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Chen C, Zhu Y, Zhang H, Xiao L. Prognostic Effects of RASSF1A, BRCA1, APC, and p16 Promoter Methylation in Ovarian Cancer: A Meta-Analysis. Gynecol Obstet Invest 2024:1-13. [PMID: 38615670 DOI: 10.1159/000538673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 03/25/2024] [Indexed: 04/16/2024]
Abstract
INTRODUCTION DNA methylation plays an important role in the carcinogenesis, progression, and prognosis of various human cancers. RASSF1A, BRCA1, APC, and p16 are the frequently methylated genes among patients with ovarian cancer. Therefore, our study aimed to better determine the prognostic and cancer characteristics effects of RASSF1A, BRCA1, APC, and p16 promoter methylation in ovarian cancer patients. METHODS Databases such as PubMed, Web of Science, EMBASE, CNKI, and WanFang were searched for published studies up to March 4, 2024. The outcomes are shown as OR and HR with their 95% CIs. Then, the random or fixed-effect model was performed to evaluate the effect sizes. RESULTS Finally, 27 articles were included in this meta-analysis. No significant relationships were observed between RASSF1A, BRCA1, and APC promoter methylation and the clinical prognostic (including overall survival and progression-free survival) and cancer characteristics (including ascites, lymph node metastasis, and pelvic peritoneal metastasis) in ovarian cancer. p16 promoter methylation was significantly related to poor progression-free survival (PFS) (HR = 1.52, 95% CI = 1.14-2.04) and overall survival (OS) (HR = 1.39, 95% CI = 1.06, to 1.83) in univariate and poor PFS in multivariate Cox regression models (HR = 1.42, 95% CI = 1.05-1.92). Besides, our results indicated that the clinical stage was associated with inferior OS while there was no significant association between tumor grade and OS. CONCLUSION RASSF1A, BRCA1, and APC promoter methylation were not significantly associated with clinical prognostic and cancer characteristics. p16 may be a useful biomarker for predicting PFS in ovarian cancer. Furthermore, the clinical stage was significantly associated with OS. In further research, more prospective and multicenter validation studies remain needed.
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Affiliation(s)
- Cheng Chen
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Ying Zhu
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Haibo Zhang
- Central Laboratory, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Lan Xiao
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Anhui Medical University, Hefei, China
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Moore JA, Chen KT, Madison R, Newberg JY, Fleischmann Z, Wang S, Sharaf R, Murugesan K, Fendler BJ, Hughes J, Schrock AB, Hegde PS, Oxnard GR, Fabrizio D, Frampton GM, Antonarakis ES, Sokol ES, Jin DX. Pan-Cancer Analysis of Copy-Number Features Identifies Recurrent Signatures and a Homologous Recombination Deficiency Biomarker to Predict Poly (ADP-Ribose) Polymerase Inhibitor Response. JCO Precis Oncol 2023; 7:e2300093. [PMID: 37769224 DOI: 10.1200/po.23.00093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 06/21/2023] [Accepted: 07/21/2023] [Indexed: 09/30/2023] Open
Abstract
PURPOSE Copy-number (CN) features reveal the molecular state of cancers and may have predictive and prognostic value in the treatment of cancer. We sought to apply published CN analysis methods to a large pan-cancer data set and characterize ubiquitous CN signatures across tumor types, including potential utility for treatment selection. METHODS We analyzed the landscape of CN features in 260,333 pan-cancer samples. We examined the association of 10 signatures with genomic alterations and clinical characteristics and trained a machine learning classifier using CN and insertion and deletion features to detect homologous recombination deficiency signature (HRDsig) positivity. Clinical outcomes were assessed using a real-world clinicogenomic database (CGDB) of comprehensive genomic profiling linked to deidentified, electronic health record-derived clinical data. RESULTS CN signatures were prevalent across cancer types and associated with diverse processes including focal tandem duplications, seismic amplifications, genome-wide loss of heterozygosity (gLOH), and HRD. Our novel HRDsig outperformed gLOH in predicting BRCAness and effectively distinguished biallelic BRCA and homologous recombination-repair wild-type (HRRwt) samples pan-tumor, demonstrating high sensitivity to detect biallelic BRCA in ovarian (93%) and other HRD-associated cancers (80%-87%). Pan-tumor prevalence of HRDsig was 6.4%. HRRwt cases represented a significant fraction of the HRDsig-positive cohort, likely reflecting a population with nongenomic mechanisms of HRD. In ovarian and prostate CGDBs, HRDsig identified more patients than gLOH and had predictive value for poly (ADP-ribose) polymerase inhibitor (PARPi) benefit. CONCLUSION Tumor CN profiles are informative, revealing diverse processes active in cancer. We describe the landscape of 10 CN signatures in a large pan-cancer cohort, including two associated with HRD. We trained a machine learning-based HRDsig that robustly identified BRCAness and associated with biallelic BRCA pan-tumor, and was predictive of PARPi benefit in real-world ovarian and prostate data sets.
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Blanc-Durand F, Tang R, Pommier M, Nashvi M, Cotteret S, Genestie C, Le Formal A, Pautier P, Michels J, Kfoury M, Hervé R, Mengue S, Wafo E, Elies A, Miailhe G, Uzan J, Rouleau E, Leary A. Clinical Relevance of BRCA1 Promoter Methylation Testing in Patients with Ovarian Cancer. Clin Cancer Res 2023; 29:3124-3129. [PMID: 37067532 DOI: 10.1158/1078-0432.ccr-22-3328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/12/2022] [Accepted: 04/13/2023] [Indexed: 04/18/2023]
Abstract
PURPOSE Homologous recombination deficiency (HRD) is closely related to PARP inhibitor (PARPi) benefit in ovarian cancer. The capacity of BRCA1 promoter methylation to predict prognosis and HRD status remains unclear. We aimed to correlate BRCA1 promoter methylation levels in patients with high-grade ovarian cancer to HRD status and clinical behavior to assess its clinical relevance. EXPERIMENTAL DESIGN This is a retrospective monocentric analysis of patients centrally tested for genomic instability score (GIS) by MyChoice CDx (Myriad Genetics). The detection of BRCA1 promoter methylation and quantification of methylation levels were performed by quantitative droplet digital PCR methodology. High BRCA1 methylation was defined as ≥70% and deemed to be associated with homozygous silencing. RESULTS Of 100 patients, 11% harbored a deleterious BRCA1/2 mutation. GIS was considered positive (score ≥ 42) for 52 patients and negative for 48 patients. Using a 70% cutoff, 19% (15/79) of BRCA wild-type ovarian cancer had high BRCA1 methylation levels. All of the highly methylated tumors were classified as HRD, achieving a positive predictive value of 100%. We detected 14% (11/79) low-methylated tumors (1%-69%), and all of them were also classified as HRD. Mean GIS was 61.5 for BRCAmut, 66.4 for high-BRCAmeth, 58.9 for low-BRCAmeth, and 33.3 for BRCAwt unmethylated (P < 0.001). Low methylation levels detected in samples previously exposed to chemotherapy appeared to be associated with poor outcome post-platinum. CONCLUSIONS Patients with ovarian cancer with high levels of BRCA1 hypermethylation are very likely to have high GIS and therefore represent good candidates for PARPi treatment. These results may be highly relevant to other tumor types for HRD prediction. See related commentary by Garg and Oza, p. 2957.
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Affiliation(s)
- Félix Blanc-Durand
- Medical Oncology Department, Gynecology Unit, Institut Gustave Roussy, Villejuif, France
| | - Roseline Tang
- Cancer Genetics Unit, Department of Biology and Pathology, Institut Gustave Roussy, Villejuif, France
| | - Margaux Pommier
- Cancer Genetics Unit, Department of Biology and Pathology, Institut Gustave Roussy, Villejuif, France
| | - Marzieh Nashvi
- Cancer Genetics Unit, Department of Biology and Pathology, Institut Gustave Roussy, Villejuif, France
| | - Sophie Cotteret
- Cancer Genetics Unit, Department of Biology and Pathology, Institut Gustave Roussy, Villejuif, France
| | - Catherine Genestie
- Pathology Unit, Department of Biology and Pathology, Institut Gustave Roussy, Villejuif, France
| | | | - Patricia Pautier
- Medical Oncology Department, Gynecology Unit, Institut Gustave Roussy, Villejuif, France
| | - Judith Michels
- Medical Oncology Department, Gynecology Unit, Institut Gustave Roussy, Villejuif, France
| | - Maria Kfoury
- Medical Oncology Department, Gynecology Unit, Institut Gustave Roussy, Villejuif, France
| | - Robert Hervé
- Oncology Unit, Centre Hospitalier Polynesie Francaise, Papeete, French Polynesia
| | - Sylvie Mengue
- Oncology Unit, Centre Hospitalier Polynesie Francaise, Papeete, French Polynesia
| | - Estelle Wafo
- Gynecology Unit, Centre Hospitalier Intercommunal Creteil, Créteil, France
| | - Antoine Elies
- Gynecology Unit, Centre Hospitalier Intercommunal Creteil, Créteil, France
| | - Gregoire Miailhe
- Gynecology Unit, Groupe Hospitalier Est Francilien, Jossigny, France
| | - Jennifer Uzan
- Gynecology Unit, Groupe Hospitalier Est Francilien, Jossigny, France
| | - Etienne Rouleau
- Cancer Genetics Unit, Department of Biology and Pathology, Institut Gustave Roussy, Villejuif, France
- INSERM U981, Institut Gustave Roussy, Villejuif, France
| | - Alexandra Leary
- Medical Oncology Department, Gynecology Unit, Institut Gustave Roussy, Villejuif, France
- INSERM U981, Institut Gustave Roussy, Villejuif, France
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Rădoi VE, Țurcan M, Maioru OV, Dan A, Bohîlțea LC, Dumitrescu EA, Gheorghe AS, Stănculeanu DL, Thodi G, Loukas YL, Săbău ID. Homologous Recombination Deficiency Score Determined by Genomic Instability in a Romanian Cohort. Diagnostics (Basel) 2023; 13:diagnostics13111896. [PMID: 37296748 DOI: 10.3390/diagnostics13111896] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/02/2023] [Accepted: 05/19/2023] [Indexed: 06/12/2023] Open
Abstract
The Homologous Recombination Deficiency (HRD) Score, determined by evaluating genomic instability through the assessment of loss of heterozygosity (LOH), telomeric allelic imbalance (TAI), and large-scale state transitions (LST), serves as a crucial biomarker for identifying patients who might benefit from targeted therapies, such as PARP inhibitors (PARPi). This study aimed to investigate the efficacy of HRD testing in high-grade serous ovarian carcinoma, tubal, and peritoneal cancer patients who are negative for somatic BRCA1 and BRCA2 mutations and to evaluate the impact of HRD status on Bevacizumab and PARPi therapy response. A cohort of 100 Romanian female patients, aged 42-77, was initially selected. Among them, 30 patients had unsuitable samples for HRD testing due to insufficient tumor content or DNA integrity. Using the OncoScan C.N.V. platform, HRD testing was successfully performed on the remaining 70 patients, with 20 testing negative and 50 testing positive for HRD. Among the HRD-positive patients, 35 were eligible for and benefited from PARPi maintenance therapy, resulting in a median progression-free survival (PFS) increase from 4 months to 8.2 months. Our findings support the importance of HRD testing in ovarian cancer patients, demonstrating the potential therapeutic advantage of PARPi therapy in HRD-positive patients without somatic BRCA1/2 mutations.
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Affiliation(s)
- Viorica-Elena Rădoi
- Department of Medical Genetics, "Carol Davila" University of Medicine and Pharmacy, 020021 Bucharest, Romania
- "Alessandrescu-Rusescu" National Institute for Maternal and Child Health, 20382 Bucharest, Romania
- Independent Researcher, 010987 Bucharest, Romania
- Sanador, 011026 Bucharest, Romania
| | - Mihaela Țurcan
- Department of Medical Genetics, "Carol Davila" University of Medicine and Pharmacy, 020021 Bucharest, Romania
- Independent Researcher, 010987 Bucharest, Romania
| | - Ovidiu Virgil Maioru
- Department of Medical Genetics, "Carol Davila" University of Medicine and Pharmacy, 020021 Bucharest, Romania
| | - Andra Dan
- Department of Medical Genetics, "Carol Davila" University of Medicine and Pharmacy, 020021 Bucharest, Romania
| | - Laurentiu Camil Bohîlțea
- Department of Medical Genetics, "Carol Davila" University of Medicine and Pharmacy, 020021 Bucharest, Romania
- "Alessandrescu-Rusescu" National Institute for Maternal and Child Health, 20382 Bucharest, Romania
| | - Elena Adriana Dumitrescu
- Department of Oncology, "Carol Davila" University of Medicine and Pharmacy, 020021 Bucharest, Romania
| | - Adelina Silvana Gheorghe
- Department of Oncology, "Carol Davila" University of Medicine and Pharmacy, 020021 Bucharest, Romania
- Department of Medical Oncology I, Institute of Oncology "Prof. Dr. Al. Trestioreanu" Bucharest, 022328 Bucharest, Romania
| | - Dana Lucia Stănculeanu
- Department of Oncology, "Carol Davila" University of Medicine and Pharmacy, 020021 Bucharest, Romania
- Department of Medical Oncology I, Institute of Oncology "Prof. Dr. Al. Trestioreanu" Bucharest, 022328 Bucharest, Romania
| | - Georgia Thodi
- Neoscreen Diagnostic Laboratory, Voreiou Ipeirou, 15235 Athens, Greece
| | - Yannis L Loukas
- School of Pharmacy, University of Athens, Panepistimiolopis, 15771 Zografou, Greece
| | - Ileana-Delia Săbău
- Department of Medical Genetics, "Carol Davila" University of Medicine and Pharmacy, 020021 Bucharest, Romania
- Independent Researcher, 010987 Bucharest, Romania
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Sahnane N, Rivera D, Libera L, Carnevali I, Banelli B, Facchi S, Gismondi V, Paudice M, Cirmena G, Vellone VG, Sessa F, Varesco L, Tibiletti MG. Pyrosequencing Assay for BRCA1 Methylation Analysis: Results from a Cross-Validation Study. J Mol Diagn 2023; 25:217-226. [PMID: 36739964 DOI: 10.1016/j.jmoldx.2023.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 12/14/2022] [Accepted: 01/10/2023] [Indexed: 02/05/2023] Open
Abstract
Epithelial ovarian cancers (EOCs) harboring germline or somatic pathogenic variants in BRCA1 and BRCA2 genes show sensitivity to poly(ADP-ribose) polymerase inhibition. It has been suggested that BRCA1 promoter methylation is perhaps a better determinant of therapy response, because of its intrinsic dynamic feature, with respect to genomic scars or gene mutation. Conflicting evidence was reported so far, and the lack of a validated assay to measure promoter methylation was considered a main confounding factor in data interpretation. To contribute to the validation process of a pyrosequencing assay for BRCA1 promoter methylation, 109 EOCs from two Italian centers were reciprocally blindly investigated. By comparing two different pyrosequencing assays, addressing a partially overlapping region of BRCA1 promoter, an almost complete concordance of results was obtained. Moreover, the clinical relevance of this approach was also supported by the finding of BRCA1 transcript down-regulation in BRCA1-methylated EOCs. These findings could lead to the development of a simple and cheap pyrosequencing assay for diagnostics, easily applicable to formalin-fixed, paraffin-embedded tissues. This technique may be implemented in routine clinical practice in the near future to identify EOCs sensitive to poly(ADP-ribose) polymerase inhibitor therapy, thus increasing the subset of women affected by EOCs who could benefit from such treatment.
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Affiliation(s)
- Nora Sahnane
- Unit of Pathology, Ospedale di Circolo, Azienda Socio Sanitaria Territoriale (ASST) Sette Laghi Hospital, Varese, Italy; Research Center for Familial and Hereditary Tumors, Department of Medicine and Surgery, University of Insubria, Varese, Italy.
| | - Daniela Rivera
- Hereditary Cancer Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ospedale Policlinico San Martino, Genoa, Italy
| | - Laura Libera
- Research Center for Familial and Hereditary Tumors, Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Ileana Carnevali
- Unit of Pathology, Ospedale di Circolo, Azienda Socio Sanitaria Territoriale (ASST) Sette Laghi Hospital, Varese, Italy; Research Center for Familial and Hereditary Tumors, Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Barbara Banelli
- Tumor Epigenetics Laboratory, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ospedale Policlinico San Martino, Genoa, Italy
| | - Sofia Facchi
- Research Center for Familial and Hereditary Tumors, Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Viviana Gismondi
- Hereditary Cancer Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ospedale Policlinico San Martino, Genoa, Italy
| | - Michele Paudice
- Department of Surgical Sciences and Integrated Diagnostics, University of Genoa, Genoa, Italy
| | - Gabriella Cirmena
- Hereditary Cancer Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ospedale Policlinico San Martino, Genoa, Italy
| | - Valerio G Vellone
- Department of Surgical Sciences and Integrated Diagnostics, University of Genoa, Genoa, Italy; Anatomic Pathology University Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ospedale Policlinico San Martino, Genoa, Italy
| | - Fausto Sessa
- Unit of Pathology, Ospedale di Circolo, Azienda Socio Sanitaria Territoriale (ASST) Sette Laghi Hospital, Varese, Italy; Research Center for Familial and Hereditary Tumors, Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Liliana Varesco
- Hereditary Cancer Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ospedale Policlinico San Martino, Genoa, Italy
| | - Maria G Tibiletti
- Unit of Pathology, Ospedale di Circolo, Azienda Socio Sanitaria Territoriale (ASST) Sette Laghi Hospital, Varese, Italy; Research Center for Familial and Hereditary Tumors, Department of Medicine and Surgery, University of Insubria, Varese, Italy
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Abstract
Ovarian carcinoma (OC) is an umbrella term for multiple distinct diseases (histotypes), each with their own developmental origins, clinical behaviour and molecular profile. Accordingly, OC management is progressing away from a one-size-fits all approach, toward more molecularly-driven, histotype-specific management strategies. Our knowledge of driver events in high grade serous OC, the most common histotype, has led to major advances in treatments, including PARP inhibitor use. However, these agents are not suitable for all patients, most notably for many of those with rare OC histotypes. Identification of additional targeted therapeutic strategies will require a detailed understanding of the molecular landscape in each OC histotype. Until recently, tumour profiling studies in rare histotypes were sparse; however, significant advances have been made over the last decade. In particular, reports of genomic characterisation in endometrioid, clear cell, mucinous and low grade serous OC have significantly expanded our understanding of mutational events in these tumour types. Nonetheless, substantial knowledge gaps remain. This review summarises our current understanding of each histotype, highlighting recent advances in these unique diseases and outlining immediate research priorities for accelerating progress toward improving patient outcomes.
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Affiliation(s)
- Robert L Hollis
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, UK.
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Oswald AJ, Gourley C. Development of Homologous Recombination Functional Assays for Targeting the DDR. Cancer Treat Res 2023; 186:43-70. [PMID: 37978130 DOI: 10.1007/978-3-031-30065-3_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Identification of tumours that have homologous recombination deficiency (HRD) has become of increasing interest following the licensing of PARP inhibitors. Potential methods to assess HRD status include; clinical selection for platinum sensitive disease, mutational/methylation status, genomic scars/signature and functional RAD51 assays. Homologous recombination (HR) is a dynamic process with the potential to evolve over a disease course, particularly in relation to previous treatment. This is one of the major drawbacks of genomic scars/signatures, as they only demonstrate historic HR status. Functional HR assays have the benefit of giving a real time HR status readout and therefore have the potential for clearer identification of patients who may benefit from PARP inhibitors at that specific time point. However, the development of RAD51 foci assays ready for clinical practice has been challenging. Pre-clinical considerations have included; controlling for variation in tumour proliferation, tissue type and whether DNA damage induction is required. Furthermore, the assays require correlation with clinical outcomes, an understanding of how they complement current testing modalities and validation of test performance in large cohorts. Despite these challenges, given the profound benefit from PARP inhibitors seen in those with an HRD phenotype to date, the ongoing development and validation of these functional HR assays remains of high clinical importance.
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Affiliation(s)
- Ailsa J Oswald
- Cancer Research UK Scotland Centre, University of Edinburgh, Edinburgh, UK.
| | - Charlie Gourley
- Cancer Research UK Scotland Centre, University of Edinburgh, Edinburgh, UK
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Tsyganov MM, Ibragimova MK, Garbukov EY, Bragina OD, Karchevskaya AA, Usynin EA, Litvyakov NV. Determination of BRCAness Phenotype in Breast Tumors for the Appointment of Neoadjuvant Chemotherapy Based on Platinum and Taxanes. Int J Mol Sci 2022; 24. [PMID: 36613648 DOI: 10.3390/ijms24010207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/19/2022] [Accepted: 12/19/2022] [Indexed: 12/25/2022] Open
Abstract
The concept of BRCAness was developed because of similarities between sporadic and hereditary breast cancer. BRCAness defines the pathogenesis and treatment sensitivity of many types of cancer, as well as the presence of a defect in the homologous recombination repair of tumor cells simulating the loss of BRCA1 or BRCA2, as in the presence of germline mutations. The question of treatment effectiveness for BRCA-like tumors is controversial and open. Thus, the aim of this work was to study the effectiveness of neoadjuvant chemotherapy (NAC) in BRCA-deficient breast cancer patients without germline mutations. The study involved 130 patients with breast cancer in stages IIA-IIIB. The treatment regimen included neoadjuvant chemotherapy, surgery, and adjuvant chemotherapy. The materials used were tumor samples from before and after chemotherapy. DNA and RNA were isolated from the tumor material. RNA was used to assess the expression level of BRCA1, while DNA was used for methyl-sensitive PCR. A microarray analysis was performed on high-density DNA chips from an Affymetrix CytoScanTM HD Array to assess DNA copy number aberration (CNA status) and loss of heterozygosity. A statistical analysis was performed using the Statistica 8.0 application package. It was noted that the existence of copy number aberrations in genes was statistically significantly associated with tumor treatment response and disease prognosis. Patients with partial regression had a statistically significantly higher amount of deletion than patients without an objective response (5/25 patients; 16%), as shown in the general sample of patients (52.9% versus 27.1%, respectively) at p = 0.0001 and in patients treated with anthracycline-containing regimen (p = 0.0001). In addition, it was shown that patients with BRCA1 deletion had higher rates of metastatic-free survival (log rank test, p = 0.009). BRCAness patients had a higher rate of 5-year metastatic survival, but not of treatment efficacy. The prospective study showed the positive effect of assessing the BRCAness phenotype of a tumor before treatment and of prescribing personalized NAC regimens. The objective response rate was statistically significantly more often observed in the group of patients with personalized chemotherapy (85.0% (34/40 patients) versus 62.3% (56/90 patients); p = 0.007). Despite the controversial effectiveness of BRCA-like tumor treatment, our data showed high predictive and prognostic significance of the BRCAness phenotype for the personalization of platinum and taxane regimens.
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van Wagensveld L, van Baal JOAM, Timmermans M, Gaillard D, Borghuis L, Coffelt SB, Rosenberg EH, Lok CAR, Nijman HW, Kooreman LFS, Sanders J, de Bruijn M, Wessels LFA, van der Wiel R, Rausch C, Broeks A, Kruitwagen RFPM, van der Aa MA, Sonke GS, Schouten PC, Van de Vijver KK, Horlings HM. Homologous Recombination Deficiency and Cyclin E1 Amplification Are Correlated with Immune Cell Infiltration and Survival in High-Grade Serous Ovarian Cancer. Cancers (Basel) 2022; 14:cancers14235965. [PMID: 36497449 PMCID: PMC9738162 DOI: 10.3390/cancers14235965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/24/2022] [Accepted: 11/28/2022] [Indexed: 12/07/2022] Open
Abstract
BACKGROUND How molecular profiles are associated with tumor microenvironment (TME) in high-grade serous ovarian cancer (HGSOC) is incompletely understood. Therefore, we analyzed the TME and molecular profiles of HGSOC and assessed their associations with overall survival (OS). METHODS Patients with advanced-stage HGSOC treated in three Dutch hospitals between 2008-2015 were included. Patient data were collected from medical records. BRCA1/2 mutation, BRCA1 promotor methylation analyses, and copy number variations were used to define molecular profiles. Immune cells were assessed with immunohistochemical staining. RESULTS 348 patients were categorized as BRCA mutation (BRCAm) (BRCAm or promotor methylation) (30%), non-BRCA mutated HRD (19%), Cyclin E1 (CCNE1)-amplification (13%), non-BRCAmut HRD and CCNE1-amplification (double classifier) (20%), and no specific molecular profile (NSMP) (18%). BRCAm showed highest immune cell densities and CCNE1-amplification lowest. BRCAm showed the most favorable OS (52.5 months), compared to non-BRCAmut HRD (41.0 months), CCNE1-amplification (28.0 months), double classifier (27.8 months), and NSMP (35.4 months). Higher immune cell densities showed a favorable OS compared to lower, also within the profiles. CD8+, CD20+, and CD103+ cells remained associated with OS in multivariable analysis. CONCLUSIONS Molecular profiles and TME are associated with OS. TME differs per profile, with higher immune cell densities showing a favorable OS, even within the profiles. HGSOC does not reflect one entity but comprises different entities based on molecular profiles and TME.
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Affiliation(s)
- Lilian van Wagensveld
- Department of Research and Development, Netherlands Comprehensive Cancer Organization (IKNL), 3511 DT Utrecht, The Netherlands
- Department of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
- GROW, School for Oncology and Reproduction, 6229 HX Maastricht, The Netherlands
- Correspondence:
| | - Juliette O. A. M. van Baal
- Department of Gynecology, Center for Gynecologic Oncology Amsterdam (CGOA), 1066 CX Amsterdam, The Netherlands
| | - Maite Timmermans
- Department of Obstetrics and Gynecology, Leiden University Medical Centre, 2333 ZA Leiden, The Netherlands
| | - Duco Gaillard
- Department of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Lauri Borghuis
- Department of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Seth B. Coffelt
- Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
- Institute of Cancer Sciences, University of Glasgow, Glasgow G12 8QQ, UK
- Cancer Research UK, Beatson Institute, Glasgow G61 1BD, UK
| | - Efraim H. Rosenberg
- Department of Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Christianne A. R. Lok
- Department of Gynecology, Center for Gynecologic Oncology Amsterdam (CGOA), 1066 CX Amsterdam, The Netherlands
| | - Hans W. Nijman
- Department of Obstetrics and Gynecology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands
| | - Loes F. S. Kooreman
- GROW, School for Oncology and Reproduction, 6229 HX Maastricht, The Netherlands
- Department of Pathology, Maastricht University Medical Centre, 6229 HX Maastricht, The Netherlands
| | - Joyce Sanders
- Department of Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Marco de Bruijn
- Department of Obstetrics and Gynecology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands
| | - Lodewyk F. A. Wessels
- Department of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Rianne van der Wiel
- Department of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Christian Rausch
- Department of Pathology, VU University Medical Center, 1081 HV Amsterdam, The Netherlands
- BioLizard nv, 9000 Ghent, Belgium
| | - Annegien Broeks
- Core Facility Molecular Pathology & Biobanking, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Roy F. P. M. Kruitwagen
- GROW, School for Oncology and Reproduction, 6229 HX Maastricht, The Netherlands
- Department of Obstetrics and Gynecology, Maastricht University Medical Centre, 6229 HX Maastricht, The Netherlands
| | - Maaike A. van der Aa
- Department of Research and Development, Netherlands Comprehensive Cancer Organization (IKNL), 3511 DT Utrecht, The Netherlands
| | - Gabe S. Sonke
- Department of Medical Oncology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Philip C. Schouten
- Department of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Koen K. Van de Vijver
- Department of Gynecology, Center for Gynecologic Oncology Amsterdam (CGOA), 1066 CX Amsterdam, The Netherlands
- Department of Pathology & Cancer Research Institute Ghent (CRIG), Ghent University Hospital, 9000 Ghent, Belgium
| | - Hugo M. Horlings
- Department of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
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10
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Ebata T, Yamashita S, Takeshima H, Yoshida H, Kawata Y, Kino N, Yasugi T, Terao Y, Yonemori K, Kato T, Ushijima T. DNA methylation of the immediate upstream region of BRCA1 major transcription start sites is an independent favorable prognostic factor in patients with high-grade serous ovarian cancer. Gynecol Oncol 2022; 167:513-8. [PMID: 36253303 DOI: 10.1016/j.ygyno.2022.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 10/05/2022] [Accepted: 10/07/2022] [Indexed: 11/04/2022]
Abstract
OBJECTIVE To establish a quantitative method to evaluate the DNA methylation level of an immediate upstream region of major BRCA1 transcriptional start sites (TSSs), and to investigate whether methylation of the region is a prognostic factor in high-grade serous ovarian cancer patients after neoadjuvant chemotherapy. METHODS Ninety-two FFPE samples of advanced high-grade serous ovarian cancers after neoadjuvant chemotherapy between 2011 and 2018 were used for mutation and methylation analysis. DNA methylation levels were assessed by pyrosequencing and DNA methylation microarray. An association between methylation level (or a mutation) and progression-free survival was assessed by Kaplan-Meier analysis. RESULT Major BRCA1 transcripts and CpG sites immediately upstream of their TSSs were identified, and a pyrosequencing method was developed. BRCA1 methylation, BRCA1/2 mutations, and a RAD51C mutation were detected in 17/79 (21.5%), 17/92 (18.5%), and 1/92 (1.1%) high-grade serious ovarian cancer samples. In univariate analysis, BRCA1 methylation and no residual tumor were associated with progression-free survival (BRCA1 methylation: P = 0.025, no residual tumor: P = 0.0026). Multivariate analysis showed that both BRCA1 methylation (P = 0.038, HR = 0.47, 95% CI: 0.21-0.96) and no residual tumor (P = 0.012, HR = 0.49, 95% CI: 0.28-0.85) were significant favorable prognostic factors. CONCLUSION A quantitative method to estimate the methylation level of the immediate upstream region of major BRCA1 TSSs was established. Methylation of the region of was an independent favorable prognostic factor in high-grade serous ovarian cancer patients.
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11
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Yuan W, Ni J, Wen H, Shi W, Chen X, Huang H, Zhang X, Lu X, Zhu C, Dong H, Yang S, Wu X, Chen X. Genomic Scar Score: A robust model predicting homologous recombination deficiency based on genomic instability. BJOG 2022; 129 Suppl 2:14-22. [PMID: 36485068 DOI: 10.1111/1471-0528.17324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
OBJECTIVE To develop a novel machine learning-based algorithm called the Genomic Scar Score (GSS) for predicting homologous recombination deficiency (HRD) events. DESIGN Method development study. SETTING AmoyDx Medical Laboratory and Jiangsu Cancer Hospital. POPULATION OR SAMPLE A cohort of individuals with ovarian or breast cancer (n = 377) were collected from the AmoyDx Medical Laboratory. Another cohort of patients with ovarian cancer treated with PARP inhibitors (n = 58) was enrolled in the Jiangsu Cancer Hospital. METHODS We used linear support vector machines to build a Genomic Scar (GS) model to predict HRD events, and Kaplan-Meier analyses were performed by comparing the progression-free survival (PFS) of patients in different groups using a two-sided log-rank test. MAIN OUTCOME MEASURES The performance of the GS model and the result of clinical validation. RESULTS The GS model displayed more than 97.0% sensitivity to detect BRCA-deficient events, and the GS model identified patients that could benefit from poly(ADP-ribose) polymerase inhibitors (PARPi), as the GS score (GSS)-positive group had a longer progression-free survival (PFS) (9.4 versus 4.4 months; hazard ratio [HR] = 0.54, P < 0.001) than the GSS-negative group after PARPi treatment. Meanwhile, the GSS showed high concordance among different NGS panels, which implied the robustness of the GS model. CONCLUSIONS The GS was a robust model to predict HRD and had broad clinical applications in predicting which patients will respond favourably to PARPi treatment.
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Affiliation(s)
| | - Jing Ni
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Hao Wen
- Department of Gynecological Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Weijie Shi
- Amoy Diagnostics Co., Ltd., Xiamen, China
| | | | | | | | - Xuan Lu
- Amoy Diagnostics Co., Ltd., Xiamen, China
| | | | - Hua Dong
- Amoy Diagnostics Co., Ltd., Xiamen, China
| | | | - Xiaohua Wu
- Department of Gynecological Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Xiaoxiang Chen
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
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12
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Menghi F, Banda K, Kumar P, Straub R, Dobrolecki L, Rodriguez IV, Yost SE, Chandok H, Radke MR, Somlo G, Yuan Y, Lewis MT, Swisher EM, Liu ET. Genomic and epigenomic
BRCA
alterations predict adaptive resistance and response to platinum-based therapy in patients with triple-negative breast and ovarian carcinomas. Sci Transl Med 2022; 14:eabn1926. [PMID: 35857626 PMCID: PMC9585706 DOI: 10.1126/scitranslmed.abn1926] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Triple-negative breast cancer (TNBC) and ovarian carcinomas (OvCas) with
BRCA1
promoter methylation (
BRCA1
meth) respond more poorly to alkylating agents compared to those bearing mutations in
BRCA1
and
BRCA2
(
BRCA
mut). This is a conundrum given the biologically equivalent homologous recombination deficiency (HRD) induced by these genetic and epigenetic
BRCA
perturbations. We dissected this problem through detailed genomic analyses of TNBC and OvCa cohorts and experimentation with patient-derived xenografts and genetically engineered cell lines. We found that despite identical downstream genomic mutational signatures associated with
BRCA1
meth and
BRCA
mut states,
BRCA1
meth uniformly associates with poor outcomes. Exposure of
BRCA1
meth TNBCs to platinum chemotherapy, either as clinical treatment of a patient or as experimental in vivo exposure of preclinical patient derived xenografts, resulted in allelic loss of
BRCA1
methylation and increased
BRCA1
expression and platinum resistance. These data suggest that, unlike
BRCA
mut cancers, where
BRCA
loss is a genetically “fixed” deficiency state,
BRCA1
meth cancers are highly adaptive to genotoxin exposure and, through reversal of promoter methylation, recover
BRCA1
expression and become resistant to therapy. We further found a specific augmented immune transcriptional signal associated with enhanced response to platinum chemotherapy but only in patients with BRCA-proficient cancers. We showed how integrating both this cancer immune signature and the presence of
BRCA
mutations results in more accurate predictions of patient response when compared to either HRD status or
BRCA
status alone. This underscores the importance of defining
BRCA
heterogeneity in optimizing the predictive precision of assigning response probabilities in TNBC and OvCa.
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Affiliation(s)
- Francesca Menghi
- Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA
| | - Kalyan Banda
- Division of Medical Oncology, UW Medical Center, Seattle, WA 98195, USA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Pooja Kumar
- Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA
| | - Robert Straub
- Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA
| | | | - Isabel V. Rodriguez
- Department of Obstetrics and Gynecology, UW Medical Center, Seattle, WA 98195, USA
| | - Susan E. Yost
- Division of Medical Oncology and Therapeutic Research, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | | | - Marc R. Radke
- Department of Obstetrics and Gynecology, UW Medical Center, Seattle, WA 98195, USA
| | - George Somlo
- Division of Medical Oncology and Therapeutic Research, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Yuan Yuan
- Division of Medical Oncology and Therapeutic Research, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Michael T. Lewis
- Departments of Molecular and Cellular Biology and Radiology, Lester and Sue Smith Breast Center, Dan L Duncan Comprehensive Cancer Center, Houston, TX 77030, USA
| | - Elizabeth M. Swisher
- Department of Obstetrics and Gynecology, UW Medical Center, Seattle, WA 98195, USA
| | - Edison T. Liu
- Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA
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13
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Mekonnen N, Yang H, Shin YK. Homologous Recombination Deficiency in Ovarian, Breast, Colorectal, Pancreatic, Non-Small Cell Lung and Prostate Cancers, and the Mechanisms of Resistance to PARP Inhibitors. Front Oncol 2022; 12:880643. [PMID: 35785170 PMCID: PMC9247200 DOI: 10.3389/fonc.2022.880643] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 05/18/2022] [Indexed: 11/30/2022] Open
Abstract
Homologous recombination (HR) is a highly conserved DNA repair mechanism that protects cells from exogenous and endogenous DNA damage. Breast cancer 1 (BRCA1) and breast cancer 2 (BRCA2) play an important role in the HR repair pathway by interacting with other DNA repair proteins such as Fanconi anemia (FA) proteins, ATM, RAD51, PALB2, MRE11A, RAD50, and NBN. These pathways are frequently aberrant in cancer, leading to the accumulation of DNA damage and genomic instability known as homologous recombination deficiency (HRD). HRD can be caused by chromosomal and subchromosomal aberrations, as well as by epigenetic inactivation of tumor suppressor gene promoters. Deficiency in one or more HR genes increases the risk of many malignancies. Another conserved mechanism involved in the repair of DNA single-strand breaks (SSBs) is base excision repair, in which poly (ADP-ribose) polymerase (PARP) enzymes play an important role. PARP inhibitors (PARPIs) convert SSBs to more cytotoxic double-strand breaks, which are repaired in HR-proficient cells, but remain unrepaired in HRD. The blockade of both HR and base excision repair pathways is the basis of PARPI therapy. The use of PARPIs can be expanded to sporadic cancers displaying the “BRCAness” phenotype. Although PARPIs are effective in many cancers, their efficacy is limited by the development of resistance. In this review, we summarize the prevalence of HRD due to mutation, loss of heterozygosity, and promoter hypermethylation of 35 DNA repair genes in ovarian, breast, colorectal, pancreatic, non-small cell lung cancer, and prostate cancer. The underlying mechanisms and strategies to overcome PARPI resistance are also discussed.
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Affiliation(s)
- Negesse Mekonnen
- Department of Pharmacy, Research Institute of Pharmaceutical Science, Seoul National University College of Pharmacy, Seoul, South Korea
- Department of Veterinary Science, School of Animal Science and Veterinary Medicine, Bahir Dar University, Bahir Dar, Ethiopia
| | - Hobin Yang
- Department of Pharmacy, Research Institute of Pharmaceutical Science, Seoul National University College of Pharmacy, Seoul, South Korea
| | - Young Kee Shin
- Department of Pharmacy, Research Institute of Pharmaceutical Science, Seoul National University College of Pharmacy, Seoul, South Korea
- Bio-MAX/N-Bio, Seoul National University, Seoul, South Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Seoul National University Graduate School of Convergence Science and Technology, Seoul, South Korea
- LOGONE Bio Convergence Research Foundation, Center for Companion Diagnostics, Seoul, South Korea
- *Correspondence: Young Kee Shin,
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14
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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: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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15
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Paulet L, Trecourt A, Leary A, Peron J, Descotes F, Devouassoux-Shisheboran M, Leroy K, You B, Lopez J. Cracking the homologous recombination deficiency code: how to identify responders to PARP inhibitors. Eur J Cancer 2022; 166:87-99. [DOI: 10.1016/j.ejca.2022.01.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 01/10/2022] [Accepted: 01/24/2022] [Indexed: 12/16/2022]
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16
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van Wijk LM, Nilas AB, Vrieling H, Vreeswijk MPG. RAD51 as a functional biomarker for homologous recombination deficiency in cancer: a promising addition to the HRD toolbox? Expert Rev Mol Diagn 2021; 22:185-199. [PMID: 34913794 DOI: 10.1080/14737159.2022.2020102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Carcinomas with defects in the homologous recombination (HR) pathway are sensitive to PARP inhibitors (PARPi). A robust method to identify HR-deficient (HRD) carcinomas is therefore of utmost clinical importance. Currently available DNA-based HRD tests either scan HR-related genes such as BRCA1 and BRCA2 for the presence of pathogenic variants or identify HRD-related genomic scars or mutational signatures by using whole-exome or whole-genome sequencing data. As an alternative to DNA-based tests, functional HRD tests have been developed that assess the actual ability of tumors to accumulate RAD51 protein at DNA double strand breaks as a proxy for HR proficiency. AREAS COVERED This review presents an overview of currently available HRD tests and discuss the pros and cons of the different methodologies including their sensitivity for the identification of HRD tumors, their concordance with other HRD tests, and their capacity to predict therapy response. EXPERT OPINION With the increasing use of PARP inhibitors in the treatment of several cancers there is an urgent need to implement HRD testing in routine clinical practice. To this end, calibration of HRD thresholds and clinical validation of both DNA-based and RAD51-based HRD tests should have top-priority in the coming years.
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Affiliation(s)
- Lise M van Wijk
- Department of Human Genetics, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Andreea B Nilas
- Department of Human Genetics, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Harry Vrieling
- Department of Human Genetics, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Maaike P G Vreeswijk
- Department of Human Genetics, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
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17
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Chiang YC, Lin PH, Cheng WF. Homologous Recombination Deficiency Assays in Epithelial Ovarian Cancer: Current Status and Future Direction. Front Oncol 2021; 11:675972. [PMID: 34722237 PMCID: PMC8551835 DOI: 10.3389/fonc.2021.675972] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 09/17/2021] [Indexed: 01/02/2023] Open
Abstract
Epithelial ovarian cancer (EOC) patients are generally diagnosed at an advanced stage, usually relapse after initial treatments, which include debulking surgery and adjuvant platinum-based chemotherapy, and eventually have poor 5-year survival of less than 50%. In recent years, promising survival benefits from maintenance therapy with poly(ADP-ribose) polymerase (PARP) inhibitor (PARPi) has changed the management of EOC in newly diagnosed and recurrent disease. Identification of BRCA mutations and/or homologous recombination deficiency (HRD) is critical for selecting patients for PARPi treatment. However, the currently available HRD assays are not perfect predictors of the clinical response to PARPis in EOC patients. In this review, we introduce the concept of synthetic lethality, the rationale of using PARPi when HRD is present in tumor cells, the clinical trials of PARPi incorporating the HRD assays for EOC, the current HRD assays, and other HRD assays in development.
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Affiliation(s)
- Ying-Cheng Chiang
- Department of Obstetrics and Gynecology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Po-Han Lin
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan.,Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Wen-Fang Cheng
- Department of Obstetrics and Gynecology, College of Medicine, National Taiwan University, Taipei, Taiwan.,Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan.,Graduate Institute of Oncology, College of Medicine, National Taiwan University, Taipei, Taiwan
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18
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Abstract
Ovarian clear cell carcinoma (OCCC) is one of the major types of ovarian cancer and is of higher relative prevalence in Asians. It also shows higher possibility of resistance to cisplatin-based chemotherapy leading to poor prognosis. This may be attributed to the relative lack of mutations and aberrations in homologous recombination-associated genes, which are crucial in DNA damage response (DDR), such as BRCA1, BRCA2, p53, RAD51, and genes in the Fanconi anemia pathway. On the other hand, OCCC is characterized by a number of genetic defects rendering it vulnerable to DDR-targeting therapy, which is emerging as a potent treatment strategy for various cancer types. Mutations of ARID1A, PIK3CA, PTEN, and catenin beta 1 (CTNNB1), as well as overexpression of transcription factor hepatocyte nuclear factor-1β (HNF-1β), and microsatellite instability are common in OCCC. Of particular note is the loss-of-function mutations in ARID1A, which is found in approximately 50% of OCCC. ARID1A is crucial for processing of DNA double-strand break (DSB) and for sustaining DNA damage signaling, rendering ARID1A-deficient cells prone to impaired DNA damage checkpoint regulation and hence sensitive to poly ADP ribose polymerase (PARP) inhibitors. However, while preclinical studies have demonstrated the possibility to exploit DDR deficiency in OCCC for therapeutic purpose, progress in clinical application is lagging. In this review, we will recapitulate the preclinical studies supporting the potential of DDR targeting in OCCC treatment, with emphasis on the role of ARID1A in DDR. Companion diagnostic tests (CDx) for predicting susceptibility to PARP inhibitors are rapidly being developed for solid tumors including ovarian cancers and may readily be applicable on OCCC. The potential of various available DDR-targeting drugs for treating OCCC by drawing analogies with other solid tumors sharing similar genetic characteristics with OCCC will also be discussed.
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19
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Nesic K, Kondrashova O, Hurley RM, McGehee CD, Vandenberg CJ, Ho GY, Lieschke E, Dall G, Bound N, Shield-Artin K, Radke M, Musafer A, Chai ZQ, Eftekhariyan Ghamsari MR, Harrell MI, Kee D, Olesen I, McNally O, Traficante N, Cancer Study AO, DeFazio A, Bowtell DDL, Swisher EM, Weroha SJ, Nones K, Waddell N, Kaufmann SH, Dobrovic A, Wakefield MJ, Scott CL. Acquired RAD51C promoter methylation loss causes PARP inhibitor resistance in high grade serous ovarian carcinoma. Cancer Res 2021; 81:4709-4722. [PMID: 34321239 DOI: 10.1158/0008-5472.can-21-0774] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/10/2021] [Accepted: 07/07/2021] [Indexed: 11/16/2022]
Abstract
In high-grade serous ovarian carcinoma (HGSC), deleterious mutations in DNA repair gene RAD51C are established drivers of defective homologous recombination and are emerging biomarkers of PARP inhibitor (PARPi) sensitivity. RAD51C promoter methylation (meRAD51C) is detected at similar frequencies to mutations, yet its effects on PARPi responses remain unresolved. In this study, three HGSC patient-derived xenograft (PDX) models with methylation at most or all examined CpG sites in the RAD51C promoter show responses to PARPi. Both complete and heterogeneous methylation patterns were associated with RAD51C gene silencing and homologous recombination deficiency (HRD). PDX models lost meRAD51C following treatment with PARPi rucaparib or niraparib, where a single unmethylated copy of RAD51C was sufficient to drive PARPi resistance. Genomic copy number profiling of one of the PDX models using SNP arrays revealed that this resistance was acquired independently in two genetically distinct lineages. In a cohort of 11 patients with RAD51C-methylated HGSC, various patterns of meRAD51C were associated with genomic 'scarring', indicative of HRD history, but exhibited no clear correlations with clinical outcome. Differences in methylation stability under treatment pressure were also observed between patients, where one HGSC was found to maintain meRAD51C after 6 lines of therapy (4 platinum-based), whilst another HGSC sample was found to have heterozygous meRAD51C and elevated RAD51C gene expression (relative to homozygous meRAD51C controls) after only neo-adjuvant chemotherapy. As meRAD51C loss in a single gene copy was sufficient to cause PARPi resistance in PDX, methylation zygosity should be carefully assessed in previously treated patients when considering PARPi therapy.
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Affiliation(s)
- Ksenija Nesic
- Cancer Biology and Stem Cells, Walter and Eliza Hall Institute of Medical Research
| | - Olga Kondrashova
- Genetics and Computational Biology, QIMR Berghofer Medical Research Institute
| | | | | | | | - Gwo-Yaw Ho
- Stem Cells and Cancer Division, Walter and Eliza Hall Institute of Medical Research
| | - Elizabeth Lieschke
- Stem Cells and Cancer Division, Walter and Eliza Hall Institute of Medical Research
| | | | | | - Kristy Shield-Artin
- Stem Cells and Cancer Division, Walter and Eliza Hall Institute of Medical Research
| | - Marc Radke
- Obstetrics and Gynecology, University of Washington Medical Center
| | - Ashan Musafer
- Translational Genomics and Epigenomics Group, Olivia Newton-John Cancer Wellness & Research Centre
| | - Zi Qing Chai
- Olivia Newton-John Cancer Wellness & Research Centre
| | | | - Maria I Harrell
- Obstetrics and Gynecology, University of Washington Medical Center
| | | | | | - Orla McNally
- Department of Obstetrics and Gynaecology, Royal Women's Hospital
| | - Nadia Traficante
- Cancer Genetics and Genomics Laboratory and Australian Ovarian Cancer Study, Peter MacCallum Cancer Centre
| | | | - Anna DeFazio
- Centre for Cancer Research, University of Sydney, Westmead Institute for Medical Research
| | - David D L Bowtell
- Cancer Genetics and Genomics Laboratory and Austrialian Ovarian Cancer Study, Peter MacCallum Cancer Centre
| | | | | | - Katia Nones
- Cell and Molecular Biology, QIMR Berghofer Medical Research Institute
| | - Nicola Waddell
- Medical Genomics Laboratory, QIMR Berghofer Medical Research Institute
| | | | - Alexander Dobrovic
- Translational Genomics and Epigenomics Laboratory, University of Melbourne
| | - Matthew J Wakefield
- Stem Cells and Cancer Division, Walter and Eliza Hall Institute of Medical Research
| | - Clare L Scott
- Cancer Biology and Stem Cells Division Division, Walter and Eliza Hall Institute of Medical Research
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20
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Fernandes SG, Shah P, Khattar E. Recent Advances in Therapeutic Application of DNA Damage Response Inhibitors against Cancer. Anticancer Agents Med Chem 2021; 22:469-484. [PMID: 34102988 DOI: 10.2174/1871520621666210608105735] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 02/02/2021] [Accepted: 02/22/2021] [Indexed: 11/22/2022]
Abstract
DNA integrity is continuously challenged by intrinsic cellular processes and environmental agents. To overcome this genomic damage, cells have developed multiple signaling pathways collectively named as DNA damage response (DDR) and composed of three components: (i) sensor proteins, which detect DNA damage, (ii) mediators that relay the signal downstream and recruit the repair machinery, and (iii) the repair proteins, which restore the damaged DNA. A flawed DDR and failure to repair the damage lead to the accumulation of genetic lesions and increased genomic instability, which is recognized as a hallmark of cancer. Cancer cells tend to harbor increased mutations in DDR genes and often have fewer DDR pathways than normal cells. This makes cancer cells more dependent on particular DDR pathways and thus become more susceptible to compounds inhibiting those pathways compared to normal cells, which have all the DDR pathways intact. Understanding the roles of different DDR proteins in the DNA damage response and repair pathways and identification of their structures have paved the way for the development of their inhibitors as targeted cancer therapy. In this review, we describe the major participants of various DDR pathways, their significance in carcinogenesis, and focus on the inhibitors developed against several key DDR proteins.
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Affiliation(s)
- Stina George Fernandes
- Sunandan Divatia School of Science, SVKM's NMIMS (Deemed to be) University, Mumbai, India
| | - Prachi Shah
- Sunandan Divatia School of Science, SVKM's NMIMS (Deemed to be) University, Mumbai, India
| | - Ekta Khattar
- Sunandan Divatia School of Science, SVKM's NMIMS (Deemed to be) University, Mumbai, India
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21
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Ngoi NYL, Tan DSP. The role of homologous recombination deficiency testing in ovarian cancer and its clinical implications: do we need it? ESMO Open 2021; 6:100144. [PMID: 34015643 PMCID: PMC8141874 DOI: 10.1016/j.esmoop.2021.100144] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 03/19/2021] [Accepted: 04/09/2021] [Indexed: 12/20/2022] Open
Abstract
The recognition of homologous recombination deficiency (HRD) as a frequent feature of high-grade serous ovarian cancer (HGSOC) has transformed treatment paradigms. Poly(ADP-ribose) polymerase inhibitors (PARPis), developed based on the rationale of synthetic lethality that predicates antitumor efficacy in tumors harboring underlying HRD, now represents an important class of therapy for HGSOC. Recent data have drawn attention to the assessment of homologous recombination DNA repair (HRR) as a prognostic and predictive biomarker in HGSOC, leading to increasing debate on the optimal means of defining and evaluating HRD, both genotypically and phenotypically. At present, clinical-grade assays such as myChoice CDx and FoundationOne CDx are approved companion diagnostics which can identify patients with HRD-positive HGSOC by diagnosing a 'genomic scar' reflecting underlying genomic instability. Yet despite the rapid maturation of this field, tumoral HRD status has been recognized to be dynamic over time and with treatment pressure. In practice, this means that restoration of HRR through mechanisms of platinum and PARPi resistance are not adequately represented by genomic scar assays, and contribute toward discordance with clinical PARPi response, or lack-thereof. It is thus critical that HRD testing is optimized to address the controversies of diverse HRD testing methodology, appropriate thresholds for HRD identification, and relevant timepoints for HRD testing, in order to realize the potential for PARPis to maximally benefit patients with HGSOC. Here, we discuss the premise of HRD testing in HGSOC, current methodologies for HRD identification and their performance in the clinic, highlight upcoming strategies, and discuss the challenges faced in moving this field forward.
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Affiliation(s)
- N Y L Ngoi
- Department of Haematology-Oncology, National University Cancer Institute, National University Health System, Singapore, Singapore
| | - D S P Tan
- Department of Haematology-Oncology, National University Cancer Institute, National University Health System, Singapore, Singapore; Cancer Science Institute, National University of Singapore, Singapore, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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22
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Kalachand RD, Stordal B, Madden S, Chandler B, Cunningham J, Goode EL, Ruscito I, Braicu EI, Sehouli J, Ignatov A, Yu H, Katsaros D, Mills GB, Lu KH, Carey MS, Timms KM, Kupryjanczyk J, Rzepecka IK, Podgorska A, McAlpine JN, Swisher EM, Bernards SS, O'Riain C, O'Toole S, O'Leary JJ, Bowtell DD, Thomas DM, Prieske K, Joosse SA, Woelber L, Chaudhry P, Häfner N, Runnebaum IB, Hennessy BT. BRCA1 Promoter Methylation and Clinical Outcomes in Ovarian Cancer: An Individual Patient Data Meta-Analysis. J Natl Cancer Inst 2021; 112:1190-1203. [PMID: 32413141 DOI: 10.1093/jnci/djaa070] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 04/23/2020] [Accepted: 05/11/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND BRCA1 methylation has been associated with homologous recombination deficiency, a biomarker of platinum sensitivity. Studies evaluating BRCA1-methylated tubal and ovarian cancer (OC) do not consistently support improved survival following platinum chemotherapy. We examine the characteristics of BRCA1-methylated OC in a meta-analysis of individual participant data. METHODS Data of 2636 participants across 15 studies were analyzed. BRCA1-methylated tumors were defined according to their original study. Associations between BRCA1 methylation and clinicopathological characteristics were evaluated. The effects of methylation on overall survival (OS) and progression-free survival (PFS) were examined using mixed-effects models. All statistical tests were 2-sided. RESULTS 430 (16.3%) tumors were BRCA1-methylated. BRCA1 methylation was associated with younger age and advanced-stage, high-grade serous OC. There were no survival differences between BRCA1-methylated and non-BRCA1-methylated OC (median PFS = 20.0 vs 18.5 months, hazard ratio [HR] = 1.01, 95% CI = 0.87 to 1.16; P = .98; median OS = 46.6 vs 48.0 months, HR = 1.02, 95% CI = 0.87 to 1.18; P = .96). Where BRCA1/2 mutations were evaluated (n = 1248), BRCA1 methylation displayed no survival advantage over BRCA1/2-intact (BRCA1/2 wild-type non-BRCA1-methylated) OC. Studies used different methods to define BRCA1 methylation. Where BRCA1 methylation was determined using methylation-specific polymerase chain reaction and gel electrophoresis (n = 834), it was associated with improved survival (PFS: HR = 0.80, 95% CI = 0.66 to 0.97; P = .02; OS: HR = 0.80, 95% CI = 0.63 to 1.00; P = .05) on mixed-effects modeling. CONCLUSION BRCA1-methylated OC displays similar clinicopathological features to BRCA1-mutated OC but is not associated with survival. Heterogeneity within BRCA1 methylation assays influences associations. Refining these assays may better identify cases with silenced BRCA1 function and improved patient outcomes.
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Affiliation(s)
- Roshni D Kalachand
- Medical Oncology Group, Department of Molecular Medicine, Royal College of Surgeons in Ireland, Beaumont Hospital, Dublin, Ireland
| | - Britta Stordal
- Department of Natural Sciences, Middlesex University, Hendon, London NW4 4BT, UK
| | - Stephen Madden
- Data Science Centre, Royal College of Surgeons in Ireland, Beaux Lane House, Dublin, Ireland
| | - Benjamin Chandler
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Julie Cunningham
- Division of Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Ellen L Goode
- Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Ilary Ruscito
- Department of Gynecology, European Competence Center for Ovarian Cancer, Campus Virchow Klinikum, Charité-Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Berlin, Germany.,Cell Therapy Unit and Laboratory of Tumor Immunology, Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Elena I Braicu
- Department of Gynecology, European Competence Center for Ovarian Cancer, Campus Virchow Klinikum, Charité-Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Berlin, Germany
| | - Jalid Sehouli
- Department of Gynecology, European Competence Center for Ovarian Cancer, Campus Virchow Klinikum, Charité-Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Berlin, Germany
| | - Atanas Ignatov
- Department of Gynecology and Obstetrics, University Medical Center, Regensburg, Germany
| | - Herbert Yu
- University of Hawaii Cancer Centre, Honolulu, HI, USA
| | - Dionyssios Katsaros
- AOU Citta della Salute and Department of Surgical Sciences, Gynecologic Oncology, University of Torino, Italy
| | - Gordon B Mills
- Department of Cell, Development and Cancer Biology Knight Cancer Institute, Oregon Health and Sciences University, Portland, OR, USA
| | - Karen H Lu
- University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mark S Carey
- Division of Gynecologic Oncology, Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Jolanta Kupryjanczyk
- Department of Pathology and Laboratory Diagnostics, Maria Sklodowska-Curie Institute-Oncology Center, Warsaw, Poland
| | - Iwona K Rzepecka
- Department of Pathology and Laboratory Diagnostics, Maria Sklodowska-Curie Institute-Oncology Center, Warsaw, Poland
| | - Agnieszka Podgorska
- Department of Pathology and Laboratory Diagnostics, Maria Sklodowska-Curie Institute-Oncology Center, Warsaw, Poland
| | - Jessica N McAlpine
- Division of Gynecologic Oncology, Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, British Columbia, Canada
| | | | | | - Ciaran O'Riain
- Department of Histopathology, Trinity College Dublin, Central Pathology Laboratory, St. James's Hospital, Dublin, Ireland
| | - Sharon O'Toole
- Department of Obstetrics and Gynaecology/Histopathology, Trinity College Dublin, Trinity Centre for Health Sciences, St. James's Hospital, Dublin, Ireland.,Emer Casey Research Laboratory, Molecular Pathology Laboratory, The Coombe Women and Infants University Hospital, Dublin, Ireland
| | - John J O'Leary
- Department of Histopathology, Trinity College Dublin, Central Pathology Laboratory, St. James's Hospital, Dublin, Ireland.,Emer Casey Research Laboratory, Molecular Pathology Laboratory, The Coombe Women and Infants University Hospital, Dublin, Ireland
| | | | - David M Thomas
- Genomic Cancer Medicine, Cancer Division, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Darlinghurst, Australia
| | - Katharina Prieske
- Department of Gynecology and Gynecologic Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Simon A Joosse
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Linn Woelber
- Department of Gynecology and Gynecologic Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Parvesh Chaudhry
- Department of Radiotherapy, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Norman Häfner
- Department for Gynaecology and Reproductive Medicine, Jena University Hospital-Friedrich Schiller University Jena, Jena, Germany
| | - Ingo B Runnebaum
- Department for Gynaecology and Reproductive Medicine, Jena University Hospital-Friedrich Schiller University Jena, Jena, Germany
| | - Bryan T Hennessy
- Medical Oncology Group, Department of Molecular Medicine, Royal College of Surgeons in Ireland, Beaumont Hospital, Dublin, Ireland.,Department of Medical Oncology, Beaumont Hospital, Dublin, Ireland.,Our Lady of Lourdes Hospital, Drogheda, Ireland
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Andrei P, Battuello P, Grasso G, Rovera E, Tesio N, Bardelli A. Integrated approaches for precision oncology in colorectal cancer: The more you know, the better. Semin Cancer Biol 2021:S1044-579X(21)00108-5. [PMID: 33848627 DOI: 10.1016/j.semcancer.2021.04.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 03/30/2021] [Accepted: 04/07/2021] [Indexed: 12/24/2022]
Abstract
Colorectal cancer (CRC) is one of the most common human malignancies accounting for approximately 10 % of worldwide cancer incidence and mortality. While early-stage CRC is mainly a preventable and curable disease, metastatic colorectal cancer (mCRC) remains an unmet clinical need. Moreover, about 25 % of CRC cases are diagnosed only at the metastatic stage. Despite the extensive molecular and functional knowledge on this disease, systemic therapy for mCRC still relies on traditional 5-fluorouracil (5-FU)-based chemotherapy regimens. On the other hand, targeted therapies and immunotherapy have shown effectiveness only in a limited subset of patients. For these reasons, there is a growing need to define the molecular and biological landscape of individual patients to implement novel, rationally driven, tailored therapies. In this review, we explore current and emerging approaches for CRC management such as genomic, transcriptomic and metabolomic analysis, the use of liquid biopsies and the implementation of patients' preclinical avatars. In particular, we discuss the contribution of each of these tools in elucidating patient specific features, with the aim of improving our ability in advancing the diagnosis and treatment of colorectal tumors.
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24
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Ramarao-Milne P, Kondrashova O, Barry S, Hooper JD, Lee JS, Waddell N. Histone Modifying Enzymes in Gynaecological Cancers. Cancers (Basel) 2021; 13:cancers13040816. [PMID: 33669182 PMCID: PMC7919659 DOI: 10.3390/cancers13040816] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/10/2021] [Accepted: 02/11/2021] [Indexed: 12/16/2022] Open
Abstract
Simple Summary Epigenetics is a process that allows genetic control, without the involvement of sequence changes to DNA or genes. In cancer, epigenetics is a key event in tumour development that can alter the expression of cancer driver genes and result in genomic instability. Due to the critical role of epigenetics in malignant transformation, therapies that target these processes have been developed to treat cancer. Here, we provide a summary of the epigenetic changes that have been described in a variety of gynaecological cancers. We then highlight how these changes are being targeted in preclinical models and clinical trials for gynaecological cancers. Abstract Genetic and epigenetic factors contribute to the development of cancer. Epigenetic dysregulation is common in gynaecological cancers and includes altered methylation at CpG islands in gene promoter regions, global demethylation that leads to genome instability and histone modifications. Histones are a major determinant of chromosomal conformation and stability, and unlike DNA methylation, which is generally associated with gene silencing, are amenable to post-translational modifications that induce facultative chromatin regions, or condensed transcriptionally silent regions that decondense resulting in global alteration of gene expression. In comparison, other components, crucial to the manipulation of chromatin dynamics, such as histone modifying enzymes, are not as well-studied. Inhibitors targeting DNA modifying enzymes, particularly histone modifying enzymes represent a potential cancer treatment. Due to the ability of epigenetic therapies to target multiple pathways simultaneously, tumours with complex mutational landscapes affected by multiple driver mutations may be most amenable to this type of inhibitor. Interrogation of the actionable landscape of different gynaecological cancer types has revealed that some patients have biomarkers which indicate potential sensitivity to epigenetic inhibitors. In this review we describe the role of epigenetics in gynaecological cancers and highlight how it may exploited for treatment.
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Affiliation(s)
- Priya Ramarao-Milne
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; (P.R.-M.); (O.K.); (N.W.)
- Faculty of Medicine, The University of Queensland, Brisbane, QLD 4006, Australia
| | - Olga Kondrashova
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; (P.R.-M.); (O.K.); (N.W.)
| | - Sinead Barry
- Department of Gynaecological Oncology, Mater Hospital Brisbane, Brisbane, QLD 4101, Australia;
- Mater Research Institute, The University of Queensland, Translational Research Institute, Woolloongabba, QLD 4102, Australia;
| | - John D. Hooper
- Mater Research Institute, The University of Queensland, Translational Research Institute, Woolloongabba, QLD 4102, Australia;
| | - Jason S. Lee
- Faculty of Medicine, The University of Queensland, Brisbane, QLD 4006, Australia
- Epigenetics and Disease Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
- School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD 4000, Australia
- Correspondence: ; Tel.: +61-7-38453951
| | - Nicola Waddell
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; (P.R.-M.); (O.K.); (N.W.)
- Faculty of Medicine, The University of Queensland, Brisbane, QLD 4006, Australia
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Heinze K, Rengsberger M, Gajda M, Jansen L, Osmers L, Oliveira-Ferrer L, Schmalfeldt B, Dürst M, Häfner N, Runnebaum IB. CAMK2N1/RUNX3 methylation is an independent prognostic biomarker for progression-free and overall survival of platinum-sensitive epithelial ovarian cancer patients. Clin Epigenetics 2021; 13:15. [PMID: 33482905 PMCID: PMC7824928 DOI: 10.1186/s13148-021-01006-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 01/05/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND To date, no predictive or prognostic molecular biomarkers except BRCA mutations are clinically established for epithelial ovarian cancer (EOC) despite being the deadliest gynecological malignancy. Aim of this biomarker study was the analysis of DNA methylation biomarkers for their prognostic value independent from clinical variables in a heterogeneous cohort of 203 EOC patients from two university medical centers. RESULTS The marker combination CAMK2N1/RUNX3 exhibited a significant prognostic value for progression-free (PFS) and overall survival (OS) of sporadic platinum-sensitive EOC (n = 188) both in univariate Kaplan-Meier (LogRank p < 0.05) and multivariate Cox regression analysis (p < 0.05; hazard ratio HR = 1.587). KRT86 methylation showed a prognostic value only in univariate analysis because of an association with FIGO staging (Fisher's exact test p < 0.01). Thus, it may represent a marker for EOC staging. Dichotomous prognostic values were observed for KATNAL2 methylation depending on BRCA aberrations. KATNAL2 methylation exhibited a negative prognostic value for PFS in sporadic EOC patients without BRCA1 methylation (HR 1.591, p = 0.012) but positive prognostic value in sporadic EOC with BRCA1 methylation (HR 0.332, p = 0.04) or BRCA-mutated EOC (HR 0.620, n.s.). CONCLUSION The retrospective analysis of 188 sporadic platinum-sensitive EOC proved an independent prognostic value of the methylation marker combination CAMK2N1/RUNX3 for PFS and OS. If validated prospectively this combination may identify EOC patients with worse prognosis after standard therapy potentially benefiting from intensive follow-up, maintenance therapies or inclusion in therapeutic studies. The dichotomous prognostic value of KATNAL2 should be validated in larger sample sets of EOC.
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Affiliation(s)
- Karolin Heinze
- Department of Gynecology and Reproduction Medicine, Jena University Hospital-Friedrich Schiller University Jena, 07747, Jena, Germany
| | - Matthias Rengsberger
- Department of Gynecology and Reproduction Medicine, Jena University Hospital-Friedrich Schiller University Jena, 07747, Jena, Germany
| | - Mieczyslaw Gajda
- Department of Forensic Medicine, Section of Pathology, Jena University Hospital - Friedrich Schiller University Jena, 07747, Jena, Germany
| | - Lars Jansen
- Department of Gynecology and Reproduction Medicine, Jena University Hospital-Friedrich Schiller University Jena, 07747, Jena, Germany
| | - Linea Osmers
- Department of Gynecology and Reproduction Medicine, Jena University Hospital-Friedrich Schiller University Jena, 07747, Jena, Germany
| | - Leticia Oliveira-Ferrer
- Department of Gynecology, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Barbara Schmalfeldt
- Department of Gynecology, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Matthias Dürst
- Department of Gynecology and Reproduction Medicine, Jena University Hospital-Friedrich Schiller University Jena, 07747, Jena, Germany
| | - Norman Häfner
- Department of Gynecology and Reproduction Medicine, Jena University Hospital-Friedrich Schiller University Jena, 07747, Jena, Germany.
| | - Ingo B Runnebaum
- Department of Gynecology and Reproduction Medicine, Jena University Hospital-Friedrich Schiller University Jena, 07747, Jena, Germany.
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Sahnane N, Carnevali I, Formenti G, Casarin J, Facchi S, Bombelli R, Di Lauro E, Memoli D, Salvati A, Rizzo F, Sessa F, Tibiletti MG. BRCA Methylation Testing Identifies a Subset of Ovarian Carcinomas without Germline Variants That Can Benefit from PARP Inhibitor. Int J Mol Sci 2020; 21:ijms21249708. [PMID: 33352687 PMCID: PMC7767143 DOI: 10.3390/ijms21249708] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/16/2020] [Accepted: 12/17/2020] [Indexed: 12/15/2022] Open
Abstract
Homologous Recombination Deficiency (HRD) is a frequent feature of high-grade epithelial ovarian carcinoma (EOC), associated with sensitivity to PARP-inhibitors (PARPi). The best characterized causes of HRD in EOCs are germline or somatic mutations in BRCA1 and BRCA2 genes. Although promoter methylation is a well-known mechanism of gene transcriptional repression, few data have been published about BRCA gene methylation in EOCs. In this retrospective study, we quantitatively analyzed by pyrosequencing a selected series of 90 formalin-fixed (FFPE) primary EOCs without BRCA germline mutations. We identified 20/88 (22.7%) EOCs showing BRCA promoter methylation, including 17/88 (19.3%) in BRCA1 and 4/86 (4.6%) in BRCA2 promoters, one of which showing concomitant BRCA1 methylation. Mean methylation levels were 49.6% and 45.8% for BRCA1 and BRCA2, respectively, with methylation levels ≥50% in 10/20 methylated EOCs. Constitutive BRCA methylation was excluded by testing blood-derived DNA. In conclusion, pyrosequencing methylation analysis of BRCA genes is a robust, quantitative and sensitive assay applicable to FFPE samples. Remarkably, a considerable subset of germline BRCA-negative EOCs showed somatic methylation and, likely, HRD. A subpopulation of women with BRCA methylation, even without BRCA mutations, could potentially benefit from PARP-inhibitors; further clinical studies are needed to clarify the predictive role of somatic BRCA methylation of PARP-therapy response.
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Affiliation(s)
- Nora Sahnane
- SC Anatomia Patologica, Ospedale di Circolo, ASST Settelaghi, 21100 Varese, Italy; (N.S.); (I.C.); (E.D.L.); (F.S.)
- Centro di Ricerca dei Tumori Eredo-Familiari, Dipartimento di Medicina e Chirurgia, University of Insubria, 21100 Varese, Italy
| | - Ileana Carnevali
- SC Anatomia Patologica, Ospedale di Circolo, ASST Settelaghi, 21100 Varese, Italy; (N.S.); (I.C.); (E.D.L.); (F.S.)
- Centro di Ricerca dei Tumori Eredo-Familiari, Dipartimento di Medicina e Chirurgia, University of Insubria, 21100 Varese, Italy
| | - Giorgio Formenti
- Dipartimento di Ostetricia e Ginecologia, ASST Settelaghi, University of Insubria, 21100 Varese, Italy; (G.F.); (J.C.)
| | - Jvan Casarin
- Dipartimento di Ostetricia e Ginecologia, ASST Settelaghi, University of Insubria, 21100 Varese, Italy; (G.F.); (J.C.)
| | - Sofia Facchi
- Dipartimento di Medicina e Chirurgia, University of Insubria, 21100 Varese, Italy; (S.F.); (R.B.)
| | - Raffaella Bombelli
- Dipartimento di Medicina e Chirurgia, University of Insubria, 21100 Varese, Italy; (S.F.); (R.B.)
| | - Eleonora Di Lauro
- SC Anatomia Patologica, Ospedale di Circolo, ASST Settelaghi, 21100 Varese, Italy; (N.S.); (I.C.); (E.D.L.); (F.S.)
| | - Domenico Memoli
- Programma di Genomica Medica, AOU SS Giovanni di Dio e Ruggi d’Aragona Università di Salerno, 84131 Salerno, Italy; (D.M.); (A.S.); (F.R.)
| | - Annamaria Salvati
- Programma di Genomica Medica, AOU SS Giovanni di Dio e Ruggi d’Aragona Università di Salerno, 84131 Salerno, Italy; (D.M.); (A.S.); (F.R.)
| | - Francesca Rizzo
- Programma di Genomica Medica, AOU SS Giovanni di Dio e Ruggi d’Aragona Università di Salerno, 84131 Salerno, Italy; (D.M.); (A.S.); (F.R.)
- Laboratorio di Medicina Molecolare e Genomica Dipartimento di Medicina, Chirurgia e Odontoiatria “Scuola Medica Salernitana” Università di Salerno, Baronissi, 84084 Salerno, Italy
| | - Fausto Sessa
- SC Anatomia Patologica, Ospedale di Circolo, ASST Settelaghi, 21100 Varese, Italy; (N.S.); (I.C.); (E.D.L.); (F.S.)
- Centro di Ricerca dei Tumori Eredo-Familiari, Dipartimento di Medicina e Chirurgia, University of Insubria, 21100 Varese, Italy
- Dipartimento di Medicina e Chirurgia, University of Insubria, 21100 Varese, Italy; (S.F.); (R.B.)
| | - Maria Grazia Tibiletti
- SC Anatomia Patologica, Ospedale di Circolo, ASST Settelaghi, 21100 Varese, Italy; (N.S.); (I.C.); (E.D.L.); (F.S.)
- Centro di Ricerca dei Tumori Eredo-Familiari, Dipartimento di Medicina e Chirurgia, University of Insubria, 21100 Varese, Italy
- Correspondence: ; Tel.: +39-0332-270601
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Miller RE, Leary A, Scott CL, Serra V, Lord CJ, Bowtell D, Chang DK, Garsed DW, Jonkers J, Ledermann JA, Nik-Zainal S, Ray-Coquard I, Shah SP, Matias-Guiu X, Swisher EM, Yates LR. ESMO recommendations on predictive biomarker testing for homologous recombination deficiency and PARP inhibitor benefit in ovarian cancer. Ann Oncol 2020; 31:1606-1622. [PMID: 33004253 DOI: 10.1016/j.annonc.2020.08.2102] [Citation(s) in RCA: 191] [Impact Index Per Article: 47.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 08/14/2020] [Accepted: 08/17/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Homologous recombination repair deficiency (HRD) is a frequent feature of high-grade serous ovarian, fallopian tube and peritoneal carcinoma (HGSC) and is associated with sensitivity to PARP inhibitor (PARPi) therapy. HRD testing provides an opportunity to optimise PARPi use in HGSC but methodologies are diverse and clinical application remains controversial. MATERIALS AND METHODS To define best practice for HRD testing in HGSC the ESMO Translational Research and Precision Medicine Working Group launched a collaborative project that incorporated a systematic review approach. The main aims were to (i) define the term 'HRD test'; (ii) provide an overview of the biological rationale and the level of evidence supporting currently available HRD tests; (iii) provide recommendations on the clinical utility of HRD tests in clinical management of HGSC. RESULTS A broad range of repair genes, genomic scars, mutational signatures and functional assays are associated with a history of HRD. Currently, the clinical validity of HRD tests in ovarian cancer is best assessed, not in terms of biological HRD status per se, but in terms of PARPi benefit. Clinical trials evidence supports the use of BRCA mutation testing and two commercially available assays that also incorporate genomic instability for identifying subgroups of HGSCs that derive different magnitudes of benefit from PARPi therapy, albeit with some variation by clinical scenario. These tests can be used to inform treatment selection and scheduling but their use is limited by a failure to consistently identify a subgroup of patients who derive no benefit from PARPis in most studies. Existing tests lack negative predictive value and inadequately address the complex and dynamic nature of the HRD phenotype. CONCLUSIONS Currently available HRD tests are useful for predicting likely magnitude of benefit from PARPis but better biomarkers are urgently needed to better identify current homologous recombination proficiency status and stratify HGSC management.
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Affiliation(s)
- R E Miller
- Department of Medical Oncology, University College London, London, UK; Department of Medical Oncology, St Bartholomew's Hospital, London, UK
| | - A Leary
- Department of Medicine and INSERM U981, Gustave Roussy Cancer Center, Université Paris-Saclay, Paris, France
| | - C L Scott
- Peter MacCallum Cancer Centre, Melbourne, Australia; The University of Melbourne, Melbourne, Australia
| | - V Serra
- Experimental Therapeutics Group Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - C J Lord
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK; CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK
| | - D Bowtell
- Peter MacCallum Cancer Centre, Melbourne, Australia; The University of Melbourne, Melbourne, Australia
| | - D K Chang
- Glasgow Precision Oncology Laboratory, Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, UK
| | - D W Garsed
- Peter MacCallum Cancer Centre, Melbourne, Australia; The University of Melbourne, Melbourne, Australia
| | - J Jonkers
- Division of Molecular Pathology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - J A Ledermann
- UCL Cancer Institute, University College London, London, UK
| | - S Nik-Zainal
- Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK; MRC Cancer Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - I Ray-Coquard
- Centre Leon Berard, Lyon, France; University Claude Bernard Groupe University of Lyon, France
| | - S P Shah
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, USA
| | - X Matias-Guiu
- Departments of Pathology, Hospital U Arnau de Vilanova and Hospital U de Bellvitge, Universities of Lleida and Barcelona, Irblleida, Idibell, Ciberonc, Barcelona, Spain
| | - E M Swisher
- Department of Obstetrics and Gynecology, University of Washington, Seattle, USA
| | - L R Yates
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge; Guy's Cancer Centre, Guys and St Thomas' NHS Foundation Trust, London, UK.
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van Wijk LM, Vermeulen S, Meijers M, van Diest MF, ter Haar NT, de Jonge MM, Solleveld-Westerink N, van Wezel T, van Gent DC, Kroep JR, Bosse T, Gaarenstroom KN, Vrieling H, Vreeswijk MPG. The RECAP Test Rapidly and Reliably Identifies Homologous Recombination-Deficient Ovarian Carcinomas. Cancers (Basel) 2020; 12:E2805. [PMID: 33003546 PMCID: PMC7650677 DOI: 10.3390/cancers12102805] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/25/2020] [Accepted: 09/26/2020] [Indexed: 12/14/2022] Open
Abstract
Recent studies have shown that the efficacy of PARP inhibitors in epithelial ovarian carcinoma (EOC) is related to tumor-specific defects in homologous recombination (HR) and extends beyond BRCA1/2 deficient EOC. A robust method with which to identify HR-deficient (HRD) carcinomas is therefore of utmost clinical importance. In this study, we investigated the proficiency of a functional HR assay based on the detection of RAD51 foci, the REcombination CAPacity (RECAP) test, in identifying HRD tumors in a cohort of prospectively collected epithelial ovarian carcinomas (EOCs). Of the 39 high-grade serous ovarian carcinomas (HGSOC), the RECAP test detected 26% (10/39) to be HRD, whereas ovarian carcinomas of other histologic subtypes (n = 10) were all HR-proficient (HRP). Of the HRD tumors that could be sequenced, 8/9 showed pathogenic BRCA1/2 variants or BRCA1 promoter hypermethylation, indicating that the RECAP test reliably identifies HRD, including but not limited to tumors related to BRCA1/2 deficiency. Furthermore, we found a trend towards better overall survival (OS) of HGSOC patients with RECAP-identified HRD tumors compared to patients with HRP tumors. This study shows that the RECAP test is an attractive alternative to DNA-based HRD tests, and further development of a clinical grade RECAP test is clearly warranted.
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Affiliation(s)
- Lise M. van Wijk
- Department of Human Genetics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (L.M.v.W.); (S.V.); (M.M.); (M.F.v.D.); (H.V.)
| | - Sylvia Vermeulen
- Department of Human Genetics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (L.M.v.W.); (S.V.); (M.M.); (M.F.v.D.); (H.V.)
| | - Matty Meijers
- Department of Human Genetics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (L.M.v.W.); (S.V.); (M.M.); (M.F.v.D.); (H.V.)
| | - Manuela F. van Diest
- Department of Human Genetics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (L.M.v.W.); (S.V.); (M.M.); (M.F.v.D.); (H.V.)
| | - Natalja T. ter Haar
- Department of Pathology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (N.T.t.H.); (M.M.d.J.); (N.S.-W.); (T.v.W.); (T.B.)
| | - Marthe M. de Jonge
- Department of Pathology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (N.T.t.H.); (M.M.d.J.); (N.S.-W.); (T.v.W.); (T.B.)
| | - Nienke Solleveld-Westerink
- Department of Pathology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (N.T.t.H.); (M.M.d.J.); (N.S.-W.); (T.v.W.); (T.B.)
| | - Tom van Wezel
- Department of Pathology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (N.T.t.H.); (M.M.d.J.); (N.S.-W.); (T.v.W.); (T.B.)
| | - Dik C. van Gent
- Department of Molecular Genetics, Erasmus MC, 3000 CA Rotterdam, The Netherlands;
| | - Judith R. Kroep
- Department of Medical Oncology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands;
| | - Tjalling Bosse
- Department of Pathology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (N.T.t.H.); (M.M.d.J.); (N.S.-W.); (T.v.W.); (T.B.)
| | - Katja N. Gaarenstroom
- Department of Gynecology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands;
| | - Harry Vrieling
- Department of Human Genetics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (L.M.v.W.); (S.V.); (M.M.); (M.F.v.D.); (H.V.)
| | - Maaike P. G. Vreeswijk
- Department of Human Genetics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (L.M.v.W.); (S.V.); (M.M.); (M.F.v.D.); (H.V.)
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Kalachand RD, O'Riain C, Toomey S, Carr A, Timms KM, O'Toole S, Madden S, Bates M, O'Leary JJ, Gleeson N, O'Donnell D, Grogan L, Breathnach O, Farrelly A, Stordal B, Hennessy BT. Prevalence of tumor BRCA1 and BRCA2 dysfunction in unselected patients with ovarian cancer. Obstet Gynecol Sci 2020; 63:643-54. [PMID: 32872764 DOI: 10.5468/ogs.20033] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 05/06/2020] [Indexed: 12/14/2022] Open
Abstract
Objective The therapeutic benefits of poly(ADP-ribose) polymerase inhibitors highlight the need to evaluate BRCA1/2 defects in tubal/ovarian cancer (OC). We sought to determine the pattern and disease characteristics associated with tumor BRCA1/2 mutations and BRCA1 methylation in women with OC. Methods We obtained 111 OC specimens from 2 university hospitals and assessed BRCA1/2 mutations and BRCA1 methylation in tumor DNA. The frequency and pattern of BRCA1/2 defects were examined. Associations between patient/disease characteristics and BRCA1/2 defects were ascertained (Fisher’s exact test). Platinum-free interval (PFI), progression-free survival (PFS), and overall survival (OS) based on the underlying BRCA1/2 defect were determined (Kaplan-Meier analysis [log-rank test]). Results We observed a BRCA1/2 dysfunction rate of 40% (28/70) in high-grade serous tubal/ovarian cancer (HGSC), including 14.3% BRCA1 methylation (n=10), 7.1% BRCA1 mutation (n=5), and 18.6% BRCA2 mutation (n=13). Defects in BRCA1/2 genes were associated with stage III/IV HGSC (BRCA1 methylation: P=0.005 [stage III/IV] and P=0.004 [HGSC]; BRCA1/2 mutation: P=0.03 [stage III/IV] and P<0.001 [HGSC]). Patients with BRCA1/2-mutated cancers showed improved OS (hazard ratio [HR], 0.65; 95% confidence interval [CI], 0.43–0.99; P=0.045) and a trend toward improved PFI (HR, 0.48; 95% CI, 0.22–1.06; P=0.07) and PFS (HR, 0.72; 95% CI, 0.51–1.03; P=0.07). No survival differences were observed between BRCA1-methylated and BRCA1/2 wild-type non-BRCA1-methylated cancers. Conclusion We observed a high tumor BRCA1/2 dysfunction rate in HGSC with a unique predominance of BRCA2 over BRCA1 mutations. While BRCA1/2 mutations conferred survival benefits in OC, no such association was observed with BRCA1 methylation.
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Romero I, Leskelä S, Mies BP, Velasco AP, Palacios J. Morphological and molecular heterogeneity of epithelial ovarian cancer: Therapeutic implications. EJC Suppl 2020; 15:1-15. [PMID: 33240438 DOI: 10.1016/j.ejcsup.2020.02.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 02/03/2020] [Accepted: 02/09/2020] [Indexed: 12/11/2022] Open
Abstract
Ovarian epithelial cancer (OEC) is the most lethal gynecologic malignancy. Despite current chemotherapeutic and surgical options, this high lethality can be attributed to multiple factors, including late-stage presentation. In order to optimize OEC treatment, it is important to highlight that it is composed of five main subtypes: high-grade serous ovarian carcinoma (HGSOC), low-grade serous ovarian carcinoma (LGSOC), endometrioid ovarian carcinoma (EOC), ovarian clear cell carcinoma (CCOC), and mucinous ovarian carcinoma (MOC). These subtypes differ in their precursor lesions, as well as in epidemiological, morphological, molecular and clinical features. OEC is one of the tumours in which most pathogenic germline mutations have been identified. Accordingly, up to 20% OC show alterations in BRCA1/2 genes, and also, although with a lower frequency, in other low penetrance genes associated with homologous recombination deficiency (HRD), mismatch repair genes (Lynch syndrome) and TP53. The most important prognostic factor is the 2014 FIGO staging, while older age is also associated with worse survival. HGSOC in all stages and CCC and MOC in advanced stages have the worse prognosis among histological types. Molecular markers have emerged as prognostic factors, particularly mutations in BRCA1/2, which are associated with a better outcome. Regarding treatment, whereas a proportion of HGSOC is sensible to platinum-based treatment and PARP inhibitors due to HRD, the rest of the histological types are relatively chemoresistant. New treatments based in specific molecular alterations are being tested in different histological types. In addition, immunotherapy could be an option, especially for EOC carrying mismatch repair deficiency or POLE mutations. The five different histological types have different precursor lesions and epidemiological, morphological, genetic, epigenetic and clinical features. Histological type is an important prognostic factor. Drugs targeting homologous recombination deficiency have been approved for treatment. The use of immunotherapy is limited due to lack of predictive biomarkers
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31
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Le Page C, Amuzu S, Rahimi K, Gotlieb W, Ragoussis J, Tonin PN. Lessons learned from understanding chemotherapy resistance in epithelial tubo-ovarian carcinoma from BRCA1and BRCA2mutation carriers. Semin Cancer Biol 2020; 77:110-126. [PMID: 32827632 DOI: 10.1016/j.semcancer.2020.08.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/20/2020] [Accepted: 08/12/2020] [Indexed: 02/07/2023]
Abstract
BRCA1 and BRCA2 are multi-functional proteins and key factors for maintaining genomic stability through their roles in DNA double strand break repair by homologous recombination, rescuing stalled or damaged DNA replication forks, and regulation of cell cycle DNA damage checkpoints. Impairment of any of these critical roles results in genomic instability, a phenotypic hallmark of many cancers including breast and epithelial ovarian carcinomas (EOC). Damaging, usually loss of function germline and somatic variants in BRCA1 and BRCA2, are important drivers of the development, progression, and management of high-grade serous tubo-ovarian carcinoma (HGSOC). However, mutations in these genes render patients particularly sensitive to platinum-based chemotherapy, and to the more innovative targeted therapies with poly-(ADP-ribose) polymerase inhibitors (PARPis) that are targeted to BRCA1/BRCA2 mutation carriers. Here, we reviewed the literature on the responsiveness of BRCA1/2-associated HGSOC to platinum-based chemotherapy and PARPis, and propose mechanisms underlying the frequent development of resistance to these therapeutic agents.
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Affiliation(s)
- Cécile Le Page
- McGill Research Institute of the McGill University Health Center, Montreal, QC, Canada.
| | - Setor Amuzu
- McGill Genome Centre, and Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Kurosh Rahimi
- Department of Pathology du Centre hospitalier de l'Université de Montréal, Montreal, QC, Canada
| | - Walter Gotlieb
- Laboratory of Gynecologic Oncology, Lady Davis Research Institute, Jewish General Hospital, Montreal, QC, Canada
| | - Jiannis Ragoussis
- McGill Genome Centre, and Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Patricia N Tonin
- Departments of Medicine and Human Genetics, McGill University, Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada.
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Tomasova K, Cumova A, Seborova K, Horak J, Koucka K, Vodickova L, Vaclavikova R, Vodicka P. DNA Repair and Ovarian Carcinogenesis: Impact on Risk, Prognosis and Therapy Outcome. Cancers (Basel) 2020; 12:E1713. [PMID: 32605254 DOI: 10.3390/cancers12071713] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 06/24/2020] [Indexed: 12/13/2022] Open
Abstract
There is ample evidence for the essential involvement of DNA repair and DNA damage response in the onset of solid malignancies, including ovarian cancer. Indeed, high-penetrance germline mutations in DNA repair genes are important players in familial cancers: BRCA1, BRCA2 mutations or mismatch repair, and polymerase deficiency in colorectal, breast, and ovarian cancers. Recently, some molecular hallmarks (e.g., TP53, KRAS, BRAF, RAD51C/D or PTEN mutations) of ovarian carcinomas were identified. The manuscript overviews the role of DNA repair machinery in ovarian cancer, its risk, prognosis, and therapy outcome. We have attempted to expose molecular hallmarks of ovarian cancer with a focus on DNA repair system and scrutinized genetic, epigenetic, functional, and protein alterations in individual DNA repair pathways (homologous recombination, non-homologous end-joining, DNA mismatch repair, base- and nucleotide-excision repair, and direct repair). We suggest that lack of knowledge particularly in non-homologous end joining repair pathway and the interplay between DNA repair pathways needs to be confronted. The most important genes of the DNA repair system are emphasized and their targeting in ovarian cancer will deserve further attention. The function of those genes, as well as the functional status of the entire DNA repair pathways, should be investigated in detail in the near future.
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Teraoka S, Muguruma M, Takano N, Miyahara K, Kawate T, Kaise H, Yamada K, Miyazawa K, Ishikawa T. Association of BRCA Mutations and BRCAness Status With Anticancer Drug Sensitivities in Triple-Negative Breast Cancer Cell Lines. J Surg Res 2020; 250:200-8. [PMID: 32092597 DOI: 10.1016/j.jss.2019.12.040] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 12/02/2019] [Accepted: 12/26/2019] [Indexed: 12/15/2022]
Abstract
BACKGROUND Many triple-negative breast cancers (TNBCs) show impaired breast cancer susceptibility gene I (BRCA1) function, called BRCAness. BRCAness tumors may show similar sensitivities to anticancer drugs as tumors with BRCA1 mutations. In this study, we investigated the association of BRCA mutations or BRCAness with drug sensitivities in TNBC. METHODS BRCAness was evaluated as BRCA1-like scores, using multiplex ligation-dependent probe amplification in 12 TNBC cell lines, including four with mutations. Sensitivities to docetaxel, cisplatin, and epirubicin were compared with BRCA mutations and BRCA1-like scores. Cisplatin sensitivity was examined in BRCA1 knockdown Michigan Cancer Foundation-7 cell lines. RESULTS Eight and four cell lines had characteristics of BRCAness and non-BRCAness, respectively. The 50% inhibitory concentration of docetaxel was higher in BRCA mutant and BRCAness cell lines than their counterparts. BRCA1-like scores showed a weak positive correlation with docetaxel sensitivity (r = 0.377; P = 0.039). Regarding cisplatin, scores were lower in BRCA mutants and BRCAness tumors than their counterparts. A negative correlation was found between BRCA1-like scores and cisplatin sensitivity (r = -0.407; P = 0.013). No differences were found for epirubicin. BRCA1 gene knockdown increased the cisplatin sensitivity of Michigan Cancer Foundation-7 cells. CONCLUSIONS BRCA1-like scores were associated with cisplatin sensitivity and docetaxel resistance. BRCA1-like score is hence a promising indicator for estimating drug sensitivities in TNBC.
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Takaya H, Nakai H, Takamatsu S, Mandai M, Matsumura N. Homologous recombination deficiency status-based classification of high-grade serous ovarian carcinoma. Sci Rep. 2020;10:2757. [PMID: 32066851 PMCID: PMC7026096 DOI: 10.1038/s41598-020-59671-3] [Citation(s) in RCA: 109] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 02/03/2020] [Indexed: 12/25/2022] Open
Abstract
Homologous recombination repair (HRR) pathway deficiency (HRD) is involved in the tumorigenesis and progression of high-grade serous ovarian carcinoma (HGSOC) as well as in the sensitivity to platinum chemotherapy drugs. In this study, we obtained data from The Cancer Genome Atlas (TCGA) on HGSOC and identified scores for the loss of heterozygosity, telomeric allelic imbalance, and large-scale state transitions, and calculated the HRD score. We then investigated the relationships among the score, genetic/epigenetic alterations in HRR-related genes, and the clinical data. We found that BRCA1/2 mutations were enriched in the group with HRD scores ≥63. Compared with the groups with scores ≤62, this group had a good prognosis; we thus considered HRD scores ≥63 to be the best cutoff point for identifying HRD cases in HGSOC. Classification of HGSOC cases by the HRD status revealed a better prognosis for HRD cases caused by genetic alterations (genetic HRD) than those caused by epigenetic changes and those caused by undetermined reasons (p = 0.0002). Among cases without macroscopic residual tumors after primary debulking surgery, 11 of 12 genetic HRD cases survived after the median observation period of 6.6 years, showing remarkably high survival rates (p = 0.0059). In conclusion, HGSOC can be classified into subtypes with different prognoses according to HRD status. This classification could be useful for personalized HGSOC treatment.
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Franzese E, Centonze S, Diana A, Lombardi A, Carlino F, Guerrera LP, De Vita F, Caraglia M, Pignata S, Ciardiello F, Orditura M. Genomic Profile and BRCA-1 Promoter Methylation Status in BRCA Mutated Ovarian Cancer: New Insights in Predictive Biomarkers of Olaparib Response. Front Oncol 2019; 9:1289. [PMID: 31850198 PMCID: PMC6895028 DOI: 10.3389/fonc.2019.01289] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 11/06/2019] [Indexed: 11/13/2022] Open
Abstract
Objective: We assessed the genomic profile of four representative BRCA-mutated ovarian cancer (OC) patients treated with olaparib to investigate the relationship between intratumor heterogeneity and response to olaparib treatment. The main aim is to identify possible predictive biomarkers of response to olaparib through the analysis of HRD or not HRD genes and the definition of BRCA1 promoter methylation status. Methods: DNA, isolated from formalin-fixed, paraffin-embedded (FFPE) diagnostic OC tissues, was analyzed by FoundationOneCDx™. This assay detects alterations in a total panel of 324 genes, using the Illumina® HiSeq 4000 platform. Methylation analysis of the BRCA gene promoter was carried out by pyrosequencing with PyroMark Q24 platform (Qiagen), an in vitro nucleic acid sequence-based detection test based on pyrosequencing technology for quantitative measurements of methylation status. Results: Case #1 and #2 were defined Long-term responders since they received olaparib for 27 and 36 months, respectively. These remarkable results could be explained, at least in part, by the presence of somatic IDH1 mutation in case #1 and PI3K and SOX2 amplification in the case #2. In case #3, the somatic NF1 mutation appeared to be related to the short duration of response. In the case #4, in which the patients is on olaparib from 1 year achieving a stable disease, a somatic mutation of BRCA1 was recorded. Moreover, in all cases, levels of BRCA1 promoter were strictly related to olaparib response. Conclusions: Based on our experience, genomic analysis of tumor tissue at diagnosis might help to determine the future response to olaparib in advanced OC setting, revealing predictive biomarkers beyond BRCA 1-2 and HRD status.
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Affiliation(s)
- Elisena Franzese
- Division of Medical Oncology, Department of Precision Medicine, School of Medicine, Luigi Vanvitelli University of Campania, Naples, Italy
| | - Sara Centonze
- Division of Medical Oncology, Department of Precision Medicine, School of Medicine, Luigi Vanvitelli University of Campania, Naples, Italy
| | - Anna Diana
- Division of Medical Oncology, Department of Precision Medicine, School of Medicine, Luigi Vanvitelli University of Campania, Naples, Italy
| | - Angela Lombardi
- Division of Medical Oncology, Department of Precision Medicine, School of Medicine, Luigi Vanvitelli University of Campania, Naples, Italy
| | - Francesca Carlino
- Division of Medical Oncology, Department of Precision Medicine, School of Medicine, Luigi Vanvitelli University of Campania, Naples, Italy
| | - Luigi Pio Guerrera
- Division of Medical Oncology, Department of Precision Medicine, School of Medicine, Luigi Vanvitelli University of Campania, Naples, Italy
| | - Ferdinando De Vita
- Division of Medical Oncology, Department of Precision Medicine, School of Medicine, Luigi Vanvitelli University of Campania, Naples, Italy
| | - Michele Caraglia
- Division of Medical Oncology, Department of Precision Medicine, School of Medicine, Luigi Vanvitelli University of Campania, Naples, Italy
| | - Sandro Pignata
- Istituto Nazionale per lo Studio e la Cura dei Tumori "Fondazione G. Pascale", IRCCS, Naples, Italy
| | - Fortunato Ciardiello
- Division of Medical Oncology, Department of Precision Medicine, School of Medicine, Luigi Vanvitelli University of Campania, Naples, Italy
| | - Michele Orditura
- Division of Medical Oncology, Department of Precision Medicine, School of Medicine, Luigi Vanvitelli University of Campania, Naples, Italy
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Kanakkanthara A, Huntoon CJ, Hou X, Zhang M, Heinzen EP, O'Brien DR, Oberg AL, John Weroha S, Kaufmann SH, Karnitz LM. ZC3H18 specifically binds and activates the BRCA1 promoter to facilitate homologous recombination in ovarian cancer. Nat Commun 2019; 10:4632. [PMID: 31604914 PMCID: PMC6789141 DOI: 10.1038/s41467-019-12610-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 09/18/2019] [Indexed: 01/27/2023] Open
Abstract
Reduced BRCA1 expression causes homologous recombination (HR) repair defects in high-grade serous ovarian cancers (HGSOCs). Here, we demonstrate that BRCA1 is transcriptionally activated by a previously unknown function of ZC3H18. We show that ZC3H18 is a DNA-binding protein that interacts with an E2F site in the BRCA1 promoter where it facilitates recruitment of E2F4 to an adjacent E2F site to promote BRCA1 transcription. Consistent with ZC3H18 role in activating BRCA1 expression, ZC3H18 depletion induces BRCA1 promoter methylation, reduces BRCA1 expression, disrupts HR, and sensitizes cells to DNA crosslinkers and poly(ADP-ribose) polymerase inhibitors. Moreover, in patient-derived xenografts and primary HGSOC tumors, ZC3H18 and E2F4 mRNA levels are positively correlated with BRCA1 mRNA levels, further supporting ZC3H18 role in regulating BRCA1. Given that ZC3H18 lies within 16q24.2, a region with frequent copy number loss in HGSOC, these findings suggest that ZC3H18 copy number losses could contribute to HR defects in HGSOC.
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Affiliation(s)
- Arun Kanakkanthara
- Division of Oncology Research, Mayo Clinic, Rochester, MN, USA
- Department of Pharmacology, Mayo Clinic, Rochester, MN, USA
| | | | - Xiaonan Hou
- Division of Medical Oncology, Mayo Clinic, Rochester, MN, USA
| | - Minzhi Zhang
- Division of Medical Oncology, Mayo Clinic, Rochester, MN, USA
| | - Ethan P Heinzen
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Daniel R O'Brien
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Ann L Oberg
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - S John Weroha
- Division of Medical Oncology, Mayo Clinic, Rochester, MN, USA
| | - Scott H Kaufmann
- Division of Oncology Research, Mayo Clinic, Rochester, MN, USA
- Department of Pharmacology, Mayo Clinic, Rochester, MN, USA
| | - Larry M Karnitz
- Division of Oncology Research, Mayo Clinic, Rochester, MN, USA.
- Department of Pharmacology, Mayo Clinic, Rochester, MN, USA.
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Hoppe MM, Sundar R, Tan DSP, Jeyasekharan AD. Biomarkers for Homologous Recombination Deficiency in Cancer. J Natl Cancer Inst 2019; 110:704-713. [PMID: 29788099 DOI: 10.1093/jnci/djy085] [Citation(s) in RCA: 203] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 04/06/2018] [Indexed: 12/11/2022] Open
Abstract
Defective DNA repair is a common hallmark of cancer. Homologous recombination is a DNA repair pathway of clinical interest due to the sensitivity of homologous recombination-deficient cells to poly-ADP ribose polymerase (PARP) inhibitors. The measurement of homologous recombination deficiency (HRD) in cancer is therefore vital to the appropriate design of clinical trials incorporating PARP inhibitors. However, methods to identify HRD in tumors are varied and controversial. Understanding existing and new methods to measure HRD is important to their appropriate use in clinical trials and practice. The aim of this review is to summarize the biology and clinical validation of current methods to measure HRD, to aid decision-making for patient stratification and translational research in PARP inhibitor trials. We discuss the current clinical development of PARP inhibitors, along with established indicators for HRD such as germline BRCA1/2 mutation status and clinical response to platinum-based therapy. We then examine newer assays undergoing clinical validation, including 1) somatic mutations in homologous recombination genes, 2) "genomic scar" assays using array-based comparative genomic hybridization (aCGH), single nucleotide polymorphism (SNP) analysis or mutational signatures derived from next-generation sequencing, 3) transcriptional profiles of HRD, and 4) phenotypic or functional assays of protein expression and localization. We highlight the strengths and weaknesses of each of these assays, for consideration during the design of studies involving PARP inhibitors.
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Affiliation(s)
- Michal M Hoppe
- Cancer Science Institute of Singapore, National University Hospital, Singapore
| | - Raghav Sundar
- Department of Haematology-Oncology, National University Hospital, Singapore
| | - David S P Tan
- Cancer Science Institute of Singapore, National University Hospital, Singapore.,Department of Haematology-Oncology, National University Hospital, Singapore
| | - Anand D Jeyasekharan
- Cancer Science Institute of Singapore, National University Hospital, Singapore.,Department of Haematology-Oncology, National University Hospital, Singapore
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Abstract
Objective This study aimed to assess the relationship between BRCA1 gene methylation, PD-L1 protein expression, and the clinicopathologic features of sporadic ovarian cancer (OC). Methods Bisulfite pyrosequencing and immunohistochemistry were used to detect BRCA1 gene methylation and PD-L1 protein expression, respectively, in tumor tissues from 112 patients with sporadic OC. Their levels were analyzed against clinicopathologic characteristics and prognosis using standard statistical methods. Results Twenty percent (22/112) of the OC cases exhibited BRCA1 gene hypermethylation. The frequency of BRCA1 hypermethylation was significantly higher in serous OC (25%) than in nonserous OC (8%; P < 0.05). No significant correlations were discovered between BRCA1 hypermethylation and age, menstrual status, tumor location, stage, lymph node metastasis, and prognosis (P > 0.05). Among the 112 OC cases, 59% (66/112) cases were positive for PD-L1 protein expression. No significant difference existed between PD-L1 expression and age, menstrual status, histological type, tumor location, stage, lymph node metastasis, and prognosis (P > 0.05). Moreover, no correlation existed between BRCA1 methylation and PD-L1 expression (P > 0.05, r = 0.002). Conclusions This is the first study linking BRCA1 hypermethylation variability to PD-L1 protein expression and the clinicopathologic features of OC. The data demonstrated that an epigenetic alteration of BRCA1 was closely associated with serous OC. The expression of PD-L1 was unrelated to the clinicopathologic features or BRCA1 hypermethylation in sporadic OC.
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Zhu X, Yang H, Lang J, Zhang Y. Ras association domain family protein 1a hypermethylation and PD-L1 expression in ovarian cancer: A retrospective study of 112 cases. Eur J Obstet Gynecol Reprod Biol 2019; 240:103-108. [PMID: 31242460 DOI: 10.1016/j.ejogrb.2019.06.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Accepted: 06/05/2019] [Indexed: 12/13/2022]
Abstract
OBJECTIVE This study assessed the interrelationships between Ras association domain family protein 1a (RASSF1A) gene hypermethylation, PD-L1 protein expression, and the clinicopathological characteristics of 112 ovarian cancer (OC) samples. METHODS Formalin-fixed paraffin-embedded OC tissue samples from surgical resection were assessed. Bisulfite pyrosequencing and immunohistochemistry were applied to detect RASSF1A gene methylation and PD-L1 protein expression in tumor cells, respectively. RASSF1A gene methylation and PD-L1 protein expression levels were analyzed against clinicopathological features and prognosis through standard statistical methods. RESULTS Of the 112 OC samples, 49.1% (55/112) exhibited RASSF1A gene hypermethylation. The frequency of RASSF1A hypermethylation was significantly higher in nonserous subtype (73.0%), early stage (66.7%), and nonrecurrent OC (62.9%, p < 0.05). Among all samples, 61.6% (69/112) were positive for PD-L1 protein expression in tumor cells. No significant differences in PD-L1 expression were identified for age, menstrual status, histological type, tumor location, grade, stage, lymph node metastasis, or prognosis (p > 0.05). RASSF1A methylation and PD-L1 expression were not correlated (p > 0.05). CONCLUSIONS This was the first study linking RASSF1A hypermethylation variability to PD-L1 expression and clinicopathological characteristics of OC. Epigenetic alteration of RASSF1A was closely associated with nonserous subtype, early stage, and nonrecurrent OC, indicating that RASSF1A hypermethylation may play a role in early detection of OC. Expression of PD-L1 had no relationship with the studied clinicopathological characteristics or RASSF1A hypermethylation in the 112 OC samples.
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Affiliation(s)
- Xinxin Zhu
- Department of Obstetrics and Gynecology, Peking University First Hospital, Beijing, China
| | - Huixia Yang
- Department of Obstetrics and Gynecology, Peking University First Hospital, Beijing, China
| | - Jinghe Lang
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Yan Zhang
- Department of Obstetrics and Gynecology, Peking University First Hospital, Beijing, China.
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Lønning PE, Eikesdal HP, Løes IM, Knappskog S. Constitutional Mosaic Epimutations - a hidden cause of cancer? Cell Stress 2019; 3:118-135. [PMID: 31225507 PMCID: PMC6551830 DOI: 10.15698/cst2019.04.183] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 03/04/2019] [Accepted: 03/05/2019] [Indexed: 12/11/2022] Open
Abstract
Silencing of tumor suppressor genes by promoter hypermethylation is a key mechanism to facilitate cancer progression in many malignancies. While promoter hypermethylation can occur at later stages of the carcinogenesis process, constitutional methylation of key tumor suppressors may be an initiating event whereby cancer is started. Constitutional BRCA1 methylation due to cis-acting germline genetic variants is associated with a high risk of breast and ovarian cancer. However, this seems to be a rare event, restricted to a very limited number of families. In contrast, mosaic constitutional BRCA1 methylation is detected in 4-7% of newborn females without germline BRCA1 mutations. While the cause of such methylation is poorly understood, mosaic normal tissue BRCA1 methylation is associated with a 2-3 fold increased risk of high-grade serous ovarian cancer (HGSOC). As such, BRCA1 methylation may be the cause of a significant number of ovarian cancers. Given the molecular similarities between HGSOC and basal-like breast cancer, the findings with respect to HGSOC suggest that constitutional BRCA1 methylation could be a risk factor for basal-like breast cancer as well. Similar to BRCA1, some specific germline variants in MLH1 and MSH2 are associated with promoter methylation and a high risk of colorectal cancers in rare hereditary cases of the disease. However, as many as 15% of all colorectal cancers are of the microsatellite instability (MSI) "high" subtype, in which commonly the tumors harbor MLH1 hypermethylation. Constitutional mosaic methylation of MLH1 in normal tissues has been detected but not formally evaluated as a potential risk factor for incidental colorectal cancers. However, the findings with respect to BRCA1 in breast and ovarian cancer raises the question whether mosaic MLH1 methylation is a risk factor for MSI positive colorectal cancer as well. As for MGMT, a promoter variant is associated with elevated methylation across a panel of solid cancers, and MGMT promoter methylation may contribute to an elevated cancer risk in several of these malignancies. We hypothesize that constitutional mosaic promoter methylation of crucial tumor suppressors may trigger certain types of cancer, similar to germline mutations inactivating the same particular genes. Such constitutional methylation events may be a spark to ignite cancer development, and if associated with a significant cancer risk, screening for such epigenetic alterations could be part of cancer prevention programs to reduce cancer mortality in the future.
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Affiliation(s)
- Per E. Lønning
- K.G.Jebsen Center for Genome Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Norway
- Department of Oncology, Haukeland University Hospital, Bergen, Norway
| | - Hans P. Eikesdal
- K.G.Jebsen Center for Genome Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Norway
- Department of Oncology, Haukeland University Hospital, Bergen, Norway
| | - Inger M. Løes
- K.G.Jebsen Center for Genome Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Norway
- Department of Oncology, Haukeland University Hospital, Bergen, Norway
| | - Stian Knappskog
- K.G.Jebsen Center for Genome Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Norway
- Department of Oncology, Haukeland University Hospital, Bergen, Norway
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Nicolas E, Bertucci F, Sabatier R, Gonçalves A. Targeting BRCA Deficiency in Breast Cancer: What are the Clinical Evidences and the Next Perspectives? Cancers (Basel) 2018; 10:cancers10120506. [PMID: 30544963 PMCID: PMC6316565 DOI: 10.3390/cancers10120506] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 11/27/2018] [Accepted: 12/09/2018] [Indexed: 12/24/2022] Open
Abstract
Breast cancers (BC) associated with germline mutations of BRCA1/2 represent 3–5% of cases. BRCA1/2-associated BC have biological features leading to genomic instability and potential sensitivity to DNA damaging agents, including poly(ADP-ribose) polymerase (PARP) and platinum agents. In this review, we will summarize clinical trials of chemotherapy and PARP inhibitors (PARPi), alone or in combination, at the early or late stage of BRCA1/2-associated BC. We will also present the mechanisms of resistance to PARPi as well as the new therapeutic strategies of association with PARPi. Finally, we will discuss under which conditions the use of DNA damaging agents can be extended to the BRCA1/2-wild type population, the BRCAness concept.
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Affiliation(s)
- Emanuel Nicolas
- Department of Medical Oncology, Institut Paoli-Calmettes, 13009 Marseille, France.
| | - François Bertucci
- Department of Medical Oncology, Institut Paoli-Calmettes, 13009 Marseille, France.
- CRCM-Predictive Oncology laboratory, Institut Paoli-Calmettes, Inserm U1068, CNRS UMR7258, Aix-Marseille Univ, 13009 Marseille, France.
| | - Renaud Sabatier
- Department of Medical Oncology, Institut Paoli-Calmettes, 13009 Marseille, France.
- CRCM-Predictive Oncology laboratory, Institut Paoli-Calmettes, Inserm U1068, CNRS UMR7258, Aix-Marseille Univ, 13009 Marseille, France.
| | - Anthony Gonçalves
- Department of Medical Oncology, Institut Paoli-Calmettes, 13009 Marseille, France.
- CRCM-Predictive Oncology laboratory, Institut Paoli-Calmettes, Inserm U1068, CNRS UMR7258, Aix-Marseille Univ, 13009 Marseille, France.
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Hodgson DR, Dougherty BA, Lai Z, Fielding A, Grinsted L, Spencer S, O'Connor MJ, Ho TW, Robertson JD, Lanchbury JS, Timms KM, Gutin A, Orr M, Jones H, Gilks B, Womack C, Gourley C, Ledermann J, Barrett JC. Candidate biomarkers of PARP inhibitor sensitivity in ovarian cancer beyond the BRCA genes. Br J Cancer. 2018;119:1401-1409. [PMID: 30353044 DOI: 10.1038/s41416-018-0274-8] [Citation(s) in RCA: 159] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 08/20/2018] [Accepted: 09/04/2018] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Olaparib (Lynparza™) is a PARP inhibitor approved for advanced BRCA-mutated (BRCAm) ovarian cancer. PARP inhibitors may benefit patients whose tumours are dysfunctional in DNA repair mechanisms unrelated to BRCA1/2. We report exploratory analyses, including the long-term outcome of candidate biomarkers of sensitivity to olaparib in BRCA wild-type (BRCAwt) tumours. METHODS Tumour samples from an olaparib maintenance monotherapy trial (Study 19, D0810C00019; NCT00753545) were analysed. Analyses included classification of mutations in genes involved in homologous recombination repair (HRR), BRCA1 promoter methylation status, measurement of BRCA1 protein and Myriad HRD score. RESULTS Patients with BRCAm tumours gained most benefit from olaparib; a similar treatment benefit was also observed in 21/95 patients whose tumours were BRCAwt but had loss-of-function HRR mutations compared to patients with no detectable HRR mutations (58/95). A higher median Myriad MyChoice® HRD score was observed in BRCAm and BRCAwt tumours with BRCA1 methylation. Patients without BRCAm tumours derived benefit from olaparib treatment vs placebo although to a lesser extent than BRCAm patients. CONCLUSIONS Ovarian cancer patients with tumours harbouring loss-of-function mutations in HRR genes other than BRCA1/2 may constitute a small, molecularly identifiable and clinically relevant population who derive treatment benefit from olaparib similar to patients with BRCAm.
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Kondrashova O, Topp M, Nesic K, Lieschke E, Ho GY, Harrell MI, Zapparoli GV, Hadley A, Holian R, Boehm E, Heong V, Sanij E, Pearson RB, Krais JJ, Johnson N, McNally O, Ananda S, Alsop K, Hutt KJ, Kaufmann SH, Lin KK, Harding TC, Traficante N, deFazio A, McNeish IA, Bowtell DD, Swisher EM, Dobrovic A, Wakefield MJ, Scott CL. Methylation of all BRCA1 copies predicts response to the PARP inhibitor rucaparib in ovarian carcinoma. Nat Commun 2018; 9:3970. [PMID: 30266954 PMCID: PMC6162272 DOI: 10.1038/s41467-018-05564-z] [Citation(s) in RCA: 172] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Accepted: 06/25/2018] [Indexed: 01/17/2023] Open
Abstract
Accurately identifying patients with high-grade serous ovarian carcinoma (HGSOC) who respond to poly(ADP-ribose) polymerase inhibitor (PARPi) therapy is of great clinical importance. Here we show that quantitative BRCA1 methylation analysis provides new insight into PARPi response in preclinical models and ovarian cancer patients. The response of 12 HGSOC patient-derived xenografts (PDX) to the PARPi rucaparib was assessed, with variable dose-dependent responses observed in chemo-naive BRCA1/2-mutated PDX, and no responses in PDX lacking DNA repair pathway defects. Among BRCA1-methylated PDX, silencing of all BRCA1 copies predicts rucaparib response, whilst heterozygous methylation is associated with resistance. Analysis of 21 BRCA1-methylated platinum-sensitive recurrent HGSOC (ARIEL2 Part 1 trial) confirmed that homozygous or hemizygous BRCA1 methylation predicts rucaparib clinical response, and that methylation loss can occur after exposure to chemotherapy. Accordingly, quantitative BRCA1 methylation analysis in a pre-treatment biopsy could allow identification of patients most likely to benefit, and facilitate tailoring of PARPi therapy.
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Affiliation(s)
- Olga Kondrashova
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Monique Topp
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medicine and Health Sciences, Monash University, Clayton, VIC, 3168, Australia
| | - Ksenija Nesic
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Elizabeth Lieschke
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
| | - Gwo-Yaw Ho
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3010, Australia
- Royal Women's Hospital, Parkville, VIC, 3052, Australia
- Research Division, Peter MacCallum Cancer Centre, Grattan Street, Parkville, VIC, 3010, Australia
| | - Maria I Harrell
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA, 98195, USA
| | - Giada V Zapparoli
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC, 3084, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Alison Hadley
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Robert Holian
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- School of Medicine, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Emma Boehm
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- School of Medicine, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Valerie Heong
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3010, Australia
- Royal Women's Hospital, Parkville, VIC, 3052, Australia
| | - Elaine Sanij
- Research Division, Peter MacCallum Cancer Centre, Grattan Street, Parkville, VIC, 3010, Australia
- Department of Clinical Pathology, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Richard B Pearson
- Research Division, Peter MacCallum Cancer Centre, Grattan Street, Parkville, VIC, 3010, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, 3010, Australia
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC, 3010, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3168, Australia
| | - John J Krais
- Fox Chase Cancer Centre, Philadelphia, PA, 19111, USA
| | - Neil Johnson
- Fox Chase Cancer Centre, Philadelphia, PA, 19111, USA
| | - Orla McNally
- Royal Women's Hospital, Parkville, VIC, 3052, Australia
| | | | - Kathryn Alsop
- Research Division, Peter MacCallum Cancer Centre, Grattan Street, Parkville, VIC, 3010, Australia
| | - Karla J Hutt
- Department of Medicine and Health Sciences, Monash University, Clayton, VIC, 3168, Australia
| | - Scott H Kaufmann
- Departments of Oncology and Molecular Pharmacology, Mayo Clinic, Rochester, MN, 55905, USA
| | | | | | - Nadia Traficante
- Research Division, Peter MacCallum Cancer Centre, Grattan Street, Parkville, VIC, 3010, Australia
- Department of Clinical Pathology, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Anna deFazio
- Centre for Cancer Research, The Westmead Institute for Medical Research, Sydney Medical School, The University of Sydney and Department of Gynaecological Oncology, Westmead Hospital, Sydney, NSW, 2145, Australia
| | - Iain A McNeish
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, Kensington, London, SW7 2AZ, United Kingdom
| | - David D Bowtell
- Research Division, Peter MacCallum Cancer Centre, Grattan Street, Parkville, VIC, 3010, Australia
- Department of Clinical Pathology, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Elizabeth M Swisher
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA, 98195, USA
| | - Alexander Dobrovic
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC, 3084, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, VIC, 3086, Australia
- Department of Clinical Pathology, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Matthew J Wakefield
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Melbourne Bioinformatics, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Clare L Scott
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.
- Department of Medicine and Health Sciences, Monash University, Clayton, VIC, 3168, Australia.
- Research Division, Peter MacCallum Cancer Centre, Grattan Street, Parkville, VIC, 3010, Australia.
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Tsibulak I, Wieser V, Degasper C, Shivalingaiah G, Wenzel S, Sprung S, Lax SF, Marth C, Fiegl H, Zeimet AG. BRCA1 and BRCA2 mRNA-expression prove to be of clinical impact in ovarian cancer. Br J Cancer 2018; 119:683-692. [PMID: 30111871 PMCID: PMC6173779 DOI: 10.1038/s41416-018-0217-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/12/2018] [Accepted: 07/16/2018] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Mutations in BRCA1 and BRCA2 are associated with better survival in ovarian cancer (OC) patients due to a better response to platinum-based chemotherapy. However, the impact of the BRCA1/2 mRNA-expression is not well characterized in OC. PATIENTS AND METHODS We investigated BRCA1/2 mRNA-expression in 12 non-neoplastic fallopian tubes and 201 epithelial OCs in relation to their clinical characteristics. RESULTS We found higher BRCA1/2 mRNA-expression in OCs compared to controls (P = 0.011, P < 0.001, respectively). BRCA1 mutated OCs exhibited lower BRCA1 (P = 0.014) but higher BRCA2 mRNA-expression (P = 0.001). Low BRCA1-expression was associated with favorable overall survival (OS) (P = 0.012) and low BRCA2-expression with better progression-free survival (PFS) and OS (P = 0.004, P = 0.001, respectively). A subgroup-analysis showed that this effect was confined only to the BRCA1-wildtype cancers. Cox-regression confirmed the prognostic significance of BRCA1-expression for OS (P = 0.028). Independency of the prognostic value of BRCA2-expression for PFS (P = 0.045) and OS (P = 0.015) was restricted to high-grade serous OCs. Fully platinum-sensitivity was characterized by lower BRCA1/2 mRNA-expression in BRCA1-wildtype cancers in comparison to platinum-refractory OC. CONCLUSION Our findings may reflect higher platinum-sensitivity due to reduced capacity of DNA damage repair in tissues with low BRCA1/2-expression. In this context, especially in BRCA-wildtype cancers both parameters could also be potential predictors for PARP-sensitivity.
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Affiliation(s)
- Irina Tsibulak
- Department of Obstetrics and Gynecology, Medical University of Innsbruck, Innsbruck, Austria
| | - Verena Wieser
- Department of Obstetrics and Gynecology, Medical University of Innsbruck, Innsbruck, Austria
| | - Christine Degasper
- Department of Obstetrics and Gynecology, Medical University of Innsbruck, Innsbruck, Austria
| | - Giridhar Shivalingaiah
- Division of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria.,Division Biological Chemistry, Biocenter, Innsbruck, Medical University of Innsbruck, Innsbruck, Austria
| | - Sören Wenzel
- Division of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Susanne Sprung
- Institute of Pathology, Medical University of Innsbruck, Innsbruck, Austria
| | - Sigurd F Lax
- Department of Pathology, Hospital Graz Süd-West, Academic Teaching Hospital of the Medical University Graz, Graz, Austria
| | - Christian Marth
- Department of Obstetrics and Gynecology, Medical University of Innsbruck, Innsbruck, Austria
| | - Heidelinde Fiegl
- Department of Obstetrics and Gynecology, Medical University of Innsbruck, Innsbruck, Austria.
| | - Alain G Zeimet
- Department of Obstetrics and Gynecology, Medical University of Innsbruck, Innsbruck, Austria.
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Vos S, van Diest PJ, Moelans CB. A systematic review on the frequency of BRCA promoter methylation in breast and ovarian carcinomas of BRCA germline mutation carriers: Mutually exclusive, or not? Crit Rev Oncol Hematol 2018; 127:29-41. [DOI: 10.1016/j.critrevonc.2018.05.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Revised: 04/10/2018] [Accepted: 05/09/2018] [Indexed: 12/12/2022] Open
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Tucker DW, Getchell CR, McCarthy ET, Ohman AW, Sasamoto N, Xu S, Ko JY, Gupta M, Shafrir A, Medina JE, Lee JJ, MacDonald LA, Malik A, Hasselblatt KT, Li W, Zhang H, Kaplan SJ, Murphy GF, Hirsch MS, Liu JF, Matulonis UA, Terry KL, Lian CG, Dinulescu DM. Epigenetic Reprogramming Strategies to Reverse Global Loss of 5-Hydroxymethylcytosine, a Prognostic Factor for Poor Survival in High-grade Serous Ovarian Cancer. Clin Cancer Res 2018; 24:1389-1401. [PMID: 29263182 PMCID: PMC5951622 DOI: 10.1158/1078-0432.ccr-17-1958] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 10/11/2017] [Accepted: 12/14/2017] [Indexed: 01/10/2023]
Abstract
Purpose: A major challenge in platinum-based cancer therapy is the clinical management of chemoresistant tumors, which have a largely unknown pathogenesis at the level of epigenetic regulation.Experimental Design: We evaluated the potential of using global loss of 5-hydroxymethylcytosine (5-hmC) levels as a novel diagnostic and prognostic epigenetic marker to better assess platinum-based chemotherapy response and clinical outcome in high-grade serous tumors (HGSOC), the most common and deadliest subtype of ovarian cancer. Furthermore, we identified a targetable pathway to reverse these epigenetic changes, both genetically and pharmacologically.Results: This study shows that decreased 5-hmC levels are an epigenetic hallmark for malignancy and tumor progression in HGSOC. In addition, global 5-hmC loss is associated with a decreased response to platinum-based chemotherapy, shorter time to relapse, and poor overall survival in patients newly diagnosed with HGSOC. Interestingly, the rescue of 5-hmC loss restores sensitivity to platinum chemotherapy in vitro and in vivo, decreases the percentage of tumor cells with cancer stem cell markers, and increases overall survival in an aggressive animal model of platinum-resistant disease.Conclusions: Consequently, a global analysis of patient 5-hmC levels should be included in future clinical trials, which use pretreatment with epigenetic adjuvants to elevate 5-hmC levels and improve the efficacy of current chemotherapies. Identifying prognostic epigenetic markers and altering chemotherapeutic regimens to incorporate DNMTi pretreatment in tumors with low 5-hmC levels could have important clinical implications for newly diagnosed HGSOC disease. Clin Cancer Res; 24(6); 1389-401. ©2017 AACR.
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Affiliation(s)
- Douglass W Tucker
- Department of Pathology, Division of Women's and Perinatal Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Christopher R Getchell
- Department of Pathology, Division of Women's and Perinatal Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Eric T McCarthy
- Department of Pathology, Division of Women's and Perinatal Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Anders W Ohman
- Department of Pathology, Division of Women's and Perinatal Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Naoko Sasamoto
- Epidemiology Center, Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Shuyun Xu
- Department of Pathology, Division of Dermatopathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Joo Yeon Ko
- Department of Dermatology, Hanyang University College of Medicine, Seoul, Korea
| | - Mamta Gupta
- Epidemiology Center, Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Amy Shafrir
- Epidemiology Center, Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jamie E Medina
- Department of Pathology, Division of Women's and Perinatal Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jonathan J Lee
- Department of Pathology, Division of Dermatopathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Lauren A MacDonald
- Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, Massachusetts
| | - Ammara Malik
- Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, Massachusetts
| | - Kathleen T Hasselblatt
- Gynecologic Oncology Laboratory, Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Wenjing Li
- Department of Medicine, Division of Endocrinology, Brigham and Women's Hospital, Harvard Medical School Boston, Massachusetts
| | - Hong Zhang
- Department of Pathology, Division of Women's and Perinatal Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Samuel J Kaplan
- Department of Pathology, Division of Women's and Perinatal Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - George F Murphy
- Department of Pathology, Division of Dermatopathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Michelle S Hirsch
- Department of Pathology, Division of Women's and Perinatal Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Joyce F Liu
- Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, Massachusetts
| | - Ursula A Matulonis
- Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, Massachusetts
| | - Kathryn L Terry
- Epidemiology Center, Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.
| | - Christine G Lian
- Department of Pathology, Division of Dermatopathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.
| | - Daniela M Dinulescu
- Department of Pathology, Division of Women's and Perinatal Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.
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Bernards SS, Pennington KP, Harrell MI, Agnew KJ, Garcia RL, Norquist BM, Swisher EM. Clinical characteristics and outcomes of patients with BRCA1 or RAD51C methylated versus mutated ovarian carcinoma. Gynecol Oncol 2018; 148:281-5. [DOI: 10.1016/j.ygyno.2017.12.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Revised: 11/28/2017] [Accepted: 12/04/2017] [Indexed: 02/08/2023]
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Eetezadi S, Evans JC, Shen YT, De Souza R, Piquette-Miller M, Allen C. Ratio-Dependent Synergism of a Doxorubicin and Olaparib Combination in 2D and Spheroid Models of Ovarian Cancer. Mol Pharm 2018; 15:472-485. [DOI: 10.1021/acs.molpharmaceut.7b00843] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Sina Eetezadi
- Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - James C. Evans
- Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Yen-Ting Shen
- Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Raquel De Souza
- Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Micheline Piquette-Miller
- Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Christine Allen
- Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
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Saini U, Suarez AA, Naidu S, Wallbillich JJ, Bixel K, Wanner RA, Bice J, Kladney RD, Lester J, Karlan BY, Goodfellow PJ, Cohn DE, Selvendiran K. STAT3/PIAS3 Levels Serve as "Early Signature" Genes in the Development of High-Grade Serous Carcinoma from the Fallopian Tube. Cancer Res 2018; 78:1739-1750. [PMID: 29339537 DOI: 10.1158/0008-5472.can-17-1671] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 11/13/2017] [Accepted: 01/10/2018] [Indexed: 01/23/2023]
Abstract
The initial molecular events that lead to malignant transformation of the fimbria of the fallopian tube (FT) through high-grade serous ovarian carcinoma (HGSC) remain poorly understood. In this study, we report that increased expression of signal transducer and activator of transcription 3 (pSTAT3 Tyr705) and suppression or loss of protein inhibitor of activated STAT3 (PIAS3) in FT likely drive HGSC. We evaluated human tissues-benign normal FT, tubal-peritoneal junction (TPJ), p53 signature FT tissue, tubal intraepithelial lesion in transition (TILT), serous tubal intraepithelial carcinoma (STIC) without ovarian cancer, and HGSC for expression of STAT3/PIAS3 (compared with their known TP53 signature) and their target proliferation genes. We observed constitutive activation of STAT3 and low levels or loss of PIAS3 in the TPJ, p53 signature, TILT, and STIC through advanced stage IV (HGSC) tissues. Elevated expression of pSTAT3 Tyr705 and decreased levels of PIAS3 appeared as early as TPJ and the trend continued until very advanced stage HGSC (compared with high PIAS3 and low pSTAT3 expression in normal benign FT). Exogenous expression of STAT3 in FT cells mediated translocation of pSTAT3 and c-Myc into the nucleus. In vivo experiments demonstrated that overexpression of STAT3 in FT secretory epithelial cells promoted tumor progression and metastasis, mimicking the clinical disease observed in patients with HGSC. Thus, we conclude that the STAT3 pathway plays a role in the development and progression of HGSC from its earliest premalignant states.Significance: Concomitant gain of pSTAT3 Tyr705 and loss of PIAS3 appear critical for initiation and development of high-grade serous carcinoma. Cancer Res; 78(7); 1739-50. ©2018 AACR.
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Affiliation(s)
- Uksha Saini
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Comprehensive Cancer Center, the Ohio State University Wexner Medical Center, Columbus, Ohio
| | - Adrian A Suarez
- Department of Pathology, Gynecological Pathology and Cytopathology Unit, the Ohio State University Wexner Medical Center, Columbus, Ohio
| | - Shan Naidu
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Comprehensive Cancer Center, the Ohio State University Wexner Medical Center, Columbus, Ohio
| | - John J Wallbillich
- Division of Gynecologic Oncology, Department of OB/GYN, Georgia Cancer Center, Augusta University, Augusta, Georgia
| | - Kristin Bixel
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Comprehensive Cancer Center, the Ohio State University Wexner Medical Center, Columbus, Ohio
| | - Ross A Wanner
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Comprehensive Cancer Center, the Ohio State University Wexner Medical Center, Columbus, Ohio
| | - Jason Bice
- Pathology Core Lab, Comprehensive Cancer Center, the Ohio State University Wexner Medical Center, Columbus, Ohio
| | - Raleigh D Kladney
- Pathology Core Lab, Comprehensive Cancer Center, the Ohio State University Wexner Medical Center, Columbus, Ohio
| | - Jenny Lester
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars Sinai Medical Center, Los Angeles, California
| | - Beth Y Karlan
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars Sinai Medical Center, Los Angeles, California
| | - Paul J Goodfellow
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Comprehensive Cancer Center, the Ohio State University Wexner Medical Center, Columbus, Ohio
| | - David E Cohn
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Comprehensive Cancer Center, the Ohio State University Wexner Medical Center, Columbus, Ohio
| | - Karuppaiyah Selvendiran
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Comprehensive Cancer Center, the Ohio State University Wexner Medical Center, Columbus, Ohio.
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Cai FF, Chen S, Wang MH, Lin XY, Zhang L, Zhang JX, Wang LX, Yang J, Ding JH, Pan X, Shao ZM, Biskup E. Pyrosequencing quantified methylation level of BRCA1 promoter as prognostic factor for survival in breast cancer patient. Oncotarget 2016; 7:27499-510. [PMID: 27027444 DOI: 10.18632/oncotarget.8355] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Accepted: 03/16/2016] [Indexed: 12/11/2022] Open
Abstract
BRCA1 promoter methylation is an essential epigenetic transcriptional silencing mechanism, related to breast cancer (BC) occurrence and progression. We quantified the methylation level of BRCA1 promoter and evaluated its significance as prognostic and predictive factor. BRCA1 promoter methylation level was quantified by pyrosequencing in surgical cancerous and adjacent normal specimens from 154 BC patients. A follow up of 98 months was conducted to assess the correlation between BRCA1-methylation level vs. overall survival (OS) and disease free survival (DFS). The mean methylation level in BC tissues was significantly higher (mean 32.6%; median 31.9%) than in adjacent normal samples (mean 16.2%; median 13.0%) (P < 0.0001). Tumor stage (R = 0.6165, P < 0.0001) and size (R = 0.7328, P < 0.0001) were significantly correlated with the methylation level. Patients with unmethylated BRCA1 had a better OS and DFS compared to the methylated group (each P < 0.0001). BRCA1 promoter methylation level has a statistically significance on survival in BC patients (HazR = 1.465, P = 0.000) and is an independent prognostic factor for OS in BC patients (HazR = 2.042, P = 0.000). Patients with ductal type, HER2 negative, lymph node negative stage 1+2 tumors had a better OS and DFS. Classification of grades and molecular subtypes did not show any prognostic significance. Pyrosequencing is a precise and efficient method to quantify BRCA1 promoter methylation level, with a high potential for future clinical implication, as it identifies subgroups of patients with poorer prognosis.
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