1
|
Wang Y, Dackus GMHE, Rosenberg EH, Cornelissen S, de Boo LW, Broeks A, Brugman W, Chan TWS, van Diest PJ, Hauptmann M, Ter Hoeve ND, Isaeva OI, de Jong VMT, Jóźwiak K, Kluin RJC, Kok M, Koop E, Nederlof PM, Opdam M, Schouten PC, Siesling S, van Steenis C, Voogd AC, Vreuls W, Salgado RF, Linn SC, Schmidt MK. Long-term outcomes of young, node-negative, chemotherapy-naïve, triple-negative breast cancer patients according to BRCA1 status. BMC Med 2024; 22:9. [PMID: 38191387 PMCID: PMC10775514 DOI: 10.1186/s12916-023-03233-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 12/15/2023] [Indexed: 01/10/2024] Open
Abstract
BACKGROUND Due to the abundant usage of chemotherapy in young triple-negative breast cancer (TNBC) patients, the unbiased prognostic value of BRCA1-related biomarkers in this population remains unclear. In addition, whether BRCA1-related biomarkers modify the well-established prognostic value of stromal tumor-infiltrating lymphocytes (sTILs) is unknown. This study aimed to compare the outcomes of young, node-negative, chemotherapy-naïve TNBC patients according to BRCA1 status, taking sTILs into account. METHODS We included 485 Dutch women diagnosed with node-negative TNBC under age 40 between 1989 and 2000. During this period, these women were considered low-risk and did not receive chemotherapy. BRCA1 status, including pathogenic germline BRCA1 mutation (gBRCA1m), somatic BRCA1 mutation (sBRCA1m), and tumor BRCA1 promoter methylation (BRCA1-PM), was assessed using DNA from formalin-fixed paraffin-embedded tissue. sTILs were assessed according to the international guideline. Patients' outcomes were compared using Cox regression and competing risk models. RESULTS Among the 399 patients with BRCA1 status, 26.3% had a gBRCA1m, 5.3% had a sBRCA1m, 36.6% had tumor BRCA1-PM, and 31.8% had BRCA1-non-altered tumors. Compared to BRCA1-non-alteration, gBRCA1m was associated with worse overall survival (OS) from the fourth year after diagnosis (adjusted HR, 2.11; 95% CI, 1.18-3.75), and this association attenuated after adjustment for second primary tumors. Every 10% sTIL increment was associated with 16% higher OS (adjusted HR, 0.84; 95% CI, 0.78-0.90) in gBRCA1m, sBRCA1m, or BRCA1-non-altered patients and 31% higher OS in tumor BRCA1-PM patients. Among the 66 patients with tumor BRCA1-PM and ≥ 50% sTILs, we observed excellent 15-year OS (97.0%; 95% CI, 92.9-100%). Conversely, among the 61 patients with gBRCA1m and < 50% sTILs, we observed poor 15-year OS (50.8%; 95% CI, 39.7-65.0%). Furthermore, gBRCA1m was associated with higher (adjusted subdistribution HR, 4.04; 95% CI, 2.29-7.13) and tumor BRCA1-PM with lower (adjusted subdistribution HR, 0.42; 95% CI, 0.19-0.95) incidence of second primary tumors, compared to BRCA1-non-alteration. CONCLUSIONS Although both gBRCA1m and tumor BRCA1-PM alter BRCA1 gene transcription, they are associated with different outcomes in young, node-negative, chemotherapy-naïve TNBC patients. By combining sTILs and BRCA1 status for risk classification, we were able to identify potential subgroups in this population to intensify and optimize adjuvant treatment.
Collapse
Affiliation(s)
- Yuwei Wang
- Division of Molecular Pathology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Gwen M H E Dackus
- Division of Molecular Pathology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Efraim H Rosenberg
- Division of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Sten Cornelissen
- Division of Molecular Pathology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
- Core Facility Molecular Pathology and Biobanking, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Leonora W de Boo
- Division of Molecular Pathology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Annegien Broeks
- Core Facility Molecular Pathology and Biobanking, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Wim Brugman
- Genomics Core Facility, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Terry W S Chan
- Division of Molecular Pathology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Paul J van Diest
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Michael Hauptmann
- Institute of Biostatistics and Registry Research, Brandenburg Medical School Theodor Fontane, Neuruppin, Germany
| | - Natalie D Ter Hoeve
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Olga I Isaeva
- Division of Tumor Biology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Vincent M T de Jong
- Division of Molecular Pathology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Katarzyna Jóźwiak
- Institute of Biostatistics and Registry Research, Brandenburg Medical School Theodor Fontane, Neuruppin, Germany
| | - Roelof J C Kluin
- Genomics Core Facility, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Marleen Kok
- Division of Tumor Biology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Esther Koop
- Department of Pathology, Gelre Ziekenhuizen, Apeldoorn, The Netherlands
| | - Petra M Nederlof
- Division of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Mark Opdam
- Division of Molecular Pathology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Philip C Schouten
- Division of Molecular Pathology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Sabine Siesling
- Department of Research and Development, Netherlands Comprehensive Cancer Organization, Utrecht, The Netherlands
- Department of Health Technology and Services Research, Technical Medical Centre, University of Twente, Enschede, The Netherlands
| | | | - Adri C Voogd
- Department of Epidemiology, Maastricht University, Maastricht, The Netherlands
| | - Willem Vreuls
- Department of Pathology, Canisius Wilhelmina Ziekenhuis, Nijmegen, The Netherlands
| | - Roberto F Salgado
- Department of Pathology, GZA-ZNA Hospitals, Antwerp, Belgium
- Division of Research, Peter MacCallum Cancer Center, Melbourne, Australia
| | - Sabine C Linn
- Division of Molecular Pathology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Marjanka K Schmidt
- Division of Molecular Pathology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands.
| |
Collapse
|
2
|
de Jong VMT, Pruntel R, Steenbruggen TG, Bleeker FE, Nederlof P, Hogervorst FBL, Linn SC. Identifying the BRCA1 c.-107A > T variant in Dutch patients with a tumor BRCA1 promoter hypermethylation. Fam Cancer 2023; 22:151-154. [PMID: 36112334 PMCID: PMC10020283 DOI: 10.1007/s10689-022-00314-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 06/02/2022] [Indexed: 11/26/2022]
Abstract
An inherited single nucleotide variant (SNV) in the 5'UTR of the BRCA1 gene c.-107A > T was identified to be related to BRCA1 promoter hypermethylation and a hereditary breast and ovarian cancer phenotype in two UK families. We investigated whether this BRCA1 variant was also present in a Dutch cohort of breast and ovarian cancer patients with tumor BRCA1 promoter hypermethylation. We selected all breast and ovarian cancer cases that tested positive for tumor BRCA1 promoter hypermethylation at the Netherlands Cancer Institute and Sanger sequenced the specific mutation in the tumor DNA. In total, we identified 193 tumors with BRCA1 promoter hypermethylation in 178 unique patients. The wild-type allele was identified in 100% (193/193) of sequenced tumor samples. In a large cohort of 178 patients, none had tumors harboring the previously identified c.-107A > T SNV in BRCA1. We therefore can conclude that the germline SNV is not pervasive in patients with tumor BRCA1 promoter hypermethylation.
Collapse
Affiliation(s)
- Vincent M T de Jong
- Department of Molecular Pathology, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX, Amsterdam, Netherlands
| | - Roelof Pruntel
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Tessa G Steenbruggen
- Department of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Fonnet E Bleeker
- Department of Clinical Genetics, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Petra Nederlof
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Frans B L Hogervorst
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Sabine C Linn
- Department of Molecular Pathology, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX, Amsterdam, Netherlands.
- Department of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, Netherlands.
- Department of Pathology, University Medical Center Utrecht, Utrecht, Netherlands.
| |
Collapse
|
3
|
van den Bosch T, Derks S, Miedema DM. Chromosomal Instability, Selection and Competition: Factors That Shape the Level of Karyotype Intra-Tumor Heterogeneity. Cancers (Basel) 2022; 14:cancers14204986. [PMID: 36291770 PMCID: PMC9600040 DOI: 10.3390/cancers14204986] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/07/2022] [Accepted: 10/09/2022] [Indexed: 12/03/2022] Open
Abstract
Simple Summary Each cancer consists of billions of cells. These cells are far from identical; hence, the population of cells that constitute a tumor is heterogeneous. A salient property that varies between cells in a tumor is their karyotype, the number and configuration of the chromosomes. The level of karyotype heterogeneity can be used to predict the survival of a patient. In this review, we describe the processes that shape the level of karyotype heterogeneity in a cancer. Abstract Intra-tumor heterogeneity (ITH) is a pan-cancer predictor of survival, with high ITH being correlated to a dismal prognosis. The level of ITH is, hence, a clinically relevant characteristic of a malignancy. ITH of karyotypes is driven by chromosomal instability (CIN). However, not all new karyotypes generated by CIN are viable or competitive, which limits the amount of ITH. Here, we review the cellular processes and ecological properties that determine karyotype ITH. We propose a framework to understand karyotype ITH, in which cells with new karyotypes emerge through CIN, are selected by cell intrinsic and cell extrinsic selective pressures, and propagate through a cancer in competition with other malignant cells. We further discuss how CIN modulates the cell phenotype and immune microenvironment, and the implications this has for the subsequent selection of karyotypes. Together, we aim to provide a comprehensive overview of the biological processes that shape the level of karyotype heterogeneity.
Collapse
Affiliation(s)
- Tom van den Bosch
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam and Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers—Location AMC, 1105 AZ Amsterdam, The Netherlands
- Oncode Institute, 1105 AZ Amsterdam, The Netherlands
| | - Sarah Derks
- Oncode Institute, 1105 AZ Amsterdam, The Netherlands
- Department of Medical Oncology, Amsterdam University Medical Centers—Location VUmc, 1081 HV Amsterdam, The Netherlands
- Correspondence: (S.D.); (D.M.M.)
| | - Daniël M. Miedema
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam and Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers—Location AMC, 1105 AZ Amsterdam, The Netherlands
- Oncode Institute, 1105 AZ Amsterdam, The Netherlands
- Correspondence: (S.D.); (D.M.M.)
| |
Collapse
|
4
|
Meijer TG, Nguyen L, Van Hoeck A, Sieuwerts AM, Verkaik NS, Ladan MM, Ruigrok-Ritstier K, van Deurzen CHM, van de Werken HJG, Lips EH, Linn SC, Memari Y, Davies H, Nik-Zainal S, Kanaar R, Martens JWM, Cuppen E, Jager A, van Gent DC. Functional RECAP (REpair CAPacity) assay identifies homologous recombination deficiency undetected by DNA-based BRCAness tests. Oncogene 2022; 41:3498-3506. [PMID: 35662281 PMCID: PMC9232391 DOI: 10.1038/s41388-022-02363-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 05/19/2022] [Accepted: 05/25/2022] [Indexed: 12/18/2022]
Abstract
Germline BRCA1/2 mutation status is predictive for response to Poly-[ADP-Ribose]-Polymerase (PARP) inhibitors in breast cancer (BC) patients. However, non-germline BRCA1/2 mutated and homologous recombination repair deficient (HRD) tumors are likely also PARP-inhibitor sensitive. Clinical validity and utility of various HRD biomarkers are under investigation. The REpair CAPacity (RECAP) test is a functional method to select HRD tumors based on their inability to form RAD51 foci. We investigated whether this functional test defines a similar group of HRD tumors as DNA-based tests. An HRD enriched cohort (n = 71; 52 primary and 19 metastatic BCs) selected based on the RECAP test (26 RECAP-HRD; 37%), was subjected to DNA-based HRD tests (i.e., Classifier of HOmologous Recombination Deficiency (CHORD) and BRCA1/2-like classifier). Whole genome sequencing (WGS) was carried out for 38 primary and 19 metastatic BCs. The RECAP test identified all bi-allelic BRCA deficient samples (n = 15) in this cohort. RECAP status partially correlated with DNA-based HRD test outcomes (70% concordance for both RECAP-CHORD and RECAP-BRCA1/2-like classifier). RECAP selected additional samples unable to form RAD51 foci, suggesting that this functional assay identified deficiencies in other DNA repair genes, which could also result in PARP-inhibitor sensitivity. Direct comparison of these HRD tests in clinical trials will be required to evaluate the optimal predictive test for clinical decision making.
Collapse
Affiliation(s)
- Titia G Meijer
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands. .,Department of Pathology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands. .,Oncode Institute, Utrecht, The Netherlands.
| | - Luan Nguyen
- Oncode Institute, Utrecht, The Netherlands.,Department of Molecular Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Arne Van Hoeck
- Oncode Institute, Utrecht, The Netherlands.,Department of Molecular Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Anieta M Sieuwerts
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Nicole S Verkaik
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Marjolijn M Ladan
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Kirsten Ruigrok-Ritstier
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Carolien H M van Deurzen
- Department of Pathology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Harmen J G van de Werken
- Cancer Computational Biology Center, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Urology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Immunology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Esther H Lips
- Department of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Sabine C Linn
- Department of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Department of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Department of Pathology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Yasin Memari
- Academic Department of Medical Genetics, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK.,MRC Cancer Unit, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
| | - Helen Davies
- Academic Department of Medical Genetics, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK.,MRC Cancer Unit, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
| | - Serena Nik-Zainal
- Academic Department of Medical Genetics, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK.,MRC Cancer Unit, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
| | - Roland Kanaar
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Edwin Cuppen
- Oncode Institute, Utrecht, The Netherlands.,Department of Molecular Genetics, University Medical Center Utrecht, Utrecht, The Netherlands.,Science Park, Hartwig Medical Foundation, Amsterdam, The Netherlands
| | - Agnes Jager
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Dik C van Gent
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| |
Collapse
|
5
|
Koole SN, Schouten PC, Hauke J, Kluin RJC, Nederlof P, Richters LK, Krebsbach G, Sikorska K, Alkemade M, Opdam M, Schagen van Leeuwen JH, Schreuder HWR, Hermans RHM, de Hingh IHJT, Mom CH, Arts HJG, van Ham M, van Dam P, Vuylsteke P, Sanders J, Horlings HM, van de Vijver KK, Hahnen E, van Driel WJ, Schmutzler R, Sonke GS, Linn SC. Effect of HIPEC according to HRD/BRCAwt genomic profile in stage III ovarian cancer - results from the phase III OVHIPEC trial. Int J Cancer 2022; 151:1394-1404. [PMID: 35583992 DOI: 10.1002/ijc.34124] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 04/09/2022] [Accepted: 04/21/2022] [Indexed: 11/07/2022]
Abstract
The addition of hyperthermic intraperitoneal chemotherapy (HIPEC) with cisplatin to interval cytoreductive surgery improves recurrence-free (RFS) and overall survival (OS) in patients with stage III ovarian cancer. Homologous recombination deficient (HRD) ovarian tumors are usually more platinum sensitive. Since hyperthermia impairs BRCA1/2 protein function, we hypothesized that HRD tumors respond best to treatment with HIPEC. We analyzed the effect of HIPEC in patients in the OVHIPEC trial, stratified by HRD status and BRCAm status. Clinical data and tissue samples were collected from patients included in the randomized, phase III OVHIPEC-1 trial. DNA copy number variation (CNV) profiles, HRD-related pathogenic mutations, and BRCA1 promotor hypermethylation were determined. CNV-profiles were categorized as HRD or non-HRD, based on a previously validated algorithm-based BRCA1-like classifier. Hazard ratios (HR) and corresponding 99% confidence intervals (CI) for the effect of RFS and OS of HIPEC in the BRCAm, the HRD/BRCAwt and the non-HRD group were estimated using Cox proportional hazard models. DNA was available from 200/245 (82%) patients. Seventeen (9%) tumors carried a pathogenic mutation in BRCA1 and 14 (7%) in BRCA2. Ninety-one (46%) tumors classified as BRCA1-like. The effect of HIPEC on RFS and OS was absent in BRCAm tumors (HR 1.25; 99%CI 0.48-3.29), and most present in HRD/BRCAwt (HR 0.44; 99%CI 0.21-0.91), and non-HRD/BRCAwt tumors (HR 0.82; 99%CI 0.48-1.42), interaction p-value: 0.024. Patients with HRD tumors without pathogenic BRCA1/2 mutation appear to benefit most from treatment with HIPEC, while benefit in patients with BRCA1/2 pathogenic mutations and patients without HRD seems less evident.
Collapse
Affiliation(s)
- Simone N Koole
- Department of Gynecology, The Netherlands Cancer Institute, Center of Gynecologic Oncology Amsterdam, Amsterdam, The Netherlands
- Department of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Philip C Schouten
- Department of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jan Hauke
- Faculty of Medicine and Center for Familial Breast and Ovarian Cancer and Center for Integrated Oncology (CIO), Cologne, University Hospital Cologne, Cologne, Germany
| | - Roel J C Kluin
- Genomics Core Facility, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Petra Nederlof
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Lisa K Richters
- Faculty of Medicine and Center for Familial Breast and Ovarian Cancer and Center for Integrated Oncology (CIO), Cologne, University Hospital Cologne, Cologne, Germany
| | - Gabriele Krebsbach
- Faculty of Medicine and Center for Familial Breast and Ovarian Cancer and Center for Integrated Oncology (CIO), Cologne, University Hospital Cologne, Cologne, Germany
| | - Karolina Sikorska
- Department of Biometrics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Maartje Alkemade
- Core Facility of Molecular Pathology and Biobanking, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Mark Opdam
- Core Facility of Molecular Pathology and Biobanking, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Henk W R Schreuder
- Department of Gynecological Oncology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ralph H M Hermans
- Department of Gynecology and Obstetrics, Catharina Hospital, Eindhoven, The Netherlands
| | | | - Constantijne H Mom
- Department of Obstetrics and Gynecology, Amsterdam University Medical Center, Center of Gynecologic Oncology Amsterdam, Amsterdam, The Netherlands
| | - Henriette J G Arts
- Department of Gynecological Oncology, University Medical Center Groningen, Groningen, The Netherlands
| | - Maaike van Ham
- Department of Gynecological Oncology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Peter van Dam
- Department of Gynecologic Oncology, University Hospital Antwerp, Antwerp, Belgium
| | - Peter Vuylsteke
- Department of Medical Oncology, UCL Louvain, CHU Namur Sainte-Elisabeth, Namur, Belgium
- University of Botswana, Gaborone, Botswana
| | - Joyce Sanders
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Hugo M Horlings
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Eric Hahnen
- Faculty of Medicine and Center for Familial Breast and Ovarian Cancer and Center for Integrated Oncology (CIO), Cologne, University Hospital Cologne, Cologne, Germany
| | - Willemien J van Driel
- Department of Gynecology, The Netherlands Cancer Institute, Center of Gynecologic Oncology Amsterdam, Amsterdam, The Netherlands
| | - Rita Schmutzler
- Faculty of Medicine and Center for Familial Breast and Ovarian Cancer and Center for Integrated Oncology (CIO), Cologne, University Hospital Cologne, Cologne, Germany
| | - Gabe S Sonke
- Department of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Sabine C Linn
- Department of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| |
Collapse
|
6
|
de Boo LW, Jóźwiak K, Joensuu H, Lindman H, Lauttia S, Opdam M, van Steenis C, Brugman W, Kluin RJC, Schouten PC, Kok M, Nederlof PM, Hauptmann M, Linn SC. Adjuvant capecitabine-containing chemotherapy benefit and homologous recombination deficiency in early-stage triple-negative breast cancer patients. Br J Cancer 2022; 126:1401-1409. [PMID: 35124703 PMCID: PMC9090783 DOI: 10.1038/s41416-022-01711-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 12/16/2021] [Accepted: 01/17/2022] [Indexed: 12/21/2022] Open
Abstract
Background The addition of adjuvant capecitabine to standard chemotherapy of early-stage triple-negative breast cancer (TNBC) patients has improved survival in a few randomised trials and in meta-analyses. However, many patients did not benefit. We evaluated the BRCA1-like DNA copy number signature, indicative of homologous recombination deficiency, as a predictive biomarker for capecitabine benefit in the TNBC subgroup of the FinXX trial. Methods Early-stage TNBC patients were randomised between adjuvant capecitabine-containing (TX + CEX: capecitabine-docetaxel, followed by cyclophosphamide-epirubicin-capecitabine) and conventional chemotherapy (T + CEF: docetaxel, followed by cyclophosphamide-epirubicin-fluorouracil). Tumour BRCA1-like status was determined on low-coverage, whole genome next-generation sequencing data using an established DNA comparative genomic hybridisation algorithm. Results For 129/202 (63.9%) patients the BRCA1-like status could be determined, mostly due to lack of tissue. During a median follow-up of 10.7 years, 35 recurrences and 32 deaths occurred. Addition of capecitabine appears to improve recurrence-free survival more among 61 (47.3%) patients with non-BRCA1-like tumours (HR 0.23, 95% CI 0.08–0.70) compared to 68 (52.7%) patients with BRCA1-like tumours (HR 0.66, 95% CI 0.24–1.81) (P-interaction = 0.17). Conclusion Based on our data, patients with non-BRCA1-like TNBC appear to benefit from the addition of capecitabine to adjuvant chemotherapy. Patients with BRCA1-like TNBC may also benefit. Additional research is needed to define the subgroup within BRCA1-like TNBC patients who may not benefit from adjuvant capecitabine.
Collapse
|
7
|
Collet L, Péron J, Penault-Llorca F, Pujol P, Lopez J, Freyer G, You B. PARP Inhibitors: A Major Therapeutic Option in Endocrine-Receptor Positive Breast Cancers. Cancers (Basel) 2022; 14:cancers14030599. [PMID: 35158866 PMCID: PMC8833594 DOI: 10.3390/cancers14030599] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/13/2022] [Accepted: 01/21/2022] [Indexed: 01/01/2023] Open
Abstract
Simple Summary OlympiAD and EMBRACA trials demonstrated the efficacy of PARPi, compared to chemotherapy, in patients with HER2-negative metastatic breast cancers (mBC) carrying a germline BRCA mutation. Patients with ER+/HER2-BRCA-mutated mBC seemed to have a higher risk of early disease progression while on CDK4/6 inhibitors and benefit from PARPi, especially when prescribed before chemotherapy. Importantly, the frequency of BRCA pathogenic variant (PV) carriers among ER+/HER2- breast cancer patients has been underestimated, and 50% of all BRCA1/2 mutated breast cancers are actually of ER+/HER2- subtype. Recent studies also highlight the benefit of PARPi in BRCA wild type mBC with HRD representing up to 20% of ER+/HER2- breast cancers. The OLYMPIA trial also demonstrated PARPi utility in patients with ER+/HER2- early breast cancers with BRCA PV at high risk of relapse. Consequently, implementation of early genotyping and new strategies for identifying patients with high-risk ER+/HER2- HRD breast cancers likely to benefit from PARPi is of high importance. Abstract Recently, OlympiAD and EMBRACA trials demonstrated the favorable efficacy/toxicity ratio of PARPi, compared to chemotherapy, in patients with HER2-negative metastatic breast cancers (mBC) carrying a germline BRCA mutation. PARPi have been largely adopted in triple-negative metastatic breast cancer, but their place has been less clearly defined in endocrine-receptor positive, HER2 negative (ER+/ HER2-) mBC. The present narrative review aims at addressing this question by identifying the patients that are more likely benefit from PARPi. Frequencies of BRCA pathogenic variant (PV) carriers among ER+/HER2- breast cancer patients have been underestimated, and many experts assume than 50% of all BRCA1/2 mutated breast cancers are of ER+/HER2- subtype. Patients with ER+/HER2- BRCA-mutated mBC seemed to have a higher risk of early disease progression while on CDK4/6 inhibitors and PARPi are effective especially when prescribed before exposure to chemotherapy. The OLYMPIA trial also highlighted the utility of PARPi in patients with early breast cancers at high risk of relapse and carrying PV of BRCA. PARPi might also be effective in patients with HRD diseases, representing up to 20% of ER+/HER2- breast cancers. Consequently, the future implementation of early genotyping strategies for identifying the patients with high-risk ER+/HER2- HRD breast cancers likely to benefit from PARPi is of high importance.
Collapse
Affiliation(s)
- Laetitia Collet
- Oncology Department, CITOHL, Lyon-Sud Hospital, Cancer Institute of Hospices Civils de Lyon (IC-HCL), Hospices Civils de Lyon, 69495 Lyon, France; (L.C.); (J.P.); (G.F.)
- Lyon-Sud Medicine School, University of Lyon, University Claude Bernard Lyon 1, 69008 Lyon, France
| | - Julien Péron
- Oncology Department, CITOHL, Lyon-Sud Hospital, Cancer Institute of Hospices Civils de Lyon (IC-HCL), Hospices Civils de Lyon, 69495 Lyon, France; (L.C.); (J.P.); (G.F.)
- Lyon-Sud Medicine School, University of Lyon, University Claude Bernard Lyon 1, 69008 Lyon, France
- Laboratoire de Biométrie et Biologie Evolutive, Equipe Biostatistique-Santé, CNRS UMR 5558, Université Claude Bernard Lyon 1, 69100 Villeurbanne, France
| | - Frédérique Penault-Llorca
- Department of Pathology and Biopathology, Jean Perrin Comprehensive Cancer Center, UMR INSERM 1240, University Clermont Auvergne, 63011 Clermont-Ferrand, France;
| | - Pascal Pujol
- Department of Cancer Genetics, CHU Montpellier, UMR IRD 224-CNRS 5290, Université Montpellier, 34295 Montpellier, France;
- Centre de Recherches Écologiques et Évolutives sur le Cancer (CREEC), UMR 224 CNRS-5290, University of Montpellier, 34394 Montpellier, France
| | - Jonathan Lopez
- Biochemistry and Molecular Biology Department, Hopital Lyon Sud, Hospices Civils de Lyon, Université Claude Bernard Lyon 1, 69008 Lyon, France;
| | - Gilles Freyer
- Oncology Department, CITOHL, Lyon-Sud Hospital, Cancer Institute of Hospices Civils de Lyon (IC-HCL), Hospices Civils de Lyon, 69495 Lyon, France; (L.C.); (J.P.); (G.F.)
- Lyon-Sud Medicine School, University of Lyon, University Claude Bernard Lyon 1, 69008 Lyon, France
| | - Benoît You
- Oncology Department, CITOHL, Lyon-Sud Hospital, Cancer Institute of Hospices Civils de Lyon (IC-HCL), Hospices Civils de Lyon, 69495 Lyon, France; (L.C.); (J.P.); (G.F.)
- Lyon-Sud Medicine School, University of Lyon, University Claude Bernard Lyon 1, 69008 Lyon, France
- Correspondence: ; Tel.: +33-(0)4-78-86-43-18; Fax: +33-(0)4-78-86-43-56
| |
Collapse
|
8
|
Schouten PC, Richters L, Vis DJ, Kommoss S, van Dijk E, Ernst C, Kluin RJ, Marmé F, Lips EH, Schmidt S, Scheerman E, Prieske K, van Deurzen CH, Burges A, Ewing-Graham PC, Dietrich D, Jager A, de Gregorio N, Hauke J, du Bois A, Nederlof PM, Wessels LF, Hahnen E, Harter P, Linn SC, Schmutzler RK. Ovarian Cancer-Specific BRCA-like Copy-Number Aberration Classifiers Detect Mutations Associated with Homologous Recombination Deficiency in the AGO-TR1 Trial. Clin Cancer Res 2021; 27:6559-6569. [PMID: 34593530 PMCID: PMC9401539 DOI: 10.1158/1078-0432.ccr-21-1673] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 09/12/2021] [Accepted: 09/23/2021] [Indexed: 01/07/2023]
Abstract
PURPOSE Previously, we developed breast cancer BRCA1-like and BRCA2-like copy-number profile shrunken centroid classifiers predictive for mutation status and response to therapy, targeting homologous recombination deficiency (HRD). Therefore, we investigated BRCA1- and BRCA2-like classification in ovarian cancer, aiming to acquire classifiers with similar properties as those in breast cancer.Experimental Design: We analyzed DNA copy-number profiles of germline BRCA1- and BRCA2-mutant ovarian cancers and control tumors and observed that existing breast cancer classifiers did not sufficiently predict mutation status. Hence, we trained new shrunken centroid classifiers on this set and validated them in the independent The Cancer Genome Atlas dataset. Subsequently, we assessed BRCA1/2-like classification and obtained germline and tumor mutation and methylation status of cancer predisposition genes, among them several involved in HR repair, of 300 ovarian cancer samples derived from the consecutive cohort trial AGO-TR1 (NCT02222883). RESULTS The detection rate of the BRCA1-like classifier for BRCA1 mutations and promoter hypermethylation was 95.6%. The BRCA2-like classifier performed less accurately, likely due to a smaller training set. Furthermore, three quarters of the BRCA1/2-like tumors could be explained by (epi)genetic alterations in BRCA1/2, germline RAD51C mutations and alterations in other genes involved in HR. Around half of the non-BRCA-mutated ovarian cancer cases displayed a BRCA-like phenotype. CONCLUSIONS The newly trained classifiers detected most BRCA-mutated and methylated cancers and all tumors harboring a RAD51C germline mutations. Beyond that, we found an additional substantial proportion of ovarian cancers to be BRCA-like.
Collapse
Affiliation(s)
- Philip C. Schouten
- Department of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands.,Corresponding Author: Philip C. Schouten, Department of Molecular Pathology, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands. Phone: 312-051-2449; E-mail:
| | - Lisa Richters
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - Daniel J. Vis
- Department of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Stefan Kommoss
- Department of Women's Health, Tübingen University Hospital, Tübingen, Germany
| | - Ewald van Dijk
- Department of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Corinna Ernst
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - Roelof J.C. Kluin
- Genomics Core Facility, Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Frederik Marmé
- Department of Gynecologic Oncology, Medical Faculty Mannheim, University of Heidelberg, University Hospital Mannheim, Mannheim, Germany
| | - Esther H. Lips
- Department of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Sandra Schmidt
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - Esther Scheerman
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Katharina Prieske
- Department of Gynecology and Gynecologic Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Alexander Burges
- Department of Gynecology and Obstetrics, University Hospital Munich-Großhadern, Munich, Germany
| | | | - Dimo Dietrich
- Department of Otolaryngology, Head and Neck Surgery, University Hospital Bonn, Bonn, Germany
| | - Agnes Jager
- Department of Medical Oncology, Erasmus MC, Rotterdam, the Netherlands
| | - Nikolaus de Gregorio
- Department of Gynecology and Obstetrics, University Hospital, University of Ulm, Ulm, Germany
| | - Jan Hauke
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - Andreas du Bois
- Department of Gynecology and Gynecologic Oncology, Ev. Kliniken Essen-Mitte, Essen, Germany
| | - Petra M. Nederlof
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Lodewyk F. Wessels
- Department of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, the Netherlands.,Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Delft, the Netherlands
| | - Eric Hahnen
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - Philipp Harter
- Department of Gynecology and Gynecologic Oncology, Ev. Kliniken Essen-Mitte, Essen, Germany
| | - Sabine C. Linn
- Department of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands.,Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, the Netherlands.,Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Rita K. Schmutzler
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hospital Cologne, Cologne, Germany
| |
Collapse
|
9
|
A survey of cancer genome signatures identifies genes connected to distinct chromosomal instability phenotypes. THE PHARMACOGENOMICS JOURNAL 2021; 21:390-401. [PMID: 33731882 DOI: 10.1038/s41397-021-00217-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 01/16/2021] [Accepted: 01/27/2021] [Indexed: 01/31/2023]
Abstract
Certain breast and ovarian cancers are characterised by high levels of chromosomal instability. We established a suite of eleven SNP array-based signatures of various forms of chromosomal instability. To understand what biological mechanisms might underpin these signatures, we generated and assembled genetic-feature data including allele-specific expression, fusion genes, gene expression, methylation, somatic coding mutations and protein expression. For each signature, we extracted a compendium of significantly associated genetic features using machine learning. We established an association between subchromosomal allelic imbalance-based measures and DNA repair genes. Numerical chromosomal instability and chromothripsis were found to have distinct genetic associations but shared a relationship to mitotic processes, while whole-genome doubling was characterised by TP53 mutation, and high AURKA and GINS1 expression. Furthermore, we identified two genetically distinct forms of tandem duplicator phenotypes. These findings identify potentially novel genomic targets for validation and drug development for specific subsets of breast and ovarian cancer.
Collapse
|
10
|
Sipos O, Tovey H, Quist J, Haider S, Nowinski S, Gazinska P, Kernaghan S, Toms C, Maguire S, Orr N, Linn SC, Owen J, Gillett C, Pinder SE, Bliss JM, Tutt A, Cheang MCU, Grigoriadis A. Assessment of structural chromosomal instability phenotypes as biomarkers of carboplatin response in triple negative breast cancer: the TNT trial. Ann Oncol 2021; 32:58-65. [PMID: 33098992 PMCID: PMC7784666 DOI: 10.1016/j.annonc.2020.10.475] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 08/05/2020] [Accepted: 10/13/2020] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND In the TNT trial of triple negative breast cancer (NCT00532727), germline BRCA1/2 mutations were present in 28% of carboplatin responders. We assessed quantitative measures of structural chromosomal instability (CIN) to identify a wider patient subgroup within TNT with preferential benefit from carboplatin over docetaxel. PATIENTS AND METHODS Copy number aberrations (CNAs) were established from 135 formalin-fixed paraffin-embedded primary carcinomas using Illumina OmniExpress SNP-arrays. Seven published [allelic imbalanced CNA (AiCNA); allelic balanced CNA (AbCNA); copy number neutral loss of heterozygosity (CnLOH); number of telomeric allelic imbalances (NtAI); BRCA1-like status; percentage of genome altered (PGA); homologous recombination deficiency (HRD) scores] and two novel [Shannon diversity index (SI); high-level amplifications (HLAMP)] CIN-measurements were derived. HLAMP was defined based on the presence of at least one of the top 5% amplified cytobands located on 1q, 8q and 10p. Continuous CIN-measurements were divided into tertiles. All nine CIN-measurements were used to analyse objective response rate (ORR) and progression-free survival (PFS). RESULTS Patients with tumours without HLAMP had a numerically higher ORR and significantly longer PFS in the carboplatin (C) than in the docetaxel (D) arm [56% (C) versus 29% (D), PHLAMP,quiet = 0.085; PFS 6.1 months (C) versus 4.1 months (D), Pinteraction/HLAMP = 0.047]. In the carboplatin arm, patients with tumours showing intermediate telomeric NtAI and AiCNA had higher ORR [54% (C) versus 20% (D), PNtAI,intermediate = 0.03; 62% (C) versus 33% (D), PAiCNA,intermediate = 0.076]. Patients with high AiCNA and PGA had shorter PFS in the carboplatin arm [3.4 months (high) versus 5.7 months (low/intermediate); and 3.8 months (high) versus 5.6 months (low/intermediate), respectively; Pinteraction/AiCNA = 0.027, Padj.interaction/AiCNA = 0.125 and Pinteraction/PGA = 0.053, Padj.interaction/PGA = 0.176], whilst no difference was observed in the docetaxel arm. CONCLUSIONS Patients with tumours lacking HLAMP and demonstrating intermediate CIN-measurements formed a subgroup benefitting from carboplatin relative to docetaxel treatment within the TNT trial. This suggests a complex and paradoxical relationship between the extent of genomic instability in primary tumours and treatment response in the metastatic setting.
Collapse
Affiliation(s)
- O Sipos
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - H Tovey
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, UK
| | - J Quist
- Breast Cancer Now Unit, King's College London Faculty of Life Sciences and Medicine, London, UK; School of Cancer and Pharmaceutical Sciences, King's College London Faculty of Life Sciences and Medicine, London, UK
| | - S Haider
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - S Nowinski
- School of Cancer and Pharmaceutical Sciences, King's College London Faculty of Life Sciences and Medicine, London, UK
| | - P Gazinska
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - S Kernaghan
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, UK
| | - C Toms
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, UK
| | - S Maguire
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - N Orr
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - S C Linn
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - J Owen
- King's Health Partners Cancer Biobank, London, UK
| | - C Gillett
- King's Health Partners Cancer Biobank, London, UK
| | - S E Pinder
- School of Cancer and Pharmaceutical Sciences, King's College London Faculty of Life Sciences and Medicine, London, UK
| | - J M Bliss
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, UK
| | - A Tutt
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK; Breast Cancer Now Unit, King's College London Faculty of Life Sciences and Medicine, London, UK; School of Cancer and Pharmaceutical Sciences, King's College London Faculty of Life Sciences and Medicine, London, UK
| | - M C U Cheang
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, UK
| | - A Grigoriadis
- Breast Cancer Now Unit, King's College London Faculty of Life Sciences and Medicine, London, UK; School of Cancer and Pharmaceutical Sciences, King's College London Faculty of Life Sciences and Medicine, London, UK.
| |
Collapse
|
11
|
Przybytkowski E, Davis T, Hosny A, Eismann J, Matulonis UA, Wulf GM, Nabavi S. An immune-centric exploration of BRCA1 and BRCA2 germline mutation related breast and ovarian cancers. BMC Cancer 2020; 20:197. [PMID: 32164626 PMCID: PMC7068944 DOI: 10.1186/s12885-020-6605-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 02/04/2020] [Indexed: 12/28/2022] Open
Abstract
Background BRCA1/2 germline mutation related cancers are candidates for new immune therapeutic interventions. This study was a hypothesis generating exploration of genomic data collected at diagnosis for 19 patients. The prominent tumor mutation burden (TMB) in hereditary breast and ovarian cancers in this cohort was not correlated with high global immune activity in their microenvironments. More information is needed about the relationship between genomic instability, phenotypes and immune microenvironments of these hereditary tumors in order to find appropriate markers of immune activity and the most effective anticancer immune strategies. Methods Mining and statistical analyses of the original DNA and RNA sequencing data and The Cancer Genome Atlas data were performed. To interpret the data, we have used published literature and web available resources such as Gene Ontology, The Cancer immunome Atlas and the Cancer Research Institute iAtlas. Results We found that BRCA1/2 germline related breast and ovarian cancers do not represent a unique phenotypic identity, but they express a range of phenotypes similar to sporadic cancers. All breast and ovarian BRCA1/2 related tumors are characterized by high homologous recombination deficiency (HRD) and low aneuploidy. Interestingly, all sporadic high grade serous ovarian cancers (HGSOC) and most of the subtypes of triple negative breast cancers (TNBC) also express a high degree of HRD. Conclusions TMB is not associated with the magnitude of the immune response in hereditary BRCA1/2 related breast and ovarian cancers or in sporadic TNBC and sporadic HGSOC. Hereditary tumors express phenotypes as heterogenous as sporadic tumors with various degree of “BRCAness” and various characteristics of the immune microenvironments. The subtyping criteria developed for sporadic tumors can be applied for the classification of hereditary tumors and possibly also characterization of their immune microenvironment. A high HRD score may be a good candidate biomarker for response to platinum, and potentially PARP-inhibition. Trial registration Phase I Study of the Oral PI3kinase Inhibitor BKM120 or BYL719 and the Oral PARP Inhibitor Olaparib in Patients With Recurrent TNBC or HGSOC (NCT01623349), first posted on June 20, 2012. The design and the outcome of the clinical trial is not in the scope of this study.
Collapse
Affiliation(s)
- Ewa Przybytkowski
- Department of Computer Science and Engineering, University of Connecticut, Institute of System Genomics, Boston, MA, USA
| | - Thomas Davis
- Department of Computer Science and Engineering, University of Connecticut, Institute of System Genomics, Boston, MA, USA
| | - Abdelrahman Hosny
- Department of Computer Science and Engineering, University of Connecticut, Institute of System Genomics, Boston, MA, USA
| | | | | | - Gerburg M Wulf
- Beth Israel Deaconess Medical Center, Department of Hematology/Oncology, Harvard Medical School, Boston, MA, USA
| | - Sheida Nabavi
- Department of Computer Science and Engineering, University of Connecticut, Institute of System Genomics, Boston, MA, USA.
| |
Collapse
|
12
|
Puppe J, Opdam M, Schouten PC, Jóźwiak K, Lips E, Severson T, van de Ven M, Brambillasca C, Bouwman P, van Tellingen O, Bernards R, Wesseling J, Eichler C, Thangarajah F, Malter W, Pandey GK, Ozretić L, Caldas C, van Lohuizen M, Hauptmann M, Rhiem K, Hahnen E, Reinhardt HC, Büttner R, Mallmann P, Schömig-Markiefka B, Schmutzler R, Linn S, Jonkers J. EZH2 Is Overexpressed in BRCA1-like Breast Tumors and Predictive for Sensitivity to High-Dose Platinum-Based Chemotherapy. Clin Cancer Res 2019; 25:4351-4362. [PMID: 31036541 DOI: 10.1158/1078-0432.ccr-18-4024] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 02/25/2019] [Accepted: 04/24/2019] [Indexed: 11/16/2022]
Abstract
PURPOSE BRCA1-deficient breast cancers carry a specific DNA copy-number signature ("BRCA1-like") and are hypersensitive to DNA double-strand break (DSB) inducing compounds. Here, we explored whether (i) EZH2 is overexpressed in human BRCA1-deficient breast tumors and might predict sensitivity to DSB-inducing drugs; (ii) EZH2 inhibition potentiates cisplatin efficacy in Brca1-deficient murine mammary tumors. EXPERIMENTAL DESIGN EZH2 expression was analyzed in 497 breast cancers using IHC or RNA sequencing. We classified 370 tumors by copy-number profiles as BRCA1-like or non-BRCA1-like and examined its association with EZH2 expression. Additionally, we assessed BRCA1 loss through mutation or promoter methylation status and investigated the predictive value of EZH2 expression in a study population of breast cancer patients treated with adjuvant high-dose platinum-based chemotherapy compared with standard anthracycline-based chemotherapy. To explore whether EZH2 inhibition by GSK126 enhances sensitivity to platinum drugs in EZH2-overexpressing breast cancers we used a Brca1-deficient mouse model. RESULTS The highest EZH2 expression was found in BRCA1-associated tumors harboring a BRCA1 mutation, BRCA1-promoter methylation or were classified as BRCA1 like. We observed a greater benefit from high-dose platinum-based chemotherapy in BRCA1-like and non-BRCA1-like patients with high EZH2 expression. Combined treatment with the EZH2 inhibitor GSK126 and cisplatin decreased cell proliferation and improved survival in Brca1-deficient mice in comparison with single agents. CONCLUSIONS Our findings demonstrate that EZH2 is expressed at significantly higher levels in BRCA1-deficient breast cancers. EZH2 overexpression can identify patients with breast cancer who benefit significantly from intensified DSB-inducing platinum-based chemotherapy independent of BRCA1-like status. EZH2 inhibition improves the antitumor effect of platinum drugs in Brca1-deficient breast tumors in vivo.
Collapse
Affiliation(s)
- Julian Puppe
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands.
- Department of Obstetrics and Gynecology, Medical Faculty, University Hospital Cologne, Cologne, Germany
- Center of Familial Breast and Ovarian Cancer, University Hospital of Cologne, Cologne, Germany
| | - Mark Opdam
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Philip C Schouten
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Katarzyna Jóźwiak
- Department of Epidemiology and Biostatistics, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Esther Lips
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Tesa Severson
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Marieke van de Ven
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Chiara Brambillasca
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Peter Bouwman
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Olaf van Tellingen
- Division of Pharmacology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - René Bernards
- Oncode Institute, Utrecht, the Netherlands
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Jelle Wesseling
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Christian Eichler
- Department of Obstetrics and Gynecology, Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - Fabinshy Thangarajah
- Department of Obstetrics and Gynecology, Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - Wolfram Malter
- Department of Obstetrics and Gynecology, Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - Gaurav Kumar Pandey
- Oncode Institute, Utrecht, the Netherlands
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Luka Ozretić
- Department of Pathology, University Hospital of Cologne, Cologne, Germany
| | | | - Maarten van Lohuizen
- Oncode Institute, Utrecht, the Netherlands
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Michael Hauptmann
- Department of Epidemiology and Biostatistics, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Kerstin Rhiem
- Center of Familial Breast and Ovarian Cancer, University Hospital of Cologne, Cologne, Germany
| | - Eric Hahnen
- Center of Familial Breast and Ovarian Cancer, University Hospital of Cologne, Cologne, Germany
| | | | - Reinhard Büttner
- Department of Pathology, University Hospital of Cologne, Cologne, Germany
| | - Peter Mallmann
- Department of Obstetrics and Gynecology, Medical Faculty, University Hospital Cologne, Cologne, Germany
| | | | - Rita Schmutzler
- Center of Familial Breast and Ovarian Cancer, University Hospital of Cologne, Cologne, Germany
| | - Sabine Linn
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Jos Jonkers
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Center of Familial Breast and Ovarian Cancer, University Hospital of Cologne, Cologne, Germany
| |
Collapse
|
13
|
Immune induction strategies in metastatic triple-negative breast cancer to enhance the sensitivity to PD-1 blockade: the TONIC trial. Nat Med 2019; 25:920-928. [PMID: 31086347 DOI: 10.1038/s41591-019-0432-4] [Citation(s) in RCA: 537] [Impact Index Per Article: 107.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 03/19/2019] [Indexed: 12/19/2022]
Abstract
The efficacy of programmed cell death protein 1 (PD-1) blockade in metastatic triple-negative breast cancer (TNBC) is low1-5, highlighting a need for strategies that render the tumor microenvironment more sensitive to PD-1 blockade. Preclinical research has suggested immunomodulatory properties for chemotherapy and irradiation6-13. In the first stage of this adaptive, non-comparative phase 2 trial, 67 patients with metastatic TNBC were randomized to nivolumab (1) without induction or with 2-week low-dose induction, or with (2) irradiation (3 × 8 Gy), (3) cyclophosphamide, (4) cisplatin or (5) doxorubicin, all followed by nivolumab. In the overall cohort, the objective response rate (ORR; iRECIST14) was 20%. The majority of responses were observed in the cisplatin (ORR 23%) and doxorubicin (ORR 35%) cohorts. After doxorubicin and cisplatin induction, we detected an upregulation of immune-related genes involved in PD-1-PD-L1 (programmed death ligand 1) and T cell cytotoxicity pathways. This was further supported by enrichment among upregulated genes related to inflammation, JAK-STAT and TNF-α signaling after doxorubicin. Together, the clinical and translational data of this study indicate that short-term doxorubicin and cisplatin may induce a more favorable tumor microenvironment and increase the likelihood of response to PD-1 blockade in TNBC. These data warrant confirmation in TNBC and exploration of induction treatments prior to PD-1 blockade in other cancer types.
Collapse
|
14
|
Pellegrino B, Mateo J, Serra V, Balmaña J. Controversies in oncology: are genomic tests quantifying homologous recombination repair deficiency (HRD) useful for treatment decision making? ESMO Open 2019; 4:e000480. [PMID: 31231558 PMCID: PMC6555601 DOI: 10.1136/esmoopen-2018-000480] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 02/01/2019] [Accepted: 02/04/2019] [Indexed: 12/25/2022] Open
Affiliation(s)
- Benedetta Pellegrino
- Experimental Therapeutics Group, Vall d'Hebron Institut d'Oncologia, Barcelona, Spain
- Oncology, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Joaquin Mateo
- Prostate Cancer Translational Research Group, Vall d'Hebron Institut d'Oncologia, Barcelona, Spain
| | - Violeta Serra
- Experimental Therapeutics Group, Vall d'Hebron Institut d'Oncologia, Barcelona, Spain
| | - Judith Balmaña
- High Risk and Cancer Prevention Group, Vall d'Hebron Institut d'Oncologia, Barcelona, Spain
| |
Collapse
|
15
|
Salvagno C, Ciampricotti M, Tuit S, Hau CS, van Weverwijk A, Coffelt SB, Kersten K, Vrijland K, Kos K, Ulas T, Song JY, Ooi CH, Rüttinger D, Cassier PA, Jonkers J, Schultze JL, Ries CH, de Visser KE. Therapeutic targeting of macrophages enhances chemotherapy efficacy by unleashing type I interferon response. Nat Cell Biol 2019; 21:511-521. [PMID: 30886344 PMCID: PMC6451630 DOI: 10.1038/s41556-019-0298-1] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 02/13/2019] [Indexed: 12/18/2022]
Abstract
Recent studies have revealed a role for macrophages and neutrophils in limiting chemotherapy efficacy; however, the mechanisms underlying the therapeutic benefit of myeloid-targeting agents in combination with chemotherapy are incompletely understood. Here, we show that targeting tumour-associated macrophages by colony-stimulating factor-1 receptor (CSF-1R) blockade in the K14cre;Cdh1F/F;Trp53F/F transgenic mouse model for breast cancer stimulates intratumoural type I interferon (IFN) signalling, which enhances the anticancer efficacy of platinum-based chemotherapeutics. Notably, anti-CSF-1R treatment also increased intratumoural expression of type I IFN-stimulated genes in patients with cancer, confirming that CSF-1R blockade is a powerful strategy to trigger an intratumoural type I IFN response. By inducing an inflamed, type I IFN-enriched tumour microenvironment and by further targeting immunosuppressive neutrophils during cisplatin therapy, antitumour immunity was activated in this poorly immunogenic breast cancer mouse model. These data illustrate the importance of breaching multiple layers of immunosuppression during cytotoxic therapy to successfully engage antitumour immunity in breast cancer.
Collapse
Affiliation(s)
- Camilla Salvagno
- Division of Tumor Biology & Immunology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Metamia Ciampricotti
- Division of Tumor Biology & Immunology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Molecular Pharmacology Program and Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sander Tuit
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, Bonn, Germany.,Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, The Netherlands
| | - Cheei-Sing Hau
- Division of Tumor Biology & Immunology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Antoinette van Weverwijk
- Division of Tumor Biology & Immunology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Seth B Coffelt
- Division of Tumor Biology & Immunology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Cancer Research UK Beatson Institute and Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Kelly Kersten
- Division of Tumor Biology & Immunology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Kim Vrijland
- Division of Tumor Biology & Immunology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Kevin Kos
- Division of Tumor Biology & Immunology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Thomas Ulas
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, Bonn, Germany
| | - Ji-Ying Song
- Division of Experimental Animal Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Chia-Huey Ooi
- Roche Innovation Center Basel, Roche Pharma Research and Early Development, Basel, Switzerland
| | - Dominik Rüttinger
- Roche Innovation Center Munich, Roche Pharma Research and Early Development, Penzberg, Germany
| | | | - Jos Jonkers
- Division of Molecular Pathology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Joachim L Schultze
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, Bonn, Germany.,Platform for Single Cell Genomics and Epigenomics (PRECISE) at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Carola H Ries
- Roche Innovation Center Munich, Roche Pharma Research and Early Development, Penzberg, Germany
| | - Karin E de Visser
- Division of Tumor Biology & Immunology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands.
| |
Collapse
|
16
|
Chen Y, Wang Y, Salas LA, Miller TW, Mark K, Marotti JD, Kettenbach AN, Cheng C, Christensen BC. Molecular and epigenetic profiles of BRCA1-like hormone-receptor-positive breast tumors identified with development and application of a copy-number-based classifier. Breast Cancer Res 2019; 21:14. [PMID: 30683142 PMCID: PMC6347811 DOI: 10.1186/s13058-018-1090-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 12/20/2018] [Indexed: 02/09/2023] Open
Abstract
Background BRCA1-mutated cancers exhibit deficient homologous recombination (HR) DNA repair, resulting in extensive copy number alterations and genome instability. HR deficiency can also arise in tumors without a BRCA1 mutation. Compared with other breast tumors, HR-deficient, BRCA1-like tumors exhibit worse prognosis but selective chemotherapeutic sensitivity. Presently, patients with triple negative breast cancer (TNBC) who do not respond to hormone endocrine-targeting therapy are given cytotoxic chemotherapy. However, more recent evidence showed a similar genomic profile between BRCA1-deficient TNBCs and hormone-receptor-positive tumors. Characterization of the somatic alterations of BRCA1-like hormone-receptor-positive breast tumors as a group, which is currently lacking, can potentially help develop biomarkers for identifying additional patients who might respond to chemotherapy. Methods We retrained and validated a copy-number-based support vector machine (SVM) classifier to identify HR-deficient, BRCA1-like breast tumors. We applied this classifier to The Cancer Genome Atlas (TCGA) and Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) breast tumors. We assessed mutational profiles and proliferative capacity by covariate-adjusted linear models and identified differentially methylated regions using DMRcate in BRCA1-like hormone-receptor-positive tumors. Results Of the breast tumors in TCGA and METABRIC, 22% (651/2925) were BRCA1-like. Stratifying on hormone-receptor status, 13% (302/2405) receptor-positive and 69% (288/417) triple-negative tumors were BRCA1-like. Among the hormone-receptor-positive subgroup, BRCA1-like tumors showed significantly increased mutational burden and proliferative capacity (both P < 0.05). Genome-scale DNA methylation analysis of BRCA1-like tumors identified 202 differentially methylated gene regions, including hypermethylated BRCA1. Individually significant CpGs were enriched for enhancer regions (P < 0.05). The hypermethylated gene sets were enriched for DNA and chromatin conformation (all Bonferroni P < 0.05). Conclusions To provide insights into alternative classification and potential therapeutic targeting strategies of BRCA1-like hormone-receptor-positive tumors we developed and applied a novel copy number classifier to identify BRCA1-like hormone-receptor-positive tumors and their characteristic somatic alteration profiles. Electronic supplementary material The online version of this article (10.1186/s13058-018-1090-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Youdinghuan Chen
- Department of Epidemiology, Lebanon, USA.,Department of Molecular and Systems Biology, Lebanon, USA
| | - Yue Wang
- Department of Molecular and Systems Biology, Lebanon, USA
| | - Lucas A Salas
- Department of Epidemiology, Lebanon, USA.,Department of Molecular and Systems Biology, Lebanon, USA
| | - Todd W Miller
- Department of Molecular and Systems Biology, Lebanon, USA
| | - Kenneth Mark
- Department of Molecular and Systems Biology, Lebanon, USA
| | | | - Arminja N Kettenbach
- Department of Molecular and Systems Biology, Lebanon, USA.,Department of Biochemistry and Cell Biology, Lebanon, USA
| | - Chao Cheng
- Department of Molecular and Systems Biology, Lebanon, USA. .,Department of Biomedical Data Science, Lebanon, USA. .,Present address: Department of Medicine, Baylor College of Medicine, Room ICTR 100D, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Brock C Christensen
- Department of Epidemiology, Lebanon, USA. .,Department of Molecular and Systems Biology, Lebanon, USA. .,Department of Community and Family Medicine, Dartmouth-Hitchcock Medical Center, 660 Williamson, HB 7650. One Medical Center Drive, Lebanon, NH, 03756, USA.
| |
Collapse
|
17
|
Chartron E, Theillet C, Guiu S, Jacot W. Targeting homologous repair deficiency in breast and ovarian cancers: Biological pathways, preclinical and clinical data. Crit Rev Oncol Hematol 2018; 133:58-73. [PMID: 30661659 DOI: 10.1016/j.critrevonc.2018.10.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 09/25/2018] [Accepted: 10/30/2018] [Indexed: 12/16/2022] Open
Abstract
Mutation or epigenetic silencing of homologous recombination (HR) repair genes is characteristic of a growing proportion of triple-negative breast cancers (TNBCs) and high-grade serous ovarian carcinomas. Defects in HR lead to genome instability, allowing cells to acquire the multiple genetic alterations essential for cancer development. However, this deficiency can also be exploited by using DNA damaging agents or by targeting compensatory repair pathways. A noteworthy example is treatment of TNBC and epithelial ovarian cancer harboring BRCA1/2 germline mutations using platinum salts and/or PARP inhibitors. Dramatic responses to PARP inhibitors may support a wider use in the HR-deficient population beyond those with mutated germline BRCA1 and 2. In this review, we discuss HR deficiency hallmarks as predictive biomarkers for platinum salt and PARP inhibitor sensitivity for selecting patients affected by TNBC or epithelial ovarian cancer who could benefit from these therapeutic options.
Collapse
Affiliation(s)
- Elodie Chartron
- Department of medical oncology, Montpellier Academic Hospital, Montpellier, France
| | - Charles Theillet
- IRCM, INSERM, Université de Montpellier, ICM, Montpellier, France
| | - Séverine Guiu
- Department of Medical Oncology, Institut du Cancer de Montpellier, Montpellier, France
| | - William Jacot
- IRCM, INSERM, Université de Montpellier, ICM, Montpellier, France; Department of Medical Oncology, Institut du Cancer de Montpellier, Montpellier, France.
| |
Collapse
|
18
|
Computational Investigation of Homologous Recombination DNA Repair Deficiency in Sporadic Breast Cancer. Sci Rep 2017; 7:15742. [PMID: 29146938 PMCID: PMC5691048 DOI: 10.1038/s41598-017-16138-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 11/03/2017] [Indexed: 12/17/2022] Open
Abstract
BRCAness has important implications in the management and treatment of patients with breast and ovarian cancer. In this study, we propose a computational framework to measure the BRCAness of breast and ovarian tumor samples based on their gene expression profiles. We define a characteristic profile for BRCAness by comparing gene expression differences between BRCA1/2 mutant familial tumors and sporadic breast cancer tumors while adjusting for relevant clinical factors. With this BRCAness profile, our framework calculates sample-specific BRCA scores, which indicates homologous recombination (HR)-mediated DNA repair pathway activity of samples. We found that in sporadic breast cancer high BRCAness score is associated with aberrant copy number of HR genes rather than somatic mutation and other genomic features. Moreover, we observed significant correlations of BRCA score with genome instability and neoadjuvant chemotherapy. More importantly, BRCA score provides significant prognostic value in both breast and ovarian cancers after considering established clinical variables. In summary, the inferred BRCAness from our framework can be used as a robust biomarker for the prediction of prognosis and treatment response in breast and ovarian cancers.
Collapse
|
19
|
BRCA1-like profile is not significantly associated with survival benefit of non-myeloablative intensified chemotherapy in the GAIN randomized controlled trial. Breast Cancer Res Treat 2017; 166:775-785. [PMID: 28822007 DOI: 10.1007/s10549-017-4444-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 08/05/2017] [Indexed: 01/06/2023]
Abstract
PURPOSE The BRCA1-like profile identifies tumors with a defect in homologous recombination due to inactivation of BRCA1. This profile has been shown to predict which stage III breast cancer patients benefit from myeloablative, DNA double-strand-break-inducing chemotherapy. We tested the predictive potential of the BRCA1-like profile for adjuvant non-myeloablative, intensified dose-dense chemotherapy in the GAIN trial. METHODS Lymph node positive breast cancer patients were randomized to 3 × 3 dose-dense cycles of intensified epirubicin, paclitaxel, and cyclophosphamide (ETC) or 4 cycles concurrent epirubicin and cyclophosphamide followed by 10 cycles of weekly paclitaxel combined with 4 cycles capecitabine (EC-TX). Only triple negative breast cancer patients (TNBC) for whom tissue was available were included in these planned analyses. BRCA1-like or non-BRCA1-like copy number profiles were derived from low coverage sequencing data. RESULTS 119 out of 163 TNBC patients (73%) had a BRCA1-like profile. After median follow-up of 83 months, disease free survival (DFS) was not significantly different between BRCA1-like and non-BRCA1-like patients [adjusted hazard ratio (adj.HR) 1.02; 95% confidence interval (CI) 0.55-1.86], neither was overall survival (OS; adj.HR 1.26; 95% CI 0.58-2.71). When split by BRCA1-like status, DFS and OS were not significantly different between treatments. However, EC-TX seemed to result in a trend to an improvement in DFS in patients with a BRCA1-like tumor, while the reverse accounted for ETC treatment in patients with a non-BRCA1-like tumor (p for interaction = 0.094). CONCLUSIONS The BRCA1-like profile is not associated with survival benefit for a non-myeloablative, intensified regimen in this study population. Considering the limited cohort size, capecitabine might have additional benefit for TNBC patients.
Collapse
|
20
|
Murria Estal R, Palanca Suela S, de Juan Jiménez I, Alenda Gonzalez C, Egoavil Rojas C, García-Casado Z, López Guerrero JA, Juan Fita MJ, Sánchez Heras AB, Segura Huerta Á, Santaballa Bertrán A, Chirivella González I, Llop García M, Pérez Simó G, Barragán González E, Bolufer Gilabert P. Relationship of immunohistochemistry, copy number aberrations and epigenetic disorders with BRCAness pattern in hereditary and sporadic breast cancer. Fam Cancer 2016; 15:193-200. [PMID: 26723934 DOI: 10.1007/s10689-015-9864-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The study aims to identify the relevance of immunohistochemistry (IHC), copy number aberrations (CNA) and epigenetic disorders in BRCAness breast cancers (BCs). We studied 95 paraffin included BCs, of which 41 carried BRCA1/BRCA2 germline mutations and 54 were non hereditary (BRCAX/Sporadic). Samples were assessed for BRCA1ness and CNAs by Multiplex Ligation-dependent Probe Amplification (MLPA); promoter methylation (PM) was assessed by methylation-specific-MLPA and the expression of miR-4417, miR-423-3p, miR-590-5p and miR-187-3p by quantitative RT-PCR. IHC markers Ki67, ER, PR, HER2, CK5/6, EGFR and CK18 were detected with specific primary antibodies (DAKO, Denmark). BRCAness association with covariates was performed using multivariate binary logistic regression (stepwise backwards Wald option). BRCA1/2 mutational status (p = 0.027), large tumor size (p = 0.041) and advanced histological grade (p = 0.017) among clinic-pathological variables; ER (p < 0.001) among IHC markers; MYC (p < 0.001) among CNA; APC (p = 0.065), ATM (p = 0.014) and RASSF1 (p = 0.044) among PM; and miR-590-5p (p = 0.001), miR-4417 (p = 0.019) and miR-423 (p = 0.013) among microRNA expression, were the selected parameters significantly related with the BRCAness status. The logistic regression performed with all these parameters selected ER+ as linked with the lack of BRCAness (p = 0.001) and MYC CNA, APC PM and miR-590-5p expression with BRCAness (p = 0.014, 0.045 and 0.007, respectively). In conclusion, the parameters ER expression, APC PM, MYC CNA and miR-590-5p expression, allowed detection of most BRCAness BCs. The identification of BRCAness can help establish a personalized medicine addressed to predict the response to specific treatments.
Collapse
Affiliation(s)
- Rosa Murria Estal
- Laboratory of Molecular Biology, Service of Clinical Analysis, University Hospital La Fe, Torre A 4ª planta, Avenida de Fernando Abril Martorell, no 106, 46026, Valencia, Spain
| | - Sarai Palanca Suela
- Laboratory of Molecular Biology, Service of Clinical Analysis, University Hospital La Fe, Torre A 4ª planta, Avenida de Fernando Abril Martorell, no 106, 46026, Valencia, Spain
| | - Inmaculada de Juan Jiménez
- Laboratory of Molecular Biology, Service of Clinical Analysis, University Hospital La Fe, Torre A 4ª planta, Avenida de Fernando Abril Martorell, no 106, 46026, Valencia, Spain
| | | | | | | | | | | | | | | | | | | | - Marta Llop García
- Laboratory of Molecular Biology, Service of Clinical Analysis, University Hospital La Fe, Torre A 4ª planta, Avenida de Fernando Abril Martorell, no 106, 46026, Valencia, Spain
| | - Gema Pérez Simó
- Laboratory of Molecular Biology, Service of Clinical Analysis, University Hospital La Fe, Torre A 4ª planta, Avenida de Fernando Abril Martorell, no 106, 46026, Valencia, Spain
| | - Eva Barragán González
- Laboratory of Molecular Biology, Service of Clinical Analysis, University Hospital La Fe, Torre A 4ª planta, Avenida de Fernando Abril Martorell, no 106, 46026, Valencia, Spain
| | - Pascual Bolufer Gilabert
- Laboratory of Molecular Biology, Service of Clinical Analysis, University Hospital La Fe, Torre A 4ª planta, Avenida de Fernando Abril Martorell, no 106, 46026, Valencia, Spain.
| |
Collapse
|
21
|
Gross E, van Tinteren H, Li Z, Raab S, Meul C, Avril S, Laddach N, Aubele M, Propping C, Gkazepis A, Schmitt M, Meindl A, Nederlof PM, Kiechle M, Lips EH. Identification of BRCA1-like triple-negative breast cancers by quantitative multiplex-ligation-dependent probe amplification (MLPA) analysis of BRCA1-associated chromosomal regions: a validation study. BMC Cancer 2016; 16:811. [PMID: 27756336 PMCID: PMC5070367 DOI: 10.1186/s12885-016-2848-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 10/07/2016] [Indexed: 12/11/2022] Open
Abstract
Background Triple-negative breast cancer (TNBC) with a BRCA1-like molecular signature has been demonstrated to remarkably respond to platinum-based chemotherapy and might be suited for a future treatment with poly(ADP-ribose)polymerase (PARP) inhibitors. In order to rapidly assess this signature we have previously developed a multiplex-ligation-dependent probe amplification (MLPA)-based assay. Here we present an independent validation of this assay to confirm its important clinical impact. Methods One-hundred-forty-four TNBC tumor specimens were analysed by the MLPA-based “BRCA1-like” test. Classification into BRCA1-like vs. non-BRCA1-like samples was performed by our formerly established nearest shrunken centroids classifier. Data were subsequently compared with the BRCA1-mutation/methylation status of the samples. T-lymphocyte infiltration and expression of the main target of PARP inhibitors, PARP1, were assessed on a subset of samples by immunohistochemistry. Data acquisition and interpretation was performed in a blinded manner. Results In the studied TNBC cohort, 63 out of 144 (44 %) tumors were classified into the BRCA1-like category. Among these, the MLPA test correctly predicted 15 out of 18 (83 %) samples with a pathogenic BRCA1-mutation and 20 of 22 (91 %) samples exhibiting BRCA1-promoter methylation. Five false-negative samples were observed. We identified high lymphocyte infiltration as one possible basis for misclassification. However, two falsely classified BRCA1-mutated tumors were also characterized by rather non-BRCA1-associated histopathological features such as borderline ER expression. The BRCA1-like vs. non-BRCA1-like signature was specifically enriched in high-grade (G3) cancers (90 % vs. 58 %, p = 0.0004) and was also frequent in tumors with strong (3+) nuclear PARP1 expression (37 % vs. 16 %; p = 0.087). Conclusions This validation study confirmed the good performance of the initial MLPA assay which might thus serve as a valuable tool to select patients for platinum-based chemotherapy regimens. Moreover, frequent PARP1 upregulation in BRCA1-like tumors may also point to susceptibility to treatment with PARP inhibitors. Limitations are the requirement of high tumor content and high-quality DNA.
Collapse
Affiliation(s)
- Eva Gross
- Department of Gynecology and Obstetrics, Technische Universität München, Ismaninger Strasse 22, D-81675, Munich, Germany.
| | - Harm van Tinteren
- Biometrics Department, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Zhou Li
- Department of Gynecology and Obstetrics, Technische Universität München, Ismaninger Strasse 22, D-81675, Munich, Germany
| | - Sandra Raab
- Department of Gynecology and Obstetrics, Technische Universität München, Ismaninger Strasse 22, D-81675, Munich, Germany
| | - Christina Meul
- Department of Gynecology and Obstetrics, Technische Universität München, Ismaninger Strasse 22, D-81675, Munich, Germany
| | - Stefanie Avril
- Institute of Pathology, Technische Universität München, Ismaninger Strasse 22, D-81675, Munich, Germany.,Present address: Department of Pathology, Case Western Reserve University School of Medicine, University Hospitals Case Medical Center, Cleveland, OH, USA
| | - Nadja Laddach
- MRC-Holland, Willem Schoutenstraat 6, 1057 DN, Amsterdam, The Netherlands
| | - Michaela Aubele
- Helmholtz Zentrum München, Institute of Pathology, Ingolstädter Landstrasse 1, D-85764, Neuherberg, Germany
| | - Corinna Propping
- Department of Gynecology and Obstetrics, Technische Universität München, Ismaninger Strasse 22, D-81675, Munich, Germany
| | - Apostolos Gkazepis
- Department of Gynecology and Obstetrics, Technische Universität München, Ismaninger Strasse 22, D-81675, Munich, Germany
| | - Manfred Schmitt
- Department of Gynecology and Obstetrics, Technische Universität München, Ismaninger Strasse 22, D-81675, Munich, Germany
| | - Alfons Meindl
- Department of Gynecology and Obstetrics, Technische Universität München, Ismaninger Strasse 22, D-81675, Munich, Germany
| | - Petra M Nederlof
- Department of Pathology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Marion Kiechle
- Department of Gynecology and Obstetrics, Technische Universität München, Ismaninger Strasse 22, D-81675, Munich, Germany
| | - Esther H Lips
- Department of Pathology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.,Department of Molecular Pathology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| |
Collapse
|
22
|
Wulaningsih W, Serrano FEC, Utarini A, Matsuguchi T, Watkins J. Smoking, second-hand smoke exposure and smoking cessation in relation to leukocyte telomere length and mortality. Oncotarget 2016; 7:60419-60431. [PMID: 27509177 PMCID: PMC5312393 DOI: 10.18632/oncotarget.11051] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 07/19/2016] [Indexed: 11/29/2022] Open
Abstract
OBJECTIVES To investigate the link between smoking exposure, telomere length and mortality, with emphasis on second-hand smoke (SHS) exposure and the duration of smoking cessation. RESULTS A total of 1,018 participants died during follow-up (mean: 10.3 years). A 50 base-pair decrease in LTL was shown among cotinine-confirmed current versus never smokers. The 90th quantile of LTL decreased with increasing cotinine among never smokers, indicating a role of SHS. Longer telomeres with smoking cessation were indicated but limited to a 3-16 year period of abstaining smoking. When assessing mortality, we observed a lower risk of all-cause death for the second quintile compared to the first among never smokers (HR: 0.67, 95% CI: 0.52-0.87), and a higher risk was found among current smokers (HR: 1.89, 1.19-2.92). MATERIALS AND METHODS We studied 6,456 nationally representative U.S. respondents with mortality follow-up through to 31 December 2011. Smoking status was assessed by interviews and cotinine levels. Relative leukocyte telomere length (LTL) was quantified by polymerase chain reaction (PCR). Multivariable linear regression was performed to examine LTL by smoking exposure, adjusted for age, sex, race/ethnicity, socioeconomic status, education, body mass index, alcohol consumption, and physical activity. We further estimated the association of LTL with cotinine levels using quantile regression, and with smoking cessation dynamics. Cox regression was used to estimate mortality by smoking status and LTL. CONCLUSION Our findings indicated a complex association between smoking, telomere length, and mortality. LTL alterations with SHS and smoking cessation warrant further investigation for translation to public health measures.
Collapse
Affiliation(s)
- Wahyu Wulaningsih
- Division of Cancer Studies, King's College London, London, UK
- MRC Unit for Lifelong Health and Ageing, University College London, London, UK
- Division of Haematology/Oncology, Faculty of Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
- PILAR Research and Education, Cambridge, UK
| | - Fidel Emmanuel C. Serrano
- National Institute of Molecular Biology and Biotechnology, University of The Philippines Diliman, Diliman, Quezon City, Metro Manila, The Philippines
| | - Adi Utarini
- Department of Health Policy and Management, Faculty of Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Tetsuya Matsuguchi
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
- Driver Group, L.L.C., San Francisco, CA, USA
| | - Johnathan Watkins
- PILAR Research and Education, Cambridge, UK
- Institute for Mathematical and Molecular Biomedicine, King's College London, London, UK
| | | |
Collapse
|
23
|
Tandem duplications contribute to not one but two distinct phenotypes. Proc Natl Acad Sci U S A 2016; 113:E5257-8. [PMID: 27543336 DOI: 10.1073/pnas.1610228113] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
|
24
|
RUBIC identifies driver genes by detecting recurrent DNA copy number breaks. Nat Commun 2016; 7:12159. [PMID: 27396759 PMCID: PMC4942583 DOI: 10.1038/ncomms12159] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Accepted: 06/07/2016] [Indexed: 01/12/2023] Open
Abstract
The frequent recurrence of copy number aberrations across tumour samples is a reliable hallmark of certain cancer driver genes. However, state-of-the-art algorithms for detecting recurrent aberrations fail to detect several known drivers. In this study, we propose RUBIC, an approach that detects recurrent copy number breaks, rather than recurrently amplified or deleted regions. This change of perspective allows for a simplified approach as recursive peak splitting procedures and repeated re-estimation of the background model are avoided. Furthermore, we control the false discovery rate on the level of called regions, rather than at the probe level, as in competing algorithms. We benchmark RUBIC against GISTIC2 (a state-of-the-art approach) and RAIG (a recently proposed approach) on simulated copy number data and on three SNP6 and NGS copy number data sets from TCGA. We show that RUBIC calls more focal recurrent regions and identifies a much larger fraction of known cancer genes. Analysis of cancer genome sequencing data has been used to predict genes associated with the pathogenesis of cancer. Here, the authors propose a new algorithm entitled RUBIC that predicts breaks in DNA as opposed to previously published methods that predict amplifications and deletions of DNA.
Collapse
|
25
|
Singh RR, Mehrotra M, Chen H, Almohammedsalim AA, Sahin A, Bosamra A, Patel KP, Routbort MJ, Lu X, Ronald A, Mishra BM, Virani S, Medeiros LJ, Luthra R. Comprehensive Screening of Gene Copy Number Aberrations in Formalin-Fixed, Paraffin-Embedded Solid Tumors Using Molecular Inversion Probe-Based Single-Nucleotide Polymorphism Array. J Mol Diagn 2016; 18:676-687. [PMID: 27392636 DOI: 10.1016/j.jmoldx.2016.03.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 02/23/2016] [Accepted: 03/29/2016] [Indexed: 02/08/2023] Open
Abstract
Gene copy number aberrations (CNAs) represent a major class of cancer-related genomic alterations that drive solid tumors. Comprehensive and sensitive detection of CNAs is challenging because of often low quality and quantity of DNA isolated from the formalin-fixed, paraffin-embedded (FFPE) solid tumor samples. Here, in a clinical molecular diagnostic laboratory, we tested the utility and validated a molecular inversion probe-based (MIP) array to routinely screen for CNAs in solid tumors. Using low-input FFPE DNA, the array detects genome-wide CNAs with a special focus on 900 cancer-related genes. A cohort of 76 solid tumors of various types and tumor cellularity (20% to 100%), and four cancer cell lines were used. These harbored CNAs in clinically important genes (ERBB2, EGFR, FGFR1, KRAS, MYC) as detected by orthogonal techniques like next-generation sequencing or fluorescence in situ hybridization. Results of the MIP array were concordant with results from orthogonal techniques, and also provided additional information regarding the allelic nature of the CNAs. Limit-of-detection and assay reproducibility studies showed a high degree of sensitivity and reproducibility of detection, respectively. FFPE compatibility, ability to detect CNAs with high sensitivity, accuracy, and provide valuable information such as loss of heterozygosity along with relatively short turnaround times makes the MIP array a desirable clinical platform for routine screening of solid tumors in a clinical laboratory.
Collapse
Affiliation(s)
- Rajesh R Singh
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Meenakshi Mehrotra
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Hui Chen
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Alaa A Almohammedsalim
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ayesagul Sahin
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Alex Bosamra
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Keyur P Patel
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Mark J Routbort
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Xinyan Lu
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Abraham Ronald
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Bal Mukund Mishra
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Shumaila Virani
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - L Jeffrey Medeiros
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rajyalakshmi Luthra
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| |
Collapse
|
26
|
Schouten PC, Gluz O, Harbeck N, Mohrmann S, Diallo-Danebrock R, Pelz E, Kruizinga J, Velds A, Nieuwland M, Kerkhoven RM, Liedtke C, Frick M, Kates R, Linn SC, Nitz U, Marme F. BRCA1-like profile predicts benefit of tandem high dose epirubicin-cyclophospamide-thiotepa in high risk breast cancer patients randomized in the WSG-AM01 trial. Int J Cancer 2016; 139:882-9. [PMID: 26946057 DOI: 10.1002/ijc.30078] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 01/13/2016] [Indexed: 01/07/2023]
Abstract
BRCA1 is an important protein in the repair of DNA double strand breaks (DSBs), which are induced by alkylating chemotherapy. A BRCA1-like DNA copy number signature derived from tumors with a BRCA1 mutation is indicative for impaired BRCA1 function and associated with good outcome after high dose (HD) and tandem HD DSB inducing chemotherapy. We investigated whether BRCA1-like status was a predictive biomarker in the WSG AM 01 trial. WSG AM 01 randomized high-risk breast cancer patients to induction (2× epirubicin-cyclophosphamide) followed by tandem HD chemotherapy with epirubicin, cyclophosphamide and thiotepa versus dose dense chemotherapy (4× epirubicin-cyclophospamide followed by 3× cyclophosphamide-methotrexate-5-fluorouracil). We generated copy number profiles for 143 tumors and classified them as being BRCA1-like or non-BRCA1-like. Twenty-six out of 143 patients were BRCA1-like. BRCA1-like status was associated with high grade and triple negative tumors. With regard to event-free-survival, the primary endpoint of the trial, patients with a BRCA1-like tumor had a hazard rate of 0.2, 95% confidence interval (CI): 0.07-0.63, p = 0.006. In the interaction analysis, the combination of BRCA1-like status and HD chemotherapy had a hazard rate of 0.19, 95% CI: 0.067-0.54, p = 0.003. Similar results were observed for overall survival. These findings suggest that BRCA1-like status is a predictor for benefit of tandem HD chemotherapy with epirubicin-thiotepa-cyclophosphamide.
Collapse
Affiliation(s)
- Philip C Schouten
- Department of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Oleg Gluz
- West German Study Group, Germany.,Breast Centre Niederrhein, Moenchengladbach, Germany
| | - Nadia Harbeck
- West German Study Group, Germany.,Brustzentrum, Ludwig-Maximillian University Munich, Germany
| | | | | | - Enrico Pelz
- Breast Centre Niederrhein, Moenchengladbach, Germany
| | | | - Arno Velds
- Genomics Core Facility, NKI-AVL, Amsterdam, The Netherlands
| | | | | | - Cornelia Liedtke
- West German Study Group, Germany.,Universitäts-Frauenklinik Lübeck, Germany
| | | | | | - Sabine C Linn
- Department of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Division of Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ulrike Nitz
- West German Study Group, Germany.,Breast Centre Niederrhein, Moenchengladbach, Germany
| | - Frederik Marme
- Universitäts-Frauenklinik, University of Heidelberg, Germany.,National Center for Tumour Diseases, University of Heidelberg, Germany
| |
Collapse
|
27
|
Schouten PC, Grigoriadis A, Kuilman T, Mirza H, Watkins JA, Cooke SA, van Dyk E, Severson TM, Rueda OM, Hoogstraat M, Verhagen CVM, Natrajan R, Chin SF, Lips EH, Kruizinga J, Velds A, Nieuwland M, Kerkhoven RM, Krijgsman O, Vens C, Peeper D, Nederlof PM, Caldas C, Tutt AN, Wessels LF, Linn SC. Robust BRCA1-like classification of copy number profiles of samples repeated across different datasets and platforms. Mol Oncol 2015; 9:1274-86. [PMID: 25825120 PMCID: PMC5528812 DOI: 10.1016/j.molonc.2015.03.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 03/01/2015] [Accepted: 03/11/2015] [Indexed: 11/30/2022] Open
Abstract
Breast cancers with BRCA1 germline mutation have a characteristic DNA copy number (CN) pattern. We developed a test that assigns CN profiles to be 'BRCA1-like' or 'non-BRCA1-like', which refers to resembling a BRCA1-mutated tumor or resembling a tumor without a BRCA1 mutation, respectively. Approximately one third of the BRCA1-like breast cancers have a BRCA1 mutation, one third has hypermethylation of the BRCA1 promoter and one third has an unknown reason for being BRCA1-like. This classification is indicative of patients' response to high dose alkylating and platinum containing chemotherapy regimens, which targets the inability of BRCA1 deficient cells to repair DNA double strand breaks. We investigated whether this classification can be reliably obtained with next generation sequencing and copy number platforms other than the bacterial artificial chromosome (BAC) array Comparative Genomic Hybridization (aCGH) on which it was originally developed. We investigated samples from 230 breast cancer patients for which a CN profile had been generated on two to five platforms, comprising low coverage CN sequencing, CN extraction from targeted sequencing panels (CopywriteR), Affymetrix SNP6.0, 135K/720K oligonucleotide aCGH, Affymetrix Oncoscan FFPE (MIP) technology, 3K BAC and 32K BAC aCGH. Pairwise comparison of genomic position-mapped profiles from the original aCGH platform and other platforms revealed concordance. For most cases, biological differences between samples exceeded the differences between platforms within one sample. We observed the same classification across different platforms in over 80% of the patients and kappa values of at least 0.36. Differential classification could be attributed to CN profiles that were not strongly associated to one class. In conclusion, we have shown that the genomic regions that define our BRCA1-like classifier are robustly measured by different CN profiling technologies, providing the possibility to retro- and prospectively investigate BRCA1-like classification across a wide range of CN platforms.
Collapse
Affiliation(s)
- Philip C Schouten
- Department of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Anita Grigoriadis
- Breakthrough Breast Cancer Research Unit, Department of Research Oncology, Guy's Hospital, King's College London School of Medicine, London, United Kingdom
| | - Thomas Kuilman
- Division of Molecular Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Hasan Mirza
- Breakthrough Breast Cancer Research Unit, Department of Research Oncology, Guy's Hospital, King's College London School of Medicine, London, United Kingdom
| | - Johnathan A Watkins
- Breakthrough Breast Cancer Research Unit, Department of Research Oncology, Guy's Hospital, King's College London School of Medicine, London, United Kingdom
| | - Saskia A Cooke
- Breakthrough Breast Cancer Research Unit, Department of Research Oncology, Guy's Hospital, King's College London School of Medicine, London, United Kingdom
| | - Ewald van Dyk
- Department of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Tesa M Severson
- Department of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Oscar M Rueda
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Cambridge, UK
| | - Marlous Hoogstraat
- Department of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands; Department of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands; Department of Medical Oncology, University Medical Center Utrecht, Utrecht, The Netherlands; Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
| | - Caroline V M Verhagen
- Division of Biological Stress Response, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Rachael Natrajan
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
| | - Suet-Feung Chin
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Cambridge, UK
| | - Esther H Lips
- Department of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Janneke Kruizinga
- Genomics Core Facility, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Arno Velds
- Genomics Core Facility, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Marja Nieuwland
- Genomics Core Facility, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ron M Kerkhoven
- Genomics Core Facility, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Oscar Krijgsman
- Division of Molecular Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Conchita Vens
- Division of Biological Stress Response, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Daniel Peeper
- Division of Molecular Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Petra M Nederlof
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Carlos Caldas
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Cambridge, UK; Department of Oncology, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK; Cambridge Experimental Cancer Medicine Centre and NIHR Cambridge Biomedical, Research Centre, Cambridge University Hospitals NHS, Cambridge, UK
| | - Andrew N Tutt
- Breakthrough Breast Cancer Research Unit, Department of Research Oncology, Guy's Hospital, King's College London School of Medicine, London, United Kingdom
| | - Lodewyk F Wessels
- Department of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands; Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Delft, The Netherlands
| | - Sabine C Linn
- Department of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands; Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands; Division of Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands.
| |
Collapse
|