1
|
Lin J, Wu X, Liu Z, Yang H, Chen Y, Li H, Yu Y, Tu Q, Chen Y. Identification, expression and molecular polymorphism of T-cell receptors α and β from the glacial relict Hucho bleekeri. Fish & Shellfish Immunology 2024; 148:109475. [PMID: 38447781 DOI: 10.1016/j.fsi.2024.109475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/01/2024] [Accepted: 03/03/2024] [Indexed: 03/08/2024]
Abstract
The T-cell receptor (TCR) is a specific molecule on the surface of all T cells that mediates cellular adaptive immune responses to antigens. Hucho bleekeri is a critically endangered species and is regarded as a glacial relict that has the lowest-latitude distribution compared with any Eurasian salmonid. In the present study, two TCR genes, namely, TCR α and β, were identified and characterized in H. bleekeri. Both TCR α and TCR β have typical TCR structures, including the IgV domain, IgC domain, connecting peptide, transmembrane and cytoplasmic domains. The two TCR genes were constitutionally expressed in various tissues, with the highest expression found in the spleen for TCR α and in the trunk kidney for TCR β. Challenge of H. bleekeri with LPS or poly(I:C) resulted in significant upregulation of both TCR α and β expression in headkidney and spleen primary cells, indicating their potential roles in the immune response. Molecular polymorphism analysis of the whole ORF regions of TCR α and β in different individuals revealed high diversity of IgV domains of these two genes, especially in complementarity-determining region (CDR) 3. The ratio of nonsynonymous substitution occurred at a significantly higher frequency than synonymous substitution in the CDR of TCR α and β, demonstrating the existence of positive selection. The results obtained in the present study enhance our understanding of TCR roles in regulating immune mechanisms and provide new information for the study of TCR lineage diversity in fish.
Collapse
Affiliation(s)
- Jue Lin
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu, 611730, China; Fish Resources and Environment in the Upper Reaches of the Yangtze River Observation and Research Station of Sichuan Province, Chengdu, 611730, China
| | - Xiaoyun Wu
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu, 611730, China; Fish Resources and Environment in the Upper Reaches of the Yangtze River Observation and Research Station of Sichuan Province, Chengdu, 611730, China
| | - Zhao Liu
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu, 611730, China; Fish Resources and Environment in the Upper Reaches of the Yangtze River Observation and Research Station of Sichuan Province, Chengdu, 611730, China
| | - Huanchao Yang
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu, 611730, China; Fish Resources and Environment in the Upper Reaches of the Yangtze River Observation and Research Station of Sichuan Province, Chengdu, 611730, China
| | - Yanling Chen
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu, 611730, China; Fish Resources and Environment in the Upper Reaches of the Yangtze River Observation and Research Station of Sichuan Province, Chengdu, 611730, China
| | - Hua Li
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu, 611730, China; Fish Resources and Environment in the Upper Reaches of the Yangtze River Observation and Research Station of Sichuan Province, Chengdu, 611730, China
| | - Yi Yu
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu, 611730, China; Fish Resources and Environment in the Upper Reaches of the Yangtze River Observation and Research Station of Sichuan Province, Chengdu, 611730, China
| | - Quanyu Tu
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu, 611730, China; Fish Resources and Environment in the Upper Reaches of the Yangtze River Observation and Research Station of Sichuan Province, Chengdu, 611730, China
| | - Yeyu Chen
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu, 611730, China; Fish Resources and Environment in the Upper Reaches of the Yangtze River Observation and Research Station of Sichuan Province, Chengdu, 611730, China.
| |
Collapse
|
2
|
Ehrenfried AR, Zens S, Steffens LK, Kehm H, Paul A, Lauenstein C, Volkmar M, Poschke I, Meng Z, Offringa R. T-Cell-Based Platform for Functional Screening of T-Cell Receptors Identified in Single-Cell RNA Sequencing Data Sets of Tumor-Infiltrating T-Cells. Bio Protoc 2024; 14:e4972. [PMID: 38686347 PMCID: PMC11056003 DOI: 10.21769/bioprotoc.4972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/14/2024] [Accepted: 03/14/2024] [Indexed: 05/02/2024] Open
Abstract
The advent of single-cell RNA sequencing (scRNAseq) has enabled in-depth gene expression analysis of several thousand cells isolated from tissues. We recently reported the application of scRNAseq toward the dissection of the tumor-infiltrating T-cell repertoire in human pancreatic cancer samples. In this study, we demonstrated that combined whole transcriptome and T-cell receptor (TCR) sequencing provides an effective way to identify tumor-reactive TCR clonotypes on the basis of gene expression signatures. An important aspect in this respect was the experimental validation of TCR-mediated anti-tumor reactivity by means of an in vitro functional assay, which is the subject of the present protocol. This assay involves the transient transfection of mRNA gene constructs encoding TCRα/β pairs into a well-defined human T-cell line, followed by co-cultivation with the tumor cells of interest and detection of T-cell activation by flow cytometry. Due to the high transfectability and the low background reactivity of the mock-transfected T-cell line to a wide variety of tumor cells, this assay offers a highly robust and versatile platform for the functional screening of large numbers of TCR clonotypes as identified in scRNAseq data sets. Whereas the assay was initially developed to test TCRs of human origin, it was more recently also applied successfully for the screening of TCRs of murine origin. Key features • Efficient functional screening of-and discrimination between-TCRs isolated from tumor-reactive vs. bystander T-cell clones. • Applicable to TCRs from CD8+ and CD4+ tumor-infiltrating T-cells originating from patient-derived tumor samples and syngeneic mouse tumor models. • Rapid flow cytometric detection of T-cell activation by means of TNFα and CD107a expression after a 5 h T-cell/tumor cell co-cultivation.
Collapse
Affiliation(s)
- Aaron Rodriguez Ehrenfried
- Division of Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Helmholtz-Institute for Translational Oncology by DKFZ (HI-TRON), Mainz, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Stefan Zens
- Division of Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Laura K. Steffens
- Division of Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Hannes Kehm
- Division of Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Alina Paul
- Division of Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Claudia Lauenstein
- Division of Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael Volkmar
- Helmholtz-Institute for Translational Oncology by DKFZ (HI-TRON), Mainz, Germany
| | - Isabel Poschke
- Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Immune Monitoring Unit, National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Zibo Meng
- Division of Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of General Visceral and Transplantation Surgery, University Hospital Heidelberg, Heidelberg, Germany
- Sino-German Laboratory of Personalized Medicine for Pancreatic Cancer, Union Hospital, Tongji Medical College, Wuhan, China
| | - Rienk Offringa
- Division of Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of General Visceral and Transplantation Surgery, University Hospital Heidelberg, Heidelberg, Germany
- Sino-German Laboratory of Personalized Medicine for Pancreatic Cancer, Union Hospital, Tongji Medical College, Wuhan, China
| |
Collapse
|
3
|
van Hees EP, Morton LT, Remst DFG, Wouters AK, Van den Eynde A, Falkenburg JHF, Heemskerk MH. Self-sufficient primary natural killer cells engineered to express T cell receptors and interleukin-15 exhibit improved effector function and persistence. Front Immunol 2024; 15:1368290. [PMID: 38690288 PMCID: PMC11058644 DOI: 10.3389/fimmu.2024.1368290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 04/03/2024] [Indexed: 05/02/2024] Open
Abstract
Background NK cells can be genetically engineered to express a transgenic T-cell receptor (TCR). This approach offers an alternative strategy to target heterogenous tumors, as NK:TCR cells can eradicate both tumor cells with high expression of HLA class I and antigen of interest or HLA class I negative tumors. Expansion and survival of NK cells relies on the presence of IL-15. Therefore, autonomous production of IL-15 by NK:TCR cells might improve functional persistence of NK cells. Here we present an optimized NK:TCR product harnessed with a construct encoding for soluble IL-15 (NK:TCR/IL-15), to support their proliferation, persistence and cytotoxic capabilities. Methods Expression of tumor-specific TCRs in peripheral blood derived NK-cells was achieved following retroviral transduction. NK:TCR/IL-15 cells were compared with NK:TCR cells for autonomous cytokine production, proliferation and survival. NK:BOB1-TCR/IL-15 cells, expressing a HLA-B*07:02-restricted TCR against BOB1, a B-cell lineage specific transcription factor highly expressed in all B-cell malignancies, were compared with control NK:BOB1-TCR and NK:CMV-TCR/IL-15 cells for effector function against TCR antigen positive malignant B-cell lines in vitro and in vivo. Results Viral incorporation of the interleukin-15 gene into engineered NK:TCR cells was feasible and high expression of the TCR was maintained, resulting in pure NK:TCR/IL-15 cell products generated from peripheral blood of multiple donors. Self-sufficient secretion of IL-15 by NK:TCR cells enables engineered NK cells to proliferate in vitro without addition of extra cytokines. NK:TCR/IL-15 demonstrated a marked enhancement of TCR-mediated cytotoxicity as well as enhanced NK-mediated cytotoxicity resulting in improved persistence and performance of NK:BOB1-TCR/IL-15 cells in an orthotopic multiple myeloma mouse model. However, in contrast to prolonged anti-tumor reactivity by NK:BOB1-TCR/IL-15, we observed in one of the experiments an accumulation of NK:BOB1-TCR/IL-15 cells in several organs of treated mice, leading to unexpected death 30 days post-NK infusion. Conclusion This study showed that NK:TCR/IL-15 cells secrete low levels of IL-15 and can proliferate in an environment lacking cytokines. Repeated in vitro and in vivo experiments confirmed the effectiveness and target specificity of our product, in which addition of IL-15 supports TCR- and NK-mediated cytotoxicity.
Collapse
Affiliation(s)
- Els P. van Hees
- Department of Hematology, Leiden University Medical Centre (LUMC), Leiden, Netherlands
| | - Laura T. Morton
- Department of Hematology, Leiden University Medical Centre (LUMC), Leiden, Netherlands
| | - Dennis F. G. Remst
- Department of Hematology, Leiden University Medical Centre (LUMC), Leiden, Netherlands
| | - Anne K. Wouters
- Department of Hematology, Leiden University Medical Centre (LUMC), Leiden, Netherlands
| | - Astrid Van den Eynde
- Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), Antwerp, Belgium
| | | | - Mirjam H.M. Heemskerk
- Department of Hematology, Leiden University Medical Centre (LUMC), Leiden, Netherlands
| |
Collapse
|
4
|
Zabrodskaya Y, Tsvetkov V, Shurygina AP, Vasyliev K, Shaldzhyan A, Gorshkov A, Kuklin A, Fedorova N, Egorov V. How the immune mousetrap works: Structural evidence for the immunomodulatory action of a peptide from influenza NS1 protein. Biophys Chem 2024; 307:107176. [PMID: 38219420 DOI: 10.1016/j.bpc.2024.107176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 01/08/2024] [Indexed: 01/16/2024]
Abstract
One of the critical stages of the T-cell immune response is the dimerization of the intramembrane domains of T-cell receptors (TCR). Structural similarities between the immunosuppressive domains of viral proteins and the transmembrane domains of TCR have led several authors to hypothesize the mechanism of immune response suppression by highly pathogenic viruses: viral proteins embed themselves in the membrane and act on the intramembrane domain of the TCRalpha subunit, hindering its functional oligomerization. It has also been suggested that this mechanism is used by influenza A virus in NS1-mediated immunosuppression. We have shown that the peptide corresponding to the primary structure of the potential immunosuppressive domain of NS1 protein (G51) can reduce concanavalin A-induced proliferation of PBMC cells, as well as in vitro, G51 can affect the oligomerization of the core peptide corresponding to the intramembrane domain of TCR, using AFM and small-angle neutron scattering. The results obtained using in cellulo and in vitro model systems suggest the presence of functional interaction between the NS1 fragment and the intramembrane domain of the TCR alpha subunit. We have proposed a possible scheme for such interaction obtained by computer modeling. This suggests the existence of another NS1-mediated mechanism of immunosuppression in influenza.
Collapse
Affiliation(s)
- Yana Zabrodskaya
- Institute of Biomedical Systems and Biotechnology, Peter the Great Saint Petersburg Polytechnic University, 29 Ulitsa Polytechnicheskaya, St. Petersburg 194064, Russia; Smorodintsev Research Institute of Influenza, Russian Ministry of Health, 15/17 Ulitsa Prof. Popova, St. Petersburg 197376, Russia.
| | - Vladimir Tsvetkov
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, 15/17 Ulitsa Prof. Popova, St. Petersburg 197376, Russia; Federal Research and Clinical Center for Physical Chemical Medicine, 1a Ulitsa Malaya Pirogovskaya, Moscow 119435, Russia; Center for Mathematical Modeling in Drug Development, I.M. Sechenov First Moscow State Medical University, Moscow 119146, Russia
| | - Anna-Polina Shurygina
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, 15/17 Ulitsa Prof. Popova, St. Petersburg 197376, Russia
| | - Kirill Vasyliev
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, 15/17 Ulitsa Prof. Popova, St. Petersburg 197376, Russia
| | - Aram Shaldzhyan
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, 15/17 Ulitsa Prof. Popova, St. Petersburg 197376, Russia
| | - Andrey Gorshkov
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, 15/17 Ulitsa Prof. Popova, St. Petersburg 197376, Russia
| | - Alexander Kuklin
- International Intergovernmental Organization Joint Institute for Nuclear Research, 6 Ulitsa Joliot-Curie, Dubna 141980, Russia; Moscow Institute of Physics and Technology (State University), 9 Institutskiy pereulok, 141701 Dolgoprudny, Moscow Region, Russia
| | - Natalya Fedorova
- Petersburg Nuclear Physics Institute Named by B. P. Konstantinov of National Research Center, Kurchatov Institute, 1 mkr. Orlova Roshcha, Gatchina 188300, Russia
| | - Vladimir Egorov
- Institute of Experimental Medicine, 12 Ulitsa Akademika Pavlova, St. Petersburg 197376, Russia
| |
Collapse
|
5
|
Forbes C, Nierkens S, Cornel AM. Thymic NK-Cells and Their Potential in Cancer Immunotherapy. Immunotargets Ther 2024; 13:183-194. [PMID: 38558927 PMCID: PMC10979679 DOI: 10.2147/itt.s441639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 01/20/2024] [Indexed: 04/04/2024] Open
Abstract
Natural killer (NK)-cells are innate immune cells with potent anti-tumor capacity, capable of recognizing target cells without prior exposure. For this reason, NK-cells are recognized as a useful source of cell therapy. Although most NK-cells are derived from the bone marrow (BM), a separate developmental pathway in the thymus also exists, producing so-called thymic NK-cells. Unlike conventional NK-cells, thymic NK (tNK)-cells have a combined capacity for cytokine production and a natural ability to kill tumor cells in the presence of NK-cell receptor stimulatory ligands. Furthermore, tNK-cells are reported to express CD3 subunits intracellularly, without the presence of a rearranged T-cell receptor (TCR). This unique feature may enable harnessing of these cells with a TCR to combine NK- and T-cell effector properties in one cell type. The development, phenotype, and function of tNK-cells, and potential as a cell therapy is, however, poorly explored. In this review, we provide an overview of current literature on both murine and human tNK-cells in comparison to conventional BM-derived NK-cells, and discuss the potential applications of this cellular subset in the context of cancer immunotherapy.
Collapse
Affiliation(s)
- Caitlyn Forbes
- Princess Máxima Center for Pediatric Oncology, Utrecht University, Utrecht, the Netherlands
| | - Stefan Nierkens
- Princess Máxima Center for Pediatric Oncology, Utrecht University, Utrecht, the Netherlands
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Annelisa M Cornel
- Princess Máxima Center for Pediatric Oncology, Utrecht University, Utrecht, the Netherlands
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| |
Collapse
|
6
|
Xiang J, Chang Q, McLinden JH, Bhattarai N, Welch JL, Kaufman TM, Stapleton JT. Characterization of "Off-Target" Immune Modulation Induced by Live Attenuated Yellow Fever Vaccine. J Infect Dis 2024; 229:786-794. [PMID: 36994927 PMCID: PMC10938199 DOI: 10.1093/infdis/jiad086] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/09/2023] [Accepted: 03/28/2023] [Indexed: 03/31/2023] Open
Abstract
BACKGROUND Live attenuated vaccines alter immune functions and are associated with beneficial outcomes. We previously demonstrated that live attenuated yellow fever virus (YFV) vaccine (LA-YF-Vax) dampens T-cell receptor (TCR) signaling in vitro via an RNA-based mechanism. We examined study participants before and after LA-YF-Vax to assess TCR-mediated functions in vivo. METHODS Serum samples and peripheral blood mononuclear cells (PBMCs) were obtained before and after LA-YF-Vax (with or without additional vaccines) or quadrivalent influenza vaccine. TCR-mediated activation was determined by interleukin 2 release or phosphorylation of the lymphocyte-specific Src kinase. TCR-regulating phosphatase (protein tyrosine phosphatase receptor type E [PTPRE]) expression was also measured. RESULTS Compared with prevaccination findings, LA-YF-Vax recipient PBMCs demonstrated transient reduction in interleukin 2 release after TCR stimulation and PTPRE levels, unlike in control participants who received quadrivalent influenza vaccine. YFV was detected in 8 of 14 participants after LA-YF-Vax. After incubation of healthy donor PBMCs in serum-derived extracellular vesicles prepared from LA-YF-Vax recipients, TCR signaling and PTPRE levels were reduced after vaccination, even in participants without detectable YFV RNA. CONCLUSIONS LA-YF-Vax reduces TCR functions and PTPRE levels after vaccination. Extracellular vesicles from serum recapitulated this effect in healthy cells. This likely contributes to the reduced immunogenicity for heterologous vaccines after LA-YF-Vax administration. Identification of specific immune mechanisms related to vaccines should contribute to understanding of the "off-target," beneficial effects of live vaccines.
Collapse
Affiliation(s)
- J Xiang
- Iowa City Department of Veterans Affairs Healthcare System, University of Iowa, Iowa City, Iowa, USA
| | - Q Chang
- Iowa City Department of Veterans Affairs Healthcare System, University of Iowa, Iowa City, Iowa, USA
| | - J H McLinden
- Iowa City Department of Veterans Affairs Healthcare System, University of Iowa, Iowa City, Iowa, USA
| | - N Bhattarai
- Division of Cellular and Gene Therapies, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA
| | - J L Welch
- Iowa City Department of Veterans Affairs Healthcare System, University of Iowa, Iowa City, Iowa, USA
| | - T M Kaufman
- Iowa City Department of Veterans Affairs Healthcare System, University of Iowa, Iowa City, Iowa, USA
| | - Jack T Stapleton
- Iowa City Department of Veterans Affairs Healthcare System, University of Iowa, Iowa City, Iowa, USA
| |
Collapse
|
7
|
Ibusuki A, Kawai K, Nitahara-Takeuchi A, Argüello RJ, Kanekura T. TCR signaling and cellular metabolism regulate the capacity of murine epidermal γδ T cells to rapidly produce IL-13 but not IFN-γ. Front Immunol 2024; 15:1361139. [PMID: 38482017 PMCID: PMC10933099 DOI: 10.3389/fimmu.2024.1361139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 02/08/2024] [Indexed: 04/17/2024] Open
Abstract
Resident epidermal T cells of murine skin, called dendritic epidermal T cells (DETCs), express an invariant γδ TCR that recognizes an unidentified self-ligand expressed on epidermal keratinocytes. Although their fetal thymic precursors are preprogrammed to produce IFN-γ, DETCs in the adult epidermis rapidly produce IL-13 but not IFN-γ early after activation. Here, we show that preprogrammed IFN-γ-producing DETC precursors differentiate into rapid IL-13 producers in the perinatal epidermis. The addition of various inhibitors of signaling pathways downstream of TCR to the in vitro differentiation model of neonatal DETCs revealed that TCR signaling through the p38 MAPK pathway is essential for the functional differentiation of neonatal DETCs. Constitutive TCR signaling at steady state was also shown to be needed for the maintenance of the rapid IL-13-producing capacity of adult DETCs because in vivo treatment with the p38 MAPK inhibitor decreased adult DETCs with the rapid IL-13-producing capacity. Adult DETCs under steady-state conditions had lower glycolytic capacity than proliferating neonatal DETCs. TCR stimulation of adult DETCs induced high glycolytic capacity and IFN-γ production during the late phase of activation. Inhibition of glycolysis decreased IFN-γ but not IL-13 production by adult DETCs during the late phase of activation. These results demonstrate that TCR signaling promotes the differentiation of IL-13-producing DETCs in the perinatal epidermis and is needed for maintaining the rapid IL-13-producing capacity of adult DETCs. The low glycolytic capacity of adult DETCs at steady state also regulates the rapid IL-13 response and delayed IFN-γ production after activation.
Collapse
Affiliation(s)
- Atsuko Ibusuki
- Department of Dermatology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Kazuhiro Kawai
- Department of Dermatology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
- Department of Dermatology, Kido Hospital, Niigata, Japan
| | - Ayano Nitahara-Takeuchi
- Division of Dermatology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Rafael J. Argüello
- Aix Marseille Université, CNRS, INSERM, CIML, Centre d’Immunologie de Marseille-Luminy, Marseille, France
| | - Takuro Kanekura
- Department of Dermatology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| |
Collapse
|
8
|
Migalska M, Węglarczyk K, Dudek K, Homa J. Evolutionary trade-offs constraining the MHC gene expansion: beyond simple TCR depletion model. Front Immunol 2024; 14:1240723. [PMID: 38259496 PMCID: PMC10801004 DOI: 10.3389/fimmu.2023.1240723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 12/18/2023] [Indexed: 01/24/2024] Open
Abstract
The immune system is as much shaped by the pressure of pathogens as it is by evolutionary trade-offs that constrain its structure and function. A perfect example comes from the major histocompatibility complex (MHC), molecules that initiate adaptive immune response by presentation of foreign antigens to T cells. The remarkable, population-level polymorphism of MHC genes is assumed to result mainly from a co-evolutionary arms race between hosts and pathogens, while the limited, within-individual number of functional MHC loci is thought to be the consequence of an evolutionary trade-off between enhanced pathogen recognition and excessive T cell depletion during negative selection in the thymus. Certain mathematical models and infection studies suggest that an intermediate individual MHC diversity would thus be optimal. A recent, more direct test of this hypothesis has shown that the effects of MHC diversity on T-cell receptor (TCR) repertoires may differ between MHC classes, supporting the depletion model only for MHC class I. Here, we used the bank vole (Myodes=Cletronomys glareolus), a rodent species with variable numbers of expressed MHC genes, to test how an individual MHC diversity influences the proportions and TCR repertoires of responding T cell subsets. We found a non-linear relationship between MHC diversity and T cell proportions (with intermediate MHC numbers coinciding with the largest T cell proportions), perhaps reflecting an optimality effect of balanced positive and negative thymic selection. The association was strongest for the relationship between MHC class I and splenic CD8+ T cells. The CD8+ TCR richness alone was unaffected by MHC class I diversity, suggesting that MHC class I expansion may be limited by decreasing T cell counts, rather than by direct depletion of TCR richness. In contrast, CD4+ TCR richness was positively correlated with MHC class II diversity, arguing against a universal TCR depletion. It also suggests that different evolutionary forces or trade-offs may limit the within-individual expansion of the MHC class II loci.
Collapse
Affiliation(s)
- Magdalena Migalska
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Krakow, Poland
| | - Kazimierz Węglarczyk
- Department of Clinical Immunology, Institute of Paediatrics, Jagiellonian University Medical College, Krakow, Poland
| | - Katarzyna Dudek
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Krakow, Poland
| | - Joanna Homa
- Department of Evolutionary Immunology, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Krakow, Poland
| |
Collapse
|
9
|
Dibble JJ, Ferneyhough B, Roddis M, Millington S, Fischer MD, Parkinson NJ, Ponting CP. Comparison of T-cell receptor diversity of people with myalgic encephalomyelitis versus controls. BMC Res Notes 2024; 17:17. [PMID: 38178251 PMCID: PMC10768444 DOI: 10.1186/s13104-023-06616-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 11/06/2023] [Indexed: 01/06/2024] Open
Abstract
OBJECTIVE Myalgic Encephalomyelitis (ME; sometimes referred to as Chronic Fatigue Syndrome) is a chronic disease without laboratory test, detailed aetiological understanding or effective therapy. Its symptoms are diverse, but it is distinguished from other fatiguing illnesses by the experience of post-exertional malaise, the worsening of symptoms even after minor physical or mental exertion. Its frequent onset after infection suggests autoimmune involvement or that it arises from abnormal T-cell activation. RESULTS To test this hypothesis, we sequenced the genomic loci of α/δ, β and γ T-cell receptors (TCR) from 40 human blood samples from each of four groups: severely affected people with ME; mildly or moderately affected people with ME; people diagnosed with Multiple Sclerosis, as disease controls; and, healthy controls. Seeking to automatically classify these individuals' samples by their TCR repertoires, we applied P-SVM, a machine learning method. However, despite working well on a simulated data set, this approach did not allow statistically significant partitioning of samples into the four subgroups. Our findings do not support the hypothesis that blood samples from people with ME frequently contain altered T-cell receptor diversity.
Collapse
Affiliation(s)
- Joshua J Dibble
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, UK
| | - Ben Ferneyhough
- Systems Biology Laboratory UK, Abingdon, Oxfordshire, OX14 4SA, UK
| | - Matthew Roddis
- Systems Biology Laboratory UK, Abingdon, Oxfordshire, OX14 4SA, UK
| | - Sam Millington
- Systems Biology Laboratory UK, Abingdon, Oxfordshire, OX14 4SA, UK
| | | | - Nick J Parkinson
- Systems Biology Laboratory UK, Abingdon, Oxfordshire, OX14 4SA, UK.
| | - Chris P Ponting
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, UK.
| |
Collapse
|
10
|
Chang-Gonzalez AC, Mallis RJ, Lang MJ, Reinherz EL, Hwang W. Asymmetric framework motion of TCRαβ controls load-dependent peptide discrimination. eLife 2024; 13:e91881. [PMID: 38167271 PMCID: PMC10869138 DOI: 10.7554/elife.91881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 12/21/2023] [Indexed: 01/05/2024] Open
Abstract
Mechanical force is critical for the interaction between an αβ T cell receptor (TCR) and a peptide-bound major histocompatibility complex (pMHC) molecule to initiate productive T-cell activation. However, the underlying mechanism remains unclear. We use all-atom molecular dynamics simulations to examine the A6 TCR bound to HLA-A*02:01 presenting agonist or antagonist peptides under different extensions to simulate the effects of applied load on the complex, elucidating their divergent biological responses. We found that TCR α and β chains move asymmetrically, which impacts the interface with pMHC, in particular the peptide-sensing CDR3 loops. For the wild-type agonist, the complex stabilizes in a load-dependent manner while antagonists destabilize it. Simulations of the Cβ FG-loop deletion, which reduces the catch bond response, and simulations with in silico mutant peptides further support the observed behaviors. The present results highlight the combined role of interdomain motion, fluctuating forces, and interfacial contacts in determining the mechanical response and fine peptide discrimination by a TCR, thereby resolving the conundrum of nearly identical crystal structures of TCRαβ-pMHC agonist and antagonist complexes.
Collapse
Affiliation(s)
- Ana C Chang-Gonzalez
- Department of Biomedical Engineering, Texas A&M UniversityCollege StationUnited States
| | - Robert J Mallis
- Department of Dermatology, Harvard Medical SchoolBostonUnited States
- Laboratory of Immunobiology, Dana-Farber Cancer InstituteBostonUnited States
- Department of Medicine, Oncology, Dana-Farber Cancer InstituteBostonUnited States
| | - Matthew J Lang
- Department of Chemistry and Biomolecular Engineering, Vanderbilt UniversityNashvilleUnited States
- Department of Molecular Physiology and Biophysics, Vanderbilt UniversityNashvilleUnited States
| | - Ellis L Reinherz
- Laboratory of Immunobiology, Dana-Farber Cancer InstituteBostonUnited States
- Department of Medicine, Oncology, Dana-Farber Cancer InstituteBostonUnited States
- Department of Medicine, Harvard Medical SchoolBostonUnited States
| | - Wonmuk Hwang
- Department of Biomedical Engineering, Texas A&M UniversityCollege StationUnited States
- Department of Materials Science & Engineering, Texas A&M UniversityCollege StationUnited States
- Department of Physics & Astronomy, Texas A&M UniversityCollege StationUnited States
| |
Collapse
|
11
|
Nenclares P, Larkeryd A, Manodoro F, Lee JY, Lalondrelle S, Gilbert DC, Punta M, O’Leary B, Rullan A, Sadanandam A, Chain B, Melcher A, Harrington KJ, Bhide SA. T-cell receptor determinants of response to chemoradiation in locally-advanced HPV16-driven malignancies. Front Oncol 2024; 13:1296948. [PMID: 38234396 PMCID: PMC10791873 DOI: 10.3389/fonc.2023.1296948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 11/28/2023] [Indexed: 01/19/2024] Open
Abstract
Background The effect of chemoradiation on the anti-cancer immune response is being increasingly acknowledged; however, its clinical implications in treatment responses are yet to be fully understood. Human papillomavirus (HPV)-driven malignancies express viral oncogenic proteins which may serve as tumor-specific antigens and represent ideal candidates for monitoring the peripheral T-cell receptor (TCR) changes secondary to chemoradiotherapy (CRT). Methods We performed intra-tumoral and pre- and post-treatment peripheral TCR sequencing in a cohort of patients with locally-advanced HPV16-positive cancers treated with CRT. An in silico computational pipeline was used to cluster TCR repertoire based on epitope-specificity and to predict affinity between these clusters and HPV16-derived epitopes. Results Intra-tumoral repertoire diversity, intra-tumoral and post-treatment peripheral CDR3β similarity clustering were predictive of response. In responders, CRT triggered an increase peripheral TCR clonality and clonal relatedness. Post-treatment expansion of baseline peripheral dominant TCRs was associated with response. Responders showed more baseline clustered structures of TCRs maintained post-treatment and displayed significantly more maintained clustered structures. When applying clustering by TCR-specificity methods, responders displayed a higher proportion of intra-tumoral TCRs predicted to recognise HPV16 peptides. Conclusions Baseline TCR characteristics and changes in the peripheral T-cell clones triggered by CRT are associated with treatment outcome. Maintenance and boosting of pre-existing clonotypes are key elements of an effective anti-cancer immune response driven by CRT, supporting a paradigm in which the immune system plays a central role in the success of CRT in current standard-of-care protocols.
Collapse
Affiliation(s)
- Pablo Nenclares
- Radiotherapy and Imaging Division, The Institute of Cancer Research, London, United Kingdom
- Head and Neck Unit, The Royal Marsden Hospital, London, United Kingdom
| | - Adrian Larkeryd
- Bioinformatics Unit, The Centre for Translational Immunotherapy, The Institute of Cancer Research, London, United Kingdom
| | - Floriana Manodoro
- Genomics Facility, The Institute of Cancer Research, London, United Kingdom
| | - Jen Y. Lee
- Radiotherapy and Imaging Division, The Institute of Cancer Research, London, United Kingdom
| | - Susan Lalondrelle
- Radiotherapy and Imaging Division, The Institute of Cancer Research, London, United Kingdom
| | - Duncan C. Gilbert
- Sussex Cancer Centre, University Hospitals Sussex NHS Foundation Trust, Brighton, United Kingdom
| | - Marco Punta
- Unit of Immunogenetic, Leukemia Genomics and Immunobiology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Ben O’Leary
- Radiotherapy and Imaging Division, The Institute of Cancer Research, London, United Kingdom
- Head and Neck Unit, The Royal Marsden Hospital, London, United Kingdom
| | - Antonio Rullan
- Radiotherapy and Imaging Division, The Institute of Cancer Research, London, United Kingdom
- Head and Neck Unit, The Royal Marsden Hospital, London, United Kingdom
| | - Anguraj Sadanandam
- Systems and Precision Cancer Medicine Team, The Institute of Cancer Research, London, United Kingdom
| | - Benny Chain
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Alan Melcher
- Radiotherapy and Imaging Division, The Institute of Cancer Research, London, United Kingdom
| | - Kevin J. Harrington
- Radiotherapy and Imaging Division, The Institute of Cancer Research, London, United Kingdom
- Head and Neck Unit, The Royal Marsden Hospital, London, United Kingdom
| | - Shreerang A. Bhide
- Radiotherapy and Imaging Division, The Institute of Cancer Research, London, United Kingdom
- Head and Neck Unit, The Royal Marsden Hospital, London, United Kingdom
| |
Collapse
|
12
|
Mullan KA, de Vrij N, Valkiers S, Meysman P. Current annotation strategies for T cell phenotyping of single-cell RNA-seq data. Front Immunol 2023; 14:1306169. [PMID: 38187377 PMCID: PMC10768068 DOI: 10.3389/fimmu.2023.1306169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 11/27/2023] [Indexed: 01/09/2024] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) has become a popular technique for interrogating the diversity and dynamic nature of cellular gene expression and has numerous advantages in immunology. For example, scRNA-seq, in contrast to bulk RNA sequencing, can discern cellular subtypes within a population, which is important for heterogenous populations such as T cells. Moreover, recent advancements in the technology allow the parallel capturing of the highly diverse T-cell receptor (TCR) sequence with the gene expression. However, the field of single-cell RNA sequencing data analysis is still hampered by a lack of gold-standard cell phenotype annotation. This problem is particularly evident in the case of T cells due to the heterogeneity in both their gene expression and their TCR. While current cell phenotype annotation tools can differentiate major cell populations from each other, labelling T-cell subtypes remains problematic. In this review, we identify the common automated strategy for annotating T cells and their subpopulations, and also describe what crucial information is still missing from these tools.
Collapse
Affiliation(s)
- Kerry A. Mullan
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS) Consortium, University of Antwerp, Antwerp, Belgium
| | - Nicky de Vrij
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS) Consortium, University of Antwerp, Antwerp, Belgium
- Clinical Immunology Unit, Department of Clinical Sciences, Institute for Tropical Medicine, Antwerp, Belgium
| | - Sebastiaan Valkiers
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS) Consortium, University of Antwerp, Antwerp, Belgium
| | - Pieter Meysman
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS) Consortium, University of Antwerp, Antwerp, Belgium
| |
Collapse
|
13
|
Koyama K, Hashimoto K, Nagao C, Mizuguchi K. Attention network for predicting T-cell receptor-peptide binding can associate attention with interpretable protein structural properties. Front Bioinform 2023; 3:1274599. [PMID: 38170146 PMCID: PMC10759225 DOI: 10.3389/fbinf.2023.1274599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 11/27/2023] [Indexed: 01/05/2024] Open
Abstract
Understanding how a T-cell receptor (TCR) recognizes its specific ligand peptide is crucial for gaining an insight into biological functions and disease mechanisms. Despite its importance, experimentally determining TCR-peptide-major histocompatibility complex (TCR-pMHC) interactions is expensive and time-consuming. To address this challenge, computational methods have been proposed, but they are typically evaluated by internal retrospective validation only, and few researchers have incorporated and tested an attention layer from language models into structural information. Therefore, in this study, we developed a machine learning model based on a modified version of Transformer, a source-target attention neural network, to predict the TCR-pMHC interaction solely from the amino acid sequences of the TCR complementarity-determining region (CDR) 3 and the peptide. This model achieved competitive performance on a benchmark dataset of the TCR-pMHC interaction, as well as on a truly new external dataset. Additionally, by analyzing the results of binding predictions, we associated the neural network weights with protein structural properties. By classifying the residues into large- and small-attention groups, we identified statistically significant properties associated with the largely attended residues such as hydrogen bonds within CDR3. The dataset that we created and the ability of our model to provide an interpretable prediction of TCR-peptide binding should increase our knowledge about molecular recognition and pave the way for designing new therapeutics.
Collapse
Affiliation(s)
- Kyohei Koyama
- Laboratory for Computational Biology, Institute for Protein Research, Osaka University, Osaka, Japan
- National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Kosuke Hashimoto
- Laboratory for Computational Biology, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Chioko Nagao
- Laboratory for Computational Biology, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Kenji Mizuguchi
- Laboratory for Computational Biology, Institute for Protein Research, Osaka University, Osaka, Japan
- National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| |
Collapse
|
14
|
Takayanagi SI, Wang B, Hasegawa S, Nishikawa S, Fukumoto K, Nakano K, Chuganji S, Kato Y, Kamibayashi S, Minagawa A, Kunisato A, Nozawa H, Kaneko S. Mini-TCRs: Truncated T cell receptors to generate T cells from induced pluripotent stem cells. Mol Ther Methods Clin Dev 2023; 31:101109. [PMID: 37822720 PMCID: PMC10562677 DOI: 10.1016/j.omtm.2023.101109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/13/2023] [Indexed: 10/13/2023]
Abstract
Allogeneic T cell platforms utilizing induced pluripotent stem cell (iPSC) technology exhibit significant promise for the facilitation of adoptive immunotherapies. While mature T cell receptor (TCR) signaling plays a crucial role in generating T cells from iPSCs, the introduction of exogenous mature TCR genes carries a potential risk of causing graft-versus-host disease (GvHD). In this study, we present the development of truncated TCRα and TCRβ chains, termed mini-TCRs, which lack variable domains responsible for recognizing human leukocyte antigen (HLA)-peptide complexes. We successfully induced cytotoxic T lymphocytes (CTLs) from iPSCs by employing mini-TCRs. Combinations of TCRα and TCRβ fragments were screened from mini-TCR libraries based on the surface localization of CD3 proteins and their ability to transduce T cell signaling. Consequently, mini-TCR-expressing iPSCs underwent physiological T cell development, progressing from the CD4 and CD8 double-positive stage to the CD8 single-positive stage. The resulting iPSC-derived CTLs exhibited comparable cytokine production and cytotoxicity in comparison to that of full-length TCR-expressing T lymphocytes when chimeric antigen receptors (CARs) were expressed. These findings demonstrate the potential of mini-TCR-carrying iPSCs as a versatile platform for CAR T cell therapy, offering a promising avenue for advancing adoptive immunotherapies.
Collapse
Affiliation(s)
- Shin-ichiro Takayanagi
- Kirin Central Research Institute, Kirin Holdings Company, Ltd., 26-1, Muraoka-Higashi 2, Fujisawa-shi, Kanagawa 251-8555, Japan
- Shin Kaneko Laboratory, Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Bo Wang
- Shin Kaneko Laboratory, Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
- Shinobi Therapeutics, Inc., 46-29 Yoshida-Shimo-Adachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Saki Hasegawa
- Kirin Central Research Institute, Kirin Holdings Company, Ltd., 26-1, Muraoka-Higashi 2, Fujisawa-shi, Kanagawa 251-8555, Japan
- Shin Kaneko Laboratory, Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Satoshi Nishikawa
- R&D Division, Kyowa Kirin Co. Ltd, 3-6-6 Asahi-machi, Machida-shi, Tokyo 194-8533, Japan
| | - Ken Fukumoto
- Kirin Central Research Institute, Kirin Holdings Company, Ltd., 26-1, Muraoka-Higashi 2, Fujisawa-shi, Kanagawa 251-8555, Japan
- Shin Kaneko Laboratory, Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Kohei Nakano
- Shinobi Therapeutics, Inc., 46-29 Yoshida-Shimo-Adachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Sayaka Chuganji
- Kirin Central Research Institute, Kirin Holdings Company, Ltd., 26-1, Muraoka-Higashi 2, Fujisawa-shi, Kanagawa 251-8555, Japan
- Shin Kaneko Laboratory, Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Yuya Kato
- Kirin Central Research Institute, Kirin Holdings Company, Ltd., 26-1, Muraoka-Higashi 2, Fujisawa-shi, Kanagawa 251-8555, Japan
| | - Sanae Kamibayashi
- Shin Kaneko Laboratory, Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Atsutaka Minagawa
- Shin Kaneko Laboratory, Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Atsushi Kunisato
- Kirin Central Research Institute, Kirin Holdings Company, Ltd., 26-1, Muraoka-Higashi 2, Fujisawa-shi, Kanagawa 251-8555, Japan
| | - Hajime Nozawa
- Kirin Central Research Institute, Kirin Holdings Company, Ltd., 26-1, Muraoka-Higashi 2, Fujisawa-shi, Kanagawa 251-8555, Japan
| | - Shin Kaneko
- Shin Kaneko Laboratory, Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
- Shinobi Therapeutics, Inc., 46-29 Yoshida-Shimo-Adachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| |
Collapse
|
15
|
Fang Y, Shen B, Dai Q, Xie Q, Li X, Wu W, Wang M. Composition and diversity analysis of the TCR CDR3 repertoire in patients with idiopathic orbital inflammation using high-throughput sequencing. BMC Ophthalmol 2023; 23:491. [PMID: 38044453 PMCID: PMC10694961 DOI: 10.1186/s12886-023-03248-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 11/28/2023] [Indexed: 12/05/2023] Open
Abstract
BACKGROUND Idiopathic orbital inflammation (IOI) is a nonspecific orbital inflammatory disease with the third highest prevalence among orbital diseases, and its pathogenesis is associated with T-cell-mediated immune responses. This study aimed to investigate the differences in T-cell receptor (TCR) expression between IOI patients and healthy subjects by high-throughput sequencing and to characterize TCR expression in patients with IOI and with respect to glucocorticoid response. METHODS A total of 19 subjects were enrolled in this study and were divided into the idiopathic orbital inflammation group (IOI group, n = 13) and the healthy control group (HC group, n = 6), and within the IOI group were further divided into the glucocorticoid therapy sensitive group (IOI(EF) group, n = 6) and the glucocorticoid therapy ineffective group (IOI(IN) group, n = 7) based on the degree of effectiveness to glucocorticoid therapy. High-throughput TCR sequencing was performed on peripheral blood mononuclear cells of IOI patients and healthy control individuals using 5' RACE technology combined with Unique Identifier (UID) digital tag correction technology. The TCR CDR3 region diversity, sharing patterns, and differential sequences between the IOI and HC groups, and between the IOI(EF) and IOI(IN) groups were analyzed. RESULTS It was found that the diversity of TCR CDR3 in the IOI group was significantly lower than that in the HC group, and the frequency of V gene use was significantly different between groups. The diversity of TCR CDR3 in patients in the IOI(EF) group was significantly lower than that in patients in the IOI(IN) group, and the frequency of V and J gene use was significantly different between the IOI(EF) group and the IOI(IN) group. Additionally, we found 133 nucleotide sequences shared in all IOI samples and screened two sequences with higher expression from them. CONCLUSIONS Our results suggested that abnormal clonal expansion of specific T-cells exists in IOI patients and that TCR diversity may had an impact on the prognosis of glucocorticoid-treated IOI. This study may contribute to a better understanding of the immune status of IOI and provide new insights for T-cell -associated IOI pathogenesis, diagnosis and treatment prediction.
Collapse
Affiliation(s)
- Yenan Fang
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
- Department of Ophthalmology, Children's Hospital of Fudan University, National Children's Medical Center, No. 399 Wanyuan Road, Shanghai, 201102, China
| | - Bingyan Shen
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Qin Dai
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Qiqi Xie
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Xinyu Li
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Wencan Wu
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China.
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China.
| | - Min Wang
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China.
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China.
| |
Collapse
|
16
|
Cheng C, Zhao Z, Liu G. Expression, Purification, and Crystallization of the Vγ9Vδ2 T-cell Receptor Recognizing Protein/Peptide Antigens. Protein J 2023; 42:778-791. [PMID: 37620608 DOI: 10.1007/s10930-023-10151-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2023] [Indexed: 08/26/2023]
Abstract
γδ T cells, especially Vγ9Vδ2 T cells, play an important role in mycobacterial infection. We have identified some Vγ9Vδ2 T cells that recognize protein/peptide antigens derived from mycobacteria, which may induce protective immune responses to mycobacterial infection. To clarify the structural basis of the molecular recognition mechanism, we tried many methods to express the Vγ9Vδ2 T-cell receptor (TCR). The Vγ9Vδ2 TCR was not expressed well in a prokaryotic expression system or a baculovirus expression system, even after extensive optimization. In a mammalian cell expression system, the Vγ9Vδ2 TCR was expressed in the form of a soluble heterodimer, which was suitable for crystal screening. Reduced-temperature cultivation (cold shock) increased the yield of the recombinant TCR. The recombinant purified TCR was used for crystal trials, and crystals that could be used for X-ray diffraction were obtained. Although we have not yet determined the crystal structure of the Vγ9Vδ2 TCR, we have established a procedure for Vγ9Vδ2 TCR expression and purification, which is useful for basic research and potentially for clinical application.
Collapse
Affiliation(s)
- Chaofei Cheng
- Stem Cell Research Center, Henan Key Laboratory of Stem Cell Differentiation and Modification, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, 450003, China
- People's Hospital of Henan University, Zhengzhou, 450003, China
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Centre for Tuberculosis Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
| | - Zhendong Zhao
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Centre for Tuberculosis Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China.
- Clinical Immunology Center, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China.
| | - Guangzhi Liu
- Stem Cell Research Center, Henan Key Laboratory of Stem Cell Differentiation and Modification, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, 450003, China.
- People's Hospital of Henan University, Zhengzhou, 450003, China.
| |
Collapse
|
17
|
Banerjee P, Chaudhary R, Singh AK, Parulekar P, Kumar S, Senapati S. Specific Genetic Polymorphisms Contributing in Differential Binding of Gliadin Peptides to HLA-DQ and TCR to Elicit Immunogenicity in Celiac Disease. Biochem Genet 2023; 61:2457-2480. [PMID: 37103600 DOI: 10.1007/s10528-023-10377-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 04/01/2023] [Indexed: 04/28/2023]
Abstract
Immunogenicity of gliadin peptides in celiac disease (CD) is majorly determined by the pattern of molecular interactions with HLA-DQ and T-cell receptors (TCR). Investigation of the interactions between immune-dominant gliadin peptides, DQ protein, and TCR are warranted to unravel the basis of immunogenicity and variability contributed by the genetic polymorphisms. Homology modeling of HLA and TCR done using Swiss Model and iTASSER, respectively. Molecular interactions of eight common deamidated immune-dominant gliadin with HLA-DQ allotypes and specific TCR gene pairs were evaluated. Docking of the three structures was performed with ClusPro2.0 and ProDiGY was used to predict binding energies. Effects of known allelic polymorphisms and reported susceptibility SNPs were predicted on protein-protein interactions. CD susceptible allele, HLA-DQ2.5 was shown to have considerable binding affinity to 33-mer gliadin (ΔG = - 13.9; Kd = 1.5E - 10) in the presence of TRAV26/TRBV7. Higher binding affinity was predicted (ΔG = - 14.3, Kd = 8.9E - 11) when TRBV28 was replaced with TRBV20 paired with TRAV4 suggesting its role in CD predisposition. SNP rs12722069 at HLA-DQ8 that codes Arg76α forms three H-bonds with Glu12 and two H-bonds with Asn13 of DQ2 restricted gliadin in the presence of TRAV8-3/TRBV6. None of the HLA-DQ polymorphisms was found to be in linkage disequilibrium with reported CD susceptibility markers. Haplotypic presentations of rs12722069-G, rs1130392-C, rs3188043-C and rs4193-A with CD reported SNPs were observed in sub-ethnic groups. Highly polymorphic sites of HLA alleles and TCR variable regions could be utilized for better risk prediction models in CD. Therapeutic strategies by identifying inhibitors or blockers targeting specific gliadin:HLA-DQ:TCR binding sites could be investigated.
Collapse
Affiliation(s)
- Pratibha Banerjee
- Immunogenomics Laboratory, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, 151401, India
| | - Ramprasad Chaudhary
- Immunogenomics Laboratory, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, 151401, India
| | - Atul Kumar Singh
- Molecular Signaling and Drug Discovery Laboratory, Department of Biochemistry, School of Basic Sciences, Central University of Punjab, Bathinda, 151401, India
| | - Pratima Parulekar
- Centre for Healthcare Science and Technology, Indian Institute of Engineering Science and Technology, Shibpur, Howrah, 711103, India
| | - Shashank Kumar
- Molecular Signaling and Drug Discovery Laboratory, Department of Biochemistry, School of Basic Sciences, Central University of Punjab, Bathinda, 151401, India.
| | - Sabyasachi Senapati
- Immunogenomics Laboratory, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, 151401, India.
| |
Collapse
|
18
|
Passeron T, King B, Seneschal J, Steinhoff M, Jabbari A, Ohyama M, Tobin DJ, Randhawa S, Winkler A, Telliez JB, Martin D, Lejeune A. Inhibition of T-cell activity in alopecia areata: recent developments and new directions. Front Immunol 2023; 14:1243556. [PMID: 38022501 PMCID: PMC10657858 DOI: 10.3389/fimmu.2023.1243556] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 10/05/2023] [Indexed: 12/01/2023] Open
Abstract
Alopecia areata (AA) is an autoimmune disease that has a complex underlying immunopathogenesis characterized by nonscarring hair loss ranging from small bald patches to complete loss of scalp, face, and/or body hair. Although the etiopathogenesis of AA has not yet been fully characterized, immune privilege collapse at the hair follicle (HF) followed by T-cell receptor recognition of exposed HF autoantigens by autoreactive cytotoxic CD8+ T cells is now understood to play a central role. Few treatment options are available, with the Janus kinase (JAK) 1/2 inhibitor baricitinib (2022) and the selective JAK3/tyrosine kinase expressed in hepatocellular carcinoma (TEC) inhibitor ritlecitinib (2023) being the only US Food and Drug Administration-approved systemic medications thus far for severe AA. Several other treatments are used off-label with limited efficacy and/or suboptimal safety and tolerability. With an increased understanding of the T-cell-mediated autoimmune and inflammatory pathogenesis of AA, additional therapeutic pathways beyond JAK inhibition are currently under investigation for the development of AA therapies. This narrative review presents a detailed overview about the role of T cells and T-cell-signaling pathways in the pathogenesis of AA, with a focus on those pathways targeted by drugs in clinical development for the treatment of AA. A detailed summary of new drugs targeting these pathways with expert commentary on future directions for AA drug development and the importance of targeting multiple T-cell-signaling pathways is also provided in this review.
Collapse
Affiliation(s)
- Thierry Passeron
- University Côte d’Azur, Centre Hospitalier Universitaire Nice, Department of Dermatology, Nice, France
- University Côte d’Azur, INSERM, U1065, C3M, Nice, France
| | - Brett King
- Department of Dermatology, Yale University School of Medicine, New Haven, CT, United States
| | - Julien Seneschal
- Department of Dermatology and Paediatric Dermatology, National Reference Centre for Rare Skin Diseases, Saint-André Hospital, University of Bordeaux, Bordeaux, France
- Bordeaux University, Centre national de la recherche scientifique (CNRS), ImmunoConcept, UMR5164, Bordeaux, France
| | - Martin Steinhoff
- Department of Dermatology and Venereology, Hamad Medical Corporation, Doha, Qatar
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
- Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
- Department of Dermatology and Venereology, Weill Cornell Medicine-Qatar, Doha, Qatar
- College of Medicine, Qatar University, Doha, Qatar
- Department of Dermatology, Weill Cornell Medicine, New York, NY, United States
- College of Health and Life Sciences, Hamad Bin Khalifa University-Qatar, Doha, Qatar
| | - Ali Jabbari
- Department of Dermatology, University of Iowa, Iowa City, IA, United States
- Iowa City VA Medical Center, Iowa City, IA, United States
| | - Manabu Ohyama
- Department of Dermatology, Kyorin University Faculty of Medicine, Tokyo, Japan
| | - Desmond J. Tobin
- Charles Institute of Dermatology, UCD School of Medicine, University College Dublin, Dublin, Ireland
| | | | | | | | | | | |
Collapse
|
19
|
Mifsud NA, Illing PT, Ho R, Tuomisto JE, Fettke H, Mullan KA, McCluskey J, Rossjohn J, Vivian J, Reantragoon R, Purcell AW. The allopurinol metabolite, oxypurinol, drives oligoclonal expansions of drug-reactive T cells in resolved hypersensitivity cases and drug-naïve healthy donors. Allergy 2023; 78:2980-2993. [PMID: 37452515 PMCID: PMC10952278 DOI: 10.1111/all.15814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/07/2023] [Accepted: 06/10/2023] [Indexed: 07/18/2023]
Abstract
Allopurinol (ALP) is a successful drug used in the treatment of gout. However, this drug has been implicated in hypersensitivity reactions that can cause severe to life-threatening reactions such as Stevens-Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN). Individuals who carry the human leukocyte antigen (HLA)-B*58:01 allotype are at higher risk of experiencing a hypersensitivity reaction (odds ratios ranging from 5.62 to 580.3 for mild to severe reactions, respectively). In addition to the parent drug, the metabolite oxypurinol (OXP) is implicated in triggering T cell-mediated immunopathology via a labile interaction with HLA-B*58:01. To date, there has been limited information regarding the T-cell receptor (TCR) repertoire usage of reactive T cells in patients with ALP-induced SJS or TEN and, in particular, there are no reports examining paired αβTCRs. Here, using in vitro drug-treated PBMCs isolated from both resolved ALP-induced SJS/TEN cases and drug-naïve healthy donors, we show that OXP is the driver of CD8+ T cell-mediated responses and that drug-exposed memory T cells can exhibit a proinflammatory immunophenotype similar to T cells described during active disease. Furthermore, this response supported the pharmacological interaction with immune receptors (p-i) concept by showcasing (i) the labile metabolite interaction with peptide/HLA complexes, (ii) immunogenic complex formation at the cell surface, and (iii) lack of requirement for antigen processing to elicit drug-induced T cell responsiveness. Examination of paired OXP-induced αβTCR repertoires highlighted an oligoclonal and private clonotypic profile in both resolved ALP-induced SJS/TEN cases and drug-naïve healthy donors.
Collapse
Affiliation(s)
- Nicole A. Mifsud
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonVictoriaAustralia
| | - Patricia T. Illing
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonVictoriaAustralia
| | - Rebecca Ho
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonVictoriaAustralia
| | - Johanna E. Tuomisto
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonVictoriaAustralia
| | - Heidi Fettke
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonVictoriaAustralia
- Present address:
Cancer Research, Peter MacCallum Cancer CentreMelbourneVictoriaAustralia
- Present address:
Sir Peter MacCallum Department of OncologyUniversity of MelbourneMelbourneVictoriaAustralia
| | - Kerry A. Mullan
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonVictoriaAustralia
- Present address:
ADREM Data Lab, Department of Computer ScienceUniversity of AntwerpAntwerpBelgium
| | - James McCluskey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and ImmunityUniversity of MelbourneParkvilleVictoriaAustralia
| | - Jamie Rossjohn
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonVictoriaAustralia
- Institute of Infection and ImmunityCardiff University School of MedicineCardiffUK
| | - Julian Vivian
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonVictoriaAustralia
- Present address:
St. Vincent's Institute of Medical ResearchFitzroyVictoriaAustralia
- Present address:
Department of MedicineThe University of MelbourneMelbourneVictoriaAustralia
| | - Rangsima Reantragoon
- Immunology Division, Department of Microbiology, Department of MicrobiologyChulalongkorn UniversityBangkokThailand
- Center of Excellence in Immunology and Immune‐mediated Disease, Faculty of MedicineChulalongkorn UniversityBangkokThailand
| | - Anthony W. Purcell
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonVictoriaAustralia
| |
Collapse
|
20
|
Seitz V, Gennermann K, Elezkurtaj S, Groth D, Schaper S, Dröge A, Lachmann N, Berg E, Lenze D, Kühl AA, Husemann C, Kleo K, Horst D, Lennerz V, Hennig S, Hummel M, Schumann M. Specific T-cell receptor beta-rearrangements of gluten-triggered CD8 + T-cells are enriched in celiac disease patients' duodenal mucosa. Clin Immunol 2023; 256:109795. [PMID: 37769786 DOI: 10.1016/j.clim.2023.109795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/12/2023] [Accepted: 09/25/2023] [Indexed: 10/02/2023]
Abstract
Celiac disease (CeD) is an autoimmune disorder affecting the small intestine with gluten as disease trigger. Infections including Influenza A, increase the CeD risk. While gluten-specific CD4+ T-cells, recognizing HLA-DQ2/DQ8 presented gluten-peptides, initiate and sustain the celiac immune response, CD8+ α/β intraepithelial T-cells elicit mucosal damage. Here, we subjected TCRs from a cohort of 56 CeD patients and 22 controls to an analysis employing 749 published CeD-related TCRβ-rearrangements derived from gluten-specific CD4+ T-cells and gluten-triggered peripheral blood CD8+ T-cells. We show, that in addition to TCRs from gluten-specific CD4+ T-cells, TCRs of gluten-triggered CD8+ T-cells are significantly enriched in CeD duodenal tissue samples. TCRβ-rearrangements of gluten-triggered CD8+ T-cells were even more expanded in patients than TCRs from gluten-specific CD4+ T-cells (p < 0.0002) and highest in refractory CeD. Sequence alignments with TCR-antigen databases suggest that a subgroup of these most likely indirectly gluten-triggered TCRs recognize microbial, viral, and autoantigens.
Collapse
Affiliation(s)
- V Seitz
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; HS Diagnomics GmbH, Berlin, Germany
| | | | - S Elezkurtaj
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - D Groth
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | | | - A Dröge
- HS Diagnomics GmbH, Berlin, Germany
| | - N Lachmann
- Centre for Tumor Medicine, Histocompatibility & Immunogenetics Laboratory, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - E Berg
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - D Lenze
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - A A Kühl
- iPATH.Berlin - Core Unit of the Charité Universitätsmedizin Berlin, corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - C Husemann
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; German Cancer Consortium (DKTK), Partner Site Berlin, Berlin, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - K Kleo
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - D Horst
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - S Hennig
- HS Diagnomics GmbH, Berlin, Germany
| | - M Hummel
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; German Cancer Consortium (DKTK), Partner Site Berlin, Berlin, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - M Schumann
- Medizinische Klinik m. S. Gastroenterologie, Infektiologie und Rheumatologie, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
| |
Collapse
|
21
|
Argyriou A, Horuluoglu B, Galindo‐Feria AS, Diaz‐Boada JS, Sijbranda M, Notarnicola A, Dani L, van Vollenhoven A, Ramsköld D, Nennesmo I, Dastmalchi M, Lundberg IE, Diaz‐Gallo L, Chemin K. Single-cell profiling of muscle-infiltrating T cells in idiopathic inflammatory myopathies. EMBO Mol Med 2023; 15:e17240. [PMID: 37522383 PMCID: PMC10565639 DOI: 10.15252/emmm.202217240] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 07/04/2023] [Accepted: 07/10/2023] [Indexed: 08/01/2023] Open
Abstract
Idiopathic inflammatory myopathies (IIM) are rare autoimmune systemic diseases characterized by muscle weakness and the presence of muscle-infiltrating T cells. IIM represent a clinical challenge due to heterogeneity of symptoms and variability of response to immunosuppressive treatment. Here, we performed in-depth single-cell sequencing on muscle-infiltrating T cells and peripheral blood memory T cells in six patients with recently diagnosed IIM. We identified tissue resident memory T-cell (TRM ) signatures including the expression of HOBIT, XCL1 and CXCR6 in the muscle biopsies of all patients with IIM. Clonally expanded T-cell clones were mainly found among cytotoxic and TRM implying their role in the disease pathogenesis. Finally, identical expanded T-cell clones persisting at follow-up in the muscle tissue of two patients suggest their involvement in disease chronicity. Our study reveals a muscle tissue resident memory T-cell signature in patients with IIM and a transcriptomic map to identify novel therapeutic targets in IIM.
Collapse
Affiliation(s)
- Alexandra Argyriou
- Division of Rheumatology, Department of Medicine, SolnaKarolinska InstitutetStockholmSweden
- Center for Molecular MedicineKarolinska InstitutetStockholmSweden
| | - Begum Horuluoglu
- Division of Rheumatology, Department of Medicine, SolnaKarolinska InstitutetStockholmSweden
- Center for Molecular MedicineKarolinska InstitutetStockholmSweden
| | - Angeles Shunashy Galindo‐Feria
- Division of Rheumatology, Department of Medicine, SolnaKarolinska InstitutetStockholmSweden
- Center for Molecular MedicineKarolinska InstitutetStockholmSweden
| | - Juan Sebastian Diaz‐Boada
- Division of Rheumatology, Department of Medicine, SolnaKarolinska InstitutetStockholmSweden
- Center for Molecular MedicineKarolinska InstitutetStockholmSweden
| | - Merel Sijbranda
- Division of Rheumatology, Department of Medicine, SolnaKarolinska InstitutetStockholmSweden
- Center for Molecular MedicineKarolinska InstitutetStockholmSweden
| | - Antonella Notarnicola
- Division of Rheumatology, Department of Medicine, SolnaKarolinska InstitutetStockholmSweden
- Center for Molecular MedicineKarolinska InstitutetStockholmSweden
- Department of Gastro, Dermatology and RheumatologyKarolinska University HospitalStockholmSweden
| | - Lara Dani
- Division of Rheumatology, Department of Medicine, SolnaKarolinska InstitutetStockholmSweden
- Department of Gastro, Dermatology and RheumatologyKarolinska University HospitalStockholmSweden
| | - Annika van Vollenhoven
- Division of Rheumatology, Department of Medicine, SolnaKarolinska InstitutetStockholmSweden
- Center for Molecular MedicineKarolinska InstitutetStockholmSweden
| | - Daniel Ramsköld
- Department of Cell and Molecular BiologyKarolinska InstitutetStockholmSweden
| | - Inger Nennesmo
- Department of Oncology‐PathologyKarolinska University HospitalStockholmSweden
| | - Maryam Dastmalchi
- Division of Rheumatology, Department of Medicine, SolnaKarolinska InstitutetStockholmSweden
- Center for Molecular MedicineKarolinska InstitutetStockholmSweden
- Department of Gastro, Dermatology and RheumatologyKarolinska University HospitalStockholmSweden
| | - Ingrid E Lundberg
- Division of Rheumatology, Department of Medicine, SolnaKarolinska InstitutetStockholmSweden
- Center for Molecular MedicineKarolinska InstitutetStockholmSweden
- Department of Gastro, Dermatology and RheumatologyKarolinska University HospitalStockholmSweden
| | - Lina‐Marcela Diaz‐Gallo
- Division of Rheumatology, Department of Medicine, SolnaKarolinska InstitutetStockholmSweden
- Center for Molecular MedicineKarolinska InstitutetStockholmSweden
| | - Karine Chemin
- Division of Rheumatology, Department of Medicine, SolnaKarolinska InstitutetStockholmSweden
- Center for Molecular MedicineKarolinska InstitutetStockholmSweden
| |
Collapse
|
22
|
Davydov AN, Bolotin DA, Poslavsky SV, Chudakov DM. Comment on 'rigorous benchmarking of T cell receptor repertoire profiling methods for cancer RNA sequencing'. Brief Bioinform 2023; 24:bbad354. [PMID: 37824737 PMCID: PMC10569745 DOI: 10.1093/bib/bbad354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/14/2023] [Accepted: 09/17/2023] [Indexed: 10/14/2023] Open
Abstract
Transcriptome sequencing has become common in cancer research, resulting in the generation of a substantial volume of RNA sequencing (RNA-Seq) data. The ability to extract immune repertoires from these data is crucial for obtaining information on infiltrating T- and B-lymphocyte clones when dedicated amplicon T-cell/B-cell receptors sequencing (TCR-Seq/BCR-Seq) methods are unavailable. In response to this demand, several dedicated computational methods have been developed, including MiXCR, TRUST and ImRep. In the recent publication in Briefings in Bioinformatics, Peng et al. have conducted an intensive, systematic comparison of the three previously mentioned tools. Although their effort is commendable, we do have a few constructive critiques regarding technical elements of their analysis.
Collapse
Affiliation(s)
- Alexey N Davydov
- MiLaboratories Inc, San Francisco, CA, USA
- Central European Institute of Technology, Brno, Czech Republic
| | | | | | - Dmitry M Chudakov
- MiLaboratories Inc, San Francisco, CA, USA
- Central European Institute of Technology, Brno, Czech Republic
| |
Collapse
|
23
|
Huang YN, Vahed M, Peng K, Alachkar H, Mangul S. Response to 'comment on rigorous benchmarking of T cell receptor repertoire profiling methods for cancer RNA sequencing' by Davydov A.N.; Bolotin D.A.; Poslavsky S. V. and Chudakov D.M. Brief Bioinform 2023; 24:bbad355. [PMID: 37824736 PMCID: PMC10569746 DOI: 10.1093/bib/bbad355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 09/17/2023] [Indexed: 10/14/2023] Open
Affiliation(s)
- Yu-Ning Huang
- Titus Family Department of Clinical Pharmacy, Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, California, 90089, USA
| | - Mohammad Vahed
- Titus Family Department of Clinical Pharmacy, Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, California, 90089, USA
| | - Kerui Peng
- Titus Family Department of Clinical Pharmacy, Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, California, 90089, USA
| | - Houda Alachkar
- Titus Family Department of Clinical Pharmacy, Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, California, 90089, USA
| | - Serghei Mangul
- Titus Family Department of Clinical Pharmacy, Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, California, 90089, USA
- Department of Quantitative and Computational Biology, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA 90033, USA
| |
Collapse
|
24
|
Flumens D, Gielis S, Bartholomeus E, Campillo-Davo D, van der Heijden S, Versteven M, De Reu H, Smits E, Ogunjimi B, Laukens K, Meysman P, Lion E. Training of epitope-TCR prediction models with healthy donor-derived cancer-specific T cells. Methods Cell Biol 2023; 183:143-160. [PMID: 38548410 DOI: 10.1016/bs.mcb.2023.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
Discovery of epitope-specific T-cell receptors (TCRs) for cancer therapies is a time consuming and expensive procedure that usually requires a large amount of patient cells. To maximize information from and minimize the need of precious samples in cancer research, prediction models have been developed to identify in silico epitope-specific TCRs. In this chapter, we provide a step-by-step protocol to train a prediction model using the user-friendly TCRex webtool for the nearly universal tumor-associated antigen Wilms' tumor 1 (WT1)-specific TCR repertoire. WT1 is a self-antigen overexpressed in numerous solid and hematological malignancies with a high clinical relevance. Training of computational models starts from a list of known epitope-specific TCRs which is often not available for new cancer epitopes. Therefore, we describe a workflow to assemble a training data set consisting of TCR sequences obtained from WT137-45-reactive CD8 T cell clones expanded and sorted from healthy donor peripheral blood mononuclear cells.
Collapse
Affiliation(s)
- Donovan Flumens
- Laboratory of Experimental Hematology (LEH), Vaccine & Infectious Disease Institute (VAXINFECTIO), Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Sofie Gielis
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium; Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium; Biomedical Informatics Research Network Antwerp (Biomina), University of Antwerp, Antwerp, Belgium
| | - Esther Bartholomeus
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium; Centre for Health Economics Research & Modeling Infectious Diseases (CHERMID), VAXINFECTIO, University of Antwerp, Antwerp, Belgium; Antwerp Center for Translational Immunology and Virology (ACTIV), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Diana Campillo-Davo
- Laboratory of Experimental Hematology (LEH), Vaccine & Infectious Disease Institute (VAXINFECTIO), Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Sanne van der Heijden
- Laboratory of Experimental Hematology (LEH), Vaccine & Infectious Disease Institute (VAXINFECTIO), Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium; Center for Oncological Research (CORE), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, Antwerp, Belgium
| | - Maarten Versteven
- Laboratory of Experimental Hematology (LEH), Vaccine & Infectious Disease Institute (VAXINFECTIO), Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Hans De Reu
- Laboratory of Experimental Hematology (LEH), Vaccine & Infectious Disease Institute (VAXINFECTIO), Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Evelien Smits
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium; Centre for Health Economics Research & Modeling Infectious Diseases (CHERMID), VAXINFECTIO, University of Antwerp, Antwerp, Belgium
| | - Benson Ogunjimi
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium; Centre for Health Economics Research & Modeling Infectious Diseases (CHERMID), VAXINFECTIO, University of Antwerp, Antwerp, Belgium; Antwerp Center for Translational Immunology and Virology (ACTIV), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Kris Laukens
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium; Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium; Biomedical Informatics Research Network Antwerp (Biomina), University of Antwerp, Antwerp, Belgium
| | - Pieter Meysman
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium; Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium; Biomedical Informatics Research Network Antwerp (Biomina), University of Antwerp, Antwerp, Belgium
| | - Eva Lion
- Laboratory of Experimental Hematology (LEH), Vaccine & Infectious Disease Institute (VAXINFECTIO), Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium; Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium; Center for Cell Therapy & Regenerative Medicine (CCRG), Antwerp University Hospital, Edegem, Belgium.
| |
Collapse
|
25
|
Fan Q, Li M, Zhao W, Zhang K, Li M, Li W. Hyper α2,6-Sialylation Promotes CD4 + T-Cell Activation and Induces the Occurrence of Ulcerative Colitis. Adv Sci (Weinh) 2023; 10:e2302607. [PMID: 37424034 PMCID: PMC10502867 DOI: 10.1002/advs.202302607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/23/2023] [Indexed: 07/11/2023]
Abstract
α2,6-sialylation, catalyzed by α2,6-sialyltransferase (ST6GAL1), plays a pivotal role in immune responses. However, the role of ST6GAL1 in the pathogenesis of ulcerative colitis (UC) remains unknown. ST6GAL1 mRNA is highly expressed in UC tissues compared with the corresponding adjacent normal tissues, and α2,6-sialylation is significantly increased in the colon tissues of patients with UC. The expression of ST6GAL1 and proinflammatory cytokines, such as interleukin (IL)-2, IL-6, IL-17, and interferon-gamma, is also increased. The number of CD4+ T cells increases in UC patients. St6gal1 gene knockout (St6gal1-/- ) rats are established by clustered regularly interspaced short palindromic repeats (CRISPR)-associated gene knockout system. St6gal1 deficiency reduces the levels of pro-inflammatory cytokines and alleviates colitis symptoms in UC model rats. Ablation of α2,6-sialylation inhibits the transport of the TCR to lipid rafts and suppresses CD4+ T-cell activation. The attenuation of TCR signaling downregulates the expression of NF-κB in ST6GAL1-/- CD4+ T-cells. Moreover, NF-κB could bind to the ST6GAL1 promoter to increase its transcription. Ablation of ST6GAL1 downregulates the expression of NF-κB and reduces the production of proinflammatory cytokines to relieve UC pathogenesis, which is a potential novel target for the clinical treatment of UC.
Collapse
Affiliation(s)
- Qingjie Fan
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular ImmunopathologyShantou University Medical CollegeShantouGuangdong515041China
- College of Basic Medical ScienceDalian Medical University9‐Western Section, Lvshun South RoadDalianLiaoning116044China
| | - Mechou Li
- College of Basic Medical ScienceDalian Medical University9‐Western Section, Lvshun South RoadDalianLiaoning116044China
| | - Weiwei Zhao
- College of Basic Medical ScienceDalian Medical University9‐Western Section, Lvshun South RoadDalianLiaoning116044China
| | - Kaixin Zhang
- College of Basic Medical ScienceDalian Medical University9‐Western Section, Lvshun South RoadDalianLiaoning116044China
| | - Ming Li
- College of Basic Medical ScienceDalian Medical University9‐Western Section, Lvshun South RoadDalianLiaoning116044China
| | - Wenzhe Li
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular ImmunopathologyShantou University Medical CollegeShantouGuangdong515041China
| |
Collapse
|
26
|
Carbone ML, Capone A, Guercio M, Reddel S, Silvestris DA, Lulli D, Ramondino C, Peluso D, Quintarelli C, Volpe E, Failla CM. Insight into immune profile associated with vitiligo onset and anti-tumoral response in melanoma patients receiving anti-PD-1 immunotherapy. Front Immunol 2023; 14:1197630. [PMID: 37680638 PMCID: PMC10482109 DOI: 10.3389/fimmu.2023.1197630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 08/04/2023] [Indexed: 09/09/2023] Open
Abstract
Introduction Immunotherapy with checkpoint inhibitors is an efficient treatment for metastatic melanoma. Development of vitiligo upon immunotherapy represents a specific immune-related adverse event (irAE) diagnosed in 15% of patients and associated with a positive clinical response. Therefore, a detailed characterization of immune cells during vitiligo onset in melanoma patients would give insight into the immune mechanisms mediating both the irAE and the anti-tumor response. Methods To better understand these aspects, we analyzed T cell subsets from peripheral blood of metastatic melanoma patients undergoing treatment with anti-programmed cell death protein (PD)-1 antibodies. To deeply characterize the antitumoral T cell response concomitant to vitiligo onset, we analyzed T cell content in skin biopsies collected from melanoma patients who developed vitiligo. Moreover, to further characterize T cells in vitiligo skin lesion of melanoma patients, we sequenced T cell receptor (TCR) of cells derived from biopsies of vitiligo and primary melanoma of the same patient. Results and discussion Stratification of patients for developing or not developing vitiligo during anti-PD-1 therapy revealed an association between blood reduction of CD8-mucosal associated invariant T (MAIT), T helper (h) 17, natural killer (NK) CD56bright, and T regulatory (T-reg) cells and vitiligo onset. Consistently with the observed blood reduction of Th17 cells in melanoma patients developing vitiligo during immunotherapy, we found high amount of IL-17A expressing cells in the vitiligo skin biopsy, suggesting a possible migration of Th17 cells from the blood into the autoimmune lesion. Interestingly, except for a few cases, we found different TCR sequences between vitiligo and primary melanoma lesions. In contrast, shared TCR sequences were identified between vitiligo and metastatic tissues of the same patient. These data indicate that T cell response against normal melanocytes, which is involved in vitiligo onset, is not typically mediated by reactivation of specific T cell clones infiltrating primary melanoma but may be elicited by T cell clones targeting metastatic tissues. Altogether, our data indicate that anti-PD-1 therapy induces a de novo immune response, stimulated by the presence of metastatic cells, and composed of different T cell subtypes, which may trigger the development of vitiligo and the response against metastatic tumor.
Collapse
Affiliation(s)
- Maria Luigia Carbone
- Laboratory of Experimental Immunology, Istituto Dermopatico dell’Immacolata (IDI)-IRCCS, Rome, Italy
| | - Alessia Capone
- Laboratory of Molecular Neuroimmunology, Santa Lucia Foundation-IRCCS, Rome, Italy
| | - Marika Guercio
- Department of Oncology-Hematology, and Cell and Gene Therapy, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
| | - Sofia Reddel
- Department of Oncology-Hematology, and Cell and Gene Therapy, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
| | | | - Daniela Lulli
- Laboratory of Experimental Immunology, Istituto Dermopatico dell’Immacolata (IDI)-IRCCS, Rome, Italy
| | - Carmela Ramondino
- Laboratory of Experimental Immunology, Istituto Dermopatico dell’Immacolata (IDI)-IRCCS, Rome, Italy
| | - Daniele Peluso
- Department of Biology, University “Tor Vergata”, Rome, Italy
| | - Concetta Quintarelli
- Department of Oncology-Hematology, and Cell and Gene Therapy, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
- Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Elisabetta Volpe
- Laboratory of Molecular Neuroimmunology, Santa Lucia Foundation-IRCCS, Rome, Italy
| | - Cristina Maria Failla
- Laboratory of Experimental Immunology, Istituto Dermopatico dell’Immacolata (IDI)-IRCCS, Rome, Italy
| |
Collapse
|
27
|
Dabas P, Danda A. Revolutionizing cancer treatment: a comprehensive review of CAR-T cell therapy. Med Oncol 2023; 40:275. [PMID: 37608202 DOI: 10.1007/s12032-023-02146-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 08/01/2023] [Indexed: 08/24/2023]
Abstract
Chimeric antigen receptor (CAR)-T cell therapy is a promising new treatment for cancer that involves genetically modifying a patient's T-cells to recognize and attack cancer cells. This review provides an overview of the latest discoveries and clinical trials related to CAR-T cell therapy, as well as the concept and applications of the therapy. The review also discusses the limitations and potential side effects of CAR-T cell therapy, including the high cost and the risk of cytokine release syndrome and neurotoxicity. While CAR-T cell therapy has shown promising results in the treatment of hematologic malignancies, ongoing research is needed to improve the efficacy and safety of the therapy and expand its use to solid tumors. With continued research and development, CAR-T cell therapy has the potential to revolutionize cancer treatment and improve outcomes for patients with cancer.
Collapse
Affiliation(s)
- Preeti Dabas
- St Jude Children's Research Hospital, Memphis, TN, USA.
| | - Adithi Danda
- St Jude Children's Research Hospital, Memphis, TN, USA
| |
Collapse
|
28
|
Andreatta M, Gueguen P, Borcherding N, Carmona SJ. T Cell Clonal Analysis Using Single-cell RNA Sequencing and Reference Maps. Bio Protoc 2023; 13:e4735. [PMID: 37638293 PMCID: PMC10450729 DOI: 10.21769/bioprotoc.4735] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/19/2023] [Accepted: 05/11/2023] [Indexed: 08/29/2023] Open
Abstract
T cells are endowed with T-cell antigen receptors (TCR) that give them the capacity to recognize specific antigens and mount antigen-specific adaptive immune responses. Because TCR sequences are distinct in each naïve T cell, they serve as molecular barcodes to track T cells with clonal relatedness and shared antigen specificity through proliferation, differentiation, and migration. Single-cell RNA sequencing provides coupled information of TCR sequence and transcriptional state in individual cells, enabling T-cell clonotype-specific analyses. In this protocol, we outline a computational workflow to perform T-cell states and clonal analysis from scRNA-seq data based on the R packages Seurat, ProjecTILs, and scRepertoire. Given a scRNA-seq T-cell dataset with TCR sequence information, cell states are automatically annotated by reference projection using the ProjecTILs method. TCR information is used to track individual clonotypes, assess their clonal expansion, proliferation rates, bias towards specific differentiation states, and the clonal overlap between T-cell subtypes. We provide fully reproducible R code to conduct these analyses and generate useful visualizations that can be adapted for the needs of the protocol user. Key features Computational analysis of paired scRNA-seq and scTCR-seq data Characterizing T-cell functional state by reference-based analysis using ProjecTILs Exploring T-cell clonal structure using scRepertoire Linking T-cell clonality to transcriptomic state to study relationships between clonal expansion and functional phenotype Graphical overview.
Collapse
Affiliation(s)
- Massimo Andreatta
- Ludwig Institute for Cancer Research, Lausanne Branch, and Department of Oncology, CHUV and University of Lausanne, Epalinges, Switzerland
- Agora Cancer Research Center, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Paul Gueguen
- Ludwig Institute for Cancer Research, Lausanne Branch, and Department of Oncology, CHUV and University of Lausanne, Epalinges, Switzerland
- Agora Cancer Research Center, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Nicholas Borcherding
- Department of Pathology & Immunology, Washington University in St. Louis, St. Louis, MO, USA
| | - Santiago J. Carmona
- Ludwig Institute for Cancer Research, Lausanne Branch, and Department of Oncology, CHUV and University of Lausanne, Epalinges, Switzerland
- Agora Cancer Research Center, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| |
Collapse
|
29
|
Shcherbinin DS, Karnaukhov VK, Zvyagin IV, Chudakov DM, Shugay M. Large-scale template-based structural modeling of T-cell receptors with known antigen specificity reveals complementarity features. Front Immunol 2023; 14:1224969. [PMID: 37649481 PMCID: PMC10464843 DOI: 10.3389/fimmu.2023.1224969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 07/27/2023] [Indexed: 09/01/2023] Open
Abstract
Introduction T-cell receptor (TCR) recognition of foreign peptides presented by the major histocompatibility complex (MHC) initiates the adaptive immune response against pathogens. While a large number of TCR sequences specific to different antigenic peptides are known to date, the structural data describing the conformation and contacting residues for TCR-peptide-MHC complexes is relatively limited. In the present study we aim to extend and analyze the set of available structures by performing highly accurate template-based modeling of these complexes using TCR sequences with known specificity. Methods Identification of CDR3 sequences and their further clustering, based on available spatial structures, V- and J-genes of corresponding T-cell receptors, and epitopes, was performed using the VDJdb database. Modeling of the selected CDR3 loops was conducted using a stepwise introduction of single amino acid substitutions to the template PDB structures, followed by optimization of the TCR-peptide-MHC contacting interface using the Rosetta package applications. Statistical analysis and recursive feature elimination procedures were carried out on computed energy values and properties of contacting amino acid residues between CDR3 loops and peptides, using R. Results Using the set of 29 complex templates (including a template with SARS-CoV-2 antigen) and 732 specificity records, we built a database of 1585 model structures carrying substitutions in either TCRα or TCRβ chains with some models representing the result of different mutation pathways for the same final structure. This database allowed us to analyze features of amino acid contacts in TCR - peptide interfaces that govern antigen recognition preferences and interpret these interactions in terms of physicochemical properties of interacting residues. Conclusion Our results provide a methodology for creating high-quality TCR-peptide-MHC models for antigens of interest that can be utilized to predict TCR specificity.
Collapse
Affiliation(s)
- Dmitrii S. Shcherbinin
- Institute of Translational Medicine, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Laboratory of Structural Bioinformatics, Institute of Biomedical Chemistry, Moscow, Russia
| | - Vadim K. Karnaukhov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Ivan V. Zvyagin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Dmitriy M. Chudakov
- Institute of Translational Medicine, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Center of Molecular Medicine, Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czechia
| | - Mikhail Shugay
- Institute of Translational Medicine, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| |
Collapse
|
30
|
Carty SA, Murga-Zamalloa CA, Wilcox RA. SOHO State of the Art Updates and Next Questions | New Pathways and New Targets in PTCL: Staying on Target. Clin Lymphoma Myeloma Leuk 2023; 23:561-574. [PMID: 37142534 PMCID: PMC10565700 DOI: 10.1016/j.clml.2023.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 04/05/2023] [Accepted: 04/16/2023] [Indexed: 05/06/2023]
Abstract
While the peripheral T-cell lymphomas (PTCL) remain a therapeutic challenge, and increasingly account for a disproportionate number of lymphoma-related deaths, improved understanding of disease pathogenesis and classification, and the development of novel therapeutic agents over the past decade, all provide reasons for a more optimistic outlook in the next. Despite their genetic and molecular heterogeneity, many PTCL are dependent upon signaling input provided by antigen, costimulatory, and cytokine receptors. While gain-of-function alterations effecting these pathways are recurrently observed in many PTCL, more often than not, signaling remains ligand-and tumor microenvironment (TME)-dependent. Consequently, the TME and its constituents are increasingly recognized as "on target". Utilizing a "3 signal" model, we will review new-and old-therapeutic targets that are relevant for the more common nodal PTCL subtypes.
Collapse
Affiliation(s)
- Shannon A Carty
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, MI
| | | | - Ryan A Wilcox
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, MI.
| |
Collapse
|
31
|
Gutierrez M, Bladek P, Goksu B, Murga-Zamalloa C, Bixby D, Wilcox R. T-Cell Prolymphocytic Leukemia: Diagnosis, Pathogenesis, and Treatment. Int J Mol Sci 2023; 24:12106. [PMID: 37569479 PMCID: PMC10419310 DOI: 10.3390/ijms241512106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/20/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023] Open
Abstract
T-cell prolymphocytic leukemia (T-PLL) is a rare and aggressive neoplasm of mature T-cells. Most patients with T-PLL present with lymphocytosis, anemia, thrombocytopenia, and hepatosplenomegaly. Correct identification of T-PLL is essential because treatment for this disease is distinct from that of other T-cell neoplasms. In 2019, the T-PLL International Study Group (TPLL-ISG) established criteria for the diagnosis, staging, and assessment of response to treatment of T-PLL with the goal of harmonizing research efforts and supporting clinical decision-making. T-PLL pathogenesis is commonly driven by T-cell leukemia 1 (TCL1) overexpression and ATM loss, genetic alterations that are incorporated into the TPLL-ISG diagnostic criteria. The cooperativity between TCL1 family members and ATM is seemingly unique to T-PLL across the spectrum of T-cell neoplasms. The role of the T-cell receptor, its downstream kinases, and JAK/STAT signaling are also emerging themes in disease pathogenesis and have obvious therapeutic implications. Despite improved understanding of disease pathogenesis, alemtuzumab remains the frontline therapy in the treatment of naïve patients with indications for treatment given its high response rate. Unfortunately, the responses achieved are rarely durable, and the majority of patients are not candidates for consolidation with hematopoietic stem cell transplantation. Improved understanding of T-PLL pathogenesis has unveiled novel therapeutic vulnerabilities that may change the natural history of this lymphoproliferative neoplasm and will be the focus of this concise review.
Collapse
Affiliation(s)
- Marc Gutierrez
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Patrick Bladek
- Department of Pathology, University of Illinois Chicago, Chicago, IL 60607, USA; (P.B.); (B.G.); (C.M.-Z.)
| | - Busra Goksu
- Department of Pathology, University of Illinois Chicago, Chicago, IL 60607, USA; (P.B.); (B.G.); (C.M.-Z.)
| | - Carlos Murga-Zamalloa
- Department of Pathology, University of Illinois Chicago, Chicago, IL 60607, USA; (P.B.); (B.G.); (C.M.-Z.)
| | - Dale Bixby
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, MI 60607, USA;
| | - Ryan Wilcox
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, MI 60607, USA;
| |
Collapse
|
32
|
Hu MT, Ma WC, Wang JH, Jiang XQ, Yang DQ, Ao JY. Mechanistic insights into the allosteric inactivation mechanism of ZAP-70 induced by the hot spot W165C mutation. J Biomol Struct Dyn 2023:1-10. [PMID: 37505058 DOI: 10.1080/07391102.2023.2240421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Zeta chain-associated protein kinase 70 (ZAP-70) is a non-receptor tyrosine kinase that interacts with the activated T-cell receptor to transduce downstream signals, and thus plays an important role in the adaptive immune system. The biphosphorylated immunotyrosine-based activation motifs (ITAM-Y2P) binds to the N-SH2 and C-SH2 domains of ZAP-70 to promote the activation of ZAP-70. The present study explores molecular mechanisms of allosteric inactivation of ZAP-70 induced by the hot spot W165C mutation through atomically detailed molecular dynamics simulation approaches. We report microsecond-length simulations of two states of the tandem SH2 domains of ZAP-70 in complex with the ITAM-Y2P motif, including the wild-type and W165C mutant. Extensive analysis of local flexibility and dynamical correlated motions show that W165C mutation changes coupled motions of protein domains and community networks. The binding affinities of the ITAM-Y2P motif to the wild-type and W165C mutant of ZAP-70 are predicted using binding free energy calculations. The results suggest that the driving force to decrease the binding affinity in the W165C mutant derives from the difference in the protein-protein electrostatic interactions. Moreover, the per-residue free energy decomposition unravels that the contributions from residues in the phosphorylated Tyr315 (pY315) binding site, in particular pY315 of ITAM-Y2P, and Arg43, Tyr240 of ZAP-70, are the key determinants for the loss of binding affinity. This study may insights into our understanding of the pathological mechanism of ZAP-70.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Ming-Tai Hu
- Department of Hepatobiliary and Pancreatic Surgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- Institute of Hepatobiliary and Pancreatic Surgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Wen-Cong Ma
- Department of Hepatobiliary and Pancreatic Surgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- Institute of Hepatobiliary and Pancreatic Surgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jing-Han Wang
- Department of Hepatobiliary and Pancreatic Surgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- Institute of Hepatobiliary and Pancreatic Surgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiao-Qing Jiang
- Department of Biliary Tract Surgery I, The Third Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Da-Qing Yang
- Department of General Surgery, The Second Affiliated Hospital of Shanghai University (Wenzhou Central Hospital), Wenzhou, Zhejiang, China
| | - Jian-Yang Ao
- Department of Hepatobiliary and Pancreatic Surgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- Institute of Hepatobiliary and Pancreatic Surgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| |
Collapse
|
33
|
Peng K, Nowicki TS, Campbell K, Vahed M, Peng D, Meng Y, Nagareddy A, Huang YN, Karlsberg A, Miller Z, Brito J, Nadel B, Pak VM, Abedalthagafi MS, Burkhardt AM, Alachkar H, Ribas A, Mangul S. Rigorous benchmarking of T-cell receptor repertoire profiling methods for cancer RNA sequencing. Brief Bioinform 2023; 24:bbad220. [PMID: 37291798 PMCID: PMC10359085 DOI: 10.1093/bib/bbad220] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 05/02/2023] [Accepted: 05/24/2023] [Indexed: 06/10/2023] Open
Abstract
The ability to identify and track T-cell receptor (TCR) sequences from patient samples is becoming central to the field of cancer research and immunotherapy. Tracking genetically engineered T cells expressing TCRs that target specific tumor antigens is important to determine the persistence of these cells and quantify tumor responses. The available high-throughput method to profile TCR repertoires is generally referred to as TCR sequencing (TCR-Seq). However, the available TCR-Seq data are limited compared with RNA sequencing (RNA-Seq). In this paper, we have benchmarked the ability of RNA-Seq-based methods to profile TCR repertoires by examining 19 bulk RNA-Seq samples across 4 cancer cohorts including both T-cell-rich and T-cell-poor tissue types. We have performed a comprehensive evaluation of the existing RNA-Seq-based repertoire profiling methods using targeted TCR-Seq as the gold standard. We also highlighted scenarios under which the RNA-Seq approach is suitable and can provide comparable accuracy to the TCR-Seq approach. Our results show that RNA-Seq-based methods are able to effectively capture the clonotypes and estimate the diversity of TCR repertoires, as well as provide relative frequencies of clonotypes in T-cell-rich tissues and low-diversity repertoires. However, RNA-Seq-based TCR profiling methods have limited power in T-cell-poor tissues, especially in highly diverse repertoires of T-cell-poor tissues. The results of our benchmarking provide an additional appealing argument to incorporate RNA-Seq into the immune repertoire screening of cancer patients as it offers broader knowledge into the transcriptomic changes that exceed the limited information provided by TCR-Seq.
Collapse
Affiliation(s)
- Kerui Peng
- Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | - Theodore S Nowicki
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, University of California, Los Angeles, CA, USA
- Department of Microbiology, Immunology, & Molecular Genetics, University of California, Los Angeles, CA, USA
| | - Katie Campbell
- Department of Medicine, Division of Hematology-Oncology, University of California, Los Angeles, CA, USA
| | - Mohammad Vahed
- Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | - Dandan Peng
- Department of Quantitative and Computational Biology, USC Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA, USA
| | - Yiting Meng
- Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | - Anish Nagareddy
- Viterbi School of Engineering, University of Southern California, Los Angeles, CA, USA
| | - Yu-Ning Huang
- Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | - Aaron Karlsberg
- Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | - Zachary Miller
- Department of Pharmaceutical Sciences, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | - Jaqueline Brito
- Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | - Brian Nadel
- Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
| | - Victoria M Pak
- Emory Nell Hodgson School of Nursing, Emory University, Atlanta, GA, USA
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Malak S Abedalthagafi
- Department of Pathology & Laboratory Medicine, Emory University Hospital, Atlanta, GA, USA
- King Salman Center for Disability Research, Riyadh, Saudi Arabia
| | - Amanda M Burkhardt
- Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | - Houda Alachkar
- Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | - Antoni Ribas
- Departments of Medicine (Hematology-Oncology), Surgery (Surgical Oncology) and Molecular & Medical Pharmacology, University of California, Los Angeles, CA, USA
| | - Serghei Mangul
- Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
- Department of Quantitative and Computational Biology, USC Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA, USA
| |
Collapse
|
34
|
Ashry MSE, Radwan E, Abdellateif MS, Arafah O, Hassan NM. Clinical features, laboratory characteristics, and outcome of ETP and TCRA/D aberrations in pediatric patients with T-acute lymphoblastic leukemia. J Egypt Natl Canc Inst 2023; 35:17. [PMID: 37303010 DOI: 10.1186/s43046-023-00176-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 05/06/2023] [Indexed: 06/13/2023] Open
Abstract
BACKGROUND T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignancy with few accepted prognostic factors that limit the efficiency of therapy. The aim of the current study was to assess the clinical and laboratory features of T-cell receptor (TCR) aberrations and early T-cell precursor (ETP) subtype as well as their outcome to therapy. METHODS Sixty-three newly diagnosed pediatric T-ALL patients were assessed for the ETP status using immunophenotyping. Screening of TCRA/D aberrations was done by fluorescent in situ hybridization (FISH). The data were correlated to the patients' clinical features, response to treatment, and survival rates. RESULTS Seven patients (11%) had ETP-ALL. The ETP-ALL patients were older (P = 0.013), presented with lower white blood cell (WBC) count (P = 0.001) and lower percentage of peripheral blood (PB) blast cells (P = 0.037), more likely to have hyperdiploid karyotype (P = 0.009), and had been associated with TCRA/D gene amplification (P = 0.014) compared to other T-ALL patients. Of note, the same associations had been significantly observed in patients with TCRA/D gene amplification. Patients with TCRA/D amplification frequently coincided with TCRβ aberrations (P = 0.025). TCR-β aberrations were significantly associated with negative MRD at the end of induction compared to TCR-β-negative patients. There was a nonsignificant trend of ETP-positive cases to have lower overall survival (OS) (P = 0.06). Patients with TCR aberrations had no significant differences regarding disease-free survival (DFS) or OS rates compared to those with normal TCR. CONCLUSION ETP-ALL patients tend to have increased mortalities. There was no significant impact of TCR aberrations on the survival rates of the patients.
Collapse
Affiliation(s)
- Mona S El Ashry
- Clinical Pathology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Enas Radwan
- Clinical Pathology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Mona S Abdellateif
- Medical Biochemistry and Molecular Biology, Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt.
| | - Omar Arafah
- Pediatric Oncology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Naglaa M Hassan
- Clinical Pathology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| |
Collapse
|
35
|
Viguier M, Pérals C, Poirier B, Battistella M, Aubin F, Bachelez H, Prétet JL, Gheit T, Tommasino M, Touzé A, Gougeon ML, Fazilleau N. Human papilloma virus-16-specific CD8+ T-cell expansions characterize different clinical forms of lichen planus and not lichen sclerosus et atrophicus. Exp Dermatol 2023; 32:859-868. [PMID: 36922453 DOI: 10.1111/exd.14788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 02/22/2023] [Accepted: 02/25/2023] [Indexed: 03/18/2023]
Abstract
Lichen planus (LP) is a cutaneomucosal chronic inflammatory disease characterized by a CD8+ cytotoxic T-lymphocytes (CTL) infiltrate. In erosive oral LP, we found HPV16-specific activated CTL in lesions, supporting a pathogenic contribution of HPV16. Here, we investigated whether a similar scenario occurs in other clinical forms of LP and in lichen sclerosus et atrophicus (LSA), another chronic disease also affecting the mucosa and/or the skin. Blood CTL from LP and LSA patients expressed significant higher levels of granzyme B, perforin and CD107a proteins than healthy donors. Expansions of TCRVß3+ CTL, with presence of TCR clonotypes identical to those previously detected in erosive oral LP, were found both in blood and mucosal/skin lesions of LP, and not of LSA patients. These expansions were enriched with HPV16-specific CD8+ T-cells as shown by their recognition of the E711-20 immunodominant epitope. In LSA patients, the peripheral repertoire of CTL was oligoclonal for TCRVß6+ CTL. Finally, although patients with LP and LSA have developed antibodies against HPV16 capsid L1, antibodies against HPV16 E6 were only observed in patients with LP. Overall, our data collectively suggest an involvement of HPV16-specific CTL in different clinical forms of LP, not only in erosive oral LP, while a different scenario operates in LSA.
Collapse
Affiliation(s)
- Manuelle Viguier
- Department of dermatology, Hôpital Robert-Debré, University of Reims Champagne-Ardenne (URCA), EA7509 IRMAIC, Reims, France
| | - Corine Pérals
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), CNRS U5051, INSERM U1291, University Toulouse III, Toulouse, France
| | | | - Maxime Battistella
- Sorbonne Paris Cité, Service d'Anatomo-Pathologie, Hôpital Saint-Louis, Paris, France
| | - François Aubin
- Service de Dermatologie, Centre Hospitalo-Universitaire (CHU) de Besançon, Université de Franche Comté, Besançon, France
| | - Hervé Bachelez
- Laboratory of Genetics of Skin Diseases, Imagine Institute for Human Genetic Diseases, INSERM U1163, Université de Paris, Paris, France
- Department of Dermatology, APHP Hôpital Saint-Louis, Paris, France
| | - Jean-Luc Prétet
- Centre National de Référence Papillomavirus, Laboratoire de Biologie Cellulaire et Moléculaire, CHU de Besançon, Université Bourgogne Franche Comté, Besançon, France
| | | | - Massimo Tommasino
- IARC, Lyon, France
- IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
| | | | | | - Nicolas Fazilleau
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), CNRS U5051, INSERM U1291, University Toulouse III, Toulouse, France
| |
Collapse
|
36
|
Hey S, Whyte D, Hoang MC, Le N, Natvig J, Wingfield C, Onyeama C, Howrylak J, Toby IT. Analysis of CDR3 Sequences from T-Cell Receptor β in Acute Respiratory Distress Syndrome. Biomolecules 2023; 13:biom13050825. [PMID: 37238695 DOI: 10.3390/biom13050825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/04/2023] [Accepted: 05/06/2023] [Indexed: 05/28/2023] Open
Abstract
Acute Respiratory Distress Syndrome (ARDS) is an illness that typically develops in people who are significantly ill or have serious injuries. ARDS is characterized by fluid build-up that occurs in the alveoli. T-cells are implicated as playing a role in the modulation of the aberrant response leading to excessive tissue damage and, eventually, ARDS. Complementarity Determining Region 3 (CDR3) sequences derived from T-cells are key players in the adaptive immune response. This response is governed by an elaborate specificity for distinct molecules and the ability to recognize and vigorously respond to repeated exposures to the same molecules. Most of the diversity in T-cell receptors (TCRs) is contained in the CDR3 regions of the heterodimeric cell-surface receptors. For this study, we employed the novel technology of immune sequencing to assess lung edema fluid. Our goal was to explore the landscape of CDR3 clonal sequences found within these samples. We obtained more than 3615 CDR3 sequences across samples in the study. Our data demonstrate that: (1) CDR3 sequences from lung edema fluid exhibit distinct clonal populations, and (2) CDR3 sequences can be further characterized based on biochemical features. Analysis of these CDR3 sequences offers insight into the CDR3-driven T-cell repertoire of ARDS. These findings represent the first step towards applications of this technology with these types of biological samples in the context of ARDS.
Collapse
Affiliation(s)
- Sara Hey
- Department of Biology, University of Dallas, Irving, TX 75062, USA
| | - Dayjah Whyte
- Department of Biology, University of Dallas, Irving, TX 75062, USA
| | - Minh-Chau Hoang
- Department of Biology, University of Dallas, Irving, TX 75062, USA
| | - Nick Le
- Department of Biology, University of Dallas, Irving, TX 75062, USA
| | - Joseph Natvig
- Department of Biology, University of Dallas, Irving, TX 75062, USA
| | - Claire Wingfield
- Department of Biology, University of Dallas, Irving, TX 75062, USA
| | | | - Judie Howrylak
- Pulmonary, Allergy and Critical Care Division, Penn State Milton S. Hershey Medical Center, Hershey, PA 17033, USA
| | - Inimary T Toby
- Department of Biology, University of Dallas, Irving, TX 75062, USA
| |
Collapse
|
37
|
Kalinina AA, Kazansky DB, Khromykh LM. Recombinant Human Cyclophilin A in Combination with Adoptive T-cell Therapy Improves the Efficacy of Cancer Immunotherapy in Experimental Models in vivo. Biochemistry (Mosc) 2023; 88:590-599. [PMID: 37331705 DOI: 10.1134/s0006297923050024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/08/2023] [Accepted: 02/08/2023] [Indexed: 06/20/2023]
Abstract
Adoptive T-cell therapy (ACT) is successfully applied in cancer treatment; however, its efficiency can be limited by a low viability, short persistence time, and loss of functional activity of T-cells after adoptive transfer. The search for novel immunomodulators that can improve the viability, expansion, and functions of T-cells after their infusion with the minimal side effects could contribute to the development of more efficient and safe ACT strategies. Recombinant human cyclophilin A (rhCypA) is of particular interest in this respect, as it exhibits pleiotropic immunomodulatory activity and stimulates both innate and adaptive anti-tumor immunity. Here, we evaluated the effect of rhCypA on the efficacy of ACT in the mouse EL4 lymphoma model. Lymphocytes from transgenic 1D1a mice with an inborn pool of EL4-specific T-cells were used as a source of tumor-specific T-cells for ACT. In models of immunocompetent and immunodeficient transgenic mice, the course (3 days) rhCypA administration was shown to significantly stimulate EL4 rejection and prolong the overall survival of tumor-bearing mice after adoptive transfer of lowered doses of transgenic 1D1a cells. Our studies showed that rhCypA significantly improved the efficacy of ACT by enhancing the effector functions of tumor-specific cytotoxic T-cells. These findings open up the prospects for the development of innovative strategies of adoptive T-cell immunotherapy for cancer using rhCypA as an alternative to existing cytokine therapies.
Collapse
Affiliation(s)
- Anastasiia A Kalinina
- N. N. Blokhin National Medical Research Center of Oncology, Ministry of Health of the Russian Federation, Moscow, 115478, Russia.
| | - Dmitry B Kazansky
- N. N. Blokhin National Medical Research Center of Oncology, Ministry of Health of the Russian Federation, Moscow, 115478, Russia
| | - Ludmila M Khromykh
- N. N. Blokhin National Medical Research Center of Oncology, Ministry of Health of the Russian Federation, Moscow, 115478, Russia
| |
Collapse
|
38
|
Yarza R, Bover M, Herrera-Juarez M, Rey-Cardenas M, Paz-Ares L, Lopez-Martin JA, Haanen J. Efficacy of T-Cell Receptor-Based Adoptive Cell Therapy in Cutaneous Melanoma: A Meta-Analysis. Oncologist 2023:7111821. [PMID: 37036865 DOI: 10.1093/oncolo/oyad078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 02/21/2023] [Indexed: 04/11/2023] Open
Abstract
BACKGROUND T-cell receptor (TCR-T) therapies are based on the expression of an introduced TCR targeting a tumor associated antigen (TAA) which has been studied in several trials in cutaneous melanoma. We conducted a systematic review and meta-analysis aiming to assess the primary efficacy of TCR-based adoptive cell therapy in cutaneous melanoma. METHODS We searched through PubMed electronic database from its inception until May 21, 2022. Primary endpoints were pooled objective response rate (ORR) and disease control rate (DCR). We conducted logistic regression analyses to identify potential predictive factors for tumor response. RESULTS From 187 patients, 50 showed an objective response (pooled ORR 28%; 95% CI, 20%-37%) and a pooled DCR of 38% (95% CI, 27%-50%). Median PFS was 2, 9 months (95% CI, 1.4-3.1). A trend toward higher PFS was demonstrated for patients treated with cancer/testis antigens targeting TCR-T cells (HR 0.91 95% CI, 0.64-1.3, P = .61) among whom, patients treated with NYESO-1 targeting TCR-T showed a significantly higher PFS (HR 0.63 95% CI, 0.64-0.98, P = .03). In addition, the number of infused cells was associated with a significantly higher likelihood of tumor response (OR 6.61; 95% CI, 1.68-21.6; P = .007). CONCLUSION TCR-T therapy shows promising results in terms of antitumor activity and survival similar to those reported for TILs with a significantly higher benefit for cancer/testis antigens targeting cells. Since TCR-based therapy shows advantages of great potential over classic ACT strategies, further research in solid cancers is warranted (PROSPERO ID CRD42022328011).
Collapse
Affiliation(s)
- Ramon Yarza
- Department of Medical Oncology, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Mateo Bover
- Department of Medical Oncology, Hospital Universitario 12 de Octubre, Madrid, Spain
| | | | | | - Luis Paz-Ares
- Department of Medical Oncology, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Jose A Lopez-Martin
- Virology and Inflammation Unit, PharmaMar, SA, Madrid, Spain
- GETICA (Spanish Group for Cancer Immuno-Biotherapies), Madrid, Spain
| | - John Haanen
- Division of Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| |
Collapse
|
39
|
Pettmann J, Awada L, Różycki B, Huhn A, Faour S, Kutuzov M, Limozin L, Weikl TR, van der Merwe PA, Robert P, Dushek O. Mechanical forces impair antigen discrimination by reducing differences in T-cell receptor/peptide-MHC off-rates. EMBO J 2023; 42:e111841. [PMID: 36484367 PMCID: PMC10068313 DOI: 10.15252/embj.2022111841] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 11/08/2022] [Accepted: 11/16/2022] [Indexed: 12/13/2022] Open
Abstract
T cells use their T-cell receptors (TCRs) to discriminate between lower-affinity self and higher-affinity foreign peptide major-histocompatibility-complexes (pMHCs) based on the TCR/pMHC off-rate. It is now appreciated that T cells generate mechanical forces during this process but how force impacts the TCR/pMHC off-rate remains debated. Here, we measured the effect of mechanical force on the off-rate of multiple TCR/pMHC interactions. Unexpectedly, we found that lower-affinity TCR/pMHCs with faster solution off-rates were more resistant to mechanical force (weak slip or catch bonds) than higher-affinity interactions (strong slip bonds). This was confirmed by molecular dynamics simulations. Consistent with these findings, we show that the best-characterized catch bond, involving the OT-I TCR, has a low affinity and an exceptionally fast solution off-rate. Our findings imply that reducing forces on the TCR/pMHC interaction improves antigen discrimination, and we suggest a role for the adhesion receptors CD2 and LFA-1 in force-shielding the TCR/pMHC interaction.
Collapse
Affiliation(s)
| | - Lama Awada
- Laboratoire Adhesion et InflammationAix Marseille University UM 61, INSERM UMRS 1067, CNRS UMR 7333MarseilleFrance
| | | | - Anna Huhn
- Sir William Dunn School of PathologyUniversity of OxfordOxfordUK
| | - Sara Faour
- Laboratoire Adhesion et InflammationAix Marseille University UM 61, INSERM UMRS 1067, CNRS UMR 7333MarseilleFrance
| | - Mikhail Kutuzov
- Sir William Dunn School of PathologyUniversity of OxfordOxfordUK
| | - Laurent Limozin
- Laboratoire Adhesion et InflammationAix Marseille University UM 61, INSERM UMRS 1067, CNRS UMR 7333MarseilleFrance
| | - Thomas R Weikl
- Max Planck Institute of Colloids and InterfacesPotsdamGermany
| | | | - Philippe Robert
- Laboratoire Adhesion et InflammationAix Marseille University UM 61, INSERM UMRS 1067, CNRS UMR 7333MarseilleFrance
- Assistance Publique‐Hôpitaux de MarseilleMarseilleFrance
| | - Omer Dushek
- Sir William Dunn School of PathologyUniversity of OxfordOxfordUK
| |
Collapse
|
40
|
Liu S, Bush WS, Miskimen K, Gonzalez-Vicente A, Bailey JNC, Konidari I, McCauley JL, Sedor JR, O'Toole JF, Crawford DC. T-cell receptor diversity in minimal change disease in the NEPTUNE study. Pediatr Nephrol 2023; 38:1115-1126. [PMID: 35943576 PMCID: PMC10037226 DOI: 10.1007/s00467-022-05696-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 07/15/2022] [Accepted: 07/15/2022] [Indexed: 11/28/2022]
Abstract
BACKGROUND Minimal change disease (MCD) is the major cause of childhood idiopathic nephrotic syndrome, which is characterized by massive proteinuria and debilitating edema. Proteinuria in MCD is typically rapidly reversible with corticosteroid therapy, but relapses are common, and children often have many adverse events from the repeated courses of immunosuppressive therapy. The pathobiology of MCD remains poorly understood. Prior clinical observations suggest that abnormal T-cell function may play a central role in MCD pathogenesis. Based on these observations, we hypothesized that T-cell responses to specific exposures or antigens lead to a clonal expansion of T-cell subsets, a restriction in the T-cell repertoire, and an elaboration of specific circulating factors that trigger disease onset and relapses. METHODS To test these hypotheses, we sequenced T-cell receptors in fourteen MCD, four focal segmental glomerulosclerosis (FSGS), and four membranous nephropathy (MN) patients with clinical data and blood samples drawn during active disease and during remission collected by the Nephrotic Syndrome Study Network (NEPTUNE). We calculated several T-cell receptor diversity metrics to assess possible differences between active disease and remission states in paired samples. RESULTS Median productive clonality did not differ between MCD active disease (0.0083; range: 0.0042, 0.0397) and remission (0.0088; range: 0.0038, 0.0369). We did not identify dominant clonotypes in MCD active disease, and few clonotypes were shared with FSGS and MN patients. CONCLUSIONS While these data do not support an obvious role of the adaptive immune system T-cells in MCD pathogenesis, further study is warranted given the limited sample size. A higher resolution version of the Graphical abstract is available as Supplementary information.
Collapse
Affiliation(s)
- Shiying Liu
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - William S Bush
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Kristy Miskimen
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Agustin Gonzalez-Vicente
- Glickman Urological and Kidney Disease and Lerner Research Institutes, Cleveland Clinic, Cleveland, OH, USA
| | - Jessica N Cooke Bailey
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Ioanna Konidari
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Jacob L McCauley
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - John R Sedor
- Glickman Urological and Kidney Disease and Lerner Research Institutes, Cleveland Clinic, Cleveland, OH, USA
| | - John F O'Toole
- Glickman Urological and Kidney Disease and Lerner Research Institutes, Cleveland Clinic, Cleveland, OH, USA
| | - Dana C Crawford
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA.
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA.
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA.
| |
Collapse
|
41
|
Angelakakis G, Serraneau KS, Barker VR, Callahan BM, Tong WL, Zaman S, Huda TI, Blanck G. TCR gene segment usage and HLA alleles that are associated with cancer survival rates also represent racial disparities. Int J Immunogenet 2023; 50:41-47. [PMID: 36585798 DOI: 10.1111/iji.12610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 12/08/2022] [Accepted: 12/13/2022] [Indexed: 01/01/2023]
Abstract
Understanding racial disparities in cancer outcomes continues to be a challenge, with likely many factors at play, including socioeconomic factors and genetic polymorphisms impacting basic cellular and molecular functions. Additionally, it is possible that specific combinations of environment and genetics have specific impacts. T-cell receptor (TCR) gene segment usage, HLA allele combinations have been associated with autoimmune and infectious disease courses, and more recently, TCR gene segment usage, HLA allele combinations have been associated with distinct survival outcomes in cancer as well. We examined several such, previously reported cancer-related TCR gene segment usage, HLA allele combinations for evidence of racial disparities, with regard to the prevalence of the combination in different racial groups. Results indicated that TCR gene segment usage, potentially reflecting environmental factors related to previous pathogen exposure, in combination with certain HLA alleles or independently, may represent a novel explanation for racial disparities in cancer outcomes. Overall, at this point, a genetic connection to racial disparities in cancer outcomes is detectable but remains modest, suggesting that other factors, such as socioeconomic factors, remain as important considerations.
Collapse
Affiliation(s)
- George Angelakakis
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Karisa S Serraneau
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Vayda R Barker
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Blake M Callahan
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Wei Lue Tong
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Saif Zaman
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Taha I Huda
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - George Blanck
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA.,Immunology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| |
Collapse
|
42
|
Gudmundsdottir JA, Thorgeirsdottir S, Lundbäck V, Göngrich C, Lingman Framme J, Kindgren E, Rydenman K, Ludviksson BR, Bjarnadottir H, Runarsdottir S, Nilsson S, Zetterström RH, Ekwall O, Lindgren S. Normal neonatal TREC and KREC levels in early onset juvenile idiopathic arthritis. Clin Immunol 2023; 249:109277. [PMID: 36878420 DOI: 10.1016/j.clim.2023.109277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 01/18/2023] [Accepted: 03/01/2023] [Indexed: 03/07/2023]
Abstract
OBJECTIVE Dysregulated central tolerance predisposes to autoimmune diseases. Reduced thymic output as well as compromised central B cell tolerance checkpoints have been proposed in the pathogenesis of juvenile idiopathic arthritis (JIA). The aim of this study was to investigate neonatal levels of T-cell receptor excision circles (TRECs) and kappa-deleting element excision circles (KRECs), as markers of T- and B-cell output at birth, in patients with early onset JIA. METHODS TRECs and KRECs were quantitated by multiplex qPCR from dried blood spots (DBS), collected 2-5 days after birth, in 156 children with early onset JIA and in 312 matched controls. RESULTS When analysed from neonatal dried blood spots, the median TREC level was 78 (IQR 55-113) in JIA cases and 88 (IQR 57-117) copies/well in controls. The median KREC level was 51 (IQR 35-69) and 53 (IQR 35-74) copies/well, in JIA cases and controls, respectively. Stratification by sex and age at disease onset did not reveal any difference in the levels of TRECs and KRECs. CONCLUSION T- and B-cell output at birth, as measured by TREC and KREC levels in neonatal dried blood spots, does not differ in children with early onset JIA compared to controls.
Collapse
Affiliation(s)
- Judith A Gudmundsdottir
- Children's Medical Center, Landspitali, The National University Hospital, Reykjavik, Iceland
| | - Sigridur Thorgeirsdottir
- Department of Pediatrics, Institute of Clinical Sciences, The Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Veroniqa Lundbäck
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden; Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
| | - Christina Göngrich
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden; Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
| | - Jenny Lingman Framme
- Department of Pediatrics, Institute of Clinical Sciences, The Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden; The Department of Pediatrics, Halland Hospital Halmstad, Halmstad, Region Halland, Sweden
| | - Erik Kindgren
- Division of Pediatrics, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden; Department of Pediatrics, Skaraborgs Hospital Skövde, Region Västra Götaland, Sweden
| | - Karin Rydenman
- Department of Pediatrics, Institute of Clinical Sciences, The Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Bjorn Runar Ludviksson
- Department of Immunology, Landspitali, The National University Hospital of Iceland, Reykjavik, Iceland
| | - Helga Bjarnadottir
- Department of Immunology, Landspitali, The National University Hospital of Iceland, Reykjavik, Iceland
| | - Saga Runarsdottir
- Department of Genetics and Molecular Medicine, Landspitali, The National University Hospital of Iceland, Reykjavik, Iceland
| | - Staffan Nilsson
- Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden; Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Rolf H Zetterström
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden; Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
| | - Olov Ekwall
- Department of Pediatrics, Institute of Clinical Sciences, The Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden; Department of Rheumatology and Inflammation Research, The Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Susanne Lindgren
- Department of Pediatrics, Institute of Clinical Sciences, The Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden; Department of Rheumatology and Inflammation Research, The Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden.
| |
Collapse
|
43
|
Karahan ZS, Aras M, Sütlü T. TCR-NK Cells: A Novel Source for Adoptive Immunotherapy of Cancer. Turk J Haematol 2023; 40:1-10. [PMID: 36719099 PMCID: PMC9979742 DOI: 10.4274/tjh.galenos.2022.2022.0534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2023] Open
Abstract
Antigen-specific retargeting of cytotoxic lymphocytes against tumor-associated antigens has thus far remained largely dependent on chimeric antigen receptors (CARs) that can be constructed by the fusion of an extracellular targeting domain (classically a single-chain variable fragment from an antibody) fused with intracellular signaling domains to trigger activation of T or natural killer (NK) cells. A major limitation of CAR-based therapies is that this technology only allows for the targeting of antigens that would be located on the surface of target cells while non-surface antigens, which affect approximately three-fourths of all human genes, remain out of reach. The targeting of non-surface antigens is only possible using inherent T cell receptor (TCR) mechanisms. However, introducing a second TCR into T cells via genetic modification is problematic due to the heterodimeric nature of the TCR ligand-binding domain, which is composed of TCR α and β chains. It has been observed that the delivery of a second TCR α/β pair may lead to the mispairing of new TCR chains with the endogenously expressed ones and create mixed TCR dimers, and this has negatively affected the advancement of TCR-based T cell therapies. Recently, NK cells have been put forward as possible effectors for TCR gene therapy. Since NK cells do not endogenously express TCR chains, this seems to be an infallible approach to circumventing the problem of mispairing. Moreover, the similarity of intracellular signaling pathways and mechanisms of cytotoxicity between NK and T cells ensures that the triggering of antigen-specific responses by the TCR/CD3 complex can be used to induce antigen-specific cytotoxicity by TCR-modified NK (TCR-NK) cells. This review provides an overview of the initial studies of TCR-NK cells, identifies open questions in the field, and defines the place of this approach within the spectrum of adoptive immunotherapy techniques that rely on cytotoxic lymphocytes.
Collapse
Affiliation(s)
- Zeynep Sena Karahan
- Boğaziçi University Faculty of Arts and Sciences, Department of Molecular Biology and Genetics, İstanbul, Türkiye
| | - Mertkaya Aras
- Boğaziçi University Faculty of Arts and Sciences, Department of Molecular Biology and Genetics, İstanbul, Türkiye,Sabancı University Faculty of Engineering and Natural Sciences, Department of Molecular Biology, Genetics, and Bioengineering, İstanbul, Türkiye
| | - Tolga Sütlü
- Boğaziçi University Faculty of Arts and Sciences, Department of Molecular Biology and Genetics, İstanbul, Türkiye,* Address for Correspondence: Boğaziçi University Faculty of Arts and Sciences, Department of Molecular Biology and Genetics, İstanbul, Türkiye E-mail:
| |
Collapse
|
44
|
Chen IC, Chen HH, Jiang YH, Hsiao TH, Ko TM, Chao WC. Whole transcriptome analysis to explore the impaired immunological features in critically ill elderly patients with sepsis. J Transl Med 2023; 21:141. [PMID: 36823620 PMCID: PMC9951485 DOI: 10.1186/s12967-023-04002-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 02/16/2023] [Indexed: 02/25/2023] Open
Abstract
BACKGROUND Sepsis is a frequent complication in critically ill patients, is highly heterogeneous and is associated with high morbidity and mortality rates, especially in the elderly population. Utilizing RNA sequencing (RNA-Seq) to analyze biological pathways is widely used in clinical and molecular genetic studies, but studies in elderly patients with sepsis are still lacking. Hence, we investigated the mortality-relevant biological features and transcriptomic features in elderly patients who were admitted to the intensive care unit (ICU) for sepsis. METHODS We enrolled 37 elderly patients with sepsis from the ICU at Taichung Veterans General Hospital. On day-1 and day-8, clinical and laboratory data, as well as blood samples, were collected for RNA-Seq analysis. We identified the dynamic transcriptome and enriched pathways of differentially expressed genes between day-8 and day-1 through DVID enrichment analysis and Gene Set Enrichment Analysis. Then, the diversity of the T cell repertoire was analyzed with MiXCR. RESULTS Overall, 37 patients had sepsis, and responders and non-responders were grouped through principal component analysis. Significantly higher SOFA scores at day-7, longer ventilator days, ICU lengths of stay and hospital mortality were found in the non-responder group, than in the responder group. On day-8 in elderly ICU patients with sepsis, genes related to innate immunity and inflammation, such as ZDHCC19, ALOX15, FCER1A, HDC, PRSS33, and PCSK9, were upregulated. The differentially expressed genes (DEGs) were enriched in the regulation of transcription, adaptive immune response, immunoglobulin production, negative regulation of transcription, and immune response. Moreover, there was a higher diversity of T-cell receptors on day-8 in the responder group, than on day-1, indicating that they had better regulated recovery from sepsis compared with the non-response patients. CONCLUSION Sepsis mortality and incidence were both high in elderly individuals. We identified mortality-relevant biological features and transcriptomic features with functional pathway and MiXCR analyses based on RNA-Seq data; and found that the responder group had upregulated innate immunity and increased T cell diversity; compared with the non-responder group. RNA-Seq may be able to offer additional complementary information for the accurate and early prediction of treatment outcome.
Collapse
Affiliation(s)
- I-Chieh Chen
- grid.410764.00000 0004 0573 0731Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Hsin-Hua Chen
- grid.410764.00000 0004 0573 0731Division of General Internal Medicine, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan ,grid.260542.70000 0004 0532 3749Big Data Center, National Chung Hsing University, Taichung, Taiwan ,grid.265231.10000 0004 0532 1428Department of Industrial Engineering and Enterprise Information, Tunghai University, Taichung, Taiwan ,grid.260542.70000 0004 0532 3749Institute of Biomedical Science and Rong Hsing Research Centre for Translational Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Yu-Han Jiang
- grid.410764.00000 0004 0573 0731Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Tzu-Hung Hsiao
- grid.410764.00000 0004 0573 0731Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan ,grid.256105.50000 0004 1937 1063Department of Public Health, Fu Jen Catholic University, New Taipei City, Taiwan ,grid.260542.70000 0004 0532 3749Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan
| | - Tai-Ming Ko
- grid.260539.b0000 0001 2059 7017Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan ,grid.260539.b0000 0001 2059 7017Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan ,grid.28665.3f0000 0001 2287 1366Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Wen-Cheng Chao
- Big Data Center, National Chung Hsing University, Taichung, Taiwan. .,Department of Critical Care Medicine, Taichung Veterans General Hospital, No. 1650 Taiwan Boulevard, Section 4, Xitun District, Taichung City, 40705, Taiwan. .,Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung, Taiwan. .,Department of Automatic Control Engineering, Feng Chia University, Taichung, Taiwan.
| |
Collapse
|
45
|
Groenen PJTA, van den Brand M, Kroeze LI, Amir AL, Hebeda KM. Read the clonotype: Next-generation sequencing-based lymphocyte clonality analysis and perspectives for application in pathology. Front Oncol 2023; 13:1107171. [PMID: 36845702 PMCID: PMC9945094 DOI: 10.3389/fonc.2023.1107171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 01/19/2023] [Indexed: 02/10/2023] Open
Abstract
Clonality assessment using the unique rearrangements of immunoglobulin (IG) and T-cell receptor (TR) genes in lymphocytes is a widely applied supplementary test for the diagnosis of B-cell and T-cell lymphoma. To enable a more sensitive detection and a more precise comparison of clones compared with conventional clonality analysis based on fragment analysis, the EuroClonality NGS Working Group developed and validated a next-generation sequencing (NGS)-based clonality assay for detection of the IG heavy and kappa light chain and TR gene rearrangements for formalin-fixed and paraffin-embedded tissues. We outline the features and advantages of NGS-based clonality detection and discuss potential applications for NGS-based clonality testing in pathology, including site specific lymphoproliferations, immunodeficiency and autoimmune disease and primary and relapsed lymphomas. Also, we briefly discuss the role of T-cell repertoire of reactive lymphocytic infiltrations in solid tumors and B-lymphoma.
Collapse
Affiliation(s)
- Patricia J. T. A. Groenen
- Department of Pathology, Radboud University Medical Center, Nijmegen, Netherlands,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands,*Correspondence: Patricia J. T. A. Groenen,
| | - Michiel van den Brand
- Department of Pathology, Radboud University Medical Center, Nijmegen, Netherlands,Pathology-DNA, Location Rijnstate Hospital, Arnhem, Netherlands
| | - Leonie I. Kroeze
- Department of Pathology, Radboud University Medical Center, Nijmegen, Netherlands,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Avital L. Amir
- Department of Pathology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Konnie M. Hebeda
- Department of Pathology, Radboud University Medical Center, Nijmegen, Netherlands
| |
Collapse
|
46
|
Zou J, Li B, Li D, Bao HF, She CH, Ye JF, Cai JF, Guan JL. Comprehensive analysis of T-cell receptor repertoires reveals antigen-driven T-cell clusters in patients with Behçet's syndrome. Eur J Immunol 2023; 53:e2250181. [PMID: 36747316 DOI: 10.1002/eji.202250181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 01/23/2023] [Accepted: 01/31/2023] [Indexed: 02/08/2023]
Abstract
T lymphocytes are the major components of adaptive immunity in Behçet's syndrome (BS) pathology. However, the precise mechanism of T-cell-induced inflammatory condition remains to be determined. We applied bulk sequencing of the T-cell receptor (TCR) β chain in peripheral blood samples from 45 patients with BS and 10 healthy donors as controls. TCR repertoires in BS patients displayed more clonality and less diversity than in healthy donors. Male patients exhibited lower diversity metrics of TCR and had a larger proportion in the top 10 clones than females (p = 0.016). There were no TCR clonality differences in other clinical features, such as age, disease duration, organ involvement, disease severity, and activity. By "Grouping of Lymphocyte Interactions by Paratope Hotspots" (GLIPH2) for antigen prediction, we found distinct 2477 clusters of TCR-β sequences that potentially recognize similar antigens shared between BS patients. We observed clonal T-cell expansion in BS patients. Sexual differences in TCR clonal expansion and public TCR groups deserve further study to reveal the underline T-cell-mediated immunity in BS.
Collapse
Affiliation(s)
- Jun Zou
- Division of Rheumatology and Immunology, Huadong Hospital Affiliated to Fudan University, Shanghai, China
| | - Bin Li
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University, Shanghai, China
| | - Dan Li
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University, Shanghai, China
| | - Hua-Fang Bao
- Division of Rheumatology and Immunology, Huadong Hospital Affiliated to Fudan University, Shanghai, China
| | - Chun-Hui She
- Division of Rheumatology and Immunology, Huadong Hospital Affiliated to Fudan University, Shanghai, China
| | - Jing-Fen Ye
- Division of Rheumatology and Immunology, Huadong Hospital Affiliated to Fudan University, Shanghai, China
| | - Jian-Fei Cai
- Division of Rheumatology and Immunology, Huadong Hospital Affiliated to Fudan University, Shanghai, China
| | - Jian-Long Guan
- Division of Rheumatology and Immunology, Huadong Hospital Affiliated to Fudan University, Shanghai, China
| |
Collapse
|
47
|
Geller S, Tel-Dan SF, Solar I, Sprecher E, Goldberg I. T-Cell Monoclonality in the Blood and the Skin Correlates With Poor Response to Treatment in Mycosis Fungoides. Clin Lymphoma Myeloma Leuk 2023; 23:123-6. [PMID: 36424279 DOI: 10.1016/j.clml.2022.10.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 10/30/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND The prognostic value of skin and blood T-cell receptor clonality in mycosis fungoides is a matter of debate. Our aim was to ascertain the relation between the presence of a monoclonal T-cell population in the blood and in the skin with response to treatment in patients with mycosis fungoides. PATIENTS AND METHODS Clinical features and follow-up data were retrospectively collected and analyzed in 94 patients with mycosis fungoides seen at a cutaneous lymphoma clinic in a single tertiary center. All patients had results of polymerase chain reaction analysis of T-cell receptor gamma gene rearrangement in lesional skin and in peripheral blood at time of diagnosis. Association of response to treatment with clonality in the tissue and in the blood was assessed. RESULTS T-cell monoclonality was detected in the skin in 30 of 94 patients, in the blood in 12 of 94 cases and the same clone was found in both tissues in 6 of 94 patients. The presence of a polyclonal T-cell population in the circulation was associated with complete response (P = .006). Lack of response to treatment (stable disease or progression of disease) was associated with T-cell clonality in skin (P = .009), in blood (P = .002) and in both tissues (P < .001). A multivariate analysis showed that T-cell monoclonality in the skin is independently associated with lack of response of mycosis fungoides to therapy. CONCLUSION Blood and skin should be studied for T-cell clonality as part of the routine initial workup, even in patients with early-stage disease.
Collapse
|
48
|
Farquhar R, Van Rhijn I, Moody DB, Rossjohn J, Shahine A. αβ T-cell receptor recognition of self-phosphatidylinositol presented by CD1b. J Biol Chem 2023; 299:102849. [PMID: 36587766 PMCID: PMC9900620 DOI: 10.1016/j.jbc.2022.102849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 12/21/2022] [Accepted: 12/23/2022] [Indexed: 12/31/2022] Open
Abstract
CD1 glycoproteins present lipid-based antigens to T-cell receptors (TCRs). A role for CD1b in T-cell-mediated autoreactivity was proposed when it was established that CD1b can present self-phospholipids with short alkyl chains (∼C34) to T cells; however, the structural characteristics of this presentation and recognition are unclear. Here, we report the 1.9 Å resolution binary crystal structure of CD1b presenting a self-phosphatidylinositol-C34:1 and an endogenous scaffold lipid. Moreover, we also determined the 2.4 Å structure of CD1b-phosphatidylinositol complexed to an autoreactive αβ TCR, BC8B. We show that the TCR docks above CD1b and directly contacts the presented antigen, selecting for both the phosphoinositol headgroup and glycerol neck region via antigen remodeling within CD1b and allowing lateral escape of the inositol moiety through a channel formed by the TCR α-chain. Furthermore, through alanine scanning mutagenesis and surface plasmon resonance, we identified key CD1b residues mediating this interaction, with Glu-80 abolishing TCR binding. We in addition define a role for both CD1b α1 and CD1b α2 molecular domains in modulating this interaction. These findings suggest that the BC8B TCR contacts both the presented phospholipid and the endogenous scaffold lipid via a dual mechanism of corecognition. Taken together, these data expand our understanding into the molecular mechanisms of CD1b-mediated T-cell autoreactivity.
Collapse
Affiliation(s)
- Rachel Farquhar
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Ildiko Van Rhijn
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA; Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - D Branch Moody
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Jamie Rossjohn
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia; Institute of Infection and Immunity, Cardiff University, School of Medicine, Cardiff, United Kingdom.
| | - Adam Shahine
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
| |
Collapse
|
49
|
Bensouda Koraichi M, Ferri S, Walczak AM, Mora T. Inferring the T cell repertoire dynamics of healthy individuals. Proc Natl Acad Sci U S A 2023; 120:e2207516120. [PMID: 36669107 DOI: 10.1073/pnas.2207516120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The adaptive immune system is a diverse ecosystem that responds to pathogens by selecting cells with specific receptors. While clonal expansion in response to particular immune challenges has been extensively studied, we do not know the neutral dynamics that drive the immune system in the absence of strong stimuli. Here, we learn the parameters that underlie the clonal dynamics of the T cell repertoire in healthy individuals of different ages, by applying Bayesian inference to longitudinal immune repertoire sequencing (RepSeq) data. Quantifying the experimental noise accurately for a given RepSeq technique allows us to disentangle real changes in clonal frequencies from noise. We find that the data are consistent with clone sizes following a geometric Brownian motion and show that its predicted steady state is in quantitative agreement with the observed power-law behavior of the clone-size distribution. The inferred turnover time scale of the repertoire increases with patient age and depends on the clone size in some individuals.
Collapse
|
50
|
Marrone L, D'Agostino M, Cesaro E, di Giacomo V, Urzini S, Romano MF, Romano S. Alternative splicing of FKBP5 gene exerts control over T lymphocyte expansion. J Cell Biochem 2023. [PMID: 36645880 DOI: 10.1002/jcb.30364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 11/15/2022] [Accepted: 12/15/2022] [Indexed: 01/18/2023]
Abstract
FKBP51 is constitutively expressed by immune cells. As other FKBP family members, FKBP51 acts as a coreceptor for the natural products FK506 and rapamycin, which exhibit immunosuppressive effects. However, little is known about the intrinsic role of this large FKBP in the primary function of lymphocytes, that is, the adaptive immune response against foreign antigens, for example, pathogens. This paper aimed to investigate whether FKBP51 expression was modulated during lymphocyte activation. Moreover, as we recently identified a splicing isoform of FKBP51, namely FKBP51s, we also measured this splice protein, along with the canonical one, at different times of a peripheral blood mononuclear cell culture stimulated via T cell receptor. Our results show that the two FKBP51 isoforms were alternatively induced during the proliferative burst. Canonical FKBP51 increased in the time window between 48 and 96 h and its expression levels correlated with cyclin D levels. FKBP51s transiently increased earlier, at 24-36 h to reappearing later, at 120 h, when cyclin D expression returned at resting levels and proliferation ceased. Interestingly, within these two specific timeframes, FKBP51s accumulated in the nucleus. Here FKBP51s colocalized with the Foxp3 transcription factor at 36 h. Regulatory T cell (Treg) counts significantly decreased when FKBP51s was downmodulated. The coculture suppression assay suggested that FKBP51s supports the suppressive capability of Tregs. At 120 h, chromatin immunoprecipitation experiments found FKBP51s linked to CCND1 gene, suggesting a possible effect on gene transcription regulation, as previously demonstrated in melanoma. In conclusion, our study shows that FKBP5 isoforms are upregulated during lymphocyte activation, albeit on different timeframes. The activation of canonical FKBP51 coincides with proliferation hallmarks; FKBP5 splicing occurs early to sustain Treg development and late when proliferation ceases.
Collapse
Affiliation(s)
- Laura Marrone
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Massimo D'Agostino
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Elena Cesaro
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Valeria di Giacomo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Simona Urzini
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Maria Fiammetta Romano
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Simona Romano
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| |
Collapse
|