1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Jin Y, Miyama T, Brown A, Hayase T, Song X, Singh AK, Huang L, Flores II, McDaniel LK, Glover I, Halsey TM, Prasad R, Chapa V, Ahmed S, Zhang J, Rai K, Peterson CB, Lizee G, Karmouch J, Hayase E, Molldrem JJ, Chang CC, Tsai WB, Jenq RR. Tsyn-Seq: a T-cell Synapse-Based Antigen Identification Platform. Cancer Immunol Res 2024; 12:530-543. [PMID: 38363296 PMCID: PMC11065584 DOI: 10.1158/2326-6066.cir-23-0467] [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: 06/02/2023] [Revised: 11/02/2023] [Accepted: 02/09/2024] [Indexed: 02/17/2024]
Abstract
Tools for genome-wide rapid identification of peptide-major histocompatibility complex targets of T-cell receptors (TCR) are not yet universally available. We present a new antigen screening method, the T-synapse (Tsyn) reporter system, which includes antigen-presenting cells (APC) with a Fas-inducible NF-κB reporter and T cells with a nuclear factor of activated T cells (NFAT) reporter. To functionally screen for target antigens from a cDNA library, productively interacting T cell-APC aggregates were detected by dual-reporter activity and enriched by flow sorting followed by antigen identification quantified by deep sequencing (Tsyn-seq). When applied to a previously characterized TCR specific for the E7 antigen derived from human papillomavirus type 16 (HPV16), Tsyn-seq successfully enriched the correct cognate antigen from a cDNA library derived from an HPV16-positive cervical cancer cell line. Tsyn-seq provides a method for rapidly identifying antigens recognized by TCRs of interest from a tumor cDNA library. See related Spotlight by Makani and Joglekar, p. 515.
Collapse
Affiliation(s)
- Yimei Jin
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Takahiko Miyama
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Alexandria Brown
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Tomo Hayase
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Xingzhi Song
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Anand K. Singh
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Licai Huang
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Ivonne I. Flores
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Lauren K. McDaniel
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Israel Glover
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Taylor M. Halsey
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Rishika Prasad
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Valerie Chapa
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Saira Ahmed
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Kunal Rai
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Christine B. Peterson
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Gregory Lizee
- Department of Melanoma Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Jennifer Karmouch
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Eiko Hayase
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Jeffrey J. Molldrem
- Department of Hematopoietic Biology & Malignancy, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Chia-Chi Chang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Wen-Bin Tsai
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Robert R. Jenq
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| |
Collapse
|
3
|
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.
Collapse
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.
| |
Collapse
|
4
|
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.
Collapse
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.
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Hafler D, Lu B, Lucca L, Lewis W, Wang J, Nogeuira C, Heer S, Axisa PP, Buitrago-Pocasangre N, Pham G, Kojima M, Wei W, Aizenbud L, Bacchiocchi A, Zhang L, Walewski J, Chiang V, Olino K, Clune J, Halaban R, Kluger Y, Coyle A, Kisielow J, Obermair FJ, Kluger H. Circulating Tumor Reactive KIR+CD8+ T cells Suppress Anti-Tumor Immunity in Patients with Melanoma. RESEARCH SQUARE 2024:rs.3.rs-3956671. [PMID: 38464315 PMCID: PMC10925449 DOI: 10.21203/rs.3.rs-3956671/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Effective anti-tumor immunity is largely driven by cytotoxic CD8+ T cells that can specifically recognize tumor antigens. However, the factors which ultimately dictate successful tumor rejection remain poorly understood. Here we identify a subpopulation of CD8+ T cells which are tumor antigen-specific in patients with melanoma but resemble KIR+CD8+ T cells with a regulatory function (Tregs). These tumor antigen-specific KIR+CD8+ T cells are detectable in both the tumor and the blood, and higher levels of this population are associated with worse overall survival. Our findings therefore suggest that KIR+CD8+ Tregs are tumor antigen-specific but uniquely suppress anti-tumor immunity in patients with melanoma.
Collapse
|
7
|
McBride DA, Jones RM, Bottini N, Shah NJ. The therapeutic potential of immunoengineering for systemic autoimmunity. Nat Rev Rheumatol 2024:10.1038/s41584-024-01084-x. [PMID: 38383732 DOI: 10.1038/s41584-024-01084-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/22/2024] [Indexed: 02/23/2024]
Abstract
Disease-modifying drugs have transformed the treatment options for many systemic autoimmune diseases. However, an evolving understanding of disease mechanisms, which might vary between individuals, is paving the way for the development of novel agents that operate in a patient-tailored manner through immunophenotypic regulation of disease-relevant cells and the microenvironment of affected tissue domains. Immunoengineering is a field that is focused on the application of engineering principles to the modulation of the immune system, and it could enable future personalized and immunoregulatory therapies for rheumatic diseases. An important aspect of immunoengineering is the harnessing of material chemistries to design technologies that span immunologically relevant length scales, to enhance or suppress immune responses by re-balancing effector and regulatory mechanisms in innate or adaptive immunity and rescue abnormalities underlying pathogenic inflammation. These materials are endowed with physicochemical properties that enable features such as localization in immune cells and organs, sustained delivery of immunoregulatory agents, and mimicry of key functions of lymphoid tissue. Immunoengineering applications already exist for disease management, and there is potential for this new discipline to improve disease modification in rheumatology.
Collapse
Affiliation(s)
- David A McBride
- Department of NanoEngineering and Chemical Engineering Program, University of California, San Diego, La Jolla, CA, USA
| | - Ryan M Jones
- Department of NanoEngineering and Chemical Engineering Program, University of California, San Diego, La Jolla, CA, USA
| | - Nunzio Bottini
- Kao Autoimmunity Institute and Division of Rheumatology, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
| | - Nisarg J Shah
- Department of NanoEngineering and Chemical Engineering Program, University of California, San Diego, La Jolla, CA, USA.
| |
Collapse
|
8
|
Akama-Garren EH, Yin X, Prestwood TR, Ma M, Utz PJ, Carroll MC. T cell help shapes B cell tolerance. Sci Immunol 2024; 9:eadj7029. [PMID: 38363829 DOI: 10.1126/sciimmunol.adj7029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 12/29/2023] [Indexed: 02/18/2024]
Abstract
T cell help is a crucial component of the normal humoral immune response, yet whether it promotes or restrains autoreactive B cell responses remains unclear. Here, we observe that autoreactive germinal centers require T cell help for their formation and persistence. Using retrogenic chimeras transduced with candidate TCRs, we demonstrate that a follicular T cell repertoire restricted to a single autoreactive TCR, but not a foreign antigen-specific TCR, is sufficient to initiate autoreactive germinal centers. Follicular T cell specificity influences the breadth of epitope spreading by regulating wild-type B cell entry into autoreactive germinal centers. These results demonstrate that TCR-dependent T cell help can promote loss of B cell tolerance and that epitope spreading is determined by TCR specificity.
Collapse
Affiliation(s)
- Elliot H Akama-Garren
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Harvard-MIT Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA
| | - Xihui Yin
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Tyler R Prestwood
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Minghe Ma
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Paul J Utz
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael C Carroll
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
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, Darise Farris A, 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: 2] [Impact Index Per Article: 2.0] [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.
Collapse
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.
| |
Collapse
|
11
|
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: 0] [Impact Index Per Article: 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.
Collapse
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
| |
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
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.
Collapse
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.
| |
Collapse
|
15
|
Prinz JC. Immunogenic self-peptides - the great unknowns in autoimmunity: Identifying T-cell epitopes driving the autoimmune response in autoimmune diseases. Front Immunol 2023; 13:1097871. [PMID: 36700227 PMCID: PMC9868241 DOI: 10.3389/fimmu.2022.1097871] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 12/12/2022] [Indexed: 01/11/2023] Open
Abstract
HLA-associated autoimmune diseases likely arise from T-cell-mediated autoimmune responses against certain self-peptides from the broad HLA-presented immunopeptidomes. The limited knowledge of the autoimmune target peptides has so far compromised the basic understanding of autoimmune pathogenesis. This is due to the complexity of antigen processing and presentation as well as the polyspecificity of T-cell receptors (TCRs), which pose high methodological challenges on the discovery of immunogenic self-peptides. HLA-class I molecules present peptides to CD8+ T cells primarily derived from cytoplasmic proteins. Therefore, HLA-class I-restricted autoimmune responses should be directed against target cells expressing the corresponding parental protein. In HLA-class II-associated diseases, the origin of immunogenic peptides is not pre-specified, because peptides presented by HLA-class II molecules to CD4+ T cells may originate from both extracellular and cellular self-proteins. The different origins of HLA-class I and class II presented peptides determine the respective strategy for the discovery of immunogenic self-peptides in approaches based on the TCRs isolated from clonally expanded pathogenic T cells. Both involve identifying the respective restricting HLA allele as well as determining the recognition motif of the TCR under investigation by peptide library screening, which is required to search for homologous immunogenic self-peptides. In HLA-class I-associated autoimmune diseases, identification of the target cells allows for defining the restricting HLA allotype from the 6 different HLA-class I alleles of the individual HLA haplotype. It furthermore limits the search for immunogenic self-peptides to the transcriptome or immunopeptidome of the target cells, although neoepitopes generated by peptide splicing or translational errors may complicate identification. In HLA class II-associated autoimmune diseases, the lack of a defined target cell and differential antigen processing in different antigen-presenting cells complicate identification of the HLA restriction of autoreactive TCRs from CD4+ T cells. To avoid that all corresponding HLA-class II allotypes have to be included in the peptide discovery, autoantigens defined by autoantibodies can guide the search for immunogenic self-peptides presented by the respective HLA-class II risk allele. The objective of this article is to highlight important aspects to be considered in the discovery of immunogenic self-peptides in autoimmune diseases.
Collapse
|
16
|
Garrido-Mesa J, Brown MA. T cell Repertoire Profiling and the Mechanism by which HLA-B27 Causes Ankylosing Spondylitis. Curr Rheumatol Rep 2022; 24:398-410. [PMID: 36197645 PMCID: PMC9666335 DOI: 10.1007/s11926-022-01090-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/25/2022] [Indexed: 11/25/2022]
Abstract
Purpose of Review Ankylosing spondylitis (AS) is strongly associated with the HLA-B27 gene. The canonical function of HLA-B27 is to present antigenic peptides to CD8 lymphocytes, leading to adaptive immune responses. The ‘arthritogenic peptide’ theory as to the mechanism by which HLA-B27 induces ankylosing spondylitis proposes that HLA-B27 presents peptides derived from exogenous sources such as bacteria to CD8 lymphocytes, which subsequently cross-react with antigens at the site of inflammation of the disease, causing inflammation. This review describes findings of studies in AS involving profiling of T cell expansions and discusses future research opportunities based on these findings. Recent Findings Consistent with this theory, there is an expanding body of data showing that expansion of a restricted pool of CD8 lymphocytes is found in most AS patients yet only in a small proportion of healthy HLA-B27 carriers. Summary These exciting findings strongly support the theory that AS is driven by presentation of antigenic peptides to the adaptive immune system by HLA-B27. They point to new potential approaches to identify the exogenous and endogenous antigens involved and to potential therapies for the disease.
Collapse
Affiliation(s)
- Jose Garrido-Mesa
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, England
| | - Matthew A Brown
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, England.
- Genomics England, Charterhouse Square, London, EC1M 6BQ, England.
| |
Collapse
|
17
|
Healthy-like CD4 + Regulatory and CD4 + Conventional T-Cell Receptor Repertoires Predict Protection from GVHD Following Donor Lymphocyte Infusion. Int J Mol Sci 2022; 23:ijms231810914. [PMID: 36142824 PMCID: PMC9505302 DOI: 10.3390/ijms231810914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 09/14/2022] [Accepted: 09/16/2022] [Indexed: 11/17/2022] Open
Abstract
Donor lymphocyte infusion (DLI) can (re-)induce durable remission in relapsing patients after allogeneic hematopoietic stem-cell transplantation (alloHSCT). However, DLI harbors the risk of increased non-relapse mortality due to the co-occurrence of graft-versus-host disease (GVHD). GVHD onset may be caused or accompanied by changes in the clonal T-cell receptor (TCR) repertoire. To investigate this, we analyzed T cells in a cohort of 21 patients receiving DLI after alloHSCT. We performed deep T-cell receptor β (TRB) sequencing of sorted CD4+CD25+CD127low regulatory T cells (Treg cells) and CD4+ conventional T cells (Tcon cells) in order to track longitudinal changes in the TCR repertoire. GVHD following DLI was associated with less diverse but clonally expanded CD4+CD25+CD127low Treg and CD4+ Tcon TCR repertoires, while patients without GVHD exhibited healthy-like repertoire properties. Moreover, the diversification of the repertoires upon GVHD treatment was linked to steroid-sensitive GVHD, whereas decreased diversity was observed in steroid-refractory GVHD. Finally, the unbiased sample analysis revealed that the healthy-like attributes of the CD4+CD25+CD127low Treg TCR repertoire were associated with reduced GVHD incidence. In conclusion, CD4+CD25+CD127low Treg and CD4+ Tcon TRB repertoire dynamics may provide a helpful real-time tool to improve the diagnosis and monitoring of treatment in GVHD following DLI.
Collapse
|
18
|
Camp FA, Brunetti TM, Williams MM, Christenson JL, Sreekanth V, Costello JC, Hay ZLZ, Kedl RM, Richer JK, Slansky JE. Antigens Expressed by Breast Cancer Cells Undergoing EMT Stimulate Cytotoxic CD8 + T Cell Immunity. Cancers (Basel) 2022; 14:cancers14184397. [PMID: 36139558 PMCID: PMC9496737 DOI: 10.3390/cancers14184397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/31/2022] [Accepted: 09/06/2022] [Indexed: 11/26/2022] Open
Abstract
Simple Summary The transition of cells with epithelial characteristics to those with mesenchymal characteristics (termed EMT) facilitates breast cancer invasive capacity. The EMT program can also contribute to immunosuppressive and immunoevasive properties, altering susceptibility to immune cell recognition and killing. The goal of our study was to manipulate EMT to reveal potential neoantigens that might affect the ability of tumor cells to circumvent immune escape and/or be utilized as an anticancer vaccine to kill cancer cells exhibiting the cellular plasticity that permits therapy resistance and metastatic progression. We identified potential neoantigens resulting from EMT-associated altered gene expression and alternative splicing events and observed increased immunogenicity and susceptibility to killing of the more epithelial-like cancer cells. Although the tested peptides did not protect from tumor growth, a limited number of predicted neoantigens derived from intron retention events were tested. In the future, refined prediction programs may facilitate exciting antigen discoveries. Abstract Antigenic differences formed by alterations in gene expression and alternative splicing are predicted in breast cancer cells undergoing epithelial to mesenchymal transition (EMT) and the reverse plasticity known as MET. How these antigenic differences impact immune interactions and the degree to which they can be exploited to enhance immune responses against mesenchymal cells is not fully understood. We utilized a master microRNA regulator of EMT to alter mesenchymal-like EO771 mammary carcinoma cells to a more epithelial phenotype. A computational approach was used to identify neoantigens derived from the resultant differentially expressed somatic variants (SNV) and alternative splicing events (neojunctions). Using whole cell vaccines and peptide-based vaccines, we find superior cytotoxicity against the more-epithelial cells and explore the potential of neojunction-derived antigens to elicit T cell responses through experiments designed to validate the computationally predicted neoantigens. Overall, results identify EMT-associated splicing factors common to both mouse and human breast cancer cells as well as immunogenic SNV- and neojunction-derived neoantigens in mammary carcinoma cells.
Collapse
Affiliation(s)
- Faye A. Camp
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Tonya M. Brunetti
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Michelle M. Williams
- Department of Pathology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Jessica L. Christenson
- Department of Pathology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Varsha Sreekanth
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - James C. Costello
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Zachary L. Z. Hay
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Ross M. Kedl
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Jennifer K. Richer
- Department of Pathology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Jill E. Slansky
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Correspondence:
| |
Collapse
|
19
|
Zhang Y, Liu Z, Wei W, Li Y. TCR engineered T cells for solid tumor immunotherapy. Exp Hematol Oncol 2022; 11:38. [PMID: 35725570 PMCID: PMC9210724 DOI: 10.1186/s40164-022-00291-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 06/09/2022] [Indexed: 11/26/2022] Open
Abstract
T cell immunotherapy remains an attractive approach for cancer immunotherapy. T cell immunotherapy mainly employs chimeric antigen receptor (CAR)- and T cell receptor (TCR)-engineered T cells. CAR-T cell therapy has been an essential breakthrough in treating hematological malignancies. TCR-T cells can recognize antigens expressed both on cell surfaces and in intracellular compartments. Although TCR-T cells have not been approved for clinical application, a number of clinical trials have been performed, particularly for solid tumors. In this article, we summarized current TCR-T cell advances and their potential advantages for solid tumor immunotherapy.
Collapse
Affiliation(s)
- Yikai Zhang
- Guangzhou Municipality Tianhe Nuoya Bio-engineering Co. Ltd, Guangzhou, 510663, China.,Guangdong Cord blood bank, Guangzhou, 510663, China.,Department of Hematology, First Affiliated Hospital, Jinan University, Guangzhou, 510632, China.,Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, 601 Huang Pu Da Dao Xi, Guangzhou, 510632, China
| | - Zhipeng Liu
- Guangzhou Municipality Tianhe Nuoya Bio-engineering Co. Ltd, Guangzhou, 510663, China.,Guangdong Cord blood bank, Guangzhou, 510663, China
| | - Wei Wei
- Guangzhou Municipality Tianhe Nuoya Bio-engineering Co. Ltd, Guangzhou, 510663, China. .,Guangdong Cord blood bank, Guangzhou, 510663, China.
| | - Yangqiu Li
- Department of Hematology, First Affiliated Hospital, Jinan University, Guangzhou, 510632, China. .,Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, 601 Huang Pu Da Dao Xi, Guangzhou, 510632, China.
| |
Collapse
|
20
|
Obermair FJ, Renoux F, Heer S, Lee CH, Cereghetti N, Loi M, Maestri G, Haldner Y, Wuigk R, Iosefson O, Patel P, Triebel K, Kopf M, Swain J, Kisielow J. High-resolution profiling of MHC II peptide presentation capacity reveals SARS-CoV-2 CD4 T cell targets and mechanisms of immune escape. SCIENCE ADVANCES 2022; 8:eabl5394. [PMID: 35486722 PMCID: PMC9054008 DOI: 10.1126/sciadv.abl5394] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 03/09/2022] [Indexed: 05/22/2023]
Abstract
Understanding peptide presentation by specific MHC alleles is fundamental for controlling physiological functions of T cells and harnessing them for therapeutic use. However, commonly used in silico predictions and mass spectroscopy have their limitations in precision, sensitivity, and throughput, particularly for MHC class II. Here, we present MEDi, a novel mammalian epitope display that allows an unbiased, affordable, high-resolution mapping of MHC peptide presentation capacity. Our platform provides a detailed picture by testing every antigen-derived peptide and is scalable to all the MHC II alleles. Given the urgent need to understand immune evasion for formulating effective responses to threats such as SARS-CoV-2, we provide a comprehensive analysis of the presentability of all SARS-CoV-2 peptides in the context of several HLA class II alleles. We show that several mutations arising in viral strains expanding globally resulted in reduced peptide presentability by multiple HLA class II alleles, while some increased it, suggesting alteration of MHC II presentation landscapes as a possible immune escape mechanism.
Collapse
Affiliation(s)
- Franz-Josef Obermair
- Repertoire Immune Medicines, Cambridge, MA, USA
- Repertoire Immune Medicines, Schlieren, Switzerland
| | | | | | - Chloe H. Lee
- Institute of Molecular Health Sciences, ETH Zürich, Zürich, Switzerland
| | | | - Marisa Loi
- Repertoire Immune Medicines, Schlieren, Switzerland
| | | | | | - Robin Wuigk
- Repertoire Immune Medicines, Schlieren, Switzerland
| | | | - Pooja Patel
- Repertoire Immune Medicines, Cambridge, MA, USA
| | | | - Manfred Kopf
- Institute of Molecular Health Sciences, ETH Zürich, Zürich, Switzerland
| | | | - Jan Kisielow
- Repertoire Immune Medicines, Cambridge, MA, USA
- Repertoire Immune Medicines, Schlieren, Switzerland
- Corresponding author.
| |
Collapse
|
21
|
Affiliation(s)
- Yuqian Wang
- CAMS Key Laboratory of Synthetic Biology Regulatory Element, Institute of Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Suzhou Institute of Systems Medicine, Suzhou, China
| | - Zhe Wang
- CAMS Key Laboratory of Synthetic Biology Regulatory Element, Institute of Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Suzhou Institute of Systems Medicine, Suzhou, China
| | - Guideng Li
- CAMS Key Laboratory of Synthetic Biology Regulatory Element, Institute of Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China. .,Suzhou Institute of Systems Medicine, Suzhou, China.
| |
Collapse
|
22
|
Dobson CS, Reich AN, Gaglione S, Smith BE, Kim EJ, Dong J, Ronsard L, Okonkwo V, Lingwood D, Dougan M, Dougan SK, Birnbaum ME. Antigen identification and high-throughput interaction mapping by reprogramming viral entry. Nat Methods 2022; 19:449-460. [PMID: 35396484 PMCID: PMC9012700 DOI: 10.1038/s41592-022-01436-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 03/01/2022] [Indexed: 01/11/2023]
Abstract
Deciphering immune recognition is critical for understanding a broad range of diseases and for the development of effective vaccines and immunotherapies. Efforts to do so are limited by a lack of technologies capable of simultaneously capturing the complexity of adaptive immunoreceptor repertoires and the landscape of potential antigens. To address this, we present receptor-antigen pairing by targeted retroviruses, which combines viral pseudotyping and molecular engineering approaches to enable one-pot library-on-library interaction screens by displaying antigens on the surface of lentiviruses and encoding their identity in the viral genome. Antigen-specific viral infection of cell lines expressing human T or B cell receptors allows readout of both antigen and receptor identities via single-cell sequencing. The resulting system is modular, scalable and compatible with any cell type. These techniques provide a suite of tools for targeted viral entry, molecular engineering and interaction screens with broad potential applications.
Collapse
Affiliation(s)
- Connor S Dobson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - Anna N Reich
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - Stephanie Gaglione
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Blake E Smith
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Program in Immunology, Harvard Medical School, Boston, MA, USA
| | - Ellen J Kim
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - Jiayi Dong
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | | | - Vintus Okonkwo
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | | | - Michael Dougan
- Program in Immunology, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Stephanie K Dougan
- Program in Immunology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Michael E Birnbaum
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA.
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
- Singapore-MIT Alliance for Research and Technology Centre, Singapore, Singapore.
| |
Collapse
|
23
|
Lantz O, Teyton L. Identification of T cell antigens in the 21st century, as difficult as ever. Semin Immunol 2022; 60:101659. [PMID: 36183497 PMCID: PMC10332289 DOI: 10.1016/j.smim.2022.101659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Identifying antigens recognized by T cells is still challenging, particularly for innate like T cells that do not recognize peptides but small metabolites or lipids in the context of MHC-like molecules or see non-MHC restricted antigens. The fundamental reason for this situation is the low affinity of T cell receptors for their ligands coupled with a level of degeneracy that makes them bind to similar surfaces on antigen presenting cells. Herein we will describe non-exhaustively some of the methods that were used to identify peptide antigens and briefly mention the high throughput methods more recently proposed for that purpose. We will then present how the molecules recognized by innate like T cells (NKT, MAIT and γδ T cells) were discovered. We will show that serendipity was instrumental in many cases.
Collapse
Affiliation(s)
- Olivier Lantz
- INSERM U932, PSL University, Institut Curie, 75005 Paris, France; Laboratoire d'Immunologie Clinique, Institut Curie, Paris 75005, France; Centre d'investigation Clinique en Biothérapie Gustave-Roussy Institut Curie (CIC-BT1428) Institut Curie, Paris 75005, France
| | - Luc Teyton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| |
Collapse
|
24
|
Poznyak AV, Bezsonov EE, Popkova TV, Starodubova AV, Orekhov AN. Vaccination against Atherosclerosis: Is It Real? Int J Mol Sci 2022; 23:ijms23052417. [PMID: 35269559 PMCID: PMC8910641 DOI: 10.3390/ijms23052417] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/12/2022] [Accepted: 02/18/2022] [Indexed: 02/05/2023] Open
Abstract
Atherosclerosis has been known in medicine for several centuries. As early as 1755, the Swedish anatomist Albrecht von Haller used the term "atheroma" to describe vascular lesions. Atherosclerosis may originate from an unbalanced diet or bad habits, and is mainly found in developed countries. Clinical trials have been conducted to establish the causes of atherosclerosis, and also to develop treatments for this disease. However, prevention of the disease has always been better than treatment, so vaccination may be the key to saving thousands of lives. The creation of a vaccine may be directly related to the study of autoimmune processes occurring in the body, immunity. This review considers the issues related to the involvement of the immune response in the development of atherosclerotic lesions. Modern concepts of atherogenesis, immune inflammation in atherosclerosis, and potential vaccine targets are also discussed. There is a particular focus on experimental and clinical data supporting the development of immune therapies to reduce cardiovascular risk.
Collapse
Affiliation(s)
- Anastasia V. Poznyak
- Institute for Atherosclerosis Research, Skolkovo Innovative Center, 121609 Moscow, Russia
- Correspondence: (A.V.P.); (A.N.O.)
| | - Evgeny E. Bezsonov
- Laboratory of Cellular and Molecular Pathology of Cardiovascular System, Institute of Human Morphology, 3 Tsyurupa Street, 117418 Moscow, Russia;
- Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, 8 Baltiiskaya Street, 125315 Moscow, Russia
- Department of Biology and General Genetics, I.M. Sechenov First Moscow State Medical University (Sechenov University), 8 Izmailovsky Boulevard, 105043 Moscow, Russia
| | - Tatyana V. Popkova
- V.A. Nasonova Institute of Rheumatology, 34A Kashirskoye Shosse, 115522 Moscow, Russia;
| | - Antonina V. Starodubova
- Federal Research Centre for Nutrition, Biotechnology and Food Safety, 2/14 Ustinsky Passage, 109240 Moscow, Russia;
- Medical Faculty, Pirogov Russian National Research Medical University, 1 Ostrovitianov Street, 117997 Moscow, Russia
| | - Alexander N. Orekhov
- Institute for Atherosclerosis Research, Skolkovo Innovative Center, 121609 Moscow, Russia
- Laboratory of Cellular and Molecular Pathology of Cardiovascular System, Institute of Human Morphology, 3 Tsyurupa Street, 117418 Moscow, Russia;
- Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, 8 Baltiiskaya Street, 125315 Moscow, Russia
- Correspondence: (A.V.P.); (A.N.O.)
| |
Collapse
|
25
|
V-CARMA: A tool for the detection and modification of antigen-specific T cells. Proc Natl Acad Sci U S A 2022; 119:2116277119. [PMID: 35042811 PMCID: PMC8795542 DOI: 10.1073/pnas.2116277119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/13/2021] [Indexed: 11/18/2022] Open
Abstract
Immunotherapy is a promising approach to treat cancers, infectious diseases, and autoimmunity by harnessing the power of immune cells, especially T cells. To improve the precision and efficacy of immunotherapy, the ability to genetically modify antigen-specific T cells is needed but cannot be accomplished using current methods. Here, we present a method, V-CARMA (Viral ChimAeric Receptor MHC-Antigen), to generate lentiviruses displaying peptide-MHC complex to specifically target T cells that express cognate TCRs and subsequently deliver genes into target T cells for genetic modification. Our results demonstrate that V-CARMA is a versatile tool to detect and modify antigen-specific T cells. T cells promote our body’s ability to battle cancers and infectious diseases but can act pathologically in autoimmunity. The recognition of peptides presented by major histocompatibility complex (pMHC) molecules by T cell receptors (TCRs) enables T cell–mediated responses. To modify disease-relevant T cells, new tools to genetically modify T cells and decode their antigen recognition are needed. Here, we present an approach using viruses pseudotyped with peptides loaded on MHC called V-CARMA (Viral ChimAeric Receptor MHC-Antigen) to specifically target T cells expressing cognate TCRs for antigen discovery and T cell engineering. We show that lentiviruses displaying antigens on human leukocyte antigen (HLA) class I and class II molecules can robustly infect CD8+ and CD4+ T cells expressing cognate TCRs, respectively. The infection rates of the pseudotyped lentiviruses (PLVs) are correlated with the binding affinity of the TCR to its cognate antigen. Furthermore, peptide-HLA pseudotyped lentivirus V-CARMA constructs can identify target cells from a mixed T cell population, suppress PD-1 expression on CD8+ T cells via PDCD1 shRNA delivery, and induce apoptosis in autoreactive CD4+ T cells. Thus, V-CARMA is a versatile tool for TCR ligand identification and selective T cell manipulation.
Collapse
|
26
|
Ma KY, Schonnesen AA, He C, Xia AY, Sun E, Chen E, Sebastian KR, Guo YW, Balderas R, Kulkarni-Date M, Jiang N. High-throughput and high-dimensional single-cell analysis of antigen-specific CD8 + T cells. Nat Immunol 2021; 22:1590-1598. [PMID: 34811538 PMCID: PMC9184244 DOI: 10.1038/s41590-021-01073-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 10/15/2021] [Indexed: 02/08/2023]
Abstract
Although critical to T cell function, antigen specificity is often omitted in high-throughput multiomics-based T cell profiling due to technical challenges. We describe a high-dimensional, tetramer-associated T cell antigen receptor (TCR) sequencing (TetTCR-SeqHD) method to simultaneously profile cognate antigen specificities, TCR sequences, targeted gene expression and surface-protein expression from tens of thousands of single cells. Using human polyclonal CD8+ T cells with known antigen specificity and TCR sequences, we demonstrate over 98% precision for detecting the correct antigen specificity. We also evaluate gene expression and phenotypic differences among antigen-specific CD8+ T cells and characterize phenotype signatures of influenza- and Epstein-Barr virus-specific CD8+ T cells that are unique to their pathogen targets. Moreover, with the high-throughput capacity of profiling hundreds of antigens simultaneously, we apply TetTCR-SeqHD to identify antigens that preferentially enrich cognate CD8+ T cells in patients with type 1 diabetes compared to healthy controls and discover a TCR that cross-reacts with diabetes-related and microbiome antigens. TetTCR-SeqHD is a powerful approach for profiling T cell responses in humans and mice.
Collapse
MESH Headings
- Antigens/immunology
- Antigens/metabolism
- Antigens, Viral/immunology
- Antigens, Viral/metabolism
- Autoantigens/immunology
- Autoantigens/metabolism
- Autoimmunity
- CD8-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/metabolism
- CD8-Positive T-Lymphocytes/virology
- Case-Control Studies
- Cell Separation
- Cells, Cultured
- Diabetes Mellitus, Type 1/genetics
- Diabetes Mellitus, Type 1/immunology
- Diabetes Mellitus, Type 1/metabolism
- Herpesvirus 4, Human/immunology
- Herpesvirus 4, Human/pathogenicity
- High-Throughput Nucleotide Sequencing
- Humans
- Orthomyxoviridae/immunology
- Orthomyxoviridae/pathogenicity
- Phenotype
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- Receptors, Antigen, T-Cell/metabolism
- Single-Cell Analysis
Collapse
Affiliation(s)
- Ke-Yue Ma
- Interdisciplinary Life Sciences Graduate Programs, The University of Texas at Austin, Austin, TX, USA
| | - Alexandra A Schonnesen
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Chenfeng He
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Amanda Y Xia
- Department of Molecular Biosciences, The University of Texas atAustin, Austin, TX, USA
| | - Eric Sun
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Eunise Chen
- Department of Nutritional Sciences, The University of Texas at Austin, Austin, TX, USA
| | - Katherine R Sebastian
- Department of Internal Medicine, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
| | - Yu-Wan Guo
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Mrinalini Kulkarni-Date
- Department of Internal Medicine, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
| | - Ning Jiang
- Interdisciplinary Life Sciences Graduate Programs, The University of Texas at Austin, Austin, TX, USA.
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA.
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, USA.
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
| |
Collapse
|
27
|
Wang S, Liu Y, Li Y, Lv M, Gao K, He Y, Wei W, Zhu Y, Dong X, Xu X, Li Z, Liu L, Liu Y. High-Throughput Functional Screening of Antigen-Specific T Cells Based on Droplet Microfluidics at a Single-Cell Level. Anal Chem 2021; 94:918-926. [PMID: 34852202 DOI: 10.1021/acs.analchem.1c03678] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The lack of an efficient method for the identification of tumor antigen-specific T cell receptors (TCRs) impedes the development of T cell-based cancer immunotherapies. Here, we introduce a droplet-based microfluidic platform for function-based screening and sorting of tumor antigen-specific T cells with high throughput. We built a reporter cell line by co-transducing the TCR library and reporter genes at the downstream of TCR signaling, and reporter cells fluoresced upon functionally binding with antigens. We co-encapsulated reporter cells and antigen-presenting cells in droplets to allow for stimulation on a single-cell level. Functioning reporter cells specific against the antigen were identified in the microfluidic channel based on the fluorescent signals of the droplets, which were immediately sorted out using dielectrophoresis. We validated the reporter system and sorting results using flow cytometry. We then performed single-cell RNA sequencing on the sorted cells to further validate this platform and demonstrate the compatibility with genetic characterizations. Our platform provides a means for precise and efficient T cell immunotherapy, and the droplet-based high-throughput TCR screening method could potentially facilitate immunotherapeutic screening and promote T cell-based anti-tumor therapies.
Collapse
Affiliation(s)
- Shiyu Wang
- BGI-Shenzhen, Shenzhen 518083, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Liu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Yijian Li
- BGI-Shenzhen, Shenzhen 518083, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Menghua Lv
- BGI-Shenzhen, Shenzhen 518083, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kai Gao
- BGI-Shenzhen, Shenzhen 518083, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying He
- Department of Gynaecological Oncology, Cancer Hospital Chinese Academy of Medical Sciences, Shenzhen Center, Shenzhen 518116, China
| | - Wenbo Wei
- Department of Biomedical Engineering, School of Medicine, Shenzhen University, Shenzhen 518060, China.,The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen 518035, China
| | - Yonggang Zhu
- School of Mechanical Engineering and Automation, Harbin Institute of Technology, Shenzhen 518055, China
| | - Xuan Dong
- BGI-Shenzhen, Shenzhen 518083, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen 518083, China.,Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, China
| | - Zida Li
- Department of Biomedical Engineering, School of Medicine, Shenzhen University, Shenzhen 518060, China.,Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, Department of Biomedical Engineering, School of Medicine, Shenzhen University, Shenzhen 518060, China
| | - Longqi Liu
- BGI-Shenzhen, Shenzhen 518083, China.,Shenzhen Bay Laboratory, Shenzhen 518000, China
| | - Ya Liu
- BGI-Shenzhen, Shenzhen 518083, China.,Shenzhen Key Laboratory of Single-Cell Omics, BGI-Shenzhen, Shenzhen 518100, China
| |
Collapse
|
28
|
Prinz JC. Antigen Processing, Presentation, and Tolerance: Role in Autoimmune Skin Diseases. J Invest Dermatol 2021; 142:750-759. [PMID: 34294386 DOI: 10.1016/j.jid.2021.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 05/12/2021] [Accepted: 05/16/2021] [Indexed: 10/20/2022]
Abstract
Autoreactive T cells pose a constant risk for the emergence of autoimmune skin diseases in genetically predisposed individuals carrying certain HLA risk alleles. Immune tolerance mechanisms are opposed by broad HLA-presented self-immunopeptidomes, a predefined repertoire of polyspecific TCRs, the continuous generation of new antibody specificities by somatic recombination of Ig genes in B cells, and heightened proinflammatory reactivity. Increased autoantigen presentation by HLA molecules, cross-activation of pathogen-induced T cells against autologous structures, altered metabolism of self-proteins, and excessive production of proinflammatory signals may all contribute to the breakdown of immune tolerance and the development of autoimmune skin diseases.
Collapse
Affiliation(s)
- Jörg Christoph Prinz
- Department of Dermatology and Allergy, University Hospital, Ludwig-Maximilian-University of Munich, Munich, Germany.
| |
Collapse
|
29
|
ACT Up TIL Now: The Evolution of Tumor-Infiltrating Lymphocytes in Adoptive Cell Therapy for the Treatment of Solid Tumors. IMMUNO 2021. [DOI: 10.3390/immuno1030012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The past decades of cancer immunotherapy research have provided profound evidence that the immune system is capable of inducing durable tumor regression. Although many commercialized anti-cancer immunotherapies are available to patients, these treatment options only scrape the surface of the potential immune-related treatment possibilities for cancer. Additionally, many individuals are ineligible for established immunotherapies due to their cancer type. The adoptive cell transfer of autologous tumor-infiltrating lymphocytes has been used in humans for over 30 years to treat metastatic melanoma, and continued modifications are making it increasingly more effective against other types of cancer. This comprehensive review outlines this therapy from its infancy through to the present day, bringing to light modifications and optimizations to the traditional workflow, as well as highlighting the influence of new methods and technologies.
Collapse
|
30
|
Bigot J, Lalanne AI, Lucibello F, Gueguen P, Houy A, Dayot S, Ganier O, Gilet J, Tosello J, Nemati F, Pierron G, Waterfall JJ, Barnhill R, Gardrat S, Piperno-Neumann S, Popova T, Masson V, Loew D, Mariani P, Cassoux N, Amigorena S, Rodrigues M, Alsafadi S, Stern MH, Lantz O. Splicing Patterns in SF3B1-Mutated Uveal Melanoma Generate Shared Immunogenic Tumor-Specific Neoepitopes. Cancer Discov 2021; 11:1938-1951. [PMID: 33811047 DOI: 10.1158/2159-8290.cd-20-0555] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 01/29/2021] [Accepted: 03/31/2021] [Indexed: 11/16/2022]
Abstract
Disruption of splicing patterns due to mutations of genes coding splicing factors in tumors represents a potential source of tumor neoantigens, which would be both public (shared between patients) and tumor-specific (not expressed in normal tissues). In this study, we show that mutations of the splicing factor SF3B1 in uveal melanoma generate such immunogenic neoantigens. Memory CD8+ T cells specific for these neoantigens are preferentially found in 20% of patients with uveal melanoma bearing SF3B1-mutated tumors. Single-cell analyses of neoepitope-specific T cells from the blood identified large clonal T-cell expansions, with distinct effector transcription patterns. Some of these expanded T-cell receptors are also present in the corresponding tumors. CD8+ T-cell clones specific for the neoepitopes specifically recognize and kill SF3B1-mutated tumor cells, supporting the use of this new family of neoantigens as therapeutic targets. SIGNIFICANCE: Mutations of the splicing factor SF3B1 in uveal melanoma generate shared neoantigens that are uniquely expressed by tumor cells, leading to recognition and killing by specific CD8 T cells. Mutations in splicing factors can be sources of new therapeutic strategies applicable to diverse tumors.This article is highlighted in the In This Issue feature, p. 1861.
Collapse
Affiliation(s)
- Jeremy Bigot
- INSERM U932, PSL University, Institut Curie, Paris, France
| | - Ana I Lalanne
- Laboratoire d'immunologie clinique, Institut Curie, Paris, France.,Centre d'investigation Clinique en Biothérapie, Institut Curie (CIC-BT1428), Paris, France
| | | | - Paul Gueguen
- INSERM U932, PSL University, Institut Curie, Paris, France
| | - Alexandre Houy
- INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe labellisée par la Ligue Nationale Contre le Cancer, PSL University, Institut Curie, Paris, France
| | - Stephane Dayot
- INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe labellisée par la Ligue Nationale Contre le Cancer, PSL University, Institut Curie, Paris, France
| | - Olivier Ganier
- INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe labellisée par la Ligue Nationale Contre le Cancer, PSL University, Institut Curie, Paris, France
| | - Jules Gilet
- INSERM U932, PSL University, Institut Curie, Paris, France
| | - Jimena Tosello
- INSERM U932, PSL University, Institut Curie, Paris, France
| | - Fariba Nemati
- Centre d'investigation Clinique en Biothérapie, Institut Curie (CIC-BT1428), Paris, France.,Laboratory of Preclinical Investigation, Translational Research Department, PSL Research University, Institut Curie, Paris, France
| | | | - Joshua J Waterfall
- INSERM U830, PSL University, Institut Curie, Paris, France, and Department of Translational Research, PSL University, Institut Curie, Paris, France
| | - Raymond Barnhill
- Departments of Pathology and Translational Research, Institut Curie, Paris, France
| | - Sophie Gardrat
- INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe labellisée par la Ligue Nationale Contre le Cancer, PSL University, Institut Curie, Paris, France.,Departments of Pathology and Translational Research, Institut Curie, Paris, France
| | | | - Tatiana Popova
- INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe labellisée par la Ligue Nationale Contre le Cancer, PSL University, Institut Curie, Paris, France
| | - Vanessa Masson
- Laboratoire de Spectrométrie de Masse Protéomique, PSL University, Institut Curie, Paris, France
| | - Damarys Loew
- Laboratoire de Spectrométrie de Masse Protéomique, PSL University, Institut Curie, Paris, France
| | - Pascale Mariani
- Department of Surgical Oncology, University of Paris, Institut Curie, Paris, France
| | - Nathalie Cassoux
- Department of Surgical Oncology, University of Paris, Institut Curie, Paris, France
| | | | - Manuel Rodrigues
- INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe labellisée par la Ligue Nationale Contre le Cancer, PSL University, Institut Curie, Paris, France.,Department of Medical Oncology, Institut Curie, Paris, France
| | - Samar Alsafadi
- INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe labellisée par la Ligue Nationale Contre le Cancer, PSL University, Institut Curie, Paris, France.,Laboratory of Uveal Biology, Translational Research Department, Institut Curie, Paris, France
| | - Marc-Henri Stern
- INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe labellisée par la Ligue Nationale Contre le Cancer, PSL University, Institut Curie, Paris, France
| | - Olivier Lantz
- INSERM U932, PSL University, Institut Curie, Paris, France. .,Laboratoire d'immunologie clinique, Institut Curie, Paris, France.,Centre d'investigation Clinique en Biothérapie, Institut Curie (CIC-BT1428), Paris, France
| |
Collapse
|
31
|
Zhao Q, Gong Z, Li Z, Wang J, Zhang J, Zhao Z, Zhang P, Zheng S, Miron RJ, Yuan Q, Zhang Y. Target Reprogramming Lysosomes of CD8+ T Cells by a Mineralized Metal-Organic Framework for Cancer Immunotherapy. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2100616. [PMID: 33760313 DOI: 10.1002/adma.202100616] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 02/24/2021] [Indexed: 06/12/2023]
Abstract
T cell immunotherapy holds significant challenges in solid tumors, mainly due to the T cells' low activation and the decreased synthesis-release of therapeutic proteins, including perforin and granzyme B, which are present in lysosomes. In this study, a lysosome-targeting nanoparticle (LYS-NP) is developed by way of a mineralized metal-organic framework (MOF) coupled with a lysosome-targeting aptamer (CD63-aptamer) to enhance the antitumor effect of T cells. The MOF synthesized from Zn2+ and dimethylimidazole has good protein encapsulation and acid sensitivity, and is thus an ideal lysosomal delivery vector. Calcium carbonate (CaCO3 ) is used to induce MOF mineralization, improve the composite material's stability in encapsulating therapeutic protein, and provide calcium ions with synergistic effects. Before mineralization, perforin and granzyme B-T cell-needed therapeutic proteins for tumors-are preloaded with the MOF. Moreover, T cells are pretreated with processed tumor-specific antigens to activate or produce memory before reprogramming the lysosomes, facilitating the T cell receptor (TCR) for release of the therapeutic proteins. Using T cells recombined by LYS-NPs, a significant enhancement of breast cancer control is confirmed.
Collapse
Affiliation(s)
- Qin Zhao
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China
- Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China
| | - Zijian Gong
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China
- Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China
| | - Zhihao Li
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, China
| | - Jinyang Wang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China
- Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China
| | - Jinglun Zhang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China
- Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China
| | - Zifan Zhao
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China
- Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China
| | - Peng Zhang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China
- Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China
| | - Shihang Zheng
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China
- Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China
| | - Richard J Miron
- Department of Periodontology, University of Bern, Bern, 3010, Switzerland
| | - Quan Yuan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, China
| | - Yufeng Zhang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China
- Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China
| |
Collapse
|
32
|
Harris T, Sauer K. Are T cell repertoires useful as diagnostics for SARS- CoV- 2 infection? Expert Rev Mol Diagn 2021; 21:137-139. [PMID: 33595410 PMCID: PMC7898294 DOI: 10.1080/14737159.2021.1882852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Tim Harris
- Repertoire Immune Medicines, Cambridge, MA, USA
| | | |
Collapse
|
33
|
Lee MN, Meyerson M. Antigen identification for HLA class I- and HLA class II-restricted T cell receptors using cytokine-capturing antigen-presenting cells. Sci Immunol 2021; 6:6/55/eabf4001. [PMID: 33483338 DOI: 10.1126/sciimmunol.abf4001] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 12/17/2020] [Indexed: 12/17/2022]
Abstract
A major limitation to understanding the associations of human leukocyte antigen (HLA) and CD8+ and CD4+ T cell receptor (TCR) genes with disease pathophysiology is the technological barrier of identifying which HLA molecules, epitopes, and TCRs form functional complexes. Here, we present a high-throughput epitope identification system that combines capture of T cell-secreted cytokines by barcoded antigen-presenting cells (APCs), cell sorting, and next-generation sequencing to identify class I- and class II-restricted epitopes starting from highly complex peptide-encoding oligonucleotide pools. We engineered APCs to express anti-cytokine antibodies, a library of DNA-encoded peptides, and multiple HLA class I or II molecules. We demonstrate that these engineered APCs link T cell activation-dependent cytokines with the DNA that encodes the presented peptide. We validated this technology by showing that we could select known targets of viral epitope-, neoepitope-, and autoimmune epitope-specific TCRs, starting from mixtures of peptide-encoding oligonucleotides. Then, starting from 10 TCRβ sequences that are found commonly in humans but lack known targets, we identified seven CD8+ or CD4+ TCR-targeted epitopes encoded by the human cytomegalovirus (CMV) genome. These included known epitopes, as well as a class I and a class II CMV epitope that have not been previously described. Thus, our cytokine capture-based assay makes use of a signal secreted by both CD8+ and CD4+ T cells and allows pooled screening of thousands of encoded peptides to enable epitope discovery for orphan TCRs. Our technology may enable identification of HLA-epitope-TCR complexes relevant to disease control, etiology, or treatment.
Collapse
Affiliation(s)
- Mark N Lee
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA. .,Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA.,Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Matthew Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA. .,Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA.,Departments of Genetics and Medicine, Harvard Medical School, Boston, MA 02115, USA
| |
Collapse
|
34
|
Kast F, Klein C, Umaña P, Gros A, Gasser S. Advances in identification and selection of personalized neoantigen/T-cell pairs for autologous adoptive T cell therapies. Oncoimmunology 2021; 10:1869389. [PMID: 33520408 PMCID: PMC7808433 DOI: 10.1080/2162402x.2020.1869389] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Based on the success of tumor-infiltrating lymphocytes (TIL)-based therapies, personalized adoptive cell therapies (ACT) targeting neoantigens have the potential to become a disruptive technology and lead to highly effective treatments for cancer patients for whom no other options exist. ACT of TIL, peripheral blood or gene-engineered peripheral blood lymphocytes (PBLs) targeting neoantigens is a highly personalized intervention that requires three discrete steps: i) Identification of suitable personal targets (neoantigens), ii) selection of T cells or their T cell receptors (TCRs) that are specific for the identified neoantigens and iii) expansion of the selected T cell population or generation of sufficient number of TCR modified T cells. In this review, we provide an introduction into challenges and approaches to identify neoantigens and to select the Adoptive Cell Therapy, ACT, Neoantigen, T cell, Cancer respective neoantigen-reactive T cells for use in ACT.
Collapse
Affiliation(s)
- Florian Kast
- Roche Pharma Research & Early Development, Roche Innovation Center Zurich, Schlieren, Switzerland
| | - Christian Klein
- Roche Pharma Research & Early Development, Roche Innovation Center Zurich, Schlieren, Switzerland
| | - Pablo Umaña
- Roche Pharma Research & Early Development, Roche Innovation Center Zurich, Schlieren, Switzerland
| | - Alena Gros
- Vall d'Hebron Institute of Oncology, Cellex Center, Barcelona, Spain
| | - Stephan Gasser
- Roche Pharma Research & Early Development, Roche Innovation Center Zurich, Schlieren, Switzerland
| |
Collapse
|
35
|
Landry LG, Anderson AM, Russ HA, Yu L, Kent SC, Atkinson MA, Mathews CE, Michels AW, Nakayama M. Proinsulin-Reactive CD4 T Cells in the Islets of Type 1 Diabetes Organ Donors. Front Endocrinol (Lausanne) 2021; 12:622647. [PMID: 33841327 PMCID: PMC8027116 DOI: 10.3389/fendo.2021.622647] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 02/17/2021] [Indexed: 02/06/2023] Open
Abstract
Proinsulin is an abundant protein that is selectively expressed by pancreatic beta cells and has been a focus for development of antigen-specific immunotherapies for type 1 diabetes (T1D). In this study, we sought to comprehensively evaluate reactivity to preproinsulin by CD4 T cells originally isolated from pancreatic islets of organ donors having T1D. We analyzed 187 T cell receptor (TCR) clonotypes expressed by CD4 T cells obtained from six T1D donors and determined their response to 99 truncated preproinsulin peptide pools, in the presence of autologous B cells. We identified 14 TCR clonotypes from four out of the six donors that responded to preproinsulin peptides. Epitopes were found across all of proinsulin (insulin B-chain, C-peptide, and A-chain) including four hot spot regions containing peptides commonly targeted by TCR clonotypes derived from multiple T1D donors. Of importance, these hot spots overlap with peptide regions to which CD4 T cell responses have previously been detected in the peripheral blood of T1D patients. The 14 TCR clonotypes recognized proinsulin peptides presented by various HLA class II molecules, but there was a trend for dominant restriction with HLA-DQ, especially T1D risk alleles DQ8, DQ2, and DQ8-trans. The characteristics of the tri-molecular complex including proinsulin peptide, HLA-DQ molecule, and TCR derived from CD4 T cells in islets, provides an essential basis for developing antigen-specific biomarkers as well as immunotherapies.
Collapse
Affiliation(s)
- Laurie G. Landry
- Barbara Davis Center for Childhood Diabetes, University of Colorado School of Medicine, Aurora, CO, United States
| | - Amanda M. Anderson
- Barbara Davis Center for Childhood Diabetes, University of Colorado School of Medicine, Aurora, CO, United States
| | - Holger A. Russ
- Barbara Davis Center for Childhood Diabetes, University of Colorado School of Medicine, Aurora, CO, United States
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, United States
| | - Liping Yu
- Barbara Davis Center for Childhood Diabetes, University of Colorado School of Medicine, Aurora, CO, United States
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, United States
| | - Sally C. Kent
- Diabetes Center of Excellence, Department of Medicine, Division of Diabetes, University of Massachusetts Medical School, Worcester, MA, United States
| | - Mark A. Atkinson
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
| | - Clayton E. Mathews
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
| | - Aaron W. Michels
- Barbara Davis Center for Childhood Diabetes, University of Colorado School of Medicine, Aurora, CO, United States
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, United States
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States
| | - Maki Nakayama
- Barbara Davis Center for Childhood Diabetes, University of Colorado School of Medicine, Aurora, CO, United States
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, United States
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States
- *Correspondence: Maki Nakayama,
| |
Collapse
|
36
|
Esprit A, de Mey W, Bahadur Shahi R, Thielemans K, Franceschini L, Breckpot K. Neo-Antigen mRNA Vaccines. Vaccines (Basel) 2020; 8:E776. [PMID: 33353155 PMCID: PMC7766040 DOI: 10.3390/vaccines8040776] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 12/14/2020] [Accepted: 12/16/2020] [Indexed: 12/12/2022] Open
Abstract
The interest in therapeutic cancer vaccines has caught enormous attention in recent years due to several breakthroughs in cancer research, among which the finding that successful checkpoint blockade treatments reinvigorate neo-antigen-specific T cells and that successful adoptive cell therapies are directed towards neo-antigens. Neo-antigens are cancer-specific antigens, which develop from somatic mutations in the cancer cell genome that can be highly immunogenic and are not subjected to central tolerance. As the majority of neo-antigens are unique to each patient's cancer, a vaccine technology that is flexible and potent is required to develop personalized neo-antigen vaccines. In vitro transcribed mRNA is such a technology platform and has been evaluated for delivery of neo-antigens to professional antigen-presenting cells both ex vivo and in vivo. In addition, strategies that support the activity of T cells in the tumor microenvironment have been developed. These represent a unique opportunity to ensure durable T cell activity upon vaccination. Here, we comprehensively review recent progress in mRNA-based neo-antigen vaccines, summarizing critical milestones that made it possible to bring the promise of therapeutic cancer vaccines within reach.
Collapse
Affiliation(s)
| | | | | | | | | | - Karine Breckpot
- Laboratory for Molecular and Cellular Therapy (LMCT), Department of Biomedical Sciences, Vrije Universiteit Brussel, B-1090 Brussels, Belgium; (A.E.); (W.d.M.); (R.B.S.); (K.T.); (L.F.)
| |
Collapse
|
37
|
Rahman MA, Murata K, Burt BD, Hirano N. Changing the landscape of tumor immunology: novel tools to examine T cell specificity. Curr Opin Immunol 2020; 69:1-9. [PMID: 33307272 DOI: 10.1016/j.coi.2020.11.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 11/10/2020] [Indexed: 01/14/2023]
Abstract
Immunotherapy has established itself as a stalwart arm in patient care and with precision medicine forms the new paradigm in cancer treatment. T cells are an important group of immune cells capable of potent cancer immune surveillance and immunity. The advent of bioinformatics, particularly more recent advances incorporating algorithms employing machine learning, provide a seemingly limitless ability for T cell analysis and hypothesis generation. Such endeavors have become indispensable to research efforts accelerating and evolving to such an extent that there exists an appreciable gap between knowledge and proof of function and application. Exciting new technologies such as DNA barcoding, cytometry by time-of-flight (CyTOF), and peptide-exchangeable pHLA multimers inclusive of rare and difficult HLA alleles offer high-throughput cell-by-cell analytical capabilities. These outstanding recent contributions to T cell research will help close this gap and potentially bring practical benefit to patients.
Collapse
Affiliation(s)
- Muhammed A Rahman
- University of Queensland, Australia; Tumor Immunotherapy Program, Princess Margaret Cancer Centre, University Health Network, Canada
| | - Kenji Murata
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, University Health Network, Canada; Department of Pathology, Sapporo Medical University School of Medicine, Japan
| | - Brian D Burt
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, University Health Network, Canada
| | - Naoto Hirano
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, University Health Network, Canada; Department of Immunology, University of Toronto, Canada.
| |
Collapse
|
38
|
Jost C, Darowski D, Challier J, Pulko V, Hanisch LJ, Xu W, Mössner E, Bujotzek A, Klostermann S, Umana P, Kontermann RE, Klein C. CAR-J cells for antibody discovery and lead optimization of TCR-like immunoglobulins. MAbs 2020; 12:1840709. [PMID: 33136521 PMCID: PMC7646475 DOI: 10.1080/19420862.2020.1840709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
T-cell bispecific antibodies (TCBs) are a novel class of engineered immunoglobulins that unite monovalent binding to the T-cell receptor (TCR) CD3e chain and bivalent binding to tumor-associated antigens in order to recruit and activate T-cells for tumor cell killing. In vivo, T-cell activation is usually initiated via the interaction of the TCR with the peptide-HLA complex formed by the human leukocyte antigen (HLA) and peptides derived from intracellular proteins. TCR-like antibodies (TCRLs) that recognize pHLA-epitopes extend the target space of TCBs to peptides derived from intracellular proteins, such as those overexpressed during oncogenesis or created via mutations found in cancer. One challenge during lead identification of TCRL-TCBs is to identify TCRLs that specifically, and ideally exclusively, recognize the desired pHLA, but not unrelated pHLAs. In order to identify TCRLs suitable for TCRL-TCBs, large numbers of TCRLs have to be tested in the TCB format. Here, we propose a novel approach using chimeric antigen receptors (CARs) to facilitate the identification of highly selective TCRLs. In this new so-called TCRL-CAR-J approach, TCRL-candidates are transduced as CARs into Jurkat reporter-cells, and subsequently assessed for their specificity profile. This work demonstrates that the CAR-J reporter-cell assay can be applied to predict the profile of TCRL-TCBs without the need to produce each candidate in the final TCB format. It is therefore useful in streamlining the identification of TCRL-TCBs.
Collapse
Affiliation(s)
- Christian Jost
- Roche Innovation Center Zurich, Roche Pharma Research & Early Development , Schlieren, Switzerland.,Athebio AG , Zurich, Switzerland
| | - Diana Darowski
- Roche Innovation Center Zurich, Roche Pharma Research & Early Development , Schlieren, Switzerland
| | - John Challier
- Roche Innovation Center Zurich, Roche Pharma Research & Early Development , Schlieren, Switzerland
| | - Vesna Pulko
- Roche Innovation Center Zurich, Roche Pharma Research & Early Development , Schlieren, Switzerland
| | - Lydia J Hanisch
- Roche Innovation Center Zurich, Roche Pharma Research & Early Development , Schlieren, Switzerland
| | - Wei Xu
- Roche Innovation Center Zurich, Roche Pharma Research & Early Development , Schlieren, Switzerland
| | - Ekkehard Mössner
- Roche Innovation Center Zurich, Roche Pharma Research & Early Development , Schlieren, Switzerland
| | - Alexander Bujotzek
- Roche Innovation Center Munich, Roche Pharma Research & Early Development , Penzberg, Germany
| | - Stefan Klostermann
- Roche Innovation Center Munich, Roche Pharma Research & Early Development , Penzberg, Germany
| | - Pablo Umana
- Roche Innovation Center Zurich, Roche Pharma Research & Early Development , Schlieren, Switzerland
| | | | - Christian Klein
- Roche Innovation Center Zurich, Roche Pharma Research & Early Development , Schlieren, Switzerland
| |
Collapse
|
39
|
Lee CH, Salio M, Napolitani G, Ogg G, Simmons A, Koohy H. Predicting Cross-Reactivity and Antigen Specificity of T Cell Receptors. Front Immunol 2020; 11:565096. [PMID: 33193332 PMCID: PMC7642207 DOI: 10.3389/fimmu.2020.565096] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 09/07/2020] [Indexed: 12/13/2022] Open
Abstract
Adaptive immune recognition is mediated by specific interactions between heterodimeric T cell receptors (TCRs) and their cognate peptide-MHC (pMHC) ligands, and the methods to accurately predict TCR:pMHC interaction would have profound clinical, therapeutic and pharmaceutical applications. Herein, we review recent developments in predicting cross-reactivity and antigen specificity of TCR recognition. We discuss current experimental and computational approaches to investigate cross-reactivity and antigen-specificity of TCRs and highlight how integrating kinetic, biophysical and structural features may offer valuable insights in modeling immunogenicity. We further underscore the close inter-relationship of these two interconnected notions and the need to investigate each in the light of the other for a better understanding of T cell responsiveness for the effective clinical applications.
Collapse
Affiliation(s)
- Chloe H. Lee
- MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- MRC WIMM Centre for Computational Biology, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Mariolina Salio
- MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Giorgio Napolitani
- MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Graham Ogg
- MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Alison Simmons
- MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford, United Kingdom
| | - Hashem Koohy
- MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- MRC WIMM Centre for Computational Biology, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| |
Collapse
|
40
|
Bousbaine D, Ploegh HL. Antigen discovery tools for adaptive immune receptor repertoire research. ACTA ACUST UNITED AC 2020; 24:64-70. [PMID: 33195881 DOI: 10.1016/j.coisb.2020.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The adaptive immune system has evolved to recognize with incredible precision a large diversity of molecules. Innovations in high-throughput sequencing and bioinformatics have accelerated large-scale immune repertoire analyses and given us important insights into the behavior of the adaptive immune system. However, establishing a connection between receptor sequence and its antigen-specificity remains a challenge despite its central role in determining T and B cell fate. We discuss recent large-scale antigen discovery technologies which can be combined with adaptive immune receptor repertoire (AIRR) studies. We highlight important discoveries made using repertoire analyses in the field of host-microbe interactions.
Collapse
Affiliation(s)
- Djenet Bousbaine
- Department of Bioengineering and ChEM-H, Stanford University, Stanford CA, USA
| | - Hidde L Ploegh
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston MA, USA
| |
Collapse
|
41
|
Shahnazari M, Samadi P, Pourjafar M, Jalali A. Therapeutic vaccines for colorectal cancer: The progress and future prospect. Int Immunopharmacol 2020; 88:106944. [PMID: 33182032 DOI: 10.1016/j.intimp.2020.106944] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/21/2020] [Accepted: 08/25/2020] [Indexed: 02/06/2023]
Abstract
Cancer vaccines are usually derived from the patient's tumor cells or the antigens found on their surface, which may help the immune system to identify and kill these malignant cells. Current focus of many researches is designing vaccines with the hope of triggering the immune system to attack cancer cells in a more effective, reliable and safe manner. Although colorectal cancer (CRC) is recognized as the third leading cause of death by cancer, but significant advances in therapy strategies have been made in recent years, including cancer vaccine. In this review, we present various vaccine platforms that have been used in the border battle against CRC, some of which have been approved for clinical use and some are in late-stage clinical trials. Until September 2020 there is approximately 1940 clinical trials of cancer vaccines on patients with different cancer types, and also many more trials are in the planning stages, which makes it the most important period of therapeutic cancer vaccines studies in the history of the immunotherapy. In cancer vaccines clinical trials, there are several considerations that must be taken into account including engineering of antigen-presenting cells, potential toxicity of antigenic areas, pharmacokinetics and pharmacodynamics of vaccines, and monitoring of the patients' immune response. Therefore, the need to overcome immunosuppression mechanisms/immune tolerance is a critical step for the success of introducing therapeutic vaccines into the widely used drugs on market. In this way, better understanding of neoantigens, tumor immune surveillance escape mechanisms and host-tumor interactions are required to develop more effective and safe cancer vaccines.
Collapse
Affiliation(s)
- Mina Shahnazari
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran; Student Research Committee, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Pouria Samadi
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran; Student Research Committee, Hamadan University of Medical Sciences, Hamadan, Iran.
| | - Mona Pourjafar
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran; Student Research Committee, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Akram Jalali
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran.
| |
Collapse
|
42
|
Sauer K, Harris T. An Effective COVID-19 Vaccine Needs to Engage T Cells. Front Immunol 2020; 11:581807. [PMID: 33117391 PMCID: PMC7549399 DOI: 10.3389/fimmu.2020.581807] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 08/27/2020] [Indexed: 12/28/2022] Open
Affiliation(s)
- Karsten Sauer
- Repertoire Immune Medicines, Cambridge, MA, United States
| | - Tim Harris
- Repertoire Immune Medicines, Cambridge, MA, United States
| |
Collapse
|
43
|
Deseke M, Prinz I. Ligand recognition by the γδ TCR and discrimination between homeostasis and stress conditions. Cell Mol Immunol 2020; 17:914-924. [PMID: 32709926 PMCID: PMC7608190 DOI: 10.1038/s41423-020-0503-y] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 06/22/2020] [Indexed: 12/19/2022] Open
Abstract
T lymphocytes comprise cells expressing either an αβ or a γδ TCR. The riddle how αβ TCRs are triggered by specific peptides presented in the context of MHC was elucidated some time ago. In contrast, the mechanisms that underlie antigen recognition by γδ TCRs are still baffling the scientific community. It is clear that activation of γδ TCRs does not necessarily depend on MHC antigen presentation. To date, diverse and largely host-cell-derived molecules have been identified as cognate antigens for the γδ TCR. However, for most γδ TCRs, the activating ligand is still unknown and many open questions with regard to physiological relevance and generalizable concepts remain. Especially the question of how γδ T cells can distinguish homeostatic from stress conditions via their TCR remains largely unresolved. Recent discoveries in the field might have paved the way towards a better understanding of antigen recognition by the γδ TCR and have made it conceivable to revise the current knowledge and contextualize the new findings.
Collapse
Affiliation(s)
- Malte Deseke
- Institute of Immunology, Hannover Medical School, 30625, Hannover, Germany
| | - Immo Prinz
- Institute of Immunology, Hannover Medical School, 30625, Hannover, Germany.
| |
Collapse
|
44
|
Huang D, Miller M, Ashok B, Jain S, Peppas NA. CRISPR/Cas systems to overcome challenges in developing the next generation of T cells for cancer therapy. Adv Drug Deliv Rev 2020; 158:17-35. [PMID: 32707148 DOI: 10.1016/j.addr.2020.07.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/16/2020] [Accepted: 07/17/2020] [Indexed: 12/12/2022]
Abstract
Genetically engineered immune cells with chimeric antigen receptors (CAR) or modified T cell receptors (TCR) have demonstrated their potential as a potent class of new cancer therapeutic strategy. Despite the clinical success of autologous CD19 CAR T cells in hematological malignancies, allogeneic T cells exhibit many advantages over their autologous counterparts and have recently gathered widespread attention due to the emergence of multiplex genome editing techniques, particularly CRISPR/Cas systems. Furthermore, genetically engineered T cells face a host of major challenges in solid tumors that are not as significant for blood cancers such as T cell targeted delivery, target specificity, proliferation, persistence, and the immunosuppressive tumor microenvironment. We take this opportunity to analyze recent strategies to develop allogeneic T cells, specifically in consideration of CRISPR/Cas and its delivery systems for multiplex gene editing. Additionally, we discuss the current methods used to delivery CRISPR/Cas systems for immunotherapeutic applications, and the challenges to continued development of novel delivery systems. We also provide a comprehensive analysis of the major challenges that genetically engineered T cells face in solid tumors along with the most recent strategies to overcome these barriers, with an emphasis on CRISPR-based approaches. We illustrate the synergistic prospects for how the combination of synthetic biology and immune-oncology could pave the way for designing the next generation of precision cancer therapy.
Collapse
|
45
|
Mahata B, Pramanik J, van der Weyden L, Polanski K, Kar G, Riedel A, Chen X, Fonseca NA, Kundu K, Campos LS, Ryder E, Duddy G, Walczak I, Okkenhaug K, Adams DJ, Shields JD, Teichmann SA. Tumors induce de novo steroid biosynthesis in T cells to evade immunity. Nat Commun 2020; 11:3588. [PMID: 32680985 PMCID: PMC7368057 DOI: 10.1038/s41467-020-17339-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 06/22/2020] [Indexed: 12/23/2022] Open
Abstract
Tumors subvert immune cell function to evade immune responses, yet the complex mechanisms driving immune evasion remain poorly understood. Here we show that tumors induce de novo steroidogenesis in T lymphocytes to evade anti-tumor immunity. Using a transgenic steroidogenesis-reporter mouse line we identify and characterize de novo steroidogenic immune cells, defining the global gene expression identity of these steroid-producing immune cells and gene regulatory networks by using single-cell transcriptomics. Genetic ablation of T cell steroidogenesis restricts primary tumor growth and metastatic dissemination in mouse models. Steroidogenic T cells dysregulate anti-tumor immunity, and inhibition of the steroidogenesis pathway is sufficient to restore anti-tumor immunity. This study demonstrates T cell de novo steroidogenesis as a mechanism of anti-tumor immunosuppression and a potential druggable target.
Collapse
Affiliation(s)
- Bidesh Mahata
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK.
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
| | - Jhuma Pramanik
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | | | - Krzysztof Polanski
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Gozde Kar
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
- Translational Medicine, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | - Angela Riedel
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, Cambridge, UK
| | - Xi Chen
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Nuno A Fonseca
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Kousik Kundu
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
| | - Lia S Campos
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Edward Ryder
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Graham Duddy
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Izabela Walczak
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Klaus Okkenhaug
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
| | - David J Adams
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Jacqueline D Shields
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, Cambridge, UK.
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
- Theory of Condensed Matter, Cavendish Laboratory, 19 JJ Thomson Ave, Cambridge, CB3 0HE, UK.
| |
Collapse
|
46
|
Abstract
T cells respond to threats in an antigen-specific manner using T cell receptors (TCRs) that recognize short peptide antigens presented on major histocompatibility complex (MHC) proteins. The TCR-peptide-MHC interaction mediated between a T cell and its target cell dictates its function and thereby influences its role in disease. A lack of approaches for antigen discovery has limited the fundamental understanding of the antigenic landscape of the overall T cell response. Recent advances in high-throughput sequencing, mass cytometry, microfluidics and computational biology have led to a surge in approaches to address the challenge of T cell antigen discovery. Here, we summarize the scope of this challenge, discuss in depth the recent exciting work and highlight the outstanding questions and remaining technical hurdles in this field.
Collapse
|
47
|
Dunst J, Glaros V, Englmaier L, Sandoz PA, Önfelt B, Kisielow J, Kreslavsky T. Recognition of synthetic polyanionic ligands underlies "spontaneous" reactivity of Vγ1 γδTCRs. J Leukoc Biol 2020; 107:1033-1044. [PMID: 31943366 PMCID: PMC7317387 DOI: 10.1002/jlb.2ma1219-392r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 12/05/2019] [Accepted: 12/11/2019] [Indexed: 01/02/2023] Open
Abstract
Although γδTCRs were discovered more than 30 yr ago, principles of antigen recognition by these receptors remain unclear and the nature of these antigens is largely elusive. Numerous studies reported that T cell hybridomas expressing several Vγ1-containing TCRs, including the Vγ1Vδ6 TCR of γδNKT cells, spontaneously secrete cytokines. This property was interpreted as recognition of a self-ligand expressed on the hybridoma cells themselves. Here, we revisited this finding using a recently developed reporter system and live single cell imaging. We confirmed strong spontaneous signaling by Vγ1Vδ6 and related TCRs, but not by TCRs from several other γδ or innate-like αβ T cells, and demonstrated that both γ and δ chains contributed to this reactivity. Unexpectedly, live single cell imaging showed that activation of this signaling did not require any interaction between cells. Further investigation revealed that the signaling is instead activated by interaction with negatively charged surfaces abundantly present under regular cell culture conditions and was abrogated when noncharged cell culture vessels were used. This mode of TCR signaling activation was not restricted to the reporter cell lines, as interaction with negatively charged surfaces also triggered TCR signaling in ex vivo Vγ1 γδ T cells. Taken together, these results explain long-standing observations on the spontaneous reactivity of Vγ1Vδ6 TCR and demonstrate an unexpected antigen presentation-independent mode of TCR activation by a spectrum of chemically unrelated polyanionic ligands.
Collapse
Affiliation(s)
- Josefine Dunst
- Department of Medicine, Division of Immunology and Allergy, Karolinska InstitutetKarolinska University HospitalStockholmSweden
- Center for Molecular MedicineKarolinska InstitutetStockholmSweden
| | - Vassilis Glaros
- Department of Medicine, Division of Immunology and Allergy, Karolinska InstitutetKarolinska University HospitalStockholmSweden
- Center for Molecular MedicineKarolinska InstitutetStockholmSweden
| | - Lukas Englmaier
- Department of Medicine, Division of Immunology and Allergy, Karolinska InstitutetKarolinska University HospitalStockholmSweden
- Center for Molecular MedicineKarolinska InstitutetStockholmSweden
| | - Patrick A. Sandoz
- Department of Applied PhysicsScience for Life LaboratoryKTH Royal Institute of TechnologyStockholmSweden
| | - Björn Önfelt
- Department of Applied PhysicsScience for Life LaboratoryKTH Royal Institute of TechnologyStockholmSweden
- Department of Microbiology, Tumor and Cell BiologyKarolinska InstituteSolnaSweden
| | - Jan Kisielow
- Institute of Molecular Health SciencesETHZurichSwitzerland
| | - Taras Kreslavsky
- Department of Medicine, Division of Immunology and Allergy, Karolinska InstitutetKarolinska University HospitalStockholmSweden
- Center for Molecular MedicineKarolinska InstitutetStockholmSweden
| |
Collapse
|
48
|
White J, O'Brien RL, Born WK. BW5147 and Derivatives for the Study of T Cells and their Antigen Receptors. Arch Immunol Ther Exp (Warsz) 2020; 68:15. [PMID: 32419056 DOI: 10.1007/s00005-020-00579-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 04/30/2020] [Indexed: 10/24/2022]
Abstract
Like B cells, T cells can be immortalized through hybridization with lymphoma cells, a technique that has been particularly useful in the study of the T cell receptors (TCR) for antigen. In T cell hybridizations, the AKR mouse strain-derived thymus lymphoma BW5147 is by far the most popular fusion line. However, the full potential of this technology had to await inactivation of the productively rearranged TCR-α and -β genes in the lymphoma. BWα-β-, the TCR-gene deficient variant of the original lymphoma, which has become the fusion line of choice for αβ T cells, is now available with numerous modifications, enabling the investigation of many aspects of TCR-mediated responses and TCR-structure. Unexpectedly, inactivating BW's functional TCR-α gene also rendered the lymphoma more permissive for the expression of TCR-γδ, facilitating the study of γδ T cells, their TCRs, and their TCR-mediated reactivity.
Collapse
Affiliation(s)
- Janice White
- Department of Biomedical Research, National Jewish Health, 1400 Jackson Street, Denver, CO, 80206, USA
| | - Rebecca L O'Brien
- Department of Biomedical Research, National Jewish Health, 1400 Jackson Street, Denver, CO, 80206, USA.,Department of Immunology and Microbiology, University of Colorado Health Sciences Center, Aurora, CO, 80045, USA
| | - Willi K Born
- Department of Biomedical Research, National Jewish Health, 1400 Jackson Street, Denver, CO, 80206, USA. .,Department of Immunology and Microbiology, University of Colorado Health Sciences Center, Aurora, CO, 80045, USA.
| |
Collapse
|
49
|
Alves de Lima K, Rustenhoven J, Kipnis J. Meningeal Immunity and Its Function in Maintenance of the Central Nervous System in Health and Disease. Annu Rev Immunol 2020; 38:597-620. [DOI: 10.1146/annurev-immunol-102319-103410] [Citation(s) in RCA: 109] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Neuroimmunology, albeit a relatively established discipline, has recently sparked numerous exciting findings on microglia, the resident macrophages of the central nervous system (CNS). This review addresses meningeal immunity, a less-studied aspect of neuroimmune interactions. The meninges, a triple layer of membranes—the pia mater, arachnoid mater, and dura mater—surround the CNS, encompassing the cerebrospinal fluid produced by the choroid plexus epithelium. Unlike the adjacent brain parenchyma, the meninges contain a wide repertoire of immune cells. These constitute meningeal immunity, which is primarily concerned with immune surveillance of the CNS, and—according to recent evidence—also participates in postinjury CNS recovery, chronic neurodegenerative conditions, and even higher brain function. Meningeal immunity has recently come under the spotlight owing to the characterization of meningeal lymphatic vessels draining the CNS. Here, we review the current state of our understanding of meningeal immunity and its effects on healthy and diseased brains.
Collapse
Affiliation(s)
- Kalil Alves de Lima
- Center for Brain Immunology and Glia (BIG) and Department of Neuroscience, School of Medicine, University of Virginia, Charlottesville, Virginia 22908, USA;,
| | - Justin Rustenhoven
- Center for Brain Immunology and Glia (BIG) and Department of Neuroscience, School of Medicine, University of Virginia, Charlottesville, Virginia 22908, USA;,
| | - Jonathan Kipnis
- Center for Brain Immunology and Glia (BIG) and Department of Neuroscience, School of Medicine, University of Virginia, Charlottesville, Virginia 22908, USA;,
| |
Collapse
|
50
|
Beck JD, Birtel M, Haefner E, Keil IS, Reidenbach D, Salomon N, Yildiz IG, Diken M. CIMT 2019: report on the 17th Annual Meeting of the Association for Cancer Immunotherapy. Hum Vaccin Immunother 2020; 16:808-815. [PMID: 31584850 PMCID: PMC7227697 DOI: 10.1080/21645515.2019.1675459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Jan David Beck
- TRON-Translational Oncology at the University Medical Center of the Johannes Gutenberg University Mainz gGmbH, Mainz, Germany
| | - Matthias Birtel
- TRON-Translational Oncology at the University Medical Center of the Johannes Gutenberg University Mainz gGmbH, Mainz, Germany
| | - Erik Haefner
- TRON-Translational Oncology at the University Medical Center of the Johannes Gutenberg University Mainz gGmbH, Mainz, Germany
| | - Isabell Sofia Keil
- TRON-Translational Oncology at the University Medical Center of the Johannes Gutenberg University Mainz gGmbH, Mainz, Germany
| | - Daniel Reidenbach
- TRON-Translational Oncology at the University Medical Center of the Johannes Gutenberg University Mainz gGmbH, Mainz, Germany
| | - Nadja Salomon
- TRON-Translational Oncology at the University Medical Center of the Johannes Gutenberg University Mainz gGmbH, Mainz, Germany
| | - Ikra Gizem Yildiz
- TRON-Translational Oncology at the University Medical Center of the Johannes Gutenberg University Mainz gGmbH, Mainz, Germany
| | - Mustafa Diken
- TRON-Translational Oncology at the University Medical Center of the Johannes Gutenberg University Mainz gGmbH, Mainz, Germany
| |
Collapse
|