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Gunbin KV, Kopeina GS, Zhivotovsky B, Zamaraev AV. Features of the CD1 gene family in rodents and the uniqueness of the immune system of naked mole-rat. Biol Direct 2024; 19:58. [PMID: 39075541 PMCID: PMC11285450 DOI: 10.1186/s13062-024-00503-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: 06/25/2024] [Accepted: 07/15/2024] [Indexed: 07/31/2024] Open
Abstract
Cluster of Differentiation 1 (CD1) proteins are widely expressed throughout jawed vertebrates and present lipid antigens to specific CD1-restricted T lymphocytes. CD1 molecules play an important role in immune defense with the presence or absence of particular CD1 proteins frequently associated with the functional characteristics of the immune system. Here, we show the evolution of CD1 proteins in the Rodentia family and the diversity among its members. Based on the analysis of CD1 protein-coding regions in rodent genomes and the reconstruction of protein structures, we found that Heterocephalus glaber represents a unique member of the suborder Hystricomorpha with significant changes in protein sequences and structures of the CD1 family. Multiple lines of evidence point to the absence of CD1d and CD1e and probably a dysfunctional CD1b protein in Heterocephalus glaber. In addition, the impact of CD1d loss on the CD1d/Natural killer T (NKT) cell axis in the naked mole-rat and its potential implications for immune system function are discussed in detail.
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Affiliation(s)
- Konstantin V Gunbin
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, 236016, Russia
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, 630090, Russia
| | - Gelina S Kopeina
- Engelhardt Institute of Molecular Biology, RAS, Moscow, 119991, Russia
- Faculty of Medicine, MV Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Boris Zhivotovsky
- Engelhardt Institute of Molecular Biology, RAS, Moscow, 119991, Russia.
- Faculty of Medicine, MV Lomonosov Moscow State University, Moscow, 119991, Russia.
- Division of Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Box 210, Stockholm, 17177, Sweden.
| | - Alexey V Zamaraev
- Engelhardt Institute of Molecular Biology, RAS, Moscow, 119991, Russia.
- Faculty of Medicine, MV Lomonosov Moscow State University, Moscow, 119991, Russia.
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Maerz MD, Cross DL, Seshadri C. Functional and biological implications of clonotypic diversity among human donor-unrestricted T cells. Immunol Cell Biol 2024; 102:474-486. [PMID: 38659280 PMCID: PMC11236517 DOI: 10.1111/imcb.12751] [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: 11/10/2023] [Revised: 02/04/2024] [Accepted: 04/04/2024] [Indexed: 04/26/2024]
Abstract
T cells express a T-cell receptor (TCR) heterodimer that is the product of germline rearrangement and junctional editing resulting in immense clonotypic diversity. The generation of diverse TCR repertoires enables the recognition of pathogen-derived peptide antigens presented by polymorphic major histocompatibility complex (MHC) molecules. However, T cells also recognize nonpeptide antigens through nearly monomorphic antigen-presenting systems, such as cluster of differentiation 1 (CD1), MHC-related protein 1 (MR1) and butyrophilins (BTNs). This potential for shared immune responses across genetically diverse populations led to their designation as donor-unrestricted T cells (DURTs). As might be expected, some CD1-, MR1- and BTN-restricted T cells express a TCR that is conserved across unrelated individuals. However, several recent studies have reported unexpected diversity among DURT TCRs, and increasing evidence suggests that this diversity has functional consequences. Recent reports also challenge the dogma that immune cells are either innate or adaptive and suggest that DURT TCRs may act in both capacities. Here, we review this evidence and propose an expanded view of the role for clonotypic diversity among DURTs in humans, including new perspectives on how DURT TCRs may integrate their adaptive and innate immune functions.
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Affiliation(s)
- Megan D Maerz
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
- Molecular Medicine and Mechanisms of Disease Program, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Deborah L Cross
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Chetan Seshadri
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
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Stern LJ, Clement C, Galluzzi L, Santambrogio L. Non-mutational neoantigens in disease. Nat Immunol 2024; 25:29-40. [PMID: 38168954 PMCID: PMC11075006 DOI: 10.1038/s41590-023-01664-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 09/29/2023] [Indexed: 01/05/2024]
Abstract
The ability of mammals to mount adaptive immune responses culminating with the establishment of immunological memory is predicated on the ability of the mature T cell repertoire to recognize antigenic peptides presented by syngeneic MHC class I and II molecules. Although it is widely believed that mature T cells are highly skewed towards the recognition of antigenic peptides originating from genetically diverse (for example, foreign or mutated) protein-coding regions, preclinical and clinical data rather demonstrate that novel antigenic determinants efficiently recognized by mature T cells can emerge from a variety of non-mutational mechanisms. In this Review, we describe various mechanisms that underlie the formation of bona fide non-mutational neoantigens, such as epitope mimicry, upregulation of cryptic epitopes, usage of non-canonical initiation codons, alternative RNA splicing, and defective ribosomal RNA processing, as well as both enzymatic and non-enzymatic post-translational protein modifications. Moreover, we discuss the implications of the immune recognition of non-mutational neoantigens for human disease.
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Affiliation(s)
- Lawrence J Stern
- Department of Pathology, UMass Chan Medical School, Worcester, MA, USA
- Immunology and Microbiology Program, UMass Chan Medical School, Worcester, MA, USA
| | - Cristina Clement
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA
| | - Lorenzo Galluzzi
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA.
- Sandra and Edward Meyer Cancer Center, New York, NY, USA.
- Caryl and Israel Englander Institute for Precision Medicine, New York, NY, USA.
| | - Laura Santambrogio
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA.
- Sandra and Edward Meyer Cancer Center, New York, NY, USA.
- Caryl and Israel Englander Institute for Precision Medicine, New York, NY, USA.
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Eckhardt E, Schinköthe J, Gischke M, Sehl-Ewert J, Corleis B, Dorhoi A, Teifke J, Albrecht D, Geluk A, Gilleron M, Bastian M. Phosphatidylinositolmannoside vaccination induces lipid-specific Th1-responses and partially protects guinea pigs from Mycobacterium tuberculosis challenge. Sci Rep 2023; 13:18613. [PMID: 37903877 PMCID: PMC10616071 DOI: 10.1038/s41598-023-45898-3] [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: 01/20/2023] [Accepted: 10/25/2023] [Indexed: 11/01/2023] Open
Abstract
The concept of donor-unrestricted T cells (DURTs) comprises a heterogeneity of lymphoid cells that respond to an abundance of unconventional epitopes in a non-MHC-restricted manner. Vaccinologists strive to harness this so far underexplored branch of the immune system for new vaccines against tuberculosis. A particular division of DURTs are T cells that recognize their cognate lipid antigen in the context of CD1-molecules. Mycobacteria are characterized by a particular lipid-rich cell wall. Several of these lipids have been shown to be presented to T cells via CD1b-molecules. Guinea pigs functionally express CD1b and are hence an appropriate small animal model to study the role of CD1b-restricted, lipid-specific immune responses. In the current study, guinea pigs were vaccinated with BCG or highly-purified, liposome-formulated phosphatidylinositol-hexa-mannoside (PIM6) to assess the effect of CD1-restricted DURTs on the course of infection after virulent Mycobacterium tuberculosis (Mtb) challenge. Robust PIM6-specific T cell-responses were observed both after BCG- and PIM6-vaccination. The cellular response was significantly reduced in the presence of monoclonal, CD1b-blocking antibodies, indicating that a predominant part of this reactivity was CD1b-restricted. When animals were challenged with Mtb, BCG- and PIM6-vaccinated animals showed significantly reduced pathology, smaller necrotic granulomas in lymph node and spleen and reduced bacterial loads. While BCG conferred an almost sterile protection in this setting, compared to control animals' lesions were reduced roughly by two thirds in PIM6-vaccinated. Comprehensive histological and transcriptional analyses in the draining lymph node revealed that protected animals showed reduced transcription-levels of inflammatory cyto- and chemokines and higher levels of CD1b-expression on professional antigen cells compared to controls. Although BCG as a comparator induced by far stronger effects, our observations in the guinea pig model suggest that CD1b-restricted, PIM6-reactive DURTs contribute to immune-mediated containment of virulent Mtb.
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Affiliation(s)
- Emmelie Eckhardt
- Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald - Isle of Riems, Germany
| | - Jan Schinköthe
- Institute of Veterinary Pathology, Faculty of Veterinary Medicine, Leipzig University, Leipzig, Germany
| | - Marcel Gischke
- Institute of Microbiology, Greifswald University, Greifswald, Germany
| | - Julia Sehl-Ewert
- Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald - Isle of Riems, Germany
| | - Björn Corleis
- Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald - Isle of Riems, Germany
| | - Anca Dorhoi
- Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald - Isle of Riems, Germany
| | - Jens Teifke
- Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald - Isle of Riems, Germany
| | - Dirk Albrecht
- Institute of Microbiology, Greifswald University, Greifswald, Germany
| | - Annemieke Geluk
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Martine Gilleron
- CNRS, Institut de Pharmacologie et de Biologie Structurale, Toulouse, France
| | - Max Bastian
- Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald - Isle of Riems, Germany.
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