1
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Garnica J, Sole P, Yamanouchi J, Moro J, Mondal D, Fandos C, Serra P, Santamaria P. T-follicular helper cells are epigenetically poised to transdifferentiate into T-regulatory type 1 cells. eLife 2024; 13:RP97665. [PMID: 39576679 PMCID: PMC11584177 DOI: 10.7554/elife.97665] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2024] Open
Abstract
Chronic antigenic stimulation can trigger the formation of interleukin 10 (IL-10)-producing T-regulatory type 1 (TR1) cells in vivo. We have recently shown that murine T-follicular helper (TFH) cells are precursors of TR1 cells and that the TFH-to-TR1 cell transdifferentiation process is characterized by the progressive loss and acquisition of opposing transcription factor gene expression programs that evolve through at least one transitional cell stage. Here, we use a broad range of bulk and single-cell transcriptional and epigenetic tools to investigate the epigenetic underpinnings of this process. At the single-cell level, the TFH-to-TR1 cell transition is accompanied by both, downregulation of TFH cell-specific gene expression due to loss of chromatin accessibility, and upregulation of TR1 cell-specific genes linked to chromatin regions that remain accessible throughout the transdifferentiation process, with minimal generation of new open chromatin regions. By interrogating the epigenetic status of accessible TR1 genes on purified TFH and conventional T-cells, we find that most of these genes, including Il10, are already poised for expression at the TFH cell stage. Whereas these genes are closed and hypermethylated in Tconv cells, they are accessible, hypomethylated, and enriched for H3K27ac-marked and hypomethylated active enhancers in TFH cells. These enhancers are enriched for binding sites for the TFH and TR1-associated transcription factors TOX-2, IRF4, and c-MAF. Together, these data suggest that the TR1 gene expression program is genetically imprinted at the TFH cell stage.
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Affiliation(s)
- Josep Garnica
- Institut D’Investigacions Biomèdiques August Pi i SunyerBarcelonaSpain
| | - Patricia Sole
- Institut D’Investigacions Biomèdiques August Pi i SunyerBarcelonaSpain
| | - Jun Yamanouchi
- Department of Microbiology, Immunology and Infectious Diseases, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of CalgaryCalgary, AlbertaCanada
| | - Joel Moro
- Institut D’Investigacions Biomèdiques August Pi i SunyerBarcelonaSpain
| | - Debajyoti Mondal
- Department of Microbiology, Immunology and Infectious Diseases, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of CalgaryCalgary, AlbertaCanada
| | - Cesar Fandos
- Institut D’Investigacions Biomèdiques August Pi i SunyerBarcelonaSpain
| | - Pau Serra
- Institut D’Investigacions Biomèdiques August Pi i SunyerBarcelonaSpain
| | - Pere Santamaria
- Institut D’Investigacions Biomèdiques August Pi i SunyerBarcelonaSpain
- Department of Microbiology, Immunology and Infectious Diseases, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of CalgaryCalgary, AlbertaCanada
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2
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Wu Y, Liang X, Sun Y, Ning J, Dai Y, Jin S, Xu Y, Chen S, Pan L. A general pHLA-CD80 scaffold fusion protein to promote efficient antigen-specific T cell-based immunotherapy. MOLECULAR THERAPY. ONCOLOGY 2024; 32:200827. [PMID: 39027379 PMCID: PMC11255371 DOI: 10.1016/j.omton.2024.200827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 04/23/2024] [Accepted: 06/07/2024] [Indexed: 07/20/2024]
Abstract
Inadequate antigen-specific T cells activation hampers immunotherapy due to complex antigen presentation. In addition, therapeutic in vivo T cell expansion is constrained by slow expansion rates and limited functionality. Herein, we introduce a model fusion protein termed antigen-presenting cell-mimic fusion protein (APC-mimic), designed to greatly mimicking the natural antigen presentation pattern of antigen-presenting cells and directly expand T cells both in vitro and in vivo. The APC-mimic comprises the cognate peptide-human leukocyte antigen (pHLA) complex and the co-stimulatory marker CD80, which are natural ligands on APCs. Following a single stimulation, APC-mimic leads to an approximately 400-fold increase in the polyclonal expansion of antigen-specific T cells compared with the untreated group in vitro without the requirement for specialized antigen-presenting cells. Through the combination of single-cell TCR sequencing (scTCR-seq) and single-cell RNA sequencing (scRNA-seq), we identify an approximately 600-fold monoclonal expansion clonotype among these polyclonal clonotypes. It also exhibits suitability for in vivo applications confirmed in the OT-1 mouse model. Furthermore, T cells expanded by APC-mimic effectively inhibits tumor growth in adoptive cell transfer (ACT) murine models. These findings pave the way for the versatile APC-mimic platform for personalized therapeutics, enabling direct expansion of polyfunctional antigen-specific T cell subsets in vitro and in vivo.
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Affiliation(s)
- Yue Wu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiao Liang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yanping Sun
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jiangtao Ning
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yukun Dai
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Shijie Jin
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yingchun Xu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Shuqing Chen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Department of Precision Medicine on Tumor Therapeutics, ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou 311200, China
| | - Liqiang Pan
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
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3
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Aisihaer X, Guo H, Liu C. Interchain disulfide engineering enables the efficient production of functional HLA-DQ-Fc fusion proteins. J Biol Chem 2024; 300:107652. [PMID: 39121997 PMCID: PMC11402769 DOI: 10.1016/j.jbc.2024.107652] [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: 05/02/2024] [Revised: 07/13/2024] [Accepted: 07/30/2024] [Indexed: 08/12/2024] Open
Abstract
HLA-DQ molecules drive unwanted alloimmune responses after solid-organ transplants and several autoimmune diseases, including type 1 diabetes and celiac disease. Biologics with HLA molecules as part of the design are emerging therapeutic options for these allo- and autoimmune conditions. However, the soluble α and β chains of class II HLA molecules do not dimerize efficiently without their transmembrane domains, which hinders their production. In this study, we examined the feasibility of interchain disulfide engineering by introducing paired cysteines to juxtaposed positions in the α and β chains of HLA-DQ7, encoded by HLA-DQA1∗05:01 and HLA-DQB1∗03:01 respectively. We identified three variant peptide-HLA-DQ7-Fc fusion proteins (DQ7Fc) with increased expression and production yield, namely Y19C-D6C (YCDC), A83C-E5C (ACEC), and A84C-N33C (ACNC). The mutated residues were conserved across all HLA-DQ proteins and had limited solvent exposure. Further characterizations of the YCDC variant showed that the expression of the fusion protein is peptide-dependent; inclusion of a higher-affinity peptide correlated with increased protein expression. However, high-affinity peptide alone was insufficient for stabilizing the DQ7 complex without the engineered disulfide bond. Multiple DQ7Fc variants demonstrated expected binding characteristics with commercial anti-DQ antibodies in two immunoassays and by a cell-based assay. Lastly, DQ7Fc variants demonstrated dose-dependent killing of DQ7-specific B cell hybridomas in a flow cytometric, complement-dependent cytotoxicity assay. These data support inter-chain disulfide engineering as a novel approach to efficiently producing functional HLA-DQ molecules and potentially other class II HLA molecules as candidate therapeutic agents.
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Affiliation(s)
| | - Hongjie Guo
- Antiger Therapeutics Inc., St Louis, Missouri, USA.
| | - Chang Liu
- Antiger Therapeutics Inc., St Louis, Missouri, USA.
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4
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Zmievskaya EA, Mukhametshin SA, Ganeeva IA, Gilyazova EM, Siraeva ET, Kutyreva MP, Khannanov AA, Yuan Y, Bulatov ER. Artificial Extracellular Vesicles Generated from T Cells Using Different Induction Techniques. Biomedicines 2024; 12:919. [PMID: 38672273 PMCID: PMC11048032 DOI: 10.3390/biomedicines12040919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/05/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
Cell therapy is at the forefront of biomedicine in oncology and regenerative medicine. However, there are still significant challenges to their wider clinical application such as limited efficacy, side effects, and logistical difficulties. One of the potential approaches that could overcome these problems is based on extracellular vesicles (EVs) as a cell-free therapy modality. One of the major obstacles in the translation of EVs into practice is their low yield of production, which is insufficient to achieve therapeutic amounts. Here, we evaluated two primary approaches of artificial vesicle induction in primary T cells and the SupT1 cell line-cytochalasin B as a chemical inducer and ultrasonication as a physical inducer. We found that both methods are capable of producing artificial vesicles, but cytochalasin B induction leads to vesicle yield compared to natural secretion, while ultrasonication leads to a three-fold increase in particle yield. Cytochalasin B induces the formation of vesicles full of cytoplasmic compartments without nuclear fraction, while ultrasonication induces the formation of particles rich in membranes and membrane-related components such as CD3 or HLAII proteins. The most effective approach for T-cell induction in terms of the number of vesicles seems to be the combination of anti-CD3/CD28 antibody activation with ultrasonication, which leads to a seven-fold yield increase in particles with a high content of functionally important proteins (CD3, granzyme B, and HLA II).
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Affiliation(s)
- Ekaterina A. Zmievskaya
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
| | - Sabir A. Mukhametshin
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
| | - Irina A. Ganeeva
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
| | - Elvina M. Gilyazova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
| | - Elvira T. Siraeva
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
| | - Marianna P. Kutyreva
- A.M. Butlerov Institute of Chemistry, Kazan Federal University, 420008 Kazan, Russia
| | - Artur A. Khannanov
- A.M. Butlerov Institute of Chemistry, Kazan Federal University, 420008 Kazan, Russia
| | - Youyong Yuan
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou 511442, China
| | - Emil R. Bulatov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
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5
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Wang C, Chen J, Li J, Xu Z, Huang L, Zhao Q, Chen L, Liang X, Hu H, Li G, Xiong C, Wu B, You H, Du D, Wang X, Li H, Wang Z, Chen L. An EBV-related CD4 TCR immunotherapy inhibits tumor growth in an HLA-DP5+ nasopharyngeal cancer mouse model. J Clin Invest 2024; 134:e172092. [PMID: 38412034 PMCID: PMC11014665 DOI: 10.1172/jci172092] [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: 05/09/2023] [Accepted: 02/24/2024] [Indexed: 02/29/2024] Open
Abstract
Adoptive transfer of T cell receptor-engineered T cells (TCR-T) is a promising strategy for immunotherapy against solid tumors. However, the potential of CD4+ T cells in mediating tumor regression has been neglected. Nasopharyngeal cancer is consistently associated with EBV. Here, to evaluate the therapeutic potential of CD4 TCR-T in nasopharyngeal cancer, we screened for CD4 TCRs recognizing EBV nuclear antigen 1 (EBNA1) presented by HLA-DP5. Using mass spectrometry, we identified EBNA1567-581, a peptide naturally processed and presented by HLA-DP5. We isolated TCR135, a CD4 TCR with high functional avidity, that can function in both CD4+ and CD8+ T cells and recognizes HLA-DP5-restricted EBNA1567-581. TCR135-transduced T cells functioned in two ways: directly killing HLA-DP5+EBNA1+ tumor cells after recognizing EBNA1 presented by tumor cells and indirectly killing HLA-DP5-negative tumor cells after recognizing EBNA1 presented by antigen-presenting cells. TCR135-transduced T cells preferentially infiltrated into the tumor microenvironment and significantly inhibited tumor growth in xenograft nasopharyngeal tumor models. Additionally, we found that 62% of nasopharyngeal cancer patients showed 50%-100% expression of HLA-DP on tumor cells, indicating that nasopharyngeal cancer is well suited for CD4 TCR-T therapy. These findings suggest that TCR135 may provide a new strategy for EBV-related nasopharyngeal cancer immunotherapy in HLA-DP5+ patients.
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Affiliation(s)
- Chenwei Wang
- Guangzhou Medical University–Guangzhou Institute of Biomedicine and Health (GMU-GIBH) Joint School of Life Sciences and Guangdong–Hong Kong–Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jiewen Chen
- Guangzhou Medical University–Guangzhou Institute of Biomedicine and Health (GMU-GIBH) Joint School of Life Sciences and Guangdong–Hong Kong–Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jingyao Li
- Guangzhou Medical University–Guangzhou Institute of Biomedicine and Health (GMU-GIBH) Joint School of Life Sciences and Guangdong–Hong Kong–Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Zhihong Xu
- Guangzhou Medical University–Guangzhou Institute of Biomedicine and Health (GMU-GIBH) Joint School of Life Sciences and Guangdong–Hong Kong–Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Lihong Huang
- Guangzhou Medical University–Guangzhou Institute of Biomedicine and Health (GMU-GIBH) Joint School of Life Sciences and Guangdong–Hong Kong–Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Qian Zhao
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China
| | - Lei Chen
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Hong Kong, China
| | - Xiaolong Liang
- Guangzhou Medical University–Guangzhou Institute of Biomedicine and Health (GMU-GIBH) Joint School of Life Sciences and Guangdong–Hong Kong–Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Hai Hu
- Department of Pathology, Air Force Hospital of Southern Theater Command, Guangzhou, Guangdong, China
| | - Gang Li
- Department of Otolaryngology–Head and Neck Surgery, Huiqiao Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Chengjie Xiong
- Guangzhou Medical University–Guangzhou Institute of Biomedicine and Health (GMU-GIBH) Joint School of Life Sciences and Guangdong–Hong Kong–Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Bin Wu
- Guangzhou Medical University–Guangzhou Institute of Biomedicine and Health (GMU-GIBH) Joint School of Life Sciences and Guangdong–Hong Kong–Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Hua You
- Laboratory for Excellence in Systems Biomedicine of Pediatric Oncology, Department of Pediatric Hematology and Oncology, Children’s Hospital of Chongqing Medical University, Chongqing, China
| | - Danyi Du
- Department of Otolaryngology–Head and Neck Surgery, Precision Medical Center, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Xiaoling Wang
- Guangzhou Medical University–Guangzhou Institute of Biomedicine and Health (GMU-GIBH) Joint School of Life Sciences and Guangdong–Hong Kong–Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Hongle Li
- Department of Immunotherapy, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, Henan, China
| | - Zibing Wang
- Department of Immunotherapy, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, Henan, China
| | - Lin Chen
- Guangzhou Medical University–Guangzhou Institute of Biomedicine and Health (GMU-GIBH) Joint School of Life Sciences and Guangdong–Hong Kong–Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangzhou, Guangdong, China
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6
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Stražar M, Park J, Abelin JG, Taylor HB, Pedersen TK, Plichta DR, Brown EM, Eraslan B, Hung YM, Ortiz K, Clauser KR, Carr SA, Xavier RJ, Graham DB. HLA-II immunopeptidome profiling and deep learning reveal features of antigenicity to inform antigen discovery. Immunity 2023; 56:1681-1698.e13. [PMID: 37301199 PMCID: PMC10519123 DOI: 10.1016/j.immuni.2023.05.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 02/08/2023] [Accepted: 05/11/2023] [Indexed: 06/12/2023]
Abstract
CD4+ T cell responses are exquisitely antigen specific and directed toward peptide epitopes displayed by human leukocyte antigen class II (HLA-II) on antigen-presenting cells. Underrepresentation of diverse alleles in ligand databases and an incomplete understanding of factors affecting antigen presentation in vivo have limited progress in defining principles of peptide immunogenicity. Here, we employed monoallelic immunopeptidomics to identify 358,024 HLA-II binders, with a particular focus on HLA-DQ and HLA-DP. We uncovered peptide-binding patterns across a spectrum of binding affinities and enrichment of structural antigen features. These aspects underpinned the development of context-aware predictor of T cell antigens (CAPTAn), a deep learning model that predicts peptide antigens based on their affinity to HLA-II and full sequence of their source proteins. CAPTAn was instrumental in discovering prevalent T cell epitopes from bacteria in the human microbiome and a pan-variant epitope from SARS-CoV-2. Together CAPTAn and associated datasets present a resource for antigen discovery and the unraveling genetic associations of HLA alleles with immunopathologies.
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Affiliation(s)
- Martin Stražar
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jihye Park
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Hannah B Taylor
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Thomas K Pedersen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Eric M Brown
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Basak Eraslan
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yuan-Mao Hung
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Kayla Ortiz
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Karl R Clauser
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Daniel B Graham
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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7
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Solé P, Parras D, Yamanouchi J, Garnica J, Garabatos N, Moro J, Montaño J, Mondal D, Fandos C, Yang Y, Serra P, Santamaria P. Transcriptional re-programming of insulin B-chain epitope-specific T-follicular helper cells into anti-diabetogenic T-regulatory type-1 cells. Front Immunol 2023; 14:1177722. [PMID: 37153608 PMCID: PMC10154693 DOI: 10.3389/fimmu.2023.1177722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 03/27/2023] [Indexed: 05/09/2023] Open
Abstract
Systemic delivery of nanoparticles (NPs) coated with mono-specific autoimmune disease-relevant peptide-major histocompatibility complex class II (pMHCII) molecules can resolve organ inflammation in various disease models in a disease-specific manner without impairing normal immunity. These compounds invariably trigger the formation and systemic expansion of cognate pMHCII-specific T-regulatory type 1 (TR1) cells. By focusing on type 1 diabetes (T1D)-relevant pMHCII-NP types that display an epitope from the insulin B-chain bound to the same MHCII molecule (IAg7) on three different registers, we show that pMHCII-NP-induced TR1 cells invariably co-exist with cognate T-Follicular Helper (TFH)-like cells of quasi-identical clonotypic composition and are oligoclonal, yet transcriptionally homogeneous. Furthermore, these three different TR1 specificities have similar diabetes reversal properties in vivo despite being uniquely reactive against the peptide MHCII-binding register displayed on the NPs. Thus, pMHCII-NP treatment using nanomedicines displaying different epitope specificities results in the simultaneous differentiation of multiple antigen-specific TFH-like cell clones into TR1-like cells that inherit the fine antigenic specificity of their precursors while acquiring a defined transcriptional immunoregulatory program.
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Affiliation(s)
- Patricia Solé
- Department of Liver, Digestive System and Metabolism, Institut D’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Daniel Parras
- Department of Liver, Digestive System and Metabolism, Institut D’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Jun Yamanouchi
- Department of Microbiology, Immunology and Infectious Diseases, Snyder Institute for Chronic Diseases and Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Josep Garnica
- Department of Liver, Digestive System and Metabolism, Institut D’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Nahir Garabatos
- Department of Liver, Digestive System and Metabolism, Institut D’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Joel Moro
- Department of Liver, Digestive System and Metabolism, Institut D’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Javier Montaño
- Department of Liver, Digestive System and Metabolism, Institut D’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Debajyoti Mondal
- Department of Microbiology, Immunology and Infectious Diseases, Snyder Institute for Chronic Diseases and Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - César Fandos
- Department of Liver, Digestive System and Metabolism, Institut D’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Yang Yang
- Department of Microbiology, Immunology and Infectious Diseases, Snyder Institute for Chronic Diseases and Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Pau Serra
- Department of Liver, Digestive System and Metabolism, Institut D’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Pere Santamaria
- Department of Liver, Digestive System and Metabolism, Institut D’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Department of Microbiology, Immunology and Infectious Diseases, Snyder Institute for Chronic Diseases and Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- *Correspondence: Pere Santamaria,
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8
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Erausquin E, Serra P, Parras D, Santamaria P, López-Sagaseta J. Structural plasticity in I-Ag7 links autoreactivity to hybrid insulin peptides in type I diabetes. Front Immunol 2022; 13:924311. [PMID: 35967292 PMCID: PMC9365947 DOI: 10.3389/fimmu.2022.924311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
We recently provided evidence for promiscuous recognition of several different hybrid insulin peptides (HIPs) by the highly diabetogenic, I-Ag7-restricted 4.1-T cell receptor (TCR). To understand the structural determinants of this phenomenon, we solved the structure of an agonistic HIP/I-Ag7 complex, both in isolation as well as bound to the 4.1-TCR. We find that HIP promiscuity of the 4.1-TCR is dictated, on the one hand, by an amino acid sequence pattern that ensures I-Ag7 binding and, on the other hand, by the presence of three acidic residues at positions P5, P7 and P8 that favor an optimal engagement by the 4.1-TCR’s complementary determining regions. Surprisingly, comparison of the TCR-bound and unbound HIP/I-Ag7 structures reveals that 4.1-TCR binding triggers several novel and unique structural motions in both the I-Ag7 molecule and the peptide that are essential for docking. This observation indicates that the type 1 diabetes-associated I-Ag7 molecule is structurally malleable and that this plasticity allows the recognition of multiple peptides by individual TCRs that would otherwise be unable to do so.
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Affiliation(s)
- Elena Erausquin
- Unit of Protein Crystallography and Structural Immunology, Navarrabiomed, Navarra, Spain
- Public University of Navarra (UPNA), Pamplona, Spain
- Navarra University Hospital, Pamplona, Spain
| | - Pau Serra
- Institut D’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Daniel Parras
- Institut D’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Pere Santamaria
- Institut D’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Julia McFarlane Diabetes Research Centre (JMDRC) and Department of Microbiology, Immunology and Infectious Diseases, Snyder Institute for Chronic Diseases and Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- *Correspondence: Jacinto López-Sagaseta, ; Pere Santamaria,
| | - Jacinto López-Sagaseta
- Unit of Protein Crystallography and Structural Immunology, Navarrabiomed, Navarra, Spain
- Public University of Navarra (UPNA), Pamplona, Spain
- Navarra University Hospital, Pamplona, Spain
- *Correspondence: Jacinto López-Sagaseta, ; Pere Santamaria,
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9
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Patel S, Ramnoruth N, Wehr P, Rossjohn J, Reid HH, Campbell K, Nel HJ, Thomas R. Evaluation of a fit-for-purpose assay to monitor antigen-specific functional CD4+ T-cell subpopulations in rheumatoid arthritis using flow cytometry-based peptide-MHC class-II tetramer staining. Clin Exp Immunol 2022; 207:72-83. [PMID: 35020859 PMCID: PMC8802177 DOI: 10.1093/cei/uxab008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 09/13/2021] [Accepted: 12/01/2021] [Indexed: 12/11/2022] Open
Abstract
Antigen-specific T cells can serve as a response biomarker in non-clinical or clinical immunotherapy studies in autoimmune disease. There are protocols with optimized multimer staining methods to detect peptide (p)MHCII+ CD4+ T cells, and some qualified and validated protocols for pMHCI+ CD8+ T cells. However, no protocol is fully or partially qualified to enumerate and characterize antigen-specific pMHCII+ CD4+ T cells from patient samples. Implementing such an assay requires a desired level of specificity and precision, in terms of assay repeatability and reproducibility. In transgenic type II collagen (CII)-immunized HLA-DR1/DR4 humanized mouse models of collagen-induced arthritis (CIA), CII259-273-specific T cells dominantly expand. Therefore antigen-specific T cells recognizing this epitope presented by rheumatoid arthritis (RA)-associated risk HLA-DR allomorphs are of interest to understand disease progression and responses to immunotherapy in RA patients. Using HLA-DRB1∗04:01 or ∗01:01-collagen type II (CII)259-273 tetramers, we evaluated parameters influencing precision and reproducibility of an optimized flow cytometry-based method for antigen-specific CD4+ T cells and eight specific subpopulations with and without tetramer positivity. We evaluated specificity, precision, and reproducibility for research environments and non-regulated laboratories. The assay has excellent overall precision with %CV<25% for intra-assay repeatability, inter-analyst precision, and inter-assay reproducibility. The precision of the assay correlated negatively with the cell viability after thawing, indicating that post-thaw viability is a critical parameter for reproducibility. This assay is suitable for longitudinal analysis of treatment response and disease activity outcome in RA patients, and adaptable for translational or immunotherapy clinical trial settings.
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Affiliation(s)
- Swati Patel
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Nishta Ramnoruth
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Pascale Wehr
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program and The Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC, Australia
- Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK
| | - Hugh H Reid
- Infection and Immunity Program and The Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC, Australia
| | - Kim Campbell
- Janssen Research & Development, LLC, Spring House, PA, USA
- Janssen Research & Development, LLC, La Jolla, CA, USA
| | - Hendrik J Nel
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Ranjeny Thomas
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
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10
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Yang Y, Ellestad KK, Singha S, Uddin MM, Clarke R, Mondal D, Garabatos N, Solé P, Fandos C, Serra P, Santamaria P. Extremely short bioavailability and fast pharmacodynamic effects of pMHC-based nanomedicines. J Control Release 2021; 338:557-570. [PMID: 34474072 DOI: 10.1016/j.jconrel.2021.08.043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 08/10/2021] [Accepted: 08/25/2021] [Indexed: 01/25/2023]
Abstract
Nanoparticles (NPs) coated with autoimmune disease-relevant peptide-major histocompatibility complexes (pMHCs) can blunt autoimmune diseases by re-programming cognate effector T-lymphocytes into disease-suppressing regulatory T-cells, followed by massive expansion. Here, a method to quantify the absolute amounts of the active drug product is developed, to understand the relationship between bioavailability and pharmacodynamics. Incubation with plasma results in the formation of a protein corona that stabilizes the directional pMHC coat, shielding it from proteolysis or anti-drug antibody recognition, without any appreciable loss in biological potency. A quantitative method that harnesses these features indicates that the half-life of these compounds in the circulation and organs is an order of magnitude shorter (minutes vs. hours) than that measured using commonly-used semi-quantitative methods. Extensive transmission electron microscopy-based organ scanning and flow cytometry-based enumeration of pMHCII-NP capturing cells confirmed that these compounds are rapidly captured (within 1 min) by liver sinusoidal endothelial cells, Kupffer cells, splenic phagocytes and cognate T-cells, leading to a fast decline in the circulation. Therefore, the powerful pharmacodynamic effects of these compounds are dissociated from long bioavailability, implying a hit-and-run event. Collectively, these data provide a detailed view of the life-cycle of a nanoimmunomedicine, and suggest that the real half-lives of intact nanomedicines may be much shorter than those estimated using indirect approaches.
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Affiliation(s)
- Yang Yang
- Julia McFarlane Diabetes Research Centre (JMDRC) and Department of Microbiology, Immunology and Infectious Diseases, Snyder Institute for Chronic Diseases and Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Alberta T2N 4N1, Canada; Department of Biochemistry and Molecular Biology and Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Alberta T2N 4N1, Canada.
| | - Kristofor K Ellestad
- Julia McFarlane Diabetes Research Centre (JMDRC) and Department of Microbiology, Immunology and Infectious Diseases, Snyder Institute for Chronic Diseases and Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Alberta T2N 4N1, Canada
| | - Santiswarup Singha
- Julia McFarlane Diabetes Research Centre (JMDRC) and Department of Microbiology, Immunology and Infectious Diseases, Snyder Institute for Chronic Diseases and Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Alberta T2N 4N1, Canada
| | - Muhammad Myn Uddin
- Julia McFarlane Diabetes Research Centre (JMDRC) and Department of Microbiology, Immunology and Infectious Diseases, Snyder Institute for Chronic Diseases and Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Alberta T2N 4N1, Canada
| | - Robert Clarke
- Julia McFarlane Diabetes Research Centre (JMDRC) and Department of Microbiology, Immunology and Infectious Diseases, Snyder Institute for Chronic Diseases and Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Alberta T2N 4N1, Canada
| | - Debajyoti Mondal
- Julia McFarlane Diabetes Research Centre (JMDRC) and Department of Microbiology, Immunology and Infectious Diseases, Snyder Institute for Chronic Diseases and Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Alberta T2N 4N1, Canada
| | - Nahir Garabatos
- Institut D'Investigacions Biomèdiques August Pi i Sunyer, Barcelona 08036, Spain
| | - Patricia Solé
- Institut D'Investigacions Biomèdiques August Pi i Sunyer, Barcelona 08036, Spain
| | - Cesar Fandos
- Institut D'Investigacions Biomèdiques August Pi i Sunyer, Barcelona 08036, Spain
| | - Pau Serra
- Institut D'Investigacions Biomèdiques August Pi i Sunyer, Barcelona 08036, Spain
| | - Pere Santamaria
- Julia McFarlane Diabetes Research Centre (JMDRC) and Department of Microbiology, Immunology and Infectious Diseases, Snyder Institute for Chronic Diseases and Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Alberta T2N 4N1, Canada; Institut D'Investigacions Biomèdiques August Pi i Sunyer, Barcelona 08036, Spain.
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11
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Parras D, Solé P, Delong T, Santamaría P, Serra P. Recognition of Multiple Hybrid Insulin Peptides by a Single Highly Diabetogenic T-Cell Receptor. Front Immunol 2021; 12:737428. [PMID: 34527002 PMCID: PMC8435627 DOI: 10.3389/fimmu.2021.737428] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 08/03/2021] [Indexed: 12/11/2022] Open
Abstract
The mechanisms underlying the major histocompatibility complex class II (MHCII) type 1 diabetes (T1D) association remain incompletely understood. We have previously shown that thymocytes expressing the highly diabetogenic, I-Ag7-restricted 4.1-T-cell receptor (TCR) are MHCII-promiscuous, and that, in MHCII-heterozygous mice, they sequentially undergo positive and negative selection/Treg deviation by recognizing pro- and anti-diabetogenic MHCII molecules on cortical thymic epithelial cells and medullary hematopoietic antigen-presenting cells (APCs), respectively. Here, we use a novel autoantigen discovery approach to define the antigenic specificity of this TCR in the context of I-Ag7. This was done by screening the ability of random epitope-GS linker-I- A β g 7 chain fusion pools to form agonistic peptide-MHCII complexes on the surface of I- A α d chain-transgenic artificial APCs. Pool deconvolution, I-Ag7-binding register-fixing, TCR contact residue mapping, and alanine scanning mutagenesis resulted in the identification of a 4.1-TCR recognition motif XL(G/A)XEXE(D/E)X that was shared by seven agonistic hybrid insulin peptides (HIPs) resulting from the fusion of several different chromogranin A and/or insulin C fragments, including post-translationally modified variants. These data validate a novel, highly sensitive MHCII-restricted epitope discovery approach for orphan TCRs and suggest thymic selection of autoantigen-promiscuous TCRs as a mechanism for the murine T1D-I-Ag7-association.
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MESH Headings
- Animals
- Autoantigens/genetics
- Autoantigens/immunology
- Autoantigens/metabolism
- CD4-Positive T-Lymphocytes/immunology
- CD4-Positive T-Lymphocytes/metabolism
- CHO Cells
- Coculture Techniques
- Cricetulus
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Diabetes Mellitus, Type 1/genetics
- Diabetes Mellitus, Type 1/immunology
- Diabetes Mellitus, Type 1/metabolism
- Epitopes
- HEK293 Cells
- Histocompatibility Antigens Class II/genetics
- Histocompatibility Antigens Class II/immunology
- Histocompatibility Antigens Class II/metabolism
- Humans
- Insulin/genetics
- Insulin/immunology
- Insulin/metabolism
- Jurkat Cells
- Mice, Inbred NOD
- Mice, Knockout
- Peptide Fragments/genetics
- Peptide Fragments/immunology
- Peptide Fragments/metabolism
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- Receptors, Antigen, T-Cell/metabolism
- Mice
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Affiliation(s)
- Daniel Parras
- Institut D’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Patricia Solé
- Institut D’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Thomas Delong
- Skaggs School of Pharmacy and Pharmaceutical Sciences (SSPPS), Department of Pharmaceutical Sciences, University of Colorado, Aurora, CO, United States
| | - Pere Santamaría
- Institut D’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Julia McFarlane Diabetes Research Centre (JMDRC) and Department of Microbiology, Immunology and Infectious Diseases, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Pau Serra
- Institut D’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
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12
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Liu R, Jiang W, Mellins ED. Yeast display of MHC-II enables rapid identification of peptide ligands from protein antigens (RIPPA). Cell Mol Immunol 2021; 18:1847-1860. [PMID: 34117370 PMCID: PMC8193015 DOI: 10.1038/s41423-021-00717-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 05/25/2021] [Indexed: 11/12/2022] Open
Abstract
CD4+ T cells orchestrate adaptive immune responses via binding of antigens to their receptors through specific peptide/MHC-II complexes. To study these responses, it is essential to identify protein-derived MHC-II peptide ligands that constitute epitopes for T cell recognition. However, generating cells expressing single MHC-II alleles and isolating these proteins for use in peptide elution or binding studies is time consuming. Here, we express human MHC alleles (HLA-DR4 and HLA-DQ6) as native, noncovalent αβ dimers on yeast cells for direct flow cytometry-based screening of peptide ligands from selected antigens. We demonstrate rapid, accurate identification of DQ6 ligands from pre-pro-hypocretin, a narcolepsy-related immunogenic target. We also identify 20 DR4-binding SARS-CoV-2 spike peptides homologous to SARS-CoV-1 epitopes, and one spike peptide overlapping with the reported SARS-CoV-2 epitope recognized by CD4+ T cells from unexposed individuals carrying DR4 subtypes. Our method is optimized for immediate application upon the emergence of novel pathogens.
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Affiliation(s)
- Rongzeng Liu
- Department of Pediatrics-Human Gene Therapy, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Immunology, Henan University of Science and Technology School of Medicine, Luoyang, China
| | - Wei Jiang
- Department of Pediatrics-Human Gene Therapy, Stanford University School of Medicine, Stanford, CA, USA.
- Stanford Immunology, Stanford University School of Medicine, Stanford, CA, USA.
| | - Elizabeth D Mellins
- Department of Pediatrics-Human Gene Therapy, Stanford University School of Medicine, Stanford, CA, USA.
- Stanford Immunology, Stanford University School of Medicine, Stanford, CA, USA.
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13
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Mallajosyula V, Ganjavi C, Chakraborty S, McSween AM, Pavlovitch-Bedzyk AJ, Wilhelmy J, Nau A, Manohar M, Nadeau KC, Davis MM. CD8 + T cells specific for conserved coronavirus epitopes correlate with milder disease in COVID-19 patients. Sci Immunol 2021; 6:eabg5669. [PMID: 34210785 PMCID: PMC8975171 DOI: 10.1126/sciimmunol.abg5669] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 06/28/2021] [Indexed: 12/13/2022]
Abstract
A central feature of the SARS-CoV-2 pandemic is that some individuals become severely ill or die, whereas others have only a mild disease course or are asymptomatic. Here we report development of an improved multimeric αβ T cell staining reagent platform, with each maxi-ferritin "spheromer" displaying 12 peptide-MHC complexes. Spheromers stain specific T cells more efficiently than peptide-MHC tetramers and capture a broader portion of the sequence repertoire for a given peptide-MHC. Analyzing the response in unexposed individuals, we find that T cells recognizing peptides conserved amongst coronaviruses are more abundant and tend to have a "memory" phenotype, compared to those unique to SARS-CoV-2. Significantly, CD8+ T cells with these conserved specificities are much more abundant in COVID-19 patients with mild disease versus those with a more severe illness, suggesting a protective role.
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Affiliation(s)
- Vamsee Mallajosyula
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Conner Ganjavi
- Department of Biology, Stanford University School of Humanities and Sciences, Stanford, CA 94305, USA
| | - Saborni Chakraborty
- Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA 94305, USA
| | - Alana M McSween
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - Julie Wilhelmy
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Allison Nau
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Monali Manohar
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University and Division of Pulmonary, Allergy, Critical Care Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kari C Nadeau
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University and Division of Pulmonary, Allergy, Critical Care Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Mark M Davis
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA.
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
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14
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Willis RA, Ramachandiran V, Shires JC, Bai G, Jeter K, Bell DL, Han L, Kazarian T, Ugwu KC, Laur O, Contreras-Alcantara S, Long DL, Altman JD. Production of Class II MHC Proteins in Lentiviral Vector-Transduced HEK-293T Cells for Tetramer Staining Reagents. Curr Protoc 2021; 1:e36. [PMID: 33539685 PMCID: PMC7880703 DOI: 10.1002/cpz1.36] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Class II major histocompatibility complex peptide (MHC-IIp) multimers are precisely engineered reagents used to detect T cells specific for antigens from pathogens, tumors, and self-proteins. While the related Class I MHC/peptide (MHC-Ip) multimers are usually produced from subunits expressed in E. coli, most Class II MHC alleles cannot be produced in bacteria, and this has contributed to the perception that MHC-IIp reagents are harder to produce. Herein, we present a robust constitutive expression system for soluble biotinylated MHC-IIp proteins that uses stable lentiviral vector-transduced derivatives of HEK-293T cells. The expression design includes allele-specific peptide ligands tethered to the amino-terminus of the MHC-II β chain via a protease-cleavable linker. Following cleavage of the linker, HLA-DM is used to catalyze efficient peptide exchange, enabling high-throughput production of many distinct MHC-IIp complexes from a single production cell line. Peptide exchange is monitored using either of two label-free methods, native isoelectric focusing gel electrophoresis or matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry of eluted peptides. Together, these methods produce MHC-IIp complexes that are highly homogeneous and that form the basis for excellent MHC-IIp multimer reagents. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Lentivirus production and expression line creation Support Protocol 1: Six-well assay for estimation of production cell line yield Support Protocol 2: Universal ELISA for quantifying proteins with fused leucine zippers and His-tags Basic Protocol 2: Cultures for production of Class II MHC proteins Basic Protocol 3: Purification of Class II MHC proteins by anti-leucine zipper affinity chromatography Alternate Protocol 1: IMAC purification of His-tagged Class II MHC Support Protocol 3: Protein concentration measurements and adjustments Support Protocol 4: Polishing purification by anion-exchange chromatography Support Protocol 5: Estimating biotinylation percentage by streptavidin precipitation Basic Protocol 4: Peptide exchange Basic Protocol 5: Analysis of peptide exchange by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry Alternate Protocol 2: Native isoelectric focusing to validate MHC-II peptide loading Basic Protocol 6: Multimerization Basic Protocol 7: Staining cells with Class II MHC tetramers.
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Affiliation(s)
- Richard A Willis
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia
- Yerkes National Primate Research Center, Atlanta, Georgia
| | - Vasanthi Ramachandiran
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia
- Yerkes National Primate Research Center, Atlanta, Georgia
| | - John C Shires
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia
- Yerkes National Primate Research Center, Atlanta, Georgia
| | - Ge Bai
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia
- Yerkes National Primate Research Center, Atlanta, Georgia
| | - Kelly Jeter
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia
- Yerkes National Primate Research Center, Atlanta, Georgia
| | - Donielle L Bell
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia
- Yerkes National Primate Research Center, Atlanta, Georgia
| | - Lixia Han
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia
- Yerkes National Primate Research Center, Atlanta, Georgia
| | - Tamara Kazarian
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia
- Yerkes National Primate Research Center, Atlanta, Georgia
| | - Kyla C Ugwu
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia
- Yerkes National Primate Research Center, Atlanta, Georgia
| | - Oskar Laur
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia
- Emory Custom Cloning Core Facility, Emory University School of Medicine, Atlanta, Georgia
| | - Susana Contreras-Alcantara
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia
- Yerkes National Primate Research Center, Atlanta, Georgia
| | - Dale L Long
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia
- Yerkes National Primate Research Center, Atlanta, Georgia
| | - John D Altman
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia
- Yerkes National Primate Research Center, Atlanta, Georgia
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia
- Center for AIDS Research, Emory University, Atlanta, Georgia
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15
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Serra P, Santamaria P. Peptide-MHC-Based Nanomedicines for the Treatment of Autoimmunity: Engineering, Mechanisms, and Diseases. Front Immunol 2021; 11:621774. [PMID: 33574822 PMCID: PMC7870702 DOI: 10.3389/fimmu.2020.621774] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 12/09/2020] [Indexed: 12/17/2022] Open
Abstract
The development of autoimmunity results from a breakdown of immunoregulation and involves cellularly complex immune responses against broad repertoires of epitope specificities. As a result, selective targeting of specific effector autoreactive T- or B-cells is not a realistic therapeutic option for most autoimmune diseases. Induction of autoantigen-specific regulatory T-cells capable of effecting bystander (dominant), yet tissue-specific, immunoregulation has thus emerged as a preferred therapeutic alternative. We have shown that peptide-major histocompatibility complex (pMHC)-based nanomedicines can re-program cognate autoantigen-experienced T-cells into disease-suppressing regulatory T-cells, which in turn elicit the formation of complex regulatory cell networks capable of comprehensively suppressing organ-specific autoimmunity without impairing normal immunity. Here, we summarize the various pMHC-based nanomedicines and disease models tested to date, the engineering principles underpinning the pharmacodynamic and therapeutic potency of these compounds, and the underlying mechanisms of action.
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Affiliation(s)
- Pau Serra
- Institut D'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Pere Santamaria
- Institut D'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain.,Julia McFarlane Diabetes Research Centre (JMDRC) and Department of Microbiology, Immunology and Infectious Diseases, Snyder Institute for Chronic Diseases and Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
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16
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Rahman MA, Murata K, Burt BD, Hirano N. Changing the landscape of tumor immunology: novel tools to examine T cell specificity. Curr Opin Immunol 2020; 69:1-9. [PMID: 33307272 DOI: 10.1016/j.coi.2020.11.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 11/10/2020] [Indexed: 01/14/2023]
Abstract
Immunotherapy has established itself as a stalwart arm in patient care and with precision medicine forms the new paradigm in cancer treatment. T cells are an important group of immune cells capable of potent cancer immune surveillance and immunity. The advent of bioinformatics, particularly more recent advances incorporating algorithms employing machine learning, provide a seemingly limitless ability for T cell analysis and hypothesis generation. Such endeavors have become indispensable to research efforts accelerating and evolving to such an extent that there exists an appreciable gap between knowledge and proof of function and application. Exciting new technologies such as DNA barcoding, cytometry by time-of-flight (CyTOF), and peptide-exchangeable pHLA multimers inclusive of rare and difficult HLA alleles offer high-throughput cell-by-cell analytical capabilities. These outstanding recent contributions to T cell research will help close this gap and potentially bring practical benefit to patients.
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Affiliation(s)
- Muhammed A Rahman
- University of Queensland, Australia; Tumor Immunotherapy Program, Princess Margaret Cancer Centre, University Health Network, Canada
| | - Kenji Murata
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, University Health Network, Canada; Department of Pathology, Sapporo Medical University School of Medicine, Japan
| | - Brian D Burt
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, University Health Network, Canada
| | - Naoto Hirano
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, University Health Network, Canada; Department of Immunology, University of Toronto, Canada.
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17
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Pan W, Zheng X, Chen G, Su L, Luo S, Wang W, Ye S, Weng J, Min Y. Nanotechnology's application in Type 1 diabetes. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2020; 12:e1645. [PMID: 32558337 DOI: 10.1002/wnan.1645] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/17/2020] [Accepted: 04/17/2020] [Indexed: 12/16/2022]
Abstract
Type 1 diabetes mellitus (T1D) is an autoimmune disease caused by the immune system attacking islet cells. T1D, with a long prediabetes period, and the incidence of T1D increases with age during childhood and peaks at 10-14 years. And once it gets overt, it requires lifelong insulin replace treatment. Therefore, the diagnosis of early-stage T1D and effective treatments are important for the management of T1D patients. The imaging methods, such as magnetic resonance imaging (MRI) and so on, were applied in diagnosis of the early stage T1D and its development tracking. The addition of nanomaterials, especially in MRI, can improve the quality of T1D imaging for the diagnosis of T1D at early stage and cause less harm to human body. Meantime, among various treatment options, islet transplantation and immunotherapy are promising, effective, and less independent on insulin. The addition of nanotechnology can effectively reduce the attack of the immune system on drugs and cells, making the therapeutic drug more targeted in the body and prolonging the action time between drugs and cells, thus its addition makes these therapy safer and more efficient. In this review, we attempt to summarize the recent advances in the development of nanotechnology advances of T1D including using nanomaterials for the diagnosis and immunological imaging of T1D, protecting the transplanted islet cells from immune system attack, and delivering relevant molecules to targeted immunocytes. This article is categorized under: Diagnostic Tools > in vivo Nanodiagnostics and Imaging Therapeutic Approaches and Drug Discovery > Emerging Technologies Implantable Materials and Surgical Technologies > Nanotechnology in Tissue Repair and Replacement.
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Affiliation(s)
- Wen Pan
- Department of Endocrinology, The First Affiliated Hospital of USTC, Anhui Provincial Hospital, University of Science and Technology of China, Hefei, China.,CAS Key Lab of Soft Matter Chemistry, University of Science and Technology of China, Hefei, China.,Department of Chemistry, University of Science and Technology of China, Hefei, China
| | - Xueying Zheng
- Department of Endocrinology, The First Affiliated Hospital of USTC, Anhui Provincial Hospital, University of Science and Technology of China, Hefei, China
| | - Guiyuan Chen
- Department of Endocrinology, The First Affiliated Hospital of USTC, Anhui Provincial Hospital, University of Science and Technology of China, Hefei, China.,CAS Key Lab of Soft Matter Chemistry, University of Science and Technology of China, Hefei, China.,Department of Chemistry, University of Science and Technology of China, Hefei, China
| | - Lanhong Su
- Department of Endocrinology, The First Affiliated Hospital of USTC, Anhui Provincial Hospital, University of Science and Technology of China, Hefei, China.,CAS Key Lab of Soft Matter Chemistry, University of Science and Technology of China, Hefei, China.,Department of Chemistry, University of Science and Technology of China, Hefei, China
| | - Sihui Luo
- Department of Endocrinology, The First Affiliated Hospital of USTC, Anhui Provincial Hospital, University of Science and Technology of China, Hefei, China
| | - Wei Wang
- Department of Endocrinology, The First Affiliated Hospital of USTC, Anhui Provincial Hospital, University of Science and Technology of China, Hefei, China
| | - Shandong Ye
- Department of Endocrinology, The First Affiliated Hospital of USTC, Anhui Provincial Hospital, University of Science and Technology of China, Hefei, China
| | - Jianping Weng
- Department of Endocrinology, The First Affiliated Hospital of USTC, Anhui Provincial Hospital, University of Science and Technology of China, Hefei, China.,Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Yuanzeng Min
- Department of Endocrinology, The First Affiliated Hospital of USTC, Anhui Provincial Hospital, University of Science and Technology of China, Hefei, China.,CAS Key Lab of Soft Matter Chemistry, University of Science and Technology of China, Hefei, China.,Department of Chemistry, University of Science and Technology of China, Hefei, China.,Department of Bio-X Interdisciplinary Science at Hefei National Laboratory (HFNL) for Physical Science at the Microscale, University of Science and Technology of China, Hefei, China
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