1
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Grant M, Ni Lee L, Chinnakannan S, Tong O, Kwok J, Cianci N, Tillman L, Saha A, Pereira Almeida V, Leung C. Unlocking cancer vaccine potential: What are the key factors? Hum Vaccin Immunother 2024; 20:2331486. [PMID: 38564321 DOI: 10.1080/21645515.2024.2331486] [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: 01/08/2024] [Accepted: 03/13/2024] [Indexed: 04/04/2024] Open
Abstract
Cancer is a global health challenge, with changing demographics and lifestyle factors producing an increasing burden worldwide. Screening advancements are enabling earlier diagnoses, but current cancer immunotherapies only induce remission in a small proportion of patients and come at a high cost. Cancer vaccines may offer a solution to these challenges, but they have been mired by poor results in past decades. Greater understanding of tumor biology, coupled with the success of vaccine technologies during the COVID-19 pandemic, has reinvigorated cancer vaccine development. With the first signs of efficacy being reported, cancer vaccines may be beginning to fulfill their potential. Solid tumors, however, present different hurdles than infectious diseases. Combining insights from previous cancer vaccine clinical development and contemporary knowledge of tumor immunology, we ask: who are the 'right' patients, what are the 'right' targets, and which are the 'right' modalities to maximize the chances of cancer vaccine success?
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2
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Pogorelyy MV, Kirk AM, Adhikari S, Minervina AA, Sundararaman B, Vegesana K, Brice DC, Scott ZB, Thomas PG. TIRTL-seq: Deep, quantitative, and affordable paired TCR repertoire sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.16.613345. [PMID: 39345544 PMCID: PMC11430070 DOI: 10.1101/2024.09.16.613345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
α/β T cells are key players in adaptive immunity. The specificity of T cells is determined by the sequences of the hypervariable T cell receptor (TCR) α and β chains. Although bulk TCR sequencing offers a cost-effective approach for in-depth TCR repertoire profiling, it does not provide chain pairings, which are essential for determining T cell specificity. In contrast, single-cell TCR sequencing technologies produce paired chain data, but are limited in throughput to thousands of cells and are cost-prohibitive for cohort-scale studies. Here, we present TIRTL-seq (Throughput-Intensive Rapid TCR Library sequencing), a novel approach that generates ready-to-sequence TCR libraries from live cells in less than 7 hours. The protocol is optimized for use with non-contact liquid handlers in an automation-friendly 384-well plate format. Reaction volume miniaturization reduces library preparation costs to <$0.50 per well. The core principle of TIRTL-seq is the parallel generation of hundreds of libraries providing multiple biological replicates from a single sample that allows precise inference of both frequencies of individual clones and TCR chain pairings from well-occurrence patterns. We demonstrate scalability of our approach up to 1 million unique paired αβTCR clonotypes corresponding to over 30 million T cells per sample at a cost of less than $2000. For a sample of 10 million cells the cost is ~$200. We benchmarked TIRTL-seq against state-of-the-art 5'RACE bulk TCR-seq and 10x Genomics Chromium technologies on longitudinal samples. We show that TIRTL-seq is able to quantitatively identify expanding and contracting clonotypes between timepoints while providing accurate TCR chain pairings, including distinct temporal dynamics of SARS-CoV-2-specific and EBV-specific CD8+ T cell responses after infection. While clonal expansion was followed by sharp contraction for SARS-CoV-2 specific TCRs, EBV-specific TCRs remained stable once established. The sequences of both α and β TCR chains are essential for determining T cell specificity. As the field moves towards greater applications in diagnostics and immunotherapy that rely on TCR specificity, we anticipate that our scalable paired TCR sequencing methodology will be instrumental for collecting large paired-chain datasets and ultimately extracting therapeutically relevant information from the TCR repertoire.
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Affiliation(s)
| | | | | | | | | | - Kasi Vegesana
- St. Jude Children's Research Hospital, Memphis, TN, USA
| | - David C Brice
- St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Paul G Thomas
- St. Jude Children's Research Hospital, Memphis, TN, 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; 32:2905-2929. [PMID: 38734902 PMCID: PMC11403233 DOI: 10.1016/j.ymthe.2024.05.021] [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: 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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Talucci I, Maric HM. Epitope landscape in autoimmune neurological disease and beyond. Trends Pharmacol Sci 2024; 45:768-780. [PMID: 39181736 DOI: 10.1016/j.tips.2024.07.007] [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: 06/05/2024] [Revised: 07/08/2024] [Accepted: 07/19/2024] [Indexed: 08/27/2024]
Abstract
Autoantibody binding has a central role in autoimmune diseases and has also been linked to cancer, infections, and behavioral disorders. Autoimmune neurological diseases remain misclassified also due to an incomplete understanding of the underlying disease-specific epitopes. Such epitopes are crucial for both pathology and diagnosis, but have historically been overlooked. Recent technological advancements have enabled the exploration of these epitopes, potentially opening novel clinical avenues. The precise identification of novel B and T cell epitopes and their autoreactivity has led to the discovery of autoantigen-specific biomarkers for patients at high risk of autoimmune neurological diseases. In this review, we propose utilizing newly available synthetic and cellular-surface display technologies and guide epitope-focused studies to unlock the potential of disease-specific epitopes for improving diagnosis and treatments. Additionally, we offer recommendations to guide emerging epitope-focused studies to broaden the current landscape.
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Affiliation(s)
- Ivan Talucci
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, Germany; Department of Neurology, University Hospital Würzburg, Germany
| | - Hans M Maric
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, Germany.
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5
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Sugrue JA, Duffy D. Systems vaccinology studies - achievements and future potential. Microbes Infect 2024; 26:105318. [PMID: 38460935 DOI: 10.1016/j.micinf.2024.105318] [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: 07/02/2023] [Revised: 02/22/2024] [Accepted: 03/01/2024] [Indexed: 03/11/2024]
Abstract
Human immune responses to vaccination are variable both within and between populations. Systems vaccinology, which is the application of multi-omics technologies to vaccine studies, seeks to understand such variation and predict responses to optimise vaccine strategies. Here, we outline new approaches to systems vaccinology, focusing on the incorporation of additional cohorts, endpoints and technologies.
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Affiliation(s)
- Jamie A Sugrue
- Translational Immunology Unit, Institut Pasteur, Université de Paris Cité, F75015, Paris, France
| | - Darragh Duffy
- Translational Immunology Unit, Institut Pasteur, Université de Paris Cité, F75015, Paris, France.
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6
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Sharma G, Round J, Teng F, Ali Z, May C, Yung E, Holt RA. A synthetic cytotoxic T cell platform for rapidly prototyping TCR function. NPJ Precis Oncol 2024; 8:182. [PMID: 39160299 PMCID: PMC11333705 DOI: 10.1038/s41698-024-00669-9] [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: 01/02/2024] [Accepted: 07/30/2024] [Indexed: 08/21/2024] Open
Abstract
Current tools for functionally profiling T cell receptors with respect to cytotoxic potency and cross-reactivity are hampered by difficulties in establishing model systems to test these proteins in the contexts of different HLA alleles and against broad arrays of potential antigens. We have implemented a granzyme-activatable sensor of T cell cytotoxicity in a universal prototyping platform which enables facile recombinant expression of any combination of TCR-, peptide-, and class I MHC-coding sequences and direct assessment of resultant responses. This system consists of an engineered cell platform based on the immortalized natural killer cell line, YT-Indy, and the MHC-null antigen-presenting cell line, K562. These cells were engineered to furnish the YT-Indy/K562 pair with appropriate protein domains required for recombinant TCR expression and function in a non-T cell chassis, integrate a fluorescence-based target-centric early detection reporter of cytotoxic function, and deploy a set of protective genetic interventions designed to preserve antigen-presenting cells for subsequent capture and downstream characterization. Our data show successful reconstitution of the surface TCR complex in the YT-Indy cell line at biologically relevant levels. We also demonstrate successful induction and highly sensitive detection of antigen-specific response in multiple distinct model TCRs. Additionally, we monitored destruction of targets in co-culture and found that our survival-optimized system allowed for complete preservation after 24 h exposure to cytotoxic effectors. With this bioplatform, we anticipate investigators will be empowered to rapidly express and characterize T cell receptor responses, generate knowledge regarding the patterns of T cell receptor recognition, and optimize therapeutic T cell receptors.
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Affiliation(s)
- Govinda Sharma
- Michael Smith Genome Sciences Centre, British Columbia Cancer Research Institute, Vancouver, BC, Canada
| | - James Round
- Michael Smith Genome Sciences Centre, British Columbia Cancer Research Institute, Vancouver, BC, Canada
| | - Fei Teng
- Michael Smith Genome Sciences Centre, British Columbia Cancer Research Institute, Vancouver, BC, Canada
| | - Zahra Ali
- Michael Smith Genome Sciences Centre, British Columbia Cancer Research Institute, Vancouver, BC, Canada
| | - Chris May
- Michael Smith Genome Sciences Centre, British Columbia Cancer Research Institute, Vancouver, BC, Canada
| | - Eric Yung
- Michael Smith Genome Sciences Centre, British Columbia Cancer Research Institute, Vancouver, BC, Canada
| | - Robert A Holt
- Michael Smith Genome Sciences Centre, British Columbia Cancer Research Institute, Vancouver, BC, Canada.
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.
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7
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Hayashi H, Mak TW, Tanaka Y, Kubo Y, Izumida M, Urae R, Matsuyama T. Development of a highly sensitive platform for protein-protein interaction detection and regulation of T cell function. Proc Natl Acad Sci U S A 2024; 121:e2318190121. [PMID: 39106307 PMCID: PMC11331103 DOI: 10.1073/pnas.2318190121] [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: 10/19/2023] [Accepted: 06/28/2024] [Indexed: 08/09/2024] Open
Abstract
We developed a highly sensitive assay for detecting protein-protein interaction using chimeric receptors comprising two molecules of interest in the extracellular domain and interferon alpha and beta receptor subunit 1 or 2 (IFNAR1/2) in the intracellular domain. This intracellular IFNAR1/2 reconstitution system (IFNARRS) proved markedly more sensitive than the NanoBiT system, currently considered one of the best detection systems for protein interaction. Employing chimeric receptors with extracellular domains from the IFNγ or IL-2 receptor and the intracellular domains of IFNAR1/2, the IFNARRS system effectively identifies low IFNγ or IL-2 levels. Cells stably expressing these chimeric receptors responded to IFNγ secreted by activated T cells following various stimuli, including a specific peptide-antigen. The activation signals were further enhanced by the expression of relevant genes, such as costimulators, via IFN-stimulated response elements in the promoters. Besides IFNγ or IL-2, the IFNARRS system demonstrated the capability to detect other cytokines by using the corresponding extracellular domains from these target cytokine receptors.
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Affiliation(s)
- Hideki Hayashi
- Medical University Research Administrator, Nagasaki University School of Medicine, Nagasaki852-8523, Japan
- Centre for Oncology and Immunology, Hong Kong Science Park, Hong Kong Special Administrative Region 999077, China
| | - Tak Wah Mak
- Center for Medical Innovation, Nagasaki University, Nagasaki852-8588, Japan
- Princess Margaret Cancer Center, University Health Network, Toronto, ONM5G 2M9, Canada
- Department of Pathology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region 999077, China
| | - Yoshimasa Tanaka
- Centre for Oncology and Immunology, Hong Kong Science Park, Hong Kong Special Administrative Region 999077, China
| | - Yoshinao Kubo
- Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Nagasaki852-8523, Japan
| | - Mai Izumida
- Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Nagasaki852-8523, Japan
| | - Ryuji Urae
- Souseikai Clinical Research Center, Fukuoka812-0025, Japan
| | - Toshifumi Matsuyama
- Department of Forensic Pathology and Science, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki852-8523, Japan
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8
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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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9
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Welters ML, Stadler S, Anastasopoulou V, Bullinger L, Leisegang M, Kammertöns T, Welters C, Hansmann L. Oligonucleotide library screening for identification of virus-specific T-cell receptors. Eur J Immunol 2024; 54:e2350908. [PMID: 38501894 DOI: 10.1002/eji.202350908] [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: 11/19/2023] [Revised: 03/04/2024] [Accepted: 03/06/2024] [Indexed: 03/20/2024]
Abstract
We demonstrate an optimized oligonucleotide library-based approach for the identification of virus-reactive T-cell receptors using Epstein-Barr virus as an example. HEK293T served as antigen-presenting cells and were co-cultured with human T cells that were transduced with T-cell receptors in question. T-cell activation was detected by CD137 expression.
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Affiliation(s)
- Marthe-Lina Welters
- Department of Hematology, Oncology and Tumor Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Serena Stadler
- Department of Hematology, Oncology and Tumor Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Lars Bullinger
- Department of Hematology, Oncology and Tumor Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matthias Leisegang
- German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Charité - Universitätsmedizin Berlin, Institute of Immunology, Berlin, Germany
- David and Etta Jonas Center for Cellular Therapy, The University of Chicago, Chicago, Illinois, USA
| | - Thomas Kammertöns
- Charité - Universitätsmedizin Berlin, Institute of Immunology, Berlin, Germany
| | - Carlotta Welters
- Department of Hematology, Oncology and Tumor Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Leo Hansmann
- Department of Hematology, Oncology and Tumor Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
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10
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Bulashevska A, Nacsa Z, Lang F, Braun M, Machyna M, Diken M, Childs L, König R. Artificial intelligence and neoantigens: paving the path for precision cancer immunotherapy. Front Immunol 2024; 15:1394003. [PMID: 38868767 PMCID: PMC11167095 DOI: 10.3389/fimmu.2024.1394003] [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: 02/29/2024] [Accepted: 05/13/2024] [Indexed: 06/14/2024] Open
Abstract
Cancer immunotherapy has witnessed rapid advancement in recent years, with a particular focus on neoantigens as promising targets for personalized treatments. The convergence of immunogenomics, bioinformatics, and artificial intelligence (AI) has propelled the development of innovative neoantigen discovery tools and pipelines. These tools have revolutionized our ability to identify tumor-specific antigens, providing the foundation for precision cancer immunotherapy. AI-driven algorithms can process extensive amounts of data, identify patterns, and make predictions that were once challenging to achieve. However, the integration of AI comes with its own set of challenges, leaving space for further research. With particular focus on the computational approaches, in this article we have explored the current landscape of neoantigen prediction, the fundamental concepts behind, the challenges and their potential solutions providing a comprehensive overview of this rapidly evolving field.
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Affiliation(s)
- Alla Bulashevska
- Host-Pathogen-Interactions, Paul-Ehrlich-Institut, Langen, Germany
| | - Zsófia Nacsa
- Host-Pathogen-Interactions, Paul-Ehrlich-Institut, Langen, Germany
| | - Franziska Lang
- TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg University gGmbH, Mainz, Germany
| | - Markus Braun
- Host-Pathogen-Interactions, Paul-Ehrlich-Institut, Langen, Germany
| | - Martin Machyna
- Host-Pathogen-Interactions, Paul-Ehrlich-Institut, Langen, Germany
| | - Mustafa Diken
- TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg University gGmbH, Mainz, Germany
| | - Liam Childs
- Host-Pathogen-Interactions, Paul-Ehrlich-Institut, Langen, Germany
| | - Renate König
- Host-Pathogen-Interactions, Paul-Ehrlich-Institut, Langen, Germany
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11
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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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12
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Tan D, Kang N, Zhu Y, Hou J, Wang H, Xu H, Zu C, Gao Z, Liu M, Liu N, Deng Q, Lu H, Liu J, Xie Y. Construction and efficacy testing of DNA vaccines containing HLA-A*02:01-restricted SARS-CoV-2 T-cell epitopes predicted by immunoinformatics. Acta Biochim Biophys Sin (Shanghai) 2024; 56:986-996. [PMID: 38655616 PMCID: PMC11322877 DOI: 10.3724/abbs.2024039] [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: 12/25/2023] [Accepted: 01/31/2024] [Indexed: 04/26/2024] Open
Abstract
Vaccines play essential roles in the fight against the COVID-19 pandemic. The development and assessment of COVID-19 vaccines have generally focused on the induction and boosting of neutralizing antibodies targeting the SARS-CoV-2 spike (S) protein. Due to rapid and continuous variation in the S protein, such vaccines need to be regularly updated to match newly emerged dominant variants. T-cell vaccines that target MHC I- or II-restricted epitopes in both structural and non-structural viral proteins have the potential to induce broadly cross-protective and long-lasting responses. In this work, the entire proteome encoded by SARS-CoV-2 (Wuhan-hu-1) is subjected to immunoinformatics-based prediction of HLA-A*02:01-restricted epitopes. The immunogenicity of the predicted epitopes is evaluated using peripheral blood mononuclear cells from convalescent Wuhan-hu-1-infected patients. Furthermore, predicted epitopes that are conserved across major SARS-CoV-2 lineages and variants are used to construct DNA vaccines expressing multi-epitope polypeptides. Most importantly, two DNA vaccine constructs induce epitope-specific CD8 + T-cell responses in a mouse model of HLA-A*02:01 restriction and protect immunized mice from challenge with Wuhan-hu-1 virus after hACE2 transduction. These data provide candidate T-cell epitopes useful for the development of T-cell vaccines against SARS-CoV-2 and demonstrate a strategy for quick T-cell vaccine candidate development applicable to other emerging pathogens.
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Affiliation(s)
- Dan Tan
- Key Laboratory of Medical Molecular Virology (NHC & MOE & CAMS)Shanghai Institute of Infectious Diseases and BiosecurityDepartment of Medical Microbiology and ParasitologySchool of Basic Medical SciencesShanghai Medical CollegeFudan UniversityShanghai200031China
| | - Ning Kang
- Key Laboratory of Medical Molecular Virology (NHC & MOE & CAMS)Shanghai Institute of Infectious Diseases and BiosecurityDepartment of Medical Microbiology and ParasitologySchool of Basic Medical SciencesShanghai Medical CollegeFudan UniversityShanghai200031China
| | - Yuanfei Zhu
- Key Laboratory of Medical Molecular Virology (NHC & MOE & CAMS)Shanghai Institute of Infectious Diseases and BiosecurityDepartment of Medical Microbiology and ParasitologySchool of Basic Medical SciencesShanghai Medical CollegeFudan UniversityShanghai200031China
| | - Jia Hou
- Key Laboratory of Medical Molecular Virology (NHC & MOE & CAMS)Shanghai Institute of Infectious Diseases and BiosecurityDepartment of Medical Microbiology and ParasitologySchool of Basic Medical SciencesShanghai Medical CollegeFudan UniversityShanghai200031China
| | - Hanqing Wang
- Key Laboratory of Medical Molecular Virology (NHC & MOE & CAMS)Shanghai Institute of Infectious Diseases and BiosecurityDepartment of Medical Microbiology and ParasitologySchool of Basic Medical SciencesShanghai Medical CollegeFudan UniversityShanghai200031China
| | - Huijun Xu
- Key Laboratory of Medical Molecular Virology (NHC & MOE & CAMS)Shanghai Institute of Infectious Diseases and BiosecurityDepartment of Medical Microbiology and ParasitologySchool of Basic Medical SciencesShanghai Medical CollegeFudan UniversityShanghai200031China
| | - Cheng Zu
- Key Laboratory of Medical Molecular Virology (NHC & MOE & CAMS)Shanghai Institute of Infectious Diseases and BiosecurityDepartment of Medical Microbiology and ParasitologySchool of Basic Medical SciencesShanghai Medical CollegeFudan UniversityShanghai200031China
| | - Zixiang Gao
- Key Laboratory of Medical Molecular Virology (NHC & MOE & CAMS)Shanghai Institute of Infectious Diseases and BiosecurityDepartment of Medical Microbiology and ParasitologySchool of Basic Medical SciencesShanghai Medical CollegeFudan UniversityShanghai200031China
| | - Mu Liu
- Key Laboratory of Medical Molecular Virology (NHC & MOE & CAMS)Shanghai Institute of Infectious Diseases and BiosecurityDepartment of Medical Microbiology and ParasitologySchool of Basic Medical SciencesShanghai Medical CollegeFudan UniversityShanghai200031China
| | - Nannan Liu
- Key Laboratory of Medical Molecular Virology (NHC & MOE & CAMS)Shanghai Institute of Infectious Diseases and BiosecurityDepartment of Medical Microbiology and ParasitologySchool of Basic Medical SciencesShanghai Medical CollegeFudan UniversityShanghai200031China
| | - Qiang Deng
- Key Laboratory of Medical Molecular Virology (NHC & MOE & CAMS)Shanghai Institute of Infectious Diseases and BiosecurityDepartment of Medical Microbiology and ParasitologySchool of Basic Medical SciencesShanghai Medical CollegeFudan UniversityShanghai200031China
| | - Hongzhou Lu
- Shanghai Public Health Clinical CenterFudan UniversityShanghai201508China
- National Clinical Research Centre for Infectious Diseasesthe Third People’s Hospital of ShenzhenThe Second Affiliated Hospital of Southern University of Science and TechnologyShenzhen518112China
| | - Jing Liu
- Key Laboratory of Medical Molecular Virology (NHC & MOE & CAMS)Shanghai Institute of Infectious Diseases and BiosecurityDepartment of Medical Microbiology and ParasitologySchool of Basic Medical SciencesShanghai Medical CollegeFudan UniversityShanghai200031China
| | - Youhua Xie
- Key Laboratory of Medical Molecular Virology (NHC & MOE & CAMS)Shanghai Institute of Infectious Diseases and BiosecurityDepartment of Medical Microbiology and ParasitologySchool of Basic Medical SciencesShanghai Medical CollegeFudan UniversityShanghai200031China
- Shanghai Public Health Clinical CenterFudan UniversityShanghai201508China
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13
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Marrer-Berger E, Nicastri A, Augustin A, Kramar V, Liao H, Hanisch LJ, Carpy A, Weinzierl T, Durr E, Schaub N, Nudischer R, Ortiz-Franyuti D, Breous-Nystrom E, Stucki J, Hobi N, Raggi G, Cabon L, Lezan E, Umaña P, Woodhouse I, Bujotzek A, Klein C, Ternette N. The physiological interactome of TCR-like antibody therapeutics in human tissues. Nat Commun 2024; 15:3271. [PMID: 38627373 PMCID: PMC11021511 DOI: 10.1038/s41467-024-47062-5] [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: 07/05/2022] [Accepted: 03/19/2024] [Indexed: 04/19/2024] Open
Abstract
Selective binding of TCR-like antibodies that target a single tumour-specific peptide antigen presented by human leukocyte antigens (HLA) is the absolute prerequisite for their therapeutic suitability and patient safety. To date, selectivity assessment has been limited to peptide library screening and predictive modeling. We developed an experimental platform to de novo identify interactomes of TCR-like antibodies directly in human tissues using mass spectrometry. As proof of concept, we confirm the target epitope of a MAGE-A4-specific TCR-like antibody. We further determine cross-reactive peptide sequences for ESK1, a TCR-like antibody with known off-target activity, in human liver tissue. We confirm off-target-induced T cell activation and ESK1-mediated liver spheroid killing. Off-target sequences feature an amino acid motif that allows a structural groove-coordination mimicking that of the target peptide, therefore allowing the interaction with the engager molecule. We conclude that our strategy offers an accurate, scalable route for evaluating the non-clinical safety profile of TCR-like antibody therapeutics prior to first-in-human clinical application.
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Affiliation(s)
- Estelle Marrer-Berger
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, 4070, Basel, Switzerland
| | - Annalisa Nicastri
- The Jenner Institute, Old Road Campus Research Building, Oxford, OX37DQ, UK
- Centre for Immuno-Oncology, Old Road Campus Research Building, Oxford, OX37DQ, UK
| | - Angelique Augustin
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, 4070, Basel, Switzerland
| | - Vesna Kramar
- Roche Innovation Center Zürich, 8952, Schlieren, Switzerland
| | - Hanqing Liao
- The Jenner Institute, Old Road Campus Research Building, Oxford, OX37DQ, UK
- Centre for Immuno-Oncology, Old Road Campus Research Building, Oxford, OX37DQ, UK
| | | | - Alejandro Carpy
- Roche Pharma Research & Early Development, Roche Innovation Center Munich, 82377, Penzberg, Germany
| | - Tina Weinzierl
- Roche Innovation Center Zürich, 8952, Schlieren, Switzerland
| | - Evelyne Durr
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, 4070, Basel, Switzerland
| | - Nathalie Schaub
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, 4070, Basel, Switzerland
| | - Ramona Nudischer
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, 4070, Basel, Switzerland
| | - Daniela Ortiz-Franyuti
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, 4070, Basel, Switzerland
| | - Ekaterina Breous-Nystrom
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, 4070, Basel, Switzerland
| | - Janick Stucki
- Alveolix AG, Swiss Organs-on-Chip Innovation, 3010, Bern, Switzerland
| | - Nina Hobi
- Alveolix AG, Swiss Organs-on-Chip Innovation, 3010, Bern, Switzerland
| | - Giulia Raggi
- Alveolix AG, Swiss Organs-on-Chip Innovation, 3010, Bern, Switzerland
| | - Lauriane Cabon
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, 4070, Basel, Switzerland
| | - Emmanuelle Lezan
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, 4070, Basel, Switzerland
| | - Pablo Umaña
- Roche Innovation Center Zürich, 8952, Schlieren, Switzerland
| | - Isaac Woodhouse
- The Jenner Institute, Old Road Campus Research Building, Oxford, OX37DQ, UK
- Centre for Immuno-Oncology, Old Road Campus Research Building, Oxford, OX37DQ, UK
| | - Alexander Bujotzek
- Roche Pharma Research & Early Development, Roche Innovation Center Munich, 82377, Penzberg, Germany
| | - Christian Klein
- Roche Innovation Center Zürich, 8952, Schlieren, Switzerland.
| | - Nicola Ternette
- The Jenner Institute, Old Road Campus Research Building, Oxford, OX37DQ, UK.
- Centre for Immuno-Oncology, Old Road Campus Research Building, Oxford, OX37DQ, UK.
- Department of Pharmaceutical Sciences, University of Utrecht, 3584, CH, Utrecht, The Netherlands.
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14
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Shao W, Yao Y, Yang L, Li X, Ge T, Zheng Y, Zhu Q, Ge S, Gu X, Jia R, Song X, Zhuang A. Novel insights into TCR-T cell therapy in solid neoplasms: optimizing adoptive immunotherapy. Exp Hematol Oncol 2024; 13:37. [PMID: 38570883 PMCID: PMC10988985 DOI: 10.1186/s40164-024-00504-8] [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: 12/08/2023] [Accepted: 03/21/2024] [Indexed: 04/05/2024] Open
Abstract
Adoptive immunotherapy in the T cell landscape exhibits efficacy in cancer treatment. Over the past few decades, genetically modified T cells, particularly chimeric antigen receptor T cells, have enabled remarkable strides in the treatment of hematological malignancies. Besides, extensive exploration of multiple antigens for the treatment of solid tumors has led to clinical interest in the potential of T cells expressing the engineered T cell receptor (TCR). TCR-T cells possess the capacity to recognize intracellular antigen families and maintain the intrinsic properties of TCRs in terms of affinity to target epitopes and signal transduction. Recent research has provided critical insight into their capability and therapeutic targets for multiple refractory solid tumors, but also exposes some challenges for durable efficacy. In this review, we describe the screening and identification of available tumor antigens, and the acquisition and optimization of TCRs for TCR-T cell therapy. Furthermore, we summarize the complete flow from laboratory to clinical applications of TCR-T cells. Last, we emerge future prospects for improving therapeutic efficacy in cancer world with combination therapies or TCR-T derived products. In conclusion, this review depicts our current understanding of TCR-T cell therapy in solid neoplasms, and provides new perspectives for expanding its clinical applications and improving therapeutic efficacy.
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Affiliation(s)
- Weihuan Shao
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China
| | - Yiran Yao
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China
| | - Ludi Yang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China
| | - Xiaoran Li
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China
| | - Tongxin Ge
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China
| | - Yue Zheng
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China
| | - Qiuyi Zhu
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China
| | - Shengfang Ge
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China
| | - Xiang Gu
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China
| | - Renbing Jia
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China.
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China.
| | - Xin Song
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China.
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China.
| | - Ai Zhuang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China.
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China.
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15
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Wang Y, Wang Z, Yang J, Lei X, Liu Y, Frankiw L, Wang J, Li G. Deciphering Membrane-Protein Interactions and High-Throughput Antigen Identification with Cell Doublets. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305750. [PMID: 38342599 PMCID: PMC10987144 DOI: 10.1002/advs.202305750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 01/02/2024] [Indexed: 02/13/2024]
Abstract
Deciphering cellular interactions is essential to both understand the mechanisms underlying a broad range of human diseases, but also to manipulate therapies targeting these diseases. Here, the formation of cell doublets resulting from specific membrane ligand-receptor interactions is discovered. Based on this phenomenon, the study developed DoubletSeeker, a novel high-throughput method for the reliable identification of ligand-receptor interactions. The study shows that DoubletSeeker can accurately identify T cell receptor (TCR)-antigen interactions with high sensitivity and specificity. Notably, DoubletSeeker effectively captured paired TCR-peptide major histocompatibility complex (pMHC) information during a highly complex library-on-library screening and successfully identified three mutant TCRs that specifically recognize the MART-1 epitope. In turn, DoubletSeeker can act as an antigen discovery platform that allows for the development of novel immunotherapy targets, making it valuable for investigating fundamental tumor immunology.
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Affiliation(s)
- Yuqian Wang
- National Key Laboratory of Immunity and InflammationSuzhou Institute of Systems MedicineChinese Academy of Medical Sciences & Peking Union Medical CollegeSuzhouJiangsu215123China
- Key Laboratory of Synthetic Biology Regulatory ElementSuzhou Institute of Systems MedicineChinese Academy of Medical Sciences & Peking Union Medical CollegeSuzhouJiangsu215123China
| | - Zhe Wang
- National Key Laboratory of Immunity and InflammationSuzhou Institute of Systems MedicineChinese Academy of Medical Sciences & Peking Union Medical CollegeSuzhouJiangsu215123China
- Key Laboratory of Synthetic Biology Regulatory ElementSuzhou Institute of Systems MedicineChinese Academy of Medical Sciences & Peking Union Medical CollegeSuzhouJiangsu215123China
| | - Juan Yang
- National Key Laboratory of Immunity and InflammationSuzhou Institute of Systems MedicineChinese Academy of Medical Sciences & Peking Union Medical CollegeSuzhouJiangsu215123China
- Key Laboratory of Synthetic Biology Regulatory ElementSuzhou Institute of Systems MedicineChinese Academy of Medical Sciences & Peking Union Medical CollegeSuzhouJiangsu215123China
| | - Xiaobo Lei
- NHC Key Laboratory of Systems Biology of PathogensInstitute of Pathogen BiologyChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100730China
| | - Yisu Liu
- National Key Laboratory of Immunity and InflammationSuzhou Institute of Systems MedicineChinese Academy of Medical Sciences & Peking Union Medical CollegeSuzhouJiangsu215123China
- Key Laboratory of Synthetic Biology Regulatory ElementSuzhou Institute of Systems MedicineChinese Academy of Medical Sciences & Peking Union Medical CollegeSuzhouJiangsu215123China
| | - Luke Frankiw
- Department of PediatricsBoston Children's HospitalBostonMA02115USA
| | - Jianwei Wang
- NHC Key Laboratory of Systems Biology of PathogensInstitute of Pathogen BiologyChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100730China
| | - Guideng Li
- National Key Laboratory of Immunity and InflammationSuzhou Institute of Systems MedicineChinese Academy of Medical Sciences & Peking Union Medical CollegeSuzhouJiangsu215123China
- Key Laboratory of Synthetic Biology Regulatory ElementSuzhou Institute of Systems MedicineChinese Academy of Medical Sciences & Peking Union Medical CollegeSuzhouJiangsu215123China
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16
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Ren Y, Manoharan T, Liu B, Cheng CZM, En Siew B, Cheong WK, Lee KY, Tan IJW, Lieske B, Tan KK, Chia G. Circular RNA as a source of neoantigens for cancer vaccines. J Immunother Cancer 2024; 12:e008402. [PMID: 38508656 PMCID: PMC10952939 DOI: 10.1136/jitc-2023-008402] [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] [Accepted: 03/03/2024] [Indexed: 03/22/2024] Open
Abstract
BACKGROUND The effectiveness of somatic neoantigen-based immunotherapy is often hindered by the limited number of mutations in tumors with low to moderate mutation burden. Focusing on microsatellite-stable colorectal cancer (CRC), this study investigates the potential of tumor-associated circular RNAs (circRNAs) as an alternative source of neoepitopes in CRC. METHODS Tumor-associated circRNAs in CRC were identified using the MiOncoCirc database and ribo-depletion RNA sequencing of paired clinical normal and tumor samples. Candidate circRNA expression was validated by quantitative real-time PCR (RT-qPCR) using divergent primers. TransCirc database was used for translation prediction. Human leukocyte antigen binding affinity of open reading frames from potentially translatable circRNA was predicted using pVACtools. Strong binders from messenger RNA-encoded proteins were excluded using BlastP. The immunogenicity of the candidate antigens was functionally validated through stimulation of naïve CD8+ T cells against the predicted neoepitopes and subsequent analysis of the T cells through enzyme-linked immunospot (ELISpot) assay, intracellular cytokine staining (ICS) and granzyme B (GZMB) reporter. The cytotoxicity of T cells trained with antigen peptides was further tested using patient-derived organoids. RESULTS We identified a neoepitope from circRAPGEF5 that is upregulated in CRC tumor samples from MiOncoCirc database, and two neoepitopes from circMYH9, which is upregulated across various tumor samples from our matched clinical samples. The translation potential of candidate peptides was supported by Clinical Proteomic Tumor Analysis Consortium database using PepQuery. The candidate peptides elicited antigen-specific T cells response and expansion, evidenced by various assays including ELISpot, ICS and GZMB reporter. Furthermore, T cells trained with circMYH9 peptides were able to specifically target and eliminate tumor-derived organoids but not match normal organoids. This observation underscores the potential of circRNAs as a source of immunogenic neoantigens. Lastly, circMYH9 was enriched in the liquid biopsies of patients with CRC, thus enabling a detection-to-vaccination treatment strategy for patients with CRC. CONCLUSIONS Our findings underscore the feasibility of tumor-associated circRNAs as an alternative source of neoantigens for cancer vaccines targeting tumors with moderate mutation levels.
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Affiliation(s)
- Yi Ren
- Department of Pharmacy, National University of Singapore, Singapore
- NUS iHealthtech, Singapore
| | - Thamizhanban Manoharan
- Department of Pharmacy, National University of Singapore, Singapore
- NUS iHealthtech, Singapore
| | - Beijia Liu
- Department of Pharmacy, National University of Singapore, Singapore
| | - Cyrus Zai Ming Cheng
- Department of Pharmacy, National University of Singapore, Singapore
- NUS iHealthtech, Singapore
| | - Bei En Siew
- Department of Surgery, National University of Singapore, Singapore
- Department of Surgery, National University Hospital, Singapore
| | - Wai-Kit Cheong
- Department of Surgery, National University Hospital, Singapore
| | - Kai Yin Lee
- Department of Surgery, National University Hospital, Singapore
| | - Ian Jse-Wei Tan
- Department of Surgery, National University Hospital, Singapore
| | - Bettina Lieske
- Department of Surgery, National University Hospital, Singapore
| | - Ker-Kan Tan
- Department of Surgery, National University of Singapore, Singapore
- Department of Surgery, National University Hospital, Singapore
| | - Gloryn Chia
- Department of Pharmacy, National University of Singapore, Singapore
- NUS iHealthtech, Singapore
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17
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Antunes DA, Baker BM, Cornberg M, Selin LK. Editorial: Quantification and prediction of T-cell cross-reactivity through experimental and computational methods. Front Immunol 2024; 15:1377259. [PMID: 38444853 PMCID: PMC10912571 DOI: 10.3389/fimmu.2024.1377259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 02/05/2024] [Indexed: 03/07/2024] Open
Affiliation(s)
- Dinler A. Antunes
- Department of Biology and Biochemistry, University of Houston, Houston, TX, United States
| | - Brian M. Baker
- Department of Chemistry and Biochemistry, and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, United States
| | - Markus Cornberg
- Department of Gastroenterology, Hepatology, Infectious Diseases and Endocrinology, Hannover Medical School, Hannover, Germany
- Centre for Individualized Infection Medicine (CiiM), c/o CRC Hannover, Hannover, Germany
- German Center for Infection Research (DZIF), Partner-site Hannover-Braunschweig, Hannover, Germany
| | - Liisa K. Selin
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, United States
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18
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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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19
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Cetin M, Pinamonti V, Schmid T, Boschert T, Mellado Fuentes A, Kromer K, Lerner T, Zhang J, Herzig Y, Ehlert C, Hernandez-Hernandez M, Samaras G, Torres CM, Fisch L, Dragan V, Kouwenhoven A, Van Schoubroeck B, Wils H, Van Hove C, Platten M, Green EW, Stevenaert F, Felix NJ, Lindner JM. T-FINDER: A highly sensitive, pan-HLA platform for functional T cell receptor and ligand discovery. SCIENCE ADVANCES 2024; 10:eadk3060. [PMID: 38306432 PMCID: PMC10836725 DOI: 10.1126/sciadv.adk3060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 01/03/2024] [Indexed: 02/04/2024]
Abstract
Effective, unbiased, high-throughput methods to functionally identify both class II and class I HLA-presented T cell epitopes and their cognate T cell receptors (TCRs) are essential for and prerequisite to diagnostic and therapeutic applications, yet remain underdeveloped. Here, we present T-FINDER [T cell Functional Identification and (Neo)-antigen Discovery of Epitopes and Receptors], a system to rapidly deconvolute CD4 and CD8 TCRs and targets physiologically processed and presented by an individual's unmanipulated, complete human leukocyte antigen (HLA) haplotype. Combining a highly sensitive TCR signaling reporter with an antigen processing system to overcome previously undescribed limitations to target expression, T-FINDER both robustly identifies unknown peptide:HLA ligands from antigen libraries and rapidly screens and functionally validates the specificity of large TCR libraries against known or predicted targets. To demonstrate its capabilities, we apply the platform to multiple TCR-based applications, including diffuse midline glioma, celiac disease, and rheumatoid arthritis, providing unique biological insights and showcasing T-FINDER's potency and versatility.
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Affiliation(s)
- Miray Cetin
- BioMed X GmbH, Im Neuenheimer Feld 515, 69120 Heidelberg, Germany
| | - Veronica Pinamonti
- BioMed X GmbH, Im Neuenheimer Feld 515, 69120 Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Theresa Schmid
- BioMed X GmbH, Im Neuenheimer Feld 515, 69120 Heidelberg, Germany
| | - Tamara Boschert
- Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
- DKTK CCU Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Helmoltz Institute for Translational Oncology (HI-TRON), Heidelberg, Germany
| | | | - Kristina Kromer
- BioMed X GmbH, Im Neuenheimer Feld 515, 69120 Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Taga Lerner
- BioMed X GmbH, Im Neuenheimer Feld 515, 69120 Heidelberg, Germany
| | - Jing Zhang
- BioMed X GmbH, Im Neuenheimer Feld 515, 69120 Heidelberg, Germany
| | - Yonatan Herzig
- BioMed X GmbH, Im Neuenheimer Feld 515, 69120 Heidelberg, Germany
| | - Christopher Ehlert
- Heidelberg Institute for Theoretical Studies (HITS gGmbH), 69118 Heidelberg, Germany
| | | | - Georgios Samaras
- BioMed X GmbH, Im Neuenheimer Feld 515, 69120 Heidelberg, Germany
| | | | - Laura Fisch
- BioMed X GmbH, Im Neuenheimer Feld 515, 69120 Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Valeriia Dragan
- BioMed X GmbH, Im Neuenheimer Feld 515, 69120 Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | | | | | - Hans Wils
- Janssen Research and Development, Beerse, Belgium
| | | | - Michael Platten
- DKTK CCU Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Helmoltz Institute for Translational Oncology (HI-TRON), Heidelberg, Germany
- Department of Neurology, Medical Faculty Mannheim, MCTN Heidelberg University, Mannheim, Germany
| | - Edward W. Green
- DKTK CCU Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Department of Neurology, Medical Faculty Mannheim, MCTN Heidelberg University, Mannheim, Germany
| | | | | | - John M. Lindner
- BioMed X GmbH, Im Neuenheimer Feld 515, 69120 Heidelberg, Germany
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20
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Zhu C, Jiao S, Xu W. CD8 + Trms against malaria liver-stage: prospects and challenges. Front Immunol 2024; 15:1344941. [PMID: 38318178 PMCID: PMC10839007 DOI: 10.3389/fimmu.2024.1344941] [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: 11/27/2023] [Accepted: 01/08/2024] [Indexed: 02/07/2024] Open
Abstract
Attenuated sporozoites provide a valuable model for exploring protective immunity against the malarial liver stage, guiding the design of highly efficient vaccines to prevent malaria infection. Liver tissue-resident CD8+ T cells (CD8+ Trm cells) are considered the host front-line defense against malaria and are crucial to developing prime-trap/target strategies for pre-erythrocytic stage vaccine immunization. However, the spatiotemporal regulatory mechanism of the generation of liver CD8+ Trm cells and their responses to sporozoite challenge, as well as the protective antigens they recognize remain largely unknown. Here, we discuss the knowledge gap regarding liver CD8+ Trm cell formation and the potential strategies to identify predominant protective antigens expressed in the exoerythrocytic stage, which is essential for high-efficacy malaria subunit pre-erythrocytic vaccine designation.
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Affiliation(s)
- Chengyu Zhu
- The School of Medicine, Chongqing University, Chongqing, China
- Department of Pathogenic Biology, Army Medical University (Third Military Medical University), Chongqing, China
| | - Shiming Jiao
- Department of Pathogenic Biology, Army Medical University (Third Military Medical University), Chongqing, China
| | - Wenyue Xu
- The School of Medicine, Chongqing University, Chongqing, China
- Department of Pathogenic Biology, Army Medical University (Third Military Medical University), Chongqing, China
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21
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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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22
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Tennant M, O'Neil R. Transposon-Based Manufacturing of Human CAR-T Cells. Methods Mol Biol 2024; 2748:187-199. [PMID: 38070116 DOI: 10.1007/978-1-0716-3593-3_14] [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] [Indexed: 12/18/2023]
Abstract
In this chapter, the methodologies are outlined for generating CAR-T from PBMCs using transposon engineering. Additionally, some methods and guidance related to basic functional and phenotypic analysis are described. This methodology can be applied to manufacture and assess chimeric antigen receptors for preclinical applications targeting a variety of molecules.
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Affiliation(s)
- Megan Tennant
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC, USA
| | - Richard O'Neil
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC, USA.
- Department of Veterans Affairs, Ralph H Johnson VA Medical Center, Charleston, SC, USA.
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23
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Han Y, Yang Y, Tian Y, Fattah FJ, von Itzstein MS, Hu Y, Zhang M, Kang X, Yang DM, Liu J, Xue Y, Liang C, Raman I, Zhu C, Xiao O, Dowell JE, Homsi J, Rashdan S, Yang S, Gwin ME, Hsiehchen D, Gloria-McCutchen Y, Pan K, Wu F, Gibbons D, Wang X, Yee C, Huang J, Reuben A, Cheng C, Zhang J, Gerber DE, Wang T. pan-MHC and cross-Species Prediction of T Cell Receptor-Antigen Binding. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.01.569599. [PMID: 38105939 PMCID: PMC10723300 DOI: 10.1101/2023.12.01.569599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Profiling the binding of T cell receptors (TCRs) of T cells to antigenic peptides presented by MHC proteins is one of the most important unsolved problems in modern immunology. Experimental methods to probe TCR-antigen interactions are slow, labor-intensive, costly, and yield moderate throughput. To address this problem, we developed pMTnet-omni, an Artificial Intelligence (AI) system based on hybrid protein sequence and structure information, to predict the pairing of TCRs of αβ T cells with peptide-MHC complexes (pMHCs). pMTnet-omni is capable of handling peptides presented by both class I and II pMHCs, and capable of handling both human and mouse TCR-pMHC pairs, through information sharing enabled this hybrid design. pMTnet-omni achieves a high overall Area Under the Curve of Receiver Operator Characteristics (AUROC) of 0.888, which surpasses competing tools by a large margin. We showed that pMTnet-omni can distinguish binding affinity of TCRs with similar sequences. Across a range of datasets from various biological contexts, pMTnet-omni characterized the longitudinal evolution and spatial heterogeneity of TCR-pMHC interactions and their functional impact. We successfully developed a biomarker based on pMTnet-omni for predicting immune-related adverse events of immune checkpoint inhibitor (ICI) treatment in a cohort of 57 ICI-treated patients. pMTnet-omni represents a major advance towards developing a clinically usable AI system for TCR-pMHC pairing prediction that can aid the design and implementation of TCR-based immunotherapeutics.
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24
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Shah RK, Cygan E, Kozlik T, Colina A, Zamora AE. Utilizing immunogenomic approaches to prioritize targetable neoantigens for personalized cancer immunotherapy. Front Immunol 2023; 14:1301100. [PMID: 38149253 PMCID: PMC10749952 DOI: 10.3389/fimmu.2023.1301100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 11/29/2023] [Indexed: 12/28/2023] Open
Abstract
Advancements in sequencing technologies and bioinformatics algorithms have expanded our ability to identify tumor-specific somatic mutation-derived antigens (neoantigens). While recent studies have shown neoantigens to be compelling targets for cancer immunotherapy due to their foreign nature and high immunogenicity, the need for increasingly accurate and cost-effective approaches to rapidly identify neoantigens remains a challenging task, but essential for successful cancer immunotherapy. Currently, gene expression analysis and algorithms for variant calling can be used to generate lists of mutational profiles across patients, but more care is needed to curate these lists and prioritize the candidate neoantigens most capable of inducing an immune response. A growing amount of evidence suggests that only a handful of somatic mutations predicted by mutational profiling approaches act as immunogenic neoantigens. Hence, unbiased screening of all candidate neoantigens predicted by Whole Genome Sequencing/Whole Exome Sequencing may be necessary to more comprehensively access the full spectrum of immunogenic neoepitopes. Once putative cancer neoantigens are identified, one of the largest bottlenecks in translating these neoantigens into actionable targets for cell-based therapies is identifying the cognate T cell receptors (TCRs) capable of recognizing these neoantigens. While many TCR-directed screening and validation assays have utilized bulk samples in the past, there has been a recent surge in the number of single-cell assays that provide a more granular understanding of the factors governing TCR-pMHC interactions. The goal of this review is to provide an overview of existing strategies to identify candidate neoantigens using genomics-based approaches and methods for assessing neoantigen immunogenicity. Additionally, applications, prospects, and limitations of some of the current single-cell technologies will be discussed. Finally, we will briefly summarize some of the recent models that have been used to predict TCR antigen specificity and analyze the TCR receptor repertoire.
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Affiliation(s)
- Ravi K. Shah
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Erin Cygan
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Tanya Kozlik
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Alfredo Colina
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Anthony E. Zamora
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, United States
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
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25
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Zhao M, Xu SX, Yang Y, Yuan M. GGNpTCR: A Generative Graph Structure Neural Network for Predicting Immunogenic Peptides for T-cell Immune Response. J Chem Inf Model 2023; 63:7557-7567. [PMID: 37990917 DOI: 10.1021/acs.jcim.3c01293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
Identifying the interactions between T-cell receptor (TCRs) and human antigens is a crucial step in developing new vaccines, diagnostics, and immunotherapy. Current methods primarily focus on learning binding patterns from known TCR binding repertoires by using sequence information alone without considering the binding specificity of new antigens or exogenous peptides that have not appeared in the training set. Furthermore, the spatial structure of antigens plays a critical role in immune studies and immunotherapy, which should be addressed properly in the identification of interacting TCR-antigen pairs. In this study, we introduced a novel deep learning framework based on generative graph structures, GGNpTCR, for predicting interactions between TCR and peptides from sequence information. Results of real data analysis indicate that our model achieved excellent prediction for new antigens unseen in the training data set, making significant improvements compared to existing methods. We also applied the model to a large COVID-19 data set with no antigens in the training data set, and the improvement was also significant. Furthermore, through incorporation of additional supervised mechanisms, GGNpTCR demonstrated the ability to precisely forecast the locations of peptide-TCR interactions within 3D configurations. This enhancement substantially improved the model's interpretability. In summary, based on the performance on multiple data sets, GGNpTCR has made significant progress in terms of performance, universality, and interpretability.
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Affiliation(s)
- Minghua Zhao
- Department of Statistics and Finance, University of Science and Technology of China, Hefei 230026, China
| | - Steven X Xu
- Genmab US, Inc., Princeton, New Jersey 08540, United States
| | - Yaning Yang
- Department of Statistics and Finance, University of Science and Technology of China, Hefei 230026, China
| | - Min Yuan
- School of Public Health Administration, Anhui Medical University, Hefei 230032, China
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26
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Dezfulian MH, Kula T, Pranzatelli T, Kamitaki N, Meng Q, Khatri B, Perez P, Xu Q, Chang A, Kohlgruber AC, Leng Y, Jupudi AA, Joachims ML, Chiorini JA, Lessard CJ, Farris AD, Muthuswamy SK, Warner BM, Elledge SJ. TScan-II: A genome-scale platform for the de novo identification of CD4 + T cell epitopes. Cell 2023; 186:5569-5586.e21. [PMID: 38016469 PMCID: PMC10841602 DOI: 10.1016/j.cell.2023.10.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 07/12/2023] [Accepted: 10/25/2023] [Indexed: 11/30/2023]
Abstract
CD4+ T cells play fundamental roles in orchestrating immune responses and tissue homeostasis. However, our inability to associate peptide human leukocyte antigen class-II (HLA-II) complexes with their cognate T cell receptors (TCRs) in an unbiased manner has hampered our understanding of CD4+ T cell function and role in pathologies. Here, we introduce TScan-II, a highly sensitive genome-scale CD4+ antigen discovery platform. This platform seamlessly integrates the endogenous HLA-II antigen-processing machinery in synthetic antigen-presenting cells and TCR signaling in T cells, enabling the simultaneous screening of multiple HLAs and TCRs. Leveraging genome-scale human, virome, and epitope mutagenesis libraries, TScan-II facilitates de novo antigen discovery and deep exploration of TCR specificity. We demonstrate TScan-II's potential for basic and translational research by identifying a non-canonical antigen for a cancer-reactive CD4+ T cell clone. Additionally, we identified two antigens for clonally expanded CD4+ T cells in Sjögren's disease, which bind distinct HLAs and are expressed in HLA-II-positive ductal cells within affected salivary glands.
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Affiliation(s)
- Mohammad H Dezfulian
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Tomasz Kula
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Thomas Pranzatelli
- Adeno-Associated Virus Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Nolan Kamitaki
- Department of Genetics, Harvard Medical School, Boston, MA, USA; Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Qingda Meng
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Bhuwan Khatri
- Genes and Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Paola Perez
- Salivary Disorders Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Qikai Xu
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Aiquan Chang
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Ayano C Kohlgruber
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Yumei Leng
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Ananth Aditya Jupudi
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA; Departmentment of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Michelle L Joachims
- Genes and Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA; Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - John A Chiorini
- Adeno-Associated Virus Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Christopher J Lessard
- Genes and Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA; Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - A Darise Farris
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA; Departmentment of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Senthil K Muthuswamy
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Blake M Warner
- Salivary Disorders Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Stephen J Elledge
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA.
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27
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Klebanoff CA, Chandran SS, Baker BM, Quezada SA, Ribas A. T cell receptor therapeutics: immunological targeting of the intracellular cancer proteome. Nat Rev Drug Discov 2023; 22:996-1017. [PMID: 37891435 PMCID: PMC10947610 DOI: 10.1038/s41573-023-00809-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/08/2023] [Indexed: 10/29/2023]
Abstract
The T cell receptor (TCR) complex is a naturally occurring antigen sensor that detects, amplifies and coordinates cellular immune responses to epitopes derived from cell surface and intracellular proteins. Thus, TCRs enable the targeting of proteins selectively expressed by cancer cells, including neoantigens, cancer germline antigens and viral oncoproteins. As such, TCRs have provided the basis for an emerging class of oncology therapeutics. Herein, we review the current cancer treatment landscape using TCRs and TCR-like molecules. This includes adoptive cell transfer of T cells expressing endogenous or engineered TCRs, TCR bispecific engagers and antibodies specific for human leukocyte antigen (HLA)-bound peptides (TCR mimics). We discuss the unique complexities associated with the clinical development of these therapeutics, such as HLA restriction, TCR retrieval, potency assessment and the potential for cross-reactivity. In addition, we highlight emerging clinical data that establish the antitumour potential of TCR-based therapies, including tumour-infiltrating lymphocytes, for the treatment of diverse human malignancies. Finally, we explore the future of TCR therapeutics, including emerging genome editing methods to safely enhance potency and strategies to streamline patient identification.
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Affiliation(s)
- Christopher A Klebanoff
- Memorial Sloan Kettering Cancer Center (MSKCC), Human Oncology and Pathogenesis Program, New York, NY, USA.
| | - Smita S Chandran
- Memorial Sloan Kettering Cancer Center (MSKCC), Human Oncology and Pathogenesis Program, New York, NY, USA
- Parker Institute for Cancer Immunotherapy, New York, NY, USA
- Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - Brian M Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, ID, USA
- The Harper Cancer Research Institute, University of Notre Dame, Notre Dame, ID, USA
| | - Sergio A Quezada
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Achilles Therapeutics, London, UK
| | - Antoni Ribas
- Jonsson Comprehensive Cancer Center at the University of California, Los Angeles (UCLA), Los Angeles, CA, USA
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28
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Pang Z, Lu MM, Zhang Y, Gao Y, Bai JJ, Gu JY, Xie L, Wu WZ. Neoantigen-targeted TCR-engineered T cell immunotherapy: current advances and challenges. Biomark Res 2023; 11:104. [PMID: 38037114 PMCID: PMC10690996 DOI: 10.1186/s40364-023-00534-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 10/22/2023] [Indexed: 12/02/2023] Open
Abstract
Adoptive cell therapy using T cell receptor-engineered T cells (TCR-T) is a promising approach for cancer therapy with an expectation of no significant side effects. In the human body, mature T cells are armed with an incredible diversity of T cell receptors (TCRs) that theoretically react to the variety of random mutations generated by tumor cells. The outcomes, however, of current clinical trials using TCR-T cell therapies are not very successful especially involving solid tumors. The therapy still faces numerous challenges in the efficient screening of tumor-specific antigens and their cognate TCRs. In this review, we first introduce TCR structure-based antigen recognition and signaling, then describe recent advances in neoantigens and their specific TCR screening technologies, and finally summarize ongoing clinical trials of TCR-T therapies against neoantigens. More importantly, we also present the current challenges of TCR-T cell-based immunotherapies, e.g., the safety of viral vectors, the mismatch of T cell receptor, the impediment of suppressive tumor microenvironment. Finally, we highlight new insights and directions for personalized TCR-T therapy.
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Affiliation(s)
- Zhi Pang
- Liver Cancer Institute, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- Clinical Center for Biotherapy, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Man-Man Lu
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, 200237, China
| | - Yu Zhang
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, 200237, China
| | - Yuan Gao
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, 200237, China
| | - Jin-Jin Bai
- Liver Cancer Institute, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- Clinical Center for Biotherapy, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Jian-Ying Gu
- Clinical Center for Biotherapy, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Lu Xie
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, 200237, China.
| | - Wei-Zhong Wu
- Liver Cancer Institute, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
- Clinical Center for Biotherapy, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
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29
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Chen G, Kong D, Lin Y. Neo-Antigen-Reactive T Cells Immunotherapy for Colorectal Cancer: A More Personalized Cancer Therapy Approach. GLOBAL CHALLENGES (HOBOKEN, NJ) 2023; 7:2200186. [PMID: 37970536 PMCID: PMC10632666 DOI: 10.1002/gch2.202200186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 05/09/2023] [Indexed: 11/17/2023]
Abstract
Colorectal cancer (CRC) is the second most common malignancy in women and the third most frequent cancer in men. Evidence has revealed that the survival of patients with metastatic CRC is very low, between one and three years. Neoantigens are known proteins encoded by mutations in tumor cells. It is theorized that recognizing neoantigens by T cells leads to T cell activation and further antitumor responses. Neoantigen-reactive T cells (NRTs) are designed against the mentioned neoantigens expressed by tumor cells. NRTs selectively kill tumor cells without damage to non-cancerous cells. Identifying patient-specific and high immunogen neoantigens is important in NRT immunotherapy of patients with CRC. However, the main challenges are the side effects and preparation of NRTs, as well as the effectiveness of these cells in vivo. This review summarized the properties of neoantigens as well as the preparation and therapeutic outcomes of NRTs for the treatment of CRC.
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Affiliation(s)
- Guan‐Liang Chen
- Department of Gastroenterology SurgeryAffiliated Hospital of Shaoxing UniversityShaoxing312000China
| | - De‐Xia Kong
- Center for General Practice MedicineDepartment of GastroenterologyZhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical CollegeNo. 158 Shangtang RoadHangzhouZhejiang310014China
| | - Yan Lin
- Center for General Practice MedicineDepartment of GastroenterologyZhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical CollegeNo. 158 Shangtang RoadHangzhouZhejiang310014China
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30
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Marks ME, Botta RK, Abe R, Beachkofsky TM, Boothman I, Carleton BC, Chung WH, Cibotti RR, Dodiuk-Gad RP, Grimstein C, Hasegawa A, Hoofnagle JH, Hung SI, Kaffenberger B, Kroshinsky D, Lehloenya RJ, Martin-Pozo M, Micheletti RG, Mockenhaupt M, Nagao K, Pakala S, Palubinsky A, Pasieka HB, Peter J, Pirmohamed M, Reyes M, Saeed HN, Shupp J, Sukasem C, Syu JY, Ueta M, Zhou L, Chang WC, Becker P, Bellon T, Bonnet K, Cavalleri G, Chodosh J, Dewan AK, Dominguez A, Dong X, Ezhkova E, Fuchs E, Goldman J, Himed S, Mallal S, Markova A, McCawley K, Norton AE, Ostrov D, Phan M, Sanford A, Schlundt D, Schneider D, Shear N, Shinkai K, Tkaczyk E, Trubiano JA, Volpi S, Bouchard CS, Divito SJ, Phillips EJ. Updates in SJS/TEN: collaboration, innovation, and community. Front Med (Lausanne) 2023; 10:1213889. [PMID: 37901413 PMCID: PMC10600400 DOI: 10.3389/fmed.2023.1213889] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 07/31/2023] [Indexed: 10/31/2023] Open
Abstract
Stevens-Johnson Syndrome/Toxic Epidermal Necrolysis (SJS/TEN) is a predominantly drug-induced disease, with a mortality rate of 15-20%, that engages the expertise of multiple disciplines: dermatology, allergy, immunology, clinical pharmacology, burn surgery, ophthalmology, urogynecology, and psychiatry. SJS/TEN has an incidence of 1-5/million persons per year in the United States, with even higher rates globally. One of the challenges of SJS/TEN has been developing the research infrastructure and coordination to answer questions capable of transforming clinical care and leading to improved patient outcomes. SJS/TEN 2021, the third research meeting of its kind, was held as a virtual meeting on August 28-29, 2021. The meeting brought together 428 international scientists, in addition to a community of 140 SJS/TEN survivors and family members. The goal of the meeting was to brainstorm strategies to support the continued growth of an international SJS/TEN research network, bridging science and the community. The community workshop section of the meeting focused on eight primary themes: mental health, eye care, SJS/TEN in children, non-drug induced SJS/TEN, long-term health complications, new advances in mechanisms and basic science, managing long-term scarring, considerations for skin of color, and COVID-19 vaccines. The meeting featured several important updates and identified areas of unmet research and clinical need that will be highlighted in this white paper.
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Affiliation(s)
- Madeline E. Marks
- Center for Drug Interactions and Immunology, Division of Infectious Disease, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Ramya Krishna Botta
- Center for Drug Interactions and Immunology, Division of Infectious Disease, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Riichiro Abe
- Division of Dermatology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Thomas M. Beachkofsky
- Departments of Dermatology and Medicine, Uniformed Services University, Bethesda, MD, United States
| | - Isabelle Boothman
- The SFI Centre for Research Training in Genomics Data Science, Dublin, Ireland
| | - Bruce C. Carleton
- Division of Translational Therapeutics, Department of Pediatrics, Faculty of Medicine, University of British Columbia and the British Columbia Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Wen-Hung Chung
- Department of Dermatology, Drug Hypersensitivity Clinical and Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Ricardo R. Cibotti
- National Institute of Arthritis and Musculoskeletal and Skin (NIAMS), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Roni P. Dodiuk-Gad
- Department of Dermatology, Emek Medical Center, Afula, Israel
- Division of Dermatology, Department of Medicine, University of Toronto, Toronto, ON, Canada
- Department of Dermatology, Bruce Rappaport Faculty of Medicine, Technion Institute of Technology, Haifa, Israel
| | - Christian Grimstein
- Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, United States
| | - Akito Hasegawa
- Division of Dermatology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Jay H. Hoofnagle
- Liver Disease Research Branch, Division of Digestive Diseases and Nutrition of NIDDK, National Institutes of Health (NIH), Bethesda, MD, United States
| | - Shuen-Iu Hung
- Cancer Vaccine and Immune Cell Therapy Core Laboratory, Department of Medical Research, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Benjamin Kaffenberger
- Department of Dermatology, Ohio State University Wexner Medical Center, Columbus, OH, United States
| | - Daniela Kroshinsky
- Department of Dermatology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Rannakoe J. Lehloenya
- Division of Dermatology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Michelle Martin-Pozo
- Center for Drug Interactions and Immunology, Division of Infectious Disease, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Robert G. Micheletti
- Department of Dermatology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Maja Mockenhaupt
- Dokumentationszentrum schwerer Hautreaktionen (dZh), Department of Dermatology, Medical Center and Medical Faculty, University of Freiburg, Freiburg, Germany
| | - Keisuke Nagao
- National Institute of Arthritis and Musculoskeletal and Skin (NIAMS), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Suman Pakala
- Center for Drug Interactions and Immunology, Division of Infectious Disease, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Amy Palubinsky
- Center for Drug Interactions and Immunology, Division of Infectious Disease, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Helena B. Pasieka
- Departments of Dermatology and Medicine, Uniformed Services University, Bethesda, MD, United States
- The Burn Center, MedStar Washington Hospital Center, Washington, D.C., DC, United States
- Department of Dermatology, MedStar Health/Georgetown University, Washington, D.C., DC, United States
| | - Jonathan Peter
- Division of Allergy and Clinical Immunology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Munir Pirmohamed
- Department of Pharmacology and Therapeutics, University of Liverpool, Liverpool, United Kingdom
| | - Melissa Reyes
- Center for Drug Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, United States
| | - Hajirah N. Saeed
- Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, United States
| | - Jeffery Shupp
- Department of Surgery, Plastic and Reconstructive Surgery, Biochemistry, and Molecular and Cellular Biology, MedStar Washington Hospital Center, Georgetown University School of Medicine, Washington, D.C., DC, United States
| | - Chonlaphat Sukasem
- Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Jhih Yu Syu
- Department of Cell Biology and Anatomy, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Mayumi Ueta
- Department of Frontier Medical Science and Technology for Ophthalmology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Li Zhou
- Division of General Internal Medicine and Primary Care, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Wan-Chun Chang
- Division of Translational Therapeutics, Department of Pediatrics, Faculty of Medicine, University of British Columbia and the British Columbia Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Patrice Becker
- Division of Allergy, Immunology, and Transplantation, National Institute of Allergy and Infectious Disease, Bethesda, MD, United States
| | - Teresa Bellon
- Drug Hypersensitivity Laboratory, La Paz Health Research Institute (IdiPAZ), Madrid, Spain
| | - Kemberlee Bonnet
- Department of Psychology, Vanderbilt University, Nashville, TN, United States
| | - Gianpiero Cavalleri
- The SFI Centre for Research Training in Genomics Data Science, Dublin, Ireland
| | - James Chodosh
- University of New Mexico School of Medicine, Albuquerque, NM, United States
| | - Anna K. Dewan
- Department of Dermatology, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Arturo Dominguez
- Department of Dermatology and Internal Medicine, UT Southwestern Medical Center, Dallas, TX, United States
| | - Xinzhong Dong
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Elena Ezhkova
- Department of Cell, Developmental, and Regenerative Biology and Dermatology, Black Family Stem Cell Institute, Mount Sinai School of Medicine, New York, NY, United States
| | - Esther Fuchs
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA, United States
| | - Jennifer Goldman
- Division of Pediatric Infectious Diseases and Clinical Pharmacology, Children’s Mercy, Kansas City, MO, United States
| | - Sonia Himed
- College of Medicine, University of Cincinnati, Cincinnati, OH, United States
| | - Simon Mallal
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Alina Markova
- Department of Dermatology, Memorial Sloan Kettering Cancer Center, Weill Cornell Medical College, New York, NY, United States
| | - Kerry McCawley
- Stevens-Johnson Syndrome Foundation, Westminster, CO, United States
| | - Allison E. Norton
- Division of Pediatric Allergy, Immunology, and Pulmonary Medicine, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, United States
| | - David Ostrov
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, United States
| | - Michael Phan
- Division of Pharmacovigilance-I, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, United States
| | - Arthur Sanford
- Division of Trauma, Surgical Critical Care, and Burns, Loyola University Medical Center, Chicago, IL, United States
| | - David Schlundt
- Department of Psychology, Vanderbilt University, Nashville, TN, United States
| | - Daniel Schneider
- Department of Psychiatry and Surgery, MedStar Washington Hospital Center, Georgetown University School of Medicine, Washington, D.C., DC, United States
| | - Neil Shear
- Department of Dermatology, Emek Medical Center, Afula, Israel
| | - Kanade Shinkai
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, United States
| | - Eric Tkaczyk
- Department of Veterans Affairs, Vanderbilt Dermatology Translational Research Clinic (VDTRC.org), Nashville, TN, United States
| | - Jason A. Trubiano
- Department of Infectious Diseases and Medicine, Austin Health, University of Melbourne, Melbourne, VIC, Australia
| | - Simona Volpi
- National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Charles S. Bouchard
- Department of Opthalmology, Loyola University Medical Center, Chicago, IL, United States
| | - Sherrie J. Divito
- Department of Dermatology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Elizabeth J. Phillips
- Center for Drug Interactions and Immunology, Division of Infectious Disease, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
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31
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To TL, Li X, Shu X. Spying on SARS-CoV-2 with Fluorescent Tags and Protease Reporters. Viruses 2023; 15:2005. [PMID: 37896782 PMCID: PMC10612051 DOI: 10.3390/v15102005] [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: 09/06/2023] [Revised: 09/23/2023] [Accepted: 09/26/2023] [Indexed: 10/29/2023] Open
Abstract
The SARS-CoV-2 coronavirus has caused worldwide disruption through the COVID-19 pandemic, providing a sobering reminder of the profound impact viruses can have on human well-being. Understanding virus life cycles and interactions with host cells lays the groundwork for exploring therapeutic strategies against virus-related diseases. Fluorescence microscopy plays a vital role in virus imaging, offering high spatiotemporal resolution, sensitivity, and spectroscopic versatility. In this opinion piece, we first highlight two recent techniques, SunTag and StayGold, for the in situ imaging of viral RNA translation and viral assembly. Next, we discuss a new class of genetically encoded fluorogenic protease reporters, such as FlipGFP, which can be customized to monitor SARS-CoV-2's main (Mpro) or papain-like (PLpro) protease activity. These assays have proven effective in identifying potential antivirals through high-throughput screening, making fluorogenic viral protease reporters a promising platform for viral disease diagnostics and therapeutics.
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Affiliation(s)
| | - Xiaoquan Li
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, UC San Francisco, San Francisco, CA 94158, USA
| | - Xiaokun Shu
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, UC San Francisco, San Francisco, CA 94158, USA
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32
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Hu D, Irving AT. Massively-multiplexed epitope mapping techniques for viral antigen discovery. Front Immunol 2023; 14:1192385. [PMID: 37818363 PMCID: PMC10561112 DOI: 10.3389/fimmu.2023.1192385] [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: 03/23/2023] [Accepted: 09/04/2023] [Indexed: 10/12/2023] Open
Abstract
Following viral infection, viral antigens bind specifically to receptors on the surface of lymphocytes thereby activating adaptive immunity in the host. An epitope, the smallest structural and functional unit of an antigen, binds specifically to an antibody or antigen receptor, to serve as key sites for the activation of adaptive immunity. The complexity and diverse range of epitopes are essential to study and map for the diagnosis of disease, the design of vaccines and for immunotherapy. Mapping the location of these specific epitopes has become a hot topic in immunology and immune therapy. Recently, epitope mapping techniques have evolved to become multiplexed, with the advent of high-throughput sequencing and techniques such as bacteriophage-display libraries and deep mutational scanning. Here, we briefly introduce the principles, advantages, and disadvantages of the latest epitope mapping techniques with examples for viral antigen discovery.
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Affiliation(s)
- Diya Hu
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, Haining, China
| | - Aaron T. Irving
- Department of Clinical Laboratory Studies, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Centre for Infection, Immunity & Cancer, Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, Haining, China
- Biomedical and Health Translational Research Centre of Zhejiang Province (BIMET), Haining, China
- College of Medicine & Veterinary Medicine, The University of Edinburgh, Edinburgh, United Kingdom
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33
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Li J, Xiao Z, Wang D, Jia L, Nie S, Zeng X, Hu W. The screening, identification, design and clinical application of tumor-specific neoantigens for TCR-T cells. Mol Cancer 2023; 22:141. [PMID: 37649123 PMCID: PMC10466891 DOI: 10.1186/s12943-023-01844-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 08/16/2023] [Indexed: 09/01/2023] Open
Abstract
Recent advances in neoantigen research have accelerated the development of tumor immunotherapies, including adoptive cell therapies (ACTs), cancer vaccines and antibody-based therapies, particularly for solid tumors. With the development of next-generation sequencing and bioinformatics technology, the rapid identification and prediction of tumor-specific antigens (TSAs) has become possible. Compared with tumor-associated antigens (TAAs), highly immunogenic TSAs provide new targets for personalized tumor immunotherapy and can be used as prospective indicators for predicting tumor patient survival, prognosis, and immune checkpoint blockade response. Here, the identification and characterization of neoantigens and the clinical application of neoantigen-based TCR-T immunotherapy strategies are summarized, and the current status, inherent challenges, and clinical translational potential of these strategies are discussed.
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Affiliation(s)
- Jiangping Li
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, People's Republic of China.
| | - Zhiwen Xiao
- Department of Otolaryngology Head and Neck Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, People's Republic of China
| | - Donghui Wang
- Department of Radiation Oncology, The Third Affiliated Hospital Sun Yat-Sen University, Guangzhou, 510630, People's Republic of China
| | - Lei Jia
- International Health Medicine Innovation Center, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Shihong Nie
- Department of Radiation Oncology, West China Hospital, Sichuan University, Cancer Center, Chengdu, 610041, People's Republic of China
| | - Xingda Zeng
- Department of Parasitology of Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Wei Hu
- Division of Vascular Surgery, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072, People's Republic of China
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34
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Foldvari Z, Knetter C, Yang W, Gjerdingen TJ, Bollineni RC, Tran TT, Lund-Johansen F, Kolstad A, Drousch K, Klopfleisch R, Leisegang M, Olweus J. A systematic safety pipeline for selection of T-cell receptors to enter clinical use. NPJ Vaccines 2023; 8:126. [PMID: 37607971 PMCID: PMC10444760 DOI: 10.1038/s41541-023-00713-y] [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: 10/19/2022] [Accepted: 07/31/2023] [Indexed: 08/24/2023] Open
Abstract
Cancer immunotherapy using T cell receptor-engineered T cells (TCR-Ts) represents a promising treatment option. However, technologies for pre-clinical safety assessment are incomplete or inaccessible to most laboratories. Here, TCR-T off-target reactivity was assessed in five steps: (1) Mapping target amino acids necessary for TCR-T recognition, followed by (2) a computational search for, and (3) reactivity screening against, candidate cross-reactive peptides in the human proteome. Natural processing and presentation of recognized peptides was evaluated using (4) short mRNAs, and (5) full-length proteins. TCR-Ts were screened for recognition of unintended HLA alleles, and as proxy for off-target reactivity in vivo, a syngeneic, HLA-A*02:01-transgenic mouse model was used. Validation demonstrated importance of studying recognition of full-length candidate off-targets, and that the clinically applied 1G4 TCR has a hitherto unknown reactivity to unintended HLA alleles, relevant for patient selection. This widely applicable strategy should facilitate evaluation of candidate therapeutic TCRs and inform clinical decision-making.
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Affiliation(s)
- Zsofia Foldvari
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
- Precision Immunotherapy Alliance, University of Oslo, Oslo, Norway
| | - Cathrine Knetter
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
- Precision Immunotherapy Alliance, University of Oslo, Oslo, Norway
| | - Weiwen Yang
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
- Precision Immunotherapy Alliance, University of Oslo, Oslo, Norway
| | - Thea Johanne Gjerdingen
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
- Precision Immunotherapy Alliance, University of Oslo, Oslo, Norway
| | - Ravi Chand Bollineni
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
- Precision Immunotherapy Alliance, University of Oslo, Oslo, Norway
| | - Trung The Tran
- Precision Immunotherapy Alliance, University of Oslo, Oslo, Norway
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Fridtjof Lund-Johansen
- Precision Immunotherapy Alliance, University of Oslo, Oslo, Norway
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Arne Kolstad
- Department of Oncology, Oslo University Hospital Radiumhospitalet, Oslo, Norway
| | - Kimberley Drousch
- Institute of Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Robert Klopfleisch
- Institute of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany
| | - Matthias Leisegang
- Institute of Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany.
- David and Etta Jonas Center for Cellular Therapy, The University of Chicago, Chicago, IL, USA.
- German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Johanna Olweus
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway.
- Precision Immunotherapy Alliance, University of Oslo, Oslo, Norway.
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Rappazzo CG, Fernández-Quintero ML, Mayer A, Wu NC, Greiff V, Guthmiller JJ. Defining and Studying B Cell Receptor and TCR Interactions. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 211:311-322. [PMID: 37459189 PMCID: PMC10495106 DOI: 10.4049/jimmunol.2300136] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 04/15/2023] [Indexed: 07/20/2023]
Abstract
BCRs (Abs) and TCRs (or adaptive immune receptors [AIRs]) are the means by which the adaptive immune system recognizes foreign and self-antigens, playing an integral part in host defense, as well as the emergence of autoimmunity. Importantly, the interaction between AIRs and their cognate Ags defies a simple key-in-lock paradigm and is instead a complex many-to-many mapping between an individual's massively diverse AIR repertoire, and a similarly diverse antigenic space. Understanding how adaptive immunity balances specificity with epitopic coverage is a key challenge for the field, and terms such as broad specificity, cross-reactivity, and polyreactivity remain ill-defined and are used inconsistently. In this Immunology Notes and Resources article, a group of experimental, structural, and computational immunologists define commonly used terms associated with AIR binding, describe methodologies to study these binding modes, as well as highlight the implications of these different binding modes for therapeutic design.
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Affiliation(s)
| | | | - Andreas Mayer
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Nicholas C. Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Victor Greiff
- Department of Immunology, University of Oslo and Oslo University Hospital, 0372 Oslo, Norway
| | - Jenna J. Guthmiller
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
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36
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Yang M, Huang ZA, Zhou W, Ji J, Zhang J, He S, Zhu Z. MIX-TPI: a flexible prediction framework for TCR-pMHC interactions based on multimodal representations. Bioinformatics 2023; 39:btad475. [PMID: 37527015 PMCID: PMC10423027 DOI: 10.1093/bioinformatics/btad475] [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: 04/28/2023] [Revised: 07/05/2023] [Accepted: 07/29/2023] [Indexed: 08/03/2023] Open
Abstract
MOTIVATION The interactions between T-cell receptors (TCR) and peptide-major histocompatibility complex (pMHC) are essential for the adaptive immune system. However, identifying these interactions can be challenging due to the limited availability of experimental data, sequence data heterogeneity, and high experimental validation costs. RESULTS To address this issue, we develop a novel computational framework, named MIX-TPI, to predict TCR-pMHC interactions using amino acid sequences and physicochemical properties. Based on convolutional neural networks, MIX-TPI incorporates sequence-based and physicochemical-based extractors to refine the representations of TCR-pMHC interactions. Each modality is projected into modality-invariant and modality-specific representations to capture the uniformity and diversities between different features. A self-attention fusion layer is then adopted to form the classification module. Experimental results demonstrate the effectiveness of MIX-TPI in comparison with other state-of-the-art methods. MIX-TPI also shows good generalization capability on mutual exclusive evaluation datasets and a paired TCR dataset. AVAILABILITY AND IMPLEMENTATION The source code of MIX-TPI and the test data are available at: https://github.com/Wolverinerine/MIX-TPI.
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Affiliation(s)
- Minghao Yang
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen 518060, China
| | - Zhi-An Huang
- Research Office, City University of Hong Kong (Dongguan), Dongguan 523000, China
| | - Wei Zhou
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen 518060, China
| | - Junkai Ji
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen 518060, China
| | - Jun Zhang
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen 518060, China
| | - Shan He
- School of Computer Science, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Zexuan Zhu
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen 518060, China
- National Engineering Laboratory for Big Data System Computing Technology, Shenzhen University, Shenzhen 518060, China
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37
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Hudson D, Fernandes RA, Basham M, Ogg G, Koohy H. Can we predict T cell specificity with digital biology and machine learning? Nat Rev Immunol 2023; 23:511-521. [PMID: 36755161 PMCID: PMC9908307 DOI: 10.1038/s41577-023-00835-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2022] [Indexed: 02/10/2023]
Abstract
Recent advances in machine learning and experimental biology have offered breakthrough solutions to problems such as protein structure prediction that were long thought to be intractable. However, despite the pivotal role of the T cell receptor (TCR) in orchestrating cellular immunity in health and disease, computational reconstruction of a reliable map from a TCR to its cognate antigens remains a holy grail of systems immunology. Current data sets are limited to a negligible fraction of the universe of possible TCR-ligand pairs, and performance of state-of-the-art predictive models wanes when applied beyond these known binders. In this Perspective article, we make the case for renewed and coordinated interdisciplinary effort to tackle the problem of predicting TCR-antigen specificity. We set out the general requirements of predictive models of antigen binding, highlight critical challenges and discuss how recent advances in digital biology such as single-cell technology and machine learning may provide possible solutions. Finally, we describe how predicting TCR specificity might contribute to our understanding of the broader puzzle of antigen immunogenicity.
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Affiliation(s)
- Dan Hudson
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- The Rosalind Franklin Institute, Didcot, UK
| | - Ricardo A Fernandes
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK
| | | | - Graham Ogg
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK
| | - Hashem Koohy
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
- Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
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38
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Wang Y, Zhang K, Zhao Y, Li Y, Su W, Li S. Construction and Applications of Mammalian Cell-Based DNA-Encoded Peptide/Protein Libraries. ACS Synth Biol 2023; 12:1874-1888. [PMID: 37315219 DOI: 10.1021/acssynbio.3c00043] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
DNA-encoded peptide/protein libraries are the starting point for protein evolutionary modification and functional peptide/antibody selection. Different display technologies, protein directed evolution, and deep mutational scanning (DMS) experiments employ DNA-encoded libraries to provide sequence variations for downstream affinity- or function-based selections. Mammalian cells promise the inherent post-translational modification and near-to-natural conformation of exogenously expressed mammalian proteins and thus are the best platform for studying transmembrane proteins or human disease-related proteins. However, due to the current technical bottlenecks of constructing mammalian cell-based large size DNA-encoded libraries, the advantages of mammalian cells as screening platforms have not been fully exploited. In this review, we summarize the current efforts in constructing DNA-encoded libraries in mammalian cells and the existing applications of these libraries in different fields.
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Affiliation(s)
- Yi Wang
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin; Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Kaili Zhang
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin; Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Yanjie Zhao
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin; Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Yifan Li
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin; Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Weijun Su
- School of Medicine, Nankai University, Tianjin 300071, China
| | - Shuai Li
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin; Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
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39
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Afroz S, Bartolo L, Su LF. Pre-existing T Cell Memory to Novel Pathogens. Immunohorizons 2023; 7:543-553. [PMID: 37436166 PMCID: PMC10587503 DOI: 10.4049/immunohorizons.2200003] [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: 05/12/2023] [Accepted: 06/22/2023] [Indexed: 07/13/2023] Open
Abstract
Immunological experiences lead to the development of specific T and B cell memory, which readies the host for a later pathogen rechallenge. Currently, immunological memory is best understood as a linear process whereby memory responses are generated by and directed against the same pathogen. However, numerous studies have identified memory cells that target pathogens in unexposed individuals. How "pre-existing memory" forms and impacts the outcome of infection remains unclear. In this review, we discuss differences in the composition of baseline T cell repertoire in mice and humans, factors that influence pre-existing immune states, and recent literature on their functional significance. We summarize current knowledge on the roles of pre-existing T cells in homeostasis and perturbation and their impacts on health and disease.
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Affiliation(s)
- Sumbul Afroz
- Division of Rheumatology, Department of Medicine, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA
| | - Laurent Bartolo
- Division of Rheumatology, Department of Medicine, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA
| | - Laura F. Su
- Division of Rheumatology, Department of Medicine, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA
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40
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Bruno PM, Timms RT, Abdelfattah NS, Leng Y, Lelis FJN, Wesemann DR, Yu XG, Elledge SJ. High-throughput, targeted MHC class I immunopeptidomics using a functional genetics screening platform. Nat Biotechnol 2023; 41:980-992. [PMID: 36593401 PMCID: PMC10314971 DOI: 10.1038/s41587-022-01566-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 10/13/2022] [Indexed: 01/03/2023]
Abstract
Identification of CD8+ T cell epitopes is critical for the development of immunotherapeutics. Existing methods for major histocompatibility complex class I (MHC class I) ligand discovery are time intensive, specialized and unable to interrogate specific proteins on a large scale. Here, we present EpiScan, which uses surface MHC class I levels as a readout for whether a genetically encoded peptide is an MHC class I ligand. Predetermined starting pools composed of >100,000 peptides can be designed using oligonucleotide synthesis, permitting large-scale MHC class I screening. We exploit this programmability of EpiScan to uncover an unappreciated role for cysteine that increases the number of predicted ligands by 9-21%, reveal affinity hierarchies by analysis of biased anchor peptide libraries and screen viral proteomes for MHC class I ligands. Using these data, we generate and iteratively refine peptide binding predictions to create EpiScan Predictor. EpiScan Predictor performs comparably to other state-of-the-art MHC class I peptide binding prediction algorithms without suffering from underrepresentation of cysteine-containing peptides. Thus, targeted immunopeptidomics using EpiScan will accelerate CD8+ T cell epitope discovery toward the goal of individual-specific immunotherapeutics.
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Affiliation(s)
- Peter M Bruno
- Department of Genetics, Harvard Medical School and Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Richard T Timms
- Department of Genetics, Harvard Medical School and Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
| | - Nouran S Abdelfattah
- Department of Genetics, Harvard Medical School and Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Yumei Leng
- Department of Genetics, Harvard Medical School and Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Felipe J N Lelis
- Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Duane R Wesemann
- Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA
| | - Xu G Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Stephen J Elledge
- Department of Genetics, Harvard Medical School and Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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41
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Li X, Pak HS, Huber F, Michaux J, Taillandier-Coindard M, Altimiras ER, Bassani-Sternberg M. A microfluidics-enabled automated workflow of sample preparation for MS-based immunopeptidomics. CELL REPORTS METHODS 2023; 3:100479. [PMID: 37426762 PMCID: PMC10326370 DOI: 10.1016/j.crmeth.2023.100479] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/22/2023] [Accepted: 04/19/2023] [Indexed: 07/11/2023]
Abstract
Mass spectrometry (MS)-based immunopeptidomics is an attractive antigen discovery method with growing clinical implications. However, the current experimental approach to extract HLA-restricted peptides requires a bulky sample source, which remains a challenge for obtaining clinical specimens. We present an innovative workflow that requires a low sample volume, which streamlines the immunoaffinity purification (IP) and C18 peptide cleanup on a single microfluidics platform with automated liquid handling and minimal sample transfers, resulting in higher assay sensitivity. We also demonstrate how the state-of-the-art data-independent acquisition (DIA) method further enhances the depth of tandem MS spectra-based peptide sequencing. Consequently, over 4,000 and 5,000 HLA-I-restricted peptides were identified from as few as 0.2 million RA957 cells and a melanoma tissue of merely 5 mg, respectively. We also identified multiple immunogenic tumor-associated antigens and hundreds of peptides derived from non-canonical protein sources. This workflow represents a powerful tool for identifying the immunopeptidome of sparse samples.
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Affiliation(s)
- Xiaokang Li
- Ludwig Institute for Cancer Research, University of Lausanne, Rue du Bugnon 25A, 1005 Lausanne, Switzerland
- Department of Oncology, Centre Hospitalier Universitaire Vaudois (CHUV), Rue du Bugnon 46, 1005 Lausanne, Switzerland
- Agora Cancer Research Centre, Rue du Bugnon 25A, 1005 Lausanne, Switzerland
| | - Hui Song Pak
- Ludwig Institute for Cancer Research, University of Lausanne, Rue du Bugnon 25A, 1005 Lausanne, Switzerland
- Department of Oncology, Centre Hospitalier Universitaire Vaudois (CHUV), Rue du Bugnon 46, 1005 Lausanne, Switzerland
- Agora Cancer Research Centre, Rue du Bugnon 25A, 1005 Lausanne, Switzerland
| | - Florian Huber
- Ludwig Institute for Cancer Research, University of Lausanne, Rue du Bugnon 25A, 1005 Lausanne, Switzerland
- Department of Oncology, Centre Hospitalier Universitaire Vaudois (CHUV), Rue du Bugnon 46, 1005 Lausanne, Switzerland
- Agora Cancer Research Centre, Rue du Bugnon 25A, 1005 Lausanne, Switzerland
| | - Justine Michaux
- Ludwig Institute for Cancer Research, University of Lausanne, Rue du Bugnon 25A, 1005 Lausanne, Switzerland
- Department of Oncology, Centre Hospitalier Universitaire Vaudois (CHUV), Rue du Bugnon 46, 1005 Lausanne, Switzerland
- Agora Cancer Research Centre, Rue du Bugnon 25A, 1005 Lausanne, Switzerland
| | - Marie Taillandier-Coindard
- Ludwig Institute for Cancer Research, University of Lausanne, Rue du Bugnon 25A, 1005 Lausanne, Switzerland
- Department of Oncology, Centre Hospitalier Universitaire Vaudois (CHUV), Rue du Bugnon 46, 1005 Lausanne, Switzerland
- Agora Cancer Research Centre, Rue du Bugnon 25A, 1005 Lausanne, Switzerland
| | - Emma Ricart Altimiras
- Ludwig Institute for Cancer Research, University of Lausanne, Rue du Bugnon 25A, 1005 Lausanne, Switzerland
- Department of Oncology, Centre Hospitalier Universitaire Vaudois (CHUV), Rue du Bugnon 46, 1005 Lausanne, Switzerland
- Agora Cancer Research Centre, Rue du Bugnon 25A, 1005 Lausanne, Switzerland
| | - Michal Bassani-Sternberg
- Ludwig Institute for Cancer Research, University of Lausanne, Rue du Bugnon 25A, 1005 Lausanne, Switzerland
- Department of Oncology, Centre Hospitalier Universitaire Vaudois (CHUV), Rue du Bugnon 46, 1005 Lausanne, Switzerland
- Agora Cancer Research Centre, Rue du Bugnon 25A, 1005 Lausanne, Switzerland
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42
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Fonseca AF, Antunes DA. CrossDome: an interactive R package to predict cross-reactivity risk using immunopeptidomics databases. Front Immunol 2023; 14:1142573. [PMID: 37377956 PMCID: PMC10291144 DOI: 10.3389/fimmu.2023.1142573] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023] Open
Abstract
T-cell-based immunotherapies hold tremendous potential in the fight against cancer, thanks to their capacity to specifically targeting diseased cells. Nevertheless, this potential has been tempered with safety concerns regarding the possible recognition of unknown off-targets displayed by healthy cells. In a notorious example, engineered T-cells specific to MAGEA3 (EVDPIGHLY) also recognized a TITIN-derived peptide (ESDPIVAQY) expressed by cardiac cells, inducing lethal damage in melanoma patients. Such off-target toxicity has been related to T-cell cross-reactivity induced by molecular mimicry. In this context, there is growing interest in developing the means to avoid off-target toxicity, and to provide safer immunotherapy products. To this end, we present CrossDome, a multi-omics suite to predict the off-target toxicity risk of T-cell-based immunotherapies. Our suite provides two alternative protocols, i) a peptide-centered prediction, or ii) a TCR-centered prediction. As proof-of-principle, we evaluate our approach using 16 well-known cross-reactivity cases involving cancer-associated antigens. With CrossDome, the TITIN-derived peptide was predicted at the 99+ percentile rank among 36,000 scored candidates (p-value < 0.001). In addition, off-targets for all the 16 known cases were predicted within the top ranges of relatedness score on a Monte Carlo simulation with over 5 million putative peptide pairs, allowing us to determine a cut-off p-value for off-target toxicity risk. We also implemented a penalty system based on TCR hotspots, named contact map (CM). This TCR-centered approach improved upon the peptide-centered prediction on the MAGEA3-TITIN screening (e.g., from 27th to 6th, out of 36,000 ranked peptides). Next, we used an extended dataset of experimentally-determined cross-reactive peptides to evaluate alternative CrossDome protocols. The level of enrichment of validated cases among top 50 best-scored peptides was 63% for the peptide-centered protocol, and up to 82% for the TCR-centered protocol. Finally, we performed functional characterization of top ranking candidates, by integrating expression data, HLA binding, and immunogenicity predictions. CrossDome was designed as an R package for easy integration with antigen discovery pipelines, and an interactive web interface for users without coding experience. CrossDome is under active development, and it is available at https://github.com/AntunesLab/crossdome.
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Affiliation(s)
| | - Dinler A. Antunes
- Antunes Lab, Center for Nuclear Receptors and Cell Signaling (CNRCS), Department of Biology and Biochemistry, University of Houston, Houston, TX, United States
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43
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Deering RP, Blumenberg L, Li L, Dhanik A, Jeong S, Pourpe S, Song H, Boucher L, Ragunathan S, Li Y, Zhong M, Kuhnert J, Adler C, Hawkins P, Gupta NT, Moore M, Ni M, Hansen J, Wei Y, Thurston G. Rapid TCR:Epitope Ranker (RAPTER): a primary human T cell reactivity screening assay pairing epitope and TCR at single cell resolution. Sci Rep 2023; 13:8452. [PMID: 37231180 DOI: 10.1038/s41598-023-35710-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 05/22/2023] [Indexed: 05/27/2023] Open
Abstract
Identifying epitopes that T cells respond to is critical for understanding T cell-mediated immunity. Traditional multimer and other single cell assays often require large blood volumes and/or expensive HLA-specific reagents and provide limited phenotypic and functional information. Here, we present the Rapid TCR:Epitope Ranker (RAPTER) assay, a single cell RNA sequencing (scRNA-SEQ) method that uses primary human T cells and antigen presenting cells (APCs) to assess functional T cell reactivity. Using hash-tag oligonucleotide (HTO) coding and T cell activation-induced markers (AIM), RAPTER defines paired epitope specificity and TCR sequence and can include RNA- and protein-level T cell phenotype information. We demonstrate that RAPTER identified specific reactivities to viral and tumor antigens at sensitivities as low as 0.15% of total CD8+ T cells, and deconvoluted low-frequency circulating HPV16-specific T cell clones from a cervical cancer patient. The specificities of TCRs identified by RAPTER for MART1, EBV, and influenza epitopes were functionally confirmed in vitro. In summary, RAPTER identifies low-frequency T cell reactivities using primary cells from low blood volumes, and the resulting paired TCR:ligand information can directly enable immunogenic antigen selection from limited patient samples for vaccine epitope inclusion, antigen-specific TCR tracking, and TCR cloning for further therapeutic development.
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Affiliation(s)
- Raquel P Deering
- Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, USA.
| | - Lili Blumenberg
- Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, USA
| | - Lianjie Li
- Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, USA
| | - Ankur Dhanik
- Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, USA
| | - Se Jeong
- Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, USA
| | - Stephane Pourpe
- Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, USA
| | - Hang Song
- Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, USA
| | - Lauren Boucher
- Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, USA
| | - Shoba Ragunathan
- Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, USA
| | - Yanxia Li
- Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, USA
| | - Maggie Zhong
- Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, USA
| | - Jessica Kuhnert
- Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, USA
| | - Christina Adler
- Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, USA
| | - Peter Hawkins
- Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, USA
| | - Namita T Gupta
- Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, USA
| | - Michael Moore
- Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, USA
| | - Min Ni
- Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, USA
| | - Johanna Hansen
- Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, USA
| | - Yi Wei
- Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, USA
| | - Gavin Thurston
- Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, USA
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44
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Tai W, Feng S, Chai B, Lu S, Zhao G, Chen D, Yu W, Ren L, Shi H, Lu J, Cai Z, Pang M, Tan X, Wang P, Lin J, Sun Q, Peng X, Cheng G. An mRNA-based T-cell-inducing antigen strengthens COVID-19 vaccine against SARS-CoV-2 variants. Nat Commun 2023; 14:2962. [PMID: 37221158 DOI: 10.1038/s41467-023-38751-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 05/12/2023] [Indexed: 05/25/2023] Open
Abstract
Herd immunity achieved through mass vaccination is an effective approach to prevent contagious diseases. Nonetheless, emerging SARS-CoV-2 variants with frequent mutations largely evaded humoral immunity induced by Spike-based COVID-19 vaccines. Herein, we develop a lipid nanoparticle (LNP)-formulated mRNA-based T-cell-inducing antigen, which targeted three SARS-CoV-2 proteome regions that enriched human HLA-I epitopes (HLA-EPs). Immunization of HLA-EPs induces potent cellular responses to prevent SARS-CoV-2 infection in humanized HLA-A*02:01/DR1 and HLA-A*11:01/DR1 transgenic mice. Of note, the sequences of HLA-EPs are highly conserved among SARS-CoV-2 variants of concern. In humanized HLA-transgenic mice and female rhesus macaques, dual immunization with the LNP-formulated mRNAs encoding HLA-EPs and the receptor-binding domain of the SARS-CoV-2 B.1.351 variant (RBDbeta) is more efficacious in preventing infection of SARS-CoV-2 Beta and Omicron BA.1 variants than single immunization of LNP-RBDbeta. This study demonstrates the necessity to strengthen the vaccine effectiveness by comprehensively stimulating both humoral and cellular responses, thereby offering insight for optimizing the design of COVID-19 vaccines.
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Affiliation(s)
- Wanbo Tai
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen, 518132, China
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510182, China
| | - Shengyong Feng
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Benjie Chai
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Shuaiyao Lu
- National Kunming High-level Biosafety Primate Research Center, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650118, China
| | - Guangyu Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, 100071, China
| | - Dong Chen
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
- Wenzhou Central Hospital, Wenzhou, 325000, China
| | - Wenhai Yu
- National Kunming High-level Biosafety Primate Research Center, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650118, China
| | - Liting Ren
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China
| | - Huicheng Shi
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Jing Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, 200438, China
| | - Zhuming Cai
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen, 518132, China
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Mujia Pang
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen, 518132, China
| | - Xu Tan
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China
| | - Penghua Wang
- Department of Immunology, School of Medicine, the University of Connecticut Health Center, Farmington, CT, 06030, USA
| | - Jinzhong Lin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, 200438, China.
| | - Qiangming Sun
- National Kunming High-level Biosafety Primate Research Center, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650118, China.
| | - Xiaozhong Peng
- National Kunming High-level Biosafety Primate Research Center, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650118, China.
| | - Gong Cheng
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China.
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45
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Christodoulou MI, Zaravinos A. Single-Cell Analysis in Immuno-Oncology. Int J Mol Sci 2023; 24:ijms24098422. [PMID: 37176128 PMCID: PMC10178969 DOI: 10.3390/ijms24098422] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/01/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023] Open
Abstract
The complexity of the cellular and non-cellular milieu surrounding human tumors plays a decisive role in the course and outcome of disease. The high variability in the distribution of the immune and non-immune compartments within the tumor microenvironments (TME) among different patients governs the mode of their response or resistance to current immunotherapeutic approaches. Through deciphering this diversity, one can tailor patients' management to meet an individual's needs. Single-cell (sc) omics technologies have given a great boost towards this direction. This review gathers recent data about how multi-omics profiling, including the utilization of single-cell RNA sequencing (scRNA-seq), assay for transposase-accessible chromatin with sequencing (scATAC-seq), T-cell receptor sequencing (scTCR-seq), mass, tissue-based, or microfluidics cytometry, and related bioinformatics tools, contributes to the high-throughput assessment of a large number of analytes at single-cell resolution. Unravelling the exact TCR clonotype of the infiltrating T cells or pinpointing the classical or novel immune checkpoints across various cell subsets of the TME provide a boost to our comprehension of adaptive immune responses, their antigen specificity and dynamics, and grant suggestions for possible therapeutic targets. Future steps are expected to merge high-dimensional data with tissue localization data, which can serve the investigation of novel multi-modal biomarkers for the selection and/or monitoring of the optimal treatment from the current anti-cancer immunotherapeutic armamentarium.
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Affiliation(s)
- Maria-Ioanna Christodoulou
- Tumor Immunology and Biomarkers Group, Basic and Translational Cancer Research Center (BTCRC), 1516 Nicosia, Cyprus
- Department of Life Sciences, School of Sciences, European University Cyprus, 2404 Nicosia, Cyprus
| | - Apostolos Zaravinos
- Department of Life Sciences, School of Sciences, European University Cyprus, 2404 Nicosia, Cyprus
- Cancer Genetics, Genomics and Systems Biology Group, Basic and Translational Cancer Research Center (BTCRC), 1516 Nicosia, Cyprus
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46
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Hederman AP, Ackerman ME. Leveraging deep learning to improve vaccine design. Trends Immunol 2023; 44:333-344. [PMID: 37003949 PMCID: PMC10485910 DOI: 10.1016/j.it.2023.03.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/05/2023] [Accepted: 03/05/2023] [Indexed: 04/03/2023]
Abstract
Deep learning has led to incredible breakthroughs in areas of research, from self-driving vehicles to solutions, to formal mathematical proofs. In the biomedical sciences, however, the revolutionary results seen in other fields are only now beginning to be realized. Vaccine research and development efforts represent an application with high public health significance. Protein structure prediction, immune repertoire analysis, and phylogenetics are three principal areas in which deep learning is poised to provide key advances. Here, we opine on some of the current challenges with deep learning and how they are being addressed. Despite the nascent stage of deep learning applications in immunological studies, there is ample opportunity to utilize this new technology to address the most challenging and burdensome infectious diseases confronting global populations.
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Affiliation(s)
| | - Margaret E Ackerman
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA; Department of Microbiology and Immunology, Geisel School of Medicine, Hanover, NH, USA.
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47
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Abstract
Recent advances in cancer immunotherapy - ranging from immune-checkpoint blockade therapy to adoptive cellular therapy and vaccines - have revolutionized cancer treatment paradigms, yet the variability in clinical responses to these agents has motivated intense interest in understanding how the T cell landscape evolves with respect to response to immune intervention. Over the past decade, the advent of multidimensional single-cell technologies has provided the unprecedented ability to dissect the constellation of cell states of lymphocytes within a tumour microenvironment. In particular, the rapidly expanding capacity to definitively link intratumoural phenotypes with the antigen specificity of T cells provided by T cell receptors (TCRs) has now made it possible to focus on investigating the properties of T cells with tumour-specific reactivity. Moreover, the assessment of TCR clonality has enabled a molecular approach to track the trajectories, clonal dynamics and phenotypic changes of antitumour T cells over the course of immunotherapeutic intervention. Here, we review the current knowledge on the cellular states and antigen specificities of antitumour T cells and examine how fine characterization of T cell dynamics in patients has provided meaningful insights into the mechanisms underlying effective cancer immunotherapy. We highlight those T cell subsets associated with productive T cell responses and discuss how diverse immunotherapies might leverage the pre-existing tumour-reactive T cell pool or instruct de novo generation of antitumour specificities. Future studies aimed at elucidating the factors associated with the elicitation of productive antitumour T cell immunity are anticipated to instruct the design of more efficacious treatment strategies.
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Affiliation(s)
- Giacomo Oliveira
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
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48
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Dunlap GS, DiToro D, Henderson J, Shah SI, Manos M, Severgnini M, Weins A, Guleria I, Ott PA, Murakami N, Rao DA. Clonal dynamics of alloreactive T cells in kidney allograft rejection after anti-PD-1 therapy. Nat Commun 2023; 14:1549. [PMID: 36941274 PMCID: PMC10027853 DOI: 10.1038/s41467-023-37230-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 03/08/2023] [Indexed: 03/23/2023] Open
Abstract
Kidney transplant recipients are at particular risk for developing tumors, many of which are now routinely treated with immune checkpoint inhibitors (ICIs); however, ICI therapy can precipitate transplant rejection. Here, we use TCR sequencing to identify and track alloreactive T cells in a patient with melanoma who experienced kidney transplant rejection following PD-1 inhibition. The treatment was associated with a sharp increase in circulating alloreactive CD8+ T cell clones, which display a unique transcriptomic signature and were also detected in the rejected kidney but not at tumor sites. Longitudinal and cross-tissue TCR analyses indicate unintended expansion of alloreactive CD8+ T cells induced by ICI therapy for cancer, coinciding with ICI-associated organ rejection.
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Affiliation(s)
- Garrett S Dunlap
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Daniel DiToro
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Joel Henderson
- Department of Pathology, Boston Medical Center and Boston University, Boston, MA, USA
| | - Sujal I Shah
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Mike Manos
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mariano Severgnini
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Astrid Weins
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Indira Guleria
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Patrick A Ott
- Harvard Medical School, Boston, MA, USA
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Naoka Murakami
- Harvard Medical School, Boston, MA, USA.
- Division of Renal Medicine, Brigham and Women's Hospital, Boston, MA, USA.
| | - Deepak A Rao
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
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49
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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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50
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Charabati M, Wheeler MA, Weiner HL, Quintana FJ. Multiple sclerosis: Neuroimmune crosstalk and therapeutic targeting. Cell 2023; 186:1309-1327. [PMID: 37001498 PMCID: PMC10119687 DOI: 10.1016/j.cell.2023.03.008] [Citation(s) in RCA: 54] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 01/23/2023] [Accepted: 03/03/2023] [Indexed: 04/03/2023]
Abstract
Multiple sclerosis (MS) is a chronic inflammatory and degenerative disease of the central nervous system afflicting nearly three million individuals worldwide. Neuroimmune interactions between glial, neural, and immune cells play important roles in MS pathology and offer potential targets for therapeutic intervention. Here, we review underlying risk factors, mechanisms of MS pathogenesis, available disease modifying therapies, and examine the value of emerging technologies, which may address unmet clinical needs and identify novel therapeutic targets.
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Affiliation(s)
- Marc Charabati
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Michael A Wheeler
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Howard L Weiner
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Francisco J Quintana
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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