1
|
Angelats E, Santamaria P. Lineage origin and transcriptional control of autoantigen-specific T-regulatory type 1 cells. Front Immunol 2023; 14:1267697. [PMID: 37818381 PMCID: PMC10560755 DOI: 10.3389/fimmu.2023.1267697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 09/04/2023] [Indexed: 10/12/2023] Open
Abstract
T Regulatory type-1 (TR1) cells represent an immunosuppressive T cell subset, discovered over 25 years ago, that produces high levels of interleukin-10 (IL-10) but, unlike its FoxP3+ T regulatory (Treg) cell counterpart, does not express FoxP3 or CD25. Experimental evidence generated over the last few years has exposed a promising role for TR1 cells as targets of therapeutic intervention in immune-mediated diseases. The discovery of cell surface markers capable of distinguishing these cells from related T cell types and the application of next generation sequencing techniques to defining their transcriptional make-up have enabled a more accurate description of this T cell population. However, the developmental biology of TR1 cells has long remained elusive, in particular the identity of the cell type(s) giving rise to bona fide TR1 cells in vivo. Here, we review the fundamental phenotypic, transcriptional and functional properties of this T cell subset, and summarize recent lines of evidence shedding light into its ontogeny.
Collapse
Affiliation(s)
- Edgar Angelats
- Pathogenesis and Treatment of Autoimmunity Group, Institut D’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Pere Santamaria
- Pathogenesis and Treatment of Autoimmunity Group, Institut D’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Department of Microbiology, Immunology and Infectious Diseases, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| |
Collapse
|
2
|
Wang SS, Pandey K, Watson KA, Abbott RC, Mifsud NA, Gracey FM, Ramarathinam SH, Cross RS, Purcell AW, Jenkins MR. Endogenous H3.3K27M derived peptide restricted to HLA-A∗02:01 is insufficient for immune-targeting in diffuse midline glioma. Mol Ther Oncolytics 2023; 30:167-180. [PMID: 37674626 PMCID: PMC10477804 DOI: 10.1016/j.omto.2023.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 08/11/2023] [Indexed: 09/08/2023] Open
Abstract
Diffuse midline glioma (DMG) is a childhood brain tumor with an extremely poor prognosis. Chimeric antigen receptor (CAR) T cell therapy has recently demonstrated some success in DMG, but there may a need to target multiple tumor-specific targets to avoid antigen escape. We developed a second-generation CAR targeting an HLA-A∗02:01 restricted histone 3K27M epitope in DMG, the target of previous peptide vaccination and T cell receptor-mimics. These CAR T cells demonstrated specific, titratable, binding to cells pulsed with the H3.3K27M peptide. However, we were unable to observe scFv binding, CAR T cell activation, or cytotoxic function against H3.3K27M+ patient-derived models. Despite using sensitive immunopeptidomics, we could not detect the H3.3K27M26-35-HLA-A∗02:01 peptide on these patient-derived models. Interestingly, other non-mutated peptides from DMG were detected bound to HLA-A∗02:01 and other class I molecules, including a novel HLA-A3-restricted peptide encompassing the K27M mutation and overlapping with the H3 K27M26-35-HLA-A∗02:01 peptide. These results suggest that targeting the H3 K27M26-35 mutation in context of HLA-A∗02:01 may not be a feasible immunotherapy strategy because of its lack of presentation. These findings should inform future investigations and clinical trials in DMG.
Collapse
Affiliation(s)
- Stacie S. Wang
- The Walter and Eliza Hall Institute of Medical Research, Immunology Division, Parkville, VIC 3052, Australia
- Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
- The University of Melbourne, Department of Medical Biology, Parkville, VIC 3052, Australia
| | - Kirti Pandey
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Katherine A. Watson
- The Walter and Eliza Hall Institute of Medical Research, Immunology Division, Parkville, VIC 3052, Australia
| | - Rebecca C. Abbott
- The Walter and Eliza Hall Institute of Medical Research, Immunology Division, Parkville, VIC 3052, Australia
- The University of Melbourne, Department of Medical Biology, Parkville, VIC 3052, Australia
| | - Nicole A. Mifsud
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Fiona M. Gracey
- Myrio Therapeutics, 6-16 Joseph St, Blackburn North, Melbourne, VIC 3130, Australia
| | - Sri H. Ramarathinam
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Ryan S. Cross
- The Walter and Eliza Hall Institute of Medical Research, Immunology Division, Parkville, VIC 3052, Australia
| | - Anthony W. Purcell
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Misty R. Jenkins
- The Walter and Eliza Hall Institute of Medical Research, Immunology Division, Parkville, VIC 3052, Australia
- The University of Melbourne, Department of Medical Biology, Parkville, VIC 3052, Australia
- La Trobe University, La Trobe Institute for Molecular Science, Bundoora, VIC, Australia
| |
Collapse
|
3
|
Huisman BD, Dai Z, Gifford DK, Birnbaum ME. A high-throughput yeast display approach to profile pathogen proteomes for MHC-II binding. eLife 2022; 11:e78589. [PMID: 35781135 PMCID: PMC9292997 DOI: 10.7554/elife.78589] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
T cells play a critical role in the adaptive immune response, recognizing peptide antigens presented on the cell surface by major histocompatibility complex (MHC) proteins. While assessing peptides for MHC binding is an important component of probing these interactions, traditional assays for testing peptides of interest for MHC binding are limited in throughput. Here, we present a yeast display-based platform for assessing the binding of tens of thousands of user-defined peptides in a high-throughput manner. We apply this approach to assess a tiled library covering the SARS-CoV-2 proteome and four dengue virus serotypes for binding to human class II MHCs, including HLA-DR401, -DR402, and -DR404. While the peptide datasets show broad agreement with previously described MHC-binding motifs, they additionally reveal experimentally validated computational false positives and false negatives. We therefore present this approach as able to complement current experimental datasets and computational predictions. Further, our yeast display approach underlines design considerations for epitope identification experiments and serves as a framework for examining relationships between viral conservation and MHC binding, which can be used to identify potentially high-interest peptide binders from viral proteins. These results demonstrate the utility of our approach to determine peptide-MHC binding interactions in a manner that can supplement and potentially enhance current algorithm-based approaches.
Collapse
Affiliation(s)
- Brooke D Huisman
- Koch Institute for Integrative Cancer ResearchCambridgeUnited States
- Department of Biological Engineering, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Zheng Dai
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of TechnologyCambridgeUnited States
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of TechnologyCambridgeUnited States
| | - David K Gifford
- Department of Biological Engineering, Massachusetts Institute of TechnologyCambridgeUnited States
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of TechnologyCambridgeUnited States
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Michael E Birnbaum
- Koch Institute for Integrative Cancer ResearchCambridgeUnited States
- Department of Biological Engineering, Massachusetts Institute of TechnologyCambridgeUnited States
- Ragon Institute of MGH, MIT and HarvardCambridgeUnited States
| |
Collapse
|
4
|
Brown SD, Holt RA. Neoantigen characteristics in the context of the complete predicted MHC class I self-immunopeptidome. Oncoimmunology 2018; 8:1556080. [PMID: 30723589 PMCID: PMC6350689 DOI: 10.1080/2162402x.2018.1556080] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 11/20/2018] [Accepted: 11/27/2018] [Indexed: 01/21/2023] Open
Abstract
The self-immunopeptidome is the repertoire of all self-peptides that can be presented by the combination of MHC variants carried by an individual, defined by their HLA genotype. Each MHC variant presents a distinct set of self-peptides, and the number of peptides in a set is variable. Subjects carrying MHC variants that present fewer self-peptides should also present fewer mutated peptides, resulting in decreased immune pressure on tumor cells. To explore this, we predicted peptide-MHC binding values using all unique 8-11mer human peptides in the human proteome and all available HLA class I allelic variants, for a total of 134 billion unique peptide--MHC binding predictions. From these predictions, we observe that most peptides are able to be presented by relatively few (< 250) MHC, while some can be presented by upwards of 1,500 different MHC. There is substantial overlap among the repertoires of peptides presented by different MHC and no relationship between the number of peptides presented and HLA population frequency. Nearly 30% of self-peptides are presentable by at least one MHC, leaving 70% of the human peptidome unsurveyed by T cells. We observed similar distributions of predicted self-immunopeptidome sizes in cancer subjects compared to controls, and within the pan-cancer population, predicted self-immunopeptidome size combined with mutational load to predict survival. Self-immunopeptidome analysis revealed evidence for tumor immunoediting and identified specific peptide positions that most influence immunogenicity. Because self-immunopeptidome size is defined by HLA genotypes and approximates neoantigen load, HLA genotyping could offer a rapid predictive biomarker for response to immunotherapy.
Collapse
Affiliation(s)
- Scott D Brown
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada.,Genome Science and Technology Program, University of British Columbia, Vancouver, British Columbia, Canada
| | - Robert A Holt
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada.,Genome Science and Technology Program, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| |
Collapse
|
5
|
Wang Y, Singh NK, Spear TT, Hellman LM, Piepenbrink KH, McMahan RH, Rosen HR, Vander Kooi CW, Nishimura MI, Baker BM. How an alloreactive T-cell receptor achieves peptide and MHC specificity. Proc Natl Acad Sci U S A 2017; 114:E4792-801. [PMID: 28572406 DOI: 10.1073/pnas.1700459114] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
T-cell receptor (TCR) allorecognition is often presumed to be relatively nonspecific, attributable to either a TCR focus on exposed major histocompatibility complex (MHC) polymorphisms or the degenerate recognition of allopeptides. However, paradoxically, alloreactivity can proceed with high peptide and MHC specificity. Although the underlying mechanisms remain unclear, the existence of highly specific alloreactive TCRs has led to their use as immunotherapeutics that can circumvent central tolerance and limit graft-versus-host disease. Here, we show how an alloreactive TCR achieves peptide and MHC specificity. The HCV1406 TCR was cloned from T cells that expanded when a hepatitis C virus (HCV)-infected HLA-A2- individual received an HLA-A2+ liver allograft. HCV1406 was subsequently shown to recognize the HCV nonstructural protein 3 (NS3):1406-1415 epitope with high specificity when presented by HLA-A2. We show that NS3/HLA-A2 recognition by the HCV1406 TCR is critically dependent on features unique to both the allo-MHC and the NS3 epitope. We also find cooperativity between structural mimicry and a crucial peptide "hot spot" and demonstrate its role, along with the MHC, in directing the specificity of allorecognition. Our results help explain the paradox of specificity in alloreactive TCRs and have implications for their use in immunotherapy and related efforts to manipulate TCR recognition, as well as alloreactivity in general.
Collapse
|
6
|
Huang J, Zeng X, Sigal N, Lund PJ, Su LF, Huang H, Chien YH, Davis MM. Detection, phenotyping, and quantification of antigen-specific T cells using a peptide-MHC dodecamer. Proc Natl Acad Sci U S A 2016; 113:E1890-7. [PMID: 26979955 DOI: 10.1073/pnas.1602488113] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Here we report a peptide-MHC (pMHC) dodecamer as a "next generation" technology that is a significantly more sensitive and versatile alternative to pMHC tetramers for the detection, isolation, and phenotypic analysis of antigen-specific T cells. In particular, dodecamers are able to detect two- to fivefold more antigen-specific T cells in both human and murine CD4(+)and CD8(+)αβ T-cell compartments compared with the equivalent tetramers. The low-affinity, tetramer-negative, dodecamer-positive T cells showed comparable effector cytokine responses as those of high-affinity, tetramer-positive T cells. Dodecamers are able to detect early stage CD4(+)CD8(+)double-positive thymocytes on which T-cell receptors are 10- to 30-fold less dense than mature T cells. Dodecamers also show utility in the analysis of γδ T cells and in cytometry by time-of-flight applications. This construct has a simple structure with a central scaffold protein linked to four streptavidin molecules, each having three pMHC ligands or other molecules. The dodecamer is straightforward and inexpensive to produce and is compatible with current tetramer technology and commercially available streptavidin conjugates.
Collapse
|
7
|
Spear TT, Riley TP, Lyons GE, Callender GG, Roszkowski JJ, Wang Y, Simms PE, Scurti GM, Foley KC, Murray DC, Hellman LM, McMahan RH, Iwashima M, Garrett-Mayer E, Rosen HR, Baker BM, Nishimura MI. Hepatitis C virus-cross-reactive TCR gene-modified T cells: a model for immunotherapy against diseases with genomic instability. J Leukoc Biol 2016; 100:545-57. [PMID: 26921345 DOI: 10.1189/jlb.2a1215-561r] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 02/08/2016] [Indexed: 12/20/2022] Open
Abstract
A major obstacle hindering the development of effective immunity against viral infections, their associated disease, and certain cancers is their inherent genomic instability. Accumulation of mutations can alter processing and presentation of antigens recognized by antibodies and T cells that can lead to immune escape variants. Use of an agent that can intrinsically combat rapidly mutating viral or cancer-associated antigens would be quite advantageous in developing effective immunity against such disease. We propose that T cells harboring cross-reactive TCRs could serve as a therapeutic agent in these instances. With the use of hepatitis C virus, known for its genomic instability as a model for mutated antigen recognition, we demonstrate cross-reactivity against immunogenic and mutagenic nonstructural protein 3:1406-1415 and nonstructural protein 3:1073-1081 epitopes in PBL-derived, TCR-gene-modified T cells. These single TCR-engineered T cells can CD8-independently recognize naturally occurring and epidemiologically relevant mutant variants. TCR-peptide MHC modeling data allow us to rationalize how TCR structural properties accommodate recognition of certain mutated epitopes and how these substitutions impact the requirement of CD8 affinity enhancement for recognition. A better understanding of such TCRs' promiscuous behavior may allow for exploitation of these properties to develop novel, adoptive T cell-based therapies for viral infections and cancers exhibiting similar genomic instability.
Collapse
Affiliation(s)
- Timothy T Spear
- Department of Surgery, Cardinal Bernardin Cancer Center, Loyola University Chicago, Maywood, Illinois, USA;
| | - Timothy P Riley
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana, USA
| | - Gretchen E Lyons
- Department of Surgery, University of Chicago, Chicago, Illinois, USA; Department of Biology, Northeastern Illinois University, Chicago, Illinois, USA
| | - Glenda G Callender
- Department of Surgery, University of Chicago, Chicago, Illinois, USA; Department of Surgery, Yale University School of Medicine, New Haven, Connecticut, USA
| | | | - Yuan Wang
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana, USA
| | - Patricia E Simms
- Flow Cytometry Core Facility, Cardinal Bernardin Cancer Center, Loyola University Chicago, Maywood, Illinois, USA
| | - Gina M Scurti
- Department of Surgery, Cardinal Bernardin Cancer Center, Loyola University Chicago, Maywood, Illinois, USA
| | - Kendra C Foley
- Department of Surgery, Cardinal Bernardin Cancer Center, Loyola University Chicago, Maywood, Illinois, USA
| | - David C Murray
- Department of Surgery, Cardinal Bernardin Cancer Center, Loyola University Chicago, Maywood, Illinois, USA
| | - Lance M Hellman
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana, USA
| | - Rachel H McMahan
- Division of Gastroenterology and Hepatology, Hepatitis C Center, and Department of Medicine, University of Colorado Health Sciences Center, Aurora, Colorado, USA; and
| | - Makio Iwashima
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois, USA
| | - Elizabeth Garrett-Mayer
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, South Carolina, USA Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Hugo R Rosen
- Division of Gastroenterology and Hepatology, Hepatitis C Center, and Department of Medicine, University of Colorado Health Sciences Center, Aurora, Colorado, USA; and
| | - Brian M Baker
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana, USA
| | - Michael I Nishimura
- Department of Surgery, Cardinal Bernardin Cancer Center, Loyola University Chicago, Maywood, Illinois, USA; Department of Surgery, University of Chicago, Chicago, Illinois, USA
| |
Collapse
|