1
|
Stamatopoulos K, Bruford E, Campo E, Lefranc MP. Immunogenetics in hematopathology and hematology: why a common language is important. Leukemia 2024; 38:1474-1476. [PMID: 38664547 PMCID: PMC11216993 DOI: 10.1038/s41375-024-02260-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 07/03/2024]
Affiliation(s)
- Kostas Stamatopoulos
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece.
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden.
| | - Elspeth Bruford
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - Elias Campo
- Hematopathology Section, Pathology Department, Hospital Clínic, University of Barcelona, Barcelona, Spain
- Molecular Pathology of Lymphoid Neoplasms Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Marie-Paule Lefranc
- IMGT®, the international ImMunoGeneTics information system®, Laboratoire d'ImmunoGénétique Moléculaire (LIGM), Institut de Génétique Humaine (IGH), Centre National de la Recherche Scientifique (CNRS), Université de Montpellier, Montpellier, France.
| |
Collapse
|
2
|
Yared N, Papadopoulou M, Barennes P, Pham HP, Quiniou V, Netzer S, Kaminski H, Burguet L, Demeste A, Colas P, Mora-Charrot L, Rousseau B, Izotte J, Zouine A, Gauthereau X, Vermijlen D, Déchanet-Merville J, Capone M. Long-lived central memory γδ T cells confer protection against murine cytomegalovirus reinfection. PLoS Pathog 2024; 20:e1010785. [PMID: 38976755 PMCID: PMC11257398 DOI: 10.1371/journal.ppat.1010785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 07/18/2024] [Accepted: 06/12/2024] [Indexed: 07/10/2024] Open
Abstract
The involvement of γδ TCR-bearing lymphocytes in immunological memory has gained increasing interest due to their functional duality between adaptive and innate immunity. γδ T effector memory (TEM) and central memory (TCM) subsets have been identified, but their respective roles in memory responses are poorly understood. In the present study, we used subsequent mouse cytomegalovirus (MCMV) infections of αβ T cell deficient mice in order to analyze the memory potential of γδ T cells. As for CMV-specific αβ T cells, MCMV induced the accumulation of cytolytic, KLRG1+CX3CR1+ γδ TEM that principally localized in infected organ vasculature. Typifying T cell memory, γδ T cell expansion in organs and blood was higher after secondary viral challenge than after primary infection. Viral control upon MCMV reinfection was prevented when masking γδ T-cell receptor, and was associated with a preferential amplification of private and unfocused TCR δ chain repertoire composed of a combination of clonotypes expanded post-primary infection and, more unexpectedly, of novel expanded clonotypes. Finally, long-term-primed γδ TCM cells, but not γδ TEM cells, protected T cell-deficient hosts against MCMV-induced death upon adoptive transfer, probably through their ability to survive and to generate TEM in the recipient host. This better survival potential of TCM cells was confirmed by a detailed scRNASeq analysis of the two γδ T cell memory subsets which also revealed their similarity to classically adaptive αβ CD8 T cells. Overall, our study uncovered memory properties of long-lived TCM γδ T cells that confer protection in a chronic infection, highlighting the interest of this T cell subset in vaccination approaches.
Collapse
Affiliation(s)
- Nathalie Yared
- Bordeaux University, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, ImmunoConcEpt, UMR 5164, ERL 1303, ImmunoConcEpt, Bordeaux, France
| | - Maria Papadopoulou
- Department of Pharmacotherapy and Pharmaceutics, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Institute for Medical Immunology, Université Libre de Bruxelles (ULB), Gosselies, Belgium
- Université Libre de Bruxelles Center for Research in Immunology, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | | | | | | | - Sonia Netzer
- Bordeaux University, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, ImmunoConcEpt, UMR 5164, ERL 1303, ImmunoConcEpt, Bordeaux, France
| | - Hanna Kaminski
- Bordeaux University, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, ImmunoConcEpt, UMR 5164, ERL 1303, ImmunoConcEpt, Bordeaux, France
| | - Laure Burguet
- Bordeaux University, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, ImmunoConcEpt, UMR 5164, ERL 1303, ImmunoConcEpt, Bordeaux, France
| | - Amandine Demeste
- Bordeaux University, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, ImmunoConcEpt, UMR 5164, ERL 1303, ImmunoConcEpt, Bordeaux, France
| | - Pacôme Colas
- Bordeaux University, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, ImmunoConcEpt, UMR 5164, ERL 1303, ImmunoConcEpt, Bordeaux, France
| | - Lea Mora-Charrot
- Bordeaux University, Service Commun des Animaleries, Bordeaux, France
| | - Benoit Rousseau
- Bordeaux University, Service Commun des Animaleries, Bordeaux, France
| | - Julien Izotte
- Bordeaux University, Service Commun des Animaleries, Bordeaux, France
| | - Atika Zouine
- Bordeaux University, Centre National de la Recherche Scientifique, Institut national de la santé et de la recherche médicale, FACSility, TBM Core, Bordeaux, France
| | - Xavier Gauthereau
- Bordeaux University, Centre National de la Recherche Scientifique, Institut national de la santé et de la recherche médicale, OneCell, RT-PCR and Single Cell Libraries, TBM Core, Bordeaux, France
| | - David Vermijlen
- Department of Pharmacotherapy and Pharmaceutics, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Institute for Medical Immunology, Université Libre de Bruxelles (ULB), Gosselies, Belgium
- Université Libre de Bruxelles Center for Research in Immunology, Université Libre de Bruxelles (ULB), Brussels, Belgium
- WELBIO department, Walloon ExceLlence Research Institute, Wavre, Belgium
| | - Julie Déchanet-Merville
- Bordeaux University, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, ImmunoConcEpt, UMR 5164, ERL 1303, ImmunoConcEpt, Bordeaux, France
| | - Myriam Capone
- Bordeaux University, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, ImmunoConcEpt, UMR 5164, ERL 1303, ImmunoConcEpt, Bordeaux, France
| |
Collapse
|
3
|
Chupp DP, Rivera CE, Zhou Y, Xu Y, Ramsey PS, Xu Z, Zan H, Casali P. A humanized mouse that mounts mature class-switched, hypermutated and neutralizing antibody responses. Nat Immunol 2024:10.1038/s41590-024-01880-3. [PMID: 38918608 DOI: 10.1038/s41590-024-01880-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 05/18/2024] [Indexed: 06/27/2024]
Abstract
Humanized mice are limited in terms of modeling human immunity, particularly with regards to antibody responses. Here we constructed a humanized (THX) mouse by grafting non-γ-irradiated, genetically myeloablated KitW-41J mutant immunodeficient pups with human cord blood CD34+ cells, followed by 17β-estradiol conditioning to promote immune cell differentiation. THX mice reconstitute a human lymphoid and myeloid immune system, including marginal zone B cells, germinal center B cells, follicular helper T cells and neutrophils, and develop well-formed lymph nodes and intestinal lymphoid tissue, including Peyer's patches, and human thymic epithelial cells. These mice have diverse human B cell and T cell antigen receptor repertoires and can mount mature T cell-dependent and T cell-independent antibody responses, entailing somatic hypermutation, class-switch recombination, and plasma cell and memory B cell differentiation. Upon flagellin or a Pfizer-BioNTech coronavirus disease 2019 (COVID-19) mRNA vaccination, THX mice mount neutralizing antibody responses to Salmonella or severe acute respiratory syndrome coronavirus 2 Spike S1 receptor-binding domain, with blood incretion of human cytokines, including APRIL, BAFF, TGF-β, IL-4 and IFN-γ, all at physiological levels. These mice can also develop lupus autoimmunity after pristane injection. By leveraging estrogen activity to support human immune cell differentiation and maturation of antibody responses, THX mice provide a platform to study the human immune system and to develop human vaccines and therapeutics.
Collapse
Affiliation(s)
- Daniel P Chupp
- The Antibody Laboratory, Department of Microbiology, Immunology & Molecular Genetics, The University of Texas Long School of Medicine, San Antonio, TX, USA
- Invivyd, Waltham, MA, USA
| | - Carlos E Rivera
- The Antibody Laboratory, Department of Microbiology, Immunology & Molecular Genetics, The University of Texas Long School of Medicine, San Antonio, TX, USA
| | - Yulai Zhou
- The Antibody Laboratory, Department of Microbiology, Immunology & Molecular Genetics, The University of Texas Long School of Medicine, San Antonio, TX, USA
| | - Yijiang Xu
- The Antibody Laboratory, Department of Microbiology, Immunology & Molecular Genetics, The University of Texas Long School of Medicine, San Antonio, TX, USA
| | - Patrick S Ramsey
- Department of Obstetrics & Gynecology, The University of Texas Long School of Medicine, San Antonio, TX, USA
| | - Zhenming Xu
- The Antibody Laboratory, Department of Microbiology, Immunology & Molecular Genetics, The University of Texas Long School of Medicine, San Antonio, TX, USA
| | - Hong Zan
- The Antibody Laboratory, Department of Microbiology, Immunology & Molecular Genetics, The University of Texas Long School of Medicine, San Antonio, TX, USA
- Prellis Biologics, Berkeley, CA, USA
| | - Paolo Casali
- The Antibody Laboratory, Department of Microbiology, Immunology & Molecular Genetics, The University of Texas Long School of Medicine, San Antonio, TX, USA.
- Department of Medicine, The University of Texas Long School of Medicine, San Antonio, TX, USA.
| |
Collapse
|
4
|
Sanchez Sanchez G, Emmrich S, Georga M, Papadaki A, Kossida S, Seluanov A, Gorbunova V, Vermijlen D. Invariant γδTCR natural killer-like effector T cells in the naked mole-rat. Nat Commun 2024; 15:4248. [PMID: 38762584 PMCID: PMC11102460 DOI: 10.1038/s41467-024-48652-z] [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: 07/20/2023] [Accepted: 05/03/2024] [Indexed: 05/20/2024] Open
Abstract
The naked mole-rat (Heterocephalus glaber) is a long-lived rodent species showing resistance to the development of cancer. Although naked mole-rats have been reported to lack natural killer (NK) cells, γδ T cell-based immunity has been suggested in this species, which could represent an important arm of the immune system for antitumor responses. Here, we investigate the biology of these unconventional T cells in peripheral tissues (blood, spleen) and thymus of the naked mole-rat at different ages by TCR repertoire profiling and single-cell gene expression analysis. Using our own TCR annotation in the naked mole-rat genome, we report that the γδ TCR repertoire is dominated by a public invariant Vγ4-2/Vδ1-4 TCR, containing the complementary-determining-region-3 (CDR3)γ CTYWDSNYAKKLF / CDR3δ CALWELRTGGITAQLVF that are likely generated by short-homology-repeat-driven DNA rearrangements. This invariant TCR is specifically found in γδ T cells expressing genes associated with NK cytotoxicity and is generated in both the thoracic and cervical thymus of the naked mole-rat until adult life. Our results indicate that invariant Vγ4-2/Vδ1-4 NK-like effector T cells in the naked mole-rat can contribute to tumor immunosurveillance by γδ TCR-mediated recognition of a common molecular signal.
Collapse
MESH Headings
- Animals
- Mole Rats/immunology
- Receptors, Antigen, T-Cell, gamma-delta/metabolism
- Receptors, Antigen, T-Cell, gamma-delta/genetics
- Receptors, Antigen, T-Cell, gamma-delta/immunology
- Thymus Gland/immunology
- Thymus Gland/cytology
- Killer Cells, Natural/immunology
- Spleen/immunology
- Complementarity Determining Regions/genetics
- Natural Killer T-Cells/immunology
Collapse
Affiliation(s)
- Guillem Sanchez Sanchez
- Department of Pharmacotherapy and Pharmaceutics, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Institute for Medical Immunology, Université Libre de Bruxelles (ULB), Gosselies, Belgium
- ULB Center for Research in Immunology (U-CRI), Université Libre de Bruxelles (ULB), Gosselies, Belgium
- WELBIO Department, WEL Research Institute, Wavre, Belgium
| | - Stephan Emmrich
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Maria Georga
- IMGT®, the international ImMunoGenetics information system®, Institut de Génétique Humaine (IGH), Centre National de la Recherche Scientifique (CNRS), Université de Montpellier (UM), Montpellier, France
| | - Ariadni Papadaki
- IMGT®, the international ImMunoGenetics information system®, Institut de Génétique Humaine (IGH), Centre National de la Recherche Scientifique (CNRS), Université de Montpellier (UM), Montpellier, France
| | - Sofia Kossida
- IMGT®, the international ImMunoGenetics information system®, Institut de Génétique Humaine (IGH), Centre National de la Recherche Scientifique (CNRS), Université de Montpellier (UM), Montpellier, France
| | - Andrei Seluanov
- Department of Biology, University of Rochester, Rochester, NY, USA
- Department of Medicine, University of Rochester Medical Center and Medicine, University of Rochester, Rochester, NY, USA
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, NY, USA
- Department of Medicine, University of Rochester Medical Center and Medicine, University of Rochester, Rochester, NY, USA
| | - David Vermijlen
- Department of Pharmacotherapy and Pharmaceutics, Université Libre de Bruxelles (ULB), Brussels, Belgium.
- Institute for Medical Immunology, Université Libre de Bruxelles (ULB), Gosselies, Belgium.
- ULB Center for Research in Immunology (U-CRI), Université Libre de Bruxelles (ULB), Gosselies, Belgium.
- WELBIO Department, WEL Research Institute, Wavre, Belgium.
| |
Collapse
|
5
|
Kovacheva E, Gevezova M, Maes M, Sarafian V. The mast cells - Cytokines axis in Autism Spectrum Disorder. Neuropharmacology 2024; 249:109890. [PMID: 38431049 DOI: 10.1016/j.neuropharm.2024.109890] [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: 01/22/2024] [Revised: 02/19/2024] [Accepted: 02/24/2024] [Indexed: 03/05/2024]
Abstract
Autism Spectrum Disorder (ASD) is a neurodevelopmental disturbance, diagnosed in early childhood. It is associated with varying degrees of dysfunctional communication and social skills, repetitive and stereotypic behaviors. Regardless of the constant increase in the number of diagnosed patients, there are still no established treatment schemes in global practice. Many children with ASD have allergic symptoms, often in the absence of mast cell (MC) positive tests. Activation of MCs may release molecules related to inflammation and neurotoxicity, which contribute to the pathogenesis of ASD. The aim of the present paper is to enrich the current knowledge regarding the relationship between MCs and ASD by providing PPI network analysis-based data that reveal key molecules and immune pathways associated with MCs in the pathogenesis of autism. Network and enrichment analyzes were performed using receptor information and secreted molecules from activated MCs identified in ASD patients. Our analyses revealed cytokines and key marker molecules for MCs degranulation, molecular pathways of key mediators released during cell degranulation, as well as various receptors. Understanding the relationship between ASD and the activation of MCs, as well as the involved molecules and interactions, is important for elucidating the pathogenesis of ASD and developing effective future treatments for autistic patients by discovering new therapeutic target molecules.
Collapse
Affiliation(s)
- Eleonora Kovacheva
- Department of Medical Biology, Medical University-Plovdiv, Plovdiv, Bulgaria; Research Institute at Medical University-Plovdiv, Plovdiv, Bulgaria
| | - Maria Gevezova
- Department of Medical Biology, Medical University-Plovdiv, Plovdiv, Bulgaria; Research Institute at Medical University-Plovdiv, Plovdiv, Bulgaria
| | - Michael Maes
- Research Institute at Medical University-Plovdiv, Plovdiv, Bulgaria; Sichuan Provincial Center for Mental Health, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072, China; Key Laboratory of Psychosomatic Medicine, Chinese Academy of Medical Sciences, Chengdu, 610072, China; Department of Psychiatry, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand; Cognitive Fitness and Technology Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; Department of Psychiatry, Medical University-Plovdiv, Plovdiv, Bulgaria; Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447, South Korea
| | - Victoria Sarafian
- Department of Medical Biology, Medical University-Plovdiv, Plovdiv, Bulgaria; Research Institute at Medical University-Plovdiv, Plovdiv, Bulgaria.
| |
Collapse
|
6
|
Hahn WO, Parks KR, Shen M, Ozorowski G, Janes H, Ballweber-Fleming L, Woodward Davis AS, Duplessis C, Tomai M, Dey AK, Sagawa ZK, De Rosa SC, Seese A, Siddaramaiah LK, Stamatatos L, Lee WH, Sewall LM, Karlinsey D, Turner HL, Rubin V, Furth S, MacPhee K, Duff M, Corey L, Keefer MC, Edupuganti S, Frank I, Maenza J, Baden LR, Hyrien O, Sanders RW, Moore JP, Ward AB, Tomaras GD, Montefiori DC, Rouphael N, McElrath MJ. HIV BG505 SOSIP.664 trimer with 3M-052-AF/alum induces human autologous tier-2 neutralizing antibodies. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.08.24306957. [PMID: 38766048 PMCID: PMC11100857 DOI: 10.1101/2024.05.08.24306957] [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
Stabilized trimers preserving the native-like HIV envelope structure may be key components of a preventive HIV vaccine regimen to induce broadly neutralizing antibodies (bnAbs). We evaluated trimeric BG505 SOSIP.664 gp140, formulated with a novel TLR7/8 signaling adjuvant, 3M-052-AF/Alum, for safety, adjuvant dose-finding and immunogenicity in a first-in-healthy adult (n=17), randomized, placebo-controlled trial (HVTN 137A). The vaccine regimen appeared safe. Robust, trimer-specific antibody, B-cell and CD4+ T-cell responses emerged post-vaccination. Five vaccinees developed serum autologous tier-2 nAbs (ID50 titer, 1:28-1:8647) after 2-3 doses targeting C3/V5 and/or V1/V2/V3 Env regions by electron microscopy and mutated pseudovirus-based neutralization analyses. Trimer-specific, B-cell-derived monoclonal antibody activities confirmed these results and showed weak heterologous neutralization in the strongest responder. Our findings demonstrate the clinical utility of the 3M-052-AF/alum adjuvant and support further improvements of trimer-based Env immunogens to focus responses on multiple broad nAb epitopes. KEY TAKEAWAY/TAKE-HOME MESSAGES HIV BG505 SOSIP.664 trimer with novel 3M-052-AF/alum adjuvant in humans appears safe and induces serum neutralizing antibodies to matched clade A, tier 2 virus, that map to diverse Env epitopes with relatively high titers. The novel adjuvant may be an important mediator of vaccine response.
Collapse
|
7
|
Zou JL, Chen KX, Wang XJ, Lu ZC, Wu XH, Wu YD. Structure-Based Rational and General Strategy for Stabilizing Single-Chain T-Cell Receptors to Enhance Affinity. J Med Chem 2024. [PMID: 38661304 DOI: 10.1021/acs.jmedchem.4c00503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The T-cell receptor (TCR) is a crucial molecule in cellular immunity. The single-chain T-cell receptor (scTCR) is a potential format in TCR therapeutics because it eliminates the possibility of αβ-TCR mispairing. However, its poor stability and solubility impede the in vitro study and manufacturing of therapeutic applications. In this study, some conserved structural motifs are identified in variable domains regardless of germlines and species. Theoretical analysis helps to identify those unfavored factors and leads to a general strategy for stabilizing scTCRs by substituting residues at exact IMGT positions with beneficial propensities on the consensus sequence of germlines. Several representative scTCRs are displayed to achieve stability optimization and retain comparable binding affinities with the corresponding αβ-TCRs in the range of μM to pM. These results demonstrate that our strategies for scTCR engineering are capable of providing the affinity-enhanced and specificity-retained format, which are of great value in facilitating the development of TCR-related therapeutics.
Collapse
Affiliation(s)
- Jia-Ling Zou
- Lab of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | | | | | | | - Xian-Hui Wu
- Tianmu Institute of Health, Changzhou 213399, China
| | - Yun-Dong Wu
- Lab of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- Shenzhen Bay Laboratory, Shenzhen 518132, China
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| |
Collapse
|
8
|
Auer PL, Farazi M, Zhang T, Dong J, Bolon YT, Spellman SR, Saber W. Donor germ-line variants associate with outcomes of allogeneic hematopoietic stem cell transplantation in patients with myelodysplastic syndromes. Am J Hematol 2024; 99:770-773. [PMID: 38339773 PMCID: PMC10947828 DOI: 10.1002/ajh.27243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 01/10/2024] [Accepted: 01/19/2024] [Indexed: 02/12/2024]
Abstract
Overall survival probability for MDS patients who underwent allo-HCT and were matched to donors that are wild-type (red) and heterozygous (blue) for the rs111224634 SNP.
Collapse
Affiliation(s)
- Paul L. Auer
- Division of Biostatistics, Institute for Health & Equity, Medical College of Wisconsin, Milwaukee, WI, USA
- Medical College of Wisconsin Cancer Center, Milwaukee, WI, USA
| | - Manzur Farazi
- Division of Biostatistics, Institute for Health & Equity, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Tao Zhang
- CIBMTR (Center for International Blood and Marrow Transplant Research), National Marrow Donor Program/Be The Match, Minneapolis, MN, USA
| | - Jing Dong
- Medical College of Wisconsin Cancer Center, Milwaukee, WI, USA
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
- Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Yung-Tsi Bolon
- CIBMTR (Center for International Blood and Marrow Transplant Research), National Marrow Donor Program/Be The Match, Minneapolis, MN, USA
| | - Stephen R. Spellman
- CIBMTR (Center for International Blood and Marrow Transplant Research), National Marrow Donor Program/Be The Match, Minneapolis, MN, USA
| | - Wael Saber
- Division of Hematology and Oncology, Department of Medicine, CIBMTR (Center for International Blood and Marrow Transplant Research), Medical College of Wisconsin, Milwaukee, WI, USA
| |
Collapse
|
9
|
Gu X, Wang S, Zhang W, Li C, Guo L, Wang Z, Li H, Zhang H, Zhou Y, Liang W, Li H, Liu Y, Wang Y, Huang L, Dong T, Zhang D, Wong CCL, Cao B. Probing long COVID through a proteomic lens: a comprehensive two-year longitudinal cohort study of hospitalised survivors. EBioMedicine 2023; 98:104851. [PMID: 37924708 PMCID: PMC10660018 DOI: 10.1016/j.ebiom.2023.104851] [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: 08/01/2023] [Revised: 10/12/2023] [Accepted: 10/12/2023] [Indexed: 11/06/2023] Open
Abstract
BACKGROUND As a debilitating condition that can impact a whole spectrum of people and involve multi-organ systems, long COVID has aroused the most attention than ever. However, mechanisms of long COVID are not clearly understood, and underlying biomarkers that can affect the long-term consequences of COVID-19 are paramount to be identified. METHODS Participants for the current study were from a cohort study of COVID-19 survivors discharged from hospital between Jan 7, and May 29, 2020. We profiled the proteomic of plasma samples from hospitalised COVID-19 survivors at 6-month, 1-year, and 2-year after symptom onset and age and sex matched healthy controls. Fold-change of >2 or <0.5, and false-discovery rate adjusted P value of 0.05 were used to filter differentially expressed proteins (DEPs). In-genuity pathway analysis was performed to explore the down-stream effects in the dataset of significantly up- or down-regulated proteins. Proteins were integrated with long-term consequences of COVID-19 survivors to explore potential biomarkers of long COVID. FINDINGS The proteomic of 709 plasma samples from 181 COVID-19 survivors and 181 matched healthy controls was profiled. In both COVID-19 and control group, 114 (63%) were male. The results indicated four major recovery modes of biological processes. Pathways related to cell-matrix interactions and cytoskeletal remodeling and hypertrophic cardiomyopathy and dilated cardiomyopathy pathways recovered relatively earlier which was before 1-year after infection. Majority of immune response pathways, complement and coagulation cascade, and cholesterol metabolism returned to similar status of matched healthy controls later but before 2-year after infection. Fc receptor signaling pathway still did not return to status similar to healthy controls at 2-year follow-up. Pathways related to neuron generation and differentiation showed persistent suppression across 2-year after infection. Among 98 DEPs from the above pathways, evidence was found for association of 11 proteins with lung function recovery, with the associations consistent at two consecutive or all three follow-ups. These proteins were mainly enriched in complement and coagulation (COMP, PLG, SERPINE1, SRGN, COL1A1, FLNA, and APOE) and hypertrophic/dilated cardiomyopathy (TPM2, TPM1, and AGT) pathways. Two DEPs (APOA4 and LRP1) involved in both neuron and cholesterol pathways showed associations with smell disorder. INTERPRETATION The study findings provided molecular insights into potential mechanism of long COVID, and put forward biomarkers for more precise intervention to reduce burden of long COVID. FUNDING National Natural Science Foundation of China; Chinese Academy of Medical Sciences (CAMS) Innovation Fund for Medical Sciences; Clinical Research Operating Fund of Central High Level Hospitals; the Talent Program of the Chinese Academy of Medical Science; Training Program of the Big Science Strategy Plan; Ministry of Science and Technology of the People's Republic of China; New Cornerstone Science Foundation; Peking Union Medical College Education Foundation; Research Funds from Health@InnoHK Program.
Collapse
Affiliation(s)
- Xiaoying Gu
- National Center for Respiratory Medicine; State Key Laboratory of Respiratory Health and Multimorbidity; National Clinical Research Center for Respiratory Diseases; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences; Department of Clinical Research and Data Management, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, PR China; Changping Laboratory, Beijing, PR China
| | - Siyuan Wang
- State Key Laboratory of Complex Severe and Rare Diseases, Clinical Research Institute, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, PR China
| | - Wanying Zhang
- National Center for Respiratory Medicine; State Key Laboratory of Respiratory Health and Multimorbidity; National Clinical Research Center for Respiratory Diseases; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences; Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, PR China
| | - Caihong Li
- Wuhan Jinyintan Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei Province, PR China; Wuhan Research Center for Communicable Disease Diagnosis and Treatment, Chinese Academy of Medical Sciences, Wuhan, Hubei Province, PR China
| | - Li Guo
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR China; NHC Key Laboratory of Systems Biology of Pathogens and Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences, Beijing, PR China
| | - Zai Wang
- Changping Laboratory, Beijing, PR China; Institute of Clinical Medical Sciences, China-Japan Friendship Hospital, Beijing, PR China
| | - Haibo Li
- Changping Laboratory, Beijing, PR China; National Center for Respiratory Medicine; State Key Laboratory of Respiratory Health and Multimorbidity; National Clinical Research Center for Respiratory Diseases; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences; Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, PR China
| | - Hui Zhang
- State Key Laboratory of Complex Severe and Rare Diseases, Clinical Research Institute, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, PR China; Department of Pulmonary and Critical Care Medicine, Capital Medical University, Beijing, PR China
| | - Yuhan Zhou
- Foreseen Biotechnology, Beijing, PR China
| | | | - Hui Li
- Changping Laboratory, Beijing, PR China; State Key Laboratory of Complex Severe and Rare Diseases, Clinical Research Institute, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, PR China
| | - Yan Liu
- State Key Laboratory of Complex Severe and Rare Diseases, Clinical Research Institute, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, PR China; Department of Infectious Disease, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, PR China
| | - Yeming Wang
- Changping Laboratory, Beijing, PR China; State Key Laboratory of Complex Severe and Rare Diseases, Clinical Research Institute, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, PR China
| | - Lixue Huang
- Department of Respiratory and Critical Care Medicine, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, PR China
| | - Tao Dong
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Dingyu Zhang
- Wuhan Jinyintan Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei Province, PR China; Wuhan Research Center for Communicable Disease Diagnosis and Treatment, Chinese Academy of Medical Sciences, Wuhan, Hubei Province, PR China; Hubei Clinical Research Center for Infectious Diseases, Wuhan, Hubei Province, PR China.
| | - Catherine C L Wong
- State Key Laboratory of Complex Severe and Rare Diseases, Clinical Research Institute, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, PR China; Tsinghua University-Peking University Joint Center for Life Sciences, Beijing, PR China.
| | - Bin Cao
- Changping Laboratory, Beijing, PR China; National Center for Respiratory Medicine; State Key Laboratory of Respiratory Health and Multimorbidity; National Clinical Research Center for Respiratory Diseases; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences; Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, PR China; Department of Pulmonary and Critical Care Medicine, Capital Medical University, Beijing, PR China; Tsinghua University-Peking University Joint Center for Life Sciences, Beijing, PR China.
| |
Collapse
|
10
|
Bachar-Wikstrom E, Dhillon B, Gill Dhillon N, Abbo L, Lindén SK, Wikstrom JD. Mass Spectrometry Analysis of Shark Skin Proteins. Int J Mol Sci 2023; 24:16954. [PMID: 38069276 PMCID: PMC10707392 DOI: 10.3390/ijms242316954] [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: 10/26/2023] [Revised: 11/21/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
The mucus layer covering the skin of fish has several roles, including protection against pathogens and mechanical damage in which proteins play a key role. While proteins in the skin mucus layer of various common bony fish species have been explored, the proteins of shark skin mucus remain unexplored. In this pilot study, we examine the protein composition of the skin mucus in spiny dogfish sharks and chain catsharks through mass spectrometry (NanoLC-MS/MS). Overall, we identified 206 and 72 proteins in spiny dogfish (Squalus acanthias) and chain catsharks (Scyliorhinus retifer), respectively. Categorization showed that the proteins belonged to diverse biological processes and that most proteins were cellular albeit a significant minority were secreted, indicative of mucosal immune roles. The secreted proteins are reviewed in detail with emphasis on their immune potentials. Moreover, STRING protein-protein association network analysis showed that proteins of closely related shark species were more similar as compared to a more distantly related shark and a bony fish, although there were also significant overlaps. This study contributes to the growing field of molecular shark studies and provides a foundation for further research into the functional roles and potential human biomedical implications of shark skin mucus proteins.
Collapse
Affiliation(s)
- Etty Bachar-Wikstrom
- Dermatology and Venereology Division, Department of Medicine (Solna), Karolinska Institutet, 17177 Stockholm, Sweden
- Whitman Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Braham Dhillon
- Department of Plant Pathology, Fort Lauderdale Research and Education Center, IFAS, University of Florida, Davie, FL 33314, USA
| | - Navi Gill Dhillon
- Department of Biological Sciences, Nova Southeastern University, Davie, FL 33314, USA
| | - Lisa Abbo
- Whitman Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Sara K. Lindén
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Jakob D. Wikstrom
- Dermatology and Venereology Division, Department of Medicine (Solna), Karolinska Institutet, 17177 Stockholm, Sweden
- Whitman Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
- Dermato-Venereology Clinic, Karolinska University Hospital, 17176 Stockholm, Sweden
| |
Collapse
|
11
|
Volkmar M, Fakhr E, Zens S, Bury A, Offringa R, Gordon J, Huduti E, Wölfel T, Wölfel C. Identification of TRDV-TRAJ V domains in human and mouse T-cell receptor repertoires. Front Immunol 2023; 14:1286688. [PMID: 38077312 PMCID: PMC10702483 DOI: 10.3389/fimmu.2023.1286688] [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: 08/31/2023] [Accepted: 10/30/2023] [Indexed: 12/18/2023] Open
Abstract
Here, we describe the identification of two T-cell receptors (TRs) containing TRDV genes in their TRA chains, the first one in human and the second one in mouse. First, using 5'RACE on a mixed lymphocyte-tumor cell culture (MLTC), we identified TRDV1 5'-untranslated region (UTR) and complete coding sequence rearranged productively to TRAJ24. Single-cell TR RNA sequencing (RNA-seq) of the MLTC, conducted to identify additional clonotypes, revealed that the analysis software detected the hybrid TRDV-TRAJ TRA (TRA) chain but excluded it from the final results. In a separate project, we performed TR sequencing of tumor-infiltrating lymphocytes (TILs) in a murine tumor model. Here, the predominant clonotype contained a TRA chain with a TRDV2-2-TRAJ49 rearrangement. Again, the hybrid TRA chain was not reported in the final results. Transfection of both TR cDNAs resulted in cell surface localization of TR together with CD3, suggesting a productive protein in both cases. Tumor recognition of the Homo sapiens (Homsap) TRDV1-containing TR could be demonstrated by IFN Gamma ELISA ELISpot kit, whereas the Mus musculus (Musmus) TR did not recognize a tumor-derived cell line. To determine whether the TRDV-containing TRA chains we detected were rare events or whether TRDV genes are commonly incorporated into TRA chains, we queried the NCBI Sequence Read Archive for TR single-cell RNA-seq data and analyzed 21 human and 23 murine datasets. We found that especially Homsap TRDV1, Musmus TRDV1, and to some extent Musmus TRDV2-2 are more commonly incorporated into TRA chains than several TRAV genes, making those TRDV genes a relevant contribution to TRA diversity. TRDV-containing TRA chains are currently excluded from the final results of V-(D)-J dataset analyses with the CellRanger software. We provide a work-around to avoid exclusion of those hybrid TRA chains from the final analysis results.
Collapse
Affiliation(s)
- Michael Volkmar
- TCR Discovery Platform, Helmholtz Institute for Translational Oncology (HI-TRON) Mainz, Mainz, Germany
| | - Elham Fakhr
- TCR Discovery Platform, Helmholtz Institute for Translational Oncology (HI-TRON) Mainz, Mainz, Germany
| | - Stefan Zens
- Department D200, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Alice Bury
- Helmholtz Institute for Translational Oncology (HI-TRON) Mainz, Mainz, Germany
| | - Rienk Offringa
- Department D200, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jessica Gordon
- BioNtech, Deptartment Immunotherapies & Preclinical Research, Cellular Biomarker and Immunology Research Team, Mainz, Germany
| | - Enes Huduti
- Helmholtz Institute for Translational Oncology (HI-TRON) Mainz, Mainz, Germany
| | - Thomas Wölfel
- Internal Medicine III, University Cancer Center (UCT), Research Center for Immunotherapy (FZI), University Medical Center (UMC) of the Johannes Gutenberg University Mainz and German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, Mainz, Germany
| | - Catherine Wölfel
- Internal Medicine III, University Cancer Center (UCT), Research Center for Immunotherapy (FZI), University Medical Center (UMC) of the Johannes Gutenberg University Mainz and German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, Mainz, Germany
| |
Collapse
|
12
|
Nagano Y, Chain B. tidytcells: standardizer for TR/MH nomenclature. Front Immunol 2023; 14:1276106. [PMID: 37954585 PMCID: PMC10634431 DOI: 10.3389/fimmu.2023.1276106] [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: 08/11/2023] [Accepted: 10/09/2023] [Indexed: 11/14/2023] Open
Abstract
T cell receptors (TR) underpin the diversity and specificity of T cell activity. As such, TR repertoire data is valuable both as an adaptive immune biomarker, and as a way to identify candidate therapeutic TR. Analysis of TR repertoires relies heavily on computational analysis, and therefore it is of vital importance that the data is standardized and computer-readable. However in practice, the usage of different abbreviations and non-standard nomenclature in different datasets makes this data pre-processing non-trivial. tidytcells is a lightweight, platform-independent Python package that provides easy-to-use standardization tools specifically designed for TR nomenclature. The software is open-sourced under the MIT license and is available to install from the Python Package Index (PyPI). At the time of publishing, tidytcells is on version 2.0.0.
Collapse
Affiliation(s)
- Yuta Nagano
- Division of Medicine, Faculty of Medical Scienecs, University College London (UCL), London, United Kingdom
| | - Benjamin Chain
- Division of Infection and Immunity, Faculty of Medical Sciences, University College London (UCL), London, United Kingdom
| |
Collapse
|
13
|
Pospiech M, Tamizharasan M, Wei YC, Kumar AMS, Lou M, Milstein J, Alachkar H. Features of the TCR repertoire associate with patients' clinical and molecular characteristics in acute myeloid leukemia. Front Immunol 2023; 14:1236514. [PMID: 37928542 PMCID: PMC10620936 DOI: 10.3389/fimmu.2023.1236514] [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: 06/07/2023] [Accepted: 09/07/2023] [Indexed: 11/07/2023] Open
Abstract
Background Allogeneic hematopoietic stem cell transplant remains the most effective strategy for patients with high-risk acute myeloid leukemia (AML). Leukemia-specific neoantigens presented by the major histocompatibility complexes (MHCs) are recognized by the T cell receptors (TCR) triggering the graft-versus-leukemia effect. A unique TCR signature is generated by a complex V(D)J rearrangement process to form TCR capable of binding to the peptide-MHC. The generated TCR repertoire undergoes dynamic changes with disease progression and treatment. Method Here we applied two different computational tools (TRUST4 and MIXCR) to extract the TCR sequences from RNA-seq data from The Cancer Genome Atlas (TCGA) and examine the association between features of the TCR repertoire in adult patients with AML and their clinical and molecular characteristics. Results We found that only ~30% of identified TCR CDR3s were shared by the two computational tools. Yet, patterns of TCR associations with patients' clinical and molecular characteristics based on data obtained from either tool were similar. The numbers of unique TCR clones were highly correlated with patients' white blood cell counts, bone marrow blast percentage, and peripheral blood blast percentage. Multivariable regressions of TCRA and TCRB median normalized number of unique clones with mutational status of AML patients using TRUST4 showed significant association of TCRA or TCRB with WT1 mutations, WBC count, %BM blast, and sex (adjusted in TCRB model). We observed a correlation between TCRA/B number of unique clones and the expression of T cells inhibitory signal genes (TIGIT, LAG3, CTLA-4) and foxp3, but not IL2RA, CD69 and TNFRSF9 suggestive of exhausted T cell phenotypes in AML. Conclusion Benchmarking of computational tools is needed to increase the accuracy of the identified clones. The utilization of RNA-seq data enables identification of highly abundant TCRs and correlating these clones with patients' clinical and molecular characteristics. This study further supports the value of high-resolution TCR-Seq analyses to characterize the TCR repertoire in patients.
Collapse
Affiliation(s)
- Mateusz Pospiech
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA, United States
| | - Mukund Tamizharasan
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA, United States
- Department of Computer Science, University of Southern California, Los Angeles, CA, United States
| | - Yu-Chun Wei
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA, United States
| | - Advaith Maya Sanjeev Kumar
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA, United States
- Department of Computer Science, University of Southern California, Los Angeles, CA, United States
| | - Mimi Lou
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA, United States
| | - Joshua Milstein
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Houda Alachkar
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA, United States
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, United States
| |
Collapse
|
14
|
He W, Ou T, Skamangas N, Bailey CC, Bronkema N, Guo Y, Yin Y, Kobzarenko V, Zhang X, Pan A, Liu X, Xu J, Zhang L, Allwardt AE, Mitra D, Quinlan B, Sanders RW, Choe H, Farzan M. Heavy-chain CDR3-engineered B cells facilitate in vivo evaluation of HIV-1 vaccine candidates. Immunity 2023; 56:2408-2424.e6. [PMID: 37531955 PMCID: PMC11092302 DOI: 10.1016/j.immuni.2023.07.003] [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: 12/19/2022] [Revised: 05/09/2023] [Accepted: 07/05/2023] [Indexed: 08/04/2023]
Abstract
V2-glycan/apex broadly neutralizing antibodies (bnAbs) recognize a closed quaternary epitope of the HIV-1 envelope glycoprotein (Env). This closed structure is necessary to elicit apex antibodies and useful to guide the maturation of other bnAb classes. To compare antigens designed to maintain this conformation, we evaluated apex-specific responses in mice engrafted with a diverse repertoire of B cells expressing the HCDR3 of the apex bnAb VRC26.25. Engineered B cells affinity matured, guiding the improvement of VRC26.25 itself. We found that soluble Env (SOSIP) variants differed significantly in their ability to raise anti-apex responses. A transmembrane SOSIP (SOSIP-TM) delivered as an mRNA-lipid nanoparticle elicited more potent neutralizing responses than multimerized SOSIP proteins. Importantly, SOSIP-TM elicited neutralizing sera from B cells engineered with the predicted VRC26.25-HCDR3 progenitor, which also affinity matured. Our data show that HCDR3-edited B cells facilitate efficient in vivo comparisons of Env antigens and highlight the potential of an HCDR3-focused vaccine approach.
Collapse
Affiliation(s)
- Wenhui He
- Division of Infectious Disease, Boston Children's Hospital, Boston, MA 02115, USA; The Center for Integrated Solutions to Infectious Diseases, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Department of Immunology and Microbiology, UF Scripps Biomedical Research, Jupiter, FL 33458, USA
| | - Tianling Ou
- Division of Infectious Disease, Boston Children's Hospital, Boston, MA 02115, USA; The Center for Integrated Solutions to Infectious Diseases, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Department of Immunology and Microbiology, UF Scripps Biomedical Research, Jupiter, FL 33458, USA
| | - Nickolas Skamangas
- Division of Infectious Disease, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Department of Immunology and Microbiology, UF Scripps Biomedical Research, Jupiter, FL 33458, USA
| | - Charles C Bailey
- The Center for Integrated Solutions to Infectious Diseases, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Immunology and Microbiology, UF Scripps Biomedical Research, Jupiter, FL 33458, USA
| | - Naomi Bronkema
- Division of Infectious Disease, Boston Children's Hospital, Boston, MA 02115, USA; The Center for Integrated Solutions to Infectious Diseases, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Skaggs Graduate School, Scripps Research, La Jolla, CA 92037, USA
| | - Yan Guo
- Department of Immunology and Microbiology, UF Scripps Biomedical Research, Jupiter, FL 33458, USA
| | - Yiming Yin
- Division of Infectious Disease, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Valerie Kobzarenko
- Department of Computer Engineering and Sciences, Florida Institute of Technology, Melbourne, FL 32901, USA
| | - Xia Zhang
- Department of Immunology and Microbiology, UF Scripps Biomedical Research, Jupiter, FL 33458, USA
| | - Andi Pan
- Division of Infectious Disease, Boston Children's Hospital, Boston, MA 02115, USA; The Center for Integrated Solutions to Infectious Diseases, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Skaggs Graduate School, Scripps Research, La Jolla, CA 92037, USA
| | - Xin Liu
- Division of Infectious Disease, Boston Children's Hospital, Boston, MA 02115, USA; The Center for Integrated Solutions to Infectious Diseases, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Jinge Xu
- Division of Infectious Disease, Boston Children's Hospital, Boston, MA 02115, USA; The Center for Integrated Solutions to Infectious Diseases, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Lizhou Zhang
- Division of Infectious Disease, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Department of Immunology and Microbiology, UF Scripps Biomedical Research, Jupiter, FL 33458, USA
| | - Ava E Allwardt
- Division of Infectious Disease, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Debasis Mitra
- Department of Computer Engineering and Sciences, Florida Institute of Technology, Melbourne, FL 32901, USA
| | - Brian Quinlan
- Department of Immunology and Microbiology, UF Scripps Biomedical Research, Jupiter, FL 33458, USA
| | - Rogier W Sanders
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Hyeryun Choe
- Division of Infectious Disease, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Michael Farzan
- Division of Infectious Disease, Boston Children's Hospital, Boston, MA 02115, USA; The Center for Integrated Solutions to Infectious Diseases, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Skaggs Graduate School, Scripps Research, La Jolla, CA 92037, USA.
| |
Collapse
|
15
|
Freedman AN, Roell K, Engwall E, Bulka C, Kuban KCK, Herring L, Mills CA, Parsons PJ, Galusha A, O’Shea TM, Fry RC. Prenatal Metal Exposure Alters the Placental Proteome in a Sex-Dependent Manner in Extremely Low Gestational Age Newborns: Links to Gestational Age. Int J Mol Sci 2023; 24:14977. [PMID: 37834424 PMCID: PMC10573797 DOI: 10.3390/ijms241914977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 10/15/2023] Open
Abstract
Prenatal exposure to toxic metals is associated with altered placental function and adverse infant and child health outcomes. Adverse outcomes include those that are observed at the time of birth, such as low birthweight, as well as those that arise later in life, such as neurological impairment. It is often the case that these adverse outcomes show sex-specific responses in relation to toxicant exposures. While the precise molecular mechanisms linking in utero toxic metal exposures with later-in-life health are unknown, placental inflammation is posited to play a critical role. Here, we sought to understand whether in utero metal exposure is associated with alterations in the expression of the placental proteome by identifying metal associated proteins (MAPs). Within the Extremely Low Gestational Age Newborns (ELGAN) cohort (n = 230), placental and umbilical cord tissue samples were collected at birth. Arsenic (As), cadmium (Cd), lead (Pb), selenium (Se), and manganese (Mn) concentrations were measured in umbilical cord tissue samples via ICP-MS/MS. Protein expression was examined in placental samples using an LC-MS/MS-based, global, untargeted proteomics analysis measuring more than 3400 proteins. MAPs were then evaluated for associations with pregnancy and neonatal outcomes, including placental weight and gestational age. We hypothesized that metal levels would be positively associated with the altered expression of inflammation/immune-associated pathways and that sex-specific patterns of metal-associated placental protein expression would be observed. Sex-specific analyses identified 89 unique MAPs expressed in female placentas and 41 unique MAPs expressed in male placentas. Notably, many of the female-associated MAPs are known to be involved in immune-related processes, while the male-associated MAPs are associated with intracellular transport and cell localization. Further, several MAPs were significantly associated with gestational age in males and females and placental weight in males. These data highlight the linkage between prenatal metal exposure and an altered placental proteome, with implications for altering the trajectory of fetal development.
Collapse
Affiliation(s)
- Anastasia N. Freedman
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina, Chapel Hill, NC 27599, USA; (A.N.F.); (E.E.)
- Institute for Environmental Health Solutions, Gillings School of Global Public Health, The University of North Carolina, Chapel Hill, NC 27599, USA;
| | - Kyle Roell
- Institute for Environmental Health Solutions, Gillings School of Global Public Health, The University of North Carolina, Chapel Hill, NC 27599, USA;
| | - Eiona Engwall
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina, Chapel Hill, NC 27599, USA; (A.N.F.); (E.E.)
| | - Catherine Bulka
- College of Public Health, University of South Florida, Tampa, FL 33612, USA;
| | - Karl C. K. Kuban
- Department of Pediatrics, Division of Child Neurology, Boston Medical Center, Boston, MA 02118, USA;
| | - Laura Herring
- UNC Proteomics Core Facility, Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (L.H.); (C.A.M.)
| | - Christina A. Mills
- UNC Proteomics Core Facility, Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (L.H.); (C.A.M.)
| | - Patrick J. Parsons
- Wadsworth Center, New York State Department of Health, Albany, NY 12201, USA; (P.J.P.); (A.G.)
- Department of Environmental Health Sciences, School of Public Health, University of Albany, Rensselaer, NY 12222, USA
| | - Aubrey Galusha
- Wadsworth Center, New York State Department of Health, Albany, NY 12201, USA; (P.J.P.); (A.G.)
- Department of Environmental Health Sciences, School of Public Health, University of Albany, Rensselaer, NY 12222, USA
| | - Thomas Michael O’Shea
- Department of Pediatrics, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA;
| | - Rebecca C. Fry
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina, Chapel Hill, NC 27599, USA; (A.N.F.); (E.E.)
- Institute for Environmental Health Solutions, Gillings School of Global Public Health, The University of North Carolina, Chapel Hill, NC 27599, USA;
- Curriculum in Toxicology & Environmental Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| |
Collapse
|
16
|
Berckmueller K, Thomas J, Taha EA, Choo S, Madhu R, Kanestrom G, Rupert PB, Strong R, Kiem HP, Radtke S. CD90-targeted lentiviral vectors for HSC gene therapy. Mol Ther 2023; 31:2901-2913. [PMID: 37550965 PMCID: PMC10556220 DOI: 10.1016/j.ymthe.2023.08.003] [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: 02/27/2023] [Revised: 06/12/2023] [Accepted: 08/03/2023] [Indexed: 08/09/2023] Open
Abstract
Hematopoietic stem cell (HSC) gene therapy is currently performed on CD34+ hematopoietic stem and progenitor cells containing less than 1% true HSCs and requiring a highly specialized infrastructure for cell manufacturing and transplantation. We have previously identified the CD34+CD90+ subset to be exclusively responsible for short- and long-term engraftment. However, purification and enrichment of this subset is laborious and expensive. HSC-specific delivery agents for the direct modification of rare HSCs are currently lacking. Here, we developed novel targeted viral vectors to specifically transduce CD90-expressing HSCs. Anti-CD90 single chain variable fragments (scFvs) were engineered onto measles- and VSV-G-pseudotyped lentiviral vectors that were knocked out for native targeting. We further developed a custom hydrodynamic titration methodology to assess the loading of surface-engineered capsids, measure antigen recognition of the scFv, and predict the performance on cells. Engineered vectors formed with minimal impairment in the functional titer, maintained their ability to fuse with the target cells, and showed highly specific recognition of CD90 on cells ex vivo. Most important, targeted vectors selectively transduced human HSCs with secondary colony-forming potential. Our novel HSC-targeted viral vectors have the potential to significantly enhance the feasibility of ex vivo gene therapy and pave the way for future in vivo applications.
Collapse
Affiliation(s)
- Kurt Berckmueller
- Stem Cell and Gene Therapy Program, Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Justin Thomas
- Stem Cell and Gene Therapy Program, Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Eman A Taha
- Stem Cell and Gene Therapy Program, Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Department of Biochemistry, Ain Shams University Faculty of Science, Cairo 11566, Egypt
| | - Seunga Choo
- Stem Cell and Gene Therapy Program, Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Ravishankar Madhu
- Stem Cell and Gene Therapy Program, Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Greta Kanestrom
- Stem Cell and Gene Therapy Program, Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Peter B Rupert
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Roland Strong
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Hans-Peter Kiem
- Stem Cell and Gene Therapy Program, Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA; Department of Pathology, University of Washington School of Medicine, Seattle, WA 98195, USA.
| | - Stefan Radtke
- Stem Cell and Gene Therapy Program, Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.
| |
Collapse
|
17
|
Früh SP, Adu OF, López-Astacio RA, Weichert WS, Wasik BR, Parrish CR. Isolation, cloning and analysis of parvovirus-specific canine antibodies from peripheral blood B cells. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 147:104894. [PMID: 37467826 PMCID: PMC10542859 DOI: 10.1016/j.dci.2023.104894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 07/05/2023] [Accepted: 07/16/2023] [Indexed: 07/21/2023]
Abstract
B-cell cloning methods enable the analysis of antibody responses against target antigens and can be used to reveal the host antibody repertoire, antigenic sites (epitopes), and details of protective immunity against pathogens. Here, we describe improved methods for isolation of canine peripheral blood B cells producing antibodies against canine parvovirus (CPV) capsids by fluorescence-activated cell sorting, followed by cell cloning. We cultured sorted B cells from an immunized dog in vitro and screened for CPV-specific antibody production. Updated canine-specific primer sets were used to amplify and clone the heavy and light chain immunoglobulin sequences directly from the B cells by reverse transcription and PCR. Monoclonal canine IgGs were produced by cloning heavy and light chain sequences into antibody expression vectors, which were screened for CPV binding. Three different canine monoclonal antibodies were analyzed, including two that shared the same heavy chain, and one that had distinct heavy and light chains. The antibodies showed broad binding to CPV variants, and epitopes were mapped to antigenic sites on the capsid. The methods described here are applicable for the isolation of canine B cells and monoclonal antibodies against many antigens.
Collapse
Affiliation(s)
- Simon P Früh
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA; Department of Veterinary Sciences, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Oluwafemi F Adu
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Robert A López-Astacio
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Wendy S Weichert
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Brian R Wasik
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Colin R Parrish
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA.
| |
Collapse
|
18
|
Massari S, Giannico F, Paolillo NV, Pala A, Jambrenghi AC, Antonacci R. Genomic and comparative analysis of the T cell receptor gamma locus in two Equus species. Front Immunol 2023; 14:1264949. [PMID: 37781375 PMCID: PMC10540303 DOI: 10.3389/fimmu.2023.1264949] [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: 07/21/2023] [Accepted: 08/31/2023] [Indexed: 10/03/2023] Open
Abstract
The genus Equus is the only extant genus of the Equidae family, which belongs to Perissodactyla, an order of mammals characterized by an odd number of toes (odd-toes ungulates). Taking advantage of the latest release of the genome assembly, we studied, for the first time in two organisms belonging to the Equus genus, the horse (Equus caballus) and the donkey (Equus asinus), the T cell receptor gamma (TRG) locus encoding the gamma chain of the γδ T cell receptor. Forty-five Variable (TRGV) genes belonging to the seven IMGT-NC validated mammalian TRGV subgroups, 25 Joining (TRGJ) and 17 Constant (TRGC) genes organized in 17 V-J-(J)-C cassettes, in tandem on about 1100 Kb, characterize the horse TRG locus, making the horse TRG locus the one with the greatest extension and with a significantly higher number of genes than the orthologous loci of the other mammalian species. A clonotype analysis of an RNA-seq transcriptomic dataset derived from spleen of an adult healthy horse, using the complete set of the horse TRGJ germline gene sequences as a probe, revealed that, in addition to the most prominent V-J rearrangements within each cassette, there is a relevant proportion of trans-cassette V-J recombination, whereby the same TRGV genes can recombine with different TRGJ genes spliced to the corresponding TRGC genes. This recombinant event strongly contributes to the diversity of the γ chain repertoire. In the donkey TRG locus, 34 TRGV, 21 TRGJ and 14 TRGC genes distributed in 14 V-J-(J)-C cassettes were found in a region of approximately 860 kb. Although the donkey's TRG is smaller than that of the horse, in Equus genus, this is still the second largest locus so far found in any mammalian species. Finally, the comparative analysis highlighted differences in size and gene content between the horse and donkey TRG loci, despite belonging to the same genus, indicating a good level of diversification within Equus. These data is in agreement with the evolutionary idea of the existence of a Equus recent common ancestor in rapid evolution, for which a mutation rate between horses and donkeys is more comparable to that between species belonging to different genera rather than to species of the same genus.
Collapse
Affiliation(s)
- Serafina Massari
- Department of Biological and Environmental Science and Technologies, University of Salento, Lecce, Italy
| | - Francesco Giannico
- Department of Veterinary Medicine, University of Bari "Aldo Moro", Bari, Italy
| | - Nunzia Valentina Paolillo
- Department of Biosciences, Biotechnologies and Environment, University of Bari "Aldo Moro", Bari, Italy
| | - Angela Pala
- Department of Biosciences, Biotechnologies and Environment, University of Bari "Aldo Moro", Bari, Italy
| | | | - Rachele Antonacci
- Department of Biosciences, Biotechnologies and Environment, University of Bari "Aldo Moro", Bari, Italy
| |
Collapse
|
19
|
Smirnova AO, Miroshnichenkova AM, Belyaeva LD, Kelmanson IV, Lebedev YB, Mamedov IZ, Chudakov DM, Komkov AY. Novel bimodal TRBD1-TRBD2 rearrangements with dual or absent D-region contribute to TRB V-(D)-J combinatorial diversity. Front Immunol 2023; 14:1245175. [PMID: 37744336 PMCID: PMC10513440 DOI: 10.3389/fimmu.2023.1245175] [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: 06/23/2023] [Accepted: 08/23/2023] [Indexed: 09/26/2023] Open
Abstract
T-cell receptor (TR) diversity of the variable domains is generated by recombination of both the alpha (TRA) and beta (TRB) chains. The textbook process of TRB chain production starts with TRBD and TRBJ gene rearrangement, followed by the rearrangement of a TRBV gene to the partially rearranged D-J gene. Unsuccessful V-D-J TRB rearrangements lead to apoptosis of the cell. Here, we performed deep sequencing of the poorly explored pool of partial TRBD1-TRBD2 rearrangements in T-cell genomic DNA. We reconstructed full repertoires of human partial TRBD1-TRBD2 rearrangements using novel sequencing and validated them by detecting V-D-J recombination-specific byproducts: excision circles containing the recombination signal (RS) joint 5'D2-RS - 3'D1-RS. Identified rearrangements were in compliance with the classical 12/23 rule, common for humans, rats, and mice and contained typical V-D-J recombination footprints. Interestingly, we detected a bimodal distribution of D-D junctions indicating two active recombination sites producing long and short D-D rearrangements. Long TRB D-D rearrangements with two D-regions are coding joints D1-D2 remaining classically on the chromosome. The short TRB D-D rearrangements with no D-region are signal joints, the coding joint D1-D2 being excised from the chromosome. They both contribute to the TRB V-(D)-J combinatorial diversity. Indeed, short D-D rearrangements may be followed by direct V-J2 recombination. Long D-D rearrangements may recombine further with J2 and V genes forming partial D1-D2-J2 and then complete V-D1-D2-J2 rearrangement. Productive TRB V-D1-D2-J2 chains are present and expressed in thousands of clones of human antigen-experienced memory T cells proving their capacity for antigen recognition and actual participation in the immune response.
Collapse
Affiliation(s)
- Anastasia O. Smirnova
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | | | - Laima D. Belyaeva
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Ilya V. Kelmanson
- Department of Biomolecular Sciences and Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Yuri B. Lebedev
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Ilgar Z. Mamedov
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Dmitriy M. Chudakov
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Abu Dhabi Stem Cells Center (ADSCC), Abu Dhabi, United Arab Emirates
- Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Alexander Y. Komkov
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Abu Dhabi Stem Cells Center (ADSCC), Abu Dhabi, United Arab Emirates
- Dmitry Rogachev National Medical and Research Center of Pediatric Hematology, Oncology, and Immunology, Moscow, Russia
| |
Collapse
|
20
|
Boudinot P, Novas S, Jouneau L, Mondot S, Lefranc MP, Grimholt U, Magadán S. Evolution of T cell receptor beta loci in salmonids. Front Immunol 2023; 14:1238321. [PMID: 37649482 PMCID: PMC10464911 DOI: 10.3389/fimmu.2023.1238321] [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: 06/11/2023] [Accepted: 07/17/2023] [Indexed: 09/01/2023] Open
Abstract
T-cell mediated immunity relies on a vast array of antigen specific T cell receptors (TR). Characterizing the structure of TR loci is essential to study the diversity and composition of T cell responses in vertebrate species. The lack of good-quality genome assemblies, and the difficulty to perform a reliably mapping of multiple highly similar TR sequences, have hindered the study of these loci in non-model organisms. High-quality genome assemblies are now available for the two main genera of Salmonids, Salmo and Oncorhynchus. We present here a full description and annotation of the TRB loci located on chromosomes 19 and 25 of rainbow trout (Oncorhynchus mykiss). To get insight about variations of the structure and composition of TRB locus across salmonids, we compared rainbow trout TRB loci with other salmonid species and confirmed that the basic structure of salmonid TRB locus is a double set of two TRBV-D-J-C loci in opposite orientation on two different chromosomes. Our data shed light on the evolution of TRB loci in Salmonids after their whole genome duplication (WGD). We established a coherent nomenclature of salmonid TRB loci based on comprehensive annotation. Our work provides a fundamental basis for monitoring salmonid T cell responses by TRB repertoire sequencing.
Collapse
Affiliation(s)
- Pierre Boudinot
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France
| | - Samuel Novas
- Immunology Laboratory, Research Center for Nanomaterials and Biomedicine (CINBIO), Universidade de Vigo, Vigo, Spain
| | - Luc Jouneau
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France
| | - Stanislas Mondot
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Marie-Paule Lefranc
- IMGT, The International ImMunoGeneTics Information System® (IMGT), Laboratoire d´ImmunoGénétique Moléculaire (LIGM), Institut de Génétique Humaine (IGH), Centre National de la Recherche Scientifique (CNRS), University of Montpellier, Montpellier, France
| | - Unni Grimholt
- Fish Health Research Section, Norwegian Veterinary Institute, Oslo, Norway
| | - Susana Magadán
- Immunology Laboratory, Research Center for Nanomaterials and Biomedicine (CINBIO), Universidade de Vigo, Vigo, Spain
| |
Collapse
|
21
|
Ott JA, Mitchell C, Sheppard M, Deiss TC, Horton JMC, Haakenson JK, Huang R, Kelley AR, Davis BW, Derr JN, Smider VV, Criscitiello MF. Evolution of immunogenetic components encoding ultralong CDR H3. Immunogenetics 2023; 75:323-339. [PMID: 37084012 PMCID: PMC10119515 DOI: 10.1007/s00251-023-01305-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 04/03/2023] [Indexed: 04/22/2023]
Abstract
The genomes of most vertebrates contain many V, D, and J gene segments within their Ig loci to construct highly variable CDR3 sequences through combinatorial diversity. This nucleotide variability translates into an antibody population containing extensive paratope diversity. Cattle have relatively few functional VDJ gene segments, requiring innovative approaches for generating diversity like the use of ultralong-encoding IGHV and IGHD gene segments that yield dramatically elongated CDR H3. Unique knob and stalk microdomains create protracted paratopes, where the antigen-binding knob sits atop a long stalk, allowing the antibody to bind both surface and recessed antigen epitopes. We examined genomes of twelve species of Bovidae to determine when ultralong-encoding IGHV and IGHD gene segments evolved. We located the 8-bp duplication encoding the unique TTVHQ motif in ultralong IGHV segments in six Bovid species (cattle, zebu, wild yak, domestic yak, American bison, and domestic gayal), but we did not find evidence of the duplication in species beyond the Bos and Bison genera. Additionally, we analyzed mRNA from bison spleen and identified a rich repertoire of expressed ultralong CDR H3 antibody mRNA, suggesting that bison use ultralong IGHV transcripts in their host defense. We found ultralong-encoding IGHD gene segments in all the same species except domestic yak, but again not beyond the Bos and Bison clade. Thus, the duplication event leading to this ultralong-encoding IGHV gene segment and the emergence of the ultralong-encoding IGHD gene segment appears to have evolved in a common ancestor of the Bos and Bison genera 5-10 million years ago.
Collapse
Affiliation(s)
- Jeannine A Ott
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Christian Mitchell
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Morgan Sheppard
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Thad C Deiss
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - J M Cody Horton
- Department of Veterinary Integrative Sciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Jeremy K Haakenson
- Applied Biomedical Science Institute, San Diego, CA, 92127, USA
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Ruiqi Huang
- Applied Biomedical Science Institute, San Diego, CA, 92127, USA
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | | | - Brian W Davis
- Department of Veterinary Integrative Sciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - James N Derr
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Vaughn V Smider
- Applied Biomedical Science Institute, San Diego, CA, 92127, USA
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Michael F Criscitiello
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA.
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health Science Center, Texas A&M University, Bryan, TX, 77807, USA.
| |
Collapse
|
22
|
Ravindranath MH, Ravindranath NM, Selvan SR, Hilali FE, Amato-Menker CJ, Filippone EJ. Cell Surface B2m-Free Human Leukocyte Antigen (HLA) Monomers and Dimers: Are They Neo-HLA Class and Proto-HLA? Biomolecules 2023; 13:1178. [PMID: 37627243 PMCID: PMC10452486 DOI: 10.3390/biom13081178] [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: 05/19/2023] [Revised: 07/17/2023] [Accepted: 07/17/2023] [Indexed: 08/27/2023] Open
Abstract
Cell surface HLA-I molecules (Face-1) consist of a polypeptide heavy chain (HC) with two groove domains (G domain) and one constant domain (C-domain) as well as a light chain, B2-microglobulin (B2m). However, HCs can also independently emerge unfolded on the cell surface without peptides as B2m-free HC monomers (Face-2), B2m-free HC homodimers (Face 3), and B2m-free HC heterodimers (Face-4). The transport of these HLA variants from ER to the cell surface was confirmed by antiviral antibiotics that arrest the release of newly synthesized proteins from the ER. Face-2 occurs at low levels on the normal cell surface of the lung, bronchi, epidermis, esophagus, breast, stomach, ilium, colorectum, gall bladder, urinary bladder, seminal vesicles ovarian epithelia, endometrium, thymus, spleen, and lymphocytes. They are upregulated on immune cells upon activation by proinflammatory cytokines, anti-CD3 antibodies, antibiotics (e.g., ionomycin), phytohemagglutinin, retinoic acid, and phorbol myristate acetate. Their density on the cell surface remains high as long as the cells remain in an activated state. After activation-induced upregulation, the Face-2 molecules undergo homo- and hetero-dimerization (Face-3 and Face-4). Alterations in the redox environment promote dimerization. Heterodimerization can occur among and between the alleles of different haplotypes. The glycosylation of these variants differ from that of Face-1, and they may occur with bound exogenous peptides. Spontaneous arthritis occurs in HLA-B27+ mice lacking B2m (HLA-B27+ B2m-/-) but not in HLA-B27+ B2m+/- mice. The mice with HLA-B27 in Face-2 spontaneous configuration develop symptoms such as changes in nails and joints, hair loss, and swelling in paws, leading to ankyloses. Anti-HC-specific mAbs delay disease development. Some HLA-I polyreactive mAbs (MEM series) used for immunostaining confirm the existence of B2m-free variants in several cancer cells. The upregulation of Face-2 in human cancers occurs concomitantly with the downregulation of intact HLAs (Face-1). The HLA monomeric and dimeric variants interact with inhibitory and activating ligands (e.g., KIR), growth factors, cytokines, and neurotransmitters. Similarities in the amino acid sequences of the HLA-I variants and HLA-II β-chain suggest that Face-2 could be the progenitor of both HLA classes. These findings may support the recognition of these variants as a neo-HLA class and proto-HLA.
Collapse
Affiliation(s)
- Mepur H. Ravindranath
- Department of Hematology and Oncology, Children’s Hospital, Los Angeles, CA 90027, USA
- Terasaki Foundation Laboratory, Santa Monica, CA 90064, USA
| | - Narendranath M. Ravindranath
- Norris Dental Science Center, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA 90089, USA;
| | - Senthamil R. Selvan
- Division of Immunology and Hematology Devices, OHT 7: Office of In Vitro Diagnostics, Office of Product Evaluation and Quality, Center for Devices and Radiological Health, Food and Drug Administration (FDA), Silver Spring, MD 20993, USA;
| | - Fatiha El Hilali
- Medico-Surgical, Biomedicine and Infectiology Research Laboratory, The Faculty of Medicine and Pharmacy of Laayoune & Agadir, Ibnou Zohr University, Agadir 80000, Morocco;
| | - Carly J. Amato-Menker
- Department of Microbiology, Immunology and Cell Biology, School of Medicine, West Virginia University, Morgantown, WV 26506, USA;
| | - Edward J. Filippone
- Division of Nephrology, Department of Medicine, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19145, USA;
| |
Collapse
|
23
|
Brunson T, Sanati N, Matthews L, Haw R, Beavers D, Shorser S, Sevilla C, Viteri G, Conley P, Rothfels K, Hermjakob H, Stein L, D’Eustachio P, Wu G. Illuminating Dark Proteins using Reactome Pathways. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.05.543335. [PMID: 37333417 PMCID: PMC10274615 DOI: 10.1101/2023.06.05.543335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Limited knowledge about a substantial portion of protein coding genes, known as "dark" proteins, hinders our understanding of their functions and potential therapeutic applications. To address this, we leveraged Reactome, the most comprehensive, open source, open-access pathway knowledgebase, to contextualize dark proteins within biological pathways. By integrating multiple resources and employing a random forest classifier trained on 106 protein/gene pairwise features, we predicted functional interactions between dark proteins and Reactome-annotated proteins. We then developed three scores to measure the interactions between dark proteins and Reactome pathways, utilizing enrichment analysis and fuzzy logic simulations. Correlation analysis of these scores with an independent single-cell RNA sequencing dataset provided supporting evidence for this approach. Furthermore, systematic natural language processing (NLP) analysis of over 22 million PubMed abstracts and manual checking of the literature associated with 20 randomly selected dark proteins reinforced the predicted interactions between proteins and pathways. To enhance the visualization and exploration of dark proteins within Reactome pathways, we developed the Reactome IDG portal, deployed at https://idg.reactome.org, a web application featuring tissue-specific protein and gene expression overlay, as well as drug interactions. Our integrated computational approach, together with the user-friendly web platform, offers a valuable resource for uncovering potential biological functions and therapeutic implications of dark proteins.
Collapse
Affiliation(s)
| | - Nasim Sanati
- Oregon Health & Science University, Portland, OR 97239, USA
| | | | - Robin Haw
- Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Deidre Beavers
- Oregon Health & Science University, Portland, OR 97239, USA
| | - Solomon Shorser
- Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Cristoffer Sevilla
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Guilherme Viteri
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Patrick Conley
- Oregon Health & Science University, Portland, OR 97239, USA
| | - Karen Rothfels
- Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Henning Hermjakob
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Lincoln Stein
- Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S1A1, Canada
| | | | - Guanming Wu
- Oregon Health & Science University, Portland, OR 97239, USA
| |
Collapse
|
24
|
Pomarici ND, Cacciato R, Kokot J, Fernández-Quintero ML, Liedl KR. Evolution of the Immunoglobulin Isotypes-Variations of Biophysical Properties among Animal Classes. Biomolecules 2023; 13:801. [PMID: 37238671 PMCID: PMC10216798 DOI: 10.3390/biom13050801] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/03/2023] [Accepted: 05/05/2023] [Indexed: 05/28/2023] Open
Abstract
The adaptive immune system arose around 500 million years ago in jawed fish, and, since then, it has mediated the immune defense against pathogens in all vertebrates. Antibodies play a central role in the immune reaction, recognizing and attacking external invaders. During the evolutionary process, several immunoglobulin isotypes emerged, each having a characteristic structural organization and dedicated function. In this work, we investigate the evolution of the immunoglobulin isotypes, in order to highlight the relevant features that were preserved over time and the parts that, instead, mutated. The residues that are coupled in the evolution process are often involved in intra- or interdomain interactions, meaning that they are fundamental to maintaining the immunoglobulin fold and to ensuring interactions with other domains. The explosive growth of available sequences allows us to point out the evolutionary conserved residues and compare the biophysical properties among different animal classes and isotypes. Our study offers a general overview of the evolution of immunoglobulin isotypes and advances the knowledge of their characteristic biophysical properties, as a first step in guiding protein design from evolution.
Collapse
Affiliation(s)
| | | | | | - Monica L. Fernández-Quintero
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Klaus R. Liedl
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
| |
Collapse
|
25
|
Tamasi V, Németh K, Csala M. Role of Extracellular Vesicles in Liver Diseases. Life (Basel) 2023; 13:life13051117. [PMID: 37240762 DOI: 10.3390/life13051117] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 04/24/2023] [Accepted: 04/27/2023] [Indexed: 05/28/2023] Open
Abstract
Extracellular vesicles (EVs) are cell-derived membrane structures that are formed by budding from the plasma membrane or originate from the endosomal system. These microparticles (100 nm-100 µm) or nanoparticles (>100 nm) can transport complex cargos to other cells and, thus, provide communication and intercellular regulation. Various cells, such as hepatocytes, liver sinusoidal endothelial cells (LSECs) or hepatic stellate cells (HSCs), secrete and take up EVs in the healthy liver, and the amount, size and content of these vesicles are markedly altered under pathophysiological conditions. A comprehensive knowledge of the modified EV-related processes is very important, as they are of great value as biomarkers or therapeutic targets. In this review, we summarize the latest knowledge on hepatic EVs and the role they play in the homeostatic processes in the healthy liver. In addition, we discuss the characteristic changes of EVs and their potential exacerbating or ameliorating effects in certain liver diseases, such as non-alcoholic fatty liver disease (NAFLD), alcoholic fatty liver disease (AFLD), drug induced liver injury (DILI), autoimmune hepatitis (AIH), hepatocarcinoma (HCC) and viral hepatitis.
Collapse
Affiliation(s)
- Viola Tamasi
- Department of Molecular Biology, Semmelweis University, 1094 Budapest, Hungary
| | - Krisztina Németh
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, 1089 Budapest, Hungary
- ELKH-SE Translational Extracellular Vesicle Research Group, 1085 Budapest, Hungary
| | - Miklós Csala
- Department of Molecular Biology, Semmelweis University, 1094 Budapest, Hungary
| |
Collapse
|
26
|
Genolet R, Bobisse S, Chiffelle J, Arnaud M, Petremand R, Queiroz L, Michel A, Reichenbach P, Cesbron J, Auger A, Baumgaertner P, Guillaume P, Schmidt J, Irving M, Kandalaft LE, Speiser DE, Coukos G, Harari A. TCR sequencing and cloning methods for repertoire analysis and isolation of tumor-reactive TCRs. CELL REPORTS METHODS 2023; 3:100459. [PMID: 37159666 PMCID: PMC10163020 DOI: 10.1016/j.crmeth.2023.100459] [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: 10/17/2022] [Revised: 02/27/2023] [Accepted: 03/27/2023] [Indexed: 05/11/2023]
Abstract
T cell receptor (TCR) technologies, including repertoire analyses and T cell engineering, are increasingly important in the clinical management of cellular immunity in cancer, transplantation, and other immune diseases. However, sensitive and reliable methods for repertoire analyses and TCR cloning are still lacking. Here, we report on SEQTR, a high-throughput approach to analyze human and mouse repertoires that is more sensitive, reproducible, and accurate as compared with commonly used assays, and thus more reliably captures the complexity of blood and tumor TCR repertoires. We also present a TCR cloning strategy to specifically amplify TCRs from T cell populations. Positioned downstream of single-cell or bulk TCR sequencing, it allows time- and cost-effective discovery, cloning, screening, and engineering of tumor-specific TCRs. Together, these methods will accelerate TCR repertoire analyses in discovery, translational, and clinical settings and permit fast TCR engineering for cellular therapies.
Collapse
Affiliation(s)
- Raphael Genolet
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
- Corresponding author
| | - Sara Bobisse
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Johanna Chiffelle
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Marion Arnaud
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Rémy Petremand
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Lise Queiroz
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Alexandra Michel
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Patrick Reichenbach
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
| | - Julien Cesbron
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Aymeric Auger
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Petra Baumgaertner
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Philippe Guillaume
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Julien Schmidt
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Melita Irving
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
| | - Lana E. Kandalaft
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Daniel E. Speiser
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
| | - George Coukos
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Corresponding author
| | - Alexandre Harari
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Corresponding author
| |
Collapse
|
27
|
García-Valiente R, Merino Tejero E, Stratigopoulou M, Balashova D, Jongejan A, Lashgari D, Pélissier A, Caniels TG, Claireaux MAF, Musters A, van Gils MJ, Rodríguez Martínez M, de Vries N, Meyer-Hermann M, Guikema JEJ, Hoefsloot H, van Kampen AHC. Understanding repertoire sequencing data through a multiscale computational model of the germinal center. NPJ Syst Biol Appl 2023; 9:8. [PMID: 36927990 PMCID: PMC10019394 DOI: 10.1038/s41540-023-00271-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 02/20/2023] [Indexed: 03/18/2023] Open
Abstract
Sequencing of B-cell and T-cell immune receptor repertoires helps us to understand the adaptive immune response, although it only provides information about the clonotypes (lineages) and their frequencies and not about, for example, their affinity or antigen (Ag) specificity. To further characterize the identified clones, usually with special attention to the particularly abundant ones (dominant), additional time-consuming or expensive experiments are generally required. Here, we present an extension of a multiscale model of the germinal center (GC) that we previously developed to gain more insight in B-cell repertoires. We compare the extent that these simulated repertoires deviate from experimental repertoires established from single GCs, blood, or tissue. Our simulations show that there is a limited correlation between clonal abundance and affinity and that there is large affinity variability among same-ancestor (same-clone) subclones. Our simulations suggest that low-abundance clones and subclones, might also be of interest since they may have high affinity for the Ag. We show that the fraction of plasma cells (PCs) with high B-cell receptor (BcR) mRNA content in the GC does not significantly affect the number of dominant clones derived from single GCs by sequencing BcR mRNAs. Results from these simulations guide data interpretation and the design of follow-up experiments.
Collapse
Affiliation(s)
- Rodrigo García-Valiente
- Amsterdam UMC location University of Amsterdam, Epidemiology and Data Science, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Public Health, Methodology, Amsterdam, The Netherlands
- Amsterdam Infection and Immunity, Inflammatory Diseases, Amsterdam, The Netherlands
| | - Elena Merino Tejero
- Amsterdam UMC location University of Amsterdam, Epidemiology and Data Science, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Public Health, Methodology, Amsterdam, The Netherlands
- Amsterdam Infection and Immunity, Inflammatory Diseases, Amsterdam, The Netherlands
| | - Maria Stratigopoulou
- Cancer Center Amsterdam, Amsterdam, The Netherlands
- Amsterdam UMC location University of Amsterdam, Medical Microbiology and Infection Prevention, Meibergdreef 9, Amsterdam, The Netherlands
| | - Daria Balashova
- Amsterdam UMC location University of Amsterdam, Epidemiology and Data Science, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Public Health, Methodology, Amsterdam, The Netherlands
- Amsterdam Infection and Immunity, Inflammatory Diseases, Amsterdam, The Netherlands
| | - Aldo Jongejan
- Amsterdam UMC location University of Amsterdam, Epidemiology and Data Science, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Public Health, Methodology, Amsterdam, The Netherlands
- Amsterdam Infection and Immunity, Inflammatory Diseases, Amsterdam, The Netherlands
| | - Danial Lashgari
- Amsterdam UMC location University of Amsterdam, Epidemiology and Data Science, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Public Health, Methodology, Amsterdam, The Netherlands
- Amsterdam Infection and Immunity, Inflammatory Diseases, Amsterdam, The Netherlands
| | - Aurélien Pélissier
- IBM Research Zurich, 8803, Rüschlikon, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
| | - Tom G Caniels
- Amsterdam UMC location University of Amsterdam, Medical Microbiology and Infection Prevention, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
| | - Mathieu A F Claireaux
- Amsterdam UMC location University of Amsterdam, Medical Microbiology and Infection Prevention, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
| | - Anne Musters
- Amsterdam UMC location University of Amsterdam, Experimental Immunology, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Rheumatology & Immunology Center, Amsterdam, The Netherlands
| | - Marit J van Gils
- Amsterdam UMC location University of Amsterdam, Medical Microbiology and Infection Prevention, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
| | | | - Niek de Vries
- Amsterdam UMC location University of Amsterdam, Experimental Immunology, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Rheumatology & Immunology Center, Amsterdam, The Netherlands
| | - Michael Meyer-Hermann
- Department for Systems Immunology and Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Jeroen E J Guikema
- Cancer Center Amsterdam, Amsterdam, The Netherlands
- Amsterdam UMC location University of Amsterdam, Pathology, Lymphoma and Myeloma Center Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Huub Hoefsloot
- Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Antoine H C van Kampen
- Amsterdam UMC location University of Amsterdam, Epidemiology and Data Science, Meibergdreef 9, Amsterdam, The Netherlands.
- Amsterdam Public Health, Methodology, Amsterdam, The Netherlands.
- Amsterdam Infection and Immunity, Inflammatory Diseases, Amsterdam, The Netherlands.
- Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands.
| |
Collapse
|
28
|
Chen ST, Oliveira TY, Gazumyan A, Cipolla M, Nussenzweig MC. B cell receptor signaling in germinal centers prolongs survival and primes B cells for selection. Immunity 2023; 56:547-561.e7. [PMID: 36882061 PMCID: PMC10424567 DOI: 10.1016/j.immuni.2023.02.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 10/28/2022] [Accepted: 02/08/2023] [Indexed: 03/08/2023]
Abstract
Germinal centers (GCs) are sites of B cell clonal expansion, diversification, and antibody affinity selection. This process is limited and directed by T follicular helper cells that provide helper signals to B cells that endocytose, process, and present cognate antigens in proportion to their B cell receptor (BCR) affinity. Under this model, the BCR functions as an endocytic receptor for antigen capture. How signaling through the BCR contributes to selection is not well understood. To investigate the role of BCR signaling in GC selection, we developed a tracker for antigen binding and presentation and a Bruton's tyrosine kinase drug-resistant-mutant mouse model. We showed that BCR signaling per se is necessary for the survival and priming of light zone B cells to receive T cell help. Our findings provide insight into how high-affinity antibodies are selected within GCs and are fundamental to our understanding of adaptive immunity and vaccine development.
Collapse
Affiliation(s)
- Spencer T Chen
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA.
| | - Thiago Y Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Anna Gazumyan
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Melissa Cipolla
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute (HHMI), The Rockefeller University, New York, NY 10065, USA.
| |
Collapse
|
29
|
Wen J, Ling R, Chen R, Zhang S, Dai Y, Zhang T, Guo F, Wang Q, Wang G, Jiang Y. Diversity of arterial cell and phenotypic heterogeneity induced by high-fat and high-cholesterol diet. Front Cell Dev Biol 2023; 11:971091. [PMID: 36910156 PMCID: PMC9997679 DOI: 10.3389/fcell.2023.971091] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 02/03/2023] [Indexed: 02/25/2023] Open
Abstract
Lipid metabolism disorder is the basis of atherosclerotic lesions, in which cholesterol and low-density lipoprotein (LDL) is the main factor involved with the atherosclerotic development. A high-fat and high-cholesterol diet can lead to this disorder in the human body, thus accelerating the process of disease. The development of single-cell RNA sequencing in recent years has opened the possibility to unbiasedly map cellular heterogeneity with high throughput and high resolution; alterations mediated by a high-fat and high-cholesterol diet at the single-cell transcriptomic level can be explored with this mean afterward. We assessed the aortic arch of 16-week old Apoe-/- mice of two control groups (12 weeks of chow diet) and two HFD groups (12 weeks of high fat, high cholesterol diet) to process single-cell suspension and use single-cell RNA sequencing to anatomize the transcripts of 5,416 cells from the control group and 2,739 from the HFD group. Through unsupervised clustering, 14 cell types were divided and defined. Among these cells, the cellular heterogeneity exhibited in endothelial cells and immune cells is the most prominent. Subsequent screening delineated ten endothelial cell subsets with various function based on gene expression profiling. The distribution of endothelial cells and immune cells differs significantly between the control group versus the HFD one. The existence of pathways that inhibit atherosclerosis was found in both dysfunctional endothelial cells and foam cells. Our data provide a comprehensive transcriptional landscape of aortic arch cells and unravel the cellular heterogeneity brought by a high-fat and high-cholesterol diet. All these findings open new perspectives at the transcriptomic level to studying the pathology of atherosclerosis.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Yizhou Jiang
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
| |
Collapse
|
30
|
Mullan KA, Zhang JB, Jones CM, Goh SJ, Revote J, Illing PT, Purcell AW, La Gruta NL, Li C, Mifsud NA. TCR_Explore: A novel webtool for T cell receptor repertoire analysis. Comput Struct Biotechnol J 2023; 21:1272-1282. [PMID: 36814721 PMCID: PMC9939424 DOI: 10.1016/j.csbj.2023.01.046] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 01/31/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
T cells expressing either alpha-beta or gamma-delta T cell receptors (TCR) are critical sentinels of the adaptive immune system, with receptor diversity being essential for protective immunity against a broad array of pathogens and agents. Programs available to profile TCR clonotypic signatures can be limiting for users with no coding expertise. Current analytical pipelines can be inefficient due to manual processing steps, open to data entry errors and have multiple analytical tools with unique inputs that require coding expertise. Here we present a bespoke webtool designed for users irrespective of coding expertise, coined 'TCR_Explore', enabling analysis either derived via Sanger sequencing or next generation sequencing (NGS) platforms. Further, TCR_Explore incorporates automated quality control steps for Sanger sequencing. The creation of flexible and publication ready figures are enabled for different sequencing platforms following universal conversion to the TCR_Explore file format. TCR_Explore will enhance a user's capacity to undertake in-depth TCR repertoire analysis of both new and pre-existing datasets for identification of T cell clonotypes associated with health and disease. The web application is located at https://tcr-explore.erc.monash.edu for users to interactively explore TCR repertoire datasets.
Collapse
Affiliation(s)
- Kerry A. Mullan
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia,Corresponding authors.
| | - Justin B. Zhang
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Claerwen M. Jones
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Shawn J.R. Goh
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Jerico Revote
- Monash eResearch Centre, Monash University, Melbourne, VIC 3800, Australia
| | - Patricia T. Illing
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Anthony W. Purcell
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Nicole L. La Gruta
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Chen Li
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Nicole A. Mifsud
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia,Corresponding authors.
| |
Collapse
|
31
|
Huang J, Chen Y, Guo Z, Yu Y, Zhang Y, Li P, Shi L, Lv G, Sun B. Prospective study and validation of early warning marker discovery based on integrating multi-omics analysis in severe burn patients with sepsis. BURNS & TRAUMA 2023; 11:tkac050. [PMID: 36659877 PMCID: PMC9840905 DOI: 10.1093/burnst/tkac050] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 09/22/2022] [Indexed: 01/17/2023]
Abstract
Background Early detection, timely diagnosis and rapid response are essential for case management and precautions of burn-associated sepsis. However, studies on indicators for early warning and intervention have rarely been conducted. This study was performed to better understand the pathophysiological changes and targets for prevention of severe burn injuries. Methods We conducted a multi-center, prospective multi-omics study, including genomics, microRNAomics, proteomics and single-cell transcriptomics, in 60 patients with severe burn injuries. A mouse model of severe burn injuries was also constructed to verify the early warning ability and therapeutic effects of potential markers. Results Through genomic analysis, we identified seven important susceptibility genes (DNAH11, LAMA2, ABCA2, ZFAND4, CEP290, MUC20 and ENTPD1) in patients with severe burn injuries complicated with sepsis. Through plasma miRNAomics studies, we identified four miRNAs (hsa-miR-16-5p, hsa-miR-185-5p, hsa-miR-451a and hsa-miR-423-5p) that may serve as early warning markers of burn-associated sepsis. A proteomic study indicated the changes in abundance of major proteins at different time points after severe burn injury and revealed the candidate early warning markers S100A8 and SERPINA10. In addition, the proteomic analysis indicated that neutrophils play an important role in the pathogenesis of severe burn injuries, as also supported by findings from single-cell transcriptome sequencing of neutrophils. Through further studies on severely burned mice, we determined that S100A8 is also a potential early therapeutic target for severe burn injuries, beyond being an early warning indicator. Conclusions Our multi-omics study identified seven susceptibility genes, four miRNAs and two proteins as early warning markers for severe burn-associated sepsis. In severe burn-associated sepsis, the protein S100A8 has both warning and therapeutic effects.
Collapse
Affiliation(s)
| | | | | | - Yanzhen Yu
- Department of Burns and Plastic Surgery, Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou 215002, Jiangsu Province, China
| | - Yi Zhang
- Department of Burns and Plastic Surgery, Affiliated Hospital of Nantong University, Nantong 226000, Jiangsu, China
| | - Pingsong Li
- Department of Burns and Plastic Surgery, Northern Jiangsu People’s Hospital, Yangzhou 225001, Jiangsu, China
| | - Lei Shi
- Department of Burns and Plastic Surgery, Affiliated Hospital of Jiangsu University, Zhenjiang 212001, Jiangsu, China
| | - Guozhong Lv
- Department of Burns and Plastic Surgery, Affiliated Hospital of Jiangnan University, Wuxi 214041, Jiangsu, China
| | | |
Collapse
|
32
|
Dacon C, Peng L, Lin TH, Tucker C, Lee CCD, Cong Y, Wang L, Purser L, Cooper AJR, Williams JK, Pyo CW, Yuan M, Kosik I, Hu Z, Zhao M, Mohan D, Peterson M, Skinner J, Dixit S, Kollins E, Huzella L, Perry D, Byrum R, Lembirik S, Murphy M, Zhang Y, Yang ES, Chen M, Leung K, Weinberg RS, Pegu A, Geraghty DE, Davidson E, Doranz BJ, Douagi I, Moir S, Yewdell JW, Schmaljohn C, Crompton PD, Mascola JR, Holbrook MR, Nemazee D, Wilson IA, Tan J. Rare, convergent antibodies targeting the stem helix broadly neutralize diverse betacoronaviruses. Cell Host Microbe 2023; 31:97-111.e12. [PMID: 36347257 PMCID: PMC9639329 DOI: 10.1016/j.chom.2022.10.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 09/04/2022] [Accepted: 10/13/2022] [Indexed: 11/09/2022]
Abstract
Humanity has faced three recent outbreaks of novel betacoronaviruses, emphasizing the need to develop approaches that broadly target coronaviruses. Here, we identify 55 monoclonal antibodies from COVID-19 convalescent donors that bind diverse betacoronavirus spike proteins. Most antibodies targeted an S2 epitope that included the K814 residue and were non-neutralizing. However, 11 antibodies targeting the stem helix neutralized betacoronaviruses from different lineages. Eight antibodies in this group, including the six broadest and most potent neutralizers, were encoded by IGHV1-46 and IGKV3-20. Crystal structures of three antibodies of this class at 1.5-1.75-Å resolution revealed a conserved mode of binding. COV89-22 neutralized SARS-CoV-2 variants of concern including Omicron BA.4/5 and limited disease in Syrian hamsters. Collectively, these findings identify a class of IGHV1-46/IGKV3-20 antibodies that broadly neutralize betacoronaviruses by targeting the stem helix but indicate these antibodies constitute a small fraction of the broadly reactive antibody response to betacoronaviruses after SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Cherrelle Dacon
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Linghang Peng
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ting-Hui Lin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Courtney Tucker
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA; Department of Biology, The Catholic University of America, Washington, DC 20064, USA
| | - Chang-Chun D Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yu Cong
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Lingshu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lauren Purser
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Andrew J R Cooper
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | | | - Chul-Woo Pyo
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ivan Kosik
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zhe Hu
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ming Zhao
- Protein Chemistry Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Divya Mohan
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Mary Peterson
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Jeff Skinner
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Saurabh Dixit
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Erin Kollins
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Louis Huzella
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Donna Perry
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Russell Byrum
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Sanae Lembirik
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Michael Murphy
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Yi Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eun Sung Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Man Chen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kwanyee Leung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rona S Weinberg
- New York Blood Center, Lindsley F. Kimball Research Institute, New York, NY 10065, USA
| | - Amarendra Pegu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel E Geraghty
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | | | - Iyadh Douagi
- Flow Cytometry Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Susan Moir
- B Cell Immunology Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jonathan W Yewdell
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Connie Schmaljohn
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Peter D Crompton
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael R Holbrook
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - David Nemazee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Joshua Tan
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA.
| |
Collapse
|
33
|
Sanchez Sanchez G, Tafesse Y, Papadopoulou M, Vermijlen D. Surfing on the waves of the human γδ T cell ontogenic sea. Immunol Rev 2023; 315:89-107. [PMID: 36625367 DOI: 10.1111/imr.13184] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
While γδ T cells are present virtually in all vertebrates, there is a remarkable lack of conservation of the TRG and TRD loci underlying the generation of the γδ T cell receptor (TCR), which is associated with the generation of species-specific γδ T cells. A prominent example is the human phosphoantigen-reactive Vγ9Vδ2 T cell subset that is absent in mice. Murine γδ thymocyte cells were among the first immune cells identified to follow a wave-based layered development during embryonic and early life, and since this initial observation, in-depth insight has been obtained in their thymic ontogeny. By contrast, less is known about the development of human γδ T cells, especially regarding the generation of γδ thymocyte waves. Here, after providing an overview of thymic γδ wave generation in several vertebrate classes, we review the evidence for γδ waves in the human fetal thymus, where single-cell technologies have allowed the breakdown of human γδ thymocytes into functional waves with important TCR associations. Finally, we discuss the possible mechanisms contributing to the generation of waves of γδ thymocytes and their possible significance in the periphery.
Collapse
Affiliation(s)
- Guillem Sanchez Sanchez
- Department of Pharmacotherapy and Pharmaceutics, Université Libre de Bruxelles (ULB), Brussels, Belgium.,Institute for Medical Immunology, Université Libre de Bruxelles (ULB), Gosselies, Belgium.,ULB Center for Research in Immunology (U-CRI), Université Libre de Bruxelles (ULB), Brussels, Belgium.,WELBIO Department, WEL Research Institute, Wavre, Belgium
| | - Yohannes Tafesse
- Department of Pharmacotherapy and Pharmaceutics, Université Libre de Bruxelles (ULB), Brussels, Belgium.,Institute for Medical Immunology, Université Libre de Bruxelles (ULB), Gosselies, Belgium.,ULB Center for Research in Immunology (U-CRI), Université Libre de Bruxelles (ULB), Brussels, Belgium.,WELBIO Department, WEL Research Institute, Wavre, Belgium
| | - Maria Papadopoulou
- Department of Pharmacotherapy and Pharmaceutics, Université Libre de Bruxelles (ULB), Brussels, Belgium.,Institute for Medical Immunology, Université Libre de Bruxelles (ULB), Gosselies, Belgium.,ULB Center for Research in Immunology (U-CRI), Université Libre de Bruxelles (ULB), Brussels, Belgium.,WELBIO Department, WEL Research Institute, Wavre, Belgium
| | - David Vermijlen
- Department of Pharmacotherapy and Pharmaceutics, Université Libre de Bruxelles (ULB), Brussels, Belgium.,Institute for Medical Immunology, Université Libre de Bruxelles (ULB), Gosselies, Belgium.,ULB Center for Research in Immunology (U-CRI), Université Libre de Bruxelles (ULB), Brussels, Belgium.,WELBIO Department, WEL Research Institute, Wavre, Belgium
| |
Collapse
|
34
|
Lefranc MP, Lefranc G. Antibody Sequence and Structure Analyses Using IMGT ®: 30 Years of Immunoinformatics. Methods Mol Biol 2023; 2552:3-59. [PMID: 36346584 DOI: 10.1007/978-1-0716-2609-2_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org , the global reference in immunogenetics and immunoinformatics, was created in 1989 by Marie-Paule Lefranc (Université de Montpellier and CNRS) to manage the huge diversity of the antigen receptors, immunoglobulins (IG) or antibodies, and T cell receptors (TR) of the adaptive immune responses. The founding of IMGT® marked the advent of immunoinformatics, which emerged at the interface between immunogenetics and bioinformatics. IMGT® standardized analysis of the IG, TR, and major histocompatibility (MH) genes and proteins bridges the gap between sequences and three-dimensional (3D) structures, for all jawed vertebrates from fish to humans. This is achieved through the IMGT Scientific chart rules, based on the IMGT-ONTOLOGY axioms, and primarily CLASSIFICATION (IMGT gene and allele nomenclature) and NUMEROTATION (IMGT unique numbering and IMGT Colliers de Perles). IMGT® comprises seven databases (IMGT/LIGM-DB for nucleotide sequences, IMGT/GENE-DB for genes and alleles, etc.), 17 tools (IMGT/V-QUEST, IMGT/JunctionAnalysis, IMGT/HighV-QUEST for NGS, etc.), and more than 20,000 Web resources. In this chapter, the focus is on the tools for amino acid sequences per domain (IMGT/DomainGapAlign and IMGT/Collier-de-Perles), and on the databases for receptors (IMGT/2Dstructure-DB and IMGT/3D-structure-DB) described per receptor, chain, and domain and, for 3D, with contact analysis, paratope, and epitope. The IMGT/mAb-DB is the query interface for monoclonal antibodies (mAb), fusion proteins for immune applications (FPIA), composite proteins for clinical applications (CPCA), and related proteins of interest (RPI) with links to IMGT® 2D and 3D databases and to the World Health Organization (WHO) International Nonproprietary Names (INN) program lists. The chapter includes the human IG allotypes and antibody engineered variants for effector properties used in the description of therapeutical mAb.
Collapse
Affiliation(s)
- Marie-Paule Lefranc
- IMGT®, the international ImMunoGeneTics information system®, Laboratoire d'ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, UMR 9002 CNRS, Université de Montpellier, Montpellier cedex 5, France.
| | - Gérard Lefranc
- IMGT®, the international ImMunoGeneTics information system®, Laboratoire d'ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, UMR 9002 CNRS, Université de Montpellier, Montpellier cedex 5, France.
| |
Collapse
|
35
|
Zhang Y, Yang S, Jiang D, Li Y, Ma S, Wang L, Li G, Wang H, Zhang A, Xu G. Screening and identification of an anti-PD-1 nanobody with antitumor activity. Biosci Rep 2022; 43:BSR20221546. [PMID: 36475449 PMCID: PMC9867944 DOI: 10.1042/bsr20221546] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 11/25/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022] Open
Abstract
Blocking of PD-1 or PD-L1 with corresponding antibody to enhance T cell response and mediate antitumor activity has been successfully applied in clinical practice. Several immune checkpoint inhibitors including monoclonal antibodies targeting PD-1 have been approved by the Food and Drug Administration (FDA) in cancer immunotherapy. However, the application of traditional antibodies has limited due to their drawbacks of large molecular weight and low tissue penetration. As the high specificity and strong tissue penetration of nanobodies (Nbs), efforts have been taken to develop Nbs for cancer therapy. Herein, we aim to screen a specific Nb against human PD-1 derived from a naïve camel Nb phage display library and further study its biological characteristic and anti-tumor activity. Finally, an anti-PD-1 Nb with high specificity and affinity was screened and generated, its cytotoxicity and antitumor effect was also confirmed in vitro and vivo. All of these indicate that the anti-PD-1 Nb may provide an alternative and appealing therapeutic agent for cancer immunotherapy.
Collapse
Affiliation(s)
- Yanting Zhang
- General Hospital of Ningxia Medical University, Yinchuan, Ningxia 750004, China
- Department of Laboratory Medicine, School of Clinical Medicine, Ningxia Medical University, Yinchuan, Ningxia 750004, China
| | - Shaoqi Yang
- General Hospital of Ningxia Medical University, Yinchuan, Ningxia 750004, China
| | - Dan Jiang
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, Guangdong 523808, China
| | - Yanning Li
- Department of Laboratory Medicine, School of Clinical Medicine, Ningxia Medical University, Yinchuan, Ningxia 750004, China
| | - Shuo Ma
- General Hospital of Ningxia Medical University, Yinchuan, Ningxia 750004, China
| | - Liyan Wang
- Department of Laboratory Medicine, School of Clinical Medicine, Ningxia Medical University, Yinchuan, Ningxia 750004, China
| | - Guangqi Li
- Department of Laboratory Medicine, School of Clinical Medicine, Ningxia Medical University, Yinchuan, Ningxia 750004, China
| | - Hongxia Wang
- Department of Laboratory Medicine, School of Clinical Medicine, Ningxia Medical University, Yinchuan, Ningxia 750004, China
| | - Aijun Zhang
- Department of Laboratory Medicine, School of Clinical Medicine, Ningxia Medical University, Yinchuan, Ningxia 750004, China
| | - Guangxian Xu
- Department of Laboratory Medicine, School of Clinical Medicine, Ningxia Medical University, Yinchuan, Ningxia 750004, China
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, Guangdong 523808, China
| |
Collapse
|
36
|
Hu Y, Paris S, Bertolet G, Barsoumian HB, Wang Q, Da Silva J, Patel NB, Nguyen N, Doss DJ, Huang A, Hsu E, Leyton CSK, Voss TA, Masrorpour F, Leuschner C, Pietz JT, Puebla-Osorio N, Gandhi S, Nguyen QN, Wang J, Cortez MA, Welsh JW. NBTXR3 improves the efficacy of immunoradiotherapy combining nonfucosylated anti-CTLA4 in an anti-PD1 resistant lung cancer model. Front Immunol 2022; 13:1022011. [PMID: 36405757 PMCID: PMC9669748 DOI: 10.3389/fimmu.2022.1022011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 10/19/2022] [Indexed: 01/01/2024] Open
Abstract
The efficacy of immunoradiotherapy consisting of radiation therapy and immune checkpoint blockade relies on effectively promoting the systemic antitumor immune response's activation while simultaneously reducing local factors favoring immune suppression. We previously demonstrated that NBTXR3, a nanoparticle radioenhancer, significantly improved immune responses in a murine anti-PD1-resistant metastatic lung cancer model. We hypothesize that radioactivated-NBTXR3 addition to anti-PD1 and a second-generation anti-CTLA4 could improve treatment effectiveness. To test this hypothesis, we inoculated mice with 344SQR cells in the right and left legs to establish primary and secondary tumors. The primary tumors were intratumorally injected with NBTXR3 nanoparticles on day 7, followed by three fractions of 12 Gy radiation on days 8, 9, and 10. The secondary tumors received two fractions of 1Gy radiation on days 13 and 14. Multiple rounds of anti-PD1, anti-CTLA4 or nonfucosylated anti-CTLA4 were given to the mice. Immune profiling of the tumors revealed that the combination of NBTXR3 with immunoradiotherapy significantly upregulated the activities of a wide range of antitumor immune pathways and reduced the abundance of regulatory suppressor T cells. This combination effectively eradicated the primary and secondary tumors and increased animal survival to 75%. Remarkably, previously treated with NBTXR3-containing treatment, the survivor mice exhibited a long-lasting antitumor memory immune response. This data provides compelling evidence of the efficacy of NBTXR3 to synergize with the immunoradiotherapy approach when combined with an anti-PD1 and multiple checkpoints such as a second generation anti-CTLA4 and show the potential for clinical uses of antitumor immunomodulatory effects of NBTXR3.
Collapse
Affiliation(s)
- Yun Hu
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Sébastien Paris
- Department of Translational Science, Nanobiotix, Paris, France
| | - Genevieve Bertolet
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Hampartsoum B. Barsoumian
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Qi Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Jordan Da Silva
- Department of Translational Science, Nanobiotix, Paris, France
| | - Nalini B. Patel
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Nguyen Nguyen
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Denaha J. Doss
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Ailing Huang
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Ethan Hsu
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Claudia S. Kettlun Leyton
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Tiffany A. Voss
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Fatemeh Masrorpour
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Carola Leuschner
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Jordan T. Pietz
- Department of Strategic Communication, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Nahum Puebla-Osorio
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Saumil Gandhi
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Quynh-Nhu Nguyen
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Jing Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Maria Angelica Cortez
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - James W. Welsh
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| |
Collapse
|
37
|
Sezen D, Barsoumian HB, He K, Hu Y, Wang Q, Abana CO, Puebla-Osorio N, Hsu EY, Wasley M, Masrorpour F, Wang J, Cortez MA, Welsh JW. Pulsed radiotherapy to mitigate high tumor burden and generate immune memory. Front Immunol 2022; 13:984318. [PMID: 36275767 PMCID: PMC9582356 DOI: 10.3389/fimmu.2022.984318] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 09/23/2022] [Indexed: 11/19/2022] Open
Abstract
Radiation therapy (XRT) has a well-established role in cancer treatment. Given the encouraging results on immunostimulatory effects, radiation has been increasingly used with immune-check-point inhibitors in metastatic disease, especially when immunotherapy fails due to tumor immune evasion. We hypothesized that using high-dose stereotactic radiation in cycles (pulses) would increase T-cell priming and repertoire with each pulse and build immune memory in an incremental manner. To prove this hypothesis, we studied the combination of anti-CTLA-4 and Pulsed radiation therapy in our 344SQ non-small cell lung adenocarcinoma murine model. Primary and secondary tumors were bilaterally implanted in 129Sv/Ev mice. In the Pulsed XRT group, both primary and secondary tumors received 12Gyx2 radiation one week apart, and blood was collected seven days afterwards for TCR repertoire analysis. As for the delayed-Pulse group, primary tumors received 12Gyx2, and after a window of two weeks, the secondary tumors received 12Gyx2. Blood was collected seven days after the second cycle of radiation. The immunotherapy backbone for both groups was anti-CTLA-4 antibody to help with priming. Treatment with Pulsed XRT + anti-CTLA-4 led to significantly improved survival and resulted in a delayed tumor growth, where we observed enhanced antitumor efficacy at primary tumor sites beyond XRT + anti-CTLA-4 treatment group. More importantly, Pulsed XRT treatment led to increased CD4+ effector memory compared to single-cycle XRT. Pulsed XRT demonstrated superior efficacy to XRT in driving antitumor effects that were largely dependent on CD4+ T cells and partially dependent on CD8+ T cells. These results suggest that combinatorial strategies targeting multiple points of tumor immune evasion may lead to a robust and sustained antitumor response.
Collapse
Affiliation(s)
- Duygu Sezen
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
- Department of Radiation Oncology, Koç University School of Medicine, Istanbul, Turkey
| | - Hampartsoum B. Barsoumian
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Kewen He
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Yun Hu
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Qi Wang
- Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Chike O. Abana
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Nahum Puebla-Osorio
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Ethan Y. Hsu
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Mark Wasley
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Fatemeh Masrorpour
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Jing Wang
- Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Maria Angelica Cortez
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - James W. Welsh
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| |
Collapse
|
38
|
Ye B, Shen Y, Chen H, Lin S, Mao W, Dong Y, Li X. Differential proteomic analysis of plasma-derived exosomes as diagnostic biomarkers for chronic HBV-related liver disease. Sci Rep 2022; 12:14428. [PMID: 36002595 PMCID: PMC9402575 DOI: 10.1038/s41598-022-13272-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 05/23/2022] [Indexed: 11/25/2022] Open
Abstract
Hepatitis B virus (HBV) infection is still a major public health problem worldwide. We aimed to identify new, non-invasive biomarkers for the early diagnosis of chronic HBV-related diseases, reveal alterations in the progression of chronic hepatitis B (CHB), liver cirrhosis (LC), and hepatocellular carcinoma (HCC). Here, exosomes were isolated and characterized through size exclusion chromatography and nanoparticle tracking analysis. Profiles of differentially expressed proteins (DEPs) were analyzed through liquid chromatography-tandem mass spectrometry (LC–MS/MS), Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes analyses. Results showed that the DEPs, including CO9, LBP, SVEP1, and VWF levels in extracellular vesicles (EVs) were significantly higher in CHB than in healthy controls (HCs). VWF expression levels in EVs were significantly lower in CHB than in those with LC. KV311 expression levels in EVs were significantly higher, whereas LBP levels were significantly lower in patients with CHB than in those with HCC. All biomarkers seemed to exhibit a high diagnostic capacity for HBV-related liver disease. Patients with HBV-induced chronic liver disease exhibit characteristic protein profiles in their EVs. Thus, serum exosomes may be used as novel, liquid biopsy biomarkers to provide useful clinical information for the diagnosis of HBV-related liver diseases at different stages.
Collapse
Affiliation(s)
- Bo Ye
- Department of Laboratory Medicine, Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, The First Affiliated Hospital, College of Medicine, Zhejiang University School of Medicine, No. 79 Qingchun Road, Hangzhou, 310003, People's Republic of China
| | - Yifei Shen
- Department of Laboratory Medicine, Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, The First Affiliated Hospital, College of Medicine, Zhejiang University School of Medicine, No. 79 Qingchun Road, Hangzhou, 310003, People's Republic of China
| | - Hui Chen
- Department of Laboratory Medicine, Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, The First Affiliated Hospital, College of Medicine, Zhejiang University School of Medicine, No. 79 Qingchun Road, Hangzhou, 310003, People's Republic of China
| | - Sha Lin
- Department of Laboratory Medicine, Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, The First Affiliated Hospital, College of Medicine, Zhejiang University School of Medicine, No. 79 Qingchun Road, Hangzhou, 310003, People's Republic of China
| | - Weilin Mao
- Department of Laboratory Medicine, Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, The First Affiliated Hospital, College of Medicine, Zhejiang University School of Medicine, No. 79 Qingchun Road, Hangzhou, 310003, People's Republic of China
| | - Yuejiao Dong
- Department of Laboratory Medicine, Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, The First Affiliated Hospital, College of Medicine, Zhejiang University School of Medicine, No. 79 Qingchun Road, Hangzhou, 310003, People's Republic of China
| | - Xuefen Li
- Department of Laboratory Medicine, Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, The First Affiliated Hospital, College of Medicine, Zhejiang University School of Medicine, No. 79 Qingchun Road, Hangzhou, 310003, People's Republic of China.
| |
Collapse
|
39
|
Covalent TCR-peptide-MHC interactions induce T cell activation and redirect T cell fate in the thymus. Nat Commun 2022; 13:4951. [PMID: 35999236 PMCID: PMC9399087 DOI: 10.1038/s41467-022-32692-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 08/10/2022] [Indexed: 11/24/2022] Open
Abstract
Interactions between a T cell receptor (TCR) and a peptide-major histocompatibility complex (pMHC) ligand are typically mediated by noncovalent bonds. By studying T cells expressing natural or engineered TCRs, here we describe covalent TCR-pMHC interactions that involve a cysteine-cysteine disulfide bond between the TCR and the peptide. By introducing cysteines into a known TCR-pMHC combination, we demonstrate that disulfide bond formation does not require structural rearrangement of the TCR or the peptide. We further show these disulfide bonds still form even when the initial affinity of the TCR-pMHC interaction is low. Accordingly, TCR-peptide disulfide bonds facilitate T cell activation by pMHC ligands with a wide spectrum of affinities for the TCR. Physiologically, this mechanism induces strong Zap70-dependent TCR signaling, which triggers T cell deletion or agonist selection in the thymus cortex. Covalent TCR-pMHC interactions may thus underlie a physiological T cell activation mechanism that has applications in basic immunology and potentially in immunotherapy. Differentiation and activation of T cells are normally modulated by non-covalent interactions between T cell receptor (TCR) and antigenic peptides. Here the authors use step-wise mutations, biochemical characterization and structural insights to describe the contributions of natural covalent bonds between TCR and antigenic peptides during these processes.
Collapse
|
40
|
Dacon C, Tucker C, Peng L, Lee CCD, Lin TH, Yuan M, Cong Y, Wang L, Purser L, Williams JK, Pyo CW, Kosik I, Hu Z, Zhao M, Mohan D, Cooper AJR, Peterson M, Skinner J, Dixit S, Kollins E, Huzella L, Perry D, Byrum R, Lembirik S, Drawbaugh D, Eaton B, Zhang Y, Yang ES, Chen M, Leung K, Weinberg RS, Pegu A, Geraghty DE, Davidson E, Douagi I, Moir S, Yewdell JW, Schmaljohn C, Crompton PD, Holbrook MR, Nemazee D, Mascola JR, Wilson IA, Tan J. Broadly neutralizing antibodies target the coronavirus fusion peptide. Science 2022; 377:728-735. [PMID: 35857439 PMCID: PMC9348754 DOI: 10.1126/science.abq3773] [Citation(s) in RCA: 102] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 07/06/2022] [Indexed: 02/05/2023]
Abstract
The potential for future coronavirus outbreaks highlights the need to broadly target this group of pathogens. We used an epitope-agnostic approach to identify six monoclonal antibodies that bind to spike proteins from all seven human-infecting coronaviruses. All six antibodies target the conserved fusion peptide region adjacent to the S2' cleavage site. COV44-62 and COV44-79 broadly neutralize alpha- and betacoronaviruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron subvariants BA.2 and BA.4/5, albeit with lower potency than receptor binding domain-specific antibodies. In crystal structures of COV44-62 and COV44-79 antigen-binding fragments with the SARS-CoV-2 fusion peptide, the fusion peptide epitope adopts a helical structure and includes the arginine residue at the S2' cleavage site. COV44-79 limited disease caused by SARS-CoV-2 in a Syrian hamster model. These findings highlight the fusion peptide as a candidate epitope for next-generation coronavirus vaccine development.
Collapse
Affiliation(s)
- Cherrelle Dacon
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Courtney Tucker
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Linghang Peng
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Chang-Chun D. Lee
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ting-Hui Lin
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yu Cong
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Lingshu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lauren Purser
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | | | - Chul-Woo Pyo
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Ivan Kosik
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zhe Hu
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ming Zhao
- Protein Chemistry Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health; Rockville, MD 20852, USA
| | - Divya Mohan
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Andrew J. R. Cooper
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Mary Peterson
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Jeff Skinner
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Saurabh Dixit
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Erin Kollins
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Louis Huzella
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Donna Perry
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Russell Byrum
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Sanae Lembirik
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - David Drawbaugh
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Brett Eaton
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Yi Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eun Sung Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Man Chen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kwanyee Leung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rona S. Weinberg
- New York Blood Center, Lindsley F. Kimball Research Institute, New York, NY 10065, USA
| | - Amarendra Pegu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel E. Geraghty
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | - Iyadh Douagi
- Flow Cytometry Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Susan Moir
- B Cell Immunology Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jonathan W. Yewdell
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Connie Schmaljohn
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Peter D. Crompton
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Michael R. Holbrook
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - David Nemazee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - John R. Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Joshua Tan
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| |
Collapse
|
41
|
Gao J, He J, Zhang F, Xiao Q, Cai X, Yi X, Zheng S, Zhang Y, Wang D, Zhu G, Wang J, Shen B, Ralser M, Guo T, Zhu Y. Integration of protein context improves protein-based COVID-19 patient stratification. Clin Proteomics 2022; 19:31. [PMID: 35953823 PMCID: PMC9366758 DOI: 10.1186/s12014-022-09370-0] [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: 02/03/2022] [Accepted: 07/30/2022] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Classification of disease severity is crucial for the management of COVID-19. Several studies have shown that individual proteins can be used to classify the severity of COVID-19. Here, we aimed to investigate whether integrating four types of protein context data, namely, protein complexes, stoichiometric ratios, pathways and network degrees will improve the severity classification of COVID-19. METHODS We performed machine learning based on three previously published datasets. The first was a SWATH (sequential window acquisition of all theoretical fragment ion spectra) MS (mass spectrometry) based proteomic dataset. The second was a TMTpro 16plex labeled shotgun proteomics dataset. The third was a SWATH dataset of an independent patient cohort. RESULTS Besides twelve proteins, machine learning also prioritized two complexes, one stoichiometric ratio, five pathways, and five network degrees, resulting a 25-feature panel. As a result, a model based on the 25 features led to effective classification of severe cases with an AUC of 0.965, outperforming the models with proteins only. Complement component C9, transthyretin (TTR) and TTR-RBP (transthyretin-retinol binding protein) complex, the stoichiometric ratio of SAA2 (serum amyloid A proteins 2)/YLPM1 (YLP Motif Containing 1), and the network degree of SIRT7 (Sirtuin 7) and A2M (alpha-2-macroglobulin) were highlighted as potential markers by this classifier. This classifier was further validated with a TMT-based proteomic data set from the same cohort (test dataset 1) and an independent SWATH-based proteomic data set from Germany (test dataset 2), reaching an AUC of 0.900 and 0.908, respectively. Machine learning models integrating protein context information achieved higher AUCs than models with only one feature type. CONCLUSION Our results show that the integration of protein context including protein complexes, stoichiometric ratios, pathways, network degrees, and proteins improves phenotype prediction.
Collapse
Affiliation(s)
- Jinlong Gao
- grid.494629.40000 0004 8008 9315Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang China
| | - Jiale He
- grid.494629.40000 0004 8008 9315Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang China
| | - Fangfei Zhang
- grid.494629.40000 0004 8008 9315Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang China
| | - Qi Xiao
- grid.494629.40000 0004 8008 9315Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang China
| | - Xue Cai
- grid.494629.40000 0004 8008 9315Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang China
| | - Xiao Yi
- grid.494629.40000 0004 8008 9315Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang China
| | - Siqi Zheng
- grid.494629.40000 0004 8008 9315Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang China
| | - Ying Zhang
- grid.268099.c0000 0001 0348 3990Taizhou Hospital, Wenzhou Medical University, Linhai, Zhejiang China
| | - Donglian Wang
- grid.268099.c0000 0001 0348 3990Taizhou Hospital, Wenzhou Medical University, Linhai, Zhejiang China
| | - Guangjun Zhu
- grid.268099.c0000 0001 0348 3990Taizhou Hospital, Wenzhou Medical University, Linhai, Zhejiang China
| | - Jing Wang
- grid.268099.c0000 0001 0348 3990Taizhou Hospital, Wenzhou Medical University, Linhai, Zhejiang China
| | - Bo Shen
- grid.268099.c0000 0001 0348 3990Taizhou Hospital, Wenzhou Medical University, Linhai, Zhejiang China
| | - Markus Ralser
- grid.451388.30000 0004 1795 1830Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK ,grid.6363.00000 0001 2218 4662Department of Biochemistry, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität Zu Berlin, Berlin, Germany
| | - Tiannan Guo
- grid.494629.40000 0004 8008 9315Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang China
| | - Yi Zhu
- grid.494629.40000 0004 8008 9315Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang China
| |
Collapse
|
42
|
Linguiti G, Tragni V, Pierri CL, Massari S, Lefranc MP, Antonacci R, Ciccarese S. 3D structures inferred from cDNA clones identify the CD1D-Restricted γδ T cell receptor in dromedaries. Front Immunol 2022; 13:928860. [PMID: 36016959 PMCID: PMC9396240 DOI: 10.3389/fimmu.2022.928860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 07/15/2022] [Indexed: 11/13/2022] Open
Abstract
The Camelidae species occupy an important immunological niche within the humoral as well as cell mediated immune response. Although recent studies have highlighted that the somatic hypermutation (SHM) shapes the T cell receptor gamma (TRG) and delta (TRD) repertoire in Camelus dromedarius, it is still unclear how γδ T cells use the TRG/TRD receptors and their respective variable V-GAMMA and V-DELTA domains to recognize antigen in an antibody-like fashion. Here we report about 3D structural analyses of the human and dromedary γδ T cell receptor. First, we have estimated the interaction energies at the interface within the human crystallized paired TRG/TRD chains and quantified interaction energies within the same human TRG/TRD chains in complex with the CD1D, an RPI-MH1-LIKE antigen presenting glycoprotein. Then, we used the human TRG/TRD-CD1D complex as template for the 3D structure of the dromedary TRG/TRD-CD1D complex and for guiding the 3D human/dromedary comparative analysis. The choice of mutated TRG alternatively combined with mutated TRD cDNA clones originating from the spleen of one single dromedary was crucial to quantify the strength of the interactions at the protein-protein interface between the paired C. dromedarius TRG and TRD V-domains and between the C. dromedarius TRG/TRD V-domains and CD1D G-domains. Interacting amino acids located in the V-domain Complementarity Determining Regions (CDR) and Framework Regions (FR) according to the IMGT unique numbering for V-domains were identified. The resulting 3D dromedary TRG V-GAMMA combined with TRD V-DELTA protein complexes allowed to deduce the most stable gamma/delta chains pairings and to propose a candidate CD1D-restricted γδ T cell receptor complex.
Collapse
Affiliation(s)
| | - Vincenzo Tragni
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari “Aldo Moro”, Bari, Italy
| | - Ciro Leonardo Pierri
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari “Aldo Moro”, Bari, Italy
| | - Serafina Massari
- Department of Biological and Environmental Science and Technologies, University of Salento, Lecce, Italy
| | - Marie-Paule Lefranc
- The International ImMunoGeneTics Information System (IMGT), Laboratoire d’ImmunoGénétique Moléculaire (LIGM), Institut de Génétique Humaine (IGH), Montpellier, France
| | | | - Salvatrice Ciccarese
- Department of Biology, University of Bari “Aldo Moro”, Bari, Italy
- *Correspondence: Salvatrice Ciccarese,
| |
Collapse
|
43
|
diaPASEF Proteomics and Feature Selection for the Description of Sputum Proteome Profiles in a Cohort of Different Subtypes of Lung Cancer Patients and Controls. Int J Mol Sci 2022; 23:ijms23158737. [PMID: 35955870 PMCID: PMC9369298 DOI: 10.3390/ijms23158737] [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: 07/12/2022] [Revised: 07/29/2022] [Accepted: 08/03/2022] [Indexed: 11/21/2022] Open
Abstract
The high mortality, the presence of an initial asymptomatic stage and the fact that diagnosis in early stages reduces mortality justify the implementation of screening programs in the populations at risk of lung cancer. It is imperative to develop less aggressive methods that can complement existing diagnosis technologies. In this study, we aimed to identify lung cancer protein biomarkers and pathways affected in sputum samples, using the recently developed diaPASEF mass spectrometry (MS) acquisition mode. The sputum proteome of lung cancer cases and controls was analyzed through nano-HPLC–MS using the diaPASEF mode. For functional analysis, the results from differential expression analysis were further analyzed in the STRING platform, and feature selection was performed using sparse partial least squares discriminant analysis (sPLS-DA). Our results showed an activation of inflammation, with an alteration of pathways and processes related to acute-phase, complement, and immune responses. The resulting sPLS-DA model separated between case and control groups with high levels of sensitivity and specificity. In conclusion, we showed how new-generation proteomics can be used to detect potential biomarkers in sputum samples, and ultimately to discriminate patients from controls and even to help to differentiate between different cancer subtypes.
Collapse
|
44
|
Das D, Podder S. Deregulation of ceRNA Networks in Frontal Cortex and Choroid Plexus of Brain during SARS-CoV-2 Infection Aggravates Neurological Manifestations: An Insight from Bulk and Single-Cell Transcriptomic Analyses. Adv Biol (Weinh) 2022; 6:e2101310. [PMID: 35661455 PMCID: PMC9348399 DOI: 10.1002/adbi.202101310] [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: 11/30/2021] [Revised: 05/20/2022] [Indexed: 01/28/2023]
Abstract
Although transcriptomic studies of SARS-CoV-2-infected brains have depicted variability in gene expression, the landscape of deregulated cell-specific regulatory circuits has not been elucidated yet. Hence, bulk and single-cell RNA-seq data are analyzed to gain detailed insights. Initially, two ceRNA networks with 19 and 3 differentially expressed (DE) hub lncRNAs are reconstructed in SARS-CoV-2 infected Frontal Cortex (FC) and Choroid Plexus (CP), respectively. Functional and pathway enrichment analyses of downstream mRNAs of deregulated ceRNA axes demonstrate impairment of neurological processes. Mapping of hub lncRNA-mRNA pairs from bulk RNA-seq with snRNA-seq data has indicated that NORAD, NEAT1, and STXBP5-AS1 are downregulated across 4, 4, and 2 FC cell types, respectively. At the same time, MIRLET7BHG and MALAT1 are upregulated in excitatory neurons of FC and neurons of CP, respectively. Here, it is hypothesized that downregulation of NORAD, NEAT1, and STXBP5-AS1, and upregulation of MIRLET7BHG and MALAT1 might deregulate respectively 51, 6, and 37, and 31 and 19 mRNAs in cell types of FC and CP. Afterward, 13 therapeutic miRNAs are traced that might safeguard against deregulated lncRNA-mRNA pairs of NORAD, NEAT1, and MIRLET7BHG in FC. This study helps to explain the plausible mechanism of post-COVID neurological manifestation and also to devise therapeutics against it.
Collapse
Affiliation(s)
- Deepyaman Das
- Department of MicrobiologyRaiganj UniversityRaiganjUttar DinajpurWest Bengal733134India
| | - Soumita Podder
- Department of MicrobiologyRaiganj UniversityRaiganjUttar DinajpurWest Bengal733134India
| |
Collapse
|
45
|
Fu Q, Zhang H, Li Y, Zhang P, Gao C, Li J, Li X, Cao M, Li C. Transcriptomic characterization of Atlantic salmon (Salmo salar) head kidney following administration of Aeromonas salmonicida subsp. masoucida vaccine. FISH & SHELLFISH IMMUNOLOGY 2022; 126:150-163. [PMID: 35580798 DOI: 10.1016/j.fsi.2022.05.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 05/09/2022] [Accepted: 05/11/2022] [Indexed: 06/15/2023]
Abstract
Atlantic salmon is one of the most famous and economically important fish species globally. However, bacterial diseases constantly constrain salmon aquaculture. Thereinto, Aeromonas salmonicida subsp. masoucida (ASM), classified as atypical A. salmonicida, caused huge losses to salmonid industry in China. In this regard, we conducted transcriptome analysis in Atlantic salmon head kidney following the administration of ASM vaccination to reveal genes, their expression patterns, and pathways involved in immune responses. A total of 448.71 million clean reads were obtained, and 397.69 million reads were mapped onto the Atlantic salmon reference genome. In addition, 117, 1891, 741, 207, and 377 genes were significantly up-regulated, and 183, 1920, 695, 83, and 539 genes were significantly down-regulated post ASM vaccination at 12 h, 24 h, 1 m, 2 m, and 3 m, respectively. Furthermore, KEGG pathway analysis revealed that many differentially expressed genes (DEGs) following ASM vaccination were involved in cell adhesion molecules (H2-Aa-l and CD28-l),cytokine-cytokine receptor interaction (IL10, CXCL9, CXCL11, CXCR3, and CCL19), herpes simplex infection (IL1B, SOCS3-l, and C3-l), HTLV-I infection (Il1r2 and BCL2L1), influenza A (CXCL8 and Il12b), and PI3K-Akt signaling pathway (PIK3R3-l and Ddit4-l). Finally, the results of qRT-PCR showed a significant correlation with RNA-Seq results, suggesting the reliability of RNA-Seq for gene expression analysis. This study sets the foundation for further study on the vaccine protective mechanism in Atlantic salmon as well as other teleost species.
Collapse
Affiliation(s)
- Qiang Fu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Hao Zhang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yuqing Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Pei Zhang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Chengbin Gao
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Jie Li
- Key Laboratory of Maricultural Organism Disease Control, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Xingchun Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Min Cao
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Chao Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China.
| |
Collapse
|
46
|
Jia J, Yang JQ, Du YR, Xu Y, Kong D, Zhang XL, Mao JH, Hu GF, Wang KH, Kuang YQ. Transcriptomic Profiling Reveals Underlying Immunoregulation Mechanisms of Resistant Hypertension in Injection Drug Users. J Inflamm Res 2022; 15:3409-3420. [PMID: 35706529 PMCID: PMC9191201 DOI: 10.2147/jir.s361634] [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: 02/23/2022] [Accepted: 05/25/2022] [Indexed: 12/18/2022] Open
Abstract
Background Hypertension is a common complication in injection drug users (IDU), especially a high proportion of resistant hypertension occurs among them. However, the involving mechanisms remain largely unknown. Methods We here investigated the key signaling moieties in resistant hypertension in drug users. Analyses were performed with high-throughput transcriptomic sequencing data of peripheral blood from individuals with drug-sensitive hypertension (Ctrl-DS), IDU with resistant hypertension (IDU-DR), and IDU with sensitive hypertension (IDU-DS). Results We showed that 17 and 1 genes in IDU-DS, 48 and 4 genes in IDU-DR were upregulated and downregulated compared Ctrl-DS, and 2 and 4 genes were upregulated and downregulated in IDU-DR compared with IDU-DS, respectively (p ≤ 0.01 and |log2(FC)| ≥ 1). Differentially expressed genes (DEGs) between Ctrl-DS and IDU-DS were mainly involved in Gene ontology terms of immunoglobulin complex and blood microparticle. DEGs between IDU-DS and IDU-DR were mainly involved in immune system process and immunoglobulin complex. DEGs between Ctrl-DS and IDU-DR were mainly involved in immunoglobulin complex, blood microparticle and cytoplasmic vesicle lumen. We identified 2 gene clusters (brown modules, MEbrown; turquoise module, MEturquoise) correlated with IDU-DR and a gene cluster (magenta module, MEmagenta) correlated with IDU-DS by weighted gene co-expression network analysis (WGCNA). Functional analysis demonstrated that pathways of focal adhesion and focalin-1-rich granule lumen were involved in the development of IDU-DR, and the cytosolic large ribosomal subunit may relate to IDU-DR. Further, immune cell infiltration analysis demonstrated that the abundance of dendritic cells (DCs), natural Treg cells (nTreg), and exhausted T cells (Tex) in IDU-DR and IDU-DS, naïve CD8+ T cells in IDU-DS was significantly different compared with that in Ctrl-DS. The abundance of cytotoxic T cells (Tc) was significantly different between IDU-DS and IDU-DR. Conclusion Our findings indicated a potential function of immunoregulation mechanisms for resistant hypertension.
Collapse
Affiliation(s)
- Jie Jia
- NHC Key Laboratory of Drug Addiction Medicine, First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming, 650032, People's Republic of China.,Scientific Research Laboratory Center, First Affiliated Hospital of Kunming Medical University, Kunming, 650032, People's Republic of China
| | - Ji-Qun Yang
- Third People's Hospital of Kunming City/Drug Rehabilitation Hospital of Kunming City, Kunming, 650041, People's Republic of China
| | - Ying-Rong Du
- Third People's Hospital of Kunming City/Drug Rehabilitation Hospital of Kunming City, Kunming, 650041, People's Republic of China
| | - Yu Xu
- Scientific Research Laboratory Center, First Affiliated Hospital of Kunming Medical University, Kunming, 650032, People's Republic of China
| | - Deshenyue Kong
- NHC Key Laboratory of Drug Addiction Medicine, First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming, 650032, People's Republic of China.,Scientific Research Laboratory Center, First Affiliated Hospital of Kunming Medical University, Kunming, 650032, People's Republic of China
| | - Xiu-Ling Zhang
- Third People's Hospital of Kunming City/Drug Rehabilitation Hospital of Kunming City, Kunming, 650041, People's Republic of China
| | - Jun-Hong Mao
- NHC Key Laboratory of Drug Addiction Medicine, First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming, 650032, People's Republic of China.,Scientific Research Laboratory Center, First Affiliated Hospital of Kunming Medical University, Kunming, 650032, People's Republic of China
| | - Gui-Fang Hu
- Third People's Hospital of Kunming City/Drug Rehabilitation Hospital of Kunming City, Kunming, 650041, People's Republic of China
| | - Kun-Hua Wang
- NHC Key Laboratory of Drug Addiction Medicine, First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming, 650032, People's Republic of China.,Scientific Research Laboratory Center, First Affiliated Hospital of Kunming Medical University, Kunming, 650032, People's Republic of China.,School of Medicine, Yunnan University, Kunming, 650500, People's Republic of China
| | - Yi-Qun Kuang
- NHC Key Laboratory of Drug Addiction Medicine, First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming, 650032, People's Republic of China.,Scientific Research Laboratory Center, First Affiliated Hospital of Kunming Medical University, Kunming, 650032, People's Republic of China
| |
Collapse
|
47
|
Gaudreault F, Corbeil CR, Purisima EO, Sulea T. Coevolved Canonical Loops Conformations of Single-Domain Antibodies: A Tale of Three Pockets Playing Musical Chairs. Front Immunol 2022; 13:884132. [PMID: 35720356 PMCID: PMC9203998 DOI: 10.3389/fimmu.2022.884132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 05/05/2022] [Indexed: 11/13/2022] Open
Abstract
Single-domain antibodies (sdAbs) are a promising class of biotherapeutics with unique structural traits within their paratope region. The distribution of canonical conformations explored by their complementarity determining region (CDR) loops differs to some extent from conventional two-chain Fv fragments of monoclonal antibodies (mAbs). In this study, we explored in detail the canonical structures of sdAb CDR-H1 and CDR-H2 loops and compared those with mAbs from the IGHV3 and IGHV1 gene families. We surveyed the antibody structures catalogued in SAbDab and clustered the CDR canonical loops in Cartesian space. While most of the sdAb clusters were sub-populations of previously defined canonical Fv conformations of CDR-H1 and CDR-H2, our stricter clustering approach defined narrower clusters in sequence-space. Meticulous visual inspection of sub-populations allowed a clearer understanding of sequence-structure relationships. The packing densities within structural pockets contacted by CDR-H1 and CDR-H2 canonical conformations were analyzed on the premise that these pockets cannot be left vacant as they would leave exposed supportive hydrophobic residues. The fine resolution of the canonical clusters defined here revealed unique signatures within these pockets, including distinct structural complementarities between CDR-H1 and CDR-H2 canonical clusters, which could not be perceived with the previous coarser clusters. We highlight examples where a single residue change in CDR-H1 sequence is sufficient to induce a dramatic population shift in CDR-H2 conformation. This suggests that preferences in combining CDR-H1 and CDR-H2 emerged naturally during antibody evolution, leading to preferred sets of conserved amino acids at key positions in the framework as well as within the CDR loops. We outline a game of musical chairs that is necessary to maintain the integrity of the antibody structures that arose during evolution. Our study also provides refined CDR-H1 and CDR-H2 structural templates for sdAb homology modeling that could be leveraged for improved antibody design.
Collapse
|
48
|
Kraivong R, Traewachiwiphak S, Nilchan N, Tangthawornchaikul N, Pornmun N, Poraha R, Sriruksa K, Limpitikul W, Avirutnan P, Malasit P, Puttikhunt C. Cross-reactive antibodies targeting surface-exposed non-structural protein 1 (NS1) of dengue virus-infected cells recognize epitopes on the spaghetti loop of the β-ladder domain. PLoS One 2022; 17:e0266136. [PMID: 35617160 PMCID: PMC9135231 DOI: 10.1371/journal.pone.0266136] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 03/14/2022] [Indexed: 11/30/2022] Open
Abstract
Non-structural protein 1 (NS1) is a glycoprotein component of dengue virus (DENV) that is essential for viral replication, infection and immune evasion. Immunization with NS1 has been shown to elicit antibody-mediated immune responses which protect mice against DENV infections. Here, we obtained peripheral blood mononuclear cells from human subjects with secondary dengue infections, which were used to construct a dengue immune phage library displaying single-chain variable fragments. Phage selective for DENV NS1 were obtained by biopanning. Twenty-one monoclonal antibodies (mAbs) against DENV NS1 were generated from the selected phage and characterized in detail. We found most anti-NS1 mAbs used IGHV1 heavy chain antibody genes. The mAbs were classified into strongly and weakly-reactive groups based on their binding to NS1 expressed in dengue virus 2 (DENV2)-infected cells. Antibody binding experiments with recombinant NS1 proteins revealed that the mAbs recognize conformational epitopes on the β-ladder domain (amino acid residues 178–273) of DENV NS1. Epitope mapping studies on alanine-substituted NS1 proteins identified distinct but overlapping epitopes. Protruding amino acids distributed around the spaghetti loop are required for the binding of the strongly-reactive mAbs, whereas the recognition residues of the weakly-reactive mAbs are likely to be located in inaccessible sites facing toward the cell membrane. This information could guide the design of an NS1 epitope-based vaccine that targets cross-reactive conserved epitopes on cell surface-associated DENV NS1.
Collapse
Affiliation(s)
- Romchat Kraivong
- Molecular Biology of Dengue and Flaviviruses Research Team, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
- Medical Biotechnology Research Unit, National Center for Genetic Engineering and Biotechnology, Siriraj Hospital, Bangkok, Thailand
- Faculty of Medicine Siriraj Hospital, Siriraj Center of Research Excellence in Dengue and Emerging Pathogens, Mahidol University, Bangkok, Thailand
| | - Somchoke Traewachiwiphak
- Molecular Biology of Dengue and Flaviviruses Research Team, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Napon Nilchan
- Molecular Biology of Dengue and Flaviviruses Research Team, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
- Medical Biotechnology Research Unit, National Center for Genetic Engineering and Biotechnology, Siriraj Hospital, Bangkok, Thailand
- Faculty of Medicine Siriraj Hospital, Siriraj Center of Research Excellence in Dengue and Emerging Pathogens, Mahidol University, Bangkok, Thailand
| | - Nattaya Tangthawornchaikul
- Molecular Biology of Dengue and Flaviviruses Research Team, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
- Medical Biotechnology Research Unit, National Center for Genetic Engineering and Biotechnology, Siriraj Hospital, Bangkok, Thailand
| | - Nuntaya Pornmun
- Faculty of Medicine Siriraj Hospital, Siriraj Center of Research Excellence in Dengue and Emerging Pathogens, Mahidol University, Bangkok, Thailand
- Faculty of Medicine Siriraj Hospital, Division of Dengue Hemorrhagic Fever Research, Mahidol University, Bangkok, Thailand
| | - Ranyikar Poraha
- Faculty of Medicine Siriraj Hospital, Siriraj Center of Research Excellence in Dengue and Emerging Pathogens, Mahidol University, Bangkok, Thailand
- Faculty of Medicine Siriraj Hospital, Division of Dengue Hemorrhagic Fever Research, Mahidol University, Bangkok, Thailand
| | - Kanokwan Sriruksa
- Pediatric Department, Khon Kaen Hospital, Ministry of Public Health, Khon Kaen, Thailand
| | - Wannee Limpitikul
- Pediatric Department, Songkhla Hospital, Ministry of Public Health, Songkhla, Thailand
| | - Panisadee Avirutnan
- Medical Biotechnology Research Unit, National Center for Genetic Engineering and Biotechnology, Siriraj Hospital, Bangkok, Thailand
- Faculty of Medicine Siriraj Hospital, Siriraj Center of Research Excellence in Dengue and Emerging Pathogens, Mahidol University, Bangkok, Thailand
- Faculty of Medicine Siriraj Hospital, Division of Dengue Hemorrhagic Fever Research, Mahidol University, Bangkok, Thailand
| | - Prida Malasit
- Medical Biotechnology Research Unit, National Center for Genetic Engineering and Biotechnology, Siriraj Hospital, Bangkok, Thailand
- Faculty of Medicine Siriraj Hospital, Siriraj Center of Research Excellence in Dengue and Emerging Pathogens, Mahidol University, Bangkok, Thailand
- Faculty of Medicine Siriraj Hospital, Division of Dengue Hemorrhagic Fever Research, Mahidol University, Bangkok, Thailand
| | - Chunya Puttikhunt
- Molecular Biology of Dengue and Flaviviruses Research Team, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
- Medical Biotechnology Research Unit, National Center for Genetic Engineering and Biotechnology, Siriraj Hospital, Bangkok, Thailand
- Faculty of Medicine Siriraj Hospital, Siriraj Center of Research Excellence in Dengue and Emerging Pathogens, Mahidol University, Bangkok, Thailand
- * E-mail:
| |
Collapse
|
49
|
One-Step Next-Generation Sequencing of Immunoglobulin and T-Cell Receptor Gene Recombinations for MRD Marker Identification in Acute Lymphoblastic Leukemia. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2453:43-59. [PMID: 35622319 DOI: 10.1007/978-1-0716-2115-8_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Within the EuroClonality-NGS group, immune repertoire analysis for target identification in lymphoid malignancies was initially developed using two-stage amplicon approaches, essentially as a progressive modification of preceding methods developed for Sanger sequencing. This approach has, however, limitations with respect to sample handling, adaptation to automation, and risk of contamination by amplicon products. We therefore developed one-step PCR amplicon methods with individual barcoding for batched analysis for IGH, IGK, TRD, TRG, and TRB rearrangements, followed by Vidjil-based data analysis.
Collapse
|
50
|
Lefranc MP, Lefranc G. IMGT/3Dstructure-DB: T-Cell Receptor TR Paratope and Peptide/Major Histocompatibility pMH Contact Sites and Epitope. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2453:533-570. [PMID: 35622341 DOI: 10.1007/978-1-0716-2115-8_25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
T-cell receptors (TR), the antigen receptors of T cells, specifically recognize peptides presented by the major histocompatibility (MH) proteins, as peptide/MH (pMH), on the cell surface. The structure characterization of the trimolecular TR/pMH complexes is crucial to the fields of immunology, vaccination, and immunotherapy. IMGT/3Dstructure-DB is the three-dimensional (3-D) structure database of IMGT®, the international ImMunoGenetics information system®. By its creation, IMGT® marks the advent of immunoinformatics, which emerged at the interface between immunogenetics and bioinformatics. The IMGT® immunoglobulin (IG) and TR gene and allele nomenclature (CLASSIFICATION axiom) and the IMGT unique numbering and IMGT/Collier-de-Perles (NUMEROTATION axiom) are the two founding breakthroughs of immunoinformatics. IMGT-ONTOLOGY concepts and IMGT Scientific chart rules generated from these axioms allowed IMGT® bridging genes, structures, and functions. IMGT/3Dstructure-DB contains 3-D structures of IG or antibodies, TR and MH proteins of the adaptive immune responses of jawed vertebrates (gnathostomata), IG or TR complexes with antigens (IG/Ag, TR/pMH), related proteins of the immune system of any species belonging to the IG and MH superfamilies, and fusion proteins for immune applications. The focus of this chapter is on the TR V domains and MH G domains and the contact analysis comparison in TR/pMH interactions. Standardized molecular characterization includes "IMGT pMH contact sites" for peptide and MH groove interactions and "IMGT paratopes and epitopes" for TR/pMH complexes. Data are available in the IMGT/3Dstructure database, at the IMGT Home page http://www.imgt.org .
Collapse
Affiliation(s)
- Marie-Paule Lefranc
- IMGT®, the international ImMunoGenetics information system®, Laboratoire d'ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, UMR 9002, CNRS, Université de Montpellier, Montpellier cedex 5, France.
| | - Gérard Lefranc
- IMGT®, the international ImMunoGenetics information system®, Laboratoire d'ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, UMR 9002, CNRS, Université de Montpellier, Montpellier cedex 5, France.
| |
Collapse
|