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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] [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.
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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.
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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] [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.
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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:
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A loss-of-adhesion CRISPR-Cas9 screening platform to identify cell adhesion-regulatory proteins and signaling pathways. Nat Commun 2022; 13:2136. [PMID: 35440579 PMCID: PMC9018714 DOI: 10.1038/s41467-022-29835-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 04/04/2022] [Indexed: 11/09/2022] Open
Abstract
The clinical introduction of the Bruton’s tyrosine kinase (BTK) inhibitor ibrutinib, which targets B-cell antigen-receptor (BCR)-controlled integrin-mediated retention of malignant B cells in their growth-supportive lymphoid organ microenvironment, provided a major breakthrough in lymphoma and leukemia treatment. Unfortunately, a significant subset of patients is intrinsically resistant or acquires resistance against ibrutinib. Here, to discover novel therapeutic targets, we present an unbiased loss-of-adhesion CRISPR-Cas9 knockout screening method to identify proteins involved in BCR-controlled integrin-mediated adhesion. Illustrating the validity of our approach, several kinases with an established role in BCR-controlled adhesion, including BTK and PI3K, both targets for clinically applied inhibitors, are among the top hits of our screen. We anticipate that pharmacological inhibitors of the identified targets, e.g. PAK2 and PTK2B/PYK2, may have great clinical potential as therapy for lymphoma and leukemia patients. Furthermore, this screening platform 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. Targeting integrin-mediated retention of malignant B cells in their protective microenvironment is an efficacious treatment for lymphoma and leukemia. Here, the authors present an unbiased loss-of-adhesion CRISPR screening method, identifying therapeutic targets for these B-cell malignancies.
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Matsumoto K, Yoshida M. Mammalian Chemical Genomics towards Identifying Targets and Elucidating Modes-of-Action of Bioactive Compounds. Chembiochem 2021; 23:e202100561. [PMID: 34813140 DOI: 10.1002/cbic.202100561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 11/22/2021] [Indexed: 11/08/2022]
Abstract
The step of identifying target molecules and elucidating the mode of action of bioactive compounds is a major bottleneck for drug discovery from phenotypic screening. Genetic screening for genes that affect drug sensitivity or phenotypes of mammalian cultured cells is a powerful tool to obtain clues to their modes of action. Chemical genomic screening systems for comprehensively identifying such genes or genetic pathways have been established using shRNA libraries for RNA interference-mediated mRNA knockdown or sgRNA libraries for CRISPR/Cas9-mediated gene knockout. The combination of chemical genomic screening in mammalian cells with other approaches such as biochemical searches for target molecules, phenotypic profiling, and yeast genetics provides a systematic way to elucidate the mode of action by converging various pieces of information regarding target molecules, target pathways, and synthetic lethal pathways.
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Affiliation(s)
- Ken Matsumoto
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Saitama, 351-0198, Japan.,Seed Compounds Exploratory Unit for Drug Discovery Platform, Drug Discovery Platforms Cooperation Division, RIKEN Center for Sustainable Resource Science, Saitama, 351-0198, Japan
| | - Minoru Yoshida
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Saitama, 351-0198, Japan.,Seed Compounds Exploratory Unit for Drug Discovery Platform, Drug Discovery Platforms Cooperation Division, RIKEN Center for Sustainable Resource Science, Saitama, 351-0198, Japan.,Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Tokyo, 113-8657, Japan
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