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Tan C, xiao Y, Liu T, Chen S, Zhou J, Zhang S, Hu Y, Wu A, Li C. Development of multi-epitope mRNA vaccine against Clostridioides difficile using reverse vaccinology and immunoinformatics approaches. Synth Syst Biotechnol 2024; 9:667-683. [PMID: 38817826 PMCID: PMC11137598 DOI: 10.1016/j.synbio.2024.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 04/28/2024] [Accepted: 05/15/2024] [Indexed: 06/01/2024] Open
Abstract
Clostridioides difficile (C. difficile), as the major pathogen of diarrhea in healthcare settings, has become increasingly prevalent within community populations, resulting in significant morbidity and mortality. However, the therapeutic options for Clostridioides difficile infection (CDI) remain limited, and as of now, no authorized vaccine is available to combat this disease. Therefore, the development of a novel vaccine against C. difficile is of paramount importance. In our study, the complete proteome sequences of 118 strains of C. difficile were downloaded and analyzed. We found four antigenic proteins that were highly conserved and can be used for epitope identification. We designed two vaccines, WLcd1 and WLcd2, that contain the ideal T-cell and B-cell epitopes, adjuvants, and the pan HLA DR-binding epitope (PADRE) sequences. The biophysical and chemical assessments of these vaccine candidates indicated that they were suitable for immunogenic applications. Molecular docking analyses revealed that WLcd1 bonded with higher affinity to Toll-like receptors (TLRs) than WLcd2. Furthermore, molecular dynamics (MD) simulations, performed using Gmx_MMPBSA v1.56, confirmed the binding stability of WLcd1 with TLR2 and TLR4. The preliminary findings suggested that this multi-epitope vaccine could be a promising candidate for protection against CDI; however, experimental studies are necessary to confirm these predictions.
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Affiliation(s)
- Caixia Tan
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, Hunan Province, 410008, China
- National Clinical Research Center for Geriatric Disorders (XiangYa Hospital), Changsha, Hunan Province, 410008, China
| | - Yuanyuan xiao
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, Hunan Province, 410008, China
- National Clinical Research Center for Geriatric Disorders (XiangYa Hospital), Changsha, Hunan Province, 410008, China
| | - Ting Liu
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, Hunan Province, 410008, China
- National Clinical Research Center for Geriatric Disorders (XiangYa Hospital), Changsha, Hunan Province, 410008, China
| | - Siyao Chen
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, Hunan Province, 410008, China
- National Clinical Research Center for Geriatric Disorders (XiangYa Hospital), Changsha, Hunan Province, 410008, China
| | - Juan Zhou
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, Hunan Province, 410008, China
- National Clinical Research Center for Geriatric Disorders (XiangYa Hospital), Changsha, Hunan Province, 410008, China
| | - Sisi Zhang
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, Hunan Province, 410008, China
- National Clinical Research Center for Geriatric Disorders (XiangYa Hospital), Changsha, Hunan Province, 410008, China
| | - Yiran Hu
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, Hunan Province, 410008, China
- National Clinical Research Center for Geriatric Disorders (XiangYa Hospital), Changsha, Hunan Province, 410008, China
| | - Anhua Wu
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, Hunan Province, 410008, China
- National Clinical Research Center for Geriatric Disorders (XiangYa Hospital), Changsha, Hunan Province, 410008, China
| | - Chunhui Li
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, Hunan Province, 410008, China
- National Clinical Research Center for Geriatric Disorders (XiangYa Hospital), Changsha, Hunan Province, 410008, China
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2
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Shi J, Yin W, Chen W. Mathematical models of TCR initial triggering. Front Immunol 2024; 15:1411614. [PMID: 39091495 PMCID: PMC11291225 DOI: 10.3389/fimmu.2024.1411614] [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: 04/03/2024] [Accepted: 07/05/2024] [Indexed: 08/04/2024] Open
Abstract
T cell receptors (TCRs) play crucial roles in regulating T cell response by rapidly and accurately recognizing foreign and non-self antigens. The process involves multiple molecules and regulatory mechanisms, forming a complex network to achieve effective antigen recognition. Mathematical modeling techniques can help unravel the intricate network of TCR signaling and identify key regulators that govern it. In this review, we introduce and briefly discuss relevant mathematical models of TCR initial triggering, with a focus on kinetic proofreading (KPR) models with different modified structures. We compare the topology structures, biological hypotheses, parameter choices, and simulation performance of each model, and summarize the advantages and limitations of them. Further studies on TCR modeling design, aiming for an optimized balance of specificity and sensitivity, are expected to contribute to the development of new therapeutic strategies.
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Affiliation(s)
- Jiawei Shi
- Department of Cardiology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory for Biomedical Engineering of the Ministry of Education, College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, China
| | - Weiwei Yin
- Department of Cardiology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Zhejiang University, Hangzhou, China
| | - Wei Chen
- Department of Cardiology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory for Biomedical Engineering of the Ministry of Education, College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, China
- Department of Cell Biology, School of Medicine, Zhejiang University, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
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3
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Millan AJ, Allain V, Nayak I, Aguilar OA, Arakawa-Hoyt JS, Ureno G, Rothrock AG, Shemesh A, Eyquem J, Das J, Lanier LL. Spleen Tyrosine Kinase (SYK) negatively regulates ITAM-mediated human NK cell signaling and CD19-CAR NK cell efficacy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.09.602676. [PMID: 39026749 PMCID: PMC11257556 DOI: 10.1101/2024.07.09.602676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
NK cells express activating receptors that signal through ITAM-bearing adapter proteins. The phosphorylation of each ITAM creates binding sites for SYK and ZAP70 protein tyrosine kinases to propagate downstream signaling including the induction ofCa 2 + influx. While all immature and mature human NK cells co-express SYK and ZAP70, clonally driven memory or adaptive NK cells can methylate SYK genes and signaling is mediated exclusively using ZAP70. Here, we examined the role of SYK and ZAP70 in a clonal human NK cell line KHYG1 by CRISPR-based deletion using a combination of experiments and mechanistic computational modeling. Elimination of SYK resulted in more robustCa + + influx after cross-linking of the CD16 and NKp30 receptors and enhanced phosphorylation of downstream proteins, whereas ZAP70 deletion diminished these responses. By contrast, ZAP70 depletion increased proliferation of the NK cells. As immature T cells express both SYK and ZAP70 but mature T cells often express only ZAP70, we transduced the human Jurkat cell line with SYK and found that expression of SYK increased proliferation but diminished TCR-inducedCa 2 + flux and activation. We performed transcriptional analysis of the matched sets of variant Jurkat and KHYG1 cells and observed profound alterations caused by SYK expression. As depletion of SYK in NK cells increased their activation, primary human NK cells were transduced with a CD19-targeting CAR and were CRISPR edited to ablate SYK or ZAP70. Deletion of SYK resulted in more robust cytotoxic activity and cytokine production, providing a new therapeutic strategy of NK cell engineering for cancer immunotherapy.
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Affiliation(s)
- Alberto J. Millan
- Department of Microbiology and Immunology and the Parker Institute for Cancer Immunotherapy, University of California-San Francisco, San Francisco, CA, USA
| | - Vincent Allain
- Department of Medicine, University of California-San Francisco, San Francisco, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Université Paris Cité, INSERM UMR976, Hôpital Saint-Louis, Paris, France
| | - Indrani Nayak
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Biomedical Sciences Graduate Program, Department of Pediatrics, Pelotonia Institute for Immuno-Oncology, College of Medicine, The Ohio State University, Columbus OH
| | - Oscar A. Aguilar
- Department of Microbiology and Immunology and the Parker Institute for Cancer Immunotherapy, University of California-San Francisco, San Francisco, CA, USA
| | - Janice S. Arakawa-Hoyt
- Department of Microbiology and Immunology and the Parker Institute for Cancer Immunotherapy, University of California-San Francisco, San Francisco, CA, USA
| | - Gabriella Ureno
- Department of Microbiology and Immunology and the Parker Institute for Cancer Immunotherapy, University of California-San Francisco, San Francisco, CA, USA
| | - Allison Grace Rothrock
- Department of Medicine, University of California-San Francisco, San Francisco, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Avishai Shemesh
- Department of Microbiology and Immunology and the Parker Institute for Cancer Immunotherapy, University of California-San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California-San Francisco, San Francisco, CA, USA
| | - Justin Eyquem
- Department of Medicine, University of California-San Francisco, San Francisco, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Jayajit Das
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Biomedical Sciences Graduate Program, Department of Pediatrics, Pelotonia Institute for Immuno-Oncology, College of Medicine, The Ohio State University, Columbus OH
| | - Lewis L. Lanier
- Department of Microbiology and Immunology and the Parker Institute for Cancer Immunotherapy, University of California-San Francisco, San Francisco, CA, USA
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Balasenthilkumaran NV, Whitesell JC, Pyle L, Friedman RS, Kravets V. Network approach reveals preferential T-cell and macrophage association with α-linked β-cells in early stage of insulitis in NOD mice. FRONTIERS IN NETWORK PHYSIOLOGY 2024; 4:1393397. [PMID: 38979061 PMCID: PMC11228247 DOI: 10.3389/fnetp.2024.1393397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 05/21/2024] [Indexed: 07/10/2024]
Abstract
One of the challenges in studying islet inflammation-insulitis-is that it is a transient phenomenon. Traditional reporting of the insulitis progression is based on cumulative, donor-averaged values of leucocyte density in the vicinity of pancreatic islets, that hinder intra- and inter-islet heterogeneity of disease progression. Here, we aimed to understand why insulitis is non-uniform, often with peri-insulitis lesions formed on one side of an islet. To achieve this, we demonstrated the applicability of network theory in detangling intra-islet multi-cellular interactions during insulitis. Specifically, we asked the question "What is unique about regions of the islet that interact with immune cells first". This study utilized the non-obese diabetic mouse model of type one diabetes and examined the interplay among α-, β-, T-cells, myeloid cells, and macrophages in pancreatic islets during the progression of insulitis. Disease evolution was tracked based on the T/β cell ratio in individual islets. In the early stage, we found that immune cells are preferentially interacting with α-cell-rich regions of an islet. At the islet periphery α-linked β-cells were found to be targeted significantly more compared to those without α-cell neighbors. Additionally, network analysis revealed increased T-myeloid, and T-macrophage interactions with all β-cells.
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Affiliation(s)
- Nirmala V. Balasenthilkumaran
- Department of Bioengineering, Jacobs School of Engineering, University of California San Diego, San Diego, CA, United States
| | - Jennifer C. Whitesell
- Department of Immunology and Microbiology, School of Medicine, Barbara Davis Center for Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Laura Pyle
- Department of Pediatrics, University of Colorado School of Medicine, Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO, United States
| | - Rachel S. Friedman
- Department of Immunology and Microbiology, School of Medicine, Barbara Davis Center for Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Vira Kravets
- Department of Bioengineering, Jacobs School of Engineering, University of California San Diego, San Diego, CA, United States
- Department of Pediatrics, School of Medicine, University of California San Diego, San Diego, CA, United States
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5
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Menon AP, Villanueva H, Meraviglia-Crivelli D, van Santen HM, Hellmeier J, Zheleva A, Nonateli F, Peters T, Wachsmann TL, Hernandez-Rueda M, Huppa JB, Schütz GJ, Sevcsik E, Moreno B, Pastor F. CD3 aptamers promote expansion and persistence of tumor-reactive T cells for adoptive T cell therapy in cancer. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102198. [PMID: 38745854 PMCID: PMC11091522 DOI: 10.1016/j.omtn.2024.102198] [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: 09/14/2023] [Accepted: 04/21/2024] [Indexed: 05/16/2024]
Abstract
The CD3/T cell receptor (TCR) complex is responsible for antigen-specific pathogen recognition by T cells, and initiates the signaling cascade necessary for activation of effector functions. CD3 agonistic antibodies are commonly used to expand T lymphocytes in a wide range of clinical applications, including in adoptive T cell therapy for cancer patients. A major drawback of expanding T cell populations ex vivo using CD3 agonistic antibodies is that they expand and activate T cells independent of their TCR antigen specificity. Therapeutic agents that facilitate expansion of T cells in an antigen-specific manner and reduce their threshold of T cell activation are therefore of great interest for adoptive T cell therapy protocols. To identify CD3-specific T cell agonists, several RNA aptamers were selected against CD3 using Systematic Evolution of Ligands by EXponential enrichment combined with high-throughput sequencing. The extent and specificity of aptamer binding to target CD3 were assessed through surface plasma resonance, P32 double-filter assays, and flow cytometry. Aptamer-mediated modulation of the threshold of T cell activation was observed in vitro and in preclinical transgenic TCR mouse models. The aptamers improved efficacy and persistence of adoptive T cell therapy by low-affinity TCR-reactive T lymphocytes in melanoma-bearing mice. Thus, CD3-specific aptamers can be applied as therapeutic agents which facilitate the expansion of tumor-reactive T lymphocytes while conserving their tumor specificity. Furthermore, selected CD3 aptamers also exhibit cross-reactivity to human CD3, expanding their potential for clinical translation and application in the future.
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Affiliation(s)
- Ashwathi Puravankara Menon
- Molecular Therapeutics Program, Center for Applied Medical Research, CIMA, University of Navarra, 31008 Pamplona, Spain
| | - Helena Villanueva
- Molecular Therapeutics Program, Center for Applied Medical Research, CIMA, University of Navarra, 31008 Pamplona, Spain
| | - Daniel Meraviglia-Crivelli
- Molecular Therapeutics Program, Center for Applied Medical Research, CIMA, University of Navarra, 31008 Pamplona, Spain
| | - Hisse M. van Santen
- Immune System Development and Function Unit, Centro Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas/Universidad Autónoma de Madrid (CSIC/UAM), 28049 Madrid, Spain
| | - Joschka Hellmeier
- Institute of Applied Physics, TU Wien, Lehargasse 6, 1060 Vienna, Austria
| | - Angelina Zheleva
- Molecular Therapeutics Program, Center for Applied Medical Research, CIMA, University of Navarra, 31008 Pamplona, Spain
| | - Francesca Nonateli
- Molecular Therapeutics Program, Center for Applied Medical Research, CIMA, University of Navarra, 31008 Pamplona, Spain
| | - Timo Peters
- Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology, Immunology, Medical University of Vienna, 1090 Vienna, Austria
| | | | - Mercedes Hernandez-Rueda
- Molecular Therapeutics Program, Center for Applied Medical Research, CIMA, University of Navarra, 31008 Pamplona, Spain
| | - Johannes B. Huppa
- Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology, Immunology, Medical University of Vienna, 1090 Vienna, Austria
| | - Gerhard J. Schütz
- Institute of Applied Physics, TU Wien, Lehargasse 6, 1060 Vienna, Austria
| | - Eva Sevcsik
- Institute of Applied Physics, TU Wien, Lehargasse 6, 1060 Vienna, Austria
| | - Beatriz Moreno
- Molecular Therapeutics Program, Center for Applied Medical Research, CIMA, University of Navarra, 31008 Pamplona, Spain
| | - Fernando Pastor
- Molecular Therapeutics Program, Center for Applied Medical Research, CIMA, University of Navarra, 31008 Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
- Spanish Center for Biomedical Research Network in Oncology (CIBERONC), 28029 Madrid, Spain
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6
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Chen X, Hu G, Ning D, Wang D. Exploring gut microbiota's role in rheumatic valve disease: insights from a Mendelian randomization study and mediation analysis. Front Immunol 2024; 15:1362753. [PMID: 38895120 PMCID: PMC11183100 DOI: 10.3389/fimmu.2024.1362753] [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: 12/28/2023] [Accepted: 05/16/2024] [Indexed: 06/21/2024] Open
Abstract
Background Investigating the relationship between gut microbiota and Rheumatic Valve Disease (RVD) is crucial for understanding the disease's etiology and developing effective interventions. Our study adopts a novel approach to examine the potential causal connections between these factors. Methods Utilizing a two-sample Mendelian Randomization (MR) framework, we incorporated a multi-variable MR (MVMR) strategy to assess the mediatory mechanisms involved. This approach involved analyzing data from the MiBioGen consortium for gut microbiota and the FinnGen for RVD, among other sources. Instrumental variables (IVs) were carefully selected based on rigorous MR principles, and statistical analysis was conducted using bidirectional two-sample MR, such as inverse variance-weighted (IVW), weighted median, MR-Egger regression and MR Steiger Test methods. The MR-PRESSO strategy was employed for outlier detection, and MVMR was used to untangle the complex relationships between multiple microbiota and RVD. Results Our analysis highlighted several gut microbiota classes and families with potential protective effects against RVD, including Lentisphaerae, Alphaproteobacteria, and Streptococcaceae. In contrast, certain genera, such as Eubacterium eligens and Odoribacter, were identified as potential risk factors. The MVMR analysis revealed significant mediation effects of various immune cell traits and biomarkers, such as CD4-CD8- T cells, CD3 on Terminally Differentiated CD8+ T cell and Pentraxin-related protein PTX, elucidating the complex pathways linking gut microbiota to RVD. Conclusion This study underscores the intricate and potentially causal relationship between gut microbiota and RVD, mediated through a range of immune and hormonal factors. The use of MVMR in our methodological approach provides a more comprehensive understanding of these interactions, highlighting the gut microbiota's potential as therapeutic targets in RVD management. Our findings pave the way for further research to explore these complex relationships and develop targeted interventions for RVD.
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Affiliation(s)
- Xiwei Chen
- The Hospital Affiliated to Medical School of Yangzhou University (Taizhou People's Hospital), Taizhou, Jiangsu, China
| | - Guangwen Hu
- The Hospital Affiliated to Medical School of Yangzhou University (Taizhou People's Hospital), Taizhou, Jiangsu, China
| | - Dong Ning
- Department of Physiology, Human Biology Building, School of Medicine, National University of Ireland (NUI), Galway, Ireland
| | - Daxin Wang
- The Hospital Affiliated to Medical School of Yangzhou University (Taizhou People's Hospital), Taizhou, Jiangsu, China
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Notti RQ, Yi F, Heissel S, Bush MW, Molvi Z, Das P, Molina H, Klebanoff CA, Walz T. The resting and ligand-bound states of the membrane-embedded human T-cell receptor-CD3 complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.22.554360. [PMID: 37662363 PMCID: PMC10473723 DOI: 10.1101/2023.08.22.554360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
The T-cell receptor (TCR) is central to the ligand-dependent activation of T lymphocytes and as such orchestrates both adaptive and pathologic immune processes. However, major questions remain regarding the structure and function of the human TCR. Here, we present cryogenic electron microscopy structures for the unliganded and HLA-bound human TCR-CD3 complex in nanodiscs that provide a native-like lipid environment. The unliganded structures reveal two related conformations that are distinct from its structure in detergent. These new "closed and compacted" conformations afford insights into the interactions between the TCR-CD3 and the membrane, including conserved surface patches that make extensive outer leaflet contact, and suggest novel conformational regulation by glycans. We show that the closed/compacted conformations, not the extended one previously reported in detergent, represent the unliganded resting state for the TCR-CD3 in vivo, underscoring the importance of structural interrogation of membrane proteins in native-like environments. By contrast, the structure of the HLA-bound complex in nanodiscs is in an open and extended conformation, showing that physiologic ligand binding is sufficient to induce substantial conformational change in the TCR-CD3 complex. We use conformation-locking disulfide mutants to show that ectodomain opening is necessary for maximal ligand-dependent TCR-CD3 activation, demonstrating that TCR-intrinsic conformational change is necessary for full TCR-CD3 activation and opening numerous avenues for immunoreceptor engineering.
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8
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Mohan N, Ayinde S, Peng H, Dutta S, Shen Y, Falkowski VM, Biel TG, Ju T, Wu WJ. Structural and functional characterization of IgG- and non-IgG-based T-cell-engaging bispecific antibodies. Front Immunol 2024; 15:1376096. [PMID: 38863707 PMCID: PMC11165055 DOI: 10.3389/fimmu.2024.1376096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 05/06/2024] [Indexed: 06/13/2024] Open
Abstract
Bispecific T-cell-engaging antibodies are a growing class of therapeutics with numerous molecules being tested in clinical trials and, currently, seven of them have received market approval. They are structurally complex and function as adaptors to redirect the cytotoxicity of T cells to kill tumor cells. T-cell-engaging bispecific antibodies can be generally divided into two categories: IgG/IgG-like and non-IgG-like formats. Different formats may have different intrinsic potencies and physiochemical properties, and comprehensive studies are needed to gain a better understanding of how the differences in formats impact on structural and functional characteristics. In this study, we designed and generated bispecific T-cell-engaging antibodies with IgG-like (DVD-Ig) and non-IgG (BiTE) formats. Both target the same pair of antigens (EGFR and CD3) to minimize the possible influence of targets on functional characterization. We performed a side-by-side comparison to assess differences in the physiochemical and biological properties of these two bispecific T-cell-engaging antibodies using a variety of breast and ovarian cancer cell-based functional assays to delineate the structural-functional relationships and anti-tumor activities/potency. We found that the Fc portion of T-cell-engaging bispecific antibodies can significantly impact antigen binding activity, potency, and stability in addition to eliciting different mechanisms of action that contribute the killing of cancer cells.
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Affiliation(s)
- Nishant Mohan
- Office of Pharmaceutical Quality Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, United States
| | - Safiat Ayinde
- Office of Pharmaceutical Quality Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, United States
| | - Hanjing Peng
- Office of Pharmaceutical Manufacturing Assessment, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, United States
| | - Shraboni Dutta
- Office of Pharmaceutical Quality Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, United States
| | - Yi Shen
- Office of Pharmaceutical Quality Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, United States
| | - Vincent M. Falkowski
- Office of Pharmaceutical Quality Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, United States
| | - Thomas G. Biel
- Office of Pharmaceutical Quality Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, United States
| | - Tongzhong Ju
- Office of Pharmaceutical Quality Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, United States
| | - Wen Jin Wu
- Office of Pharmaceutical Quality Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, United States
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9
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Balasenthilkumaran NV, Whitesell JC, Pyle L, Friedman R, Kravets V. Network approach reveals preferential T-cell and macrophage association with α-linked β-cells in early stage of insulitis in NOD mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.06.592831. [PMID: 38766090 PMCID: PMC11100702 DOI: 10.1101/2024.05.06.592831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
One of the challenges in studying islet inflammation - insulitis - is that it is a transient phenomenon. Traditional reporting of the insulitis progression is based on cumulative, donor-averaged values of leucocyte density in the vicinity of pancreatic islets, that hinders intra- and inter-islet heterogeneity of disease progression. Here, we aimed to understand why insulitis is non-uniform, often with peri-insulitis lesions formed on one side of an islet. To achieve this, we demonstrated applicability of network theory in detangling intra-islet multi-cellular interactions during insulitis. Specifically, we asked the question "what is unique about regions of the islet which interact with immune cells first". This study utilized the non-obese diabetic mouse model of type one diabetes and examined the interplay among α-, β-, T-cells, myeloid cells, and macrophages in pancreatic islets during the progression of insulitis. Disease evolution was tracked based on T/β cell ratio in individual islets. In the early stage, we found that immune cells are preferentially interacting with α-cell-rich regions of an islet. At the islet periphery α-linked β-cells were found to be targeted significantly more compared to those without α-cell neighbors. Additionally, network analysis revealed increased T-myeloid, and T-macrophage interactions with all β-cells.
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10
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Gao Y, Kennelly JP, Xiao X, Whang E, Ferrari A, Bedard AH, Mack JJ, Nguyen AH, Weston T, Uchiyama LF, Lee MS, Young SG, Bensinger SJ, Tontonoz P. T cell cholesterol transport is a metabolic checkpoint that links intestinal immune responses to dietary lipid absorption. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.08.584164. [PMID: 38559079 PMCID: PMC10979874 DOI: 10.1101/2024.03.08.584164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The intrinsic pathways that control membrane organization in immune cells and the impact of such pathways on cellular function are not well defined. Here we report that the non-vesicular cholesterol transporter Aster-A links plasma membrane (PM) cholesterol availability in T cells to immune signaling and systemic metabolism. Aster-A is recruited to the PM during T-cell receptor (TCR) activation, where it facilitates the removal of newly generated "accessible" membrane cholesterol. Loss of Aster-A leads to excess PM cholesterol accumulation, resulting in enhanced TCR nano-clustering and signaling, and Th17 cytokine production. Finally, we show that the mucosal Th17 response is restrained by PM cholesterol remodeling. Ablation of Aster-A in T cells leads to enhanced IL-22 production, reduced intestinal fatty acid absorption, and resistance to diet-induced obesity. These findings delineate a multi-tiered regulatory scheme linking immune cell lipid flux to nutrient absorption and systemic physiology.
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11
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Liang W, Li K, Gao H, Li K, Zhang J, Zhang Q, Jiao X, Yang J, Wei X. Full T-cell activation and function in teleosts require collaboration of first and co-stimulatory signals. Zool Res 2024; 45:13-24. [PMID: 38114429 PMCID: PMC10839663 DOI: 10.24272/j.issn.2095-8137.2023.053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 09/08/2023] [Indexed: 12/21/2023] Open
Abstract
Mammalian T-cell responses require synergism between the first signal and co-stimulatory signal. However, whether and how dual signaling regulates the T-cell response in early vertebrates remains unknown. In the present study, we discovered that the Nile tilapia ( Oreochromis niloticus) encodes key components of the LAT signalosome, namely, LAT, ITK, GRB2, VAV1, SLP-76, GADS, and PLC-γ1. These components are evolutionarily conserved, and CD3ε mAb-induced T-cell activation markedly increased their expression. Additionally, at least ITK, GRB2, and VAV1 were found to interact with LAT for signalosome formation. Downstream of the first signal, the NF-κB, MAPK/ERK, and PI3K-AKT pathways were activated upon CD3ε mAb stimulation. Furthermore, treatment of lymphocytes with CD28 mAbs triggered the AKT-mTORC1 pathway downstream of the co-stimulatory signal. Combined CD3ε and CD28 mAb stimulation enhanced ERK1/2 and S6 phosphorylation and elevated NFAT1, c-Fos, IL-2, CD122, and CD44 expression, thereby signifying T-cell activation. Moreover, rather than relying on the first or co-stimulatory signal alone, both signals were required for T-cell proliferation. Full T-cell activation was accompanied by marked apoptosis and cytotoxic responses. These findings suggest that tilapia relies on dual signaling to maintain an optimal T-cell response, providing a novel perspective for understanding the evolution of the adaptive immune system.
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Affiliation(s)
- Wei Liang
- State Key Laboratory of Estuarine and Coastal Research, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Kang Li
- State Key Laboratory of Estuarine and Coastal Research, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Haiyou Gao
- State Key Laboratory of Estuarine and Coastal Research, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Kunming Li
- State Key Laboratory of Estuarine and Coastal Research, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jiansong Zhang
- State Key Laboratory of Estuarine and Coastal Research, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Qian Zhang
- State Key Laboratory of Estuarine and Coastal Research, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Xinying Jiao
- State Key Laboratory of Estuarine and Coastal Research, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jialong Yang
- State Key Laboratory of Estuarine and Coastal Research, School of Life Sciences, East China Normal University, Shanghai 200241, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China. E-mail:
| | - Xiumei Wei
- State Key Laboratory of Estuarine and Coastal Research, School of Life Sciences, East China Normal University, Shanghai 200241, China. E-mail:
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12
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Lee HN, Lee SE, Inn KS, Seong J. Optical sensing and control of T cell signaling pathways. Front Physiol 2024; 14:1321996. [PMID: 38269062 PMCID: PMC10806162 DOI: 10.3389/fphys.2023.1321996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 12/20/2023] [Indexed: 01/26/2024] Open
Abstract
T cells regulate adaptive immune responses through complex signaling pathways mediated by T cell receptor (TCR). The functional domains of the TCR are combined with specific antibodies for the development of chimeric antigen receptor (CAR) T cell therapy. In this review, we first overview current understanding on the T cell signaling pathways as well as traditional methods that have been widely used for the T cell study. These methods, however, are still limited to investigating dynamic molecular events with spatiotemporal resolutions. Therefore, genetically encoded biosensors and optogenetic tools have been developed to study dynamic T cell signaling pathways in live cells. We review these cutting-edge technologies that revealed dynamic and complex molecular mechanisms at each stage of T cell signaling pathways. They have been primarily applied to the study of dynamic molecular events in TCR signaling, and they will further aid in understanding the mechanisms of CAR activation and function. Therefore, genetically encoded biosensors and optogenetic tools offer powerful tools for enhancing our understanding of signaling mechanisms in T cells and CAR-T cells.
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Affiliation(s)
- Hae Nim Lee
- Brain Science Institute, Korea Institute of Science and Technoloy, Seoul, Republic of Korea
- Department of Converging Science and Technology, Kyung Hee University, Seoul, Republic of Korea
| | - Seung Eun Lee
- Department of Pharmacology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Kyung-Soo Inn
- Department of Converging Science and Technology, Kyung Hee University, Seoul, Republic of Korea
| | - Jihye Seong
- Department of Pharmacology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Wide River Institute of Immunology, Seoul National University, Hongcheon, Republic of Korea
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13
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Chang-Gonzalez AC, Mallis RJ, Lang MJ, Reinherz EL, Hwang W. Asymmetric framework motion of TCRαβ controls load-dependent peptide discrimination. eLife 2024; 13:e91881. [PMID: 38167271 PMCID: PMC10869138 DOI: 10.7554/elife.91881] [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: 08/14/2023] [Accepted: 12/21/2023] [Indexed: 01/05/2024] Open
Abstract
Mechanical force is critical for the interaction between an αβ T cell receptor (TCR) and a peptide-bound major histocompatibility complex (pMHC) molecule to initiate productive T-cell activation. However, the underlying mechanism remains unclear. We use all-atom molecular dynamics simulations to examine the A6 TCR bound to HLA-A*02:01 presenting agonist or antagonist peptides under different extensions to simulate the effects of applied load on the complex, elucidating their divergent biological responses. We found that TCR α and β chains move asymmetrically, which impacts the interface with pMHC, in particular the peptide-sensing CDR3 loops. For the wild-type agonist, the complex stabilizes in a load-dependent manner while antagonists destabilize it. Simulations of the Cβ FG-loop deletion, which reduces the catch bond response, and simulations with in silico mutant peptides further support the observed behaviors. The present results highlight the combined role of interdomain motion, fluctuating forces, and interfacial contacts in determining the mechanical response and fine peptide discrimination by a TCR, thereby resolving the conundrum of nearly identical crystal structures of TCRαβ-pMHC agonist and antagonist complexes.
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Affiliation(s)
- Ana C Chang-Gonzalez
- Department of Biomedical Engineering, Texas A&M UniversityCollege StationUnited States
| | - Robert J Mallis
- Department of Dermatology, Harvard Medical SchoolBostonUnited States
- Laboratory of Immunobiology, Dana-Farber Cancer InstituteBostonUnited States
- Department of Medicine, Oncology, Dana-Farber Cancer InstituteBostonUnited States
| | - Matthew J Lang
- Department of Chemistry and Biomolecular Engineering, Vanderbilt UniversityNashvilleUnited States
- Department of Molecular Physiology and Biophysics, Vanderbilt UniversityNashvilleUnited States
| | - Ellis L Reinherz
- Laboratory of Immunobiology, Dana-Farber Cancer InstituteBostonUnited States
- Department of Medicine, Oncology, Dana-Farber Cancer InstituteBostonUnited States
- Department of Medicine, Harvard Medical SchoolBostonUnited States
| | - Wonmuk Hwang
- Department of Biomedical Engineering, Texas A&M UniversityCollege StationUnited States
- Department of Materials Science & Engineering, Texas A&M UniversityCollege StationUnited States
- Department of Physics & Astronomy, Texas A&M UniversityCollege StationUnited States
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14
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Takayanagi SI, Wang B, Hasegawa S, Nishikawa S, Fukumoto K, Nakano K, Chuganji S, Kato Y, Kamibayashi S, Minagawa A, Kunisato A, Nozawa H, Kaneko S. Mini-TCRs: Truncated T cell receptors to generate T cells from induced pluripotent stem cells. Mol Ther Methods Clin Dev 2023; 31:101109. [PMID: 37822720 PMCID: PMC10562677 DOI: 10.1016/j.omtm.2023.101109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/13/2023] [Indexed: 10/13/2023]
Abstract
Allogeneic T cell platforms utilizing induced pluripotent stem cell (iPSC) technology exhibit significant promise for the facilitation of adoptive immunotherapies. While mature T cell receptor (TCR) signaling plays a crucial role in generating T cells from iPSCs, the introduction of exogenous mature TCR genes carries a potential risk of causing graft-versus-host disease (GvHD). In this study, we present the development of truncated TCRα and TCRβ chains, termed mini-TCRs, which lack variable domains responsible for recognizing human leukocyte antigen (HLA)-peptide complexes. We successfully induced cytotoxic T lymphocytes (CTLs) from iPSCs by employing mini-TCRs. Combinations of TCRα and TCRβ fragments were screened from mini-TCR libraries based on the surface localization of CD3 proteins and their ability to transduce T cell signaling. Consequently, mini-TCR-expressing iPSCs underwent physiological T cell development, progressing from the CD4 and CD8 double-positive stage to the CD8 single-positive stage. The resulting iPSC-derived CTLs exhibited comparable cytokine production and cytotoxicity in comparison to that of full-length TCR-expressing T lymphocytes when chimeric antigen receptors (CARs) were expressed. These findings demonstrate the potential of mini-TCR-carrying iPSCs as a versatile platform for CAR T cell therapy, offering a promising avenue for advancing adoptive immunotherapies.
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Affiliation(s)
- Shin-ichiro Takayanagi
- Kirin Central Research Institute, Kirin Holdings Company, Ltd., 26-1, Muraoka-Higashi 2, Fujisawa-shi, Kanagawa 251-8555, Japan
- Shin Kaneko Laboratory, Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Bo Wang
- Shin Kaneko Laboratory, Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
- Shinobi Therapeutics, Inc., 46-29 Yoshida-Shimo-Adachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Saki Hasegawa
- Kirin Central Research Institute, Kirin Holdings Company, Ltd., 26-1, Muraoka-Higashi 2, Fujisawa-shi, Kanagawa 251-8555, Japan
- Shin Kaneko Laboratory, Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Satoshi Nishikawa
- R&D Division, Kyowa Kirin Co. Ltd, 3-6-6 Asahi-machi, Machida-shi, Tokyo 194-8533, Japan
| | - Ken Fukumoto
- Kirin Central Research Institute, Kirin Holdings Company, Ltd., 26-1, Muraoka-Higashi 2, Fujisawa-shi, Kanagawa 251-8555, Japan
- Shin Kaneko Laboratory, Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Kohei Nakano
- Shinobi Therapeutics, Inc., 46-29 Yoshida-Shimo-Adachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Sayaka Chuganji
- Kirin Central Research Institute, Kirin Holdings Company, Ltd., 26-1, Muraoka-Higashi 2, Fujisawa-shi, Kanagawa 251-8555, Japan
- Shin Kaneko Laboratory, Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Yuya Kato
- Kirin Central Research Institute, Kirin Holdings Company, Ltd., 26-1, Muraoka-Higashi 2, Fujisawa-shi, Kanagawa 251-8555, Japan
| | - Sanae Kamibayashi
- Shin Kaneko Laboratory, Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Atsutaka Minagawa
- Shin Kaneko Laboratory, Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Atsushi Kunisato
- Kirin Central Research Institute, Kirin Holdings Company, Ltd., 26-1, Muraoka-Higashi 2, Fujisawa-shi, Kanagawa 251-8555, Japan
| | - Hajime Nozawa
- Kirin Central Research Institute, Kirin Holdings Company, Ltd., 26-1, Muraoka-Higashi 2, Fujisawa-shi, Kanagawa 251-8555, Japan
| | - Shin Kaneko
- Shin Kaneko Laboratory, Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
- Shinobi Therapeutics, Inc., 46-29 Yoshida-Shimo-Adachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
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15
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Wu J, Lu Z, Zhao H, Lu M, Gao Q, Che N, Wang J, Ma T. The expanding Pandora's toolbox of CD8 +T cell: from transcriptional control to metabolic firing. J Transl Med 2023; 21:905. [PMID: 38082437 PMCID: PMC10714647 DOI: 10.1186/s12967-023-04775-3] [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: 08/17/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
CD8+ T cells are the executor in adaptive immune response, especially in anti-tumor immunity. They are the subset immune cells that are of high plasticity and multifunction. Their development, differentiation, activation and metabolism are delicately regulated by multiple factors. Stimuli from the internal and external environment could remodel CD8+ T cells, and correspondingly they will also make adjustments to the microenvironmental changes. Here we describe the most updated progresses in CD8+ T biology from transcriptional regulation to metabolism mechanisms, and also their interactions with the microenvironment, especially in cancer and immunotherapy. The expanding landscape of CD8+ T cell biology and discovery of potential targets to regulate CD8+ T cells will provide new viewpoints for clinical immunotherapy.
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Affiliation(s)
- Jinghong Wu
- Cancer Research Center, Beijing Chest Hospital, Beijing Tuberculosis and Thoracic Tumor Research Institute, Capital Medical University, Beijing, 101149, China
| | - Zhendong Lu
- Cancer Research Center, Beijing Chest Hospital, Beijing Tuberculosis and Thoracic Tumor Research Institute, Capital Medical University, Beijing, 101149, China
| | - Hong Zhao
- Department of Pathology, Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, China
| | - Mingjun Lu
- Cancer Research Center, Beijing Chest Hospital, Beijing Tuberculosis and Thoracic Tumor Research Institute, Capital Medical University, Beijing, 101149, China
| | - Qing Gao
- Cancer Research Center, Beijing Chest Hospital, Beijing Tuberculosis and Thoracic Tumor Research Institute, Capital Medical University, Beijing, 101149, China
| | - Nanying Che
- Department of Pathology, Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, China
| | - Jinghui Wang
- Cancer Research Center, Beijing Chest Hospital, Beijing Tuberculosis and Thoracic Tumor Research Institute, Capital Medical University, Beijing, 101149, China.
| | - Teng Ma
- Cancer Research Center, Beijing Chest Hospital, Beijing Tuberculosis and Thoracic Tumor Research Institute, Capital Medical University, Beijing, 101149, China.
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16
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Dumonteil E, Tu W, Desale H, Goff K, Marx P, Ortega-Lopez J, Herrera C. Immunoglobin and T cell receptor repertoire changes induced by a prototype vaccine against Chagas disease in naïve rhesus macaques. RESEARCH SQUARE 2023:rs.3.rs-3453582. [PMID: 37961272 PMCID: PMC10635379 DOI: 10.21203/rs.3.rs-3453582/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
A vaccine against Trypanosoma cruzi, the agent of Chagas disease, would be an excellent additional tool for disease control. A recombinant vaccine based on Tc24 and TSA1 parasite antigens was found to be safe and immunogenic in naïve macaques. Here we performed a transcriptomic analysis of PBMC responses to vaccination, to shed light on the immunogenicity of this vaccine and guide the optimization of doses and formulation. RNA-sequencing analysis indicated a clear transcriptomic response of PBMCs from macaques after three vaccine doses, with the up-regulation of several immune cell activation pathways and a broad non-polarized immune profile. Analysis of the IgG repertoire showed that it had a rapid turnover with novel IgGs produced following each vaccine dose, while the TCR repertoire presented several persisting clones that were expanded after each vaccine dose. These data suggest that three vaccine doses may be needed for optimum immunogenecity and support the further evaluation of the protective efficacy of this vaccine.
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17
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Malviya M, Aretz Z, Molvi Z, Lee J, Pierre S, Wallisch P, Dao T, Scheinberg DA. Challenges and solutions for therapeutic TCR-based agents. Immunol Rev 2023; 320:58-82. [PMID: 37455333 PMCID: PMC11141734 DOI: 10.1111/imr.13233] [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: 05/30/2023] [Accepted: 06/18/2023] [Indexed: 07/18/2023]
Abstract
Recent development of methods to discover and engineer therapeutic T-cell receptors (TCRs) or antibody mimics of TCRs, and to understand their immunology and pharmacology, lag two decades behind therapeutic antibodies. Yet we have every expectation that TCR-based agents will be similarly important contributors to the treatment of a variety of medical conditions, especially cancers. TCR engineered cells, soluble TCRs and their derivatives, TCR-mimic antibodies, and TCR-based CAR T cells promise the possibility of highly specific drugs that can expand the scope of immunologic agents to recognize intracellular targets, including mutated proteins and undruggable transcription factors, not accessible by traditional antibodies. Hurdles exist regarding discovery, specificity, pharmacokinetics, and best modality of use that will need to be overcome before the full potential of TCR-based agents is achieved. HLA restriction may limit each agent to patient subpopulations and off-target reactivities remain important barriers to widespread development and use of these new agents. In this review we discuss the unique opportunities for these new classes of drugs, describe their unique antigenic targets, compare them to traditional antibody therapeutics and CAR T cells, and review the various obstacles that must be overcome before full application of these drugs can be realized.
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Affiliation(s)
- Manish Malviya
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065
| | - Zita Aretz
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065
- Physiology, Biophysics & Systems Biology Program, Weill Cornell Graduate School of Medical Sciences, 1300 York Avenue, New York, NY 10021
| | - Zaki Molvi
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065
- Physiology, Biophysics & Systems Biology Program, Weill Cornell Graduate School of Medical Sciences, 1300 York Avenue, New York, NY 10021
| | - Jayop Lee
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065
| | - Stephanie Pierre
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065
- Tri-Institutional Medical Scientist Program, 1300 York Avenue, New York, NY 10021
| | - Patrick Wallisch
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065
- Pharmacology Program, Weill Cornell Graduate School of Medical Sciences, 1300 York Avenue, New York, NY 10021
| | - Tao Dao
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065
| | - David A. Scheinberg
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065
- Pharmacology Program, Weill Cornell Graduate School of Medical Sciences, 1300 York Avenue, New York, NY 10021
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18
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Ye Y, Morita S, Chang JJ, Buckley PM, Wilhelm KB, DiMaio D, Groves JT, Barrera FN. Allosteric inhibition of the T cell receptor by a designed membrane ligand. eLife 2023; 12:e82861. [PMID: 37796108 PMCID: PMC10554751 DOI: 10.7554/elife.82861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 09/20/2023] [Indexed: 10/06/2023] Open
Abstract
The T cell receptor (TCR) is a complex molecular machine that directs the activation of T cells, allowing the immune system to fight pathogens and cancer cells. Despite decades of investigation, the molecular mechanism of TCR activation is still controversial. One of the leading activation hypotheses is the allosteric model. This model posits that binding of pMHC at the extracellular domain triggers a dynamic change in the transmembrane (TM) domain of the TCR subunits, which leads to signaling at the cytoplasmic side. We sought to test this hypothesis by creating a TM ligand for TCR. Previously we described a method to create a soluble peptide capable of inserting into membranes and binding to the TM domain of the receptor tyrosine kinase EphA2 (Alves et al., eLife, 2018). Here, we show that the approach is generalizable to complex membrane receptors, by designing a TM ligand for TCR. We observed that the designed peptide caused a reduction of Lck phosphorylation of TCR at the CD3ζ subunit in T cells. As a result, in the presence of this peptide inhibitor of TCR (PITCR), the proximal signaling cascade downstream of TCR activation was significantly dampened. Co-localization and co-immunoprecipitation in diisobutylene maleic acid (DIBMA) native nanodiscs confirmed that PITCR was able to bind to the TCR. AlphaFold-Multimer predicted that PITCR binds to the TM region of TCR, where it interacts with the two CD3ζ subunits. Our results additionally indicate that PITCR disrupts the allosteric changes in the compactness of the TM bundle that occur upon TCR activation, lending support to the allosteric TCR activation model. The TCR inhibition achieved by PITCR might be useful to treat inflammatory and autoimmune diseases and to prevent organ transplant rejection, as in these conditions aberrant activation of TCR contributes to disease.
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Affiliation(s)
- Yujie Ye
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee at KnoxvilleKnoxvilleUnited States
| | - Shumpei Morita
- Department of Chemistry, University of California, BerkeleyBerkeleyUnited States
| | - Justin J Chang
- Department of Genetics, Yale UniversityNew HavenUnited States
| | - Patrick M Buckley
- Department of Microbial Pathogenesis, Yale UniversityNew HavenUnited States
| | - Kiera B Wilhelm
- Department of Chemistry, University of California, BerkeleyBerkeleyUnited States
| | - Daniel DiMaio
- Department of Genetics, Yale UniversityNew HavenUnited States
| | - Jay T Groves
- Department of Chemistry, University of California, BerkeleyBerkeleyUnited States
- Institute for Digital Molecular Analytics and Science, Nanyang Technological UniversitySingaporeSingapore
| | - Francisco N Barrera
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee at KnoxvilleKnoxvilleUnited States
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19
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Chang-Gonzalez AC, Mallis RJ, Lang MJ, Reinherz EL, Hwang W. Asymmetric framework motion of TCR αβ controls load-dependent peptide discrimination. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.10.557064. [PMID: 37745603 PMCID: PMC10515854 DOI: 10.1101/2023.09.10.557064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Mechanical force is critical for the interaction between an αβT cell receptor (TCR) and a peptide-bound major histocompatibility complex (pMHC) molecule to initiate productive T-cell activation. However, the underlying mechanism remains unclear. We use all-atom molecular dynamics simulations to examine the A6 TCR bound to HLA-A*02:01 presenting agonist or antagonist peptides under different extensions to simulate the effects of applied load on the complex, elucidating their divergent biological responses. We found that TCR α and β chains move asymmetrically, which impacts the interface with pMHC, in particular the peptide-sensing CDR3 loops. For the wild-type agonist, the complex stabilizes in a load-dependent manner while antagonists destabilize it. Simulations of the Cβ FG-loop deletion, which reduces the catch bond response, and simulations with in silico mutant peptides further support the observed behaviors. The present results highlight the combined role of interdomain motion, fluctuating forces, and interfacial contacts in determining the mechanical response and fine peptide discrimination by a TCR, thereby resolving the conundrum of nearly identical crystal structures of TCRαβ-pMHC agonist and antagonist complexes.
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Affiliation(s)
- Ana C. Chang-Gonzalez
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, USA
| | - Robert J. Mallis
- Dept. Dermatology, Harvard Medical School, Boston, MA, USA
- Lab. of Immunobio., Dana-Farber Cancer Inst., Boston, MA, USA
- Dept. Med. Oncology, Dana-Farber Cancer Inst., Boston, MA, USA
| | - Matthew J. Lang
- Dept. Chem. and Biomolec. Eng., Vanderbilt Univ., Nashville, TN, USA
- Dept. Molec. Physiology and Biophys., Vanderbilt Univ., Nashville, TN, USA
| | - Ellis L. Reinherz
- Dept. Medicine, Harvard Medical School, Boston, MA, USA
- Lab. of Immunobio., Dana-Farber Cancer Inst., Boston, MA, USA
- Dept. Med. Oncology, Dana-Farber Cancer Inst., Boston, MA, USA
| | - Wonmuk Hwang
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, USA
- Department of Materials Science & Engineering, Texas A&M University, College Station, TX, USA
- Dept. Phys. & Astronomy, Texas A&M Univ., College Station, TX, USA
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20
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Prakaash D, Fagnen C, Cook GP, Acuto O, Kalli AC. Molecular dynamics simulations reveal membrane lipid interactions of the full-length lymphocyte specific kinase (Lck). Sci Rep 2022; 12:21121. [PMID: 36476673 PMCID: PMC9729596 DOI: 10.1038/s41598-022-25603-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
The membrane-bound lymphocyte-specific protein-tyrosine kinase (Lck) triggers T cell antigen receptor signalling to initiate adaptive immune responses. Despite many structure-function studies, the mode of action of Lck and the potential role of plasma membrane lipids in regulating Lck's activity remains elusive. Advances in molecular dynamics simulations of membrane proteins in complex lipid bilayers have opened a new perspective in gathering such information. Here, we have modelled the full-length Lck open and closed conformations using data available from different crystalographic studies and simulated its interaction with the inner leaflet of the T cell plasma membrane. In both conformations, we found that the unstructured unique domain and the structured domains including the kinase interacted with the membrane with a preference for PIP lipids. Interestingly, our simulations suggest that the Lck-SH2 domain interacts with lipids differently in the open and closed Lck conformations, demonstrating that lipid interaction can potentially regulate Lck's conformation and in turn modulate T cell signalling. Additionally, the Lck-SH2 and kinase domain residues that significantly contacted PIP lipids are found to be conserved among the Src family of kinases, thereby potentially representing similar PIP interactions within the family.
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Affiliation(s)
- Dheeraj Prakaash
- Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds, UK
- Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Charline Fagnen
- Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds, UK
- Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Graham P Cook
- School of Medicine, Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Oreste Acuto
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Antreas C Kalli
- Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds, UK.
- Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, UK.
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21
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Shevyrev DV, Tereshchenko VP, Sennikov SV. The Enigmatic Nature of the TCR-pMHC Interaction: Implications for CAR-T and TCR-T Engineering. Int J Mol Sci 2022; 23:ijms232314728. [PMID: 36499057 PMCID: PMC9740949 DOI: 10.3390/ijms232314728] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/11/2022] [Accepted: 11/21/2022] [Indexed: 11/29/2022] Open
Abstract
The interaction of the T-cell receptor (TCR) with a peptide in the major histocompatibility complex (pMHC) plays a central role in the adaptive immunity of higher chordates. Due to the high specificity and sensitivity of this process, the immune system quickly recognizes and efficiently responds to the appearance of foreign and altered self-antigens. This is important for ensuring anti-infectious and antitumor immunity, in addition to maintaining self-tolerance. The most common parameter used for assessing the specificity of TCR-pMHC interaction is affinity. This thermodynamic characteristic is widely used not only in various theoretical aspects, but also in practice, for example, in the engineering of various T-cell products with a chimeric (CAR-T) or artificial (TCR-engineered T-cell) antigen receptor. However, increasing data reveal the fact that, in addition to the thermodynamic component, the specificity of antigen recognition is based on the kinetics and mechanics of the process, having even greater influence on the selectivity of the process and T lymphocyte activation than affinity. Therefore, the kinetic and mechanical aspects of antigen recognition should be taken into account when designing artificial antigen receptors, especially those that recognize antigens in the MHC complex. This review describes the current understanding of the nature of the TCR-pMHC interaction, in addition to the thermodynamic, kinetic, and mechanical principles underlying the specificity and high sensitivity of this interaction.
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Affiliation(s)
- D. V. Shevyrev
- Laboratory of molecular Immunology, Research Institute for Fundamental and Clinical Immunology, 630099 Novosibirsk, Russia
- Center for Cell Technology and Immunology, Sirius University of Science and Technology, 354340 Sochi, Russia
- Correspondence: ; Tel.: +7-9231345505
| | - V. P. Tereshchenko
- Laboratory of molecular Immunology, Research Institute for Fundamental and Clinical Immunology, 630099 Novosibirsk, Russia
- Center for Cell Technology and Immunology, Sirius University of Science and Technology, 354340 Sochi, Russia
| | - S. V. Sennikov
- Laboratory of molecular Immunology, Research Institute for Fundamental and Clinical Immunology, 630099 Novosibirsk, Russia
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22
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Current and Future Perspectives for Chimeric Antigen Receptor T Cells Development in Poland. Biomedicines 2022; 10:biomedicines10112912. [PMID: 36428480 PMCID: PMC9687915 DOI: 10.3390/biomedicines10112912] [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: 10/06/2022] [Revised: 11/03/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
Chimeric antigen receptor T (CAR-T) cells are genetically modified autologous T cells that have revolutionized the treatment of relapsing and refractory haematological malignancies. In this review we present molecular pathways involved in the activation of CAR-T cells, describe in details the structures of receptors and the biological activity of CAR-T cells currently approved for clinical practice in the European Union, and explain the functional differences between them. Finally, we present the potential for the development of CAR-T cells in Poland, as well as indicate the possible directions of future research in this area, including novel modifications and applications of CAR-T cells and CAR-natural killer (NK) cells.
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The challenge of selecting tumor antigens for chimeric antigen receptor T-cell therapy in ovarian cancer. MEDICAL ONCOLOGY (NORTHWOOD, LONDON, ENGLAND) 2022; 39:232. [PMID: 36175774 DOI: 10.1007/s12032-022-01824-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 08/14/2022] [Indexed: 10/14/2022]
Abstract
Ovarian cancer (OC) is one of the most common cancers in women, with a high mortality rate and very few available and effective treatments. Evidence shows that immunotherapy in OC has not been very successful because immune checkpoint blockers have not achieved satisfactory clinical outcomes. On the other hand, as one of the effective treatment approaches, chimeric antigen receptor T-cell (CAR T-cell) therapy has gained a moral position, especially in blood malignancies. Although in solid tumors, CAR T-cell therapy faces various complications and challenges. One of these challenges is selecting the appropriate tumor antigen targeted by CAR T cells, making the selection difficult due to the expression of antigens by tumor cells and normal cells. In addition, the rate of tumor antigen expression and CAR T-cell access to the desired antigen and proper stimulation of CAR T cells can be other important points in antigen selection. This review summarized common tumor antigens and the challenges of selecting them in CAR T cells therapy of OC.
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Lima BP, Davies JR, Wickström C, Johnstone KF, Hall JW, Svensater G, Herzberg MC. Streptococcus gordonii Poised for Glycan Feeding through a MUC5B-Discriminating, Lipoteichoic Acid-Mediated Outside-In Signaling Circuit. J Bacteriol 2022; 204:e0011822. [PMID: 35652671 PMCID: PMC9210975 DOI: 10.1128/jb.00118-22] [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: 03/30/2022] [Accepted: 05/09/2022] [Indexed: 11/20/2022] Open
Abstract
Many oral bacteria employ cell wall-anchored adhesins to bind to the salivary films coating the teeth and mucosal surfaces. Surface binding prevents clearance and facilitates catabolism of salivary film glycoproteins. We asked whether Streptococcus gordonii adhesin expression changes in response to surface salivary cues using a eukaryote-like, outside-in recognition and signaling circuit. To determine whether the cues were discriminated, S. gordonii was tested during cell adhesion and biofilm formation on a MUC5B-rich or lower-molecular-mass salivary fraction or an uncoated abiotic surface. Cells were recovered and analyzed for differences in gene expression and proteins in cell wall fractions. In salivary-free conditions, planktonic S. gordonii presented three prominent cell wall LPXTG-motif proteins, SGO_1487, SGO_0890, and MbpA (mucin-binding protein A; SGO_0707). During biofilm formation on MUC5B-coated surfaces, MbpA, a MUC5B-binding protein, and key genes in the tagatose and quorum-sensing pathways were strongly promoted. The response to MUC5B required the two-component system (TCS), streptococcal regulator of adhesins sensor and regulator (SraSR, SGO_1180/81), lipoteichoic acid (LTA), and the homologous paired adhesins, SspA and SspB (SspAB). LTA appears to link the outside signal (MUC5B) to intramembrane SraSR. Tagatose pathway gene expression may poise cells to metabolize MUC5B glycans and, with a quorum-sensing gene (luxS), may direct formation of a consortium to facilitate glycan cross-feeding by S. gordonii. We now show that a Gram-positive bacterium discriminates specific surface environmental cues using an outside-in signaling mechanism to apparently optimize colonization of saliva-coated surfaces. IMPORTANCE All organisms throughout the tree of life sense and respond to their surface environments. To discriminate among mucosal surface environmental cues, we report that Streptococcus gordonii recognizes a high-molecular-weight mucin glycoprotein, MUC5B, using the paired adhesins SspAB and lipoteichoic acid; the latter bridges the outside signal to an intramembrane two-component system to transcriptionally regulate a MUC5B-specific adhesin and genes that may facilitate glycan catabolism.
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Affiliation(s)
- Bruno P. Lima
- Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, Minnesota, USA
| | - Julia R. Davies
- Section for Oral Biology and Pathology, Faculty of Odontology, Malmö University, Malmö, Sweden
| | - Claes Wickström
- Section for Oral Biology and Pathology, Faculty of Odontology, Malmö University, Malmö, Sweden
| | - Karen F. Johnstone
- Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, Minnesota, USA
| | - Jeffrey W. Hall
- Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, Minnesota, USA
| | - Gunnel Svensater
- Section for Oral Biology and Pathology, Faculty of Odontology, Malmö University, Malmö, Sweden
| | - Mark C. Herzberg
- Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, Minnesota, USA
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Grimholt U, Sundaram AYM, Bøe CA, Dahle MK, Lukacs M. Tetraploid Ancestry Provided Atlantic Salmon With Two Paralogue Functional T Cell Receptor Beta Regions Whereof One Is Completely Novel. Front Immunol 2022; 13:930312. [PMID: 35784332 PMCID: PMC9247247 DOI: 10.3389/fimmu.2022.930312] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Abstract
Protective cellular immune responses have been difficult to study in fish, due to lack of basic understanding of their T cell populations, and tools to study them. Cellular immunity is thus mostly ignored in vaccination and infection studies compared to humoral responses. High throughput sequencing, as well as access to well assembled genomes, now advances studies of cellular responses. Here we have used such resources to describe organization of T cell receptor beta genes in Atlantic salmon. Salmonids experienced a unique whole genome duplication approximately 94 million years ago, which provided these species with many functional duplicate genes, where some duplicates have evolved new functions or sub-functions of the original gene copy. This is also the case for T cell receptor beta, where Atlantic salmon has retained two paralogue T cell receptor beta regions on chromosomes 01 and 09. Compared to catfish and zebrafish, the genomic organization in both regions is unique, each chromosomal region organized with dual variable- diversity- joining- constant genes in a head to head orientation. Sequence identity of the chromosomal constant sequences between TRB01 and TRB09 is suggestive of rapid diversification, with only 67 percent as opposed to the average 82-90 percent for other duplicated genes. Using virus challenged samples we find both regions expressing bona fide functional T cell receptor beta molecules. Adding the 292 variable T cell receptor alpha genes to the 100 variable TRB genes from 14 subgroups, Atlantic salmon has one of the most diverse T cell receptor alpha beta repertoire of any vertebrate studied so far. Perhaps salmonid cellular immunity is more advanced than we have imagined.
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Affiliation(s)
- Unni Grimholt
- Fish Health Research Section, Norwegian Veterinary Institute, Oslo, Norway
- *Correspondence: Unni Grimholt,
| | - Arvind Y. M. Sundaram
- Fish Health Research Section, Norwegian Veterinary Institute, Oslo, Norway
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | | | - Maria K. Dahle
- Fish Health Research Section, Norwegian Veterinary Institute, Oslo, Norway
| | - Morten Lukacs
- Fish Health Research Section, Norwegian Veterinary Institute, Oslo, Norway
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Tempark T, John S, Rerknimitr P, Satapornpong P, Sukasem C. Drug-Induced Severe Cutaneous Adverse Reactions: Insights Into Clinical Presentation, Immunopathogenesis, Diagnostic Methods, Treatment, and Pharmacogenomics. Front Pharmacol 2022; 13:832048. [PMID: 35517811 PMCID: PMC9065683 DOI: 10.3389/fphar.2022.832048] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 03/01/2022] [Indexed: 12/19/2022] Open
Abstract
SCARs are rare and life-threatening hypersensitivity reactions. In general, the increased duration of hospital stays and the associated cost burden are common issues, and in the worst-case scenario, they can result in mortality. SCARs are delayed T cell-mediated hypersensitivity reactions. Recovery can take from 2 weeks to many months after dechallenging the culprit drugs. Genetic polymorphism of the HLA genes may change the selection and presentation of antigens, allowing toxic drug metabolites to initiate immunological reactions. However, each SCARs has a different onset latency period, clinical features, or morphological pattern. This explains that, other than HLA mutations, other immuno-pathogenesis may be involved in drug-induced severe cutaneous reactions. This review will discuss the clinical morphology of various SCARs, various immune pathogenesis models, diagnostic criteria, treatments, the association of various drug-induced reactions and susceptible alleles in different populations, and the successful implementation of pharmacogenomics in Thailand for the prevention of SCARs.
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Affiliation(s)
- Therdpong Tempark
- Division of Dermatology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,The Pediatrics-Thai Severe Cutaneous Adverse Drug Reaction (Ped-Thai-SCAR) Research Group, Bangkok, Thailand
| | - Shobana John
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.,Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center (SDMC), Ramathibodi Hospital, Bangkok, Thailand
| | - Pawinee Rerknimitr
- The Thai Severe Cutaneous Adverse Drug Reaction (Thai-SCAR) Research Group, Bangkok, Thailand.,Division of Dermatology, Department of Medicine, Faculty of Medicine, Skin, and Allergy Research Unit, Chulalongkorn University, Bangkok, Thailand
| | - Patompong Satapornpong
- Division of General Pharmacy Practice, Department of Pharmaceutical Care, College of Pharmacy, Rangsit University, Pathum Thani, Thailand.,Excellence Pharmacogenomics and Precision Medicine Centre, College of Pharmacy, Rangsit University, Pathum Thani, Thailand
| | - Chonlaphat Sukasem
- The Pediatrics-Thai Severe Cutaneous Adverse Drug Reaction (Ped-Thai-SCAR) Research Group, Bangkok, Thailand.,Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.,Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center (SDMC), Ramathibodi Hospital, Bangkok, Thailand.,The Thai Severe Cutaneous Adverse Drug Reaction (Thai-SCAR) Research Group, Bangkok, Thailand.,Pharmacogenomics and Precision Medicine, The Preventive Genomics & Family Check-up Services Center, Bumrungrad International Hospital, Bangkok, Thailand.,MRC Centre for Drug Safety Science, Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
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27
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Boettcher M, Joechner A, Li Z, Yang SF, Schlegel P. Development of CAR T Cell Therapy in Children-A Comprehensive Overview. J Clin Med 2022; 11:jcm11082158. [PMID: 35456250 PMCID: PMC9024694 DOI: 10.3390/jcm11082158] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/08/2022] [Accepted: 04/11/2022] [Indexed: 01/27/2023] Open
Abstract
CAR T cell therapy has revolutionized immunotherapy in the last decade with the successful establishment of chimeric antigen receptor (CAR)-expressing cellular therapies as an alternative treatment in relapsed and refractory CD19-positive leukemias and lymphomas. There are fundamental reasons why CAR T cell therapy has been approved by the Food and Drug administration and the European Medicines Agency for pediatric and young adult patients first. Commonly, novel therapies are developed for adult patients and then adapted for pediatric use, due to regulatory and commercial reasons. Both strategic and biological factors have supported the success of CAR T cell therapy in children. Since there is an urgent need for more potent and specific therapies in childhood malignancies, efforts should also include the development of CAR therapeutics and expand applicability by introducing new technologies. Basic aspects, the evolution and the drawbacks of childhood CAR T cell therapy are discussed as along with the latest clinically relevant information.
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Affiliation(s)
- Michael Boettcher
- Department of Pediatric Surgery, University Medical Centre Mannheim, University of Heidelberg, 69117 Heidelberg, Germany;
| | - Alexander Joechner
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney 2006, Australia;
- Cellular Cancer Therapeutics Unit, Children’s Medical Research Institute, Sydney 2145, Australia; (Z.L.); (S.F.Y.)
| | - Ziduo Li
- Cellular Cancer Therapeutics Unit, Children’s Medical Research Institute, Sydney 2145, Australia; (Z.L.); (S.F.Y.)
| | - Sile Fiona Yang
- Cellular Cancer Therapeutics Unit, Children’s Medical Research Institute, Sydney 2145, Australia; (Z.L.); (S.F.Y.)
| | - Patrick Schlegel
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney 2006, Australia;
- Cellular Cancer Therapeutics Unit, Children’s Medical Research Institute, Sydney 2145, Australia; (Z.L.); (S.F.Y.)
- Department of Pediatric Hematology and Oncology, Westmead Children’s Hospital, Sydney 2145, Australia
- Correspondence:
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28
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Manry D, Bolanos K, DiAndreth B, Mock JY, Kamb A. Robust In Vitro Pharmacology of Tmod, a Synthetic Dual-Signal Integrator for Cancer Cell Therapy. Front Immunol 2022; 13:826747. [PMID: 35359952 PMCID: PMC8960424 DOI: 10.3389/fimmu.2022.826747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/18/2022] [Indexed: 01/09/2023] Open
Abstract
Progress toward improved solid-tumor treatment has long been hindered by the lack of truly tumor-specific targets. We have developed an approach to T cell therapy based on a dual-receptor system called Tmod™ that addresses this problem. The Tmod system exploits one of the few common genetic differences between tumor and normal cells: loss of heterozygosity (LOH). It utilizes the basic mechanistic logic that evolved in early vertebrates to mediate self vs. non-self discrimination, where an activation stimulus is blocked by self-ligands. Tmod constructs employ a chimeric antigen receptor (CAR) or T cell receptor (TCR) as activator component and a modified LIR-1 inhibitory receptor (blocker) to achieve high selectivity based on expression of the blocker antigen (Ag). Here we explore the in vitro pharmacology of a blocker directed at the HLA-A*02 Ag paired with either a mesothelin CAR or an HLA-A*11-restricted KRAS peptide TCR. While more sensitive to receptor expression changes on effector cells, we show that Tmod response is well-buffered against variations in Ag levels on target cells. In addition, the data reveal at least two distinguishable pharmacologic mechanisms of Tmod blocker function: (1) reducing activator sensitivity and (2) decreasing activation magnitude.
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Affiliation(s)
- Diane Manry
- A2 Biotherapeutics, Inc., Agoura Hills, CA, United States
| | | | | | - Jee-Young Mock
- A2 Biotherapeutics, Inc., Agoura Hills, CA, United States
| | - Alexander Kamb
- A2 Biotherapeutics, Inc., Agoura Hills, CA, United States
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29
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The Full Model of the pMHC-TCR-CD3 Complex: A Structural and Dynamical Characterization of Bound and Unbound States. Cells 2022; 11:cells11040668. [PMID: 35203317 PMCID: PMC8869815 DOI: 10.3390/cells11040668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/31/2022] [Accepted: 02/10/2022] [Indexed: 11/23/2022] Open
Abstract
The machinery involved in cytotoxic T-cell activation requires three main characters: the major histocompatibility complex class I (MHC I) bound to the peptide (p), the T-cell receptor (TCR), and the CD3 complex, a multidimer interfaced with the intracellular side. The pMHC:TCR interaction has been largely studied by means of both experimental and computational models, giving a contribution in understanding the complexity of the TCR triggering. Nevertheless, a detailed study of the structural and dynamical characterization of the full complex (pMHC:TCR:CD3 complex) is still missing due to a lack of structural information of the CD3-chains arrangement around the TCR. Very recently, the determination of the TCR:CD3 complex structure by means of Cryo-EM technique has given a chance to build the entire system essential in the activation of T-cells, a fundamental mechanism in the adaptive immune response. Here, we present the first complete model of the pMHC interacting with the TCR:CD3 complex, built in a lipid environment. To describe the conformational behavior associated with the unbound and the bound states, all-atom Molecular Dynamics simulations were performed for the TCR:CD3 complex and for two pMHC:TCR:CD3 complex systems, bound to two different peptides. Our data point out that a conformational change affecting the TCR Constant β (Cβ) region occurs after the binding to the pMHC, revealing a key role of this region in the propagation of the signal. Moreover, we found that TCR reduces the flexibility of the MHC I binding groove, confirming our previous results.
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30
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Ge C, Weisse S, Xu B, Dobritzsch D, Viljanen J, Kihlberg J, Do NN, Schneider N, Lanig H, Holmdahl R, Burkhardt H. Key interactions in the trimolecular complex consisting of the rheumatoid arthritis-associated DRB1*04:01 molecule, the major glycosylated collagen II peptide and the T-cell receptor. Ann Rheum Dis 2022; 81:480-489. [PMID: 35027402 PMCID: PMC8921575 DOI: 10.1136/annrheumdis-2021-220500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 12/10/2021] [Indexed: 12/30/2022]
Abstract
Objectives Rheumatoid arthritis (RA) is an autoimmune disease strongly associated with the major histocompatibility complex (MHC) class II allele DRB1*04:01, which encodes a protein that binds self-peptides for presentation to T cells. This study characterises the autoantigen-presenting function of DRB1*04:01 (HLA-DRA*01:01/HLA-DRB1*04:01) at a molecular level for prototypic T-cell determinants, focusing on a post-translationally modified collagen type II (Col2)-derived peptide. Methods The crystal structures of DRB1*04:01 molecules in complex with the peptides HSP70289-306, citrullinated CILP982-996 and galactosylated Col2259-273 were determined on cocrystallisation. T cells specific for Col2259-273 were investigated in peripheral blood mononuclear cells from patients with DRB1*04:01-positive RA by cytofluorometric detection of the activation marker CD154 on peptide stimulation and binding of fluorescent DRB1*0401/Col2259-273 tetramer complexes. The cDNAs encoding the T-cell receptor (TCR) α-chains and β-chains were cloned from single-cell sorted tetramer-positive T cells and transferred via a lentiviral vector into TCR-deficient Jurkat 76 cells. Results The crystal structures identified peptide binding to DRB1*04:01 and potential side chain exposure to T cells. The main TCR recognition sites in Col2259-273 were lysine residues that can be galactosylated. RA T-cell responses to DRB1*04:01-presented Col2259-273 were dependent on peptide galactosylation at lysine 264. Dynamic molecular modelling of a functionally characterised Col2259-273-specific TCR complexed with DRB1*04:01/Col2259-273 provided evidence for differential allosteric T-cell recognition of glycosylated lysine 264. Conclusions The MHC-peptide-TCR interactions elucidated in our study provide new molecular insights into recognition of a post-translationally modified RA T-cell determinant with a known dominant role in arthritogenic and tolerogenic responses in murine Col2-induced arthritis.
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Affiliation(s)
- Changrong Ge
- Section for Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Sylvia Weisse
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Frankfurt am Main, Germany
| | - Bingze Xu
- Section for Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Doreen Dobritzsch
- Section of Biochemistry, Department of Chemistry-BMC, Uppsala University, Uppsala, Sweden
| | - Johan Viljanen
- Section of Organic Chemistry, Department of Chemistry-BMC, Uppsala University, Uppsala, Sweden
| | - Jan Kihlberg
- Section of Organic Chemistry, Department of Chemistry-BMC, Uppsala University, Uppsala, Sweden
| | - Nhu-Nguyen Do
- Section for Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden.,Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Frankfurt am Main, Germany
| | - Nadine Schneider
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Frankfurt am Main, Germany
| | - Harald Lanig
- Central Institute for Scientific Computing (ZISC), Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.,Erlangen National High Performance Computing Center, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany (current affiliation)
| | - Rikard Holmdahl
- Section for Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden.,Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Harald Burkhardt
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Frankfurt am Main, Germany .,Fraunhofer Cluster of Excellence Immune-Mediated Diseases CIMD, Frankfurt am Main, Germany.,Division of Rheumatology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
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T Cell Aging in Patients with Colorectal Cancer-What Do We Know So Far? Cancers (Basel) 2021; 13:cancers13246227. [PMID: 34944847 PMCID: PMC8699226 DOI: 10.3390/cancers13246227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/07/2021] [Accepted: 12/07/2021] [Indexed: 01/02/2023] Open
Abstract
Simple Summary This review describes the role of T cell aging in colorectal cancer development. T cells are important mediators in cancer immunity. Aging affects T cells, leading to various dysfunctions which can impede antitumor immunity. While some hallmarks of T cell aging have been observed in colorectal cancer patients, the functional role of such cells is not clear. Therefore, understanding how aged T cells influence overall patient outcome could potentially help in the pursue to develop new therapies for the elderly. Abstract Colorectal cancer (CRC) continues to be one of the most frequently diagnosed types of cancers in the world. CRC is considered to affect mostly elderly patients, and the number of diagnosed cases increases with age. Even though general screening improves outcomes, the overall survival and recurrence-free CRC rates in aged individuals are highly dependent on their history of comorbidities. Furthermore, aging is also known to alter the immune system, and especially the adaptive immune T cells. Many studies have emphasized the importance of T cell responses to CRC. Therefore, understanding how age-related changes affect the outcome in CRC patients is crucial. This review focuses on what is so far known about age-related T cell dysfunction in elderly patients with colorectal cancer and how aged T cells can mediate its development. Last, this study describes the advances in basic animal models that have potential to be used to elucidate the role of aged T cells in CRC.
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CD3/TCRE Expression and Immunoregulatory Milieu Induced in a Secondary Intermediate Host by Different Phases of Hydatid Cyst. Acta Parasitol 2021; 66:1490-1498. [PMID: 34110592 DOI: 10.1007/s11686-021-00408-1] [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: 01/21/2021] [Accepted: 04/28/2021] [Indexed: 10/21/2022]
Abstract
BACKGROUND Echinococcosis is a common health problem in the Mediterranean and the Middle East, and manifests without any symptoms, even in the advanced stages. OBJECTIVE The present study aimed to investigate the cell mediated-immunoregulatory milieu in rats' echinococcosis induced by three different viability status of Echinococcus granulosus especially in the semi-calcareous stage, which can be used as novel biomarkers to monitor disease progression and open the door to a deeper understanding of the pathways that could contribute to complementary echinococcosis therapies. MATERIALS AND METHODS Rat infection with echinococcosis was induced by three different viable statuses of Echinococcus granulosus (G6) camel strain. During the different stages of parasitic infection, blood serum was harvested from rats containing low-, high-, and not viable (not completely transformed to the calcareous status) protoscoleces fluid. The host Th1/Th2 cytokines-mediated immune cell activation, as well as CD3/TCRE immunoregulation, and proliferation responses were investigated; especially in the semi-calcareous stage as this is the first report characterizing this stage. RESULTS Both IFN-γ and IL-6 levels significantly increased in the infected groups (P < 0.05), in addition, increased positive immunoreactions in splenic tissue for both CD3/TCRE and Ki-67 monoclonal antibodies. CONCLUSION E. granuloses infection-induced immune tolerance is involved in disease progression, and modulates the activation and regulation of host immune response, even in the early stages of infection, rather than the last stages of viability (semi-calcareous) is not neglected stage. This study is the first to report that the semi-calcareous stage causes a severe immunological response.
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Garcia P, Wang Y, Viallet J, Macek Jilkova Z. The Chicken Embryo Model: A Novel and Relevant Model for Immune-Based Studies. Front Immunol 2021; 12:791081. [PMID: 34868080 PMCID: PMC8640176 DOI: 10.3389/fimmu.2021.791081] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/02/2021] [Indexed: 12/18/2022] Open
Abstract
Dysregulation of the immune system is associated with many pathologies, including cardiovascular diseases, diabetes, and cancer. To date, the most commonly used models in biomedical research are rodents, and despite the various advantages they offer, their use also raises numerous drawbacks. Recently, another in vivo model, the chicken embryo and its chorioallantoic membrane, has re-emerged for various applications. This model has many benefits compared to other classical models, as it is cost-effective, time-efficient, and easier to use. In this review, we explain how the chicken embryo can be used as a model for immune-based studies, as it gradually develops an embryonic immune system, yet which is functionally similar to humans'. We mainly aim to describe the avian immune system, highlighting the differences and similarities with the human immune system, including the repertoire of lymphoid tissues, immune cells, and other key features. We also describe the general in ovo immune ontogeny. In conclusion, we expect that this review will help future studies better tailor their use of the chicken embryo model for testing specific experimental hypotheses or performing preclinical testing.
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Affiliation(s)
- Paul Garcia
- Université Grenoble Alpes, Grenoble, France
- R&D Department, Inovotion, La Tronche, France
- Institute for Advanced Biosciences, Research Center Université Grenoble Alpes (UGA)/Inserm U 1209/CNRS 5309, La Tronche, France
| | - Yan Wang
- R&D Department, Inovotion, La Tronche, France
| | | | - Zuzana Macek Jilkova
- Université Grenoble Alpes, Grenoble, France
- Institute for Advanced Biosciences, Research Center Université Grenoble Alpes (UGA)/Inserm U 1209/CNRS 5309, La Tronche, France
- Service d’Hépato-Gastroentérologie, Pôle Digidune, Centre Hospitalo-Universitaire (USA) Grenoble Alpes, La Tronche, France
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Puech PH, Bongrand P. Mechanotransduction as a major driver of cell behaviour: mechanisms, and relevance to cell organization and future research. Open Biol 2021; 11:210256. [PMID: 34753321 PMCID: PMC8586914 DOI: 10.1098/rsob.210256] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
How do cells process environmental cues to make decisions? This simple question is still generating much experimental and theoretical work, at the border of physics, chemistry and biology, with strong implications in medicine. The purpose of mechanobiology is to understand how biochemical and physical cues are turned into signals through mechanotransduction. Here, we review recent evidence showing that (i) mechanotransduction plays a major role in triggering signalling cascades following cell-neighbourhood interaction; (ii) the cell capacity to continually generate forces, and biomolecule properties to undergo conformational changes in response to piconewton forces, provide a molecular basis for understanding mechanotransduction; and (iii) mechanotransduction shapes the guidance cues retrieved by living cells and the information flow they generate. This includes the temporal and spatial properties of intracellular signalling cascades. In conclusion, it is suggested that the described concepts may provide guidelines to define experimentally accessible parameters to describe cell structure and dynamics, as a prerequisite to take advantage of recent progress in high-throughput data gathering, computer simulation and artificial intelligence, in order to build a workable, hopefully predictive, account of cell signalling networks.
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Affiliation(s)
- Pierre-Henri Puech
- Lab Adhesion and Inflammation (LAI), Inserm UMR 1067, CNRS UMR 7333, Aix-Marseille Université UM61, Marseille, France
| | - Pierre Bongrand
- Lab Adhesion and Inflammation (LAI), Inserm UMR 1067, CNRS UMR 7333, Aix-Marseille Université UM61, Marseille, France
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35
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Zhu Y, Huang D, Zhao Z, Lu C. Bioinformatic analysis identifies potential key genes of epilepsy. PLoS One 2021; 16:e0254326. [PMID: 34555062 PMCID: PMC8459949 DOI: 10.1371/journal.pone.0254326] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 08/31/2021] [Indexed: 12/19/2022] Open
Abstract
Background Epilepsy is one of the most common brain disorders worldwide. It is usually hard to be identified properly, and a third of patients are drug-resistant. Genes related to the progression and prognosis of epilepsy are particularly needed to be identified. Methods In our study, we downloaded the Gene Expression Omnibus (GEO) microarray expression profiling dataset GSE143272. Differentially expressed genes (DEGs) with a fold change (FC) >1.2 and a P-value <0.05 were identified by GEO2R and grouped in male, female and overlapping DEGs. Functional enrichment analysis and Protein-Protein Interaction (PPI) network analysis were performed. Results In total, 183 DEGs overlapped (77 ups and 106 downs), 302 DEGs (185 ups and 117 downs) in the male dataset, and 750 DEGs (464 ups and 286 downs) in the female dataset were obtained from the GSE143272 dataset. These DEGs were markedly enriched under various Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) terms. 16 following hub genes were identified based on PPI network analysis: ADCY7, C3AR1, DEGS1, CXCL1 in male-specific DEGs, TOLLIP, ORM1, ELANE, QPCT in female-specific DEGs and FCAR, CD3G, CLEC12A, MOSPD2, CD3D, ALDH3B1, GPR97, PLAUR in overlapping DEGs. Conclusion This discovery-driven study may be useful to provide a novel insight into the diagnosis and treatment of epilepsy. However, more experiments are needed in the future to study the functional roles of these genes in epilepsy.
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Affiliation(s)
- Yike Zhu
- Department of Respiratory Medicine, Hainan General Hospital, Haikou, China
| | - Dan Huang
- Department of Neurology, Hainan General Hospital, Haikou, China
| | - Zhongyan Zhao
- Department of Neurology, Hainan General Hospital, Haikou, China
| | - Chuansen Lu
- Department of Neurology, Hainan General Hospital, Haikou, China
- * E-mail:
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Mehdizadeh M, Karami S, Ghaffari Nazari H, Sankanian G, Hamidpour M, Hajifathali A. Immunotherapy with adoptive cytomegalovirus-specific T cells transfer: Summarizing latest gene engineering techniques. Health Sci Rep 2021; 4:e322. [PMID: 34263085 PMCID: PMC8264956 DOI: 10.1002/hsr2.322] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 05/30/2021] [Accepted: 06/04/2021] [Indexed: 01/02/2023] Open
Abstract
Cytomegalovirus (CMV) infection remains a major complication following allogeneic hematopoietic stem cell transplantation (HSCT). T cell response plays a critical role in inducing long-term immunity against CMV infection/reactivation that impairs during HSCT. Adoptive T cell therapy (ACT) via transferring CMV-specific T cells from a seropositive donor to the recipient can accelerate virus-specific immune reconstitution. ACT, as an alternative approach, can restore protective antiviral T cell immunity in patients. Different manufacturing protocols have been introduced to isolate and expand specific T cells for the ACT clinical setting. Nevertheless, HLA restriction, long-term manufacturing process, risk of alloreactivity, and CMV seropositive donor availability have limited ACT broad applicability. Genetic engineering has developed new strategies to produce TCR-modified T cells for diagnosis, prevention, and treatment of infectious disease. In this review, we presented current strategies required for ACT in posttransplant CMV infection. We also introduced novel gene-modified T cell discoveries in the context of ACT for CMV infection. It seems that these innovations are enabling to improvement and development of ACT utilization to combat posttransplant CMV infection.
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Affiliation(s)
- Mahshid Mehdizadeh
- Hematopoietic Stem Cell Research CenterShahid Beheshti University of Medical SciencesTehranIran
| | - Samira Karami
- Hematopoietic Stem Cell Research CenterShahid Beheshti University of Medical SciencesTehranIran
| | - Haniyeh Ghaffari Nazari
- Hematopoietic Stem Cell Research CenterShahid Beheshti University of Medical SciencesTehranIran
| | - Ghazaleh Sankanian
- Hematopoietic Stem Cell Research CenterShahid Beheshti University of Medical SciencesTehranIran
| | - Mohsen Hamidpour
- Hematopoietic Stem Cell Research CenterShahid Beheshti University of Medical SciencesTehranIran
| | - Abbas Hajifathali
- Hematopoietic Stem Cell Research CenterShahid Beheshti University of Medical SciencesTehranIran
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Prakaash D, Cook GP, Acuto O, Kalli AC. Multi-scale simulations of the T cell receptor reveal its lipid interactions, dynamics and the arrangement of its cytoplasmic region. PLoS Comput Biol 2021; 17:e1009232. [PMID: 34280187 PMCID: PMC8321403 DOI: 10.1371/journal.pcbi.1009232] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 07/29/2021] [Accepted: 07/01/2021] [Indexed: 12/27/2022] Open
Abstract
The T cell receptor (TCR-CD3) initiates T cell activation by binding to peptides of Major Histocompatibility Complexes (pMHC). The TCR-CD3 topology is well understood but the arrangement and dynamics of its cytoplasmic tails remains unknown, limiting our grasp of the signalling mechanism. Here, we use molecular dynamics simulations and modelling to investigate the entire TCR-CD3 embedded in a model membrane. Our study demonstrates conformational changes in the extracellular and transmembrane domains, and the arrangement of the TCR-CD3 cytoplasmic tails. The cytoplasmic tails formed highly interlaced structures while some tyrosines within the immunoreceptor tyrosine-based activation motifs (ITAMs) penetrated the hydrophobic core of the membrane. Interactions between the cytoplasmic tails and phosphatidylinositol phosphate lipids in the inner membrane leaflet led to the formation of a distinct anionic lipid fingerprint around the TCR-CD3. These results increase our understanding of the TCR-CD3 dynamics and the importance of membrane lipids in regulating T cell activation.
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Affiliation(s)
- Dheeraj Prakaash
- Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds, United Kingdom
- Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Graham P. Cook
- Leeds Institute of Medical Research at St James’s, School of Medicine, University of Leeds, Leeds, United Kingdom
| | - Oreste Acuto
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Antreas C. Kalli
- Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds, United Kingdom
- Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
- * E-mail:
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38
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Lanz AL, Masi G, Porciello N, Cohnen A, Cipria D, Prakaash D, Bálint Š, Raggiaschi R, Galgano D, Cole DK, Lepore M, Dushek O, Dustin ML, Sansom MSP, Kalli AC, Acuto O. Allosteric activation of T cell antigen receptor signaling by quaternary structure relaxation. Cell Rep 2021; 36:109375. [PMID: 34260912 PMCID: PMC8293630 DOI: 10.1016/j.celrep.2021.109375] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 05/05/2021] [Accepted: 06/18/2021] [Indexed: 01/05/2023] Open
Abstract
The mechanism of T cell antigen receptor (TCR-CD3) signaling remains elusive. Here, we identify mutations in the transmembrane region of TCRβ or CD3ζ that augment peptide T cell antigen receptor (pMHC)-induced signaling not explicable by enhanced ligand binding, lateral diffusion, clustering, or co-receptor function. Using a biochemical assay and molecular dynamics simulation, we demonstrate that the gain-of-function mutations loosen the interaction between TCRαβ and CD3ζ. Similar to the activating mutations, pMHC binding reduces TCRαβ cohesion with CD3ζ. This event occurs prior to CD3ζ phosphorylation and at 0°C. Moreover, we demonstrate that soluble monovalent pMHC alone induces signaling and reduces TCRαβ cohesion with CD3ζ in membrane-bound or solubilised TCR-CD3. Our data provide compelling evidence that pMHC binding suffices to activate allosteric changes propagating from TCRαβ to the CD3 subunits, reconfiguring interchain transmembrane region interactions. These dynamic modifications could change the arrangement of TCR-CD3 boundary lipids to license CD3ζ phosphorylation and initiate signal propagation. Mutations in TCRβ and CD3ζ TMRs that reduce their interaction augment signaling pMHC and anti-CD3 binding to TCR-CD3 induce similar quaternary structure relaxation Soluble monovalent pMHC alone signals and reduces TCRαβ cohesion with CD3ζ Allosteric changes in TCR-CD3 dynamics instigate T cell activation
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Affiliation(s)
- Anna-Lisa Lanz
- T-cell signalling laboratory, Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Giulia Masi
- T-cell signalling laboratory, Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Nicla Porciello
- T-cell signalling laboratory, Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - André Cohnen
- T-cell signalling laboratory, Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Deborah Cipria
- T-cell signalling laboratory, Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Dheeraj Prakaash
- Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds LS2 9JT, UK
| | - Štefan Bálint
- Kennedy Institute of Rheumatology, University of Oxford, Oxford OX3 7FY, UK
| | - Roberto Raggiaschi
- T-cell signalling laboratory, Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Donatella Galgano
- T-cell signalling laboratory, Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - David K Cole
- Division Infection & Immunity, Cardiff University, Cardiff CF14 4XN, UK; Immunocore Ltd., Abingdon OX14 4RY, UK
| | | | - Omer Dushek
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Michael L Dustin
- Kennedy Institute of Rheumatology, University of Oxford, Oxford OX3 7FY, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
| | - Antreas C Kalli
- Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds LS2 9JT, UK; Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
| | - Oreste Acuto
- T-cell signalling laboratory, Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK.
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Gunasinghe SD, Peres NG, Goyette J, Gaus K. Biomechanics of T Cell Dysfunctions in Chronic Diseases. Front Immunol 2021; 12:600829. [PMID: 33717081 PMCID: PMC7948521 DOI: 10.3389/fimmu.2021.600829] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 01/12/2021] [Indexed: 12/12/2022] Open
Abstract
Understanding the mechanisms behind T cell dysfunctions during chronic diseases is critical in developing effective immunotherapies. As demonstrated by several animal models and human studies, T cell dysfunctions are induced during chronic diseases, spanning from infections to cancer. Although factors governing the onset and the extent of the functional impairment of T cells can differ during infections and cancer, most dysfunctional phenotypes share common phenotypic traits in their immune receptor and biophysical landscape. Through the latest developments in biophysical techniques applied to explore cell membrane and receptor-ligand dynamics, we are able to dissect and gain further insights into the driving mechanisms behind T cell dysfunctions. These insights may prove useful in developing immunotherapies aimed at reinvigorating our immune system to fight off infections and malignancies more effectively. The recent success with checkpoint inhibitors in treating cancer opens new avenues to develop more effective, targeted immunotherapies. Here, we highlight the studies focused on the transformation of the biophysical landscape during infections and cancer, and how T cell biomechanics shaped the immunopathology associated with chronic diseases.
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Affiliation(s)
- Sachith D Gunasinghe
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Sydney, NSW, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, NSW, Australia
| | - Newton G Peres
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Sydney, NSW, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, NSW, Australia
| | - Jesse Goyette
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Sydney, NSW, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, NSW, Australia
| | - Katharina Gaus
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Sydney, NSW, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, NSW, Australia
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Dam T, Junghans V, Humphrey J, Chouliara M, Jönsson P. Calcium Signaling in T Cells Is Induced by Binding to Nickel-Chelating Lipids in Supported Lipid Bilayers. Front Physiol 2021; 11:613367. [PMID: 33551841 PMCID: PMC7859345 DOI: 10.3389/fphys.2020.613367] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 12/30/2020] [Indexed: 12/26/2022] Open
Abstract
Supported lipid bilayers (SLBs) are one of the most common cell-membrane model systems to study cell-cell interactions. Nickel-chelating lipids are frequently used to functionalize the SLB with polyhistidine-tagged ligands. We show here that these lipids by themselves can induce calcium signaling in T cells, also when having protein ligands on the SLB. This is important to avoid "false" signaling events in cell studies with SLBs, but also to better understand the molecular mechanisms involved in T-cell signaling. Jurkat T cells transfected with the non-signaling molecule rat CD48 were found to bind to ligand-free SLBs containing ≥2 wt% nickel-chelating lipids upon which calcium signaling was induced. This signaling fraction steadily increased from 24 to 60% when increasing the amount of nickel-chelating lipids from 2 to 10 wt%. Both the signaling fraction and signaling time did not change significantly compared to ligand-free SLBs when adding the CD48-ligand rat CD2 to the SLB. Blocking the SLB with bovine serum albumin reduced the signaling fraction to 11%, while preserving CD2 binding and the exclusion of the phosphatase CD45 from the cell-SLB contacts. Thus, CD45 exclusion alone was not sufficient to result in calcium signaling. In addition, more cells signaled on ligand-free SLBs with copper-chelating lipids instead of nickel-chelating lipids and the signaling was found to be predominantly via T-cell receptor (TCR) triggering. Hence, it is possible that the nickel-chelating lipids act as ligands to the cell's TCRs, an interaction that needs to be blocked to avoid unwanted cell activation.
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Affiliation(s)
- Tommy Dam
- Department of Chemistry, Lund University, Lund, Sweden
| | | | - Jane Humphrey
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | | | - Peter Jönsson
- Department of Chemistry, Lund University, Lund, Sweden
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41
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Calcineurin and Systemic Lupus Erythematosus: The Rationale for Using Calcineurin Inhibitors in the Treatment of Lupus Nephritis. Int J Mol Sci 2021; 22:ijms22031263. [PMID: 33514066 PMCID: PMC7865978 DOI: 10.3390/ijms22031263] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/24/2021] [Accepted: 01/25/2021] [Indexed: 12/18/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is a chronic autoimmune disease with a broad spectrum of clinical presentations that can affect almost all organ systems. Lupus nephritis (LN) is a severe complication that affects approximately half of the systemic erythematosus lupus (SLE) patients, which significantly increases the morbidity and the mortality risk. LN is characterized by the accumulation of immune complexes, ultimately leading to renal failure. Aberrant activation of T cells plays a critical role in the pathogenesis of both SLE and LN and is involved in the production of inflammatory cytokines, the recruitment of inflammatory cells to the affected tissues and the co-stimulation of B cells. Calcineurin is a serine-threonine phosphatase that, as a consequence of the T cell hyperactivation, induces the production of inflammatory mediators. Moreover, calcineurin is also involved in the alterations of the podocyte phenotype, which contribute to proteinuria and kidney damage observed in LN patients. Therefore, calcineurin inhibitors have been postulated as a potential treatment strategy in LN, since they reduce T cell activation and promote podocyte cytoskeleton stabilization, both being key aspects in the development of LN. Here, we review the role of calcineurin in SLE and the latest findings about calcineurin inhibitors and their mechanisms of action in the treatment of LN.
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Fölser M, Motsch V, Platzer R, Huppa JB, Schütz GJ. A Multimodal Platform for Simultaneous T-Cell Imaging, Defined Activation, and Mechanobiological Characterization. Cells 2021; 10:235. [PMID: 33504075 PMCID: PMC7910839 DOI: 10.3390/cells10020235] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/18/2021] [Accepted: 01/20/2021] [Indexed: 11/16/2022] Open
Abstract
T-cell antigen recognition is accompanied by extensive morphological rearrangements of the contact zone between the T-cell and the antigen-presenting cell (APC). This process involves binding of the T-cell receptor (TCR) complex to antigenic peptides presented via MHC on the APC surface, the interaction of costimulatory and adhesion proteins, remodeling of the actin cytoskeleton, and the initiation of downstream signaling processes such as the release of intracellular calcium. However, multiparametric time-resolved analysis of these processes is hampered by the difficulty in recording the different readout modalities at high quality in parallel. In this study, we present a platform for simultaneous quantification of TCR distribution via total internal reflection fluorescence microscopy, of intracellular calcium levels, and of T-cell-exerted forces via atomic force microscopy (AFM). In our method, AFM cantilevers were used to bring single T-cells into contact with the activating surface. We designed the platform specifically to enable the study of T-cell triggering via functionalized fluid-supported lipid bilayers, which represent a widely accepted model system to stimulate T-cells in an antigen-specific manner. In this paper, we showcase the possibilities of this platform using primary transgenic T-cells triggered specifically via their cognate antigen presented by MHCII.
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Affiliation(s)
- Martin Fölser
- Institute of Applied Physics, TU Wien, 1060 Vienna, Austria; (M.F.); (V.M.)
| | - Viktoria Motsch
- Institute of Applied Physics, TU Wien, 1060 Vienna, Austria; (M.F.); (V.M.)
- Institute of Agricultural Engineering, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - René Platzer
- Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, 1090 Vienna, Austria; (R.P.); (J.B.H.)
| | - Johannes B. Huppa
- Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, 1090 Vienna, Austria; (R.P.); (J.B.H.)
| | - Gerhard J. Schütz
- Institute of Applied Physics, TU Wien, 1060 Vienna, Austria; (M.F.); (V.M.)
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43
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Wilson IA, Stanfield RL. 50 Years of structural immunology. J Biol Chem 2021; 296:100745. [PMID: 33957119 PMCID: PMC8163984 DOI: 10.1016/j.jbc.2021.100745] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/24/2021] [Accepted: 04/30/2021] [Indexed: 12/12/2022] Open
Abstract
Fifty years ago, the first landmark structures of antibodies heralded the dawn of structural immunology. Momentum then started to build toward understanding how antibodies could recognize the vast universe of potential antigens and how antibody-combining sites could be tailored to engage antigens with high specificity and affinity through recombination of germline genes (V, D, J) and somatic mutation. Equivalent groundbreaking structures in the cellular immune system appeared some 15 to 20 years later and illustrated how processed protein antigens in the form of peptides are presented by MHC molecules to T cell receptors. Structures of antigen receptors in the innate immune system then explained their inherent specificity for particular microbial antigens including lipids, carbohydrates, nucleic acids, small molecules, and specific proteins. These two sides of the immune system act immediately (innate) to particular microbial antigens or evolve (adaptive) to attain high specificity and affinity to a much wider range of antigens. We also include examples of other key receptors in the immune system (cytokine receptors) that regulate immunity and inflammation. Furthermore, these antigen receptors use a limited set of protein folds to accomplish their various immunological roles. The other main players are the antigens themselves. We focus on surface glycoproteins in enveloped viruses including SARS-CoV-2 that enable entry and egress into host cells and are targets for the antibody response. This review covers what we have learned over the past half century about the structural basis of the immune response to microbial pathogens and how that information can be utilized to design vaccines and therapeutics.
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MESH Headings
- Adaptive Immunity
- Allergy and Immunology/history
- Animals
- Antibodies, Viral/chemistry
- Antibodies, Viral/genetics
- Antibodies, Viral/immunology
- Antibody Specificity
- Antigen Presentation
- Antigens, Viral/chemistry
- Antigens, Viral/genetics
- Antigens, Viral/immunology
- COVID-19/immunology
- COVID-19/virology
- Crystallography/history
- Crystallography/methods
- History, 20th Century
- History, 21st Century
- Humans
- Immunity, Innate
- Protein Folding
- Protein Interaction Domains and Motifs
- Receptors, Antigen, T-Cell/chemistry
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- Receptors, Cytokine/chemistry
- Receptors, Cytokine/genetics
- Receptors, Cytokine/immunology
- SARS-CoV-2/immunology
- SARS-CoV-2/pathogenicity
- V(D)J Recombination
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Affiliation(s)
- Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA.
| | - Robyn L Stanfield
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
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44
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He Y, Agnihotri P, Rangarajan S, Chen Y, Kerzic MC, Ma B, Nussinov R, Mariuzza RA, Orban J. Peptide-MHC Binding Reveals Conserved Allosteric Sites in MHC Class I- and Class II-Restricted T Cell Receptors (TCRs). J Mol Biol 2020; 432:166697. [PMID: 33157083 PMCID: PMC8356565 DOI: 10.1016/j.jmb.2020.10.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 09/29/2020] [Accepted: 10/27/2020] [Indexed: 12/31/2022]
Abstract
T cells are vital for adaptive immune responses that protect against pathogens and cancers. The T cell receptor (TCR)-CD3 complex comprises a diverse αβ TCR heterodimer in noncovalent association with three invariant CD3 dimers. The TCR is responsible for recognizing antigenic peptides bound to MHC molecules (pMHC), while the CD3 dimers relay activation signals to the T cell. However, the mechanisms by which TCR engagement by pMHC is transmitted to CD3 remain mysterious, although there is growing evidence that mechanosensing and allostery both play a role. Here, we carried out NMR analysis of a human autoimmune TCR (MS2-3C8) that recognizes a self-peptide from myelin basic protein presented by the MHC class II molecule HLA-DR4. We observed pMHC-induced NMR signal perturbations in MS2-3C8 that indicate long-range effects on TCR β chain conformation and dynamics. Our results demonstrate that, in addition to expected changes in the NMR resonances of pMHC-contacting residues, perturbations extend to the Vβ/Vα, Vβ/Cβ, and Cβ/Cα interfacial regions. Moreover, the pattern of long-range perturbations is similar to that detected previously in the β chains of two MHC class I-restricted TCRs, thereby revealing a common allosteric pathway among three unrelated TCRs. Molecular dynamics (MD) simulations predict similar pMHC-induced effects. Taken together, our results demonstrate that pMHC binding induces long-range allosteric changes in the TCR β chain at conserved sites in both representative MHC class I- and class II-restricted TCRs, and that these sites may play a role in the transmission of signaling information.
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Affiliation(s)
- Yanan He
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA; Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
| | - Pragati Agnihotri
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Sneha Rangarajan
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Yihong Chen
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA; Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
| | - Melissa C Kerzic
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Buyong Ma
- Engineering Research Center of Cell & Therapeutic Antibody, MOE, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China; Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Roy A Mariuzza
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA.
| | - John Orban
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA; Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA.
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45
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Ramesh S, Park S, Call MJ, Im W, Call ME. Experimentally Guided Computational Methods Yield Highly Accurate Insights into Transmembrane Interactions within the T Cell Receptor Complex. J Phys Chem B 2020; 124:10303-10310. [PMID: 33030343 DOI: 10.1021/acs.jpcb.0c06403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Understanding how molecular interactions within the plasma membrane govern assembly, clustering, and conformational changes in single-pass transmembrane (TM) receptors has long presented substantial experimental challenges. Our previous work on activating immune receptors has combined direct biochemical and biophysical characterizations with both independent and experimentally restrained computational methods to provide novel insights into the key TM interactions underpinning assembly and stability of complex, multisubunit receptor systems. The recently published cryo-EM structure of the intact T cell receptor (TCR)-CD3 complex provides a unique opportunity to test the models and predictions arising from these studies, and we find that they are accurate, which we attribute to robust simulation environments and careful consideration of limitations related to studying TM interactions in isolation from additional receptor domains. With this in mind, we revisit results in other immune receptors and look forward to how similar methods may be applied to understand receptors for which little or no structural information is currently available.
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Affiliation(s)
- Samyuktha Ramesh
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Soohyung Park
- Departments of Biological Sciences, Chemistry, Bioengineering, and Computer Science and Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Melissa J Call
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Wonpil Im
- Departments of Biological Sciences, Chemistry, Bioengineering, and Computer Science and Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Matthew E Call
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
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46
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Mørch AM, Bálint Š, Santos AM, Davis SJ, Dustin ML. Coreceptors and TCR Signaling - the Strong and the Weak of It. Front Cell Dev Biol 2020; 8:597627. [PMID: 33178706 PMCID: PMC7596257 DOI: 10.3389/fcell.2020.597627] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 09/28/2020] [Indexed: 12/02/2022] Open
Abstract
The T-cell coreceptors CD4 and CD8 have well-characterized and essential roles in thymic development, but how they contribute to immune responses in the periphery is unclear. Coreceptors strengthen T-cell responses by many orders of magnitude - beyond a million-fold according to some estimates - but the mechanisms underlying these effects are still debated. T-cell receptor (TCR) triggering is initiated by the binding of the TCR to peptide-loaded major histocompatibility complex (pMHC) molecules on the surfaces of other cells. CD4 and CD8 are the only T-cell proteins that bind to the same pMHC ligand as the TCR, and can directly associate with the TCR-phosphorylating kinase Lck. At least three mechanisms have been proposed to explain how coreceptors so profoundly amplify TCR signaling: (1) the Lck recruitment model and (2) the pseudodimer model, both invoked to explain receptor triggering per se, and (3) two-step coreceptor recruitment to partially triggered TCRs leading to signal amplification. More recently it has been suggested that, in addition to initiating or augmenting TCR signaling, coreceptors effect antigen discrimination. But how can any of this be reconciled with TCR signaling occurring in the absence of CD4 or CD8, and with their interactions with pMHC being among the weakest specific protein-protein interactions ever described? Here, we review each theory of coreceptor function in light of the latest structural, biochemical, and functional data. We conclude that the oldest ideas are probably still the best, i.e., that their weak binding to MHC proteins and efficient association with Lck allow coreceptors to amplify weak incipient triggering of the TCR, without comprising TCR specificity.
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Affiliation(s)
- Alexander M. Mørch
- The Kennedy Institute of Rheumatology, University of Oxford, Oxford, United Kingdom
- Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Štefan Bálint
- The Kennedy Institute of Rheumatology, University of Oxford, Oxford, United Kingdom
| | - Ana Mafalda Santos
- Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Simon J. Davis
- Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Michael L. Dustin
- The Kennedy Institute of Rheumatology, University of Oxford, Oxford, United Kingdom
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47
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Chandler NJ, Call MJ, Call ME. T Cell Activation Machinery: Form and Function in Natural and Engineered Immune Receptors. Int J Mol Sci 2020; 21:E7424. [PMID: 33050044 PMCID: PMC7582382 DOI: 10.3390/ijms21197424] [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: 09/22/2020] [Revised: 10/05/2020] [Accepted: 10/07/2020] [Indexed: 12/15/2022] Open
Abstract
The impressive success of chimeric antigen receptor (CAR)-T cell therapies in treating advanced B-cell malignancies has spurred a frenzy of activity aimed at developing CAR-T therapies for other cancers, particularly solid tumors, and optimizing engineered T cells for maximum clinical benefit in many different disease contexts. A rapidly growing body of design work is examining every modular component of traditional single-chain CARs as well as expanding out into many new and innovative engineered immunoreceptor designs that depart from this template. New approaches to immune cell and receptor engineering are being reported with rapidly increasing frequency, and many recent high-quality reviews (including one in this special issue) provide comprehensive coverage of the history and current state of the art in CAR-T and related cellular immunotherapies. In this review, we step back to examine our current understanding of the structure-function relationships in natural and engineered lymphocyte-activating receptors, with an eye towards evaluating how well the current-generation CAR designs recapitulate the most desirable features of their natural counterparts. We identify key areas that we believe are under-studied and therefore represent opportunities to further improve our grasp of form and function in natural and engineered receptors and to rationally design better therapeutics.
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Affiliation(s)
- Nicholas J. Chandler
- Structural Biology Division, Walter and Eliza Hall Institute, Parkville, VIC 3052, Australia; (N.J.C.); (M.J.C.)
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Melissa J. Call
- Structural Biology Division, Walter and Eliza Hall Institute, Parkville, VIC 3052, Australia; (N.J.C.); (M.J.C.)
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Matthew E. Call
- Structural Biology Division, Walter and Eliza Hall Institute, Parkville, VIC 3052, Australia; (N.J.C.); (M.J.C.)
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
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48
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Tremblay MM, Ollinger T, Houtman JCD. The membrane proximal proline-rich region and correct order of C-terminal tyrosines on the adaptor protein LAT are required for TCR-mediated signaling and downstream functions. Cell Signal 2020; 76:109790. [PMID: 32979494 DOI: 10.1016/j.cellsig.2020.109790] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 09/21/2020] [Accepted: 09/22/2020] [Indexed: 12/11/2022]
Abstract
The primary activating receptor for T cells is the T cell receptor (TCR), which is stimulated upon binding to an antigen/MHC complex. TCR activation results in the induction of regulated signaling pathways vital for T cell differentiation, cellular adhesion and cytokine release. A critical TCR-induced signaling protein is the adaptor protein LAT. Upon TCR stimulation, LAT is phosphorylated on conserved tyrosines, which facilitates the formation of multiprotein complexes needed for propagation of signaling pathways. Although the role of the conserved tyrosines in LAT-mediated signaling has been investigated, few studies have examined the role of larger regions of LAT in TCR-induced pathways. In this study, a sequence alignment of 97 mammalian LAT proteins was used to identify several "functional" domains on LAT. Using LAT mutants expressed in Jurkat E6.1 cells, we observed that the membrane proximal, proline-rich region of LAT and the correct order of domains containing conserved tyrosines are necessary for optimal TCR-mediated early signaling, cytokine production, and cellular adhesion. Together, these data show that LAT contains distinct regions whose presence and correct order are required for the propagation of TCR-mediated signaling pathways.
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Affiliation(s)
- Mikaela M Tremblay
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, USA
| | - Tomye Ollinger
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, USA
| | - Jon C D Houtman
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, USA.
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49
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Kolan SS, Li G, Wik JA, Malachin G, Guo S, Kolan P, Skålhegg BS. Cellular metabolism dictates T cell effector function in health and disease. Scand J Immunol 2020; 92:e12956. [PMID: 32767795 DOI: 10.1111/sji.12956] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/13/2020] [Accepted: 08/03/2020] [Indexed: 12/23/2022]
Abstract
In a healthy person, metabolically quiescent T lymphocytes (T cells) circulate between lymph nodes and peripheral tissues in search of antigens. Upon infection, some T cells will encounter cognate antigens followed by proliferation and clonal expansion in a context-dependent manner, to become effector T cells. These events are accompanied by changes in cellular metabolism, known as metabolic reprogramming. The magnitude and variation of metabolic reprogramming are, in addition to antigens, dependent on factors such as nutrients and oxygen to ensure host survival during various diseases. Herein, we describe how metabolic programmes define T cell subset identity and effector functions. In addition, we will discuss how metabolic programs can be modulated and affect T cell activity in health and disease using cancer and autoimmunity as examples.
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Affiliation(s)
- Shrikant S Kolan
- Division for Molecular Nutrition, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Gaoyang Li
- Division for Molecular Nutrition, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Jonas A Wik
- Department of Pathology, Oslo University Hospital, Rikshopitalet, Oslo, Norway
| | - Giulia Malachin
- Division for Molecular Nutrition, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Shuai Guo
- Division for Molecular Nutrition, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Pratibha Kolan
- Division for Molecular Nutrition, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Bjørn S Skålhegg
- Division for Molecular Nutrition, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
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50
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The αβTCR mechanosensor exploits dynamic ectodomain allostery to optimize its ligand recognition site. Proc Natl Acad Sci U S A 2020; 117:21336-21345. [PMID: 32796106 DOI: 10.1073/pnas.2005899117] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Each [Formula: see text]T cell receptor (TCR) functions as a mechanosensor. The TCR is comprised of a clonotypic TCR[Formula: see text] ligand-binding heterodimer and the noncovalently associated CD3 signaling subunits. When bound by ligand, an antigenic peptide arrayed by a major histocompatibility complex molecule (pMHC), the TCR[Formula: see text] has a longer bond lifetime under piconewton-level loads. The atomistic mechanism of this "catch bond" behavior is unknown. Here, we perform molecular dynamics simulation of a TCR[Formula: see text]-pMHC complex and its variants under physiologic loads to identify this mechanism and any attendant TCR[Formula: see text] domain allostery. The TCR[Formula: see text]-pMHC interface is dynamically maintained by contacts with a spectrum of occupancies, introducing a level of control via relative motion between Vα and Vβ variable domains containing the pMHC-binding complementarity-determining region (CDR) loops. Without adequate load, the interfacial contacts are unstable, whereas applying sufficient load suppresses Vα-Vβ motion, stabilizing the interface. A second level of control is exerted by Cα and Cβ constant domains, especially Cβ and its protruding FG-loop, that create mismatching interfaces among the four TCR[Formula: see text] domains and with a pMHC ligand. Applied load enhances fit through deformation of the TCR[Formula: see text] molecule. Thus, the catch bond involves the entire TCR[Formula: see text] conformation, interdomain motion, and interfacial contact dynamics, collectively. This multilayered architecture of the machinery fosters fine-tuning of cellular response to load and pMHC recognition. Since the germline-derived TCR[Formula: see text] ectodomain is structurally conserved, the proposed mechanism can be universally adopted to operate under load during immune surveillance by diverse [Formula: see text]TCRs constituting the T cell repertoire.
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