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Rollins ZA, Curtis MB, George SC, Faller R. A Computational Strategy for the Rapid Identification and Ranking of Patient-Specific T Cell Receptors Bound to Neoantigens. Macromol Rapid Commun 2024:e2400225. [PMID: 38839076 DOI: 10.1002/marc.202400225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 06/02/2024] [Indexed: 06/07/2024]
Abstract
T cell receptor (TCR) recognition of a peptide-major histocompatibility complex (pMHC) is crucial for adaptive immune response. The identification of therapeutically relevant TCR-pMHC protein pairs is a bottleneck in the implementation of TCR-based immunotherapies. The ability to computationally design TCRs to target a specific pMHC requires automated integration of next-generation sequencing, protein-protein structure prediction, molecular dynamics, and TCR ranking. A pipeline to evaluate patient-specific, sequence-based TCRs to a target pMHC is presented. Using the three most frequently expressed TCRs from 16 colorectal cancer patients, the protein-protein structure of the TCRs to the target CEA peptide-MHC is predicted using Modeller and ColabFold. TCR-pMHC structures are compared using automated equilibration and successive analysis. ColabFold generated configurations require an ≈2.5× reduction in equilibration time of TCR-pMHC structures compared to Modeller. The structural differences between Modeller and ColabFold are demonstrated by root mean square deviation (≈0.20 nm) between clusters of equilibrated configurations, which impact the number of hydrogen bonds and Lennard-Jones contacts between the TCR and pMHC. TCR ranking criteria that may prioritize TCRs for evaluation of in vitro immunogenicity are identified, and this ranking is validated by comparing to state-of-the-art machine learning-based methods trained to predict the probability of TCR-pMHC binding.
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Affiliation(s)
- Zachary A Rollins
- Department of Chemical Engineering, University of California, Davis, 1 Shields Ave, Bainer Hall, Davis, CA, 95616, USA
| | - Matthew B Curtis
- Department of Biomedical Engineering, University of California, Davis, 451 E. Health Sciences Dr., GBSF 2303, Davis, CA, 95616, USA
| | - Steven C George
- Department of Biomedical Engineering, University of California, Davis, 451 E. Health Sciences Dr., GBSF 2303, Davis, CA, 95616, USA
| | - Roland Faller
- Department of Chemical Engineering, University of California, Davis, 1 Shields Ave, Bainer Hall, Davis, CA, 95616, USA
- Department of Chemical Engineering, Texas Tech University, Lubbock, TX, 79409, USA
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2
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Ishimoto T, Arakawa Y, Vural S, Stöhr J, Vollmer S, Galinski A, Siewert K, Rühl G, Poluektov Y, Delcommenne M, Horvath O, He M, Summer B, Pohl R, Alharbi R, Dornmair K, Arakawa A, Prinz JC. Multiple environmental antigens may trigger autoimmunity in psoriasis through T-cell receptor polyspecificity. Front Immunol 2024; 15:1374581. [PMID: 38524140 PMCID: PMC10958380 DOI: 10.3389/fimmu.2024.1374581] [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: 01/22/2024] [Accepted: 02/16/2024] [Indexed: 03/26/2024] Open
Abstract
Introduction Psoriasis is a T-cell mediated autoimmune skin disease. HLA-C*06:02 is the main psoriasis-specific risk gene. Using a Vα3S1/Vβ13S1 T-cell receptor (TCR) from a lesional psoriatic CD8+ T-cell clone we had discovered that, as an underlying pathomechanism, HLA-C*06:02 mediates an autoimmune response against melanocytes in psoriasis, and we had identified an epitope from ADAMTS-like protein 5 (ADAMTSL5) as a melanocyte autoantigen. The conditions activating the psoriatic autoimmune response in genetically predisposed individuals throughout life remain incompletely understood. Here, we aimed to identify environmental antigens that might trigger autoimmunity in psoriasis because of TCR polyspecificity. Methods We screened databases with the peptide recognition motif of the Vα3S1/Vβ13S1 TCR for environmental proteins containing peptides activating this TCR. We investigated the immunogenicity of these peptides for psoriasis patients and healthy controls by lymphocyte stimulation experiments and peptide-loaded HLA-C*06:02 tetramers. Results We identified peptides from wheat, Saccharomyces cerevisiae, microbiota, tobacco, and pathogens that activated both the Vα3S1/Vβ13S1 TCR and CD8+ T cells from psoriasis patients. Using fluorescent HLA-C*06:02 tetramers loaded with ADAMTSL5 or wheat peptides, we find that the same CD8+ T cells may recognize both autoantigen and environmental antigens. A wheat-free diet could alleviate psoriasis in several patients. Discussion Our results show that due to TCR polyspecificity, several environmental antigens corresponding to previously suspected psoriasis risk conditions converge in the reactivity of a pathogenic psoriatic TCR and might thus be able to stimulate the psoriatic autoimmune response against melanocytes. Avoiding the corresponding environmental risk factors could contribute to the management of psoriasis.
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Affiliation(s)
- Tatsushi Ishimoto
- Department of Dermatology and Allergy, University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany
| | - Yukiyasu Arakawa
- Department of Dermatology and Allergy, University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany
| | - Secil Vural
- Department of Dermatology and Allergy, University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany
| | - Julia Stöhr
- Department of Dermatology and Allergy, University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany
| | - Sigrid Vollmer
- Department of Dermatology and Allergy, University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany
| | - Adrian Galinski
- Department of Dermatology and Allergy, University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany
| | - Katherina Siewert
- Institute of Clinical Neuroimmunology, Biomedical Center and University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany
| | - Geraldine Rühl
- Institute of Clinical Neuroimmunology, Biomedical Center and University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany
| | | | | | - Orsolya Horvath
- Department of Dermatology and Allergy, University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany
| | - Mengwen He
- Department of Dermatology and Allergy, University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany
| | - Burkhard Summer
- Department of Dermatology and Allergy, University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany
| | - Ralf Pohl
- Department of Dermatology and Allergy, University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany
| | - Rehab Alharbi
- Department of Dermatology and Allergy, University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany
| | - Klaus Dornmair
- Institute of Clinical Neuroimmunology, Biomedical Center and University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany
| | - Akiko Arakawa
- Department of Dermatology and Allergy, University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany
| | - Jörg C. Prinz
- Department of Dermatology and Allergy, University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany
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3
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Kishimoto M, Komine M, Okada H, Sato A, Kamiya K, Maekawa T, Murata S, Ohtsuki M. Three cases of subcorneal pustular dermatosis with immunohistochemical examinations. J Dermatol 2023; 50:1150-1155. [PMID: 37288510 DOI: 10.1111/1346-8138.16850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 04/25/2023] [Accepted: 05/12/2023] [Indexed: 06/09/2023]
Abstract
Subcorneal pustular dermatosis, a rare, benign skin disease, is a type of neutrophilic dermatosis. The authors reported three cases of subcorneal pustular dermatosis. In case 1, a 9-year-old girl developed a skin rash with blisters following a mycoplasma infection and had a flare-up due to a common cold. She was successfully treated with a topical corticosteroid. In case 2, a 70-year-old woman who had been treated for rheumatoid arthritis with adalimumab, salazosulfapyridine, and leflunomide developed 3- to 5-mm pustules on her trunk and thighs 4 days after flu vaccination. The rash disappeared with drug withdrawal and treatment with diaminodiphenyl sulfone. In case 3, an 81-year-old man, who was diagnosed with pyoderma gangrenosum at 61 years old, developed multiple small flaccid pustules on his trunk and extremities due to an infection in the arteriovenous shunt area on the forearm. The pustule disappeared with intravenous antibiotic therapy; however, the pustules subsequently flared up along with ulcers typical of pyoderma gangrenosum. He was given oral prednisolone therapy, which was effective for the small pustules and some ulcers. Immunohistochemical examination of the three cases revealed neutrophilic infiltration in the subcorneal layer of the epidermis. The pustules contained neutrophils as well as some CD68+ and a few CD1a+ cells. The epidermis and dermis were more predominantly infiltrated by CD4+ cells than by CD8+ cells. Positive stainings for interleukin 8, interleukin 36γ, and phospho-extracellular signal-regulated kinases 1 and 2 were observed in the upper layers of the epidermis below the pustules. Although the pathogenesis of subcorneal pustular dermatosis has not been clarified, the current results suggest that a variety of inflammatory cells, including those responsible for both innate and acquired immunity, are involved in the accumulation of neutrophils in subcorneal pustular dermatosis.
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Affiliation(s)
- Megumi Kishimoto
- Department of Dermatology, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Mayumi Komine
- Department of Dermatology, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Hirofumi Okada
- Department of Dermatology, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Atsuko Sato
- Department of Dermatology, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Koji Kamiya
- Department of Dermatology, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Takeo Maekawa
- Department of Dermatology, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Satoru Murata
- Murata Dermatology Clinic, Shimotsuke, Tochigi, Japan
| | - Mamitaro Ohtsuki
- Department of Dermatology, Jichi Medical University, Shimotsuke, Tochigi, Japan
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4
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Li J, Xiao Z, Wang D, Jia L, Nie S, Zeng X, Hu W. The screening, identification, design and clinical application of tumor-specific neoantigens for TCR-T cells. Mol Cancer 2023; 22:141. [PMID: 37649123 PMCID: PMC10466891 DOI: 10.1186/s12943-023-01844-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 08/16/2023] [Indexed: 09/01/2023] Open
Abstract
Recent advances in neoantigen research have accelerated the development of tumor immunotherapies, including adoptive cell therapies (ACTs), cancer vaccines and antibody-based therapies, particularly for solid tumors. With the development of next-generation sequencing and bioinformatics technology, the rapid identification and prediction of tumor-specific antigens (TSAs) has become possible. Compared with tumor-associated antigens (TAAs), highly immunogenic TSAs provide new targets for personalized tumor immunotherapy and can be used as prospective indicators for predicting tumor patient survival, prognosis, and immune checkpoint blockade response. Here, the identification and characterization of neoantigens and the clinical application of neoantigen-based TCR-T immunotherapy strategies are summarized, and the current status, inherent challenges, and clinical translational potential of these strategies are discussed.
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Affiliation(s)
- Jiangping Li
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, People's Republic of China.
| | - Zhiwen Xiao
- Department of Otolaryngology Head and Neck Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, People's Republic of China
| | - Donghui Wang
- Department of Radiation Oncology, The Third Affiliated Hospital Sun Yat-Sen University, Guangzhou, 510630, People's Republic of China
| | - Lei Jia
- International Health Medicine Innovation Center, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Shihong Nie
- Department of Radiation Oncology, West China Hospital, Sichuan University, Cancer Center, Chengdu, 610041, People's Republic of China
| | - Xingda Zeng
- Department of Parasitology of Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Wei Hu
- Division of Vascular Surgery, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072, People's Republic of China
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5
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Muhowski EM, Rogers LM. Dual TCR-Expressing T Cells in Cancer: How Single-Cell Technologies Enable New Investigation. Immunohorizons 2023; 7:299-306. [PMID: 37129560 PMCID: PMC10354877 DOI: 10.4049/immunohorizons.2200062] [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: 02/01/2023] [Accepted: 04/11/2023] [Indexed: 05/03/2023] Open
Abstract
TCR diversity measures are often used to understand the immune response in cancer. Traditional measures of diversity rely on bulk RNA sequencing (RNAseq) of the β-chain variable regions. However, the full αβ TCR repertoire is a combination of both the α- and β-chains, which are encoded by separate genes. In contrast with bulk RNAseq, single-cell RNAseq (scRNAseq) allows paired chain analyses, yielding a more accurate measure of the repertoire. Interestingly, ∼30% of mature peripheral T cells express multiple TCR alleles (e.g., two α-chains) and may exhibit dual Ag specificity. scRNAseq has become increasingly common, and data from both human and animal studies are publicly available. However, routine workflows discard secondary TCR alleles and focus on a single TCR clone per cell. This perspectives piece emphasizes why this may not be good practice and highlights unanswered questions in the field of T cell dual specificity.
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6
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Islam SR, Maeda T, Tamaoki N, Good ML, Kishton RJ, Paria BC, Yu Z, Bosch-Marce M, Bedanova NM, Liu C, Kruhlak MJ, Restifo NP, Vizcardo R. Reprogramming of Tumor-reactive Tumor-infiltrating Lymphocytes to Human-induced Pluripotent Stem Cells. CANCER RESEARCH COMMUNICATIONS 2023; 3:917-932. [PMID: 37377887 PMCID: PMC10211394 DOI: 10.1158/2767-9764.crc-22-0265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 03/01/2023] [Accepted: 05/05/2023] [Indexed: 06/29/2023]
Abstract
UNLABELLED Tumor-infiltrating lymphocytes (TIL) that can recognize and kill tumor cells have curative potential in subsets of patients treated with adoptive cell transfer (ACT). However, lack of TIL therapeutic efficacy in many patients may be due in large part to a paucity of tumor-reactive T cells in TIL and the exhausted and terminally differentiated status of those tumor-reactive T cells. We sought to reprogram exhausted TIL that possess T-cell receptors (TCR) specific for tumor antigens into induced pluripotent stem cells (iPSC) to rejuvenate them for more potent ACT. We first attempted to reprogram tumor neoantigen-specific TIL by αCD3 Ab prestimulation which resulted in failure of establishing tumor-reactive TIL-iPSCs, instead, T cell-derived iPSCs from bystander T cells were established. To selectively activate and enrich tumor-reactive T cells from the heterogenous TIL population, CD8+ PD-1+ 4-1BB+ TIL population were isolated after coculture with autologous tumor cells, followed by direct reprogramming into iPSCs. TCR sequencing analysis of the resulting iPSC clones revealed that reprogrammed TIL-iPSCs encoded TCRs that were identical to the pre-identified tumor-reactive TCRs found in minimally cultured TIL. Moreover, reprogrammed TIL-iPSCs contained rare tumor antigen-specific TCRs, which were not detectable by TCR sequencing of the starting cell population. Thus, reprogramming of PD-1+ 4-1BB+ TIL after coculture with autologous tumor cells selectively generates tumor antigen-specific TIL-iPSCs, and is a distinctive method to enrich and identify tumor antigen-specific TCRs of low frequency from TIL. SIGNIFICANCE Reprogramming of TIL into iPSC holds great promise for the future treatment of cancer due to their rejuvenated nature and the retention of tumor-specific TCRs. One limitation is the lack of selective and efficient methods for reprogramming tumor-specific T cells from polyclonal TIL. Here we addressed this limitation and present a method to efficiently reprogram TIL into iPSC colonies carrying diverse tumor antigen reactive TCR recombination.
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Affiliation(s)
- S.M. Rafiqul Islam
- Surgery Branch, NCI, NIH, Bethesda, Maryland
- Center for Cell-Based Therapy, NCI, NIH, Bethesda, Maryland
| | - Takuya Maeda
- Surgery Branch, NCI, NIH, Bethesda, Maryland
- Center for Cell-Based Therapy, NCI, NIH, Bethesda, Maryland
| | - Naritaka Tamaoki
- Surgery Branch, NCI, NIH, Bethesda, Maryland
- Center for Cell-Based Therapy, NCI, NIH, Bethesda, Maryland
| | - Meghan L. Good
- Surgery Branch, NCI, NIH, Bethesda, Maryland
- Center for Cell-Based Therapy, NCI, NIH, Bethesda, Maryland
| | - Rigel J. Kishton
- Surgery Branch, NCI, NIH, Bethesda, Maryland
- Center for Cell-Based Therapy, NCI, NIH, Bethesda, Maryland
| | | | - Zhiya Yu
- Surgery Branch, NCI, NIH, Bethesda, Maryland
| | | | | | - Chengyu Liu
- Transgenic Core, Division of Intramural Research, National Heart, Lung and Blood Institute, NIH, Bethesda, Maryland
| | | | - Nicholas P. Restifo
- Surgery Branch, NCI, NIH, Bethesda, Maryland
- Center for Cell-Based Therapy, NCI, NIH, Bethesda, Maryland
| | - Raul Vizcardo
- Surgery Branch, NCI, NIH, Bethesda, Maryland
- Center for Cell-Based Therapy, NCI, NIH, Bethesda, Maryland
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7
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Kuiper JJ, Prinz JC, Stratikos E, Kuśnierczyk P, Arakawa A, Springer S, Mintoff D, Padjen I, Shumnalieva R, Vural S, Kötter I, van de Sande MG, Boyvat A, de Boer JH, Bertsias G, de Vries N, Krieckaert CL, Leal I, Vidovič Valentinčič N, Tugal-Tutkun I, El Khaldi Ahanach H, Costantino F, Glatigny S, Mrazovac Zimak D, Lötscher F, Kerstens FG, Bakula M, Viera Sousa E, Böhm P, Bosman K, Kenna TJ, Powis SJ, Breban M, Gul A, Bowes J, Lories RJ, Nowatzky J, Wolbink GJ, McGonagle DG, Turkstra F. EULAR study group on ‘MHC-I-opathy’: identifying disease-overarching mechanisms across disciplines and borders. Ann Rheum Dis 2023:ard-2022-222852. [PMID: 36987655 DOI: 10.1136/ard-2022-222852] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 01/25/2023] [Indexed: 03/29/2023]
Abstract
The ‘MHC-I (major histocompatibility complex class I)-opathy’ concept describes a family of inflammatory conditions with overlapping clinical manifestations and a strong genetic link to the MHC-I antigen presentation pathway. Classical MHC-I-opathies such as spondyloarthritis, Behçet’s disease, psoriasis and birdshot uveitis are widely recognised for their strong association with certain MHC-I alleles and gene variants of the antigen processing aminopeptidases ERAP1 and ERAP2 that implicates altered MHC-I peptide presentation to CD8+T cells in the pathogenesis. Progress in understanding the cause and treatment of these disorders is hampered by patient phenotypic heterogeneity and lack of systematic investigation of the MHC-I pathway.Here, we discuss new insights into the biology of MHC-I-opathies that strongly advocate for disease-overarching and integrated molecular and clinical investigation to decipher underlying disease mechanisms. Because this requires transformative multidisciplinary collaboration, we introduce the EULAR study group on MHC-I-opathies to unite clinical expertise in rheumatology, dermatology and ophthalmology, with fundamental and translational researchers from multiple disciplines such as immunology, genomics and proteomics, alongside patient partners. We prioritise standardisation of disease phenotypes and scientific nomenclature and propose interdisciplinary genetic and translational studies to exploit emerging therapeutic strategies to understand MHC-I-mediated disease mechanisms. These collaborative efforts are required to address outstanding questions in the etiopathogenesis of MHC-I-opathies towards improving patient treatment and prognostication.
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Affiliation(s)
- Jonas Jw Kuiper
- Department of Ophthalmology, Center for Translational Immunology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Jörg C Prinz
- University Hospital, department of Dermatology and Allergy, Ludwig Maximilians University Munich, Munchen, Germany
| | - Efstratios Stratikos
- Laboratory of Biochemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
| | - Piotr Kuśnierczyk
- Laboratory of Immunogenetics and Tissue Immunology, Institute of Immunology and Experimental Therapy Ludwik Hirszfeld Polish Academy of Sciences, Wroclaw, Poland
| | - Akiko Arakawa
- University Hospital, department of Dermatology and Allergy, Ludwig Maximilians University Munich, Munchen, Germany
| | | | - Dillon Mintoff
- Department of Dermatology, Mater Dei Hospital, Msida, Malta
- Department of Pathology, University of Malta Faculty of Medicine and Surgery, Msida, Malta
| | - Ivan Padjen
- Division of Clinical Immunology and Rheumatology, University Hospital Centre Zagreb Department of Internal Medicine, Zagreb, Croatia
- University of Zagreb School of Medicine, Zagreb, Croatia
| | - Russka Shumnalieva
- Clinic of Rheumatology, Department of Rheumatology, Medical University of Sofia, Sofia, Bulgaria
| | - Seçil Vural
- School of Medicine, Department of Dermatology, Koç University, Istanbul, Turkey
| | - Ina Kötter
- Clinic for Rheumatology and Immunology, Bad Bramdsted Hospital, Bad Bramstedt, Germany
- Division of Rheumatology and Systemic Inflammatory Diseases, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marleen G van de Sande
- University of Amsterdam, Department of Rheumatology & Clinical Immunology and Department of Experimental Immunology, Amsterdam Institute for Infection & Immunity, Amsterdam UMC Location AMC, Amsterdam, The Netherlands
- Amsterdam Rheumatology and Immunology Center (ARC) | Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Ayşe Boyvat
- Department of Dermatology, Ankara University Faculty of Medicine, Ankara, Turkey
| | - Joke H de Boer
- Department of Ophthalmology, Center for Translational Immunology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - George Bertsias
- Department of Rheumatology and Clinical Immunology, University of Crete School of Medicine, Iraklio, Greece
- Laboratory of Autoimmunity-Inflammation, Institute of Molecular Biology and Biotechnology, Heraklion, Greece
| | - Niek de Vries
- University of Amsterdam, Department of Rheumatology & Clinical Immunology and Department of Experimental Immunology, Amsterdam Institute for Infection & Immunity, Amsterdam UMC Location AMC, Amsterdam, The Netherlands
- Amsterdam Rheumatology and Immunology Center (ARC) | Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Charlotte Lm Krieckaert
- Amsterdam Rheumatology and immunology Center (ARC)| Reade, Amsterdam, The Netherlands
- Department of Rheumatology, Reade Hoofdlocatie Dr Jan van Breemenstraat, Amsterdam, The Netherlands
| | - Inês Leal
- Department of Ophthalmology, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte EPE, Lisboa, Portugal
- Centro de Estudeos das Ciencias da Visão, Universidade de Lisboa Faculdade de Medicina, Lisboa, Portugal
| | - Nataša Vidovič Valentinčič
- University Eye Clinic, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Ilknur Tugal-Tutkun
- Department of Ophthalmology, Istanbul University Istanbul Faculty of Medicine, Istanbul, Turkey
| | - Hanane El Khaldi Ahanach
- Departement of Ophthalmology, Amsterdam UMC Location AMC, Amsterdam, The Netherlands
- Department of Ophthalmology, Onze Lieve Vrouwe Gasthuis, Amsterdam, The Netherlands
| | - Félicie Costantino
- Service de Rheumatology, Hospital Ambroise-Pare, Boulogne-Billancourt, France
- Infection & Inflammation, UMR 1173, Inserm, UVSQ, University Paris-Saclay, Montigny-le-Bretonneux, France
| | - Simon Glatigny
- Infection & Inflammation, UMR 1173, Inserm, UVSQ/Université Paris Saclay, Montigny-le-Bretonneux, France
- Laboratoire d'Excellence Inflamex, Paris, France
| | | | - Fabian Lötscher
- Department of Rheumatology and Immunology, Inselspital University Hospital Bern, University of Bern, Bern, Switzerland
| | - Floor G Kerstens
- Amsterdam Rheumatology and immunology Center (ARC)| Reade, Amsterdam, The Netherlands
- Department of Rheumatology, Reade Hoofdlocatie Dr Jan van Breemenstraat, Amsterdam, The Netherlands
| | - Marija Bakula
- Division of Clinical Immunology and Rheumatology, University Hospital Centre Zagreb Department of Internal Medicine, Zagreb, Croatia
| | - Elsa Viera Sousa
- Rheumatology Research Unit Molecular João Lobo Antunes, University of Lisbon Medical Faculty, Lisboa, Portugal
- Rheumatology DepartmentSanta Maria Centro Hospital, Academic Medical Centre of Lisbon, Lisboa, Portugal
| | - Peter Böhm
- Patientpartner, German League against Rheumatism, Bonn, Germany
| | - Kees Bosman
- Patientpartner, Nationale Vereniging ReumaZorg, Nijmegen, The Netherlands
| | - Tony J Kenna
- Translational Research Institute, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Simon J Powis
- School of Medicine, University of St Andrews School of Medicine, St Andrews, UK
| | - Maxime Breban
- Service de Rheumatology, Hospital Ambroise-Pare, Boulogne-Billancourt, France
- Infection & Inflammation, UMR 1173, Inserm, UVSQ, University Paris-Saclay, Montigny-le-Bretonneux, France
| | - Ahmet Gul
- Division of Rheumatology, Istanbul University Istanbul Faculty of Medicine, Istanbul, Turkey
| | - John Bowes
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Center, The University of Manchester, Manchester, UK
- NIHR Manchester Musculoskeletal Biomedical Research Unit, Manchester University NHS Foundation Trust, Manchester, UK
| | - Rik Ju Lories
- Department of Rheumatology, KU Leuven University Hospitals Leuven, Leuven, Belgium
- Skeletal Biology and Engineering Research Center, Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Johannes Nowatzky
- Department of Medicine, Division of Rheumatology, NYU Langone Behçet's Disease Program, NYU Langone Ocular Rheumatology Program, New York University Grossman School of Medicine, New York University, New York, New York, USA
- Department of Pathology, New York University Grossman School of Medicine, New York, New York, USA
| | - Gerrit Jan Wolbink
- Amsterdam Rheumatology and immunology Center (ARC)| Reade, Amsterdam, The Netherlands
- Department Immunopathology, Sanquin Research, Amsterdam, The Netherlands
| | - Dennis G McGonagle
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK
- NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Franktien Turkstra
- Amsterdam Rheumatology and immunology Center (ARC)| Reade, Amsterdam, The Netherlands
- Department of Rheumatology, Reade Hoofdlocatie Dr Jan van Breemenstraat, Amsterdam, The Netherlands
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8
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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.
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9
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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.
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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.
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10
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Roesner LM, Farag AK, Pospich R, Traidl S, Werfel T. T-cell receptor sequencing specifies psoriasis as a systemic and atopic dermatitis as a skin-focused, allergen-driven disease. Allergy 2022; 77:2737-2747. [PMID: 35255168 DOI: 10.1111/all.15272] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 01/28/2022] [Accepted: 02/12/2022] [Indexed: 01/27/2023]
Abstract
BACKGROUND Atopic dermatitis (AD) and psoriasis represent two of the most common inflammatory skin diseases in developed countries. A hallmark of both diseases is T-cell infiltration into the skin. However, it is still not clarified to what extent these infiltrating T cells are antigen-specific skin-homing T cells or unspecific heterogeneous bystander cells. METHODS To elucidate this, T cells from lesional skin and from blood of 9 AD and 10 psoriasis patients were compared by receptor (TCR) sequencing. Therefore, peripheral blood mononuclear cells (PBMC) were cell-sorted according to expression of the cutaneous leukocyte antigen (CLA) into skin-homing (CLA+ ) and non-skin-homing (CLA- ) subfractions. Aeroallergen-specific T-cell lines were grown from AD patients' PBMC in parallel. RESULTS Intra-individual comparison of TCRB CDR3 regions revealed that clonally expanded T cells in skin lesions of both AD and psoriasis patients corresponded to skin-homing circulating T cells. However, in psoriasis patients, these T-cell clones were also detectable to a larger extent among CLA- circulating T cells. Up to 28% of infiltrating cells in AD skin were identified as allergen-specific by overlapping TCR sequences. CONCLUSIONS Our data show that in line with the systemic nature of psoriasis, T-cell clones that infiltrate psoriatic skin lesions do not exclusively possess skin-homing ability and are therefore most probably specific to antigens that are not exclusively expressed or located in the skin. T cells driving AD skin inflammation appear to home nearly exclusively to the skin and are, to a certain extent, specific to aeroallergens.
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Affiliation(s)
- Lennart M Roesner
- Division of Immunodermatology and Allergy Research, Department of Dermatology and Allergy, Hannover Medical School, Hannover, Germany.,Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | - Ahmed K Farag
- Division of Immunodermatology and Allergy Research, Department of Dermatology and Allergy, Hannover Medical School, Hannover, Germany
| | - Rebecca Pospich
- Division of Immunodermatology and Allergy Research, Department of Dermatology and Allergy, Hannover Medical School, Hannover, Germany
| | - Stephan Traidl
- Division of Immunodermatology and Allergy Research, Department of Dermatology and Allergy, Hannover Medical School, Hannover, Germany.,Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | - Thomas Werfel
- Division of Immunodermatology and Allergy Research, Department of Dermatology and Allergy, Hannover Medical School, Hannover, Germany.,Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
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11
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Tian G, Li M, Lv G. Analysis of T-Cell Receptor Repertoire in Transplantation: Fingerprint of T Cell-mediated Alloresponse. Front Immunol 2022; 12:778559. [PMID: 35095851 PMCID: PMC8790170 DOI: 10.3389/fimmu.2021.778559] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 12/22/2021] [Indexed: 11/13/2022] Open
Abstract
T cells play a key role in determining allograft function by mediating allogeneic immune responses to cause rejection, and recent work pointed their role in mediating tolerance in transplantation. The unique T-cell receptor (TCR) expressed on the surface of each T cell determines the antigen specificity of the cell and can be the specific fingerprint for identifying and monitoring. Next-generation sequencing (NGS) techniques provide powerful tools for deep and high-throughput TCR profiling, and facilitate to depict the entire T cell repertoire profile and trace antigen-specific T cells in circulation and local tissues. Tailing T cell transcriptomes and TCR sequences at the single cell level provides a full landscape of alloreactive T-cell clones development and biofunction in alloresponse. Here, we review the recent advances in TCR sequencing techniques and computational tools, as well as the recent discovery in overall TCR profile and antigen-specific T cells tracking in transplantation. We further discuss the challenges and potential of using TCR sequencing-based assays to profile alloreactive TCR repertoire as the fingerprint for immune monitoring and prediction of rejection and tolerance.
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Affiliation(s)
| | - Mingqian Li
- Department of Hepatobiliary and Pancreatic Surgery, The First Hospital of Jilin University, Changchun, China
| | - Guoyue Lv
- Department of Hepatobiliary and Pancreatic Surgery, The First Hospital of Jilin University, Changchun, China
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12
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Pasetto A, Buggert M. T-Cell Repertoire Characterization. Methods Mol Biol 2022; 2574:209-219. [PMID: 36087203 DOI: 10.1007/978-1-0716-2712-9_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
T-cell repertoire characterization is a methodology that enables the identification of T-cell receptor (TCR) gene sequences in a T-cell population. TCR genes are composed of modular gene segments V (D) J that undergo somatic recombination, resulting in unique and unpredictable sequences that can be utilized to identify each T-cell clone. The analysis of the TCR composition in a T-cell population can give information on the biological phenomenon such as antigen-driven expansion and heterogeneity of T-cell responses. Bulk TCR analysis can give useful information on the clonality and can help track a specific clonotype over time or in different compartments, although the information about pairing cannot be provided. Single-cell TCR sequencing, on the other hand, can provide pairing information that are necessary to reconstruct the TCR and confirm antigen specificity.Here we describe common methods to characterize T-cell repertoires based on both bulk and single-cell next-generation sequencing.
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Affiliation(s)
- Anna Pasetto
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.
| | - Marcus Buggert
- Department of Medicine Huddinge, Center for Infectious Medicine (CIM), Karolinska Institutet, Stockholm, Sweden.
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13
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AIRR Community Guide to Planning and Performing AIRR-Seq Experiments. Methods Mol Biol 2022; 2453:261-278. [PMID: 35622331 PMCID: PMC9761540 DOI: 10.1007/978-1-0716-2115-8_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The development of high-throughput sequencing of adaptive immune receptor repertoires (AIRR-seq of IG and TR rearrangements) has provided a new frontier for in-depth analysis of the immune system. The last decade has witnessed an explosion in protocols, experimental methodologies, and computational tools. In this chapter, we discuss the major considerations in planning a successful AIRR-seq experiment together with basic strategies for controlling and evaluating the outcome of the experiment. Members of the AIRR Community have authored several chapters in this edition, which cover step-by-step instructions to successfully conduct, analyze, and share an AIRR-seq project.
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14
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Jahn S, Diamanti E, Föhr J, Papageorgiou A, Herbst M. Psoriasisarthritis (PsA) – retrospektive Datenanalyse einer Praxis-Kohorte und Schlussfolgerungen für Diagnostik und Therapie. AKTUELLE DERMATOLOGIE 2021. [DOI: 10.1055/a-1509-4679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
ZusammenfassungEs wurden 40 Patienten mit Psoriasisarthritis (PsA) aus unserer Praxis nach dem Kriterium „Vorstellung in der Spezialsprechstunde Immundermatologie“ ausgewählt und einer retrospektiven Datenanalyse unterzogen. Entsprechend wurden nur vorhandene Angaben zu Krankheitsmerkmalen, -schwere und -verlauf, zu Therapien sowie zu Laborparametern ausgewertet, keine neuen oder ergänzenden nachträglich erhoben. Unsere Patientenkohorte wird charakterisiert durch epidemiologische Daten wie Geschlechtsverteilung (weiblich:männlich = 1,2:1), Alter (Mittelwert 52 Jahre), Erkrankungsdauer (23 Jahre, 5/40 Patienten mit Late-Onset-Erkrankung). In den meisten Fällen traten die Gelenkbeschwerden deutlich nach, bei nur wenigen Patienten zeitnah zu den Hautsymptomen, auf oder wurden dann bemerkt. Für die Diagnosestellung wurden die CASPAR-Kriterien und der DAPSA-Score verwendet. Die röntgenologische Diagnostik erwies sich als wenig hilfreich. Soweit möglich, wurde bei der Diagnosestellung und Therapieeinleitung mit Kollegen der Rheumatologie oder Kliniken zusammengearbeitet. Entsprechend der Vielzahl zur Verfügung stehender therapeutischer Optionen wurden verschiedene Substanzen eingesetzt und ein Therapiealgorithmus ausgearbeitet. In einigen Fällen wurde versucht, Therapieverläufe mittels DAPSA, PASI, NAPSI und DLQI zu objektivieren. Kasuistische Berichte aus der Kohorte veranlassten uns zur Analyse von Hinweisen auf Atopie (klinische Symptome, Labor- und Testparameter, entsprechende Therapien), wobei wir bei 12/40 Patienten mit PsA atopische Phänomene feststellten. Wir möchten mit dieser retrospektiven, klinischen Datenanalyse einen Beitrag leisten für ein gutes interdisziplinäres Management einer sehr komplexen und häufig schweren Erkrankung in unseren dermatologischen Praxen.
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Affiliation(s)
- Sigbert Jahn
- Dermatologische Facharztpraxis Dr. Herbst & Kollegen, Darmstadt
| | | | - Julia Föhr
- Dermatologische Facharztpraxis Dr. Herbst & Kollegen, Darmstadt
| | | | - Matthias Herbst
- Dermatologische Facharztpraxis Dr. Herbst & Kollegen, Darmstadt
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15
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Arakawa A, Reeves E, Vollmer S, Arakawa Y, He M, Galinski A, Stöhr J, Dornmair K, James E, Prinz JC. ERAP1 Controls the Autoimmune Response against Melanocytes in Psoriasis by Generating the Melanocyte Autoantigen and Regulating Its Amount for HLA-C*06:02 Presentation. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2021; 207:2235-2244. [PMID: 34580106 PMCID: PMC7611875 DOI: 10.4049/jimmunol.2100686] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 08/17/2021] [Indexed: 01/05/2023]
Abstract
Autoimmune diseases develop when autoantigens activate previously quiescent self-reactive lymphocytes. Gene-gene interaction between certain HLA class I risk alleles and variants of the endoplasmic reticulum aminopeptidase ERAP1 controls the risk for common immune-mediated diseases, including psoriasis, ankylosing spondylitis, and Behçet disease. The functional mechanisms underlying this statistical association are unknown. In psoriasis, HLA-C*06:02 mediates an autoimmune response against melanocytes by autoantigen presentation. Using various genetically modified cell lines together with an autoreactive psoriatic TCR in a TCR activation assay, we demonstrate in this study that in psoriasis, ERAP1 generates the causative melanocyte autoantigen through trimming N-terminal elongated peptide precursors to the appropriate length for presentation by HLA-C*06:02. An ERAP1 risk haplotype for psoriasis produced the autoantigen much more efficiently and increased HLA-C expression and stimulation of the psoriatic TCR by melanocytes significantly more than a protective haplotype. Compared with the overall HLA class I molecules, cell surface expression of HLA-C decreased significantly more upon ERAP1 knockout. The combined upregulation of ERAP1 and HLA-C on melanocytes in psoriasis lesions emphasizes the pathogenic relevance of their interaction in patients. We conclude that in psoriasis pathogenesis, the increased generation of an ERAP1-dependent autoantigen by an ERAP1 risk haplotype enhances the likelihood that autoantigen presentation by HLA-C*06:02 will exceed the threshold for activation of potentially autoreactive T cells, thereby triggering CD8+ T cell-mediated autoimmune disease. These data identify ERAP1 function as a central checkpoint and promising therapeutic target in psoriasis and possibly other HLA class I-associated diseases with a similar genetic predisposition.
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Affiliation(s)
- Akiko Arakawa
- Department of Dermatology and Allergy, University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany;
| | - Emma Reeves
- Centre for Cancer Immunology, University Hospital Southampton, Southampton, United Kingdom; and
| | - Sigrid Vollmer
- Department of Dermatology and Allergy, University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany
| | - Yukiyasu Arakawa
- Department of Dermatology and Allergy, University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany
| | - Mengwen He
- Department of Dermatology and Allergy, University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany
| | - Adrian Galinski
- Department of Dermatology and Allergy, University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany
| | - Julia Stöhr
- Department of Dermatology and Allergy, University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany
| | - Klaus Dornmair
- Institute of Clinical Neuroimmunology, Biomedical Center and University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany
| | - Edward James
- Centre for Cancer Immunology, University Hospital Southampton, Southampton, United Kingdom; and
| | - Jörg C Prinz
- Department of Dermatology and Allergy, University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany;
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16
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Interleukin-1 Links Autoimmune and Autoinflammatory Pathophysiology in Mixed-Pattern Psoriasis. Mediators Inflamm 2021; 2021:2503378. [PMID: 34697538 PMCID: PMC8541875 DOI: 10.1155/2021/2503378] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/07/2021] [Accepted: 09/29/2021] [Indexed: 01/25/2023] Open
Abstract
Autoinflammatory and autoimmune diseases are characterized by an oversensitive immune system with loss of the physiological endogenous regulation, involving multifactorial self-reactive pathological mechanisms of mono- or polygenic nature. Failure in regulatory mechanisms triggers a complex network of dynamic relationships between innate and adaptive immunity, leading to coexistent autoinflammatory and autoimmune processes. Sustained exposure to a trigger or a genetic alteration at the level of the receptors of the natural immune system may lead to abnormal activation of the innate immune system, adaptive system activation, loss of self-tolerance, and systemic inflammation. The IL-1 family members critically activate and regulate innate and adaptive immune responses' diversity and plasticity in autoimmune and/or autoinflammatory conditions. The IL-23/IL-17 axis is key in the communication between innate immunity (IL-23-producing myeloid cells) and adaptive immunity (Th17- and IL-17-expressing CD8+ T cells). In psoriasis, these cytokines are decisive to the different clinical presentations, whether as plaque psoriasis (psoriasis vulgaris), generalized pustular psoriasis (pustular psoriasis), or mixed forms. These forms reflect a gradient between autoimmune pathophysiology with predominant adaptive immune response and autoinflammatory pathophysiology with predominant innate immune response.
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17
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Arnaud M, Bobisse S, Chiffelle J, Harari A. The Promise of Personalized TCR-Based Cellular Immunotherapy for Cancer Patients. Front Immunol 2021; 12:701636. [PMID: 34394096 PMCID: PMC8363295 DOI: 10.3389/fimmu.2021.701636] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 07/01/2021] [Indexed: 12/14/2022] Open
Abstract
Mutation-derived neoantigens are now established as attractive targets for cancer immunotherapy. The field of adoptive T cell transfer (ACT) therapy was significantly reshaped by tumor neoantigens and is now moving towards the genetic engineering of T cells with neoantigen-specific T cell receptors (TCRs). Yet, the identification of neoantigen-reactive TCRs remains challenging and the process needs to be adapted to clinical timelines. In addition, the state of recipient T cells for TCR transduction is critical and can affect TCR-ACT efficacy. Here we provide an overview of the main strategies for TCR-engineering, describe the selection and expansion of optimal carrier cells for TCR-ACT and discuss the next-generation methods for rapid identification of relevant TCR candidates for gene transfer therapy.
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Affiliation(s)
- Marion Arnaud
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Sara Bobisse
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Johanna Chiffelle
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Alexandre Harari
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
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18
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Yamaguchi S, Hamana H, Shitaoka K, Sukegawa K, Nagata T, Hayee A, Kobayashi E, Ozawa T, Fujii T, Muraguchi A, Tobe K, Kishi H. TCR function analysis using a novel system reveals the multiple unconventional tumor-reactive T cells in human breast cancer-infiltrating lymphocytes. Eur J Immunol 2021; 51:2306-2316. [PMID: 34171120 DOI: 10.1002/eji.202049070] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 04/27/2021] [Accepted: 06/22/2020] [Indexed: 11/06/2022]
Abstract
Tumor-infiltrating lymphocytes (TILs) are a potent source for obtaining tumor-reactive T cell receptors (TCRs). Although comprehensive methods to analyze the TCR repertoire in TILs have been reported, the evaluation system for TCR-reactivity to endogenously expressed antigen in tumor cells remains laborious and time consuming. Consequently, very limited numbers of TCRs in TILs have been analyzed for their reactivity to tumor cells. In this study, we developed an efficient evaluation system for TCR function designated c-FIT (comprehensive functional investigation of TCRs) to analyze TCR reactivity. The c-FIT system enabled us to analyze up to 90 TCRs for their reactivity to tumor cells by a single assay within a month. Using c-FIT, we analyzed 70 TCRs of CD8+ TILs derived from two breast cancer patients and obtained 23 TCRs that reacted to tumor cells. Surprisingly, although two TCRs were HLA class I-restricted, the remaining 21 TCRs were non-HLA-restricted. Thus, c-FIT can be applied for monitoring multiple conventional and unconventional antigen-specific killer T cells in TILs, leading to the development of new designs for more effective T-cell-based immunotherapies.
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Affiliation(s)
- Satoshi Yamaguchi
- Department of Immunology, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama, Japan.,Department of First Internal Medicine, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama, Japan
| | - Hiroshi Hamana
- Department of Immunology, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama, Japan
| | - Kiyomi Shitaoka
- Department of Immunology, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama, Japan.,Department of Immunology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Kenta Sukegawa
- Department of Immunology, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama, Japan.,Department of Surgery and Science, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama, Japan.,Niigata Medical-Care-Cooperative Kido-Hospital, Niigata, Japan
| | - Takuya Nagata
- Department of Surgery and Science, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama, Japan.,Toho University Ohashi Medical Center, Tokyo, Japan
| | - Abdul Hayee
- Department of Immunology, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama, Japan
| | - Eiji Kobayashi
- Department of Immunology, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama, Japan
| | - Tatsuhiko Ozawa
- Department of Immunology, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama, Japan
| | - Tsutomu Fujii
- Department of Surgery and Science, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama, Japan
| | - Atsushi Muraguchi
- Department of Immunology, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama, Japan
| | - Kazuyuki Tobe
- Department of First Internal Medicine, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama, Japan
| | - Hiroyuki Kishi
- Department of Immunology, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama, Japan
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19
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Wiendl H, Gross CC, Bauer J, Merkler D, Prat A, Liblau R. Fundamental mechanistic insights from rare but paradigmatic neuroimmunological diseases. Nat Rev Neurol 2021; 17:433-447. [PMID: 34050331 DOI: 10.1038/s41582-021-00496-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/13/2021] [Indexed: 02/04/2023]
Abstract
The pathophysiology of complex neuroimmunological diseases, such as multiple sclerosis and autoimmune encephalitis, remains puzzling - various mechanisms that are difficult to dissect seem to contribute, hampering the understanding of the processes involved. Some rare neuroimmunological diseases are easier to study because their presentation and pathogenesis are more homogeneous. The investigation of these diseases can provide fundamental insights into neuroimmunological pathomechanisms that can in turn be applied to more complex diseases. In this Review, we summarize key mechanistic insights into three such rare but paradigmatic neuroimmunological diseases - Susac syndrome, Rasmussen encephalitis and narcolepsy type 1 - and consider the implications of these insights for the study of other neuroimmunological diseases. In these diseases, the combination of findings in humans, different modalities of investigation and animal models has enabled the triangulation of evidence to validate and consolidate the pathomechanistic features and to develop diagnostic and therapeutic strategies; this approach has provided insights that are directly relevant to other neuroimmunological diseases and applicable in other contexts. We also outline how next-generation technologies and refined animal models can further improve our understanding of pathomechanisms, including cell-specific and antigen-specific CNS immune responses, thereby paving the way for the development of targeted therapeutic approaches.
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Affiliation(s)
- Heinz Wiendl
- Department of Neurology with Institute of Translational Neurology, University and University Hospital Münster, Münster, Germany.
| | - Catharina C Gross
- Department of Neurology with Institute of Translational Neurology, University and University Hospital Münster, Münster, Germany
| | - Jan Bauer
- Department of Neuroimmunology, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Doron Merkler
- Department of Pathology and Immunology, Division of Clinical Pathology, University and University Hospitals of Geneva, Geneva, Switzerland
| | - Alexandre Prat
- Department of Neuroscience, University of Montreal, Montreal, Canada
| | - Roland Liblau
- Infinity, Université Toulouse, CNRS, Inserm, Toulouse, France.,CHU Toulouse, Hôpital Purpan, Immunology Department, Toulouse, France
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20
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Pasetto A, Lu YC. Single-Cell TCR and Transcriptome Analysis: An Indispensable Tool for Studying T-Cell Biology and Cancer Immunotherapy. Front Immunol 2021; 12:689091. [PMID: 34163487 PMCID: PMC8215674 DOI: 10.3389/fimmu.2021.689091] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/10/2021] [Indexed: 12/18/2022] Open
Abstract
T cells have been known to be the driving force for immune response and cancer immunotherapy. Recent advances on single-cell sequencing techniques have empowered scientists to discover new biology at the single-cell level. Here, we review the single-cell techniques used for T-cell studies, including T-cell receptor (TCR) and transcriptome analysis. In addition, we summarize the approaches used for the identification of T-cell neoantigens, an important aspect for T-cell mediated cancer immunotherapy. More importantly, we discuss the applications of single-cell techniques for T-cell studies, including T-cell development and differentiation, as well as the role of T cells in autoimmunity, infectious disease and cancer immunotherapy. Taken together, this powerful tool not only can validate previous observation by conventional approaches, but also can pave the way for new discovery, such as previous unidentified T-cell subpopulations that potentially responsible for clinical outcomes in patients with autoimmunity or cancer.
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Affiliation(s)
- Anna Pasetto
- Department of Laboratory Medicine, Division of Clinical Microbiology, ANA FUTURA, Karolinska Institutet, Stockholm, Sweden
| | - Yong-Chen Lu
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, United States.,Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, United States
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21
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Phadungsaksawasdi P, Fujiyama T, Kurihara K, Ito T, Honda T, Tokura Y. PD-1 Expression Defines Epidermal CD8 +CD103 + T Cells Preferentially Producing IL-17A and Using Skewed TCR Repertoire in Psoriasis. J Invest Dermatol 2021; 141:2426-2435.e5. [PMID: 33845077 DOI: 10.1016/j.jid.2021.03.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 03/12/2021] [Accepted: 03/12/2021] [Indexed: 11/17/2022]
Abstract
In psoriasis, CD8+CD103+ memory T cells residing in the epidermis represent an effector population capable of maintaining the condition and driving a recurrence of the disease. Tissue-infiltrating CD8+ T cells expressing PD-1 are regarded as antigen-primed effector cells in others chronic inflammatory diseases. However, the expression and significance of PD-1 on skin-infiltrating CD8+ T cells in human psoriasis is not known. By analyzing skin-infiltrating T cells from human psoriasis, we found that active psoriatic epidermis contained PD-1 expressing CD8+CD103+ T cells that correlated with the disease severity and histopathology. PD-1+CD8+CD103+ T cells possessed a canonical psoriasis-specific resident memory phenotype with IL-23R expression and produced IL-17A, whereas PD-1-CD8+CD103+ T cells preferentially produced IFN-γ. The diversity of skin-infiltrating T cells was dominated by CD4+ T cells, while CD8+ T cells, especially CD8+CD103+T cells, represented an oligoclonal population in active psoriasis. In addition, PD-1+CD8+CD103+T cells used different TCR Vβs from PD-1-CD8+CD103+T cells counterpart. In the early resolved lesion, the composition and functional status of PD-1+CD8+CD103+T cells were markedly altered, while PD-1-CD8+CD103+ T cells population was minimally changed. Collectively, PD-1 expression delineates a putative pathogenic subset of epidermal CD8+CD103+ T cells, which possibly play a role in psoriasis pathogenesis.
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Affiliation(s)
| | - Toshiharu Fujiyama
- Department of Dermatology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Kazuo Kurihara
- Department of Dermatology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Taisuke Ito
- Department of Dermatology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Tetsuya Honda
- Department of Dermatology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Yoshiki Tokura
- Department of Dermatology, Hamamatsu University School of Medicine, Hamamatsu, Japan; Allergic Disease Research Center, Chutoen General Medical Center, Kakegawa, Japan.
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22
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Zhang H, Sun M, Wang J, Zeng B, Cao X, Han Y, Tan S, Gao GF. Identification of NY-ESO-1 157-165 Specific Murine T Cell Receptors With Distinct Recognition Pattern for Tumor Immunotherapy. Front Immunol 2021; 12:644520. [PMID: 33833762 PMCID: PMC8021954 DOI: 10.3389/fimmu.2021.644520] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 02/15/2021] [Indexed: 01/02/2023] Open
Abstract
New York esophageal squamous cell carcinoma 1 (NY-ESO-1) is a promising target for T-cell receptor-engineered T cell (TCR-T) therapy, and targeting the human leukocyte antigen (HLA)-A2 restricted NY-ESO-1157-165 epitope has yielded remarkable clinical benefits in the treatment of multiple advanced malignancies. Herein, we report the identification of two NY-ESO-1157-165 epitope-specific murine TCRs obtained from HLA-A*0201 transgenic mice. NY-ESO-1157-165 specific TCRs were isolated after vaccinating HLA-A2 transgenic mice with epitope peptides. HZ6 and HZ8 TCRs could specifically bind to NY-ESO-1157-165/HLA-A2 and were capable of cytokine secretion with engineered Jurkat T cells and primary T cells upon recognition with K562 target cells expressing the single-chain trimer (SCT) of NY-ESO-1157-165/HLA-A2. The reactivity profiles of the HZ6 and HZ8 TCRs were found to be distinct from one another when co-cultured with K562 target cells carrying alanine-substituted NY-ESO-1157-165 SCTs. The binding characterization revealed that the recognition pattern of the HZ6 TCR to NY-ESO-1157-165/HLA-A2 was substantially different from the widely used 1G4 TCR. These findings would broaden the understanding of immunogenicity of the NY-ESO-1157-165, and the two identified TCRs may serve as promising candidates for the future development of TCR-T therapy for tumors.
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Affiliation(s)
- Helin Zhang
- Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Meng Sun
- Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jie Wang
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Bin Zeng
- College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, China.,College of Pharmacy, Shenzhen Technology University, Shenzhen, China
| | - Xiaoqing Cao
- Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Yi Han
- Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Shuguang Tan
- University of Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - George F Gao
- Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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23
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Paria BC, Levin N, Lowery F, Pasetto A, Deniger DC, Parkhurst MR, Yossef R, Kim SP, Florentin M, Ngo L, Ray S, Krishna S, Robbins PF, Rosenberg SA. Rapid Identification and Evaluation of Neoantigen-reactive T-Cell Receptors From Single Cells. J Immunother 2021; 44:1-8. [PMID: 33086340 PMCID: PMC7725897 DOI: 10.1097/cji.0000000000000342] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Engineered T cells expressing tumor-specific T-cell receptors (TCRs) are emerging as a mode of personalized cancer immunotherapy that requires identification of TCRs against the products of known driver mutations and novel mutations in a timely fashion. We present a nonviral and non-next-generation sequencing platform for rapid, and efficient neoantigen-specific TCR identification and evaluation that does not require the use of recombinant cloning techniques. The platform includes an innovative method of TCRα detection using Sanger sequencing, TCR pairings and the use of TCRα/β gene fragments for putative TCR evaluation. Using patients' samples, we validated and compared our new methods head-to-head with conventional approaches used for TCR discovery. Development of a unique demultiplexing method for identification of TCRα, adaptation of synthetic TCRs for gene transfer, and a reliable reporter system significantly shortens TCR discovery time over conventional methods and increases throughput to facilitate testing prospective personalized TCRs for adoptive cell therapy.
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Affiliation(s)
- Biman C. Paria
- Surgery Branch, National Cancer Institute, Bethesda, Maryland, 20892, USA
| | - Noam Levin
- Surgery Branch, National Cancer Institute, Bethesda, Maryland, 20892, USA
| | - Frank Lowery
- Surgery Branch, National Cancer Institute, Bethesda, Maryland, 20892, USA
| | - Anna Pasetto
- Surgery Branch, National Cancer Institute, Bethesda, Maryland, 20892, USA
| | - Drew C. Deniger
- Surgery Branch, National Cancer Institute, Bethesda, Maryland, 20892, USA
| | - Maria R. Parkhurst
- Surgery Branch, National Cancer Institute, Bethesda, Maryland, 20892, USA
| | - Rami Yossef
- Surgery Branch, National Cancer Institute, Bethesda, Maryland, 20892, USA
| | - Sanghyun P. Kim
- Surgery Branch, National Cancer Institute, Bethesda, Maryland, 20892, USA
| | - Maria Florentin
- Surgery Branch, National Cancer Institute, Bethesda, Maryland, 20892, USA
| | - Lien Ngo
- Surgery Branch, National Cancer Institute, Bethesda, Maryland, 20892, USA
| | - Satyajit Ray
- Surgery Branch, National Cancer Institute, Bethesda, Maryland, 20892, USA
| | - Sri Krishna
- Surgery Branch, National Cancer Institute, Bethesda, Maryland, 20892, USA
| | - Paul F. Robbins
- Surgery Branch, National Cancer Institute, Bethesda, Maryland, 20892, USA
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24
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Liu Y, Wang X, Zhu Y, Zhang M, Nasri U, Sun SS, Forman SJ, Riggs AD, Zhang X, Zeng D. Haploidentical mixed chimerism cures autoimmunity in established type 1 diabetic mice. J Clin Invest 2020; 130:6457-6476. [PMID: 32817590 DOI: 10.1172/jci131799] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 08/13/2020] [Indexed: 12/21/2022] Open
Abstract
Clinical trials are currently testing whether induction of haploidentical mixed chimerism (Haplo-MC) induces organ transplantation tolerance. Whether Haplo-MC can be used to treat established autoimmune diseases remains unknown. Here, we show that established autoimmunity in euthymic and adult-thymectomized NOD (H-2g7) mice was cured by induction of Haplo-MC under a non-myeloablative anti-thymocyte globulin-based conditioning regimen and infusion of CD4+ T cell-depleted hematopoietic graft from H-2b/g7 F1 donors that expressed autoimmune-resistant H-2b or from H-2s/g7 F1 donors that expressed autoimmune-susceptible H-2s. The cure was associated with enhanced thymic negative selection, increased thymic Treg (tTreg) production, and anergy or exhaustion of residual host-type autoreactive T cells in the periphery. The peripheral tolerance was accompanied by expansion of donor- and host-type CD62L-Helios+ tTregs as well as host-type Helios-Nrp1+ peripheral Tregs (pTregs) and PD-L1hi plasmacytoid DCs (pDCs). Depletion of donor- or host-type Tregs led to reduction of host-type PD-L1hi pDCs and recurrence of autoimmunity, whereas PD-L1 deficiency in host-type DCs led to reduction of host-type pDCs and Helios-Nrp1+ pTregs. Thus, induction of Haplo-MC reestablished both central and peripheral tolerance through mechanisms that depend on allo-MHC+ donor-type DCs, PD-L1hi host-type DCs, and the generation and persistence of donor- and host-type tTregs and pTregs.
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Affiliation(s)
- Yuqing Liu
- Diabetes and Metabolism Research Institute, and.,Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute of City of Hope, Duarte, California, USA.,Medical Center of Hematology, Xinqiao Hospital of Army Medical University, Chongqing, China
| | - Xiaoqi Wang
- Diabetes and Metabolism Research Institute, and.,Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute of City of Hope, Duarte, California, USA.,Medical Center of Hematology, Xinqiao Hospital of Army Medical University, Chongqing, China
| | - Yongping Zhu
- Diabetes and Metabolism Research Institute, and.,Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute of City of Hope, Duarte, California, USA.,Department of Cardiovascular Surgery, Fujian Medical University Union Hospital, Fuzhou, China
| | - Mingfeng Zhang
- Diabetes and Metabolism Research Institute, and.,Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute of City of Hope, Duarte, California, USA
| | - Ubaydah Nasri
- Diabetes and Metabolism Research Institute, and.,Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute of City of Hope, Duarte, California, USA
| | - Sharne S Sun
- Eugene and Ruth Roberts Summer Student Academy of City of Hope, Duarte, California, USA
| | - Stephen J Forman
- Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute of City of Hope, Duarte, California, USA
| | | | - Xi Zhang
- Medical Center of Hematology, Xinqiao Hospital of Army Medical University, Chongqing, China
| | - Defu Zeng
- Diabetes and Metabolism Research Institute, and.,Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute of City of Hope, Duarte, California, USA
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25
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Abstract
T cells are an integral component of the adaptive immune response via the recognition of peptides by the cell surface-expressed T cell receptor (TCR). Rearrangement of the TCR genes results in a highly polymorphic repertoire on the T cells within a given individual. Although the diverse repertoire is beneficial for immune responses to foreign pathogens, recognition of self-peptides by T cells can contribute to the development of autoimmune disorders. Increasing evidence supports a pathogenic role for T cells in autoimmune pathology, and it is of interest to determine the TCR repertoires involved in autoimmune disease development. In this review, we summarize methodologies and advancements in the TCR sequencing field and discuss recent studies focused on TCR sequencing in a variety of autoimmune conditions. The rapidly evolving methodology of TCR sequencing has the potential to allow for a better understanding of autoimmune disease pathogenesis, identify disease-specific biomarkers, and aid in developing therapies to prevent and treat a number of these disorders.
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Affiliation(s)
- Angela M Mitchell
- Barbara Davis Center for Diabetes, University of Colorado, Aurora, CO, USA, 80045
| | - Aaron W Michels
- Barbara Davis Center for Diabetes, University of Colorado, Aurora, CO, USA, 80045
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26
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Cerboni S, Gehrmann U, Preite S, Mitra S. Cytokine-regulated Th17 plasticity in human health and diseases. Immunology 2020; 163:3-18. [PMID: 33064842 DOI: 10.1111/imm.13280] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/30/2020] [Accepted: 10/04/2020] [Indexed: 02/06/2023] Open
Abstract
Upon activation, naïve CD4+ T helper (Th) cells differentiate into distinct Th effector cell lineages depending on the local cytokine environment. However, these polarized Th cells can also adapt their function and phenotype depending on the changing cytokine environment, demonstrating functional plasticity. Here, Th17 cells, which play a critical role in host protection from extracellular pathogens and in autoimmune disorders, are of particular interest. While being able to shift phenotype within their lineage, Th17 cells can also acquire characteristics of Th1, Th2, T follicular helper (Tfh) or regulatory T cells. Th17 cell identity is determined by a spectrum of extracellular signals, including cytokines, which are critical orchestrators of cellular immune responses. Cytokine induces changes in epigenetic, transcriptional, translational and metabolomic parameters. How these signals are integrated to determine Th17 plasticity is not well defined, yet this is a crucial point of investigation as it represents a potential target to treat autoimmune and inflammatory diseases. The goal of this review was to discuss how cytokines regulate intracellular networks, focusing on the regulation of lineage-specific transcription factors, chromatin remodelling and metabolism, to control human Th17 cell plasticity. We discuss the importance of Th17 plasticity in autoimmunity and cancer and present current strategies and challenges in targeting pathogenic Th17 cells with cytokine-based approaches, considering human genetic variants associated with altered Th17 differentiation. Finally, we discuss how modulating Th17 plasticity rather than targeting the Th17 lineage as a whole might preserve its essential immune function while purging its adverse effects.
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Affiliation(s)
- Silvia Cerboni
- Translational Science and Experimental Medicine, Research and Early Development, Respiratory and Immunology (R&I, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Ulf Gehrmann
- Translational Science and Experimental Medicine, Research and Early Development, Respiratory and Immunology (R&I, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Silvia Preite
- Bioscience, In vivo, Research and Early Development, Respiratory & Immunology (R&I, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Suman Mitra
- CNRS, INSERM, CHU Lille, Institut pour la Recherche contre le Cancer de Lille, UMR9020 - UMR-S 1277 - CANTHER - Cancer Heterogeneity, Plasticity and Resistance to Therapies, Univ. Lille, Lille, France
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27
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Sulen A, Islam S, Wolff ASB, Oftedal BE. The prospects of single-cell analysis in autoimmunity. Scand J Immunol 2020; 92:e12964. [PMID: 32869859 DOI: 10.1111/sji.12964] [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: 05/01/2020] [Revised: 07/18/2020] [Accepted: 08/21/2020] [Indexed: 12/29/2022]
Abstract
In the last decade, there has been a tremendous development of technologies focused on analysing various molecular attributes in single cells, with an ever-increasing number of parameters becoming available at the DNA, RNA and protein levels. Much of this progress has involved cells in suspension, but also in situ analysis of tissues has taken great leaps. Paralleling the development in the laboratory, and because of increasing complexity, the analysis of single-cell data is also constantly being updated with new algorithms and analysis platforms. Our immune system shares this complexity, and immunologists have therefore been in the forefront of this technological development. These technologies clearly open new avenues for immunology research, maybe particularly within autoimmunity where the interaction between the faulty immune system and the thymus or the target organ is important. However, the technologies currently available can seem overwhelming and daunting. The aim of this review is to remedy this by giving a balanced overview of the prospects of using single-cell analysis in basal and clinical autoimmunity research, with an emphasis on endocrine autoimmunity.
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Affiliation(s)
- André Sulen
- KG Jebsen Center for Autoimmune Disorders, University of Bergen, Bergen, Norway.,Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Shahinul Islam
- KG Jebsen Center for Autoimmune Disorders, University of Bergen, Bergen, Norway.,Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Anette S B Wolff
- KG Jebsen Center for Autoimmune Disorders, University of Bergen, Bergen, Norway.,Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Bergithe E Oftedal
- KG Jebsen Center for Autoimmune Disorders, University of Bergen, Bergen, Norway.,Department of Clinical Science, University of Bergen, Bergen, Norway
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28
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Sukegawa K, Shitaoka K, Hamana H, Kobayashi E, Miyahara Y, Fujii K, Tsuda K, Saeki S, Nagata T, Ozawa T, Saito S, Fujii T, Muraguchi A, Shiku H, Kishi H. Relationship between T cell receptor clonotype and PD‐1 expression of tumor‐infiltrating lymphocytes in colorectal cancer. Eur J Immunol 2020; 50:1580-1590. [DOI: 10.1002/eji.201948399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 04/15/2020] [Accepted: 05/19/2020] [Indexed: 01/04/2023]
Affiliation(s)
- Kenta Sukegawa
- Department of Immunology, Faculty of Medicine, Academic Assembly University of Toyama Toyama Japan
- Department of Surgery and Science, Faculty of Medicine, Academic Assembly University of Toyama Toyama Japan
| | - Kiyomi Shitaoka
- Department of Immunology, Faculty of Medicine, Academic Assembly University of Toyama Toyama Japan
| | - Hiroshi Hamana
- Department of Immunology, Faculty of Medicine, Academic Assembly University of Toyama Toyama Japan
| | - Eiji Kobayashi
- Department of Immunology, Faculty of Medicine, Academic Assembly University of Toyama Toyama Japan
| | - Yoshihiro Miyahara
- Department of Personalized Cancer Immunotherapy Mie University Graduate School of Medicine Mie Japan
| | - Keisuke Fujii
- Department of Immuno‐Gene Therapy Mie University Graduate School of Medicine Mie Japan
| | - Kei Tsuda
- Department of Immunology, Faculty of Medicine, Academic Assembly University of Toyama Toyama Japan
- Department of Obstetrics and Gynecology, Faculty of Medicine, Academic Assembly University of Toyama Toyama Japan
| | - Shiori Saeki
- Department of Immunology, Faculty of Medicine, Academic Assembly University of Toyama Toyama Japan
- Department of Surgery and Science, Faculty of Medicine, Academic Assembly University of Toyama Toyama Japan
| | - Takuya Nagata
- Department of Surgery and Science, Faculty of Medicine, Academic Assembly University of Toyama Toyama Japan
| | - Tatsuhiko Ozawa
- Department of Immunology, Faculty of Medicine, Academic Assembly University of Toyama Toyama Japan
| | - Shigeru Saito
- Department of Obstetrics and Gynecology, Faculty of Medicine, Academic Assembly University of Toyama Toyama Japan
| | - Tsutomu Fujii
- Department of Surgery and Science, Faculty of Medicine, Academic Assembly University of Toyama Toyama Japan
| | - Atsushi Muraguchi
- Department of Immunology, Faculty of Medicine, Academic Assembly University of Toyama Toyama Japan
| | - Hiroshi Shiku
- Department of Personalized Cancer Immunotherapy Mie University Graduate School of Medicine Mie Japan
| | - Hiroyuki Kishi
- Department of Immunology, Faculty of Medicine, Academic Assembly University of Toyama Toyama Japan
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29
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Bracher A, Alcalá C, Ferrer J, Melzer N, Hohlfeld R, Casanova B, Beltrán E, Dornmair K. An expanded parenchymal CD8+ T cell clone in GABA A receptor encephalitis. Ann Clin Transl Neurol 2020; 7:239-244. [PMID: 31943946 PMCID: PMC7034500 DOI: 10.1002/acn3.50974] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 11/12/2019] [Accepted: 12/05/2019] [Indexed: 12/28/2022] Open
Abstract
The role of T cells in autoimmune encephalitis syndromes with autoantibodies against cell surface antigens is still enigmatic. Here we analyzed the T cell receptor repertoires of CD8+ and CD4+ T cells in a patient with "idiopathic" gamma-aminobutyric-acid-A receptor (GABAA -R) encephalitis by next-generation sequencing and single-cell analyses. We identified a CD8+ T cell clone that was strongly expanded in the cerebrospinal fluid and in the hippocampus but not in the operculo-insular cortex. By contrast, CD4+ T cells were polyclonal in these tissues. Such a strong clonal expansion suggests that CD8+ T cells may play a significant role in the pathogenesis.
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Affiliation(s)
- Aline Bracher
- Institute of Clinical Neuroimmunology, Biomedical Center and Hospital of the Ludwig-Maximilians Universität München, Munich, Germany
| | - Carmen Alcalá
- Department of Neurology, Hospital Universitari i Politècnic la Fe, Valencia, Spain
| | - Jaime Ferrer
- Department of Pathology, Hospital Universitari i Politècnic la Fe, Valencia, Spain
| | - Nico Melzer
- Clinic of Neurology and Institute of Translational Neurology, University Hospital Münster, Münster, Germany
| | - Reinhard Hohlfeld
- Institute of Clinical Neuroimmunology, Biomedical Center and Hospital of the Ludwig-Maximilians Universität München, Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Bonaventura Casanova
- Department of Neurology, Hospital Universitari i Politècnic la Fe, Valencia, Spain
| | - Eduardo Beltrán
- Institute of Clinical Neuroimmunology, Biomedical Center and Hospital of the Ludwig-Maximilians Universität München, Munich, Germany
| | - Klaus Dornmair
- Institute of Clinical Neuroimmunology, Biomedical Center and Hospital of the Ludwig-Maximilians Universität München, Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
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30
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Gupta S, Witas R, Voigt A, Semenova T, Nguyen CQ. Single-Cell Sequencing of T cell Receptors: A Perspective on the Technological Development and Translational Application. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1255:29-50. [PMID: 32949388 DOI: 10.1007/978-981-15-4494-1_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
T cells recognize peptides bound to major histocompatibility complex (MHC) class I and class II molecules at the cell surface. This recognition is accomplished by the expression of T cell receptors (TCR) which are required to be diverse and adaptable in order to accommodate the various and vast number of antigens presented on the MHCs. Thus, determining TCR repertoires of effector T cells is necessary to understand the immunological process in responding to cancer progression, infection, and autoimmune development. Furthermore, understanding the TCR repertoires will provide a solid framework to predict and test the antigen which is more critical in autoimmunity. However, it has been a technical challenge to sequence the TCRs and provide a conceptual context in correlation to the vast number of TCR repertoires in the immunological system. The exploding field of single-cell sequencing has changed how the repertoires are being investigated and analyzed. In this review, we focus on the biology of TCRs, TCR signaling and its implication in autoimmunity. We discuss important methods in bulk sequencing of many cells. Lastly, we explore the most pertinent platforms in single-cell sequencing and its application in autoimmunity.
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Affiliation(s)
- Shivai Gupta
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, Gainesville, FL, USA
| | - Richard Witas
- Department of Oral Biology, College of Dentistry, Gainesville, FL, USA
| | - Alexandria Voigt
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, Gainesville, FL, USA
| | - Touyana Semenova
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, Gainesville, FL, USA
| | - Cuong Q Nguyen
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, Gainesville, FL, USA. .,Department of Oral Biology, College of Dentistry, Gainesville, FL, USA. .,Center of Orphaned Autoimmune Diseases, University of Florida, Gainesville, FL, USA.
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31
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Soon CF, Zhang S, Suneetha PV, Antunes DA, Manns MP, Raha S, Schultze-Florey C, Prinz I, Wedemeyer H, Sällberg Chen M, Cornberg M. Hepatitis E Virus (HEV)-Specific T Cell Receptor Cross-Recognition: Implications for Immunotherapy. Front Immunol 2019; 10:2076. [PMID: 31552033 PMCID: PMC6738269 DOI: 10.3389/fimmu.2019.02076] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 08/16/2019] [Indexed: 12/26/2022] Open
Abstract
T cell immunotherapy is a concept developed for the treatment of cancer and infectious diseases, based on cytotoxic T lymphocytes to target tumor- or pathogen-specific antigens. Antigen-specificity of the T cell receptors (TCRs) is an important selection criterion in the developmental design of immunotherapy. However, off-target specificity is a possible autoimmunity concern if the engineered antigen-specific T cells are cross-reacting to self-peptides in-vivo. In our recent work, we identified several hepatitis E virus (HEV)-specific TCRs as potential candidates to be developed into T cell therapy to treat chronic hepatitis E. One of the identified TCRs, targeting a HLA-A2-restricted epitope at the RNA-dependent RNA polymerase (HEV-1527: LLWNTVWNM), possessed a unique multiple glycine motif in the TCR-β CDR3, which might be a factor inducing cross-reactivity. The aim of our study was to explore if this TCR could cross-recognize self-peptides to underlay autoimmunity. Indeed, we found that this HEV-1527-specific TCR could also cross-recognize an apoptosis-related epitope, Nonmuscle Myosin Heavy Chain 9 (MYH9-478: QLFNHTMFI). While this TCR had dual specificities to both viral epitope and a self-antigen by double Dextramer binding, it was selectively functional against HEV-1527 but not activated against MYH9-478. The consecutive glycine motif in β chain may be the reason promoting TCR binding promiscuity to recognize a secondary target, thereby facilitating cross-recognition. In conclusion, candidate TCRs for immunotherapy development should be screened for autoimmune potential, especially when the TCRs exhibit unique sequence pattern.
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Affiliation(s)
- Chai Fen Soon
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hanover, Germany.,Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hanover, Germany
| | - Shihong Zhang
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hanover, Germany
| | | | | | - Michael Peter Manns
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hanover, Germany.,Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hanover, Germany
| | - Solaiman Raha
- Hannover Medical School, Institute of Immunology, Hanover, Germany
| | - Christian Schultze-Florey
- Hannover Medical School, Institute of Immunology, Hanover, Germany.,Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hanover, Germany
| | - Immo Prinz
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hanover, Germany.,Hannover Medical School, Institute of Immunology, Hanover, Germany
| | - Heiner Wedemeyer
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hanover, Germany.,German Center for Infection Research, Partner Site Hannover-Braunschweig, Hanover, Germany.,Department of Gastroenterology and Hepatology, University Clinic Essen, Essen, Germany
| | - Margaret Sällberg Chen
- Department of Dental Medicine and Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.,Shanghai Tenth People's Hospital, Tongji University, Shanghai, China
| | - Markus Cornberg
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hanover, Germany.,Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hanover, Germany.,German Center for Infection Research, Partner Site Hannover-Braunschweig, Hanover, Germany.,Centre for Individualised Infection Medicine, Hanover, Germany.,Helmholtz Centre for Infection Research, Braunschweig, Germany
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32
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Peng S, Zaretsky JM, Ng AHC, Chour W, Bethune MT, Choi J, Hsu A, Holman E, Ding X, Guo K, Kim J, Xu AM, Heath JE, Noh WJ, Zhou J, Su Y, Lu Y, McLaughlin J, Cheng D, Witte ON, Baltimore D, Ribas A, Heath JR. Sensitive Detection and Analysis of Neoantigen-Specific T Cell Populations from Tumors and Blood. Cell Rep 2019; 28:2728-2738.e7. [PMID: 31484081 PMCID: PMC6774618 DOI: 10.1016/j.celrep.2019.07.106] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 05/04/2019] [Accepted: 07/29/2019] [Indexed: 12/30/2022] Open
Abstract
Neoantigen-specific T cells are increasingly viewed as important immunotherapy effectors, but physically isolating these rare cell populations is challenging. Here, we describe a sensitive method for the enumeration and isolation of neoantigen-specific CD8+ T cells from small samples of patient tumor or blood. The method relies on magnetic nanoparticles that present neoantigen-loaded major histocompatibility complex (MHC) tetramers at high avidity by barcoded DNA linkers. The magnetic particles provide a convenient handle to isolate the desired cell populations, and the barcoded DNA enables multiplexed analysis. The method exhibits superior recovery of antigen-specific T cell populations relative to literature approaches. We applied the method to profile neoantigen-specific T cell populations in the tumor and blood of patients with metastatic melanoma over the course of anti-PD1 checkpoint inhibitor therapy. We show that the method has value for monitoring clinical responses to cancer immunotherapy and might help guide the development of personalized mutational neoantigen-specific T cell therapies and cancer vaccines.
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Affiliation(s)
- Songming Peng
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA
| | - Jesse M Zaretsky
- Department of Medicine, University of California Los Angeles and Jonsson Comprehensive Cancer Center, 10833 Le Conte Avenue, Los Angeles, CA 90095, USA
| | - Alphonsus H C Ng
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA; Institute for Systems Biology, Seattle, WA 98109, USA
| | - William Chour
- Institute for Systems Biology, Seattle, WA 98109, USA; Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Michael T Bethune
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Jongchan Choi
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Alice Hsu
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Elizabeth Holman
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA
| | - Xiaozhe Ding
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA; Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Katherine Guo
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA
| | - Jungwoo Kim
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA
| | - Alexander M Xu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA; Institute for Systems Biology, Seattle, WA 98109, USA
| | - John E Heath
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA
| | - Won Jun Noh
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Jing Zhou
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA
| | - Yapeng Su
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA; Institute for Systems Biology, Seattle, WA 98109, USA
| | - Yue Lu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA; Institute for Systems Biology, Seattle, WA 98109, USA
| | - Jami McLaughlin
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Donghui Cheng
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Owen N Witte
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA 90095, USA; Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - David Baltimore
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Antoni Ribas
- Department of Medicine, University of California Los Angeles and Jonsson Comprehensive Cancer Center, 10833 Le Conte Avenue, Los Angeles, CA 90095, USA
| | - James R Heath
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA; Institute for Systems Biology, Seattle, WA 98109, USA.
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33
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Lanzarotti E, Marcatili P, Nielsen M. T-Cell Receptor Cognate Target Prediction Based on Paired α and β Chain Sequence and Structural CDR Loop Similarities. Front Immunol 2019; 10:2080. [PMID: 31555288 PMCID: PMC6724566 DOI: 10.3389/fimmu.2019.02080] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 08/16/2019] [Indexed: 12/21/2022] Open
Abstract
T-cell receptors (TCR) mediate immune responses recognizing peptides in complex with major histocompatibility complexes (pMHC) displayed on the surface of cells. Resolving the challenge of predicting the cognate pMHC target of a TCR would benefit many applications in the field of immunology, including vaccine design/discovery and the development of immunotherapies. Here, we developed a model for prediction of TCR targets based on similarity to a database of TCRs with known targets. Benchmarking the model on a large set of TCRs with known target, we demonstrated how the predictive performance is increased (i) by focusing on CDRs rather than the full length TCR protein sequences, (ii) by incorporating information from paired α and β chains, and (iii) integrating information for all 6 CDR loops rather than just CDR3. Finally, we show how integration of the structure of CDR loops, as obtained through homology modeling, boosts the predictive power of the model, in particular in situations where no high-similarity TCRs are available for the query. These findings demonstrate that TCRs that bind to the same target also share, to a very high degree, sequence, and structural features. This observation has profound impact for future development of prediction models for TCR-pMHC interactions and for the use of such models for the rational design of T cell based therapies.
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Affiliation(s)
- Esteban Lanzarotti
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Paolo Marcatili
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Morten Nielsen
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina.,Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
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34
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Schön MP. Adaptive and Innate Immunity in Psoriasis and Other Inflammatory Disorders. Front Immunol 2019; 10:1764. [PMID: 31402919 PMCID: PMC6676248 DOI: 10.3389/fimmu.2019.01764] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 07/11/2019] [Indexed: 12/14/2022] Open
Abstract
Over the past three decades, a considerable body of evidence has highlighted T cells as pivotal culprits in the pathogenesis of psoriasis. This includes the association of psoriasis with certain MHC (HLA) alleles, oligoclonal expansion of T cells in some cases, therapeutic response to T cell-directed immunomodulation, the onset of psoriasis following bone marrow transplantation, or induction of psoriasis-like inflammation by T cells in experimental animals. There is accumulating clinical and experimental evidence suggesting that both autoimmune and autoinflammatory mechanisms lie at the core of the disease. Indeed, some studies suggested antigenic functions of structural proteins, and complexes of self-DNA with cathelicidin (LL37) or melanocytic ADAMTSL5 have been proposed more recently as actual auto-antigens in some cases of psoriasis. These findings are accompanied by various immunoregulatory mechanisms, which we increasingly understand and which connect innate and adaptive immunity. Specific adaptive autoimmune responses, together with our current view of psoriasis as a systemic inflammatory disorder, raise the question of whether psoriasis may have connections to autoimmune or autoinflammatory disorders elsewhere in the body. While such associations have been suspected for many years, compelling mechanistic evidence in support of this notion is still scant. This review sets into context the current knowledge about innate and adaptive immunological processes in psoriasis and other autoimmune or autoinflammatory diseases.
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Affiliation(s)
- Michael P Schön
- Department of Dermatology, Venereology and Allergology, University Medical Center Göttingen, Göttingen, Germany
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35
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Arakawa A, Vollmer S, Tietze J, Galinski A, Heppt MV, Bürdek M, Berking C, Prinz JC. Clonality of CD4 + Blood T Cells Predicts Longer Survival With CTLA4 or PD-1 Checkpoint Inhibition in Advanced Melanoma. Front Immunol 2019; 10:1336. [PMID: 31275310 PMCID: PMC6591437 DOI: 10.3389/fimmu.2019.01336] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 05/28/2019] [Indexed: 12/31/2022] Open
Abstract
Recognition of cancer antigens drives the clonal expansion of cancer-reactive T cells, which is thought to contribute to restricted T-cell receptor (TCR) repertoires in tumor-infiltrating lymphocytes (TILs). To understand how tumors escape anti-tumor immunity, we investigated tumor-associated T-cell repertoires of patients with advanced melanoma and after blockade of the cytotoxic T-lymphocyte-associated protein 4 (CTLA4) or programmed cell death 1 (PD-1). TCR Vβ-gene spectratyping allowed us to quantify restrictions of T-cell repertoires and, further, diversities of T-cell clones. In this study, we show that the blood TCR repertoires were variably restricted in CD4+ and extensively restricted in CD8+ T cells of patients with advanced melanoma, and contained clones in both T-cell fractions prior to the start of immunotherapy. A greater diversification especially of CD4+ blood T-cell clones before immunotherapy showed statistically significant correlations with long-term survival upon CTLA4 or PD-1 inhibition. Analysis of TILs and corresponding blood available in one patient indicated that blood clonality may at least partially be related to the clonal expansion in the tumor microenvironment. In patients who developed severe immune-related adverse events (IrAEs), CD4+ and CD8+ TCR spectratypes became more restricted during anti-CTLA4 treatment, suggesting that newly expanded oligoclonal T-cell responses may contribute to IrAEs. This study reveals diverse T-cell clones in the blood of melanoma patients prior to immunotherapy, which may reflect the extent to which T cells are able to react against melanoma and potentially control melanoma progression. Therefore, the T-cell clonality in the circulation may have predictive value for antitumor responses from checkpoint inhibition.
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Affiliation(s)
- Akiko Arakawa
- Department of Dermatology and Allergology, University Hospital Munich, Ludwig-Maximilian-University Munich, Munich, Germany
| | - Sigrid Vollmer
- Department of Dermatology and Allergology, University Hospital Munich, Ludwig-Maximilian-University Munich, Munich, Germany
| | - Julia Tietze
- Department of Dermatology and Allergology, University Hospital Munich, Ludwig-Maximilian-University Munich, Munich, Germany
| | - Adrian Galinski
- Department of Dermatology and Allergology, University Hospital Munich, Ludwig-Maximilian-University Munich, Munich, Germany
| | - Markus V Heppt
- Department of Dermatology and Allergology, University Hospital Munich, Ludwig-Maximilian-University Munich, Munich, Germany
| | - Maja Bürdek
- Department of Dermatology and Allergology, University Hospital Munich, Ludwig-Maximilian-University Munich, Munich, Germany
| | - Carola Berking
- Department of Dermatology and Allergology, University Hospital Munich, Ludwig-Maximilian-University Munich, Munich, Germany
| | - Jörg C Prinz
- Department of Dermatology and Allergology, University Hospital Munich, Ludwig-Maximilian-University Munich, Munich, Germany
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36
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Dupic T, Marcou Q, Walczak AM, Mora T. Genesis of the αβ T-cell receptor. PLoS Comput Biol 2019; 15:e1006874. [PMID: 30830899 PMCID: PMC6417744 DOI: 10.1371/journal.pcbi.1006874] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 03/14/2019] [Accepted: 02/17/2019] [Indexed: 11/18/2022] Open
Abstract
The T-cell (TCR) repertoire relies on the diversity of receptors composed of two chains, called α and β, to recognize pathogens. Using results of high throughput sequencing and computational chain-pairing experiments of human TCR repertoires, we quantitively characterize the αβ generation process. We estimate the probabilities of a rescue recombination of the β chain on the second chromosome upon failure or success on the first chromosome. Unlike β chains, α chains recombine simultaneously on both chromosomes, resulting in correlated statistics of the two genes which we predict using a mechanistic model. We find that ∼35% of cells express both α chains. Altogether, our statistical analysis gives a complete quantitative mechanistic picture that results in the observed correlations in the generative process. We learn that the probability to generate any TCRαβ is lower than 10(-12) and estimate the generation diversity and sharing properties of the αβ TCR repertoire.
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MESH Headings
- Chromosomes, Human
- Humans
- Probability
- Receptors, Antigen, T-Cell, alpha-beta/biosynthesis
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Recombination, Genetic
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Affiliation(s)
- Thomas Dupic
- Laboratoire de physique théorique et hautes énergies, CNRS and Sorbonne Université, 4 Place Jussieu, 75005 Paris, France
- Laboratoire de physique de l’ENS, CNRS, Sorbonne Université, and École normale supérieure (PSL), 24 rue Lhomond, 75005 Paris, France
| | - Quentin Marcou
- Laboratoire de physique de l’ENS, CNRS, Sorbonne Université, and École normale supérieure (PSL), 24 rue Lhomond, 75005 Paris, France
| | - Aleksandra M. Walczak
- Laboratoire de physique de l’ENS, CNRS, Sorbonne Université, and École normale supérieure (PSL), 24 rue Lhomond, 75005 Paris, France
- * E-mail: (AMW); (TM)
| | - Thierry Mora
- Laboratoire de physique de l’ENS, CNRS, Sorbonne Université, and École normale supérieure (PSL), 24 rue Lhomond, 75005 Paris, France
- * E-mail: (AMW); (TM)
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37
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Dey S, Kamil Reza K, Wuethrich A, Korbie D, Ibn Sina AA, Trau M. Tracking antigen specific T-cells: Technological advancement and limitations. Biotechnol Adv 2018; 37:145-153. [PMID: 30508573 DOI: 10.1016/j.biotechadv.2018.11.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 10/30/2018] [Accepted: 11/20/2018] [Indexed: 11/18/2022]
Abstract
Assessing T-cell mediated immune status can help to understand the body's response to disease and also provide essential diagnostic information. However, detection and characterization of immune response are challenging due to the rarity of signature biomolecules in biological fluid and require highly sensitive and specific assay technique for the analysis. Until now, several techniques spanning from flow cytometry to microsensors have been developed or under investigation for T-cell mediated immune response monitoring. Most of the current assays are designed to estimate average immune responses, i.e., total functional protein analysis and detection of total T-cells irrespective of their antigen specificity. Although potential, immune response analysis without detecting and characterizing the rare subset of T-cell population could lead to over or underestimation of patient's immune status. Addressing this limitation, recently a number of technological advancements in biosensing have been developed for this. The potential of simple and precise micro-technologies including microarray and microfluidic platforms for assessing antigen-specific T-cells will be highlighted in this review, together with a discussion on existing challenges and future aspects of immune-sensor development.
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Affiliation(s)
- Shuvashis Dey
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, QLD 4072, Australia
| | - K Kamil Reza
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, QLD 4072, Australia
| | - Alain Wuethrich
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, QLD 4072, Australia
| | - Darren Korbie
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, QLD 4072, Australia
| | - Abu Ali Ibn Sina
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, QLD 4072, Australia.
| | - Matt Trau
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, QLD 4072, Australia; School of Chemistry and Molecular Biosciences, The University of Queensland, QLD 4072, Australia.
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38
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Bai Y, Wang D, Li W, Huang Y, Ye X, Waite J, Barry T, Edelmann KH, Levenkova N, Guo C, Skokos D, Wei Y, Macdonald LE, Fury W. Evaluation of the capacities of mouse TCR profiling from short read RNA-seq data. PLoS One 2018; 13:e0207020. [PMID: 30439982 PMCID: PMC6237323 DOI: 10.1371/journal.pone.0207020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 10/22/2018] [Indexed: 11/18/2022] Open
Abstract
Profiling T cell receptor (TCR) repertoire via short read transcriptome sequencing (RNA-Seq) has a unique advantage of probing simultaneously TCRs and the genome-wide RNA expression of other genes. However, compared to targeted amplicon approaches, the shorter read length is more prone to mapping error. In addition, only a small percentage of the genome-wide reads may cover the TCR loci and thus the repertoire could be significantly under-sampled. Although this approach has been applied in a few studies, the utility of transcriptome sequencing in probing TCR repertoires has not been evaluated extensively. Here we present a systematic assessment of RNA-Seq in TCR profiling. We evaluate the power of both Fluidigm C1 full-length single cell RNA-Seq and bulk RNA-Seq in characterizing the repertoires of different diversities under either naïve conditions or after immunogenic challenges. Standard read length and sequencing coverage were employed so that the evaluation was conducted in accord with the current RNA-Seq practices. Despite high sequencing depth in bulk RNA-Seq, we encountered difficulty quantifying TCRs with low transcript abundance (<1%). Nevertheless, top enriched TCRs with an abundance of 1–3% or higher can be faithfully detected and quantified. When top TCR sequences are of interest and transcriptome sequencing is available, it is worthwhile to conduct a TCR profiling using the RNA-Seq data.
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Affiliation(s)
- Yu Bai
- Regeneron Pharmaceuticals, Tarrytown, New York, United States of America
- * E-mail: (YB); (WF)
| | - David Wang
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
| | - Wentian Li
- Robert S. Boas Center for Genomics & Human Genetics, Feinstein Institute for Medical Research, Northwell Health, Manhasset, New York, United States of America
| | - Ying Huang
- Regeneron Pharmaceuticals, Tarrytown, New York, United States of America
| | - Xuan Ye
- Regeneron Pharmaceuticals, Tarrytown, New York, United States of America
| | - Janelle Waite
- Regeneron Pharmaceuticals, Tarrytown, New York, United States of America
| | - Thomas Barry
- Regeneron Pharmaceuticals, Tarrytown, New York, United States of America
| | - Kurt H. Edelmann
- Regeneron Pharmaceuticals, Tarrytown, New York, United States of America
| | - Natasha Levenkova
- Regeneron Pharmaceuticals, Tarrytown, New York, United States of America
| | - Chunguang Guo
- Regeneron Pharmaceuticals, Tarrytown, New York, United States of America
| | - Dimitris Skokos
- Regeneron Pharmaceuticals, Tarrytown, New York, United States of America
| | - Yi Wei
- Regeneron Pharmaceuticals, Tarrytown, New York, United States of America
| | - Lynn E. Macdonald
- Regeneron Pharmaceuticals, Tarrytown, New York, United States of America
| | - Wen Fury
- Regeneron Pharmaceuticals, Tarrytown, New York, United States of America
- * E-mail: (YB); (WF)
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39
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Querfeld C, Leung S, Myskowski PL, Curran SA, Goldman DA, Heller G, Wu X, Kil SH, Sharma S, Finn KJ, Horwitz S, Moskowitz A, Mehrara B, Rosen ST, Halpern AC, Young JW. Primary T Cells from Cutaneous T-cell Lymphoma Skin Explants Display an Exhausted Immune Checkpoint Profile. Cancer Immunol Res 2018; 6:900-909. [PMID: 29895574 PMCID: PMC6074045 DOI: 10.1158/2326-6066.cir-17-0270] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Revised: 01/23/2018] [Accepted: 06/04/2018] [Indexed: 02/04/2023]
Abstract
Cutaneous T-cell lymphoma (CTCL) develops from clonally expanded CD4+ T cells in a background of chronic inflammation. Although dendritic cells (DCs) stimulate T cells and are present in skin, cutaneous T cells in CTCL do not respond with effective antitumor immunity. We evaluated primary T-cell and DC émigrés from epidermal and dermal explant cultures of skin biopsies from CTCL patients (n = 37) and healthy donors (n = 5). Compared with healthy skin, CD4+ CTCL populations contained more T cells expressing PD-1, CTLA-4, and LAG-3. CD8+ CTCL populations contained more T cells expressing CTLA-4 and LAG-3. CTCL populations also contained more T cells expressing the inducible T-cell costimulator (ICOS), a marker of T-cell activation. DC émigrés from healthy or CTCL skin biopsies expressed PD-L1, indicating that maturation during migration resulted in PD-L1 expression irrespective of disease. Most T cells did not express PD-L1. Using skin samples from 49 additional CTCL patients for an unsupervised analysis of genome-wide mRNA expression profiles corroborated that advanced T3/T4-stage samples expressed more checkpoint inhibition mRNA compared with T1/T2 stage patients or healthy controls. Exhaustion of activated T cells is therefore a hallmark of both CD4+ and CD8+ T cells isolated from the lesional skin of patients with CTCL, with increasing expression as the disease progresses. These results justify identification of antigens driving T-cell exhaustion and the evaluation of immune checkpoint inhibition to reverse T-cell exhaustion earlier in the treatment of CTCL. Cancer Immunol Res; 6(8); 900-9. ©2018 AACR.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- B7-H1 Antigen/analysis
- CD4-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/immunology
- Dendritic Cells/immunology
- Epidermis/immunology
- Female
- Gene Expression Profiling/methods
- Genes, cdc/genetics
- Humans
- Immunophenotyping
- Lymphocyte Activation/immunology
- Lymphoma, T-Cell, Cutaneous/genetics
- Lymphoma, T-Cell, Cutaneous/immunology
- Lymphoma, T-Cell, Cutaneous/pathology
- Male
- Middle Aged
- Neoplasm Staging
- RNA, Messenger/genetics
- RNA, Neoplasm/genetics
- Skin Neoplasms/genetics
- Skin Neoplasms/immunology
- Skin Neoplasms/pathology
- Tumor Cells, Cultured
- Young Adult
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Affiliation(s)
- Christiane Querfeld
- Laboratory of Cellular Immunobiology, Immunology Program, Sloan Kettering Institute for Cancer Research, New York, New York.
- Dermatology Service, Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell Medical College, New York, New York
- Beckman Research Institute, City of Hope, Duarte, California
| | - Samantha Leung
- Laboratory of Cellular Immunobiology, Immunology Program, Sloan Kettering Institute for Cancer Research, New York, New York
| | - Patricia L Myskowski
- Dermatology Service, Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell Medical College, New York, New York
| | - Shane A Curran
- Laboratory of Cellular Immunobiology, Immunology Program, Sloan Kettering Institute for Cancer Research, New York, New York
| | - Debra A Goldman
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Glenn Heller
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Xiwei Wu
- Beckman Research Institute, City of Hope, Duarte, California
| | - Sung Hee Kil
- Beckman Research Institute, City of Hope, Duarte, California
| | - Sneh Sharma
- Laboratory of Cellular Immunobiology, Immunology Program, Sloan Kettering Institute for Cancer Research, New York, New York
| | - Kathleen J Finn
- Laboratory of Cellular Immunobiology, Immunology Program, Sloan Kettering Institute for Cancer Research, New York, New York
| | - Steven Horwitz
- Weill Cornell Medical College, New York, New York
- Lymphoma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alison Moskowitz
- Weill Cornell Medical College, New York, New York
- Lymphoma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Babak Mehrara
- Weill Cornell Medical College, New York, New York
- Plastic and Reconstructive Surgery Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Steven T Rosen
- Beckman Research Institute, City of Hope, Duarte, California
| | - Allan C Halpern
- Dermatology Service, Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell Medical College, New York, New York
| | - James W Young
- Laboratory of Cellular Immunobiology, Immunology Program, Sloan Kettering Institute for Cancer Research, New York, New York
- Weill Cornell Medical College, New York, New York
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- The Rockefeller University, Memorial Sloan Kettering Cancer Center, New York, New York
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40
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De Simone M, Rossetti G, Pagani M. Single Cell T Cell Receptor Sequencing: Techniques and Future Challenges. Front Immunol 2018; 9:1638. [PMID: 30072991 PMCID: PMC6058020 DOI: 10.3389/fimmu.2018.01638] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 07/03/2018] [Indexed: 12/19/2022] Open
Abstract
The peculiarity of T cell is their ability to recognize an infinite range of self and foreign antigens. This ability is achieved during thymic development through a complex molecular mechanism based on somatic recombination that leads to the expression of a very heterogeneous population of surface antigen receptors, the T Cell Receptors (TCRs). TCRs are cell specific and represent a sort of “molecular tag” of T cells and have been widely studied to monitor the dynamics of T cells in terms of clonality and diversity in several contexts including lymphoid malignancies, infectious diseases, autoimmune diseases, and tumor immunology. In this review, we provide an overview of the strategies used to investigate the TCR repertoire from the pioneering techniques based on the V segments identification to the revolution introduced by Next-Generation Sequencing that allows for high-throughput sequencing of alpha and beta chains. Single cell based approaches brought the analysis to a higher level of complexity and now provide the opportunity to sequence paired alpha and beta chains. We also discuss novel approaches that through the integration of TCR tracking and mRNA single cell sequencing offer a valuable tool to associate antigen specificity to transcriptional dynamics and to understand the molecular mechanisms of T cell plasticity.
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Affiliation(s)
- Marco De Simone
- Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi', Milan, Italy
| | - Grazisa Rossetti
- Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi', Milan, Italy
| | - Massimiliano Pagani
- Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi', Milan, Italy.,Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Milan, Italy
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41
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Zewde M, Kiyotani K, Park JH, Fang H, Yap KL, Yew PY, Alachkar H, Kato T, Mai TH, Ikeda Y, Matsuda T, Liu X, Ren L, Deng B, Harada M, Nakamura Y. The era of immunogenomics/immunopharmacogenomics. J Hum Genet 2018; 63:865-875. [PMID: 29785006 DOI: 10.1038/s10038-018-0468-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 05/01/2018] [Accepted: 05/02/2018] [Indexed: 11/09/2022]
Abstract
Although germline alterations and somatic mutations in disease cells have been extensively analyzed, molecular changes in immune cells associated with disease conditions have not been characterized in depth. It is clear that our immune system has a critical role in various biological and pathological conditions, such as infectious diseases, autoimmune diseases, drug-induced skin and liver toxicity, food allergy, and rejection of transplanted organs. The recent development of cancer immunotherapies, particularly drugs modulating the immune checkpoint molecules, has clearly demonstrated the importance of host immune cells in cancer treatments. However, the molecular mechanisms by which these new therapies kill tumor cells are still not fully understood. In this regard, we have begun to explore the role of newly developed tools such as next-generation sequencing in the genetic characterization of both cancer cells and host immune cells, a field that is called immunogenomics/ immunopharmacogenomics. This new field has enormous potential to help us better understand changes in our immune system during the course of various disease conditions. Here we report the potential of deep sequencing of T-cell and B-cell receptors in capturing the molecular contribution of the immune system, which we believe plays critical roles in the pathogenesis of various human diseases.
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Affiliation(s)
- Makda Zewde
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Kazuma Kiyotani
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA.,Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, 135-8550, Japan
| | - Jae-Hyun Park
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Hua Fang
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Kai Lee Yap
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Poh Yin Yew
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Houda Alachkar
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Taigo Kato
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Tu H Mai
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Yuji Ikeda
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Tatsuo Matsuda
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Xiao Liu
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Lili Ren
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Boya Deng
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Makiko Harada
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Yusuke Nakamura
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA.
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42
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Prinz JC. Human Leukocyte Antigen-Class I Alleles and the Autoreactive T Cell Response in Psoriasis Pathogenesis. Front Immunol 2018; 9:954. [PMID: 29760713 PMCID: PMC5936982 DOI: 10.3389/fimmu.2018.00954] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 04/17/2018] [Indexed: 01/08/2023] Open
Abstract
Psoriasis is a complex immune-mediated inflammatory skin disease characterized by T-cell-driven epidermal hyperplasia. It occurs on a strong genetic predisposition. The human leukocyte antigen (HLA)-class I allele HLA-C*06:02 on psoriasis susceptibility locus 1 (PSORS1 on 6p21.3) is the main psoriasis risk gene. Other HLA-class I alleles encoding HLA molecules presenting overlapping peptide repertoires show associations with psoriasis as well. Outside the major histocompatibility complex region, genome-wide association studies identified more than 60 psoriasis-associated common gene variants exerting only modest individual effects. They mainly refer to innate immune activation and the interleukin-23/Th/c17 pathway. Given their strong risk association, explaining the role of the HLA-risk alleles is essential for elucidating psoriasis pathogenesis. Psoriasis lesions develop upon epidermal infiltration, activation, and expansion of CD8+ T cells. The unbiased analysis of a paradigmatic Vα3S1/Vβ13S1-T-cell receptor from a pathogenic epidermal CD8+ T-cell clone of an HLA-C*06:02+ psoriasis patient had revealed that HLA-C*06:02 directs an autoimmune response against melanocytes through autoantigen presentation, and it identified a peptide form ADAMTS-like protein 5 as an HLA-C*06:02-presented melanocyte autoantigen. These data demonstrate that psoriasis is an autoimmune disease, where the predisposing HLA-class I alleles promote organ-specific inflammation through facilitating a T-cell response against a particular skin-specific cell population. This review discusses the role of HLA-class I alleles in the pathogenic psoriatic T-cell immune response. It concludes that as a principle of T-cell driven HLA-associated inflammatory diseases proinflammatory traits promote autoimmunity in the context of certain HLA molecules that present particular autoantigens.
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Affiliation(s)
- Jörg Christoph Prinz
- Department of Dermatology, University Clinics, Ludwig-Maximilian-University of Munich, Munich, Germany
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43
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44
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Shitaoka K, Hamana H, Kishi H, Hayakawa Y, Kobayashi E, Sukegawa K, Piao X, Lyu F, Nagata T, Sugiyama D, Nishikawa H, Tanemura A, Katayama I, Murahashi M, Takamatsu Y, Tani K, Ozawa T, Muraguchi A. Identification of Tumoricidal TCRs from Tumor-Infiltrating Lymphocytes by Single-Cell Analysis. Cancer Immunol Res 2018; 6:378-388. [PMID: 29475880 DOI: 10.1158/2326-6066.cir-17-0489] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 12/08/2017] [Accepted: 02/16/2018] [Indexed: 11/16/2022]
Abstract
T-cell receptor (TCR) gene therapy is a promising next-generation antitumor treatment. We previously developed a single-T-cell analysis protocol that allows the rapid capture of paired TCRα and β cDNAs. Here, we applied the protocol to analyze the TCR repertoire of tumor-infiltrating lymphocytes (TIL) of various cancer patients. We found clonally expanded populations of T cells that expressed the same clonotypic TCR in 50% to 70% of CD137+CD8+ TILs, indicating that they responded to certain antigens in the tumor environment. To assess the tumor reactivity of the TCRs derived from those clonally expanded TILs in detail, we then analyzed the CD137+CD8+ TILs from the tumor of B16F10 melanoma cells in six C57BL/6 mice and analyzed their TCR repertoire. We also found clonally expanded T cells in 60% to 90% of CD137+CD8+ TILs. When the tumor reactivity of dominant clonotypic TCRs in each mouse was analyzed, 9 of 13 TCRs induced the secretion of IFNγ in response to, and showed killing of, B16F10 cells in vitro, and 2 of them showed strong antitumor activity in vivo Concerning their antigen specificity, 7 of them reacted to p15E peptide of endogenous murine leukemia virus-derived envelope glycoprotein 70, and the rest reacted to tumor-associated antigens expressed on EL4 lymphoma as well as B16 melanoma cells. These results show that our strategy enables us to simply and rapidly obtain the tumor-specific TCR repertoire with high fidelity in an antigen- and MHC haplotype-independent manner from primary TILs. Cancer Immunol Res; 6(4); 378-88. ©2018 AACR.
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Affiliation(s)
- Kiyomi Shitaoka
- Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences (Medicine), Toyama, Japan
| | - Hiroshi Hamana
- Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences (Medicine), Toyama, Japan
| | - Hiroyuki Kishi
- Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences (Medicine), Toyama, Japan.
| | - Yoshihiro Hayakawa
- Division of Pathogenic Biochemistry, Institute of Natural Medicine, University of Toyama, Toyama, Japan
| | - Eiji Kobayashi
- Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences (Medicine), Toyama, Japan
| | - Kenta Sukegawa
- Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences (Medicine), Toyama, Japan.,Department of Surgery and Science, Graduate School of Medicine and Pharmaceutical Sciences (Medicine), Toyama, Japan
| | - Xiuhong Piao
- Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences (Medicine), Toyama, Japan
| | - Fulian Lyu
- Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences (Medicine), Toyama, Japan
| | - Takuya Nagata
- Department of Surgery and Science, Graduate School of Medicine and Pharmaceutical Sciences (Medicine), Toyama, Japan
| | - Daisuke Sugiyama
- Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hiroyoshi Nishikawa
- Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Division of Cancer Immunology, Research Institute/Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa, Japan
| | - Atsushi Tanemura
- Department of Dermatology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Ichiro Katayama
- Department of Dermatology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Mutsunori Murahashi
- Department of Advanced Cell and Molecular Therapy, Kyushu University Hospital, Fukuoka, Japan
| | - Yasushi Takamatsu
- Division of Medical Oncology, Hematology and Infectious Diseases, Department of Internal Medicine, Fukuoka University, Fukuoka, Japan
| | - Kenzaburo Tani
- Project Division of ALA Advanced Medical Research, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Tatsuhiko Ozawa
- Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences (Medicine), Toyama, Japan
| | - Atsushi Muraguchi
- Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences (Medicine), Toyama, Japan
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45
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Prinz JC. Melanocytes: Target Cells of an HLA-C*06:02-Restricted Autoimmune Response in Psoriasis. J Invest Dermatol 2017; 137:2053-2058. [PMID: 28941475 DOI: 10.1016/j.jid.2017.05.023] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 05/08/2017] [Accepted: 05/26/2017] [Indexed: 12/17/2022]
Abstract
HLA-C*06:02 is the main psoriasis risk allele. By the unbiased analysis of a Vα3S1/Vβ13S1 T-cell receptor from pathogenic psoriatic CD8+ T cells, we had recently proven that HLA-C*06:02 directs an autoimmune response against melanocytes through autoantigen presentation in psoriasis and identified ADAMTSL5 as a melanocyte autoantigen. We concluded that psoriasis is based on a melanocyte-specific immune response and that HLA-C*06:02 may predispose to psoriasis via this newly identified autoimmune pathway. Understanding this pathway, however, requires more detailed explanation. It is based on the fact that an HLA class I-restricted autoreactive CD8+ T-cell response must be directed against a particular target cell type, because HLA class I molecules present peptide antigens generated from cytoplasmic (i.e., intracellular) proteins. This review summarizes the findings on the melanocyte-specific autoimmune response in the context of the immune mechanisms related to HLA function and T-cell receptor-antigen recognition. Identifying melanocytes as target cells of the psoriatic immune response now explains psoriasis as a primary autoimmune skin disease.
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Affiliation(s)
- Jörg Christoph Prinz
- Department of Dermatology, University Clinics, Ludwig Maximilian University of Munich, Munich, Germany.
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46
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Elder JT. The Quest for Psoriasis Autoantigens: Genetics Meets Immunology in the Melanocyte. J Invest Dermatol 2017; 137:2042-2045. [PMID: 28941471 PMCID: PMC8223235 DOI: 10.1016/j.jid.2017.08.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 08/16/2017] [Indexed: 10/18/2022]
Affiliation(s)
- James T Elder
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA; Ann Arbor Veterans Affairs Hospital, Ann Arbor, Michigan, USA.
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47
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Mobbs JI, Illing PT, Dudek NL, Brooks AG, Baker DG, Purcell AW, Rossjohn J, Vivian JP. The molecular basis for peptide repertoire selection in the human leucocyte antigen (HLA) C*06:02 molecule. J Biol Chem 2017; 292:17203-17215. [PMID: 28855257 DOI: 10.1074/jbc.m117.806976] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 08/18/2017] [Indexed: 12/31/2022] Open
Abstract
Human leukocyte antigen (HLA)-C*06:02 is identified as the allele associated with the highest risk for the development of the autoimmune skin disease psoriasis. However, the diversity and mode of peptide presentation by the HLA-C*06:02 molecule remains unclear. Here, we describe the endogenous peptide repertoire of ∼3,000 sequences for HLA-C*06:02 that defines the peptide-binding motif for this HLA allomorph. We found that HLA-C*06:02 predominantly presents nonamer peptides with dominant arginine anchors at the P2 and P7 positions and a preference for small hydrophobic residues at the C terminus (PΩ). To determine the structural basis of this selectivity, we determined crystal structures of HLA-C*06:02 in complex with two self-peptides (ARTELYRSL and ARFNDLRFV) and an analogue of a melanocyte autoantigen (ADAMTSL5, VRSRR-abu-LRL) implicated in psoriasis. These structures revealed that HLA-C*06:02 possesses a deep peptide-binding groove comprising two electronegative B- and E-pockets that coincide with the preference for P2 and P7 arginine anchors. The ADAMTSL5 autoantigen possessed a P7-Leu instead of the P7-Arg residue, but nevertheless was accommodated within the HLA-C*06:02 antigen-binding cleft. Collectively, our results provide the structural basis for understanding peptide repertoire selection in HLA-C*06:02.
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Affiliation(s)
- Jesse I Mobbs
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Victoria, Australia
| | - Patricia T Illing
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Victoria, Australia
| | - Nadine L Dudek
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Victoria, Australia
| | - Andrew G Brooks
- the Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Daniel G Baker
- Janssen Research & Development, LLC, Horsham, Philadelphia, Pennsylvania 19044
| | - Anthony W Purcell
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Victoria, Australia,
| | - Jamie Rossjohn
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Victoria, Australia, .,the Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton 3800, Victoria, Australia, and.,the Institute of Infection and Immunity, Cardiff University, School of Medicine, Cardiff CF14 4XN, Wales, United Kingdom
| | - Julian P Vivian
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Victoria, Australia, .,the Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton 3800, Victoria, Australia, and
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48
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Rosati E, Dowds CM, Liaskou E, Henriksen EKK, Karlsen TH, Franke A. Overview of methodologies for T-cell receptor repertoire analysis. BMC Biotechnol 2017; 17:61. [PMID: 28693542 PMCID: PMC5504616 DOI: 10.1186/s12896-017-0379-9] [Citation(s) in RCA: 194] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 06/26/2017] [Indexed: 12/13/2022] Open
Abstract
Background The T-cell receptor (TCR), located on the surface of T cells, is responsible for the recognition of the antigen-major histocompatibility complex, leading to the initiation of an inflammatory response. Analysing the TCR repertoire may help to gain a better understanding of the immune system features and of the aetiology and progression of diseases, in particular those with unknown antigenic triggers. The extreme diversity of the TCR repertoire represents a major analytical challenge; this has led to the development of specialized methods which aim to characterize the TCR repertoire in-depth. Currently, next generation sequencing based technologies are most widely employed for the high-throughput analysis of the immune cell repertoire. Results Here, we report on the latest methodological advancements in the field by describing and comparing the available tools; from the choice of the starting material and library preparation method, to the sequencing technologies and data analysis. Finally, we provide a practical example and our own experience by reporting some exemplary results from a small internal benchmark study, where current approaches from the literature and the market are employed and compared. Conclusions Several valid methods for clonotype identification and TCR repertoire analysis exist, however, a gold standard method for the field has not yet been identified. Depending on the purpose of the scientific study, some approaches may be more suitable than others. Finally, due to possible method specific biases, scientists must be careful when comparing results obtained using different methods. Electronic supplementary material The online version of this article (doi:10.1186/s12896-017-0379-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elisa Rosati
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Str. 12, 24105, Kiel, Germany
| | - C Marie Dowds
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Str. 12, 24105, Kiel, Germany
| | - Evaggelia Liaskou
- Centre for Liver Research and NIHR Birmingham Liver Biomedical Research Unit, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Eva Kristine Klemsdal Henriksen
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway.,Research Institute of Internal Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway.,K.G. Jebsen Inflammation Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Tom H Karlsen
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway.,Section of Gastroenterology, Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Str. 12, 24105, Kiel, Germany.
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49
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Identifying T Cell Receptors from High-Throughput Sequencing: Dealing with Promiscuity in TCRα and TCRβ Pairing. PLoS Comput Biol 2017; 13:e1005313. [PMID: 28103239 PMCID: PMC5289640 DOI: 10.1371/journal.pcbi.1005313] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 02/02/2017] [Accepted: 12/15/2016] [Indexed: 12/20/2022] Open
Abstract
Characterisation of the T cell receptors (TCR) involved in immune responses is important for the design of vaccines and immunotherapies for cancer and autoimmune disease. The specificity of the interaction between the TCR heterodimer and its peptide-MHC ligand derives largely from the juxtaposed hypervariable CDR3 regions on the TCRα and TCRβ chains, and obtaining the paired sequences of these regions is a standard for functionally defining the TCR. A brute force approach to identifying the TCRs in a population of T cells is to use high-throughput single-cell sequencing, but currently this process remains costly and risks missing small clones. Alternatively, CDR3α and CDR3β sequences can be associated using their frequency of co-occurrence in independent samples, but this approach can be confounded by the sharing of CDR3α and CDR3β across clones, commonly observed within epitope-specific T cell populations. The accurate, exhaustive, and economical recovery of TCR sequences from such populations therefore remains a challenging problem. Here we describe an algorithm for performing frequency-based pairing (alphabetr) that accommodates CDR3α- and CDR3β-sharing, cells expressing two TCRα chains, and multiple forms of sequencing error. The algorithm also yields accurate estimates of clonal frequencies.
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50
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Attayek PJ, Hunsucker SA, Sims CE, Allbritton NL, Armistead PM. Identification and isolation of antigen-specific cytotoxic T lymphocytes with an automated microraft sorting system. Integr Biol (Camb) 2016; 8:1208-1220. [PMID: 27853786 PMCID: PMC5138107 DOI: 10.1039/c6ib00168h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The simultaneous measurement of T cell function with recovery of individual T cells would greatly facilitate characterizing antigen-specific responses both in vivo and in model systems. We have developed a microraft array methodology that automatically measures the ability of individual T cells to kill a population of target cells and viably sorts specific cells into a 96-well plate for expansion. A human T cell culture was generated against the influenza M1p antigen. Individual microrafts on a 70 × 70 array were loaded with on average 1 CD8+ cell from the culture and a population of M1p presenting target cells. Target cell killing, measured by fluorescence microscopy, was quantified in each microraft. The rates of target cell death among the individual CD8+ T cells varied greatly; however, individual T cells maintained their rates of cytotoxicity throughout the time course of the experiment enabling rapid identification of highly cytotoxic CD8+ T cells. Microrafts with highly active CD8+ T cells were individually transferred to wells of a 96-well plate, using a needle-release device coupled to the microscope. Three sorted T cells clonally expanded. All of these expressed high-avidity T cell receptors for M1p/HLA*02:01 tetramers, and 2 of the 3 receptors were sequenced. While this study investigated single T cell cytotoxicity rates against simple targets with subsequent cell sorting, future studies will involve measuring T cell mediated cytotoxicity in more complex cellular environments, enlarging the arrays to identify very rare antigen specific T cells, and measuring single cell CD4+ and CD8+ T cell proliferation.
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Affiliation(s)
- Peter J. Attayek
- Department of Biomedical Engineering, University of North Carolina, Chapel Hill NC and North Carolina State University, Raleigh NC
| | - Sally A. Hunsucker
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC
| | - Christopher E. Sims
- Department of Chemistry, University of North Carolina, Chapel Hill, NC
- Department of Medicine, University of North Carolina, Chapel Hill, NC
| | - Nancy L. Allbritton
- Department of Biomedical Engineering, University of North Carolina, Chapel Hill NC and North Carolina State University, Raleigh NC
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC
- Department of Chemistry, University of North Carolina, Chapel Hill, NC
| | - Paul M. Armistead
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC
- Department of Medicine, University of North Carolina, Chapel Hill, NC
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