1
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Guffanti F, Mengoli I, Damia G. Current HRD assays in ovarian cancer: differences, pitfalls, limitations, and novel approaches. Front Oncol 2024; 14:1405361. [PMID: 39220639 PMCID: PMC11361952 DOI: 10.3389/fonc.2024.1405361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 07/26/2024] [Indexed: 09/04/2024] Open
Abstract
Ovarian carcinoma (OC) still represents an insidious and fatal malignancy, and few significant results have been obtained in the last two decades to improve patient survival. Novel targeted therapies such as poly (ADP-ribose) polymerase inhibitors (PARPi) have been successfully introduced in the clinical management of OC, but not all patients will benefit, and drug resistance almost inevitably occurs. The identification of patients who are likely to respond to PARPi-based therapies relies on homologous recombination deficiency (HRD) tests, as this condition is associated with response to these treatments. This review summarizes the genomic and functional HRD assays currently used in clinical practice and those under evaluation, the clinical implications of HRD testing in OC, and their current pitfalls and limitations. Special emphasis will be placed on the functional HRD assays under development and the use of machine learning and artificial intelligence technologies as novel strategies to overcome the current limitations of HRD tests for a better-personalized treatment to improve patient outcomes.
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Affiliation(s)
| | | | - Giovanna Damia
- Laboratory of Preclinical Gynaecological Oncology, Department of Experimental Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
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2
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Oufkir N, Rouzier R, Paoletti X, Bonneau C. External validation of Standardized KELIM and platinum-resistant recurrence scores in patients with advanced epithelial ovarian cancer. J Ovarian Res 2024; 17:152. [PMID: 39039554 PMCID: PMC11265035 DOI: 10.1186/s13048-024-01476-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 07/11/2024] [Indexed: 07/24/2024] Open
Abstract
BACKGROUND Neoadjuvant chemotherapy followed by interval debulking surgery is currently a common treatment option for advanced epithelial ovarian cancer (EOC). The Standardized CA-125 ELIMination rate constant K (Std KELIM) and the Platinum Resistant Recurrence (PtRR) Score have been proposed as markers of tumor chemosensitivity. The aim of our study was to validate these tools for predicting platinum sensitivity in a real-world population of patients with advanced EOC treated with neoadjuvant chemotherapy. EXPERIMENTAL DESIGN All patients with advanced EOC treated with neoadjuvant chemotherapy at the Institut Curie between 2000 and 2015 were included. The Std KELIM was calculated with the CA-125 concentrations during the first 100 days of chemotherapy. The predictive value of Std KELIM and PtRR scores for the risk of subsequent PtRR was assessed using receiver operating characteristic (ROC) curve analysis, logistic regression and calibration curve. Kaplan-Meier survival analysis was performed for the treatment-free interval from platinum (TFIp) therapy and overall survival (OS). RESULTS Std KELIM data were available for 149 patients. The AUC was 0.67 for PtRR. A low Std KELIM was significantly associated with PtRR (OR = 0.19 (95% CI [0.06, 0.53], p = 0.002)) according to the univariate analysis. The calibration curve of the PtRR showed a slight but significant underestimation (p = 0.02) of the probability of platinum resistance. Favorable Std KELIM (≥ 1) alone and combined with the completeness of surgery were associated with significantly better survival in terms of TFIp and OS. CONCLUSIONS Std KELIM is an early prognostic marker of chemosensitivity in a real-life setting complementary to surgical status. It could help the clinician in the early management of patients by identifying those with a worse prognosis.
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Affiliation(s)
- Nina Oufkir
- Institut Curie, Inserm U900 - Bioinformatics, Biostatistics, Epidemiology and Computational Systems. Cancer Biology, 35, Rue Dailly, 92210, Saint-Cloud, France
- Department of Surgery, Institut Curie, 92210, St Cloud, France
| | - Roman Rouzier
- Institut Curie, Inserm U900 - Bioinformatics, Biostatistics, Epidemiology and Computational Systems. Cancer Biology, 35, Rue Dailly, 92210, Saint-Cloud, France
- Department of Surgery, Centre François Baclesse, 3, Av. du Général Harris , 14000, Caen, France
| | - Xavier Paoletti
- Institut Curie, Inserm U900 - Bioinformatics, Biostatistics, Epidemiology and Computational Systems. Cancer Biology, 35, Rue Dailly, 92210, Saint-Cloud, France
| | - Claire Bonneau
- Institut Curie, Inserm U900 - Bioinformatics, Biostatistics, Epidemiology and Computational Systems. Cancer Biology, 35, Rue Dailly, 92210, Saint-Cloud, France.
- Department of Surgery, Institut Curie, 92210, St Cloud, France.
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3
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Bulanova D, Akimov Y, Senkowski W, Oikkonen J, Gall-Mas L, Timonen S, Elmadani M, Hynninen J, Hautaniemi S, Aittokallio T, Wennerberg K. A synthetic lethal dependency on casein kinase 2 in response to replication-perturbing therapeutics in RB1-deficient cancer cells. SCIENCE ADVANCES 2024; 10:eadj1564. [PMID: 38781347 PMCID: PMC11114247 DOI: 10.1126/sciadv.adj1564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 04/16/2024] [Indexed: 05/25/2024]
Abstract
Resistance to therapy commonly develops in patients with high-grade serous ovarian carcinoma (HGSC) and triple-negative breast cancer (TNBC), urging the search for improved therapeutic combinations and their predictive biomarkers. Starting from a CRISPR knockout screen, we identified that loss of RB1 in TNBC or HGSC cells generates a synthetic lethal dependency on casein kinase 2 (CK2) for surviving the treatment with replication-perturbing therapeutics such as carboplatin, gemcitabine, or PARP inhibitors. CK2 inhibition in RB1-deficient cells resulted in the degradation of another RB family cell cycle regulator, p130, which led to S phase accumulation, micronuclei formation, and accelerated PARP inhibition-induced aneuploidy and mitotic cell death. CK2 inhibition was also effective in primary patient-derived cells. It selectively prevented the regrowth of RB1-deficient patient HGSC organoids after treatment with carboplatin or niraparib. As about 25% of HGSCs and 40% of TNBCs have lost RB1 expression, CK2 inhibition is a promising approach to overcome resistance to standard therapeutics in large strata of patients.
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Affiliation(s)
- Daria Bulanova
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
- Institute for Molecular Medicine Finland, Helsinki Institute for Life Sciences, University of Helsinki, Helsinki, Finland
| | - Yevhen Akimov
- Institute for Molecular Medicine Finland, Helsinki Institute for Life Sciences, University of Helsinki, Helsinki, Finland
| | - Wojciech Senkowski
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Jaana Oikkonen
- Research Program in Systems Oncology (ONCOSYS), University of Helsinki, Helsinki, Finland
| | - Laura Gall-Mas
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Sanna Timonen
- Institute for Molecular Medicine Finland, Helsinki Institute for Life Sciences, University of Helsinki, Helsinki, Finland
| | | | - Johanna Hynninen
- Department of Obstetrics and Gynecology, Turku University Hospital and University of Turku, Turku, Finland
| | - Sampsa Hautaniemi
- Research Program in Systems Oncology (ONCOSYS), University of Helsinki, Helsinki, Finland
| | - Tero Aittokallio
- Institute for Molecular Medicine Finland, Helsinki Institute for Life Sciences, University of Helsinki, Helsinki, Finland
- Institute for Cancer Research, Department of Cancer Genetics, Oslo University Hospital, Oslo, Norway
- Oslo Centre for Biostatistics and Epidemiology (OCBE), University of Oslo, Oslo, Norway
| | - Krister Wennerberg
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
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4
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Kim YN, Kim K, Joung JG, Kim SW, Kim S, Lee JY, Park E. RAD51 as an immunohistochemistry-based marker of poly(ADP-ribose) polymerase inhibitor resistance in ovarian cancer. Front Oncol 2024; 14:1351778. [PMID: 38725623 PMCID: PMC11079140 DOI: 10.3389/fonc.2024.1351778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 03/28/2024] [Indexed: 05/12/2024] Open
Abstract
Objective Effective functional biomarkers that can be readily used in clinical practice to predict poly(ADP-ribose) polymerase inhibitor (PARPi) sensitivity are lacking. With the widespread adoption of PARPi maintenance therapy in ovarian cancer, particularly in patients with BRCA mutation or HR deficiencies, accurately identifying de novo or acquired resistance to PARPi has become critical in clinical practice. We investigated RAD51 immunohistochemistry (IHC) as a functional biomarker for predicting PARPi sensitivity in ovarian cancer. Methods Ovarian cancer patients who had received PARPi and had archival tissue samples prior to PARPi exposure ("pre-PARPi") and/or after progression on PARPi ("post-PARPi") were selected. RAD51 IHC expression was semi-quantitatively evaluated using the H-score in geminin (a G2/S phase marker)- and γH2AX (a DNA damage marker)-positive tissues. A RAD51 H-score of 20 was used as the cutoff value. Results In total, 72 samples from 56 patients were analyzed. The median RAD51 H-score was 20 (range: 0-90) overall, 10 (0-190) in pre-PARPi samples (n = 34), and 25 (1-170) in post-PARPi samples (n = 19). Among patients with BRCA mutations, RAD51-low patients had better progression-free survival (PFS) after PARPi treatment than RAD51-high patients (P = 0.029). No difference was found in PFS with respect to the genomic scar score (P = 0.930). Analysis of matched pre- and post-PARPi samples collected from 15 patients indicated an increase in the RAD51 H-score upon progression on PARPi, particularly among pre-PARPi low-RAD51-expressing patients. Conclusion RAD51 is a potential functional IHC biomarker of de novo and acquired PARPi resistance in BRCA-mutated ovarian cancer and can be used to fine-tune ovarian cancer treatment.
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Affiliation(s)
- Yoo-Na Kim
- Department of Obstetrics and Gynecology, Institute of Women’s Life Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Kyeongmin Kim
- Graduate School of Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department of Pathology, Soonchunhyang University, Seoul, Republic of Korea
| | - Je-Gun Joung
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam, Republic of Korea
| | - Sang Wun Kim
- Department of Obstetrics and Gynecology, Institute of Women’s Life Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Sunghoon Kim
- Department of Obstetrics and Gynecology, Institute of Women’s Life Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jung-Yun Lee
- Department of Obstetrics and Gynecology, Institute of Women’s Life Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Eunhyang Park
- Department of Pathology, Yonsei University College of Medicine, Seoul, Republic of Korea
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5
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Chiappa M, Guffanti F, Grasselli C, Panini N, Corbelli A, Fiordaliso F, Damia G. Different Patterns of Platinum Resistance in Ovarian Cancer Cells with Homologous Recombination Proficient and Deficient Background. Int J Mol Sci 2024; 25:3049. [PMID: 38474294 DOI: 10.3390/ijms25053049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024] Open
Abstract
Platinum compounds are very active in first-line treatments of ovarian carcinoma. In fact, high rates of complete remission are achieved, but most patients eventually relapse with resistant disease. Many mechanisms underlying the platinum-resistant phenotype have been reported. However, there are no data in the same isogenic cell system proficient and deficient in homologous recombination (HR) on platinum-acquired resistance that might unequivocally clarify the most important mechanism associated with resistance. We generated and characterized cisplatin (DDP)-resistant murine ovarian ID8 cell lines in a HR-deficient and -proficient background. Specific upregulation of the NER pathway in the HR-proficient and -resistant cells and partial restoration of HR in Brca1-/--resistant cells were found. Combinations of different inhibitors of the DNA damage response pathways with cisplatin were strongly active in both resistant and parental cells. The data from the ID8 isogenic system are in line with current experimental and clinical evidence and strongly suggest that platinum resistance develops in different ways depending on the cell DNA repair status (i.e., HR-proficient or HR-deficient), and the upregulation and/or restoration of repair pathways are major determinants of DDP resistance.
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Affiliation(s)
- Michela Chiappa
- Department of Experimental Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via M. Negri 2, 20156 Milan, Italy
| | - Federica Guffanti
- Department of Experimental Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via M. Negri 2, 20156 Milan, Italy
| | - Chiara Grasselli
- Department of Experimental Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via M. Negri 2, 20156 Milan, Italy
| | - Nicolò Panini
- Department of Experimental Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via M. Negri 2, 20156 Milan, Italy
| | - Alessandro Corbelli
- Department of Biochemistry and Molecular Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via M. Negri 2, 20156 Milan, Italy
| | - Fabio Fiordaliso
- Department of Biochemistry and Molecular Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via M. Negri 2, 20156 Milan, Italy
| | - Giovanna Damia
- Department of Experimental Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via M. Negri 2, 20156 Milan, Italy
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Dai J, Zheng S, Falco MM, Bao J, Eriksson J, Pikkusaari S, Forstén S, Jiang J, Wang W, Gao L, Perez-Villatoro F, Dufva O, Saeed K, Wang Y, Amiryousefi A, Färkkilä A, Mustjoki S, Kauppi L, Tang J, Vähärautio A. Tracing back primed resistance in cancer via sister cells. Nat Commun 2024; 15:1158. [PMID: 38326354 PMCID: PMC10850087 DOI: 10.1038/s41467-024-45478-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 01/24/2024] [Indexed: 02/09/2024] Open
Abstract
Exploring non-genetic evolution of cell states during cancer treatments has become attainable by recent advances in lineage-tracing methods. However, transcriptional changes that drive cells into resistant fates may be subtle, necessitating high resolution analysis. Here, we present ReSisTrace that uses shared transcriptomic features of sister cells to predict the states priming treatment resistance. Applying ReSisTrace in ovarian cancer cells perturbed with olaparib, carboplatin or natural killer (NK) cells reveals pre-resistant phenotypes defined by proteostatic and mRNA surveillance features, reflecting traits enriched in the upcoming subclonal selection. Furthermore, we show that DNA repair deficiency renders cells susceptible to both DNA damaging agents and NK killing in a context-dependent manner. Finally, we leverage the obtained pre-resistance profiles to predict and validate small molecules driving cells to sensitive states prior to treatment. In summary, ReSisTrace resolves pre-existing transcriptional features of treatment vulnerability, facilitating both molecular patient stratification and discovery of synergistic pre-sensitizing therapies.
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Affiliation(s)
- Jun Dai
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Shuyu Zheng
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Matías M Falco
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jie Bao
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Johanna Eriksson
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Sanna Pikkusaari
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Sofia Forstén
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jing Jiang
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Wenyu Wang
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Luping Gao
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Fernando Perez-Villatoro
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine, Helsinki, Finland
| | - Olli Dufva
- Research Program in Translational Immunology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Khalid Saeed
- Research Program in Translational Immunology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Yinyin Wang
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Ali Amiryousefi
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Anniina Färkkilä
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine, Helsinki, Finland
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland
- Department of Obstetrics and Gynecology, and Clinical Trial Unit, Comprehensive Cancer Centre, Helsinki University Hospital, Helsinki, Finland
| | - Satu Mustjoki
- Research Program in Translational Immunology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Liisa Kauppi
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jing Tang
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
| | - Anna Vähärautio
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
- Foundation for the Finnish Cancer Institute, Helsinki, Finland.
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7
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Korsholm LM, Kjeldsen M, Perino L, Mariani L, Nyvang GB, Kristensen E, Bagger FO, Mirza MR, Rossing M. Combining Homologous Recombination-Deficient Testing and Functional RAD51 Analysis Enhances the Prediction of Poly(ADP-Ribose) Polymerase Inhibitor Sensitivity. JCO Precis Oncol 2024; 8:e2300483. [PMID: 38427930 PMCID: PMC10919475 DOI: 10.1200/po.23.00483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/03/2023] [Accepted: 12/21/2023] [Indexed: 03/03/2024] Open
Abstract
PURPOSE To meet the urgent need for accessible homologous recombination-deficient (HRD) test options, we validated a laboratory-developed test (LDT) and a functional RAD51 assay to assess patients with ovarian cancer and predict the clinical benefit of poly(ADP-ribose) polymerase inhibitor therapy. METHODS Optimization of the LDT cutoff and validation on the basis of samples from 91 patients enrolled in the ENGOT-ov24/NSGO-AVANOVA1&2 trial (ClinicalTrials.gov identifier: NCT02354131), previously subjected to commercial CDx HRD testing (CDx). RAD51 foci analysis was performed and tumors with ≥five foci/nucleus were classified as RAD51-positive (homologous recombination-proficient). RESULTS The optimal LDT cutoff is 54. Comparing CDx genome instability score and LDT HRD scores show a Spearman's correlation of rho = 0.764 (P < .0001). Cross-tabulation analysis shows that the sensitivity of the LDT HRD score is 86% and of the LDT HRD status is 91.8% (Fisher's exact test P < .001). Survival analysis on progression-free survival (PFS) of LDT-assessed patients show a Cox regression P < .05. RAD51 assays show a correlation between low RAD51 foci detection (<20% RAD51+ cells) and significantly prolonged PFS (P < .001). CONCLUSION The robust concordance between the open standard LDT and the CDx, especially the correlation with PFS, warrants future validation and implementation of the open standard LDT for HRD testing in diagnostic settings.
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Affiliation(s)
- Lea M. Korsholm
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Maj Kjeldsen
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Oncology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Lorenzo Perino
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Luca Mariani
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | | | - Elisabeth Kristensen
- Department of Pathology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Frederik O. Bagger
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Mansoor Raza Mirza
- Department of Oncology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Maria Rossing
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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8
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Ali U, Vungarala S, Tiriveedhi V. Genomic Features of Homologous Recombination Deficiency in Breast Cancer: Impact on Testing and Immunotherapy. Genes (Basel) 2024; 15:162. [PMID: 38397152 PMCID: PMC10887603 DOI: 10.3390/genes15020162] [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: 12/28/2023] [Revised: 01/21/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
Genomic instability is one of the well-established hallmarks of cancer. The homologous recombination repair (HRR) pathway plays a critical role in correcting the double-stranded breaks (DSB) due to DNA damage in human cells. Traditionally, the BRCA1/2 genes in the HRR pathway have been tested for their association with breast cancer. However, defects in the HRR pathway (HRD, also termed 'BRCAness'), which has up to 50 genes, have been shown to be involved in tumorigenesis and treatment susceptibility to poly-ADP ribose polymerase inhibitors (PARPis), platinum-based chemotherapy, and immune checkpoint inhibitors (ICIs). A reliable consensus on HRD scores is yet to be established. Emerging evidence suggests that only a subset of breast cancer patients benefit from ICI-based immunotherapy. Currently, albeit with limitations, the expression of programmed death-ligand 1 (PDL1) and tumor mutational burden (TMB) are utilized as biomarkers to predict the favorable outcomes of ICI therapy in breast cancer patients. Preclinical studies demonstrate an interplay between the HRR pathway and PDL1 expression. In this review, we outline the current understanding of the role of HRD in genomic instability leading to breast tumorigenesis and delineate outcomes from various clinical trials. Furthermore, we discuss potential strategies for combining HRD-targeted therapy with immunotherapy to achieve the best healthcare outcomes in breast cancer patients.
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Affiliation(s)
- Umer Ali
- Department of Biological Sciences, Tennessee State University, Nashville, TN 37209, USA;
| | - Sunitha Vungarala
- Meharry-Vanderbilt Alliance, Vanderbilt University Medical Center, Nashville, TN 37209, USA;
| | - Venkataswarup Tiriveedhi
- Department of Biological Sciences, Tennessee State University, Nashville, TN 37209, USA;
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37209, USA
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9
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Payton M, Belmontes B, Hanestad K, Moriguchi J, Chen K, McCarter JD, Chung G, Ninniri MS, Sun J, Manoukian R, Chambers S, Ho SM, Kurzeja RJM, Edson KZ, Dahal UP, Wu T, Wannberg S, Beltran PJ, Canon J, Boghossian AS, Rees MG, Ronan MM, Roth JA, Minocherhomji S, Bourbeau MP, Allen JR, Coxon A, Tamayo NA, Hughes PE. Small-molecule inhibition of kinesin KIF18A reveals a mitotic vulnerability enriched in chromosomally unstable cancers. NATURE CANCER 2024; 5:66-84. [PMID: 38151625 PMCID: PMC10824666 DOI: 10.1038/s43018-023-00699-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 11/30/2023] [Indexed: 12/29/2023]
Abstract
Chromosomal instability (CIN) is a hallmark of cancer, caused by persistent errors in chromosome segregation during mitosis. Aggressive cancers like high-grade serous ovarian cancer (HGSOC) and triple-negative breast cancer (TNBC) have a high frequency of CIN and TP53 mutations. Here, we show that inhibitors of the KIF18A motor protein activate the mitotic checkpoint and selectively kill chromosomally unstable cancer cells. Sensitivity to KIF18A inhibition is enriched in TP53-mutant HGSOC and TNBC cell lines with CIN features, including in a subset of CCNE1-amplified, CDK4-CDK6-inhibitor-resistant and BRCA1-altered cell line models. Our KIF18A inhibitors have minimal detrimental effects on human bone marrow cells in culture, distinct from other anti-mitotic agents. In mice, inhibition of KIF18A leads to robust anti-cancer effects with tumor regression observed in human HGSOC and TNBC models at well-tolerated doses. Collectively, our results provide a rational therapeutic strategy for selective targeting of CIN cancers via KIF18A inhibition.
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Affiliation(s)
- Marc Payton
- Oncology Research, Amgen Research, Thousand Oaks, CA, USA.
| | | | - Kelly Hanestad
- Oncology Research, Amgen Research, Thousand Oaks, CA, USA
| | - Jodi Moriguchi
- Oncology Research, Amgen Research, Thousand Oaks, CA, USA
| | - Kui Chen
- Lead Discovery and Characterization, Amgen Research, Thousand Oaks, CA, USA
| | - John D McCarter
- Lead Discovery and Characterization, Amgen Research, Thousand Oaks, CA, USA
| | - Grace Chung
- Oncology Research, Amgen Research, Thousand Oaks, CA, USA
| | | | - Jan Sun
- Oncology Research, Amgen Research, Thousand Oaks, CA, USA
| | | | | | - Seok-Man Ho
- Research Biomics, Amgen Research, San Francisco, CA, USA
| | | | | | | | - Tian Wu
- Pre-Pivotal Drug Product, Amgen Process Development, Thousand Oaks, CA, USA
| | | | | | - Jude Canon
- Oncology Research, Amgen Research, Thousand Oaks, CA, USA
| | | | | | | | | | - Sheroy Minocherhomji
- Translational Safety and Bioanalytical Sciences, Amgen Research, Thousand Oaks, CA, USA
| | | | | | - Angela Coxon
- Oncology Research, Amgen Research, Thousand Oaks, CA, USA
| | - Nuria A Tamayo
- Medicinal Chemistry, Amgen Research, Thousand Oaks, CA, USA
| | - Paul E Hughes
- Oncology Research, Amgen Research, Thousand Oaks, CA, USA
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10
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van Wijk LM, Vermeulen S, Ter Haar NT, Kramer CJH, Terlouw D, Vrieling H, Cohen D, Vreeswijk MPG. Performance of a RAD51-based functional HRD test on paraffin-embedded breast cancer tissue. Breast Cancer Res Treat 2023; 202:607-616. [PMID: 37725154 PMCID: PMC10564840 DOI: 10.1007/s10549-023-07102-y] [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: 06/13/2023] [Accepted: 08/18/2023] [Indexed: 09/21/2023]
Abstract
PURPOSE BRCA-deficient breast cancers (BC) are highly sensitive to platinum-based chemotherapy and PARP inhibitors due to their deficiency in the homologous recombination (HR) pathway. However, HR deficiency (HRD) extends beyond BRCA-associated BC, highlighting the need for a sensitive method to enrich for HRD tumors in an alternative way. A promising approach is the use of functional HRD tests which evaluate the HR capability of tumor cells by measuring RAD51 protein accumulation at DNA damage sites. This study aims to evaluate the performance of a functional RAD51-based HRD test for the identification of HRD BC. METHODS The functional HR status of 63 diagnostic formalin-fixed paraffin-embedded (FFPE) BC samples was determined by applying the RAD51-FFPE test. Samples were screened for the presence of (epi)genetic defects in HR and matching tumor samples were analyzed with the RECAP test, which requires ex vivo irradiated fresh tumor tissue on the premise that the HRD status as determined by the RECAP test faithfully represented the functional HR status. RESULTS The RAD51-FFPE test identified 23 (37%) of the tumors as HRD, including three tumors with pathogenic variants in BRCA1/2. The RAD51-FFPE test showed a sensitivity of 88% and a specificity of 76% in determining the HR-class as defined by the RECAP test. CONCLUSION Given its high sensitivity and compatibility with FFPE samples, the RAD51-FFPE test holds great potential to enrich for HRD tumors, including those associated with BRCA-deficiency. This potential extends to situations where DNA-based testing may be challenging or not easily accessible in routine clinical practice. This is particularly important considering the potential implications for treatment decisions and patient stratification.
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Affiliation(s)
- Lise M van Wijk
- Department of Human Genetics, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
| | - Sylvia Vermeulen
- Department of Human Genetics, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
| | - Natalja T Ter Haar
- Department of Pathology, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
| | - Claire J H Kramer
- Department of Pathology, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
| | - Diantha Terlouw
- Department of Pathology, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
| | - Harry Vrieling
- Department of Human Genetics, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
| | - Danielle Cohen
- Department of Pathology, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
| | - Maaike P G Vreeswijk
- Department of Human Genetics, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands.
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11
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Lee CY, Cheng WF, Lin PH, Chen YL, Huang SH, Lei KH, Chang KY, Ko MY, Chi P. An activity-based functional test for identifying homologous recombination deficiencies across cancer types in real time. Cell Rep Med 2023; 4:101247. [PMID: 37863059 PMCID: PMC10694588 DOI: 10.1016/j.xcrm.2023.101247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 08/17/2023] [Accepted: 09/26/2023] [Indexed: 10/22/2023]
Abstract
Homologous recombination (HR)-mediated DNA repair is a prerequisite for maintaining genome stability. Cancer cells displaying HR deficiency (HRD) are selectively eliminated by poly(ADP-ribose) polymerase inhibitors (PARPis). To date, sequencing of HR-associated genes and analyzing genome instability have been used as clinical predictions for PARPi therapy. However, these genetic tests cannot reflect dynamic changes in the HR status. Here, we have developed a virus- and activity-based functional assay to quantify real-time HR activity directly. Instead of focusing on a few HR-associated genes, our functional assay detects endpoint HR activity and establishes an activity threshold for identifying HRD across cancer types, validated by PARPi sensitivity and BRCA status. Notably, this fluorescence-based assay can be applied to primary ovarian cancer cells from patients to reflect their level of HRD, which is associated with survival benefits. Thus, our work provides a functional test to predict the response of primary cancer cells to PARPis.
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Affiliation(s)
- Chih-Ying Lee
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Wen-Fang Cheng
- Department of Obstetrics & Gynecology, National Taiwan University Hospital, Taipei, Taiwan
| | - Po-Han Lin
- Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, Taiwan; Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Yu-Li Chen
- Department of Obstetrics & Gynecology, National Taiwan University Hospital, Taipei, Taiwan
| | - Shih-Han Huang
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Kai-Hang Lei
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Ko-Yu Chang
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Min-Yu Ko
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Peter Chi
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan; Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.
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12
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Alizzi Z, Saravi S, Khalique S, McDonald T, Karteris E, Hall M. Identification of RAD51 foci in cancer-associated circulating cells of patients with high-grade serous ovarian cancer: association with treatment outcomes. Int J Gynecol Cancer 2023; 33:1427-1433. [PMID: 37541687 PMCID: PMC10511972 DOI: 10.1136/ijgc-2023-004483] [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: 03/24/2023] [Accepted: 07/20/2023] [Indexed: 08/06/2023] Open
Abstract
OBJECTIVE Fifty percent of patients with high-grade serous ovarian cancer harbor defects in the homologous recombination repair pathway. RAD51 foci form where DNA is damaged, indicating its involvement in repairing double-stranded breaks. High levels of RAD51 in ovarian cancer tissue have been associated with a poorer prognosis. OBJECTIVE To demonstrate RAD51 foci in circulating cancer-associated cells of patients with ovarian cancer and their association with clinical outcomes. METHODS One hundred and twenty-four patients with high-grade serous ovarian cancer had blood samples taken at strategic points during treatment and follow-up. Cells were stained using WT1 and RAD51 antibodies with immunofluorescence and reviewed under Leica camera microscopy; RAD51 foci were counted. Correlations were made between numbers of RAD51 foci and treatment response, BRCA status, and progression-free survival. RESULTS RAD51 foci were identified in all patients (n=42) with wild-type BRCA. BRCA mutant/homologous recombination deficiency-positive patients (n=8) had significantly lower numbers of RAD51 foci (p=0.009). Responders to treatment (n=32) had a reduction in circulating cells (p=0.02) and RAD51 foci (p=0.0007). Numbers of RAD51 foci were significantly higher in the platinum-resistant population throughout treatment: at the start of treatment, in 56 platinum-sensitive patients there was a mean of 3.6 RAD51 foci versus 6.2 in 15 platinum-resistant patients (p=0.02). Patients with a high number of RAD51 foci had worse median progression-free survival: in 39 patients with a mean of <3 RAD51 foci at treatment start, median progression-free survival had not been reached, compared with 32 patients with >3 RAD51 foci whose progression-free survival was 13 months (p=0.04). CONCLUSIONS Levels of RAD51 foci in circulating cancer-associated cells of patients with high-grade serous ovarian cancer are associated with clinical outcomes and may be a more pragmatic method of determining a homologous repair-deficient population.
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Affiliation(s)
- Zena Alizzi
- Cancer Biomarker and Cellular Endocrinology Laboratory, College of Life Sciences, Brunel University London, Uxbridge, UK
- Mount Vernon Cancer Centre, Northwood, UK
| | - Sayeh Saravi
- Cancer Biomarker and Cellular Endocrinology Laboratory, College of Life Sciences, Brunel University London, Uxbridge, UK
| | - Saira Khalique
- Cancer Biomarker and Cellular Endocrinology Laboratory, College of Life Sciences, Brunel University London, Uxbridge, UK
- Mount Vernon Cancer Centre, Northwood, UK
| | | | - Emmanouil Karteris
- Cancer Biomarker and Cellular Endocrinology Laboratory, College of Life Sciences, Brunel University London, Uxbridge, UK
| | - Marcia Hall
- Cancer Biomarker and Cellular Endocrinology Laboratory, College of Life Sciences, Brunel University London, Uxbridge, UK
- Mount Vernon Cancer Centre, Northwood, UK
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13
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Pikkusaari S, Tumiati M, Virtanen A, Oikkonen J, Li Y, Perez-Villatoro F, Muranen T, Salko M, Huhtinen K, Kanerva A, Koskela H, Tapper J, Koivisto-Korander R, Joutsiniemi T, Haltia UM, Lassus H, Hautaniemi S, Färkkilä A, Hynninen J, Hietanen S, Carpén O, Kauppi L. Functional Homologous Recombination Assay on FFPE Specimens of Advanced High-Grade Serous Ovarian Cancer Predicts Clinical Outcomes. Clin Cancer Res 2023; 29:3110-3123. [PMID: 36805632 PMCID: PMC10425726 DOI: 10.1158/1078-0432.ccr-22-3156] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/29/2022] [Accepted: 02/15/2023] [Indexed: 02/22/2023]
Abstract
PURPOSE Deficiency in homologous recombination (HR) repair of DNA damage is characteristic of many high-grade serous ovarian cancers (HGSC). It is imperative to identify patients with homologous recombination-deficient (HRD) tumors as they are most likely to benefit from platinum-based chemotherapy and PARP inhibitors (PARPi). Existing methods measure historical, not necessarily current HRD and/or require high tumor cell content, which is not achievable for many patients. We set out to develop a clinically feasible assay for identifying functionally HRD tumors that can predict clinical outcomes. EXPERIMENTAL DESIGN We quantified RAD51, a key HR protein, in immunostained formalin-fixed, paraffin-embedded (FFPE) tumor samples obtained from chemotherapy-naïve and neoadjuvant chemotherapy (NACT)-treated HGSC patients. We defined cutoffs for functional HRD separately for these sample types, classified the patients accordingly as HRD or HR-proficient, and analyzed correlations with clinical outcomes. From the same specimens, genomics-based HRD estimates (HR gene mutations, genomic signatures, and genomic scars) were also determined, and compared with functional HR (fHR) status. RESULTS fHR status significantly predicted several clinical outcomes, including progression-free survival (PFS) and overall survival (OS), when determined from chemo-naïve (PFS, P < 0.0001; OS, P < 0.0001) as well as NACT-treated (PFS, P < 0.0001; OS, P = 0.0033) tumor specimens. The fHR test also identified as HRD those PARPi-at-recurrence-treated patients with longer OS (P = 0.0188). CONCLUSIONS We developed an fHR assay performed on routine FFPE specimens, obtained from either chemo-naïve or NACT-treated HGSC patients, that can significantly predict real-world platinum-based chemotherapy and PARPi response. See related commentary by Garg and Oza, p. 2957.
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Affiliation(s)
- Sanna Pikkusaari
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Manuela Tumiati
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Anni Virtanen
- Department of Pathology, University of Helsinki and HUS Diagnostic Center, Helsinki University Hospital, Helsinki, Finland
| | - Jaana Oikkonen
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Yilin Li
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Fernando Perez-Villatoro
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Taru Muranen
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Matilda Salko
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Kaisa Huhtinen
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Anna Kanerva
- Department of Obstetrics and Gynecology, Helsinki University Hospital, Helsinki, Finland
| | - Heidi Koskela
- Department of Obstetrics and Gynecology, Turku University Hospital, Turku, Finland
| | - Johanna Tapper
- Department of Obstetrics and Gynecology, Helsinki University Hospital, Helsinki, Finland
| | | | - Titta Joutsiniemi
- Department of Obstetrics and Gynecology, Turku University Hospital, Turku, Finland
| | - Ulla-Maija Haltia
- Department of Obstetrics and Gynecology, Helsinki University Hospital, Helsinki, Finland
| | - Heini Lassus
- Department of Obstetrics and Gynecology, Helsinki University Hospital, Helsinki, Finland
| | - Sampsa Hautaniemi
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Anniina Färkkilä
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- iCAN digital precision cancer medicine flagship, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Johanna Hynninen
- Department of Obstetrics and Gynecology, Turku University Hospital, Turku, Finland
| | - Sakari Hietanen
- Department of Obstetrics and Gynecology, Turku University Hospital, Turku, Finland
| | - Olli Carpén
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Pathology, University of Helsinki and HUS Diagnostic Center, Helsinki University Hospital, Helsinki, Finland
| | - Liisa Kauppi
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- iCAN digital precision cancer medicine flagship, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
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14
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Ye T, Lin A, Qiu Z, Hu S, Zhou C, Liu Z, Cheng Q, Zhang J, Luo P. Microsatellite instability states serve as predictive biomarkers for tumors chemotherapy sensitivity. iScience 2023; 26:107045. [PMID: 37448561 PMCID: PMC10336167 DOI: 10.1016/j.isci.2023.107045] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 03/17/2023] [Accepted: 06/01/2023] [Indexed: 07/15/2023] Open
Abstract
There is an urgent need for markers to predict the efficacy of different chemotherapy drugs. Herein, we examined whether microsatellite instability (MSI) status can predict tumor multidrug sensitivity and explored the underlying mechanisms. We downloaded data from several public databases. Drug sensitivity was compared between the high microsatellite instability (MSI-H) and microsatellite-stable/low microsatellite instability (MSS/MSI-L) groups. In addition, we performed pathway enrichment analysis and cellular chemosensitivity assays to explore the mechanisms by which MSI status may affect drug sensitivity and assessed the differences between drug-treated and control cell lines. We found that multiple MSI-H tumors were more sensitive to a variety of chemotherapy drugs than MSS/MSI-L tumors, and especially for CRC, chemosensitivity is enhanced through the downregulation of DDR pathways such as NHEJ. Additional DNA damage caused by chemotherapeutic drugs results in further downregulation of DDR pathways and enhances drug sensitivity, forming a cycle of increasing drug sensitivity.
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Affiliation(s)
- Taojun Ye
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- The First Clinical Medical School, Southern Medical University, Guangzhou, Guangdong, China
| | - Anqi Lin
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- The First Clinical Medical School, Southern Medical University, Guangzhou, Guangdong, China
| | - Zhengang Qiu
- The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
| | - Shulu Hu
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- The First Clinical Medical School, Southern Medical University, Guangzhou, Guangdong, China
| | - Chaozheng Zhou
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- The First Clinical Medical School, Southern Medical University, Guangzhou, Guangdong, China
| | - Zaoqu Liu
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Quan Cheng
- Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jian Zhang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- The First Clinical Medical School, Southern Medical University, Guangzhou, Guangdong, China
| | - Peng Luo
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- The First Clinical Medical School, Southern Medical University, Guangzhou, Guangdong, China
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15
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Dey G, Bharti R, Braley C, Alluri R, Esakov E, Crean-Tate K, McCrae K, Joehlin-Price A, Rose PG, Lathia J, Gong Z, Reizes O. LCK facilitates DNA damage repair by stabilizing RAD51 and BRCA1 in the nucleus of chemoresistant ovarian cancer. J Ovarian Res 2023; 16:122. [PMID: 37370140 PMCID: PMC10294509 DOI: 10.1186/s13048-023-01194-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
Poly-ADP Ribose Polymerase (PARP) targeted therapy is clinically approved for the treatment of homologous recombination (HR) repair deficient tumors. The remarkable success of this therapy in the treatment of HR repair deficient cancers has not translated to HR-proficient cancers. Our studies identify the novel role of non-receptor lymphocyte-specific protein tyrosine kinase (LCK) in the regulation of HR repair in endometrioid epithelial ovarian cancer (eEOC) model. We show that DNA damage leads to direct interaction of LCK with the HR repair proteins RAD51 and BRCA1 in a kinase dependent manner RAD51 and BRCA1 stabilization. LCK expression is induced and activated in the nucleus in response to DNA damage insult. Disruption of LCK expression attenuates RAD51, BRCA1, and BRCA2 protein expression by hampering there stability and results in inhibition of HR-mediated DNA repair including suppression of RAD51 foci formation, and augmentation of γH2AX foci formation. In contrast LCK overexpression leads to increased RAD51 and BRCA1 expression with a concomitant increase in HR DNA damage repair. Importantly, attenuation of LCK sensitizes HR-proficient eEOC cells to PARP inhibitor in cells and pre-clinical mouse studies. Collectively, our findings identify a novel therapeutic strategy to expand the utility of PARP targeted therapy in HR proficient ovarian cancer.
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Affiliation(s)
- Goutam Dey
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, OH, 44195, USA
| | - Rashmi Bharti
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, OH, 44195, USA
| | - Chad Braley
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, OH, 44195, USA
| | - Ravi Alluri
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, OH, 44195, USA
| | - Emily Esakov
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, OH, 44195, USA
| | - Katie Crean-Tate
- Division of Gynecologic Cancer, Women's Health Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Keith McCrae
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, OH, 44195, USA
- Case Comprehensive Cancer Center, Cleveland, OH, USA
| | | | - Peter G Rose
- Division of Gynecologic Cancer, Women's Health Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Justin Lathia
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, OH, 44195, USA
- Case Comprehensive Cancer Center, Cleveland, OH, USA
| | - Zihua Gong
- Case Comprehensive Cancer Center, Cleveland, OH, USA
- Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Ofer Reizes
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, OH, 44195, USA.
- Case Comprehensive Cancer Center, Cleveland, OH, USA.
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16
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Biegała Ł, Gajek A, Marczak A, Rogalska A. Olaparib-Resistant BRCA2MUT Ovarian Cancer Cells with Restored BRCA2 Abrogate Olaparib-Induced DNA Damage and G2/M Arrest Controlled by the ATR/CHK1 Pathway for Survival. Cells 2023; 12:cells12071038. [PMID: 37048111 PMCID: PMC10093185 DOI: 10.3390/cells12071038] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/07/2023] [Accepted: 03/27/2023] [Indexed: 03/31/2023] Open
Abstract
The PARP inhibitor (PARPi) olaparib is currently the drug of choice for serous ovarian cancer (OC), especially in patients with homologous recombination (HR) repair deficiency associated with deleterious BRCA1/2 mutations. Unfortunately, OC patients who fail to respond to PARPi or relapse after treatment have limited therapeutic options. To elucidate olaparib resistance and enhance the efficacy of olaparib, intracellular factors exploited by OC cells to achieve decreased sensitivity to PARPi were examined. An olaparib-resistant OC cell line, PEO1-OR, was established from BRCA2MUT PEO1 cells. The anticancer activity and action of olaparib combined with inhibitors of the ATR/CHK1 pathway (ceralasertib as ATRi, MK-8776 as CHK1i) in olaparib-sensitive and -resistant OC cell lines were evaluated. Whole-exome sequencing revealed that PEO1-OR cells acquire resistance through subclonal enrichment of BRCA2 secondary mutations that restore functional full-length protein. Moreover, PEO1-OR cells upregulate HR repair-promoting factors (BRCA1, BRCA2, RAD51) and PARP1. Olaparib-inducible activation of the ATR/CHK1 pathway and G2/M arrest is abrogated in olaparib-resistant cells. Drug sensitivity assays revealed that PEO1-OR cells are less sensitive to ATRi and CHK1i agents. Combined treatment is less effective in olaparib-resistant cells considering inhibition of metabolic activity, colony formation, survival, accumulation of DNA double-strand breaks, and chromosomal aberrations. However, synergistic antitumor activity between compounds is achievable in PEO1-OR cells. Collectively, olaparib-resistant cells display co-existing HR repair-related mechanisms that confer resistance to olaparib, which may be effectively utilized to resensitize them to PARPi via combination therapy. Importantly, the addition of ATR/CHK1 pathway inhibitors to olaparib has the potential to overcome acquired resistance to PARPi.
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17
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Clinical Utility of Genomic Tests Evaluating Homologous Recombination Repair Deficiency (HRD) for Treatment Decisions in Early and Metastatic Breast Cancer. Cancers (Basel) 2023; 15:cancers15041299. [PMID: 36831640 PMCID: PMC9954086 DOI: 10.3390/cancers15041299] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/17/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
Breast cancer is the most frequently occurring cancer worldwide. With its increasing incidence, it is a major public health problem, with many therapeutic challenges such as precision medicine for personalized treatment. Thanks to next-generation sequencing (NGS), progress in biomedical technologies, and the use of bioinformatics, it is now possible to identify specific molecular alterations in tumor cells-such as homologous recombination deficiencies (HRD)-enabling us to consider using DNA-damaging agents such as platinum salts or PARP inhibitors. Different approaches currently exist to analyze impairment of the homologous recombination pathway, e.g., the search for specific mutations in homologous recombination repair (HRR) genes, such as BRCA1/2; the use of genomic scars or mutational signatures; or the development of functional tests. Nevertheless, the role and value of these different tests in breast cancer treatment decisions remains to be clarified. In this review, we summarize current knowledge on the clinical utility of genomic tests, evaluating HRR deficiency for treatment decisions in early and metastatic breast cancer.
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18
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Kim K, Kim SH, Lee JY, Kim YN, Lee ST, Park E. RAD51/geminin/γH2AX immunohistochemical expression predicts platinum-based chemotherapy response in ovarian high-grade serous carcinoma. J Gynecol Oncol 2023:34.e45. [PMID: 36807748 DOI: 10.3802/jgo.2023.34.e45] [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: 09/26/2022] [Revised: 12/28/2022] [Accepted: 01/18/2023] [Indexed: 02/11/2023] Open
Abstract
OBJECTIVE The RAD51 assay is a recently developed functional assay for homologous recombination deficiency (HRD) that reflects real-time HRD status. We aimed to identify the applicability and predictive value of RAD51 immunohistochemical expression in pre- and post-neoadjuvant chemotherapy (NAC) samples of ovarian high-grade serous carcinoma (HGSC). METHODS We evaluated the immunohistochemical expression of RAD51/geminin/γH2AX in ovarian HGSC before and after NAC. RESULTS In pre-NAC tumors (n=51), 74.5% (39/51) showed at least 25% of γH2AX-positive tumor cells, suggesting endogenous DNA damage. The RAD51-high group (41.0%, 16/39) showed significantly worse progression-free survival (PFS) compared to the RAD51-low group (51.3%, 20/39) (p=0.032). In post-NAC tumors (n=50), the RAD51-high group (36.0%, 18/50) showed worse PFS (p=0.013) and tended to present worse overall survival (p=0.067) compared to the RAD51-low group (64.0%, 32/50). RAD51-high cases were more likely to progress than RAD51-low cases at both 6 months and 12 months (p=0.046 and p=0.019, respectively). Of 34 patients with matched pre- and post-NAC RAD51 results, 44% (15/34) of pre-NAC RAD51 results were changed in the post-NAC tissue, and the RAD51 high-to-high group showed the worst PFS, while the low-to-low group showed the best PFS (p=0.031). CONCLUSION High RAD51 expression was significantly associated with worse PFS in HGSC, and post-NAC RAD51 status showed higher association than pre-NAC RAD51 status. Moreover, RAD51 status can be evaluated in a significant proportion of treatment-naïve HGSC samples. As RAD51 status dynamically changes, sequential follow-up of RAD51 status might reflect the biological behavior of HGSCs.
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Affiliation(s)
- Kyeongmin Kim
- Department of Pathology, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea.,Department of Pathology, Soonchunhyang University, Seoul, Korea
| | - Se Hoon Kim
- Department of Pathology, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Jung-Yun Lee
- Department of Obstetrics and Gynecology, Institute of Women's Life Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Yoo-Na Kim
- Department of Obstetrics and Gynecology, Institute of Women's Life Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Seung-Tae Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Eunhyang Park
- Department of Pathology, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea.
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19
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Oswald AJ, Gourley C. Development of Homologous Recombination Functional Assays for Targeting the DDR. Cancer Treat Res 2023; 186:43-70. [PMID: 37978130 DOI: 10.1007/978-3-031-30065-3_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Identification of tumours that have homologous recombination deficiency (HRD) has become of increasing interest following the licensing of PARP inhibitors. Potential methods to assess HRD status include; clinical selection for platinum sensitive disease, mutational/methylation status, genomic scars/signature and functional RAD51 assays. Homologous recombination (HR) is a dynamic process with the potential to evolve over a disease course, particularly in relation to previous treatment. This is one of the major drawbacks of genomic scars/signatures, as they only demonstrate historic HR status. Functional HR assays have the benefit of giving a real time HR status readout and therefore have the potential for clearer identification of patients who may benefit from PARP inhibitors at that specific time point. However, the development of RAD51 foci assays ready for clinical practice has been challenging. Pre-clinical considerations have included; controlling for variation in tumour proliferation, tissue type and whether DNA damage induction is required. Furthermore, the assays require correlation with clinical outcomes, an understanding of how they complement current testing modalities and validation of test performance in large cohorts. Despite these challenges, given the profound benefit from PARP inhibitors seen in those with an HRD phenotype to date, the ongoing development and validation of these functional HR assays remains of high clinical importance.
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Affiliation(s)
- Ailsa J Oswald
- Cancer Research UK Scotland Centre, University of Edinburgh, Edinburgh, UK.
| | - Charlie Gourley
- Cancer Research UK Scotland Centre, University of Edinburgh, Edinburgh, UK
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20
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Coelho R, Tozzi A, Disler M, Lombardo F, Fedier A, López MN, Freuler F, Jacob F, Heinzelmann-Schwarz V. Overlapping gene dependencies for PARP inhibitors and carboplatin response identified by functional CRISPR-Cas9 screening in ovarian cancer. Cell Death Dis 2022; 13:909. [PMID: 36307400 PMCID: PMC9616819 DOI: 10.1038/s41419-022-05347-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 10/11/2022] [Accepted: 10/13/2022] [Indexed: 11/23/2022]
Abstract
PARP inhibitors (PARPi) have revolutionized the therapeutic landscape of epithelial ovarian cancer (EOC) treatment with outstanding benefits in regard to progression-free survival, especially in patients either carrying BRCA1/2 mutations or harboring defects in the homologous recombination repair system. Yet, it remains uncertain which PARPi to apply and how to predict responders when platinum sensitivity is unknown. To shed light on the predictive power of genes previously suggested to be associated with PARPi response, we systematically reviewed the literature and identified 79 publications investigating a total of 93 genes. The top candidate genes were further tested using a comprehensive CRISPR-Cas9 mutagenesis screening in combination with olaparib treatment. Therefore, we generated six constitutive Cas9+ EOC cell lines and profiled 33 genes in a CRISPR-Cas9 cell competition assay using non-essential (AAVS1) and essential (RPA3 and PCNA) genes for cell fitness as negative and positive controls, respectively. We identified only ATM, MUS81, NBN, BRCA2, and RAD51B as predictive markers for olaparib response. As the major survival benefit of PARPi treatment was reported in platinum-sensitive tumors, we next assessed nine top candidate genes in combination with three PARPi and carboplatin. Interestingly, we observed similar dropout rates in a gene and compound independent manner, supporting the strong correlation of cancer cell response to compounds that rely on DNA repair for their effectiveness. In addition, we report on CDK12 as a common vulnerability for EOC cell survival and proliferation without altering the olaparib response, highlighting its potential as a therapeutic target in EOC.
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Affiliation(s)
- Ricardo Coelho
- grid.410567.1Ovarian Cancer Research, Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Alessandra Tozzi
- grid.410567.1Ovarian Cancer Research, Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland ,grid.410567.1Hospital for Women, University Hospital Basel, Basel, Switzerland
| | - Muriel Disler
- grid.410567.1Ovarian Cancer Research, Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Flavio Lombardo
- grid.410567.1Ovarian Cancer Research, Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
| | - André Fedier
- grid.410567.1Ovarian Cancer Research, Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Mónica Núñez López
- grid.410567.1Ovarian Cancer Research, Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Florian Freuler
- grid.410567.1Ovarian Cancer Research, Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Francis Jacob
- grid.410567.1Ovarian Cancer Research, Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Viola Heinzelmann-Schwarz
- grid.410567.1Ovarian Cancer Research, Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland ,grid.410567.1Hospital for Women, University Hospital Basel, Basel, Switzerland
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21
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Dotolo S, Esposito Abate R, Roma C, Guido D, Preziosi A, Tropea B, Palluzzi F, Giacò L, Normanno N. Bioinformatics: From NGS Data to Biological Complexity in Variant Detection and Oncological Clinical Practice. Biomedicines 2022; 10:biomedicines10092074. [PMID: 36140175 PMCID: PMC9495893 DOI: 10.3390/biomedicines10092074] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/12/2022] [Accepted: 08/22/2022] [Indexed: 11/22/2022] Open
Abstract
The use of next-generation sequencing (NGS) techniques for variant detection has become increasingly important in clinical research and in clinical practice in oncology. Many cancer patients are currently being treated in clinical practice or in clinical trials with drugs directed against specific genomic alterations. In this scenario, the development of reliable and reproducible bioinformatics tools is essential to derive information on the molecular characteristics of each patient’s tumor from the NGS data. The development of bioinformatics pipelines based on the use of machine learning and statistical methods is even more relevant for the determination of complex biomarkers. In this review, we describe some important technologies, computational algorithms and models that can be applied to NGS data from Whole Genome to Targeted Sequencing, to address the problem of finding complex cancer-associated biomarkers. In addition, we explore the future perspectives and challenges faced by bioinformatics for precision medicine both at a molecular and clinical level, with a focus on an emerging complex biomarker such as homologous recombination deficiency (HRD).
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Affiliation(s)
- Serena Dotolo
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori—IRCCS—Fondazione G. Pascale, 80131 Naples, Italy
| | - Riziero Esposito Abate
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori—IRCCS—Fondazione G. Pascale, 80131 Naples, Italy
| | - Cristin Roma
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori—IRCCS—Fondazione G. Pascale, 80131 Naples, Italy
| | - Davide Guido
- Bioinformatics Research Core Facility, Gemelli Science and Technology Park (GSTeP), Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Largo A. Gemelli, 8, 00168 Rome, Italy
| | - Alessia Preziosi
- Bioinformatics Research Core Facility, Gemelli Science and Technology Park (GSTeP), Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Largo A. Gemelli, 8, 00168 Rome, Italy
| | - Beatrice Tropea
- Bioinformatics Research Core Facility, Gemelli Science and Technology Park (GSTeP), Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Largo A. Gemelli, 8, 00168 Rome, Italy
| | - Fernando Palluzzi
- Bioinformatics Research Core Facility, Gemelli Science and Technology Park (GSTeP), Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Largo A. Gemelli, 8, 00168 Rome, Italy
| | - Luciano Giacò
- Bioinformatics Research Core Facility, Gemelli Science and Technology Park (GSTeP), Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Largo A. Gemelli, 8, 00168 Rome, Italy
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori—IRCCS—Fondazione G. Pascale, 80131 Naples, Italy
- Correspondence:
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22
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Roering P, Siddiqui A, Heuser VD, Potdar S, Mikkonen P, Oikkonen J, Li Y, Pikkusaari S, Wennerberg K, Hynninen J, Grenman S, Huhtinen K, Auranen A, Carpén O, Kaipio K. Effects of Wee1 inhibitor adavosertib on patient-derived high-grade serous ovarian cancer cells are multiple and independent of homologous recombination status. Front Oncol 2022; 12:954430. [PMID: 36081565 PMCID: PMC9445195 DOI: 10.3389/fonc.2022.954430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 07/27/2022] [Indexed: 11/25/2022] Open
Abstract
Objective A major challenge in the treatment of platinum-resistant high-grade serous ovarian cancer (HGSOC) is lack of effective therapies. Much of ongoing research on drug candidates relies on HGSOC cell lines that are poorly documented. The goal of this study was to screen for effective, state-of-the-art drug candidates using primary HGSOC cells. In addition, our aim was to dissect the inhibitory activities of Wee1 inhibitor adavosertib on primary and conventional HGSOC cell lines. Methods A comprehensive drug sensitivity and resistance testing (DSRT) on 306 drug compounds was performed on three patient-derived genetically unique HGSOC cell lines and two commonly used ovarian cancer cell lines. The effect of adavosertib on the cell lines was tested in several assays, including cell-cycle analysis, apoptosis induction, proliferation, wound healing, DNA damage, and effect on nuclear integrity. Results Several compounds exerted cytotoxic activity toward all cell lines, when tested in both adherent and spheroid conditions. In further cytotoxicity tests, adavosertib exerted the most consistent cytotoxic activity. Adavosertib affected cell-cycle control in patient-derived and conventional HGSOC cells, inducing G2/M accumulation and reducing cyclin B1 levels. It induced apoptosis and inhibited proliferation and migration in all cell lines. Furthermore, the DNA damage marker γH2AX and the number of abnormal cell nuclei were clearly increased following adavosertib treatment. Based on the homologous recombination (HR) signature and functional HR assays of the cell lines, the effects of adavosertib were independent of the cells' HR status. Conclusion Our study indicates that Wee1 inhibitor adavosertib affects several critical functions related to proliferation, cell cycle and division, apoptosis, and invasion. Importantly, the effects are consistent in all tested cell lines, including primary HGSOC cells, and independent of the HR status of the cells. Wee1 inhibition may thus provide treatment opportunities especially for patients, whose cancer has acquired resistance to platinum-based chemotherapy or PARP inhibitors.
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Affiliation(s)
- Pia Roering
- Institute of Biomedicine and Finnish Cancer Center (FICAN) West Cancer Centre, University of Turku and Turku University Hospital, Turku, Finland
- *Correspondence: Pia Roering, ; Olli Carpén,
| | - Arafat Siddiqui
- Institute of Biomedicine and Finnish Cancer Center (FICAN) West Cancer Centre, University of Turku and Turku University Hospital, Turku, Finland
| | - Vanina D. Heuser
- Institute of Biomedicine and Finnish Cancer Center (FICAN) West Cancer Centre, University of Turku and Turku University Hospital, Turku, Finland
| | - Swapnil Potdar
- High Throughput Biomedicine Unit, Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Piia Mikkonen
- Helsinki Institute of Life Science (HiLIFE), Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Jaana Oikkonen
- Research Program in Systems Oncology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Yilin Li
- Research Program in Systems Oncology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Sanna Pikkusaari
- Institute of Biomedicine and Finnish Cancer Center (FICAN) West Cancer Centre, University of Turku and Turku University Hospital, Turku, Finland
| | - Krister Wennerberg
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Johanna Hynninen
- Department of Obstetrics and Gynecology, Turku University Hospital and University of Turku, Turku, Finland
| | - Seija Grenman
- Department of Obstetrics and Gynecology, Turku University Hospital and University of Turku, Turku, Finland
| | - Kaisa Huhtinen
- Institute of Biomedicine and Finnish Cancer Center (FICAN) West Cancer Centre, University of Turku and Turku University Hospital, Turku, Finland
- Research Program in Systems Oncology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Annika Auranen
- Department of Obstetrics and Gynecology and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
| | - Olli Carpén
- Department of Pathology, Precision Cancer Pathology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- *Correspondence: Pia Roering, ; Olli Carpén,
| | - Katja Kaipio
- Institute of Biomedicine and Finnish Cancer Center (FICAN) West Cancer Centre, University of Turku and Turku University Hospital, Turku, Finland
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23
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Combinations of ATR, Chk1 and Wee1 Inhibitors with Olaparib Are Active in Olaparib Resistant Brca1 Proficient and Deficient Murine Ovarian Cells. Cancers (Basel) 2022; 14:cancers14071807. [PMID: 35406579 PMCID: PMC8997432 DOI: 10.3390/cancers14071807] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 03/10/2022] [Accepted: 03/30/2022] [Indexed: 01/03/2023] Open
Abstract
Simple Summary Poly(ADP-ribose) polymerases inhibitors (PARPis), including olaparib, have been recently approved for ovarian carcinoma treatment and PARPi resistance has already been observed in the clinics. With the aim of dissecting the molecular mechanisms of PARPi resistance, we generated olaparib resistant cells lines, both in a homologous recombination (HR)-deficient and -proficient background by continuous in vitro drug treatment. In the HR proficient background, olaparib resistance was caused by overexpression of multidrug resistance 1 gene (MDR1), while multiple heterogeneous co-existing mechanisms were found in olaparib resistant HR-deficient cells, including overexpression of MDR1, a decrease in PARP1 protein level and partial reactivation of HR repair. We found that combinations of ATR, Chk1 and Wee1 inhibitors with olaparib were synergistic in sensitive and resistant sublines, regardless of the HR status. These new olaparib resistant models will be instrumental to screen new therapeutic options for PARPi-resistant ovarian tumors. Abstract Background. Poly(ADP-ribose) polymerases inhibitor (PARPi) have shown clinical efficacy in ovarian carcinoma, especially in those harboring defects in homologous recombination (HR) repair, including BRCA1 and BRCA2 mutated tumors. There is increasing evidence however that PARPi resistance is common and develops through multiple mechanisms. Methods. ID8 F3 (HR proficient) and ID8 Brca1-/- (HR deficient) murine ovarian cells resistant to olaparib, a PARPi, were generated through stepwise drug concentrations in vitro. Both sensitive and resistant cells lines were pharmacologically characterized and the molecular mechanisms underlying olaparib resistance. Results. In ID8, cells with a HR proficient background, olaparib resistance was mainly caused by overexpression of multidrug resistance 1 gene (MDR1), while multiple heterogeneous co-existing mechanisms were found in ID8 Brca1-/- HR-deficient cells resistant to olaparib, including overexpression of MDR1, a decrease in PARP1 protein level and partial reactivation of HR repair. Importantly, combinations of ATR, Chk1 and Wee1 inhibitors with olaparib were synergistic in sensitive and resistant sublines, regardless of the HR cell status. Conclusion. Olaparib-resistant cell lines were generated and displayed multiple mechanisms of resistance, which will be instrumental in selecting new possible therapeutic options for PARPi-resistant ovarian tumors.
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24
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Toward More Comprehensive Homologous Recombination Deficiency Assays in Ovarian Cancer, Part 1: Technical Considerations. Cancers (Basel) 2022; 14:cancers14051132. [PMID: 35267439 PMCID: PMC8909526 DOI: 10.3390/cancers14051132] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/19/2022] [Accepted: 02/22/2022] [Indexed: 02/05/2023] Open
Abstract
Simple Summary High-grade serous ovarian cancer (HGSOC) is the most frequent and lethal form of ovarian cancer and is associated with homologous recombination deficiency (HRD) in 50% of cases. This specific alteration is associated with sensitivity to PARP inhibitors (PARPis). Despite vast prognostic improvements due to PARPis, current molecular assays assessing HRD status suffer from several limitations, and there is an urgent need for a more accurate evaluation. In these companion reviews (Part 1: Technical considerations; Part 2: Medical perspectives), we develop an integrative review to provide physicians and researchers involved in HGSOC management with a holistic perspective, from translational research to clinical applications. Abstract High-grade serous ovarian cancer (HGSOC), the most frequent and lethal form of ovarian cancer, exhibits homologous recombination deficiency (HRD) in 50% of cases. In addition to mutations in BRCA1 and BRCA2, which are the best known thus far, defects can also be caused by diverse alterations to homologous recombination-related genes or epigenetic patterns. HRD leads to genomic instability (genomic scars) and is associated with PARP inhibitor (PARPi) sensitivity. HRD is currently assessed through BRCA1/2 analysis, which produces a genomic instability score (GIS). However, despite substantial clinical achievements, FDA-approved companion diagnostics (CDx) based on GISs have important limitations. Indeed, despite the use of GIS in clinical practice, the relevance of such assays remains controversial. Although international guidelines include companion diagnostics as part of HGSOC frontline management, they also underscore the need for more powerful and alternative approaches for assessing patient eligibility to PARP inhibitors. In these companion reviews, we review and present evidence to date regarding HRD definitions, achievements and limitations in HGSOC. Part 1 is dedicated to technical considerations and proposed perspectives that could lead to a more comprehensive and dynamic assessment of HR, while Part 2 provides a more integrated approach for clinicians.
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25
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Ramsden DA, Carvajal-Garcia J, Gupta GP. Mechanism, cellular functions and cancer roles of polymerase-theta-mediated DNA end joining. Nat Rev Mol Cell Biol 2022; 23:125-140. [PMID: 34522048 DOI: 10.1038/s41580-021-00405-2] [Citation(s) in RCA: 87] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/21/2021] [Indexed: 02/08/2023]
Abstract
Cellular pathways that repair chromosomal double-strand breaks (DSBs) have pivotal roles in cell growth, development and cancer. These DSB repair pathways have been the target of intensive investigation, but one pathway - alternative end joining (a-EJ) - has long resisted elucidation. In this Review, we highlight recent progress in our understanding of a-EJ, especially the assignment of DNA polymerase theta (Polθ) as the predominant mediator of a-EJ in most eukaryotes, and discuss a potential molecular mechanism by which Polθ-mediated end joining (TMEJ) occurs. We address possible cellular functions of TMEJ in resolving DSBs that are refractory to repair by non-homologous end joining (NHEJ), DSBs generated following replication fork collapse and DSBs present owing to stalling of repair by homologous recombination. We also discuss how these context-dependent cellular roles explain how TMEJ can both protect against and cause genome instability, and the emerging potential of Polθ as a therapeutic target in cancer.
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Affiliation(s)
- Dale A Ramsden
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Juan Carvajal-Garcia
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Gaorav P Gupta
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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26
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Brady SW, Gout AM, Zhang J. Therapeutic and prognostic insights from the analysis of cancer mutational signatures. Trends Genet 2022; 38:194-208. [PMID: 34483003 PMCID: PMC8752466 DOI: 10.1016/j.tig.2021.08.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 08/06/2021] [Accepted: 08/11/2021] [Indexed: 02/08/2023]
Abstract
The somatic mutations in each cancer genome are caused by multiple mutational processes, each of which leaves a characteristic imprint (or 'signature'), potentially caused by specific etiologies or exposures. Deconvolution of these signatures offers a glimpse into the evolutionary history of individual tumors. Recent work has shown that mutational signatures may also yield therapeutic and prognostic insights, including the identification of cell-intrinsic signatures as biomarkers of drug response and prognosis. For example, mutational signatures indicating homologous recombination deficiency are associated with poly(ADP)-ribose polymerase (PARP) inhibitor sensitivity, whereas APOBEC-associated signatures are associated with ataxia telangiectasia and Rad3-related kinase (ATR) inhibitor sensitivity. Furthermore, therapy-induced mutational signatures implicated in cancer progression have also been uncovered, including the identification of thiopurine-induced TP53 mutations in leukemia. In this review, we explore the various ways mutational signatures can reveal new therapeutic and prognostic insights, thus extending their traditional role in identifying disease etiology.
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Affiliation(s)
- Samuel W Brady
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
| | - Alexander M Gout
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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27
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Lodewijk I, Bernardini A, Suárez-Cabrera C, Bernal E, Sánchez R, Garcia JL, Rojas K, Morales L, Wang S, Han X, Dueñas M, Paramio JM, Manso L. Genomic landscape and immune-related gene expression profiling of epithelial ovarian cancer after neoadjuvant chemotherapy. NPJ Precis Oncol 2022; 6:7. [PMID: 35087175 PMCID: PMC8795445 DOI: 10.1038/s41698-021-00247-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 12/16/2021] [Indexed: 02/04/2023] Open
Abstract
Platinum-based neoadjuvant chemotherapy followed by interval debulking surgery is an accepted treatment for patients with stage III or IV epithelial ovarian cancer who are not suitable for primary debulking surgery. The identification of suitable adjuvant treatments in these patients is an unmet need. Here, we explore potential genomic characteristics (mutational and immune-associated expression profiles) in a series of patients undergoing neoadjuvant chemotherapy. Tumor samples from biopsy and interval debulking surgery were analyzed for mutational landscape and immune profiling, together with detailed immunohistochemistry using different immune cell markers, and correlated with clinicopathological characteristics and potential response to neoadjuvant chemotherapy. No major differences in the mutational landscape were observed in paired biopsy and surgery samples. Genomic loss of heterozygosity was found to be higher in patients with total/near-total tumor response. The immune gene expression profile after neoadjuvant chemotherapy revealed activation of several immune regulation-related pathways in patients with no/minimal or partial response. In parallel, neoadjuvant therapy caused a significant increase of tumor-infiltrating lymphocyte population abundance, primarily due to an augmentation of the CD8+ T cell population. Remarkably, these changes occurred irrespective of potential homologous recombination defects, such as those associated with BRCA1/2 mutations. Our study strengthens the use of loss of heterozygosity as a biomarker of homologous repair deficiency. The changes of immune states during neoadjuvant chemotherapy reveal the dynamic nature of tumor-host immune interactions and suggest the potential use of immune checkpoint inhibitors or their combination with poly-ADP polymerase inhibitors in high stage and grade epithelial ovarian cancer patients undergoing neoadjuvant therapy.
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Affiliation(s)
- I Lodewijk
- Biomedical Research Institute I+12, University Hospital "12 de Octubre", Madrid, Spain.,Molecular Oncology Unit, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain.,Centro de Investigación Biomédica en Red Cáncer, Madrid, Spain
| | - A Bernardini
- Centro de Investigación Biomédica en Red Cáncer, Madrid, Spain
| | - C Suárez-Cabrera
- Molecular Oncology Unit, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain.,Centro de Investigación Biomédica en Red Cáncer, Madrid, Spain
| | - E Bernal
- Medical Oncology, University Hospital 12 De Octubre, Madrid, Spain.,Medical Oncology, Infant Cristina University Hospital, Madrid, Spain
| | - R Sánchez
- Medical Oncology, University Hospital 12 De Octubre, Madrid, Spain
| | - J L Garcia
- Pathology Department, University Hospital 12 De Octubre, Madrid, Spain
| | - K Rojas
- Medical Oncology, Vall d'Hebron University Hospital, Barcelona, Spain
| | - L Morales
- Biomedical Research Institute I+12, University Hospital "12 de Octubre", Madrid, Spain.,Molecular Oncology Unit, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain
| | - S Wang
- Experimental Medicine Unit, Oncology, GlaxoSmithKline, Waltham, MA, USA
| | - X Han
- Experimental Medicine Unit, Oncology, GlaxoSmithKline, Waltham, MA, USA
| | - M Dueñas
- Biomedical Research Institute I+12, University Hospital "12 de Octubre", Madrid, Spain.,Molecular Oncology Unit, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain.,Centro de Investigación Biomédica en Red Cáncer, Madrid, Spain
| | - J M Paramio
- Biomedical Research Institute I+12, University Hospital "12 de Octubre", Madrid, Spain.,Molecular Oncology Unit, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain.,Centro de Investigación Biomédica en Red Cáncer, Madrid, Spain
| | - L Manso
- Medical Oncology, University Hospital 12 De Octubre, Madrid, Spain.
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28
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van Wijk LM, Nilas AB, Vrieling H, Vreeswijk MPG. RAD51 as a functional biomarker for homologous recombination deficiency in cancer: a promising addition to the HRD toolbox? Expert Rev Mol Diagn 2021; 22:185-199. [PMID: 34913794 DOI: 10.1080/14737159.2022.2020102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Carcinomas with defects in the homologous recombination (HR) pathway are sensitive to PARP inhibitors (PARPi). A robust method to identify HR-deficient (HRD) carcinomas is therefore of utmost clinical importance. Currently available DNA-based HRD tests either scan HR-related genes such as BRCA1 and BRCA2 for the presence of pathogenic variants or identify HRD-related genomic scars or mutational signatures by using whole-exome or whole-genome sequencing data. As an alternative to DNA-based tests, functional HRD tests have been developed that assess the actual ability of tumors to accumulate RAD51 protein at DNA double strand breaks as a proxy for HR proficiency. AREAS COVERED This review presents an overview of currently available HRD tests and discuss the pros and cons of the different methodologies including their sensitivity for the identification of HRD tumors, their concordance with other HRD tests, and their capacity to predict therapy response. EXPERT OPINION With the increasing use of PARP inhibitors in the treatment of several cancers there is an urgent need to implement HRD testing in routine clinical practice. To this end, calibration of HRD thresholds and clinical validation of both DNA-based and RAD51-based HRD tests should have top-priority in the coming years.
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Affiliation(s)
- Lise M van Wijk
- Department of Human Genetics, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Andreea B Nilas
- Department of Human Genetics, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Harry Vrieling
- Department of Human Genetics, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Maaike P G Vreeswijk
- Department of Human Genetics, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
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29
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Xiang J, Zhou L, He Y, Wu S. LDH-A inhibitors as remedies to enhance the anticancer effects of PARP inhibitors in ovarian cancer cells. Aging (Albany NY) 2021; 13:25920-25930. [PMID: 34919531 PMCID: PMC8751605 DOI: 10.18632/aging.203780] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 12/03/2021] [Indexed: 12/23/2022]
Abstract
Ovarian cancer is one of the most lethal gynecologic malignancies. It has been shown that PARP inhibitors can selectively target BRCA-mutated ovarian cancer and exert some effects on ovarian cancer without BRCA mutations. However, the mechanism is still unclear. In this study, wild-type BRCA ovarian cancer cells (A2780 and SKOV3) were used. Our results showed that using a PARP inhibitor (olaparib or AG14361) alone significantly inhibited the proliferation of A2780 cells but negligibly inhibited the proliferation of SKOV3 cells. We used RNA sequencing to explore differentially expressed genes and found that PARP inhibitors increased LDH-A in SKOV3 cells, which was confirmed by RT-PCR. Oxamate (a specific inhibitor of LDH-A) was used to investigate whether LDH-A inhibition enhances the suppressive effects of PARP inhibitors on ovarian cancer without BRCA mutations. CCK-8 assays, scratch assays and Transwell assays were used to determine cell proliferation, cell migration ability and invasion ability, respectively. Both olaparib and AG14361 significantly inhibited the proliferation/invasion ability of A2780 cells but not SKOV3 cells. Inhibition of LDH-A can remarkably promote the inhibitory effects of PARP inhibitors on both A2780 and SKOV3 cells. Thus, high expression level of LDH-A influenced the suppressive effects of PARP inhibitors on ovarian cancer with wild-type BRCA, and LDH-A inhibition notably enhanced this effect.
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Affiliation(s)
- Jiangdong Xiang
- Department of Obstetrics and Gynecology, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200080, P.R. China
| | - Lina Zhou
- Department of Obstetrics and Gynecology, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200080, P.R. China
| | - Yinyan He
- Department of Obstetrics and Gynecology, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200080, P.R. China
| | - Sufang Wu
- Department of Obstetrics and Gynecology, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200080, P.R. China
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30
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Lin H, Xie Y, Kong Y, Yang L, Li M. Identification of molecular subtypes and prognostic signature for hepatocellular carcinoma based on genes associated with homologous recombination deficiency. Sci Rep 2021; 11:24022. [PMID: 34912005 PMCID: PMC8674316 DOI: 10.1038/s41598-021-03432-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 12/03/2021] [Indexed: 01/15/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a rapidly developing digestive tract carcinoma. The prognosis of patients and side effects caused by clinical treatment should be better improved. Nonnegative matrix factorization (NMF) clustering was performed using 109 homologous recombination deficiency (HRD)-related of HCC genes from The Cancer Genome Atlas (TCGA) database. Limma was applied to analyze subtype differences. Immune scores and clinical characteristics of different subtypes were compared. An HRD signature were built with least absolute shrinkage operator (LASSO) and multivariate Cox analysis. Performance of the signature system was then assessed by Kaplan–Meier curves and receiver operating characteristic (ROC) curves. We identified two molecular subtypes (C1 and C2), with C2 showing a significantly better prognosis than C1. C1 contained 3623 differentially expressed genes. A 4-gene prognostic signature for HCC was established, and showed a high predicting accuracy in validation sets, entire TCGA data set, HCCDB18 and GSE14520 queues. Moreover, the risk score was validated as an independent prognostic marker for HCC. Our research identified two molecular subtypes of HCC, and proposed a novel scoring system for evaluating the prognosis of HCC in clinical practice.
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Affiliation(s)
- Hongsheng Lin
- Guangxi University of Chinese Medicine, Nanning, 530200, China.,Department of Laboratory, The First Affiliated Hospital of Guangxi University of Chinese Medicine, Nanning, 530023, China.,Guangxi Medical University, Nanning, 530021, China.,Department of Microbiology, School of Basic Medical Sciences, Guangxi Medical University, Nanning, 530021, China
| | - Yangyi Xie
- Guangxi University of Chinese Medicine, Nanning, 530200, China.,The First Clinical Faculty of Guangxi University of Chinese Medicine, Nanning, 530200, China
| | - Yinzhi Kong
- Guangxi University of Chinese Medicine, Nanning, 530200, China.,The First Clinical Faculty of Guangxi University of Chinese Medicine, Nanning, 530200, China
| | - Li Yang
- Guangxi University of Chinese Medicine, Nanning, 530200, China.,Department of Laboratory, The First Affiliated Hospital of Guangxi University of Chinese Medicine, Nanning, 530023, China
| | - Mingfen Li
- Guangxi University of Chinese Medicine, Nanning, 530200, China. .,Department of Laboratory, The First Affiliated Hospital of Guangxi University of Chinese Medicine, Nanning, 530023, China.
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31
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DiSilvestro P, Colombo N, Harter P, González-Martín A, Ray-Coquard I, Coleman RL. Maintenance Treatment of Newly Diagnosed Advanced Ovarian Cancer: Time for a Paradigm Shift? Cancers (Basel) 2021; 13:5756. [PMID: 34830911 PMCID: PMC8616471 DOI: 10.3390/cancers13225756] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/01/2021] [Accepted: 11/06/2021] [Indexed: 11/16/2022] Open
Abstract
Recent data have demonstrated substantial efficacy with poly (ADP-ribose) polymerase (PARP) inhibitors as treatment and/or maintenance therapy in patients with newly diagnosed advanced epithelial ovarian cancer (EOC). Here, we review efficacy and safety results from four recent Phase III trials in newly diagnosed EOC: SOLO1 (olaparib), PAOLA-1 (olaparib in combination with bevacizumab), PRIMA (niraparib), and VELIA (veliparib). The implications of these data for current clinical practice and areas for future research are discussed, including ongoing studies of targeted agents in the newly diagnosed setting. Data from SOLO1, PAOLA-1, PRIMA, and VELIA confirm the benefit of PARP inhibitors (olaparib, niraparib, veliparib) for women with newly diagnosed EOC. The greatest benefit was seen in patients with a BRCA1 and/or BRCA2 mutation or in the homologous recombination deficiency (HRD)-test positive subgroup. These four well-conducted studies have generated practice-changing data. However, deciding how to apply these results in clinical practice is challenging, and substantial differences in trial design impede cross-trial comparisons. Recent PARP inhibitor approvals (olaparib, niraparib) in the newly diagnosed EOC setting have provided new maintenance treatment options for a broader patient population. The results of these studies call for personalized medicine based on biomarker profile and other factors, including tolerability, cost considerations, and physician and patient preference. Important areas for future research include appropriate use of both BRCA mutation and HRD testing to inform magnitude of PARP inhibitor benefit as well as exploring further options for patients who are HRD-test negative and for those who become PARP inhibitor resistant.
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Affiliation(s)
- Paul DiSilvestro
- Program in Women’s Oncology, Women & Infants Hospital, Providence, RI 02905, USA
| | - Nicoletta Colombo
- IRCCS European Institute of Oncology (IEO), University of Milan-Bicocca, 20126 Milan, Italy;
| | - Philipp Harter
- Department of Gynecology & Gynecologic Oncology, Ev. Kliniken Essen Mitte, 45136 Essen, Germany;
| | - Antonio González-Martín
- Department of Oncology, Clínica Universidad de Navarra, 28027 Madrid, Spain;
- Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain
| | - Isabelle Ray-Coquard
- Centre Leon Berard, Claude Bernard, Claude Bernard University, 69008 Lyon, France;
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32
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Barenboim M, Kovac M, Ameline B, Jones DTW, Witt O, Bielack S, Burdach S, Baumhoer D, Nathrath M. DNA methylation-based classifier and gene expression signatures detect BRCAness in osteosarcoma. PLoS Comput Biol 2021; 17:e1009562. [PMID: 34762643 PMCID: PMC8584788 DOI: 10.1371/journal.pcbi.1009562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 10/14/2021] [Indexed: 11/29/2022] Open
Abstract
Although osteosarcoma (OS) is a rare cancer, it is the most common primary malignant bone tumor in children and adolescents. BRCAness is a phenotypical trait in tumors with a defect in homologous recombination repair, resembling tumors with inactivation of BRCA1/2, rendering these tumors sensitive to poly (ADP)-ribose polymerase inhibitors (PARPi). Recently, OS was shown to exhibit molecular features of BRCAness. Our goal was to develop a method complementing existing genomic methods to aid clinical decision making on administering PARPi in OS patients. OS samples with DNA-methylation data were divided to BRCAness-positive and negative groups based on the degree of their genomic instability (n = 41). Methylation probes were ranked according to decreasing variance difference between two groups. The top 2000 probes were selected for training and cross-validation of the random forest algorithm. Two-thirds of available OS RNA-Seq samples (n = 17) from the top and bottom of the sample list ranked according to genome instability score were subjected to differential expression and, subsequently, to gene set enrichment analysis (GSEA). The combined accuracy of trained random forest was 85% and the average area under the ROC curve (AUC) was 0.95. There were 449 upregulated and 1,079 downregulated genes in the BRCAness-positive group (fdr < 0.05). GSEA of upregulated genes detected enrichment of DNA replication and mismatch repair and homologous recombination signatures (FWER < 0.05). Validation of the BRCAness classifier with an independent OS set (n = 20) collected later in the course of study showed AUC of 0.87 with an accuracy of 90%. GSEA signatures computed for this test set were matching the ones observed in the training set enrichment analysis. In conclusion, we developed a new classifier based on DNA-methylation patterns that detects BRCAness in OS samples with high accuracy. GSEA identified genome instability signatures. Machine-learning and gene expression approaches add new epigenomic and transcriptomic aspects to already established genomic methods for evaluation of BRCAness in osteosarcoma and can be extended to cancers characterized by genome instability. Osteosarcoma (OS) is the most common primary malignant tumor of bone in children and young adults with poor prognosis for patients with refractory or metastatic disease. A common feature, so-called BRCAness, exists in multiple cancers including OS and is characterized by homologous recombination deficiency. Tumors exhibiting BRCAness have been shown to respond to therapy with PARP inhibitors. Currently, BRCAness is mostly assessed by the genomic instability score. This method based on the DNA sequencing requires normal tissue DNA as control and is vulnerable to subjective interpretation of "genomic scarring" events. In this study, we implemented a classifier based on DNA methylation patterns. It is capable of detecting BRCAness in OS samples and does not require control tissue DNA. Therefore, it has the potential to support clinical decision making on administering PARPi in OS patients. We further corroborated the presence of BRCAness in OS by detecting homologous recombination signatures through gene expression analysis.
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Affiliation(s)
- Maxim Barenboim
- Department of Pediatrics and Children’s Cancer Research Center, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
- * E-mail: (MB); (MN)
| | - Michal Kovac
- University Hospital Basel and University of Basel, Bone Tumour Reference Centre at the Institute of Pathology, Basel, Switzerland
- Faculty of Informatics and Information Technologies, Slovak University of Technology, Bratislava, Slovakia
| | - Baptiste Ameline
- University Hospital Basel and University of Basel, Bone Tumour Reference Centre at the Institute of Pathology, Basel, Switzerland
| | - David T. W. Jones
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Olaf Witt
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- University Hospital Heidelberg, Hematology and Immunology at the Department of Pediatric Oncology, Heidelberg, Germany
| | - Stefan Bielack
- Klinikum Stuttgart–Olgahospital, Stuttgart Cancer Center, Pediatrics 5 (Oncology, Hematology, Immunology), Stuttgart, Germany
| | - Stefan Burdach
- Department of Pediatrics and Children’s Cancer Research Center, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
- CCC München—Comprehensive Cancer Center, DKTK German Cancer Consortium, Munich, Germany
| | - Daniel Baumhoer
- University Hospital Basel and University of Basel, Bone Tumour Reference Centre at the Institute of Pathology, Basel, Switzerland
| | - Michaela Nathrath
- Department of Pediatrics and Children’s Cancer Research Center, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
- Klinikum Kassel, Department of Pediatric Oncology, Kassel, Germany
- * E-mail: (MB); (MN)
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33
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Chiang YC, Lin PH, Cheng WF. Homologous Recombination Deficiency Assays in Epithelial Ovarian Cancer: Current Status and Future Direction. Front Oncol 2021; 11:675972. [PMID: 34722237 PMCID: PMC8551835 DOI: 10.3389/fonc.2021.675972] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 09/17/2021] [Indexed: 01/02/2023] Open
Abstract
Epithelial ovarian cancer (EOC) patients are generally diagnosed at an advanced stage, usually relapse after initial treatments, which include debulking surgery and adjuvant platinum-based chemotherapy, and eventually have poor 5-year survival of less than 50%. In recent years, promising survival benefits from maintenance therapy with poly(ADP-ribose) polymerase (PARP) inhibitor (PARPi) has changed the management of EOC in newly diagnosed and recurrent disease. Identification of BRCA mutations and/or homologous recombination deficiency (HRD) is critical for selecting patients for PARPi treatment. However, the currently available HRD assays are not perfect predictors of the clinical response to PARPis in EOC patients. In this review, we introduce the concept of synthetic lethality, the rationale of using PARPi when HRD is present in tumor cells, the clinical trials of PARPi incorporating the HRD assays for EOC, the current HRD assays, and other HRD assays in development.
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Affiliation(s)
- Ying-Cheng Chiang
- Department of Obstetrics and Gynecology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Po-Han Lin
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan.,Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Wen-Fang Cheng
- Department of Obstetrics and Gynecology, College of Medicine, National Taiwan University, Taipei, Taiwan.,Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan.,Graduate Institute of Oncology, College of Medicine, National Taiwan University, Taipei, Taiwan
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34
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Yang C, Zhang Z, Tang X, Zhang X, Chen Y, Hu T, Zhang H, Guan M, Zhang X, Wu Z. Pan-cancer analysis reveals homologous recombination deficiency score as a predictive marker for immunotherapy responders. Hum Cell 2021; 35:199-213. [PMID: 34628623 DOI: 10.1007/s13577-021-00630-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 10/02/2021] [Indexed: 02/07/2023]
Abstract
The immune context of the tumor microenvironment (TME) is critical for effective immunotherapy. Nonetheless, DNA-based biomarkers for the immune-sensitive TME and the identification of immune checkpoint inhibitor (ICI) responders are under-explored. This study aims to comprehensively landscape the homologous recombination deficiency (HRD) score, an emerging hallmark for tumor genome instability that triggers immune responsiveness across major cancer types, and to unveil their link to the TME and immunotherapeutic response. The HRD-associated genomic scars were characterized in 9088 tumor samples across 32 cancer types from TCGA. We evaluated the HRD score's performance in classifying ICI responders using an independent breast cancer cohort (GSE87049) and 11 in vivo murine mammary tumor models treated with anti-PD1/CTLA4 regimen (GSE124821). This study revealed a broad association between HRD-high genotype and neoantigenesis in the major cancer types including bladder cancer, breast cancer, head and neck squamous carcinoma, lung adenocarcinoma, lung squamous cell carcinoma, ovarian cancer, and sarcoma. Tumors with high HRD score bears increased leukocyte infiltration and lymphocyte fraction and demonstrated immune-sensitive microenvironment. The tumor immune dysfunction and exclusion (TIDE) model further confirmed HRD score-high genotype as a potential predictor for ICI immunotherapy responders in breast cancer. In conclusion, tumors with high HRD score exhibit an immune-sensitive TME. The HRD-high genotype is a promising marker for identifying ICI therapy responders among breast cancer patients.
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Affiliation(s)
- Can Yang
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Zijing Zhang
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Xuemei Tang
- Central Laboratory, Huashan Hospital North, Fudan University, Shanghai, 201907, China
| | - Xinju Zhang
- Central Laboratory, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Yuming Chen
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Tingting Hu
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Huating Zhang
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Ming Guan
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China.
- Central Laboratory, Huashan Hospital North, Fudan University, Shanghai, 201907, China.
- Central Laboratory, Huashan Hospital, Fudan University, Shanghai, 200040, China.
- Clinical Laboratory, Huashan Hospital North, Fudan University, Shanghai, 201907, China.
| | - Xiuming Zhang
- Medical Laboratory, Shenzhen Luohu People's Hospital, Shenzhen, 518002, China.
| | - Zhiyuan Wu
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China.
- Central Laboratory, Huashan Hospital North, Fudan University, Shanghai, 201907, China.
- Clinical Laboratory, Huashan Hospital North, Fudan University, Shanghai, 201907, China.
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35
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Siddiqui A, Tumiati M, Joko A, Sandholm J, Roering P, Aakko S, Vainionpää R, Kaipio K, Huhtinen K, Kauppi L, Tuomela J, Hietanen S. Targeting DNA Homologous Repair Proficiency With Concomitant Topoisomerase II and c-Abl Inhibition. Front Oncol 2021; 11:733700. [PMID: 34616682 PMCID: PMC8488401 DOI: 10.3389/fonc.2021.733700] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/27/2021] [Indexed: 12/21/2022] Open
Abstract
Critical DNA repair pathways become deranged during cancer development. This vulnerability may be exploited with DNA-targeting chemotherapy. Topoisomerase II inhibitors induce double-strand breaks which, if not repaired, are detrimental to the cell. This repair process requires high-fidelity functional homologous recombination (HR) or error-prone non-homologous end joining (NHEJ). If either of these pathways is defective, a compensatory pathway may rescue the cells and induce treatment resistance. Consistently, HR proficiency, either inherent or acquired during the course of the disease, enables tumor cells competent to repair the DNA damage, which is a major problem for chemotherapy in general. In this context, c-Abl is a protein tyrosine kinase that is involved in DNA damage-induced stress. We used a low-dose topoisomerase II inhibitor mitoxantrone to induce DNA damage which caused a transient cell cycle delay but allowed eventual passage through this checkpoint in most cells. We show that the percentage of HR and NHEJ efficient HeLa cells decreased more than 50% by combining c-Abl inhibitor imatinib with mitoxantrone. This inhibition of DNA repair caused more than 87% of cells in G2/M arrest and a significant increase in apoptosis. To validate the effect of the combination treatment, we tested it on commercial and patient-derived cell lines in high-grade serous ovarian cancer (HGSOC), where chemotherapy resistance correlates with HR proficiency and is a major clinical problem. Results obtained with HR-proficient and deficient HGSOC cell lines show a 50–85% increase of sensitivity by the combination treatment. Our data raise the possibility of successful targeting of treatment-resistant HR-proficient cancers.
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Affiliation(s)
- Arafat Siddiqui
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Manuela Tumiati
- ONCOSYS, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Alia Joko
- Department of Biology, Åbo Akademi University, Turku, Finland
| | - Jouko Sandholm
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Pia Roering
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Sofia Aakko
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Reetta Vainionpää
- Laboratory of Genetics, HUS Diagnostic Center, Helsinki University Hospital, Helsinki, Finland
| | - Katja Kaipio
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Kaisa Huhtinen
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Liisa Kauppi
- ONCOSYS, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Johanna Tuomela
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Sakari Hietanen
- Turku University Hospital, FICAN West Cancer Centre, Turku, Finland
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36
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Identifying patients eligible for PARP inhibitor treatment: from NGS-based tests to 3D functional assays. Br J Cancer 2021; 125:7-14. [PMID: 33767416 PMCID: PMC8257604 DOI: 10.1038/s41416-021-01295-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 01/14/2021] [Accepted: 01/28/2021] [Indexed: 02/08/2023] Open
Abstract
Within the past few years, poly (ADP-ribose) polymerase inhibitors (PARPi) have been added to the standard of care for cancer patients, mainly for those exhibiting specific genomic alterations in the homologous recombination (HR) pathway. Until now, patients who are eligible to receive PARPi have been identified using next-generation sequencing (NGS) of gene panels. However, NGS analyses do have some limitations, with a subset of patients with negative NGS-based results can exhibit a clinical benefit, responding positively to PARPi, despite the failure to detect dynamic and predictive biomarkers such as mutated BRCA1/2 genes. Furthermore, the sequencing of initial tumour does not allow to detect reversions or secondary mutations that can restore proficient HR and lead to PARPi resistance. Therefore, it is crucial to better identify patients who are likely to benefit from PARPi treatment. In this context, tumour models such as patient-derived xenografts or tumour-derived organoids could help to guide clinicians in their decision making as these models accurately mimic phenotypic and genetic tumour heterogeneity, and could reflect treatment response in an integrative manner. In this Perspective article, we provide an overview of the currently available NGS-based tests that enable the identification of patients who might benefit from PARPi, and outline breakthroughs and discoveries to expand this selection using 3D functional assays. Combining NGS with functional assays could facilitate the efficient identification of patients, thereby improving patient survival.
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37
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Setton J, Zinda M, Riaz N, Durocher D, Zimmermann M, Koehler M, Reis-Filho JS, Powell SN. Synthetic Lethality in Cancer Therapeutics: The Next Generation. Cancer Discov 2021; 11:1626-1635. [PMID: 33795234 PMCID: PMC8295179 DOI: 10.1158/2159-8290.cd-20-1503] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 01/01/2021] [Accepted: 02/23/2021] [Indexed: 12/25/2022]
Abstract
Synthetic lethality (SL) provides a conceptual framework for tackling targets that are not classically "druggable," including loss-of-function mutations in tumor suppressor genes required for carcinogenesis. Recent technological advances have led to an inflection point in our understanding of genetic interaction networks and ability to identify a wide array of novel SL drug targets. Here, we review concepts and lessons emerging from first-generation trials aimed at testing SL drugs, discuss how the nature of the targeted lesion can influence therapeutic outcomes, and highlight the need to develop clinical biomarkers distinct from those based on the paradigms developed to target activated oncogenes. SIGNIFICANCE: SL offers an approach for the targeting of loss of function of tumor suppressor and DNA repair genes, as well as of amplification and/or overexpression of genes that cannot be targeted directly. A next generation of tumor-specific alterations targetable through SL has emerged from high-throughput CRISPR technology, heralding not only new opportunities for drug development, but also important challenges in the development of optimal predictive biomarkers.
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Affiliation(s)
- Jeremy Setton
- Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Nadeem Riaz
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Daniel Durocher
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | | | | | - Simon N Powell
- Memorial Sloan Kettering Cancer Center, New York, New York.
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38
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Lazo JS, Sharlow ER, Cornelison R, Hart DJ, Llaneza DC, Mendelson AJ, Rastelli EJ, Tasker NR, Landen CN, Wipf P. Credentialing and Pharmacologically Targeting PTP4A3 Phosphatase as a Molecular Target for Ovarian Cancer. Biomolecules 2021; 11:969. [PMID: 34209460 PMCID: PMC8329922 DOI: 10.3390/biom11070969] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 06/26/2021] [Accepted: 06/28/2021] [Indexed: 01/02/2023] Open
Abstract
High grade serous ovarian cancer (OvCa) frequently becomes drug resistant and often recurs. Consequently, new drug targets and therapies are needed. Bioinformatics-based studies uncovered a relationship between high Protein Tyrosine Phosphatase of Regenerating Liver-3 (PRL3 also known as PTP4A3) expression and poor patient survival in both early and late stage OvCa. PTP4A3 mRNA levels were 5-20 fold higher in drug resistant or high grade serous OvCa cell lines compared to nonmalignant cells. JMS-053 is a potent allosteric small molecule PTP4A3 inhibitor and to explore further the role of PTP4A3 in OvCa, we synthesized and interrogated a series of JMS-053-based analogs in OvCa cell line-based phenotypic assays. While the JMS-053 analogs inhibit in vitro PTP4A3 enzyme activity, none were superior to JMS-053 in reducing high grade serous OvCa cell survival. Because PTP4A3 controls cell migration, we interrogated the effect of JMS-053 on this cancer-relevant process. Both JMS-053 and CRISPR/Cas9 PTP4A3 depletion blocked cell migration. The inhibition caused by JMS-053 required the presence of PTP4A3. JMS-053 caused additive or synergistic in vitro cytotoxicity when combined with paclitaxel and reduced in vivo OvCa dissemination. These results indicate the importance of PTP4A3 in OvCa and support further investigations of the lead inhibitor, JMS-053.
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Affiliation(s)
- John S. Lazo
- Department of Pharmacology, University of Virginia, Charlottesville, VA 22908, USA; (R.C.); (D.J.H.); (D.C.L.); (A.J.M.)
- KeViRx, Inc., Charlottesville, VA 22904, USA
| | - Elizabeth R. Sharlow
- Department of Pharmacology, University of Virginia, Charlottesville, VA 22908, USA; (R.C.); (D.J.H.); (D.C.L.); (A.J.M.)
- KeViRx, Inc., Charlottesville, VA 22904, USA
| | - Robert Cornelison
- Department of Pharmacology, University of Virginia, Charlottesville, VA 22908, USA; (R.C.); (D.J.H.); (D.C.L.); (A.J.M.)
- KeViRx, Inc., Charlottesville, VA 22904, USA
| | - Duncan J. Hart
- Department of Pharmacology, University of Virginia, Charlottesville, VA 22908, USA; (R.C.); (D.J.H.); (D.C.L.); (A.J.M.)
| | - Danielle C. Llaneza
- Department of Pharmacology, University of Virginia, Charlottesville, VA 22908, USA; (R.C.); (D.J.H.); (D.C.L.); (A.J.M.)
| | - Anna J. Mendelson
- Department of Pharmacology, University of Virginia, Charlottesville, VA 22908, USA; (R.C.); (D.J.H.); (D.C.L.); (A.J.M.)
| | - Ettore J. Rastelli
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA; (E.J.R.); (N.R.T.); (P.W.)
| | - Nikhil R. Tasker
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA; (E.J.R.); (N.R.T.); (P.W.)
| | - Charles N. Landen
- Department of Obstetrics and Gynecology, University of Virginia, Charlottesville, VA 22908, USA;
| | - Peter Wipf
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA; (E.J.R.); (N.R.T.); (P.W.)
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Co-evolution of matrisome and adaptive adhesion dynamics drives ovarian cancer chemoresistance. Nat Commun 2021; 12:3904. [PMID: 34162871 PMCID: PMC8222388 DOI: 10.1038/s41467-021-24009-8] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 05/20/2021] [Indexed: 02/05/2023] Open
Abstract
Due to its dynamic nature, the evolution of cancer cell-extracellular matrix (ECM) crosstalk, critically affecting metastasis and treatment resistance, remains elusive. Our results show that platinum-chemotherapy itself enhances resistance by progressively changing the cancer cell-intrinsic adhesion signaling and cell-surrounding ECM. Examining ovarian high-grade serous carcinoma (HGSC) transcriptome and histology, we describe the fibrotic ECM heterogeneity at primary tumors and distinct metastatic sites, prior and after chemotherapy. Using cell models from systematic ECM screen to collagen-based 2D and 3D cultures, we demonstrate that both specific ECM substrates and stiffness increase resistance to platinum-mediated, apoptosis-inducing DNA damage via FAK and β1 integrin-pMLC-YAP signaling. Among such substrates around metastatic HGSCs, COL6 was upregulated by chemotherapy and enhanced the resistance of relapse, but not treatment-naïve, HGSC organoids. These results identify matrix adhesion as an adaptive response, driving HGSC aggressiveness via co-evolving ECM composition and sensing, suggesting stromal and tumor strategies for ECM pathway targeting.
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Diossy M, Sztupinszki Z, Borcsok J, Krzystanek M, Tisza V, Spisak S, Rusz O, Timar J, Csabai I, Fillinger J, Moldvay J, Pedersen AG, Szuts D, Szallasi Z. A subset of lung cancer cases shows robust signs of homologous recombination deficiency associated genomic mutational signatures. NPJ Precis Oncol 2021; 5:55. [PMID: 34145376 PMCID: PMC8213828 DOI: 10.1038/s41698-021-00199-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 05/28/2021] [Indexed: 01/14/2023] Open
Abstract
PARP inhibitors are approved for the treatment of solid tumor types that frequently harbor alterations in the key homologous recombination (HR) genes, BRCA1/2. Other tumor types, such as lung cancer, may also be HR deficient, but the frequency of such cases is less well characterized. Specific DNA aberration profiles (mutational signatures) are induced by homologous recombination deficiency (HRD) and their presence can be used to assess the presence or absence of HR deficiency in a given tumor biopsy even in the absence of an observed alteration of an HR gene. We derived various HRD-associated mutational signatures from whole-genome and whole-exome sequencing data in the lung adenocarcinoma and lung squamous carcinoma cases from TCGA, and in a patient of ours with stage IVA lung cancer with exceptionally good response to platinum-based therapy, and in lung cancer cell lines. We found that a subset of the investigated cases, both with and without biallelic loss of BRCA1 or BRCA2, showed robust signs of HR deficiency. The extreme platinum responder case also showed a robust HRD-associated genomic mutational profile. HRD-associated mutational signatures were also associated with PARP inhibitor sensitivity in lung cancer cell lines. Consequently, lung cancer cases with HRD, as identified by diagnostic mutational signatures, may benefit from PARP inhibitor therapy.
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Affiliation(s)
- Miklos Diossy
- Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, DTU, Kgs. Lyngby, Denmark
- Danish Cancer Society Research Center, Copenhagen, Denmark
| | | | - Judit Borcsok
- Danish Cancer Society Research Center, Copenhagen, Denmark
| | | | - Viktoria Tisza
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
| | - Sandor Spisak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Orsolya Rusz
- 2nd Department of Pathology, SE NAP, Brain Metastasis Research Group, Semmelweis University, Budapest, Hungary
| | - Jozsef Timar
- 2nd Department of Pathology, SE NAP, Brain Metastasis Research Group, Semmelweis University, Budapest, Hungary
| | - István Csabai
- Department of Physics of Complex Systems, Eötvös Loránd University, Budapest, Hungary
| | - Janos Fillinger
- Department of Pathology, National Korányi Institute of Pulmonology, Budapest, Hungary
| | - Judit Moldvay
- 2nd Department of Pathology, SE NAP, Brain Metastasis Research Group, Semmelweis University, Budapest, Hungary
- Department of Tumor Biology, National Korányi Institute of Pulmonology-Semmelweis University, Budapest, Hungary
| | - Anders Gorm Pedersen
- Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, DTU, Kgs. Lyngby, Denmark
| | - David Szuts
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Zoltan Szallasi
- Danish Cancer Society Research Center, Copenhagen, Denmark.
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA.
- 2nd Department of Pathology, SE NAP, Brain Metastasis Research Group, Semmelweis University, Budapest, Hungary.
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41
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The RAD51-FFPE Test; Calibration of a Functional Homologous Recombination Deficiency Test on Diagnostic Endometrial and Ovarian Tumor Blocks. Cancers (Basel) 2021; 13:cancers13122994. [PMID: 34203855 PMCID: PMC8232577 DOI: 10.3390/cancers13122994] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/08/2021] [Accepted: 06/11/2021] [Indexed: 11/18/2022] Open
Abstract
Simple Summary Rapid and reliable identification of patients with homologous recombination deficient (HRD) tumors is important for treatment choice as these tumors tend to respond well to platinum-based chemotherapy and PARP inhibitors (PARPi). In this study, a RAD51-based functional HRD test that can be performed on routine diagnostic formalin-fixed paraffin-embedded (FFPE) tissues (RAD51-FFPE test), was further improved and optimal test parameters were determined. The RAD51-FFPE test was able to determine tumor HR status with high sensitivity and specificity, making it an attractive test to be applied as routine diagnostic tool in the near future. Abstract PARP inhibitor (PARPi) sensitivity is related to tumor-specific defects in homologous recombination (HR). Therefore, there is great clinical interest in tests that can rapidly and reliably identify HR deficiency (HRD). Functional HRD tests determine the actual HR status by using the (dis)ability to accumulate RAD51 protein at sites of DNA damage as read-out. In this study, we further improved and calibrated a previously described RAD51-based functional HRD test on 74 diagnostic formalin-fixed paraffin-embedded (FFPE) specimens (RAD51-FFPE test) from endometrial cancer (EC n = 25) and epithelial ovarian cancer (OC n = 49) patients. We established optimal parameters with regard to RAD51 foci cut-off (≥2) and HRD threshold (15%) using matched endometrial and ovarian carcinoma specimens for which HR status had been established using a RAD51-based test that required ex vivo irradiation of fresh tissue (RECAP test). The RAD51-FFPE test detected BRCA deficient tumors with 90% sensitivity and RECAP-HRD tumors with 87% sensitivity, indicating that it is an attractive alternative to DNA-based tests with the potential to be applied in routine diagnostic pathology.
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Hoppe MM, Jaynes P, Wardyn JD, Upadhyayula SS, Tan TZ, Lie S, Lim DGZ, Pang BNK, Lim S, P S Yeong J, Karnezis A, Chiu DS, Leung S, Huntsman DG, Sedukhina AS, Sato K, Topp MD, Scott CL, Choi H, Patel NR, Brown R, Kaye SB, Pitt JJ, Tan DSP, Jeyasekharan AD. Quantitative imaging of RAD51 expression as a marker of platinum resistance in ovarian cancer. EMBO Mol Med 2021; 13:e13366. [PMID: 33709473 PMCID: PMC8103098 DOI: 10.15252/emmm.202013366] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 02/04/2021] [Accepted: 02/09/2021] [Indexed: 12/23/2022] Open
Abstract
Early relapse after platinum chemotherapy in epithelial ovarian cancer (EOC) portends poor survival. A-priori identification of platinum resistance is therefore crucial to improve on standard first-line carboplatin-paclitaxel treatment. The DNA repair pathway homologous recombination (HR) repairs platinum-induced damage, and the HR recombinase RAD51 is overexpressed in cancer. We therefore designed a REMARK-compliant study of pre-treatment RAD51 expression in EOC, using fluorescent quantitative immunohistochemistry (qIHC) to overcome challenges in quantitation of protein expression in situ. In a discovery cohort (n = 284), RAD51-High tumours had shorter progression-free and overall survival compared to RAD51-Low cases in univariate and multivariate analyses. The association of RAD51 with relapse/survival was validated in a carboplatin monotherapy SCOTROC4 clinical trial cohort (n = 264) and was predominantly noted in HR-proficient cancers (Myriad HRDscore < 42). Interestingly, overexpression of RAD51 modified expression of immune-regulatory pathways in vitro, while RAD51-High tumours showed exclusion of cytotoxic T cells in situ. Our findings highlight RAD51 expression as a determinant of platinum resistance and suggest possible roles for therapy to overcome immune exclusion in RAD51-High EOC. The qIHC approach is generalizable to other proteins with a continuum instead of discrete/bimodal expression.
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Affiliation(s)
- Michal M Hoppe
- Cancer Science Institute of SingaporeNational University of SingaporeSingapore
| | - Patrick Jaynes
- Cancer Science Institute of SingaporeNational University of SingaporeSingapore
| | - Joanna D Wardyn
- Cancer Science Institute of SingaporeNational University of SingaporeSingapore
| | | | - Tuan Zea Tan
- Cancer Science Institute of SingaporeNational University of SingaporeSingapore
| | - Stefanus Lie
- Cancer Science Institute of SingaporeNational University of SingaporeSingapore
| | - Diana G Z Lim
- Department of PathologyNational University HospitalSingapore
| | - Brendan N K Pang
- Cancer Science Institute of SingaporeNational University of SingaporeSingapore
- Department of PathologyNational University HospitalSingapore
| | - Sherlly Lim
- Cancer Science Institute of SingaporeNational University of SingaporeSingapore
| | - Joe P S Yeong
- Cancer Science Institute of SingaporeNational University of SingaporeSingapore
| | - Anthony Karnezis
- British Columbia Cancer AgencyVancouverBCCanada
- Present address:
Pathology and Lab medicineUC Davis Medical CentreSacramentoCAUSA
| | | | | | | | - Anna S Sedukhina
- Department of PharmacogenomicsSt. Marianna UniversityKawasakiJapan
| | - Ko Sato
- Department of PharmacogenomicsSt. Marianna UniversityKawasakiJapan
| | - Monique D Topp
- The Walter and Eliza Hall Institute of Medical ResearchParkvilleVic.Australia
| | - Clare L Scott
- The Walter and Eliza Hall Institute of Medical ResearchParkvilleVic.Australia
| | - Hyungwon Choi
- Saw Swee Hock School of Public HealthNational University of SingaporeSingapore
| | | | - Robert Brown
- Division of CancerImperial College LondonLondonUK
| | - Stan B Kaye
- Department of Haematology‐OncologyNational University HospitalSingapore
| | - Jason J Pitt
- Cancer Science Institute of SingaporeNational University of SingaporeSingapore
| | - David S P Tan
- Cancer Science Institute of SingaporeNational University of SingaporeSingapore
- Department of Haematology‐OncologyNational University HospitalSingapore
| | - Anand D Jeyasekharan
- Cancer Science Institute of SingaporeNational University of SingaporeSingapore
- Department of Haematology‐OncologyNational University HospitalSingapore
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43
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Excision Repair Cross-Complementation Group 6 Gene Polymorphism Is Associated with the Response to FOLFIRINOX Chemotherapy in Asian Patients with Pancreatic Cancer. Cancers (Basel) 2021; 13:cancers13061196. [PMID: 33801891 PMCID: PMC7998301 DOI: 10.3390/cancers13061196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/23/2021] [Accepted: 03/05/2021] [Indexed: 11/29/2022] Open
Abstract
Simple Summary FOLFIRINOX is a platinum-based chemotherapy regimen for patients with pancreatic cancer and is known to be more effective in the presence of the BRCA mutation, one of the DNA damage repair (DDR) gene mutations. However, BRCA mutations are less common in pancreatic cancer patients, accounting for only about 5% of cases worldwide, and are known to be even rarer in Asians. Therefore, this study aimed to uncover new genetic variants of DDR genes related to the response of FOLFIRINOX by analyzing variants of DDR genes using whole exome sequencing. Multivariable Cox regression analysis adjusted for clinical variables showed that a single nucleotide polymorphism (SNP) of the ERCC6 gene is an independent predictor for progression-free survival. If validated, the ERCC6 SNP found in this study could be used as a biomarker to predict responses to FOLFIRINOX. Abstract FOLFIRINOX is currently one of the standard chemotherapy regimens for pancreatic cancer patients, but little is known about the factors that can predict a response to it. We performed a study to discover novel DNA damage repair (DDR) gene variants associated with the response to FOLFIRINOX chemotherapy in patients with pancreatic cancer. We queried a cohort of pancreatic cancer patients who received FOLFIRINOX chemotherapy as the first treatment and who had tissue obtained through an endoscopic ultrasound-guided biopsy that was suitable for DNA sequencing. We explored variants of 148 DDR genes based on whole exome sequencing and performed multivariate Cox regression to find genetic variants associated with progression-free survival (PFS). Overall, 103 patients were included. Among 2384 variants of 141 DDR genes, 612 non-synonymous variants of 123 genes were selected for Cox regression analysis. The multivariate Cox model showed that rs2228528 in ERCC6 was significantly associated with improved PFS (hazard ratio 0.54, p = 0.001). The median PFS was significantly longer in patients with rs2228528 genotype AA vs. genotype GA and GG (23.5 vs. 16.2 and 8.6 months; log-rank p < 0.001). This study suggests that rs2228528 in ERCC6 could be a potential predictor of response to FOLFIRINOX chemotherapy in patients with pancreatic cancer.
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Li Y, Zhang X, Gao Y, Shang C, Yu B, Wang T, Su J, Huang C, Wu Y, Guo H, Ha C. Development of a Genomic Signatures-Based Predictor of Initial Platinum-Resistance in Advanced High-Grade Serous Ovarian Cancer Patients. Front Oncol 2021; 10:625866. [PMID: 33747898 PMCID: PMC7977004 DOI: 10.3389/fonc.2020.625866] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 12/30/2020] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND High grade serous ovarian cancer (HGSOC) is the most common subtype of ovarian cancer. Although platinum-based chemotherapy has been the cornerstone for HGSOC treatment, nearly 25% of patients would have less than 6 months of interval since the last platinum chemotherapy, referred to as platinum-resistance. Currently, no precise tools to predict platinum resistance have been developed yet. METHODS Ninety-nine HGSOC patients, who have finished cytoreductive surgery and platinum-based chemotherapy in Peking University Third Hospital from 2018 to 2019, were enrolled. Whole-genome sequencing (WGS) and whole-exome sequencing (WES) were performed on the collected tumor tissue samples to establish a platinum-resistance predictor in a discovery cohort of 57 patients, and further validated in another 42 HGSOC patients. RESULTS A high prevalence of alterations in DNA damage repair (DDR) pathway, including BRCA1/2, was identified both in the platinum-sensitive and resistant HGSOC patients. Compared with the resistant subgroup, there was a trend of higher prevalence of homologous recombination deficiency (HRD) in the platinum-sensitive subgroup (78.95% vs. 47.37%, p=0.0646). Based on the HRD score, microhomology insertions and deletions (MHID), copy number changes load, duplication load of 1-100 kb, single nucleotide variants load, and eight other mutational signatures, a combined predictor of platinum-resistance, named as DRDscore, was established. DRDscore outperformed in predicting the platinum-sensitivity than the previously reported biomarkers with a predictive accuracy of 0.860 at a threshold of 0.7584. The predictive performance of DRDscore was validated in an independent cohort of 42 HGSOC patients with a sensitivity of 90.9%. CONCLUSIONS A multi-genomic signature-based analysis enabled the prediction of initial platinum resistance in advanced HGSOC patients, which may serve as a novel assessment of platinum resistance, provide therapeutic guidance, and merit further validation.
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Affiliation(s)
- Yuan Li
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Xiaolan Zhang
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Yan Gao
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Chunliang Shang
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Bo Yu
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Tongxia Wang
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Junyan Su
- Lifehealthcare Clinical Laboratories, Hangzhou, China
| | - Cuiyu Huang
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Yu Wu
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Hongyan Guo
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Chunfang Ha
- Department of Gynecology and Obstetrics Department, General Hospital of Ningxia Medical University, Yinchuan, China
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Sorrells S, McKinnon KE, McBratney A, Sumey C. Longitudinal and multi-tissue molecular diagnostics track somatic BRCA2 reversion mutations that correct the open reading frame of germline alteration upon clinical relapse. NPJ Genom Med 2021; 6:17. [PMID: 33619265 PMCID: PMC7900170 DOI: 10.1038/s41525-021-00181-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 01/12/2021] [Indexed: 12/28/2022] Open
Abstract
BRCA-mutant cancers often develop therapeutic resistance through several mechanisms. Here, we report a case of pathogenic germline BRCA2-driven breast cancer monitored for disease progression and acquired resistance using longitudinal multi-tissue genomic testing. Briefly, genomic testing was performed throughout the course of disease on tumor tissue from multiple sites, circulating tumor DNA from blood plasma, and matched normal tissue. Genomic analyses identified actionable variants for targeted therapies, as well as emerging resistance mutations over time. Two unique BRCA2 somatic alterations (p.N255fs and p.D252fs) were identified upon resistance to PARP inhibitor and platinum treatment, respectively. Both alterations restored the open reading frame of the original germline alteration, likely accounting for acquired resistance. This case exemplifies the evolution of multiple subclonal BRCA reversion alterations over time and demonstrates the value of longitudinal multi-tissue genomic testing for monitoring disease progression, predicting measures of response, and evaluating treatment outcomes in oncology patients.
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Färkkilä A, Rodríguez A, Oikkonen J, Gulhan DC, Nguyen H, Domínguez J, Ramos S, Mills CE, Pérez-Villatoro F, Lazaro JB, Zhou J, Clairmont CS, Moreau LA, Park PJ, Sorger PK, Hautaniemi S, Frias S, D'Andrea AD. Heterogeneity and Clonal Evolution of Acquired PARP Inhibitor Resistance in TP53- and BRCA1-Deficient Cells. Cancer Res 2021; 81:2774-2787. [PMID: 33514515 DOI: 10.1158/0008-5472.can-20-2912] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 12/17/2020] [Accepted: 01/25/2021] [Indexed: 12/13/2022]
Abstract
Homologous recombination (HR)-deficient cancers are sensitive to poly-ADP ribose polymerase inhibitors (PARPi), which have shown clinical efficacy in the treatment of high-grade serous cancers (HGSC). However, the majority of patients will relapse, and acquired PARPi resistance is emerging as a pressing clinical problem. Here we generated seven single-cell clones with acquired PARPi resistance derived from a PARPi-sensitive TP53 -/- and BRCA1 -/- epithelial cell line generated using CRISPR/Cas9. These clones showed diverse resistance mechanisms, and some clones presented with multiple mechanisms of resistance at the same time. Genomic analysis of the clones revealed unique transcriptional and mutational profiles and increased genomic instability in comparison with a PARPi-sensitive cell line. Clonal evolutionary analyses suggested that acquired PARPi resistance arose via clonal selection from an intrinsically unstable and heterogenous cell population in the sensitive cell line, which contained preexisting drug-tolerant cells. Similarly, clonal and spatial heterogeneity in tumor biopsies from a clinical patient with BRCA1-mutant HGSC with acquired PARPi resistance was observed. In an imaging-based drug screening, the clones showed heterogenous responses to targeted therapeutic agents, indicating that not all PARPi-resistant clones can be targeted with just one therapy. Furthermore, PARPi-resistant clones showed mechanism-dependent vulnerabilities to the selected agents, demonstrating that a deeper understanding on the mechanisms of resistance could lead to improved targeting and biomarkers for HGSC with acquired PARPi resistance. SIGNIFICANCE: This study shows that BRCA1-deficient cells can give rise to multiple genomically and functionally heterogenous PARPi-resistant clones, which are associated with various vulnerabilities that can be targeted in a mechanism-specific manner.
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Affiliation(s)
- Anniina Färkkilä
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Research Program in Systems Oncology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Alfredo Rodríguez
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Jaana Oikkonen
- Research Program in Systems Oncology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | | | - Huy Nguyen
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Julieta Domínguez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Sandra Ramos
- Laboratorio de Citogenética, Instituto Nacional de Pediatría, Ciudad de México, México
| | - Caitlin E Mills
- Laboratory of Systems Pharmacology, Harvard Medical School, Massachusetts
| | - Fernando Pérez-Villatoro
- Research Program in Systems Oncology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Jean-Bernard Lazaro
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Jia Zhou
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Connor S Clairmont
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Lisa A Moreau
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | | | - Peter K Sorger
- Laboratory of Systems Pharmacology, Harvard Medical School, Massachusetts
| | - Sampsa Hautaniemi
- Research Program in Systems Oncology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Sara Frias
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, México.,Laboratorio de Citogenética, Instituto Nacional de Pediatría, Ciudad de México, México
| | - Alan D D'Andrea
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.
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Ding J, Zhang Q, Chen S, Huang H, He L. Construction of a new tumor immunity-related signature to assess and classify the prognostic risk of ovarian cancer. Aging (Albany NY) 2020; 12:21316-21328. [PMID: 33154188 PMCID: PMC7695433 DOI: 10.18632/aging.103868] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 07/21/2020] [Indexed: 12/16/2022]
Abstract
Ovarian cancer is associated with a high mortality rate. In this study, we established a new immune-related signature that can stratify ovarian cancer patients. First, we obtained immune-related genes through IMMUPORT, and DEGs (Differential Expression Genes) by analyzing the GSE26712 dataset. The APP (Antigen Processing and Presentation) and DEG signatures were established using univariate and multivariate Cox models. Kaplan-Meier analysis revealed the signatures' prognostic value in training and validation cohorts (HR: 0.379 VS. 0.450; 0.333 VS. 0.327). Nomogram analysis was used to assess the signatures' ability to predict the 30-month prognosis, which was evaluated using the calibration curve and time-dependent ROC curve (30-month AUC: 0.665 VS. 0.743). Time-dependent ROC, Decision Curve Analysis (DCA) and Integrated discrimination improvement (IDI) was used to compare the new model to previously published gene signatures. 30-month AUC composite variable (0.736) was higher than 9-gene signature (0.657), and composite variable had a larger net benefit and a higher IDI (+2.436%) relative to the 9-gene signature. Tumor immune infiltration and tumor microenvironment scores of the 2 groups separated by APP signature were compared. GSEA was used to identify enriched KEGG pathways. Conclusively, the proposed signature can stratify ovarian cancer patients by risk-score and guide clinical decisions.
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Affiliation(s)
- Jiashan Ding
- Obstetrics and Gynecology, The First Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, Jiangxi, China
| | - Qiaoling Zhang
- Obstetrics and Gynecology, The First Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, Jiangxi, China
| | - Shichao Chen
- Obstetrics and Gynecology, The First Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, Jiangxi, China
| | - Huikai Huang
- Obstetrics and Gynecology, The First Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, Jiangxi, China
| | - Linsheng He
- Obstetrics and Gynecology, The First Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, Jiangxi, China
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Cardillo TM, Rossi DL, Zalath MB, Liu D, Arrojo R, Sharkey RM, Chang CH, Goldenberg DM. Predictive biomarkers for sacituzumab govitecan efficacy in Trop-2-expressing triple-negative breast cancer. Oncotarget 2020; 11:3849-3862. [PMID: 33196706 PMCID: PMC7597411 DOI: 10.18632/oncotarget.27766] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 09/23/2020] [Indexed: 12/21/2022] Open
Abstract
Sacituzumab govitecan (SG) is an antibody-drug conjugate composed of a humanized anti-Trop-2 IgG antibody conjugated via a hydrolysable linker to SN-38, the topoisomerase I-inhibitory active component of irinotecan. We investigated whether Trop-2-expression and homologous recombination repair (HRR) of SN-38-mediated double-strand DNA (dsDNA) breaks play a role in the sensitivity of triple-negative breast cancer (TNBC) to SG. Activation of HRR pathways, as evidenced by Rad51 expression, was assessed in SG-sensitive cell lines with low and moderate Trop-2-expression (SK-MES-1 squamous cell lung carcinoma and HCC1806 TNBC, respectively), compared to a low Trop-2-expressing, less SG-sensitive TNBC cell line (MDA-MB-231). Further, two Trop-2-transfectants of MDA-MB-231, C13 and C39 (4- and 25-fold higher Trop-2, respectively), were treated in mice with SG to determine whether increasing Trop-2 expression improves SG efficacy. SG mediated >2-fold increase in Rad51 in MDA-MB-231 but had no effect in SK-MES-1 or HCC1806, resulting in lower levels of dsDNA breaks in MDA-MB-231. SG and saline produced similar effects in parental MDA-MB-231 tumor-bearing mice (median survival time (MST) = 21d and 19.5d, respectively). However, in mice bearing higher Trop-2-expressing C13 and C39 tumors after Trop-2 transfection, SG provided a significant survival benefit, even compared to irinotecan (MST = 97d vs. 35d for C13, and 81d vs. 28d for C39, respectively; P < 0.0007). These results suggest that SG could provide better clinical benefit than irinotecan in patients with HRR-proficient tumors expressing high levels of Trop-2, as well as to patients with HRR-deficient tumors expressing low/moderate levels of Trop-2.
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Affiliation(s)
| | | | | | - Donglin Liu
- Immunomedics, Inc., Morris Plains, NJ 07950, USA.,Currently employed with FrontAim Biomedicines Inc., Princeton, NJ 08540, USA
| | | | - Robert M Sharkey
- Immunomedics, Inc., Morris Plains, NJ 07950, USA.,At the time the work was conducted, these authors were employees of Immunomedics, Inc., Morris Plains, NJ 07950, USA
| | - Chien-Hsing Chang
- Immunomedics, Inc., Morris Plains, NJ 07950, USA.,At the time the work was conducted, these authors were employees of Immunomedics, Inc., Morris Plains, NJ 07950, USA
| | - David M Goldenberg
- Immunomedics, Inc., Morris Plains, NJ 07950, USA.,Current address: Center for Molecular Medicine and Immunology, Mendham, NJ 07945, USA.,At the time the work was conducted, this author was Chairman and Chief Scientific Officer of Immunomedics, Inc., Morris Plains, NJ 07950, USA
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49
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van Wijk LM, Vermeulen S, Meijers M, van Diest MF, ter Haar NT, de Jonge MM, Solleveld-Westerink N, van Wezel T, van Gent DC, Kroep JR, Bosse T, Gaarenstroom KN, Vrieling H, Vreeswijk MPG. The RECAP Test Rapidly and Reliably Identifies Homologous Recombination-Deficient Ovarian Carcinomas. Cancers (Basel) 2020; 12:E2805. [PMID: 33003546 PMCID: PMC7650677 DOI: 10.3390/cancers12102805] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/25/2020] [Accepted: 09/26/2020] [Indexed: 12/14/2022] Open
Abstract
Recent studies have shown that the efficacy of PARP inhibitors in epithelial ovarian carcinoma (EOC) is related to tumor-specific defects in homologous recombination (HR) and extends beyond BRCA1/2 deficient EOC. A robust method with which to identify HR-deficient (HRD) carcinomas is therefore of utmost clinical importance. In this study, we investigated the proficiency of a functional HR assay based on the detection of RAD51 foci, the REcombination CAPacity (RECAP) test, in identifying HRD tumors in a cohort of prospectively collected epithelial ovarian carcinomas (EOCs). Of the 39 high-grade serous ovarian carcinomas (HGSOC), the RECAP test detected 26% (10/39) to be HRD, whereas ovarian carcinomas of other histologic subtypes (n = 10) were all HR-proficient (HRP). Of the HRD tumors that could be sequenced, 8/9 showed pathogenic BRCA1/2 variants or BRCA1 promoter hypermethylation, indicating that the RECAP test reliably identifies HRD, including but not limited to tumors related to BRCA1/2 deficiency. Furthermore, we found a trend towards better overall survival (OS) of HGSOC patients with RECAP-identified HRD tumors compared to patients with HRP tumors. This study shows that the RECAP test is an attractive alternative to DNA-based HRD tests, and further development of a clinical grade RECAP test is clearly warranted.
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Affiliation(s)
- Lise M. van Wijk
- Department of Human Genetics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (L.M.v.W.); (S.V.); (M.M.); (M.F.v.D.); (H.V.)
| | - Sylvia Vermeulen
- Department of Human Genetics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (L.M.v.W.); (S.V.); (M.M.); (M.F.v.D.); (H.V.)
| | - Matty Meijers
- Department of Human Genetics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (L.M.v.W.); (S.V.); (M.M.); (M.F.v.D.); (H.V.)
| | - Manuela F. van Diest
- Department of Human Genetics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (L.M.v.W.); (S.V.); (M.M.); (M.F.v.D.); (H.V.)
| | - Natalja T. ter Haar
- Department of Pathology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (N.T.t.H.); (M.M.d.J.); (N.S.-W.); (T.v.W.); (T.B.)
| | - Marthe M. de Jonge
- Department of Pathology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (N.T.t.H.); (M.M.d.J.); (N.S.-W.); (T.v.W.); (T.B.)
| | - Nienke Solleveld-Westerink
- Department of Pathology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (N.T.t.H.); (M.M.d.J.); (N.S.-W.); (T.v.W.); (T.B.)
| | - Tom van Wezel
- Department of Pathology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (N.T.t.H.); (M.M.d.J.); (N.S.-W.); (T.v.W.); (T.B.)
| | - Dik C. van Gent
- Department of Molecular Genetics, Erasmus MC, 3000 CA Rotterdam, The Netherlands;
| | - Judith R. Kroep
- Department of Medical Oncology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands;
| | - Tjalling Bosse
- Department of Pathology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (N.T.t.H.); (M.M.d.J.); (N.S.-W.); (T.v.W.); (T.B.)
| | - Katja N. Gaarenstroom
- Department of Gynecology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands;
| | - Harry Vrieling
- Department of Human Genetics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (L.M.v.W.); (S.V.); (M.M.); (M.F.v.D.); (H.V.)
| | - Maaike P. G. Vreeswijk
- Department of Human Genetics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (L.M.v.W.); (S.V.); (M.M.); (M.F.v.D.); (H.V.)
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50
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Chen CW, Buj R, Dahl ES, Leon KE, Aird KM. ATM inhibition synergizes with fenofibrate in high grade serous ovarian cancer cells. Heliyon 2020; 6:e05097. [PMID: 33024871 PMCID: PMC7527645 DOI: 10.1016/j.heliyon.2020.e05097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/04/2020] [Accepted: 09/24/2020] [Indexed: 11/09/2022] Open
Abstract
While therapies targeting deficiencies in the homologous recombination (HR) pathway are emerging as the standard treatment for high grade serous ovarian cancer (HGSOC) patients, this strategy is limited to the ~50% of patients with a deficiency in this pathway. Therefore, patients with HR-proficient tumors are likely to be resistant to these therapies and require alternative strategies. We found that the HR gene Ataxia Telangiectasia Mutated (ATM) is wildtype and its activity is upregulated in HGSOC compared to normal fallopian tube tissue. Interestingly, multiple pathways related to metabolism are inversely correlated with ATM expression in HGSOC specimens, suggesting that combining ATM inhibition with metabolic drugs would be effective. Analysis of FDA-approved drugs from the Dependency Map demonstrated that ATM-low cells are more sensitive to fenofibrate, a PPARα agonist that affects multiple cellular metabolic pathways. Consistently, PPARα signaling is associated with ATM expression. We validated that combined inhibition of ATM and treatment with fenofibrate is synergistic in multiple HGSOC cell lines by inducing senescence. Together, our results suggest that metabolic changes induced by ATM inhibitors are a potential target for the treatment of HGSOC.
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