1
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Roessner PM, Seufert I, Chapaprieta V, Jayabalan R, Briesch H, Massoni-Badosa R, Boskovic P, Beckendorff J, Roider T, Arseni L, Coelho M, Chakraborty S, Vaca A, Sivina M, Muckenhuber M, Rodriguez-Rodriguez S, Bonato A, Herbst SA, Zapatka M, Sun C, Kretzmer H, Naake T, Bruch PM, Czernilofsky F, Ten Hacken E, Schneider M, Helm D, Yosifov DY, Kauer J, Danilov AV, Bewarder M, Heyne K, Schneider C, Stilgenbauer S, Wiestner A, Mallm JP, Burger JA, Efremov DG, Lichter P, Dietrich S, Martín-Subero JI, Rippe K, Seiffert M. T-bet suppresses proliferation of malignant B cells in chronic lymphocytic leukemia. Blood 2024:blood.2023021990. [PMID: 38684038 DOI: 10.1182/blood.2023021990] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 03/28/2024] [Accepted: 04/13/2024] [Indexed: 05/02/2024] Open
Abstract
The T-box transcription factor T-bet is known as a master regulator of T-cell response but its role in malignant B cells is not sufficiently explored. Here, we conducted single-cell resolved multi-omics analyses of malignant B cells from patients with chronic lymphocytic leukemia (CLL) and studied a CLL mouse model with genetic knockout of TBX21. We found that T-bet acts as a tumor suppressor in malignant B cells by decreasing their proliferation rate. NF-κB activity induced by inflammatory signals provided by the microenvironment, triggered T-bet expression which impacted on promoter proximal and distal chromatin co-accessibility and controlled a specific gene signature by mainly suppressing transcription. Gene set enrichment analysis identified a positive regulation of interferon signaling, and a negative control of proliferation by T-bet. In line, we showed that T-bet represses cell cycling and is associated with longer overall survival of CLL patients. Our study uncovers a novel tumor suppressive role of T-bet in malignant B cells via its regulation of inflammatory processes and cell cycling which has implications for stratification and therapy of CLL patients. Linking T-bet activity to inflammation explains the good prognostic role of genetic alterations in inflammatory signaling pathways in CLL.
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Affiliation(s)
| | | | - Vicente Chapaprieta
- Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | | | | | | | - Pavle Boskovic
- Washington University in St. Louis School of Medicine, Saint Louis, Missouri, United States
| | | | | | | | | | - Supriya Chakraborty
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Alicia Vaca
- The University of Texas MD Anderson Cancer Center, Houston, Texas, United States
| | - Mariela Sivina
- MD Anderson Cancer Center, Houston, Texas, United States
| | | | | | - Alice Bonato
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | | | - Marc Zapatka
- German Cancer Research Center, Heidelberg, Germany
| | - Clare Sun
- National Heart, Lung, and Blood Institute, Bethesda, Maryland, United States
| | - Helene Kretzmer
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Thomas Naake
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | | | | | - Elisa Ten Hacken
- Dana Farber Cancer Institute, Boston, Massachusetts, United States
| | | | - Dominic Helm
- German Cancer Research Center, Heidelberg, Germany
| | | | - Joseph Kauer
- University Hospital Heidelberg, Heidelberg, Germany
| | | | | | | | | | | | | | | | - Jan A Burger
- University of Texas M.D. Anderson Cancer Center, Houston, Texas, United States
| | - Dimitar G Efremov
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | | | | | - José Ignacio Martín-Subero
- Department of Pathology, Hematopathology Section, Hospital Clinic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Spain, Barcelona, Spain
| | - Karsten Rippe
- German Cancer Research Center (DKFZ), Heidelberg, Germany
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2
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Bundschuh C, Weidner N, Klein J, Rausch T, Azevedo N, Telzerow A, Mallm JP, Kim H, Steiger S, Seufert I, Börner K, Bauer K, Hübschmann D, Jost KL, Parthé S, Schnitzler P, Boutros M, Rippe K, Müller B, Bartenschlager R, Kräusslich HG, Benes V. Evolution of SARS-CoV-2 in the Rhine-Neckar/Heidelberg Region 01/2021 - 07/2023. Infect Genet Evol 2024; 119:105577. [PMID: 38403035 DOI: 10.1016/j.meegid.2024.105577] [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: 10/12/2023] [Revised: 01/31/2024] [Accepted: 02/21/2024] [Indexed: 02/27/2024]
Abstract
In January 2021, the monitoring of circulating variants of SARS-CoV-2 was initiated in Germany under the Corona Surveillance Act, which was discontinued after July 2023. This initiative aimed to enhance pandemic containment, as specific amino acid changes, particularly in the spike protein, were associated with increased transmission and reduced vaccine efficacy. Our group conducted whole genome sequencing using the ARTIC protocol (currently V4) on Illumina's NextSeq 500 platform (and, starting in May 2023, on the MiSeq DX platform) for SARS-CoV-2 positive specimen from patients at Heidelberg University Hospital, associated hospitals, and the public health office in the Rhine-Neckar/Heidelberg region. In total, we sequenced 26,795 SARS-CoV-2-positive samples between January 2021 and July 2023. Valid sequences, meeting the requirements for upload to the German electronic sequencing data hub (DESH) operated by the Robert Koch Institute (RKI), were determined for 24,852 samples, and the lineage/clade could be identified for 25,912 samples. The year 2021 witnessed significant dynamics in the circulating variants in the Rhine-Neckar/Heidelberg region, including A.27.RN, followed by the emergence of B.1.1.7 (Alpha), subsequently displaced by B.1.617.2 (Delta), and the initial occurrences of B.1.1.529 (Omicron). By January 2022, B.1.1.529 had superseded B.1.617.2, dominating with over 90%. The years 2022 and 2023 were then characterized by the dominance of B.1.1.529 and its sublineages, particularly BA.5 and BA.2, and more recently, the emergence of recombinant variants like XBB.1.5. Since the global dominance of B.1.617.2, the identified variant distribution in our local study, apart from a time delay in the spread of new variants, can be considered largely representative of the global distribution. om a time delay in the spread of new variants, can be considered largely representative of the global distribution.
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Affiliation(s)
- Christian Bundschuh
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Virology, Heidelberg, Germany.
| | - Niklas Weidner
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Virology, Heidelberg, Germany; Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Microbiology and Hygiene, Heidelberg, Germany
| | - Julian Klein
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Virology, Heidelberg, Germany
| | - Tobias Rausch
- Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Nayara Azevedo
- Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Anja Telzerow
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Virology, Heidelberg, Germany; Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Jan-Philipp Mallm
- Single Cell Open Lab, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Heeyoung Kim
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Simon Steiger
- Division Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Isabelle Seufert
- Division Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Kathleen Börner
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Virology, Heidelberg, Germany
| | - Katharina Bauer
- Single Cell Open Lab, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Daniel Hübschmann
- Division Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Katharina Laurence Jost
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Virology, Heidelberg, Germany
| | - Sylvia Parthé
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Virology, Heidelberg, Germany
| | - Paul Schnitzler
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Virology, Heidelberg, Germany
| | - Michael Boutros
- Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Department for Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Karsten Rippe
- Division Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Barbara Müller
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Virology, Heidelberg, Germany
| | - Ralf Bartenschlager
- Single Cell Open Lab, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany; Division Virus-Associated Carcinogenesis, German Cancer Research Center, Heidelberg, Germany; Deutsches Zentrum für Infektionsforschung, partner site Heidelberg, Germany
| | - Hans-Georg Kräusslich
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Virology, Heidelberg, Germany; Deutsches Zentrum für Infektionsforschung, partner site Heidelberg, Germany
| | - Vladimir Benes
- Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
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3
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Groth C, Maric J, Garcés Lázaro I, Hofman T, Zhang Z, Ni Y, Keller F, Seufert I, Hofmann M, Neumann-Haefelin C, Sticht C, Rippe K, Urban S, Cerwenka A. Hepatitis D infection induces IFN-β-mediated NK cell activation and TRAIL-dependent cytotoxicity. Front Immunol 2023; 14:1287367. [PMID: 38143742 PMCID: PMC10739304 DOI: 10.3389/fimmu.2023.1287367] [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: 09/01/2023] [Accepted: 10/23/2023] [Indexed: 12/26/2023] Open
Abstract
Background and aims The co-infection of hepatitis B (HBV) patients with the hepatitis D virus (HDV) causes the most severe form of viral hepatitis and thus drastically worsens the course of the disease. Therapy options for HBV/HDV patients are still limited. Here, we investigated the potential of natural killer (NK) cells that are crucial drivers of the innate immune response against viruses to target HDV-infected hepatocytes. Methods We established in vitro co-culture models using HDV-infected hepatoma cell lines and human peripheral blood NK cells. We determined NK cell activation by flow cytometry, transcriptome analysis, bead-based cytokine immunoassays, and NK cell-mediated effects on T cells by flow cytometry. We validated the mechanisms using CRISPR/Cas9-mediated gene deletions. Moreover, we assessed the frequencies and phenotype of NK cells in peripheral blood of HBV and HDV superinfected patients. Results Upon co-culture with HDV-infected hepatic cell lines, NK cells upregulated activation markers, interferon-stimulated genes (ISGs) including the death receptor ligand tumor necrosis factor-related apoptosis-inducing ligand (TRAIL), produced interferon (IFN)-γ and eliminated HDV-infected cells via the TRAIL-TRAIL-R2 axis. We identified IFN-β released by HDV-infected cells as an important enhancer of NK cell activity. In line with our in vitro data, we observed activation of peripheral blood NK cells from HBV/HDV co-infected, but not HBV mono-infected patients. Conclusion Our data demonstrate NK cell activation in HDV infection and their potential to eliminate HDV-infected hepatoma cells via the TRAIL/TRAIL-R2 axis which implies a high relevance of NK cells for the design of novel anti-viral therapies.
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Affiliation(s)
- Christopher Groth
- Department of Immunobiochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Jovana Maric
- Department of Immunobiochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Irene Garcés Lázaro
- Department of Immunobiochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Tomáš Hofman
- Department of Immunobiochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Zhenfeng Zhang
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Yi Ni
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
- German Center for Infection Research Deutsches Zentrum für Infektionsforschung (DZFI) - Heidelberg Partner Site, Heidelberg, Germany
| | - Franziska Keller
- Department of Medicine II (Gastroenterology, Hepatology, Endocrinology and Infectious Diseases), Faculty of Medicine, Medical Center-University of Freiburg, Freiburg, Germany
| | - Isabelle Seufert
- Division of Chromatin Networks, German Cancer Research Center Deutsches Krebsforschungszentrum (DKFZ) and Bioquant, Heidelberg, Germany
| | - Maike Hofmann
- Department of Medicine II (Gastroenterology, Hepatology, Endocrinology and Infectious Diseases), Faculty of Medicine, Medical Center-University of Freiburg, Freiburg, Germany
| | - Christoph Neumann-Haefelin
- Department of Medicine II (Gastroenterology, Hepatology, Endocrinology and Infectious Diseases), Faculty of Medicine, Medical Center-University of Freiburg, Freiburg, Germany
| | - Carsten Sticht
- Medical Research Center, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Karsten Rippe
- Division of Chromatin Networks, German Cancer Research Center Deutsches Krebsforschungszentrum (DKFZ) and Bioquant, Heidelberg, Germany
| | - Stephan Urban
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
- German Center for Infection Research Deutsches Zentrum für Infektionsforschung (DZFI) - Heidelberg Partner Site, Heidelberg, Germany
| | - Adelheid Cerwenka
- Department of Immunobiochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
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4
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Schuster LC, Syed AP, Tirier SM, Steiger S, Seufert I, Becker H, Duque-Afonso J, Ma T, Ogawa S, Mallm JP, Lübbert M, Rippe K. Progenitor-like cell type of an MLL-EDC4 fusion in acute myeloid leukemia. Blood Adv 2023; 7:7079-7083. [PMID: 37820244 PMCID: PMC10694518 DOI: 10.1182/bloodadvances.2022009096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 09/24/2023] [Accepted: 09/29/2023] [Indexed: 10/13/2023] Open
Affiliation(s)
- Linda C. Schuster
- Division of Chromatin Networks, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Center for Quantitative Analysis of Molecular and Cellular Biosystems, Heidelberg University, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Afzal P. Syed
- Division of Chromatin Networks, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Center for Quantitative Analysis of Molecular and Cellular Biosystems, Heidelberg University, Heidelberg, Germany
- Single Cell Open Lab, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stephan M. Tirier
- Division of Chromatin Networks, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Simon Steiger
- Division of Chromatin Networks, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Center for Quantitative Analysis of Molecular and Cellular Biosystems, Heidelberg University, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Isabelle Seufert
- Division of Chromatin Networks, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Center for Quantitative Analysis of Molecular and Cellular Biosystems, Heidelberg University, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Heiko Becker
- Department of Medicine I, University Freiburg Medical Center, Freiburg, Germany
| | - Jesus Duque-Afonso
- Department of Medicine I, University Freiburg Medical Center, Freiburg, Germany
| | - Tobias Ma
- Department of Medicine I, University Freiburg Medical Center, Freiburg, Germany
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Jan-Philipp Mallm
- Center for Quantitative Analysis of Molecular and Cellular Biosystems, Heidelberg University, Heidelberg, Germany
- Single Cell Open Lab, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael Lübbert
- Department of Medicine I, University Freiburg Medical Center, Freiburg, Germany
| | - Karsten Rippe
- Division of Chromatin Networks, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Center for Quantitative Analysis of Molecular and Cellular Biosystems, Heidelberg University, Heidelberg, Germany
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5
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Wu Y, Seufert I, Al-Shaheri FN, Kurilov R, Bauer AS, Manoochehri M, Moskalev EA, Brors B, Tjaden C, Giese NA, Hackert T, Büchler MW, Hoheisel JD. DNA-methylation signature accurately differentiates pancreatic cancer from chronic pancreatitis in tissue and plasma. Gut 2023; 72:2344-2353. [PMID: 37709492 DOI: 10.1136/gutjnl-2023-330155] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 08/31/2023] [Indexed: 09/16/2023]
Abstract
OBJECTIVE Pancreatic ductal adenocarcinoma (PDAC) is a lethal malignancy. Differentiation from chronic pancreatitis (CP) is currently inaccurate in about one-third of cases. Misdiagnoses in both directions, however, have severe consequences for patients. We set out to identify molecular markers for a clear distinction between PDAC and CP. DESIGN Genome-wide variations of DNA-methylation, messenger RNA and microRNA level as well as combinations thereof were analysed in 345 tissue samples for marker identification. To improve diagnostic performance, we established a random-forest machine-learning approach. Results were validated on another 48 samples and further corroborated in 16 liquid biopsy samples. RESULTS Machine-learning succeeded in defining markers to differentiate between patients with PDAC and CP, while low-dimensional embedding and cluster analysis failed to do so. DNA-methylation yielded the best diagnostic accuracy by far, dwarfing the importance of transcript levels. Identified changes were confirmed with data taken from public repositories and validated in independent sample sets. A signature of six DNA-methylation sites in a CpG-island of the protein kinase C beta type gene achieved a validated diagnostic accuracy of 100% in tissue and in circulating free DNA isolated from patient plasma. CONCLUSION The success of machine-learning to identify an effective marker signature documents the power of this approach. The high diagnostic accuracy of discriminating PDAC from CP could have tremendous consequences for treatment success, once the result from still a limited number of liquid biopsy samples would be confirmed in a larger cohort of patients with suspected pancreatic cancer.
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Affiliation(s)
- Yenan Wu
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Isabelle Seufert
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Fawaz N Al-Shaheri
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Medical Faculty Heidelberg, University of Heidelberg, Heidelberg, Germany
| | - Roman Kurilov
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andrea S Bauer
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mehdi Manoochehri
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Evgeny A Moskalev
- Institute of Pathology, Universitätsklinikum Erlangen, Friedrich Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Benedikt Brors
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christin Tjaden
- Department of Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Nathalia A Giese
- Department of Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Thilo Hackert
- Department of Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Markus W Büchler
- Department of Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Jörg D Hoheisel
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
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6
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Poos AM, Prokoph N, Przybilla MJ, Mallm JP, Steiger S, Seufert I, John L, Tirier SM, Bauer K, Baumann A, Rohleder J, Munawar U, Rasche L, Kortüm KM, Giesen N, Reichert P, Huhn S, Müller-Tidow C, Goldschmidt H, Stegle O, Raab MS, Rippe K, Weinhold N. Resolving therapy resistance mechanisms in multiple myeloma by multiomics subclone analysis. Blood 2023; 142:1633-1646. [PMID: 37390336 PMCID: PMC10733835 DOI: 10.1182/blood.2023019758] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [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: 01/17/2023] [Revised: 05/17/2023] [Accepted: 06/12/2023] [Indexed: 07/02/2023] Open
Abstract
Intratumor heterogeneity as a clinical challenge becomes most evident after several treatment lines, when multidrug-resistant subclones accumulate. To address this challenge, the characterization of resistance mechanisms at the subclonal level is key to identify common vulnerabilities. In this study, we integrate whole-genome sequencing, single-cell (sc) transcriptomics (scRNA sequencing), and chromatin accessibility (scATAC sequencing) together with mitochondrial DNA mutations to define subclonal architecture and evolution for longitudinal samples from 15 patients with relapsed or refractory multiple myeloma. We assess transcriptomic and epigenomic changes to resolve the multifactorial nature of therapy resistance and relate it to the parallel occurrence of different mechanisms: (1) preexisting epigenetic profiles of subclones associated with survival advantages, (2) converging phenotypic adaptation of genetically distinct subclones, and (3) subclone-specific interactions of myeloma and bone marrow microenvironment cells. Our study showcases how an integrative multiomics analysis can be applied to track and characterize distinct multidrug-resistant subclones over time for the identification of molecular targets against them.
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Affiliation(s)
- Alexandra M. Poos
- Department of Internal Medicine V, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center, Heidelberg, Germany
| | - Nina Prokoph
- Department of Internal Medicine V, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center, Heidelberg, Germany
| | - Moritz J. Przybilla
- Division Computational Genomics and Systems Genetics, German Cancer Research Center, Heidelberg, Germany
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | - Jan-Philipp Mallm
- Single Cell Open Lab, German Cancer Research Center and BioQuant, Heidelberg, Germany
| | - Simon Steiger
- Division of Chromatin Networks, German Cancer Research Center and BioQuant, Heidelberg, Germany
| | - Isabelle Seufert
- Division of Chromatin Networks, German Cancer Research Center and BioQuant, Heidelberg, Germany
| | - Lukas John
- Department of Internal Medicine V, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center, Heidelberg, Germany
| | - Stephan M. Tirier
- Division of Chromatin Networks, German Cancer Research Center and BioQuant, Heidelberg, Germany
| | - Katharina Bauer
- Single Cell Open Lab, German Cancer Research Center and BioQuant, Heidelberg, Germany
| | - Anja Baumann
- Department of Internal Medicine V, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center, Heidelberg, Germany
| | - Jennifer Rohleder
- Department of Internal Medicine V, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center, Heidelberg, Germany
| | - Umair Munawar
- Department of Internal Medicine 2, University Hospital of Würzburg, Würzburg, Germany
| | - Leo Rasche
- Department of Internal Medicine 2, University Hospital of Würzburg, Würzburg, Germany
- Mildred Scheel Early Career Center, University Hospital of Würzburg, Würzburg, Germany
| | - K. Martin Kortüm
- Department of Internal Medicine 2, University Hospital of Würzburg, Würzburg, Germany
| | - Nicola Giesen
- Department of Internal Medicine V, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center, Heidelberg, Germany
| | - Philipp Reichert
- Department of Internal Medicine V, University Hospital Heidelberg, Heidelberg, Germany
| | - Stefanie Huhn
- Department of Internal Medicine V, University Hospital Heidelberg, Heidelberg, Germany
| | - Carsten Müller-Tidow
- Department of Internal Medicine V, University Hospital Heidelberg, Heidelberg, Germany
- National Center for Tumor Diseases, Heidelberg, Germany
| | - Hartmut Goldschmidt
- Department of Internal Medicine V, GMMG-Study Group at University Hospital Heidelberg, Heidelberg, Germany
| | - Oliver Stegle
- Division Computational Genomics and Systems Genetics, German Cancer Research Center, Heidelberg, Germany
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Marc S. Raab
- Department of Internal Medicine V, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center, Heidelberg, Germany
| | - Karsten Rippe
- Division of Chromatin Networks, German Cancer Research Center and BioQuant, Heidelberg, Germany
| | - Niels Weinhold
- Department of Internal Medicine V, University Hospital Heidelberg, Heidelberg, Germany
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7
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Muckenhuber M, Seufert I, Müller-Ott K, Mallm JP, Klett LC, Knotz C, Hechler J, Kepper N, Erdel F, Rippe K. Epigenetic signals that direct cell type-specific interferon beta response in mouse cells. Life Sci Alliance 2023; 6:e202201823. [PMID: 36732019 PMCID: PMC9900254 DOI: 10.26508/lsa.202201823] [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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 01/14/2023] [Accepted: 01/16/2023] [Indexed: 02/04/2023] Open
Abstract
The antiviral response induced by type I interferon (IFN) via the JAK-STAT signaling cascade activates hundreds of IFN-stimulated genes (ISGs) across human and mouse tissues but varies between cell types. However, the links between the underlying epigenetic features and the ISG profile are not well understood. We mapped ISGs, binding sites of the STAT1 and STAT2 transcription factors, chromatin accessibility, and histone H3 lysine modification by acetylation (ac) and mono-/tri-methylation (me1, me3) in mouse embryonic stem cells and fibroblasts before and after IFNβ treatment. A large fraction of ISGs and STAT-binding sites was cell type specific with promoter binding of a STAT1/2 complex being a key driver of ISGs. Furthermore, STAT1/2 binding to putative enhancers induced ISGs as inferred from a chromatin co-accessibility analysis. STAT1/2 binding was dependent on the chromatin context and positively correlated with preexisting H3K4me1 and H3K27ac marks in an open chromatin state, whereas the presence of H3K27me3 had an inhibitory effect. Thus, chromatin features present before stimulation represent an additional regulatory layer for the cell type-specific antiviral response.
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Affiliation(s)
- Markus Muckenhuber
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Isabelle Seufert
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Katharina Müller-Ott
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Jan-Philipp Mallm
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
- Single Cell Open Lab, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lara C Klett
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Caroline Knotz
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Jana Hechler
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Nick Kepper
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Fabian Erdel
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Karsten Rippe
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
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