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Kang J, Na K, Kang H, Cho U, Kwon SY, Hwang S, Lee A. Prediction of homologous recombination deficiency from Oncomine Comprehensive Assay Plus correlating with SOPHiA DDM HRD Solution. PLoS One 2024; 19:e0298128. [PMID: 38527014 PMCID: PMC10962813 DOI: 10.1371/journal.pone.0298128] [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: 10/20/2023] [Accepted: 01/19/2024] [Indexed: 03/27/2024] Open
Abstract
OBJECTIVE Poly(ADP-ribose) polymerase (PARP) inhibitors are used for targeted therapy for ovarian cancer with homologous recombination deficiency (HRD). In this study, we aimed to develop a homologous recombination deficiency prediction model to predict the genomic integrity (GI) index of the SOPHiA DDM HRD Solution from the Oncomine Comprehensive Assay (OCA) Plus. We also tried to a find cut-off value of the genomic instability metric (GIM) of the OCA Plus that correlates with the GI index of the SOPHiA DDM HRD Solution. METHODS We included 87 cases with high-grade ovarian serous carcinoma from five tertiary referral hospitals in Republic of Korea. We developed an HRD prediction model to predict the GI index of the SOPHiA DDM HRD Solution. As predictor variables in the model, we used the HRD score, which included percent loss of heterozygosity (%LOH), percent telomeric allelic imbalance (%TAI), percent large-scale state transitions (%LST), and the genomic instability metric (GIM). To build the model, we employed a penalized logistic regression technique. RESULTS The final model equation is -21.77 + 0.200 × GIM + 0.102 × %LOH + 0.037 × %TAI + 0.261 × %LST. To improve the performance of the prediction model, we added a borderline result category to the GI results. The accuracy of our HRD status prediction model was 0.958 for the test set. The accuracy of HRD status using GIM with a cut-off value of 16 was 0.911. CONCLUSION The Oncomine Comprehensive Assay Plus provides a reliable biomarker for homologous recombination deficiency.
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Affiliation(s)
- Jun Kang
- Department of Hospital Pathology, Seoul St. Mary’s Hospital, College of Medicine, Catholic University of Korea, Seoul, Korea
| | - Kiyong Na
- Department of Pathology, Kyung Hee University College of Medicine, Kyung Hee University Hospital, Seoul, Republic of Korea
| | - Haeyoun Kang
- Department of Pathology, CHA Bundang Medical Center, CHA University, Seongnam, Korea
| | - Uiju Cho
- Department of Pathology, St. Vincent’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Sun Young Kwon
- Department of Pathology, Dongsan Hospital, School of Medicine, Keimyung University, Daegu, South Korea
| | - Sohyun Hwang
- CHA Future Medicine Research Institute, CHA Bundang Medical Center, Seongnam, Korea
| | - Ahwon Lee
- Department of Hospital Pathology, Seoul St. Mary’s Hospital, College of Medicine, Catholic University of Korea, Seoul, Korea
- Cancer Research Institute, Catholic University of Korea, Seoul, Korea
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Leslie AR, Ning S, Armstrong CM, D’Abronzo LS, Sharifi M, Schaaf ZA, Lou W, Liu C, Evans CP, Lombard AP, Gao AC. IGFBP3 promotes resistance to Olaparib via modulating EGFR signaling in advanced prostate cancer. iScience 2024; 27:108984. [PMID: 38327800 PMCID: PMC10847745 DOI: 10.1016/j.isci.2024.108984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 11/07/2023] [Accepted: 01/17/2024] [Indexed: 02/09/2024] Open
Abstract
Olaparib is a pioneering PARP inhibitor (PARPi) approved for treating castration-resistant prostate cancer (CRPC) tumors harboring DNA repair defects, but clinical resistance has been documented. To study acquired resistance, we developed Olaparib-resistant (OlapR) cell lines through chronic Olaparib treatment of LNCaP and C4-2B cell lines. Here, we found that IGFBP3 is highly expressed in acquired (OlapR) and intrinsic (Rv1) models of Olaparib resistance. We show that IGFBP3 expression promotes Olaparib resistance by enhancing DNA repair capacity through activation of EGFR and DNA-PKcs. IGFBP3 depletion enhances efficacy of Olaparib by promoting DNA damage accumulation and subsequently, cell death in resistant models. Mechanistically, we show that silencing IGFBP3 or EGFR expression reduces cell viability and resensitizes OlapR cells to Olaparib treatment. Inhibition of EGFR by Gefitinib suppressed growth of OlapR cells and improved Olaparib sensitivity, thereby phenocopying IGFBP3 inhibition. Collectively, our results highlight IGFBP3 and EGFR as critical mediators of Olaparib resistance.
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Affiliation(s)
- Amy R. Leslie
- Department of Urologic Surgery, University of California Davis, Davis, CA, USA
| | - Shu Ning
- Department of Urologic Surgery, University of California Davis, Davis, CA, USA
| | | | | | - Masuda Sharifi
- Department of Urologic Surgery, University of California Davis, Davis, CA, USA
| | - Zachary A. Schaaf
- Department of Urologic Surgery, University of California Davis, Davis, CA, USA
| | - Wei Lou
- Department of Urologic Surgery, University of California Davis, Davis, CA, USA
| | - Chengfei Liu
- Department of Urologic Surgery, University of California Davis, Davis, CA, USA
- UC Davis Comprehensive Cancer Center, University of California Davis, Davis, CA, USA
| | - Christopher P. Evans
- Department of Urologic Surgery, University of California Davis, Davis, CA, USA
- UC Davis Comprehensive Cancer Center, University of California Davis, Davis, CA, USA
| | - Alan P. Lombard
- Department of Urologic Surgery, University of California Davis, Davis, CA, USA
- Department of Biochemistry and Molecular Medicine, University of California Davis, Davis, CA, USA
| | - Allen C. Gao
- Department of Urologic Surgery, University of California Davis, Davis, CA, USA
- UC Davis Comprehensive Cancer Center, University of California Davis, Davis, CA, USA
- VA Northern California Health Care System, Sacramento, CA, USA
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Fanale D, Corsini LR, Pedone E, Randazzo U, Fiorino A, Di Piazza M, Brando C, Magrin L, Contino S, Piraino P, Bazan Russo TD, Cipolla C, Russo A, Bazan V. Potential agnostic role of BRCA alterations in patients with several solid tumors: One for all, all for one? Crit Rev Oncol Hematol 2023; 190:104086. [PMID: 37536445 DOI: 10.1016/j.critrevonc.2023.104086] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 07/27/2023] [Accepted: 07/30/2023] [Indexed: 08/05/2023] Open
Abstract
Germline BRCA1/2 alterations in the Homologous Recombination (HR) pathway are considered as main susceptibility biomarkers to Hereditary Breast and Ovarian Cancers (HBOC). The modern molecular biology technologies allowed to characterize germline and somatic BRCA1/2 alterations in several malignancies, broadening the landscape of BRCA1/2-alterated tumors. In the last years, BRCA genetic testing, beyond the preventive value, also assumed a predictive and prognostic significance for patient management. The approval of molecules with agnostic indication is leading to a new clinical model, defined "mutational". Among these drugs, the Poly (ADP)-Ribose Polymerase inhibitors (PARPi) for BRCA1/2-deficient tumors were widely studied leading to increasing therapeutic implications. In this Review we provided an overview of the main clinical studies describing the association between BRCA-mutated tumors and PARPi response, focusing on the controversial evidence about the potential agnostic indication based on BRCA1/2 alterations in several solid tumors.
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Affiliation(s)
- Daniele Fanale
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Lidia Rita Corsini
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Erika Pedone
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Ugo Randazzo
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Alessia Fiorino
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Marianna Di Piazza
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Chiara Brando
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Luigi Magrin
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Silvia Contino
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Paola Piraino
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Tancredi Didier Bazan Russo
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Calogero Cipolla
- Division of General and Oncological Surgery, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Antonio Russo
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy.
| | - Viviana Bazan
- Department of Biomedicine, Neuroscience and Advanced Diagnostics, University of Palermo, 90127 Palermo, Italy
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Kang J, Lee J, Lee A, Lee YS. Prediction of homologous recombination deficiency from cancer gene expression data. J Int Med Res 2022; 50:3000605221133655. [DOI: 10.1177/03000605221133655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Objective Homologous recombination deficiency (HRD) is the main mechanism of tumorigenesis in some cancers. HRD causes abnormal double-strand break repair, resulting in genomic scars. Some scoring HRD tests have been approved as companion diagnostics of polyadenosine diphosphate-ribose polymerase (PARP) inhibitor treatment. This study aimed to build an HRD prediction model using gene expression data from various cancer types. Methods The cancer genome atlas data were used for HRD prediction modeling. A total of 10,567 cases of 33 cancer types were included, and expression data from 5128 out of 20,502 genes were included as predictors. A penalized logistic regression model was chosen as a modeling technique. Results The area under the curve of the receiver operating characteristic curve of HRD status prediction was 0.98 for the training set and 0.93 for the test set. The accuracy of HRD status prediction was 0.93 for the training set and 0.88 for the test set. Conclusions Our study suggests that the HRD prediction model based on penalized logistic regression using gene expression data can be used to select patients for treatment with PARP inhibitors.
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Affiliation(s)
- Jun Kang
- Department of Hospital Pathology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jieun Lee
- Division of Medical Oncology, Department of Internal Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Ahwon Lee
- Department of Hospital Pathology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
- Cancer Research Institute, The Catholic University of Korea, Seoul, Korea
| | - Youn Soo Lee
- Department of Hospital Pathology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
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Cresta Morgado P, Mateo J. Clinical implications of homologous recombination repair mutations in prostate cancer. Prostate 2022; 82 Suppl 1:S45-S59. [PMID: 35657156 DOI: 10.1002/pros.24352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 03/28/2022] [Indexed: 11/06/2022]
Abstract
Prostate cancer is a disease with significant interpatient genomics, with a proportion of patients presenting mutations in key homologous recombination repair (HRR) gene aberrations, particularly in late-stage disease. A better understanding of the genomic landscape of prostate cancer and the prognostic and predictive value of HRR mutations could lead to more precise care for prostate cancer patients. BRCA1/2 mutations are associated with a more aggressive disease course and higher risk of developing lethal prostate cancer, but also identify patients who could benefit from directed therapeutic strategies with PARP inhibitors. Other HRR mutations are also frequent but their prognostic and predictive value for prostate cancer patients is less clear. Moreover, a proportion of these mutations are associated with inherited germline defects, being relevant for the patients' risk of second malignancies but also to inform their relatives' risk of cancer through cascade testing. In this manuscript, we review current knowledge of the prognostic and predictive value for different HHR alterations across the different prostate cancer disease states. Additionally, we assess the challenges to implement genomic testing in clinical practice for prostate cancer patients.
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Affiliation(s)
- Pablo Cresta Morgado
- Medical Oncology Department, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Prostate Cancer Translational Research Group, Barcelona, Spain
| | - Joaquin Mateo
- Medical Oncology Department, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Prostate Cancer Translational Research Group, Barcelona, Spain
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Bieńkowski M, Tomasik B, Braun M, Jassem J. PARP inhibitors for metastatic castration-resistant prostate cancer: Biological rationale and current evidence. Cancer Treat Rev 2022; 104:102359. [DOI: 10.1016/j.ctrv.2022.102359] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 02/06/2022] [Accepted: 02/07/2022] [Indexed: 12/27/2022]
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Harnessing Synthetic Lethal Interactions for Personalized Medicine. J Pers Med 2022; 12:jpm12010098. [PMID: 35055413 PMCID: PMC8779047 DOI: 10.3390/jpm12010098] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 01/07/2022] [Accepted: 01/09/2022] [Indexed: 02/01/2023] Open
Abstract
Two genes are said to have synthetic lethal (SL) interactions if the simultaneous mutations in a cell lead to lethality, but each individual mutation does not. Targeting SL partners of mutated cancer genes can kill cancer cells but leave normal cells intact. The applicability of translating this concept into clinics has been demonstrated by three drugs that have been approved by the FDA to target PARP for tumors bearing mutations in BRCA1/2. This article reviews applications of the SL concept to translational cancer medicine over the past five years. Topics are (1) exploiting the SL concept for drug combinations to circumvent tumor resistance, (2) using synthetic lethality to identify prognostic and predictive biomarkers, (3) applying SL interactions to stratify patients for targeted and immunotherapy, and (4) discussions on challenges and future directions.
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