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Pan JN, Li PC, Wang M, Li MW, Ding XW, Zhou T, Wang HN, Wang YK, Chen LB, Wang R, Ye WW, Wu WZ, Lou F, Wang XJ, Cao WM. AcornHRD: an HRD algorithm highly associated with anthracycline-based neoadjuvant chemotherapy in breast cancer in China. Eur J Med Res 2024; 29:366. [PMID: 39014466 PMCID: PMC11253386 DOI: 10.1186/s40001-024-01936-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 06/11/2024] [Indexed: 07/18/2024] Open
Abstract
PURPOSE Our study aimed to develop and validate a homologous recombination deficiency (HRD) scoring algorithm in the Chinese breast cancer population. METHODS AND MATERIALS Ninety-six in-house breast cancer (BC) samples and 6 HRD-positive standard cells were analyzed by whole-genome sequencing (WGS). Besides, 122 BCs from the TCGA database were down-sampled to ~ 1X WGS. We constructed an algorithm named AcornHRD for HRD score calculated based on WGS at low coverage as input data to estimate large-scale copy number alteration (LCNA) events on the genome. A clinical cohort of 50 BCs (15 cases carrying BRCA mutation) was used to assess the association between HRD status and anthracyclines-based neoadjuvant treatment outcomes. RESULTS A 100-kb window was defined as the optimal size using 41 in-house cases and the TCGA dataset. HRD score high threshold was determined as HRD score ≥ 10 using 55 in-house BCs with BRCA mutation to achieve a 95% BRCA-positive agreement rate. Furthermore, the HRD status agreement rate of AcornHRD is 100%, while the ShallowHRD is 60% in standard cells. BRCA mutation was significantly associated with a high HRD score evaluated by AcornHRD and ShallowHRD (p = 0.008 and p = 0.003, respectively) in the TCGA dataset. However, AcornHRD showed a higher positive agreement rate than did the ShallowHRD algorithm (70% vs 60%). In addition, the BRCA-positive agreement rate of AcornHRD was superior to that of ShallowHRD (87% vs 13%) in the clinical cohort. Importantly, the high HRD score assessed by AcornHRD was significantly correlated with a residual cancer burden score of 0 or 1 (RCB0/1). Besides, the HRD-positive group was more likely to respond to anthracycline-based chemotherapy than the HRD-negative group (pCR [OR = 9.5, 95% CI 1.11-81.5, p = 0.040] and RCB0/1 [OR = 10.29, 95% CI 2.02-52.36, p = 0.005]). CONCLUSION Using the AcornHRD algorithm evaluation, our analysis demonstrated the high performance of the LCNA genomic signature for HRD detection in breast cancers.
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Affiliation(s)
- Jia-Ni Pan
- Department of Breast Medical Oncology, Zhejiang Cancer Hospital, Hangzhou, 310022, China
- Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310018, China
- Cancer Centre, Faculty of Health Sciences, University of Macau, Macau, 999078, SAR, China
| | - Pu-Chun Li
- Department of Breast Medical Oncology, Zhejiang Cancer Hospital, Hangzhou, 310022, China
- Wenzhou Medical University, Wenzhou, 325035, China
| | - Meng Wang
- AcornMed Biotechnology Co., Ltd., Floor 18, Block 5, Yard 18, Kechuang 13 RD, Beijing, 100176, China
| | - Ming-Wei Li
- AcornMed Biotechnology Co., Ltd., Floor 18, Block 5, Yard 18, Kechuang 13 RD, Beijing, 100176, China
| | - Xiao-Wen Ding
- Department of Breast Surgery, Zhejiang Cancer Hospital, Hangzhou, 310022, China
| | - Tao Zhou
- AcornMed Biotechnology Co., Ltd., Floor 18, Block 5, Yard 18, Kechuang 13 RD, Beijing, 100176, China
| | - Hui-Na Wang
- AcornMed Biotechnology Co., Ltd., Floor 18, Block 5, Yard 18, Kechuang 13 RD, Beijing, 100176, China
| | - Yun-Kai Wang
- AcornMed Biotechnology Co., Ltd., Floor 18, Block 5, Yard 18, Kechuang 13 RD, Beijing, 100176, China
| | - Li-Bin Chen
- AcornMed Biotechnology Co., Ltd., Floor 18, Block 5, Yard 18, Kechuang 13 RD, Beijing, 100176, China
| | - Rong Wang
- Department of Breast Medical Oncology, Zhejiang Cancer Hospital, Hangzhou, 310022, China
| | - Wei-Wu Ye
- Department of Breast Medical Oncology, Zhejiang Cancer Hospital, Hangzhou, 310022, China
| | - Wei-Zhu Wu
- Lihuili Hospital of Ningbo Medical Center, Ningbo, 315040, China
| | - Feng Lou
- AcornMed Biotechnology Co., Ltd., Floor 18, Block 5, Yard 18, Kechuang 13 RD, Beijing, 100176, China.
| | - Xiao-Jia Wang
- Department of Breast Medical Oncology, Zhejiang Cancer Hospital, Hangzhou, 310022, China.
| | - Wen-Ming Cao
- Department of Breast Medical Oncology, Zhejiang Cancer Hospital, Hangzhou, 310022, China.
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Fan Y, Liu Z, Chen Y, He Z. Homologous Recombination Repair Gene Mutations in Prostate Cancer: Prevalence and Clinical Value. Adv Ther 2024; 41:2196-2216. [PMID: 38767824 PMCID: PMC11133173 DOI: 10.1007/s12325-024-02844-7] [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: 01/30/2024] [Accepted: 03/12/2024] [Indexed: 05/22/2024]
Abstract
Despite advances in our understanding of the molecular landscape of prostate cancer and the development of novel biomarker-driven therapies, the prognosis of patients with metastatic prostate cancer that is resistant to conventional hormonal therapy remains poor. Data suggest that a significant proportion of patients with metastatic castration-resistant prostate cancer (mCRPC) have mutations in homologous recombination repair (HRR) genes and may benefit from poly(ADP-ribose) polymerase (PARP) inhibitors. However, the adoption of HRR gene mutation testing in prostate cancer remains low, meaning there is a missed opportunity to identify patients who may benefit from targeted therapy with PARP inhibition, with or without novel hormonal agents. Here, we review the current knowledge regarding the clinical significance of HRR gene mutations in prostate cancer and discuss the efficacy of PARP inhibition in patients with mCRPC. This comprehensive overview aims to increase the clinical implementation of HRR gene mutation testing and inform future efforts in personalized treatment of prostate cancer.
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Affiliation(s)
- Yu Fan
- Department of Urology, Peking University First Hospital, No. 8 Xishiku Street, Xicheng District, Beijing, China
| | - Zhenhua Liu
- Global Medical Affairs, MSD China, Shanghai, China
| | - Yuke Chen
- Department of Urology, Peking University First Hospital, No. 8 Xishiku Street, Xicheng District, Beijing, China
| | - Zhisong He
- Department of Urology, Peking University First Hospital, No. 8 Xishiku Street, Xicheng District, Beijing, China.
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Fallah J, Xu J, Weinstock C, Gao X, Heiss BL, Maguire WF, Chang E, Agrawal S, Tang S, Amiri-Kordestani L, Pazdur R, Kluetz PG, Suzman DL. Efficacy of Poly(ADP-ribose) Polymerase Inhibitors by Individual Genes in Homologous Recombination Repair Gene-Mutated Metastatic Castration-Resistant Prostate Cancer: A US Food and Drug Administration Pooled Analysis. J Clin Oncol 2024; 42:1687-1698. [PMID: 38484203 PMCID: PMC11095872 DOI: 10.1200/jco.23.02105] [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: 09/27/2023] [Revised: 11/29/2023] [Accepted: 12/20/2023] [Indexed: 05/09/2024] Open
Abstract
PURPOSE We performed a pooled analysis of multiple trials of poly(ADP-ribose) polymerase inhibitors (PARPi) in metastatic castration-resistant prostate cancer (mCRPC) to investigate the efficacy of PARPi in each individual homologous recombination repair (HRR) mutated (m) gene. PATIENTS AND METHODS We pooled patient-level data from trials of PARPi in mCRPC that reported mutation status in individual HRR genes. Any HRR gene with available data across all the randomized trials of PARPi in first-line mCRPC was selected. The hazard ratios (HRs; 95% CI) for radiographic progression-free survival (rPFS; by blinded independent review) and overall survival (OS) of a PARPi plus an androgen receptor pathway inhibitor (ARPI) relative to placebo plus an ARPI in the pool of three randomized trials in first-line mCRPC were calculated using Kaplan-Meier estimates and a Cox proportional hazards model. RESULTS In ATMm (N = 268), rPFS HR was 1.05 (0.74 to 1.49) and OS HR was 1.18 (0.82 to 1.71). In BRCA1m (N = 64), rPFS HR was 0.51 (0.23 to 1.1) and OS HR was 0.74 (0.34 to 1.61). In BRCA2m (N = 422), rPFS HR was 0.31 (0.23 to 0.42) and OS HR was 0.66 (0.49 to 0.89). In CDK12m (N = 164), rPFS HR was 0.50 (0.32 to 0.80) and OS HR was 0.63 (0.39 to 0.99). In CHEK2m (N = 172), rPFS HR was 1.06 (0.67 to 1.66) and OS HR was 1.53 (0.95 to 2.46). In PALB2m (N = 41) rPFS HR was 0.52 (0.23 to 1.17) and OS HR was 0.78 (0.34 to 1.8). CONCLUSION In this pooled analysis, benefit from PARPi appeared greatest for patients with BRCA1m, BRCA2m, CDK12m, and PALB2m. Given limitations of this exploratory analysis, the apparent lack of benefit from PARPi in patients with CHEK2m or ATMm should be further explored in future clinical trials.
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Affiliation(s)
- Jaleh Fallah
- Center for Drug Evaluation and Research (CDER), U.S. Food and Drug Administration, Silver Spring, MD
| | - Jianjin Xu
- Center for Drug Evaluation and Research (CDER), U.S. Food and Drug Administration, Silver Spring, MD
| | - Chana Weinstock
- Center for Drug Evaluation and Research (CDER), U.S. Food and Drug Administration, Silver Spring, MD
| | - Xin Gao
- Center for Drug Evaluation and Research (CDER), U.S. Food and Drug Administration, Silver Spring, MD
| | - Brian L. Heiss
- Center for Drug Evaluation and Research (CDER), U.S. Food and Drug Administration, Silver Spring, MD
| | - William F. Maguire
- Center for Drug Evaluation and Research (CDER), U.S. Food and Drug Administration, Silver Spring, MD
| | - Elaine Chang
- Center for Drug Evaluation and Research (CDER), U.S. Food and Drug Administration, Silver Spring, MD
| | - Sundeep Agrawal
- Center for Drug Evaluation and Research (CDER), U.S. Food and Drug Administration, Silver Spring, MD
| | - Shenghui Tang
- Center for Drug Evaluation and Research (CDER), U.S. Food and Drug Administration, Silver Spring, MD
| | - Laleh Amiri-Kordestani
- Center for Drug Evaluation and Research (CDER), U.S. Food and Drug Administration, Silver Spring, MD
- Oncology Center of Excellence (OCE), U.S. Food and Drug Administration, Silver Spring, MD
| | - Richard Pazdur
- Center for Drug Evaluation and Research (CDER), U.S. Food and Drug Administration, Silver Spring, MD
- Oncology Center of Excellence (OCE), U.S. Food and Drug Administration, Silver Spring, MD
| | - Paul G. Kluetz
- Center for Drug Evaluation and Research (CDER), U.S. Food and Drug Administration, Silver Spring, MD
- Oncology Center of Excellence (OCE), U.S. Food and Drug Administration, Silver Spring, MD
| | - Daniel L. Suzman
- Center for Drug Evaluation and Research (CDER), U.S. Food and Drug Administration, Silver Spring, MD
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Sardar S, McNair CM, Ravindranath L, Chand SN, Yuan W, Bogdan D, Welti J, Sharp A, Ryan NK, Schiewer MJ, DeArment EG, Janas T, Su XA, Butler LM, de Bono JS, Frese K, Brooks N, Pegg N, Knudsen KE, Shafi AA. AR coactivators, CBP/p300, are critical mediators of DNA repair in prostate cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.07.592966. [PMID: 38766099 PMCID: PMC11100730 DOI: 10.1101/2024.05.07.592966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Castration resistant prostate cancer (CRPC) remains an incurable disease stage with ineffective treatments options. Here, the androgen receptor (AR) coactivators CBP/p300, which are histone acetyltransferases, were identified as critical mediators of DNA damage repair (DDR) to potentially enhance therapeutic targeting of CRPC. Key findings demonstrate that CBP/p300 expression increases with disease progression and selects for poor prognosis in metastatic disease. CBP/p300 bromodomain inhibition enhances response to standard of care therapeutics. Functional studies, CBP/p300 cistrome mapping, and transcriptome in CRPC revealed that CBP/p300 regulates DDR. Further mechanistic investigation showed that CBP/p300 attenuation via therapeutic targeting and genomic knockdown decreases homologous recombination (HR) factors in vitro, in vivo, and in human prostate cancer (PCa) tumors ex vivo. Similarly, CBP/p300 expression in human prostate tissue correlates with HR factors. Lastly, targeting CBP/p300 impacts HR-mediate repair and patient outcome. Collectively, these studies identify CBP/p300 as drivers of PCa tumorigenesis and lay the groundwork to optimize therapeutic strategies for advanced PCa via CBP/p300 inhibition, potentially in combination with AR-directed and DDR therapies.
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Affiliation(s)
- Sumaira Sardar
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, Maryland, 20817, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, 20817 USA
| | - Christopher M. McNair
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, 19107, USA
| | - Lakshmi Ravindranath
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, Maryland, 20817, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, 20817 USA
| | - Saswati N. Chand
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, 19107, USA
| | - Wei Yuan
- The Institute of Cancer Research, London, United Kingdom
| | - Denisa Bogdan
- The Institute of Cancer Research, London, United Kingdom
| | - Jon Welti
- The Institute of Cancer Research, London, United Kingdom
| | - Adam Sharp
- The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden Hospital, London, United Kingdom
| | - Natalie K. Ryan
- South Australian Immunogenomics Cancer Institute, The University of Adelaide, Australia
- South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Matthew J. Schiewer
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, 19107, USA
| | - Elise G. DeArment
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, Maryland, 20817, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, 20817 USA
| | - Thomas Janas
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, Maryland, 20817, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, 20817 USA
| | - Xiaofeng A. Su
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, Maryland, 20817, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, 20817 USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Lisa M. Butler
- South Australian Immunogenomics Cancer Institute, The University of Adelaide, Australia
- South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Johann S. de Bono
- The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden Hospital, London, United Kingdom
| | - Kris Frese
- CellCentric Ltd., Cambridge, United Kingdom
| | | | - Neil Pegg
- CellCentric Ltd., Cambridge, United Kingdom
| | - Karen E. Knudsen
- The American Cancer Society, Philadelphia, Pennsylvania, 19103, USA
| | - Ayesha A. Shafi
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, Maryland, 20817, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, 20817 USA
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5
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Koguchi D, Tsumura H, Tabata KI, Shimura S, Satoh T, Ikeda M, Watanabe A, Yoshida T, Sasaki J, Matsumoto K, Iwamura M. Real-world data on the comprehensive genetic profiling test for Japanese patients with metastatic castration-resistant prostate cancer. Jpn J Clin Oncol 2024; 54:569-576. [PMID: 38305663 DOI: 10.1093/jjco/hyae003] [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: 10/26/2023] [Accepted: 01/10/2024] [Indexed: 02/03/2024] Open
Abstract
OBJECTIVE comprehensive genomic profiling test has been covered by Japanese health insurance since June 2019. However, no real-world data on the test have been reported with a focus on Japanese patients with prostate cancer. METHODS we retrospectively reviewed the data of 45 consecutive patients with metastatic castration-resistant prostate cancer, who underwent the comprehensive genomic profiling tests at Kitasato University Hospital between August 2019 and December 2022. Patients' characteristics, prevalence of gene alterations and therapeutic impact of genotype-matched therapy were assessed. RESULTS genomic data were obtained using a tissue-based test (n = 32) and liquid-based test (n = 13). Actionable genomic alternations were identified in 51.1% of patients, and 22.2% were treated with genotype-matched therapy. The main reason for not receiving genotype-matched therapy was disease progression, accounting for 46.2% (6/13). Kaplan-Meier analysis showed significantly longer overall survival after the comprehensive genomic profiling tests in patients with genotype-matched therapy under public insurance (17.8%, n = 8) than those without it (median: not reached vs. 18.1 months; P = 0.003). Five (62.5%) out of the eight patients with genotype-matched therapy under public insurance had BRCA1 or 2 deleterious alteration. Multivariate analyses showed that BRCA deleterious alteration (17.8%, n = 8) was an independent risk factor for shorter time to castration-resistant prostate cancer (hazard ratio: 2.46, 95% confidence interval: 1.04-5.87; P = 0.041), and no patients with the alteration had ≤5 bone metastases. CONCLUSIONS the results of this study showed the promising survival outcomes in patients with genotype-matched therapy under public insurance, even in the castration-resistant prostate cancer setting. Further detection of promising therapeutic target gene is expected to increase the number of patients who reach genotype-matched therapies.
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Affiliation(s)
- Dai Koguchi
- Department of Urology, Kitasato University School of Medicine, Kanagawa, Japan
| | - Hideyasu Tsumura
- Department of Urology, Kitasato University School of Medicine, Kanagawa, Japan
| | - Ken-Ichi Tabata
- Department of Urology, Kitasato Institute Hospital, Tokyo, Japan
| | - Soichiro Shimura
- Department of Urology, Kitasato University School of Medicine, Kanagawa, Japan
| | - Takefumi Satoh
- Department of Urology, Kitasato University School of Medicine, Kanagawa, Japan
| | - Masaomi Ikeda
- Department of Urology, Kitasato University School of Medicine, Kanagawa, Japan
| | - Akinori Watanabe
- Department of Gastroenterology, Kitasato University School of Medicine, Kanagawa, Japan
| | - Tsutomu Yoshida
- Department of Pathology, Kitasato University School of Medicine, Kanagawa, Japan
| | - Jiichiro Sasaki
- Department of Respiratory Medicine, Kitasato University School of Medicine, Kanagawa, Japan
| | - Kazumasa Matsumoto
- Department of Urology, Kitasato University School of Medicine, Kanagawa, Japan
| | - Masatsugu Iwamura
- Department of Urology, Kitasato University School of Medicine, Kanagawa, Japan
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Slootbeek PHJ, Tolmeijer SH, Mehra N, Schalken JA. Therapeutic biomarkers in metastatic castration-resistant prostate cancer: does the state matter? Crit Rev Clin Lab Sci 2024; 61:178-204. [PMID: 37882463 DOI: 10.1080/10408363.2023.2266482] [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: 06/07/2023] [Accepted: 09/28/2023] [Indexed: 10/27/2023]
Abstract
The treatment of metastatic castration-resistant prostate cancer (mCRPC) has been fundamentally transformed by our greater understanding of its complex biological mechanisms and its entrance into the era of precision oncology. A broad aim is to use the extreme heterogeneity of mCRPC by matching already approved or new targeted therapies to the correct tumor genotype. To achieve this, tumor DNA must be obtained, sequenced, and correctly interpreted, with individual aberrations explored for their druggability, taking into account the hierarchy of driving molecular pathways. Although tumor tissue sequencing is the gold standard, tumor tissue can be challenging to obtain, and a biopsy from one metastatic site or primary tumor may not provide an accurate representation of the current genetic underpinning. Sequencing of circulating tumor DNA (ctDNA) might catalyze precision oncology in mCRPC, as it enables real-time observation of genomic changes in tumors and allows for monitoring of treatment response and identification of resistance mechanisms. Moreover, ctDNA can be used to identify mutations that may not be detected in solitary metastatic lesions and can provide a more in-depth understanding of inter- and intra-tumor heterogeneity. Finally, ctDNA abundance can serve as a prognostic biomarker in patients with mCRPC.The androgen receptor (AR)-axis is a well-established therapeutical target for prostate cancer, and through ctDNA sequencing, insights have been obtained in (temporal) resistance mechanisms that develop through castration resistance. New third-generation AR-axis inhibitors are being developed to overcome some of these resistance mechanisms. The druggability of defects in the DNA damage repair machinery has impacted the treatment landscape of mCRPC in recent years. For patients with deleterious gene aberrations in genes linked to homologous recombination, particularly BRCA1 or BRCA2, PARP inhibitors have shown efficacy compared to the standard of care armamentarium, but platinum-based chemotherapy may be equally effective. A hierarchy exists in genes associated with homologous recombination, where, besides the canonical genes in this pathway, not every other gene aberration predicts the same likelihood of response. Moreover, evidence is emerging on cross-resistance between therapies such as PARP inhibitors, platinum-based chemotherapy and even radioligand therapy that target this genotype. Mismatch repair-deficient patients can experience a beneficial response to immune checkpoint inhibitors. Activation of other cellular signaling pathways such as PI3K, cell cycle, and MAPK have shown limited success with monotherapy, but there is potential in co-targeting these pathways with combination therapy, either already witnessed or anticipated. This review outlines precision medicine in mCRPC, zooming in on the role of ctDNA, to identify genomic biomarkers that may be used to tailor molecularly targeted therapies. The most common druggable pathways and outcomes of therapies matched to these pathways are discussed.
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Affiliation(s)
- Peter H J Slootbeek
- Department of Medical Oncology, Radboud university medical center, Nijmegen, The Netherland
| | - Sofie H Tolmeijer
- Department of Medical Oncology, Radboud university medical center, Nijmegen, The Netherland
| | - Niven Mehra
- Department of Medical Oncology, Radboud university medical center, Nijmegen, The Netherland
| | - Jack A Schalken
- Department of Experimental Urology, Research Institute of Medical Innovation, Radboud university medical center, Nijmegen, The Netherlands
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7
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Paul AK, Melson JW, Hirani S, Muthusamy S. Systemic therapy landscape of advanced prostate cancer. Adv Cancer Res 2024; 161:367-402. [PMID: 39032954 DOI: 10.1016/bs.acr.2024.04.004] [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: 07/23/2024]
Abstract
Prostate cancer is the most commonly diagnosed cancer in American men and 2nd leading cause of cancer-related deaths in the United States. Androgen deprivation therapy (ADT) is the backbone of treatment for advanced prostate cancer. Over the past several decades a number of new therapeutics, such as novel androgen receptor pathway inhibitors, targeted agents and radionuclide therapies, have been introduced for the treatment of prostate cancers. These agents have been demonstrated to improve clinical outcomes of prostate cancer patients in randomized clinical trials. In addition, new therapeutic strategies, such as early intensification of ADT, novel treatment combinations, and treatment sequencing, are expected to improve outcomes further. In this clinical review, we discuss the changing treatment landscape for advanced prostate cancer with a focus on new therapeutics.
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Affiliation(s)
- Asit K Paul
- Department of Internal Medicine, Division of Hematology, Oncology and Palliative Care, Virginia Commonwealth University, Richmond, VA, United States; VCU Massey Comprehensive Cancer Center, Richmond, VA, United States.
| | - John W Melson
- Department of Internal Medicine, Division of Hematology, Oncology and Palliative Care, Virginia Commonwealth University, Richmond, VA, United States; VCU Massey Comprehensive Cancer Center, Richmond, VA, United States
| | - Samina Hirani
- Department of Internal Medicine, Division of Hematology, Oncology and Palliative Care, Virginia Commonwealth University, Richmond, VA, United States
| | - Selvaraj Muthusamy
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, United States
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8
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Aleksakhina SN, Ivantsov AO, Imyanitov EN. Agnostic Administration of Targeted Anticancer Drugs: Looking for a Balance between Hype and Caution. Int J Mol Sci 2024; 25:4094. [PMID: 38612902 PMCID: PMC11012409 DOI: 10.3390/ijms25074094] [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: 02/18/2024] [Revised: 03/27/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
Many tumors have well-defined vulnerabilities, thus potentially allowing highly specific and effective treatment. There is a spectrum of actionable genetic alterations which are shared across various tumor types and, therefore, can be targeted by a given drug irrespective of tumor histology. Several agnostic drug-target matches have already been approved for clinical use, e.g., immune therapy for tumors with microsatellite instability (MSI) and/or high tumor mutation burden (TMB), NTRK1-3 and RET inhibitors for cancers carrying rearrangements in these kinases, and dabrafenib plus trametinib for BRAF V600E mutated malignancies. Multiple lines of evidence suggest that this histology-independent approach is also reasonable for tumors carrying ALK and ROS1 translocations, biallelic BRCA1/2 inactivation and/or homologous recombination deficiency (HRD), strong HER2 amplification/overexpression coupled with the absence of other MAPK pathway-activating mutations, etc. On the other hand, some well-known targets are not agnostic: for example, PD-L1 expression is predictive for the efficacy of PD-L1/PD1 inhibitors only in some but not all cancer types. Unfortunately, the individual probability of finding a druggable target in a given tumor is relatively low, even with the use of comprehensive next-generation sequencing (NGS) assays. Nevertheless, the rapidly growing utilization of NGS will significantly increase the number of patients with highly unusual or exceptionally rare tumor-target combinations. Clinical trials may provide only a framework for treatment attitudes, while the decisions for individual patients usually require case-by-case consideration of the probability of deriving benefit from agnostic versus standard therapy, drug availability, associated costs, and other circumstances. The existing format of data dissemination may not be optimal for agnostic cancer medicine, as conventional scientific journals are understandably biased towards the publication of positive findings and usually discourage the submission of case reports. Despite all the limitations and concerns, histology-independent drug-target matching is certainly feasible and, therefore, will be increasingly utilized in the future.
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Affiliation(s)
- Svetlana N. Aleksakhina
- Department of Tumor Growth Biology, N. N. Petrov Institute of Oncology, 197758 St. Petersburg, Russia
| | - Alexander O. Ivantsov
- Department of Tumor Growth Biology, N. N. Petrov Institute of Oncology, 197758 St. Petersburg, Russia
- Department of Medical Genetics, St. Petersburg Pediatric Medical University, 194100 St. Petersburg, Russia
| | - Evgeny N. Imyanitov
- Department of Tumor Growth Biology, N. N. Petrov Institute of Oncology, 197758 St. Petersburg, Russia
- Department of Medical Genetics, St. Petersburg Pediatric Medical University, 194100 St. Petersburg, Russia
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Ditonno F, Bianchi A, Malandra S, Porcaro AB, Fantinel E, Negrelli R, Ferro M, Milella M, Brunelli M, Autorino R, Cerruto MA, Veccia A, Antonelli A. PARP Inhibitors in Metastatic Prostate Cancer: A Comprehensive Systematic Review and Meta-analysis of Existing Evidence. Clin Genitourin Cancer 2024; 22:402-412.e17. [PMID: 38281877 DOI: 10.1016/j.clgc.2023.12.011] [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: 09/15/2023] [Revised: 12/05/2023] [Accepted: 12/16/2023] [Indexed: 01/30/2024]
Abstract
Poly (ADP-ribose) polymerase inhibitors (PARPi) represent an option in selected cases of metastatic castration-resistant prostate cancer (mCRPC). The aim of the present systematic review and meta-analysis is to evaluate the efficacy and safety of approved (Olaparib, Rucaparib) and investigational (Talazoparib, Niraparib, Veliparib) PARPi in mCRPC patients. Three databases were queried for studies analyzing oncological outcomes and adverse events of mCRPC patients receiving PARPi. Primary outcome was a PSA decline ≥ 50% from baseline. Secondary outcomes were objective response rate, progression-free survival (PFS), radiological PFS, overall survival (OS), conversion of circulating tumor cell count, and time to PSA progression. The number and rate of any grade adverse events (AEs), grade ≥ 3 AEs, and most common grade ≥ 3 AEs were registered. A subanalysis of outcomes per mutation type, prospective trials, and studies adopting combination therapies was performed. Overall, 31 studies were included in this systematic review, 28 of which are available for meta-analysis. The most frequently investigated drug was Olaparib. The most frequent mutation was BRCA2. A PSA decline rate of 43% (95% CI 0.32-0.54) was observed in the overall population. Mean OS was 15.9 (95% CI 12.9-19.0) months. In BRCA2 patients, PSA decline rate was 66% (95% CI 0.57-0.7) and OS 23.4 months (95% CI 22.8-24.1). Half of the patients suffered from grade 3 and 4 AEs (0.50 [95% CI 0.39-0.60]). Most common AEs were hematological, the most frequent being anemia (21.5%). PARP inhibitors represent a viable option for mCRPC patients. Current evidence suggests an increased effectiveness in homologous recombination repair (HRR) gene mutation carriers, especially BRCA2.
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Affiliation(s)
- Francesco Ditonno
- Department of Urology, University of Verona, Azienda Ospedaliera Universitaria Integrata (AOUI) Verona, Verona, Italy; Department of Urology, Rush University, Chicago, IL, USA
| | - Alberto Bianchi
- Department of Urology, University of Verona, Azienda Ospedaliera Universitaria Integrata (AOUI) Verona, Verona, Italy
| | - Sarah Malandra
- Department of Surgery, Dentistry, Pediatrics and Ginecology, University of Verona, Azienda Ospedaliera Universitaria Integrata (AOUI) Verona, Verona, Italy
| | - Antonio Benito Porcaro
- Department of Urology, University of Verona, Azienda Ospedaliera Universitaria Integrata (AOUI) Verona, Verona, Italy
| | - Emanuela Fantinel
- Section of Oncology, Department of Medicine, University of Verona, Azienda Ospedaliera Universitaria Integrata, Verona, Italy
| | - Riccardo Negrelli
- Department of Radiology, University of Verona, Azienda Ospedaliera Universitaria Integrata, Verona, Italy
| | - Matteo Ferro
- Department of Urology, European Institute of Oncology (IEO) IRCCS, Milan, Italy
| | - Michele Milella
- Section of Oncology, Department of Medicine, University of Verona, Azienda Ospedaliera Universitaria Integrata, Verona, Italy
| | - Matteo Brunelli
- Department of Diagnostic and Public Health, Section of Pathology, University of Verona, Italy
| | | | - Maria Angela Cerruto
- Department of Urology, University of Verona, Azienda Ospedaliera Universitaria Integrata (AOUI) Verona, Verona, Italy
| | - Alessandro Veccia
- Department of Urology, University of Verona, Azienda Ospedaliera Universitaria Integrata (AOUI) Verona, Verona, Italy.
| | - Alessandro Antonelli
- Department of Urology, University of Verona, Azienda Ospedaliera Universitaria Integrata (AOUI) Verona, Verona, Italy
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10
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Akhoundova D, Francica P, Rottenberg S, Rubin MA. DNA Damage Response and Mismatch Repair Gene Defects in Advanced and Metastatic Prostate Cancer. Adv Anat Pathol 2024; 31:61-69. [PMID: 38008971 PMCID: PMC10846598 DOI: 10.1097/pap.0000000000000422] [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: 11/28/2023]
Abstract
Alterations in DNA damage response (DDR) and related genes are present in up to 25% of advanced prostate cancers (PCa). Most frequently altered genes are involved in the homologous recombination repair, the Fanconi anemia, and the mismatch repair pathways, and their deficiencies lead to a highly heterogeneous spectrum of DDR-deficient phenotypes. More than half of these alterations concern non- BRCA DDR genes. From a therapeutic perspective, poly-ADP-ribose polymerase inhibitors have demonstrated robust clinical efficacy in tumors with BRCA2 and BRCA1 alterations. Mismatch repair-deficient PCa, and a subset of CDK12-deficient PCa, are vulnerable to immune checkpoint inhibitors. Emerging data point to the efficacy of ATR inhibitors in PCa with ATM deficiencies. Still, therapeutic implications are insufficiently clarified for most of the non- BRCA DDR alterations, and no successful targeted treatment options have been established.
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Affiliation(s)
- Dilara Akhoundova
- Department for BioMedical Research
- Department of Medical Oncology
- Bern Center for Precision Medicine, Inselspital, University Hospital of Bern, Bern, Switzerland
| | - Paola Francica
- Department for BioMedical Research
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern
- Bern Center for Precision Medicine, Inselspital, University Hospital of Bern, Bern, Switzerland
| | - Sven Rottenberg
- Department for BioMedical Research
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern
- Bern Center for Precision Medicine, Inselspital, University Hospital of Bern, Bern, Switzerland
| | - Mark A. Rubin
- Department for BioMedical Research
- Bern Center for Precision Medicine, Inselspital, University Hospital of Bern, Bern, Switzerland
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11
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Wang X, Waldman L, Silberman Y, Wang M, Tackey C, Hanna L, Vesprini D, Emmenegger U, Eisen A, Smoragiewicz M. Mainstream Model of Genetic Testing for Prostate Cancer at a Large Tertiary Cancer Centre. Clin Genitourin Cancer 2024:102052. [PMID: 38461085 DOI: 10.1016/j.clgc.2024.02.003] [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: 12/04/2023] [Revised: 02/01/2024] [Accepted: 02/03/2024] [Indexed: 03/11/2024]
Abstract
BACKGROUND An estimated 20% to 30% of men with advanced prostate cancer carry a mutation in DNA damage repair genes, of which half are estimated to be germline. Eligibility criteria for germline genetic testing expanded significantly for Ontario patients in May 2021 and many centers adopted a "mainstream" model, defined as oncologist-initiated genetic testing. METHODS We conducted a retrospective chart review to report on the first-year mainstream experience of a large tertiary oncologic center, the Sunnybrook Odette Cancer Centre. All patients who underwent mainstream at the discretion of their treating physician were included. A subset underwent somatic profiling as part of clinical trial screening. Descriptive statistics were used to report baseline clinicopathologic characteristics and treatments received. RESULTS Between May 1, 2021, and May 30, 2022, 174 patients with prostate cancer underwent mainstream germline genetic testing with a 19-gene panel. Median age was 75 (IQR 68-80), and 82% of patients were diagnosed with either de novo metastatic or high-risk localized prostate adenocarcinoma. Fourteen patients (8%; 95% CI 4%-12%) were found to have a deleterious germline mutation, including pathogenic or likely pathogenic variants in BRCA1/2, ATM, CHEK2, PMS2, RAD51C, HOXB13, and BRIP1. Forty-nine patients (28%; 95% CI 21%-35%) were found to have a variant of uncertain significance. Thirty-four patients also had next-generation sequencing (NGS) of their somatic tissue. Among this subset, 8 of 34 (23%) had an alteration in homologous recombination repair (HRR) genes. Of the 14 patients with a germline mutation, none had a prior personal history of malignancy and 6 (43%) did not have any first- or second-degree relatives with history of prostate, pancreatic, breast, or ovarian cancer. CONCLUSION We report on the real-world characteristics of prostate cancer patients who underwent mainstream germline genetic testing. Personal history and family history of cancer cannot reliably stratify patients for the presence of pathogenic germline variants.
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Affiliation(s)
- Xin Wang
- Department of Medical Oncology, Princess Margaret Cancer Centre, Toronto, Ontario, Canada; Department of Medical Oncology, Sunnybrook Odette Cancer Centre, Toronto, Ontario, Canada
| | - Larissa Waldman
- Cancer Genetics and High-Risk Program, Sunnybrook Odette Cancer Centre, Toronto, Ontario, Canada; Department of Molecular Genetics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Yael Silberman
- Cancer Genetics and High-Risk Program, Sunnybrook Odette Cancer Centre, Toronto, Ontario, Canada
| | - Michael Wang
- Department of Medical Oncology, Sunnybrook Odette Cancer Centre, Toronto, Ontario, Canada; Department of Bio-Medical Science, Guelph University, Guelph, Ontario, Canada
| | - Caleb Tackey
- Department of Medical Oncology, Sunnybrook Odette Cancer Centre, Toronto, Ontario, Canada
| | - Lilian Hanna
- Department of Medical Oncology, Sunnybrook Odette Cancer Centre, Toronto, Ontario, Canada
| | - Danny Vesprini
- Department of Radiation Oncology, Sunnybrook Odette Cancer Centre, Toronto, Ontario, Canada
| | - Urban Emmenegger
- Department of Medical Oncology, Sunnybrook Odette Cancer Centre, Toronto, Ontario, Canada
| | - Andrea Eisen
- Cancer Genetics and High-Risk Program, Sunnybrook Odette Cancer Centre, Toronto, Ontario, Canada; Department of Medical Oncology, Sunnybrook Odette Cancer Centre, Toronto, Ontario, Canada
| | - Martin Smoragiewicz
- Department of Medical Oncology, Sunnybrook Odette Cancer Centre, Toronto, Ontario, Canada.
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12
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Dimitrov G, Mangaldzhiev R, Slavov C, Popov E. Precision Medicine in Castration-Resistant Prostate Cancer: Advances, Challenges, and the Landscape of PARPi Therapy-A Narrative Review. Int J Mol Sci 2024; 25:2184. [PMID: 38396858 PMCID: PMC10889419 DOI: 10.3390/ijms25042184] [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: 01/13/2024] [Revised: 02/08/2024] [Accepted: 02/10/2024] [Indexed: 02/25/2024] Open
Abstract
After recent approvals, poly-adenosine diphosphate [ADP]-ribose polymerase inhibitors (PARPis) have emerged as a frontline treatment for metastatic castration-resistant prostate cancer (mCRPC). Unlike their restricted use in breast or ovarian cancers, where approval is limited to those with BRCA1/2 alterations, PARPis in mCRPC are applied across a broader spectrum of genetic aberrations. Key findings from the phase III PROPEL trial suggest that PARPis' accessibility may broaden, even without mandatory testing. An increasing body of evidence underscores the importance of distinct alterations in homologous recombination repair (HRR) genes, revealing unique sensitivities to PARPis. Nonetheless, despite the initial effectiveness of PARPis in treating BRCA-mutated tumors, resistance to therapy is frequently encountered. This review aims to discuss patient stratification based on biomarkers and genetic signatures, offering insights into the nuances of first-line PARPis' efficacy in the intricate landscape of mCRPC.
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Affiliation(s)
- George Dimitrov
- Department of Medical Oncology, Medical University of Sofia, University Hospital “Tsaritsa Yoanna”, 1527 Sofia, Bulgaria; (G.D.)
| | - Radoslav Mangaldzhiev
- Department of Medical Oncology, Medical University of Sofia, University Hospital “Tsaritsa Yoanna”, 1527 Sofia, Bulgaria; (G.D.)
| | - Chavdar Slavov
- Department of Urology, Medical University of Sofia, University Hospital “Tsaritsa Yoanna”, 1527 Sofia, Bulgaria;
| | - Elenko Popov
- Department of Urology, Medical University of Sofia, University Hospital “Tsaritsa Yoanna”, 1527 Sofia, Bulgaria;
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13
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Qiu X, Lu C, Sha H, Zhu Y, Kong W, Tong F, Wang Q, Meng F, Liu B, Du J. Efficacy and safety of second-line therapy by S-1 combined with sintilimab and anlotinib in pancreatic cancer patients with liver metastasis: a single-arm, phase II clinical trial. Front Immunol 2024; 15:1210859. [PMID: 38361920 PMCID: PMC10867188 DOI: 10.3389/fimmu.2024.1210859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 01/11/2024] [Indexed: 02/17/2024] Open
Abstract
Background Pancreatic adenocarcinoma carries a grim prognosis, and there are few recognized effective second-line treatment strategies. We attempted to evaluate the efficacy and safety of a combination of S-1, sintilimab, and anlotinib as a second-line treatment in pancreatic cancer patients with liver metastasis. Methods Pancreatic cancer patients with liver metastases were recruited. S-1 was administered orally at 25 mg/m2 bid, anlotinib was administered orally at 12 mg qd from day 1 to day 14, and sintilimab was administered intravenously at 200 mg on day 1. This method was repeated every 21 days, and the therapeutic effect was evaluated every 3 cycles. The primary outcome was the objective response rate (ORR). Results Overall, 23 patients were enrolled in this study of whom 19 patients had objective efficacy evaluation. The ORR was 10.5% (95% CI 0.4%-25.7%) in the evaluable population. The progression-free survival (PFS) was 3.53 (95% CI 2.50-7.50) months, and the overall survival (mOS) was 8.53 (95% CI 4.97-14.20) months. Grade 3 adverse events were 26.1%, and no grade 4 or above adverse events occurred. High-throughput sequencing was performed on the tumor tissues of 16 patients; patients with HRD-H (n = 10) had shorter PFS than those with HRD-L (n = 6) (2.43 vs. 5.45 months; P = 0.043), but there was no significant difference in OS between the two groups (4.43 vs. 9.35 months; P = 0.11). Conclusions This study suggests the advantage of S-1 combined with sintilimab and anlotinib in extending OS as a second-line therapy in pancreatic cancer patients with liver metastasis. Clinical Trial Registration: ChiCTR2000030659.
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Affiliation(s)
- Xin Qiu
- The Comprehensive Cancer Center of Drum Tower Hospital, Medical School of Nanjing University & Clinical Cancer Institute of Nanjing University, Nanjing, China
- The Comprehensive Cancer Center of Drum Tower Hospital, Clinical College of Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Changchang Lu
- The Comprehensive Cancer Center of Drum Tower Hospital, Clinical College of Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Huizi Sha
- The Comprehensive Cancer Center of Drum Tower Hospital, Medical School of Nanjing University & Clinical Cancer Institute of Nanjing University, Nanjing, China
| | - Yahui Zhu
- The Comprehensive Cancer Center of Drum Tower Hospital, Medical School of Nanjing University & Clinical Cancer Institute of Nanjing University, Nanjing, China
| | - Weiwei Kong
- The Comprehensive Cancer Center of Drum Tower Hospital, Medical School of Nanjing University & Clinical Cancer Institute of Nanjing University, Nanjing, China
| | - Fan Tong
- The Comprehensive Cancer Center of Drum Tower Hospital, Clinical College of Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Qiaoli Wang
- The Comprehensive Cancer Center of Drum Tower Hospital, Clinical College of Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Fanyan Meng
- The Comprehensive Cancer Center of Drum Tower Hospital, Medical School of Nanjing University & Clinical Cancer Institute of Nanjing University, Nanjing, China
| | - Baorui Liu
- The Comprehensive Cancer Center of Drum Tower Hospital, Medical School of Nanjing University & Clinical Cancer Institute of Nanjing University, Nanjing, China
| | - Juan Du
- The Comprehensive Cancer Center of Drum Tower Hospital, Medical School of Nanjing University & Clinical Cancer Institute of Nanjing University, Nanjing, China
- The Comprehensive Cancer Center of Drum Tower Hospital, Clinical College of Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
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14
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Vogel A, Haupts A, Kloth M, Roth W, Hartmann N. A novel targeted NGS panel identifies numerous homologous recombination deficiency (HRD)-associated gene mutations in addition to known BRCA mutations. Diagn Pathol 2024; 19:9. [PMID: 38184614 PMCID: PMC10770950 DOI: 10.1186/s13000-023-01431-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 12/15/2023] [Indexed: 01/08/2024] Open
Abstract
Deleterious mutations in the BRCA1 and BRCA2 genes have significant therapeutic relevance in clinical settings regarding personalized therapy approaches. BRCA1 and BRCA2 play a pivotal role in homologous recombination (HR) and thus are sensitive for PARP inhibitors (PARPi). Beyond the narrow scope of evaluating only the BRCA mutation status, PARPi can be beneficial for HR deficient (HRD) patients, who harbor mutations in other HR-associated genes. In the present retrospective study, a novel targeted HRD gene panel was validated and implemented for use with FFPE tissue. Samples of patients with ovarian, breast, pancreatic and prostate cancer were included. Variants were robustly detected with various DNA input amounts and the use of test samples showed complete concordance between previously known mutations and HRD panel results. From all the 90 samples included in this cohort, TP53 was the most frequently altered gene (73%). Deleterious BRCA1/2 mutations were found in 20 (22%) of all samples. New pathogenic or likely pathogenic mutations in additional HR-associated genes were identified in 22 (24%) patients. Taken together, the present study proves the feasibility of a new HRD gene panel with reliable panel performance and offers the possibility to easily screen for resistance mutations acquired over treatment time.Mutations in HR-associated genes, besides BRCA1/2, might represent promising potential targets for synthetic lethality approaches. Thus, a substantial number of patients may benefit from expanding the scope of therapeutic agents like PARPi.
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Affiliation(s)
- Anne Vogel
- Institute of Pathology, University Medical Center Mainz, Langenbeckstraße 1, Mainz, 55131, Germany
| | - Anna Haupts
- Institute of Pathology, University Medical Center Mainz, Langenbeckstraße 1, Mainz, 55131, Germany
| | - Michael Kloth
- Institute of Pathology, University Medical Center Mainz, Langenbeckstraße 1, Mainz, 55131, Germany
| | - Wilfried Roth
- Institute of Pathology, University Medical Center Mainz, Langenbeckstraße 1, Mainz, 55131, Germany
| | - Nils Hartmann
- Institute of Pathology, University Medical Center Mainz, Langenbeckstraße 1, Mainz, 55131, Germany.
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15
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Altwerger G, Ghazarian M, Glazer PM. Harnessing the effects of hypoxia-like inhibition on homology-directed DNA repair. Semin Cancer Biol 2024; 98:11-18. [PMID: 38029867 PMCID: PMC10872265 DOI: 10.1016/j.semcancer.2023.11.007] [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: 07/14/2023] [Revised: 11/08/2023] [Accepted: 11/16/2023] [Indexed: 12/01/2023]
Abstract
Hypoxia is a hallmark feature of the tumor microenvironment which can promote mutagenesis and instability. This increase in mutational burden occurs as a result of the downregulation of DNA repair systems. Deficits in the DNA damage response can be exploited to induce cytotoxicity and treat advanced stage cancers. With the advent of precision medicine, agents such as Poly (ADP-ribose) polymerase (PARP) inhibitors have been used to achieve synthetic lethality in homology directed repair (HDR) deficient cancers. However, most cancers lack these predictive biomarkers. Treatment for the HDR proficient population represents an important unmet clinical need. There has been interest in the use of anti-angiogenic agents to promote tumor hypoxia and induce deficiency in a HDR proficient background. For example, the use of cediranib to inhibit PDGFR and downregulate enzymes of the HDR pathway can be used synergistically with a PARP inhibitor. This combination can improve therapeutic responses in HDR proficient cancers. Preclinical results and Phase II and III clinical trial data support the mechanistic rationale for the efficacy of these agents in combination. Future investigations should explore the effectiveness of cediranib and other anti-angiogenic agents with a PARP inhibitor to elicit an antitumor response and sensitize cancers to immunotherapy.
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Affiliation(s)
- Gary Altwerger
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, New Haven, CT 06511, USA
| | - Maddie Ghazarian
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, New Haven, CT 06511, USA
| | - Peter M Glazer
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06511, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06511, USA.
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16
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Akbıyık I, Ürün Y. Determining magnitude of benefit from poly(ADP-ribose) polymerase inhibitors in prostate cancer. Future Oncol 2023; 19:2585-2591. [PMID: 38073492 DOI: 10.2217/fon-2023-0550] [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: 12/21/2023] Open
Abstract
The treatment landscape for castration-resistant prostate cancer (mCRPC) is undergoing significant advancements, particularly with the emergence of poly(ADP-ribose) polymerase inhibitors and their recent US FDA authorizations. The combination of olaparib with abiraterone and prednisone/prednisolone has gained approval for mCRPC patients harboring confirmed BRCA mutations. Subsequently, talazoparib in combination with enzalutamide was approved for patients with mutations in homologous recombination repair genes. Nevertheless, emerging evidence suggests that these treatments may confer benefits irrespective of specific biomarkers. While the understanding of biomarkers in therapy selection for mCRPC is expanding, further data are warranted to provide comprehensive elucidation for guiding clinical practice.
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Affiliation(s)
- Ilgın Akbıyık
- Department of Medical Oncology, Ankara University School of Medicine, Ankara, Turkey
- Ankara University Cancer Research Institute, Ankara, Turkey
| | - Yüksel Ürün
- Department of Medical Oncology, Ankara University School of Medicine, Ankara, Turkey
- Ankara University Cancer Research Institute, Ankara, Turkey
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17
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Cussenot O, Cancel-Tassin G, Rao SR, Woodcock DJ, Lamb AD, Mills IG, Hamdy FC. Aligning germline and somatic mutations in prostate cancer. Are genetics changing practice? BJU Int 2023; 132:472-484. [PMID: 37410655 DOI: 10.1111/bju.16120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
OBJECTIVE To review the current status of germline and somatic (tumour) genetic testing for prostate cancer (PCa), and its relevance for clinical practice. METHODS A narrative synthesis of various molecular profiles related to their clinical context was carried out. Current guidelines for genetic testing and its feasibility in clinical practice were analysed. We report the main identified genetic sequencing results or functional genomic scores for PCa published in the literature or obtained from the French PROGENE study. RESULTS The molecular alterations observed in PCa are mostly linked to disruption of the androgen receptor (AR) pathway or DNA repair deficiency. The main known germline mutations affect the BReast CAncer gene 2 (BRCA2) and homeobox B13 (HOXB13) genes, whereas AR and tumour protein p53 (TP53) are the genes with most frequent somatic alterations in tumours from men with metastatic PCa. Molecular tests are now available for detecting some of these germline or somatic alterations and sometimes recommended by guidelines, but their utilisation must combine rationality and feasibility. They can guide specific therapies, notably for the management of metastatic disease. Indeed, following androgen deprivation, targeted therapies for PCa currently include poly-(ADP-ribose)-polymerase (PARP) inhibitors, immune checkpoint inhibitors, and prostate-specific membrane antigen (PSMA)-guided radiotherapy. The genetic tests currently approved for targeted therapies remain limited to the detection of BRCA1 and BRCA2 mutation and DNA mismatch repair deficiency, while large panels are recommended for germline analyses, not only for inherited cancer predisposing syndrome, but also for metastatic PCa. CONCLUSIONS Further consensus aligning germline with somatic molecular analysis in metastatic PCa is required, including genomics scars, emergent immunohistochemistry, or functional pre-screen imaging. With rapid advances in knowledge and technology in the field, continuous updating of guidelines to help the clinical management of these individuals, and well-conducted studies to evaluate the benefits of genetic testing are needed.
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Affiliation(s)
- Olivier Cussenot
- Centre de Recherche sur les Pathologies Prostatiques et Urologiques (CeRePP), Paris, France
- GRC 5 Predictive Onco-Urology, Sorbonne University, Paris, France
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Geraldine Cancel-Tassin
- Centre de Recherche sur les Pathologies Prostatiques et Urologiques (CeRePP), Paris, France
- GRC 5 Predictive Onco-Urology, Sorbonne University, Paris, France
| | - Srinivasa R Rao
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Dan J Woodcock
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Alastair D Lamb
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Ian G Mills
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Freddie C Hamdy
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
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18
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Cancel-Tassin G, Koutros S. Use of genomic markers to improve epidemiologic and clinical research in urology. Curr Opin Urol 2023; 33:414-420. [PMID: 37642472 DOI: 10.1097/mou.0000000000001126] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
PURPOSE OF REVIEW Urologic cancers result from the appearance of genomic alterations in the target organ due to the combination of genetic and environmental factors. Knowledge of the genomic markers involved in their etiology and mechanisms for their development continue to progress. This reviewed provides an update on recent genomic studies that have informed epidemiologic and clinical research in urology. RECENT FINDINGS Inherited variations are an established risk factor for urologic cancers with significant estimates of heritability for prostate, kidney, and bladder cancer. The roles of both rare germline variants, identified from family-based studies, and common variants, identified from genome-wide association studies, have provided important information about the genetic architecture for urologic cancers. Large-scale analyses of tumors have generated genomic, epigenomic, transcriptomic, and proteomic data that have also provided novel insights into etiology and mechanisms. These tumors characteristics, along with the associated tumor microenvironment, have attempted to provide more accurate risk stratification, prognosis of disease and therapeutic management. SUMMARY Genomic studies of inherited and acquired variation are changing the landscape of our understanding of the causes of urologic cancers and providing important translational insights for their management. Their use in epidemiologic and clinical studies is thus essential.
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Affiliation(s)
- Géraldine Cancel-Tassin
- Centre for Research on Prostatic Diseases (CeRePP), Paris, France
- GRC 5 Predictive Onco-Urology, Sorbonne University, Paris, France
| | - Stella Koutros
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, USA
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Liu C, Fang J, Kang W, Yang Y, Yu C, Chen H, Zhang Y, Ouyang H. Identification of novel potential homologous repair deficiency-associated genes in pancreatic adenocarcinoma via WGCNA coexpression network analysis and machine learning. Cell Cycle 2023; 22:2392-2408. [PMID: 38124367 PMCID: PMC10802216 DOI: 10.1080/15384101.2023.2293594] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 12/05/2023] [Indexed: 12/23/2023] Open
Abstract
Homologous repair deficiency (HRD) impedes double-strand break repair, which is a common driver of carcinogenesis. Positive HRD status can be used as theranostic markers of response to platinum- and PARP inhibitor-based chemotherapies. Here, we aimed to fully investigate the therapeutic and prognostic potential of HRD in pancreatic adenocarcinoma (PAAD) and identify effective biomarkers related to HRD using comprehensive bioinformatics analysis. The HRD score was defined as the unweighted sum of the LOH, TAI, and LST scores, and it was obtained based on the previous literature. To characterize PAAD immune infiltration subtypes, the "ConsensusClusterPlus" package in R was used to conduct unsupervised clustering. A WGCNA was conducted to elucidate the gene coexpression modules and hub genes in the HRD-related gene module of PAAD. The functional enrichment study was performed using Metascape. LASSO analysis was performed using the "glmnet" package in R, while the random forest algorithm was realized using the "randomForest" package in R. The prognostic variables were evaluated using univariate Cox analysis. The prognostic risk model was built using the LASSO approach. ROC curve and KM survival analyses were performed to assess the prognostic potential of the risk model. The half-maximal inhibitory concentration (IC50) of the PARP inhibitors was estimated using the "pRRophetic" package in R and the Genomics of Drug Sensitivity in Cancer database. The "rms" package in R was used to create the nomogram. A high HRD score indicated a poor prognosis and an advanced clinical process in PAAD patients. PAAD tumors with high HRD levels revealed significant T helper lymphocyte depletion, upregulated levels of cancer stem cells, and increased sensitivity to rucaparib, Olaparib, and veliparib. Using WGCNA, 11 coexpression modules were obtained. The red module and 122 hub genes were identified as the most correlated with HRD in PAAD. Functional enrichment analysis revealed that the 122 hub genes were mainly concentrated in cell cycle pathways. One novel HRD-related gene signature consisting of CKS1B, HJURP, and TPX2 were screened via LASSO analysis and a random forest algorithm, and they were validated using independent validation sets. No direct association between HRD and CKS1B, HJURP, or TPX2 has not been reported in the literature so far. Thus, these findings indicated that CKS1B, HJURP, and TPX2 have potential as diagnostic and prognostic biomarkers for PAAD. We constructed a novel HRD-related prognostic model that provides new insights into PAAD prognosis and immunotherapy. Based on bioinformatics analysis, we comprehensively explored the therapeutic and prognostic potential of HRD in PAAD. One novel HRD-related gene signature consisting of CKS1B, HJURP, and TPX2 were identified through the combination of WGCNA, LASSO analysis and a random forest algorithm. A novel HRD-related risk model that can predict clinical prognosis and immunotherapeutic response in PAAD patients was constructed.
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Affiliation(s)
- Chun Liu
- Department of General surgery, The People’s Hospital of Chizhou, Chizhou, Anhui Province, China
| | - Jingyun Fang
- Department of Nursing, The People’s Hospital of Chizhou, Chizhou, Anhui Province, China
| | - Weibiao Kang
- Department of General surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui Province, China
| | - Yang Yang
- Department of General surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui Province, China
| | - Changjun Yu
- Department of General surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui Province, China
| | - Hao Chen
- Department of Emergency Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui Province, China
| | - Yongwei Zhang
- Department of general surgery, Anqing First People’s Hospital, Anqing, Anhui Province, China
| | - Huan Ouyang
- Department of General surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui Province, China
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Dai Z, Peng X, Cui X, Guo Y, Zhang J, Shen X, Liu CY, Liu Y. Innovative molecular subtypes of multiple signaling pathways in colon cancer and validation of FMOD as a prognostic-related marker. J Cancer Res Clin Oncol 2023; 149:13087-13106. [PMID: 37474678 DOI: 10.1007/s00432-023-05163-6] [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: 06/06/2023] [Accepted: 07/09/2023] [Indexed: 07/22/2023]
Abstract
PURPOSE Colon cancer is highly heterogeneous in terms of the immune and stromal microenvironment, genomic integrity, and oncogenic properties; therefore, molecular subtypes of the four characteristic dimensions are expected to provide novel clues for immunotherapy of colon cancer. METHODS According to the enrichment of four dimensions, we performed consensus cluster analysis and identified three robust molecular subtypes for colon cancer, namely immune enriched, immune deficiency, and stroma enriched. We characterized and validated the immune infiltration, gene mutations, copy number variants, methylation, protein expression, and clinical features in different datasets. Finally, we developed an 8-gene risk prognostic model and proposed the innovative RiskScore. In addition, a nomogram model was constructed combining clinical characteristics and RiskScore to validate its excellent clinical predictive power. RESULTS Combining clinical patient tissue samples and histochemical microarray data, we found that high FMOD expression in tumor epithelial cells was associated with poorer patient prognosis, but FMOD expression in the mesenchyme was not associated with prognosis. In pan-cancer, RiskScore, a prognostic model constructed based on characteristic pathway scores, was a poor prognostic factor for malignancy and was negatively associated with immunotherapy response. CONCLUSION The identification of molecular subtypes could provide innovative ideas for immunotherapy of colon cancer.
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Affiliation(s)
- Zhujiang Dai
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200092, China
- Shanghai Colorectal Cancer Research Center, Shanghai, 200092, China
| | - Xiang Peng
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200092, China
- Shanghai Colorectal Cancer Research Center, Shanghai, 200092, China
| | - Xuewei Cui
- Department of Anesthesiology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
| | - Yuegui Guo
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200092, China
- Shanghai Colorectal Cancer Research Center, Shanghai, 200092, China
| | - Jie Zhang
- Department of Gastroenterology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200092, China
| | - Xia Shen
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200092, China
- Shanghai Colorectal Cancer Research Center, Shanghai, 200092, China
| | - Chen-Ying Liu
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200092, China.
- Shanghai Colorectal Cancer Research Center, Shanghai, 200092, China.
| | - Yun Liu
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200092, China.
- Shanghai Colorectal Cancer Research Center, Shanghai, 200092, China.
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21
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Elias R, Antonarakis ES. Rucaparib for metastatic castration-resistant prostate cancer: did TRITON3 deliver a trifecta? Transl Cancer Res 2023; 12:2448-2453. [PMID: 37969378 PMCID: PMC10643943 DOI: 10.21037/tcr-23-1279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 09/19/2023] [Indexed: 11/17/2023]
Affiliation(s)
- Roy Elias
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
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Feng J, Lan Y, Liu F, Yuan Y, Ge J, Wei S, Luo H, Li J, Luo T, Bian X. Combination of genomic instability score and TP53 status for prognosis prediction in lung adenocarcinoma. NPJ Precis Oncol 2023; 7:110. [PMID: 37907595 PMCID: PMC10618567 DOI: 10.1038/s41698-023-00465-x] [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: 01/18/2023] [Accepted: 10/13/2023] [Indexed: 11/02/2023] Open
Abstract
The genomic instability (GI) /homologous recombination deficiency (HRD) score, calculated as the sum of the events of loss of heterozygosity (LOH), large-scale state transition (LST) and telomere allele imbalance (TAI), is used to guide the choice of treatment in several cancers, but its relationship with genomic features, clinicopathological characteristics and prognosis in lung cancer is poorly understood, which could lead to population bias in prospective studies. We retrospectively analyzed 1011 lung cancer patients whose tumor samples were successfully profiled by high-throughput sequencing panel including GI/HRD score. Alterations of many cancer suppressor genes were associated with higher GI/HRD scores, biallelic inactivation of TP53 was correlated with a high GI/HRD score. A combination of two gene alterations exhibited a higher GI/HRD scores than single gene alterations. The GI/HRD score was associated with advanced stages in lung adenocarcinoma but not in lung squamous cell carcinoma. Furthermore, patients with higher GI/HRD scores had significantly shorter overall survival and progression-free survival than patients with lower GI/HRD scores. Finally, patients with a combination of a higher GI/HRD scores and TP53 alteration exhibited an extremely poor prognosis compared with patients with a lower GI/HRD scores and wild-type TP53 (overall survival, training cohort, hazard ratio (HR) = 8.56, P < 0.001; validation cohort, HR = 6.47, P < 0.001; progression-free survival, HR = 4.76, P < 0.001). Our study revealed the prognostic value of the GI/HRD score in lung adenocarcinoma, but not for all lung cancer. Moreover, the combination of the GI/HRD score and TP53 status could be a promising strategy to predict the prognosis of patients with lung adenocarcinoma.
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Affiliation(s)
- Juan Feng
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University) and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, 400038, Chongqing, China
| | - Yang Lan
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University) and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, 400038, Chongqing, China
| | - Feng Liu
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University) and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, 400038, Chongqing, China
| | - Ye Yuan
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University) and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, 400038, Chongqing, China
| | - Jia Ge
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University) and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, 400038, Chongqing, China
| | - Sen Wei
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University) and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, 400038, Chongqing, China
| | - Hu Luo
- Department of Respiratory and Critical Care Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 400038, Chongqing, China
| | - Jianjun Li
- Department of Oncology, Southwest Hospital, Third Military Medical University (Army Medical University), 400038, Chongqing, China
| | - Tao Luo
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University) and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, 400038, Chongqing, China.
| | - Xiuwu Bian
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University) and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, 400038, Chongqing, China.
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Tsantikidi A, Papadopoulou E, Metaxa-Mariatou V, Kapetsis G, Tsaousis G, Meintani A, Florou-Chatzigiannidou C, Gazouli M, Papadimitriou C, Timotheadou E, Kotsakis A, Boutis A, Boukovinas I, Kampletsas E, Kontovinis L, Fountzilas E, Andreadis C, Karanikiotis C, Filippou D, Theodoropoulos G, Özdoğan M, Nasioulas G. The Utility of NGS Analysis in Homologous Recombination Deficiency Tracking. Diagnostics (Basel) 2023; 13:2962. [PMID: 37761329 PMCID: PMC10529941 DOI: 10.3390/diagnostics13182962] [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: 08/11/2023] [Revised: 09/05/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Several tumor types have been efficiently treated with PARP inhibitors (PARPis), which are now approved for the treatment of ovarian, breast, prostate, and pancreatic cancers. The BRCA1/2 genes and mutations in many additional genes involved in the HR pathway may be responsible for the HRD phenomenon. The aim of the present study was to investigate the association between genomic loss of heterozygosity (gLOH) and alterations in 513 genes with targeted and immuno-oncology therapies in 406 samples using an NGS assay. In addition, the %gLOHs of 24 samples were calculated using the Affymetrix technology in order to compare the results obtained via the two methodologies. HR variations occurred in 20.93% of the malignancies, while BRCA1/2 gene alterations occurred in 5.17% of the malignancies. The %LOH was highly correlated with alterations in the BRCA1/2 genes, since 76.19% (16/21) of the BRCA1/2 positive tumors had a high %LOH value (p = 0.007). Moreover, the LOH status was highly correlated with the TP53 and KRAS statuses, but there was no association with the TMB value. Lin's concordance correlation coefficient for the 24 samples simultaneously examined via both assays was 0.87, indicating a nearly perfect agreement. In conclusion, the addition of gLOH analysis could assist in the detection of additional patients eligible for treatment with PARPis.
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Affiliation(s)
- Aikaterini Tsantikidi
- Genekor Medical S.A., 15344 Athens, Greece; (V.M.-M.); (G.K.); (G.T.); (A.M.); (C.F.-C.)
| | - Eirini Papadopoulou
- Genekor Medical S.A., 15344 Athens, Greece; (V.M.-M.); (G.K.); (G.T.); (A.M.); (C.F.-C.)
| | | | - George Kapetsis
- Genekor Medical S.A., 15344 Athens, Greece; (V.M.-M.); (G.K.); (G.T.); (A.M.); (C.F.-C.)
| | - Georgios Tsaousis
- Genekor Medical S.A., 15344 Athens, Greece; (V.M.-M.); (G.K.); (G.T.); (A.M.); (C.F.-C.)
| | - Angeliki Meintani
- Genekor Medical S.A., 15344 Athens, Greece; (V.M.-M.); (G.K.); (G.T.); (A.M.); (C.F.-C.)
| | | | - Maria Gazouli
- Department of Basic Medical Sciences, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece;
| | - Christos Papadimitriou
- Second Department of Surgery, Aretaieion Hospital, Medical School, National and Kapodistrian University of Athens, 11528 Athens, Greece;
| | - Eleni Timotheadou
- Department of Medical Oncology, Papageorgiou Hospital, School of Medicine, Aristotle University of Thessaloniki, 56429 Thessaloniki, Greece;
| | - Athanasios Kotsakis
- Oncology Department, University General Hospital of Larissa, 41334 Larissa, Greece;
| | - Anastasios Boutis
- First Department of Clinical Oncology, Theagenio Hospital, 54639 Thessaloniki, Greece;
| | - Ioannis Boukovinas
- Oncology Department, Bioclinic of Thessaloniki, 54622 Thessaloniki, Greece;
| | - Eleftherios Kampletsas
- Department of Medical, Oncology, University Hospital of Ioannina, 45500 Ioannina, Greece
| | - Loukas Kontovinis
- Oncology Department, “Euromedica” General Clinic, 54645 Thessaloniki, Greece;
| | - Elena Fountzilas
- Second Department of Medical Oncology, Euromedica General Clinic, 54645 Thessaloniki, Greece; (E.F.); (G.N.)
| | - Charalampos Andreadis
- Second Department of Clinical Oncology, Theagenio Hospital, 54639 Thessaloniki, Greece;
| | | | - Dimitrios Filippou
- Department of Anatomy, Faculty of Health Sciences, Medical School, National and Kapodistrian University of Athens, 15772 Athens, Greece;
| | - Georgios Theodoropoulos
- Department of Surgery, National and Kapodistrian University of Athens, Hippocration General Hospital, 15772 Athens, Greece;
| | - Mustafa Özdoğan
- Division of Medical Oncology, Memorial Hospital, Antalya 07025, Turkey;
| | - George Nasioulas
- Second Department of Medical Oncology, Euromedica General Clinic, 54645 Thessaloniki, Greece; (E.F.); (G.N.)
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Brown LC, Zhu J, Mauer E, Thiede SN, Macera L, Stein MM, Taxter T, Raghavan D, Burgess EF. RNA-Based Homologous Recombination Deficiency Signature Detects Homologous Recombination Deficiency-RNA+ Patients With and Without Homologous Recombination Repair Gene Pathogenic Alterations in Men With Prostate Cancer. JCO Precis Oncol 2023; 7:e2300378. [PMID: 38061006 DOI: 10.1200/po.23.00378] [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: 07/18/2023] [Revised: 08/29/2023] [Accepted: 09/20/2023] [Indexed: 12/18/2023] Open
Abstract
PURPOSE Homologous recombination deficiency (HRD) is a well-described phenotype of some prostate cancers; however, current biomarkers for HRD are imperfect and rely on detection of single gene alterations in the homologous recombination repair (HRR) pathway, which may not capture the complexity of HRD biology. RNA signature-based methods of HRD identification present a potentially dynamic assessment of the HRD phenotype; however, its relationship with HRR gene alterations is not well characterized in prostate cancer. METHODS A HRD assay on the basis of an RNA signature associated with biallelic BRCA1/2 loss was applied to a retrospective cohort study of 985 men with prostate cancer analyzed on the Tempus xT platform. HRD status was defined by a binary threshold on a continuous scale. RESULTS In this cohort, of the 126 (13%) patients found to be HRD+ by RNA signature (HRD-RNA+), 100 (79%) had no coexisting HRR gene alteration. Among samples with biallelic BRCA1/2 loss, 78% (7/9) were classified as HRD-RNA+, while 8% (2/25) of samples with BRCA1/2 monoallelic loss were HRD-RNA+. Biallelic and monoallelic ATM loss exhibited HRD-RNA+ at a lower prevalence: 6.7% (1/15) and 7.1% (1/14), respectively, compared with HRD-RNA+ prevalence among samples without any HRR gene loss (13%; 100/782). HRD-RNA+ was associated with a significantly higher prevalence of TP53 and AR gene alterations relative to HRD-RNA- after correction for multiple comparisons, 59% versus 39% (q = 0.003) and 23% versus 12% (q = 0.024), respectively. CONCLUSION Use of an RNA-based HRD signature significantly expands the fraction of patients with prostate cancer who may derive benefit from poly (ADP-ribose) polymerase inhibitors (PARPis) compared with using HRR gene mutations alone. Further studies are needed to evaluate functional HRD significance and inform future usage as a predictive biomarker for PARPi selection.
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Affiliation(s)
| | - Jason Zhu
- Levine Cancer Institute, Atrium Health, Charlotte, NC
| | | | | | | | | | | | - Derek Raghavan
- Levine Cancer Institute, Atrium Health, Charlotte, NC
- Veterans Administration Health Care Center, Charlotte, NC
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Fröhlich LM, Niessner H, Sauer B, Kämereit S, Chatziioannou E, Riel S, Sinnberg T, Schittek B. PARP Inhibitors Effectively Reduce MAPK Inhibitor Resistant Melanoma Cell Growth and Synergize with MAPK Inhibitors through a Synthetic Lethal Interaction In Vitro and In Vivo. CANCER RESEARCH COMMUNICATIONS 2023; 3:1743-1755. [PMID: 37674529 PMCID: PMC10478790 DOI: 10.1158/2767-9764.crc-23-0101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/03/2023] [Accepted: 07/27/2023] [Indexed: 09/08/2023]
Abstract
The efficacy of targeting the MAPK signaling pathway in patients with melanoma is limited by the rapid development of resistance mechanisms that result in disease relapse. In this article, we focus on targeting the DNA repair pathway as an antimelanoma therapy, especially in MAPK inhibitor resistant melanoma cells using PARP inhibitors. We found that MAPK inhibitor resistant melanoma cells are particularly sensitive to PARP inhibitor treatment due to a lower basal expression of the DNA damage sensor ataxia-telangiectasia mutated (ATM). As a consequence, MAPK inhibitor resistant melanoma cells have decreased homologous recombination repair activity leading to a reduced repair of double-strand breaks caused by the PARP inhibitors. We validated the clinical relevance of our findings by ATM expression analysis in biopsies from patients with melanoma before and after development of resistance to MAPK inhibitors. Furthermore, we show that inhibition of the MAPK pathway induces a homologous recombination repair deficient phenotype in melanoma cells irrespective of their MAPK inhibitor sensitivity status. MAPK inhibition results in a synthetic lethal interaction of a combinatorial treatment with PARP inhibitors, which significantly reduces melanoma cell growth in vitro and in vivo. In conclusion, this study shows that PARP inhibitor treatment is a valuable therapy option for patients with melanoma, either as a single treatment or as a combination with MAPK inhibitors depending on ATM expression. Significance We show that MAPK inhibitor resistant melanoma cells exhibit low ATM expression increasing their sensitivity toward PARP inhibitors and that a combination of MAPK/PARP inhibitors act synthetically lethal in melanoma cells. Our study shows that PARP inhibitor treatment is a valuable therapy option for patients with melanoma, either as a single treatment or as a combination with MAPK inhibitors depending on ATM expression, which could serve as a novel biomarker for treatment response.
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Affiliation(s)
- Lisa Marie Fröhlich
- Division of Dermatooncology, Department of Dermatology, University of Tübingen, Tübingen, Germany
| | - Heike Niessner
- Division of Dermatooncology, Department of Dermatology, University of Tübingen, Tübingen, Germany
| | - Birgit Sauer
- Division of Dermatooncology, Department of Dermatology, University of Tübingen, Tübingen, Germany
| | - Sofie Kämereit
- Division of Dermatooncology, Department of Dermatology, University of Tübingen, Tübingen, Germany
| | - Eftychia Chatziioannou
- Division of Dermatooncology, Department of Dermatology, University of Tübingen, Tübingen, Germany
| | - Simon Riel
- Department of Dermatology, University of Tübingen, Tübingen, Germany
| | - Tobias Sinnberg
- Division of Dermatooncology, Department of Dermatology, University of Tübingen, Tübingen, Germany
- Department of Dermatology, Venereology and Allergology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Birgit Schittek
- Division of Dermatooncology, Department of Dermatology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) “Image-Guided and Functionally Instructed Tumor Therapies,” University of Tübingen, Tübingen, Germany
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Moore JA, Chen KT, Madison R, Newberg JY, Fleischmann Z, Wang S, Sharaf R, Murugesan K, Fendler BJ, Hughes J, Schrock AB, Hegde PS, Oxnard GR, Fabrizio D, Frampton GM, Antonarakis ES, Sokol ES, Jin DX. Pan-Cancer Analysis of Copy-Number Features Identifies Recurrent Signatures and a Homologous Recombination Deficiency Biomarker to Predict Poly (ADP-Ribose) Polymerase Inhibitor Response. JCO Precis Oncol 2023; 7:e2300093. [PMID: 37769224 DOI: 10.1200/po.23.00093] [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: 02/24/2023] [Revised: 06/21/2023] [Accepted: 07/21/2023] [Indexed: 09/30/2023] Open
Abstract
PURPOSE Copy-number (CN) features reveal the molecular state of cancers and may have predictive and prognostic value in the treatment of cancer. We sought to apply published CN analysis methods to a large pan-cancer data set and characterize ubiquitous CN signatures across tumor types, including potential utility for treatment selection. METHODS We analyzed the landscape of CN features in 260,333 pan-cancer samples. We examined the association of 10 signatures with genomic alterations and clinical characteristics and trained a machine learning classifier using CN and insertion and deletion features to detect homologous recombination deficiency signature (HRDsig) positivity. Clinical outcomes were assessed using a real-world clinicogenomic database (CGDB) of comprehensive genomic profiling linked to deidentified, electronic health record-derived clinical data. RESULTS CN signatures were prevalent across cancer types and associated with diverse processes including focal tandem duplications, seismic amplifications, genome-wide loss of heterozygosity (gLOH), and HRD. Our novel HRDsig outperformed gLOH in predicting BRCAness and effectively distinguished biallelic BRCA and homologous recombination-repair wild-type (HRRwt) samples pan-tumor, demonstrating high sensitivity to detect biallelic BRCA in ovarian (93%) and other HRD-associated cancers (80%-87%). Pan-tumor prevalence of HRDsig was 6.4%. HRRwt cases represented a significant fraction of the HRDsig-positive cohort, likely reflecting a population with nongenomic mechanisms of HRD. In ovarian and prostate CGDBs, HRDsig identified more patients than gLOH and had predictive value for poly (ADP-ribose) polymerase inhibitor (PARPi) benefit. CONCLUSION Tumor CN profiles are informative, revealing diverse processes active in cancer. We describe the landscape of 10 CN signatures in a large pan-cancer cohort, including two associated with HRD. We trained a machine learning-based HRDsig that robustly identified BRCAness and associated with biallelic BRCA pan-tumor, and was predictive of PARPi benefit in real-world ovarian and prostate data sets.
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Wang Y, Zhang X, Chen G, Xing Q, Zhu B, Wang X. Integrated analyses reveal the prognostic, immunological features and mechanisms of cuproptosis critical mediator gene FDX1 in KIRC. Genes Immun 2023; 24:171-182. [PMID: 37430022 DOI: 10.1038/s41435-023-00211-0] [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: 01/23/2023] [Revised: 06/25/2023] [Accepted: 06/29/2023] [Indexed: 07/12/2023]
Abstract
The ferredoxin 1 (FDX1) gene had been recently reported as a critical mediator of cuproptosis, and without doubt, its roles in KIRC would be of importance. Hence, this paper was to explore the roles of FDX1 in kidney renal clear cell carcinoma (KIRC) and its potential molecular mechanisms via scRNA-sequencing and bulk RNA-sequencing analyses. FDX1 was lowly expressed in KIRC and validated both at the protein and mRNA levels (all p < 0.05). Moreover, its elevated expression was linked with a better overall survival (OS) prognosis in KIRC (p < 0.01). The independent impact of FDX1 on KIRC prognosis was demonstrated by univariate/multivariate regression analysis (p < 0.01). Gene set enrichment analysis (GSEA) identified seven pathways strongly associated with FDX1 in KIRC. Furthermore, FDX1 was also revealed to be significantly related with immunity (p < 0.05). In addition, patients with low expression of FDX1 might be more sensitive to immunotherapies. ScRNA-seq analysis found that FDX1 could be expressed in immune cells and was mainly differently expressed in Mono/Macro cells. Ultimately, we also identified several LncRNA/RBP/FDX1 mRNA networks to reveal its underlying mechanisms in KIRC. Taken together, FDX1 was closely related to prognosis and immunity in KIRC, and its RBP-involved mechanisms of LncRNA/RBP/FDX1 networks were also revealed by us.
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Affiliation(s)
- Yi Wang
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
- Department of Urology, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu Province, China
| | - Xinyu Zhang
- Department of Urology, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu Province, China
| | - Guihua Chen
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Qianwei Xing
- Department of Urology, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu Province, China
| | - Bingye Zhu
- Department of Urology, Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), Nantong, 226001, Jiangsu Province, China.
| | - Xiang Wang
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China.
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Li L, Gu Y, Zhang M, Shi X, Li Z, Xu X, Sun T, Dong Y, Xue C, Zhu X, Lv R, Jiao K, Ji X, Wang LJ, Zhang Y, Liang Z, Jin Y, Yin R, Wu M, Liang H. HRD effects on first-line adjuvant chemotherapy and PARPi maintenance therapy in Chinese ovarian cancer patients. NPJ Precis Oncol 2023; 7:51. [PMID: 37258600 DOI: 10.1038/s41698-023-00402-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 05/15/2023] [Indexed: 06/02/2023] Open
Abstract
Homologous recombination deficiency (HRD) testing has been approved by FDA for selecting epithelial ovarian cancer (EOC) patients who may benefit from the first-line poly (ADP-ribose) polymerase inhibitor (PARPi) maintenance therapy. However, the effects of HRD on the clinical outcomes of first-line chemotherapy and first-line PARPi maintenance therapy have not been rigorously evaluated in Chinese EOC patients. Here, we developed an HRD assay and applied it to two large retrospectively collected Chinese EOC patient cohorts. In the first-line adjuvant chemotherapy cohort (FACT, N = 380), HRD status significantly improved PFS (median, 15.6 months vs. 9.4 months; HR, 0.688; 95% CI, 0.526-0.899; P = 0.003) and OS (median, 89.5 months vs. 60.9 months; HR, 0.636; 95% CI, 0.423-0.955; P = 0.008). In the first-line PARPi maintenance therapy cohort (FPMT, N = 83), HRD status significantly improved PFS (median, NA vs. 12 months; HR, 0.438; 95% CI, 0.201-0.957; P = 0.033) and OS (median, NA vs. NA months; HR, 0.12; 95% CI, 0.029-0.505; P = 0.001). Our results demonstrate that HRD status is a significant predictor for PFS and OS in both first-line chemotherapy and first-line PARPi maintenance therapy, providing strong real-world evidence for conducting genetic testing and improving clinical recommendations for Chinese EOC patients.
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Affiliation(s)
- Lei Li
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- National Clinical Research Center for Obstetric & Gynecologic Diseases, Beijing, China
| | - Yu Gu
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- National Clinical Research Center for Obstetric & Gynecologic Diseases, Beijing, China
| | - Mengpei Zhang
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Xiaohua Shi
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Zhe Li
- Precision Scientific (Beijing) Co., Ltd., Beijing, China
| | - Xinyun Xu
- Precision Scientific (Beijing) Co., Ltd., Beijing, China
| | - Tianqi Sun
- Precision Scientific (Beijing) Co., Ltd., Beijing, China
| | - Yu Dong
- Precision Scientific (Beijing) Co., Ltd., Beijing, China
| | - Chao Xue
- Precision Scientific (Beijing) Co., Ltd., Beijing, China
| | - Xiaoru Zhu
- Precision Scientific (Beijing) Co., Ltd., Beijing, China
| | - Ran Lv
- Precision Scientific (Beijing) Co., Ltd., Beijing, China
| | - Kai Jiao
- Precision Scientific (Beijing) Co., Ltd., Beijing, China
| | - Xuwo Ji
- Precision Scientific (Beijing) Co., Ltd., Beijing, China
| | - Li-Juan Wang
- Department of Gynecological Oncology, Sun Yat-Sen Memorial Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Yang Zhang
- Precision Scientific (Beijing) Co., Ltd., Beijing, China
| | - Zhiyong Liang
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
| | - Ying Jin
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
- National Clinical Research Center for Obstetric & Gynecologic Diseases, Beijing, China.
| | - Rutie Yin
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China.
| | - Ming Wu
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
- National Clinical Research Center for Obstetric & Gynecologic Diseases, Beijing, China.
| | - Han Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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29
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Krumm N, Khasnavis NS, Radke M, Banda K, Davies HR, Pennil C, McLean K, Paulson VA, Konnick EQ, Johnson WC, Huff G, Nik-Zainal S, Swisher EM, Lockwood CM, Salipante SJ. Diagnosis of Ovarian Carcinoma Homologous Recombination DNA Repair Deficiency From Targeted Gene Capture Oncology Assays. JCO Precis Oncol 2023; 7:e2200720. [PMID: 37196218 PMCID: PMC10309534 DOI: 10.1200/po.22.00720] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/08/2023] [Accepted: 03/17/2023] [Indexed: 05/19/2023] Open
Abstract
PURPOSE Homologous recombination DNA repair deficiency (HRD) is a therapeutic biomarker for sensitivity to platinum and poly(ADP-ribose) polymerase inhibitor therapies in breast and ovarian cancers. Several molecular phenotypes and diagnostic strategies have been developed to assess HRD; however, their clinical implementation remains both technically challenging and methodologically unstandardized. METHODS We developed and validated an efficient and cost-effective strategy for HRD determination on the basis of calculation of a genome-wide loss of heterozygosity (LOH) score through targeted, hybridization capture and next-generation DNA sequencing augmented with 3,000 common, polymorphic single-nucleotide polymorphism (SNP) sites distributed genome-wide. This approach requires minimal sequence reads and can be readily integrated into targeted gene capture workflows already in use for molecular oncology. We interrogated 99 ovarian neoplasm-normal pairs using this method and compared results with patient mutational genotypes and orthologous predictors of HRD derived from whole-genome mutational signatures. RESULTS LOH scores of ≥11% had >86% sensitivity for identifying tumors with HRD-causing mutations in an independent validation set (90.6% sensitivity for all specimens). We found strong agreement of our analytic approach with genome-wide mutational signature assays for determining HRD, yielding an estimated 96.7% sensitivity and 50% specificity. We observed poor concordance with mutational signatures inferred using only mutations detected by the targeted gene capture panel, suggesting inadequacy of the latter approach. LOH score did not significantly correlate with treatment outcomes. CONCLUSION Targeted sequencing of genome-wide polymorphic SNP sites can be used to infer LOH events and subsequently diagnose HRD in ovarian tumors. The methods presented here are readily generalizable to other targeted gene oncology assays and could be adapted for HRD diagnosis in other tumor types.
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Affiliation(s)
- Niklas Krumm
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA
| | - Nithisha S. Khasnavis
- Department of Obstetrics & Gynecology, University of Washington School of Medicine, Seattle, WA
| | - Marc Radke
- Department of Obstetrics & Gynecology, University of Washington School of Medicine, Seattle, WA
| | - Kalyan Banda
- Department of Medicine, Oncology Division, University of Washington School of Medicine, Seattle, WA
| | - Helen R. Davies
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom
- Early Cancer Institute, University of Cambridge, Cambridge, United Kingdom
| | - Christopher Pennil
- Department of Obstetrics & Gynecology, University of Washington School of Medicine, Seattle, WA
| | - Kathryn McLean
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA
| | - Vera A. Paulson
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA
| | - Eric Q. Konnick
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA
| | - Winslow C. Johnson
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA
| | - Grogan Huff
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA
| | - Serena Nik-Zainal
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Elizabeth M. Swisher
- Department of Obstetrics & Gynecology, University of Washington School of Medicine, Seattle, WA
| | - Christina M. Lockwood
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA
| | - Stephen J. Salipante
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA
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30
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Patel L, Pritchard CC. Molecular testing of DNA damage response pathways in prostate cancer patients. Curr Opin Oncol 2023; 35:224-230. [PMID: 36966502 DOI: 10.1097/cco.0000000000000934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2023]
Abstract
PURPOSE OF REVIEW Personalizing prostate cancer therapy requires germline and tumor molecular tests that predict who will respond to specific treatments and who may not. The review covers molecular testing of DNA damage response pathways, the first biomarker-driven precision target with clinical utility for treatment selection in patients with castration resistant prostate cancer (CRPC). RECENT FINDINGS Recurrent somatic and germline variants cause deficiency of the mismatch repair (MMR) or homologous recombination (HR) pathways in about a quarter of CRPC patients. In prospective clinical trials, patients with deleterious variants in the MMR pathway more frequently experience a therapeutic response to immune checkpoint inhibitors (ICI). Similarly, somatic and germline events affecting HR predict response to poly(ADP) ribose polymerase inhibitor (PARPi) therapy. Molecular testing of these pathways currently involves assaying for loss of function variants in individual genes and for the genome-wide consequences of repair deficiency. SUMMARY DNA damage response pathways are the first major area of molecular genetic testing in CRPC settings and offer insights into this new paradigm. Our hope is that eventually an arsenal of molecularly-guided therapies will be developed across many pathways to enable precision medicine options for most men with prostate cancer.
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Affiliation(s)
- Lalit Patel
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Colin C Pritchard
- Department of Laboratory Medicine and Pathology, University of Washington
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
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31
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Chen H, Liu Y, Yin Z, Chen H, Wang Y, Qian Y. Homologous repair deficiency-associated genes in invasive breast cancer revealed by WGCNA co-expression network analysis and genetic perturbation similarity analysis. Cell Cycle 2023; 22:1077-1100. [PMID: 36757135 PMCID: PMC10081085 DOI: 10.1080/15384101.2023.2174339] [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: 10/25/2022] [Revised: 11/28/2022] [Accepted: 12/06/2022] [Indexed: 02/10/2023] Open
Abstract
BACKGROUND Homologous repair deficiency (HRD) causes double-strand break repair to be impeded, which is a common driver of carcinogenesis. However, the therapeutic and prognostic potential of HRD in invasive breast cancer (BRCA) has not been fully explored using comprehensive bioinformatics analysis. MATERIALS AND METHODS HRD score was defined as the unweighted sum of LOH, TAI, and LST scores and obtained from the previous study according to Theo A et al. To characterize BRCA tumor microenvironment (TME) subtypes, "ConsensusClusterPlus" R package was used to conduct unsupervised clustering. The xCell algorithm was utilized for tumor composition analysis to estimate the TME in TCGA-BRCA. A WGCNA analysis was conducted to uncover the gene coexpression modules and hub genes in the HRD-related gene module of BRCA. The functional enrichment study was carried out using Metascape. A novel analysis pipeline, Genetic Perturbation Similarity Analysis (GPSA), was used to explore the single-gene perturbation closely related to HRD based on 3048 stable knockdown/knockout cell lines. The prognostic variables were evaluated using univariate COX analysis. Kaplan-Meier (KM) survival analysis was performed to assess the prognostic potential of HRD score. Receiver operator characteristic (ROC) curve was utilized to judge the diagnostic utility. Drug sensitivity was estimated through the R package "oncoPredict" and Genomics of Drug Sensitivity in Cancer (GDSC) database. XSum algorithm was performed to screen the candidate small molecule drugs based on the connectivity map (CMAP) database. RESULTS Low HRD score suggested a better prognosis in BRCA patients. The tumor with low HRD score had considerably greater degree of infiltration of stromal cells and infiltration of immunocytes was significantly enhanced in the high HRD score group. Using WGCNA, ten co-expression modules were obtained. The turquoise module and 25 hub genes were identified as the most correlated with HRD in BRCA. Functional enrichment analysis revealed that the turquoise gene module was mainly concentrated in the "cell cycle" pathways. Candidate HRD-related gene signatures (MELK) were screened out through WGCNA and GPSA analysis pipeline and then validated on independent validation sets. A small molecule drug (Clofibrate) that has the potential to reverse the increase of high HRD score was screened out to improve oncological outcomes in BRCA. Molecular docking suggested MELK to be one of possible molecular targets in the Clofibrate treatment of BRCA. CONCLUSION Based on bioinformatic analysis, we fully explored the therapeutic and prognostic potential of HRD in BRCA. A novel HRD-related gene signature (MELK) were identified through the combination of WGCNA and GPSA analysis. In addition, we detailed the TME landscape in BRCA and identified four unique TME subtypes in group with high or low HRD score group. Moreover, Clofibrate were screened out to improve oncological outcomes in BRCA by reversing the increase of high HRD score. Thus, our study contributes to the development of personalized clinical management and treatment regimens of BRCA.
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Affiliation(s)
- Haohao Chen
- Department of General surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Department of General surgery, The Third Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yanyan Liu
- Department of General surgery, The Third Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Zhenglang Yin
- Department of General surgery, The Third Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Hao Chen
- Department of Emergency Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yao Wang
- Department of Digestive Endoscopy, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
| | - Yeben Qian
- Department of General surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
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32
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Wei B, Zheng J, Jiang C, Zhang H, Zhang M, Cheng T, Li J, Wang Z, Deng L, Wang L, Xia Q, Ma J. Improved detection of homologous recombination deficiency in Chinese patients with ovarian cancer: a novel non-exonic single-nucleotide polymorphism-based next-generation sequencing panel. Mol Oncol 2023. [PMID: 36852736 PMCID: PMC10399708 DOI: 10.1002/1878-0261.13411] [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: 09/07/2022] [Revised: 01/18/2023] [Accepted: 02/14/2023] [Indexed: 03/01/2023] Open
Abstract
As homologous recombination deficiency (HRD) is a biomarker to predict the efficiency of PARP inhibitor treatment, this study developed a non-exonic single-nucleotide polymorphism (SNP)-based targeted next-generation sequencing panel and comprehensively examined it both on standard and clinical ovarian cancer tissues. The HRD scores calculated by the panel and whole-genome sequencing were consistent, with the analysis by sequenza being the most reliable. The results on clinical samples revealed that the panel performed better in HRD analysis compared with the SNP microarray. There are several distinctions between this newly developed kit and reported HRD detection panels. First, the panel covers only 52 592 SNPs, which makes it capable of detecting genomic instability. Secondly, all the SNPs are non-exonic; as a result, the panel can be used cooperatively with any exon panel. Thirdly, all the SNPs selected have a high minor allele frequency in Chinese people, making it a better choice for HRD detection in Chinese patients. In summary, this panel shows promise as a clinical application to guide PARP inhibitors or platinum drugs used in the treatment of ovarian and other cancers.
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Affiliation(s)
- Bing Wei
- Department of Molecular Pathology, Henan Key Laboratory of Molecular Pathology, Zhengzhou, China.,The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, China
| | - Jinxiang Zheng
- Department of Molecular Pathology, Henan Key Laboratory of Molecular Pathology, Zhengzhou, China.,The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, China
| | - Cai Jiang
- Nanodigmbio (Nanjing) Biotechnology Co., Ltd., China
| | - He Zhang
- Department of Molecular Pathology, Henan Key Laboratory of Molecular Pathology, Zhengzhou, China.,The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, China
| | - Mingye Zhang
- Nanodigmbio (Nanjing) Biotechnology Co., Ltd., China
| | - Taoran Cheng
- Nanodigmbio (Nanjing) Biotechnology Co., Ltd., China
| | - Jun Li
- Department of Molecular Pathology, Henan Key Laboratory of Molecular Pathology, Zhengzhou, China.,The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, China
| | - Zhizhong Wang
- Department of Molecular Pathology, Henan Key Laboratory of Molecular Pathology, Zhengzhou, China.,The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, China
| | - Lijun Deng
- Department of Molecular Pathology, Henan Key Laboratory of Molecular Pathology, Zhengzhou, China.,The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, China
| | - Li Wang
- Department of Molecular Pathology, Henan Key Laboratory of Molecular Pathology, Zhengzhou, China.,The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, China
| | - Qingxin Xia
- Department of Molecular Pathology, Henan Key Laboratory of Molecular Pathology, Zhengzhou, China.,The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, China
| | - Jie Ma
- Department of Molecular Pathology, Henan Key Laboratory of Molecular Pathology, Zhengzhou, China.,The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, China
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33
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Miyahira AK, Hawley JE, Adelaiye-Ogala R, Calais J, Nappi L, Parikh R, Seibert TM, Wasmuth EV, Wei XX, Pienta KJ, Soule HR. Exploring new frontiers in prostate cancer research: Report from the 2022 Coffey-Holden prostate cancer academy meeting. Prostate 2023; 83:207-226. [PMID: 36443902 DOI: 10.1002/pros.24461] [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: 10/21/2022] [Accepted: 11/02/2022] [Indexed: 12/03/2022]
Abstract
INTRODUCTION The 2022 Coffey-Holden Prostate Cancer Academy (CHPCA) Meeting, "Exploring New Frontiers in Prostate Cancer Research," was held from June 23 to 26, 2022, at the University of California, Los Angeles, Luskin Conference Center, in Los Angeles, CA. METHODS The CHPCA Meeting is an annual discussion-oriented scientific conference organized by the Prostate Cancer Foundation, that focuses on emerging and next-step topics deemed critical for making the next major advances in prostate cancer research and clinical care. The 2022 CHPCA Meeting included 35 talks over 10 sessions and was attended by 73 academic investigators. RESULTS Major topic areas discussed at the meeting included: prostate cancer diversity and disparities, the impact of social determinants on research and patient outcomes, leveraging real-world and retrospective data, development of artificial intelligence biomarkers, androgen receptor (AR) signaling biology and new strategies for targeting AR, features of homologous recombination deficient prostate cancer, and future directions in immunotherapy and nuclear theranostics. DISCUSSION This article summarizes the scientific presentations from the 2022 CHPCA Meeting, with the goal that dissemination of this knowledge will contribute to furthering global prostate cancer research efforts.
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Affiliation(s)
| | - Jessica E Hawley
- Department of Medicine, Division of Medical Oncology, University of Washington, Seattle, Washington, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Remi Adelaiye-Ogala
- Department of Medicine, Division of Hematology and Oncology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York, USA
- Department of Pharmacology and Toxicology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York, USA
| | - Jeremie Calais
- Department of Molecular and Medical Pharmacology, Ahmanson Translational Imaging Division, University of California, Los Angeles, Los Angeles, California, USA
| | - Lucia Nappi
- Department of Urologic Sciences, Vancouver Prostate Centre, University of British Columbia, British Columbia, Canada
- Department of Medical Oncology, BC Cancer, British Columbia, Canada
| | - Ravi Parikh
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Medical Ethics and Health Policy, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, Pennsylvania, USA
| | - Tyler M Seibert
- Department of Radiation Medicine and Applied Sciences, University of California San Diego, La Jolla, California, USA
- Department of Radiology, University of California San Diego, La Jolla, California, USA
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
- Research Service, VA San Diego Healthcare System, San Diego, California, USA
| | - Elizabeth V Wasmuth
- Department of Biochemistry and Structural Biology, University of Texas Health at San Antonio, San Antonio, Texas, USA
| | - Xiao X Wei
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Kenneth J Pienta
- The James Buchanan Brady Urological Institute, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Howard R Soule
- Prostate Cancer Foundation, Santa Monica, California, USA
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Winkelmann R, Bankov K, Döring C, Cinatl J, Grothe S, Rothweiler F, Michaelis M, Schmitt C, Wild PJ, Demes M, Cinatl J, Vallo S. Increased HRD score in cisplatin resistant penile cancer cells. BMC Cancer 2022; 22:1352. [PMID: 36564761 PMCID: PMC9789628 DOI: 10.1186/s12885-022-10432-7] [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: 09/16/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND/INTRODUCTION Penile cancer is a rare disease in demand for new therapeutic options. Frequently used combination chemotherapy with 5 fluorouracil (5-FU) and cisplatin (CDDP) in patients with metastatic penile cancer mostly results in the development of acquired drug resistance. Availability of cell culture models with acquired resistance against standard therapy could help to understand molecular mechanisms underlying chemotherapy resistance and to identify candidate treatments for an efficient second line therapy. METHODS We generated a cell line from a humanpapilloma virus (HPV) negative penile squamous cell carcinoma (UKF-PEC-1). This cell line was subject to chronic exposure to chemotherapy with CDDP and / or 5-FU to induce acquired resistance in the newly established chemo-resistant sublines (PEC-1rCDDP2500, adapted to 2500 ng/ml CDDP; UKF-PEC-1r5-FU500, adapted to 500 ng/ml 5- FU; UKF-PEC1rCDDP2500/r5-FU500, adapted to 2500 ng/ml CDDP and 500 ng/ml 5 -FU). Afterwards cell line pellets were formalin-fixed, paraffin embedded and subject to sequencing as well as testing for homologous recombination deficiency (HRD). Additionally, exemplary immunohistochemical stainings for p53 and gammaH2AX were applied for verification purposes. Finally, UKF-PEC-1rCDDP2500, UKF-PEC-1r5-FU500, UKF-PEC1rCDDP2500/r5-FU500, and UKF-PEC-3 (an alternative penis cancer cell line) were tested for sensitivity to paclitaxel, docetaxel, olaparib, and rucaparib. RESULTS AND CONCLUSIONS The chemo-resistant sublines differed in their mutational landscapes. UKF-PEC-1rCDDP2500 was characterized by an increased HRD score, which is supposed to be associated with increased PARP inhibitor and immune checkpoint inhibitor sensitivity in cancer. However, UKF-PEC-1rCDDP2500 did not display sensitivity to PARP inhibitors.
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Affiliation(s)
- Ria Winkelmann
- grid.411088.40000 0004 0578 8220Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt Am Main, Germany
| | - Katrin Bankov
- grid.411088.40000 0004 0578 8220Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt Am Main, Germany
| | - Claudia Döring
- grid.411088.40000 0004 0578 8220Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt Am Main, Germany
| | | | - Sebastian Grothe
- Dr. Petra Joh Forschungshaus, Frankfurt Am Main, Germany ,grid.411088.40000 0004 0578 8220Institute of Medical Virology, University Hospital Frankfurt, Frankfurt Am Main, Germany
| | - Florian Rothweiler
- Dr. Petra Joh Forschungshaus, Frankfurt Am Main, Germany ,grid.411088.40000 0004 0578 8220Institute of Medical Virology, University Hospital Frankfurt, Frankfurt Am Main, Germany
| | - Martin Michaelis
- grid.9759.20000 0001 2232 2818School of Biosciences, University of Kent, Canterbury, UK
| | - Christina Schmitt
- grid.411088.40000 0004 0578 8220Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt Am Main, Germany
| | - Peter J. Wild
- grid.411088.40000 0004 0578 8220Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt Am Main, Germany ,grid.417999.b0000 0000 9260 4223Frankfurt Institute for Advanced Studies (FIAS), Frankfurt Am Main, Germany
| | - Melanie Demes
- grid.411088.40000 0004 0578 8220Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt Am Main, Germany
| | - Jindrich Cinatl
- Dr. Petra Joh Forschungshaus, Frankfurt Am Main, Germany ,grid.411088.40000 0004 0578 8220Institute of Medical Virology, University Hospital Frankfurt, Frankfurt Am Main, Germany
| | - Stefan Vallo
- grid.411088.40000 0004 0578 8220Institute of Medical Virology, University Hospital Frankfurt, Frankfurt Am Main, Germany ,grid.411088.40000 0004 0578 8220Department of Urology, University Hospital Frankfurt, Frankfurt Am Main, Germany ,Urologie an der Zeil, Frankfurt Am Main, Germany
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35
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Akhoundova D, Feng FY, Pritchard CC, Rubin MA. Molecular Genetics of Prostate Cancer and Role of Genomic Testing. Surg Pathol Clin 2022; 15:617-628. [PMID: 36344179 DOI: 10.1016/j.path.2022.08.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Prostate cancer (PCa) is characterized by profound genomic heterogeneity. Recent advances in personalized treatment entail an increasing need of genomic profiling. For localized PCa, gene expression assays can support clinical decisions regarding active surveillance and adjuvant treatment. In metastatic PCa, homologous recombination deficiency, microsatellite instability-high (MSI-H), and CDK12 deficiency constitute main actionable alterations. Alterations in DNA repair genes confer variable sensitivities to poly(ADP-ribose)polymerase inhibitors, and the use of genomic instability assays as predictive biomarker is still incipient. MSI can be assessed by immunohistochemistry To date there is a lack of consensus as to testing standards.
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Affiliation(s)
- Dilara Akhoundova
- Department for BioMedical Research, University of Bern, Murtenstrasse 24, Bern 3008, Switzerland; Department of Medical Oncology, Inselspital, University Hospital of Bern, Bern 3010, Switzerland
| | - Felix Y Feng
- Department of Radiation Oncology, University of California, 1600 Divisadero Street, Suite H-1031, San Francisco, CA 94115, USA
| | - Colin C Pritchard
- Department of Laboratory Medicine and Pathology, University of Washington, 1959 NE Pacific St Seattle, WA 98195-7110, USA
| | - Mark A Rubin
- Department for BioMedical Research, University of Bern, Murtenstrasse 24, Bern 3008, Switzerland; Bern Center for Precision Medicine, Inselspital, University Hospital of Bern, Bern, 3008, Switzerland.
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36
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Risk Allele Frequency Analysis and Risk Prediction of Single-Nucleotide Polymorphisms for Prostate Cancer. Genes (Basel) 2022; 13:genes13112039. [DOI: 10.3390/genes13112039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/29/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022] Open
Abstract
The incidence of prostate cancer (PCa) varies by ethnicity. This study aimed to provide insights into the genetic cause of PCa, which can result in differences in incidence among individuals of diverse ancestry. We collected data on PCa-associated single-nucleotide polymorphisms (SNPs) from a genome-wide association study catalog. Fisher’s exact tests were used to analyze the significance of enrichment or depletion of the effect on the allele at a given SNP. A network analysis was performed based on PCa-related SNPs that showed significant differences among ethnicities. The SNP-based polygenic risk score (PRS) was calculated, and its correlation with PCa incidence was evaluated. European, African, and East Asian populations had different heatmap patterns. Calculated PRS from the allele frequencies of PCa was the highest among Africans, followed by Europeans, and was the lowest among East Asians. PRS was positively correlated with the incidence and mortality of PCa. Network analysis revealed that AR, CDKN1B, and MAD1L1 are genes related to ethnic differences in PCa. The incidence and mortality of PCa showed a strong correlation with PRS according to ethnicity, which may suggest the effect of genetic factors, such as the AR gene, on PCa pathogenesis.
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Imyanitov E, Sokolenko A. Integrative Genomic Tests in Clinical Oncology. Int J Mol Sci 2022; 23:13129. [PMID: 36361916 PMCID: PMC9656402 DOI: 10.3390/ijms232113129] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 10/24/2022] [Accepted: 10/25/2022] [Indexed: 09/12/2023] Open
Abstract
Many clinical decisions in oncology practice rely on the presence or absence of an alteration in a single genetic locus, be it a pathogenic variant in a hereditary cancer gene or activating mutation in a drug target. In addition, there are integrative tests that produce continuous variables and evaluate complex characteristics of the entire tumor genome. Microsatellite instability (MSI) analysis identifies tumors with the accumulation of mutations in short repetitive nucleotide sequences. This procedure is utilized in Lynch syndrome diagnostic pipelines and for the selection of patients for immunotherapy. MSI analysis is well-established for colorectal malignancies, but its applications in other cancer types lack standardization and require additional research. Homologous repair deficiency (HRD) indicates tumor sensitivity to PARP inhibitors and some cytotoxic drugs. HRD-related "genomic scars" are manifested by a characteristic pattern of allelic imbalances, accumulation of deletions with flanking homology, and specific mutation signatures. The detection of the genetic consequences of HRD is particularly sophisticated and expensive, as it involves either whole genome sequencing (WGS) or the utilization of large next-generation sequencing (NGS) panels. Tumor mutation burden (TMB) can be determined by whole exome sequencing (WES) or middle-throughput NGS multigene testing. Although TMB is regarded as an agnostic indicator of tumor sensitivity to immunotherapy, the clinical utility of this test is proven only for a few cancer types.
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Affiliation(s)
- Evgeny Imyanitov
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St. Petersburg, Russia
- Department of Medical Genetics, St.-Petersburg Pediatric Medical University, 194100 St. Petersburg, Russia
| | - Anna Sokolenko
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St. Petersburg, Russia
- Department of Medical Genetics, St.-Petersburg Pediatric Medical University, 194100 St. Petersburg, Russia
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Li S, Wang L, Wang Y, Zhang C, Hong Z, Han Z. The synthetic lethality of targeting cell cycle checkpoints and PARPs in cancer treatment. J Hematol Oncol 2022; 15:147. [PMID: 36253861 PMCID: PMC9578258 DOI: 10.1186/s13045-022-01360-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 09/30/2022] [Indexed: 11/17/2022] Open
Abstract
Continuous cell division is a hallmark of cancer, and the underlying mechanism is tumor genomics instability. Cell cycle checkpoints are critical for enabling an orderly cell cycle and maintaining genome stability during cell division. Based on their distinct functions in cell cycle control, cell cycle checkpoints are classified into two groups: DNA damage checkpoints and DNA replication stress checkpoints. The DNA damage checkpoints (ATM-CHK2-p53) primarily monitor genetic errors and arrest cell cycle progression to facilitate DNA repair. Unfortunately, genes involved in DNA damage checkpoints are frequently mutated in human malignancies. In contrast, genes associated with DNA replication stress checkpoints (ATR-CHK1-WEE1) are rarely mutated in tumors, and cancer cells are highly dependent on these genes to prevent replication catastrophe and secure genome integrity. At present, poly (ADP-ribose) polymerase inhibitors (PARPi) operate through “synthetic lethality” mechanism with mutant DNA repair pathways genes in cancer cells. However, an increasing number of patients are acquiring PARP inhibitor resistance after prolonged treatment. Recent work suggests that a combination therapy of targeting cell cycle checkpoints and PARPs act synergistically to increase the number of DNA errors, compromise the DNA repair machinery, and disrupt the cell cycle, thereby increasing the death rate of cancer cells with DNA repair deficiency or PARP inhibitor resistance. We highlight a combinational strategy involving PARP inhibitors and inhibition of two major cell cycle checkpoint pathways, ATM-CHK2-TP53 and ATR-CHK1-WEE1. The biological functions, resistance mechanisms against PARP inhibitors, advances in preclinical research, and clinical trials are also reviewed.
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Affiliation(s)
- Shuangying Li
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Liangliang Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Yuanyuan Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Changyi Zhang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Zhenya Hong
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China.
| | - Zhiqiang Han
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China.
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van der Wiel AMA, Schuitmaker L, Cong Y, Theys J, Van Hoeck A, Vens C, Lambin P, Yaromina A, Dubois LJ. Homologous Recombination Deficiency Scar: Mutations and Beyond-Implications for Precision Oncology. Cancers (Basel) 2022; 14:cancers14174157. [PMID: 36077694 PMCID: PMC9454578 DOI: 10.3390/cancers14174157] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 02/05/2023] Open
Abstract
Homologous recombination deficiency (HRD) is a prevalent in approximately 17% of tumors and is associated with enhanced sensitivity to anticancer therapies inducing double-strand DNA breaks. Accurate detection of HRD would therefore allow improved patient selection and outcome of conventional and targeted anticancer therapies. However, current clinical assessment of HRD mainly relies on determining germline BRCA1/2 mutational status and is insufficient for adequate patient stratification as mechanisms of HRD occurrence extend beyond functional BRCA1/2 loss. HRD, regardless of BRCA1/2 status, is associated with specific forms of genomic and mutational signatures termed HRD scar. Detection of this HRD scar might therefore be a more reliable biomarker for HRD. This review discusses and compares different methods of assessing HRD and HRD scar, their advances into the clinic, and their potential implications for precision oncology.
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Affiliation(s)
- Alexander M. A. van der Wiel
- The M-Lab, Department of Precision Medicine, GROW—School for Oncology and Reproduction, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Lesley Schuitmaker
- The M-Lab, Department of Precision Medicine, GROW—School for Oncology and Reproduction, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Ying Cong
- The M-Lab, Department of Precision Medicine, GROW—School for Oncology and Reproduction, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Jan Theys
- The M-Lab, Department of Precision Medicine, GROW—School for Oncology and Reproduction, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Arne Van Hoeck
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, 3584 CG Utrecht, The Netherlands
| | - Conchita Vens
- Institute of Cancer Science, University of Glasgow, Glasgow G61 1BD, Scotland, UK
- Department of Radiation Oncology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Philippe Lambin
- The M-Lab, Department of Precision Medicine, GROW—School for Oncology and Reproduction, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Ala Yaromina
- The M-Lab, Department of Precision Medicine, GROW—School for Oncology and Reproduction, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Ludwig J. Dubois
- The M-Lab, Department of Precision Medicine, GROW—School for Oncology and Reproduction, Maastricht University, 6229 ER Maastricht, The Netherlands
- Correspondence:
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Boussios S, Rassy E, Moschetta M, Ghose A, Adeleke S, Sanchez E, Sheriff M, Chargari C, Pavlidis N. BRCA Mutations in Ovarian and Prostate Cancer: Bench to Bedside. Cancers (Basel) 2022; 14:cancers14163888. [PMID: 36010882 PMCID: PMC9405840 DOI: 10.3390/cancers14163888] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/09/2022] [Accepted: 08/10/2022] [Indexed: 11/17/2022] Open
Abstract
Simple Summary DNA damage is one of the hallmarks of cancer. Epithelial ovarian cancer (EOC) —especially the high-grade serous subtype—harbors a defect in at least one DNA damage response (DDR) pathway. Defective DDR results from a variety of lesions affecting homologous recombination (HR) and nonhomologous end joining (NHEJ) for double strand breaks, base excision repair (BER), and nucleotide excision repair (NER) for single strand breaks and mismatch repair (MMR). Apart from the EOC, mutations in the DDR genes, such as BRCA1 and BRCA2, are common in prostate cancer as well. Among them, BRCA2 lesions are found in 12% of metastatic castration-resistant prostate cancers, but very rarely in primary prostate cancer. Better understanding of the DDR pathways is essential in order to optimize the therapeutic choices, and has led to the design of biomarker-driven clinical trials. Poly(ADP-ribose) polymerase (PARP) inhibitors are now a standard therapy for EOC patients, and more recently have been approved for the metastatic castration-resistant prostate cancer with alterations in DDR genes. They are particularly effective in tumours with HR deficiency. Abstract DNA damage repair (DDR) defects are common in different cancer types, and these alterations can be exploited therapeutically. Epithelial ovarian cancer (EOC) is among the tumours with the highest percentage of hereditary cases. BRCA1 and BRCA2 predisposing pathogenic variants (PVs) were the first to be associated with EOC, whereas additional genes comprising the homologous recombination (HR) pathway have been discovered with DNA sequencing technologies. The incidence of DDR alterations among patients with metastatic prostate cancer is much higher compared to those with localized disease. Genetic testing is playing an increasingly important role in the treatment of patients with ovarian and prostate cancer. The development of poly (ADP-ribose) polymerase (PARP) inhibitors offers a therapeutic strategy for patients with EOC. One of the mechanisms of PARP inhibitors exploits the concept of synthetic lethality. Tumours with BRCA1 or BRCA2 mutations are highly sensitive to PARP inhibitors. Moreover, the synthetic lethal interaction may be exploited beyond germline BRCA mutations in the context of HR deficiency, and this is an area of ongoing research. PARP inhibitors are in advanced stages of development as a treatment for metastatic castration-resistant prostate cancer. However, there is a major concern regarding the need to identify reliable biomarkers predictive of treatment response. In this review, we explore the mechanisms of DDR, the potential for genomic analysis of ovarian and prostate cancer, and therapeutics of PARP inhibitors, along with predictive biomarkers.
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Affiliation(s)
- Stergios Boussios
- Department of Medical Oncology, Medway NHS Foundation Trust, Windmill Road, Gillingham ME7 5NY, UK
- Faculty of Life Sciences & Medicine, School of Cancer & Pharmaceutical Sciences, King’s College London, London SE1 9RT, UK
- AELIA Organization, 9th Km Thessaloniki-Thermi, 57001 Thessaloniki, Greece
- Correspondence:
| | - Elie Rassy
- Department of Medical Oncology, Gustave Roussy Institut, 94805 Villejuif, France
| | - Michele Moschetta
- Novartis Institutes for BioMedical Research, CH 4033 Basel, Switzerland
| | - Aruni Ghose
- Department of Medical Oncology, Medway NHS Foundation Trust, Windmill Road, Gillingham ME7 5NY, UK
- Department of Medical Oncology, Barts Cancer Centre, St. Bartholomew’s Hospital, Barts Health NHS Trust, London E1 1BB, UK
- Department of Medical Oncology, Mount Vernon Cancer Centre, East and North Hertfordshire NHS Trust, London KT1 2EE, UK
- Centre for Education, Faculty of Life Sciences and Medicine, King’s College London, London SE1 9RT, UK
| | - Sola Adeleke
- High Dimensional Neurology Group, UCL Queen’s Square Institute of Neurology, London WC1N 3BG, UK
- Department of Oncology, Guy’s and St Thomas’ Hospital, London SE1 9RT, UK
- School of Cancer & Pharmaceutical Sciences, King’s College London, Strand, London WC2R 2LS, UK
| | - Elisabet Sanchez
- Department of Medical Oncology, Medway NHS Foundation Trust, Windmill Road, Gillingham ME7 5NY, UK
| | - Matin Sheriff
- Department of Urology, Medway NHS Foundation Trust, Windmill Road, Gillingham ME7 5NY, UK
| | - Cyrus Chargari
- Department of Medical Oncology, Gustave Roussy Institut, 94805 Villejuif, France
| | - Nicholas Pavlidis
- Medical School, University of Ioannina, Stavros Niarchou Avenue, 45110 Ioannina, Greece
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Homologous recombination deficiency (HRD) score in aggressive prostatic adenocarcinoma with or without intraductal carcinoma of the prostate (IDC-P). BMC Med 2022; 20:237. [PMID: 35864546 PMCID: PMC9306093 DOI: 10.1186/s12916-022-02430-0] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 06/07/2022] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Intraductal carcinoma of the prostate (IDC-P) is a subtype of prostate cancer featured by poor prognosis. Previous studies suggested IDC-P could have a potentially unstable genome. Homologous recombination deficiency (HRD) score is a result-oriented method to describe the genomic instability status. This study investigates the association of HRD scores with IDC-P and other clinicopathological factors and the prognostic implication of HRD scores in an aggressive prostate cancer cohort. METHODS This study involved 123 PCa patients, including high-risk localized (M0) and de novo metastatic (M1) diseases. HRD score is calculated based on over 10,000 single-nucleotide polymorphisms distributed across the human genome. We explored the association between HRD scores and clinicopathological characteristics, genomic alterations, and patients' prognoses using rank-sum tests, chi-square tests, Kaplan-Meier curves, and Cox proportional hazards method. RESULTS The median HRD score of this cohort is 21.0, with 65 (52.8%) patients showing HRD score≥21. Tumors with IDC-P displayed higher HRD scores than adenocarcinoma (P=0.002); other high HRD score-related factors included M1 (P =0.008) and high ISUP grades (4-5) (P=0.001). MYC mutations were associated with high HRD scores (P<0.001) in the total cohort. TP53 mutations (P=0.010) and HRR pathway mutations (P=0.028) corresponded to high HRD scores in IDC-P positive and non-IDC-P patients, respectively, but not vice versa. HRD scores higher than 21 indicated significantly worse survival in the total cohort. CONCLUSIONS M1, high Gleason score, and IDC-P pathology represent higher HRD scores in PCa. Tumors with IDC-P might have different driven mechanisms for high HRD scores than non-IDC-P. HRD score displayed prognostic value in this aggressive prostate cancer cohort.
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Luo C, Liu Z, Gan Y, Gao X, Zu X, Zhang Y, Ye W, Cai Y. SLC26A4 correlates with homologous recombination deficiency and patient prognosis in prostate cancer. J Transl Med 2022; 20:313. [PMID: 35836192 PMCID: PMC9281181 DOI: 10.1186/s12967-022-03513-5] [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: 04/09/2022] [Accepted: 06/29/2022] [Indexed: 11/29/2022] Open
Abstract
Background Homologous recombination deficiency (HRD) is closely associated with patient prognosis and treatment options in prostate cancer (PCa). However, there is a lack of quantitative indicators related to HRD to predict the prognosis of PCa accurately. Methods We screened HRD-related genes based on the HRD scores and constructed an HRD cluster system to explore different clinicopathological, genomic, and immunogenomic patterns among the clusters. A risk signature, HRDscore, was established and evaluated by multivariate Cox regression analysis. We noticed that SLC26A4, a model gene, demonstrated unique potential to predict prognosis and HRD in PCa. Multi-omics analysis was conducted to explore its role in PCa, and the results were validated by qRT-PCR and immunohistochemistry. Results Three HRD clusters were identified with significant differences in patient prognosis, clinicopathological characteristics, biological pathways, immune infiltration characteristics, and regulation of immunomodulators. Further analyses revealed that the constructed HRDscore system was an independent prognostic factor of PCa patients with good stability. Finally, we identified a single gene, SLC26A4, which significantly correlated with prognosis in three independent cohorts. Importantly, SLC26A4 was confirmed to distinguish PCa (AUC for mRNA 0.845; AUC for immunohistochemistry score 0.769) and HRD (AUC for mRNA 0.911; AUC for immunohistochemistry score 0.689) at both RNA and protein levels in our cohort. Conclusion This study introduces HRDscore to quantify the HRD pattern of individual PCa patients. Meanwhile, SLC26A4 is a novel biomarker and can reasonably predict the prognosis and HRD in PCa. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-022-03513-5.
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Affiliation(s)
- Cong Luo
- Department of Urology, Disorders of Prostate Cancer Multidisciplinary Team, Xiangya Hospital, Central South University, No. 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, No. 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China
| | - Zhi Liu
- Department of Urology, Disorders of Prostate Cancer Multidisciplinary Team, Xiangya Hospital, Central South University, No. 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, No. 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China.,Department of Urology, The Second Affiliated Hospital of Guizhou Medical University, Kaili City, 556000, Guizhou, People's Republic of China
| | - Yu Gan
- Department of Urology, Disorders of Prostate Cancer Multidisciplinary Team, Xiangya Hospital, Central South University, No. 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, No. 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China
| | - Xiaomei Gao
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, No. 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China.,Department of Pathology, Disorders of Prostate Cancer Multidisciplinary Team, Xiangya Hospital, Central South University, No. 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China
| | - Xiongbing Zu
- Department of Urology, Disorders of Prostate Cancer Multidisciplinary Team, Xiangya Hospital, Central South University, No. 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, No. 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China
| | - Ye Zhang
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, No. 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China. .,Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Xiangya Hospital, Central South University, Hunan Province, No. 87 Xiangya Road, Changsha, 410008, People's Republic of China.
| | - Wenrui Ye
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, No. 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China. .,Department of Neurosurgery, Xiangya Hospital, Central South University, No. 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China.
| | - Yi Cai
- Department of Urology, Disorders of Prostate Cancer Multidisciplinary Team, Xiangya Hospital, Central South University, No. 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China. .,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, No. 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China.
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Gillessen S, Armstrong A, Attard G, Beer TM, Beltran H, Bjartell A, Bossi A, Briganti A, Bristow RG, Bulbul M, Caffo O, Chi KN, Clarke CS, Clarke N, Davis ID, de Bono JS, Duran I, Eeles R, Efstathiou E, Efstathiou J, Ekeke ON, Evans CP, Fanti S, Feng FY, Fizazi K, Frydenberg M, George D, Gleave M, Halabi S, Heinrich D, Higano C, Hofman MS, Hussain M, James N, Jones R, Kanesvaran R, Khauli RB, Klotz L, Leibowitz R, Logothetis C, Maluf F, Millman R, Morgans AK, Morris MJ, Mottet N, Mrabti H, Murphy DG, Murthy V, Oh WK, Ost P, O'Sullivan JM, Padhani AR, Parker C, Poon DMC, Pritchard CC, Rabah DM, Rathkopf D, Reiter RE, Rubin M, Ryan CJ, Saad F, Sade JP, Sartor O, Scher HI, Shore N, Skoneczna I, Small E, Smith M, Soule H, Spratt DE, Sternberg CN, Suzuki H, Sweeney C, Sydes MR, Taplin ME, Tilki D, Tombal B, Türkeri L, Uemura H, Uemura H, van Oort I, Yamoah K, Ye D, Zapatero A, Omlin A. Management of Patients with Advanced Prostate Cancer: Report from the Advanced Prostate Cancer Consensus Conference 2021. Eur Urol 2022; 82:115-141. [PMID: 35450732 DOI: 10.1016/j.eururo.2022.04.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 04/01/2022] [Indexed: 12/14/2022]
Abstract
BACKGROUND Innovations in treatments, imaging, and molecular characterisation in advanced prostate cancer have improved outcomes, but various areas of management still lack high-level evidence to inform clinical practice. The 2021 Advanced Prostate Cancer Consensus Conference (APCCC) addressed some of these questions to supplement guidelines that are based on level 1 evidence. OBJECTIVE To present the voting results from APCCC 2021. DESIGN, SETTING, AND PARTICIPANTS The experts identified three major areas of controversy related to management of advanced prostate cancer: newly diagnosed metastatic hormone-sensitive prostate cancer (mHSPC), the use of prostate-specific membrane antigen ligands in diagnostics and therapy, and molecular characterisation of tissue and blood. A panel of 86 international prostate cancer experts developed the programme and the consensus questions. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS The panel voted publicly but anonymously on 107 pre-defined questions, which were developed by both voting and non-voting panel members prior to the conference following a modified Delphi process. RESULTS AND LIMITATIONS The voting reflected the opinions of panellists and did not incorporate a standard literature review or formal meta-analysis. The answer options for the consensus questions received varying degrees of support from panellists, as reflected in this article and the detailed voting results reported in the Supplementary material. CONCLUSIONS These voting results from a panel of experts in advanced prostate cancer can help clinicians and patients to navigate controversial areas of management for which high-level evidence is scant. However, diagnostic and treatment decisions should always be individualised according to patient characteristics, such as the extent and location of disease, prior treatment(s), comorbidities, patient preferences, and treatment recommendations, and should also incorporate current and emerging clinical evidence and logistic and economic constraints. Enrolment in clinical trials should be strongly encouraged. Importantly, APCCC 2021 once again identified salient questions that merit evaluation in specifically designed trials. PATIENT SUMMARY The Advanced Prostate Cancer Consensus Conference is a forum for discussing current diagnosis and treatment options for patients with advanced prostate cancer. An expert panel votes on predefined questions focused on the most clinically relevant areas for treatment of advanced prostate cancer for which there are gaps in knowledge. The voting results provide a practical guide to help clinicians in discussing treatment options with patients as part of shared decision-making.
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Affiliation(s)
- Silke Gillessen
- Oncology Institute of Southern Switzerland, Bellinzona, Switzerland; Universita della Svizzera Italiana, Lugano, Switzerland; University of Berne, Berne, Switzerland; Division of Cancer Sciences, University of Manchester, Manchester, UK.
| | - Andrew Armstrong
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Durham, NC, USA
| | - Gert Attard
- University College London Cancer Institute, London, UK
| | - Tomasz M Beer
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Himisha Beltran
- Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Anders Bjartell
- Department of Urology, Skåne University Hospital, Malmö, Sweden
| | - Alberto Bossi
- Genitourinary Oncology, Prostate Brachytherapy Unit, Gustave Roussy, Paris, France
| | - Alberto Briganti
- Unit of Urology/Division of Oncology, Urological Research Institute, IRCCS Ospedale San Raffaele, Vita-Salute San Raffaele University, Milan, Italy
| | - Robert G Bristow
- Division of Cancer Sciences, University of Manchester, Manchester, UK; Christie NHS Trust and CRUK Manchester Institute and Cancer Centre, Manchester, UK
| | - Muhammad Bulbul
- Division of Urology, Department of Surgery, American University of Beirut Medical Center, Beirut, Lebanon
| | - Orazio Caffo
- Department of Medical Oncology, Santa Chiara Hospital, Trento, Italy
| | - Kim N Chi
- BC Cancer, Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
| | - Caroline S Clarke
- Research Department of Primary Care & Population Health, Royal Free Campus, University College London, London, UK
| | - Noel Clarke
- The Christie and Salford Royal Hospitals, Manchester, UK
| | - Ian D Davis
- Monash University and Eastern Health, Victoria, Australia
| | - Johann S de Bono
- The Institute of Cancer Research, Royal Marsden NHS Foundation Trust, Sutton, UK
| | - Ignacio Duran
- Department of Medical Oncology, Hospital Universitario Marques de Valdecilla, IDIVAL, Santander, Spain
| | - Ros Eeles
- The Institute of Cancer Research, Royal Marsden NHS Foundation Trust, Sutton, UK
| | | | - Jason Efstathiou
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA, USA
| | - Onyeanunam Ngozi Ekeke
- Department of Surgery, University of Port Harcourt Teaching Hospital, Port Harcourt, Nigeria
| | | | - Stefano Fanti
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Felix Y Feng
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California-San Francisco, San Francisco, CA, USA
| | - Karim Fizazi
- Institut Gustave Roussy, University of Paris Saclay, Villejuif, France
| | - Mark Frydenberg
- Department of Surgery, Prostate Cancer Research Program, Monash University, Melbourne, Australia
| | - Dan George
- Departments of Medicine and Surgery, Duke Cancer Institute, Duke University, Durham, NC, USA
| | - Martin Gleave
- Urological Sciences, Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
| | - Susan Halabi
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - Daniel Heinrich
- Department of Oncology and Radiotherapy, Innlandet Hospital Trust, Gjøvik, Norway
| | | | - Michael S Hofman
- Prostate Cancer Theranostics and Imaging Centre of Excellence, Department of Molecular Imaging and Therapeutic Nuclear Medicine, Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Maha Hussain
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA
| | - Nick James
- The Institute of Cancer Research, Royal Marsden NHS Foundation Trust, Sutton, UK
| | - Robert Jones
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | | | - Raja B Khauli
- Department of Urology and the Naef K. Basile Cancer Institute, American University of Beirut Medical Center, Beirut, Lebanon
| | - Laurence Klotz
- Division of Urology, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, ON, Canada
| | - Raya Leibowitz
- Oncology Institute, Shamir Medical Center and Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Chris Logothetis
- Department of Genitourinary Medical Oncology, David H. Koch Centre, MD Anderson Cancer Centre, Houston, TX, USA; Department of Clinical Therapeutics, University of Athens Alexandra Hospital, Athens, Greece
| | - Fernando Maluf
- Beneficiência Portuguesa de São Paulo, São Paulo, SP, Brazil; Departamento de Oncologia, Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | | | - Alicia K Morgans
- Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael J Morris
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Hind Mrabti
- National Institute of Oncology, Mohamed V University, Rabat, Morocco
| | - Declan G Murphy
- Division of Cancer Surgery, Peter MacCallum Cancer Centre, Melbourne, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Australia
| | | | - William K Oh
- Division of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, The Tisch Cancer Institute, New York, NY, USA
| | - Piet Ost
- Department of Radiation Oncology, Iridium Netwerk, Antwerp, Belgium; Department of Human Structure and Repair, Ghent University, Ghent, Belgium
| | - Joe M O'Sullivan
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Northern Ireland Cancer Centre, Belfast City Hospital, Belfast, UK
| | - Anwar R Padhani
- The Institute of Cancer Research, Royal Marsden NHS Foundation Trust, Sutton, UK; Mount Vernon Cancer Centre, London, UK
| | - Chris Parker
- The Institute of Cancer Research, Royal Marsden NHS Foundation Trust, Sutton, UK
| | - Darren M C Poon
- Comprehensive Oncology Centre, Hong Kong Sanatorium & Hospital, The Chinese University of Hong Kong, Hong Kong
| | - Colin C Pritchard
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Danny M Rabah
- The Cancer Research Chair, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Dana Rathkopf
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rob E Reiter
- University of California-Los Angeles, Los Angeles, CA, USA
| | - Mark Rubin
- Bern Center for Precision Medicine and Department for Biomedical Research, Bern, Switzerland
| | - Charles J Ryan
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Fred Saad
- Centre Hospitalier de Université de Montréal, Montreal, Canada
| | - Juan P Sade
- Instituto Alexander Fleming, Buenos Aires, Argentina
| | | | - Howard I Scher
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Neal Shore
- Carolina Urologic Research Center, Myrtle Beach, SC, USA
| | - Iwona Skoneczna
- Rafal Masztak Grochowski Hospital and Maria Sklodowska Curie National Research Institute of Oncology, Warsaw, Poland
| | - Eric Small
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California-San Francisco, San Francisco, CA, USA
| | - Matthew Smith
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Howard Soule
- Prostate Cancer Foundation, Santa Monica, CA, USA
| | - Daniel E Spratt
- University Hospitals Seidman Cancer Center, Cleveland, OH, USA
| | - Cora N Sternberg
- Englander Institute for Precision Medicine, Weill Cornell Medicine Division of Hematology and Oncology, Meyer Cancer Center, New York Presbyterian Hospital, New York, NY, USA
| | | | - Christopher Sweeney
- Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Matthew R Sydes
- MRC Clinical Trials Unit, Institute of Clinical Trials and Methodology, University College London, London, UK
| | - Mary-Ellen Taplin
- Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Derya Tilki
- Martini-Klinik Prostate Cancer Center, University Hospital Hamburg-Eppendorf, Hamburg, Germany; Department of Urology, University Hospital Hamburg-Eppendorf, Hamburg, Germany; Department of Urology, Koc University Hospital, Istanbul, Turkey
| | | | - Levent Türkeri
- Department of Urology, M.A. Aydınlar Acıbadem University, Altunizade Hospital, Istanbul, Turkey
| | - Hiroji Uemura
- Yokohama City University Medical Center, Yokohama, Japan
| | - Hirotsugu Uemura
- Department of Urology, Kindai University Faculty of Medicine, Osaka, Japan
| | - Inge van Oort
- Radboud University Medical Center, Nijmegen, The Netherlands
| | - Kosj Yamoah
- Department of Radiation Oncology & Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, University of South Florida, Tampa, FL, USA
| | - Dingwei Ye
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Almudena Zapatero
- Department of Radiation Oncology, Hospital Universitario de La Princesa, Health Research Institute, Madrid, Spain
| | - Aurelius Omlin
- Department of Medical Oncology and Haematology, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
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The Homologous Recombination Deficiency Scar in Advanced Cancer: Agnostic Targeting of Damaged DNA Repair. Cancers (Basel) 2022; 14:cancers14122950. [PMID: 35740616 PMCID: PMC9221128 DOI: 10.3390/cancers14122950] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/09/2022] [Accepted: 06/10/2022] [Indexed: 12/24/2022] Open
Abstract
Simple Summary Tumor-suppressor genes are involved in DNA break repair through the homologous recombination system and are widely known for their role in hereditary cancer. Beyond breast and ovarian cancer, prostate and pancreatic cancer also have targetable homologous recombination deficiency (HRD) beyond the well-known BRCA1 and BRCA2 with relevance that exceeds diagnostic purposes. In this review, we aim to summarize the roles of HRD across tumor types and the treatment landscape to guide the targeting of damaged DNA repair based on the cancer’s genetic features. Abstract BRCA1 and BRCA2 are the most recognized tumor-suppressor genes involved in double-strand DNA break repair through the homologous recombination (HR) system. Widely known for its role in hereditary cancer, HR deficiency (HRD) has turned out to be critical beyond breast and ovarian cancer: for prostate and pancreatic cancer also. The relevance for the identification of these patients exceeds diagnostic purposes, since results published from clinical trials with poly-ADP ribose polymerase (PARP) inhibitors (PARPi) have shown how this type of targeted therapy can modify the long-term evolution of patients with HRD. Somatic aberrations in other HRD pathway genes, but also indirect genomic instability as a sign of this DNA repair impairment (known as HRD scar), have been reported to be relevant events that lead to more frequently than expected HR loss of function in several tumor types, and should therefore be included in the current diagnostic and therapeutic algorithm. However, the optimal strategy to identify HRD and potential PARPi responders in cancer remains undefined. In this review, we summarize the role and prevalence of HRD across tumor types and the current treatment landscape to guide the agnostic targeting of damaged DNA repair. We also discuss the challenge of testing patients and provide a special insight for new strategies to select patients who benefit from PARPi due to HRD scarring.
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Yi H, Li L, Huang J, Ma Z, Li H, Chen J, Zheng X, Chen J, He H, Song J. Biomarker Assessment of Homologous Recombination Deficiency in Epithelial Ovarian Cancer: Association With Progression-Free Survival After Surgery. Front Mol Biosci 2022; 9:906922. [PMID: 35769916 PMCID: PMC9234295 DOI: 10.3389/fmolb.2022.906922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 05/17/2022] [Indexed: 11/15/2022] Open
Abstract
Identifying BRCA mutations and homologous recombination deficiency (HRD) is the key to choosing patients for poly (ADP-ribose) polymerase inhibitor (PARPi) therapy. At present, a large amount of research focuses on the application of HRD detection in ovarian cancer. However, few studies have discussed the relationship between HRD detection and postoperative survival in patients with epithelial ovarian cancer (EOC). This study included 38 consecutive patients with EOC who underwent cytoreduction surgery. Owing to tissue availability, only 29 patients underwent molecular profiling and survival analysis. Overall, 21 (72.4%) tumors had HRD scores of ≥42. Mutations in BRCA were observed in 5/29 (17.2%) patients. In this cohort, an HRD score of ≥42 was more common in serous ovarian tumors. We found no statistically significant association between homologous recombination repair (HRR) genes and HRD scores except for tumor protein P53 (TP53) mutation. We also found a strong positive association between HRD scores and chromosomal instability (CIN). In the survival analysis, an HRD score of >23 was correlated with better postoperative progression-free survival (pPFS). With increased depth of research, an appropriate HRD score threshold may serve as a prognostic tool and should be assessed in future studies to predict the clinical value of PARPi.
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Affiliation(s)
- Huan Yi
- Department of Gynecology Oncology, Fujian Key Laboratory of Women and Children’s Critical Diseases Research [Fujian Maternity and Child Health Hospital(Fujian Women and Children’s Hospital)], Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
| | - Linhong Li
- Research and Development Division, Oriomics Biotech Inc, Hangzhou, China
| | - Jimiao Huang
- Department of Gynecology Oncology, Fujian Key Laboratory of Women and Children’s Critical Diseases Research [Fujian Maternity and Child Health Hospital(Fujian Women and Children’s Hospital)], Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
| | - Zhiming Ma
- Research and Development Division, Oriomics Biotech Inc, Hangzhou, China
| | - Hongping Li
- Research and Development Division, Oriomics Biotech Inc, Hangzhou, China
| | - Jian Chen
- Department of Gynecology Oncology, Fujian Provincial Cancer Hospital, Fuzhou, China
| | - Xiangqin Zheng
- Department of Gynecology Oncology, Fujian Key Laboratory of Women and Children’s Critical Diseases Research [Fujian Maternity and Child Health Hospital(Fujian Women and Children’s Hospital)], Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
| | - Jingjing Chen
- Department of Obstetrics and Gynecology, Fuding General Hospital, Fuding, China
| | - Haixin He
- Department of Gynecology Oncology, Fujian Provincial Cancer Hospital, Fuzhou, China
| | - Jianrong Song
- Department of Gynecology Oncology, Fujian Key Laboratory of Women and Children’s Critical Diseases Research [Fujian Maternity and Child Health Hospital(Fujian Women and Children’s Hospital)], Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
- *Correspondence: Jianrong Song,
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Leibowitz BD, Dougherty BV, Bell JSK, Kapilivsky J, Michuda J, Sedgewick AJ, Munson WA, Chandra TA, Dry JR, Beaubier N, Igartua C, Taxter T. Validation of genomic and transcriptomic models of homologous recombination deficiency in a real-world pan-cancer cohort. BMC Cancer 2022; 22:587. [PMID: 35643464 PMCID: PMC9148513 DOI: 10.1186/s12885-022-09669-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 05/11/2022] [Indexed: 12/14/2022] Open
Abstract
Background With the introduction of DNA-damaging therapies into standard of care cancer treatment, there is a growing need for predictive diagnostics assessing homologous recombination deficiency (HRD) status across tumor types. Following the strong clinical evidence for the utility of DNA-sequencing-based HRD testing in ovarian cancer, and growing evidence in breast cancer, we present analytical validation of the Tempus HRD-DNA test. We further developed, validated, and explored the Tempus HRD-RNA model, which uses gene expression data from 16,750 RNA-seq samples to predict HRD status from formalin-fixed paraffin-embedded tumor samples across numerous cancer types. Methods Genomic and transcriptomic profiling was performed using next-generation sequencing from Tempus xT, Tempus xO, Tempus xE, Tempus RS, and Tempus RS.v2 assays on 48,843 samples. Samples were labeled based on their BRCA1, BRCA2 and selected Homologous Recombination Repair pathway gene (CDK12, PALB2, RAD51B, RAD51C, RAD51D) mutational status to train and validate HRD-DNA, a genome-wide loss-of-heterozygosity biomarker, and HRD-RNA, a logistic regression model trained on gene expression. Results In a sample of 2058 breast and 1216 ovarian tumors, BRCA status was predicted by HRD-DNA with F1-scores of 0.98 and 0.96, respectively. Across an independent set of 1363 samples across solid tumor types, the HRD-RNA model was predictive of BRCA status in prostate, pancreatic, and non-small cell lung cancer, with F1-scores of 0.88, 0.69, and 0.62, respectively. Conclusions We predict HRD-positive patients across many cancer types and believe both HRD models may generalize to other mechanisms of HRD outside of BRCA loss. HRD-RNA complements DNA-based HRD detection methods, especially for indications with low prevalence of BRCA alterations. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09669-z.
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Rao A, Antonarakis ES. The growing role of rucaparib in contemporary treatment of metastatic prostate cancer: a review of efficacy and guidance for side effect management. Expert Rev Anticancer Ther 2022; 22:671-679. [PMID: 35594523 DOI: 10.1080/14737140.2022.2081154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
INTRODUCTION In May 2020, the approval of rucaparib - a poly-ADP-ribose polymerase (PARP) inhibitor - in the USA marked the arrival of a new class of targeted therapeutics for a subset of metastatic castration-resistant prostate cancer patients whose tumors harbor germline or somatic BRCA1/2 gene alterations. It has now become critical for physicians to be aware of the role and nuances of management of PARP inhibitor therapies in prostate cancer. AREAS COVERED We focus on rucaparib's pharmacology, key clinical trials that support its current indication, the competitive landscape, and our considerations for management of adverse events. We also review the ongoing clinical trials that may expand its utility in prostate cancer in our expert opinion. Finally, we discuss the opportunities that exist for further development of this class of targeted agents in prostate cancer. EXPERT OPINION We believe that the time has come to develop functional assays of HRR proficiency or deficiency in order to better guide PARP inhibitor selection for patients with prostate cancer and beyond.
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Affiliation(s)
- Arpit Rao
- Hematology and Oncology, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Emmanuel S Antonarakis
- Hematology, Oncology and Transplantation, Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
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Takamatsu S, Brown JB, Yamaguchi K, Hamanishi J, Yamanoi K, Takaya H, Kaneyasu T, Mori S, Mandai M, Matsumura N. Utility of Homologous Recombination Deficiency Biomarkers Across Cancer Types. JCO Precis Oncol 2022; 6:e2200085. [PMID: 35613413 PMCID: PMC9200383 DOI: 10.1200/po.22.00085] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Homologous recombination DNA repair deficiency (HRD) is associated with sensitivity to platinum and poly (ADP-ribose) polymerase inhibitors in certain cancer types, including breast, ovarian, pancreatic, and prostate. In these cancers, BRCA1/2 alterations and genomic scar signatures are useful indicators for assessing HRD. However, alterations in other homologous recombination repair (HRR)-related genes and their clinical significance in other cancer types have not been adequately and systematically investigated. A comprehensive pan-cancer analysis on the clinical significance of homologous recombination deficiency![]()
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Affiliation(s)
- Shiro Takamatsu
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - J B Brown
- Life Science Informatics Research Unit, Department of Molecular Biosciences, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Center for Cancer Immunotherapy and Immunobiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ken Yamaguchi
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Junzo Hamanishi
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Koji Yamanoi
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hisamitsu Takaya
- Department of Obstetrics and Gynecology, Kindai University Faculty of Medicine, Osaka, Japan
| | - Tomoko Kaneyasu
- Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Seiichi Mori
- Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Masaki Mandai
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Noriomi Matsumura
- Department of Obstetrics and Gynecology, Kindai University Faculty of Medicine, Osaka, Japan
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Kaur HB, Vidotto T, Mendes AA, Salles DC, Isaacs WB, Antonarakis ES, Lotan TL. Association between pathogenic germline mutations in BRCA2 and ATM and tumor-infiltrating lymphocytes in primary prostate cancer. Cancer Immunol Immunother 2022; 71:943-951. [PMID: 34533610 PMCID: PMC9254167 DOI: 10.1007/s00262-021-03050-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 09/05/2021] [Indexed: 01/15/2023]
Abstract
Pathogenic mutations in homologous recombination (HR) DNA repair genes may be associated with increased tumor mutational burden and numbers of tumor-infiltrating lymphocytes (TIL). Though HR-deficient prostate tumors have been anecdotally associated with improved responses to immunotherapy, it is unclear whether HR mutations or HR deficiency (HRD) scores predict for increased T-cell densities in this cancer. We evaluated 17 primary prostate tumors from patients with pathogenic germline BRCA2 mutations (gBRCA2) and 21 primary prostate tumors from patients with pathogenic germline ATM (gATM) mutations, which were compared to 19 control tumors lacking HR gene mutations, as well as the TCGA prostate cancer cohort. HRD score was estimated by targeted sequencing (gBRCA2 and gATM) or by SNP microarray (TCGA). Tumor-associated T-cell densities were assessed using validated automated digital image analysis of CD8 and FOXP3 immunostaining (gBRCA2 or gATM) or by methylCIBERSORT (TCGA). CD8 + and FOXP3 + T-cell densities were significantly correlated with each other in gBRCA2 and gATM cases. There was no significant difference between CD8 + or FOXP3 + TIL densities in gBRCA2 or gATM cases compared to controls. In the TCGA cohort, HRD score was associated with predicted CD8 + and FOXP3 + TILs. Associations were also seen for HRD score and TIL density among the germline-mutated cases. In contrast to mismatch repair-deficient primary prostate tumors, cancers from germline BRCA2 or ATM mutation carriers do not appear to be associated with elevated TIL density. However, measures of genomic scarring, such as HRD score, may be associated with increased tumor-infiltrating T-cells.
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Affiliation(s)
- Harsimar B Kaur
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Thiago Vidotto
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Adrianna A Mendes
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Daniela C Salles
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - William B Isaacs
- Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Emmanuel S Antonarakis
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, CRB2, Room 316, 1550 Orleans Street, Baltimore, MD, 21287, USA
| | - Tamara L Lotan
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, CRB2, Room 316, 1550 Orleans Street, Baltimore, MD, 21287, USA.
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Vergote I, González-Martín A, Ray-Coquard I, Harter P, Colombo N, Pujol P, Lorusso D, Mirza MR, Brasiuniene B, Madry R, Brenton JD, Ausems MGEM, Büttner R, Lambrechts D. European experts consensus: BRCA/homologous recombination deficiency testing in first-line ovarian cancer. Ann Oncol 2022; 33:276-287. [PMID: 34861371 DOI: 10.1016/j.annonc.2021.11.013] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/18/2021] [Accepted: 11/22/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Homologous recombination repair (HRR) enables fault-free repair of double-stranded DNA breaks. HRR deficiency is predicted to occur in around half of high-grade serous ovarian carcinomas. Ovarian cancers harbouring HRR deficiency typically exhibit sensitivity to poly-ADP ribose polymerase inhibitors (PARPi). Current guidelines recommend a range of approaches for genetic testing to identify predictors of sensitivity to PARPi in ovarian cancer and to identify genetic predisposition. DESIGN To establish a European-wide consensus for genetic testing (including the genetic care pathway), decision making and clinical management of patients with recently diagnosed advanced ovarian cancer, and the validity of biomarkers to predict the effectiveness of PARPi in the first-line setting. The collaborative European experts' consensus group consisted of a steering committee (n = 14) and contributors (n = 84). A (modified) Delphi process was used to establish consensus statements based on a systematic literature search, conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-analyses guidelines. RESULTS A consensus was reached on 34 statements amongst 98 caregivers (including oncologists, pathologists, clinical geneticists, genetic researchers, and patient advocates). The statements concentrated on (i) the value of testing for BRCA1/2 mutations and HRR deficiency testing, including when and whom to test; (ii) the importance of developing new and better HRR deficiency tests; (iii) the importance of germline non-BRCA HRR and mismatch repair gene mutations for predicting familial risk, but not for predicting sensitivity to PARPi, in the first-line setting; (iv) who should be able to inform patients about genetic testing, and what training and education should these caregivers receive. CONCLUSION These consensus recommendations, from a multidisciplinary panel of experts from across Europe, provide clear guidance on the use of BRCA and HRR deficiency testing for recently diagnosed patients with advanced ovarian cancer.
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Affiliation(s)
- I Vergote
- Division of Gynaecological Oncology, Department of Gynaecology and Obstetrics and Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium.
| | - A González-Martín
- Clinica Universidad de Navarra, Madrid, Spain; Program for Solid Tumors at Centro de Investigación Médica Aplicada (CIMA), Pamplona, Spain
| | - I Ray-Coquard
- Medical Oncology, Centre Leon Bérard and Université Claude Bernard Lyon, Lyon, France
| | - P Harter
- Department of Gynaecology & Gynaecologic Oncology, Ev. Kliniken Essen-Mitte, Essen, Germany
| | - N Colombo
- University of Milan-Bicocca and European Institute of Oncology IRCCS, Milan, Italy
| | - P Pujol
- Montpellier Faculty of Medicine, University Hospital of Montpellier, Montpellier, France
| | - D Lorusso
- Department of Women and Child Science and Public Health, Catholic University of Rome, Fondazione Policlinico Gemelli IRCCS, Rome, Italy
| | - M R Mirza
- Department of Oncology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - B Brasiuniene
- Department of Medical Oncology, National Cancer Institute of Lithuania, Faculty of Medicine of Vilnius University, Vilnius, Lithuania
| | - R Madry
- Oncological Gynaecology Department, Poznan University of Medical Sciences, Poznan, Poland
| | - J D Brenton
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - M G E M Ausems
- Division Laboratories, Pharmacy and Biomedical Genetics, Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - R Büttner
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | - D Lambrechts
- Department of Human Genetics, VIB and KU Leuven, Leuven, Belgium
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