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Kulkarni S, Gajjar K, Madhusudan S. Poly (ADP-ribose) polymerase inhibitor therapy and mechanisms of resistance in epithelial ovarian cancer. Front Oncol 2024; 14:1414112. [PMID: 39135999 PMCID: PMC11317305 DOI: 10.3389/fonc.2024.1414112] [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: 04/08/2024] [Accepted: 07/15/2024] [Indexed: 08/15/2024] Open
Abstract
Advanced epithelial ovarian cancer is the commonest cause of gynaecological cancer deaths. First-line treatment for advanced disease includes a combination of platinum-taxane chemotherapy (post-operatively or peri-operatively) and maximal debulking surgery whenever feasible. Initial response rate to chemotherapy is high (up to 80%) but most patients will develop recurrence (approximately 70-90%) and succumb to the disease. Recently, poly-ADP-ribose polymerase (PARP) inhibition (by drugs such as Olaparib, Niraparib or Rucaparib) directed synthetic lethality approach in BRCA germline mutant or platinum sensitive disease has generated real hope for patients. PARP inhibitor (PARPi) maintenance therapy can prolong survival but therapeutic response is not sustained due to intrinsic or acquired secondary resistance to PARPi therapy. Reversion of BRCA1/2 mutation can lead to clinical PARPi resistance in BRCA-germline mutated ovarian cancer. However, in the more common platinum sensitive sporadic HGSOC, the clinical mechanisms of development of PARPi resistance remains to be defined. Here we provide a comprehensive review of the current status of PARPi and the mechanisms of resistance to therapy.
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Affiliation(s)
- Sanat Kulkarni
- Department of Medicine, Sandwell and West Birmingham NHS Trust, West Bromwich, United Kingdom
| | - Ketankumar Gajjar
- Department of Gynaecological Oncology, Nottingham University Hospitals, Nottingham, United Kingdom
| | - Srinivasan Madhusudan
- Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, Nottingham, United Kingdom
- Department of Oncology, Nottingham University Hospitals, Nottingham, United Kingdom
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2
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Dibitetto D, Widmer CA, Rottenberg S. PARPi, BRCA, and gaps: controversies and future research. Trends Cancer 2024:S2405-8033(24)00134-1. [PMID: 39004561 DOI: 10.1016/j.trecan.2024.06.008] [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: 04/30/2024] [Revised: 06/17/2024] [Accepted: 06/21/2024] [Indexed: 07/16/2024]
Abstract
In recent years, various poly(ADP-ribose) polymerase (PARP) inhibitors (PARPis) have been approved for the treatment of several cancers to target the vulnerability of homologous recombination (HR) deficiency (e.g., due to BRCA1/2 dysfunction). In this review we analyze the ongoing debates and recent breakthroughs in the use of PARPis for BRCA1/2-deficient cancers, juxtaposing the 'double-strand break (DSB)' and 'single-stranded DNA (ssDNA) gap' models of synthetic lethality induced by PARPis. We spotlight the complexity of this interaction, highlighting emerging research on the role of DNA polymerase theta (POLθ) and ssDNA gaps in shaping therapy responses. We scrutinize the clinical ramifications of these findings, especially concerning PARPi efficacy and resistance mechanisms, underscoring the heterogeneity of BRCA-mutated tumors and the urgent need for advanced research to bridge the gap between laboratory models and patient outcomes.
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Affiliation(s)
- Diego Dibitetto
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Länggassstrasse 122, 3012 Bern, Switzerland; Bern Center for Precision Medicine and Cancer Therapy Research Cluster, Department for Biomedical Research, University of Bern, 3012 Bern, Switzerland; Molecular Oncology and DNA Damage Response Laboratory, Department of Experimental Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, 20156 Milan, Italy.
| | - Carmen A Widmer
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Länggassstrasse 122, 3012 Bern, Switzerland; Bern Center for Precision Medicine and Cancer Therapy Research Cluster, Department for Biomedical Research, University of Bern, 3012 Bern, Switzerland
| | - Sven Rottenberg
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Länggassstrasse 122, 3012 Bern, Switzerland; Bern Center for Precision Medicine and Cancer Therapy Research Cluster, Department for Biomedical Research, University of Bern, 3012 Bern, Switzerland; Division of Molecular Pathology, The Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands.
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3
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Casartelli C, Tommasi C, Lazzarin A, Corianò M, Tornali C, Serra O, Campanini N, Gutiérrez-Enríquez S, Sikokis A, Zanoni D, Minari R, Bortesi B, Michiara M, Boggiani D, Uliana V, Llop-Guevara A, Serra V, Musolino A, Pellegrino B. Functional HRD by RAD51 identifies BRCA1 VUS associated with loss of gene function and response to DNA-damaging agents. ESMO Open 2024; 9:103629. [PMID: 38970842 DOI: 10.1016/j.esmoop.2024.103629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 05/20/2024] [Accepted: 05/21/2024] [Indexed: 07/08/2024] Open
Affiliation(s)
- C Casartelli
- Department of Medicine and Surgery, University of Parma, Parma, Italy; Medical Oncology Unit, University Hospital of Parma, Parma, Italy; Gruppo Oncologico Italiano di Ricerca Clinica (GOIRC), Parma, Italy
| | - C Tommasi
- Department of Medicine and Surgery, University of Parma, Parma, Italy; Medical Oncology Unit, University Hospital of Parma, Parma, Italy; Gruppo Oncologico Italiano di Ricerca Clinica (GOIRC), Parma, Italy
| | - A Lazzarin
- Department of Medicine and Surgery, University of Parma, Parma, Italy; Medical Oncology Unit, University Hospital of Parma, Parma, Italy; Gruppo Oncologico Italiano di Ricerca Clinica (GOIRC), Parma, Italy
| | - M Corianò
- Department of Medicine and Surgery, University of Parma, Parma, Italy; Medical Oncology Unit, University Hospital of Parma, Parma, Italy; Gruppo Oncologico Italiano di Ricerca Clinica (GOIRC), Parma, Italy
| | - C Tornali
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - O Serra
- Department of Medicine and Surgery, University of Parma, Parma, Italy; Medical Oncology Unit, University Hospital of Parma, Parma, Italy; Gruppo Oncologico Italiano di Ricerca Clinica (GOIRC), Parma, Italy
| | - N Campanini
- Pathology Unit, University Hospital of Parma, Parma, Italy
| | - S Gutiérrez-Enríquez
- Hereditary Cancer Genetics Group, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - A Sikokis
- Medical Oncology Unit, University Hospital of Parma, Parma, Italy; Gruppo Oncologico Italiano di Ricerca Clinica (GOIRC), Parma, Italy
| | - D Zanoni
- Medical Oncology Unit, University Hospital of Parma, Parma, Italy; Gruppo Oncologico Italiano di Ricerca Clinica (GOIRC), Parma, Italy
| | - R Minari
- Medical Oncology Unit, University Hospital of Parma, Parma, Italy
| | - B Bortesi
- Medical Oncology Unit, University Hospital of Parma, Parma, Italy
| | - M Michiara
- Medical Oncology Unit, University Hospital of Parma, Parma, Italy; Gruppo Oncologico Italiano di Ricerca Clinica (GOIRC), Parma, Italy
| | - D Boggiani
- Medical Oncology Unit, University Hospital of Parma, Parma, Italy; Gruppo Oncologico Italiano di Ricerca Clinica (GOIRC), Parma, Italy
| | - V Uliana
- Medical Genetics Unit, University Hospital of Parma, Parma, Italy
| | - A Llop-Guevara
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - V Serra
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - A Musolino
- Department of Medicine and Surgery, University of Parma, Parma, Italy; Medical Oncology Unit, University Hospital of Parma, Parma, Italy; Gruppo Oncologico Italiano di Ricerca Clinica (GOIRC), Parma, Italy.
| | - B Pellegrino
- Department of Medicine and Surgery, University of Parma, Parma, Italy; Medical Oncology Unit, University Hospital of Parma, Parma, Italy; Gruppo Oncologico Italiano di Ricerca Clinica (GOIRC), Parma, Italy
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4
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Guffanti F, Mengoli I, Alvisi MF, Dellavedova G, Giavazzi R, Fruscio R, Rulli E, Damia G. BRCA1 foci test as a predictive biomarker of olaparib response in ovarian cancer patient-derived xenograft models. Front Pharmacol 2024; 15:1390116. [PMID: 38989145 PMCID: PMC11234799 DOI: 10.3389/fphar.2024.1390116] [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: 02/22/2024] [Accepted: 06/05/2024] [Indexed: 07/12/2024] Open
Abstract
Standard therapy for high-grade ovarian carcinoma includes surgery followed by platinum-based chemotherapy and poly-ADP ribose polymerase inhibitors (PARPis). Deficiency in homologous recombination repair (HRD) characterizes almost half of high-grade ovarian carcinomas and is due to genetic and epigenetic alterations in genes involved in HR repair, mainly BRCA1/BRCA2, and predicts response to PARPi. The academic and commercial tests set up to define the HRD status of the tumor rely on DNA sequencing analysis, while functional tests such as the RAD51 foci assay are currently under study, but have not been validated yet and are available for patients. In a well-characterized ovarian carcinoma patient-derived xenograft platform whose response to cisplatin and olaparib, a PARPi, is known, we assessed the association between the BRCA1 foci score, determined in formalin-fixed paraffin-embedded tumor slices with an immunofluorescence technique, and other HRD biomarkers and explored the potential of the BRCA1 foci test to predict tumors' response to cisplatin and olaparib. The BRCA1 foci score was associated with both tumors' HRD status and RAD51 foci score. A low BRCA1 foci score predicted response to olaparib and cisplatin, while a high score was associated with resistance to therapy. As we recently published that a low RAD51 foci score predicted olaparib sensitivity in our xenobank, we combined the two scores and showed that the predictive value was better than with the single tests. This study reports for the first time the capacity of the BRCA1 foci test to identify HRD ovarian carcinomas and possibly predict response to olaparib.
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Affiliation(s)
- Federica Guffanti
- Laboratory of Preclinical Gynaecological Oncology, Experimental Oncology Department, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Ilaria Mengoli
- Laboratory of Preclinical Gynaecological Oncology, Experimental Oncology Department, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Maria Francesca Alvisi
- Laboratory of Methodology for Clinical Research, Clinical Oncology Department, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Giulia Dellavedova
- Laboratory of Cancer Metastasis Therapeutics, Experimental Oncology Department, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Raffaella Giavazzi
- Laboratory of Cancer Metastasis Therapeutics, Experimental Oncology Department, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Robert Fruscio
- Clinic of Obstetrics and Gynecology, Department of Medicine and Surgery, San Gerardo Hospital, University of Milan Bicocca, Monza, Italy
| | - Eliana Rulli
- Laboratory of Methodology for Clinical Research, Clinical Oncology Department, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Giovanna Damia
- Laboratory of Preclinical Gynaecological Oncology, Experimental Oncology Department, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
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Perrone F, Facchinetti F, Pellegrino B, Minari R, Gnetti L, Azzoni C, Bottarelli L, Campanini N, Grau-Bejar JF, Mingozzi A, Cognigni V, Tiseo M. Multiple targets, germline BRCA1 mutation and HRD in a lung cancer patient: Molecular considerations and treatment decision-making. TUMORI JOURNAL 2024:3008916241257754. [PMID: 38869029 DOI: 10.1177/03008916241257754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
Abstract
INTRODUCTION Several biomarkers are currently available to address targeted treatments in cancer patients, with lung malignancies representing one of the best examples. CASE DESCRIPTION We report the case of a patient affected by advanced non-small cell lung cancer with an uncommon histology and a complex biology. The use of a large next-generation sequencing (NGS) NGS panel allowed us to identify an extremely rare BRAF mutation (V600Q), a MET amplification, a high tumor mutational burden, a germline pathogenetic BRCA1 mutation and a homologous recombination deficiency through RAD51 assay. The treatment decision was driven by the abundance of molecular information. CONCLUSIONS This case highlights that an attentive and critical evaluation of molecular reports is key for the tailoring of treatment algorithms at the patient-level scale.
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Affiliation(s)
- Fabiana Perrone
- Medical Oncology Unit, University Hospital of Parma, Parma, Italy
| | - Francesco Facchinetti
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Roberta Minari
- Medical Oncology Unit, University Hospital of Parma, Parma, Italy
| | - Letizia Gnetti
- Pathology Unit, University Hospital of Parma, Parma, Italy
| | - Cinzia Azzoni
- Pathology Unit, University Hospital of Parma, Parma, Italy
| | | | | | | | - Anna Mingozzi
- Medical Oncology Unit, University Hospital of Parma, Parma, Italy
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Valeria Cognigni
- Oncology Clinic, Polytechnic University of Marche, United Hospitals of Ancona, Ancona, Italy
| | - Marcello Tiseo
- Medical Oncology Unit, University Hospital of Parma, Parma, Italy
- Department of Medicine and Surgery, University of Parma, Parma, Italy
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6
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Huang Y, Ren S, Ding L, Jiang Y, Luo J, Huang J, Yin X, Zhao J, Fu S, Liao J. TP53-specific mutations serve as a potential biomarker for homologous recombination deficiency in breast cancer: a clinical next-generation sequencing study. PRECISION CLINICAL MEDICINE 2024; 7:pbae009. [PMID: 38745917 PMCID: PMC11092399 DOI: 10.1093/pcmedi/pbae009] [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: 01/08/2024] [Accepted: 04/07/2024] [Indexed: 05/16/2024] Open
Abstract
Background TP53 mutations and homologous recombination deficiency (HRD) occur frequently in breast cancer. However, the characteristics of TP53 pathogenic mutations in breast cancer patients with/without HRD are not clear. Methods Clinical next-generation sequencing (NGS) of both tumor and paired blood DNA from 119 breast cancer patients (BRCA-119 cohort) was performed with a 520-gene panel. Mutations, tumor mutation burden (TMB), and genomic HRD scores were assessed from NGS data. NGS data from 47 breast cancer patients in the HRD test cohort were analyzed for further verification. Results All TP53 pathogenic mutations in patients had somatic origin, which was associated with the protein expression of estrogen receptor and progestogen receptor. Compared to patients without TP53 pathologic mutations, patients with TP53 pathologic mutations had higher levels of HRD scores and different genomic alterations. The frequency of TP53 pathologic mutation was higher in the HRD-high group (HRD score ≥ 42) relative to that in the HRD-low group (HRD score < 42). TP53 has different mutational characteristics between the HRD-low and HRD-high groups. TP53-specific mutation subgroups had diverse genomic features and TMB. Notably, TP53 pathogenic mutations predicted the HRD status of breast cancer patients with an area under the curve (AUC) of 0.61. TP53-specific mutations, namely HRD-low mutation, HRD-high mutation, and HRD common mutation, predicted the HRD status of breast cancer patients with AUC values of 0.32, 0.72, and 0.58, respectively. Interestingly, TP53 HRD-high mutation and HRD common mutation combinations showed the highest AUC values (0.80) in predicting HRD status. Conclusions TP53-specific mutation combinations predict the HRD status of patients, indicating that TP53 pathogenic mutations could serve as a potential biomarker for poly-ADP-ribose polymerase (PARP) inhibitors in breast cancer patients .
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Affiliation(s)
- Yongsheng Huang
- Cellular & Molecular Diagnostics Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Shuwei Ren
- Department of Clinical Laboratory, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
| | - Linxiaoxiao Ding
- Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
- Guangzhou Regenerative Medicine and Health, Guangdong Laboratory, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Yuanling Jiang
- Cellular & Molecular Diagnostics Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Jiahuan Luo
- Cellular & Molecular Diagnostics Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Jinghua Huang
- Cellular & Molecular Diagnostics Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Xinke Yin
- Cellular & Molecular Diagnostics Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Jianli Zhao
- Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
- Guangzhou Regenerative Medicine and Health, Guangdong Laboratory, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Sha Fu
- Cellular & Molecular Diagnostics Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Jianwei Liao
- Cellular & Molecular Diagnostics Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
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7
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Torrado C, Plummer R, Yap TA. Poly(ADP-Ribose) Polymerase Inhibitor Development: Promising Strategies to Move Beyond Approved Indications. JCO Precis Oncol 2024; 8:e2400204. [PMID: 38865670 DOI: 10.1200/po.24.00204] [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: 03/26/2024] [Accepted: 04/08/2024] [Indexed: 06/14/2024] Open
Abstract
Biomarker-based patient selection and rational combinations show promise in expanding the use of PARP inhibitors.
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Affiliation(s)
- Carlos Torrado
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ruth Plummer
- Newcastle University and Northern Centre for Cancer Care, Newcastle Hospitals NHS Trust, Newcastle Upon Tyne, United Kigdom
| | - Timothy A Yap
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, TX
- Therapeutics Discovery Division, The University of Texas MD Anderson Cancer Center, Houston, TX
- Khalifa Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX
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8
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Morganti S, Marra A, De Angelis C, Toss A, Licata L, Giugliano F, Taurelli Salimbeni B, Berton Giachetti PPM, Esposito A, Giordano A, Bianchini G, Garber JE, Curigliano G, Lynce F, Criscitiello C. PARP Inhibitors for Breast Cancer Treatment: A Review. JAMA Oncol 2024; 10:658-670. [PMID: 38512229 DOI: 10.1001/jamaoncol.2023.7322] [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: 03/22/2024]
Abstract
Importance Poly(adenosine diphosphate-ribose) polymerase (PARP) inhibitors have revolutionized the treatment of patients with germline BRCA1/2-associated breast cancer, representing the first targeted therapy capable of improving outcomes in patients with hereditary tumors. However, resistance to PARP inhibitors occurs in almost all patients. Observations This narrative review summarizes the biological rationale behind the use of PARP inhibitors in breast cancer, as well as the available evidence, recent progress, and potential future applications of these agents. Recent studies have shown that the benefit of PARP inhibitors extends beyond patients with germline BRCA1/2-associated metastatic breast cancer to patients with somatic BRCA1/2 variants and to those with germline PALB2 alterations. Moreover, these agents proved to be effective both in the metastatic and adjuvant settings. However, patients with metastatic breast cancer usually do not achieve the long-term benefit from PARP inhibitors observed in other tumor types. Mechanisms of resistance have been identified, but how to effectively target them is largely unknown. Ongoing research is investigating both novel therapeutics and new combination strategies to overcome resistance. PARP1-selective inhibitors, by sparing the hematological toxic effects induced by the PARP2 blockade, are promising agents to be combined with chemotherapy, antibody-drug conjugates, and other targeted therapies. Conclusions and Relevance Although the efficacy of PARP inhibitors is well established, many questions persist. Future research should focus on identifying predictive biomarkers and therapeutic strategies to overcome resistance. Integrating well-designed translational efforts into all clinical studies is thereby crucial to laying the groundwork for future insights from ongoing research.
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Affiliation(s)
- Stefania Morganti
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | - Carmine De Angelis
- Department of Clinical Medicine and Surgery, University Federico II, Naples, Italy
- Laster and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Angela Toss
- Department of Oncology and Hematology, Azienda Ospedaliero-Universitaria di Modena, Modena, Italy
- Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Luca Licata
- Department of Medical Oncology, San Raffaele Hospital, Milan, Italy
- School of Medicine and Surgery, Vita-Salute San Raffaele University, Milan, Italy
| | - Federica Giugliano
- European Institute of Oncology IRCCS, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
- INSERM U981-Molecular Predictors and New Targets in Oncology, PRISM Center for Precision Medicine, Gustave Roussy, Villejuif, France
| | | | | | - Angela Esposito
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Antonio Giordano
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Giampaolo Bianchini
- Department of Medical Oncology, San Raffaele Hospital, Milan, Italy
- School of Medicine and Surgery, Vita-Salute San Raffaele University, Milan, Italy
| | - Judy E Garber
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Giuseppe Curigliano
- European Institute of Oncology IRCCS, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Filipa Lynce
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Carmen Criscitiello
- European Institute of Oncology IRCCS, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
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9
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Torres-Esquius S, Llop-Guevara A, Gutiérrez-Enríquez S, Romey M, Teulé À, Llort G, Herrero A, Sánchez-Henarejos P, Vallmajó A, González-Santiago S, Chirivella I, Cano JM, Graña B, Simonetti S, Díaz de Corcuera I, Ramon y Cajal T, Sanz J, Serrano S, Otero A, Churruca C, Sánchez-Heras AB, Servitja S, Guillén-Ponce C, Brunet J, Denkert C, Serra V, Balmaña J. Prevalence of Homologous Recombination Deficiency Among Patients With Germline RAD51C/D Breast or Ovarian Cancer. JAMA Netw Open 2024; 7:e247811. [PMID: 38648056 PMCID: PMC11036141 DOI: 10.1001/jamanetworkopen.2024.7811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 02/21/2024] [Indexed: 04/25/2024] Open
Abstract
Importance RAD51C and RAD51D are involved in DNA repair by homologous recombination. Germline pathogenic variants (PVs) in these genes are associated with an increased risk of ovarian and breast cancer. Understanding the homologous recombination deficiency (HRD) status of tumors from patients with germline PVs in RAD51C/D could guide therapeutic decision-making and improve survival. Objective To characterize the clinical and tumor characteristics of germline RAD51C/D PV carriers, including the evaluation of HRD status. Design, Setting, and Participants This retrospective cohort study included 91 index patients plus 90 relatives carrying germline RAD51C/D PV (n = 181) in Spanish hospitals from January 1, 2014, to December 31, 2021. Genomic and functional HRD biomarkers were assessed in untreated breast and ovarian tumor samples (n = 45) from June 2022 to February 2023. Main Outcomes and Measures Clinical and pathologic characteristics were assessed using descriptive statistics. Genomic HRD by genomic instability scores, functional HRD by RAD51, and gene-specific loss of heterozygosity were analyzed. Associations between HRD status and tumor subtype, age at diagnosis, and gene-specific loss of heterozygosity in RAD51C/D were investigated using logistic regression or the t test. Results A total of 9507 index patients were reviewed, and 91 patients (1.0%) were found to carry a PV in RAD51C/D; 90 family members with a germline PV in RAD51C/D were also included. A total of 157 of carriers (86.7%) were women and 181 (55.8%) had received a diagnosis of cancer, mainly breast cancer or ovarian cancer. The most prevalent PVs were c.1026+5_1026+7del (11 of 56 [19.6%]) and c.709C>T (9 of 56 [16.1%]) in RAD51C and c.694C>T (20 of 35 [57.1%]) in RAD51D. In untreated breast cancer and ovarian cancer, the prevalence of functional and genomic HRD was 55.2% (16 of 29) and 61.1% (11 of 18) for RAD51C, respectively, and 66.7% (6 of 9) and 90.0% (9 of 10) for RAD51D. The concordance between HRD biomarkers was 91%. Tumors with the same PV displayed contrasting HRD status, and age at diagnosis did not correlate with the occurrence of HRD. All breast cancers retaining the wild-type allele were estrogen receptor positive and lacked HRD. Conclusions and Relevance In this cohort study of germline RAD51C/D breast cancer and ovarian cancer, less than 70% of tumors displayed functional HRD, and half of those that did not display HRD were explained by retention of the wild-type allele, which was more frequent among estrogen receptor-positive breast cancers. Understanding which tumors are associated with RAD51C/D and HRD is key to identify patients who can benefit from targeted therapies, such as PARP (poly [adenosine diphosphate-ribose] polymerase) inhibitors.
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Affiliation(s)
- Sara Torres-Esquius
- Hereditary Cancer Genetics Group, Vall d’Hebron Institute of Oncology, Barcelona, Spain
| | - Alba Llop-Guevara
- Experimental Therapeutics Group, Vall d’Hebron Institute of Oncology, Barcelona, Spain
- Translational Medicine, DNA Damage Response Department, AstraZeneca, Barcelona, Spain
| | | | - Marcel Romey
- Institute of Pathology, Universitätsklinikum Marburg, Marburg, Germany
| | - Àlex Teulé
- Hereditary Cancer Program, Catalan Institute of Oncology, Bellvitge Biomedical Research Institute (IDIBELL), Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Gemma Llort
- Department of Medical Oncology, Hospital Universitari Parc Taulí, Sabadell, Spain
| | - Ana Herrero
- Department of Medical Oncology, Hospital Miguel Servet de Zaragoza, Zaragoza, Spain
| | | | - Anna Vallmajó
- Genetic Counseling Unit, Arnau de Vilanova University Hospital, Lleida, Spain
| | | | - Isabel Chirivella
- Cancer Genetic Counseling, Hospital Clínico Universitario de Valencia, Valencia, Spain
| | - Juana Maria Cano
- Department of Medical Oncology, Hospital General Universitario de Ciudad Real, Ciudad Real, Spain
| | - Begoña Graña
- Department of Medical Oncology, Xerencia de Xestión Integrada de A Coruña, Coruña, Spain
| | - Sara Simonetti
- Molecular Oncology Group, Vall d’Hebron Institute of Oncology, Barcelona, Spain
| | | | - Teresa Ramon y Cajal
- Department of Medical Oncology, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Judit Sanz
- Unidad de Cáncer Familiar y Hereditario, Althaia Xarxa Assistencial Universitària de Manresa, Manresa, Spain
| | - Sara Serrano
- Department of Medical Oncology, Institute of Oncology of Southern Catalonia (IOCS), Hospital Universitari Sant Joan de Reus, Reus, Spain
| | - Andrea Otero
- Institute of Oncology and Molecular Medicine of Asturias (IMOMA) S. A., Oviedo, Spain
| | - Cristina Churruca
- Department of Medical Oncology, Hospital Universitario Donostia, San Sebastián, Gipuzkoa, Spain
| | - Ana Beatriz Sánchez-Heras
- Cancer Genetic Counselling Unit, Medical Oncology Department, Hospital General Universitario de Elche, Elche, Spain
| | - Sonia Servitja
- Department of Medical Oncology, Hospital del Mar-CIBERONC, Barcelona, Spain
| | - Carmen Guillén-Ponce
- Department of Medical Oncology, Hospital Universitario Ramón y Cajal (IRYCIS), Madrid, Spain
| | - Joan Brunet
- Hereditary Cancer Program, Catalan Institute of Oncology, Girona, Spain
- Precision Oncology Group (OncoGIR-Pro), Institut d’Investigació Biomèdica de Girona (IDIBGI), Girona, Spain
| | - Carsten Denkert
- Institute of Pathology, Universitätsklinikum Marburg, Marburg, Germany
| | - Violeta Serra
- Experimental Therapeutics Group, Vall d’Hebron Institute of Oncology, Barcelona, Spain
| | - Judith Balmaña
- Hereditary Cancer Genetics Group, Vall d’Hebron Institute of Oncology, Barcelona, Spain
- Medical Oncology Department, Hospital Universitari Vall d’Hebron, Barcelona, Spain
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10
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Lewis MT, Caldas C. The Power and Promise of Patient-Derived Xenografts of Human Breast Cancer. Cold Spring Harb Perspect Med 2024; 14:a041329. [PMID: 38052483 PMCID: PMC10982691 DOI: 10.1101/cshperspect.a041329] [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: 12/07/2023]
Abstract
In 2016, a group of researchers engaged in the development of patient-derived xenografts (PDXs) of human breast cancer provided a comprehensive review of the state of the field. In that review, they summarized the clinical problem that PDXs might address, the technical approaches to their generation (including a discussion of host animals and transplant conditions tested), and presented transplantation success (take) rates across groups and across transplantation conditions. At the time, there were just over 500 unique PDX models created by these investigators representing all three clinically defined subtypes (ER+, HER2+, and TNBC). Today, many of these PDX resources have at least doubled in size, and several more PDX development groups now exist, such that there may be well upward of 1000 PDX models of human breast cancer in existence worldwide. They also presented a series of open questions for the field. Many of these questions have been addressed. However, several remain open, or only partially addressed. Herein, we revisit these questions, and recount the progress that has been made in a number of areas with respect to generation, characterization, and use of PDXs in translational research, and re-present questions that remain open. These open questions, and others, are now being addressed not only by individual investigators, but also large, well-funded consortia including the PDXNet program of the National Cancer Institute in the United States, and the EuroPDX Consortium, an organization of PDX developers across Europe. Finally, we discuss the new opportunities in PDX-based research.
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Affiliation(s)
- Michael T Lewis
- Baylor College of Medicine, The Lester and Sue Smith Breast Center, Departments of Molecular and Cellular Biology and Radiology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
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11
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Longoria O, Beije N, de Bono JS. PARP inhibitors for prostate cancer. Semin Oncol 2024; 51:25-35. [PMID: 37783649 DOI: 10.1053/j.seminoncol.2023.09.003] [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: 09/07/2023] [Accepted: 09/11/2023] [Indexed: 10/04/2023]
Abstract
Poly(ADP-ribose) polymerase (PARP) inhibitors have transformed the treatment landscape for patients with metastatic castration-resistant prostate cancer (mCRPC) and alterations in DNA damage response genes. This has also led to widespread use of genomic testing in all patients with mCRPC. The current review will give an overview of (1) the current understanding of the interplay between DNA damage response and PARP enzymes; (2) the clinical landscape of PARP inhibitors, including the combination of PARP inhibitors with other agents such as androgen-receptor signaling agents; (3) biomarkers related to PARP inhibitor response and resistance; and (4) considerations for interpreting genomic testing results and treating patients with PARP inhibitors.
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Affiliation(s)
- Ossian Longoria
- The Institute of Cancer Research, London, United Kingdom; The Royal Marsden NHS Foundation Trust, Sutton, United Kingdom
| | - Nick Beije
- The Institute of Cancer Research, London, United Kingdom; The Royal Marsden NHS Foundation Trust, Sutton, United Kingdom
| | - Johann S de Bono
- The Institute of Cancer Research, London, United Kingdom; The Royal Marsden NHS Foundation Trust, Sutton, United Kingdom.
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12
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Korsholm LM, Kjeldsen M, Perino L, Mariani L, Nyvang GB, Kristensen E, Bagger FO, Mirza MR, Rossing M. Combining Homologous Recombination-Deficient Testing and Functional RAD51 Analysis Enhances the Prediction of Poly(ADP-Ribose) Polymerase Inhibitor Sensitivity. JCO Precis Oncol 2024; 8:e2300483. [PMID: 38427930 PMCID: PMC10919475 DOI: 10.1200/po.23.00483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/03/2023] [Accepted: 12/21/2023] [Indexed: 03/03/2024] Open
Abstract
PURPOSE To meet the urgent need for accessible homologous recombination-deficient (HRD) test options, we validated a laboratory-developed test (LDT) and a functional RAD51 assay to assess patients with ovarian cancer and predict the clinical benefit of poly(ADP-ribose) polymerase inhibitor therapy. METHODS Optimization of the LDT cutoff and validation on the basis of samples from 91 patients enrolled in the ENGOT-ov24/NSGO-AVANOVA1&2 trial (ClinicalTrials.gov identifier: NCT02354131), previously subjected to commercial CDx HRD testing (CDx). RAD51 foci analysis was performed and tumors with ≥five foci/nucleus were classified as RAD51-positive (homologous recombination-proficient). RESULTS The optimal LDT cutoff is 54. Comparing CDx genome instability score and LDT HRD scores show a Spearman's correlation of rho = 0.764 (P < .0001). Cross-tabulation analysis shows that the sensitivity of the LDT HRD score is 86% and of the LDT HRD status is 91.8% (Fisher's exact test P < .001). Survival analysis on progression-free survival (PFS) of LDT-assessed patients show a Cox regression P < .05. RAD51 assays show a correlation between low RAD51 foci detection (<20% RAD51+ cells) and significantly prolonged PFS (P < .001). CONCLUSION The robust concordance between the open standard LDT and the CDx, especially the correlation with PFS, warrants future validation and implementation of the open standard LDT for HRD testing in diagnostic settings.
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Affiliation(s)
- Lea M. Korsholm
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Maj Kjeldsen
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Oncology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Lorenzo Perino
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Luca Mariani
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | | | - Elisabeth Kristensen
- Department of Pathology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Frederik O. Bagger
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Mansoor Raza Mirza
- Department of Oncology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Maria Rossing
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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13
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Fu X, Li P, Zhou Q, He R, Wang G, Zhu S, Bagheri A, Kupfer G, Pei H, Li J. Mechanism of PARP inhibitor resistance and potential overcoming strategies. Genes Dis 2024; 11:306-320. [PMID: 37588193 PMCID: PMC10425807 DOI: 10.1016/j.gendis.2023.02.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/27/2023] [Accepted: 02/02/2023] [Indexed: 08/18/2023] Open
Abstract
PARP inhibitors (PARPi) are a kind of cancer therapy that targets poly (ADP-ribose) polymerase. PARPi is the first clinically approved drug to exert synthetic lethality by obstructing the DNA single-strand break repair process. Despite the significant therapeutic effect in patients with homologous recombination (HR) repair deficiency, innate and acquired resistance to PARPi is a main challenge in the clinic. In this review, we mainly discussed the underlying mechanisms of PARPi resistance and summarized the promising solutions to overcome PARPi resistance, aiming at extending PARPi application and improving patient outcomes.
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Affiliation(s)
- Xiaoyu Fu
- Department of Oncology, Georgetown Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, China
| | - Ping Li
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, China
| | - Qi Zhou
- Department of Oncology, Georgetown Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, China
| | - Ruyuan He
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, China
| | - Guannan Wang
- Department of Oncology, Georgetown Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Shiya Zhu
- Department of Oncology, Georgetown Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Amir Bagheri
- Department of Oncology, Georgetown Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Gary Kupfer
- Department of Oncology, Georgetown Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Huadong Pei
- Department of Oncology, Georgetown Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Juanjuan Li
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, China
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14
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Tsang ES, Gallinger S. Deciphering the Pathways to PARP Sensitivity in Pancreatic Cancer. Clin Cancer Res 2023; 29:5005-5007. [PMID: 37787975 DOI: 10.1158/1078-0432.ccr-23-2260] [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: 08/15/2023] [Revised: 09/01/2023] [Accepted: 09/15/2023] [Indexed: 10/04/2023]
Abstract
A recent article analyzed paired cell-free DNA among patients with platinum-sensitive BRCA- or PALB2-mutated pancreatic cancer who received maintenance olaparib. Reversion mutations were linked with worse outcomes. These types of paired correlative studies are needed to improve our understanding of drug resistance and guide future clinical trials. See related article by Brown et al., p. 5207.
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Affiliation(s)
- Erica S Tsang
- Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario, Canada
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15
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van Wijk LM, Vermeulen S, Ter Haar NT, Kramer CJH, Terlouw D, Vrieling H, Cohen D, Vreeswijk MPG. Performance of a RAD51-based functional HRD test on paraffin-embedded breast cancer tissue. Breast Cancer Res Treat 2023; 202:607-616. [PMID: 37725154 PMCID: PMC10564840 DOI: 10.1007/s10549-023-07102-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/18/2023] [Indexed: 09/21/2023]
Abstract
PURPOSE BRCA-deficient breast cancers (BC) are highly sensitive to platinum-based chemotherapy and PARP inhibitors due to their deficiency in the homologous recombination (HR) pathway. However, HR deficiency (HRD) extends beyond BRCA-associated BC, highlighting the need for a sensitive method to enrich for HRD tumors in an alternative way. A promising approach is the use of functional HRD tests which evaluate the HR capability of tumor cells by measuring RAD51 protein accumulation at DNA damage sites. This study aims to evaluate the performance of a functional RAD51-based HRD test for the identification of HRD BC. METHODS The functional HR status of 63 diagnostic formalin-fixed paraffin-embedded (FFPE) BC samples was determined by applying the RAD51-FFPE test. Samples were screened for the presence of (epi)genetic defects in HR and matching tumor samples were analyzed with the RECAP test, which requires ex vivo irradiated fresh tumor tissue on the premise that the HRD status as determined by the RECAP test faithfully represented the functional HR status. RESULTS The RAD51-FFPE test identified 23 (37%) of the tumors as HRD, including three tumors with pathogenic variants in BRCA1/2. The RAD51-FFPE test showed a sensitivity of 88% and a specificity of 76% in determining the HR-class as defined by the RECAP test. CONCLUSION Given its high sensitivity and compatibility with FFPE samples, the RAD51-FFPE test holds great potential to enrich for HRD tumors, including those associated with BRCA-deficiency. This potential extends to situations where DNA-based testing may be challenging or not easily accessible in routine clinical practice. This is particularly important considering the potential implications for treatment decisions and patient stratification.
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Affiliation(s)
- Lise M van Wijk
- Department of Human Genetics, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
| | - Sylvia Vermeulen
- Department of Human Genetics, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
| | - Natalja T Ter Haar
- Department of Pathology, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
| | - Claire J H Kramer
- Department of Pathology, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
| | - Diantha Terlouw
- Department of Pathology, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
| | - Harry Vrieling
- Department of Human Genetics, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
| | - Danielle Cohen
- Department of Pathology, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
| | - Maaike P G Vreeswijk
- Department of Human Genetics, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands.
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16
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Lee CY, Cheng WF, Lin PH, Chen YL, Huang SH, Lei KH, Chang KY, Ko MY, Chi P. An activity-based functional test for identifying homologous recombination deficiencies across cancer types in real time. Cell Rep Med 2023; 4:101247. [PMID: 37863059 PMCID: PMC10694588 DOI: 10.1016/j.xcrm.2023.101247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 08/17/2023] [Accepted: 09/26/2023] [Indexed: 10/22/2023]
Abstract
Homologous recombination (HR)-mediated DNA repair is a prerequisite for maintaining genome stability. Cancer cells displaying HR deficiency (HRD) are selectively eliminated by poly(ADP-ribose) polymerase inhibitors (PARPis). To date, sequencing of HR-associated genes and analyzing genome instability have been used as clinical predictions for PARPi therapy. However, these genetic tests cannot reflect dynamic changes in the HR status. Here, we have developed a virus- and activity-based functional assay to quantify real-time HR activity directly. Instead of focusing on a few HR-associated genes, our functional assay detects endpoint HR activity and establishes an activity threshold for identifying HRD across cancer types, validated by PARPi sensitivity and BRCA status. Notably, this fluorescence-based assay can be applied to primary ovarian cancer cells from patients to reflect their level of HRD, which is associated with survival benefits. Thus, our work provides a functional test to predict the response of primary cancer cells to PARPis.
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Affiliation(s)
- Chih-Ying Lee
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Wen-Fang Cheng
- Department of Obstetrics & Gynecology, National Taiwan University Hospital, Taipei, Taiwan
| | - Po-Han Lin
- Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, Taiwan; Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Yu-Li Chen
- Department of Obstetrics & Gynecology, National Taiwan University Hospital, Taipei, Taiwan
| | - Shih-Han Huang
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Kai-Hang Lei
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Ko-Yu Chang
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Min-Yu Ko
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Peter Chi
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan; Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.
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17
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Kramer CJH, Llop‐Guevara A, Yaniz‐Galende E, Pellegrino B, ter Haar NT, Herencia‐Ropero A, Campanini N, Musolino A, Bosse T, Leary A, Serra V, Vreeswijk MPG. RAD51 as a biomarker for homologous recombination deficiency in high-grade serous ovarian carcinoma: robustness and interobserver variability of the RAD51 test. J Pathol Clin Res 2023; 9:442-448. [PMID: 37504067 PMCID: PMC10556259 DOI: 10.1002/cjp2.336] [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: 04/19/2023] [Revised: 05/30/2023] [Accepted: 07/02/2023] [Indexed: 07/29/2023]
Abstract
The RAD51 test is emerging as a promising biomarker for the assessment of functional homologous recombination deficiency (HRD). Yet, the robustness and reproducibility of the immunofluorescence-based RAD51 test, in different academic laboratories, have not been systematically investigated. Therefore, we tested the performance of the RAD51 assay in formalin-fixed paraffin-embedded (FFPE) high-grade serous ovarian carcinoma (HGSOC) samples in four European laboratories. Here, we confirm that subtle differences in staining procedures result in low variability of RAD51 and γH2AX scores. However, substantial variability in RAD51 scoring was observed in some samples, likely due to complicating technical and biological features, such as high RAD51 signal-to-noise ratio and RAD51 heterogeneity. These results support the need to identify and perform additional quality control steps and/or automating image analysis. Altogether, resolving technical issues should be a priority, as identifying tumours with functional HRD is urgently needed to guide the individual treatment of HGSOC patients. Follow-up studies are needed to define the key tissue quality requirements to assess HRD by RAD51 in FFPE tumour samples, as this test could help in guiding the individual treatment of HGSOC patients.
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Affiliation(s)
- Claire JH Kramer
- Department of PathologyLeiden University Medical CenterLeidenThe Netherlands
| | - Alba Llop‐Guevara
- Experimental Therapeutics GroupVall d'Hebron Institute of OncologyBarcelonaSpain
| | | | - Benedetta Pellegrino
- Department of Medicine and SurgeryUniversity of ParmaParmaItaly
- Medical Oncology and Breast UnitUniversity Hospital of ParmaParmaItaly
| | - Natalja T ter Haar
- Department of PathologyLeiden University Medical CenterLeidenThe Netherlands
| | | | - Nicoletta Campanini
- Department of Medicine and SurgeryUniversity of ParmaParmaItaly
- Medical Oncology and Breast UnitUniversity Hospital of ParmaParmaItaly
| | - Antonino Musolino
- Department of Medicine and SurgeryUniversity of ParmaParmaItaly
- Medical Oncology and Breast UnitUniversity Hospital of ParmaParmaItaly
| | - Tjalling Bosse
- Department of PathologyLeiden University Medical CenterLeidenThe Netherlands
| | - Alexandra Leary
- Department of OncologyInstitute Gustave RoussyVillejuifFrance
| | - Violeta Serra
- Experimental Therapeutics GroupVall d'Hebron Institute of OncologyBarcelonaSpain
| | - Maaike PG Vreeswijk
- Department of Human GeneticsLeiden University Medical CenterLeidenThe Netherlands
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18
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Hong L, Braden DC, Zhao Y, Skoko JJ, Chang F, Woodcock SR, Uvalle C, Casey A, Wood K, Salvatore SR, Asan A, Harkness T, Fagunloye A, Razzaghi M, Straub A, Spies M, Brown DD, Lee AV, Schopfer F, Freeman BA, Neumann CA. Small molecule nitroalkenes inhibit RAD51-mediated homologous recombination and amplify triple-negative breast cancer cell killing by DNA-directed therapies. Redox Biol 2023; 66:102856. [PMID: 37633047 PMCID: PMC10472314 DOI: 10.1016/j.redox.2023.102856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/09/2023] [Accepted: 08/16/2023] [Indexed: 08/28/2023] Open
Abstract
Nitro fatty acids (NO2-FAs) are endogenously generated lipid signaling mediators from metabolic and inflammatory reactions between conjugated diene fatty acids and nitric oxide or nitrite-derived reactive species. NO2-FAs undergo reversible Michael addition with hyperreactive protein cysteine thiolates to induce posttranslational protein modifications that can impact protein function. Herein, we report a novel mechanism of action of natural and non-natural nitroalkenes structurally similar to (E) 10-nitro-octadec-9-enoic acid (CP-6), recently de-risked by preclinical Investigational New Drug-enabling studies and Phase 1 and Phase 2 clinical trials and found to induce DNA damage in a TNBC xenograft by inhibiting homologous-recombination (HR)-mediated repair of DNA double-strand breaks (DSB). CP-6 specifically targets Cys319, essential in RAD51-controlled HR-mediated DNA DSB repair in cells. A nitroalkene library screen identified two structurally different nitroalkenes, a non-natural fatty acid [(E) 8-nitro-nonadec-7-enoic acid (CP-8)] and a dicarboxylate ester [dimethyl (E)nitro-oct-4-enedioate (CP-23)] superior to CP-6 in TNBC cells killing, synergism with three different inhibitors of the poly ADP-ribose polymerase (PARP) and γ-IR. CP-8 and CP-23 effectively inhibited γ-IR-induced RAD51 foci formation and HR in a GFP-reported assay but did not affect benign human epithelial cells or cell cycle phases. In vivo, CP-8 and CP-23's efficacies diverged as only CP-8 showed promising anticancer activities alone and combined with the PARP inhibitor talazoparib in an HR-proficient TNBC mouse model. As preliminary preclinical toxicology analysis also suggests CP-8 as safe, our data endorse CP-8 as a novel anticancer molecule for treating cancers sensitive to homologous recombination-mediated DNA repair inhibitors.
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Affiliation(s)
- Lisa Hong
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA; Women's Cancer Research Center, UPMC Hillman Cancer Center, Magee-Women's Research Institute, Pittsburgh, PA, USA
| | - Dennis C Braden
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA; Women's Cancer Research Center, UPMC Hillman Cancer Center, Magee-Women's Research Institute, Pittsburgh, PA, USA
| | - Yaoning Zhao
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA; Women's Cancer Research Center, UPMC Hillman Cancer Center, Magee-Women's Research Institute, Pittsburgh, PA, USA; School of Medicine, Tsinghua University, Beijing, China
| | - John J Skoko
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA; Women's Cancer Research Center, UPMC Hillman Cancer Center, Magee-Women's Research Institute, Pittsburgh, PA, USA
| | - Fei Chang
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Steven R Woodcock
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Crystall Uvalle
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Allison Casey
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA; Women's Cancer Research Center, UPMC Hillman Cancer Center, Magee-Women's Research Institute, Pittsburgh, PA, USA
| | - Katherine Wood
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sonia R Salvatore
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Alparslan Asan
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA; Women's Cancer Research Center, UPMC Hillman Cancer Center, Magee-Women's Research Institute, Pittsburgh, PA, USA
| | - Trey Harkness
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA; Women's Cancer Research Center, UPMC Hillman Cancer Center, Magee-Women's Research Institute, Pittsburgh, PA, USA
| | - Adeola Fagunloye
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA; Women's Cancer Research Center, UPMC Hillman Cancer Center, Magee-Women's Research Institute, Pittsburgh, PA, USA
| | - Mortezaali Razzaghi
- Department of Biochemistry and Molecular Biology, University of Iowa, Iowa City, IA, USA
| | - Adam Straub
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Maria Spies
- Department of Biochemistry and Molecular Biology, University of Iowa, Iowa City, IA, USA
| | - Daniel D Brown
- Institute for Precision Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Adrian V Lee
- Institute for Precision Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Francisco Schopfer
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Bruce A Freeman
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Carola A Neumann
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA; Women's Cancer Research Center, UPMC Hillman Cancer Center, Magee-Women's Research Institute, Pittsburgh, PA, USA.
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19
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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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20
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Ganzinelli M, Guffanti F, Ianza A, Sobhani N, Crovella S, Zanconati F, Bottin C, Confalonieri M, Fumagalli S, Guglielmi A, Generali D, Damia G. Epithelioid Mesothelioma Patients with Very Long Survival Display Defects in DNA Repair. Cancers (Basel) 2023; 15:4309. [PMID: 37686585 PMCID: PMC10486625 DOI: 10.3390/cancers15174309] [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: 06/28/2023] [Revised: 08/21/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
AIM DNA repair has an important role in malignant pleural mesothelioma (MPM) tumorigenesis and progression. Prognostic/predictive biomarkers for better management of MPM patients are needed. In the present manuscript, we analyzed the expression of more than 700 genes in a cohort of MPM patients to possibly find biomarkers correlated with survival. METHODS A total of 54 MPM patients, all with epithelioid histology, whose survival follow-up and formalin-fixed paraffin-embedded tumors were available, were included in the study. Gene expression profiles were evaluated using a Nanostring platform analyzing 760 genes involved in different cellular pathways. The percentages of proliferating tumor cells positive for RAD51 and BRCA1 foci were evaluated using an immunofluorescence assay, as a readout of homologous recombination repair status. RESULTS Patient median survival time was 16.9 months, and based on this value, they were classified as long and short survivors (LS/SS) with, respectively, an overall survival ≥ and <16.9 months as well as very long and very short survivors (VLS/VSS) with an overall survival ≥ than 33.8 and < than 8.45 months. A down-regulation in the DNA damage/repair expression score was observed in LS and VLS as compared to SS and VSS. These findings were validated by the lower number of both RAD51 and BRCA1-positive tumor cells in VLS as compared to VSS. CONCLUSIONS The down-regulation of DNA repair signature in VLS was functionally validated by a lower % of RAD51 and BRCA1-positive tumor cells. If these data can be corroborated in a prospective trial, an easy, cost-effective test could be routinely used to better manage treatment in MPM patients.
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Affiliation(s)
- Monica Ganzinelli
- Unit of Thoracic Oncology, Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy;
| | - Federica Guffanti
- Laboratory of Preclinical Gynecological Oncology, Department of Experimental Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy;
| | - Anna Ianza
- Oncology Department, University Health Organization Giuliano Isontina, ASUGI, Piazza Ospitale 1, 34129 Trieste, Italy; (A.I.); (A.G.); (D.G.)
| | - Navid Sobhani
- Department of Medical, Surgical and Health Sciences, University of Trieste, 34139 Trieste, Italy; (N.S.); (F.Z.); (C.B.); (M.C.)
| | - Sergio Crovella
- IRCCS Burlo Garofolo, Via dell’Istria 65/1, 34137 Trieste, Italy;
| | - Fabrizio Zanconati
- Department of Medical, Surgical and Health Sciences, University of Trieste, 34139 Trieste, Italy; (N.S.); (F.Z.); (C.B.); (M.C.)
| | - Cristina Bottin
- Department of Medical, Surgical and Health Sciences, University of Trieste, 34139 Trieste, Italy; (N.S.); (F.Z.); (C.B.); (M.C.)
| | - Marco Confalonieri
- Department of Medical, Surgical and Health Sciences, University of Trieste, 34139 Trieste, Italy; (N.S.); (F.Z.); (C.B.); (M.C.)
| | - Stefano Fumagalli
- Laboratory of Biology of Neurodegenerative Disorders, Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy;
| | - Alessandra Guglielmi
- Oncology Department, University Health Organization Giuliano Isontina, ASUGI, Piazza Ospitale 1, 34129 Trieste, Italy; (A.I.); (A.G.); (D.G.)
| | - Daniele Generali
- Oncology Department, University Health Organization Giuliano Isontina, ASUGI, Piazza Ospitale 1, 34129 Trieste, Italy; (A.I.); (A.G.); (D.G.)
| | - Giovanna Damia
- Laboratory of Preclinical Gynecological Oncology, Department of Experimental Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy;
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21
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Karmokar A, Sargeant R, Hughes AM, Baakza H, Wilson Z, Talbot S, Bloomfield S, Leo E, Jones GN, Likhatcheva M, Tobalina L, Dean E, Cadogan EB, Lau A. Relevance of ATM Status in Driving Sensitivity to DNA Damage Response Inhibitors in Patient-Derived Xenograft Models. Cancers (Basel) 2023; 15:4195. [PMID: 37627223 PMCID: PMC10453052 DOI: 10.3390/cancers15164195] [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: 07/14/2023] [Revised: 08/05/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
Ataxia-telangiectasia mutated gene (ATM) is a key component of the DNA damage response (DDR) and double-strand break repair pathway. The functional loss of ATM (ATM deficiency) is hypothesised to enhance sensitivity to DDR inhibitors (DDRi). Whole-exome sequencing (WES), immunohistochemistry (IHC), and Western blotting (WB) were used to characterise the baseline ATM status across a panel of ATM mutated patient-derived xenograft (PDX) models from a range of tumour types. Antitumour efficacy was assessed with poly(ADP-ribose)polymerase (PARP, olaparib), ataxia- telangiectasia and rad3-related protein (ATR, AZD6738), and DNA-dependent protein kinase (DNA-PK, AZD7648) inhibitors as a monotherapy or in combination to associate responses with ATM status. Biallelic truncation/frameshift ATM mutations were linked to ATM protein loss while monoallelic or missense mutations, including the clinically relevant recurrent R3008H mutation, did not confer ATM protein loss by IHC. DDRi agents showed a mixed response across the PDX's but with a general trend toward greater activity, particularly in combination in models with biallelic ATM mutation and protein loss. A PDX with an ATM splice-site mutation, 2127T > C, with a high relative baseline ATM expression and KAP1 phosphorylation responded to all DDRi treatments. These data highlight the heterogeneity and complexity in describing targetable ATM-deficiencies and the fact that current patient selection biomarker methods remain imperfect; although, complete ATM loss was best able to enrich for DDRi sensitivity.
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Affiliation(s)
- Ankur Karmokar
- Bioscience, Oncology R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - Rebecca Sargeant
- Imaging & Data Analytics, Clinical Pharmacology & Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - Adina M. Hughes
- Bioscience, Oncology R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - Hana Baakza
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - Zena Wilson
- Bioscience, Oncology R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - Sara Talbot
- Bioscience, Oncology R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | | | - Elisabetta Leo
- Bioscience, Oncology R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - Gemma N. Jones
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - Maria Likhatcheva
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - Luis Tobalina
- Oncology Data Science, Oncology R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - Emma Dean
- Oncology R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | | | - Alan Lau
- Bioscience, Oncology R&D, AstraZeneca, Cambridge CB2 0AA, UK
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22
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Pikkusaari S, Tumiati M, Virtanen A, Oikkonen J, Li Y, Perez-Villatoro F, Muranen T, Salko M, Huhtinen K, Kanerva A, Koskela H, Tapper J, Koivisto-Korander R, Joutsiniemi T, Haltia UM, Lassus H, Hautaniemi S, Färkkilä A, Hynninen J, Hietanen S, Carpén O, Kauppi L. Functional Homologous Recombination Assay on FFPE Specimens of Advanced High-Grade Serous Ovarian Cancer Predicts Clinical Outcomes. Clin Cancer Res 2023; 29:3110-3123. [PMID: 36805632 PMCID: PMC10425726 DOI: 10.1158/1078-0432.ccr-22-3156] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/29/2022] [Accepted: 02/15/2023] [Indexed: 02/22/2023]
Abstract
PURPOSE Deficiency in homologous recombination (HR) repair of DNA damage is characteristic of many high-grade serous ovarian cancers (HGSC). It is imperative to identify patients with homologous recombination-deficient (HRD) tumors as they are most likely to benefit from platinum-based chemotherapy and PARP inhibitors (PARPi). Existing methods measure historical, not necessarily current HRD and/or require high tumor cell content, which is not achievable for many patients. We set out to develop a clinically feasible assay for identifying functionally HRD tumors that can predict clinical outcomes. EXPERIMENTAL DESIGN We quantified RAD51, a key HR protein, in immunostained formalin-fixed, paraffin-embedded (FFPE) tumor samples obtained from chemotherapy-naïve and neoadjuvant chemotherapy (NACT)-treated HGSC patients. We defined cutoffs for functional HRD separately for these sample types, classified the patients accordingly as HRD or HR-proficient, and analyzed correlations with clinical outcomes. From the same specimens, genomics-based HRD estimates (HR gene mutations, genomic signatures, and genomic scars) were also determined, and compared with functional HR (fHR) status. RESULTS fHR status significantly predicted several clinical outcomes, including progression-free survival (PFS) and overall survival (OS), when determined from chemo-naïve (PFS, P < 0.0001; OS, P < 0.0001) as well as NACT-treated (PFS, P < 0.0001; OS, P = 0.0033) tumor specimens. The fHR test also identified as HRD those PARPi-at-recurrence-treated patients with longer OS (P = 0.0188). CONCLUSIONS We developed an fHR assay performed on routine FFPE specimens, obtained from either chemo-naïve or NACT-treated HGSC patients, that can significantly predict real-world platinum-based chemotherapy and PARPi response. See related commentary by Garg and Oza, p. 2957.
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Affiliation(s)
- Sanna Pikkusaari
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Manuela Tumiati
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Anni Virtanen
- Department of Pathology, University of Helsinki and HUS Diagnostic Center, Helsinki University Hospital, Helsinki, Finland
| | - Jaana Oikkonen
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Yilin Li
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Fernando Perez-Villatoro
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Taru Muranen
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Matilda Salko
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Kaisa Huhtinen
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Anna Kanerva
- Department of Obstetrics and Gynecology, Helsinki University Hospital, Helsinki, Finland
| | - Heidi Koskela
- Department of Obstetrics and Gynecology, Turku University Hospital, Turku, Finland
| | - Johanna Tapper
- Department of Obstetrics and Gynecology, Helsinki University Hospital, Helsinki, Finland
| | | | - Titta Joutsiniemi
- Department of Obstetrics and Gynecology, Turku University Hospital, Turku, Finland
| | - Ulla-Maija Haltia
- Department of Obstetrics and Gynecology, Helsinki University Hospital, Helsinki, Finland
| | - Heini Lassus
- Department of Obstetrics and Gynecology, Helsinki University Hospital, Helsinki, Finland
| | - Sampsa Hautaniemi
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Anniina Färkkilä
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- iCAN digital precision cancer medicine flagship, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Johanna Hynninen
- Department of Obstetrics and Gynecology, Turku University Hospital, Turku, Finland
| | - Sakari Hietanen
- Department of Obstetrics and Gynecology, Turku University Hospital, Turku, Finland
| | - Olli Carpén
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Pathology, University of Helsinki and HUS Diagnostic Center, Helsinki University Hospital, Helsinki, Finland
| | - Liisa Kauppi
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- iCAN digital precision cancer medicine flagship, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
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23
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Hong L, Braden DC, Zhao Y, Skoko JJ, Chang F, Woodcock SR, Uvalle C, Casey A, Wood K, Salvatore SR, Asan A, Harkness T, Fagunloye A, Razzaghi M, Straub A, Spies M, Brown DD, Lee AV, Schopfer F, Freeman BA, Neumann CA. Small molecule nitroalkenes inhibit RAD51-mediated homologous recombination and amplify triple-negative breast cancer cell killing by DNA-directed therapies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.11.552990. [PMID: 37645906 PMCID: PMC10462009 DOI: 10.1101/2023.08.11.552990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Nitro fatty acids (NO 2 -FAs) are endogenously generated lipid signaling mediators from metabolic and inflammatory reactions between conjugated diene fatty acids and nitric oxide or nitrite-derived reactive species. NO 2 -FAs undergo reversible Michael addition with hyperreactive protein cysteine thiolates to induce posttranslational protein modifications that can impact protein function. Herein, we report a novel mechanism of action of natural and non-natural nitroalkenes structurally similar to ( E ) 10-nitro-octadec-9-enoic acid (CP-6), recently de-risked by preclinical Investigational New Drug-enabling studies and Phase 1 and Phase 2 clinical trials and found to induce DNA damage in a TNBC xenograft by inhibiting homologous-recombination (HR)-mediated repair of DNA double-strand breaks (DSB). CP-6 specifically targets Cys319, essential in RAD51-controlled HR-mediated DNA DSB repair in cells. A nitroalkene library screen identified two structurally different nitroalkenes, a non-natural fatty acid [( E ) 8-nitro- nonadec-7-enoic acid (CP-8)] and a dicarboxylate ester [dimethyl ( E )nitro-oct-4-enedioate (CP- 23)] superior to CP-6 in TNBC cells killing, synergism with three different inhibitors of the poly ADP-ribose polymerase (PARP) and γ-IR. CP-8 and CP-23 effectively inhibited γ-IR-induced RAD51 foci formation and HR in a GFP-reported assay but did not affect benign human epithelial cells or cell cycle phases. In vivo, CP-8 and CP-23's efficacies diverged as only CP-8 showed promising anticancer activities alone and combined with the PARP inhibitor talazoparib in an HR-proficient TNBC mouse model. As preliminary preclinical toxicology analysis also suggests CP-8 as safe, our data endorse CP-8 as a novel anticancer molecule for treating cancers sensitive to homologous recombination-mediated DNA repair inhibitors.
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24
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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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25
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Hutten SJ, de Bruijn R, Lutz C, Badoux M, Eijkman T, Chao X, Ciwinska M, Sheinman M, Messal H, Herencia-Ropero A, Kristel P, Mulder L, van der Waal R, Sanders J, Almekinders MM, Llop-Guevara A, Davies HR, van Haren MJ, Martin NI, Behbod F, Nik-Zainal S, Serra V, van Rheenen J, Lips EH, Wessels LFA, Wesseling J, Scheele CLGJ, Jonkers J. A living biobank of patient-derived ductal carcinoma in situ mouse-intraductal xenografts identifies risk factors for invasive progression. Cancer Cell 2023; 41:986-1002.e9. [PMID: 37116492 PMCID: PMC10171335 DOI: 10.1016/j.ccell.2023.04.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 02/21/2023] [Accepted: 04/04/2023] [Indexed: 04/30/2023]
Abstract
Ductal carcinoma in situ (DCIS) is a non-obligate precursor of invasive breast cancer (IBC). Due to a lack of biomarkers able to distinguish high- from low-risk cases, DCIS is treated similar to early IBC even though the minority of untreated cases eventually become invasive. Here, we characterized 115 patient-derived mouse-intraductal (MIND) DCIS models reflecting the full spectrum of DCIS observed in patients. Utilizing the possibility to follow the natural progression of DCIS combined with omics and imaging data, we reveal multiple prognostic factors for high-risk DCIS including high grade, HER2 amplification, expansive 3D growth, and high burden of copy number aberrations. In addition, sequential transplantation of xenografts showed minimal phenotypic and genotypic changes over time, indicating that invasive behavior is an intrinsic phenotype of DCIS and supporting a multiclonal evolution model. Moreover, this study provides a collection of 19 distributable DCIS-MIND models spanning all molecular subtypes.
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Affiliation(s)
- Stefan J Hutten
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands
| | - Roebi de Bruijn
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands; Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Catrin Lutz
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands
| | - Madelon Badoux
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands
| | - Timo Eijkman
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands
| | - Xue Chao
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands
| | - Marta Ciwinska
- Center for Cancer Biology, VIB, Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Michael Sheinman
- Oncode Institute, Amsterdam, the Netherlands; Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Hendrik Messal
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands
| | - Andrea Herencia-Ropero
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain; Department of Biochemistry and Molecular Biology, Autonomous University of Barcelona, Barcelona, Spain
| | - Petra Kristel
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Lennart Mulder
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Rens van der Waal
- Core Facility Molecular Pathology & Biobanking, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Joyce Sanders
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Mathilde M Almekinders
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Alba Llop-Guevara
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Helen R Davies
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, CB2 0QQ Cambridge, UK; Early Cancer Institute, University of Cambridge, CB2 0XZ Cambridge, UK
| | - Matthijs J van Haren
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, 2302 BH Leiden, the Netherlands
| | - Nathaniel I Martin
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, 2302 BH Leiden, the Netherlands
| | - Fariba Behbod
- Department of Pathology and Laboratory Medicine, The University of Kansas Medical Center, Kansas City, KS 66103, USA
| | - Serena Nik-Zainal
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, CB2 0QQ Cambridge, UK; Early Cancer Institute, University of Cambridge, CB2 0XZ Cambridge, UK
| | - Violeta Serra
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Jacco van Rheenen
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands
| | - Esther H Lips
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Lodewyk F A Wessels
- Oncode Institute, Amsterdam, the Netherlands; Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Jelle Wesseling
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands; Division of Diagnostic Oncology, Netherlands Cancer Institute - Antonie van Leeuwenhoek Hospital, 1066 CX Amsterdam, the Netherlands; Department of Pathology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Colinda L G J Scheele
- Center for Cancer Biology, VIB, Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Jos Jonkers
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands.
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26
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Martini G, Belli V, Napolitano S, Ciaramella V, Ciardiello D, Belli A, Izzo F, Avallone A, Selvaggi F, Menegon Tasselli F, Santaniello W, Franco R, Puig I, Ramirez L, Chicote I, Mancuso F, Caratu G, Serres X, Fasani R, Jimenez J, Ros J, Baraibar I, Mulet N, Della Corte CM, Troiani T, Vivancos A, Dienstmann R, Elez E, Palmer HG, Tabernero J, Martinelli E, Ciardiello F, Argilés G. Establishment of patient-derived tumor organoids to functionally inform treatment decisions in metastatic colorectal cancer. ESMO Open 2023; 8:101198. [PMID: 37119788 DOI: 10.1016/j.esmoop.2023.101198] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/16/2023] [Accepted: 02/22/2023] [Indexed: 05/01/2023] Open
Abstract
BACKGROUND Metastatic colorectal cancer (mCRC) patients tend to have modest benefits from molecularly driven therapeutics. Patient-derived tumor organoids (PDTOs) represent an unmatched model to elucidate tumor resistance to therapy, due to their high capacity to resemble tumor characteristics. MATERIALS AND METHODS We used viable tumor tissue from two cohorts of patients with mCRC, naïve or refractory to treatment, respectively, for generating PDTOs. The derived models were subjected to a 6-day drug screening assay (DSA) with a comprehensive pipeline of chemotherapy and targeted drugs against almost all the actionable mCRC molecular drivers. For the second cohort DSA data were matched with those from PDTO genotyping. RESULTS A total of 40 PDTOs included in the two cohorts were derived from mCRC primary tumors or metastases. The first cohort included 31 PDTOs derived from patients treated in front line. For this cohort, DSA results were matched with patient responses. Moreover, RAS/BRAF mutational status was matched with DSA cetuximab response. Ten out of 12 (83.3%) RAS wild-type PDTOs responded to cetuximab, while all the mutant PDTOs, 8 out of 8 (100%), were resistant. For the second cohort (chemorefractory patients), we used part of tumor tissue for genotyping. Four out of nine DSA/genotyping data resulted applicable in the clinic. Two RAS-mutant mCRC patients have been treated with FOLFOX-bevacizumab and mitomycin-capecitabine in third line, respectively, based on DSA results, obtaining disease control. One patient was treated with nivolumab-second mitochondrial-derived activator of caspases mimetic (phase I trial) due to high tumor mutational burden at genotyping, experiencing stable disease. In one case, the presence of BRCA2 mutation correlated with DSA sensitivity to olaparib; however, the patient could not receive the therapy. CONCLUSIONS Using CRC as a model, we have designed and validated a clinically applicable methodology to potentially inform clinical decisions with functional data. Undoubtedly, further larger analyses are needed to improve methodology success rates and propose suitable treatment strategies for mCRC patients.
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Affiliation(s)
- G Martini
- Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Naples
| | - V Belli
- Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Naples
| | - S Napolitano
- Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Naples
| | - V Ciaramella
- Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Naples
| | - D Ciardiello
- Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Naples
| | - A Belli
- Hepatobiliary Surgical Oncology Unit, Istituto Nazionale Tumori-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Fondazione G. Pascale, Napoli
| | - F Izzo
- Hepatobiliary Surgical Oncology Unit, Istituto Nazionale Tumori-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Fondazione G. Pascale, Napoli
| | - A Avallone
- Experimental Clinical Abdominal Oncology Unit, Istituto Nazionale Tumori-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Fondazione G. Pascale, Napoli
| | - F Selvaggi
- Department of Advanced Medical and Surgical Sciences, Università degli Studi della Campania Luigi Vanvitelli, Naples
| | - F Menegon Tasselli
- Department of Advanced Medical and Surgical Sciences, Università degli Studi della Campania Luigi Vanvitelli, Naples
| | - W Santaniello
- Hepatobiliary Surgical Oncology Unit, AORN Cardarelli, Naples
| | - R Franco
- Pathology Unit, Department of Mental and Physical Health and Preventive Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - I Puig
- Translational Program, Stem Cells and Cancer Laboratory, Vall D'Hebron Institute of Oncology (VHIO), Barcelona
| | - L Ramirez
- Translational Program, Stem Cells and Cancer Laboratory, Vall D'Hebron Institute of Oncology (VHIO), Barcelona
| | - I Chicote
- Translational Program, Stem Cells and Cancer Laboratory, Vall D'Hebron Institute of Oncology (VHIO), Barcelona
| | - F Mancuso
- Cancer Genomics Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona
| | - G Caratu
- Cancer Genomics Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona
| | - X Serres
- Department of Interventional Radiology, Hospital Universitari Vall d'Hebron, Barcelona
| | - R Fasani
- Molecular Oncology Lab, Vall d'Hebron Institute of Oncology, Barcelona
| | - J Jimenez
- Molecular Oncology Lab, Vall d'Hebron Institute of Oncology, Barcelona
| | - J Ros
- Vall d'Hebron Hospital Campus and Institute of Oncology (VHIO), Barcelona
| | - I Baraibar
- Vall d'Hebron Hospital Campus and Institute of Oncology (VHIO), Barcelona
| | - N Mulet
- B-ARGO Badalona Applied Research Group in Oncology, Catalan Institute of Oncology, Badalona
| | - C M Della Corte
- Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Naples
| | - T Troiani
- Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Naples
| | - A Vivancos
- Cancer Genomics Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona
| | - R Dienstmann
- Oncology Data Science, Vall d'Hebron Institute of Oncology, Barcelona
| | - E Elez
- Vall d'Hebron Hospital Campus and Institute of Oncology (VHIO), Barcelona
| | - H G Palmer
- Translational Program, Stem Cells and Cancer Laboratory, Vall D'Hebron Institute of Oncology (VHIO), Barcelona
| | - J Tabernero
- Vall d'Hebron Hospital Campus and Institute of Oncology (VHIO), Barcelona
| | - E Martinelli
- Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Naples
| | - F Ciardiello
- Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Naples
| | - G Argilés
- Vall d'Hebron Hospital Campus and Institute of Oncology (VHIO), Barcelona; Universitat Autònoma de Barcelona, Barcelona, Spain; Memorial Sloan Kettering Cancer Center, New York, USA.
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27
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Velazquez C, Orhan E, Tabet I, Fenou L, Orsetti B, Adélaïde J, Guille A, Thézénas S, Crapez E, Colombo PE, Chaffanet M, Birnbaum D, Sardet C, Jacot W, Theillet C. BRCA1-methylated triple negative breast cancers previously exposed to neoadjuvant chemotherapy form RAD51 foci and respond poorly to olaparib. Front Oncol 2023; 13:1125021. [PMID: 37007122 PMCID: PMC10064050 DOI: 10.3389/fonc.2023.1125021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 03/03/2023] [Indexed: 03/19/2023] Open
Abstract
BackgroundAbout 15% of Triple-Negative-Breast-Cancer (TNBC) present silencing of the BRCA1 promoter methylation and are assumed to be Homologous Recombination Deficient (HRD). BRCA1-methylated (BRCA1-Me) TNBC could, thus, be eligible to treatment based on PARP-inhibitors or Platinum salts. However, their actual HRD status is discussed, as these tumors are suspected to develop resistance after chemotherapy exposure.MethodsWe interrogated the sensitivity to olaparib vs. carboplatin of 8 TNBC Patient-Derived Xenografts (PDX) models. Four PDX corresponded to BRCA1-Me, of which 3 were previously exposed to NeoAdjuvant-Chemotherapy (NACT). The remaining PDX models corresponded to two BRCA1-mutated (BRCA1-Mut) and two BRCA1-wild type PDX that were respectively included as positive and negative controls. The HRD status of our PDX models was assessed using both genomic signatures and the functional BRCA1 and RAD51 nuclear foci formation assay. To assess HR restoration associated with olaparib resistance, we studied pairs of BRCA1 deficient cell lines and their resistant subclones.ResultsThe 3 BRCA1-Me PDX that had been exposed to NACT responded poorly to olaparib, likewise BRCA1-WT PDX. Contrastingly, 3 treatment-naïve BRCA1-deficient PDX (1 BRCA1-Me and 2 BRCA1-mutated) responded to olaparib. Noticeably, the three olaparib-responsive PDX scored negative for BRCA1- and RAD51-foci, whereas all non-responsive PDX models, including the 3 NACT-exposed BRCA1-Me PDX, scored positive for RAD51-foci. This suggested HRD in olaparib responsive PDX, while non-responsive models were HR proficient. These results were consistent with observations in cell lines showing a significant increase of RAD51-foci in olaparib-resistant subclones compared with sensitive parental cells, suggesting HR restoration in these models.ConclusionOur results thus support the notion that the actual HRD status of BRCA1-Me TNBC, especially if previously exposed to chemotherapy, may be questioned and should be verified using the BRCA1- and RAD51-foci assay.
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Affiliation(s)
- Carolina Velazquez
- Institut de Recherche en Cancérologie de Montpellier, IRCM U1194, Montpellier University, INSERM, ICM, CNRS, Montpellier, France
| | - Esin Orhan
- Institut de Recherche en Cancérologie de Montpellier, IRCM U1194, Montpellier University, INSERM, ICM, CNRS, Montpellier, France
| | - Imene Tabet
- Institut de Recherche en Cancérologie de Montpellier, IRCM U1194, Montpellier University, INSERM, ICM, CNRS, Montpellier, France
| | - Lise Fenou
- Institut de Recherche en Cancérologie de Montpellier, IRCM U1194, Montpellier University, INSERM, ICM, CNRS, Montpellier, France
| | - Béatrice Orsetti
- Institut de Recherche en Cancérologie de Montpellier, IRCM U1194, Montpellier University, INSERM, ICM, CNRS, Montpellier, France
| | - José Adélaïde
- Centre de Recherche en Cancérologie de Marseille, CRCM UMR1068, Aix-Marseille University, IPC, CNRS, Marseille, France
| | - Arnaud Guille
- Centre de Recherche en Cancérologie de Marseille, CRCM UMR1068, Aix-Marseille University, IPC, CNRS, Marseille, France
| | - Simon Thézénas
- Biometry Unit, Institut du Cancer de Montpellier, Montpellier, France
| | - Evelyne Crapez
- Unité de Recherche Translationnelle, Institut du Cancer de Montpellier, Montpellier, France
| | - Pierre-Emmanuel Colombo
- Institut de Recherche en Cancérologie de Montpellier, IRCM U1194, Montpellier University, INSERM, ICM, CNRS, Montpellier, France
- Oncological Surgery, Institut du Cancer de Montpellier, Montpellier, France
| | - Max Chaffanet
- Centre de Recherche en Cancérologie de Marseille, CRCM UMR1068, Aix-Marseille University, IPC, CNRS, Marseille, France
| | - Daniel Birnbaum
- Centre de Recherche en Cancérologie de Marseille, CRCM UMR1068, Aix-Marseille University, IPC, CNRS, Marseille, France
| | - Claude Sardet
- Institut de Recherche en Cancérologie de Montpellier, IRCM U1194, Montpellier University, INSERM, ICM, CNRS, Montpellier, France
| | - William Jacot
- Institut de Recherche en Cancérologie de Montpellier, IRCM U1194, Montpellier University, INSERM, ICM, CNRS, Montpellier, France
- Clinical Oncology, Institut du Cancer de Montpellier, Montpellier, France
| | - Charles Theillet
- Institut de Recherche en Cancérologie de Montpellier, IRCM U1194, Montpellier University, INSERM, ICM, CNRS, Montpellier, France
- *Correspondence: Charles Theillet,
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28
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Loeffler CML, El Nahhas OSM, Muti HS, Seibel T, Cifci D, van Treeck M, Gustav M, Carrero ZI, Gaisa NT, Lehmann KV, Leary A, Selenica P, Reis-Filho JS, Bruechle NO, Kather JN. Direct prediction of Homologous Recombination Deficiency from routine histology in ten different tumor types with attention-based Multiple Instance Learning: a development and validation study. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.08.23286975. [PMID: 36945540 PMCID: PMC10029072 DOI: 10.1101/2023.03.08.23286975] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Background Homologous Recombination Deficiency (HRD) is a pan-cancer predictive biomarker that identifies patients who benefit from therapy with PARP inhibitors (PARPi). However, testing for HRD is highly complex. Here, we investigated whether Deep Learning can predict HRD status solely based on routine Hematoxylin & Eosin (H&E) histology images in ten cancer types. Methods We developed a fully automated deep learning pipeline with attention-weighted multiple instance learning (attMIL) to predict HRD status from histology images. A combined genomic scar HRD score, which integrated loss of heterozygosity (LOH), telomeric allelic imbalance (TAI) and large-scale state transitions (LST) was calculated from whole genome sequencing data for n=4,565 patients from two independent cohorts. The primary statistical endpoint was the Area Under the Receiver Operating Characteristic curve (AUROC) for the prediction of genomic scar HRD with a clinically used cutoff value. Results We found that HRD status is predictable in tumors of the endometrium, pancreas and lung, reaching cross-validated AUROCs of 0.79, 0.58 and 0.66. Predictions generalized well to an external cohort with AUROCs of 0.93, 0.81 and 0.73 respectively. Additionally, an HRD classifier trained on breast cancer yielded an AUROC of 0.78 in internal validation and was able to predict HRD in endometrial, prostate and pancreatic cancer with AUROCs of 0.87, 0.84 and 0.67 indicating a shared HRD-like phenotype is across tumor entities. Conclusion In this study, we show that HRD is directly predictable from H&E slides using attMIL within and across ten different tumor types.
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Affiliation(s)
- Chiara Maria Lavinia Loeffler
- Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany
- Else Kroener Fresenius Center for Digital Health, Medical Faculty Carl Gustav Carus, Technical University Dresden, Dresden, Germany
- Department of Medicine I, University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universitat Dresden, Dresden, Germany
| | - Omar S M El Nahhas
- Else Kroener Fresenius Center for Digital Health, Medical Faculty Carl Gustav Carus, Technical University Dresden, Dresden, Germany
| | - Hannah Sophie Muti
- Else Kroener Fresenius Center for Digital Health, Medical Faculty Carl Gustav Carus, Technical University Dresden, Dresden, Germany
- Department for Visceral, Thoracic and Vascular Surgery, University Hospital Carl Gustav Carus, Technical University Dresden, Dresden, Germany
| | - Tobias Seibel
- Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany
| | - Didem Cifci
- Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany
| | - Marko van Treeck
- Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany
- Else Kroener Fresenius Center for Digital Health, Medical Faculty Carl Gustav Carus, Technical University Dresden, Dresden, Germany
| | - Marco Gustav
- Else Kroener Fresenius Center for Digital Health, Medical Faculty Carl Gustav Carus, Technical University Dresden, Dresden, Germany
| | - Zunamys I Carrero
- Else Kroener Fresenius Center for Digital Health, Medical Faculty Carl Gustav Carus, Technical University Dresden, Dresden, Germany
| | - Nadine T Gaisa
- Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), Germany
| | - Kjong-Van Lehmann
- Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), Germany
| | - Alexandra Leary
- Gynecological Cancer Unit, Department of Medicine, Institut Gustave Roussy, Villejuif, France
| | - Pier Selenica
- Experimental Pathology, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jorge S Reis-Filho
- Experimental Pathology, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nadina Ortiz Bruechle
- Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), Germany
| | - Jakob Nikolas Kather
- Else Kroener Fresenius Center for Digital Health, Medical Faculty Carl Gustav Carus, Technical University Dresden, Dresden, Germany
- Department of Medicine I, University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universitat Dresden, Dresden, Germany
- Pathology & Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
- Medical Oncology, National Center for Tumor Diseases (NCT), University Hospital Heidelberg, Heidelberg, Germany
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29
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Zhu Y, Li Y, Liu W, Zhou R, Tse LA, Wang Y, Li W. Efficacy and safety of treatment regimens for patients with metastatic, locally advanced, or recurrent breast cancer carrying BRCA1/BRCA2 pathogenic variants: A network meta-analysis. Front Oncol 2023; 13:1080297. [PMID: 36865806 PMCID: PMC9971004 DOI: 10.3389/fonc.2023.1080297] [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: 10/26/2022] [Accepted: 01/24/2023] [Indexed: 02/16/2023] Open
Abstract
Objective Patients with breast cancer carrying BRCA1 and BRCA2 genetic alterations show poor prognoses. However, the efficacy of pharmacotherapies for patients with advanced breast cancer carrying BRCA1/2 pathogenic variants remains unclear. This study aimed to conduct a network meta-analysis to assess the efficacy and safety of various pharmacotherapies for patients with metastatic, locally advanced, or recurrent breast cancer carrying BRCA1/BRCA2 pathogenic variants. Methods A literature search was conducted using Embase, PubMed, and Cochrane Library (CENTRAL), from inception to 11th May 2022. The references of included articles were screened to identify relevant literature. This network meta-analysis included patients with metastatic locally advanced or recurrent breast cancer who received pharmacotherapy and carried deleterious variants of BRCA1/2. The Preferred Reporting Items for Systematic Reviews and Meta-analysis (PRISMA) guidelines were followed for conducting and reporting this systematic meta-analysis. The Grading of Recommendations Assessment, Development, and Evaluation (GRADE) method was employed to evaluate evidential certainty. Frequentist random-effect model was applied. Results of objective response rate (ORR), progression-free survival (PFS), overall survival (OS), and rates of any-grade adverse events were presented. Results Nine randomized controlled trials were obtained comprising six treatment regimens, including 1912 patients with pathogenic variants of BRCA1 and BRCA2. The orchestration of PARP inhibitors with platinum-based chemotherapy was found to be the most effective with a pooled odds ratio (OR) of 3.52 (95% CI 2.14, 5.78) for ORR; 1.53 (1.34,1.76), 3.05 (1.79, 5.19), and 5.80 (1.42, 23.77) for 3-, 12-, and 24-month PFS, respectively, and 1.04 (1.00, 1.07), 1.76 (1.25, 2.49) and 2.31 (1.41, 3.77) for 3-, 12-, and 36-month OS, respectively compared to those receiving non-platinum-based chemotherapy. However, it posed an elevated risk of some adverse events. Platinum-based chemotherapy alone or PARP inhibitors markedly improved ORR, PFS, and OS compared to non-platinum-based chemotherapy. Interestingly, platinum-based chemotherapy surpassed PARP inhibitors in terms of efficacy. Evidence on programmed death-ligand 1(PD-L1) inhibitors and sacituzumab govitecan (SG) suggested low quality and insignificant results. Conclusions Among all treatment regimens, PARP inhibitors with platinum exhibited the best efficacy, although with a trade-off of elevated risk of some types of adverse events. Future research on direct comparisons between different treatment regimens specifically targeting patients with breast cancer carrying BRCA1/2 pathogenic variants with a pre-specified adequate sample size is warranted.
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Affiliation(s)
- Yingxuan Zhu
- Medical Research and Biometrics Center, National Center for Cardiovascular Diseases, Fuwai Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
| | - Yang Li
- Medical Research and Biometrics Center, National Center for Cardiovascular Diseases, Fuwai Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
| | - Weida Liu
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Ruozhu Zhou
- Department of Oncology, China-Japan Friendship Hospital, Beijing, China
| | - Lap Ah Tse
- Jockey Club School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Yang Wang
- Medical Research and Biometrics Center, National Center for Cardiovascular Diseases, Fuwai Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
| | - Wei Li
- Medical Research and Biometrics Center, National Center for Cardiovascular Diseases, Fuwai Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China,*Correspondence: Wei Li,
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30
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Planas-Paz L, Pliego-Mendieta A, Hagedorn C, Aguilera-Garcia D, Haberecker M, Arnold F, Herzog M, Bankel L, Guggenberger R, Steiner S, Chen Y, Kahraman A, Zoche M, Rubin MA, Moch H, Britschgi C, Pauli C. Unravelling homologous recombination repair deficiency and therapeutic opportunities in soft tissue and bone sarcoma. EMBO Mol Med 2023; 15:e16863. [PMID: 36779660 PMCID: PMC10086583 DOI: 10.15252/emmm.202216863] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 01/18/2023] [Accepted: 01/24/2023] [Indexed: 02/14/2023] Open
Abstract
Defects in homologous recombination repair (HRR) in tumors correlate with poor prognosis and metastases development. Determining HRR deficiency (HRD) is of major clinical relevance as it is associated with therapeutic vulnerabilities and remains poorly investigated in sarcoma. Here, we show that specific sarcoma entities exhibit high levels of genomic instability signatures and molecular alterations in HRR genes, while harboring a complex pattern of chromosomal instability. Furthermore, sarcomas carrying HRDness traits exhibit a distinct SARC-HRD transcriptional signature that predicts PARP inhibitor sensitivity in patient-derived sarcoma cells. Concomitantly, HRDhigh sarcoma cells lack RAD51 nuclear foci formation upon DNA damage, further evidencing defects in HRR. We further identify the WEE1 kinase as a therapeutic vulnerability for sarcomas with HRDness and demonstrate the clinical benefit of combining DNA damaging agents and inhibitors of DNA repair pathways ex vivo and in the clinic. In summary, we provide a personalized oncological approach to treat sarcoma patients successfully.
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Affiliation(s)
- Lara Planas-Paz
- Laboratory for Systems Pathology and Functional Tumor Pathology, Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Alicia Pliego-Mendieta
- Laboratory for Systems Pathology and Functional Tumor Pathology, Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Catherine Hagedorn
- Laboratory for Systems Pathology and Functional Tumor Pathology, Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Domingo Aguilera-Garcia
- Molecular Tumor Profiling Laboratory, Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Martina Haberecker
- Laboratory for Systems Pathology and Functional Tumor Pathology, Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Fabian Arnold
- Molecular Tumor Profiling Laboratory, Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Marius Herzog
- Laboratory for Systems Pathology and Functional Tumor Pathology, Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Lorenz Bankel
- Department of Medical Oncology and Haematology, University Hospital Zurich, Zurich, Switzerland
| | - Roman Guggenberger
- Diagnostic and Interventional Radiology, University Hospital Zurich, Zurich, Switzerland
| | - Sabrina Steiner
- Laboratory for Systems Pathology and Functional Tumor Pathology, Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Yanjiang Chen
- Laboratory for Systems Pathology and Functional Tumor Pathology, Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Abdullah Kahraman
- Molecular Tumor Profiling Laboratory, Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Martin Zoche
- Molecular Tumor Profiling Laboratory, Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Mark A Rubin
- Precision Oncology Laboratory, Department for Biomedical Research, Bern Center for Precision Medicine, Bern, Switzerland
| | - Holger Moch
- Laboratory for Systems Pathology and Functional Tumor Pathology, Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Christian Britschgi
- Department of Medical Oncology and Haematology, University Hospital Zurich, Zurich, Switzerland
| | - Chantal Pauli
- Laboratory for Systems Pathology and Functional Tumor Pathology, Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland.,Medical Faculty, University of Zurich, Zurich, Switzerland
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31
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Simoneau A, Engel JL, Bandi M, Lazarides K, Liu S, Meier SR, Choi AH, Zhang H, Shen B, Martires L, Gotur D, Pham TV, Li F, Gu L, Gong S, Zhang M, Wilker E, Pan X, Whittington DA, Throner S, Maxwell JP, Chen Y, Yu Y, Huang A, Andersen JN, Feng T. Ubiquitinated PCNA Drives USP1 Synthetic Lethality in Cancer. Mol Cancer Ther 2023; 22:215-226. [PMID: 36228090 PMCID: PMC9891357 DOI: 10.1158/1535-7163.mct-22-0409] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 08/08/2022] [Accepted: 10/06/2022] [Indexed: 02/05/2023]
Abstract
CRISPR Cas9-based screening is a powerful approach for identifying and characterizing novel drug targets. Here, we elucidate the synthetic lethal mechanism of deubiquitinating enzyme USP1 in cancers with underlying DNA damage vulnerabilities, specifically BRCA1/2 mutant tumors and a subset of BRCA1/2 wild-type (WT) tumors. In sensitive cells, pharmacologic inhibition of USP1 leads to decreased DNA synthesis concomitant with S-phase-specific DNA damage. Genome-wide CRISPR-Cas9 screens identify RAD18 and UBE2K, which promote PCNA mono- and polyubiquitination respectively, as mediators of USP1 dependency. The accumulation of mono- and polyubiquitinated PCNA following USP1 inhibition is associated with reduced PCNA protein levels. Ectopic expression of WT or ubiquitin-dead K164R PCNA reverses USP1 inhibitor sensitivity. Our results show, for the first time, that USP1 dependency hinges on the aberrant processing of mono- and polyubiquitinated PCNA. Moreover, this mechanism of USP1 dependency extends beyond BRCA1/2 mutant tumors to selected BRCA1/2 WT cancer cell lines enriched in ovarian and lung lineages. We further show PARP and USP1 inhibition are strongly synergistic in BRCA1/2 mutant tumors. We postulate USP1 dependency unveils a previously uncharacterized vulnerability linked to posttranslational modifications of PCNA. Taken together, USP1 inhibition may represent a novel therapeutic strategy for BRCA1/2 mutant tumors and a subset of BRCA1/2 WT tumors.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Fang Li
- Tango Therapeutics, Boston, Massachusetts
| | - Lina Gu
- Tango Therapeutics, Boston, Massachusetts
| | | | | | | | - Xuewen Pan
- Tango Therapeutics, Boston, Massachusetts
| | | | | | | | | | - Yi Yu
- Tango Therapeutics, Boston, Massachusetts
| | - Alan Huang
- Tango Therapeutics, Boston, Massachusetts
| | | | - Tianshu Feng
- Tango Therapeutics, Boston, Massachusetts.,Corresponding Author: Tianshu Feng, Tango Therapeutics, 201 Brookline Avenue, Suite 901, Boston, MA 02215. E-mail:
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32
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Zheng C, Fu C, Wen Y, Liu J, Lin S, Han H, Han Z, Xu C. Clinical characteristics and overall survival prognostic nomogram for metaplastic breast cancer. Front Oncol 2023; 13:1030124. [PMID: 36937402 PMCID: PMC10018193 DOI: 10.3389/fonc.2023.1030124] [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: 08/28/2022] [Accepted: 02/09/2023] [Indexed: 03/06/2023] Open
Abstract
Background Metaplastic breast cancer (MBC) is a rare breast tumor and the prognostic factors for survival in patients still remain controversial. This study aims to develop and validate a nomogram to predict the overall survival (OS) of patients with MBC. Methods We searched the Surveillance, Epidemiology, and End Results (SEER) database for data about patients including metaplastic breast cancer and infiltrating ductal carcinoma (IDC) from 2010 to 2018. The survival outcomes of patients between MBC and IDC were analyzed and compared with the Kaplan-Meier (KM) method. MBC patients were randomly allocated to the training set and validation I set by a ratio of eight to two. Meanwhile, the performance of this model was validated again by the validation II set, which consisted of MBC patients from the Union Hospital of Fujian Medical University between 2010 and 2018. The independent prognostic factors were selected by univariate and multivariate Cox regression analyses. The nomogram was constructed to predict individual survival outcomes for MBC patients. The discriminative power, calibration, and clinical effectiveness of the nomogram were evaluated by the concordance index (C-index), the receiver operating characteristic (ROC) curve, and the decision curve analysis (DCA). Results MBC had a significantly higher T stage (T2 and above accounting for 75.1% vs 39.9%), fewer infiltrated lymph nodes (N0 accounted for 76.2% vs 67.7%), a lower proportion of ER (22.2% vs 81.2%), PR (13.6% vs 71.4%), and HER-2(6.7% vs 17.7%) positive, radiotherapy(51.6% vs 58.0%) but more chemotherapy(67.5% vs 44.7%), and a higher rate of mastectomy(53.2% vs 36.8%), which was discovered when comparing the clinical baseline data between MBC and IDC. Age at diagnosis, T, N, and M stage, as well as surgery and radiation treatment, were all significant independent prognostic factors for overall survival (OS). In the validation I cohort, the nomogram's C-index (0.769 95% CI 0.710 -0.828) was indicated to be considerably higher than the standard AJCC model's (0.700 95% CI 0.644 -0.756). Nomogram's great predictive capability capacity further was supported by the comparatively high C-index of the validation II sets (0.728 95%CI 0.588-0.869). Conclusions Metaplastic breast cancer is more aggressive, with a worse clinical prognosis than IDC. This nomogram is recommended for patients with MBC, both American and Chinese, which can help clinicians make more accurate individualized survival analyses.
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Affiliation(s)
- Caihong Zheng
- The Graduate School of Fujian Medical University, Fuzhou, Fujian, China
- Department of Breast Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
| | - Chengbin Fu
- Department of Breast Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
- Breast Cancer Institute, Fujian Medical University, Fuzhou, Fujian, China
| | - Yahui Wen
- The Graduate School of Fujian Medical University, Fuzhou, Fujian, China
- Department of Breast Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
| | - Jiameng Liu
- Department of Breast Surgery, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Shunguo Lin
- Department of Breast Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
- Breast Cancer Institute, Fujian Medical University, Fuzhou, Fujian, China
| | - Hui Han
- Department of Breast Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
- Breast Cancer Institute, Fujian Medical University, Fuzhou, Fujian, China
| | - Zhonghua Han
- Department of Breast Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
- Breast Cancer Institute, Fujian Medical University, Fuzhou, Fujian, China
- *Correspondence: Zhonghua Han, ; Chunsen Xu,
| | - Chunsen Xu
- Department of Breast Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
- Breast Cancer Institute, Fujian Medical University, Fuzhou, Fujian, China
- *Correspondence: Zhonghua Han, ; Chunsen Xu,
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O'Connor MJ, Forment JV. Mechanisms of PARP Inhibitor Resistance. Cancer Treat Res 2023; 186:25-42. [PMID: 37978129 DOI: 10.1007/978-3-031-30065-3_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Poly(ADP-ribose) polymerase (PARP) inhibitors (PARPi) represent the first medicines based on the targeting of the DNA damage response (DDR). PARPi have become standard of care for first-line maintenance treatment in ovarian cancer and have also been approved in other cancer indications including breast, pancreatic and prostate. Despite their efficacy, resistance to PARPi has been reported clinically and represents a growing patient population with unmet clinical need. Here, we describe the various mechanisms of PARPi resistance that have been identified in pre-clinical models and in the clinic.
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Affiliation(s)
- Mark J O'Connor
- Oncology R&D, AstraZeneca, Discovery Centre, Cambridge Biomedical Campus, 1 Francis Crick Avenue, Cambridge, CB2 0AA, UK.
| | - Josep V Forment
- Oncology R&D, AstraZeneca, Discovery Centre, Cambridge Biomedical Campus, 1 Francis Crick Avenue, Cambridge, CB2 0AA, UK
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34
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Sokolova A, Johnstone KJ, McCart Reed AE, Simpson PT, Lakhani SR. Hereditary breast cancer: syndromes, tumour pathology and molecular testing. Histopathology 2023; 82:70-82. [PMID: 36468211 PMCID: PMC10953374 DOI: 10.1111/his.14808] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/12/2022] [Accepted: 09/18/2022] [Indexed: 12/09/2022]
Abstract
Hereditary factors account for a significant proportion of breast cancer risk. Approximately 20% of hereditary breast cancers are attributable to pathogenic variants in the highly penetrant BRCA1 and BRCA2 genes. A proportion of the genetic risk is also explained by pathogenic variants in other breast cancer susceptibility genes, including ATM, CHEK2, PALB2, RAD51C, RAD51D and BARD1, as well as genes associated with breast cancer predisposition syndromes - TP53 (Li-Fraumeni syndrome), PTEN (Cowden syndrome), CDH1 (hereditary diffuse gastric cancer), STK11 (Peutz-Jeghers syndrome) and NF1 (neurofibromatosis type 1). Polygenic risk, the cumulative risk from carrying multiple low-penetrance breast cancer susceptibility alleles, is also a well-recognised contributor to risk. This review provides an overview of the established breast cancer susceptibility genes as well as breast cancer predisposition syndromes, highlights distinct genotype-phenotype correlations associated with germline mutation status and discusses molecular testing and therapeutic implications in the context of hereditary breast cancer.
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Affiliation(s)
- A Sokolova
- Sullivan and Nicolaides PathologyBrisbane
- Centre for Clinical Research, Faculty of MedicineThe University of QueenslandBrisbane
| | - K J Johnstone
- Centre for Clinical Research, Faculty of MedicineThe University of QueenslandBrisbane
- Pathology Queensland, The Royal Brisbane and Women's HospitalBrisbaneQueenslandAustralia
| | - A E McCart Reed
- Centre for Clinical Research, Faculty of MedicineThe University of QueenslandBrisbane
| | - P T Simpson
- Centre for Clinical Research, Faculty of MedicineThe University of QueenslandBrisbane
| | - S R Lakhani
- Centre for Clinical Research, Faculty of MedicineThe University of QueenslandBrisbane
- Pathology Queensland, The Royal Brisbane and Women's HospitalBrisbaneQueenslandAustralia
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35
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Veneziani AC, Scott C, Wakefield MJ, Tinker AV, Lheureux S. Fighting resistance: post-PARP inhibitor treatment strategies in ovarian cancer. Ther Adv Med Oncol 2023; 15:17588359231157644. [PMID: 36872947 PMCID: PMC9983116 DOI: 10.1177/17588359231157644] [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: 09/06/2022] [Accepted: 01/30/2023] [Indexed: 03/06/2023] Open
Abstract
Poly (ADP-ribose) polymerase inhibitors (PARPis) represent a therapeutic milestone in the management of epithelial ovarian cancer. The concept of 'synthetic lethality' is exploited by PARPi in tumors with defects in DNA repair pathways, particularly homologous recombination deficiency. The use of PARPis has been increasing since its approval as maintenance therapy, particularly in the first-line setting. Therefore, resistance to PARPi is an emerging issue in clinical practice. It brings an urgent need to elucidate and identify the mechanisms of PARPi resistance. Ongoing studies address this challenge and investigate potential therapeutic strategies to prevent, overcome, or re-sensitize tumor cells to PARPi. This review aims to summarize the mechanisms of resistance to PARPi, discuss emerging strategies to treat patients post-PARPi progression, and discuss potential biomarkers of resistance.
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Affiliation(s)
- Ana C Veneziani
- Division of Medical Oncology and Haematology, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Clare Scott
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia.,Royal Women's Hospital, Parkville, VIC, Australia.,Sir Peter MacCallum Department of Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Matthew J Wakefield
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Anna V Tinker
- BC Cancer Agency, Medical Oncology Vancouver, Canada
| | - Stephanie Lheureux
- Division of Medical Oncology and Haematology, Princess Margaret Cancer Centre, 610 University Ave, Toronto, ON M5B 2M9, Canada
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36
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Tsang ES, Munster PN. Targeting RAD51-Mediated Homologous Recombination as a Treatment for Advanced Solid and Hematologic Malignancies: Opportunities and Challenges Ahead. Onco Targets Ther 2022; 15:1509-1518. [PMID: 36536949 PMCID: PMC9758980 DOI: 10.2147/ott.s322297] [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] [Received: 05/10/2022] [Accepted: 11/18/2022] [Indexed: 11/26/2023] Open
Abstract
RAD51 is integral in homologous recombination DNA damage repair and has garnered much interest as both a biomarker and potential therapeutic target in oncology. Multiple in vitro and in vivo studies have demonstrated its role as a predictive marker, particularly in the context of platinum-based therapies and poly ADP-ribose polymerase (PARP) inhibitors. In this review, we highlight the development of RAD51 inhibitors, with a focus on novel molecules and ongoing clinical trials. Despite many efforts to develop effective and tolerable direct RAD51 inhibitors, identification of these agents remains challenging. Clinically, however, there may be a role of pharmacological indirect RAD51 inhibition.
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Affiliation(s)
- Erica S Tsang
- Division of Hematology and Oncology, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Pamela N Munster
- Division of Hematology and Oncology, University of California San Francisco, San Francisco, CA, 94158, USA
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37
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Punzón-Jiménez P, Lago V, Domingo S, Simón C, Mas A. Molecular Management of High-Grade Serous Ovarian Carcinoma. Int J Mol Sci 2022; 23:13777. [PMID: 36430255 PMCID: PMC9692799 DOI: 10.3390/ijms232213777] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 11/11/2022] Open
Abstract
High-grade serous ovarian carcinoma (HGSOC) represents the most common form of epithelial ovarian carcinoma. The absence of specific symptoms leads to late-stage diagnosis, making HGSOC one of the gynecological cancers with the worst prognosis. The cellular origin of HGSOC and the role of reproductive hormones, genetic traits (such as alterations in P53 and DNA-repair mechanisms), chromosomal instability, or dysregulation of crucial signaling pathways have been considered when evaluating prognosis and response to therapy in HGSOC patients. However, the detection of HGSOC is still based on traditional methods such as carbohydrate antigen 125 (CA125) detection and ultrasound, and the combined use of these methods has yet to support significant reductions in overall mortality rates. The current paradigm for HGSOC management has moved towards early diagnosis via the non-invasive detection of molecular markers through liquid biopsies. This review presents an integrated view of the relevant cellular and molecular aspects involved in the etiopathogenesis of HGSOC and brings together studies that consider new horizons for the possible early detection of this gynecological cancer.
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Affiliation(s)
- Paula Punzón-Jiménez
- Carlos Simon Foundation, INCLIVA Health Research Institute, 46010 Valencia, Spain
| | - Victor Lago
- Department of Gynecologic Oncology, La Fe University and Polytechnic Hospital, 46026 Valencia, Spain
- Department of Obstetrics and Gynecology, CEU Cardenal Herrera University, 46115 Valencia, Spain
| | - Santiago Domingo
- Department of Gynecologic Oncology, La Fe University and Polytechnic Hospital, 46026 Valencia, Spain
- Department of Pediatrics, Obstetrics and Gynecology, Universidad de Valencia, 46010 Valencia, Spain
| | - Carlos Simón
- Carlos Simon Foundation, INCLIVA Health Research Institute, 46010 Valencia, Spain
- Department of Pediatrics, Obstetrics and Gynecology, Universidad de Valencia, 46010 Valencia, Spain
- Department of Pediatrics, Obstetrics and Gynecology, Beth Israel Deaconess Medical Center, Harvard University, Boston, MA 02215, USA
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Aymara Mas
- Carlos Simon Foundation, INCLIVA Health Research Institute, 46010 Valencia, Spain
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38
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Gomez-Puerto D, Llop-Guevara A, Cruellas M, Torres-Esquius S, De La Torre J, Peg V, Balmaña J, Pimentel I. Genetic and functional homologous repair deficiency as biomarkers for platinum sensitivity in TNBC: A case report. Front Oncol 2022; 12:963728. [PMID: 36185283 PMCID: PMC9516106 DOI: 10.3389/fonc.2022.963728] [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: 06/07/2022] [Accepted: 07/26/2022] [Indexed: 11/28/2022] Open
Abstract
Triple-negative breast cancer is the most aggressive subtype of mammary carcinoma. In the early stage, neoadjuvant chemotherapy (NAC) is the standard of care for prognostic stratification and the best adjuvant treatment strategy. A 30-year-old female presented in the emergency room because of a gigantic right breast associated with an ulcerated lump at the upper quadrants. The right axillary nodes were palpable. An ultrasound was performed, showing the ulcerated neoformation with enlarged right axillary lymph nodes observed to level III. A core biopsy of the breast lesion was performed, and the pathological examination revealed a nonspecial type, grade 3, invasive, triple-negative breast cancer. No distant disease was found in the PET-CT scan. A germline genetic panel by next-generation sequencing identified a likely pathogenic variant in RAD51D (c.898C>T). Assessment of the functionality of the DNA homologous recombination repair pathway by RAD51 foci in the tumor revealed a profile of homologous recombination deficiency. NAC consisting of weekly carboplatin and paclitaxel followed by dose-dense doxorubicin/cyclophosphamide was performed with a complete metabolic response achieved in the PET-CT scan. The patient underwent a modified radical mastectomy plus axillary lymphadenectomy with a pathological complete response in the breast and axilla and remains disease-free after 2 years of follow-up. We report a young female with a triple-negative breast cancer stage cT4bN3M0 and a hereditary pathogenic mutation in RAD51D. The tumor was highly proliferative and homologous recombination-deficient by RAD51. The patient received platinum-based NAC, achieving a pathologic complete response. More effort should be made to identify predictive functional biomarkers of treatment response, such as RAD51 foci, for platinum sensitivity.
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Affiliation(s)
- Diego Gomez-Puerto
- Medical Oncology Department, Vall d’Hebron Institute of Oncology (VHIO), Hospital Universitari Vall d’Hebron, Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
- *Correspondence: Diego Gomez-Puerto,
| | - Alba Llop-Guevara
- Experimental Therapeutics Group, Vall d’Hebron Institute of Oncology (VHIO), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Mara Cruellas
- Hereditary Cancer Genetics Group, Vall d’Hebron Institute of Oncology (VHIO), Hospital Universitari Vall d’Hebron, Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Sara Torres-Esquius
- Hereditary Cancer Genetics Group, Vall d’Hebron Institute of Oncology (VHIO), Hospital Universitari Vall d’Hebron, Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Javier De La Torre
- Gynecologic Oncology and the Breast Pathology Unit, Hospital Universitari Vall d’Hebron, Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Vicente Peg
- Pathology Department, Vall d’Hebron University Hospital, Barcelona, Spain
| | - Judith Balmaña
- Hereditary Cancer Genetics Group, Vall d’Hebron Institute of Oncology (VHIO), Hospital Universitari Vall d’Hebron, Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Isabel Pimentel
- Medical Oncology Department, Vall d’Hebron Institute of Oncology (VHIO), Hospital Universitari Vall d’Hebron, Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
- Breast Cancer and Melanoma Group, Vall d’Hebron Institute of Oncology (VHIO), Hospital Universitari Vall d’Hebron, Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
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Lee HW, Seo HK. Clinical implications and practical considerations for poly-ADP-ribose polymerase inhibitors as a new horizon for the management of urothelial carcinoma of the bladder. Investig Clin Urol 2022; 63:369-372. [PMID: 35796137 PMCID: PMC9262491 DOI: 10.4111/icu.20220203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Hye Won Lee
- Department of Urology, Center for Urologic Cancer, National Cancer Center, Goyang, Korea
| | - Ho Kyung Seo
- Department of Urology, Center for Urologic Cancer, National Cancer Center, Goyang, Korea.,Division of Tumor Immunology, Research Institute, National Cancer Center, Goyang, Korea.,Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea.
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40
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Štancl P, Hamel N, Sigel KM, Foulkes WD, Karlić R, Polak P. The Great Majority of Homologous Recombination Repair-Deficient Tumors Are Accounted for by Established Causes. Front Genet 2022; 13:852159. [PMID: 35783256 PMCID: PMC9247292 DOI: 10.3389/fgene.2022.852159] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 05/03/2022] [Indexed: 11/18/2022] Open
Abstract
Background: Gene-agnostic genomic biomarkers were recently developed to identify homologous recombination deficiency (HRD) tumors that are likely to respond to treatment with PARP inhibitors. Two machine-learning algorithms that predict HRD status, CHORD, and HRDetect, utilize various HRD-associated features extracted from whole-genome sequencing (WGS) data and show high sensitivity in detecting patients with BRCA1/2 bi-allelic inactivation in all cancer types. When using only DNA mutation data for the detection of potential causes of HRD, both HRDetect and CHORD find that 30–40% of cases that have been classified as HRD are due to unknown causes. Here, we examined the impact of tumor-specific thresholds and measurement of promoter methylation of BRCA1 and RAD51C on unexplained proportions of HRD cases across various tumor types. Methods: We gathered published CHORD and HRDetect probability scores for 828 samples from breast, ovarian, and pancreatic cancer from previous studies, as well as evidence of their biallelic inactivation (by either DNA alterations or promoter methylation) in HR-related genes. ROC curve analysis evaluated the performance of each classifier in specific cancer. Tenfold nested cross-validation was used to find the optimal threshold values of HRDetect and CHORD for classifying HR-deficient samples within each cancer type. Results: With the universal threshold, HRDetect has higher sensitivity in the detection of biallelic inactivation in BRCA1/2 than CHORD and resulted in a higher proportion of unexplained cases. When promoter methylation was excluded, in ovarian carcinoma, the proportion of unexplained cases increased from 26.8 to 48.8% for HRDetect and from 14.7 to 41.2% for CHORD. A similar increase was observed in breast cancer. Applying cancer-type-specific thresholds led to similar sensitivity and specificity for both methods. The cancer-type-specific thresholds for HRDetect reduced the number of unexplained cases from 21 to 12.3% without reducing the 96% sensitivity to known events. For CHORD, unexplained cases were reduced from 10 to 9% while sensitivity increased from 85.3 to 93.9%. Conclusion: These results suggest that WGS-based HRD classifiers should be adjusted for tumor types. When applied, only ∼10% of breast, ovarian, and pancreas cancer cases are not explained by known events in our dataset.
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Affiliation(s)
- Paula Štancl
- Bioinformatics Group, Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Nancy Hamel
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Keith M. Sigel
- Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - William D. Foulkes
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Department of Human Genetics, McGill University Montreal, Montreal, QC, Canada
- Cancer Axis, Lady Davis Institute, Jewish General Hospital, Montreal, QC, Canada
| | - Rosa Karlić
- Bioinformatics Group, Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
- *Correspondence: Paz Polak, ; Rosa Karlić,
| | - Paz Polak
- Icahn School of Medicine at Mount Sinai, New York, NY, United States
- *Correspondence: Paz Polak, ; Rosa Karlić,
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