1
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Mason M, Lapuente-Santana Ó, Halkola AS, Wang W, Mall R, Xiao X, Kaufman J, Fu J, Pfeil J, Banerjee J, Chung V, Chang H, Chasalow SD, Lin HY, Chai R, Yu T, Finotello F, Mirtti T, Mäyränpää MI, Bao J, Verschuren EW, Ahmed EI, Ceccarelli M, Miller LD, Monaco G, Hendrickx WRL, Sherif S, Yang L, Tang M, Gu SS, Zhang W, Zhang Y, Zeng Z, Das Sahu A, Liu Y, Yang W, Bedognetti D, Tang J, Eduati F, Laajala TD, Geese WJ, Guinney J, Szustakowski JD, Vincent BG, Carbone DP. A community challenge to predict clinical outcomes after immune checkpoint blockade in non-small cell lung cancer. J Transl Med 2024; 22:190. [PMID: 38383458 PMCID: PMC10880244 DOI: 10.1186/s12967-023-04705-3] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 11/05/2023] [Indexed: 02/23/2024] Open
Abstract
BACKGROUND Predictive biomarkers of immune checkpoint inhibitor (ICI) efficacy are currently lacking for non-small cell lung cancer (NSCLC). Here, we describe the results from the Anti-PD-1 Response Prediction DREAM Challenge, a crowdsourced initiative that enabled the assessment of predictive models by using data from two randomized controlled clinical trials (RCTs) of ICIs in first-line metastatic NSCLC. METHODS Participants developed and trained models using public resources. These were evaluated with data from the CheckMate 026 trial (NCT02041533), according to the model-to-data paradigm to maintain patient confidentiality. The generalizability of the models with the best predictive performance was assessed using data from the CheckMate 227 trial (NCT02477826). Both trials were phase III RCTs with a chemotherapy control arm, which supported the differentiation between predictive and prognostic models. Isolated model containers were evaluated using a bespoke strategy that considered the challenges of handling transcriptome data from clinical trials. RESULTS A total of 59 teams participated, with 417 models submitted. Multiple predictive models, as opposed to a prognostic model, were generated for predicting overall survival, progression-free survival, and progressive disease status with ICIs. Variables within the models submitted by participants included tumor mutational burden (TMB), programmed death ligand 1 (PD-L1) expression, and gene-expression-based signatures. The best-performing models showed improved predictive power over reference variables, including TMB or PD-L1. CONCLUSIONS This DREAM Challenge is the first successful attempt to use protected phase III clinical data for a crowdsourced effort towards generating predictive models for ICI clinical outcomes and could serve as a blueprint for similar efforts in other tumor types and disease states, setting a benchmark for future studies aiming to identify biomarkers predictive of ICI efficacy. TRIAL REGISTRATION CheckMate 026; NCT02041533, registered January 22, 2014. CheckMate 227; NCT02477826, registered June 23, 2015.
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Affiliation(s)
- Mike Mason
- Bristol Myers Squibb, Princeton, NJ, USA
| | - Óscar Lapuente-Santana
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Anni S Halkola
- Department of Mathematics and Statistics, University of Turku, Turku, Finland
| | - Wenyu Wang
- Faculty of Medicine, Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
| | - Raghvendra Mall
- Qatar Computing Research Institute, Hamad Bin Khalifa University, P.O. Box 34110, Doha, Qatar
- Department of Immunology, St. Jude Children's Research Hospital, P.O. Box 38105, Memphis, TN, USA
- Biotechnology Research Center, Technology Innovation Institute, P.O. Box 9639, Abu Dhabi, United Arab Emirates
| | - Xu Xiao
- School of Informatics, Xiamen University, Xiamen, China
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Jacob Kaufman
- Department of Medicine, Duke University, Durham, NC, USA
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Jingxin Fu
- Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | | | - Han Chang
- Bristol Myers Squibb, Princeton, NJ, USA
| | | | | | | | | | - Francesca Finotello
- Institute of Molecular Biology, University of Innsbruck, Innsbruck, Austria
- Digital Science Center (DiSC), University of Innsbruck, Innsbruck, Austria
| | - Tuomas Mirtti
- Department of Pathology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
- iCAN-Digital Precision Cancer Medicine Flagship, Helsinki, Finland
- Department of Biomedical Engineering, School of Medicine, Emory University, Atlanta, GA, USA
| | - Mikko I Mäyränpää
- Department of Pathology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Jie Bao
- Faculty of Medicine, Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
| | - Emmy W Verschuren
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Eiman I Ahmed
- Human Immunology Department, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Michele Ceccarelli
- Department of Electrical Engineering and Information Technology (DIETI), University of Naples "Federico II", 80125, Naples, Italy
- BIOGEM Institute of Molecular Biology and Genetics, Via Camporeale, Ariano Irpino, Italy
| | - Lance D Miller
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Atrium Health Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC, USA
| | - Gianni Monaco
- BIOGEM Institute of Molecular Biology and Genetics, Via Camporeale, Ariano Irpino, Italy
| | - Wouter R L Hendrickx
- Human Immunology Department, Sidra Medicine, P.O. Box 26999, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, P.O. Box 26999, Doha, Qatar
| | - Shimaa Sherif
- Human Immunology Department, Sidra Medicine, P.O. Box 26999, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, P.O. Box 26999, Doha, Qatar
| | - Lin Yang
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ming Tang
- Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | - Yi Zhang
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Zexian Zeng
- Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Yang Liu
- Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Davide Bedognetti
- Human Immunology Department, Sidra Medicine, P.O. Box 26999, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, P.O. Box 26999, Doha, Qatar
- Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
| | - Jing Tang
- Faculty of Medicine, Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Federica Eduati
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Teemu D Laajala
- Department of Mathematics and Statistics, University of Turku, Turku, Finland
- Department of Pathology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
- iCAN-Digital Precision Cancer Medicine Flagship, Helsinki, Finland
- FICAN West Cancer Centre, University of Turku and Turku University Hospital, Turku, Finland
- Department of Pharmacology, Anschutz Medical Campus, University of Colorado, Denver, CO, USA
| | | | | | | | - Benjamin G Vincent
- Department of Medicine, Division of Hematology, Department of Microbiology and Immunology, Curriculum in Bioinformatics and Computational Biology, Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - David P Carbone
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA.
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2
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Kudling TV, Clubb JH, Pakola S, Quixabeira DC, Lähdeniemi IA, Heiniö C, Arias V, Havunen R, Cervera-Carrascon V, Santos JM, Sutinen E, Räsänen J, Borenius K, Mäyränpää MI, Aaltonen E, Sorsa S, Hemminki O, Kanerva A, Verschuren EW, Ilonen I, Hemminki A. Effective intravenous delivery of adenovirus armed with TNFα and IL-2 improves anti-PD-1 checkpoint blockade in non-small cell lung cancer. Oncoimmunology 2023; 12:2241710. [PMID: 37546696 PMCID: PMC10399490 DOI: 10.1080/2162402x.2023.2241710] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/24/2023] [Accepted: 07/24/2023] [Indexed: 08/08/2023] Open
Abstract
Lung cancer remains among the most difficult-to-treat malignancies and is the leading cause of cancer-related deaths worldwide. The introduction of targeted therapies and checkpoint inhibitors has improved treatment outcomes; however, most patients with advanced-stage non-small cell lung cancer (NSCLC) eventually fail these therapies. Therefore, there is a major unmet clinical need for checkpoint refractory/resistant NSCLC. Here, we tested the combination of aPD-1 and adenovirus armed with TNFα and IL-2 (Ad5-CMV-mTNFα/mIL-2) in an immunocompetent murine NSCLC model. Moreover, although local delivery has been standard for virotherapy, treatment was administered intravenously to facilitate clinical translation and putative routine use. We showed that treatment of tumor-bearing animals with aPD-1 in combination with intravenously injected armed adenovirus significantly decreased cancer growth, even in the presence of neutralizing antibodies. We observed an increased frequency of cytotoxic tumor-infiltrating lymphocytes, including tumor-specific cells. Combination treatment led to a decreased percentage of immunosuppressive tumor-associated macrophages and an improvement in dendritic cell maturation. Moreover, we observed expansion of the tumor-specific memory T cell compartment in secondary lymphoid organs in the group that received aPD-1 with the virus. However, although the non-replicative Ad5-CMV-mTNFα/mIL-2 virus allows high transgene expression in the murine model, it does not fully reflect the clinical outcome in humans. Thus, we complemented our findings using NSCLC ex vivo models fully permissive for the TNFα and IL-2- armed oncolytic adenovirus TILT-123. Overall, our data demonstrate the ability of systemically administered adenovirus armed with TNFα and IL-2 to potentiate the anti-tumor efficacy of aPD-1 and warrant further investigation in clinical trials.
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Affiliation(s)
- Tatiana V. Kudling
- Cancer Gene Therapy Group, Translational Immunology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - James H.A. Clubb
- Cancer Gene Therapy Group, Translational Immunology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- TILT Biotherapeutics Ltd, Helsinki, Finland
| | - Santeri Pakola
- Cancer Gene Therapy Group, Translational Immunology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Dafne C.A. Quixabeira
- Cancer Gene Therapy Group, Translational Immunology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- TILT Biotherapeutics Ltd, Helsinki, Finland
| | - Iris A.K. Lähdeniemi
- Translational Lung Cancer Research Group, Institute for Molecular Medicine Finland (FIMM), HiLife, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Camilla Heiniö
- Cancer Gene Therapy Group, Translational Immunology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Victor Arias
- Cancer Gene Therapy Group, Translational Immunology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Riikka Havunen
- Cancer Gene Therapy Group, Translational Immunology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- TILT Biotherapeutics Ltd, Helsinki, Finland
| | - Victor Cervera-Carrascon
- Cancer Gene Therapy Group, Translational Immunology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- TILT Biotherapeutics Ltd, Helsinki, Finland
| | - Joao M. Santos
- Cancer Gene Therapy Group, Translational Immunology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- TILT Biotherapeutics Ltd, Helsinki, Finland
| | - Eva Sutinen
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
- Individualized Drug Therapy Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Pulmonary Medicine, Heart and Lung Center, Helsinki University Hospital, Helsinki, Finland
| | - Jari Räsänen
- General Thoracic and Esophageal Surgery, Heart and Lung Center, Helsinki University Hospital and Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Kristian Borenius
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
- General Thoracic and Esophageal Surgery, Heart and Lung Center, Helsinki University Hospital and Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Mikko I. Mäyränpää
- Pathology, University of Helsinki and Helsinki University Hospital (HUSLAB), Helsinki, Finland
| | - Eero Aaltonen
- Faculty of Medicine, Medicum, University of Helsinki, Helsinki, Finland
| | - Suvi Sorsa
- Cancer Gene Therapy Group, Translational Immunology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- TILT Biotherapeutics Ltd, Helsinki, Finland
| | - Otto Hemminki
- Comprehensive Cancer Center, Helsinki University Hospital (HUS), Helsinki, Finland
- Department of Urology, Helsinki University Hospital, Helsinki, Finland
| | - Anna Kanerva
- Cancer Gene Therapy Group, Translational Immunology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Comprehensive Cancer Center, Helsinki University Hospital (HUS), Helsinki, Finland
- Department of Gynecology and Obstetrics, Helsinki University Hospital, Helsinki, Finland
| | - Emmy W. Verschuren
- Translational Lung Cancer Research Group, Institute for Molecular Medicine Finland (FIMM), HiLife, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Ilkka Ilonen
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
- General Thoracic and Esophageal Surgery, Heart and Lung Center, Helsinki University Hospital and Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Akseli Hemminki
- Cancer Gene Therapy Group, Translational Immunology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- TILT Biotherapeutics Ltd, Helsinki, Finland
- Comprehensive Cancer Center, Helsinki University Hospital (HUS), Helsinki, Finland
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3
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Lähdeniemi IAK, Devlin JR, Nagaraj AS, Talwelkar SS, Bao J, Linnavirta N, Şeref Vujaklija C, Kiss EA, Hemmes A, Verschuren EW. Development of an adenosquamous carcinoma histopathology - selective lung metastasis model. Biol Open 2022; 11:281292. [PMID: 36355420 PMCID: PMC9770245 DOI: 10.1242/bio.059623] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 11/02/2022] [Indexed: 11/12/2022] Open
Abstract
Preclinical tumor models with native tissue microenvironments provide essential tools to understand how heterogeneous tumor phenotypes relate to drug response. Here we present syngeneic graft models of aggressive, metastasis-prone histopathology-specific NSCLC tumor types driven by KRAS mutation and loss of LKB1 (KL): adenosquamous carcinoma (ASC) and adenocarcinoma (AC). We show that subcutaneous injection of primary KL; ASC cells results in squamous cell carcinoma (SCC) tumors with high levels of stromal infiltrates, lacking the source heterogeneous histotype. Despite forming subcutaneous tumors, intravenously injected KL;AC cells were unable to form lung tumors. In contrast, intravenous injection of KL;ASC cells leads to their lung re-colonization and lesions recapitulating the mixed AC and SCC histopathology, tumor immune suppressive microenvironment and oncogenic signaling profile of source tumors, demonstrating histopathology-selective phenotypic dominance over genetic drivers. Pan-ERBB inhibition increased survival, while selective ERBB1/EGFR inhibition did not, suggesting a role of the ERBB network crosstalk in resistance to ERBB1/EGFR. This immunocompetent NSCLC lung colonization model hence phenocopies key properties of the metastasis-prone ASC histopathology, and serves as a preclinical model to dissect therapy responses and metastasis-associated processes.
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Affiliation(s)
- Iris A. K. Lähdeniemi
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Jennifer R. Devlin
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Ashwini S. Nagaraj
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Sarang S. Talwelkar
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Jie Bao
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Nora Linnavirta
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Ceren Şeref Vujaklija
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Elina A. Kiss
- University of Helsinki and Wihuri Research Institute, Helsinki, Finland
| | - Annabrita Hemmes
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Emmy W. Verschuren
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland,Author for correspondence ()
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4
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Talwelkar SS, Mäyränpää MI, Schüler J, Linnavirta N, Hemmes A, Adinolfi S, Kankainen M, Sommergruber W, Levonen AL, Räsänen J, Knuuttila A, Verschuren EW, Wennerberg K. PI3Kβ inhibition enhances ALK-inhibitor sensitivity in ALK-rearranged lung cancer. Mol Oncol 2022; 17:747-764. [PMID: 36423211 PMCID: PMC10158778 DOI: 10.1002/1878-0261.13342] [Citation(s) in RCA: 2] [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: 04/07/2022] [Revised: 09/13/2022] [Accepted: 10/28/2022] [Indexed: 11/25/2022] Open
Abstract
Treatment with anaplastic lymphoma kinase (ALK) inhibitors significantly improves outcome for non-small-cell lung cancer (NSCLC) patients with ALK-rearranged tumors. However, clinical resistance typically develops over time and, in the majority of cases, resistance mechanisms are ALK-independent. We generated tumor cell cultures from multiple regions of an ALK-rearranged clinical tumor specimen and deployed functional drug screens to identify modulators of ALK-inhibitor response. This identified a role for PI3Kβ and EGFR inhibition in sensitizing the response regulating resistance to ALK inhibition. Inhibition of ALK elicited activation of EGFR, and subsequent MAPK and PI3K-AKT pathway reactivation. Sensitivity to ALK targeting was enhanced by inhibition or knockdown of PI3Kβ. In ALK-rearranged primary cultures, the combined inhibition of ALK and PI3Kβ prevented the EGFR-mediated ALK-inhibitor resistance, and selectively targeted the cancer cells. The combinatorial effect was seen also in the background of TP53 mutations and in epithelial-to-mesenchymal transformed cells. In conclusion, combinatorial ALK- and PI3Kβ-inhibitor treatment carries promise as a treatment for ALK-rearranged NSCLC.
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Affiliation(s)
- Sarang S Talwelkar
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Finland.,Institute of Biomedicine and MediCity Research Laboratories, University of Turku, Finland
| | - Mikko I Mäyränpää
- Department of Pathology, Helsinki University Hospital and University of Helsinki, Finland
| | - Julia Schüler
- Charles River Research Services, Germany GmbH, Freiburg im Breisgau, Germany
| | - Nora Linnavirta
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Finland
| | - Annabrita Hemmes
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Finland
| | - Simone Adinolfi
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Matti Kankainen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Finland
| | - Wolfgang Sommergruber
- Cancer Cell Signalling, Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria.,Department of Biotechnology, University of Applied Sciences, Vienna, Austria
| | - Anna-Liisa Levonen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Jari Räsänen
- Department of Thoracic Surgery, Heart and Lung Center, Helsinki University Hospital, Finland
| | - Aija Knuuttila
- Department of Pulmonary Medicine, Heart and Lung Center and Cancer Center, Helsinki University Hospital, Finland
| | - Emmy W Verschuren
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Finland.,iCAN Digital Precision Cancer Medicine Flagship, Finland.,Translational Cancer Medicine Research Program, Faculty of Medicine, University of Helsinki and Helsinki University Hospital, Finland
| | - Krister Wennerberg
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Finland.,Biotech Research & Innovation Centre (BRIC) and Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Denmark
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5
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Talwelkar SS, Lähdeniemi IA, Mäyränpää MI, Hemmes A, Linnavirta N, Räsänen J, Knuuttila A, Wennerberg K, Verschuren EW. Protocol to utilize fresh uncultured human lung tumor cells for personalized functional diagnostics. STAR Protoc 2022; 3:101720. [PMID: 36170112 PMCID: PMC9520273 DOI: 10.1016/j.xpro.2022.101720] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/02/2022] [Accepted: 08/29/2022] [Indexed: 01/26/2023] Open
Abstract
Drug sensitivity data acquired from solid tumor-derived cultures are often unsuitable for personalized treatment guidance due to the lengthy turnaround time. Here, we present a protocol for determining ex vivo drug sensitivities using fresh uncultured human lung tumor-derived EpCAM+ epithelial cells (FUTCs). We describe steps for drug testing in FUTCs to identify tumor cell-selective single or combination therapy in 72 h of sample processing. The FUTC-based approach can also be used to predict in vivo resistance to known targeted therapies. For complete details on the use and execution of this protocol, please refer to Talwelkar et al. (2021).
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Affiliation(s)
- Sarang S. Talwelkar
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, 00014 Helsinki, Finland,Institute of Biomedicine and MediCity Research Laboratories, University of Turku, Turku 20520, Finland
| | - Iris A.K. Lähdeniemi
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, 00014 Helsinki, Finland
| | - Mikko I. Mäyränpää
- Department of Pathology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Annabrita Hemmes
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, 00014 Helsinki, Finland
| | - Nora Linnavirta
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, 00014 Helsinki, Finland
| | - Jari Räsänen
- Department of Thoracic Surgery, Heart and Lung Center, Helsinki University Hospital, Helsinki, Finland
| | - Aija Knuuttila
- Department of Pulmonary Medicine, Heart and Lung Center and Cancer Center, Helsinki University Hospital, Helsinki, Finland
| | - Krister Wennerberg
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, 00014 Helsinki, Finland,BRIC - Biotech Research & Innovation Centre, University of Copenhagen, 2200 Copenhagen, Denmark,Corresponding author
| | - Emmy W. Verschuren
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, 00014 Helsinki, Finland,Corresponding author
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6
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Gao Y, Päivinen P, Tripathi S, Domènech-Moreno E, Wong IPL, Vaahtomeri K, Nagaraj AS, Talwelkar SS, Foretz M, Verschuren EW, Viollet B, Yan Y, Mäkelä TP. Inactivation of AMPK Leads to Attenuation of Antigen Presentation and Immune Evasion in Lung Adenocarcinoma. Clin Cancer Res 2021; 28:227-237. [PMID: 34667030 DOI: 10.1158/1078-0432.ccr-21-2049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 08/21/2021] [Accepted: 10/06/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE Mutations in STK11 (LKB1) occur in 17% of lung adenocarcinoma (LUAD) and drive a suppressive (cold) tumor immune microenvironment (TIME) and resistance to immunotherapy. The mechanisms underpinning the establishment and maintenance of a cold TIME in LKB1-mutant LUAD remain poorly understood. In this study, we investigated the role of the LKB1 substrate AMPK in immune evasion in human non-small cell lung cancer (NSCLC) and mouse models and explored the mechanisms involved. EXPERIMENTAL DESIGN We addressed the role of AMPK in immune evasion in NSCLC by correlating AMPK phosphorylation and immune-suppressive signatures and by deleting AMPKα1 (Prkaa1) and AMPKα2 (Prkaa2) in a KrasG12D -driven LUAD. Furthermore, we dissected the molecular mechanisms involved in immune evasion by comparing gene-expression signatures, AMPK activity, and immune infiltration in mouse and human LUAD and gain or loss-of-function experiments with LKB1- or AMPK-deficient cell lines. RESULTS Inactivation of both AMPKα1 and AMPKα2 together with Kras activation accelerated tumorigenesis and led to tumors with reduced infiltration of CD8+/CD4+ T cells and gene signatures associated with a suppressive TIME. These signatures recapitulate those in Lkb1-deleted murine LUAD and in LKB1-deficient human NSCLC. Interestingly, a similar signature is noted in human NSCLC with low AMPK activity. In mechanistic studies, we find that compromised LKB1 and AMPK activity leads to attenuated antigen presentation in both LUAD mouse models and human NSCLC. CONCLUSIONS The results provide evidence that the immune evasion noted in LKB1-inactivated lung cancer is due to subsequent inactivation of AMPK and attenuation of antigen presentation.
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Affiliation(s)
- Yajing Gao
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland.,HiLIFE-Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland.,Colorectal Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Pekka Päivinen
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland.,HiLIFE-Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Sushil Tripathi
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland.,HiLIFE-Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Eva Domènech-Moreno
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Iris P L Wong
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland.,HiLIFE-Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Kari Vaahtomeri
- Translational Cancer Medicine Research Program, Faculty of Medicine, University of Helsinki and Wihuri Research Institute, Helsinki, Finland
| | - Ashwini S Nagaraj
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Sarang S Talwelkar
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Marc Foretz
- Université de Paris, Institut Cochin, CNRS, INSERM, Paris, France
| | - Emmy W Verschuren
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Benoit Viollet
- Université de Paris, Institut Cochin, CNRS, INSERM, Paris, France
| | - Yan Yan
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland. .,HiLIFE-Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland.,Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Tomi P Mäkelä
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland.,HiLIFE-Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
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7
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Talwelkar SS, Mäyränpää MI, Søraas L, Potdar S, Bao J, Hemmes A, Linnavirta N, Lømo J, Räsänen J, Knuuttila A, Wennerberg K, Verschuren EW. Functional diagnostics using fresh uncultured lung tumor cells to guide personalized treatments. Cell Rep Med 2021; 2:100373. [PMID: 34467250 PMCID: PMC8385325 DOI: 10.1016/j.xcrm.2021.100373] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 07/08/2020] [Revised: 04/20/2021] [Accepted: 07/20/2021] [Indexed: 12/25/2022]
Abstract
Functional profiling of a cancer patient's tumor cells holds potential to tailor personalized cancer treatment. Here, we report the utility of fresh uncultured tumor-derived EpCAM+ epithelial cells (FUTCs) for ex vivo drug-response interrogation. Analysis of murine Kras mutant FUTCs demonstrates pharmacological and adaptive signaling profiles comparable to subtype-matched cultured cells. By applying FUTC profiling on non-small-cell lung cancer patient samples, we report robust drug-response data in 19 of 20 cases, with cells exhibiting targeted drug sensitivities corresponding to their oncogenic drivers. In one of these cases, an EGFR mutant lung adenocarcinoma patient refractory to osimertinib, FUTC profiling is used to guide compassionate treatment. FUTC profiling identifies selective sensitivity to disulfiram and the combination of carboplatin plus etoposide, and the patient receives substantial clinical benefit from treatment with these agents. We conclude that FUTC profiling provides a robust, rapid, and actionable assessment of personalized cancer treatment options.
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Affiliation(s)
- Sarang S. Talwelkar
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki 00014, Finland
| | - Mikko I. Mäyränpää
- HUSLAB, Division of Pathology, Helsinki University Hospital and University of Helsinki, Helsinki 00029, Finland
- Department of Pathology, University of Helsinki, Helsinki 00014, Finland
| | | | - Swapnil Potdar
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki 00014, Finland
| | - Jie Bao
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki 00014, Finland
| | - Annabrita Hemmes
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki 00014, Finland
| | - Nora Linnavirta
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki 00014, Finland
| | - Jon Lømo
- Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Jari Räsänen
- Department of Thoracic Surgery, Heart and Lung Center, Helsinki University Hospital, Helsinki, Finland
| | - Aija Knuuttila
- Department of Pulmonary Medicine, Heart and Lung Center, and Cancer Center, Helsinki University Hospital, Helsinki, Finland
| | - Krister Wennerberg
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki 00014, Finland
- BRIC-Biotech Research & Innovation Centre and Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, 2200 Copenhagen, Denmark
| | - Emmy W. Verschuren
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki 00014, Finland
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8
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Bao J, Närhi K, Teodòsio A, Hemmes A, Linnavirta NM, Mäyränpää MI, Salmenkivi K, Le Quesne J, Verschuren EW. SOX9 has distinct roles in the formation and progression of different non-small cell lung cancer histotypes. J Pathol 2021; 255:16-29. [PMID: 34021911 DOI: 10.1002/path.5733] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 04/25/2021] [Accepted: 05/19/2021] [Indexed: 12/16/2022]
Abstract
The transcription factor SOX9 is a key regulator of multiple developmental processes and is frequently re-expressed in non-small cell lung cancer (NSCLC). Its precise role in the progression of NSCLC histotypes has, however, remained elusive. We show that SOX9 expression relates to poor overall survival and invasive histopathology in human non-mucinous adenocarcinoma and is absent in murine early minimally invasive and low in human in situ adenocarcinoma. Interestingly, despite wide SOX9 expression across advanced NSCLC histotypes, its genetic deletion in the murine KrasG12D ;Lkb1fl/fl model selectively disrupted only the growth of papillary NSCLC, without affecting the initiation of precursor lesions or growth of mucinous or squamous tissue. Spatial tissue phenotyping indicated a requirement of SOX9 expression for the progression of surfactant protein C-expressing progenitor cells, which gave rise to papillary tumours. Intriguingly, while SOX9 expression was dispensable for squamous tissue formation, its loss in fact led to enhanced squamous tumour metastasis, which was associated with altered collagen IV deposition in the basement membrane. Our work therefore demonstrates histopathology-selective roles for SOX9 in NSCLC progression, namely as a promoter for papillary adenocarcinoma progression, but an opposing metastasis-suppressing role in squamous histotype tissue. This attests to a pleiotropic SOX9 function, linked to the cell of origin and microenvironmental tissue contexts. © 2021 The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd. on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Jie Bao
- Institute for Molecular Medicine Finland, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Katja Närhi
- Institute for Molecular Medicine Finland, HiLIFE, University of Helsinki, Helsinki, Finland.,GlaxoSmithKline, Espoo, Finland
| | - Ana Teodòsio
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Annabrita Hemmes
- Institute for Molecular Medicine Finland, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Nora M Linnavirta
- Institute for Molecular Medicine Finland, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Mikko I Mäyränpää
- HUSLAB, Division of Pathology, Helsinki University Hospital, Helsinki, Finland.,Department of Pathology, University of Helsinki, Helsinki, Finland
| | - Kaisa Salmenkivi
- Department of Pathology, University of Helsinki, Helsinki, Finland
| | - John Le Quesne
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK.,Leicester Cancer Research Centre, University of Leicester, Leicester, UK
| | - Emmy W Verschuren
- Institute for Molecular Medicine Finland, HiLIFE, University of Helsinki, Helsinki, Finland
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9
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Tervonen TA, Pant SM, Belitškin D, Englund JI, Närhi K, Haglund C, Kovanen PE, Verschuren EW, Klefström J. Oncogenic Ras Disrupts Epithelial Integrity by Activating the Transmembrane Serine Protease Hepsin. Cancer Res 2021; 81:1513-1527. [PMID: 33461973 DOI: 10.1158/0008-5472.can-20-1760] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 11/10/2020] [Accepted: 01/11/2021] [Indexed: 11/16/2022]
Abstract
Ras proteins play a causal role in human cancer by activating multiple pathways that promote cancer growth and invasion. However, little is known about how Ras induces the first diagnostic features of invasion in solid tumors, including loss of epithelial integrity and breaching of the basement membrane (BM). In this study, we found that oncogenic Ras strongly promotes the activation of hepsin, a member of the hepsin/TMPRSS type II transmembrane serine protease family. Mechanistically, the Ras-dependent hepsin activation was mediated via Raf-MEK-ERK signaling, which controlled hepsin protein stability through the heat shock transcription factor-1 stress pathway. In Ras-transformed three-dimensional mammary epithelial culture, ablation of hepsin restored desmosomal cell-cell junctions, hemidesmosomes, and BM integrity and epithelial cohesion. In tumor xenografts harboring mutant KRas, silencing of hepsin increased local invasion concomitantly with accumulation of collagen IV. These findings suggest that hepsin is a critical protease for Ras-dependent tumorigenesis, executing cell-cell and cell-matrix pathologies important for early tumor dissemination. SIGNIFICANCE: These findings identify the cell-surface serine protease hepsin as a potential therapeutic target for its role in oncogenic Ras-mediated deregulation of epithelial cell-cell and cell-matrix interactions and cohesion of epithelial structure.
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Affiliation(s)
- Topi A Tervonen
- Research Programs Unit/Translational Cancer Medicine and Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Shishir M Pant
- Research Programs Unit/Translational Cancer Medicine and Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Denis Belitškin
- Research Programs Unit/Translational Cancer Medicine and Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Johanna I Englund
- Research Programs Unit/Translational Cancer Medicine and Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Katja Närhi
- Research Programs Unit/Translational Cancer Medicine and Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Caj Haglund
- Research Programs Unit/Translational Cancer Medicine Research Program and Department of Surgery, Clinicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Panu E Kovanen
- Research Programs Unit/Translational Cancer Medicine and Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Department of Pathology, HUSLAB and Haartman Institute, Helsinki University Central Hospital and University of Helsinki, Helsinki, Finland
| | - Emmy W Verschuren
- Research Programs Unit/Translational Cancer Medicine and Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Juha Klefström
- Research Programs Unit/Translational Cancer Medicine and Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland. .,Finnish Cancer Institute, FICAN South, Helsinki University Hospital and Faculty of Medicine, University of Helsinki, Helsinki, Finland
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10
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Bao J, Walliander M, Kovács F, Nagaraj AS, Hemmes A, Sarhadi VK, Knuutila S, Lundin J, Horvath P, Verschuren EW. Spa-RQ: an Image Analysis Tool to Visualise and Quantify Spatial Phenotypes Applied to Non-Small Cell Lung Cancer. Sci Rep 2019; 9:17613. [PMID: 31772293 PMCID: PMC6879493 DOI: 10.1038/s41598-019-54038-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 02/20/2019] [Accepted: 11/06/2019] [Indexed: 12/14/2022] Open
Abstract
To facilitate analysis of spatial tissue phenotypes, we created an open-source tool package named ‘Spa-RQ’ for ‘Spatial tissue analysis: image Registration & Quantification’. Spa-RQ contains software for image registration (Spa-R) and quantitative analysis of DAB staining overlap (Spa-Q). It provides an easy-to-implement workflow for serial sectioning and staining as an alternative to multiplexed techniques. To demonstrate Spa-RQ’s applicability, we analysed the spatial aspects of oncogenic KRAS-related signalling activities in non-small cell lung cancer (NSCLC). Using Spa-R in conjunction with ImageJ/Fiji, we first performed annotation-guided tumour-by-tumour phenotyping using multiple signalling markers. This analysis showed histopathology-selective activation of PI3K/AKT and MAPK signalling in Kras mutant murine tumours, as well as high p38MAPK stress signalling in p53 null murine NSCLC. Subsequently, Spa-RQ was applied to measure the co-activation of MAPK, AKT, and their mutual effector mTOR pathway in individual tumours. Both murine and clinical NSCLC samples could be stratified into ‘MAPK/mTOR’, ‘AKT/mTOR’, and ‘Null’ signature subclasses, suggesting mutually exclusive MAPK and AKT signalling activities. Spa-RQ thus provides a robust and easy to use tool that can be employed to identify spatially-distributed tissue phenotypes.
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Affiliation(s)
- Jie Bao
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, 00014, Finland
| | - Margarita Walliander
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, 00014, Finland
| | | | - Ashwini S Nagaraj
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, 00014, Finland
| | - Annabrita Hemmes
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, 00014, Finland
| | - Virinder Kaur Sarhadi
- Department of Pathology, Haartman Institute, University of Helsinki, Helsinki, Finland
| | - Sakari Knuutila
- Department of Pathology, Haartman Institute, University of Helsinki, Helsinki, Finland
| | - Johan Lundin
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, 00014, Finland.,Department of Public Health Sciences, Karolinska Institutet, Stockholm, Sweden
| | - Peter Horvath
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, 00014, Finland.,Synthetic and Systems Biology Unit, Hungarian Academy of Sciences, Biological Research Center, Temesvári körút 62, 6726, Szeged, Hungary
| | - Emmy W Verschuren
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, 00014, Finland.
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11
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Talwelkar SS, Nagaraj AS, Devlin JR, Hemmes A, Potdar S, Kiss EA, Saharinen P, Salmenkivi K, Mäyränpää MI, Wennerberg K, Verschuren EW. Receptor Tyrosine Kinase Signaling Networks Define Sensitivity to ERBB Inhibition and Stratify Kras-Mutant Lung Cancers. Mol Cancer Ther 2019; 18:1863-1874. [DOI: 10.1158/1535-7163.mct-18-0573] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 07/19/2018] [Accepted: 07/10/2019] [Indexed: 11/16/2022]
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12
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Affiliation(s)
- Jennifer R Devlin
- 1 Institute for Molecular Medicine Finland (FIMM) University of Helsinki Helsinki, Finland and.,2 Division of Cancer Research Peter MacCallum Cancer Centre Parkville, Australia
| | - Emmy W Verschuren
- 1 Institute for Molecular Medicine Finland (FIMM) University of Helsinki Helsinki, Finland and
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13
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Nagaraj AS, Bao J, Hemmes A, Machado M, Närhi K, Verschuren EW. Establishment and Analysis of Tumor Slice Explants As a Prerequisite for Diagnostic Testing. J Vis Exp 2018. [PMID: 30582602 DOI: 10.3791/58569] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Organotypic primary tissue explant cultures, which include precision-cut slices, represent the three-dimensional (3-D) tissue architecture as well as the multicellular interactions of native tissue. Tissue slices immediately cut from freshly resected tumors preserve spatial aspects of intratumor heterogeneity (ITH), thus making them useful surrogates of in vivo biology. Careful optimization of tissue slice preparation and cultivation conditions is fundamental for the predictive diagnostic potential of tumor slice explants. In this regard, murine models are valuable, as these provide a consistent flow of tumor material to perform replicate and reproducible experiments. This protocol describes the culturing of murine lung tumor-derived tissue slices using a rotating incubation unit, a system that enables intermittent exposure of tissues to oxygen and nutrients. Our previous work showed that the use of rotating incubation units improves the viability of tissue compared to other culture methods, particularly floating slices and stagnant filter supports. Here, we further show that slice thickness influences the viability of cultured slices, suggesting that optimization of slice thickness should be done for different tissue types. Pronounced ITH in relevant oncogenic functions, such as signaling activities, stromal cell infiltration or expression of differentiation markers, necessitates evaluation of adjacent tissue slices for the expression of markers altered by drug treatment or cultivation itself. In summary, this protocol describes the generation of murine lung tumor slices and their culture on a rotating incubation unit and demonstrates how slices should be systematically analyzed for the expression of heterogeneous tissue markers, as a prerequisite prior to drug response studies.
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Affiliation(s)
- Ashwini S Nagaraj
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki
| | - Jie Bao
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki
| | - Annabrita Hemmes
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki
| | - Mafalda Machado
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki
| | - Katja Närhi
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki
| | - Emmy W Verschuren
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki;
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14
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Närhi K, Nagaraj AS, Parri E, Turkki R, van Duijn PW, Hemmes A, Lahtela J, Uotinen V, Mäyränpää MI, Salmenkivi K, Räsänen J, Linder N, Trapman J, Rannikko A, Kallioniemi O, Af Hällström TM, Lundin J, Sommergruber W, Anders S, Verschuren EW. Spatial aspects of oncogenic signalling determine the response to combination therapy in slice explants from Kras-driven lung tumours. J Pathol 2018; 245:101-113. [PMID: 29443392 PMCID: PMC5947161 DOI: 10.1002/path.5059] [Citation(s) in RCA: 12] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Revised: 12/21/2017] [Accepted: 02/07/2018] [Indexed: 12/23/2022]
Abstract
A key question in precision medicine is how functional heterogeneity in solid tumours informs therapeutic sensitivity. We demonstrate that spatial characteristics of oncogenic signalling and therapy response can be modelled in precision‐cut slices from Kras‐driven non‐small‐cell lung cancer with varying histopathologies. Unexpectedly, profiling of in situ tumours demonstrated that signalling stratifies mostly according to histopathology, showing enhanced AKT and SRC activity in adenosquamous carcinoma, and mitogen‐activated protein kinase (MAPK) activity in adenocarcinoma. In addition, high intertumour and intratumour variability was detected, particularly of MAPK and mammalian target of rapamycin (mTOR) complex 1 activity. Using short‐term treatment of slice explants, we showed that cytotoxic responses to combination MAPK and phosphoinositide 3‐kinase–mTOR inhibition correlate with the spatially defined activities of both pathways. Thus, whereas genetic drivers determine histopathology spectra, histopathology‐associated and spatially variable signalling activities determine drug sensitivity. Our study is in support of spatial aspects of signalling heterogeneity being considered in clinical diagnostic settings, particularly to guide the selection of drug combinations. © 2018 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Katja Närhi
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Ashwini S Nagaraj
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Elina Parri
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Riku Turkki
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Petra W van Duijn
- Department of Urology, Josephine Nefkens Institute, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Annabrita Hemmes
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Jenni Lahtela
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Virva Uotinen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Mikko I Mäyränpää
- Department of Pathology, University of Helsinki, Helsinki, Finland.,HUSLAB, Division of Pathology, Helsinki University Hospital, Helsinki, Finland
| | - Kaisa Salmenkivi
- HUSLAB, Division of Pathology, Helsinki University Hospital, Helsinki, Finland
| | - Jari Räsänen
- Heart and Lung Centre, Department of General Thoracic and Oesophageal Surgery, Helsinki University Hospital, Helsinki, Finland
| | - Nina Linder
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Jan Trapman
- Department of Pathology, Josephine Nefkens Institute, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Antti Rannikko
- Department of Urology, Helsinki University Hospital, Helsinki, Finland
| | - Olli Kallioniemi
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Taija M Af Hällström
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland.,Orion Corporation, Orion Pharma, Espoo, Finland
| | - Johan Lundin
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Wolfgang Sommergruber
- Department of Lead Discovery, Boehringer Ingelheim RCV GmbH & Co. KG, Vienna, Austria
| | - Simon Anders
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland.,Centre for Molecular Biology of the University of Heidelberg (ZMBH), Heidelberg, Germany
| | - Emmy W Verschuren
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
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15
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Nagaraj AS, Lahtela J, Hemmes A, Pellinen T, Blom S, Devlin JR, Salmenkivi K, Kallioniemi O, Mäyränpää MI, Närhi K, Verschuren EW. Cell of Origin Links Histotype Spectrum to Immune Microenvironment Diversity in Non-small-Cell Lung Cancer Driven by Mutant Kras and Loss of Lkb1. Cell Rep 2017; 18:673-684. [PMID: 28099846 DOI: 10.1016/j.celrep.2016.12.059] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [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: 07/09/2015] [Revised: 10/11/2016] [Accepted: 12/19/2016] [Indexed: 12/21/2022] Open
Abstract
Lung cancers exhibit pronounced functional heterogeneity, confounding precision medicine. We studied how the cell of origin contributes to phenotypic heterogeneity following conditional expression of KrasG12D and loss of Lkb1 (Kras;Lkb1). Using progenitor cell-type-restricted adenoviral Cre to target cells expressing surfactant protein C (SPC) or club cell antigen 10 (CC10), we show that Ad5-CC10-Cre-infected mice exhibit a shorter latency compared with Ad5-SPC-Cre cohorts. We further demonstrate that CC10+ cells are the predominant progenitors of adenosquamous carcinoma (ASC) tumors and give rise to a wider spectrum of histotypes that includes mucinous and acinar adenocarcinomas. Transcriptome analysis shows ASC histotype-specific upregulation of pro-inflammatory and immunomodulatory genes. This is accompanied by an ASC-specific immunosuppressive environment, consisting of downregulated MHC genes, recruitment of CD11b+ Gr-1+ tumor-associated neutrophils (TANs), and decreased T cell numbers. We conclude that progenitor cell-specific etiology influences the Kras;Lkb1-driven tumor histopathology spectrum and histotype-specific immune microenvironment.
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Affiliation(s)
- Ashwini S Nagaraj
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki 00014, Finland
| | - Jenni Lahtela
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki 00014, Finland
| | - Annabrita Hemmes
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki 00014, Finland
| | - Teijo Pellinen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki 00014, Finland
| | - Sami Blom
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki 00014, Finland
| | - Jennifer R Devlin
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki 00014, Finland
| | - Kaisa Salmenkivi
- HUSLAB, Division of Pathology, Helsinki University Hospital and University of Helsinki, Helsinki 00029, Finland
| | - Olli Kallioniemi
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki 00014, Finland; Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, 17165 Solna, Sweden
| | - Mikko I Mäyränpää
- HUSLAB, Division of Pathology, Helsinki University Hospital and University of Helsinki, Helsinki 00029, Finland; Department of Pathology, University of Helsinki, Helsinki 00014, Finland
| | - Katja Närhi
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki 00014, Finland
| | - Emmy W Verschuren
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki 00014, Finland.
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16
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Pekkonen P, Järviluoma A, Zinovkina N, Cvrljevic A, Prakash S, Westermarck J, Evan GI, Cesarman E, Verschuren EW, Ojala PM. KSHV viral cyclin interferes with T-cell development and induces lymphoma through Cdk6 and Notch activation in vivo. Cell Cycle 2015; 13:3670-84. [PMID: 25483078 PMCID: PMC4613844 DOI: 10.4161/15384101.2014.964118] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [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] [Indexed: 12/11/2022] Open
Abstract
Kaposi's sarcoma herpesvirus (KSHV)-encoded v-cyclin, a homolog of cellular cyclin D2, activates cellular CDK6, promotes G1-S transition of the cell cycle, induces DNA damage, apoptosis, autophagy and is reported to have oncogenic potential. Here we show that in vivo expression of v-cyclin in the B- and T-cell lymphocyte compartments results in a markedly low survival due to high penetrance of early-onset T-cell lymphoma and pancarditis. The v-cyclin transgenic mice have smaller pre-tumorigenic lymphoid organs, showing decreased cellularity, and increased proliferation and apoptosis. Furthermore, v-cyclin expression resulted in decreased amounts of CD3-expressing mature T-cells in the secondary lymphoid organs concurrent with alterations in the T-cell subpopulations of the thymus. This suggests that v-cyclin interferes with normal T-cell development. As the Notch pathway is recognized for its role in both T-cell development and lymphoma initiation, we addressed the role of Notch in the v-cyclin-induced alterations. Fittingly, we demonstrate induction of Notch3 and Hes1 in the pre-tumorigenic thymi and lymphomas of v-cyclin expressing mice, and show that lymphoma growth and viability are dependent on activated Notch signaling. Notch3 transcription and growth of the lymphomas was dependent on CDK6, as determined by silencing of CDK6 expression or chemical inhibition, respectively. Our work here reveals a viral cyclin-CDK6 complex as an upstream regulator of Notch receptor, suggesting that cyclins can play a role in the initiation of Notch-dependent lymphomagenesis.
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Affiliation(s)
- Pirita Pekkonen
- a Institute of Biotechnology ; University of Helsinki ; Helsinki , Finland
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17
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Lahtela J, Pradhan B, Närhi K, Hemmes A, Särkioja M, Kovanen PE, Brown A, Verschuren EW. The putative tumor suppressor gene EphA3 fails to demonstrate a crucial role in murine lung tumorigenesis or morphogenesis. Dis Model Mech 2015; 8:393-401. [PMID: 25713296 PMCID: PMC4381338 DOI: 10.1242/dmm.019257] [Citation(s) in RCA: 9] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 02/12/2015] [Indexed: 01/04/2023] Open
Abstract
Treatment of non-small cell lung cancer (NSCLC) is based on histological analysis and molecular profiling of targetable driver oncogenes. Therapeutic responses are further defined by the landscape of passenger mutations, or loss of tumor suppressor genes. We report here a thorough study to address the physiological role of the putative lung cancer tumor suppressor EPH receptor A3 (EPHA3), a gene that is frequently mutated in human lung adenocarcinomas. Our data shows that homozygous or heterozygous loss of EphA3 does not alter the progression of murine adenocarcinomas that result from Kras mutation or loss of Trp53, and we detected negligible postnatal expression of EphA3 in adult wild-type lungs. Yet, EphA3 was expressed in the distal mesenchyme of developing mouse lungs, neighboring the epithelial expression of its Efna1 ligand; this is consistent with the known roles of EPH receptors in embryonic development. However, the partial loss of EphA3 leads only to subtle changes in epithelial Nkx2-1, endothelial Cd31 and mesenchymal Fgf10 RNA expression levels, and no macroscopic phenotypic effects on lung epithelial branching, mesenchymal cell proliferation, or abundance and localization of CD31-positive endothelia. The lack of a discernible lung phenotype in EphA3-null mice might indicate lack of an overt role for EPHA3 in the murine lung, or imply functional redundancy between EPHA receptors. Our study shows how biological complexity can challenge in vivo functional validation of mutations identified in sequencing efforts, and provides an incentive for the design of knock-in or conditional models to assign the role of EPHA3 mutation during lung tumorigenesis.
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Affiliation(s)
- Jenni Lahtela
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki FI-00014, Finland
| | - Barun Pradhan
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki FI-00014, Finland
| | - Katja Närhi
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki FI-00014, Finland
| | - Annabrita Hemmes
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki FI-00014, Finland
| | - Merja Särkioja
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki FI-00014, Finland
| | - Panu E Kovanen
- Department of Pathology, HUSLAB and Haartman Institute, Helsinki University Central Hospital and University of Helsinki FI-00014, Finland
| | - Arthur Brown
- Spinal Cord Injury Team, Robarts Research Institute, University of Western Ontario, London, ON N6A 5K8, Canada
| | - Emmy W Verschuren
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki FI-00014, Finland.
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18
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Ho TH, Dang KX, Lintula S, Hotakainen K, Feng L, Olkkonen VM, Verschuren EW, Tenkanen T, Haglund C, Kolho KL, Stenman UH, Stenman J. Extendable blocking probe in reverse transcription for analysis of RNA variants with superior selectivity. Nucleic Acids Res 2014; 43:e4. [PMID: 25378315 PMCID: PMC4288146 DOI: 10.1093/nar/gku1048] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [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] [Indexed: 12/16/2022] Open
Abstract
Here we provide the first strategy to use a competitive Extendable Blocking Probe (ExBP) for allele-specific priming with superior selectivity at the stage of reverse transcription. In order to analyze highly similar RNA variants, a reverse-transcriptase primer whose sequence matches a specific variant selectively primes only that variant, whereas mismatch priming to the alternative variant is suppressed by virtue of hybridization and subsequent extension of the perfectly matched ExBP on that alternative variant template to form a cDNA-RNA hybrid. This hybrid will render the alternative RNA template unavailable for mismatch priming initiated by the specific primer in a hot-start protocol of reverse transcription when the temperature decreases to a level where such mismatch priming could occur. The ExBP-based reverse transcription assay detected BRAF and KRAS mutations in at least 1000-fold excess of wild-type RNA and detection was linear over a 4-log dynamic range. This novel strategy not only reveals the presence or absence of rare mutations with an exceptionally high selectivity, but also provides a convenient tool for accurate determination of RNA variants in different settings, such as quantification of allele-specific expression.
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Affiliation(s)
- Tho H Ho
- Minerva Foundation Institute for Medical Research, Helsinki, 00290, Finland
| | - Kien X Dang
- Minerva Foundation Institute for Medical Research, Helsinki, 00290, Finland
| | - Susanna Lintula
- Haartman Institute, Department of Clinical Chemistry, Biomedicum Helsinki, University of Helsinki and Helsinki University Central Hospital, Helsinki, FI-00029 HUS, Finland
| | - Kristina Hotakainen
- Haartman Institute, Department of Clinical Chemistry, Biomedicum Helsinki, University of Helsinki and Helsinki University Central Hospital, Helsinki, FI-00029 HUS, Finland Helsinki University Central Hospital, HUSLAB, Helsinki, 00029 HUS, Finland
| | - Lin Feng
- Minerva Foundation Institute for Medical Research, Helsinki, 00290, Finland
| | - Vesa M Olkkonen
- Minerva Foundation Institute for Medical Research, Helsinki, 00290, Finland
| | - Emmy W Verschuren
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, FI-00014, Finland
| | | | - Caj Haglund
- Department of Surgery, Helsinki University Central Hospital, Helsinki, 00029 HUS, Finland Research Program Unit, Translational Cancer Biology, University of Helsinki, Helsinki, FI-00014, Finland Haartman Institute, Department of Pathology, University of Helsinki, Helsinki, FI-00014, Finland
| | - Kaija-Leena Kolho
- Children's Hospital, University of Helsinki, Helsinki, FI-00014, Finland
| | - Ulf-Hakan Stenman
- Haartman Institute, Department of Clinical Chemistry, Biomedicum Helsinki, University of Helsinki and Helsinki University Central Hospital, Helsinki, FI-00029 HUS, Finland
| | - Jakob Stenman
- Minerva Foundation Institute for Medical Research, Helsinki, 00290, Finland Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, FI-00014, Finland Department of Women's and Children's Health, Karolinska Institutet, Stockholm, SE-17176, Sweden
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19
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Kakkola L, Denisova OV, Tynell J, Viiliäinen J, Ysenbaert T, Matos RC, Nagaraj A, Ohman T, Kuivanen S, Paavilainen H, Feng L, Yadav B, Julkunen I, Vapalahti O, Hukkanen V, Stenman J, Aittokallio T, Verschuren EW, Ojala PM, Nyman T, Saelens X, Dzeyk K, Kainov DE. Anticancer compound ABT-263 accelerates apoptosis in virus-infected cells and imbalances cytokine production and lowers survival rates of infected mice. Cell Death Dis 2013; 4:e742. [PMID: 23887633 PMCID: PMC3730437 DOI: 10.1038/cddis.2013.267] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [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: 02/26/2013] [Revised: 05/23/2013] [Accepted: 06/21/2013] [Indexed: 12/30/2022]
Abstract
ABT-263 and its structural analogues ABT-199 and ABT-737 inhibit B-cell lymphoma 2 (Bcl-2), BCL2L1 long isoform (Bcl-xL) and BCL2L2 (Bcl-w) proteins and promote cancer cell death. Here, we show that at non-cytotoxic concentrations, these small molecules accelerate the deaths of non-cancerous cells infected with influenza A virus (IAV) or other viruses. In particular, we demonstrate that ABT-263 altered Bcl-xL interactions with Bcl-2 antagonist of cell death (Bad), Bcl-2-associated X protein (Bax), uveal autoantigen with coiled-coil domains and ankyrin repeats protein (UACA). ABT-263 thereby activated the caspase-9-mediated mitochondria-initiated apoptosis pathway, which, together with the IAV-initiated caspase-8-mediated apoptosis pathway, triggered the deaths of IAV-infected cells. Our results also indicate that Bcl-xL, Bcl-2 and Bcl-w interact with pattern recognition receptors (PRRs) that sense virus constituents to regulate cellular apoptosis. Importantly, premature killing of IAV-infected cells by ABT-263 attenuated the production of key pro-inflammatory and antiviral cytokines. The imbalance in cytokine production was also observed in ABT-263-treated IAV-infected mice, which resulted in an inability of the immune system to clear the virus and eventually lowered the survival rates of infected animals. Thus, the results suggest that the chemical inhibition of Bcl-xL, Bcl-2 and Bcl-w could potentially be hazardous for cancer patients with viral infections.
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Affiliation(s)
- L Kakkola
- The Institute for Molecular Medicine Finland, FIMM, Helsinki 00290, Finland
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20
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Lahtela J, Corson LB, Hemmes A, Brauer MJ, Koopal S, Lee J, Hunsaker TL, Jackson PK, Verschuren EW. A high-content cellular senescence screen identifies candidate tumor suppressors, including EPHA3. Cell Cycle 2013; 12:625-34. [PMID: 23324396 PMCID: PMC3594263 DOI: 10.4161/cc.23515] [Citation(s) in RCA: 16] [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] [Indexed: 01/04/2023] Open
Abstract
Activation of a cellular senescence program is a common response to prolonged oncogene activation or tumor suppressor loss, providing a physiological mechanism for tumor suppression in premalignant cells. The link between senescence and tumor suppression supports the hypothesis that a loss-of-function screen measuring bona fide senescence marker activation should identify candidate tumor suppressors. Using a high-content siRNA screening assay for cell morphology and proliferation measures, we identify 12 senescence-regulating kinases and determine their senescence marker signatures, including elevation of senescence-associated β-galactosidase, DNA damage and p53 or p16INK4a expression. Consistent with our hypothesis, SNP array CGH data supports loss of gene copy number of five senescence-suppressing genes across multiple tumor samples. One such candidate is the EPHA3 receptor tyrosine kinase, a gene commonly mutated in human cancer. We demonstrate that selected intracellular EPHA3 tumor-associated point mutations decrease receptor expression level and/or receptor tyrosine kinase (RTK) activity. Our study therefore describes a new strategy to mine for novel candidate tumor suppressors and provides compelling evidence that EPHA3 mutations may promote tumorigenesis only when key senescence-inducing pathways have been inactivated.
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Affiliation(s)
- Jenni Lahtela
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
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21
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Peart MJ, Poyurovsky MV, Kass EM, Urist M, Verschuren EW, Summers MK, Jackson PK, Prives C. APC/C(Cdc20) targets E2F1 for degradation in prometaphase. Cell Cycle 2010; 9:3956-64. [PMID: 20948288 DOI: 10.4161/cc.9.19.13162] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The mechanisms that control E2F-1 activity are complex. We previously showed that Chk1 and Chk2 are required for E2F1 stabilization and p73 target gene induction following DNA damage. To gain further insight into the processes regulating E2F1 protein stability, we focused our investigation on the mechanisms responsible for regulating E2F1 turnover. Here we show that E2F1 is a substrate of the anaphase promoting complex or cyclosome (APC/C), a ubiquitin ligase that plays an important role in cell cycle progression. Ectopic expression of the APC/C activators Cdh1 and Cdc20 reduced the levels of co-expressed E2F-1 protein. Co-expression of DP1 with E2F1 blocked APC/C-induced E2F1 degradation, suggesting that the E2F1/DP1 heterodimer is protected from APC/C regulation. Following Cdc20 knockdown, E2F1 levels increased and remained stable in extracts over a time course, indicating that APC/C(Cdc20) is a primary regulator of E2F1 stability in vivo. Moreover, cell synchronization experiments showed that siRNA directed against Cdc20 induced an accumulation of E2F1 protein in prometaphase cells. These data suggest that APC/C(Cdc20) specifically targets E2F1 for degradation in early mitosis and reveal a novel mechanism for limiting free E2F1 levels in cells, failure of which may compromise cell survival and/or homeostasis.
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Affiliation(s)
- Melissa J Peart
- Department of Biological Sciences, Columbia University, New York, NY, USA
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22
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Verschuren EW, Ban KH, Masek MA, Lehman NL, Jackson PK. Loss of Emi1-dependent anaphase-promoting complex/cyclosome inhibition deregulates E2F target expression and elicits DNA damage-induced senescence. Mol Cell Biol 2007; 27:7955-65. [PMID: 17875940 PMCID: PMC2169152 DOI: 10.1128/mcb.00908-07] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Expression of the anaphase-promoting complex/cyclosome (APC/C) inhibitor Emi1 is required for the accumulation of APC/C substrates crucial for DNA synthesis and mitotic entry. We show that in vivo Emi1 expression correlates with the proliferative status of the cellular compartment and that cells lacking Emi1 undergo cellular senescence. Emi1 depletion leads to strong decreases in E2F target mRNA and APC/C substrate protein abundances. However, cyclin E mRNA and cyclin E protein levels and associated kinase activities are increased. Cells lacking Emi1 undergo DNA damage, likely explained by replication stress upon deregulated cyclin E- and A-associated kinase activities. Inhibition of ATM kinase prevents induction of senescence, implying that senescence is a consequence of DNA damage. Surprisingly, no senescence or no extensive amount of senescence is evident upon depletion of the Emi1-stabilizing factor Evi5 or Pin1, respectively. Our data suggest that maintenance of a protein stabilization/mRNA expression positive-feedback circuit fueled by Emi1 is required for accurate cell cycle progression, maintenance of DNA integrity, and prevention of cellular senescence.
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Affiliation(s)
- Emmy W Verschuren
- Department of Tumor Biology and Angiogenesis, Genentech Inc., 1 DNA way, South San Francisco, California 94080, USA
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23
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Abstract
The tumor suppressor function of the retinoblastoma protein (pRb) is historically attributed to inhibition of E2F gene transcription. In a recent issue of Nature Cell Biology, Binné and colleagues show that pRB is physically linked to the active anaphase-promoting complex/cyclosome (APC/C) ubiquitin ligase, suggesting that pRB-mediated tumor suppression may also function by directing the local degradation of E2F targets, including Skp2 (Binné et al., 2006).
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24
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Marangos P, Verschuren EW, Chen R, Jackson PK, Carroll J. Prophase I arrest and progression to metaphase I in mouse oocytes are controlled by Emi1-dependent regulation of APC(Cdh1). ACTA ACUST UNITED AC 2006; 176:65-75. [PMID: 17190794 PMCID: PMC2063628 DOI: 10.1083/jcb.200607070] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Mammalian oocytes are arrested in prophase of the first meiotic division. Progression into the first meiotic division is driven by an increase in the activity of maturation-promoting factor (MPF). In mouse oocytes, we find that early mitotic inhibitor 1 (Emi1), an inhibitor of the anaphase-promoting complex (APC) that is responsible for cyclin B destruction and inactivation of MPF, is present at prophase I and undergoes Skp1–Cul1–F-box/βTrCP-mediated destruction immediately after germinal vesicle breakdown (GVBD). Exogenous Emi1 or the inhibition of Emi1 destruction in prophase-arrested oocytes leads to a stabilization of cyclin B1–GFP that is sufficient to trigger GVBD. In contrast, the depletion of Emi1 using morpholino oligonucleotides increases cyclin B1–GFP destruction, resulting in an attenuation of MPF activation and a delay of entry into the first meiotic division. Finally, we show that Emi1-dependent effects on meiosis I require the presence of Cdh1. These observations reveal a novel mechanism for the control of entry into the first meiotic division: an Emi1-dependent inhibition of APCCdh1.
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Affiliation(s)
- Petros Marangos
- Department of Physiology, University College London, London WC1E 6BT, England, UK.
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25
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Lehman NL, Verschuren EW, Hsu JY, Cherry AM, Jackson PK. Overexpression of the anaphase promoting complex/cyclosome inhibitor Emi1 leads to tetraploidy and genomic instability of p53-deficient cells. Cell Cycle 2006; 5:1569-73. [PMID: 16861914 DOI: 10.4161/cc.5.14.2925] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The anaphase promoting complex/cyclosome (APC/C) is an E3 ubiquitin ligase that controls the cell cycle by directing the ubiquitin-dependent proteolysis of S-phase and mitosis promoting factors. Emi1 is an E2F transcriptional target that drives cell cycle progression from G1/S through early mitosis by inhibiting the APC/C's ubiquitin ligase activity, and thus facilitates accumulation of APC/C substrates. Using cell culture model systems, we found that Emi1 overexpression leads to proliferation, tetraploidy and genome instability of cells deficient for p53. We propose that loss of pRb repression of E2F-mediated transcription causing misregulation of Emi1 and APC/C substrates results in the generation of tetraploidy and proliferation of genomically unstable cells in the absence of normal p53 function. This represents a potentially important mechanism by which pRb and p53 dysfunction may contribute to tumorigenesis through the generation of genomic instability.
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Affiliation(s)
- Norman L Lehman
- Department of Pathology, Stanford University, Stanford, California 94305, USA.
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26
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Eldridge AG, Loktev AV, Hansen DV, Verschuren EW, Reimann JD, Jackson PK. The Evi5 Oncogene Regulates Cyclin Accumulation by Stabilizing the Anaphase-Promoting Complex Inhibitor Emi1. Cell 2006. [DOI: 10.1016/j.cell.2006.03.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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27
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Eldridge AG, Loktev AV, Hansen DV, Verschuren EW, Reimann JDR, Jackson PK. The evi5 oncogene regulates cyclin accumulation by stabilizing the anaphase-promoting complex inhibitor emi1. Cell 2006; 124:367-80. [PMID: 16439210 DOI: 10.1016/j.cell.2005.10.038] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2005] [Revised: 08/18/2005] [Accepted: 10/21/2005] [Indexed: 01/13/2023]
Abstract
The anaphase-promoting complex/cyclosome (APC/C) inhibitor Emi1 controls progression to S phase and mitosis by stabilizing key APC/C ubiquitination substrates, including cyclin A. Examining Emi1 binding proteins, we identified the Evi5 oncogene as a regulator of Emi1 accumulation. Evi5 antagonizes SCF(betaTrCP)-dependent Emi1 ubiquitination and destruction by binding to a site adjacent to Emi1's DSGxxS degron and blocking both degron phosphorylation by Polo-like kinases and subsequent betaTrCP binding. Thus, Evi5 functions as a stabilizing factor maintaining Emi1 levels in S/G2 phase. Evi5 protein accumulates in early G1 following Plk1 destruction and is degraded in a Plk1- and ubiquitin-dependent manner in early mitosis. Ablation of Evi5 induces precocious degradation of Emi1 by the Plk/SCF(betaTrCP) pathway, causing premature APC/C activation; cyclin destruction; cell-cycle arrest; centrosome overduplication; and, finally, mitotic catastrophe. We propose that the balance of Evi5 and Polo-like kinase activities determines the timely accumulation of Emi1 and cyclin, ensuring mitotic fidelity.
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Affiliation(s)
- Adam G Eldridge
- Department of Cancer Biology, Stanford University School of Medicine, CA 94305, USA
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28
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Christophorou MA, Martin-Zanca D, Soucek L, Lawlor ER, Brown-Swigart L, Verschuren EW, Evan GI. Temporal dissection of p53 function in vitro and in vivo. Nat Genet 2005; 37:718-26. [PMID: 15924142 DOI: 10.1038/ng1572] [Citation(s) in RCA: 150] [Impact Index Per Article: 7.9] [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: 11/29/2004] [Accepted: 04/22/2005] [Indexed: 11/09/2022]
Abstract
To investigate the functions of the p53 tumor suppressor, we created a new knock-in gene replacement mouse model in which the endogenous Trp53 gene is substituted by one encoding p53ER(TAM), a p53 fusion protein whose function is completely dependent on ectopic provision of 4-hydroxytamoxifen. We show here that both tissues in vivo and cells in vitro derived from such mice can be rapidly toggled between wild-type and p53 knockout states. Using this rapid perturbation model, we define the kinetics, dependence, persistence and reversibility of p53-mediated responses to DNA damage in tissues in vivo and to activation of the Ras oncoprotein and stress in vitro. This is the first example to our knowledge of a new class of genetic model that allows the specific, rapid and reversible perturbation of the function of a single endogenous gene in vivo.
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MESH Headings
- Animals
- Apoptosis/drug effects
- Apoptosis/radiation effects
- Cells, Cultured
- DNA Damage/drug effects
- Embryo, Mammalian/cytology
- Fibroblasts/metabolism
- Gamma Rays
- Gene Expression Regulation, Neoplastic
- Genes, p53
- Genes, ras/genetics
- Intestine, Small/drug effects
- Intestine, Small/pathology
- Intestine, Small/radiation effects
- Mice
- Mice, Transgenic
- Models, Animal
- Neoplasms/genetics
- Neoplasms/metabolism
- Neoplasms/pathology
- Spleen/drug effects
- Spleen/pathology
- Spleen/radiation effects
- Tamoxifen/analogs & derivatives
- Tamoxifen/pharmacology
- Thymus Gland/drug effects
- Thymus Gland/pathology
- Thymus Gland/radiation effects
- Time Factors
- Tumor Suppressor Protein p53/genetics
- Tumor Suppressor Protein p53/physiology
- Whole-Body Irradiation
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Affiliation(s)
- Maria A Christophorou
- Cancer Research Institute, University of California San Francisco Comprehensive Cancer Center, San Francisco, California 94143-0875, USA
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29
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Abstract
A timely coordination of cellular DNA synthesis and division cycles is governed by the temporal and spatial activation of cyclin-dependent kinases (Cdks). The primary regulation of Cdk activation is through binding to partner cyclin proteins. Several gammaherpesviruses encode a viral homologue of cellular cyclin D, which may function to deregulate host cell cycle progression. One of these is encoded by Kaposi's sarcoma-associated herpesvirus (KSHV) and is called K cyclin or viral cyclin (v-cyclin). v-Cyclin is expressed in most of the malignant cells that are associated with KSHV infection in humans, labelling v-cyclin as a putative viral oncogene. Here are described some of the major structural and functional properties of mammalian cyclin/Cdk complexes, some of which are phenocopied by v-cyclin. In addition, the molecular events leading to orderly progression through the G1/S and G/M cell cycle phases are reviewed. This molecular picture serves as a platform on which to explain v-cyclin-specific functional properties. Interesting but largely speculative issues concern the interplay between v-cyclin-mediated cell cycle deregulation and molecular progression of KSHV-associated neoplasms.
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Affiliation(s)
- Emmy W Verschuren
- Stanford University, Pathology Department, 300 Pasteur Drive, MC 5324, Stanford, CA 94305, USA
| | - Nic Jones
- Paterson Institute for Cancer Research, Christie Hospital NHS Trust, Manchester M20 4BX, UK
| | - Gerard I Evan
- Cancer Research Institute and Department of Cellular and Molecular Pharmacology, University of California San Francisco, CA 94143-0875, USA
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30
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Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) encodes a cyclin D homolog, K cyclin, that is thought to promote viral oncogenesis. However, expression of K cyclin in cultured cells not only triggers cell cycle progression but also engages the p53 tumor suppressor pathway, which probably restricts the oncogenic potential of K cyclin. Therefore, to assess the tumorigenic properties of K cyclin in vivo, we transgenically targeted expression of K cyclin to the B and T lymphocyte compartments via the E micro promoter/enhancer. Around 17% of E micro -K cyclin animals develop lymphoma by 9 months of age, and all such lymphomas exhibit loss of p53. A critical role of p53 in suppressing K cyclin-induced lymphomagenesis was confirmed by the greatly accelerated onset of B and T lymphomagenesis in all E micro -K cyclin/p53(-/-) mice. However, absence of p53 did not appear to accelerate K cyclin-induced lymphomagenesis by averting apoptosis: E micro -K cyclin/p53(-/-) end-stage lymphomas contained abundant apoptotic cells, and transgenic E micro -K cyclin/p53(-/-) lymphocytes in vitro were not measurably protected from DNA damage-induced apoptosis compared with E micro -K cyclin/p53(wt) cells. Notably, whereas aneuploidy was frequently evident in pre-lymphomatous tissues, end-stage E micro -K cyclin/p53(-/-) tumors showed a near-diploid DNA content with no aberrant centrosome numbers. Nonetheless, such tumor cells did harbor more restricted genomic alterations, such as single-copy chromosome losses or gains or high-level amplifications. Together, our data support a model in which K cyclin-induced genome instability arises early in the pre-tumorigenic lymphocyte population and that loss of p53 licenses subsequent expansion of tumorigenic clones.
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Affiliation(s)
- Emmy W Verschuren
- Comprehensive Cancer Center and Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, USA
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31
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Klefstrom J, Verschuren EW, Evan G. c-Myc augments the apoptotic activity of cytosolic death receptor signaling proteins by engaging the mitochondrial apoptotic pathway. J Biol Chem 2002; 277:43224-32. [PMID: 12202489 DOI: 10.1074/jbc.m206967200] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Activation of c-Myc sensitizes cells to apoptosis induction by ligand-activated death receptors. Such sensitization to death receptors by oncogenes may well be the mechanism underlying tumor cell sensitivity to tumor necrosis factor (TNF) or TNF-related apoptosis-inducing ligand (TRAIL). The mechanism by which this c-Myc-induced sensitization occurs is unclear but could involve modulation of expression of death receptors or their ligands or potentiation of the sensitivity of mitochondria to release pro-apoptotic effectors such as holocytochrome c. Here, we show that ectopic expression of the death receptor signaling protein RIP (receptor-interactive protein) triggers apoptosis via a FAS-associated death domain protein (FADD) and caspase 8-dependent pathway. Induction of apoptosis by this intracellular activation of the death receptor signaling pathway is significantly augmented by c-Myc expression. Moreover, c-Myc expression strongly promotes the potential of RIP to induce cytochrome c release from mitochondria. This implicates the mitochondrial apoptotic pathway in this synergy, a notion confirmed by the inability of c-Myc to sensitize to RIP killing in cells lacking the obligate mitochondrial apoptotic effectors Bax and Bak. We conclude that the lethality of the RIP-activated cytosolic caspase 8 pathway is augmented by c-Myc priming mitochondria to release cytochrome c. This places the intersection of apoptotic synergy between c-Myc and death receptor signaling downstream of the death receptors.
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Affiliation(s)
- Juha Klefstrom
- University of California, San Francisco Comprehensive Cancer Center, San Francisco, Calfornia 94115, USA
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32
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Abstract
Expression of the Kaposi's sarcoma-associated herpesvirus (KSHV) cyclin D homolog, K cyclin, is thought to contribute to viral oncogenesis. We show that K cyclin expression in primary cells sensitizes to apoptosis and induces growth arrest, both of which are dependent on p53 but independent of E2F1 or p19(ARF). DNA synthesis, but not cytokinesis, continues in K cyclin-expressing cells, leading to multinucleation and polyploidy. Such polyploid cells exhibit pronounced centrosome amplification and consequent aneuploidy. Our data suggest that K cyclin expression leads to cytokinesis defects and polyploidy, which activates p53. However, in the absence of p53, such cells survive and expand as an aneuploid population. Corroborating these findings, in vivo Emu; K cyclin expression cooperates with p53 loss in the induction of lymphomas.
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Affiliation(s)
- Emmy W Verschuren
- Cancer Research Institute, University of California, San Francisco, San Francisco, CA 94115, USA
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33
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Gringhuis SI, de Leij LF, Verschuren EW, Borger P, Vellenga E. Interleukin-7 upregulates the interleukin-2-gene expression in activated human T lymphocytes at the transcriptional level by enhancing the DNA binding activities of both nuclear factor of activated T cells and activator protein-1. Blood 1997; 90:2690-700. [PMID: 9326236] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
In the present report, we studied the role of the stromal-derived cytokine interleukin-7 (IL-7) in the IL-2-gene regulation in activated T lymphocytes. Production of IL-2 requires the formation of transcription factors involved in the IL-2-gene regulation. T-cell receptor (TCR)/CD3 engagement results in the activation of nuclear factor of activated T cells (NFAT), activator protein-1 (AP-1), and nuclear factor kappaB (NFkappaB), whereas the CD28 responsive complex (CD28RC) is activated in response to the CD28 signal. Costimulation of phytohemagglutinin/anti-CD28 activated T lymphocytes with IL-7 induces a fivefold enhanced IL-2-mRNA accumulation and a 2.5-fold enhanced protein secretion. The IL-2-gene transcription rate is increased 3.4-fold, indicating that the effect of IL-7 is in part mediated at the transcriptional level. The molecular mechanisms underlying the IL-7 effect involve the upregulation of the DNA binding activity of NFAT (60%) and AP-1 (120%), without affecting the activities of NFkappaB and CD28RC, which was confirmed by transfection assays. We also show that the IL-7-induced enhancement of the AP-1-DNA binding activity is not cyclosporin A-sensitive. Since AP-1 is part of the NFAT complex, we conclude that the IL-7-signaling pathway is involved in the activation of the fos and jun proteins of which AP-1 consists.
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Affiliation(s)
- S I Gringhuis
- Department of Internal Medicine, University of Groningen, The Netherlands
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