1
|
Herbst SA, Kim V, Roider T, Schitter EC, Bruch PM, Liebers N, Kolb C, Knoll M, Lu J, Dreger P, Müller-Tidow C, Zenz T, Huber W, Dietrich S. Comparing the value of mono- vs coculture for high-throughput compound screening in hematological malignancies. Blood Adv 2023; 7:5925-5936. [PMID: 37352275 PMCID: PMC10558604 DOI: 10.1182/bloodadvances.2022009652] [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: 01/19/2023] [Revised: 05/19/2023] [Accepted: 06/07/2023] [Indexed: 06/25/2023] Open
Abstract
Large-scale compound screens are a powerful model system for understanding variability of treatment response and discovering druggable tumor vulnerabilities of hematological malignancies. However, as mostly performed in a monoculture of tumor cells, these assays disregard modulatory effects of the in vivo microenvironment. It is an open question whether and to what extent coculture with bone marrow stromal cells could improve the biological relevance of drug testing assays over monoculture. Here, we established a high-throughput platform to measure ex vivo sensitivity of 108 primary blood cancer samples to 50 drugs in monoculture and coculture with bone marrow stromal cells. Stromal coculture conferred resistance to 52% of compounds in chronic lymphocytic leukemia (CLL) and 36% of compounds in acute myeloid leukemia (AML), including chemotherapeutics, B-cell receptor inhibitors, proteasome inhibitors, and Bromodomain and extraterminal domain inhibitors. Only the JAK inhibitors ruxolitinib and tofacitinib exhibited increased efficacy in AML and CLL stromal coculture. We further confirmed the importance of JAK-STAT signaling for stroma-mediated resistance by showing that stromal cells induce phosphorylation of STAT3 in CLL cells. We genetically characterized the 108 cancer samples and found that drug-gene associations strongly correlated between monoculture and coculture. However, effect sizes were lower in coculture, with more drug-gene associations detected in monoculture than in coculture. Our results justify a 2-step strategy for drug perturbation testing, with large-scale screening performed in monoculture, followed by focused evaluation of potential stroma-mediated resistances in coculture.
Collapse
Affiliation(s)
- Sophie A. Herbst
- Department of Medicine V, Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Molecular Medicine Partnership Unit, Heidelberg, Germany
- Department of Translational Medical Oncology, National Center for Tumor Diseases Heidelberg, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Vladislav Kim
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Molecular Medicine Partnership Unit, Heidelberg, Germany
- Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Tobias Roider
- Department of Medicine V, Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Molecular Medicine Partnership Unit, Heidelberg, Germany
| | - Eva C. Schitter
- Department of Medicine V, Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany
| | - Peter-Martin Bruch
- Department of Medicine V, Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Molecular Medicine Partnership Unit, Heidelberg, Germany
- Department of Hematology and Oncology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Nora Liebers
- Department of Medicine V, Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Molecular Medicine Partnership Unit, Heidelberg, Germany
- Department of Translational Medical Oncology, National Center for Tumor Diseases Heidelberg, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Carolin Kolb
- Department of Medicine V, Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany
| | - Mareike Knoll
- Department of Medicine V, Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany
| | - Junyan Lu
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Molecular Medicine Partnership Unit, Heidelberg, Germany
| | - Peter Dreger
- Department of Medicine V, Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany
| | - Carsten Müller-Tidow
- Department of Medicine V, Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Molecular Medicine Partnership Unit, Heidelberg, Germany
| | - Thorsten Zenz
- Department of Medical Oncology and Hematology, University Hospital Zürich, Zürich, Switzerland
| | - Wolfgang Huber
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Molecular Medicine Partnership Unit, Heidelberg, Germany
| | - Sascha Dietrich
- Department of Medicine V, Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Molecular Medicine Partnership Unit, Heidelberg, Germany
- Department of Hematology and Oncology, University Hospital Düsseldorf, Düsseldorf, Germany
| |
Collapse
|
2
|
Herbst SA, Vesterlund M, Helmboldt AJ, Jafari R, Siavelis I, Stahl M, Schitter EC, Liebers N, Brinkmann BJ, Czernilofsky F, Roider T, Bruch PM, Iskar M, Kittai A, Huang Y, Lu J, Richter S, Mermelekas G, Umer HM, Knoll M, Kolb C, Lenze A, Cao X, Österholm C, Wahnschaffe L, Herling C, Scheinost S, Ganzinger M, Mansouri L, Kriegsmann K, Kriegsmann M, Anders S, Zapatka M, Del Poeta G, Zucchetto A, Bomben R, Gattei V, Dreger P, Woyach J, Herling M, Müller-Tidow C, Rosenquist R, Stilgenbauer S, Zenz T, Huber W, Tausch E, Lehtiö J, Dietrich S. Proteogenomics refines the molecular classification of chronic lymphocytic leukemia. Nat Commun 2022; 13:6226. [PMID: 36266272 PMCID: PMC9584885 DOI: 10.1038/s41467-022-33385-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 09/14/2022] [Indexed: 12/24/2022] Open
Abstract
Cancer heterogeneity at the proteome level may explain differences in therapy response and prognosis beyond the currently established genomic and transcriptomic-based diagnostics. The relevance of proteomics for disease classifications remains to be established in clinically heterogeneous cancer entities such as chronic lymphocytic leukemia (CLL). Here, we characterize the proteome and transcriptome alongside genetic and ex-vivo drug response profiling in a clinically annotated CLL discovery cohort (n = 68). Unsupervised clustering of the proteome data reveals six subgroups. Five of these proteomic groups are associated with genetic features, while one group is only detectable at the proteome level. This new group is characterized by accelerated disease progression, high spliceosomal protein abundances associated with aberrant splicing, and low B cell receptor signaling protein abundances (ASB-CLL). Classifiers developed to identify ASB-CLL based on its characteristic proteome or splicing signature in two independent cohorts (n = 165, n = 169) confirm that ASB-CLL comprises about 20% of CLL patients. The inferior overall survival in ASB-CLL is also independent of both TP53- and IGHV mutation status. Our multi-omics analysis refines the classification of CLL and highlights the potential of proteomics to improve cancer patient stratification beyond genetic and transcriptomic profiling.
Collapse
Affiliation(s)
- Sophie A. Herbst
- grid.7700.00000 0001 2190 4373Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany ,grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory (EMBL), Heidelberg, Germany ,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany ,grid.461742.20000 0000 8855 0365Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Mattias Vesterlund
- grid.452834.c0000 0004 5911 2402Department of Oncology-Pathology, Karolinska Institute and Science for Life Laboratory, Stockholm, Sweden
| | - Alexander J. Helmboldt
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Rozbeh Jafari
- grid.452834.c0000 0004 5911 2402Department of Oncology-Pathology, Karolinska Institute and Science for Life Laboratory, Stockholm, Sweden
| | - Ioannis Siavelis
- grid.452834.c0000 0004 5911 2402Department of Oncology-Pathology, Karolinska Institute and Science for Life Laboratory, Stockholm, Sweden
| | - Matthias Stahl
- grid.452834.c0000 0004 5911 2402Department of Oncology-Pathology, Karolinska Institute and Science for Life Laboratory, Stockholm, Sweden
| | - Eva C. Schitter
- grid.7700.00000 0001 2190 4373Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
| | - Nora Liebers
- grid.7700.00000 0001 2190 4373Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany ,grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory (EMBL), Heidelberg, Germany ,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany ,grid.461742.20000 0000 8855 0365Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Berit J. Brinkmann
- grid.7700.00000 0001 2190 4373Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany ,grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory (EMBL), Heidelberg, Germany ,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Felix Czernilofsky
- grid.7700.00000 0001 2190 4373Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
| | - Tobias Roider
- grid.7700.00000 0001 2190 4373Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany ,grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory (EMBL), Heidelberg, Germany ,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
| | - Peter-Martin Bruch
- grid.7700.00000 0001 2190 4373Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany ,grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory (EMBL), Heidelberg, Germany ,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
| | - Murat Iskar
- grid.7497.d0000 0004 0492 0584Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Adam Kittai
- grid.261331.40000 0001 2285 7943Department of Internal Medicine, Division of Hematology, The Ohio State University, Columbus, OH USA
| | - Ying Huang
- grid.261331.40000 0001 2285 7943Department of Internal Medicine, Division of Hematology, The Ohio State University, Columbus, OH USA
| | - Junyan Lu
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory (EMBL), Heidelberg, Germany ,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
| | - Sarah Richter
- grid.7700.00000 0001 2190 4373Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
| | - Georgios Mermelekas
- grid.452834.c0000 0004 5911 2402Department of Oncology-Pathology, Karolinska Institute and Science for Life Laboratory, Stockholm, Sweden
| | - Husen Muhammad Umer
- grid.452834.c0000 0004 5911 2402Department of Oncology-Pathology, Karolinska Institute and Science for Life Laboratory, Stockholm, Sweden
| | - Mareike Knoll
- grid.7700.00000 0001 2190 4373Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
| | - Carolin Kolb
- grid.7700.00000 0001 2190 4373Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
| | - Angela Lenze
- grid.7700.00000 0001 2190 4373Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
| | - Xiaofang Cao
- grid.452834.c0000 0004 5911 2402Department of Oncology-Pathology, Karolinska Institute and Science for Life Laboratory, Stockholm, Sweden
| | - Cecilia Österholm
- grid.4714.60000 0004 1937 0626Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Linus Wahnschaffe
- grid.6190.e0000 0000 8580 3777Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf (CIO ABCD), Excellence Cluster for Cellular Stress Response and Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Carmen Herling
- grid.6190.e0000 0000 8580 3777Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf (CIO ABCD), Excellence Cluster for Cellular Stress Response and Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Sebastian Scheinost
- grid.461742.20000 0000 8855 0365Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matthias Ganzinger
- grid.7700.00000 0001 2190 4373Institute of Medical Biometry and Informatics, Heidelberg University, Heidelberg, Germany
| | - Larry Mansouri
- grid.4714.60000 0004 1937 0626Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Katharina Kriegsmann
- grid.7700.00000 0001 2190 4373Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
| | - Mark Kriegsmann
- grid.7700.00000 0001 2190 4373Institute of Pathology, University of Heidelberg, Heidelberg, Germany
| | - Simon Anders
- grid.7700.00000 0001 2190 4373Center for Molecular Biology of the University of Heidelberg (ZMBH), Heidelberg, Germany
| | - Marc Zapatka
- grid.7497.d0000 0004 0492 0584Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Giovanni Del Poeta
- grid.6530.00000 0001 2300 0941Division of Hematology, University of Tor Vergata, Rome, Italy
| | - Antonella Zucchetto
- grid.418321.d0000 0004 1757 9741Clinical and Experimental Onco-Hematology Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Riccardo Bomben
- grid.418321.d0000 0004 1757 9741Clinical and Experimental Onco-Hematology Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Valter Gattei
- grid.418321.d0000 0004 1757 9741Clinical and Experimental Onco-Hematology Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Peter Dreger
- grid.7700.00000 0001 2190 4373Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
| | - Jennifer Woyach
- grid.261331.40000 0001 2285 7943Department of Internal Medicine, Division of Hematology, The Ohio State University, Columbus, OH USA
| | - Marco Herling
- grid.6190.e0000 0000 8580 3777Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf (CIO ABCD), Excellence Cluster for Cellular Stress Response and Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Carsten Müller-Tidow
- grid.7700.00000 0001 2190 4373Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany ,grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory (EMBL), Heidelberg, Germany ,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
| | - Richard Rosenquist
- grid.4714.60000 0004 1937 0626Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden ,grid.24381.3c0000 0000 9241 5705Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Stephan Stilgenbauer
- grid.6582.90000 0004 1936 9748Department of Internal Medicine III, University of Ulm, Ulm, Germany
| | - Thorsten Zenz
- grid.461742.20000 0000 8855 0365Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.412004.30000 0004 0478 9977Department of Medical Oncology and Hematology, University Hospital Zürich, Zürich, Switzerland
| | - Wolfgang Huber
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory (EMBL), Heidelberg, Germany ,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
| | - Eugen Tausch
- grid.6582.90000 0004 1936 9748Department of Internal Medicine III, University of Ulm, Ulm, Germany
| | - Janne Lehtiö
- grid.452834.c0000 0004 5911 2402Department of Oncology-Pathology, Karolinska Institute and Science for Life Laboratory, Stockholm, Sweden
| | - Sascha Dietrich
- grid.7700.00000 0001 2190 4373Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany ,grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory (EMBL), Heidelberg, Germany ,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany ,grid.461742.20000 0000 8855 0365Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.14778.3d0000 0000 8922 7789Department of Hematolgy, Oncology and Immunolgy, University Hospital of Düsseldorf, Düsseldorf, Germany
| |
Collapse
|