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Fuchs KJ, van de Meent M, Honders MW, Khatri I, Kester MGD, Koster EAS, Koutsoumpli G, de Ru AH, van Bergen CAM, van Veelen PA, 't Hoen PAC, van Balen P, van den Akker EB, Veelken JH, Halkes CJM, Falkenburg JHF, Griffioen M. Expanding the repertoire reveals recurrent, cryptic, and hematopoietic HLA class I minor histocompatibility antigens. Blood 2024; 143:1856-1872. [PMID: 38427583 DOI: 10.1182/blood.2023022343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 02/15/2024] [Accepted: 02/15/2024] [Indexed: 03/03/2024] Open
Abstract
ABSTRACT Allogeneic stem cell transplantation (alloSCT) is a curative treatment for hematological malignancies. After HLA-matched alloSCT, antitumor immunity is caused by donor T cells recognizing polymorphic peptides, designated minor histocompatibility antigens (MiHAs), that are presented by HLA on malignant patient cells. However, T cells often target MiHAs on healthy nonhematopoietic tissues of patients, thereby inducing side effects known as graft-versus-host disease. Here, we aimed to identify the dominant repertoire of HLA-I-restricted MiHAs to enable strategies to predict, monitor or modulate immune responses after alloSCT. To systematically identify novel MiHAs by genome-wide association screening, T-cell clones were isolated from 39 transplanted patients and tested for reactivity against 191 Epstein-Barr virus transformed B cell lines of the 1000 Genomes Project. By discovering 81 new MiHAs, we more than doubled the antigen repertoire to 159 MiHAs and demonstrated that, despite many genetic differences between patients and donors, often the same MiHAs are targeted in multiple patients. Furthermore, we showed that one quarter of the antigens are cryptic, that is translated from unconventional open reading frames, for example long noncoding RNAs, showing that these antigen types are relevant targets in natural immune responses. Finally, using single cell RNA-seq data, we analyzed tissue expression of MiHA-encoding genes to explore their potential role in clinical outcome, and characterized 11 new hematopoietic-restricted MiHAs as potential targets for immunotherapy. In conclusion, we expanded the repertoire of HLA-I-restricted MiHAs and identified recurrent, cryptic and hematopoietic-restricted antigens, which are fundamental to predict, follow or manipulate immune responses to improve clinical outcome after alloSCT.
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Affiliation(s)
- Kyra J Fuchs
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Marian van de Meent
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - M Willy Honders
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Indu Khatri
- Department of Immunology, Leiden University Medical Center, Leiden, The Netherlands
| | - Michel G D Kester
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Eva A S Koster
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Georgia Koutsoumpli
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Arnoud H de Ru
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Peter A van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter A C 't Hoen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Peter van Balen
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Erik B van den Akker
- Center for Computational Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - J Hendrik Veelken
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | | | | | - Marieke Griffioen
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
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2
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Dabiri H, Habibi-Anbouhi M, Ziaei V, Moghadasi Z, Sadeghizadeh M, Hajizadeh-Saffar E. Candidate Biomarkers for Targeting in Type 1 Diabetes; A Bioinformatic Analysis of Pancreatic Cell Surface Antigens. Cell J 2024; 26:51-61. [PMID: 38351729 PMCID: PMC10864774 DOI: 10.22074/cellj.2023.1996297.1262] [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] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 08/27/2023] [Accepted: 10/24/2023] [Indexed: 02/18/2024]
Abstract
OBJECTIVE Type 1 diabetes (T1Ds) is an autoimmune disease in which the immune system invades and destroys insulin-producing cells. Nevertheless, at the time of diagnosis, about 30-40% of pancreatic beta cells are healthy and capable of producing insulin. Bi-specific antibodies, chimeric antigen receptor regulatory T cells (CAR-Treg cells), and labeled antibodies could be a new emerging option for the treatment or diagnosis of type I diabetic patients. The aim of the study is to choose appropriate cell surface antigens in the pancreas tissue for generating an antibody for type I diabetic patients. MATERIALS AND METHODS In this bioinformatics study, we extracted pancreas-specific proteins from two large databases; the Human Protein Atlas (HPA) and Genotype-Tissue Expression (GTEx) Portal. Pancreatic-enriched genes were chosen and narrowed down by Protter software for the investigation of accessible extracellular domains. The immunohistochemistry (IHC) data of the protein atlas database were used to evaluate the protein expression of selected antigens. We explored the function of candidate antigens by using the GeneCards database to evaluate the potential dysfunction or activation/hyperactivation of antigens after antibody binding. RESULTS The results showed 429 genes are highly expressed in the pancreas tissue. Also, eighteen genes encoded plasma membrane proteins that have high expression in the microarray (GEO) dataset. Our results introduced four structural proteins, including NPHS1, KIRREL2, GP2, and CUZD1, among all seventeen candidate proteins. CONCLUSION The presented antigens can potentially be used to produce specific pancreatic antibodies that guide CARTreg, bi-specific, or labeling molecules to the pancreas for treatment, detection, or other molecular targeted therapy scopes for type I diabetes.
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Affiliation(s)
- Hamed Dabiri
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | | | - Vahab Ziaei
- National Cell Bank of Iran, Pasteur Institute of Iran, Tehran, Iran
| | - Zahra Moghadasi
- National Cell Bank of Iran, Pasteur Institute of Iran, Tehran, Iran
| | - Majid Sadeghizadeh
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
| | - Ensiyeh Hajizadeh-Saffar
- Department of Regenerative Medicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.
- Advanced Therapy Medicinal Product Technology Development Center (ATMP-TDC), Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
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3
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Meeuwsen MH, Wouters AK, Wachsmann TLA, Hagedoorn RS, Kester MGD, Remst DFG, van der Steen DM, de Ru AH, van Hees EP, Kremer M, Griffioen M, van Veelen PA, Falkenburg JHF, Heemskerk MHM. Broadly applicable TCR-based therapy for multiple myeloma targeting the immunoglobulin J chain. J Hematol Oncol 2023; 16:16. [PMID: 36850001 PMCID: PMC9969645 DOI: 10.1186/s13045-023-01408-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 02/09/2023] [Indexed: 03/01/2023] Open
Abstract
BACKGROUND The immunoglobulin J chain (Jchain) is highly expressed in the majority of multiple myeloma (MM), and Jchain-derived peptides presented in HLA molecules may be suitable antigens for T-cell therapy of MM. METHODS Using immunopeptidomics, we identified Jchain-derived epitopes presented by MM cells, and pHLA tetramer technology was used to isolate Jchain-specific T-cell clones. RESULTS We identified T cells specific for Jchain peptides presented in HLA-A1, -A24, -A3, and -A11 that recognized and lysed JCHAIN-positive MM cells. TCRs of the most promising T-cell clones were sequenced, cloned into retroviral vectors, and transferred to CD8 T cells. Jchain TCR T cells recognized target cells when JCHAIN and the appropriate HLA restriction alleles were expressed, while JCHAIN or HLA-negative cells, including healthy subsets, were not recognized. Patient-derived JCHAIN-positive MM samples were also lysed by Jchain TCR T cells. In a preclinical in vivo model for established MM, Jchain-A1, -A24, -A3, and -A11 TCR T cells strongly eradicated MM cells, which resulted in 100-fold lower tumor burden in Jchain TCR versus control-treated mice. CONCLUSIONS We identified TCRs targeting Jchain-derived peptides presented in four common HLA alleles. All four TCRs demonstrated potent preclinical anti-myeloma activity, encouraging further preclinical testing and ultimately clinical development.
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Affiliation(s)
- Miranda H Meeuwsen
- Department of Hematology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Anne K Wouters
- Department of Hematology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Tassilo L A Wachsmann
- Department of Hematology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Renate S Hagedoorn
- Department of Hematology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Michel G D Kester
- Department of Hematology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Dennis F G Remst
- Department of Hematology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Dirk M van der Steen
- Department of Hematology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Arnoud H de Ru
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Els P van Hees
- Department of Hematology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Martijn Kremer
- Department of Hematology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Marieke Griffioen
- Department of Hematology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Peter A van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - J H Frederik Falkenburg
- Department of Hematology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Mirjam H M Heemskerk
- Department of Hematology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands.
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4
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Meeuwsen MH, Wouters AK, Jahn L, Hagedoorn RS, Kester MG, Remst DF, Morton LT, van der Steen DM, Kweekel C, de Ru AH, Griffioen M, van Veelen PA, Falkenburg JF, Heemskerk MH. A broad and systematic approach to identify B cell malignancy-targeting TCRs for multi-antigen-based T cell therapy. Mol Ther 2022; 30:564-578. [PMID: 34371177 PMCID: PMC8821929 DOI: 10.1016/j.ymthe.2021.08.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 12/16/2020] [Revised: 03/01/2021] [Accepted: 07/20/2021] [Indexed: 02/04/2023] Open
Abstract
CAR T cell therapy has shown great promise for the treatment of B cell malignancies. However, antigen-negative escape variants often cause disease relapse, necessitating the development of multi-antigen-targeting approaches. We propose that a T cell receptor (TCR)-based strategy would increase the number of potential antigenic targets, as peptides from both intracellular and extracellular proteins can be recognized. Here, we aimed to isolate a broad range of promising TCRs targeting multiple antigens for treatment of B cell malignancies. As a first step, 28 target genes for B cell malignancies were selected based on gene expression profiles. Twenty target peptides presented in human leukocyte antigen (HLA)-A∗01:01, -A∗24:02, -B∗08:01, or -B∗35:01 were identified from the immunopeptidome of B cell malignancies and used to form peptide-HLA (pHLA)-tetramers for T cell isolation. Target-peptide-specific CD8 T cells were isolated from HLA-mismatched healthy donors and subjected to a stringent stepwise selection procedure to ensure potency and eliminate cross-reactivity. In total, five T cell clones specific for FCRL5 in HLA-A∗01:01, VPREB3 in HLA-A∗24:02, and BOB1 in HLA-B∗35:01 recognized B cell malignancies. For all three specificities, TCR gene transfer into CD8 T cells resulted in cytokine production and efficient killing of multiple B cell malignancies. In conclusion, using this systematic approach we successfully identified three promising TCRs for T cell therapy against B cell malignancies.
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Affiliation(s)
- Miranda H. Meeuwsen
- Department of Hematology, Leiden University Medical Center, Leiden 2333ZA, the Netherlands,Corresponding author: Miranda H. Meeuwsen, Department of Hematology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands.
| | - Anne K. Wouters
- Department of Hematology, Leiden University Medical Center, Leiden 2333ZA, the Netherlands
| | - Lorenz Jahn
- Department of Hematology, Leiden University Medical Center, Leiden 2333ZA, the Netherlands,Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Renate S. Hagedoorn
- Department of Hematology, Leiden University Medical Center, Leiden 2333ZA, the Netherlands
| | - Michel G.D. Kester
- Department of Hematology, Leiden University Medical Center, Leiden 2333ZA, the Netherlands
| | - Dennis F.G. Remst
- Department of Hematology, Leiden University Medical Center, Leiden 2333ZA, the Netherlands
| | - Laura T. Morton
- Department of Hematology, Leiden University Medical Center, Leiden 2333ZA, the Netherlands
| | - Dirk M. van der Steen
- Department of Hematology, Leiden University Medical Center, Leiden 2333ZA, the Netherlands
| | - Christiaan Kweekel
- Department of Hematology, Leiden University Medical Center, Leiden 2333ZA, the Netherlands
| | - Arnoud H. de Ru
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden 2333ZA, the Netherlands
| | - Marieke Griffioen
- Department of Hematology, Leiden University Medical Center, Leiden 2333ZA, the Netherlands
| | - Peter A. van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden 2333ZA, the Netherlands
| | | | - Mirjam H.M. Heemskerk
- Department of Hematology, Leiden University Medical Center, Leiden 2333ZA, the Netherlands,Corresponding author: Mirjam H.M. Heemskerk, Department of Hematology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands.
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5
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Ma J, Li Q, Ji D, Luo L, Hong L. Predicting candidate therapeutic drugs for sepsis-induced acute respiratory distress syndrome based on transcriptome profiling. Bioengineered 2021; 12:1369-1380. [PMID: 33904373 PMCID: PMC8806268 DOI: 10.1080/21655979.2021.1917981] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/12/2021] [Accepted: 04/12/2021] [Indexed: 01/23/2023] Open
Abstract
Sepsis-induced acute respiratory distress syndrome (ARDS) remains a major threat to human health without effective therapeutic drugs. Previous studies demonstrated the power of gene expression profiling to reveal pathological changes associated with sepsis-induced ARDS. However, there is still a lack of systematic data mining framework for identifying potential targets for treatment. In this study, we demonstrated the feasibility of druggable targets prediction based on gene expression data. Through the functional enrichment analysis of microarray-based expression profiles between sepsis-induced ARDS and non-sepsis ARDS samples, we revealed genes involved in anti-microbial infection immunity were significantly altered in sepsis-induced ARDS. Protein-protein interaction (PPI) network analysis highlighted TOP2A gene as the key regulator in the dysregulated gene network of sepsis-induced ARDS. We were also able to predict several therapeutic drug candidates for sepsis-induced ARDS using Connectivity Map (Cmap) database, among which doxorubicin was identified to interact with TOP2A with a high affinity similar to its endogenous ligand. Overall, our findings suggest that doxorubicin could be a potential therapeutic for sepsis-induced ARDS by targeting TOP2A, which requires further investigation and validation. The whole study relies on publicly available dataset and publicly accessible database or bioinformatic tools for data mining. Therefore, our study benchmarks a workflow for druggable target prediction which can be widely applicable in the search of targets in other pathological conditions.
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Affiliation(s)
- Jiawei Ma
- Department of Critical Care Medicine, The Affiliated Wuxi No.2 People’s Hospital of Nanjing Medical University, Wuxi, China
| | - Qianqian Li
- Department of Critical Care Medicine, The Affiliated Wuxi No.2 People’s Hospital of Nanjing Medical University, Wuxi, China
| | - Dandan Ji
- Department of Critical Care Medicine, The Affiliated Wuxi No.2 People’s Hospital of Nanjing Medical University, Wuxi, China
| | - Liang Luo
- Department of Critical Care Medicine, The Affiliated Wuxi No.2 People’s Hospital of Nanjing Medical University, Wuxi, China
| | - Lei Hong
- Institute of Clinical Medicine Research, The Affiliated Suzhou Science and Technology Town Hospital of Nanjing Medical University, Suzhou, China
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6
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van Balen P, Jedema I, van Loenen MM, de Boer R, van Egmond HM, Hagedoorn RS, Hoogstaten C, Veld SAJ, Hageman L, van Liempt PAG, Zwaginga JJ, Meij P, Veelken H, Falkenburg JHF, Heemskerk MHM. HA-1H T-Cell Receptor Gene Transfer to Redirect Virus-Specific T Cells for Treatment of Hematological Malignancies After Allogeneic Stem Cell Transplantation: A Phase 1 Clinical Study. Front Immunol 2020; 11:1804. [PMID: 32973756 PMCID: PMC7468382 DOI: 10.3389/fimmu.2020.01804] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 12/23/2019] [Accepted: 07/06/2020] [Indexed: 12/16/2022] Open
Abstract
Graft-vs.-leukemia (GVL) reactivity after HLA-matched allogeneic stem cell transplantation (alloSCT) is mainly mediated by donor T cells recognizing minor histocompatibility antigens (MiHA). If MiHA are targeted that are exclusively expressed on hematopoietic cells of recipient origin, selective GVL reactivity without severe graft-vs.-host-disease (GVHD) may occur. In this phase I study we explored HA-1H TCR gene transfer into T cells harvested from the HA-1H negative stem-cell donor to treat HA-1H positive HLA-A*02:01 positive patients with high-risk leukemia after alloSCT. HA-1H is a hematopoiesis-restricted MiHA presented in HLA-A*02:01. Since we previously demonstrated that donor-derived virus-specific T-cell infusions did not result in GVHD, we used donor-derived EBV and/or CMV-specific T-cells to be redirected by HA-1H TCR. EBV and/or CMV-specific T-cells were purified, retrovirally transduced with HA-1H TCR, and expanded. Validation experiments illustrated dual recognition of viral antigens and HA-1H by HA-1H TCR-engineered virus-specific T-cells. Release criteria included products containing more than 60% antigen-specific T-cells. Patients with high risk leukemia following T-cell depleted alloSCT in complete or partial remission were eligible. HA-1H TCR T-cells were infused 8 and 14 weeks after alloSCT without additional pre-conditioning chemotherapy. For 4/9 included patients no appropriate products could be made. Their donors were all CMV-negative, thereby restricting the production process to EBV-specific T-cells. For 5 patients a total of 10 products could be made meeting the release criteria containing 3–280 × 106 virus and/or HA-1H TCR T-cells. No infusion-related toxicity, delayed toxicity or GVHD occurred. One patient with relapsed AML at time of infusions died due to rapidly progressing disease. Four patients were in remission at time of infusion. Two patients died of infections during follow-up, not likely related to the infusion. Two patients are alive and well without GVHD. In 2 patients persistence of HA-1H TCR T-cells could be illustrated correlating with viral reactivation, but no overt in-vivo expansion of infused T-cells was observed. In conclusion, HA-1H TCR-redirected virus-specific T-cells could be made and safely infused in 5 patients with high-risk AML, but overall feasibility and efficacy was too low to warrant further clinical development using this strategy. New strategies will be explored using patient-derived donor T-cells isolated after transplantation transduced with HA-1H-specific TCR to be infused following immune conditioning.
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Affiliation(s)
- Peter van Balen
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | - Inge Jedema
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Renate de Boer
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | - H M van Egmond
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | - Renate S Hagedoorn
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | - Conny Hoogstaten
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | - Sabrina A J Veld
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | - Lois Hageman
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | - P A G van Liempt
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | - Jaap-Jan Zwaginga
- Center for Clinical Transfusion Research, Sanquin Research, Leiden, Netherlands.,Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | - Pauline Meij
- Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, Leiden, Netherlands
| | - H Veelken
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | - J H F Falkenburg
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
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7
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Desterke C, Turhan AG, Bennaceur-Griscelli A, Griscelli F. PPARγ Cistrome Repression during Activation of Lung Monocyte-Macrophages in Severe COVID-19. iScience 2020; 23:101611. [PMID: 33015591 PMCID: PMC7518203 DOI: 10.1016/j.isci.2020.101611] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [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: 07/09/2020] [Revised: 08/06/2020] [Accepted: 09/22/2020] [Indexed: 12/19/2022] Open
Abstract
The molecular mechanisms of cytokine storm in patients with severe COVID-19 infections are poorly understood. To uncover these events, we performed transcriptome analyses of lung biopsies from patients with COVID-19, revealing a gene enrichment pattern similar to that of PPARγ-knockout macrophages. Single-cell gene expression analysis of bronchoalveolar lavage fluids revealed a characteristic trajectory of PPARγ-related disturbance in the CD14+/CD16+ cells. We identified a correlation with the disease severity and the reduced expression of several members of the PPARγ complex such as EP300, RXRA, RARA, SUMO1, NR3C1, and CCDC88A. ChIP-seq analyses confirmed repression of the PPARγ-RXRA-NR3C1 cistrome in COVID-19 lung samples. Further analysis of protein-protein networks highlighted an interaction between the PPARγ-associated protein SUMO1 and a nucleoprotein of the SARS virus. Overall, these results demonstrate for the first time the involvement of the PPARγ complex in severe COVID-19 lung disease and suggest strongly its role in the major monocyte/macrophage-mediated inflammatory storm.
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Affiliation(s)
- Christophe Desterke
- INSERM UA9- University Paris-Saclay, Institut André Lwoff, Bâtiment A CNRS, 7 rue Guy Moquet, 94800 Villejuif, France
| | - Ali G Turhan
- INSERM UA9- University Paris-Saclay, Institut André Lwoff, Bâtiment A CNRS, 7 rue Guy Moquet, 94800 Villejuif, France.,ESTeam Paris Sud, INGESTEM National IPSC Infrastructure, University Paris-Saclay, 94800 Villejuif, France.,Division of Hematology, APHP-Paris Saclay University Hospitals, Le Kremlin Bicêtre 94275, Villejuif 94800, France.,University Paris Saclay, Faculty of Medicine, Le Kremlin Bicêtre 94275, France
| | - Annelise Bennaceur-Griscelli
- INSERM UA9- University Paris-Saclay, Institut André Lwoff, Bâtiment A CNRS, 7 rue Guy Moquet, 94800 Villejuif, France.,ESTeam Paris Sud, INGESTEM National IPSC Infrastructure, University Paris-Saclay, 94800 Villejuif, France.,Division of Hematology, APHP-Paris Saclay University Hospitals, Le Kremlin Bicêtre 94275, Villejuif 94800, France.,University Paris Saclay, Faculty of Medicine, Le Kremlin Bicêtre 94275, France
| | - Frank Griscelli
- INSERM UA9- University Paris-Saclay, Institut André Lwoff, Bâtiment A CNRS, 7 rue Guy Moquet, 94800 Villejuif, France.,ESTeam Paris Sud, INGESTEM National IPSC Infrastructure, University Paris-Saclay, 94800 Villejuif, France.,University of Paris, Faculty Sorbonne Paris Cité, Faculté des Sciences Pharmaceutiques et Biologiques, Paris, France.,Gustave-Roussy Cancer Institute, Department of Biopathology, 94800 Villejuif, France
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8
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Kremer AN, Bausenwein J, Lurvink E, Kremer AE, Rutten CE, van Bergen CAM, Kretschmann S, van der Meijden E, Honders MW, Mazzeo D, Watts C, Mackensen A, Falkenburg JHF, Griffioen M. Discovery and Differential Processing of HLA Class II-Restricted Minor Histocompatibility Antigen LB-PIP4K2A-1S and Its Allelic Variant by Asparagine Endopeptidase. Front Immunol 2020; 11:381. [PMID: 32218783 PMCID: PMC7078166 DOI: 10.3389/fimmu.2020.00381] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 11/22/2019] [Accepted: 02/17/2020] [Indexed: 12/03/2022] Open
Abstract
Minor histocompatibility antigens are the main targets of donor-derived T-cells after allogeneic stem cell transplantation. Identification of these antigens and understanding their biology are a key requisite for more insight into how graft vs. leukemia effect and graft vs. host disease could be separated. We here identified four new HLA class II-restricted minor histocompatibility antigens using whole genome association scanning. For one of the new antigens, i.e., LB-PIP4K2A-1S, we measured strong T-cell recognition of the donor variant PIP4K2A-1N when pulsed as exogenous peptide, while the endogenously expressed variant in donor EBV-B cells was not recognized. We showed that lack of T-cell recognition was caused by intracellular cleavage by a protease named asparagine endopeptidase (AEP). Furthermore, microarray gene expression analysis showed that PIP4K2A and AEP are both ubiquitously expressed in a wide variety of healthy tissues, but that expression levels of AEP were lower in primary acute myeloid leukemia (AML). In line with that, we confirmed low activity of AEP in AML cells and demonstrated that HLA-DRB1*03:01 positive primary AML expressing LB-PIP4K2A-1S or its donor variant PIP4K2A-1N were both recognized by specific T-cells. In conclusion, LB-PIP4K2A-1S not only represents a novel minor histocompatibility antigen but also provides evidence that donor T-cells after allogeneic stem cell transplantation can target the autologous allelic variant as leukemia-associated antigen. Furthermore, it demonstrates that endopeptidases can play a role in cell type-specific intracellular processing and presentation of HLA class II-restricted antigens, which may be explored in future immunotherapy of AML.
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Affiliation(s)
- Anita N Kremer
- Department of Internal Medicine 5, Hematology/Oncology, Friedrich Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Judith Bausenwein
- Department of Internal Medicine 5, Hematology/Oncology, Friedrich Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Ellie Lurvink
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | - Andreas E Kremer
- Department of Internal Medicine 1, Gastroenterology, Pneumology and Endocrinology, Friedrich Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Caroline E Rutten
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Sascha Kretschmann
- Department of Internal Medicine 5, Hematology/Oncology, Friedrich Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Edith van der Meijden
- Department of Internal Medicine 5, Hematology/Oncology, Friedrich Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Maria W Honders
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | - Daniela Mazzeo
- Division of Cell Signaling & Immunology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Colin Watts
- Division of Cell Signaling & Immunology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Andreas Mackensen
- Department of Internal Medicine 5, Hematology/Oncology, Friedrich Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | | | - Marieke Griffioen
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
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9
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Loeff FC, Rijs K, van Egmond EHM, Zoutman WH, Qiao X, Kroes WGM, Veld SAJ, Griffioen M, Vermeer MH, Neefjes J, Frederik Falkenburg JH, Halkes CJM, Jedema I. Loss of the GPI-anchor in B-lymphoblastic leukemia by epigenetic downregulation of PIGH expression. Am J Hematol 2019; 94:93-102. [PMID: 30370942 PMCID: PMC6587464 DOI: 10.1002/ajh.25337] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 10/11/2018] [Accepted: 10/24/2018] [Indexed: 01/08/2023]
Abstract
Adult B-lymphoblastic leukemia (B-ALL) is a hematological malignancy characterized by genetic heterogeneity. Despite successful remission induction with classical chemotherapeutics and novel targeted agents, enduring remission is often hampered by disease relapse due to outgrowth of a pre-existing subclone resistant against the treatment. In this study, we show that small glycophosphatidylinositol (GPI)-anchor deficient CD52-negative B-cell populations are frequently present already at diagnosis in B-ALL patients, but not in patients suffering from other B-cell malignancies. We demonstrate that the GPI-anchor negative phenotype results from loss of mRNA expression of the PIGH gene, which is involved in the first step of GPI-anchor synthesis. Loss of PIGH mRNA expression within these B-ALL cells follows epigenetic silencing rather than gene mutation or deletion. The coinciding loss of CD52 membrane expression may contribute to the development of resistance to alemtuzumab (ALM) treatment in B-ALL patients resulting in the outgrowth of CD52-negative escape variants. Additional treatment with 5-aza-2'-deoxycytidine may restore expression of CD52 and revert ALM resistance.
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Affiliation(s)
- Floris C. Loeff
- Department of Hematology; Leiden University Medical Center; Leiden The Netherlands
| | - Kevin Rijs
- Department of Hematology; Leiden University Medical Center; Leiden The Netherlands
| | | | - Willem H. Zoutman
- Department of Dermatology; Leiden University Medical Center; Leiden The Netherlands
| | - Xiaohang Qiao
- Division of Cell Biology; The Netherlands Cancer Institute; Amsterdam The Netherlands
| | - Wilhelmina G. M. Kroes
- Department of Clinical Genetics; Leiden University Medical Center; Leiden The Netherlands
| | - Sabrina A. J. Veld
- Department of Hematology; Leiden University Medical Center; Leiden The Netherlands
| | - Marieke Griffioen
- Department of Hematology; Leiden University Medical Center; Leiden The Netherlands
| | - Maarten H. Vermeer
- Department of Dermatology; Leiden University Medical Center; Leiden The Netherlands
| | - Jacques Neefjes
- Division of Cell Biology; The Netherlands Cancer Institute; Amsterdam The Netherlands
- Department of Chemical Immunology; Leiden University Medical Center; Leiden The Netherlands
| | | | | | - Inge Jedema
- Department of Hematology; Leiden University Medical Center; Leiden The Netherlands
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10
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Jung S, Hartmann A, Del Sol A. RefBool: a reference-based algorithm for discretizing gene expression data. Bioinformatics 2018; 33:1953-1962. [PMID: 28334101 DOI: 10.1093/bioinformatics/btx111] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 02/21/2017] [Indexed: 12/26/2022] Open
Abstract
Motivation The identification of genes or molecular regulatory mechanisms implicated in biological processes often requires the discretization, and in particular booleanization, of gene expression measurements. However, currently used methods mostly classify each measurement into an active or inactive state regardless of its statistical support possibly leading to downstream analysis conclusions based on spurious booleanization results. Results In order to overcome the lack of certainty inherent in current methodologies and to improve the process of discretization, we introduce RefBool, a reference-based algorithm for discretizing gene expression data. Instead of requiring each measurement to be classified as active or inactive, RefBool allows for the classification of a third state that can be interpreted as an intermediate expression of genes. Furthermore, each measurement is associated to a p- and q-value indicating the significance of each classification. Validation of RefBool on a neuroepithelial differentiation study and subsequent qualitative and quantitative comparison against 10 currently used methods supports its advantages and shows clear improvements of resulting clusterings. Availability and Implementation The software is available as MATLAB files in the Supplementary Information and as an online repository ( https://github.com/saschajung/RefBool ). Contact antonio.delsol@uni.lu. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Sascha Jung
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Andras Hartmann
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Antonio Del Sol
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
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11
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Bijen HM, van der Steen DM, Hagedoorn RS, Wouters AK, Wooldridge L, Falkenburg JHF, Heemskerk MHM. Preclinical Strategies to Identify Off-Target Toxicity of High-Affinity TCRs. Mol Ther 2018; 26:1206-14. [PMID: 29567312 DOI: 10.1016/j.ymthe.2018.02.017] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 02/16/2018] [Accepted: 02/16/2018] [Indexed: 12/27/2022] Open
Abstract
Adoptive transfer of T cells engineered with a cancer-specific T cell receptor (TCR) has demonstrated clinical benefit. However, the risk for off-target toxicity of TCRs remains a concern. Here, we examined the cross-reactive profile of T cell clone (7B5) with a high functional sensitivity for the hematopoietic-restricted minor histocompatibility antigen HA-2 in the context of HLA-A*02:01. HA-2pos Epstein-Barr virus-transformed B lymphoblastic cell lines (EBV-LCLs) and primary acute myeloid leukemia samples, but not hematopoietic HA-2neg samples, are effectively recognized. However, we found unexpected off-target recognition of human fibroblasts and keratinocytes not expressing the HA-2 antigen. To uncover the origin of this off-target recognition, we performed an alanine scanning approach, identifying six out of nine positions to be important for peptide recognition. This indicates a low risk for broad cross-reactivity. However, using a combinatorial peptide library scanning approach, we identified a CDH13-derived peptide activating the 7B5 T cell clone. This was confirmed by recognition of CDH13-transduced EBV-LCLs and cell subsets endogenously expressing CDH13, such as proximal tubular epithelial cells. As such, we recommend the use of a combinatorial peptide library scan followed by screening against additional cell subsets to validate TCR specificity and detect off-target toxicity due to cross-reactivity directed against unrelated peptides before selecting candidate TCRs for clinical testing.
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12
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van Bergen CAM, van Luxemburg-Heijs SAP, de Wreede LC, Eefting M, von dem Borne PA, van Balen P, Heemskerk MHM, Mulder A, Claas FHJ, Navarrete MA, Honders WM, Rutten CE, Veelken H, Jedema I, Halkes CJM, Griffioen M, Falkenburg JHF. Selective graft-versus-leukemia depends on magnitude and diversity of the alloreactive T cell response. J Clin Invest 2017; 127:517-529. [PMID: 28067665 DOI: 10.1172/jci86175] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 11/17/2016] [Indexed: 01/10/2023] Open
Abstract
Patients with leukemia who receive a T cell-depleted allogeneic stem cell graft followed by postponed donor lymphocyte infusion (DLI) can experience graft-versus-leukemia (GVL) reactivity, with a lower risk of graft-versus-host disease (GVHD). Here, we have investigated the magnitude, diversity, and specificity of alloreactive CD8 T cells in patients who developed GVL reactivity after DLI in the absence or presence of GVHD. We observed a lower magnitude and diversity of CD8 T cells for minor histocompatibility antigens (MiHAs) in patients with selective GVL reactivity without GVHD. Furthermore, we demonstrated that MiHA-specific T cell clones from patients with selective GVL reactivity showed lower reactivity against nonhematopoietic cells, even when pretreated with inflammatory cytokines. Expression analysis of MiHA-encoding genes showed that similar types of antigens were recognized in both patient groups, but in patients who developed GVHD, T cell reactivity was skewed to target broadly expressed MiHAs. As an inflammatory environment can render nonhematopoietic cells susceptible to T cell recognition, prevention of such circumstances favors induction of selective GVL reactivity without development of GVHD.
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