1
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Baker AM, Nageswaran G, Nenclares P, Ronel T, Smith K, Kimberley C, Laclé MM, Bhide S, Harrington KJ, Melcher A, Rodriguez-Justo M, Chain B, Graham TA. FUME-TCRseq Enables Sensitive and Accurate Sequencing of the T-cell Receptor from Limited Input of Degraded RNA. Cancer Res 2024; 84:1560-1569. [PMID: 38479434 PMCID: PMC11094417 DOI: 10.1158/0008-5472.can-23-3340] [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: 10/24/2023] [Revised: 01/19/2024] [Accepted: 02/27/2024] [Indexed: 05/16/2024]
Abstract
Genomic analysis of the T-cell receptor (TCR) reveals the strength, breadth, and clonal dynamics of the adaptive immune response to pathogens or cancer. The diversity of the TCR repertoire, however, means that sequencing is technically challenging, particularly for samples with low-quality, degraded nucleic acids. Here, we developed and validated FUME-TCRseq, a robust and sensitive RNA-based TCR sequencing methodology that is suitable for formalin-fixed paraffin-embedded samples and low amounts of input material. FUME-TCRseq incorporates unique molecular identifiers into each molecule of cDNA, allowing correction for sequencing errors and PCR bias. Using RNA extracted from colorectal and head and neck cancers to benchmark the accuracy and sensitivity of FUME-TCRseq against existing methods demonstrated excellent concordance between the datasets. Furthermore, FUME-TCRseq detected more clonotypes than a commercial RNA-based alternative, with shorter library preparation time and significantly lower cost. The high sensitivity and the ability to sequence RNA of poor quality and limited amount enabled quantitative analysis of small numbers of cells from archival tissue sections, which is not possible with other methods. Spatially resolved FUME-TCRseq analysis of colorectal cancers using macrodissected archival samples revealed the shifting T-cell landscapes at the transition to an invasive phenotype and between tumor subclones containing distinct driver alterations. In summary, FUME-TCRseq represents an accurate, sensitive, and low-cost tool for the characterization of T-cell repertoires, particularly in samples with low-quality RNA that have not been accessible using existing methodology. SIGNIFICANCE FUME-TCRseq is a TCR sequencing methodology that supports sensitive and spatially resolved detection of TCR clones in archival clinical specimens, which can facilitate longitudinal tracking of immune responses through disease course and treatment.
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Affiliation(s)
- Ann-Marie Baker
- Centre for Evolution and Cancer, Institute of Cancer Research, London, United Kingdom
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Gayathri Nageswaran
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Pablo Nenclares
- Division of Radiotherapy and Imaging, Institute of Cancer Research, London, United Kingdom
| | - Tahel Ronel
- Centre for Evolution and Cancer, Institute of Cancer Research, London, United Kingdom
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Kane Smith
- Centre for Evolution and Cancer, Institute of Cancer Research, London, United Kingdom
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Christopher Kimberley
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Miangela M. Laclé
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Shreerang Bhide
- Division of Radiotherapy and Imaging, Institute of Cancer Research, London, United Kingdom
- Head and Neck Unit, The Royal Marsden Hospital NHS Trust, London, United Kingdom
| | - Kevin J. Harrington
- Division of Radiotherapy and Imaging, Institute of Cancer Research, London, United Kingdom
| | - Alan Melcher
- Division of Radiotherapy and Imaging, Institute of Cancer Research, London, United Kingdom
- Division of Breast Cancer Research, Institute of Cancer Research, London, United Kingdom
| | | | - Benny Chain
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Trevor A. Graham
- Centre for Evolution and Cancer, Institute of Cancer Research, London, United Kingdom
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
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2
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Watson RA, Ye W, Taylor CA, Jungkurth E, Cooper R, Tong O, James T, Shine B, Hofer M, Jenkins D, Pell R, Ieremia E, Jones S, Maldonado-Perez D, Roberts ISD, Coupe N, Middleton MR, Payne MJ, Fairfax BP. Severe acute myositis and myocarditis on initiation of 6-weekly pembrolizumab post-COVID-19 mRNA vaccination. J Immunother Cancer 2024; 12:e008151. [PMID: 38663935 PMCID: PMC11043765 DOI: 10.1136/jitc-2023-008151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/31/2024] [Indexed: 04/28/2024] Open
Abstract
We describe three cases of critical acute myositis with myocarditis occurring within 22 days of each other at a single institution, all within 1 month of receiving the initial cycle of the anti-PD-1 drug pembrolizumab. Analysis of T cell receptor repertoires from peripheral blood and tissues revealed a high degree of clonal expansion and public clones between cases, with several T cell clones expanded within the skeletal muscle putatively recognizing viral epitopes. All patients had recently received a COVID-19 mRNA booster vaccine prior to treatment and were positive for SARS-CoV2 Spike antibody. In conclusion, we report a series of unusually severe myositis and myocarditis following PD-1 blockade and the COVID-19 mRNA vaccination.
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Affiliation(s)
- Robert A Watson
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
- Cancer and Haematology Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Weiyu Ye
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
- Cancer and Haematology Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Chelsea A Taylor
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
| | - Elsita Jungkurth
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
| | - Rosalin Cooper
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
| | - Orion Tong
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
| | - Tim James
- Department of Clinical Biochemistry, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Brian Shine
- Department of Clinical Biochemistry, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Monika Hofer
- Department of Neuro Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Damian Jenkins
- Department of Clinical Neurology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Robert Pell
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Eleni Ieremia
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Stephanie Jones
- Oxford Centre for Histopathological Research, Oxford University Hospitals NHS Trust, Oxford, UK
| | - David Maldonado-Perez
- Oxford Centre for Histopathological Research, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Ian S D Roberts
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Nicholas Coupe
- Cancer and Haematology Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Mark R Middleton
- Department of Oncology, University of Oxford, Oxford, UK
- Cancer and Haematology Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Miranda J Payne
- Cancer and Haematology Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Benjamin P Fairfax
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
- Cancer and Haematology Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
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3
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Porcheddu V, Lhomme G, Giraudet R, Correia E, Maillère B. The self-reactive FVIII T cell repertoire in healthy individuals relies on a short set of epitopes and public clonotypes. Front Immunol 2024; 15:1345195. [PMID: 38510258 PMCID: PMC10951066 DOI: 10.3389/fimmu.2024.1345195] [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: 11/27/2023] [Accepted: 01/31/2024] [Indexed: 03/22/2024] Open
Abstract
Non-mutated FVIII-specific CD4 T cell epitopes have been recently found to contribute to the development of inhibitors in patients with hemophilia A (HA), while auto-reactive CD4 T cells specific to FVIII circulate in the blood of healthy individuals at a frequency close to the foreign protein ovalbumin. Thus, although FVIII is a self-protein, the central tolerance raised against FVIII appears to be low. In this study, we conducted a comprehensive analysis of the FVIII CD4 T cell repertoire in 29 healthy donors. Sequencing of the CDR3β TCR region from isolated FVIII-specific CD4 T cells revealed a limited usage and pairing of TRBV and TRBJ genes as well as a mostly hydrophobic composition of the CDR3β region according to their auto-reactivity. The FVIII repertoire is dominated by a few clonotypes, with only 13 clonotypes accounting for half of the FVIII response. Through a large-scale epitope mapping of the full-length FVIII sequence, we identified 18 immunodominant epitopes located in the A1, A3, C1, and C2 domains and covering half of the T cell response. These epitopes exhibited a broad specificity for HLA-DR or DP molecules or both. T cell priming with this reduced set of peptides revealed that highly expanded clonotypes specific to these epitopes were responsible individually for up to 32% of the total FVIII repertoire. These FVIII T cell epitopes and clonotypes were shared among HLA-unrelated donors tested and previously reported HA patients. Our study highlights the role of the auto-reactive T cell response against FVIII in HA and its similarity to the response observed in healthy individuals. Thus, it provides valuable insights for the development of new tolerance induction and deimmunization strategies.
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Affiliation(s)
- Valeria Porcheddu
- Université de Paris-Saclay, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut national de recherche pour l’agriculture, l’alimentation et l’environnement (INRAE), Département Médicaments et Technologies pour la Santé, Service d’Ingénierie Moléculaire pour la Santé (SIMoS), Gif-sur-Yvette, France
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4
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Shu DH, Ho WJ, Kagohara LT, Girgis A, Shin SM, Danilova L, Lee JW, Sidiropoulos DN, Mitchell S, Munjal K, Howe K, Bendinelli KJ, Qi H, Mo G, Montagne J, Leatherman JM, Lopez-Vidal TY, Zhu Q, Huff AL, Yuan X, Hernandez A, Coyne EM, Zaidi N, Zabransky DJ, Engle LL, Ogurtsova A, Baretti M, Laheru D, Durham JN, Wang H, Anders R, Jaffee EM, Fertig EJ, Yarchoan M. Immune landscape of tertiary lymphoid structures in hepatocellular carcinoma (HCC) treated with neoadjuvant immune checkpoint blockade. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.16.562104. [PMID: 37904980 PMCID: PMC10614819 DOI: 10.1101/2023.10.16.562104] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Neoadjuvant immunotherapy is thought to produce long-term remissions through induction of antitumor immune responses before removal of the primary tumor. Tertiary lymphoid structures (TLS), germinal center-like structures that can arise within tumors, may contribute to the establishment of immunological memory in this setting, but understanding of their role remains limited. Here, we investigated the contribution of TLS to antitumor immunity in hepatocellular carcinoma (HCC) treated with neoadjuvant immunotherapy. We found that neoadjuvant immunotherapy induced the formation of TLS, which were associated with superior pathologic response, improved relapse free survival, and expansion of the intratumoral T and B cell repertoire. While TLS in viable tumor displayed a highly active mature morphology, in areas of tumor regression we identified an involuted TLS morphology, which was characterized by dispersion of the B cell follicle and persistence of a T cell zone enriched for ongoing antigen presentation and T cell-mature dendritic cell interactions. Involuted TLS showed increased expression of T cell memory markers and expansion of CD8+ cytotoxic and tissue resident memory clonotypes. Collectively, these data reveal the circumstances of TLS dissolution and suggest a functional role for late-stage TLS as sites of T cell memory formation after elimination of viable tumor.
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Affiliation(s)
- Daniel H. Shu
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Convergence Institute, Johns Hopkins University, Baltimore, Maryland
| | - Won Jin Ho
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Convergence Institute, Johns Hopkins University, Baltimore, Maryland
| | - Luciane T. Kagohara
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Convergence Institute, Johns Hopkins University, Baltimore, Maryland
| | - Alexander Girgis
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Convergence Institute, Johns Hopkins University, Baltimore, Maryland
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Sarah M. Shin
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ludmila Danilova
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jae W. Lee
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Dimitrios N. Sidiropoulos
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Convergence Institute, Johns Hopkins University, Baltimore, Maryland
| | - Sarah Mitchell
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kabeer Munjal
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kathryn Howe
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kayla J. Bendinelli
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Hanfei Qi
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Guanglan Mo
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Janelle Montagne
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Convergence Institute, Johns Hopkins University, Baltimore, Maryland
| | - James M. Leatherman
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Tamara Y. Lopez-Vidal
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Convergence Institute, Johns Hopkins University, Baltimore, Maryland
| | - Qingfeng Zhu
- Convergence Institute, Johns Hopkins University, Baltimore, Maryland
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Amanda L. Huff
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Convergence Institute, Johns Hopkins University, Baltimore, Maryland
| | - Xuan Yuan
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Alexei Hernandez
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Erin M. Coyne
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Neeha Zaidi
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Convergence Institute, Johns Hopkins University, Baltimore, Maryland
| | - Daniel J. Zabransky
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Convergence Institute, Johns Hopkins University, Baltimore, Maryland
| | - Logan L. Engle
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- The Mark Foundation Center for Advanced Genomics and Imaging, Johns Hopkins University, Baltimore, Maryland
- Bloomberg∼Kimmel Institute for Cancer Immunotherapy and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Aleksandra Ogurtsova
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- The Mark Foundation Center for Advanced Genomics and Imaging, Johns Hopkins University, Baltimore, Maryland
- Bloomberg∼Kimmel Institute for Cancer Immunotherapy and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Marina Baretti
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Daniel Laheru
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Convergence Institute, Johns Hopkins University, Baltimore, Maryland
| | - Jennifer N. Durham
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Hao Wang
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Robert Anders
- Convergence Institute, Johns Hopkins University, Baltimore, Maryland
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Elizabeth M. Jaffee
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Convergence Institute, Johns Hopkins University, Baltimore, Maryland
- Bloomberg∼Kimmel Institute for Cancer Immunotherapy and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Elana J. Fertig
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Convergence Institute, Johns Hopkins University, Baltimore, Maryland
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Applied Mathematics and Statistics, Johns Hopkins University Whiting School of Engineering, Baltimore, Maryland
| | - Mark Yarchoan
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Convergence Institute, Johns Hopkins University, Baltimore, Maryland
- Bloomberg∼Kimmel Institute for Cancer Immunotherapy and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
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5
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Jayaraman S, Montagne JM, Nirschl TR, Marcisak E, Johnson J, Huff A, Hsiao MH, Nauroth J, Heumann T, Zarif JC, Jaffee EM, Azad N, Fertig EJ, Zaidi N, Larman HB. Barcoding intracellular reverse transcription enables high-throughput phenotype-coupled T cell receptor analyses. CELL REPORTS METHODS 2023; 3:100600. [PMID: 37776855 PMCID: PMC10626196 DOI: 10.1016/j.crmeth.2023.100600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/23/2023] [Accepted: 09/07/2023] [Indexed: 10/02/2023]
Abstract
Assays linking cellular phenotypes with T cell or B cell antigen receptor sequences are crucial for characterizing adaptive immune responses. Existing methodologies are limited by low sample throughput and high cost. Here, we present INtraCEllular Reverse Transcription with Sorting and sequencing (INCERTS), an approach that combines molecular indexing of receptor repertoires within intact cells and fluorescence-activated cell sorting (FACS). We demonstrate that INCERTS enables efficient processing of millions of cells from pooled human peripheral blood mononuclear cell (PBMC) samples while retaining robust association between T cell receptor (TCR) sequences and cellular phenotypes. We used INCERTS to discover antigen-specific TCRs from patients with cancer immunized with a novel mutant KRAS peptide vaccine. After ex vivo stimulation, 28 uniquely barcoded samples were pooled prior to FACS into peptide-reactive and non-reactive CD4+ and CD8+ populations. Combining complementary patient-matched single-cell RNA sequencing (scRNA-seq) data enabled retrieval of full-length, paired TCR alpha and beta chain sequences for future validation of therapeutic utility.
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Affiliation(s)
- Sahana Jayaraman
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Janelle M Montagne
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Bloomberg Kimmel Immunology Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Division of Quantitative Sciences, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Thomas R Nirschl
- Pathobiology Graduate Program, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Bloomberg∼Kimmel Institute for Cancer Immunotherapy, Johns Hopkins Medicine Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21205, USA
| | - Emily Marcisak
- Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jeanette Johnson
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Immunology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Amanda Huff
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Bloomberg Kimmel Immunology Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Meng-Hsuan Hsiao
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Julie Nauroth
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Thatcher Heumann
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Division of Hematology Oncology, Vanderbilt-Ingram Comprehensive Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jelani C Zarif
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Bloomberg∼Kimmel Institute for Cancer Immunotherapy, Johns Hopkins Medicine Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21205, USA
| | - Elizabeth M Jaffee
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Bloomberg Kimmel Immunology Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nilo Azad
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Bloomberg Kimmel Immunology Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Elana J Fertig
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Division of Quantitative Sciences, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Applied Mathematics and Statistics, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Neeha Zaidi
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Bloomberg Kimmel Immunology Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - H Benjamin Larman
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.
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6
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Chandra T, Aggarwal R. A Narrative Review of Acthar Gel for the Treatment of Myositis. Rheumatol Ther 2023; 10:523-537. [PMID: 36966453 PMCID: PMC10140234 DOI: 10.1007/s40744-023-00545-1] [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: 12/16/2022] [Accepted: 02/28/2023] [Indexed: 03/27/2023] Open
Abstract
Idiopathic inflammatory myopathies (IIMs) are autoimmune disorders characterized by symmetric proximal muscle weakness and chronic inflammation, with an increased risk of morbidity and mortality. The current standard of care includes traditional immunosuppressive pharmacotherapies; however, some patients cannot tolerate or do not adequately respond to these therapies, highlighting the need for alternative treatments for refractory disease. Acthar® Gel (repository corticotropin injection) is a naturally sourced mixture of adrenocorticotropic hormone analogs and other pituitary peptides that has been approved by the US Food and Drug Administration since 1952 for use in patients with two subgroups of IIMs, dermatomyositis (DM) and polymyositis (PM). However, it has not been routinely used in the treatment of IIMs. While Acthar may induce steroidogenesis, it also has a steroid-independent mechanism of action by exerting immunomodulatory effects through the activation of melanocortin receptors on immune cells, such as macrophages, B cells, and T cells. Recent clinical trials, retrospective analyses, and case reports add to the growing evidence suggesting that Acthar may be effective in patients with DM and PM. Here we review the current evidence supporting the safety and efficacy of Acthar for the treatment of refractory DM and PM.
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Affiliation(s)
| | - Rohit Aggarwal
- University of Pittsburgh, 3601 5th Avenue, Suite 2B, Pittsburgh, PA, 15261, USA.
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7
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Ding L, Li X, Zhu H, Luo H. Single-Cell Sequencing in Rheumatic Diseases: New Insights from the Perspective of the Cell Type. Aging Dis 2022; 13:1633-1651. [PMID: 36465169 PMCID: PMC9662270 DOI: 10.14336/ad.2022.0323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 03/23/2022] [Indexed: 11/02/2023] Open
Abstract
Rheumatic diseases are a group of highly heterogeneous autoimmune and inflammatory disorders involving multiple systems. Dysfunction of immune and non-immune cells participates in the complex pathogenesis of rheumatic diseases. Therefore, studies on the abnormal activation of cell subtypes provided a specific basis for understanding the pathogenesis of rheumatic diseases, which promoted the accuracy of disease diagnosis and the effectiveness of various treatments. However, there was still a far way to achieve individualized precision medicine as the result of heterogeneity among cell subtypes. To obtain the biological information of cell subtypes, single-cell sequencing, a cutting-edge technology, is used for analyzing their genomes, transcriptomes, epigenetics, and proteomics. Novel results identified multiple cell subtypes in tissues of patients with rheumatic diseases by single-cell sequencing. Consequently, we provide an overview of recent applications of single-cell sequencing in rheumatic disease and cross-tissue to understand the cell subtypes and functions.
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Affiliation(s)
- Liqing Ding
- The Department of Rheumatology and Immunology, Xiangya Hospital of Central South University, Changsha, Hunan, China.
| | - Xiaojing Li
- The Department of Rheumatology and Immunology, Xiangya Hospital of Central South University, Changsha, Hunan, China.
| | - Honglin Zhu
- The Department of Rheumatology and Immunology, Xiangya Hospital of Central South University, Changsha, Hunan, China.
- Provincial Clinical Research Center for Rheumatic and Immunologic Diseases, Xiangya Hospital, Changsha, Hunan, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China.
| | - Hui Luo
- The Department of Rheumatology and Immunology, Xiangya Hospital of Central South University, Changsha, Hunan, China.
- Provincial Clinical Research Center for Rheumatic and Immunologic Diseases, Xiangya Hospital, Changsha, Hunan, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China.
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8
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Nagafuchi Y, Ota M, Hatano H, Inoue M, Kobayashi S, Okubo M, Sugimori Y, Nakano M, Yamada S, Yoshida R, Tsuchida Y, Iwasaki Y, Shoda H, Okada Y, Yamamoto K, Ishigaki K, Okamura T, Fujio K. Control of naive and effector CD4 T cell receptor repertoires by rheumatoid-arthritis-risk HLA alleles. J Autoimmun 2022; 133:102907. [PMID: 36126366 DOI: 10.1016/j.jaut.2022.102907] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/30/2022] [Accepted: 08/31/2022] [Indexed: 12/13/2022]
Abstract
OBJECTIVE Human Leukocyte Antigen (HLA) alleles regulate susceptibility to rheumatoid arthritis (RA) and immune-mediated diseases. This study aims to elucidate the impact of HLA alleles to T cell subsets. METHODS We performed genome-wide and HLA allele association analysis for T cell receptor (TCR) beta chain repertoire in 13 purified T cell subsets from the ImmuNexUT database, consisting of 407 donors with ten immune-mediated diseases and healthy controls. RESULTS HLA class II alleles were associated with TRBV gene usage and the public clones of CD4 T cells, while HLA class I alleles were associated with CD8 T cells. RA-risk and immune-mediated diseases-risk HLA alleles were associated with TRBV gene usage of naive and effector CD4 T cell subsets and public clones accumulating in Th17. Clonal diversity was independent of HLA alleles and was correlated with transcriptome changes that reflect TCR signaling. CONCLUSION This study revealed in vivo evidence that both HLA alleles and environmental factors shape naive and effector TCR repertoires in RA and immune-mediated diseases patients.
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Affiliation(s)
- Yasuo Nagafuchi
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
| | - Mineto Ota
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroaki Hatano
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Laboratory for Human Immunogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Mariko Inoue
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Satomi Kobayashi
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Mai Okubo
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yusuke Sugimori
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masahiro Nakano
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Saeko Yamada
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Ryochi Yoshida
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yumi Tsuchida
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yukiko Iwasaki
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hirofumi Shoda
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan; Department of Genome Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Kazuhiko Yamamoto
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kazuyoshi Ishigaki
- Laboratory for Human Immunogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Tomohisa Okamura
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Keishi Fujio
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
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9
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Britson KA, Ling JP, Braunstein KE, Montagne JM, Kastenschmidt JM, Wilson A, Ikenaga C, Tsao W, Pinal-Fernandez I, Russell KA, Reed N, Mozaffar T, Wagner KR, Ostrow LW, Corse AM, Mammen AL, Villalta SA, Larman HB, Wong PC, Lloyd TE. Loss of TDP-43 function and rimmed vacuoles persist after T cell depletion in a xenograft model of sporadic inclusion body myositis. Sci Transl Med 2022; 14:eabi9196. [PMID: 35044790 PMCID: PMC9118725 DOI: 10.1126/scitranslmed.abi9196] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Sporadic inclusion body myositis (IBM) is the most common acquired muscle disease in adults over age 50, yet it remains unclear whether the disease is primarily driven by T cell–mediated autoimmunity. IBM muscle biopsies display nuclear clearance and cytoplasmic aggregation of TDP-43 in muscle cells, a pathologic finding observed initially in neurodegenerative diseases, where nuclear loss of TDP-43 in neurons causes aberrant RNA splicing. Here, we show that loss of TDP-43–mediated splicing repression, as determined by inclusion of cryptic exons, occurs in skeletal muscle of subjects with IBM. Of 119 muscle biopsies tested, RT-PCR–mediated detection of cryptic exon inclusion was able to diagnose IBM with 84% sensitivity and 99% specificity. To determine the role of T cells in pathogenesis, we generated a xenograft model by transplanting human IBM muscle into the hindlimb of immunodeficient mice. Xenografts from subjects with IBM displayed robust regeneration of human myofibers and recapitulated both inflammatory and degenerative features of the disease. Myofibers in IBM xenografts showed invasion by human, oligoclonal CD8+ T cells and exhibited MHC-I up-regulation, rimmed vacuoles, mitochondrial pathology, p62-positive inclusions, and nuclear clearance and cytoplasmic aggregation of TDP-43, associated with cryptic exon inclusion. Reduction of human T cells within IBM xenografts by treating mice intraperitoneally with anti-CD3 (OKT3) suppressed MHC-I up-regulation. However, rimmed vacuoles and loss of TDP-43 function persisted. These data suggest that T cell depletion does not alter muscle degenerative pathology in IBM.
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Affiliation(s)
- Kyla A. Britson
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jonathan P. Ling
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Kerstin E. Braunstein
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Janelle M. Montagne
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jenna M. Kastenschmidt
- Department of Physiology and Biophysics, Institute for Immunology, University of California Irvine, Irvine, CA 92697, USA
| | - Andrew Wilson
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Chiseko Ikenaga
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - William Tsao
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Iago Pinal-Fernandez
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Muscle Disease Unit, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Katelyn A. Russell
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nicole Reed
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Tahseen Mozaffar
- Institute for Immunology, Department of Neurology, University of California Irvine, Irvine, CA 92697, USA
| | - Kathryn R. Wagner
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Center for Genetic Muscle Disorders, Kennedy Krieger Institute, Baltimore, MD 21205, USA
| | - Lyle W. Ostrow
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Andrea M. Corse
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Andrew L. Mammen
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Muscle Disease Unit, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - S. Armando Villalta
- Department of Physiology and Biophysics, Institute for Immunology, University of California Irvine, Irvine, CA 92697, USA
| | - H. Benjamin Larman
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Philip C. Wong
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Solomon H. Synder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Thomas E. Lloyd
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Solomon H. Synder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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10
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Amoriello R, Ballerini C. An innovative and affordable quantitative assessment of human TCR repertoire. EBioMedicine 2020; 61:103021. [PMID: 33096477 PMCID: PMC7578669 DOI: 10.1016/j.ebiom.2020.103021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 09/09/2020] [Accepted: 09/09/2020] [Indexed: 11/29/2022] Open
Affiliation(s)
- Roberta Amoriello
- Department of Experimental and Clinical Medicine, University of Florence, Florence Italy
| | - Clara Ballerini
- Department of Experimental and Clinical Medicine, University of Florence, Florence Italy.
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