1
|
Dias MH, Friskes A, Wang S, Fernandes Neto JM, van Gemert F, Mourragui S, Papagianni C, Kuiken HJ, Mainardi S, Alvarez-Villanueva D, Lieftink C, Morris B, Dekker A, van Dijk E, Wilms LHS, da Silva MS, Jansen RA, Mulero-Sanchez A, Malzer E, Vidal A, Santos C, Salazar R, Wailemann RAM, Torres TEP, De Conti G, Raaijmakers JA, Snaebjornsson P, Yuan S, Qin W, Kovach JS, Armelin HA, Te Riele H, van Oudernaarden A, Jin H, Beijersbergen RL, Villanueva A, Medema RH, Bernards R. Paradoxical activation of oncogenic signaling as a cancer treatment strategy. Cancer Discov 2024:742013. [PMID: 38533987 DOI: 10.1158/2159-8290.cd-23-0216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 12/06/2023] [Accepted: 03/19/2024] [Indexed: 03/28/2024]
Abstract
Cancer homeostasis depends on a balance between activated oncogenic pathways driving tumorigenesis and engagement of stress-response programs that counteract the inherent toxicity of such aberrant signaling. While inhibition of oncogenic signaling pathways has been explored extensively, there is increasing evidence that overactivation of the same pathways can also disrupt cancer homeostasis and cause lethality. We show here that inhibition of Protein Phosphatase 2A (PP2A) hyperactivates multiple oncogenic pathways and engages stress responses in colon cancer cells. Genetic and compound screens identify combined inhibition of PP2A and WEE1 as synergistic in multiple cancer models by collapsing DNA replication and triggering premature mitosis followed by cell death. This combination also suppressed the growth of patient-derived tumors in vivo. Remarkably, acquired resistance to this drug combination suppressed the ability of colon cancer cells to form tumors in vivo. Our data suggest that paradoxical activation of oncogenic signaling can result in tumor suppressive resistance.
Collapse
Affiliation(s)
| | - Anoek Friskes
- The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Siying Wang
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | | | | | - Soufiane Mourragui
- Hubrecht Institute for Developmental Biology and Stem Cell Research, Utrecht, Netherlands
| | | | | | - Sara Mainardi
- The Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | - Cor Lieftink
- The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Ben Morris
- The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Anna Dekker
- The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Emma van Dijk
- The Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | | | - Robin A Jansen
- Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, Netherlands
| | | | - Elke Malzer
- The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - August Vidal
- Bellvitge University Hospital, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Cristina Santos
- Catalan Institute of Oncology (ICO) - Bellvitge Biomedical Research Institute (IDIBELL)-CIBERONC, L'Hospitalet de Llobregat, L'Hospitalet de Llobregat, Spain
| | - Ramon Salazar
- Instituto Catalan de Oncología-IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | | | | | | | | | | | | | - Wenxin Qin
- Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - John S Kovach
- Lixte Biotechnology Holdings, Inc., East Setauket, NY, United States
| | | | - Hein Te Riele
- Netherlands Cancer Institute, Amsterdam, N, Netherlands
| | | | - Haojie Jin
- State Key Laboratory of Oncogenes and Related Genes, Shanghai, China
| | | | - Alberto Villanueva
- Catalan Institute of Oncology (ICO/IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Rene H Medema
- University Medical Center Utrecht, Amsterdam, Netherlands
| | - Rene Bernards
- The Netherlands Cancer Institute, Amsterdam, Netherlands
| |
Collapse
|
2
|
Chen M, Mainardi S, Lieftink C, Velds A, de Rink I, Yang C, Kuiken HJ, Morris B, Edwards F, Jochems F, van Tellingen O, Boeije M, Proost N, Jansen RA, Qin S, Jin H, Koen van der Mijn JC, Schepers A, Venkatesan S, Qin W, Beijersbergen RL, Wang L, Bernards R. Targeting of vulnerabilities of drug-tolerant persisters identified through functional genetics delays tumor relapse. Cell Rep Med 2024; 5:101471. [PMID: 38508142 PMCID: PMC10983104 DOI: 10.1016/j.xcrm.2024.101471] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 12/01/2023] [Accepted: 02/21/2024] [Indexed: 03/22/2024]
Abstract
Drug-tolerant persisters (DTPs) are a rare subpopulation of cells within a tumor that can survive therapy through nongenetic adaptive mechanisms to develop relapse and repopulate the tumor following drug withdrawal. Using a cancer cell line with an engineered suicide switch to kill proliferating cells, we perform both genetic screens and compound screens to identify the inhibition of bromodomain and extraterminal domain (BET) proteins as a selective vulnerability of DTPs. BET inhibitors are especially detrimental to DTPs that have reentered the cell cycle (DTEPs) in a broad spectrum of cancer types. Mechanistically, BET inhibition induces lethal levels of ROS through the suppression of redox-regulating genes highly expressed in DTPs, including GPX2, ALDH3A1, and MGST1. In vivo BET inhibitor treatment delays tumor relapse in both melanoma and lung cancer. Our study suggests that combining standard of care therapy with BET inhibitors to eliminate residual persister cells is a promising therapeutic strategy.
Collapse
Affiliation(s)
- Mengnuo Chen
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands; State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Sara Mainardi
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Cor Lieftink
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands; NKI Robotics and Screening Center, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Arno Velds
- Genomics Core Facility, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Iris de Rink
- Genomics Core Facility, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Chen Yang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hendrik J Kuiken
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands; NKI Robotics and Screening Center, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Ben Morris
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands; NKI Robotics and Screening Center, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Finn Edwards
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Fleur Jochems
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Olaf van Tellingen
- Division of Pharmacology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Manon Boeije
- Mouse Clinic for Cancer and Aging Research, Preclinical Intervention Unit, The Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Natalie Proost
- Mouse Clinic for Cancer and Aging Research, Preclinical Intervention Unit, The Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Robin A Jansen
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Shifan Qin
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Haojie Jin
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands; State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - J C Koen van der Mijn
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands; Department of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Arnout Schepers
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Subramanian Venkatesan
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Wenxin Qin
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands; NKI Robotics and Screening Center, The Netherlands Cancer Institute, Amsterdam, the Netherlands; Genomics Core Facility, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Liqin Wang
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands; State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, China.
| | - René Bernards
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands.
| |
Collapse
|
3
|
Andronikou C, Burdova K, Dibitetto D, Lieftink C, Malzer E, Kuiken HJ, Gogola E, Ray Chaudhuri A, Beijersbergen RL, Hanzlikova H, Jonkers J, Rottenberg S. PARG-deficient tumor cells have an increased dependence on EXO1/FEN1-mediated DNA repair. EMBO J 2024; 43:1015-1042. [PMID: 38360994 PMCID: PMC10943112 DOI: 10.1038/s44318-024-00043-2] [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: 06/26/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 02/17/2024] Open
Abstract
Targeting poly(ADP-ribose) glycohydrolase (PARG) is currently explored as a therapeutic approach to treat various cancer types, but we have a poor understanding of the specific genetic vulnerabilities that would make cancer cells susceptible to such a tailored therapy. Moreover, the identification of such vulnerabilities is of interest for targeting BRCA2;p53-deficient tumors that have acquired resistance to poly(ADP-ribose) polymerase inhibitors (PARPi) through loss of PARG expression. Here, by performing whole-genome CRISPR/Cas9 drop-out screens, we identify various genes involved in DNA repair to be essential for the survival of PARG;BRCA2;p53-deficient cells. In particular, our findings reveal EXO1 and FEN1 as major synthetic lethal interactors of PARG loss. We provide evidence for compromised replication fork progression, DNA single-strand break repair, and Okazaki fragment processing in PARG;BRCA2;p53-deficient cells, alterations that exacerbate the effects of EXO1/FEN1 inhibition and become lethal in this context. Since this sensitivity is dependent on BRCA2 defects, we propose to target EXO1/FEN1 in PARPi-resistant tumors that have lost PARG activity. Moreover, EXO1/FEN1 targeting may be a useful strategy for enhancing the effect of PARG inhibitors in homologous recombination-deficient tumors.
Collapse
Affiliation(s)
- Christina Andronikou
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012, Bern, Switzerland
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066CX, Amsterdam, The Netherlands
- Oncode Institute, Amsterdam, The Netherlands
- Cancer Therapy Resistance Cluster and Bern Center for Precision Medicine, Department for Biomedical Research, University of Bern, 3088, Bern, Switzerland
| | - Kamila Burdova
- Laboratory of Genome Dynamics, Institute of Molecular Genetics of the Czech Academy of Sciences, 142 20, Prague 4, Czech Republic
| | - Diego Dibitetto
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012, Bern, Switzerland
- Cancer Therapy Resistance Cluster and Bern Center for Precision Medicine, Department for Biomedical Research, University of Bern, 3088, Bern, Switzerland
| | - Cor Lieftink
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066CX, Amsterdam, The Netherlands
- The Netherlands Cancer Institute Robotics and Screening Center, The Netherlands Cancer Institute, 1066CX, Amsterdam, The Netherlands
| | - Elke Malzer
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066CX, Amsterdam, The Netherlands
- The Netherlands Cancer Institute Robotics and Screening Center, The Netherlands Cancer Institute, 1066CX, Amsterdam, The Netherlands
| | - Hendrik J Kuiken
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066CX, Amsterdam, The Netherlands
- The Netherlands Cancer Institute Robotics and Screening Center, The Netherlands Cancer Institute, 1066CX, Amsterdam, The Netherlands
| | - Ewa Gogola
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066CX, Amsterdam, The Netherlands
| | - Arnab Ray Chaudhuri
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015GD, Rotterdam, The Netherlands
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066CX, Amsterdam, The Netherlands
- The Netherlands Cancer Institute Robotics and Screening Center, The Netherlands Cancer Institute, 1066CX, Amsterdam, The Netherlands
| | - Hana Hanzlikova
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012, Bern, Switzerland
- Laboratory of Genome Dynamics, Institute of Molecular Genetics of the Czech Academy of Sciences, 142 20, Prague 4, Czech Republic
| | - Jos Jonkers
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066CX, Amsterdam, The Netherlands.
- Oncode Institute, Amsterdam, The Netherlands.
| | - Sven Rottenberg
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012, Bern, Switzerland.
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066CX, Amsterdam, The Netherlands.
- Cancer Therapy Resistance Cluster and Bern Center for Precision Medicine, Department for Biomedical Research, University of Bern, 3088, Bern, Switzerland.
| |
Collapse
|
4
|
van Breugel ME, van Kruijsbergen I, Mittal C, Lieftink C, Brouwer I, van den Brand T, Kluin RJC, Hoekman L, Menezes RX, van Welsem T, Del Cortona A, Malik M, Beijersbergen RL, Lenstra TL, Verstrepen KJ, Pugh BF, van Leeuwen F. Locus-specific proteome decoding reveals Fpt1 as a chromatin-associated negative regulator of RNA polymerase III assembly. Mol Cell 2023; 83:4205-4221.e9. [PMID: 37995691 DOI: 10.1016/j.molcel.2023.10.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 09/27/2023] [Accepted: 10/26/2023] [Indexed: 11/25/2023]
Abstract
Transcription of tRNA genes by RNA polymerase III (RNAPIII) is tuned by signaling cascades. The emerging notion of differential tRNA gene regulation implies the existence of additional regulatory mechanisms. However, tRNA gene-specific regulators have not been described. Decoding the local chromatin proteome of a native tRNA gene in yeast revealed reprogramming of the RNAPIII transcription machinery upon nutrient perturbation. Among the dynamic proteins, we identified Fpt1, a protein of unknown function that uniquely occupied RNAPIII-regulated genes. Fpt1 binding at tRNA genes correlated with the efficiency of RNAPIII eviction upon nutrient perturbation and required the transcription factors TFIIIB and TFIIIC but not RNAPIII. In the absence of Fpt1, eviction of RNAPIII was reduced, and the shutdown of ribosome biogenesis genes was impaired upon nutrient perturbation. Our findings provide support for a chromatin-associated mechanism required for RNAPIII eviction from tRNA genes and tuning the physiological response to changing metabolic demands.
Collapse
Affiliation(s)
- Maria Elize van Breugel
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Ila van Kruijsbergen
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Chitvan Mittal
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA; Department of Molecular Biology and Genetics, Biotechnology Building, Cornell University, Ithaca, NY 14853, USA
| | - Cor Lieftink
- Division of Molecular Carcinogenesis and Robotics and Screening Center, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Ineke Brouwer
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands; Division of Gene Regulation, Netherlands Cancer Institute, Oncode Institute, Amsterdam 1066 CX, the Netherlands
| | - Teun van den Brand
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Roelof J C Kluin
- Genomics Core Facility, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Liesbeth Hoekman
- Proteomics Facility, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Renée X Menezes
- Biostatistics Centre and Division of Psychosocial Research and Epidemiology, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Tibor van Welsem
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Andrea Del Cortona
- VIB-KU Leuven Center for Microbiology, KU Leuven, 3001 Heverlee-Leuven, Belgium
| | - Muddassir Malik
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis and Robotics and Screening Center, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands; Genomics Core Facility, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Tineke L Lenstra
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands; Division of Gene Regulation, Netherlands Cancer Institute, Oncode Institute, Amsterdam 1066 CX, the Netherlands
| | - Kevin J Verstrepen
- VIB-KU Leuven Center for Microbiology, KU Leuven, 3001 Heverlee-Leuven, Belgium
| | - B Franklin Pugh
- Department of Molecular Biology and Genetics, Biotechnology Building, Cornell University, Ithaca, NY 14853, USA
| | - Fred van Leeuwen
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands; Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands.
| |
Collapse
|
5
|
Mayayo-Peralta I, Gregoricchio S, Schuurman K, Yavuz S, Zaalberg A, Kojic A, Abbott N, Geverts B, Beerthuijzen S, Siefert J, Severson TM, van Baalen M, Hoekman L, Lieftink C, Altelaar M, Beijersbergen RL, Houtsmuller A, Prekovic S, Zwart W. PAXIP1 and STAG2 converge to maintain 3D genome architecture and facilitate promoter/enhancer contacts to enable stress hormone-dependent transcription. Nucleic Acids Res 2023; 51:9576-9593. [PMID: 37070193 PMCID: PMC10570044 DOI: 10.1093/nar/gkad267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/03/2023] [Accepted: 04/12/2023] [Indexed: 04/19/2023] Open
Abstract
How steroid hormone receptors (SHRs) regulate transcriptional activity remains partly understood. Upon activation, SHRs bind the genome together with a co-regulator repertoire, crucial to induce gene expression. However, it remains unknown which components of the SHR-recruited co-regulator complex are essential to drive transcription following hormonal stimuli. Through a FACS-based genome-wide CRISPR screen, we functionally dissected the Glucocorticoid Receptor (GR) complex. We describe a functional cross-talk between PAXIP1 and the cohesin subunit STAG2, critical for regulation of gene expression by GR. Without altering the GR cistrome, PAXIP1 and STAG2 depletion alter the GR transcriptome, by impairing the recruitment of 3D-genome organization proteins to the GR complex. Importantly, we demonstrate that PAXIP1 is required for stability of cohesin on chromatin, its localization to GR-occupied sites, and maintenance of enhancer-promoter interactions. In lung cancer, where GR acts as tumor suppressor, PAXIP1/STAG2 loss enhances GR-mediated tumor suppressor activity by modifying local chromatin interactions. All together, we introduce PAXIP1 and STAG2 as novel co-regulators of GR, required to maintain 3D-genome architecture and drive the GR transcriptional programme following hormonal stimuli.
Collapse
Affiliation(s)
- Isabel Mayayo-Peralta
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Sebastian Gregoricchio
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Karianne Schuurman
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Selçuk Yavuz
- Erasmus Optical Imaging Center, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherland
| | - Anniek Zaalberg
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Aleksandar Kojic
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Nina Abbott
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Bart Geverts
- Erasmus Optical Imaging Center, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherland
- Department of Pathology, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Suzanne Beerthuijzen
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Joseph Siefert
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Tesa M Severson
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Martijn van Baalen
- Flow Cytometry Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Liesbeth Hoekman
- Proteomics Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Cor Lieftink
- Division of Molecular Carcinogenesis, The NKI Robotics and Screening Centre, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Maarten Altelaar
- Proteomics Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences, Utrecht University and Netherlands Proteomics Centre, Utrecht, The Netherlands
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis, The NKI Robotics and Screening Centre, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Adriaan B Houtsmuller
- Erasmus Optical Imaging Center, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherland
| | - Stefan Prekovic
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| |
Collapse
|
6
|
Zaalberg A, Minnee E, Mayayo-Peralta I, Schuurman K, Gregoricchio S, van Schaik TA, Hoekman L, Li D, Corey E, Janssen H, Lieftink C, Prekovic S, Altelaar M, Nelson PS, Beijersbergen RL, Zwart W, Bergman A. A genome-wide CRISPR screen in human prostate cancer cells reveals drivers of macrophage-mediated cell killing and positions AR as a tumor-intrinsic immunomodulator. bioRxiv 2023:2023.06.06.543873. [PMID: 37333335 PMCID: PMC10274642 DOI: 10.1101/2023.06.06.543873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
The crosstalk between prostate cancer (PCa) cells and the tumor microenvironment plays a pivotal role in disease progression and metastasis and could provide novel opportunities for patient treatment. Macrophages are the most abundant immune cells in the prostate tumor microenvironment (TME) and are capable of killing tumor cells. To identify genes in the tumor cells that are critical for macrophage-mediated killing, we performed a genome-wide co-culture CRISPR screen and identified AR, PRKCD, and multiple components of the NF-κB pathway as hits, whose expression in the tumor cell are essential for being targeted and killed by macrophages. These data position AR signaling as an immunomodulator, and confirmed by androgen-deprivation experiments, that rendered hormone-deprived tumor cells resistant to macrophage-mediated killing. Proteomic analyses showed a downregulation of oxidative phosphorylation in the PRKCD- and IKBKG-KO cells compared to the control, suggesting impaired mitochondrial function, which was confirmed by electron microscopy analyses. Furthermore, phosphoproteomic analyses revealed that all hits impaired ferroptosis signaling, which was validated transcriptionally using samples from a neoadjuvant clinical trial with the AR-inhibitor enzalutamide. Collectively, our data demonstrate that AR functions together with the PRKCD and the NF-κB pathway to evade macrophage-mediated killing. As hormonal intervention represents the mainstay therapy for treatment of prostate cancer patients, our findings may have direct implications and provide a plausible explanation for the clinically observed persistence of tumor cells despite androgen deprivation therapy.
Collapse
|
7
|
Bhin J, Paes Dias M, Gogola E, Rolfs F, Piersma SR, de Bruijn R, de Ruiter JR, van den Broek B, Duarte AA, Sol W, van der Heijden I, Andronikou C, Kaiponen TS, Bakker L, Lieftink C, Morris B, Beijersbergen RL, van de Ven M, Jimenez CR, Wessels LFA, Rottenberg S, Jonkers J. Multi-omics analysis reveals distinct non-reversion mechanisms of PARPi resistance in BRCA1- versus BRCA2-deficient mammary tumors. Cell Rep 2023; 42:112538. [PMID: 37209095 DOI: 10.1016/j.celrep.2023.112538] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 03/16/2023] [Accepted: 05/03/2023] [Indexed: 05/22/2023] Open
Abstract
BRCA1 and BRCA2 both function in DNA double-strand break repair by homologous recombination (HR). Due to their HR defect, BRCA1/2-deficient cancers are sensitive to poly(ADP-ribose) polymerase inhibitors (PARPis), but they eventually acquire resistance. Preclinical studies yielded several PARPi resistance mechanisms that do not involve BRCA1/2 reactivation, but their relevance in the clinic remains elusive. To investigate which BRCA1/2-independent mechanisms drive spontaneous resistance in vivo, we combine molecular profiling with functional analysis of HR of matched PARPi-naive and PARPi-resistant mouse mammary tumors harboring large intragenic deletions that prevent reactivation of BRCA1/2. We observe restoration of HR in 62% of PARPi-resistant BRCA1-deficient tumors but none in the PARPi-resistant BRCA2-deficient tumors. Moreover, we find that 53BP1 loss is the prevalent resistance mechanism in HR-proficient BRCA1-deficient tumors, whereas resistance in BRCA2-deficient tumors is mainly induced by PARG loss. Furthermore, combined multi-omics analysis identifies additional genes and pathways potentially involved in modulating PARPi response.
Collapse
Affiliation(s)
- Jinhyuk Bhin
- Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Division of Molecular Carcinogenesis, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Department of Biomedical System Informatics, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Mariana Paes Dias
- Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Ewa Gogola
- Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Frank Rolfs
- Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; OncoProteomics Laboratory, Department Medical Oncology, Amsterdam UMC, 1081HV Amsterdam, the Netherlands
| | - Sander R Piersma
- OncoProteomics Laboratory, Department Medical Oncology, Amsterdam UMC, 1081HV Amsterdam, the Netherlands
| | - Roebi de Bruijn
- Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Division of Molecular Carcinogenesis, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Julian R de Ruiter
- Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Division of Molecular Carcinogenesis, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Bram van den Broek
- Division of Cell Biology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Alexandra A Duarte
- Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Wendy Sol
- Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Ingrid van der Heijden
- Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Christina Andronikou
- Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Cancer Therapy Resistance Cluster and Bern Center for Precision Medicine, Department for Biomedical Research, University of Bern, 3088 Bern, Switzerland; Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| | - Taina S Kaiponen
- Cancer Therapy Resistance Cluster and Bern Center for Precision Medicine, Department for Biomedical Research, University of Bern, 3088 Bern, Switzerland; Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| | - Lara Bakker
- Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Cor Lieftink
- Division of Molecular Carcinogenesis, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Ben Morris
- Division of Molecular Carcinogenesis, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Marieke van de Ven
- Mouse Clinic for Cancer and Aging, Preclinical Intervention Unit, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Connie R Jimenez
- OncoProteomics Laboratory, Department Medical Oncology, Amsterdam UMC, 1081HV Amsterdam, the Netherlands
| | - Lodewyk F A Wessels
- Division of Molecular Carcinogenesis, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands.
| | - Sven Rottenberg
- Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Cancer Therapy Resistance Cluster and Bern Center for Precision Medicine, Department for Biomedical Research, University of Bern, 3088 Bern, Switzerland; Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland.
| | - Jos Jonkers
- Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands.
| |
Collapse
|
8
|
van der Noord VE, van der Stel W, Louwerens G, Verhoeven D, Kuiken HJ, Lieftink C, Grandits M, Ecker GF, Beijersbergen RL, Bouwman P, Le Dévédec SE, van de Water B. Systematic screening identifies ABCG2 as critical factor underlying synergy of kinase inhibitors with transcriptional CDK inhibitors. Breast Cancer Res 2023; 25:51. [PMID: 37147730 PMCID: PMC10161439 DOI: 10.1186/s13058-023-01648-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 04/07/2023] [Indexed: 05/07/2023] Open
Abstract
BACKGROUND Triple-negative breast cancer (TNBC) is a subtype of breast cancer with limited treatment options and poor clinical prognosis. Inhibitors of transcriptional CDKs are currently under thorough investigation for application in the treatment of multiple cancer types, including breast cancer. These studies have raised interest in combining these inhibitors, including CDK12/13 inhibitor THZ531, with a variety of other anti-cancer agents. However, the full scope of these potential synergistic interactions of transcriptional CDK inhibitors with kinase inhibitors has not been systematically investigated. Moreover, the mechanisms behind these previously described synergistic interactions remain largely elusive. METHODS Kinase inhibitor combination screenings were performed to identify kinase inhibitors that synergize with CDK7 inhibitor THZ1 and CDK12/13 inhibitor THZ531 in TNBC cell lines. CRISPR-Cas9 knockout screening and transcriptomic evaluation of resistant versus sensitive cell lines were performed to identify genes critical for THZ531 resistance. RNA sequencing analysis after treatment with individual and combined synergistic treatments was performed to gain further insights into the mechanism of this synergy. Kinase inhibitor screening in combination with visualization of ABCG2-substrate pheophorbide A was used to identify kinase inhibitors that inhibit ABCG2. Multiple transcriptional CDK inhibitors were evaluated to extend the significance of the found mechanism to other transcriptional CDK inhibitors. RESULTS We show that a very high number of tyrosine kinase inhibitors synergize with the CDK12/13 inhibitor THZ531. Yet, we identified the multidrug transporter ABCG2 as key determinant of THZ531 resistance in TNBC cells. Mechanistically, we demonstrate that most synergistic kinase inhibitors block ABCG2 function, thereby sensitizing cells to transcriptional CDK inhibitors, including THZ531. Accordingly, these kinase inhibitors potentiate the effects of THZ531, disrupting gene expression and increasing intronic polyadenylation. CONCLUSION Overall, this study demonstrates the critical role of ABCG2 in limiting the efficacy of transcriptional CDK inhibitors and identifies multiple kinase inhibitors that disrupt ABCG2 transporter function and thereby synergize with these CDK inhibitors. These findings therefore further facilitate the development of new (combination) therapies targeting transcriptional CDKs and highlight the importance of evaluating the role of ABC transporters in synergistic drug-drug interactions in general.
Collapse
Affiliation(s)
- Vera E van der Noord
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Wanda van der Stel
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Gijs Louwerens
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Danielle Verhoeven
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Hendrik J Kuiken
- Division of Molecular Carcinogenesis, The NKI Robotics and Screening Center, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Cor Lieftink
- Division of Molecular Carcinogenesis, The NKI Robotics and Screening Center, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Melanie Grandits
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Gerhard F Ecker
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis, The NKI Robotics and Screening Center, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Peter Bouwman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Sylvia E Le Dévédec
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Bob van de Water
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands.
| |
Collapse
|
9
|
Buikhuisen JY, Gomez Barila PM, Cameron K, Suijkerbuijk SJE, Lieftink C, di Franco S, Krotenberg Garcia A, Uceda Castro R, Lenos KJ, Nijman LE, Torang A, Longobardi C, de Jong JH, Dekker D, Stassi G, Vermeulen L, Beijersbergen RL, van Rheenen J, Huveneers S, Medema JP. Subtype-specific kinase dependency regulates growth and metastasis of poor-prognosis mesenchymal colorectal cancer. J Exp Clin Cancer Res 2023; 42:56. [PMID: 36869386 PMCID: PMC9983221 DOI: 10.1186/s13046-023-02600-9] [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: 09/21/2022] [Accepted: 01/15/2023] [Indexed: 03/05/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) can be divided into four consensus molecular subtypes (CMS), each with distinct biological features. CMS4 is associated with epithelial-mesenchymal transition and stromal infiltration (Guinney et al., Nat Med 21:1350-6, 2015; Linnekamp et al., Cell Death Differ 25:616-33, 2018), whereas clinically it is characterized by lower responses to adjuvant therapy, higher incidence of metastatic spreading and hence dismal prognosis (Buikhuisen et al., Oncogenesis 9:66, 2020). METHODS To understand the biology of the mesenchymal subtype and unveil specific vulnerabilities, a large CRISPR-Cas9 drop-out screen was performed on 14 subtyped CRC cell lines to uncover essential kinases in all CMSs. Dependency of CMS4 cells on p21-activated kinase 2 (PAK2) was validated in independent 2D and 3D in vitro cultures and in vivo models assessing primary and metastatic outgrowth in liver and peritoneum. TIRF microscopy was used to uncover actin cytoskeleton dynamics and focal adhesion localization upon PAK2 loss. Subsequent functional assays were performed to determine altered growth and invasion patterns. RESULTS PAK2 was identified as a key kinase uniquely required for growth of the mesenchymal subtype CMS4, both in vitro and in vivo. PAK2 plays an important role in cellular attachment and cytoskeletal rearrangements (Coniglio et al., Mol Cell Biol 28:4162-72, 2008; Grebenova et al., Sci Rep 9:17171, 2019). In agreement, deletion or inhibition of PAK2 impaired actin cytoskeleton dynamics in CMS4 cells and, as a consequence, significantly reduced invasive capacity, while it was dispensable for CMS2 cells. Clinical relevance of these findings was supported by the observation that deletion of PAK2 from CMS4 cells prevented metastatic spreading in vivo. Moreover, growth in a model for peritoneal metastasis was hampered when CMS4 tumor cells were deficient for PAK2. CONCLUSION Our data reveal a unique dependency of mesenchymal CRC and provide a rationale for PAK2 inhibition to target this aggressive subgroup of colorectal cancer.
Collapse
Affiliation(s)
- Joyce Y Buikhuisen
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental Molecular Medicine, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, location AMC, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam, The Netherlands
| | - Patricia M Gomez Barila
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental Molecular Medicine, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, location AMC, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam, The Netherlands
| | - Kate Cameron
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental Molecular Medicine, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, location AMC, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam, The Netherlands
| | - Saskia J E Suijkerbuijk
- Oncode Institute, Amsterdam, The Netherlands.,Department of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Cor Lieftink
- Oncode Institute, Amsterdam, The Netherlands.,Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Simone di Franco
- Department of Surgical Oncological and Stomatological Sciences (DICHIRONS), University of Palermo, Palermo, Italy
| | - Ana Krotenberg Garcia
- Oncode Institute, Amsterdam, The Netherlands.,Department of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Rebeca Uceda Castro
- Oncode Institute, Amsterdam, The Netherlands.,Department of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Kristiaan J Lenos
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental Molecular Medicine, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, location AMC, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam, The Netherlands
| | - Lisanne E Nijman
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental Molecular Medicine, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, location AMC, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam, The Netherlands
| | - Arezo Torang
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental Molecular Medicine, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, location AMC, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam, The Netherlands
| | - Ciro Longobardi
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental Molecular Medicine, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, location AMC, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam, The Netherlands
| | - Joan H de Jong
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental Molecular Medicine, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, location AMC, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam, The Netherlands
| | - Daniëlle Dekker
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental Molecular Medicine, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, location AMC, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam, The Netherlands
| | - Giorgio Stassi
- Department of Surgical Oncological and Stomatological Sciences (DICHIRONS), University of Palermo, Palermo, Italy
| | - Louis Vermeulen
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental Molecular Medicine, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, location AMC, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam, The Netherlands
| | - Roderick L Beijersbergen
- Oncode Institute, Amsterdam, The Netherlands.,Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jacco van Rheenen
- Oncode Institute, Amsterdam, The Netherlands.,Department of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Stephan Huveneers
- Department of Medical Biochemistry, Amsterdam Cardiovascular Sciences, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Jan Paul Medema
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental Molecular Medicine, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, location AMC, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands. .,Oncode Institute, Amsterdam, The Netherlands.
| |
Collapse
|
10
|
Thus YJ, De Rooij MFM, Swier N, Beijersbergen RL, Guikema JEJ, Kersten MJ, Eldering E, Pals ST, Kater AP, Spaargaren M. Inhibition of casein kinase 2 sensitizes mantle cell lymphoma to venetoclax through MCL-1 downregulation. Haematologica 2023; 108:797-810. [PMID: 36226498 PMCID: PMC9973496 DOI: 10.3324/haematol.2022.281668] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [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: 06/28/2022] [Indexed: 11/09/2022] Open
Abstract
BCL-2 family proteins are frequently aberrantly expressed in mantle cell lymphoma (MCL). Recently, the BCL-2-specific inhibitor venetoclax has been approved by the US Food and Drug Administration for chronic lymphocytic leukemia (CLL) and acute myeloid leukemia (AML). In MCL, venetoclax has shown promising efficacy in early clinical trials; however, a significant subset of patients is resistant. By conducting a kinome-centered CRISPR-Cas9 knockout sensitizer screen, we identified casein kinase 2 (CK2) as a major regulator of venetoclax resistance in MCL. Interestingly, CK2 is over-expressed in MCL and high CK2 expression is associated with poor patient survival. Targeting of CK2, either by inducible short hairpin RNA (shRNA)-mediated knockdown of CK2 or by the CK2-inhibitor silmitasertib, did not affect cell viability by itself, but strongly synergized with venetoclax in both MCL cell lines and primary samples, also if combined with ibrutinib. Furthermore, targeting of CK2 reduced MCL-1 levels, which involved impaired MCL-1 translation by inhibition of eIF4F complex assembly, without affecting BCL-2 and BCL-XL expression. Combined, this results in enhanced BCL-2 dependence and, consequently, venetoclax sensitization. In cocultures, targeting of CK2 overcame stroma-mediated venetoclax resistance of MCL cells. Taken together, our findings indicate that targeting of CK2 sensitizes MCL cells to venetoclax through downregulation of MCL-1. These novel insights provide a strong rationale for combining venetoclax with CK2 inhibition as therapeutic strategy for MCL patients.
Collapse
Affiliation(s)
- Yvonne J Thus
- Department of Pathology, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands; Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam, The Netherlands; Cancer Center Amsterdam (CCA), Cancer Biology and Immunology - Target and Therapy Discovery, Amsterdam
| | - Martin F M De Rooij
- Department of Pathology, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands; Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam, The Netherlands; Cancer Center Amsterdam (CCA), Cancer Biology and Immunology - Target and Therapy Discovery, Amsterdam
| | - Nathalie Swier
- Department of Pathology, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands; Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam, The Netherlands; Cancer Center Amsterdam (CCA), Cancer Biology and Immunology - Target and Therapy Discovery, Amsterdam
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands; The NKI Robotics and Screening Center, Netherlands Cancer Institute, Amsterdam
| | - Jeroen E J Guikema
- Department of Pathology, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands; Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam, The Netherlands; Cancer Center Amsterdam (CCA), Cancer Biology and Immunology - Target and Therapy Discovery, Amsterdam
| | - Marie-José Kersten
- Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam, The Netherlands; Department of Hematology, Amsterdam UMC location University of Amsterdam, Amsterdam
| | - Eric Eldering
- Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam, The Netherlands; Cancer Center Amsterdam (CCA), Cancer Biology and Immunology - Target and Therapy Discovery, Amsterdam, The Netherlands; Department of Experimental Immunology, Amsterdam UMC location University of Amsterdam, Amsterdam
| | - Steven T Pals
- Department of Pathology, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands; Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam, The Netherlands; Cancer Center Amsterdam (CCA), Cancer Biology and Immunology - Target and Therapy Discovery, Amsterdam
| | - Arnon P Kater
- Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam, The Netherlands; Cancer Center Amsterdam (CCA), Cancer Biology and Immunology - Target and Therapy Discovery, Amsterdam, The Netherlands; Department of Hematology, Amsterdam UMC location University of Amsterdam, Amsterdam
| | - Marcel Spaargaren
- Department of Pathology, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands; Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam, The Netherlands; Cancer Center Amsterdam (CCA), Cancer Biology and Immunology - Target and Therapy Discovery, Amsterdam.
| |
Collapse
|
11
|
Severson TM, Zhu Y, Prekovic S, Schuurman K, Nguyen HM, Brown LG, Hakkola S, Kim Y, Kneppers J, Linder S, Stelloo S, Lieftink C, van der Heijden M, Nykter M, van der Noort V, Sanders J, Morris B, Jenster G, van Leenders GJLH, Pomerantz M, Freedman ML, Beijersbergen RL, Urbanucci A, Wessels L, Corey E, Zwart W, Bergman AM. Enhancer profiling identifies epigenetic markers of endocrine resistance and reveals therapeutic options for metastatic castration-resistant prostate cancer patients. medRxiv 2023:2023.02.24.23286403. [PMID: 36865297 PMCID: PMC9980263 DOI: 10.1101/2023.02.24.23286403] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
Androgen Receptor (AR) signaling inhibitors, including enzalutamide, are treatment options for patients with metastatic castration-resistant prostate cancer (mCRPC), but resistance inevitably develops. Using metastatic samples from a prospective phase II clinical trial, we epigenetically profiled enhancer/promoter activities with H3K27ac chromatin immunoprecipitation followed by sequencing, before and after AR-targeted therapy. We identified a distinct subset of H3K27ac-differentially marked regions that associated with treatment responsiveness. These data were successfully validated in mCRPC patient-derived xenograft models (PDX). In silico analyses revealed HDAC3 as a critical factor that can drive resistance to hormonal interventions, which we validated in vitro . Using cell lines and mCRPC PDX tumors in vitro , we identified drug-drug synergy between enzalutamide and the pan-HDAC inhibitor vorinostat, providing therapeutic proof-of-concept. These findings demonstrate rationale for new therapeutic strategies using a combination of AR and HDAC inhibitors to improve patient outcome in advanced stages of mCRPC.
Collapse
|
12
|
Hoefsmit EP, van Royen PT, Rao D, Stunnenberg JA, Dimitriadis P, Lieftink C, Morris B, Rozeman EA, Reijers ILM, Lacroix R, Shehwana H, Ligtenberg MA, Beijersbergen RL, Peeper DS, Blank CU. Inhibitor of apoptosis proteins (IAP) antagonist induces T-cell proliferation after cross-presentation by dendritic cells. Cancer Immunol Res 2023; 11:450-465. [PMID: 36753604 DOI: 10.1158/2326-6066.cir-22-0494] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 11/28/2022] [Accepted: 02/01/2023] [Indexed: 02/10/2023]
Abstract
Cross-presentation of tumor antigens by dendritic cells (DCs) is crucial to prime, stimulate and restimulate CD8+ T cells. This process is important in initiating and maintaining an antitumor response. Here, we show that the presence of conventional type 1 DCs (cDC1), a DC subtype that excels in cross-presentation, in the tumor correlated with response to neoadjuvant immune checkpoint blockade (ICB) in melanoma. This led us to hypothesize that patients failing to respond to ICB could benefit from enhanced cross-presentation of tumor antigens. We therefore established a cross-presentation assay to screen over 5,500 compounds for enhancers of DC cross-presentation using induced T-cell proliferation as the readout. We identified 145 enhancers, including AZD5582, an antagonist of inhibitor of apoptosis proteins (IAPs) cIAP1, cIAP2 and XIAP. AZD5582 treatment led to DC activation of the non-canonical nuclear factor kappa B (NF-kB) pathway, enhanced antigen import from endolysosomes into the cytosol and increased expression of genes involved in cross-presentation. Furthermore, it upregulated expression of CD80, CD86, MHC class II, CD70 and secretion of TNF by DCs. This enhanced DC activation and maturation program was observed also in tumor-bearing mice upon AZD5582 treatment, culminating in an increased frequency of systemic tumor antigen-specific CD8+ T cells. Our results merit further exploration of AZD5582 to increase antigen cross-presentation for improving the clinical benefit of ICB in patients who are unlikely to respond to ICB.
Collapse
Affiliation(s)
- Esmee P Hoefsmit
- Netherlands Cancer Instiute, Amsterdam, Noord-Holland, Netherlands
| | | | - Disha Rao
- Netherlands Cancer Instiute, Amsterdam, Noord-Holland, Netherlands
| | | | - P Dimitriadis
- Netherlands Cancer Instiute, Amsterdam, Noord-Holland, Netherlands
| | - Cor Lieftink
- The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Ben Morris
- The Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | | | - Ruben Lacroix
- Netherlands Cancer Instiute, Amsterdam, Noord-Holland, Netherlands
| | - Huma Shehwana
- Netherlands Cancer Instiute, Amsterdam, Noord-Holland, Netherlands
| | | | | | | | - Christian U Blank
- The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital (NKI-AVL), Amsterdam, Netherlands
| |
Collapse
|
13
|
Mulero-Sánchez A, Ramirez CFA, du Chatinier A, Wang H, Koomen SJI, Song JY, de Groot MHP, Lieftink C, Bosma A, Burylo A, van Tellingen O, Beijersbergen RL, Wang C, Akkari L, Bernards R, Mainardi S. Rational combination of SHP2 and mTOR inhibition for the treatment of hepatocellular carcinoma. Mol Oncol 2023. [PMID: 36650715 DOI: 10.1002/1878-0261.13377] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 11/07/2022] [Accepted: 01/12/2023] [Indexed: 01/19/2023] Open
Abstract
Liver cancer is the fourth most common cause of cancer-related death worldwide, with hepatocellular carcinoma (HCC) being the main primary malignancy affecting the liver. Unfortunately, there are still limited therapeutic options for HCC, and even the latest advances have only increased the overall survival modestly. Thus, new treatment strategies and rational drug combinations are urgently needed. Reactivation of receptor tyrosine kinases (RTK) has been described as a mechanism of intrinsic resistance to targeted therapies in a variety of cancers, including inhibitors of mTOR. The design of rational combination therapies to overcome this type of resistance is complicated by the notion that multiple RTK can be upregulated during the acquisition of resistance. SHP2, encoded by the gene PTPN11, acts downstream of virtually all RTK, and has proven to be a good target for small molecule inhibitors. Here, we report activation of multiple RTK upon mTOR inhibition in HCC which, through SHP2, leads to reactivation of the mTOR pathway. We show that co-inhibition of both mTOR and SHP2 is highly synergistic in vitro by triggering apoptosis. More importantly, the combination is well-tolerated and outperforms the monotherapies in impairing tumor growth in multiple HCC mouse models. Our findings suggest a novel rational combination therapy for the treatment of HCC.
Collapse
Affiliation(s)
- Antonio Mulero-Sánchez
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Christel F A Ramirez
- Division of Tumor Biology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Aimée du Chatinier
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Hui Wang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, China
| | - Sofie J I Koomen
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ji-Ying Song
- Department of Experimental Animal Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Marnix H P de Groot
- Division of Tumor Biology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Cor Lieftink
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Astrid Bosma
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Artur Burylo
- Division of Pharmacology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Olaf van Tellingen
- Division of Pharmacology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Cun Wang
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, China
| | - Leila Akkari
- Division of Tumor Biology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - René Bernards
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, China
| | - Sara Mainardi
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| |
Collapse
|
14
|
Zhou Y, Wang S, Wu W, Ling J, Li H, Jia Q, Zheng J, Zheng X, Yu R, Wu Q, Shi Y, Lieftink C, Beijersbergen RL, Yuan S, Bernards R, Jin H, Qin W. Sustained activation of EGFR-ERK1/2 signaling limits the response to tigecycline-induced mitochondrial respiratory deficiency in liver cancer. EBioMedicine 2022; 87:104397. [PMID: 36502574 PMCID: PMC9763382 DOI: 10.1016/j.ebiom.2022.104397] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/17/2022] [Accepted: 11/20/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Identification of tumor dependencies is important for developing therapeutic strategies for liver cancer. METHODS A genome-wide CRISPR screen was performed for finding critical vulnerabilities in liver cancer cells. Compounds screen, RNA sequencing, and human phospho-receptor tyrosine kinase arrays were applied to explore mechanisms and search for synergistic drugs. FINDINGS We identified mitochondrial translation-related genes associated with proliferation for liver cancer cells. Tigecycline induced deficiency of respiratory chain by disturbing mitochondrial translation process and showed therapeutic potential in liver cancer. For liver cancer cells extremely insensitive to tigecycline, a compounds screen was applied to identify MEK inhibitors as synergistic drugs to tigecycline-insensitive liver cancer cells. Mechanistically, sustained activation of EGFR-ERK1/2-MYC cascade conferred the insensitivity to tigecycline, which was mediated by enhanced secretion of EREG and AREG. Moreover, glycolytic enzymes, such as HK2 and PKM2 were upregulated to stimulate glycolysisin a MYC-dependent manner. Tigecycline induced respiratory chain deficiency in combination with cutting off EGFR-ERK1/2-MYC cascade by MEK inhibitors or EGFR inhibitors, resulting in decrease of both oxidative phosphorylation and glycolysis in liver cancer cells. INTERPRETATION Our study proved that blocking EGFR-ERK1/2-MYC cascade combined with tigecycline could be a potential therapeutic strategy for liver cancer. FUNDING This work was funded by grants from the National Natural Science Foundation of China (82073039,82222047, 81920108025), Program of Shanghai Academic/Technology Research Leader (22XD1423100), Shanghai Municipal Science and Technology Project (20JC1411100), 111 Project (B21024), Innovative Research Team of High-level Local Universities in Shanghai (SHSMU-ZDCX20212700, SHSMU-ZDCX20210802) and Shanghai Jiao Tong University School of Medicine (YG2019GD01).
Collapse
Affiliation(s)
- Yangyang Zhou
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Siying Wang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei Wu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jing Ling
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Haoyu Li
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qi Jia
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiaojiao Zheng
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xingling Zheng
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ruobing Yu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qiangxin Wu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yaoping Shi
- Department of Interventional Oncology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Cor Lieftink
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Roderick L. Beijersbergen
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Shengxian Yuan
- The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Shanghai, China,Corresponding author.
| | - René Bernards
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China,Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands,Corresponding author. Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands.
| | - Haojie Jin
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China,Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands,Corresponding author. State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, No.25, Lane 2200 Xie-Tu Road, Shanghai, 200032, China.
| | - Wenxin Qin
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China,Corresponding author. State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, No.25, Lane 2200 Xie-Tu Road, Shanghai, 200032, China.
| |
Collapse
|
15
|
Llaurado Fernandez M, Hijmans EM, Gennissen AM, Wong NK, Li S, Wisman GBA, Hamilton A, Hoenisch J, Dawson A, Lee CH, Bittner M, Kim H, DiMattia GE, Lok CA, Lieftink C, Beijersbergen RL, de Jong S, Carey MS, Bernards R, Berns K. NOTCH Signaling Limits the Response of Low-Grade Serous Ovarian Cancers to MEK Inhibition. Mol Cancer Ther 2022; 21:1862-1874. [PMID: 36198031 PMCID: PMC9716250 DOI: 10.1158/1535-7163.mct-22-0004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 05/30/2022] [Accepted: 10/03/2022] [Indexed: 01/12/2023]
Abstract
Low-grade serous ovarian cancer (LGSOC) is a rare subtype of epithelial ovarian cancer with high fatality rates in advanced stages due to its chemoresistant properties. LGSOC is characterized by activation of MAPK signaling, and recent clinical trials indicate that the MEK inhibitor (MEKi) trametinib may be a good treatment option for a subset of patients. Understanding MEKi-resistance mechanisms and subsequent identification of rational drug combinations to suppress resistance may greatly improve LGSOC treatment strategies. Both gain-of-function and loss-of-function CRISPR-Cas9 genome-wide libraries were used to screen LGSOC cell lines to identify genes that modulate the response to MEKi. Overexpression of MAML2 and loss of MAP3K1 were identified, both leading to overexpression of the NOTCH target HES1, which has a causal role in this process as its knockdown reversed MEKi resistance. Interestingly, increased HES1 expression was also observed in selected spontaneous trametinib-resistant clones, next to activating MAP2K1 (MEK1) mutations. Subsequent trametinib synthetic lethality screens identified SHOC2 downregulation as being synthetic lethal with MEKis. Targeting SHOC2 with pan-RAF inhibitors (pan-RAFis) in combination with MEKi was effective in parental LGSOC cell lines, in MEKi-resistant derivatives, in primary ascites cultures from patients with LGSOC, and in LGSOC (cell line-derived and patient-derived) xenograft mouse models. We found that the combination of pan-RAFi with MEKi downregulated HES1 levels in trametinib-resistant cells, providing an explanation for the synergy that was observed. Combining MEKis with pan-RAFis may provide a promising treatment strategy for patients with LGSOC, which warrants further clinical validation.
Collapse
Affiliation(s)
- Marta Llaurado Fernandez
- Department of Obstetrics and Gynaecology, University of British Columbia Vancouver, British Columbia, Canada
| | - E. Marielle Hijmans
- Division of Molecular Carcinogenesis, Oncode Institute, Cancer Genomics Center Netherlands, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Annemiek M.C. Gennissen
- Division of Molecular Carcinogenesis, Oncode Institute, Cancer Genomics Center Netherlands, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Nelson K.Y. Wong
- Department of Obstetrics and Gynaecology, University of British Columbia Vancouver, British Columbia, Canada.,Department of Experimental Therapeutics, BC Cancer, Vancouver, British Columbia, Canada
| | - Shang Li
- Department of Medical Oncology, Cancer Research Center Groningen, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - G. Bea A. Wisman
- Department of Gynecologic Oncology, Cancer Research Center Groningen, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Aleksandra Hamilton
- Department of Obstetrics and Gynaecology, University of British Columbia Vancouver, British Columbia, Canada
| | - Joshua Hoenisch
- Department of Obstetrics and Gynaecology, University of British Columbia Vancouver, British Columbia, Canada
| | - Amy Dawson
- Department of Obstetrics and Gynaecology, University of British Columbia Vancouver, British Columbia, Canada
| | - Cheng-Han Lee
- Department of Obstetrics and Gynaecology, University of British Columbia Vancouver, British Columbia, Canada
| | - Madison Bittner
- Department of Obstetrics and Gynaecology, University of British Columbia Vancouver, British Columbia, Canada
| | - Hannah Kim
- Department of Obstetrics and Gynaecology, University of British Columbia Vancouver, British Columbia, Canada
| | - Gabriel E. DiMattia
- Mary and John Knight Translational Ovarian Cancer Research Unit, London Health Sciences Center
| | - Christianne A.R. Lok
- Center for Gynecologic Oncology Amsterdam, Antoni van Leeuwenhoek/The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Cor Lieftink
- Division of Molecular Carcinogenesis, Oncode Institute, Cancer Genomics Center Netherlands, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Roderick L. Beijersbergen
- Division of Molecular Carcinogenesis, Oncode Institute, Cancer Genomics Center Netherlands, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Steven de Jong
- Department of Medical Oncology, Cancer Research Center Groningen, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Mark S. Carey
- Department of Obstetrics and Gynaecology, University of British Columbia Vancouver, British Columbia, Canada.,Corresponding Authors: Katrien Berns, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands. Phone: 31-20-5121955. E-mail: ; and Mark S. Carey, Vancouver, British Columbia V6Z 2K8, Canada. Phone: 160-4875-4268; E-mail: ; René Bernards, Plesmanlaan 121,1066 CX Amsterdam, the Netherlands. Phone: 31-20-5121952; E-mail:
| | - René Bernards
- Division of Molecular Carcinogenesis, Oncode Institute, Cancer Genomics Center Netherlands, the Netherlands Cancer Institute, Amsterdam, the Netherlands.,Corresponding Authors: Katrien Berns, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands. Phone: 31-20-5121955. E-mail: ; and Mark S. Carey, Vancouver, British Columbia V6Z 2K8, Canada. Phone: 160-4875-4268; E-mail: ; René Bernards, Plesmanlaan 121,1066 CX Amsterdam, the Netherlands. Phone: 31-20-5121952; E-mail:
| | - Katrien Berns
- Division of Molecular Carcinogenesis, Oncode Institute, Cancer Genomics Center Netherlands, the Netherlands Cancer Institute, Amsterdam, the Netherlands.,Corresponding Authors: Katrien Berns, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands. Phone: 31-20-5121955. E-mail: ; and Mark S. Carey, Vancouver, British Columbia V6Z 2K8, Canada. Phone: 160-4875-4268; E-mail: ; René Bernards, Plesmanlaan 121,1066 CX Amsterdam, the Netherlands. Phone: 31-20-5121952; E-mail:
| |
Collapse
|
16
|
Thus YJ, De Rooij MFM, Beijersbergen RL, Spaargaren M. An Unbiased CRISPR-Cas9 Screening Method for the Identification of Positive and Negative Regulatory Proteins of Cell Adhesion. Bio Protoc 2022; 12:e4545. [PMID: 36505024 PMCID: PMC9711945 DOI: 10.21769/bioprotoc.4545] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/31/2022] [Accepted: 09/29/2022] [Indexed: 11/06/2022] Open
Abstract
Mature B-cell lymphomas are highly dependent upon the protective lymphoid organ microenvironment for their growth and survival. Targeting integrin-mediated homing and retention of the malignant B cells in the lymphoid organs, using the Bruton's tyrosine kinase (BTK) inhibitor ibrutinib, is a highly efficacious FDA-approved therapy for chronic lymphocytic leukemia (CLL), mantle cell lymphoma (MCL), and Waldenström macroglobulinemia (WM). Unfortunately, a significant subset of patients is intrinsically resistant to ibrutinib or will develop resistance upon prolonged treatment. Here, we describe an unbiased functional genomic CRISPR-Cas9 screening method to identify novel proteins involved in B-cell receptor-controlled integrin-mediated adhesion, which provides novel therapeutic targets to overcome ibrutinib resistance. This screening method is highly flexible and can be easily adapted to identify cell adhesion-regulatory proteins and signaling pathways for other stimuli, adhesion molecules, and cell types. Graphical abstract.
Collapse
Affiliation(s)
- Yvonne J. Thus
- Department of Pathology, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands
,
Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam, The Netherlands
,
Cancer Biology and Immunology – Target & Therapy Discovery, Cancer Center Amsterdam (CCA), Amsterdam, The Netherlands
| | - Martin F. M. De Rooij
- Department of Pathology, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands
,
Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam, The Netherlands
,
Cancer Biology and Immunology – Target & Therapy Discovery, Cancer Center Amsterdam (CCA), Amsterdam, The Netherlands
| | - Roderick L. Beijersbergen
- Division of Molecular Carcinogenesis and Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
,
NKI Robotics and Screening Center and Genomics Core Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Marcel Spaargaren
- Department of Pathology, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands
,
Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam, The Netherlands
,
Cancer Biology and Immunology – Target & Therapy Discovery, Cancer Center Amsterdam (CCA), Amsterdam, The Netherlands
,
*For correspondence:
| |
Collapse
|
17
|
Wang L, Jin H, Jochems F, Wang S, Lieftink C, Martinez IM, De Conti G, Edwards F, de Oliveira RL, Schepers A, Zhou Y, Zheng J, Wu W, Zheng X, Yuan S, Ling J, Jastrzebski K, Santos Dias MD, Song JY, Celie PNH, Yagita H, Yao M, Zhou W, Beijersbergen RL, Qin W, Bernards R. cFLIP suppression and DR5 activation sensitize senescent cancer cells to senolysis. Nat Cancer 2022; 3:1284-1299. [PMID: 36414711 DOI: 10.1038/s43018-022-00462-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 10/12/2022] [Indexed: 11/23/2022]
Abstract
Senolytics, drugs that kill senescent cells, have been proposed to improve the response to pro-senescence cancer therapies; however, this remains challenging due to a lack of broadly acting senolytic drugs. Using CRISPR/Cas9-based genetic screens in different senescent cancer cell models, we identify loss of the death receptor inhibitor cFLIP as a common vulnerability of senescent cancer cells. Senescent cells are primed for apoptotic death by NF-κB-mediated upregulation of death receptor 5 (DR5) and its ligand TRAIL, but are protected from death by increased cFLIP expression. Activation of DR5 signaling by agonistic antibody, which can be enhanced further by suppression of cFLIP by BRD2 inhibition, leads to efficient killing of a variety of senescent cancer cells. Moreover, senescent cells sensitize adjacent non-senescent cells to killing by DR5 agonist through a bystander effect mediated by secretion of cytokines. We validate this 'one-two punch' cancer therapy by combining pro-senescence therapy with DR5 activation in different animal models.
Collapse
Affiliation(s)
- Liqin Wang
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - Haojie Jin
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Fleur Jochems
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Siying Wang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Cor Lieftink
- Division of Molecular Carcinogenesis, NKI Robotic and Screening Center, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Isabel Mora Martinez
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Giulia De Conti
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Finn Edwards
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Rodrigo Leite de Oliveira
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Arnout Schepers
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Yangyang Zhou
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiaojiao Zheng
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei Wu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xingling Zheng
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shengxian Yuan
- The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Jing Ling
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Kathy Jastrzebski
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Matheus Dos Santos Dias
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ji-Ying Song
- Division of Experimental Animal Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Patrick N H Celie
- Division of Biochemistry, Protein facility, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Hideo Yagita
- Department of Immunology, Juntendo University School of Medicine, Tokyo, Japan
| | - Ming Yao
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Weiping Zhou
- The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis, NKI Robotic and Screening Center, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Wenxin Qin
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - René Bernards
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands. .,State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| |
Collapse
|
18
|
Pogacar Z, Johnson JL, Krenning L, De Conti G, Jochems F, Lieftink C, Velds A, Wardak L, Groot K, Schepers A, Wang L, Song JY, van de Ven M, van Tellingen O, Medema RH, Beijersbergen RL, Bernards R, Leite de Oliveira R. Indisulam synergizes with palbociclib to induce senescence through inhibition of CDK2 kinase activity. PLoS One 2022; 17:e0273182. [PMID: 36067171 PMCID: PMC9447877 DOI: 10.1371/journal.pone.0273182] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 08/03/2022] [Indexed: 11/19/2022] Open
Abstract
Inducing senescence in cancer cells is emerging as a new therapeutic strategy. In order to find ways to enhance senescence induction by palbociclib, a CDK4/6 inhibitor approved for treatment of metastatic breast cancer, we performed functional genetic screens in palbociclib-resistant cells. Using this approach, we found that loss of CDK2 results in strong senescence induction in palbociclib-treated cells. Treatment with the CDK2 inhibitor indisulam, which phenocopies genetic CDK2 inactivation, led to sustained senescence induction when combined with palbociclib in various cell lines and lung cancer xenografts. Treating cells with indisulam led to downregulation of cyclin H, which prevented CDK2 activation. Combined treatment with palbociclib and indisulam induced a senescence program and sensitized cells to senolytic therapy. Our data indicate that inhibition of CDK2 through indisulam treatment can enhance senescence induction by CDK4/6 inhibition.
Collapse
Affiliation(s)
- Ziva Pogacar
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jackie L. Johnson
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Lenno Krenning
- Division of Cell Biology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Giulia De Conti
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Fleur Jochems
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Cor Lieftink
- The NKI Robotics and Screening Center, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Arno Velds
- Genomics Core Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Leyma Wardak
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Kelvin Groot
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Arnout Schepers
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Liqin Wang
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ji-Ying Song
- Division of Animal Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Marieke van de Ven
- Mouse Clinic for Cancer and Aging, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Olaf van Tellingen
- Division of Pharmacology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Rene H. Medema
- Division of Cell Biology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Roderick L. Beijersbergen
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- The NKI Robotics and Screening Center, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Rene Bernards
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- * E-mail: (RB); (RLO)
| | - Rodrigo Leite de Oliveira
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- * E-mail: (RB); (RLO)
| |
Collapse
|
19
|
Spanjaard A, Shah R, de Groot D, Buoninfante OA, Morris B, Lieftink C, Pritchard C, Zürcher LM, Ormel S, Catsman JJI, de Korte-Grimmerink R, Siteur B, Proost N, Boadum T, van de Ven M, Song JY, Kreft M, van den Berk PCM, Beijersbergen RL, Jacobs H. Division of labor within the DNA damage tolerance system reveals non-epistatic and clinically actionable targets for precision cancer medicine. Nucleic Acids Res 2022; 50:7420-7435. [PMID: 35819193 PMCID: PMC9303390 DOI: 10.1093/nar/gkac545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/02/2022] [Accepted: 07/07/2022] [Indexed: 11/13/2022] Open
Abstract
Crosslink repair depends on the Fanconi anemia pathway and translesion synthesis polymerases that replicate over unhooked crosslinks. Translesion synthesis is regulated via ubiquitination of PCNA, and independently via translesion synthesis polymerase REV1. The division of labor between PCNA-ubiquitination and REV1 in interstrand crosslink repair is unclear. Inhibition of either of these pathways has been proposed as a strategy to increase cytotoxicity of platinating agents in cancer treatment. Here, we defined the importance of PCNA-ubiquitination and REV1 for DNA in mammalian ICL repair. In mice, loss of PCNA-ubiquitination, but not REV1, resulted in germ cell defects and hypersensitivity to cisplatin. Loss of PCNA-ubiquitination, but not REV1 sensitized mammalian cancer cell lines to cisplatin. We identify polymerase Kappa as essential in tolerating DNA damage-induced lesions, in particular cisplatin lesions. Polk-deficient tumors were controlled by cisplatin treatment and it significantly delayed tumor outgrowth and increased overall survival of tumor bearing mice. Our results indicate that PCNA-ubiquitination and REV1 play distinct roles in DNA damage tolerance. Moreover, our results highlight POLK as a critical TLS polymerase in tolerating multiple genotoxic lesions, including cisplatin lesions. The relative frequent loss of Polk in cancers indicates an exploitable vulnerability for precision cancer medicine.
Collapse
Affiliation(s)
- Aldo Spanjaard
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Ronak Shah
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Daniël de Groot
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Olimpia Alessandra Buoninfante
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Ben Morris
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Cor Lieftink
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Colin Pritchard
- Intervention unit of the Mouse Clinic for Cancer and Aging research (MCCA), The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Lisa M Zürcher
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Shirley Ormel
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Joyce J I Catsman
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Renske de Korte-Grimmerink
- Intervention unit of the Mouse Clinic for Cancer and Aging research (MCCA), The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Bjørn Siteur
- Intervention unit of the Mouse Clinic for Cancer and Aging research (MCCA), The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Natalie Proost
- Intervention unit of the Mouse Clinic for Cancer and Aging research (MCCA), The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Terry Boadum
- NKI Animal facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Marieke van de Ven
- Intervention unit of the Mouse Clinic for Cancer and Aging research (MCCA), The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Ji-Ying Song
- Division of Experimental Animal Pathology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Maaike Kreft
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Paul C M van den Berk
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Heinz Jacobs
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| |
Collapse
|
20
|
Pogacar Z, Groot K, Jochems F, Dos Santos Dias M, Mulero-Sánchez A, Morris B, Roosen M, Wardak L, De Conti G, Velds A, Lieftink C, Thijssen B, Beijersbergen RL, Bernards R, Leite de Oliveira R. Genetic and compound screens uncover factors modulating cancer cell response to indisulam. Life Sci Alliance 2022; 5:5/9/e202101348. [PMID: 35534224 PMCID: PMC9095732 DOI: 10.26508/lsa.202101348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 04/26/2022] [Accepted: 04/26/2022] [Indexed: 11/28/2022] Open
Abstract
The authors identify that loss of SRPK1 sensitises cancer cells to indisulam treatment and loss of CAND1 confers resistance. Resistance is mediated through RBM39. Furthermore, pharmacological Bcl-xL inhibition prevents acquired resistance to indisulam. Discovering biomarkers of drug response and finding powerful drug combinations can support the reuse of previously abandoned cancer drugs in the clinic. Indisulam is an abandoned drug that acts as a molecular glue, inducing degradation of splicing factor RBM39 through interaction with CRL4DCAF15. Here, we performed genetic and compound screens to uncover factors mediating indisulam sensitivity and resistance. First, a dropout CRISPR screen identified SRPK1 loss as a synthetic lethal interaction with indisulam that can be exploited therapeutically by the SRPK1 inhibitor SPHINX31. Moreover, a CRISPR resistance screen identified components of the degradation complex that mediate resistance to indisulam: DCAF15, DDA1, and CAND1. Last, we show that cancer cells readily acquire spontaneous resistance to indisulam. Upon acquiring indisulam resistance, pancreatic cancer (Panc10.05) cells still degrade RBM39 and are vulnerable to BCL-xL inhibition. The better understanding of the factors that influence the response to indisulam can assist rational reuse of this drug in the clinic.
Collapse
Affiliation(s)
- Ziva Pogacar
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Kelvin Groot
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Fleur Jochems
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Matheus Dos Santos Dias
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Antonio Mulero-Sánchez
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ben Morris
- The Netherlands Cancer Institute Robotics and Screening Center, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Mieke Roosen
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Leyma Wardak
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Giulia De Conti
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Arno Velds
- Genomics Core Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Cor Lieftink
- The Netherlands Cancer Institute Robotics and Screening Center, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Bram Thijssen
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,The Netherlands Cancer Institute Robotics and Screening Center, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Genomics Core Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - René Bernards
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Rodrigo Leite de Oliveira
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| |
Collapse
|
21
|
Paes Dias M, Tripathi V, van der Heijden I, Cong K, Manolika EM, Bhin J, Gogola E, Galanos P, Annunziato S, Lieftink C, Andújar-Sánchez M, Chakrabarty S, Smith GCM, van de Ven M, Beijersbergen RL, Bartkova J, Rottenberg S, Cantor S, Bartek J, Ray Chaudhuri A, Jonkers J. Loss of nuclear DNA ligase III reverts PARP inhibitor resistance in BRCA1/53BP1 double-deficient cells by exposing ssDNA gaps. Mol Cell 2021; 81:4692-4708.e9. [PMID: 34555355 DOI: 10.1016/j.molcel.2021.09.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [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: 09/28/2020] [Revised: 07/20/2021] [Accepted: 09/01/2021] [Indexed: 12/12/2022]
Abstract
Inhibitors of poly(ADP-ribose) (PAR) polymerase (PARPi) have entered the clinic for the treatment of homologous recombination (HR)-deficient cancers. Despite the success of this approach, preclinical and clinical research with PARPi has revealed multiple resistance mechanisms, highlighting the need for identification of novel functional biomarkers and combination treatment strategies. Functional genetic screens performed in cells and organoids that acquired resistance to PARPi by loss of 53BP1 identified loss of LIG3 as an enhancer of PARPi toxicity in BRCA1-deficient cells. Enhancement of PARPi toxicity by LIG3 depletion is dependent on BRCA1 deficiency but independent of the loss of 53BP1 pathway. Mechanistically, we show that LIG3 loss promotes formation of MRE11-mediated post-replicative ssDNA gaps in BRCA1-deficient and BRCA1/53BP1 double-deficient cells exposed to PARPi, leading to an accumulation of chromosomal abnormalities. LIG3 depletion also enhances efficacy of PARPi against BRCA1-deficient mammary tumors in mice, suggesting LIG3 as a potential therapeutic target.
Collapse
Affiliation(s)
- Mariana Paes Dias
- Division of Molecular Pathology, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Oncode Institute, 1066CX Amsterdam, the Netherlands
| | - Vivek Tripathi
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015GD Rotterdam, the Netherlands
| | - Ingrid van der Heijden
- Division of Molecular Pathology, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Oncode Institute, 1066CX Amsterdam, the Netherlands
| | - Ke Cong
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Eleni-Maria Manolika
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015GD Rotterdam, the Netherlands
| | - Jinhyuk Bhin
- Division of Molecular Pathology, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Robotics and Screening Center, Division of Molecular Carcinogenesis, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Oncode Institute, 1066CX Amsterdam, the Netherlands
| | - Ewa Gogola
- Division of Molecular Pathology, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Oncode Institute, 1066CX Amsterdam, the Netherlands
| | - Panagiotis Galanos
- Genome Integrity Unit, Danish Cancer Society Research Center, Copenhagen 2100, Denmark
| | - Stefano Annunziato
- Division of Molecular Pathology, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Oncode Institute, 1066CX Amsterdam, the Netherlands
| | - Cor Lieftink
- Robotics and Screening Center, Division of Molecular Carcinogenesis, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Miguel Andújar-Sánchez
- Pathology Department, Complejo Hospitalario Universitario Insular, Las Palmas, Gran Canaria, Spain
| | - Sanjiban Chakrabarty
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Karnataka 576104, India
| | - Graeme C M Smith
- Artios Pharma, Glenn Berge Building, Babraham Research Campus, Cambridge CB22 3FH, UK
| | - Marieke van de Ven
- Mouse Clinic for Cancer and Aging, Preclinical Intervention Unit, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Roderick L Beijersbergen
- Robotics and Screening Center, Division of Molecular Carcinogenesis, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Jirina Bartkova
- Genome Integrity Unit, Danish Cancer Society Research Center, Copenhagen 2100, Denmark; Karolinska Institutet, Department of Medical Biochemistry and Biophysics, Division of Genome Biology, Science for Life Laboratory, Stockholm 171 77, Sweden
| | - Sven Rottenberg
- Division of Molecular Pathology, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern 3012, Switzerland
| | - Sharon Cantor
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Jiri Bartek
- Genome Integrity Unit, Danish Cancer Society Research Center, Copenhagen 2100, Denmark; Karolinska Institutet, Department of Medical Biochemistry and Biophysics, Division of Genome Biology, Science for Life Laboratory, Stockholm 171 77, Sweden
| | - Arnab Ray Chaudhuri
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015GD Rotterdam, the Netherlands.
| | - Jos Jonkers
- Division of Molecular Pathology, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Oncode Institute, 1066CX Amsterdam, the Netherlands.
| |
Collapse
|
22
|
Guo Y, Wang J, Benedict B, Yang C, van Gemert F, Ma X, Gao D, Wang H, Zhang S, Lieftink C, Beijersbergen RL, Te Riele H, Qiao X, Gao Q, Sun C, Qin W, Bernards R, Wang C. Targeting CDC7 potentiates ATR-CHK1 signaling inhibition through induction of DNA replication stress in liver cancer. Genome Med 2021; 13:166. [PMID: 34663432 PMCID: PMC8524847 DOI: 10.1186/s13073-021-00981-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 09/29/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Liver cancer is one of the most commonly diagnosed cancers and the fourth leading cause of cancer-related death worldwide. Broad-spectrum kinase inhibitors like sorafenib and lenvatinib provide only modest survival benefit to patients with hepatocellular carcinoma (HCC). This study aims to identify novel therapeutic strategies for HCC patients. METHODS Integrated bioinformatics analyses and a non-biased CRISPR loss of function genetic screen were performed to identify potential therapeutic targets for HCC cells. Whole-transcriptome sequencing (RNA-Seq) and time-lapse live imaging were performed to explore the mechanisms of the synergy between CDC7 inhibition and ATR or CHK1 inhibitors in HCC cells. Multiple in vitro and in vivo assays were used to validate the synergistic effects. RESULTS Through integrated bioinformatics analyses using the Cancer Dependency Map and the TCGA database, we identified ATR-CHK1 signaling as a therapeutic target for liver cancer. Pharmacological inhibition of ATR or CHK1 leads to robust proliferation inhibition in liver cancer cells having a high basal level of replication stress. For liver cancer cells that are resistant to ATR or CHK1 inhibition, treatment with CDC7 inhibitors induces strong DNA replication stress and consequently such drugs show striking synergy with ATR or CHK1 inhibitors. The synergy between ATR-CHK1 inhibition and CDC7 inhibition probably derives from abnormalities in mitosis inducing mitotic catastrophe. CONCLUSIONS Our data highlights the potential of targeting ATR-CHK1 signaling, either alone or in combination with CDC7 inhibition, for the treatment of liver cancer.
Collapse
Affiliation(s)
- Yuchen Guo
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute & Department of Liver Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Jun Wang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute & Department of Liver Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bente Benedict
- Division of Tumour Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Chen Yang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute & Department of Liver Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Frank van Gemert
- Division of Tumour Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Xuhui Ma
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute & Department of Liver Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Dongmei Gao
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, China
| | - Hui Wang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute & Department of Liver Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shu Zhang
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, China
| | - Cor Lieftink
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Hein Te Riele
- Division of Tumour Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Xiaohang Qiao
- Division of Tumour Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Qiang Gao
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, China
| | - Chong Sun
- Immune Regulation in Cancer Group, German Cancer Research Center, D-69120, Heidelberg, Germany
| | - Wenxin Qin
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute & Department of Liver Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - René Bernards
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute & Department of Liver Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.
| | - Cun Wang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute & Department of Liver Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| |
Collapse
|
23
|
Jochems F, Thijssen B, De Conti G, Jansen R, Pogacar Z, Groot K, Wang L, Schepers A, Wang C, Jin H, Beijersbergen RL, Leite de Oliveira R, Wessels LFA, Bernards R. The Cancer SENESCopedia: A delineation of cancer cell senescence. Cell Rep 2021; 36:109441. [PMID: 34320349 PMCID: PMC8333195 DOI: 10.1016/j.celrep.2021.109441] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [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: 12/21/2020] [Revised: 05/29/2021] [Accepted: 07/02/2021] [Indexed: 12/17/2022] Open
Abstract
Cellular senescence is characterized as a stable proliferation arrest that can be triggered by multiple stresses. Most knowledge about senescent cells is obtained from studies in primary cells. However, senescence features may be different in cancer cells, since the pathways that are involved in senescence induction are often deregulated in cancer. We report here a comprehensive analysis of the transcriptome and senolytic responses in a panel of 13 cancer cell lines rendered senescent by two distinct compounds. We show that in cancer cells, the response to senolytic agents and the composition of the senescence-associated secretory phenotype are more influenced by the cell of origin than by the senescence trigger. Using machine learning, we establish the SENCAN gene expression classifier for the detection of senescence in cancer cell samples. The expression profiles and senescence classifier are available as an interactive online Cancer SENESCopedia. Senescent cancer cells respond differently to senolytic ABT-263 SASP expression in cancer is heterogeneous and influenced by cell origin The SENCAN classifier detects cancer cell senescence in vitro The Cancer SENESCopedia contains transcriptome data from 37 senescence models
Collapse
Affiliation(s)
- Fleur Jochems
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 Amsterdam, the Netherlands
| | - Bram Thijssen
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 Amsterdam, the Netherlands
| | - Giulia De Conti
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 Amsterdam, the Netherlands
| | - Robin Jansen
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 Amsterdam, the Netherlands
| | - Ziva Pogacar
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 Amsterdam, the Netherlands
| | - Kelvin Groot
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 Amsterdam, the Netherlands
| | - Liqin Wang
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 Amsterdam, the Netherlands
| | - Arnout Schepers
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 Amsterdam, the Netherlands
| | - Cun Wang
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 Amsterdam, the Netherlands
| | - Haojie Jin
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 Amsterdam, the Netherlands
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis, The NKI Robotics and Screening Center, Netherlands Cancer Institute, Plesmanlaan 121, 1066 Amsterdam, the Netherlands
| | - Rodrigo Leite de Oliveira
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 Amsterdam, the Netherlands
| | - Lodewyk F A Wessels
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 Amsterdam, the Netherlands; Faculty of EEMCS, Delft University of Technology, Delft, the Netherlands.
| | - René Bernards
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 Amsterdam, the Netherlands.
| |
Collapse
|
24
|
Lieftink C, Beijersbergen RL. It takes two to tango, and the right music: Synergistic drug combinations with cell-cycle phase-dependent sensitivities. EBioMedicine 2021; 69:103448. [PMID: 34186491 PMCID: PMC8243350 DOI: 10.1016/j.ebiom.2021.103448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 11/20/2022] Open
Affiliation(s)
- Cor Lieftink
- Division of Molecular Carcinogenesis, The NKI Robotics and Screening Center, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis, The NKI Robotics and Screening Center, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
| |
Collapse
|
25
|
Schepers A, Jochems F, Lieftink C, Wang L, Pogacar Z, Leite de Oliveira R, De Conti G, Beijersbergen RL, Bernards R. Identification of Autophagy-Related Genes as Targets for Senescence Induction Using a Customizable CRISPR-Based Suicide Switch Screen. Mol Cancer Res 2021; 19:1613-1621. [PMID: 34158393 DOI: 10.1158/1541-7786.mcr-21-0146] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 05/07/2021] [Accepted: 06/11/2021] [Indexed: 01/10/2023]
Abstract
Pro-senescence therapies are increasingly being considered for the treatment of cancer. Identifying additional targets to induce senescence in cancer cells could further enable such therapies. However, screening for targets whose suppression induces senescence on a genome-wide scale is challenging, as senescent cells become growth arrested, and senescence-associated features can take 1 to 2 weeks to develop. For a screen with a whole-genome CRISPR library, this would result in billions of undesirable proliferating cells by the time the senescent features emerge in the growth arrested cells. Here, we present a suicide switch system that allows genome-wide CRISPR screening in growth-arrested subpopulations by eliminating the proliferating cells during the screen through activation of a suicide switch in proliferating cells. Using this system, we identify in a genome-scale CRISPR screen several autophagy-related proteins as targets for senescence induction. We show that inhibiting macroautophagy with a small molecule ULK1 inhibitor can induce senescence in cancer cell lines of different origin. Finally, we show that combining ULK1 inhibition with the senolytic drug ABT-263 leads to apoptosis in a panel of cancer cell lines. IMPLICATIONS: Our suicide switch approach allows for genome-scale identification of pro-senescence targets, and can be adapted to simplify other screens depending on the nature of the promoter used to drive the switch.
Collapse
Affiliation(s)
- Arnout Schepers
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Fleur Jochems
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Cor Lieftink
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Liqin Wang
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Ziva Pogacar
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Rodrigo Leite de Oliveira
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Giulia De Conti
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Rene Bernards
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands.
| |
Collapse
|
26
|
Schep R, Brinkman EK, Leemans C, Vergara X, van der Weide RH, Morris B, van Schaik T, Manzo SG, Peric-Hupkes D, van den Berg J, Beijersbergen RL, Medema RH, van Steensel B. Impact of chromatin context on Cas9-induced DNA double-strand break repair pathway balance. Mol Cell 2021; 81:2216-2230.e10. [PMID: 33848455 PMCID: PMC8153251 DOI: 10.1016/j.molcel.2021.03.032] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 12/23/2020] [Accepted: 03/19/2021] [Indexed: 01/01/2023]
Abstract
DNA double-strand break (DSB) repair is mediated by multiple pathways. It is thought that the local chromatin context affects the pathway choice, but the underlying principles are poorly understood. Using a multiplexed reporter assay in combination with Cas9 cutting, we systematically measure the relative activities of three DSB repair pathways as a function of chromatin context in >1,000 genomic locations. This reveals that non-homologous end-joining (NHEJ) is broadly biased toward euchromatin, while the contribution of microhomology-mediated end-joining (MMEJ) is higher in specific heterochromatin contexts. In H3K27me3-marked heterochromatin, inhibition of the H3K27 methyltransferase EZH2 reverts the balance toward NHEJ. Single-stranded template repair (SSTR), often used for precise CRISPR editing, competes with MMEJ and is moderately linked to chromatin context. These results provide insight into the impact of chromatin on DSB repair pathway balance and guidance for the design of Cas9-mediated genome editing experiments.
Collapse
Affiliation(s)
- Ruben Schep
- Oncode Institute, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands; Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands
| | - Eva K Brinkman
- Oncode Institute, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands; Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands
| | - Christ Leemans
- Oncode Institute, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands; Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands
| | - Xabier Vergara
- Oncode Institute, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands; Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands; Division of Cell Biology, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands
| | - Robin H van der Weide
- Oncode Institute, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands; Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands
| | - Ben Morris
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands; Robotics Screening Center, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands
| | - Tom van Schaik
- Oncode Institute, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands; Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands
| | - Stefano G Manzo
- Oncode Institute, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands; Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands
| | - Daniel Peric-Hupkes
- Oncode Institute, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands; Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands
| | - Jeroen van den Berg
- Oncode Institute, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands; Division of Cell Biology, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands; Robotics Screening Center, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands
| | - René H Medema
- Oncode Institute, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands; Division of Cell Biology, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands
| | - Bas van Steensel
- Oncode Institute, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands; Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands; Department of Cell Biology, Erasmus University Medical Centre, 3015 CN, Rotterdam, the Netherlands.
| |
Collapse
|
27
|
Šuštić T, van Wageningen S, Bosdriesz E, Reid RJD, Dittmar J, Lieftink C, Beijersbergen RL, Wessels LFA, Rothstein R, Bernards R. Correction to: A role for the unfolded protein response stress sensor ERN1 in regulating the response to MEK inhibitors in KRAS mutant colon cancers. Genome Med 2021; 13:24. [PMID: 33568196 PMCID: PMC7877087 DOI: 10.1186/s13073-020-00815-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
An amendment to this paper has been published and can be accessed via the original article.
Collapse
Affiliation(s)
- Tonći Šuštić
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands
| | - Sake van Wageningen
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands.,Department Genetics and Development, Columbia University Vagelos College of Physicians & Surgeons, New York, NY, 10032, USA
| | - Evert Bosdriesz
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands
| | - Robert J D Reid
- Department Genetics and Development, Columbia University Vagelos College of Physicians & Surgeons, New York, NY, 10032, USA
| | - John Dittmar
- Department Genetics and Development, Columbia University Vagelos College of Physicians & Surgeons, New York, NY, 10032, USA
| | - Cor Lieftink
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands
| | - Lodewyk F A Wessels
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands
| | - Rodney Rothstein
- Department Genetics and Development, Columbia University Vagelos College of Physicians & Surgeons, New York, NY, 10032, USA.
| | - René Bernards
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands.
| |
Collapse
|
28
|
Benedict B, van Bueren MA, van Gemert FP, Lieftink C, Guerrero Llobet S, van Vugt MA, Beijersbergen RL, Te Riele H. The RECQL helicase prevents replication fork collapse during replication stress. Life Sci Alliance 2020; 3:3/10/e202000668. [PMID: 32820027 PMCID: PMC7441523 DOI: 10.26508/lsa.202000668] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 08/11/2020] [Accepted: 08/12/2020] [Indexed: 11/24/2022] Open
Abstract
Most tumors lack the G1/S phase checkpoint and are insensitive to antigrowth signals. Loss of G1/S control can severely perturb DNA replication as revealed by slow replication fork progression and frequent replication fork stalling. Cancer cells may thus rely on specific pathways that mitigate the deleterious consequences of replication stress. To identify vulnerabilities of cells suffering from replication stress, we performed an shRNA-based genetic screen. We report that the RECQL helicase is specifically essential in replication stress conditions and protects stalled replication forks against MRE11-dependent double strand break (DSB) formation. In line with these findings, knockdown of RECQL in different cancer cells increased the level of DNA DSBs. Thus, RECQL plays a critical role in sustaining DNA synthesis under conditions of replication stress and as such may represent a target for cancer therapy.
Collapse
Affiliation(s)
- Bente Benedict
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Marit Ae van Bueren
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Frank Pa van Gemert
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Cor Lieftink
- Division of Molecular Carcinogenesis, Robotics and Screening Center, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Sergi Guerrero Llobet
- Department of Medical Oncology, Cancer Research Center Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Marcel Atm van Vugt
- Department of Medical Oncology, Cancer Research Center Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis, Robotics and Screening Center, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Hein Te Riele
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| |
Collapse
|
29
|
Wang C, Wang H, Lieftink C, du Chatinier A, Gao D, Jin G, Jin H, Beijersbergen RL, Qin W, Bernards R. CDK12 inhibition mediates DNA damage and is synergistic with sorafenib treatment in hepatocellular carcinoma. Gut 2020; 69:727-736. [PMID: 31519701 DOI: 10.1136/gutjnl-2019-318506] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 08/22/2019] [Accepted: 09/03/2019] [Indexed: 02/07/2023]
Abstract
OBJECTIVES Hepatocellular carcinoma (HCC) is one of the most frequent malignancies and a major leading cause of cancer-related deaths worldwide. Several therapeutic options like sorafenib and regorafenib provide only modest survival benefit to patients with HCC. This study aims to identify novel druggable candidate genes for patients with HCC. DESIGN A non-biased CRISPR (clustered regularly interspaced short palindromic repeats) loss-of-function genetic screen targeting all known human kinases was performed to identify vulnerabilities of HCC cells. Whole-transcriptome sequencing (RNA-Seq) and bioinformatics analyses were performed to explore the mechanisms of the action of a cyclin-dependent kinase 12 (CDK12) inhibitor in HCC cells. Multiple in vitro and in vivo assays were used to study the synergistic effects of the combination of CDK12 inhibition and sorafenib. RESULTS We identify CDK12 as critically required for most HCC cell lines. Suppression of CDK12 using short hairpin RNAs (shRNAs) or its inhibition by the covalent small molecule inhibitor THZ531 leads to robust proliferation inhibition. THZ531 preferentially suppresses the expression of DNA repair-related genes and induces strong DNA damage response in HCC cell lines. The combination of THZ531 and sorafenib shows striking synergy by inducing apoptosis or senescence in HCC cells. The synergy between THZ531 and sorafenib may derive from the notion that THZ531 impairs the adaptive responses of HCC cells induced by sorafenib treatment. CONCLUSION Our data highlight the potential of CDK12 as a drug target for patients with HCC. The striking synergy of THZ531 and sorafenib suggests a potential combination therapy for this difficult to treat cancer.
Collapse
Affiliation(s)
- Cun Wang
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hui Wang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Cor Lieftink
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Aimee du Chatinier
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Dongmei Gao
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, China
| | - Guangzhi Jin
- Department of Pathology, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Haojie Jin
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Wenxin Qin
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - René Bernards
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| |
Collapse
|
30
|
|
31
|
Matlung HL, Babes L, Zhao XW, van Houdt M, Treffers LW, van Rees DJ, Franke K, Schornagel K, Verkuijlen P, Janssen H, Halonen P, Lieftink C, Beijersbergen RL, Leusen JHW, Boelens JJ, Kuhnle I, van der Werff Ten Bosch J, Seeger K, Rutella S, Pagliara D, Matozaki T, Suzuki E, Menke-van der Houven van Oordt CW, van Bruggen R, Roos D, van Lier RAW, Kuijpers TW, Kubes P, van den Berg TK. Neutrophils Kill Antibody-Opsonized Cancer Cells by Trogoptosis. Cell Rep 2019; 23:3946-3959.e6. [PMID: 29949776 DOI: 10.1016/j.celrep.2018.05.082] [Citation(s) in RCA: 209] [Impact Index Per Article: 41.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 03/30/2018] [Accepted: 05/23/2018] [Indexed: 02/07/2023] Open
Abstract
Destruction of cancer cells by therapeutic antibodies occurs, at least in part, through antibody-dependent cellular cytotoxicity (ADCC), and this can be mediated by various Fc-receptor-expressing immune cells, including neutrophils. However, the mechanism(s) by which neutrophils kill antibody-opsonized cancer cells has not been established. Here, we demonstrate that neutrophils can exert a mode of destruction of cancer cells, which involves antibody-mediated trogocytosis by neutrophils. Intimately associated with this is an active mechanical disruption of the cancer cell plasma membrane, leading to a lytic (i.e., necrotic) type of cancer cell death. Furthermore, this mode of destruction of antibody-opsonized cancer cells by neutrophils is potentiated by CD47-SIRPα checkpoint blockade. Collectively, these findings show that neutrophil ADCC toward cancer cells occurs by a mechanism of cytotoxicity called trogoptosis, which can be further improved by targeting CD47-SIRPα interactions.
Collapse
Affiliation(s)
- Hanke L Matlung
- Sanquin Research, and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Liane Babes
- Immunology Research Group, University of Calgary, Calgary, Alberta, Canada
| | - Xi Wen Zhao
- Sanquin Research, and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Michel van Houdt
- Sanquin Research, and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Louise W Treffers
- Sanquin Research, and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Dieke J van Rees
- Sanquin Research, and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Katka Franke
- Sanquin Research, and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Karin Schornagel
- Sanquin Research, and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Paul Verkuijlen
- Sanquin Research, and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Hans Janssen
- Division of Cell Biology, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Pasi Halonen
- Division of Molecular Carcinogenesis and the NKI Robotics and Screening Center, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Cor Lieftink
- Division of Molecular Carcinogenesis and the NKI Robotics and Screening Center, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis and the NKI Robotics and Screening Center, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Jeanette H W Leusen
- Immunotherapy Laboratory, Laboratory for Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jaap J Boelens
- U-DANCE, Laboratory for Translational Immunology, UMC Utrecht, Utrecht, the Netherlands; Department of Pediatrics, Blood and Marrow Transplantation Program, UMC Utrecht, Utrecht, the Netherlands
| | - Ingrid Kuhnle
- Department of Pediatrics, University Medicine Göttingen, Göttingen, Germany
| | | | - Karl Seeger
- Department of Pediatric Oncology/Hematology, Otto-Heubner-Center for Pediatric and Adolescent Medicine, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Sergio Rutella
- Division of Translational Medicine, Sidra Medical and Research Center, Doha, Qatar
| | - Daria Pagliara
- Department of Pediatric Hematology/Oncology, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Takashi Matozaki
- Department of Biochemistry and Molecular Biology, Division of Molecular and Cellular Signaling, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan
| | - Eiji Suzuki
- Department of Breast Surgery, Kyoto University Hospital, Kyoto, Japan
| | | | - Robin van Bruggen
- Sanquin Research, and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Dirk Roos
- Sanquin Research, and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Rene A W van Lier
- Sanquin Research, and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Taco W Kuijpers
- Sanquin Research, and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands; Emma Children's Hospital, Academic Medical Centre, University of Amsterdam, Amsterdam, the Netherlands
| | - Paul Kubes
- Immunology Research Group, University of Calgary, Calgary, Alberta, Canada
| | - Timo K van den Berg
- Sanquin Research, and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands; Department of Molecular Cell Biology and Immunology, VU Medical Center, Amsterdam, the Netherlands.
| |
Collapse
|
32
|
Tuijnenburg P, Aan de Kerk DJ, Jansen MH, Morris B, Lieftink C, Beijersbergen RL, van Leeuwen EMM, Kuijpers TW. High-throughput compound screen reveals mTOR inhibitors as potential therapeutics to reduce (auto)antibody production by human plasma cells. Eur J Immunol 2019; 50:73-85. [PMID: 31621069 PMCID: PMC6972998 DOI: 10.1002/eji.201948241] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 05/08/2019] [Revised: 07/18/2019] [Accepted: 10/15/2019] [Indexed: 12/14/2022]
Abstract
Antibody production by the B cell compartment is a crucial part of the adaptive immune response. Dysregulated antibody production in the form of autoantibodies can cause autoimmune disease. To date, B‐cell depletion with anti‐CD20 antibodies is commonly applied in autoimmunity, but pre‐existing plasma cells are not eliminated in this way. Alternative ways of more selective inhibition of antibody production would add to the treatment of these autoimmune diseases. To explore novel therapeutic targets in signaling pathways essential for plasmablast formation and/or immunoglobulin production, we performed a compound screen of almost 200 protein kinase inhibitors in a robust B‐cell differentiation culture system. This study yielded 35 small cell‐permeable compounds with a reproducible inhibitory effect on B‐cell activation and plasmablast formation, among which was the clinically applied mammalian target of rapamycin (mTOR) inhibitor rapamycin. Two additional compounds targeting the phosphoinositide 3‐kinase‐AKT‐mTOR pathway (BKM120 and WYE‐354) did not affect proliferation and plasmablast formation, but specifically reduced the immunoglobulin production. With this compound screen we successfully applied a method to investigate therapeutic targets for B‐cell differentiation and identified compounds in the phosphoinositide 3‐kinase‐AKT‐mTOR pathway that could specifically inhibit immunoglobulin production only. These drugs may well be explored to be of value in current B‐cell‐depleting treatment regimens in autoimmune disorders.
Collapse
Affiliation(s)
- Paul Tuijnenburg
- Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Department of Pediatric Immunology, Rheumatology and Infectious diseases, Amsterdam, The Netherlands.,Amsterdam UMC, University of Amsterdam, Department of Experimental Immunology, Amsterdam Infection & Immunity Institute, Amsterdam, The Netherlands
| | - Daan J Aan de Kerk
- Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Department of Pediatric Immunology, Rheumatology and Infectious diseases, Amsterdam, The Netherlands.,Amsterdam UMC, University of Amsterdam, Department of Experimental Immunology, Amsterdam Infection & Immunity Institute, Amsterdam, The Netherlands
| | - Machiel H Jansen
- Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Department of Pediatric Immunology, Rheumatology and Infectious diseases, Amsterdam, The Netherlands.,Amsterdam UMC, University of Amsterdam, Department of Experimental Immunology, Amsterdam Infection & Immunity Institute, Amsterdam, The Netherlands
| | - Ben Morris
- Division of Molecular Carcinogenesis and NKI Robotics and Screening Center, Netherlands Cancer Institute (NKI-AvL), The Netherlands
| | - Cor Lieftink
- Division of Molecular Carcinogenesis and NKI Robotics and Screening Center, Netherlands Cancer Institute (NKI-AvL), The Netherlands
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis and NKI Robotics and Screening Center, Netherlands Cancer Institute (NKI-AvL), The Netherlands
| | - Ester M M van Leeuwen
- Amsterdam UMC, University of Amsterdam, Department of Experimental Immunology, Amsterdam Infection & Immunity Institute, Amsterdam, The Netherlands
| | - Taco W Kuijpers
- Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Department of Pediatric Immunology, Rheumatology and Infectious diseases, Amsterdam, The Netherlands
| |
Collapse
|
33
|
Wang C, Vegna S, Jin H, Benedict B, Lieftink C, Ramirez C, de Oliveira RL, Morris B, Gadiot J, Wang W, du Chatinier A, Wang L, Gao D, Evers B, Jin G, Xue Z, Schepers A, Jochems F, Sanchez AM, Mainardi S, Te Riele H, Beijersbergen RL, Qin W, Akkari L, Bernards R. Inducing and exploiting vulnerabilities for the treatment of liver cancer. Nature 2019; 574:268-272. [PMID: 31578521 PMCID: PMC6858884 DOI: 10.1038/s41586-019-1607-3] [Citation(s) in RCA: 224] [Impact Index Per Article: 44.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 08/21/2019] [Indexed: 01/02/2023]
Abstract
Liver cancer remains difficult to treat due to a paucity of drugs that target critical dependencies1,2 and broad spectrum kinase inhibitors like sorafenib provide only modest benefit to hepatocellular carcinoma (HCC) patients3. Induction of senescence may represent a promising strategy for the treatment of cancer, especially when such pro-senescence therapy is combined with a second drug that selectively eliminates senescent cancer cells (senolysis)4,5. Through a kinome-focused genetic screen, we report here that pharmacological inhibition of the DNA replication kinase CDC7 induces senescence selectively in TP53 mutant liver cancer cells. A follow-up chemical screen identified the anti-depressant sertraline as an agent that kills HCC cells rendered senescent by CDC7 inhibition. Sertraline supressed mTOR signalling, and selective drugs targeting this pathway were highly effective in causing apoptotic cell death of CDC7 inhibitor-treated HCC cells. Mechanistically, we report that the feedback re-activation of mTOR signalling following its inhibition6 is blocked in CDC7-inhibitor treated cells, leading to sustained mTOR inhibition and cell death. Using multiple in vivo liver cancer models, we show that combination of CDC7 and mTOR inhibitors results in dramatic tumour growth inhibition. More generally, our data indicate that exploiting an induced vulnerability could be an effective treatment of liver cancer.
Collapse
Affiliation(s)
- Cun Wang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Oncode Institute, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Serena Vegna
- Oncode Institute, Division of Tumour Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Haojie Jin
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Oncode Institute, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Bente Benedict
- Oncode Institute, Division of Tumour Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Cor Lieftink
- Oncode Institute, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Christel Ramirez
- Oncode Institute, Division of Tumour Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Rodrigo Leite de Oliveira
- Oncode Institute, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ben Morris
- Oncode Institute, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jules Gadiot
- Oncode Institute, Division of Tumour Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Wei Wang
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Aimée du Chatinier
- Oncode Institute, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Liqin Wang
- Oncode Institute, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Dongmei Gao
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, China
| | - Bastiaan Evers
- Oncode Institute, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Guangzhi Jin
- Department of Pathology, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Zheng Xue
- Oncode Institute, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Arnout Schepers
- Oncode Institute, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Fleur Jochems
- Oncode Institute, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Antonio Mulero Sanchez
- Oncode Institute, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Sara Mainardi
- Oncode Institute, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Hein Te Riele
- Oncode Institute, Division of Tumour Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Roderick L Beijersbergen
- Oncode Institute, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Wenxin Qin
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Leila Akkari
- Oncode Institute, Division of Tumour Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - René Bernards
- Oncode Institute, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
| |
Collapse
|
34
|
Combès E, Andrade AF, Tosi D, Michaud HA, Coquel F, Garambois V, Desigaud D, Jarlier M, Coquelle A, Pasero P, Bonnefoy N, Moreaux J, Martineau P, Del Rio M, Beijersbergen RL, Vezzio-Vie N, Gongora C. Inhibition of Ataxia-Telangiectasia Mutated and RAD3-Related ( ATR) Overcomes Oxaliplatin Resistance and Promotes Antitumor Immunity in Colorectal Cancer. Cancer Res 2019; 79:2933-2946. [PMID: 30987998 DOI: 10.1158/0008-5472.can-18-2807] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 01/03/2019] [Accepted: 04/05/2019] [Indexed: 11/16/2022]
Abstract
Although many patients with colorectal cancer initially respond to the chemotherapeutic agent oxaliplatin, acquired resistance to this treatment remains a major challenge to the long-term management of this disease. To identify molecular targets of oxaliplatin resistance in colorectal cancer, we performed an shRNA-based loss-of-function genetic screen using a kinome library. We found that silencing of ataxia-telangiectasia mutated and RAD3-related (ATR), a serine/threonine protein kinase involved in the response to DNA stress, restored oxaliplatin sensitivity in a cellular model of oxaliplatin resistance. Combined application of the ATR inhibitor VE-822 and oxaliplatin resulted in strong synergistic effects in six different colorectal cancer cell lines and their oxaliplatin-resistant subclones, promoted DNA single- and double-strand break formation, growth arrest, and apoptosis. This treatment also increased replicative stress, cytoplasmic DNA, and signals related to immunogenic cell death such as calreticulin exposure and HMGB1 and ATP release. In a syngeneic colorectal cancer mouse model, combined administration of VE-822 and oxaliplatin significantly increased survival by promoting antitumor T-cell responses. Finally, a DNA repair gene signature discriminated sensitive from drug-resistant patients with colorectal cancer. Overall, our results highlight the potential of ATR inhibition combined with oxaliplatin to sensitize cells to chemotherapy as a therapeutic option for patients with colorectal cancer. SIGNIFICANCE: These findings demonstrate that resistance to oxaliplatin in colorectal cancer cells can be overcome with inhibitors of ATR and that combined treatment with both agents exerts synergistic antitumor effects.Graphical Abstract: http://cancerres.aacrjournals.org/content/canres/79/11/2933/F1.large.jpg.
Collapse
Affiliation(s)
- Eve Combès
- Institut de Recherche en Cancérologie de Montpellier, INSERM U1194 Université Montpellier, CNRS, France.,Institut régional du Cancer-Montpellier-Val d'Aurelle, Montpellier, France
| | - Augusto F Andrade
- Institut de Recherche en Cancérologie de Montpellier, INSERM U1194 Université Montpellier, CNRS, France.,Institut régional du Cancer-Montpellier-Val d'Aurelle, Montpellier, France
| | - Diego Tosi
- Institut de Recherche en Cancérologie de Montpellier, INSERM U1194 Université Montpellier, CNRS, France.,Institut régional du Cancer-Montpellier-Val d'Aurelle, Montpellier, France
| | - Henri-Alexandre Michaud
- Institut de Recherche en Cancérologie de Montpellier, INSERM U1194 Université Montpellier, CNRS, France.,Institut régional du Cancer-Montpellier-Val d'Aurelle, Montpellier, France
| | - Flavie Coquel
- IGH UMR9002, CNRS-Université de Montpellier, Montpellier, France
| | - Veronique Garambois
- Institut de Recherche en Cancérologie de Montpellier, INSERM U1194 Université Montpellier, CNRS, France.,Institut régional du Cancer-Montpellier-Val d'Aurelle, Montpellier, France
| | - Delphine Desigaud
- Institut de Recherche en Cancérologie de Montpellier, INSERM U1194 Université Montpellier, CNRS, France.,Institut régional du Cancer-Montpellier-Val d'Aurelle, Montpellier, France
| | - Marta Jarlier
- Institut régional du Cancer-Montpellier-Val d'Aurelle, Montpellier, France
| | - Arnaud Coquelle
- Institut de Recherche en Cancérologie de Montpellier, INSERM U1194 Université Montpellier, CNRS, France.,Institut régional du Cancer-Montpellier-Val d'Aurelle, Montpellier, France
| | - Philippe Pasero
- IGH UMR9002, CNRS-Université de Montpellier, Montpellier, France
| | - Nathalie Bonnefoy
- Institut de Recherche en Cancérologie de Montpellier, INSERM U1194 Université Montpellier, CNRS, France.,Institut régional du Cancer-Montpellier-Val d'Aurelle, Montpellier, France
| | - Jerome Moreaux
- IGH UMR9002, CNRS-Université de Montpellier, Montpellier, France
| | - Pierre Martineau
- Institut de Recherche en Cancérologie de Montpellier, INSERM U1194 Université Montpellier, CNRS, France.,Institut régional du Cancer-Montpellier-Val d'Aurelle, Montpellier, France
| | - Maguy Del Rio
- Institut de Recherche en Cancérologie de Montpellier, INSERM U1194 Université Montpellier, CNRS, France.,Institut régional du Cancer-Montpellier-Val d'Aurelle, Montpellier, France
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis and NKI Robotics and Screening Center, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Nadia Vezzio-Vie
- Institut de Recherche en Cancérologie de Montpellier, INSERM U1194 Université Montpellier, CNRS, France.,Institut régional du Cancer-Montpellier-Val d'Aurelle, Montpellier, France
| | - Celine Gongora
- Institut de Recherche en Cancérologie de Montpellier, INSERM U1194 Université Montpellier, CNRS, France. .,Institut régional du Cancer-Montpellier-Val d'Aurelle, Montpellier, France
| |
Collapse
|
35
|
Serresi M, Siteur B, Hulsman D, Company C, Schmitt MJ, Lieftink C, Morris B, Cesaroni M, Proost N, Beijersbergen RL, van Lohuizen M, Gargiulo G. Ezh2 inhibition in Kras-driven lung cancer amplifies inflammation and associated vulnerabilities. J Exp Med 2018; 215:3115-3135. [PMID: 30487290 PMCID: PMC6279402 DOI: 10.1084/jem.20180801] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [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: 04/26/2018] [Revised: 08/31/2018] [Accepted: 11/01/2018] [Indexed: 12/24/2022] Open
Abstract
Kras-driven non–small-cell-lung cancers (NSCLCs) are a leading cause of death with limited therapeutic options. Serresi et al. show that inhibiting Ezh2 in orthotopic KrasG12D-driven NSCLC unleashes an inflammatory response rewiring tumor progression and amplifying associated vulnerabilities that could be therapeutically exploited. Kras-driven non–small-cell lung cancers (NSCLCs) are a leading cause of death with limited therapeutic options. Many NSCLCs exhibit high levels of Ezh2, the enzymatic subunit of polycomb repressive complex 2 (PRC2). We tested Ezh2 inhibitors as single agents or before chemotherapy in mice with orthotopic Kras-driven NSCLC grafts, which homogeneously express Ezh2. These tumors display sensitivity to EZH2 inhibition by GSK126 but also amplify an inflammatory program involving signaling through NF-κB and genes residing in PRC2-regulated chromatin. During this process, tumor cells overcome GSK126 antiproliferative effects. We identified oncogenes that may mediate progression through an in vivo RNAi screen aimed at targets of PRC2/NF-κB. An in vitro compound screening linked GSK126-driven inflammation and therapeutic vulnerability in human cells to regulation of RNA synthesis and proteostasis. Interestingly, GSK126-treated NSCLCs in vivo also showed an enhanced response to a combination of nimesulide and bortezomib. Thus, Ezh2 inhibition may restrict cell proliferation and promote defined adaptive responses. Targeting these responses potentially improves outcomes in Kras-driven NSCLCs.
Collapse
Affiliation(s)
- Michela Serresi
- Molecular Oncology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Bjorn Siteur
- Mouse Cancer Clinic, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Danielle Hulsman
- Division of Molecular Genetics and Cancer Genomics Centre, Netherlands Cancer Institute, Amsterdam, Netherlands.,Oncode Institute, Utrecht, Netherlands
| | - Carlos Company
- Molecular Oncology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Matthias J Schmitt
- Molecular Oncology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Cor Lieftink
- Division of Molecular Carcinogenesis and Netherlands Cancer Institute Robotics and Screening Center, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Ben Morris
- Division of Molecular Carcinogenesis and Netherlands Cancer Institute Robotics and Screening Center, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Matteo Cesaroni
- Fels Institute, Temple University School of Medicine, Philadelphia, PA
| | - Natalie Proost
- Mouse Cancer Clinic, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis and Netherlands Cancer Institute Robotics and Screening Center, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Maarten van Lohuizen
- Division of Molecular Genetics and Cancer Genomics Centre, Netherlands Cancer Institute, Amsterdam, Netherlands .,Oncode Institute, Utrecht, Netherlands
| | - Gaetano Gargiulo
- Molecular Oncology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| |
Collapse
|
36
|
Šuštić T, van Wageningen S, Bosdriesz E, Reid RJD, Dittmar J, Lieftink C, Beijersbergen RL, Wessels LFA, Rothstein R, Bernards R. A role for the unfolded protein response stress sensor ERN1 in regulating the response to MEK inhibitors in KRAS mutant colon cancers. Genome Med 2018; 10:90. [PMID: 30482246 PMCID: PMC6258447 DOI: 10.1186/s13073-018-0600-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 11/13/2018] [Indexed: 12/25/2022] Open
Abstract
Background Mutations in KRAS are frequent in human cancer, yet effective targeted therapeutics for these cancers are still lacking. Attempts to drug the MEK kinases downstream of KRAS have had limited success in clinical trials. Understanding the specific genomic vulnerabilities of KRAS-driven cancers may uncover novel patient-tailored treatment options. Methods We first searched for synthetic lethal (SL) genetic interactions with mutant RAS in yeast with the ultimate aim to identify novel cancer-specific targets for therapy. Our method used selective ploidy ablation, which enables replication of cancer-specific gene expression changes in the yeast gene disruption library. Second, we used a genome-wide CRISPR/Cas9-based genetic screen in KRAS mutant human colon cancer cells to understand the mechanistic connection between the synthetic lethal interaction discovered in yeast and downstream RAS signaling in human cells. Results We identify loss of the endoplasmic reticulum (ER) stress sensor IRE1 as synthetic lethal with activated RAS mutants in yeast. In KRAS mutant colorectal cancer cell lines, genetic ablation of the human ortholog of IRE1, ERN1, does not affect growth but sensitizes to MEK inhibition. However, an ERN1 kinase inhibitor failed to show synergy with MEK inhibition, suggesting that a non-kinase function of ERN1 confers MEK inhibitor resistance. To investigate how ERN1 modulates MEK inhibitor responses, we performed genetic screens in ERN1 knockout KRAS mutant colon cancer cells to identify genes whose inactivation confers resistance to MEK inhibition. This genetic screen identified multiple negative regulators of JUN N-terminal kinase (JNK) /JUN signaling. Consistently, compounds targeting JNK/MAPK8 or TAK1/MAP3K7, which relay signals from ERN1 to JUN, display synergy with MEK inhibition. Conclusions We identify the ERN1-JNK-JUN pathway as a novel regulator of MEK inhibitor response in KRAS mutant colon cancer. The notion that multiple signaling pathways can activate JUN may explain why KRAS mutant tumor cells are traditionally seen as highly refractory to MEK inhibitor therapy. Our findings emphasize the need for the development of new therapeutics targeting JUN activating kinases, TAK1 and JNK, to sensitize KRAS mutant cancer cells to MEK inhibitors. Electronic supplementary material The online version of this article (10.1186/s13073-018-0600-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Tonći Šuštić
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands
| | - Sake van Wageningen
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands.,Department Genetics and Development, Columbia University Vagelos College of Physicians & Surgeons, New York, NY, 10032, USA
| | - Evert Bosdriesz
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands
| | - Robert J D Reid
- Department Genetics and Development, Columbia University Vagelos College of Physicians & Surgeons, New York, NY, 10032, USA
| | - John Dittmar
- Department Genetics and Development, Columbia University Vagelos College of Physicians & Surgeons, New York, NY, 10032, USA
| | - Cor Lieftink
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands
| | - Lodewyk F A Wessels
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands
| | - Rodney Rothstein
- Department Genetics and Development, Columbia University Vagelos College of Physicians & Surgeons, New York, NY, 10032, USA.
| | - René Bernards
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands.
| |
Collapse
|
37
|
Wang L, Leite de Oliveira R, Wang C, Fernandes Neto JM, Mainardi S, Evers B, Lieftink C, Morris B, Jochems F, Willemsen L, Beijersbergen RL, Bernards R. High-Throughput Functional Genetic and Compound Screens Identify Targets for Senescence Induction in Cancer. Cell Rep 2018; 21:773-783. [PMID: 29045843 DOI: 10.1016/j.celrep.2017.09.085] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [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: 05/26/2017] [Revised: 08/29/2017] [Accepted: 09/25/2017] [Indexed: 12/17/2022] Open
Abstract
Senescence is a proliferation arrest that can result from a variety of stresses. Cancer cells can also undergo senescence, but the stresses that provoke cancer cells to undergo senescence are unclear. Here, we use both functional genetic and compound screens in cancer cells harboring a reporter that is activated during senescence to find targets that induce senescence. We show that suppression of the SWI/SNF component SMARCB1 induces senescence in melanoma through strong activation of the MAP kinase pathway. From the compound screen, we identified multiple aurora kinase inhibitors as potent inducers of senescence in RAS mutant lung cancer. Senescent melanoma and lung cancer cells acquire sensitivity to the BCL2 family inhibitor ABT263. We propose a one-two punch approach for the treatment of cancer in which a drug is first used to induce senescence in cancer cells and a second drug is then used to kill senescent cancer cells.
Collapse
Affiliation(s)
- Liqin Wang
- Division of Molecular Carcinogenesis, Cancer Genomics Centre, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Rodrigo Leite de Oliveira
- Division of Molecular Carcinogenesis, Cancer Genomics Centre, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Cun Wang
- Division of Molecular Carcinogenesis, Cancer Genomics Centre, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - João M Fernandes Neto
- Division of Molecular Carcinogenesis, Cancer Genomics Centre, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Sara Mainardi
- Division of Molecular Carcinogenesis, Cancer Genomics Centre, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Bastiaan Evers
- Division of Molecular Carcinogenesis, Cancer Genomics Centre, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Cor Lieftink
- Division of Molecular Carcinogenesis, Cancer Genomics Centre, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Ben Morris
- Division of Molecular Carcinogenesis, Cancer Genomics Centre, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Fleur Jochems
- Division of Molecular Carcinogenesis, Cancer Genomics Centre, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Lisa Willemsen
- Division of Molecular Carcinogenesis, Cancer Genomics Centre, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis, Cancer Genomics Centre, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - René Bernards
- Division of Molecular Carcinogenesis, Cancer Genomics Centre, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands.
| |
Collapse
|
38
|
Jastrzebski K, Thijssen B, Kluin RJC, de Lint K, Majewski IJ, Beijersbergen RL, Wessels LFA. Integrative Modeling Identifies Key Determinants of Inhibitor Sensitivity in Breast Cancer Cell Lines. Cancer Res 2018; 78:4396-4410. [PMID: 29844118 DOI: 10.1158/0008-5472.can-17-2698] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 02/26/2018] [Accepted: 05/21/2018] [Indexed: 11/16/2022]
Abstract
Cancer cell lines differ greatly in their sensitivity to anticancer drugs as a result of different oncogenic drivers and drug resistance mechanisms operating in each cell line. Although many of these mechanisms have been discovered, it remains a challenge to understand how they interact to render an individual cell line sensitive or resistant to a particular drug. To better understand this variability, we profiled a panel of 30 breast cancer cell lines in the absence of drugs for their mutations, copy number aberrations, mRNA, protein expression and protein phosphorylation, and for response to seven different kinase inhibitors. We then constructed a knowledge-based, Bayesian computational model that integrates these data types and estimates the relative contribution of various drug sensitivity mechanisms. The resulting model of regulatory signaling explained the majority of the variability observed in drug response. The model also identified cell lines with an unexplained response, and for these we searched for novel explanatory factors. Among others, we found that 4E-BP1 protein expression, and not just the extent of phosphorylation, was a determinant of mTOR inhibitor sensitivity. We validated this finding experimentally and found that overexpression of 4E-BP1 in cell lines that normally possess low levels of this protein is sufficient to increase mTOR inhibitor sensitivity. Taken together, our work demonstrates that combining experimental characterization with integrative modeling can be used to systematically test and extend our understanding of the variability in anticancer drug response.Significance: By estimating how different oncogenic mutations and drug resistance mechanisms affect the response of cancer cells to kinase inhibitors, we can better understand and ultimately predict response to these anticancer drugs.Graphical Abstract: http://cancerres.aacrjournals.org/content/canres/78/15/4396/F1.large.jpg Cancer Res; 78(15); 4396-410. ©2018 AACR.
Collapse
Affiliation(s)
- Katarzyna Jastrzebski
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Bram Thijssen
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands.,Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Roelof J C Kluin
- Genomic Sequencing Facility, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Klaas de Lint
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Ian J Majewski
- Division of Cancer and Haematology, The Walter and Eliza Hall Institute, Parkville Victoria, Australia
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands.
| | - Lodewyk F A Wessels
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands. .,Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands.,Faculty of EEMCS, Delft University of Technology, Delft, the Netherlands
| |
Collapse
|
39
|
Berns K, Caumanns JJ, Hijmans EM, Gennissen AMC, Severson TM, Evers B, Wisman GBA, Jan Meersma G, Lieftink C, Beijersbergen RL, Itamochi H, van der Zee AGJ, de Jong S, Bernards R. ARID1A mutation sensitizes most ovarian clear cell carcinomas to BET inhibitors. Oncogene 2018; 37:4611-4625. [PMID: 29760405 PMCID: PMC6095834 DOI: 10.1038/s41388-018-0300-6] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [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: 11/27/2017] [Revised: 03/23/2018] [Accepted: 04/10/2018] [Indexed: 12/16/2022]
Abstract
Current treatment for advanced stage ovarian clear cell cancer is severely hampered by a lack of effective systemic therapy options, leading to a poor outlook for these patients. Sequencing studies revealed that ARID1A is mutated in over 50% of ovarian clear cell carcinomas. To search for a rational approach to target ovarian clear cell cancers with ARID1A mutations, we performed kinome-centered lethality screens in a large panel of ovarian clear cell carcinoma cell lines. Using the largest OCCC cell line panel established to date, we show here that BRD2 inhibition is predominantly lethal in ARID1A mutated ovarian clear cell cancer cells. Importantly, small molecule inhibitors of the BET (bromodomain and extra terminal domain) family of proteins, to which BRD2 belongs, specifically inhibit proliferation of ARID1A mutated cell lines, both in vitro and in ovarian clear cell cancer xenografts and patient-derived xenograft models. BET inhibitors cause a reduction in the expression of multiple SWI/SNF members including ARID1B, providing a potential explanation for the observed lethal interaction with ARID1A loss. Our data indicate that BET inhibition may represent a novel treatment strategy for a subset of ARID1A mutated ovarian clear cell carcinomas.
Collapse
Affiliation(s)
- Katrien Berns
- Division of Molecular Carcinogenesis and Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands.
| | - Joseph J Caumanns
- Gynaecologic Oncology, Cancer Research Centre Groningen, University Medical Center Groningen, University of Groningen, Hanzeplein 1, Groningen, 9713 GZ, The Netherlands
| | - E Marielle Hijmans
- Division of Molecular Carcinogenesis and Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands
| | - Annemiek M C Gennissen
- Division of Molecular Carcinogenesis and Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands
| | - Tesa M Severson
- Division of Molecular Carcinogenesis and Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands
| | - Bastiaan Evers
- Division of Molecular Carcinogenesis and Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands
| | - G Bea A Wisman
- Gynaecologic Oncology, Cancer Research Centre Groningen, University Medical Center Groningen, University of Groningen, Hanzeplein 1, Groningen, 9713 GZ, The Netherlands
| | - Gert Jan Meersma
- Gynaecologic Oncology, Cancer Research Centre Groningen, University Medical Center Groningen, University of Groningen, Hanzeplein 1, Groningen, 9713 GZ, The Netherlands
| | - Cor Lieftink
- Division of Molecular Carcinogenesis and Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis and Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands
| | - Hiroaki Itamochi
- Department of Obstetrics and Gynaecology, Iwate Medical University School of Medicine, Iwate, Morioka, 020-8505, Japan
| | - Ate G J van der Zee
- Gynaecologic Oncology, Cancer Research Centre Groningen, University Medical Center Groningen, University of Groningen, Hanzeplein 1, Groningen, 9713 GZ, The Netherlands
| | - Steven de Jong
- Medical Oncology, Cancer Research Centre Groningen, University Medical Center Groningen, University of Groningen, Hanzeplein 1, Groningen, 9713 GZ, The Netherlands
| | - René Bernards
- Division of Molecular Carcinogenesis and Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands.
| |
Collapse
|
40
|
Wang C, Jin H, Gao D, Wang L, Evers B, Xue Z, Jin G, Lieftink C, Beijersbergen RL, Qin W, Bernards R. A CRISPR screen identifies CDK7 as a therapeutic target in hepatocellular carcinoma. Cell Res 2018; 28:690-692. [PMID: 29507396 DOI: 10.1038/s41422-018-0020-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 01/17/2018] [Accepted: 02/06/2018] [Indexed: 02/04/2023] Open
Affiliation(s)
- Cun Wang
- Division of Molecular Carcinogenesis, Oncode Institute, Cancer Genomics Centre Netherlands, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.,State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200032, China
| | - Haojie Jin
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200032, China
| | - Dongmei Gao
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China
| | - Liqin Wang
- Division of Molecular Carcinogenesis, Oncode Institute, Cancer Genomics Centre Netherlands, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Bastiaan Evers
- Division of Molecular Carcinogenesis, Oncode Institute, Cancer Genomics Centre Netherlands, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Zheng Xue
- Division of Molecular Carcinogenesis, Oncode Institute, Cancer Genomics Centre Netherlands, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Guangzhi Jin
- Department of Pathology, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, 200438, China
| | - Cor Lieftink
- Division of Molecular Carcinogenesis, Oncode Institute, Cancer Genomics Centre Netherlands, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis, Oncode Institute, Cancer Genomics Centre Netherlands, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Wenxin Qin
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200032, China.
| | - René Bernards
- Division of Molecular Carcinogenesis, Oncode Institute, Cancer Genomics Centre Netherlands, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.
| |
Collapse
|
41
|
Brunen D, de Vries RC, Lieftink C, Beijersbergen RL, Bernards R. PIM Kinases Are a Potential Prognostic Biomarker and Therapeutic Target in Neuroblastoma. Mol Cancer Ther 2018; 17:849-857. [PMID: 29440296 DOI: 10.1158/1535-7163.mct-17-0868] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 11/01/2017] [Accepted: 01/10/2018] [Indexed: 11/16/2022]
Abstract
The majority of high-risk neuroblastoma patients are refractory to, or relapse on, current treatment regimens, resulting in 5-year survival rates of less than 50%. This emphasizes the urgent need to identify novel therapeutic targets. Here, we report that high PIM kinase expression is correlated with poor overall survival. Treatment of neuroblastoma cell lines with the pan-PIM inhibitors AZD1208 or PIM-447 suppressed proliferation through inhibition of mTOR signaling. In a panel of neuroblastoma cell lines, we observed a marked binary response to PIM inhibition, suggesting that specific genetic lesions control responses to PIM inhibition. Using a genome-wide CRISPR-Cas9 genetic screen, we identified NF1 loss as the major resistance mechanism to PIM kinase inhibitors. Treatment with AZD1208 impaired the growth of NF1 wild-type xenografts, while NF1 knockout cells were insensitive. Thus, our data indicate that PIM inhibition may be a novel targeted therapy in NF1 wild-type neuroblastoma. Mol Cancer Ther; 17(4); 849-57. ©2018 AACR.
Collapse
Affiliation(s)
- Diede Brunen
- Division of Molecular Carcinogenesis and Cancer Genomics Center Netherlands, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Romy C de Vries
- Division of Molecular Carcinogenesis and Cancer Genomics Center Netherlands, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Cor Lieftink
- Division of Molecular Carcinogenesis and Cancer Genomics Center Netherlands, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis and Cancer Genomics Center Netherlands, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - René Bernards
- Division of Molecular Carcinogenesis and Cancer Genomics Center Netherlands, The Netherlands Cancer Institute, Amsterdam, the Netherlands.
| |
Collapse
|
42
|
Brunen D, García-Barchino MJ, Malani D, Jagalur Basheer N, Lieftink C, Beijersbergen RL, Murumägi A, Porkka K, Wolf M, Zwaan CM, Fornerod M, Kallioniemi O, Martínez-Climent JÁ, Bernards R. Intrinsic resistance to PIM kinase inhibition in AML through p38α-mediated feedback activation of mTOR signaling. Oncotarget 2018; 7:37407-37419. [PMID: 27270648 PMCID: PMC5122321 DOI: 10.18632/oncotarget.9822] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [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] [Received: 04/06/2016] [Accepted: 05/23/2016] [Indexed: 01/07/2023] Open
Abstract
Although conventional therapies for acute myeloid leukemia (AML) and diffuse large B-cell lymphoma (DLBCL) are effective in inducing remission, many patients relapse upon treatment. Hence, there is an urgent need for novel therapies. PIM kinases are often overexpressed in AML and DLBCL and are therefore an attractive therapeutic target. However, in vitro experiments have demonstrated that intrinsic resistance to PIM inhibition is common. It is therefore likely that only a minority of patients will benefit from single agent PIM inhibitor treatment. In this study, we performed an shRNA-based genetic screen to identify kinases whose suppression is synergistic with PIM inhibition. Here, we report that suppression of p38α (MAPK14) is synthetic lethal with the PIM kinase inhibitor AZD1208. PIM inhibition elevates reactive oxygen species (ROS) levels, which subsequently activates p38α and downstream AKT/mTOR signaling. We found that p38α inhibitors sensitize hematological tumor cell lines to AZD1208 treatment in vitro and in vivo. These results were validated in ex vivo patient-derived AML cells. Our findings provide mechanistic and translational evidence supporting the rationale to test a combination of p38α and PIM inhibitors in clinical trials for AML and DLBCL.
Collapse
Affiliation(s)
- Diede Brunen
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Disha Malani
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Noorjahan Jagalur Basheer
- Department of Pediatric Oncology, Erasmus Medical Center/Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Cor Lieftink
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Astrid Murumägi
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | | | - Maija Wolf
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - C Michel Zwaan
- Department of Pediatric Oncology, Erasmus Medical Center/Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Maarten Fornerod
- Department of Pediatric Oncology, Erasmus Medical Center/Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Olli Kallioniemi
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | | | - René Bernards
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| |
Collapse
|
43
|
Iskit S, Lieftink C, Halonen P, Shahrabi A, Possik PA, Beijersbergen RL, Peeper DS. Integrated in vivo genetic and pharmacologic screening identifies co-inhibition of EGRF and ROCK as a potential treatment regimen for triple-negative breast cancer. Oncotarget 2018; 7:42859-42872. [PMID: 27374095 PMCID: PMC5189992 DOI: 10.18632/oncotarget.10230] [Citation(s) in RCA: 9] [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] [Received: 01/13/2016] [Accepted: 06/09/2016] [Indexed: 12/21/2022] Open
Abstract
Breast cancer is the second most common cause of cancer-related deaths worldwide among women. Despite several therapeutic options, 15% of breast cancer patients succumb to the disease owing to tumor relapse and acquired therapy resistance. Particularly in triple-negative breast cancer (TNBC), developing effective treatments remains challenging owing to the lack of a common vulnerability that can be exploited by targeted approaches. We have previously shown that tumor cells have different requirements for growth in vivo than in vitro. Therefore, to discover novel drug targets for TNBC, we performed parallel in vivo and in vitro genetic shRNA dropout screens. We identified several potential drug targets that were required for tumor growth in vivo to a greater extent than in vitro. By combining pharmacologic inhibitors acting on a subset of these candidates, we identified a synergistic interaction between EGFR and ROCK inhibitors. This combination effectively reduced TNBC cell growth by inducing cell cycle arrest. These results illustrate the power of in vivo genetic screens and warrant further validation of EGFR and ROCK as combined pharmacologic targets for breast cancer.
Collapse
Affiliation(s)
- Sedef Iskit
- Department of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan, Amsterdam, The Netherlands
| | - Cor Lieftink
- Department of Molecular Carcinogenesis, The Netherlands Cancer Institute, Plesmanlaan, Amsterdam, The Netherlands
| | - Pasi Halonen
- Drug Discovery Research and Screening Services, BioFocus, Darwinweg, Leiden
| | - Aida Shahrabi
- Department of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan, Amsterdam, The Netherlands
| | | | - Roderick L Beijersbergen
- Department of Molecular Carcinogenesis, The Netherlands Cancer Institute, Plesmanlaan, Amsterdam, The Netherlands
| | - Daniel S Peeper
- Department of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan, Amsterdam, The Netherlands
| |
Collapse
|
44
|
Berns K, Caumanns JJ, Hijmans EM, Gennissen A, Evers B, Wisman BA, Meersema GJ, Lieftink C, Beijersbergen RL, Itamochi H, Zee AGVD, Jong SD, Bernards R. Abstract 3380: Synthetic lethal interaction between ARID1A mutation and BET bromodomain inhibition in ovarian clear cell carcinoma. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-3380] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction:
Current treatment for advanced stage ovarian clear cell cancer is severely hampered by a lack of effective systemic therapy options, leading to a poor outlook for these patients. Given that ARID1A is inactivated by mutation in over 50% of ovarian clear cell carcinomas, we pursued an ARID1A synthetic lethal screening strategy to identify druggable targets in OCCC.
Experimental procedures:
We performed synthetic lethal kinome short hairpin (shRNA) screens in a large panel (n=14) of OCCC cell lines having different ARID1A mutation status. Hit validation was performed with isogenic ARID1A ko cell line pairs and in (patient-derived) xenograft mouse models.
Summary of the data:
We show here that BRD2 inhibition is synthetic lethal with ARID1A mutation in ovarian clear cell cancer cells. Importantly, inhibiting the BET family of proteins, to which BRD2 belongs, with small molecules specifically inhibits proliferation of ARID1A mutated cell lines both in vitro and in ovarian clear cell cancer xenografts and patient-derived xenograft models. We demonstrate that ARID1A loss leads to upregulation of the WNT ligand WNT10B, possibly causing a WNT dependency in the ARID1A mutant lines. BET inhibitors cause a reduction in WNT10B expression and WNT target genes such as MYC, JUN and WISP1, providing a potential explanation for the observed synthetic lethal interaction with ARID1A loss.
Conclusions:
Our study uncovered a new synthetic lethal interaction between ARID1A mutation and BET bromodomain inhibition, suggesting a new treatment strategy for ARID1A mutant ovarian clear cell carcinomas.
Citation Format: Katrien Berns, Joseph J. Caumanns, E Marielle Hijmans, Annemiek Gennissen, Bastiaan Evers, Bea A. Wisman, Gert Jan Meersema, Cor Lieftink, Roderick L. Beijersbergen, Hiroaki Itamochi, Ate G. van der Zee, Steven de Jong, René Bernards. Synthetic lethal interaction between ARID1A mutation and BET bromodomain inhibition in ovarian clear cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3380. doi:10.1158/1538-7445.AM2017-3380
Collapse
Affiliation(s)
- Katrien Berns
- 1Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | | | | | | | - Bea A. Wisman
- 2University Medical Center Groningen, Groningen, Netherlands
| | | | - Cor Lieftink
- 1Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | | | | | - Steven de Jong
- 2University Medical Center Groningen, Groningen, Netherlands
| | - René Bernards
- 1Netherlands Cancer Institute, Amsterdam, Netherlands
| |
Collapse
|
45
|
Abstract
Treatment with targeted drugs has primarily focused on the genes and pathways that are mutated in cancer, which severely limits the repertoire of drug targets. Synthetic lethality exploits the notion that the presence of a mutation in a cancer gene is often associated with a new vulnerability that can be targeted therapeutically, thus greatly expanding the arsenal of potential drug targets. Here we discuss both the experimental and the computational biology tools that can be used to identify synthetic lethal interactions. We also discuss strategies for using synthetic lethality to discover new drug targets and in the rational design of more potent drug combinations. We review the progress made and future opportunities offered by synthetic lethal approaches to treating cancer more effectively.
Collapse
Affiliation(s)
- Roderick L. Beijersbergen
- Division of Molecular Carcinogenesis and Cancer Genomics Centre Netherlands, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Lodewyk F.A. Wessels
- Division of Molecular Carcinogenesis and Cancer Genomics Centre Netherlands, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - René Bernards
- Division of Molecular Carcinogenesis and Cancer Genomics Centre Netherlands, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| |
Collapse
|
46
|
Wang L, Šuštić T, Leite de Oliveira R, Lieftink C, Halonen P, van de Ven M, Beijersbergen RL, van den Heuvel MM, Bernards R, van der Heijden MS. A Functional Genetic Screen Identifies the Phosphoinositide 3-kinase Pathway as a Determinant of Resistance to Fibroblast Growth Factor Receptor Inhibitors in FGFR Mutant Urothelial Cell Carcinoma. Eur Urol 2017; 71:858-862. [PMID: 28108151 DOI: 10.1016/j.eururo.2017.01.021] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 01/06/2017] [Indexed: 11/19/2022]
Abstract
Activating mutations and translocations of the FGFR3 gene are commonly seen in urothelial cell carcinoma (UCC) of the bladder and urinary tract. Several fibroblast growth factor receptor (FGFR) inhibitors are currently in clinical development and response rates appear promising for advanced UCC. A common problem with targeted therapeutics is intrinsic or acquired resistance of the cancer cells. To find potential drug targets that can act synergistically with FGFR inhibition, we performed a synthetic lethality screen for the FGFR inhibitor AZD4547 using a short hairpin RNA library targeting the human kinome in the UCC cell line RT112 (FGFR3-TACC3 translocation). We identified multiple members of the phosphoinositide 3-kinase (PI3K) pathway and found that inhibition of PIK3CA acts synergistically with FGFR inhibitors. The PI3K inhibitor BKM120 acted synergistically with inhibition of FGFR in multiple UCC and lung cancer cell lines having FGFR mutations. Consistently, we observed an elevated PI3K-protein kinase B pathway activity resulting from epidermal growth factor receptor or Erb-B2 receptor tyrosine kinase 3 reactivation caused by FGFR inhibition as the underlying molecular mechanism of the synergy. Our data show that feedback pathways activated by FGFR inhibition converge on the PI3K pathway. These findings provide a strong rationale to test FGFR inhibitors in combination with PI3K inhibitors in cancers harboring genetic activation of FGFR genes.
Collapse
Affiliation(s)
- Liqin Wang
- Division of Molecular Carcinogenesis, Cancer Genomics Netherlands, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Tonći Šuštić
- Division of Molecular Carcinogenesis, Cancer Genomics Netherlands, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Rodrigo Leite de Oliveira
- Division of Molecular Carcinogenesis, Cancer Genomics Netherlands, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Cor Lieftink
- Division of Molecular Carcinogenesis, Cancer Genomics Netherlands, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Pasi Halonen
- Division of Molecular Carcinogenesis, Cancer Genomics Netherlands, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Marieke van de Ven
- Mouse Clinic Intervention Unit, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis, Cancer Genomics Netherlands, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - René Bernards
- Division of Molecular Carcinogenesis, Cancer Genomics Netherlands, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - Michiel S van der Heijden
- Division of Molecular Carcinogenesis, Cancer Genomics Netherlands, The Netherlands Cancer Institute, Amsterdam, The Netherlands; Division of Medical Oncology, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands.
| |
Collapse
|
47
|
Berns K, Sonnenblick A, Gennissen A, Brohée S, Hijmans EM, Evers B, Fumagalli D, Desmedt C, Loibl S, Denkert C, Neven P, Guo W, Zhang F, Knijnenburg TA, Bosse T, van der Heijden MS, Hindriksen S, Nijkamp W, Wessels LF, Joensuu H, Mills GB, Beijersbergen RL, Sotiriou C, Bernards R. Loss of ARID1A Activates ANXA1, which Serves as a Predictive Biomarker for Trastuzumab Resistance. Clin Cancer Res 2016; 22:5238-5248. [DOI: 10.1158/1078-0432.ccr-15-2996] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 05/02/2016] [Indexed: 11/16/2022]
|
48
|
de Lint K, Poell JB, Soueidan H, Jastrzebski K, Vidal Rodriguez J, Lieftink C, Wessels LF, Beijersbergen RL. Sensitizing Triple-Negative Breast Cancer to PI3K Inhibition by Cotargeting IGF1R. Mol Cancer Ther 2016; 15:1545-56. [DOI: 10.1158/1535-7163.mct-15-0865] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 03/26/2016] [Indexed: 11/16/2022]
|
49
|
Abstract
Functional genomic screens using shRNA technology are a great tool in biomedical research. As more labs gain access to the necessary reagents and technology to perform such screens, some may lack in-depth knowledge on the difficulties often encountered. With this protocol, we aim to point out the most important caveats of performing shRNA based screens and provide a streamlined workflow that can be easily adapted to meet the specific needs of any particular screening project.
Collapse
Affiliation(s)
- Katarzyna Jastrzebski
- Division of Molecular Carcinogenesis and NKI Robotics and Screening Center, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Bastiaan Evers
- Division of Molecular Carcinogenesis and NKI Robotics and Screening Center, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis and NKI Robotics and Screening Center, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.
| |
Collapse
|
50
|
Thijssen B, Jastrzebski K, Beijersbergen RL, Wessels LFA. Abstract B2-37: Understanding the variability in drug response in a panel of breast cancer cell lines using computational models. Cancer Res 2015. [DOI: 10.1158/1538-7445.compsysbio-b2-37] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Cancer cell lines differ widely in their sensitivity to anticancer drugs. While many oncogenic drivers and drug resistance mechanisms have been discovered, it is generally unclear how these mechanisms interact in each cell line to make the cell line sensitive or resistant to a particular drug.
We set out to explain this variability in drug sensitivity in a panel of 30 breast cancer cell lines. We characterized these cell lines at the DNA, RNA and protein level, and accurately measured the proliferation under treatment with various different kinase inhibitors. We then constructed computational models encompassing several of the important driver pathways and sensitivity mechanisms, and tested how well these models describe the available data. After selecting the well-fitting models, we could use these models to estimate the relative contribution of each of the interacting mechanisms to the proliferation of the cells under drug treatment. For example, the models indicated that FGF2 autocrine signaling contributes to fast proliferation in some cell lines; that SGK1 expression provides a bypass for Akt signaling in some cell lines; or that the expression level of 4E-BP1 is a key determinant of mTOR-inhibitor sensitivity on top of other genetic alterations in the PI3K-pathway. Additionally, we could use these models to thoroughly analyze which parts of the data cannot be explained. This greatly narrows down which follow-up studies are necessary to advance our understanding of drug response.
These results show that knowledge-based computational models can be used to systematically study drug response in cell line panels. Such systematic, quantitative understanding of drug response will be useful in working towards precision medicine for individual cancer patients.
Citation Format: Bram Thijssen, Katarzyna Jastrzebski, Roderick L. Beijersbergen, Lodewyk FA Wessels. Understanding the variability in drug response in a panel of breast cancer cell lines using computational models. [abstract]. In: Proceedings of the AACR Special Conference on Computational and Systems Biology of Cancer; Feb 8-11 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 2):Abstract nr B2-37.
Collapse
Affiliation(s)
- Bram Thijssen
- Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | | | | |
Collapse
|