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Jarosch S, Köhlen J, Ghimire S, Orberg ET, Hammel M, Gaag D, Evert M, Janssen KP, Hiergeist A, Gessner A, Weber D, Meedt E, Poeck H, D'Ippolito E, Holler E, Busch DH. Multimodal immune cell phenotyping in GI biopsies reveals microbiome-related T cell modulations in human GvHD. Cell Rep Med 2023; 4:101125. [PMID: 37467715 PMCID: PMC10394271 DOI: 10.1016/j.xcrm.2023.101125] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 05/13/2023] [Accepted: 06/22/2023] [Indexed: 07/21/2023]
Abstract
Acute graft-versus-host disease (aGvHD) is a significant complication after allogeneic hematopoietic stem cell transplantation (aHSCT), but major factors determining disease severity are not well defined yet. By combining multiplexed tissue imaging and single-cell RNA sequencing on gastrointestinal biopsies from aHSCT-treated individuals with fecal microbiome analysis, we link high microbiome diversity and the abundance of short-chain fatty acid-producing bacteria to the sustenance of suppressive regulatory T cells (Tregs). Furthermore, aGvHD severity strongly associates with the clonal expansion of mainly CD8 T cells, which we find distributed over anatomically distant regions of the gut, persistent over time, and inversely correlated with the presence of suppressive Tregs. Overall, our study highlights the pathophysiological importance of expanded CD8 T cell clones in the progression of aGvHD toward more severe clinical manifestations and strongly supports the further development of microbiome interventions as GvHD treatment via repopulation of the gut Treg niche to suppress inflammation.
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Affiliation(s)
- Sebastian Jarosch
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich (TUM), 81675 Munich, Germany; Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, 88397 Biberach an der Riß, Germany
| | - Jan Köhlen
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich (TUM), 81675 Munich, Germany
| | - Sakhila Ghimire
- Department of Internal Medicine 3, University Medical Center, 93053 Regensburg, Germany
| | - Erik Thiele Orberg
- Department of Medicine III, Technical University of Munich (TUM), School of Medicine, Klinikum rechts der Isar TUM, 81675 Munich, Germany; German Cancer Consortium (DKTK), Partner Site Munich, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Monika Hammel
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich (TUM), 81675 Munich, Germany
| | - Doris Gaag
- Institute for Pathology, University of Regensburg, 93053 Regensburg, Germany
| | - Matthias Evert
- Institute for Pathology, University of Regensburg, 93053 Regensburg, Germany
| | - Klaus-Peter Janssen
- Department of Surgery, Klinikum rechts der Isar, Technical University of Munich, 81675 Munich, Germany
| | - Andreas Hiergeist
- Institute of Clinical Microbiology and Hygiene, University Medical Center, 93053 Regensburg, Germany
| | - André Gessner
- Institute of Clinical Microbiology and Hygiene, University Medical Center, 93053 Regensburg, Germany
| | - Daniela Weber
- Department of Internal Medicine 3, University Medical Center, 93053 Regensburg, Germany
| | - Elisabeth Meedt
- Department of Internal Medicine 3, University Medical Center, 93053 Regensburg, Germany
| | - Hendrik Poeck
- Department of Internal Medicine 3, University Medical Center, 93053 Regensburg, Germany; Leibniz Institute for Immuntherapie (LIT), Regensburg, Germany
| | - Elvira D'Ippolito
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich (TUM), 81675 Munich, Germany
| | - Ernst Holler
- Department of Internal Medicine 3, University Medical Center, 93053 Regensburg, Germany.
| | - Dirk H Busch
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich (TUM), 81675 Munich, Germany; German Center for Infection Research (DZIF), Partner Site Munich, 81675 Munich, Germany.
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Jarosch S, Köhlen J, Wagner S, D’Ippolito E, Busch DH. ChipCytometry for multiplexed detection of protein and mRNA markers on human FFPE tissue samples. STAR Protoc 2022; 3:101374. [PMID: 35586313 PMCID: PMC9109191 DOI: 10.1016/j.xpro.2022.101374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
In this protocol, we describe the use of ChipCytometry to combine RNA in situ hybridization and antibody staining for multiplexed tissue imaging of human formalin-fixed and paraffin-embedded tissue samples. The advantages of ChipCytometry are long-term storage for re-interrogation and advanced image quality by high dynamic range imaging of staining and background. A titrated pretreatment of tissue samples bypasses challenges because of the retrieval of antigens on coverslips and achieves an optimal staining quality at the minimal expense of tissue integrity. For complete details on the use and execution of this protocol, please refer to Jarosch et al. (2021). This protocol describes use of ChipCytometry on human FFPE samples This protocol combines mRNA staining via FISH with multiplexed immunofluorescence This protocol provides an automatic image analysis pipeline for ChipCytometry data The automated analysis pipeline can be applied on any multiplexed imaging data
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Jarosch S, Köhlen J, Sarker RS, Steiger K, Janssen KP, Christians A, Hennig C, Holler E, D'Ippolito E, Busch DH. Multiplexed imaging and automated signal quantification in formalin-fixed paraffin-embedded tissues by ChipCytometry. Cell Rep Methods 2021; 1:100104. [PMID: 35475000 PMCID: PMC9017205 DOI: 10.1016/j.crmeth.2021.100104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 08/30/2021] [Accepted: 10/06/2021] [Indexed: 12/17/2022]
Abstract
Deciphering the spatial composition of cells in tissues is essential for detailed understanding of biological processes in health and disease. Recent technological advances enabled the assessment of the enormous complexity of tissue-derived parameters by highly multiplexed tissue imaging (HMTI), but elaborate machinery and data analyses are required. This severely limits broad applicability of HMTI. Here we demonstrate for the first time the application of ChipCytometry technology, which has unique features for widespread use, on formalin-fixed paraffin-embedded samples, the most commonly used storage technique of clinically relevant patient specimens worldwide. The excellent staining quality permits workflows for automated quantification of signal intensities, which we further optimized to compensate signal spillover from neighboring cells. In combination with the high number of validated markers, the reported platform can be used from unbiased analyses of tissue composition to detection of phenotypically complex rare cells, and can be easily implemented in both routine research and clinical pathology.
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Affiliation(s)
- Sebastian Jarosch
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich (TUM), 81675 Munich, Germany
| | - Jan Köhlen
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich (TUM), 81675 Munich, Germany
| | - Rim S.J. Sarker
- Comparative Experimental Pathology, Institute for Pathology, Technical University of Munich, 81675 Munich, Germany
| | - Katja Steiger
- Comparative Experimental Pathology, Institute for Pathology, Technical University of Munich, 81675 Munich, Germany
| | - Klaus-Peter Janssen
- Department of Surgery, Klinikum rechts der Isar, Technical University of Munich, 81675 Munich, Germany
| | | | | | - Ernst Holler
- Department of Hematology/Oncology, University Medical Center, 93053 Regensburg, Germany
| | - Elvira D'Ippolito
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich (TUM), 81675 Munich, Germany
| | - Dirk H. Busch
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich (TUM), 81675 Munich, Germany
- German Center for Infection Research (DZIF), partner site Munich, 81675 Munich, Germany
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