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Rathgeber AC, Ludwig LS, Penter L. Single-cell genomics-based immune and disease monitoring in blood malignancies. Clin Hematol Int 2024; 6:62-84. [PMID: 38884110 PMCID: PMC11180218 DOI: 10.46989/001c.117961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 12/25/2023] [Indexed: 06/18/2024] Open
Abstract
Achieving long-term disease control using therapeutic immunomodulation is a long-standing concept with a strong tradition in blood malignancies. Besides allogeneic hematopoietic stem cell transplantation that continues to provide potentially curative treatment for otherwise challenging diagnoses, recent years have seen impressive progress in immunotherapies for leukemias and lymphomas with immune checkpoint blockade, bispecific monoclonal antibodies, and CAR T cell therapies. Despite their success, non-response, relapse, and immune toxicities remain frequent, thus prioritizing the elucidation of the underlying mechanisms and identifying predictive biomarkers. The increasing availability of single-cell genomic tools now provides a system's immunology view to resolve the molecular and cellular mechanisms of immunotherapies at unprecedented resolution. Here, we review recent studies that leverage these technological advancements for tracking immune responses, the emergence of immune resistance, and toxicities. As single-cell immune monitoring tools evolve and become more accessible, we expect their wide adoption for routine clinical applications to catalyze more precise therapeutic steering of personal immune responses.
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Affiliation(s)
- Anja C Rathgeber
- Berlin Institute for Medical Systems Biology Max Delbrück Center for Molecular Medicine
- Department of Hematology, Oncology, and Tumorimmunology Charité - Universitätsmedizin Berlin
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin
| | - Leif S Ludwig
- Berlin Institute for Medical Systems Biology Max Delbrück Center for Molecular Medicine
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin
| | - Livius Penter
- Department of Hematology, Oncology, and Tumorimmunology Charité - Universitätsmedizin Berlin
- BIH Biomedical Innovation Academy Berlin Institute of Health at Charité - Universitätsmedizin Berlin
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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 PMCID: PMC11076866 DOI: 10.1182/blood.2023022343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [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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Lee Y, Baek J, Park S, Kim Y, Hwang SW, Lee JL, Park SH, Kim J, Yang SK, Han B, Kweon MN, Song K, Yoon YS, Ye BD, Lee HS. Characterization of Th17 tissue-resident memory cells in non-inflamed intestinal tissue of Crohn's disease patients. J Autoimmun 2024; 145:103206. [PMID: 38554656 DOI: 10.1016/j.jaut.2024.103206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 02/28/2024] [Accepted: 03/18/2024] [Indexed: 04/02/2024]
Abstract
Crohn's disease (CD) is a chronic inflammatory disorder affecting the bowel wall. Tissue-resident memory T (Trm) cells are implicated in CD, yet their characteristics remain unclear. We aimed to investigate the transcriptional profiles and functional characteristics of Trm cells in the small bowel of CD and their interactions with immune cells. Seven patients with CD and four with ulcerative colitis as controls were included. Single-cell RNA sequencing and paired T cell receptor sequencing assessed T cell subsets and transcriptional signatures in lamina propria (LP) and submucosa/muscularis propria-enriched fractions (SM/MP) from small bowel tissue samples. We detected 58,123 T cells grouped into 16 populations, including the CD4+ Trm cells with a Th17 signature and CD8+ Trm clusters. In CD, CD4+ Trm cells with a Th17 signature, termed Th17 Trm, showed significantly increased proportions within both the LP and SM/MP areas. The Th17 Trm cluster demonstrated heightened expression of tissue-residency marker genes (ITGAE, ITGA1, and CXCR6) along with elevated levels of IL17A, IL22, CCR6, and CCL20. The clonal expansion of Th17 Trm cells in CD was accompanied by enhanced transmural dynamic potential, as indicated by significantly higher migration scores. CD-prominent Th17 Trm cells displayed an increased interferon gamma (IFNγ)-related signature possibly linked with STAT1 activation, inducing chemokines (i.e., CXCL10, CXCL8, and CXCL9) in myeloid cells. Our findings underscored the elevated Th17 Trm cells throughout the small bowel in CD, contributing to disease pathogenesis through IFNγ induction and subsequent chemokine production in myeloid cells.
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Affiliation(s)
- Yoonho Lee
- Department of Biochemistry and Molecular Biology, Asan Medical Center, Brain Korea 21 Project, University of Ulsan College of Medicine, Seoul, South Korea
| | - Jiwon Baek
- Department of Biochemistry and Molecular Biology, Asan Medical Center, Brain Korea 21 Project, University of Ulsan College of Medicine, Seoul, South Korea
| | - Sojung Park
- Department of Biochemistry and Molecular Biology, Asan Medical Center, Brain Korea 21 Project, University of Ulsan College of Medicine, Seoul, South Korea
| | - Yongjae Kim
- Department of Biochemistry and Molecular Biology, Asan Medical Center, Brain Korea 21 Project, University of Ulsan College of Medicine, Seoul, South Korea
| | - Sung Wook Hwang
- Department of Gastroenterology, Inflammatory Bowel Disease Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Jong Lyul Lee
- Division of Colon and Rectal Surgery, Department of Surgery, Inflammatory Bowel Disease Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Sang Hyoung Park
- Department of Gastroenterology, Inflammatory Bowel Disease Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Jihun Kim
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Suk-Kyun Yang
- Department of Gastroenterology, Inflammatory Bowel Disease Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Buhm Han
- Department of Biomedical Sciences, BK21 Plus Biomedical Science Project, Seoul National University College of Medicine, Seoul, South Korea
| | - Mi-Na Kweon
- Mucosal Immunology Laboratory, Asan Medical Center, Brain Korea 21 Project, University of Ulsan College of Medicine, Seoul, South Korea
| | - Kyuyoung Song
- Department of Biochemistry and Molecular Biology, Asan Medical Center, Brain Korea 21 Project, University of Ulsan College of Medicine, Seoul, South Korea
| | - Yong Sik Yoon
- Division of Colon and Rectal Surgery, Department of Surgery, Inflammatory Bowel Disease Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea.
| | - Byong Duk Ye
- Department of Gastroenterology, Inflammatory Bowel Disease Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea.
| | - Ho-Su Lee
- Department of Biochemistry and Molecular Biology, Asan Medical Center, Brain Korea 21 Project, University of Ulsan College of Medicine, Seoul, South Korea.
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Teshima T, Hashimoto D. Separation of GVL from GVHD -location, location, location. Front Immunol 2023; 14:1296663. [PMID: 38116007 PMCID: PMC10728488 DOI: 10.3389/fimmu.2023.1296663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 11/21/2023] [Indexed: 12/21/2023] Open
Abstract
Allogeneic hematopoietic cell transplantation (HCT) is a curative therapy for various hematologic malignancies. However, alloimmune response is a double-edged sword that mediates both beneficial graft-versus-leukemia (GVL) effects and harmful graft-versus-host disease (GVHD). Separation of GVL effects from GVHD has been a topic of intense research to improve transplant outcomes, but reliable clinical strategies have not yet been established. Target tissues of acute GVHD are the skin, liver, and intestine, while leukemic stem cells reside in the bone marrow. Tissue specific effector T-cell migration is determined by a combination of inflammatory and chemotactic signals that interact with specific receptors on T cells. Specific inhibition of donor T cell migration to GVHD target tissues while preserving migration to the bone marrow may represent a novel strategy to separate GVL from GVHD. Furthermore, tissue specific GVHD therapy, promoting tissue tolerance, and targeting of the tumor immune microenvironment may also help to separate GVHD and GVL.
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Affiliation(s)
- Takanori Teshima
- Department of Hematology, Hokkaido University Faculty of Medicine, Sapporo, Japan
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