diseases, Schneider Children's Medical Center of Israel, Petah Tikva 4920235, Israel;,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Gur Yaari
- The Alexander Kofkin Faculty of Engineering, Bar Ilan University, 5290002, Ramat Gan, Israel;,Bar Ilan Institute of Nanotechnology and Advanced Materials, Bar Ilan University, 5290002, Ramat Gan, Israel
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23
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Olson BJ, Schattgen SA, Thomas PG, Bradley P, Matsen IV FA. Comparing T cell receptor repertoires using optimal transport. PLoS Comput Biol 2022; 18:e1010681. [PMID: 36476997 PMCID: PMC9728925 DOI: 10.1371/journal.pcbi.1010681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 10/24/2022] [Indexed: 12/12/2022] Open
Abstract
The complexity of entire T cell receptor (TCR) repertoires makes their comparison a difficult but important task. Current methods of TCR repertoire comparison can incur a high loss of distributional information by considering overly simplistic sequence- or repertoire-level characteristics. Optimal transport methods form a suitable approach for such comparison given some distance or metric between values in the sample space, with appealing theoretical and computational properties. In this paper we introduce a nonparametric approach to comparing empirical TCR repertoires that applies the Sinkhorn distance, a fast, contemporary optimal transport method, and a recently-created distance between TCRs called TCRdist. We show that our methods identify meaningful differences between samples from distinct TCR distributions for several case studies, and compete with more complicated methods despite minimal modeling assumptions and a simpler pipeline.
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Affiliation(s)
- Branden J. Olson
- Department of Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Statistics, University of Washington, Seattle, Washington, United States of America
| | - Stefan A. Schattgen
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Paul G. Thomas
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Philip Bradley
- Department of Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Institute for Protein Design, Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
- * E-mail: (PB); (FAM)
| | - Frederick A. Matsen IV
- Department of Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Statistics, University of Washington, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Seattle, Washington, United States of America
- * E-mail: (PB); (FAM)
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24
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Komech EA, Koltakova AD, Barinova AA, Minervina AA, Salnikova MA, Shmidt EI, Korotaeva TV, Loginova EY, Erdes SF, Bogdanova EA, Shugay M, Lukyanov S, Lebedev YB, Zvyagin IV. TCR repertoire profiling revealed antigen-driven CD8+ T cell clonal groups shared in synovial fluid of patients with spondyloarthritis. Front Immunol 2022; 13:973243. [PMID: 36325356 PMCID: PMC9618624 DOI: 10.3389/fimmu.2022.973243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 09/26/2022] [Indexed: 11/16/2022] Open
Abstract
Spondyloarthritis (SpA) comprises a number of inflammatory rheumatic diseases with overlapping clinical manifestations. Strong association with several HLA-I alleles and T cell infiltration into an inflamed joint suggest involvement of T cells in SpA pathogenesis. In this study, we performed high-throughput T cell repertoire profiling of synovial fluid (SF) and peripheral blood (PB) samples collected from a large cohort of SpA patients. We showed that synovial fluid is enriched with expanded T cell clones that are shared between patients with similar HLA genotypes and persist during recurrent synovitis. Using an algorithm for identification of TCRs involved in immune response we discovered several antigen-driven CD8+ clonal groups associated with risk HLA-B*27 or HLA-B*38 alleles. We further show that these clonal groups were enriched in SF and had higher frequency in PB of SpA patients vs healthy donors, implying their relevance to SpA pathogenesis. Several of the groups were shared among patients with different SpAs that suggests a common immunopathological mechanism of the diseases. In summary, our results provide evidence for the role of specific CD8+ T cell clones in pathogenesis of SpA.
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Affiliation(s)
- Ekaterina A. Komech
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Anastasia D. Koltakova
- Department of Systemic Sclerosis, Nasonova Research Institute of Rheumatology, Moscow, Russia
| | - Anna A. Barinova
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Anastasia A. Minervina
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Maria A. Salnikova
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Evgeniya I. Shmidt
- Department of Rheumatology, Pirogov City Clinical Hospital #1, Moscow, Russia
| | - Tatiana V. Korotaeva
- Department of Spondyloarthritis, Nasonova Research Institute of Rheumatology, Moscow, Russia
| | - Elena Y. Loginova
- Department of Spondyloarthritis, Nasonova Research Institute of Rheumatology, Moscow, Russia
| | - Shandor F. Erdes
- Department of Spondyloarthritis, Nasonova Research Institute of Rheumatology, Moscow, Russia
| | - Ekaterina A. Bogdanova
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Mikhail Shugay
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Sergey Lukyanov
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Yury B. Lebedev
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Ivan V. Zvyagin
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
- *Correspondence: Ivan V. Zvyagin,
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25
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Koraichi MB, Touzel MP, Mazzolini A, Mora T, Walczak AM. NoisET: Noise Learning and Expansion Detection of T-Cell Receptors. J Phys Chem A 2022; 126:7407-7414. [PMID: 36178325 DOI: 10.1021/acs.jpca.2c05002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
High-throughput sequencing of T- and B-cell receptors makes it possible to track immune repertoires across time, in different tissues, in acute and chronic diseases and in healthy individuals. However, quantitative comparison between repertoires is confounded by variability in the read count of each receptor clonotype due to sampling, library preparation, and expression noise. We review methods for accounting for both biological and experimental noise and present an easy-to-use python package NoisET that implements and generalizes a previously developed Bayesian method. It can be used to learn experimental noise models for repertoire sequencing from replicates, and to detect responding clones following a stimulus. We test the package on different repertoire sequencing technologies and data sets. We review how such approaches have been used to identify responding clonotypes in vaccination and disease data. Availability: NoisET is freely available to use with source code at github.com/statbiophys/NoisET.
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Affiliation(s)
- Meriem Bensouda Koraichi
- Laboratoire de physique de l' École normale supérieure, CNRS, PSL University, Sorbonne Université, and Université de Paris, Paris75005, France
| | | | - Andrea Mazzolini
- Laboratoire de physique de l' École normale supérieure, CNRS, PSL University, Sorbonne Université, and Université de Paris, Paris75005, France
| | - Thierry Mora
- Laboratoire de physique de l' École normale supérieure, CNRS, PSL University, Sorbonne Université, and Université de Paris, Paris75005, France
| | - Aleksandra M Walczak
- Laboratoire de physique de l' École normale supérieure, CNRS, PSL University, Sorbonne Université, and Université de Paris, Paris75005, France
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26
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Sycheva AL, Komech EA, Pogorelyy MV, Minervina AA, Urazbakhtin SZ, Salnikova MA, Vorovitch MF, Kopantzev EP, Zvyagin IV, Komkov AY, Mamedov IZ, Lebedev YB. Inactivated tick-borne encephalitis vaccine elicits several overlapping waves of T cell response. Front Immunol 2022; 13:970285. [PMID: 36091004 PMCID: PMC9449805 DOI: 10.3389/fimmu.2022.970285] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 08/05/2022] [Indexed: 12/02/2022] Open
Abstract
The development and implementation of vaccines have been growing exponentially, remaining one of the major successes of healthcare over the last century. Nowadays, active regular immunizations prevent epidemics of many viral diseases, including tick-borne encephalitis (TBE). Along with the generation of virus-specific antibodies, a highly effective vaccine should induce T cell responses providing long-term immune defense. In this study, we performed longitudinal high-throughput T cell receptor (TCR) sequencing to characterize changes in individual T cell repertoires of 11 donors immunized with an inactivated TBE vaccine. After two-step immunization, we found significant clonal expansion of both CD4+ and CD8+ T cells, ranging from 302 to 1706 vaccine-associated TCRβ clonotypes in different donors. We detected several waves of T cell clonal expansion generated by distinct groups of vaccine-responding clones. Both CD4+ and CD8+ vaccine-responding T cell clones formed 17 motifs in TCRβ sequences shared by donors with identical HLA alleles. Our results indicate that TBE vaccination leads to a robust T cell response due to the production of a variety of T cell clones with a memory phenotype, which recognize a large set of epitopes.
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Affiliation(s)
- Anastasiia L. Sycheva
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
- *Correspondence: Anastasiia L. Sycheva, ; Yuri B. Lebedev,
| | - Ekaterina A. Komech
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
- Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Mikhail V. Pogorelyy
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Anastasia A. Minervina
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Shamil Z. Urazbakhtin
- Computational Systems Biochemistry Research Group, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Maria A. Salnikova
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
- Department of Immunology, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Mikhail F. Vorovitch
- Laboratory of Tick-Borne Encephalitis and Other Encephalitis, Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS (FSASI “Chumakov FSC R&D IBP RAS”), Moscow, Russia
- Department of Organization and Technology of Production of Immune-and-Biological Products, Institute for Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Eugene P. Kopantzev
- Department of Genomics and Postgenomic Technologies, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
| | - Ivan V. Zvyagin
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
- Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Alexander Y. Komkov
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
- Laboratory of Cytogenetics and Molecular Genetics, Dmitry Rogachev National Medical and Research Centre of Paediatric Haematology, Oncology and Immunology, Moscow, Russia
| | - Ilgar Z. Mamedov
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
| | - Yuri B. Lebedev
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
- Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
- *Correspondence: Anastasiia L. Sycheva, ; Yuri B. Lebedev,
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27
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Trofimov A, Brouillard P, Larouche JD, Séguin J, Laverdure JP, Brasey A, Ehx G, Roy DC, Busque L, Lachance S, Lemieux S, Perreault C. Two types of human TCR differentially regulate reactivity to self and non-self antigens. iScience 2022; 25:104968. [PMID: 36111255 PMCID: PMC9468382 DOI: 10.1016/j.isci.2022.104968] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/24/2022] [Accepted: 08/12/2022] [Indexed: 11/30/2022] Open
Abstract
Based on analyses of TCR sequences from over 1,000 individuals, we report that the TCR repertoire is composed of two ontogenically and functionally distinct types of TCRs. Their production is regulated by variations in thymic output and terminal deoxynucleotidyl transferase (TDT) activity. Neonatal TCRs derived from TDT-negative progenitors persist throughout life, are highly shared among subjects, and are reported as disease-associated. Thus, 10%–30% of most frequent cord blood TCRs are associated with common pathogens and autoantigens. TDT-dependent TCRs present distinct structural features and are less shared among subjects. TDT-dependent TCRs are produced in maximal numbers during infancy when thymic output and TDT activity reach a summit, are more abundant in subjects with AIRE mutations, and seem to play a dominant role in graft-versus-host disease. Factors decreasing thymic output (age, male sex) negatively impact TCR diversity. Males compensate for their lower repertoire diversity via hyperexpansion of selected TCR clonotypes. Over 108 TCR CDR3 sequences from ∼103 individuals and 7 cohorts were analyzed The TCR repertoire is composed of two layers: neonatal and TDT-dependent layer ∼70% of frequent cord blood TCRs are associated with common pathogens Acute graft-vs-host disease correlates with a high proportion of TDT-dependent TCRs
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Affiliation(s)
- Assya Trofimov
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, Quebec H3C 3J7, Canada
- Department of Computer Science and Research Operations, Université de Montréal, Montreal, Quebec H3C 3J7, Canada
- Quebec Institute for Learning Algorithms (Mila), Montreal, Quebec H2S 3H1, Canada
- Currently Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Currently Department of Physics, University of Washington, Seattle, WA 98195-1560, USA
| | - Philippe Brouillard
- Department of Computer Science and Research Operations, Université de Montréal, Montreal, Quebec H3C 3J7, Canada
- Quebec Institute for Learning Algorithms (Mila), Montreal, Quebec H2S 3H1, Canada
| | - Jean-David Larouche
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, Quebec H3C 3J7, Canada
- Department of Medicine, Université de Montréal, Montreal, Quebec H3C 3J7, Canada
| | - Jonathan Séguin
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, Quebec H3C 3J7, Canada
| | - Jean-Philippe Laverdure
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, Quebec H3C 3J7, Canada
| | - Ann Brasey
- Maisonneuve-Rosemont Hospital, Montreal, Quebec H1T 2M4, Canada
| | - Gregory Ehx
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, Quebec H3C 3J7, Canada
- Currently Interdisciplinary Cluster for Applied Geno-Proteomics (GIGA-I3), University of Liege, Liege 4000, Belgium
| | | | - Lambert Busque
- Maisonneuve-Rosemont Hospital, Montreal, Quebec H1T 2M4, Canada
| | - Silvy Lachance
- Department of Medicine, Université de Montréal, Montreal, Quebec H3C 3J7, Canada
- Maisonneuve-Rosemont Hospital, Montreal, Quebec H1T 2M4, Canada
| | - Sébastien Lemieux
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, Quebec H3C 3J7, Canada
- Department of Computer Science and Research Operations, Université de Montréal, Montreal, Quebec H3C 3J7, Canada
- Department of Biochemistry at University of Montreal, Université de Montréal, Montreal, Quebec H3C 3J7, Canada
- Corresponding author
| | - Claude Perreault
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, Quebec H3C 3J7, Canada
- Department of Medicine, Université de Montréal, Montreal, Quebec H3C 3J7, Canada
- Maisonneuve-Rosemont Hospital, Montreal, Quebec H1T 2M4, Canada
- Corresponding author
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28
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Mark M, Reich-Zeliger S, Greenstein E, Reshef D, Madi A, Chain B, Friedman N. A hierarchy of selection pressures determines the organization of the T cell receptor repertoire. Front Immunol 2022; 13:939394. [PMID: 35967295 PMCID: PMC9372880 DOI: 10.3389/fimmu.2022.939394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 07/06/2022] [Indexed: 11/13/2022] Open
Abstract
We systematically examine the receptor repertoire in T cell subsets in young, adult, and LCMV-infected mice. Somatic recombination generates diversity, resulting in the limited overlap between nucleotide sequences of different repertoires even within the same individual. However, statistical features of the repertoire, quantified by the V gene and CDR3 k-mer frequency distributions, are highly conserved. A hierarchy of immunological processes drives the evolution of this structure. Intra-thymic divergence of CD4+ and CD8+ lineages imposes subtle but dominant differences observed across repertoires of all subpopulations in both young and adult mice. Differentiation from naive through memory to effector phenotype imposes an additional gradient of repertoire diversification, which is further influenced by age in a complex and lineage-dependent manner. The distinct repertoire of CD4+ regulatory T cells is more similar to naive cells in young mice and to effectors in adults. Finally, we describe divergent (naive and memory) and convergent (CD8+ effector) evolution of the repertoire following acute infection with LCMV. This study presents a quantitative framework that captures the structure of the repertoire in terms of its fundamental statistical properties and describes how this structure evolves as individual T cells differentiate, migrate and mature in response to antigen exposure.
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Affiliation(s)
- Michal Mark
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
- *Correspondence: Michal Mark, ; Benny Chain,
| | | | - Erez Greenstein
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Dan Reshef
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Asaf Madi
- Department of Pathology, Tel-Aviv University, Tel-Aviv, Israel
| | - Benny Chain
- Department of Computer Science, University College London, UCL, London, United Kingdom
- *Correspondence: Michal Mark, ; Benny Chain,
| | - Nir Friedman
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
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29
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Katayama Y, Yokota R, Akiyama T, Kobayashi TJ. Machine Learning Approaches to TCR Repertoire Analysis. Front Immunol 2022; 13:858057. [PMID: 35911778 PMCID: PMC9334875 DOI: 10.3389/fimmu.2022.858057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
Sparked by the development of genome sequencing technology, the quantity and quality of data handled in immunological research have been changing dramatically. Various data and database platforms are now driving the rapid progress of machine learning for immunological data analysis. Of various topics in immunology, T cell receptor repertoire analysis is one of the most important targets of machine learning for assessing the state and abnormalities of immune systems. In this paper, we review recent repertoire analysis methods based on machine learning and deep learning and discuss their prospects.
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Affiliation(s)
- Yotaro Katayama
- Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
- *Correspondence: Yotaro Katayama,
| | - Ryo Yokota
- National Research Institute of Police Science, Kashiwa, Chiba, Japan
| | - Taishin Akiyama
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Tetsuya J. Kobayashi
- Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
- Institute of Industrial Science, The University of Tokyo, Tokyo, Japan
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30
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Chang CM, Peng KY, Chan CK, Lin YF, Liao HW, Chang JG, Wu MS, Wu VC, Chang WC. Divergent Characteristics of T-Cell Receptor Repertoire Between Essential Hypertension and Aldosterone-Producing Adenoma. Front Immunol 2022; 13:853403. [PMID: 35619691 PMCID: PMC9127864 DOI: 10.3389/fimmu.2022.853403] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 04/06/2022] [Indexed: 11/13/2022] Open
Abstract
Aldosterone-producing adenoma (APA) is a benign adrenal tumor that results in persistent hyperaldosteronism. As one major subtype of primary aldosteronism, APA leads to secondary hypertension that is associated with immune dysregulation. However, how the adaptive immune system, particularly the T-cell population, is altered in APA patients remains largely unknown. Here, we performed TCR sequencing to characterize the TCR repertoire between two age-matched groups of patients: one with APA and the other one with essential hypertension (EH). Strikingly, we found a significant reduction of TCR repertoire diversity in the APA group. Analyses on TCR clustering and antigen annotation further showed that the APA group possessed lower diversity in TCR clonotypes with non-common antigen-specific features, compared with the EH group. In addition, our results indicated that the strength of correlation between generation probabilities and frequencies of TCR clonotypes was significantly higher in the APA group than that in the EH group. Finally, we observed that clinical features, including plasma aldosterone level, aldosterone–renin ratio, and blood sodium level, were positively associated with the strength of correlation between generation and abundance of TCR clonotypes in the APA group. Our findings unveiled the correlation between T-cell immune repertoire and APA, suggesting a critical role of such adrenal adenoma in the T-cell immunity of patients with hypertension.
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Affiliation(s)
- Che-Mai Chang
- Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Kang-Yung Peng
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.,TAIPAI, Taiwan Primary Aldosteronism Investigation (TAIPAI) Study Group, Taipei, Taiwan
| | - Chieh-Kai Chan
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Yu-Feng Lin
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Hung-Wei Liao
- Chinru Clinic, Department of Nephrology, Taipei, Taiwan
| | - Jan-Gowth Chang
- Epigenome Research Center, China Medical University Hospital, Taichung, Taiwan.,School of Medicine, China Medical University, Taichung, Taiwan
| | - Mai-Szu Wu
- Division of Nephrology, Department of Internal Medicine, Taipei Medical University-Shuang Ho Hospital, New Taipei City, Taiwan.,Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.,TMU-Research Center of Urology and Kidney (TMU-RCUK), Taipei Medical University, Taipei, Taiwan
| | - Vin-Cent Wu
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.,TAIPAI, Taiwan Primary Aldosteronism Investigation (TAIPAI) Study Group, Taipei, Taiwan.,Division of Nephrology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Wei-Chiao Chang
- Master Program in Clinical Pharmacogenomics and Pharmacoproteomics, School of Pharmacy, Taipei Medical University, Taipei, Taiwan.,Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan.,Integrative Research Center for Critical Care, Department of Pharmacy, Wanfang Hospital, Taipei Medical University, Taipei, Taiwan.,Department of Medical Research, Taipei Medical University-Shuang Ho Hospital, New Taipei City, Taiwan
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31
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Goncharov MM, Bryushkova EA, Sharaev NI, Skatova VD, Baryshnikova AM, Sharonov GV, Karnaukhov V, Vakhitova MT, Samoylenko IV, Demidov LV, Lukyanov S, Chudakov DM, Serebrovskaya EO. Pinpointing the tumor-specific T-cells via TCR clusters. eLife 2022; 11:77274. [PMID: 35377314 PMCID: PMC9023053 DOI: 10.7554/elife.77274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Abstract
Adoptive cell transfer (ACT) is a promising approach to cancer immunotherapy, but its efficiency fundamentally depends on the extent of tumor-specific T cell enrichment within the graft. This can be estimated via activation with identifiable neoantigens, tumor-associated antigens (TAAs), or living or lysed tumor cells, but these approaches remain laborious, time-consuming, and functionally limited, hampering clinical development of ACT. Here, we demonstrate that homology cluster analysis of T cell receptor (TCR) repertoires efficiently identifies tumor-reactive TCRs allowing to: (1) detect their presence within the pool of tumor-infiltrating lymphocytes (TILs); (2) optimize TIL culturing conditions, with IL-2low/IL-21/anti-PD-1 combination showing increased efficiency; (3) investigate surface marker-based enrichment for tumor-targeting T cells in freshly isolated TILs (enrichment confirmed for CD4+ and CD8+ PD-1+/CD39+ subsets), or re-stimulated TILs (informs on enrichment in 4-1BB-sorted cells). We believe that this approach to the rapid assessment of tumor-specific TCR enrichment should accelerate T cell therapy development.
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Affiliation(s)
- Mikhail M Goncharov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russian Federation
| | | | - Nikita I Sharaev
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russian Federation
| | - Valeria D Skatova
- Pirogov Russian National Research Medical University, Moscow, Russian Federation
| | - Anastasiya M Baryshnikova
- Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
| | - George V Sharonov
- Pirogov Russian National Research Medical University, Moscow, Russian Federation
| | - Vadim Karnaukhov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russian Federation
| | - Maria T Vakhitova
- Pirogov Russian National Research Medical University, Moscow, Russian Federation
| | - Igor V Samoylenko
- Oncodermatology Department, NN Blokhin Russian Cancer Research Center, Moscow, Russian Federation
| | - Lev V Demidov
- Oncodermatology Department, NN Blokhin Russian Cancer Research Center, Moscow, Russian Federation
| | - Sergey Lukyanov
- Pirogov Russian National Research Medical University, Moscow, Russian Federation
| | - Dmitriy M Chudakov
- Department of genomics of adaptive immunity, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
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32
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Teng YHF, Quah HS, Suteja L, Dias JML, Mupo A, Bashford-Rogers RJM, Vassiliou GS, Chua MLK, Tan DSW, Lim DWT, Iyer NG. Analysis of T cell receptor clonotypes in tumor microenvironment identifies shared cancer-type-specific signatures. Cancer Immunol Immunother 2022; 71:989-998. [PMID: 34580764 PMCID: PMC8476067 DOI: 10.1007/s00262-021-03047-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 08/25/2021] [Indexed: 12/02/2022]
Abstract
Despite the conventional view that a truly random V(D)J recombination process should generate a highly diverse immune repertoire, emerging reports suggest that there is a certain bias toward the generation of shared/public immune receptor chains. These studies were performed in viral diseases where public T cell receptors (TCR) appear to confer better protective responses. Selective pressures generating common TCR clonotypes are currently not well understood, but it is believed that they confer a growth advantage. As very little is known about public TCR clonotypes in cancer, here we set out to determine the extent of shared TCR clonotypes in the intra-tumor microenvironments of virus- and non-virus-driven head and neck cancers using TCR sequencing. We report that tumor-infiltrating T cell clonotypes were indeed shared across individuals with the same cancer type, where the majority of shared sequences were specific to the cancer type (i.e., viral versus non-viral). These shared clonotypes were not particularly enriched in EBV-associated nasopharynx cancer but, in both cancers, exhibited distinct characteristics, namely shorter CDR3 lengths, restricted V- and J-gene usages, and also demonstrated convergent V(D)J recombination. Many of these shared TCRs were expressed in patients with a shared HLA background. Pattern recognition of CDR3 amino acid sequences revealed strong convergence to specific pattern motifs, and these motifs were uniquely found to each cancer type. This suggests that they may be enriched for specificity to common antigens found in the tumor microenvironment of different cancers. The identification of shared TCRs in infiltrating tumor T cells not only adds to our understanding of the tumor-adaptive immune recognition but could also serve as disease-specific biomarkers and guide the development of future immunotherapies.
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Affiliation(s)
- Yvonne H. F. Teng
- Cancer Therapeutics Research Laboratory, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610 Singapore
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Hong Sheng Quah
- Cancer Therapeutics Research Laboratory, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610 Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Lisda Suteja
- Cancer Therapeutics Research Laboratory, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610 Singapore
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - João M. L. Dias
- Hutchison/MRC Research Centre, MRC Cancer Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XZ UK
| | | | | | - George S. Vassiliou
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge Biomedical Campus, Puddicombe Way, Cambridge, CB2 0AW UK
| | - Melvin L. K. Chua
- Duke-NUS Medical School, Singapore, Singapore
- Division of Radiation Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Daniel S. W. Tan
- Cancer Therapeutics Research Laboratory, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610 Singapore
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Darren W. T. Lim
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
- Institute of Molecular and Cell Biology, A-STAR, Singapore, Singapore
| | - N. Gopalakrishna Iyer
- Cancer Therapeutics Research Laboratory, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610 Singapore
- Duke-NUS Medical School, Singapore, Singapore
- Department of Head and Neck Surgery, National Cancer Centre Singapore, Singapore, Singapore
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33
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Russell ML, Souquette A, Levine DM, Schattgen SA, Allen EK, Kuan G, Simon N, Balmaseda A, Gordon A, Thomas PG, Matsen FA, Bradley P. Combining genotypes and T cell receptor distributions to infer genetic loci determining V(D)J recombination probabilities. eLife 2022; 11:73475. [PMID: 35315770 PMCID: PMC8940181 DOI: 10.7554/elife.73475] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 01/17/2022] [Indexed: 12/12/2022] Open
Abstract
Every T cell receptor (TCR) repertoire is shaped by a complex probabilistic tangle of genetically determined biases and immune exposures. T cells combine a random V(D)J recombination process with a selection process to generate highly diverse and functional TCRs. The extent to which an individual’s genetic background is associated with their resulting TCR repertoire diversity has yet to be fully explored. Using a previously published repertoire sequencing dataset paired with high-resolution genome-wide genotyping from a large human cohort, we infer specific genetic loci associated with V(D)J recombination probabilities using genome-wide association inference. We show that V(D)J gene usage profiles are associated with variation in the TCRB locus and, specifically for the functional TCR repertoire, variation in the major histocompatibility complex locus. Further, we identify specific variations in the genes encoding the Artemis protein and the TdT protein to be associated with biasing junctional nucleotide deletion and N-insertion, respectively. These results refine our understanding of genetically-determined TCR repertoire biases by confirming and extending previous studies on the genetic determinants of V(D)J gene usage and providing the first examples of trans genetic variants which are associated with modifying junctional diversity. Together, these insights lay the groundwork for further explorations into how immune responses vary between individuals.
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Affiliation(s)
- Magdalena L Russell
- Computational Biology Program, Fred Hutch Cancer Research Center
- Molecular and Cellular Biology Program, University of Washington
| | - Aisha Souquette
- Department of Immunology, St. Jude Children’s Research Hospital
- Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center
| | | | | | | | - Guillermina Kuan
- Centro Nacional de Diagnóstico y Referencia, Ministry of Health
- Sustainable Sciences Institute
| | - Noah Simon
- Department of Biostatistics, University of Washington
| | - Angel Balmaseda
- Centro Nacional de Diagnóstico y Referencia, Ministry of Health
- Sustainable Sciences Institute
| | | | - Paul G Thomas
- Department of Immunology, St. Jude Children’s Research Hospital
| | - Frederick A Matsen
- Computational Biology Program, Fred Hutch Cancer Research Center
- Department of Genome Sciences, University of Washington
- Department of Statistics, University of Washington
- Howard Hughes Medical Institute
| | - Philip Bradley
- Computational Biology Program, Fred Hutch Cancer Research Center
- Institute for Protein Design, Department of Biochemistry, University of Washington
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34
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Gerdemann U, Fleming RA, Kaminski J, McGuckin C, Rui X, Lane JF, Keskula P, Cagnin L, Shalek AK, Tkachev V, Kean LS. Identification and Tracking of Alloreactive T Cell Clones in Rhesus Macaques Through the RM-scTCR-Seq Platform. Front Immunol 2022; 12:804932. [PMID: 35154078 PMCID: PMC8825351 DOI: 10.3389/fimmu.2021.804932] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 12/22/2021] [Indexed: 01/14/2023] Open
Abstract
T cell receptor (TCR) clonotype tracking is a powerful tool for interrogating T cell mediated immune processes. New methods to pair a single cell's transcriptional program with its TCR identity allow monitoring of T cell clonotype-specific transcriptional dynamics. While these technologies have been available for human and mouse T cells studies, they have not been developed for Rhesus Macaques (RM), a critical translational organism for autoimmune diseases, vaccine development and transplantation. We describe a new pipeline, 'RM-scTCR-Seq', which, for the first time, enables RM specific single cell TCR amplification, reconstruction and pairing of RM TCR's with their transcriptional profiles. We apply this method to a RM model of GVHD, and identify and track in vitro detected alloreactive clonotypes in GVHD target organs and explore their GVHD driven cytotoxic T cell signature. This novel, state-of-the-art platform fundamentally advances the utility of RM to study protective and pathogenic T cell responses.
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Affiliation(s)
- Ulrike Gerdemann
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, United States
| | - Ryan A Fleming
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, United States
| | - James Kaminski
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, United States.,Broad Institute of MIT and Harvard, Cambridge, MA, United States.,Department of Chemistry, Institute for Medical Engineering and Science (IMES), and Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, United States.,Ragon Institute of Massachusetts General Hospital (MGH), MIT and Harvard, Cambridge, MA, United States
| | - Connor McGuckin
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, United States
| | - Xianliang Rui
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, United States
| | - Jennifer F Lane
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, United States
| | - Paula Keskula
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, United States
| | - Lorenzo Cagnin
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, United States
| | - Alex K Shalek
- Broad Institute of MIT and Harvard, Cambridge, MA, United States.,Department of Chemistry, Institute for Medical Engineering and Science (IMES), and Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, United States.,Ragon Institute of Massachusetts General Hospital (MGH), MIT and Harvard, Cambridge, MA, United States
| | - Victor Tkachev
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, United States
| | - Leslie S Kean
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, United States
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35
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Elias G, Meysman P, Bartholomeus E, De Neuter N, Keersmaekers N, Suls A, Jansens H, Souquette A, De Reu H, Emonds MP, Smits E, Lion E, Thomas PG, Mortier G, Van Damme P, Beutels P, Laukens K, Van Tendeloo V, Ogunjimi B. Preexisting memory CD4 T cells in naïve individuals confer robust immunity upon hepatitis B vaccination. eLife 2022; 11:68388. [PMID: 35074048 PMCID: PMC8824481 DOI: 10.7554/elife.68388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 01/07/2022] [Indexed: 11/22/2022] Open
Abstract
Antigen recognition through the T cell receptor (TCR) αβ heterodimer is one of the primary determinants of the adaptive immune response. Vaccines activate naïve T cells with high specificity to expand and differentiate into memory T cells. However, antigen-specific memory CD4 T cells exist in unexposed antigen-naïve hosts. In this study, we use high-throughput sequencing of memory CD4 TCRβ repertoire and machine learning to show that individuals with preexisting vaccine-reactive memory CD4 T cell clonotypes elicited earlier and higher antibody titers and mounted a more robust CD4 T cell response to hepatitis B vaccine. In addition, integration of TCRβ sequence patterns into a hepatitis B epitope-specific annotation model can predict which individuals will have an early and more vigorous vaccine-elicited immunity. Thus, the presence of preexisting memory T cell clonotypes has a significant impact on immunity and can be used to predict immune responses to vaccination. Immune cells called CD4 T cells help the body build immunity to infections caused by bacteria and viruses, or after vaccination. Receptor proteins on the outside of the cells recognize pathogens, foreign molecules called antigens, or vaccine antigens. Vaccine antigens are usually inactivated bacteria or viruses, or fragments of these pathogens. After recognizing an antigen, CD4 T cells develop into memory CD4 T cells ready to defend against future infections with the pathogen. People who have never been exposed to a pathogen, or have never been vaccinated against it, may nevertheless have preexisting memory cells ready to defend against it. This happens because CD4 T cells can recognize multiple targets, which enables the immune system to be ready to defend against both new and familiar pathogens. Elias, Meysman, Bartholomeus et al. wanted to find out whether having preexisting memory CD4 T cells confers an advantage for vaccine-induced immunity. Thirty-four people who were never exposed to hepatitis B or vaccinated against it participated in the study. These individuals provided blood samples before vaccination, with 2 doses of the hepatitis B vaccine, and at 3 time points afterward. Using next generation immune sequencing and machine learning techniques, Elias et al. analyzed the individuals’ memory CD4 T cells before and after vaccination. The experiments showed that preexisting memory CD4 T cells may determine vaccination outcomes, and people with more preexisting memory cells develop quicker and stronger immunity after vaccination against hepatitis B. This information may help scientists to better understand how people develop immunity to pathogens. It may guide them develop better vaccines or predict who will develop immunity after vaccination.
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Affiliation(s)
- George Elias
- Laboratory of Experimental Hematology (LEH), University of Antwerp
| | - Pieter Meysman
- Biomedical Informatics Research Network Antwerp, Department of Mathematics and Informatics, University of Antwerp
| | | | - Nicolas De Neuter
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp
| | - Nina Keersmaekers
- Centre for Health Economics Research & Modeling Infectious Diseases, University of Antwerp
| | - Arvid Suls
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp
| | - Hilde Jansens
- Department of Clinical Microbiology, Antwerp University Hospital
| | - Aisha Souquette
- Department of Immunology, St. Jude Children's Research Hospital
| | - Hans De Reu
- Laboratory of Experimental Hematology, University of Antwerp
| | | | - Evelien Smits
- Laboratory of Experimental Hematology, University of Antwerp
| | - Eva Lion
- Laboratory of Experimental Hematology, University of Antwerp
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital
| | - Geert Mortier
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp
| | - Pierre Van Damme
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp
| | - Philippe Beutels
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp
| | - Kris Laukens
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp
| | - Viggo Van Tendeloo
- Janssen Research and Development, Immunosciences WWDA, Johnson and Johnson
| | - Benson Ogunjimi
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp
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36
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Marquez S, Babrak L, Greiff V, Hoehn KB, Lees WD, Luning Prak ET, Miho E, Rosenfeld AM, Schramm CA, Stervbo U. Adaptive Immune Receptor Repertoire (AIRR) Community Guide to Repertoire Analysis. Methods Mol Biol 2022; 2453:297-316. [PMID: 35622333 PMCID: PMC9761518 DOI: 10.1007/978-1-0716-2115-8_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Adaptive immune receptor repertoires (AIRRs) are rich with information that can be mined for insights into the workings of the immune system. Gene usage, CDR3 properties, clonal lineage structure, and sequence diversity are all capable of revealing the dynamic immune response to perturbation by disease, vaccination, or other interventions. Here we focus on a conceptual introduction to the many aspects of repertoire analysis and orient the reader toward the uses and advantages of each. Along the way, we note some of the many software tools that have been developed for these investigations and link the ideas discussed to chapters on methods provided elsewhere in this volume.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Chaim A Schramm
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Ulrik Stervbo
- Center for Translational Medicine, Immunology, and Transplantation, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Herne, Germany. .,Immundiagnostik, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Herne, Germany.
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37
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Aschauer C, Jelencsics K, Hu K, Heinzel A, Gregorich MG, Vetter J, Schaller S, Winkler SM, Weinberger J, Pimenov L, Gualdoni GA, Eder M, Kainz A, Troescher AR, Regele H, Reindl-Schwaighofer R, Wekerle T, Huppa JB, Sykes M, Oberbauer R. Prospective Tracking of Donor-Reactive T-Cell Clones in the Circulation and Rejecting Human Kidney Allografts. Front Immunol 2021; 12:750005. [PMID: 34721420 PMCID: PMC8552542 DOI: 10.3389/fimmu.2021.750005] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/20/2021] [Indexed: 11/13/2022] Open
Abstract
Background Antigen recognition of allo-peptides and HLA molecules leads to the activation of donor-reactive T-cells following transplantation, potentially causing T-cell-mediated rejection (TCMR). Sequencing of the T-cell receptor (TCR) repertoire can be used to track the donor-reactive repertoire in blood and tissue of patients after kidney transplantation. Methods/Design In this prospective cohort study, 117 non-sensitized kidney transplant recipients with anti-CD25 induction were included. Peripheral mononuclear cells (PBMCs) were sampled pre-transplant and at the time of protocol or indication biopsies together with graft tissue. Next-generation sequencing (NGS) of the CDR3 region of the TCRbeta chain was performed after donor stimulation in mixed lymphocyte reactions to define the donor-reactive TCR repertoire. Blood and tissue of six patients experiencing a TCMR and six patients without rejection on protocol biopsies were interrogated for these TCRs. To elucidate common features of T-cell clonotypes, a network analysis of the TCR repertoires was performed. Results After transplantation, the frequency of circulating donor-reactive CD4 T-cells increased significantly from 0.86 ± 0.40% to 2.06 ± 0.40% of all CD4 cells (p < 0.001, mean dif.: -1.197, CI: -1.802, -0.593). The number of circulating donor-reactive CD4 clonotypes increased from 0.72 ± 0.33% to 1.89 ± 0.33% (p < 0.001, mean dif.: -1.168, CI: -1.724, -0.612). No difference in the percentage of donor-reactive T-cells in the circulation at transplant biopsy was found between subjects experiencing a TCMR and the control group [p = 0.64 (CD4+), p = 0.52 (CD8+)]. Graft-infiltrating T-cells showed an up to six-fold increase of donor-reactive T-cell clonotypes compared to the blood at the same time (3.7 vs. 0.6% and 2.4 vs. 1.5%), but the infiltrating TCR repertoire was not reflected by the composition of the circulating TCR repertoire despite some overlap. Network analysis showed a distinct segregation of the donor-reactive repertoire with higher modularity than the overall TCR repertoire in the blood. These findings indicate an unchoreographed process of diverse T-cell clones directed against numerous non-self antigens found in the allograft. Conclusion Donor-reactive T-cells are enriched in the kidney allograft during a TCMR episode, and dominant tissue clones are also found in the blood. Trial Registration Clinicaltrials.gov: NCT: 03422224 (https://clinicaltrials.gov/ct2/show/NCT03422224).
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Affiliation(s)
- Constantin Aschauer
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Kira Jelencsics
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Karin Hu
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Andreas Heinzel
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Mariella Gloria Gregorich
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria.,Section for Clinical Biometrics, Center for Medical Statistics, Informatics and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | - Julia Vetter
- Bioinformatics Research Group, University of Applied Sciences Upper Austria, Hagenberg im Muehlkreis, Austria
| | - Susanne Schaller
- Bioinformatics Research Group, University of Applied Sciences Upper Austria, Hagenberg im Muehlkreis, Austria
| | - Stephan M Winkler
- Bioinformatics Research Group, University of Applied Sciences Upper Austria, Hagenberg im Muehlkreis, Austria
| | - Johannes Weinberger
- Research Laboratory of Infection Biology, Department of Medicine, Medical University of Vienna, Vienna, Austria
| | - Lisabeth Pimenov
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Guido A Gualdoni
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Michael Eder
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Alexander Kainz
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | | | - Heinz Regele
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Roman Reindl-Schwaighofer
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Thomas Wekerle
- Department of General Surgery, Division of Transplantation, Section of Transplantation Immunology, Medical University of Vienna, Vienna, Austria
| | - Johannes Bernhard Huppa
- Center for Pathophysiology, Infectiology and Immunology, Institute for Hygiene and Applied Immunology, Medical University of Vienna, Vienna, Austria
| | - Megan Sykes
- Columbian Center for Translational Immunology, Department of Medicine, Columbia University, New York City, NY, United States
| | - Rainer Oberbauer
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
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38
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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] [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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39
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Mazouz S, Boisvert M, Abdel-Hakeem MS, Khedr O, Bruneau J, Shoukry NH. Expansion of Unique Hepatitis C Virus-Specific Public CD8 + T Cell Clonotypes during Acute Infection and Reinfection. THE JOURNAL OF IMMUNOLOGY 2021; 207:1180-1193. [PMID: 34341170 DOI: 10.4049/jimmunol.2001386] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 06/09/2021] [Indexed: 11/19/2022]
Abstract
Hepatitis C virus (HCV) infection resolves spontaneously in ∼25% of acutely infected humans where viral clearance is mediated primarily by virus-specific CD8+ T cells. Previous cross-sectional analysis of the CD8+ TCR repertoire targeting two immunodominant HCV epitopes reported widespread use of public TCRs shared by different subjects, irrespective of infection outcome. However, little is known about the evolution of the public TCR repertoire during acute HCV and whether cross-reactivity to other Ags can influence infectious outcome. In this article, we analyzed the CD8+ TCR repertoire specific to the immunodominant and cross-reactive HLA-A2-restricted nonstructural 3-1073 epitope during acute HCV in humans progressing to either spontaneous resolution or chronic infection and at ∼1 y after viral clearance. TCR repertoire diversity was comparable among all groups with preferential usage of the TCR-β V04 and V06 gene families. We identified a set of 13 public clonotypes in HCV-infected humans independent of infection outcome. Six public clonotypes used the V04 gene family. Several public clonotypes were long-lived in resolvers and expanded on reinfection. By mining publicly available data, we identified several low-frequency CDR3 sequences in the HCV-specific repertoire matching human TCRs specific for other HLA-A2-restricted epitopes from melanoma, CMV, influenza A, EBV, and yellow fever viruses, but they were of low frequency and limited cross-reactivity. In conclusion, we identified 13 new public human CD8+ TCR clonotypes unique to HCV that expanded during acute infection and reinfection. The low frequency of cross-reactive TCRs suggests that they are not major determinants of infectious outcome.
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Affiliation(s)
- Sabrina Mazouz
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montreal, Quebec, Canada.,Département de Microbiologie, Infectiologie et Immunologie, Université de Montreal, Montreal, Quebec, Canada
| | - Maude Boisvert
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montreal, Quebec, Canada
| | - Mohamed S Abdel-Hakeem
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montreal, Quebec, Canada.,Département de Microbiologie, Infectiologie et Immunologie, Université de Montreal, Montreal, Quebec, Canada
| | - Omar Khedr
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montreal, Quebec, Canada
| | - Julie Bruneau
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montreal, Quebec, Canada.,Département de Médecine Familiale et de Médecine d'Urgence, Université de Montréal, Montreal, Quebec, Canada; and
| | - Naglaa H Shoukry
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montreal, Quebec, Canada; .,Département de Médecine, Université de Montréal, Montreal, Quebec, Canada
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40
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Dvorkin S, Levi R, Louzoun Y. Autoencoder based local T cell repertoire density can be used to classify samples and T cell receptors. PLoS Comput Biol 2021; 17:e1009225. [PMID: 34310600 PMCID: PMC8341707 DOI: 10.1371/journal.pcbi.1009225] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 08/05/2021] [Accepted: 06/28/2021] [Indexed: 11/18/2022] Open
Abstract
Recent advances in T cell repertoire (TCR) sequencing allow for the characterization of repertoire properties, as well as the frequency and sharing of specific TCR. However, there is no efficient measure for the local density of a given TCR. TCRs are often described either through their Complementary Determining region 3 (CDR3) sequences, or theirV/J usage, or their clone size. We here show that the local repertoire density can be estimated using a combined representation of these components through distance conserving autoencoders and Kernel Density Estimates (KDE). We present ELATE-an Encoder-based LocAl Tcr dEnsity and show that the resulting density of a sample can be used as a novel measure to study repertoire properties. The cross-density between two samples can be used as a similarity matrix to fully characterize samples from the same host. Finally, the same projection in combination with machine learning algorithms can be used to predict TCR-peptide binding through the local density of known TCRs binding a specific target.
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MESH Headings
- Algorithms
- Amino Acid Sequence
- Complementarity Determining Regions/classification
- Complementarity Determining Regions/genetics
- Computational Biology
- Databases, Genetic
- Gene Rearrangement, alpha-Chain T-Cell Antigen Receptor
- Gene Rearrangement, beta-Chain T-Cell Antigen Receptor
- Humans
- Immunoglobulin Variable Region/genetics
- Machine Learning
- Receptors, Antigen, T-Cell/classification
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell, alpha-beta/classification
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Software
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Affiliation(s)
- Shirit Dvorkin
- Department of Mathematics, Bar Ilan University, Ramat Gan, Israel
| | - Reut Levi
- Department of Mathematics, Bar Ilan University, Ramat Gan, Israel
| | - Yoram Louzoun
- Department of Mathematics, Bar Ilan University, Ramat Gan, Israel
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Van Tilbeurgh M, Lemdani K, Beignon AS, Chapon C, Tchitchek N, Cheraitia L, Marcos Lopez E, Pascal Q, Le Grand R, Maisonnasse P, Manet C. Predictive Markers of Immunogenicity and Efficacy for Human Vaccines. Vaccines (Basel) 2021; 9:579. [PMID: 34205932 PMCID: PMC8226531 DOI: 10.3390/vaccines9060579] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/22/2021] [Accepted: 05/24/2021] [Indexed: 02/07/2023] Open
Abstract
Vaccines represent one of the major advances of modern medicine. Despite the many successes of vaccination, continuous efforts to design new vaccines are needed to fight "old" pandemics, such as tuberculosis and malaria, as well as emerging pathogens, such as Zika virus and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Vaccination aims at reaching sterilizing immunity, however assessing vaccine efficacy is still challenging and underscores the need for a better understanding of immune protective responses. Identifying reliable predictive markers of immunogenicity can help to select and develop promising vaccine candidates during early preclinical studies and can lead to improved, personalized, vaccination strategies. A systems biology approach is increasingly being adopted to address these major challenges using multiple high-dimensional technologies combined with in silico models. Although the goal is to develop predictive models of vaccine efficacy in humans, applying this approach to animal models empowers basic and translational vaccine research. In this review, we provide an overview of vaccine immune signatures in preclinical models, as well as in target human populations. We also discuss high-throughput technologies used to probe vaccine-induced responses, along with data analysis and computational methodologies applied to the predictive modeling of vaccine efficacy.
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Affiliation(s)
- Matthieu Van Tilbeurgh
- Immunology of Viral Infections and Autoimmune Diseases (IMVA), IDMIT Department, Institut de Biologie François-Jacob (IBJF), University Paris-Sud—INSERM U1184, CEA, 92265 Fontenay-Aux-Roses, France; (M.V.T.); (K.L.); (A.-S.B.); (C.C.); (L.C.); (E.M.L.); (Q.P.); (R.L.G.); (P.M.)
| | - Katia Lemdani
- Immunology of Viral Infections and Autoimmune Diseases (IMVA), IDMIT Department, Institut de Biologie François-Jacob (IBJF), University Paris-Sud—INSERM U1184, CEA, 92265 Fontenay-Aux-Roses, France; (M.V.T.); (K.L.); (A.-S.B.); (C.C.); (L.C.); (E.M.L.); (Q.P.); (R.L.G.); (P.M.)
| | - Anne-Sophie Beignon
- Immunology of Viral Infections and Autoimmune Diseases (IMVA), IDMIT Department, Institut de Biologie François-Jacob (IBJF), University Paris-Sud—INSERM U1184, CEA, 92265 Fontenay-Aux-Roses, France; (M.V.T.); (K.L.); (A.-S.B.); (C.C.); (L.C.); (E.M.L.); (Q.P.); (R.L.G.); (P.M.)
| | - Catherine Chapon
- Immunology of Viral Infections and Autoimmune Diseases (IMVA), IDMIT Department, Institut de Biologie François-Jacob (IBJF), University Paris-Sud—INSERM U1184, CEA, 92265 Fontenay-Aux-Roses, France; (M.V.T.); (K.L.); (A.-S.B.); (C.C.); (L.C.); (E.M.L.); (Q.P.); (R.L.G.); (P.M.)
| | - Nicolas Tchitchek
- Unité de Recherche i3, Inserm UMR-S 959, Bâtiment CERVI, Hôpital de la Pitié-Salpêtrière, 75013 Paris, France;
| | - Lina Cheraitia
- Immunology of Viral Infections and Autoimmune Diseases (IMVA), IDMIT Department, Institut de Biologie François-Jacob (IBJF), University Paris-Sud—INSERM U1184, CEA, 92265 Fontenay-Aux-Roses, France; (M.V.T.); (K.L.); (A.-S.B.); (C.C.); (L.C.); (E.M.L.); (Q.P.); (R.L.G.); (P.M.)
| | - Ernesto Marcos Lopez
- Immunology of Viral Infections and Autoimmune Diseases (IMVA), IDMIT Department, Institut de Biologie François-Jacob (IBJF), University Paris-Sud—INSERM U1184, CEA, 92265 Fontenay-Aux-Roses, France; (M.V.T.); (K.L.); (A.-S.B.); (C.C.); (L.C.); (E.M.L.); (Q.P.); (R.L.G.); (P.M.)
| | - Quentin Pascal
- Immunology of Viral Infections and Autoimmune Diseases (IMVA), IDMIT Department, Institut de Biologie François-Jacob (IBJF), University Paris-Sud—INSERM U1184, CEA, 92265 Fontenay-Aux-Roses, France; (M.V.T.); (K.L.); (A.-S.B.); (C.C.); (L.C.); (E.M.L.); (Q.P.); (R.L.G.); (P.M.)
| | - Roger Le Grand
- Immunology of Viral Infections and Autoimmune Diseases (IMVA), IDMIT Department, Institut de Biologie François-Jacob (IBJF), University Paris-Sud—INSERM U1184, CEA, 92265 Fontenay-Aux-Roses, France; (M.V.T.); (K.L.); (A.-S.B.); (C.C.); (L.C.); (E.M.L.); (Q.P.); (R.L.G.); (P.M.)
| | - Pauline Maisonnasse
- Immunology of Viral Infections and Autoimmune Diseases (IMVA), IDMIT Department, Institut de Biologie François-Jacob (IBJF), University Paris-Sud—INSERM U1184, CEA, 92265 Fontenay-Aux-Roses, France; (M.V.T.); (K.L.); (A.-S.B.); (C.C.); (L.C.); (E.M.L.); (Q.P.); (R.L.G.); (P.M.)
| | - Caroline Manet
- Immunology of Viral Infections and Autoimmune Diseases (IMVA), IDMIT Department, Institut de Biologie François-Jacob (IBJF), University Paris-Sud—INSERM U1184, CEA, 92265 Fontenay-Aux-Roses, France; (M.V.T.); (K.L.); (A.-S.B.); (C.C.); (L.C.); (E.M.L.); (Q.P.); (R.L.G.); (P.M.)
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Montague Z, Lv H, Otwinowski J, DeWitt WS, Isacchini G, Yip GK, Ng WW, Tsang OTY, Yuan M, Liu H, Wilson IA, Peiris JSM, Wu NC, Nourmohammad A, Mok CKP. Dynamics of B cell repertoires and emergence of cross-reactive responses in patients with different severities of COVID-19. Cell Rep 2021; 35:109173. [PMID: 33991510 PMCID: PMC8106887 DOI: 10.1016/j.celrep.2021.109173] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 04/05/2021] [Accepted: 05/04/2021] [Indexed: 02/06/2023] Open
Abstract
Individuals with the 2019 coronavirus disease (COVID-19) show varying severity of the disease, ranging from asymptomatic to requiring intensive care. Although monoclonal antibodies specific to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been identified, we still lack an understanding of the overall landscape of B cell receptor (BCR) repertoires in individuals with COVID-19. We use high-throughput sequencing of bulk and plasma B cells collected at multiple time points during infection to characterize signatures of the B cell response to SARS-CoV-2 in 19 individuals. Using principled statistical approaches, we associate differential features of BCRs with different disease severity. We identify 38 significantly expanded clonal lineages shared among individuals as candidates for responses specific to SARS-CoV-2. Using single-cell sequencing, we verify the reactivity of BCRs shared among individuals to SARS-CoV-2 epitopes. Moreover, we identify the natural emergence of a BCR with cross-reactivity to SARS-CoV-1 and SARS-CoV-2 in some individuals. Our results provide insights important for development of rational therapies and vaccines against COVID-19.
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Affiliation(s)
- Zachary Montague
- Department of Physics, University of Washington, 3910 15th Ave. Northeast, Seattle, WA 98195, USA
| | - Huibin Lv
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Jakub Otwinowski
- Max Planck Institute for Dynamics and Self-Organization, Am Faßberg 17, 37077 Göttingen, Germany
| | - William S DeWitt
- Department of Genome Sciences, University of Washington, 3720 15th Ave. NE, Seattle, WA 98195, USA; Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N, Seattle, WA 98109, USA
| | - Giulio Isacchini
- Max Planck Institute for Dynamics and Self-Organization, Am Faßberg 17, 37077 Göttingen, Germany; Laboratoire de physique de l'ecole normale supérieure (PSL University), CNRS, Sorbonne Université, and Université de Paris, 75005 Paris, France
| | - Garrick K Yip
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Wilson W Ng
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Owen Tak-Yin Tsang
- Infectious Diseases Centre, Princess Margaret Hospital, Hospital Authority of Hong Kong, Hong Kong SAR, China
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hejun Liu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - J S Malik Peiris
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Nicholas C Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Armita Nourmohammad
- Department of Physics, University of Washington, 3910 15th Ave. Northeast, Seattle, WA 98195, USA; Max Planck Institute for Dynamics and Self-Organization, Am Faßberg 17, 37077 Göttingen, Germany; Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N, Seattle, WA 98109, USA.
| | - Chris Ka Pun Mok
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China; The Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong SAR, China.
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43
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Chang CM, Feng PH, Wu TH, Alachkar H, Lee KY, Chang WC. Profiling of T Cell Repertoire in SARS-CoV-2-Infected COVID-19 Patients Between Mild Disease and Pneumonia. J Clin Immunol 2021; 41:1131-1145. [PMID: 33950324 PMCID: PMC8096628 DOI: 10.1007/s10875-021-01045-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/14/2021] [Indexed: 01/01/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a public health emergency. The most common symptoms of COVID-19 are fever, cough, and fatigue. While most patients with COVID-19 present with mild illness, some patients develop pneumonia, an important risk factor for mortality, at early stage of viral infection, putting these patients at increased risk of death. So far, little has been known about differences in the T cell repertoires between COVID-19 patients with and without pneumonia during SARS-CoV-2 infection. Herein, we aimed to investigate T cell receptor (TCR) repertoire profiles and patient-specific SARS-CoV-2-associated TCR clusters between COVID-19 patients with mild disease (no sign of pneumonia) and pneumonia. The TCR sequencing was conducted to characterize the peripheral TCR repertoire profile and diversity. The TCR clustering and CDR3 annotation were exploited to further discover groups of patient-specific TCR clonotypes with potential SARS-CoV-2 antigen specificities. Our study indicated a slight decrease in the TCR repertoire diversity and a skewed CDR3 length usage in patients with pneumonia compared to those with mild disease. The SARS-CoV-2-associated TCR clusters enriched in patients with mild disease exhibited significantly higher TCR generation probabilities and most of which were highly shared among patients, compared with those from pneumonia patients. Importantly, using similarity network-based clustering followed by the sequence conservation analysis, we found different patterns of CDR3 sequence motifs between mild disease- and pneumonia-specific SARS-CoV-2-associated public TCR clusters. Our results showed that characteristics of overall TCR repertoire and SARS-CoV-2-associated TCR clusters/clonotypes were divergent between COVID-19 patients with mild disease and patients with pneumonia. These findings provide important insights into the correlation between the TCR repertoire and disease severity in COVID-19 patients.
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Affiliation(s)
- Che-Mai Chang
- Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Po-Hao Feng
- Division of Pulmonary Medicine, Department of Internal Medicine, Taipei Medical University-Shuang Ho Hospital, No. 291, Zhongzheng Rd., Zhonghe Dist., New Taipei City, 235, Taiwan
- Division of Pulmonary Medicine, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Tsung-Hsun Wu
- Master Program in Clinical Pharmacogenomics and Pharmacoproteomics, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Houda Alachkar
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA, USA
| | - Kang-Yun Lee
- Division of Pulmonary Medicine, Department of Internal Medicine, Taipei Medical University-Shuang Ho Hospital, No. 291, Zhongzheng Rd., Zhonghe Dist., New Taipei City, 235, Taiwan.
- Division of Pulmonary Medicine, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.
| | - Wei-Chiao Chang
- Master Program in Clinical Pharmacogenomics and Pharmacoproteomics, School of Pharmacy, Taipei Medical University, Taipei, Taiwan.
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, No. 250, Wuxing St., Xinyi Dist., Taipei, 110, Taiwan.
- Department of Pharmacy, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan.
- Integrative Research Center for Critical Care, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan.
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44
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Soto C, Bombardi RG, Kozhevnikov M, Sinkovits RS, Chen EC, Branchizio A, Kose N, Day SB, Pilkinton M, Gujral M, Mallal S, Crowe JE. High Frequency of Shared Clonotypes in Human T Cell Receptor Repertoires. Cell Rep 2021; 32:107882. [PMID: 32668251 PMCID: PMC7433715 DOI: 10.1016/j.celrep.2020.107882] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 04/18/2020] [Accepted: 06/16/2020] [Indexed: 01/30/2023] Open
Abstract
The collection of T cell receptors (TCRs) generated by somatic recombination is large but unknown. We generate large TCR repertoire datasets as a resource to facilitate detailed studies of the role of TCR clonotypes and repertoires in health and disease. We estimate the size of individual human recombined and expressed TCRs by sequence analysis and determine the extent of sharing between individual repertoires. Our experiments reveal that each blood sample contains between 5 million and 21 million TCR clonotypes. Three individuals share 8% of TCRβ- or 11% of TCRα-chain clonotypes. Sorting by T cell phenotypes in four individuals shows that 5% of naive CD4+ and 3.5% of naive CD8+ subsets share their TCRβ clonotypes, whereas memory CD4+ and CD8+ subsets share 2.3% and 0.4% of their clonotypes, respectively. We identify the sequences of these shared TCR clonotypes that are of interest for studies of human T cell biology. Soto et al. examine the extent to which five healthy adults share their T cell receptor (TCR) repertoire. Using sequencing and bioinformatics, they show a high prevalence of shared clonotypes even considering different T cell phenotypes. Possible functions for some clonotypes are inferred based on homology with TCRs in GenBank.
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Affiliation(s)
- Cinque Soto
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Robin G Bombardi
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Morgan Kozhevnikov
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Robert S Sinkovits
- San Diego Supercomputer Center, University of California, San Diego, San Diego, CA 92093, USA
| | - Elaine C Chen
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37212, USA
| | - Andre Branchizio
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Nurgun Kose
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Samuel B Day
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Mark Pilkinton
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Madhusudan Gujral
- San Diego Supercomputer Center, University of California, San Diego, San Diego, CA 92093, USA
| | - Simon Mallal
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37212, USA; Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - James E Crowe
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37212, USA.
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45
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Montague Z, Lv H, Otwinowski J, DeWitt WS, Isacchini G, Yip GK, Ng WW, Tsang OTY, Yuan M, Liu H, Wilson IA, Peiris JSM, Wu NC, Nourmohammad A, Mok CKP. Dynamics of B-cell repertoires and emergence of cross-reactive responses in COVID-19 patients with different disease severity. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2020.07.13.20153114. [PMID: 32699862 PMCID: PMC7373151 DOI: 10.1101/2020.07.13.20153114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
COVID-19 patients show varying severity of the disease ranging from asymptomatic to requiring intensive care. Although a number of SARS-CoV-2 specific monoclonal antibodies have been identified, we still lack an understanding of the overall landscape of B-cell receptor (BCR) repertoires in COVID-19 patients. Here, we used high-throughput sequencing of bulk and plasma B-cells collected over multiple time points during infection to characterize signatures of B-cell response to SARS-CoV-2 in 19 patients. Using principled statistical approaches, we determined differential features of BCRs associated with different disease severity. We identified 38 significantly expanded clonal lineages shared among patients as candidates for specific responses to SARS-CoV-2. Using single-cell sequencing, we verified reactivity of BCRs shared among individuals to SARS-CoV-2 epitopes. Moreover, we identified natural emergence of a BCR with cross-reactivity to SARS-CoV-1 and SARS-CoV-2 in a number of patients. Our results provide important insights for development of rational therapies and vaccines against COVID-19.
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Affiliation(s)
- Zachary Montague
- Department of Physics, University of Washington, 3910 15th Ave Northeast, Seattle, WA 98195, USA
| | - Huibin Lv
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Jakub Otwinowski
- Max Planck Institute for Dynamics and Self-organization, Am Faßberg 17, 37077 Göttingen, Germany
| | - William S. DeWitt
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA 98195, USA
- Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
| | - Giulio Isacchini
- Max Planck Institute for Dynamics and Self-organization, Am Faßberg 17, 37077 Göttingen, Germany
- Laboratoire de physique de l’ecole normale supérieure (PSL University), CNRS, Sorbonne Université, and Université de Paris, 75005 Paris, France
| | - Garrick K. Yip
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Wilson W. Ng
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Owen Tak-Yin Tsang
- Infectious Diseases Centre, Princess Margaret Hospital, Hospital Authority of Hong Kong
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hejun Liu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - J. S. Malik Peiris
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Nicholas C. Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Armita Nourmohammad
- Department of Physics, University of Washington, 3910 15th Ave Northeast, Seattle, WA 98195, USA
- Max Planck Institute for Dynamics and Self-organization, Am Faßberg 17, 37077 Göttingen, Germany
- Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
| | - Chris Ka Pun Mok
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
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46
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Yohannes DA, Kaukinen K, Kurppa K, Saavalainen P, Greco D. Clustering based approach for population level identification of condition-associated T-cell receptor β-chain CDR3 sequences. BMC Bioinformatics 2021; 22:159. [PMID: 33765908 PMCID: PMC7993519 DOI: 10.1186/s12859-021-04087-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 03/17/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Deep immune receptor sequencing, RepSeq, provides unprecedented opportunities for identifying and studying condition-associated T-cell clonotypes, represented by T-cell receptor (TCR) CDR3 sequences. However, due to the immense diversity of the immune repertoire, identification of condition relevant TCR CDR3s from total repertoires has mostly been limited to either "public" CDR3 sequences or to comparisons of CDR3 frequencies observed in a single individual. A methodology for the identification of condition-associated TCR CDR3s by direct population level comparison of RepSeq samples is currently lacking. RESULTS We present a method for direct population level comparison of RepSeq samples using immune repertoire sub-units (or sub-repertoires) that are shared across individuals. The method first performs unsupervised clustering of CDR3s within each sample. It then finds matching clusters across samples, called immune sub-repertoires, and performs statistical differential abundance testing at the level of the identified sub-repertoires. It finally ranks CDR3s in differentially abundant sub-repertoires for relevance to the condition. We applied the method on total TCR CDR3β RepSeq datasets of celiac disease patients, as well as on public datasets of yellow fever vaccination. The method successfully identified celiac disease associated CDR3β sequences, as evidenced by considerable agreement of TRBV-gene and positional amino acid usage patterns in the detected CDR3β sequences with previously known CDR3βs specific to gluten in celiac disease. It also successfully recovered significantly high numbers of previously known CDR3β sequences relevant to each condition than would be expected by chance. CONCLUSION We conclude that immune sub-repertoires of similar immuno-genomic features shared across unrelated individuals can serve as viable units of immune repertoire comparison, serving as proxy for identification of condition-associated CDR3s.
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Affiliation(s)
- Dawit A Yohannes
- Research Programs Unit, Translational Immunology, University of Helsinki, Helsinki, Finland.,Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Katri Kaukinen
- Department of Internal Medicine, Faculty of Medicine and Health Technology, Tampere University Hospital, Tampere University, Tampere, Finland
| | - Kalle Kurppa
- Department of Pediatrics, Tampere University Hospital and Center for Child Health Research, Tampere University, Tampere, Finland
| | - Päivi Saavalainen
- Research Programs Unit, Translational Immunology, University of Helsinki, Helsinki, Finland.,Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Dario Greco
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland. .,BioMediTech Institute, Tampere University, Tampere, Finland. .,Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
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47
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Fischer S, Stanke F, Tümmler B. VJ Segment Usage of TCR-Beta Repertoire in Monozygotic Cystic Fibrosis Twins. Front Immunol 2021; 12:599133. [PMID: 33708199 PMCID: PMC7940196 DOI: 10.3389/fimmu.2021.599133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 01/28/2021] [Indexed: 11/26/2022] Open
Abstract
Sixteen monozygotic cystic fibrosis (CF) twin pairs of whom 14 pairs were homozygous for the most common p.Phe508del CFTR mutation were selected from the European Cystic Fibrosis Twin and Sibling Study Cohort. The monozygotic twins were examined in their T cell receptor (TCR) repertoire in peripheral blood by amplicon sequencing of the CDR3 variable region of the ß-chain. The recruitment of TCR J and V genes for recombination and selection in the thymus showed a strong genetic influence in the CF twin cohort as indicated by the shortest Jensen-Shannon distance to the twin individual. Exceptions were the clinically most discordant and/or most severely affected twin pairs where clonal expansion probably caused by recurrent pulmonary infections overshadowed the impact of the identical genomic blueprint. In general the Simpson clonality was low indicating that the population of TCRß clonotypes of the CF twins was dominated by the naïve T-cell repertoire. Intrapair sharing of clonotypes was significantly more frequent among monozygotic CF twins than among pairs of unrelated CF patients. Complete nucleotide sequence identity was observed in about 0.11% of CDR3 sequences which partially should represent persisting fetal clones derived from the same progenitor T cells. Complete amino acid sequence identity was noted in 0.59% of clonotypes. Of the nearly 40,000 frequent amino acid clonotypes shared by at least two twin siblings 99.8% were already known within the immuneACCESS database and only 73 had yet not been detected indicating that the CDR3ß repertoire of CF children and adolescents does not carry a disease-specific signature but rather shares public clones with that of the non-CF community. Clonotypes shared within twin pairs and between unrelated CF siblings were highly abundant among healthy non-CF people, less represented in individuals with infectious disease and uncommon in patients with cancer. This subset of shared CF clonotypes defines CDR3 amino acid sequences that are more common in health than in disease.
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Affiliation(s)
- Sebastian Fischer
- Clinic for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Frauke Stanke
- Clinic for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany.,Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Hannover Medical School, Hannover, Germany
| | - Burkhard Tümmler
- Clinic for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany.,Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Hannover Medical School, Hannover, Germany
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48
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Granadier D, Iovino L, Kinsella S, Dudakov JA. Dynamics of thymus function and T cell receptor repertoire breadth in health and disease. Semin Immunopathol 2021; 43:119-134. [PMID: 33608819 PMCID: PMC7894242 DOI: 10.1007/s00281-021-00840-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 01/12/2021] [Indexed: 12/26/2022]
Abstract
T cell recognition of unknown antigens relies on the tremendous diversity of the T cell receptor (TCR) repertoire; generation of which can only occur in the thymus. TCR repertoire breadth is thus critical for not only coordinating the adaptive response against pathogens but also for mounting a response against malignancies. However, thymic function is exquisitely sensitive to negative stimuli, which can come in the form of acute insult, such as that caused by stress, infection, or common cancer therapies; or chronic damage such as the progressive decline in thymic function with age. Whether it be prolonged T cell deficiency after hematopoietic cell transplantation (HCT) or constriction in the breadth of the peripheral TCR repertoire with age; these insults result in poor adaptive immune responses. In this review, we will discuss the importance of thymic function for generation of the TCR repertoire and how acute and chronic thymic damage influences immune health. We will also discuss methods that are used to measure thymic function in patients and strategies that have been developed to boost thymic function.
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Affiliation(s)
- David Granadier
- Program in Immunology, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Immunotherapy Integrated Research Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
- Department of Molecular and Cellular Biology, University of Washington, Seattle, WA, USA
| | - Lorenzo Iovino
- Program in Immunology, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Immunotherapy Integrated Research Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Sinéad Kinsella
- Program in Immunology, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Immunotherapy Integrated Research Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jarrod A Dudakov
- Program in Immunology, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Immunotherapy Integrated Research Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Department of Immunology, University of Washington, Seattle, WA, USA.
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49
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Barennes P, Quiniou V, Shugay M, Egorov ES, Davydov AN, Chudakov DM, Uddin I, Ismail M, Oakes T, Chain B, Eugster A, Kashofer K, Rainer PP, Darko S, Ransier A, Douek DC, Klatzmann D, Mariotti-Ferrandiz E. Benchmarking of T cell receptor repertoire profiling methods reveals large systematic biases. Nat Biotechnol 2021; 39:236-245. [PMID: 32895550 DOI: 10.1038/s41587-020-0656-3] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 07/28/2020] [Indexed: 12/13/2022]
Abstract
Monitoring the T cell receptor (TCR) repertoire in health and disease can provide key insights into adaptive immune responses, but the accuracy of current TCR sequencing (TCRseq) methods is unclear. In this study, we systematically compared the results of nine commercial and academic TCRseq methods, including six rapid amplification of complementary DNA ends (RACE)-polymerase chain reaction (PCR) and three multiplex-PCR approaches, when applied to the same T cell sample. We found marked differences in accuracy and intra- and inter-method reproducibility for T cell receptor α (TRA) and T cell receptor β (TRB) TCR chains. Most methods showed a lower ability to capture TRA than TRB diversity. Low RNA input generated non-representative repertoires. Results from the 5' RACE-PCR methods were consistent among themselves but differed from the RNA-based multiplex-PCR results. Using an in silico meta-repertoire generated from 108 replicates, we found that one genomic DNA-based method and two non-unique molecular identifier (UMI) RNA-based methods were more sensitive than UMI methods in detecting rare clonotypes, despite the better clonotype quantification accuracy of the latter.
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Affiliation(s)
- Pierre Barennes
- Sorbonne Université, INSERM, Immunology-Immunopathology-Immunotherapy (i3), Paris, France
- AP-HP, Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi) and Inflammation-Immunopathology-Biotherapy Department (i2B), Paris, France
| | - Valentin Quiniou
- Sorbonne Université, INSERM, Immunology-Immunopathology-Immunotherapy (i3), Paris, France
- AP-HP, Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi) and Inflammation-Immunopathology-Biotherapy Department (i2B), Paris, France
| | - Mikhail Shugay
- Center of Life Sciences, Skoltech, Moscow, Russia
- Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Evgeniy S Egorov
- Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Alexey N Davydov
- Adaptive Immunity Group, Central European Institute of Technology, Brno, Czechia
| | - Dmitriy M Chudakov
- Center of Life Sciences, Skoltech, Moscow, Russia
- Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Adaptive Immunity Group, Central European Institute of Technology, Brno, Czechia
| | - Imran Uddin
- Division of Infection and Immunity, University College London, London, UK
| | - Mazlina Ismail
- Division of Infection and Immunity, University College London, London, UK
| | - Theres Oakes
- Division of Infection and Immunity, University College London, London, UK
| | - Benny Chain
- Division of Infection and Immunity, University College London, London, UK
| | - Anne Eugster
- DFG-Centre for Regenerative Therapies Dresden, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Karl Kashofer
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Peter P Rainer
- Division of Cardiology, Medical University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - Samuel Darko
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Amy Ransier
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - David Klatzmann
- Sorbonne Université, INSERM, Immunology-Immunopathology-Immunotherapy (i3), Paris, France
- AP-HP, Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi) and Inflammation-Immunopathology-Biotherapy Department (i2B), Paris, France
| | - Encarnita Mariotti-Ferrandiz
- Sorbonne Université, INSERM, Immunology-Immunopathology-Immunotherapy (i3), Paris, France.
- AP-HP, Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi) and Inflammation-Immunopathology-Biotherapy Department (i2B), Paris, France.
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50
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Ronel T, Harries M, Wicks K, Oakes T, Singleton H, Dearman R, Maxwell G, Chain B. The clonal structure and dynamics of the human T cell response to an organic chemical hapten. eLife 2021; 10:54747. [PMID: 33432924 PMCID: PMC7880692 DOI: 10.7554/elife.54747] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 01/12/2021] [Indexed: 12/27/2022] Open
Abstract
Diphenylcyclopropenone (DPC) is an organic chemical hapten which induces allergic contact dermatitis and is used in the treatment of warts, melanoma, and alopecia areata. This therapeutic setting therefore provided an opportunity to study T cell receptor (TCR) repertoire changes in response to hapten sensitization in humans. Repeated exposure to DPC induced highly dynamic transient expansions of a polyclonal diverse T cell population. The number of TCRs expanded early after sensitization varies between individuals and predicts the magnitude of the allergic reaction. The expanded TCRs show preferential TCR V and J gene usage and consist of clusters of TCRs with similar sequences, two characteristic features of antigen-driven responses. The expanded TCRs share subtle sequence motifs that can be captured using a dynamic Bayesian network. These observations suggest the response to DPC is mediated by a polyclonal population of T cells recognizing a small number of dominant antigens.
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Affiliation(s)
- Tahel Ronel
- Division of Infection and Immunity, University College London, London, United Kingdom.,Cancer Institute, University College London, London, United Kingdom
| | - Matthew Harries
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom.,Salford Royal NHS Foundation Trust (Dermatology Centre), Salford, United Kingdom
| | - Kate Wicks
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Theres Oakes
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Helen Singleton
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Rebecca Dearman
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Gavin Maxwell
- Safety and Environmental Assurance Centre, Unilever, Colworth Science Park, Bedford, United Kingdom
| | - Benny Chain
- Division of Infection and Immunity, University College London, London, United Kingdom.,Department of Computer Science, University College London, London, United Kingdom
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