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Borowicz P, King CG, Dustin ML, Wherry EJ, Koretzky GA, Spurkland A. The future of immunology: a Lofoten perspective. Immunol Cell Biol 2024. [PMID: 38994681 DOI: 10.1111/imcb.12805] [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] [Indexed: 07/13/2024]
Abstract
This Future Challenges article summarizes views on future directions in immunological research presented at round-table discussions at the 4th Immunology workshop in the Lofoten Islands in Norway, held in August 2023, and subsequent responses to surveys sent to meeting participants. It also summarizes some of the conversations around the responsibility of scientists to communicate with the non-science community, and the approaches that we may use to meet this obligation.
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Affiliation(s)
- Pawel Borowicz
- Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Carolyn G King
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Michael L Dustin
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - E John Wherry
- Institute of Immunology and Immune Health, University of Pennsylvania, Philadelphia, PA, USA
| | - Gary A Koretzky
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Immunology and Microbiology, Cornell University, Ithaca, NY, USA
| | - Anne Spurkland
- Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
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2
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Kohlgruber AC, Dezfulian MH, Sie BM, Wang CI, Kula T, Laserson U, Larman HB, Elledge SJ. High-throughput discovery of MHC class I- and II-restricted T cell epitopes using synthetic cellular circuits. Nat Biotechnol 2024:10.1038/s41587-024-02248-6. [PMID: 38956325 DOI: 10.1038/s41587-024-02248-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 04/16/2024] [Indexed: 07/04/2024]
Abstract
Antigen discovery technologies have largely focused on major histocompatibility complex (MHC) class I-restricted human T cell receptors (TCRs), leaving methods for MHC class II-restricted and mouse TCR reactivities relatively undeveloped. Here we present TCR mapping of antigenic peptides (TCR-MAP), an antigen discovery method that uses a synthetic TCR-stimulated circuit in immortalized T cells to activate sortase-mediated tagging of engineered antigen-presenting cells (APCs) expressing processed peptides on MHCs. Live, tagged APCs can be directly purified for deconvolution by sequencing, enabling TCRs with unknown specificity to be queried against barcoded peptide libraries in a pooled screening context. TCR-MAP accurately captures self-reactivities or viral reactivities with high throughput and sensitivity for both MHC class I-restricted and class II-restricted TCRs. We elucidate problematic cross-reactivities of clinical TCRs targeting the cancer/testis melanoma-associated antigen A3 and discover targets of myocarditis-inciting autoreactive T cells in mice. TCR-MAP has the potential to accelerate T cell antigen discovery efforts in the context of cancer, infectious disease and autoimmunity.
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Affiliation(s)
- Ayano C Kohlgruber
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Genetics, Harvard University Medical School, Boston, MA, USA
- Division of Immunology, Boston Children's Hospital, Boston, MA, USA
| | - Mohammad H Dezfulian
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Genetics, Harvard University Medical School, Boston, MA, USA
| | - Brandon M Sie
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Genetics, Harvard University Medical School, Boston, MA, USA
| | - Charlotte I Wang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Genetics, Harvard University Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Tomasz Kula
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Genetics, Harvard University Medical School, Boston, MA, USA
- Society of Fellows, Harvard University, Cambridge, MA, USA
| | - Uri Laserson
- Department of Genetics and Genomic Sciences and Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - H Benjamin Larman
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Stephen J Elledge
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
- Department of Genetics, Harvard University Medical School, Boston, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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3
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Nichols C, Do-Thi VA, Peltier DC. Noncanonical microprotein regulation of immunity. Mol Ther 2024:S1525-0016(24)00324-1. [PMID: 38734902 DOI: 10.1016/j.ymthe.2024.05.021] [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: 02/08/2024] [Revised: 04/19/2024] [Accepted: 05/09/2024] [Indexed: 05/13/2024] Open
Abstract
The immune system is highly regulated but, when dysregulated, suboptimal protective or overly robust immune responses can lead to immune-mediated disorders. The genetic and molecular mechanisms of immune regulation are incompletely understood, impeding the development of more precise diagnostics and therapeutics for immune-mediated disorders. Recently, thousands of previously unrecognized noncanonical microprotein genes encoded by small open reading frames have been identified. Many of these microproteins perform critical functions, often in a cell- and context-specific manner. Several microproteins are now known to regulate immunity; however, the vast majority are uncharacterized. Therefore, illuminating what is often referred to as the "dark proteome," may present opportunities to tune immune responses more precisely. Here, we review noncanonical microprotein biology, highlight recently discovered examples regulating immunity, and discuss the potential and challenges of modulating dysregulated immune responses by targeting microproteins.
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Affiliation(s)
- Cydney Nichols
- Morris Green Scholars Program, Department of Pediatrics, Riley Hospital for Children, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Van Anh Do-Thi
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Daniel C Peltier
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Simon Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
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4
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Zdinak PM, Trivedi N, Grebinoski S, Torrey J, Martinez EZ, Martinez S, Hicks L, Ranjan R, Makani VKK, Roland MM, Kublo L, Arshad S, Anderson MS, Vignali DAA, Joglekar AV. De novo identification of CD4 + T cell epitopes. Nat Methods 2024; 21:846-856. [PMID: 38658646 PMCID: PMC11093748 DOI: 10.1038/s41592-024-02255-0] [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: 11/20/2022] [Accepted: 03/22/2024] [Indexed: 04/26/2024]
Abstract
CD4+ T cells recognize peptide antigens presented on class II major histocompatibility complex (MHC-II) molecules to carry out their function. The remarkable diversity of T cell receptor sequences and lack of antigen discovery approaches for MHC-II make profiling the specificities of CD4+ T cells challenging. We have expanded our platform of signaling and antigen-presenting bifunctional receptors to encode MHC-II molecules presenting covalently linked peptides (SABR-IIs) for CD4+ T cell antigen discovery. SABR-IIs can present epitopes to CD4+ T cells and induce signaling upon their recognition, allowing a readable output. Furthermore, the SABR-II design is modular in signaling and deployment to T cells and B cells. Here, we demonstrate that SABR-IIs libraries presenting endogenous and non-contiguous epitopes can be used for antigen discovery in the context of type 1 diabetes. SABR-II libraries provide a rapid, flexible, scalable and versatile approach for de novo identification of CD4+ T cell ligands from single-cell RNA sequencing data using experimental and computational approaches.
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Affiliation(s)
- Paul M Zdinak
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Center for Systems Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Program in Microbiology and Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Nishtha Trivedi
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Center for Systems Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Stephanie Grebinoski
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Program in Microbiology and Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jessica Torrey
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Center for Systems Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Eduardo Zarate Martinez
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Center for Systems Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Microbiology and Immunology Diversity Scholars Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Salome Martinez
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Center for Systems Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Louise Hicks
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Center for Systems Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Rashi Ranjan
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Center for Systems Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Venkata Krishna Kanth Makani
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Center for Systems Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Mary Melissa Roland
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Center for Systems Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Lyubov Kublo
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Center for Systems Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Sanya Arshad
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Center for Systems Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Mark S Anderson
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
| | - Dario A A Vignali
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Alok V Joglekar
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
- Center for Systems Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
- Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA.
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Banerjee A, Pattinson DJ, Wincek CL, Bunk P, Chapin SR, Navlakha S, Meyer HV. BATMAN: Improved T cell receptor cross-reactivity prediction benchmarked on a comprehensive mutational scan database. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.22.576714. [PMID: 38370810 PMCID: PMC10871174 DOI: 10.1101/2024.01.22.576714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Predicting T cell receptor (TCR) activation is challenging due to the lack of both unbiased benchmarking datasets and computational methods that are sensitive to small mutations to a peptide. To address these challenges, we curated a comprehensive database encompassing complete single amino acid mutational assays of 10,750 TCR-peptide pairs, centered around 14 immunogenic peptides against 66 TCRs. We then present an interpretable Bayesian model, called BATMAN, that can predict the set of peptides that activates a TCR. When validated on our database, BATMAN outperforms existing methods by 20% and reveals important biochemical predictors of TCR-peptide interactions.
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Affiliation(s)
- Amitava Banerjee
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - David J Pattinson
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53711, USA
| | - Cornelia L. Wincek
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
- Heidelberg University, 69117 Heidelberg, Germany
| | - Paul Bunk
- School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Sarah R. Chapin
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Saket Navlakha
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Hannah V. Meyer
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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Smith BE, Chan AO, Birnbaum ME. Re-centauring T cell antigen discovery around CD4 + T cells. CELL REPORTS METHODS 2024; 4:100694. [PMID: 38262348 PMCID: PMC10832272 DOI: 10.1016/j.crmeth.2023.100694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 12/27/2023] [Accepted: 12/28/2023] [Indexed: 01/25/2024]
Abstract
In a recent issue of Cell, Dezfulian et al. develop a genome-scale platform to enable high-throughput identification of CD4+ T cell epitopes. This platform enables unbiased screens to discover antigens recognized by CD4+ T cells in cancer, infectious diseases, and autoimmunity.
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Affiliation(s)
- Blake E Smith
- Program in Immunology, Harvard Medical School, Boston, MA, USA; Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - Amanda O Chan
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Michael E Birnbaum
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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