1
|
Lazard T, Bataillon G, Naylor P, Popova T, Bidard FC, Stoppa-Lyonnet D, Stern MH, Decencière E, Walter T, Vincent-Salomon A. Deep learning identifies morphological patterns of homologous recombination deficiency in luminal breast cancers from whole slide images. Cell Rep Med 2022; 3:100872. [PMID: 36516847 PMCID: PMC9798078 DOI: 10.1016/j.xcrm.2022.100872] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 01/04/2022] [Accepted: 11/22/2022] [Indexed: 12/15/2022]
Abstract
Homologous recombination DNA-repair deficiency (HRD) is becoming a well-recognized marker of platinum salt and polyADP-ribose polymerase inhibitor chemotherapies in ovarian and breast cancers. While large-scale screening for HRD using genomic markers is logistically and economically challenging, stained tissue slides are routinely acquired in clinical practice. With the objectives of providing a robust deep-learning method for HRD prediction from tissue slides and identifying related morphological phenotypes, we first show that digital pathology workflows are sensitive to potential biases in the training set, then we propose a method to overcome the influence of these biases, and we develop an interpretation method capable of identifying complex phenotypes. Application to our carefully curated in-house dataset allows us to predict HRD with high accuracy (area under the receiver-operator characteristics curve 0.86) and to identify morphological phenotypes related to HRD. In particular, the presence of laminated fibrosis and clear tumor cells associated with HRD open new hypotheses regarding its phenotypic impact.
Collapse
Affiliation(s)
- Tristan Lazard
- Center for Computational Biology (CBIO), Mines Paris, PSL University, 60 Boulevard Saint Michel, 75006 Paris, France,Institut Curie, PSL University, 75005 Paris, France,INSERM U900, 75005 Paris, France
| | - Guillaume Bataillon
- Institut Curie, PSL University, 75005 Paris, France,INSERM U900, 75005 Paris, France,Diagnostic and Theranostic Medicine Division, Institut Curie, PSL University, Paris, France
| | - Peter Naylor
- Center for Computational Biology (CBIO), Mines Paris, PSL University, 60 Boulevard Saint Michel, 75006 Paris, France,Institut Curie, PSL University, 75005 Paris, France,INSERM U900, 75005 Paris, France
| | - Tatiana Popova
- INSERM U830, DNA Repair and Uveal Melanoma (DRUM), Equipe Labellisée par la Ligue Nationale Contre le Cancer, Institut Curie, PSL Research University, 75005 Paris, France
| | - François-Clément Bidard
- Department of Medical Oncology, Institut Curie, Université de Versailles Saint-Quentin, Saint-Cloud, France,INSERM CIC-BT 1428, Institut Curie, Paris, France
| | - Dominique Stoppa-Lyonnet
- INSERM U830, DNA Repair and Uveal Melanoma (DRUM), Equipe Labellisée par la Ligue Nationale Contre le Cancer, Institut Curie, PSL Research University, 75005 Paris, France,Université Paris Cité, 75006 Paris, France
| | - Marc-Henri Stern
- Diagnostic and Theranostic Medicine Division, Institut Curie, PSL University, Paris, France,INSERM U830, DNA Repair and Uveal Melanoma (DRUM), Equipe Labellisée par la Ligue Nationale Contre le Cancer, Institut Curie, PSL Research University, 75005 Paris, France
| | - Etienne Decencière
- Center for Mathematical Morphology (CMM), Mines Paris, PSL University, 77300 Fontainebleau, France
| | - Thomas Walter
- Center for Computational Biology (CBIO), Mines Paris, PSL University, 60 Boulevard Saint Michel, 75006 Paris, France,Institut Curie, PSL University, 75005 Paris, France,INSERM U900, 75005 Paris, France,Corresponding author
| | - Anne Vincent-Salomon
- Diagnostic and Theranostic Medicine Division, Institut Curie, PSL University, Paris, France,INSERM U934, CNRS UMR 3215, Paris, France,Corresponding author
| |
Collapse
|
2
|
Yuan W, Ni J, Wen H, Shi W, Chen X, Huang H, Zhang X, Lu X, Zhu C, Dong H, Yang S, Wu X, Chen X. Genomic Scar Score: A robust model predicting homologous recombination deficiency based on genomic instability. BJOG 2022; 129 Suppl 2:14-22. [PMID: 36485068 DOI: 10.1111/1471-0528.17324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
OBJECTIVE To develop a novel machine learning-based algorithm called the Genomic Scar Score (GSS) for predicting homologous recombination deficiency (HRD) events. DESIGN Method development study. SETTING AmoyDx Medical Laboratory and Jiangsu Cancer Hospital. POPULATION OR SAMPLE A cohort of individuals with ovarian or breast cancer (n = 377) were collected from the AmoyDx Medical Laboratory. Another cohort of patients with ovarian cancer treated with PARP inhibitors (n = 58) was enrolled in the Jiangsu Cancer Hospital. METHODS We used linear support vector machines to build a Genomic Scar (GS) model to predict HRD events, and Kaplan-Meier analyses were performed by comparing the progression-free survival (PFS) of patients in different groups using a two-sided log-rank test. MAIN OUTCOME MEASURES The performance of the GS model and the result of clinical validation. RESULTS The GS model displayed more than 97.0% sensitivity to detect BRCA-deficient events, and the GS model identified patients that could benefit from poly(ADP-ribose) polymerase inhibitors (PARPi), as the GS score (GSS)-positive group had a longer progression-free survival (PFS) (9.4 versus 4.4 months; hazard ratio [HR] = 0.54, P < 0.001) than the GSS-negative group after PARPi treatment. Meanwhile, the GSS showed high concordance among different NGS panels, which implied the robustness of the GS model. CONCLUSIONS The GS was a robust model to predict HRD and had broad clinical applications in predicting which patients will respond favourably to PARPi treatment.
Collapse
Affiliation(s)
| | - Jing Ni
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Hao Wen
- Department of Gynecological Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Weijie Shi
- Amoy Diagnostics Co., Ltd., Xiamen, China
| | | | | | | | - Xuan Lu
- Amoy Diagnostics Co., Ltd., Xiamen, China
| | | | - Hua Dong
- Amoy Diagnostics Co., Ltd., Xiamen, China
| | | | - Xiaohua Wu
- Department of Gynecological Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Xiaoxiang Chen
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| |
Collapse
|
3
|
Klaric KA, Riaz N, Asleh K, Wang XQ, Atalla T, Strickland S, Nielsen TO, Kos Z. SOX10 is a highly specific biomarker of basal-like breast cancer. Histopathology 2021; 80:589-597. [PMID: 34725848 DOI: 10.1111/his.14592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/07/2021] [Accepted: 10/31/2021] [Indexed: 11/29/2022]
Abstract
AIMS Basal-like breast cancer is an aggressive molecular subtype associated with younger age and early relapse. Most cases lack expression of estrogen receptor (ER), progesterone receptor, and human epidermal growth factor receptor 2, limiting targeted therapeutic options. Basal-like breast cancer is defined by expression of genes in the outer/basally-located epithelial layer of mammary glands including those encoding cytokeratins 5 and 14, and epidermal growth factor receptor (EGFR). SOX10, a readily available immunohistochemical stain, is expressed in a subset of breast cancers, particularly triple-negative carcinomas. In this study, we sought to (i) assess the association between SOX10 expression and intrinsic molecular subtypes as defined by PAM50 gene expression and (ii) compare the performance of SOX10 to other surrogate markers of basal-like subtype, including CK5, EGFR, nestin and INPP4b. METHODS AND RESULTS SOX10 immunostaining was performed on tissue microarrays constructed from a contemporary series enriched for ER negative and weakly positive cancers, which had also undergone PAM50 gene profiling. A total of 211 cases were informative for both SOX10 immunohistochemistry (IHC) and PAM50 subtype, including 103 basal-like. Staining for SOX10 was positive in 73/103 basal-like cancers and only 2/108 other subtypes (p<0.001), resulting in a sensitivity of 70.9% and a specificity of 98.1%. SOX10 was more specific than the other tested basal-markers and the results were independent of estrogen receptor status. CONCLUSIONS SOX10 is a moderately sensitive, but highly specific IHC biomarker for the basal-like intrinsic subtype of breast cancer, which unlike other commonly used IHC biomarkers, is independent of hormone receptor status.
Collapse
Affiliation(s)
- Kristina-Ana Klaric
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of Ottawa, ON, Canada
| | - Nazia Riaz
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.,Genetic Pathology Evaluation Centre, Vancouver, BC, Canada.,Centre for Regenerative Medicine and Stem Cell Research, Aga Khan University, Pakistan
| | - Karama Asleh
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.,Genetic Pathology Evaluation Centre, Vancouver, BC, Canada
| | - Xiu Qing Wang
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.,Genetic Pathology Evaluation Centre, Vancouver, BC, Canada
| | - Tadros Atalla
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of Ottawa, ON, Canada
| | - Sarah Strickland
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of Ottawa, ON, Canada
| | - Torsten O Nielsen
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.,Genetic Pathology Evaluation Centre, Vancouver, BC, Canada
| | - Zuzana Kos
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.,Department of Pathology, BC Cancer, Vancouver, BC, Canada
| |
Collapse
|
4
|
Brueffer C, Gladchuk S, Winter C, Vallon-Christersson J, Hegardt C, Häkkinen J, George AM, Chen Y, Ehinger A, Larsson C, Loman N, Malmberg M, Rydén L, Borg Å, Saal LH. The mutational landscape of the SCAN-B real-world primary breast cancer transcriptome. EMBO Mol Med 2020; 12:e12118. [PMID: 32926574 PMCID: PMC7539222 DOI: 10.15252/emmm.202012118] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 08/08/2020] [Accepted: 08/13/2020] [Indexed: 12/12/2022] Open
Abstract
Breast cancer is a disease of genomic alterations, of which the panorama of somatic mutations and how these relate to subtypes and therapy response is incompletely understood. Within SCAN‐B (ClinicalTrials.gov: NCT02306096), a prospective study elucidating the transcriptomic profiles for thousands of breast cancers, we developed a RNA‐seq pipeline for detection of SNVs/indels and profiled a real‐world cohort of 3,217 breast tumors. We describe the mutational landscape of primary breast cancer viewed through the transcriptome of a large population‐based cohort and relate it to patient survival. We demonstrate that RNA‐seq can be used to call mutations in genes such as PIK3CA,TP53, and ERBB2, as well as the status of molecular pathways and mutational burden, and identify potentially druggable mutations in 86.8% of tumors. To make this rich dataset available for the research community, we developed an open source web application, the SCAN‐B MutationExplorer (http://oncogenomics.bmc.lu.se/MutationExplorer). These results add another dimension to the use of RNA‐seq as a clinical tool, where both gene expression‐ and mutation‐based biomarkers can be interrogated in real‐time within 1 week of tumor sampling.
Collapse
Affiliation(s)
- Christian Brueffer
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden.,Lund University Cancer Center, Lund, Sweden
| | - Sergii Gladchuk
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden.,Lund University Cancer Center, Lund, Sweden
| | - Christof Winter
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden.,Lund University Cancer Center, Lund, Sweden
| | - Johan Vallon-Christersson
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden.,Lund University Cancer Center, Lund, Sweden.,CREATE Health Strategic Center for Translational Cancer Research, Lund University, Lund, Sweden
| | - Cecilia Hegardt
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden.,Lund University Cancer Center, Lund, Sweden.,CREATE Health Strategic Center for Translational Cancer Research, Lund University, Lund, Sweden
| | - Jari Häkkinen
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden.,Lund University Cancer Center, Lund, Sweden
| | - Anthony M George
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden.,Lund University Cancer Center, Lund, Sweden
| | - Yilun Chen
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden.,Lund University Cancer Center, Lund, Sweden
| | - Anna Ehinger
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden.,Lund University Cancer Center, Lund, Sweden.,Department of Pathology, Skåne University Hospital, Lund, Sweden
| | - Christer Larsson
- Lund University Cancer Center, Lund, Sweden.,Division of Molecular Pathology, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Niklas Loman
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden.,Lund University Cancer Center, Lund, Sweden.,Department of Oncology, Skåne University Hospital, Lund, Sweden
| | - Martin Malmberg
- Department of Oncology, Skåne University Hospital, Lund, Sweden
| | - Lisa Rydén
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden.,Lund University Cancer Center, Lund, Sweden.,Department of Surgery, Skåne University Hospital, Lund, Sweden
| | - Åke Borg
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden.,Lund University Cancer Center, Lund, Sweden.,CREATE Health Strategic Center for Translational Cancer Research, Lund University, Lund, Sweden
| | - Lao H Saal
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden.,Lund University Cancer Center, Lund, Sweden.,CREATE Health Strategic Center for Translational Cancer Research, Lund University, Lund, Sweden
| |
Collapse
|
5
|
Hatano Y, Tamada M, Matsuo M, Hara A. Molecular Trajectory of BRCA1 and BRCA2 Mutations. Front Oncol 2020; 10:361. [PMID: 32269964 PMCID: PMC7109296 DOI: 10.3389/fonc.2020.00361] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 03/02/2020] [Indexed: 12/12/2022] Open
Abstract
Every cancer carries genomic mutations. Although almost all these mutations arise after fertilization, a minimal count of cancer predisposition mutations are already present at the time of genesis of germ cells. Of the cancer predisposition genes identified to date, BRCA1 and BRCA2 have been determined to be associated with hereditary breast and ovarian cancer syndrome. Such cancer predisposition genes have recently been attracting attention owing to the emergence of molecular genetics, thus, affecting the strategy of cancer prevention, diagnostics, and therapeutics. In this review, we summarize the molecular significance of these two BRCA genes. First, we provide a brief history of BRCA1 and BRCA2, including their identification as cancer predisposition genes and recognition as members in the Fanconi anemia pathway. Next, we describe the molecular function and interaction of BRCA proteins, and thereafter, describe the patterns of BRCA dysfunction. Subsequently, we present emerging evidence on mutational signatures to determine the effects of BRCA disorders on the mutational process in cancer cells. Currently, BRCA genes serve as principal targets for clinical molecular oncology, be they germline or sporadic mutations. Moreover, comprehensive cancer genome analyses enable us to not only recognize the current status of the known cancer driver gene mutations but also divulge the past mutational processes and predict the future biological behavior of cancer through the molecular trajectory of genomic alterations.
Collapse
Affiliation(s)
- Yuichiro Hatano
- Department of Tumor Pathology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Maho Tamada
- Department of Tumor Pathology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Mikiko Matsuo
- Department of Tumor Pathology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Akira Hara
- Department of Tumor Pathology, Gifu University Graduate School of Medicine, Gifu, Japan
| |
Collapse
|
6
|
Testa U, Castelli G, Pelosi E. Breast Cancer: A Molecularly Heterogenous Disease Needing Subtype-Specific Treatments. Med Sci (Basel) 2020; 8:E18. [PMID: 32210163 PMCID: PMC7151639 DOI: 10.3390/medsci8010018] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 02/23/2020] [Accepted: 03/11/2020] [Indexed: 12/12/2022] Open
Abstract
Breast cancer is the most commonly occurring cancer in women. There were over two-million new cases in world in 2018. It is the second leading cause of death from cancer in western countries. At the molecular level, breast cancer is a heterogeneous disease, which is characterized by high genomic instability evidenced by somatic gene mutations, copy number alterations, and chromosome structural rearrangements. The genomic instability is caused by defects in DNA damage repair, transcription, DNA replication, telomere maintenance and mitotic chromosome segregation. According to molecular features, breast cancers are subdivided in subtypes, according to activation of hormone receptors (estrogen receptor and progesterone receptor), of human epidermal growth factors receptor 2 (HER2), and or BRCA mutations. In-depth analyses of the molecular features of primary and metastatic breast cancer have shown the great heterogeneity of genetic alterations and their clonal evolution during disease development. These studies have contributed to identify a repertoire of numerous disease-causing genes that are altered through different mutational processes. While early-stage breast cancer is a curable disease in about 70% of patients, advanced breast cancer is largely incurable. However, molecular studies have contributed to develop new therapeutic approaches targeting HER2, CDK4/6, PI3K, or involving poly(ADP-ribose) polymerase inhibitors for BRCA mutation carriers and immunotherapy.
Collapse
Affiliation(s)
- Ugo Testa
- Department of Oncology, Istituto Superiore di Sanità, Regina Elena 299, 00161 Rome, Italy; (G.C.); (E.P.)
| | | | | |
Collapse
|
7
|
Geenen JJJ, Linn SC, Beijnen JH, Schellens JHM. PARP Inhibitors in the Treatment of Triple-Negative Breast Cancer. Clin Pharmacokinet 2019; 57:427-437. [PMID: 29063517 DOI: 10.1007/s40262-017-0587-4] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Breast cancer is a heterogeneous disease, manifesting in a broad differentiation in phenotypes and morphologic profiles, resulting in variable clinical behavior. Between 10 and 20% of all breast cancers are triple negative. Triple-negative breast cancer (TNBC) lacks the expression of human epidermal growth factor receptor 2 (HER2) and hormone receptors; therefore, to date, chemotherapy remains the backbone of treatment. TNBC tends to be aggressive and has a high histological grade, resulting in a poor 5-year prognosis. It has a high prevalence of BRCA1 mutations and an increased Ki-67 expression. This subtype usually responds well to taxanes and/or platinum compounds and poly (ADP-ribose) polymerase (PARP) inhibitors. Studies with PARP inhibitors have demonstrated promising results in the treatment of BRCA-mutated breast and ovarian cancer, and PARP inhibitors have been studied as monotherapy and in combination with cytotoxic therapy or radiotherapy. PARP inhibitor efficacy on poly (ADP-ribose) polymer (PAR) formation in vivo can be quantified by pharmacodynamic assays that measure PAR activity in peripheral blood mononuclear cells (PBMC). Biomarkers such as TP53, ATM, PALB2 and RAD51C might be prognostic or predictive indicators for treatment response, and could also provide targets for novel treatment strategies. In summary, this review provides an overview of the treatment options for basal-like TNBC, including PARP inhibitors, and focuses on the pharmacotherapeutic options in these patients.
Collapse
Affiliation(s)
- Jill J J Geenen
- Department of Clinical Pharmacology, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands.,Division of Pharmacology, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands
| | - Sabine C Linn
- Department of Molecular Pathology, Antoni van Leeuwenhoek Hospital, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.,Division of Medical Oncology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.,Department of Pathology, Utrecht University Medical Center, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Jos H Beijnen
- Department of Clinical Pharmacology, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands.,Division of Pharmacology, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands.,Department of Pharmacy, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands.,Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, Utrecht, The Netherlands
| | - Jan H M Schellens
- Department of Clinical Pharmacology, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands. .,Division of Pharmacology, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands. .,Division of Medical Oncology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands. .,Department of Pharmacy, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands. .,Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, Utrecht, The Netherlands.
| |
Collapse
|
8
|
Gandhi N, Das GM. Metabolic Reprogramming in Breast Cancer and Its Therapeutic Implications. Cells 2019; 8:cells8020089. [PMID: 30691108 PMCID: PMC6406734 DOI: 10.3390/cells8020089] [Citation(s) in RCA: 118] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 01/20/2019] [Accepted: 01/22/2019] [Indexed: 12/22/2022] Open
Abstract
Current standard-of-care (SOC) therapy for breast cancer includes targeted therapies such as endocrine therapy for estrogen receptor-alpha (ERα) positive; anti-HER2 monoclonal antibodies for human epidermal growth factor receptor-2 (HER2)-enriched; and general chemotherapy for triple negative breast cancer (TNBC) subtypes. These therapies frequently fail due to acquired or inherent resistance. Altered metabolism has been recognized as one of the major mechanisms underlying therapeutic resistance. There are several cues that dictate metabolic reprogramming that also account for the tumors’ metabolic plasticity. For metabolic therapy to be efficacious there is a need to understand the metabolic underpinnings of the different subtypes of breast cancer as well as the role the SOC treatments play in targeting the metabolic phenotype. Understanding the mechanism will allow us to identify potential therapeutic vulnerabilities. There are some very interesting questions being tackled by researchers today as they pertain to altered metabolism in breast cancer. What are the metabolic differences between the different subtypes of breast cancer? Do cancer cells have a metabolic pathway preference based on the site and stage of metastasis? How do the cell-intrinsic and -extrinsic cues dictate the metabolic phenotype? How do the nucleus and mitochondria coordinately regulate metabolism? How does sensitivity or resistance to SOC affect metabolic reprogramming and vice-versa? This review addresses these issues along with the latest updates in the field of breast cancer metabolism.
Collapse
Affiliation(s)
- Nishant Gandhi
- Department of Pharmacology and Therapeutics, Center for Genetics & Pharmacology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA.
| | - Gokul M Das
- Department of Pharmacology and Therapeutics, Center for Genetics & Pharmacology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA.
| |
Collapse
|
9
|
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
|
10
|
Olivier M, Bouaoun L, Villar S, Robitaille A, Cahais V, Heguy A, Byrnes G, Le Calvez-Kelm F, Torres-Mejía G, Alvarado-Cabrero I, Imani-Razavi FS, Inés Sánchez G, Jaramillo R, Porras C, Rodriguez AC, Garmendia ML, Soto JL, Romieu I, Porter P, Guenthoer J, Rinaldi S. Molecular features of premenopausal breast cancers in Latin American women: Pilot results from the PRECAMA study. PLoS One 2019; 14:e0210372. [PMID: 30653559 PMCID: PMC6336331 DOI: 10.1371/journal.pone.0210372] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 12/20/2018] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND In Latin America (LA), there is a high incidence rate of breast cancer (BC) in premenopausal women, and the genomic features of these BC remain unknown. Here, we aim to characterize the molecular features of BC in young LA women within the framework of the PRECAMA study, a multicenter population-based case-control study of BC in premenopausal women. METHODS Pathological tumor tissues were collected from incident cases from four LA countries. Immunohistochemistry (IHC) was performed centrally for ER, PR, HER2, Ki67, EGFR, CK5/6, and p53 protein markers. Targeted deep sequencing was done on genomic DNA extracted from formalin-fixed, paraffin-embedded tumor tissues and their paired blood samples to screen for somatic mutations in eight genes frequently mutated in BC. A subset of samples was analyzed by exome sequencing to identify somatic mutational signatures. RESULTS The majority of cases were positive for ER or PR (168/233; 72%), and 21% were triple-negative (TN), mainly of basal type. Most tumors were positive for Ki67 (189/233; 81%). In 126 sequenced cases, TP53 and PIK3CA were the most frequently mutated genes (32.5% and 21.4%, respectively), followed by AKT1 (9.5%). TP53 mutations were more frequent in HER2-enriched and TN IHC subtypes, whereas PIK3CA/AKT1 mutations were more frequent in ER-positive tumors, as expected. Interestingly, a higher proportion of G:C>T:A mutations was observed in TP53 in PRECAMA cases compared with TCGA and METABRIC BC series (27% vs 14%). Exome-wide mutational patterns in 10 TN cases revealed alterations in signal transduction pathways and major contributions of mutational signatures caused by altered DNA repair pathways. CONCLUSIONS These pilot results on PRECAMA tumors give a preview of the molecular features of premenopausal BC in LA. Although the overall mutation burden was as expected from data in other populations, mutational patterns observed in TP53 and exome-wide suggested possible differences in mutagenic processes giving rise to these tumors compared with other populations. Further -omics analyses of a larger number of cases in the near future will enable the investigation of relationships between these molecular features and risk factors.
Collapse
Affiliation(s)
- Magali Olivier
- Section of Mechanisms of Carcinogenesis, International Agency for Research on Cancer, Lyon, France
| | - Liacine Bouaoun
- Section of Environment and Radiation, International Agency for Research on Cancer, Lyon, France
| | - Stephanie Villar
- Section of Mechanisms of Carcinogenesis, International Agency for Research on Cancer, Lyon, France
| | - Alexis Robitaille
- Section of Mechanisms of Carcinogenesis, International Agency for Research on Cancer, Lyon, France
| | - Vincent Cahais
- Section of Mechanisms of Carcinogenesis, International Agency for Research on Cancer, Lyon, France
| | - Adriana Heguy
- Department of Pathology and Genome Technology Center, New York University Langone Medical Center, New York, United States of America
| | - Graham Byrnes
- Section of Environment and Radiation, International Agency for Research on Cancer, Lyon, France
| | - Florence Le Calvez-Kelm
- Genetic Cancer Susceptibility Group, International Agency for Research on Cancer, Lyon, France
| | - Gabriela Torres-Mejía
- Center for Population Health Research, National Institute of Public Health, Cuernavaca, Mexico
| | - Isabel Alvarado-Cabrero
- Department of Pathology, Hospital de Oncología, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Fazlollah Shahram Imani-Razavi
- Department of Pathology, UMAE Hospital de Gineco Obstetricia No. 4 "Luis Castelazo Ayala", Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Gloria Inés Sánchez
- Group Infection and Cancer, School of Medicine, University of Antioquia, Medellín, Colombia
| | | | - Carolina Porras
- Agencia Costarricense de Investigaciones Biomédicas (ACIB)-Fundación INCIENSA, Costa Rica
| | - Ana Cecilia Rodriguez
- Agencia Costarricense de Investigaciones Biomédicas (ACIB)-Fundación INCIENSA, Costa Rica
| | | | | | - Isabelle Romieu
- Section of Nutrition and Metabolism, International Agency for Research on Cancer, Lyon, France
| | - Peggy Porter
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States of America
| | - Jamie Guenthoer
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, United States of America
| | - Sabina Rinaldi
- Section of Nutrition and Metabolism, International Agency for Research on Cancer, Lyon, France
| |
Collapse
|
11
|
Nesic K, Wakefield M, Kondrashova O, Scott CL, McNeish IA. Targeting DNA repair: the genome as a potential biomarker. J Pathol 2018; 244:586-597. [PMID: 29282716 DOI: 10.1002/path.5025] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 12/14/2017] [Accepted: 12/16/2017] [Indexed: 01/18/2023]
Abstract
Genomic instability and mutations are fundamental aspects of human malignancies, leading to progressive accumulation of the hallmarks of cancer. For some time, it has been clear that key mutations may be used as both prognostic and predictive biomarkers, the best-known examples being the presence of germline BRCA1 or BRCA2 mutations, which are not only associated with improved prognosis in ovarian cancer, but are also predictive of response to poly(ADP-ribose) polymerase (PARP) inhibitors. Although biomarkers as specific and powerful as these are rare in human malignancies, next-generation sequencing and improved bioinformatic analyses are revealing mutational signatures, i.e. broader patterns of alterations in the cancer genome that have the power to reveal information about underlying driver mutational processes. Thus, the cancer genome can act as a stratification factor in clinical trials and, ultimately, will be used to drive personalized treatment decisions. In this review, we use ovarian high-grade serous carcinoma (HGSC) as an example of a disease of extreme genomic complexity that is marked by widespread copy number alterations, but that lacks powerful driver oncogene mutations. Understanding of the genomics of HGSC has led to the routine introduction of germline and somatic BRCA1/2 testing, as well as testing of mutations in other homologous recombination genes, widening the range of patients who may benefit from PARP inhibitors. We will discuss how whole genome-wide analyses, including loss of heterozygosity quantification and whole genome sequencing, may extend this paradigm to allow all patients to benefit from effective targeted therapies. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Collapse
MESH Headings
- Animals
- BRCA1 Protein/genetics
- BRCA2 Protein/genetics
- Biomarkers, Tumor/genetics
- Clinical Decision-Making
- DNA Damage
- DNA Repair
- Female
- Genetic Predisposition to Disease
- Genomics/methods
- Humans
- Mutation
- Neoplasm Grading
- Neoplasms, Cystic, Mucinous, and Serous/drug therapy
- Neoplasms, Cystic, Mucinous, and Serous/genetics
- Neoplasms, Cystic, Mucinous, and Serous/pathology
- Ovarian Neoplasms/drug therapy
- Ovarian Neoplasms/genetics
- Ovarian Neoplasms/pathology
- Pathology, Molecular/methods
- Phenotype
- Precision Medicine
- Predictive Value of Tests
Collapse
Affiliation(s)
- Ksenija Nesic
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Matthew Wakefield
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Melbourne Bioinformatics, University of Melbourne, Parkville, Victoria, Australia
| | - Olga Kondrashova
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Clare L Scott
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
- Royal Women's Hospital, Parkville, Victoria, Australia
- Peter MacCallum Cancer Centre, Parkville, Victoria, Australia
| | | |
Collapse
|
12
|
Duffy MJ, Synnott NC, Crown J. Mutant p53 in breast cancer: potential as a therapeutic target and biomarker. Breast Cancer Res Treat 2018; 170:213-219. [PMID: 29564741 DOI: 10.1007/s10549-018-4753-7] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 03/13/2018] [Indexed: 12/21/2022]
Abstract
OBJECTIVE The aim of this article is to discuss mutant p53 as a possible therapeutic target and biomarker for breast cancer. RESULTS TP53 (p53) is the most frequently mutated gene in invasive breast cancer. Although mutated in 30-35% of all cases, p53 is mutated in approximately 80% of triple-negative (TN) tumors (i.e., tumors negative for ER, PR, and HER2). Because of this high prevalence, mutated p53 is both a potential biomarker and therapeutic target for patients with breast cancer, especially for those with the TN subtype. Although several retrospective studies have investigated a potential prognostic and therapy predictive role for mutant p53 in breast cancer, the results to date are mixed. Thus, at present, mutant p53 cannot be recommended as a prognostic or therapy predictive biomarker in breast cancer. In contrast to the multiple reports on a potential biomarker role, few studies had until recently, investigated mutant p53 as a potential target for breast cancer treatment. In the last decade, however, several compounds have become available which can reactivate mutant p53 protein and convert it to a conformation with wild-type properties. Some of these compounds, especially PRIMA-1, APR-246 PK11007, and COTI-2, have been found to exhibit anticancer activity in preclinical models of breast cancer. CONCLUSION Since p53 is mutated in the vast majority of TN breast cancers, compounds such as APR-246, PK11007, and COTI-2 are potential treatments for patients with this subform of the disease. Further research is necessary to identify a potential biomarker role for mutant p53 in breast cancer.
Collapse
Affiliation(s)
- Michael J Duffy
- UCD Clinical Research Centre, St. Vincent's University Hospital, Dublin 4, Ireland. .,UCD School of Medicine, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland.
| | - Naoise C Synnott
- UCD School of Medicine, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - John Crown
- Department of Medical Oncology, St. Vincent's University Hospital, Dublin, Ireland
| |
Collapse
|
13
|
Clinical outcomes based on multigene profiling in metastatic breast cancer patients. Oncotarget 2018; 7:76362-76373. [PMID: 27806348 PMCID: PMC5363515 DOI: 10.18632/oncotarget.12987] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 10/13/2016] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Identifying the clinical impact of recurrent mutations can help define their role in cancer. Here, we identify frequent hotspot mutations in metastatic breast cancer (MBC) patients and associate them with clinical outcomes. PATIENTS AND METHODS Hotspot mutation testing was conducted in 500 MBC patients using an 11 gene (N = 126) and/or 46 or 50 gene (N = 391) panel. Patients were stratified by hormone receptor (HR) and human epidermal growth factor 2 (HER2) status. Clinical outcomes were retrospectively collected. RESULTS Hotspot mutations were most frequently detected in TP53 (30%), PIK3CA (27%) and AKT1 (4%). Triple-negative breast cancer (TNBC) patients had the highest incidence of TP53 (58%) and the lowest incidence of PIK3CA (9%) mutations. TP53 mutation was associated with shorter relapse-free survival (RFS) (median 22 vs 42months; P < 0.001) and overall survival (OS) from diagnosis of distant metastatic disease (median 26 vs 51months; P < 0.001). Conversely, PIK3CA mutation was associated with a trend towards better clinical outcomes including RFS (median 41 vs 30months; P = 0.074) and OS (52 vs 40months; P = 0.066). In HR-positive patients, TP53 mutation was again associated with shorter RFS (median 30 vs 46months; P = 0.017) and OS (median 30 vs 55months; P = 0.001). When multivariable analysis was performed for RFS and OS, TP53 but not PIK3CA mutation remained a significant predictor of outcomes in the overall cohort and in HR-positive patients. CONCLUSIONS Clinical hotspot sequencing identifies potentially actionable mutations. In this cohort, TP53 mutation was associated with worse clinical outcomes, while PIK3CA mutation did not remain a significant predictor of outcomes after multivariable analysis.
Collapse
|
14
|
Survey of gynecological carcinosarcomas in families with breast and ovarian cancer predisposition. Cancer Genet 2018; 221:38-45. [DOI: 10.1016/j.cancergen.2017.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 12/13/2017] [Indexed: 12/21/2022]
|
15
|
Cyriac SL, Karakasis K, Oza AM. Rucaparib for the treatment of ovarian cancer. Expert Opin Orphan Drugs 2017. [DOI: 10.1080/21678707.2018.1419129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Sunu Lazar Cyriac
- Gynecology and Drug Development Program, Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - Katherine Karakasis
- Research Program Development, The Princess Margaret, Drug Development Program, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Amit M. Oza
- Division of Medical Oncology and Hematology, Clinical Cancer Research Unit and Bras Drug Development Program, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| |
Collapse
|
16
|
Wang X, El-Halaby AA, Zhang H, Yang Q, Laughlin TS, Rothberg PG, Skinner K, Hicks DG. p53 alteration in morphologically normal/benign breast luminal cells in BRCA carriers with or without history of breast cancer. Hum Pathol 2017; 68:22-25. [PMID: 28438622 DOI: 10.1016/j.humpath.2017.04.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 03/25/2017] [Accepted: 04/07/2017] [Indexed: 11/29/2022]
Abstract
Germline mutations in BRCA genes have been shown to predispose patients to breast cancer. Studies have suggested that p53 alteration is a necessary step in tumorigenesis in BRCA carriers. Our previous study showed p53 alteration in morphologically normal/benign breast luminal cells in sporadic breast cancer patients, the so-called breast p53 signature. Here, we studied p53 status in 66 BRCA1/2 carriers' breasts: 29 patients with breast carcinoma (2 patients with bilateral breast carcinomas) and 37 without. Seven of the 12 (58%) triple-negative breast carcinomas in BRCA carriers were positive for p53 alteration (immunohistochemical stain and/or sequencing), the same frequency as in sporadic triple-negative breast carcinomas. Focal p53 positivity in adjacent normal/benign luminal cells was identified in 4 of the 7 cases with p53-positive carcinomas but not in breasts with p53-negative carcinomas, indicating that p53 positivity in normal/benign breast luminal cells is not a random event. Furthermore, in BRCA carriers' prophylactic mastectomies, 12 of the 94 (12.77%) breasts had focal p53 positivity in normal/benign luminal cells, with 2 cases in bilateral breasts, significantly higher than in previously studied mammoplasty specimens (0%). Our study suggests that germline BRCA gene mutations could result in genomic instability and an elevated gene mutation rate (such as the p53 gene) in breast luminal cells compared with the general population, predisposing BRCA carriers to develop p53-positive/triple-negative breast carcinomas.
Collapse
Affiliation(s)
- Xi Wang
- Department of Pathology, University of Rochester Medical Center, Rochester, NY 14642.
| | - Amber A El-Halaby
- Department of Pathology, University of Rochester Medical Center, Rochester, NY 14642
| | - Hengwei Zhang
- Department of Pathology, University of Rochester Medical Center, Rochester, NY 14642
| | - Qi Yang
- Department of Pathology, University of Rochester Medical Center, Rochester, NY 14642
| | - Todd S Laughlin
- Department of Pathology, University of Rochester Medical Center, Rochester, NY 14642
| | - Paul G Rothberg
- Department of Pathology, University of Rochester Medical Center, Rochester, NY 14642
| | - Kristin Skinner
- Department of Surgery, University of Rochester Medical Center, Rochester, NY 14642
| | - David G Hicks
- Department of Pathology, University of Rochester Medical Center, Rochester, NY 14642
| |
Collapse
|
17
|
Cerrato A, Morra F, Celetti A. Use of poly ADP-ribose polymerase [PARP] inhibitors in cancer cells bearing DDR defects: the rationale for their inclusion in the clinic. J Exp Clin Cancer Res 2016; 35:179. [PMID: 27884198 PMCID: PMC5123312 DOI: 10.1186/s13046-016-0456-2] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 11/09/2016] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND DNA damage response (DDR) defects imply genomic instability and favor tumor progression but make the cells vulnerable to the pharmacological inhibition of the DNA repairing enzymes. Targeting cellular proteins like PARPs, which cooperate and complement molecular defects of the DDR process, induces a specific lethality in DDR defective cancer cells and represents an anti-cancer strategy. Normal cells can tolerate the DNA damage generated by PARP inhibition because of an efficient homologous recombination mechanism (HR); in contrast, cancer cells with a deficient HR are unable to manage the DSBs and appear especially sensitive to the PARP inhibitors (PARPi) effects. MAIN BODY In this review we discuss the proof of concept for the use of PARPi in different cancer types and the success and failure of their inclusion in clinical trials. The PARP inhibitor Olaparib [AZD2281] has been approved by the FDA for use in pretreated ovarian cancer patients with defective BRCA1/2 genes, and by the EMEA for maintenance therapy in platinum sensitive ovarian cancer patients with defective BRCA1/2 genes. BRCA mutations are now recognised as the molecular targets for PARPi sensitivity in several tumors. However, it is noteworthy that the use of PARPi has shown its efficacy also in non-BRCA related tumors. Several trials are ongoing to test different PARPi in different cancer types. Here we review the concept of BRCAness and the functional loss of proteins involved in DDR/HR mechanisms in cancer, including additional molecules that can influence the cancer cells sensitivity to PARPi. Given the complexity of the existing crosstalk between different DNA repair pathways, it is likely that a single biomarker may not be sufficient to predict the benefit of PARP inhibitors therapies. Novel general assays able to predict the DDR/HR proficiency in cancer cells and the PARPi sensitivity represent a challenge for a personalized therapy. CONCLUSIONS PARP inhibition is a potentially important strategy for managing a significant subset of tumors. The discovery of both germline and somatic DNA repair deficiencies in different cancer patients, together with the development of new PARP inhibitors that can kill selectively cancer cells is a potent example of targeting therapy to molecularly defined tumor subtypes.
Collapse
|
18
|
Asleh-Aburaya K, Sheffield BS, Kos Z, Won JR, Wang XQ, Gao D, Wolber R, Gilks CB, Bernard PS, Chia SKL, Nielsen TO. Basal biomarkers nestin and INPP4b identify intrinsic subtypes accurately in breast cancers that are weakly positive for oestrogen receptor. Histopathology 2016; 70:185-194. [DOI: 10.1111/his.13038] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 07/10/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Karama Asleh-Aburaya
- Department of Pathology and Laboratory Medicine; Genetic Pathology Evaluation Centre; University of British Columbia; Vancouver BC Canada
| | - Brandon S Sheffield
- Department of Pathology and Laboratory Medicine; Genetic Pathology Evaluation Centre; University of British Columbia; Vancouver BC Canada
| | - Zuzana Kos
- Department of Pathology and Laboratory Medicine; University of Ottawa and The Ottawa Hospital; Ottawa ON Canada
| | - Jennifer R Won
- Department of Pathology and Laboratory Medicine; Genetic Pathology Evaluation Centre; University of British Columbia; Vancouver BC Canada
- Department of Pathology and Laboratory Medicine; Canadian Immunohistochemistry Quality Control (CIQC); University of British Columbia; Vancouver BC Canada
| | - Xiu Q Wang
- Department of Pathology and Laboratory Medicine; Genetic Pathology Evaluation Centre; University of British Columbia; Vancouver BC Canada
| | - Dongxia Gao
- Department of Pathology and Laboratory Medicine; Genetic Pathology Evaluation Centre; University of British Columbia; Vancouver BC Canada
| | - Robert Wolber
- Department of Pathology and Laboratory Medicine; Lions Gate Hospital; North Vancouver BC Canada
| | - C Blake Gilks
- Department of Pathology and Laboratory Medicine; Genetic Pathology Evaluation Centre; University of British Columbia; Vancouver BC Canada
- Department of Pathology and Laboratory Medicine; Canadian Immunohistochemistry Quality Control (CIQC); University of British Columbia; Vancouver BC Canada
| | - Philip S Bernard
- Department of Pathology; University of Utah/Health Sciences; Salt Lake City UT USA
| | - Stephen K L Chia
- Department of Medical Oncology; British Columbia Cancer Agency; Vancouver BC Canada
| | - Torsten O Nielsen
- Department of Pathology and Laboratory Medicine; Genetic Pathology Evaluation Centre; University of British Columbia; Vancouver BC Canada
| |
Collapse
|
19
|
Murata S, Zhang C, Finch N, Zhang K, Campo L, Breuer EK. Predictors and Modulators of Synthetic Lethality: An Update on PARP Inhibitors and Personalized Medicine. BIOMED RESEARCH INTERNATIONAL 2016; 2016:2346585. [PMID: 27642590 PMCID: PMC5013223 DOI: 10.1155/2016/2346585] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 07/28/2016] [Indexed: 12/18/2022]
Abstract
Poly(ADP-ribose) polymerase (PARP) inhibitors have proven to be successful agents in inducing synthetic lethality in several malignancies. Several PARP inhibitors have reached clinical trial testing for treatment in different cancers, and, recently, Olaparib (AZD2281) has gained both United States Food and Drug Administration (USFDA) and the European Commission (EC) approval for use in BRCA-mutated advanced ovarian cancer treatment. The need to identify biomarkers, their interactions in DNA damage repair pathways, and their potential utility in identifying patients who are candidates for PARP inhibitor treatment is well recognized. In this review, we detail many of the biomarkers that have been investigated for their ability to predict both PARP inhibitor sensitivity and resistance in preclinical studies as well as the results of several clinical trials that have tested the safety and efficacy of different PARP inhibitor agents in BRCA and non-BRCA-mutated cancers.
Collapse
Affiliation(s)
- Stephen Murata
- Department of Radiation Oncology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
| | - Catherine Zhang
- Department of Radiation Oncology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
| | - Nathan Finch
- Department of Radiation Oncology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
| | - Kevin Zhang
- Department of Otorhinolaryngology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Loredana Campo
- Department of Radiation Oncology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
| | - Eun-Kyoung Breuer
- Department of Radiation Oncology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
| |
Collapse
|
20
|
Perez RE, Shen H, Duan L, Kim RH, Kim T, Park NH, Maki CG. Modeling the Etiology of p53-mutated Cancer Cells. J Biol Chem 2016; 291:10131-47. [PMID: 27022024 DOI: 10.1074/jbc.m116.724781] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Indexed: 12/23/2022] Open
Abstract
p53 gene mutations are among the most common alterations in cancer. In most cases, missense mutations in one TP53 allele are followed by loss-of-heterozygosity (LOH), so tumors express only mutant p53. TP53 mutations and LOH have been linked, in many cases, with poor therapy response and worse outcome. Despite this, remarkably little is known about how TP53 point mutations are acquired, how LOH occurs, or the cells involved. Nutlin-3a occupies the p53-binding site in MDM2 and blocks p53-MDM2 interaction, resulting in the stabilization and activation of p53 and subsequent growth arrest or apoptosis. We leveraged the powerful growth inhibitory activity of Nutlin-3a to select p53-mutated cells and examined how TP53 mutations arise and how the remaining wild-type allele is lost or inactivated. Mismatch repair (MMR)-deficient colorectal cancer cells formed heterozygote (p53 wild-type/mutant) colonies when cultured in low doses of Nutlin-3a, whereas MMR-corrected counterparts did not. Placing these heterozygotes in higher Nutlin-3a doses selected clones in which the remaining wild-type TP53 was silenced. Our data suggest silencing occurred through a novel mechanism that does not involve DNA methylation, histone methylation, or histone deacetylation. These data indicate MMR deficiency in colorectal cancer can give rise to initiating TP53 mutations and that TP53 silencing occurs via a copy-neutral mechanism. Moreover, the data highlight the use of MDM2 antagonists as tools to study mechanisms of TP53 mutation acquisition and wild-type allele loss or silencing in cells with defined genetic backgrounds.
Collapse
Affiliation(s)
- Ricardo E Perez
- From the Department of Anatomy and Cell Biology, Rush University Medical Center, Chicago, Illinois 60612 and
| | - Hong Shen
- From the Department of Anatomy and Cell Biology, Rush University Medical Center, Chicago, Illinois 60612 and
| | - Lei Duan
- From the Department of Anatomy and Cell Biology, Rush University Medical Center, Chicago, Illinois 60612 and
| | - Reuben H Kim
- The Shapiro Family Laboratory of Viral Oncology and Aging Research, UCLA School of Dentistry and David Geffen School of Medicine at UCLA, Los Angeles, California 90095
| | - Terresa Kim
- The Shapiro Family Laboratory of Viral Oncology and Aging Research, UCLA School of Dentistry and David Geffen School of Medicine at UCLA, Los Angeles, California 90095
| | - No-Hee Park
- The Shapiro Family Laboratory of Viral Oncology and Aging Research, UCLA School of Dentistry and David Geffen School of Medicine at UCLA, Los Angeles, California 90095
| | - Carl G Maki
- From the Department of Anatomy and Cell Biology, Rush University Medical Center, Chicago, Illinois 60612 and
| |
Collapse
|
21
|
Madaras L, Balint N, Gyorffy B, Tokes AM, Barshack I, Yosepovich A, Friedman E, Paluch-Shimon S, Zippel D, Baghy K, Timar J, Kovalszky I, Kulka J, Szasz AM. BRCA Mutation-Related and Claudin-Low Breast Cancer: Blood Relatives or Stepsisters? Pathobiology 2015; 83:1-12. [DOI: 10.1159/000439135] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 08/03/2015] [Indexed: 11/19/2022] Open
|
22
|
Ollier M, Radosevic-Robin N, Kwiatkowski F, Ponelle F, Viala S, Privat M, Uhrhammer N, Bernard-Gallon D, Penault-Llorca F, Bignon YJ, Bidet Y. DNA repair genes implicated in triple negative familial non-BRCA1/2 breast cancer predisposition. Am J Cancer Res 2015; 5:2113-2126. [PMID: 26328243 PMCID: PMC4548324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 06/11/2015] [Indexed: 06/04/2023] Open
Abstract
Among breast cancers, 10 to 15% of cases would be due to hereditary risk. In these familial cases, mutations in BRCA1 and BRCA2 are found in only 15% to 20%, meaning that new susceptibility genes remain to be found. Triple-negative breast cancers represent 15% of all breast cancers, and are generally aggressive tumours without targeted therapies available. Our hypothesis is that some patients with triple negative breast cancer could share a genetic susceptibility different from other types of breast cancers. We screened 36 candidate genes, using pyrosequencing, in all the 50 triple negative breast cancer patients with familial history of cancer but no BRCA1 or BRCA2 mutation of a population of 3000 families who had consulted for a familial breast cancer between 2005 and 2013. Any mutations were also sequenced in available relatives of cases. Protein expression and loss of heterozygosity were explored in tumours. Seven deleterious mutations in 6 different genes (RAD51D, MRE11A, CHEK2, MLH1, MSH6, PALB2) were observed in one patient each, except the RAD51D mutation found in two cases. Loss of heterozygosity in the tumour was found for 2 of the 7 mutations. Protein expression was absent in tumour tissue for 5 mutations. Taking into consideration a specific subtype of tumour has revealed susceptibility genes, most of them in the homologous recombination DNA repair pathway. This may provide new possibilities for targeted therapies, along with better screening and care of patients.
Collapse
Affiliation(s)
- Marie Ollier
- Department of Molecular Oncology, Centre Jean PerrinClermont-Ferrand 63000, France
- Université d’AuvergneEA 4677, ERTICa, BP 10448, Clermont-Ferrand 63000, France
| | - Nina Radosevic-Robin
- Department of Anatomopathology, Centre Jean PerrinClermont-Ferrand 63000, France
- Université d’AuvergneEA 4677, ERTICa, BP 10448, Clermont-Ferrand 63000, France
| | - Fabrice Kwiatkowski
- Department of Molecular Oncology, Centre Jean PerrinClermont-Ferrand 63000, France
| | - Flora Ponelle
- Department of Molecular Oncology, Centre Jean PerrinClermont-Ferrand 63000, France
| | - Sandrine Viala
- Department of Molecular Oncology, Centre Jean PerrinClermont-Ferrand 63000, France
| | - Maud Privat
- Department of Molecular Oncology, Centre Jean PerrinClermont-Ferrand 63000, France
| | - Nancy Uhrhammer
- Department of Molecular Oncology, Centre Jean PerrinClermont-Ferrand 63000, France
| | | | - Frédérique Penault-Llorca
- Department of Anatomopathology, Centre Jean PerrinClermont-Ferrand 63000, France
- Université d’AuvergneEA 4677, ERTICa, BP 10448, Clermont-Ferrand 63000, France
| | - Yves-Jean Bignon
- Department of Molecular Oncology, Centre Jean PerrinClermont-Ferrand 63000, France
- Université d’AuvergneEA 4677, ERTICa, BP 10448, Clermont-Ferrand 63000, France
| | - Yannick Bidet
- Department of Molecular Oncology, Centre Jean PerrinClermont-Ferrand 63000, France
- Université d’AuvergneEA 4677, ERTICa, BP 10448, Clermont-Ferrand 63000, France
| |
Collapse
|
23
|
Vaca-Paniagua F, Alvarez-Gomez RM, Maldonado-Martínez HA, Pérez-Plasencia C, Fragoso-Ontiveros V, Lasa-Gonsebatt F, Herrera LA, Cantú D, Bargallo-Rocha E, Mohar A, Durand G, Forey N, Voegele C, Vallée M, Le Calvez-Kelm F, McKay J, Ardin M, Villar S, Zavadil J, Olivier M. Revealing the Molecular Portrait of Triple Negative Breast Tumors in an Understudied Population through Omics Analysis of Formalin-Fixed and Paraffin-Embedded Tissues. PLoS One 2015; 10:e0126762. [PMID: 25961742 PMCID: PMC4427337 DOI: 10.1371/journal.pone.0126762] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 04/07/2015] [Indexed: 12/27/2022] Open
Abstract
Triple negative breast cancer (TNBC), defined by the lack of expression of the estrogen receptor, progesterone receptor and human epidermal receptor 2, is an aggressive form of breast cancer that is more prevalent in certain populations, in particular in low- and middle-income regions. The detailed molecular features of TNBC in these regions remain unexplored as samples are mostly accessible as formalin-fixed paraffin embedded (FFPE) archived tissues, a challenging material for advanced genomic and transcriptomic studies. Using dedicated reagents and analysis pipelines, we performed whole exome sequencing and miRNA and mRNA profiling of 12 FFPE tumor tissues collected from pathological archives in Mexico. Sequencing analyses of the tumor tissues and their blood pairs identified TP53 and RB1 genes as the most frequently mutated genes, with a somatic mutation load of 1.7 mutations/exome Mb on average. Transcriptional analyses revealed an overexpression of growth-promoting signals (EGFR, PDGFR, VEGF, PIK3CA, FOXM1), a repression of cell cycle control pathways (TP53, RB1), a deregulation of DNA-repair pathways, and alterations in epigenetic modifiers through miRNA:mRNA network de-regulation. The molecular programs identified were typical of those described in basal-like tumors in other populations. This work demonstrates the feasibility of using archived clinical samples for advanced integrated genomics analyses. It thus opens up opportunities for investigating molecular features of tumors from regions where only FFPE tissues are available, allowing retrospective studies on the search for treatment strategies or on the exploration of the geographic diversity of breast cancer.
Collapse
Affiliation(s)
- Felipe Vaca-Paniagua
- Group of Molecular Mechanisms and Biomarkers, International Agency for Research on Cancer, Lyon, France
- Subdirección de Investigación Básica, Instituto Nacional de Cancerología, México D.F., México
- Unidad de Biomedicina, FES-Iztacala, Universidad Nacional Autónoma de México (UNAM), México D.F., México
| | - Rosa María Alvarez-Gomez
- Unidad de Genómica y Secuenciación Masiva (UGESEM), Instituto Nacional de Cancerología, México D.F., México
| | | | - Carlos Pérez-Plasencia
- Subdirección de Investigación Básica, Instituto Nacional de Cancerología, México D.F., México
- Unidad de Biomedicina, FES-Iztacala, Universidad Nacional Autónoma de México (UNAM), México D.F., México
- Unidad de Genómica y Secuenciación Masiva (UGESEM), Instituto Nacional de Cancerología, México D.F., México
| | - Veronica Fragoso-Ontiveros
- Subdirección de Investigación Básica, Instituto Nacional de Cancerología, México D.F., México
- Unidad de Genómica y Secuenciación Masiva (UGESEM), Instituto Nacional de Cancerología, México D.F., México
| | | | - Luis Alonso Herrera
- Unidad de Investigaciones Biomédicas en Cáncer, Instituto Nacional de Cancerología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), México D.F., México
| | - David Cantú
- Unidad de Investigaciones Biomédicas en Cáncer, Instituto Nacional de Cancerología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), México D.F., México
| | - Enrique Bargallo-Rocha
- Departamento de Tumores Mamarios, Instituto Nacional de Cancerología, México D.F., México
| | - Alejandro Mohar
- Departamento de Epidemiología, Instituto Nacional de Cancerología, México D.F., México
| | - Geoffroy Durand
- Group of Genetic Cancer Susceptibility, International Agency for Research on Cancer, Lyon, France
| | - Nathalie Forey
- Group of Genetic Cancer Susceptibility, International Agency for Research on Cancer, Lyon, France
| | - Catherine Voegele
- Group of Genetic Cancer Susceptibility, International Agency for Research on Cancer, Lyon, France
| | - Maxime Vallée
- Group of Genetic Cancer Susceptibility, International Agency for Research on Cancer, Lyon, France
| | - Florence Le Calvez-Kelm
- Group of Genetic Cancer Susceptibility, International Agency for Research on Cancer, Lyon, France
| | - James McKay
- Group of Genetic Cancer Susceptibility, International Agency for Research on Cancer, Lyon, France
| | - Maude Ardin
- Group of Molecular Mechanisms and Biomarkers, International Agency for Research on Cancer, Lyon, France
| | - Stéphanie Villar
- Group of Molecular Mechanisms and Biomarkers, International Agency for Research on Cancer, Lyon, France
| | - Jiri Zavadil
- Group of Molecular Mechanisms and Biomarkers, International Agency for Research on Cancer, Lyon, France
| | - Magali Olivier
- Group of Molecular Mechanisms and Biomarkers, International Agency for Research on Cancer, Lyon, France
| |
Collapse
|
24
|
Liu JC, Voisin V, Wang S, Wang DY, Jones RA, Datti A, Uehling D, Al-awar R, Egan SE, Bader GD, Tsao M, Mak TW, Zacksenhaus E. Combined deletion of Pten and p53 in mammary epithelium accelerates triple-negative breast cancer with dependency on eEF2K. EMBO Mol Med 2014; 6:1542-60. [PMID: 25330770 PMCID: PMC4287974 DOI: 10.15252/emmm.201404402] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 09/23/2014] [Accepted: 09/25/2014] [Indexed: 12/17/2022] Open
Abstract
The tumor suppressors Pten and p53 are frequently lost in breast cancer, yet the consequences of their combined inactivation are poorly understood. Here, we show that mammary-specific deletion of Pten via WAP-Cre, which targets alveolar progenitors, induced tumors with shortened latency compared to those induced by MMTV-Cre, which targets basal/luminal progenitors. Combined Pten-p53 mutations accelerated formation of claudin-low, triple-negative-like breast cancer (TNBC) that exhibited hyper-activated AKT signaling and more mesenchymal features relative to Pten or p53 single-mutant tumors. Twenty-four genes that were significantly and differentially expressed between WAP-Cre:Pten/p53 and MMTV-Cre:Pten/p53 tumors predicted poor survival for claudin-low patients. Kinome screens identified eukaryotic elongation factor-2 kinase (eEF2K) inhibitors as more potent than PI3K/AKT/mTOR inhibitors on both mouse and human Pten/p53-deficient TNBC cells. Sensitivity to eEF2K inhibition correlated with AKT pathway activity. eEF2K monotherapy suppressed growth of Pten/p53-deficient TNBC xenografts in vivo and cooperated with doxorubicin to efficiently kill tumor cells in vitro. Our results identify a prognostic signature for claudin-low patients and provide a rationale for using eEF2K inhibitors for treatment of TNBC with elevated AKT signaling.
Collapse
Affiliation(s)
- Jeff C Liu
- Division of Advanced Diagnostics, Toronto General Research Institute - University Health Network, Toronto, ON, Canada
| | | | - Sharon Wang
- Division of Advanced Diagnostics, Toronto General Research Institute - University Health Network, Toronto, ON, Canada Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Dong-Yu Wang
- Princess Margaret Cancer Center, Toronto, ON, Canada Campbell Family Institute for Breast Cancer Research, Princess Margaret Hospital, Toronto, ON, Canada
| | - Robert A Jones
- Division of Advanced Diagnostics, Toronto General Research Institute - University Health Network, Toronto, ON, Canada
| | - Alessandro Datti
- SMART Laboratory for High-Throughput Screening Programs, Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Toronto, ON, Canada Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
| | - David Uehling
- Drug Discovery Program, Department of Pharmacology and Toxicology, Ontario Institute for Cancer Research, University of Toronto, Toronto, ON, Canada
| | - Rima Al-awar
- Drug Discovery Program, Department of Pharmacology and Toxicology, Ontario Institute for Cancer Research, University of Toronto, Toronto, ON, Canada
| | - Sean E Egan
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Gary D Bader
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Ming Tsao
- Princess Margaret Cancer Center, Toronto, ON, Canada Department of Medical Biophysics, University Health Network, Toronto, ON, Canada
| | - Tak W Mak
- Campbell Family Institute for Breast Cancer Research, Princess Margaret Hospital, Toronto, ON, Canada SMART Laboratory for High-Throughput Screening Programs, Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Toronto, ON, Canada Department of Medical Biophysics, University Health Network, Toronto, ON, Canada
| | - Eldad Zacksenhaus
- Division of Advanced Diagnostics, Toronto General Research Institute - University Health Network, Toronto, ON, Canada Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada Department of Medical Biophysics, University Health Network, Toronto, ON, Canada
| |
Collapse
|
25
|
Naushad SM, Reddy CA, Kumaraswami K, Divyya S, Kotamraju S, Gottumukkala SR, Digumarti RR, Kutala VK. Impact of hyperhomocysteinemia on breast cancer initiation and progression: epigenetic perspective. Cell Biochem Biophys 2014; 68:397-406. [PMID: 23934182 DOI: 10.1007/s12013-013-9720-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Our recent study showing association of hyperhomocysteinemia and hypomethioninemia in breast cancer and other studies indicating association of hyperhomocysteinemia with metastasis and development of drug resistance in breast cancer cells treated with homocysteine lead us to hypothesize that homocysteine might modulate the expression of certain tumor suppressors, i.e., RASSF1, RARβ1, CNND1, BRCA1, and p21, and might influence prognostic markers such as BNIP3 by inducing epigenetic alteration. To demonstrate this hypothesis, we have treated MCF-7 and MDA-MB-231 cells with different doses of homocysteine and observed dose-dependent inhibition of BRCA1 and RASSF1, respectively. In breast cancer tissues, we observed the following expression pattern: BNIP3 > BRCA1 > RARβ1 > CCND1 > p21 > RASSF1. Hyperhomocysteinemia was positively associated with BRAC1 hypermethylation both in breast cancer tissue and corresponding peripheral blood. Peripheral blood CpG island methylation of BRCA1 in all types of breast cancer and methylation of RASSF1 in ER/PR-negative breast cancers showed positive correlation with total plasma homocysteine. The methylation of RASSF1 and BRCA1 was associated with breast cancer initiation as well as progression, while BRCA1 methylation was associated with DNA damage. Vitamin B12 showed inverse association with the methylation at both the loci. RFC1 G80A and cSHMT C1420T variants showed positive association with methylation at both the loci. Genetic variants influencing remethylation step were associated positively with BRCA1 methylation and inversely with RASSF1 methylation. GCPII C1561T variant showed inverse association with BRCA1 methylation. We found good correlation of BRAC1 (r = 0.90) and RASSF1 (0.92) methylation pattern between the breast cancer tissue and the corresponding peripheral blood. To conclude, elevated homocysteine influences methionine dependency phenotype of breast cancer cells and is associated with breast cancer progression by epigenetic modulation of RASSF1 and BRCA1.
Collapse
Affiliation(s)
- Shaik Mohammad Naushad
- Department of Clinical Pharmacology and Therapeutics, Nizam's Institute of Medical Sciences (NIMS), Panjagutta, Hyderabad, 500082, Andhra Pradesh, India
| | | | | | | | | | | | | | | |
Collapse
|
26
|
Vollebergh MA, Klijn C, Schouten PC, Wesseling J, Israeli D, Ylstra B, Wessels LF, Jonkers J, Linn SC. Lack of genomic heterogeneity at high-resolution aCGH between primary breast cancers and their paired lymph node metastases. PLoS One 2014; 9:e103177. [PMID: 25083859 PMCID: PMC4118860 DOI: 10.1371/journal.pone.0103177] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 06/29/2014] [Indexed: 11/18/2022] Open
Abstract
Lymph-node metastasis (LNM) predict high recurrence rates in breast cancer patients. Systemic treatment aims to eliminate (micro)metastatic cells. However decisions regarding systemic treatment depend largely on clinical and molecular characteristics of primary tumours. It remains, however, unclear to what extent metastases resemble the cognate primary breast tumours, especially on a genomic level, and as such will be eradicated by the systemic therapy chosen. In this study we used high-resolution aCGH to investigate DNA copy number differences between primary breast cancers and their paired LNMs. To date, no recurrent LNM-specific genomic aberrations have been identified using array comparative genomic hybridization (aCGH) analysis. In our study we employ a high-resolution platform and we stratify on different breast cancer subtypes, both aspects that might have underpowered previously performed studies.To test the possibility that genomic instability in triple-negative breast cancers (TNBCs) might cause increased random and potentially also recurrent copy number aberrations (CNAs) in their LNMs, we studied 10 primary TNBC–LNM pairs and 10 ER-positive (ER+) pairs and verified our findings adding additionally 5 TNBC-LNM and 22 ER+-LNM pairs. We found that all LNMs clustered nearest to their matched tumour except for two cases, of which one was due to the presence of two distinct histological components in one tumour. We found no significantly altered CNAs between tumour and their LNMs in the entire group or in the subgroups. Within the TNBC subgroup, no absolute increase in CNAs was found in the LNMs compared to their primary tumours, suggesting that increased genomic instability does not lead to more CNAs in LNMs. Our findings suggest a high clonal relationship between primary breast tumours and its LNMs, at least prior to treatment, and support the use of primary tumour characteristics to guide adjuvant systemic chemotherapy in breast cancer patients.
Collapse
Affiliation(s)
- Marieke A. Vollebergh
- Division of Molecular Pathology, Netherlands Cancer Institute–Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
- Division of Medical Oncology, Netherlands Cancer Institute–Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Christiaan Klijn
- Division of Molecular Pathology, Netherlands Cancer Institute–Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Philip C. Schouten
- Division of Molecular Pathology, Netherlands Cancer Institute–Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Jelle Wesseling
- Department of Pathology, Netherlands Cancer Institute–Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Danielle Israeli
- Department of Pathology, Vrije Universiteit University Medical Center, Amsterdam, the Netherlands
| | - Bauke Ylstra
- Department of Pathology, Vrije Universiteit University Medical Center, Amsterdam, the Netherlands
| | - Lodewyk F.A. Wessels
- Department of Bioinformatics and Statistics, Netherlands Cancer Institute–Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
- Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Delft, the Netherlands
| | - Jos Jonkers
- Division of Molecular Pathology, Netherlands Cancer Institute–Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Sabine C. Linn
- Division of Molecular Pathology, Netherlands Cancer Institute–Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
- Division of Medical Oncology, Netherlands Cancer Institute–Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
- * E-mail:
| |
Collapse
|
27
|
Lupo B, Trusolino L. Inhibition of poly(ADP-ribosyl)ation in cancer: old and new paradigms revisited. Biochim Biophys Acta Rev Cancer 2014; 1846:201-15. [PMID: 25026313 DOI: 10.1016/j.bbcan.2014.07.004] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 06/02/2014] [Accepted: 07/08/2014] [Indexed: 01/31/2023]
Abstract
Inhibitors of poly(ADP-ribose) polymerases actualized the biological concept of synthetic lethality in the clinical practice, yielding a paradigmatic example of translational medicine. The profound sensitivity of tumors with germline BRCA mutations to PARP1/2 blockade owes to inherent defects of the BRCA-dependent homologous recombination machinery, which are unleashed by interruption of PARP DNA repair activity and lead to DNA damage overload and cell death. Conversely, aspirant BRCA-like tumors harboring somatic DNA repair dysfunctions (a vast entity of genetic and epigenetic defects known as "BRCAness") not always align with the familial counterpart and appear not to be equally sensitive to PARP inhibition. The acquisition of secondary resistance in initially responsive patients and the lack of standardized biomarkers to identify "BRCAness" pose serious threats to the clinical advance of PARP inhibitors; a feeling is also emerging that a BRCA-centered perspective might have missed the influence of additional, not negligible and DNA repair-independent PARP contributions onto therapy outcome. While regulatory approval for PARP1/2 inhibitors is still pending, novel therapeutic opportunities are sprouting from different branches of the PARP family, although they remain immature for clinical extrapolation. This review is an endeavor to provide a comprehensive appraisal of the multifaceted biology of PARPs and their evolving impact on cancer therapeutics.
Collapse
Affiliation(s)
- Barbara Lupo
- Department of Oncology, University of Torino Medical School, 10060 Candiolo, Torino, Italy; Laboratory of Molecular Pharmacology, Candiolo Cancer Institute, FPO IRCCS, 10060 Candiolo, Torino, Italy
| | - Livio Trusolino
- Department of Oncology, University of Torino Medical School, 10060 Candiolo, Torino, Italy; Laboratory of Molecular Pharmacology, Candiolo Cancer Institute, FPO IRCCS, 10060 Candiolo, Torino, Italy.
| |
Collapse
|
28
|
Silwal-Pandit L, Vollan HKM, Chin SF, Rueda OM, McKinney S, Osako T, Quigley DA, Kristensen VN, Aparicio S, Børresen-Dale AL, Caldas C, Langerød A. TP53 mutation spectrum in breast cancer is subtype specific and has distinct prognostic relevance. Clin Cancer Res 2014; 20:3569-80. [PMID: 24803582 DOI: 10.1158/1078-0432.ccr-13-2943] [Citation(s) in RCA: 207] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
PURPOSE In breast cancer, the TP53 gene is frequently mutated and the mutations have been associated with poor prognosis. The prognostic impact of the different types of TP53 mutations across the different molecular subtypes is still poorly understood. Here, we characterize the spectrum and prognostic significance of TP53 mutations with respect to the PAM50 subtypes and integrative clusters (IC). EXPERIMENTAL DESIGN TP53 mutation status was obtained for 1,420 tumor samples from the METABRIC cohort by sequencing all coding exons using the Sanger method. RESULTS TP53 mutations were found in 28.3% of the tumors, conferring a worse overall and breast cancer-specific survival [HR = 2.03; 95% confidence interval (CI), 1.65-2.48, P < 0.001], and were also found to be an independent marker of poor prognosis in estrogen receptor-positive cases (HR = 1.86; 95% CI, 1.39-2.49, P < 0.001). The mutation spectrum of TP53 varied between the breast cancer subtypes, and individual alterations showed subtype-specific association. TP53 mutations were associated with increased mortality in patients with luminal B, HER2-enriched, and normal-like tumors, but not in patients with luminal A and basal-like tumors. Similar observations were made in ICs, where mutation associated with poorer outcome in IC1, IC4, and IC5. The combined effect of TP53 mutation, TP53 LOH, and MDM2 amplification on mortality was additive. CONCLUSION This study reveals that TP53 mutations have different clinical relevance in molecular subtypes of breast cancer, and suggests diverse roles for TP53 in the biology underlying breast cancer development.
Collapse
Affiliation(s)
- Laxmi Silwal-Pandit
- K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Norway
| | - Hans Kristian Moen Vollan
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet; The K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine; Division of Cancer Medicine, Surgery and Transplantation, Department of Oncology, Oslo University Hospital, Oslo
| | - Suet-Feung Chin
- Cancer Research UK, Cambridge Institute; Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Oscar M Rueda
- Cancer Research UK, Cambridge Institute; Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Steven McKinney
- Department of Pathology and Laboratory Medicine, University of British Colombia; and Molecular Oncology, British Colombia Cancer Research Center, Vancouver, Canada
| | - Tomo Osako
- Department of Pathology and Laboratory Medicine, University of British Colombia; and Molecular Oncology, British Colombia Cancer Research Center, Vancouver, Canada
| | - David A Quigley
- Authors' Affiliations: Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet; The K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine; Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, California
| | - Vessela N Kristensen
- Authors' Affiliations: Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet; The K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine; Division of Medicine, Department of Clinical Molecular Oncology, Akershus University Hospital, Lørenskog, Norway
| | - Samuel Aparicio
- Department of Pathology and Laboratory Medicine, University of British Colombia; and Molecular Oncology, British Colombia Cancer Research Center, Vancouver, Canada
| | - Anne-Lise Børresen-Dale
- Authors' Affiliations: Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet; The K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine;
| | - Carlos Caldas
- Cancer Research UK, Cambridge Institute; Cambridge Experimental Cancer Medicine Centre; Cambridge Breast Unit, Addenbrooke's Hospital, Cambridge University Hospital NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre; Department of Oncology, University of Cambridge, Cambridge, United Kingdom;
| | - Anita Langerød
- Authors' Affiliations: Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet; The K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine;
| |
Collapse
|
29
|
De Summa S, Pinto R, Sambiasi D, Petriella D, Paradiso V, Paradiso A, Tommasi S. BRCAness: a deeper insight into basal-like breast tumors. Ann Oncol 2014; 24 Suppl 8:viii13-viii21. [PMID: 24131964 DOI: 10.1093/annonc/mdt306] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The molecular scenario of breast cancer has become more complex in the last few years. Distinguishing between BRCA-associated, sporadic, HER2-enriched and triple-negative tumors is not sufficient to allow effective clinical management. Basal-like breast cancer, a subtype of triple-negative breast cancer, differs from others grouped under this heading. Commonalities between BRCA-related tumors and basal-like breast cancers (BRCAness phenotype) are highly relevant to ongoing clinical trials, in particular those investigating targeted therapies (e.g. PARP inhibitors) in sporadic breast tumors. The 'gold standard' to identify basal-like phenotype is DNA microarray, but integrated results could provide a panel of biomarkers helpful in identifying 'BRCAness' tumors (e.g. copy number aberrations, abnormal protein localization and altered transcriptional levels) and other molecular targets, such as APE1,the inhibition of which is emerging as an attractive breast cancer treatment in certain therapeutic settings.
Collapse
Affiliation(s)
- S De Summa
- NCRC Istituto Tumori 'Giovanni Paolo II', Bari, Italy
| | | | | | | | | | | | | |
Collapse
|
30
|
Abstract
BACKGROUND Triple-negative breast cancers (TNBC) do not represent a single disease subgroup and are often aggressive breast cancers with poor prognoses. Unlike estrogen/progesterone receptor and HER2 (human epidermal growth factor receptor 2) breast cancers, which are responsive to targeted treatments, there is no effective targeted therapy for TNBC, although approximately 50% of patients respond to conventional chemotherapies, including taxanes, anthracyclines, cyclophosphamide, and platinum salts. CONTENT Genomic studies have helped clarify some of the possible disease groupings that make up TNBC. We discuss the findings, including copy number-transcriptome analysis, whole genome sequencing, and exome sequencing, in terms of the biological properties and phenotypes that make up the constellation of TNBC. The relationships between subgroups defined by transcriptome and genome analysis are discussed. SUMMARY TNBC is not a uniform molecular or disease entity but a constellation of variably well-defined biological properties whose relationship to each other is not understood. There is good support for the existence of a basal expression subtype, p53 mutated, high-genomic instability subtype of TNBC. This should be considered a distinct TNBC subtype. Other subtypes with variable degrees of supporting evidence exist within the nonbasal/p53wt (wild-type p53) TNBC, including a group of TNBC with PI3K (phosphoinositide 3-kinase) pathway activation that have better overall prognosis than the basal TNBC. Consistent molecular phenotyping of TNBC by whole genome sequencing, transcriptomics, and functional studies with patient-derived tumor xenograft models will be essential components in clinical and biological studies as means of resolving this heterogeneity.
Collapse
Affiliation(s)
- Hong Xu
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC
| | | | | | | |
Collapse
|
31
|
|
32
|
Elsawaf Z, Sinn HP, Rom J, Bermejo JL, Schneeweiss A, Aulmann S. Biological subtypes of triple-negative breast cancer are associated with distinct morphological changes and clinical behaviour. Breast 2013; 22:986-92. [PMID: 23806603 DOI: 10.1016/j.breast.2013.05.012] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 04/12/2013] [Accepted: 05/23/2013] [Indexed: 11/30/2022] Open
Abstract
Triple negative breast cancer (TNBC) is a heterogeneous group of tumours accounting for approximately 10-20% of all breast carcinomas. To identify biologically distinct subgroups of TNBC and to assess their clinical properties we examined a series of 142 consecutive patients all of which had received adjuvant cytotoxic chemotherapy using a comprehensive panel of immunostains. Hierarchical unsupervised cluster analysis based on the expression of 13 markers permitted separation of four distinct groups (basal A, basal B, basoluminal, luminal) with the main distinguishing features being cytokeratin (Ck5/6, Ck14, Ck19), EGFR, p53, p16, and Ki-67 expression. Clusters differed with respect to patient age, modified Bloom and Richardson grading, the presence of tumour necrosis, growth pattern and survival, both in uni- and multivariate analysis. Basal (A or B) tumours showed a substantially better outcome compared with basoluminal and luminal tumours. Our data underline the heterogeneity of TNBC and characterise potentially relevant biological subtypes.
Collapse
Affiliation(s)
- Zeinab Elsawaf
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany
| | | | | | | | | | | |
Collapse
|
33
|
Abstract
Over the last decade, our knowledge in somatic genetic events related to breast cancer has increased -enormously. Through usage of various genome-wide molecular approaches, it has become increasingly clear that breast cancer is a vastly heterogeneous disease. Microarray-based gene expression profiling has divided breast cancer into five distinct intrinsic subtypes termed basal-like, HER2-enriched, normal-like, luminal A, and luminal B. Importantly, these subtypes are closely correlated to clinical variables as well as different outcomes, with luminal A tumors as the good prognostic group. Initial studies using genome-wide DNA copy number data broadly partitioned breast cancers into three types, complex, amplifier, and simple, and moreover associated distinct copy number changes with the intrinsic subtypes defined by gene expression profiles. More recently, this genomic classification was refined into six genomic subtypes demonstrating strong resemblance to the intrinsic gene expression classification. Additionally, inherited BRCA1- and BRCA2-mutated tumors were significantly correlated to specific subtypes. In this chapter, we will review the current status regarding genomic subtypes of nonfamilial breast cancer.
Collapse
Affiliation(s)
- Markus Ringnér
- Department of Oncology, Clinical Sciences, Lund University, Lund, Sweden
| | | | | |
Collapse
|
34
|
Patterns of genomic loss of heterozygosity predict homologous recombination repair defects in epithelial ovarian cancer. Br J Cancer 2012. [PMID: 23047548 DOI: 10.1038/bjc.2012.451] [] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Defects in BRCA1, BRCA2, and other members of the homologous recombination pathway have potential therapeutic relevance when used to support agents that introduce or exploit double-stranded DNA breaks. This study examines the association between homologous recombination defects and genomic patterns of loss of heterozygosity (LOH). METHODS Ovarian tumours from two independent data sets were characterised for defects in BRCA1, BRCA2, and RAD51C, and LOH profiles were generated. Publically available data were downloaded for a third independent data set. The same analyses were performed on 57 cancer cell lines. RESULTS Loss of heterozygosity regions of intermediate size were observed more frequently in tumours with defective BRCA1 or BRCA2 (P=10(-11)). The homologous recombination deficiency (HRD) score was defined as the number of these regions observed in a tumour sample. The association between HRD score and BRCA deficiency was validated in two independent ovarian cancer data sets (P=10(-5) and 10(-29)), and identified breast and pancreatic cell lines with BRCA defects. CONCLUSION The HRD score appears capable of detecting homologous recombination defects regardless of aetiology or mechanism. This score could facilitate the use of PARP inhibitors and platinum in breast, ovarian, and other cancers.
Collapse
|
35
|
Patterns of genomic loss of heterozygosity predict homologous recombination repair defects in epithelial ovarian cancer. Br J Cancer 2012; 107:1776-82. [PMID: 23047548 PMCID: PMC3493866 DOI: 10.1038/bjc.2012.451] [Citation(s) in RCA: 534] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Background: Defects in BRCA1, BRCA2, and other members of the homologous recombination pathway have potential therapeutic relevance when used to support agents that introduce or exploit double-stranded DNA breaks. This study examines the association between homologous recombination defects and genomic patterns of loss of heterozygosity (LOH). Methods: Ovarian tumours from two independent data sets were characterised for defects in BRCA1, BRCA2, and RAD51C, and LOH profiles were generated. Publically available data were downloaded for a third independent data set. The same analyses were performed on 57 cancer cell lines. Results: Loss of heterozygosity regions of intermediate size were observed more frequently in tumours with defective BRCA1 or BRCA2 (P=10−11). The homologous recombination deficiency (HRD) score was defined as the number of these regions observed in a tumour sample. The association between HRD score and BRCA deficiency was validated in two independent ovarian cancer data sets (P=10−5 and 10−29), and identified breast and pancreatic cell lines with BRCA defects. Conclusion: The HRD score appears capable of detecting homologous recombination defects regardless of aetiology or mechanism. This score could facilitate the use of PARP inhibitors and platinum in breast, ovarian, and other cancers.
Collapse
|
36
|
Daemen A, Wolf DM, Korkola JE, Griffith OL, Frankum JR, Brough R, Jakkula LR, Wang NJ, Natrajan R, Reis-Filho JS, Lord CJ, Ashworth A, Spellman PT, Gray JW, van't Veer LJ. Cross-platform pathway-based analysis identifies markers of response to the PARP inhibitor olaparib. Breast Cancer Res Treat 2012; 135:505-17. [PMID: 22875744 PMCID: PMC3429780 DOI: 10.1007/s10549-012-2188-0] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Accepted: 07/25/2012] [Indexed: 12/15/2022]
Abstract
Poly(ADP-ribose) polymerase (PARP) is an enzyme involved in DNA repair. PARP inhibitors can act as chemosensitizers, or operate on the principle of synthetic lethality when used as single agent. Clinical trials have shown drugs in this class to be promising for BRCA mutation carriers. We postulated that inability to demonstrate response in non-BRCA carriers in which BRCA is inactivated by other mechanisms or with deficiency in homologous recombination for DNA repair is due to lack of molecular markers that define a responding subpopulation. We identified candidate markers for this purpose for olaparib (AstraZeneca) by measuring inhibitory effects of nine concentrations of olaparib in 22 breast cancer cell lines and identifying features in transcriptional and genome copy number profiles that were significantly correlated with response. We emphasized in this discovery process genes involved in DNA repair. We found that the cell lines that were sensitive to olaparib had a significant lower copy number of BRCA1 compared to the resistant cell lines (p value 0.012). In addition, we discovered seven genes from DNA repair pathways whose transcriptional levels were associated with response. These included five genes (BRCA1, MRE11A, NBS1, TDG, and XPA) whose transcript levels were associated with resistance and two genes (CHEK2 and MK2) whose transcript levels were associated with sensitivity. We developed an algorithm to predict response using the seven-gene transcription levels and applied it to 1,846 invasive breast cancer samples from 8 U133A/plus 2 (Affymetrix) data sets and found that 8–21 % of patients would be predicted to be responsive to olaparib. A similar response frequency was predicted in 536 samples analyzed on an Agilent platform. Importantly, tumors predicted to respond were enriched in basal subtype tumors. Our studies support clinical evaluation of the utility of our seven-gene signature as a predictor of response to olaparib.
Collapse
Affiliation(s)
- Anneleen Daemen
- Laboratory Medicine, University of California San Francisco, 2340 Sutter Street Box 0808, San Francisco, CA 94115, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Xu K, Usary J, Kousis PC, Prat A, Wang DY, Adams JR, Wang W, Loch AJ, Deng T, Zhao W, Cardiff RD, Yoon K, Gaiano N, Ling V, Beyene J, Zacksenhaus E, Gridley T, Leong WL, Guidos CJ, Perou CM, Egan SE. Lunatic fringe deficiency cooperates with the Met/Caveolin gene amplicon to induce basal-like breast cancer. Cancer Cell 2012; 21:626-641. [PMID: 22624713 PMCID: PMC3603366 DOI: 10.1016/j.ccr.2012.03.041] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Revised: 10/31/2011] [Accepted: 03/08/2012] [Indexed: 12/17/2022]
Abstract
Basal-like breast cancers (BLBC) express a luminal progenitor gene signature. Notch receptor signaling promotes luminal cell fate specification in the mammary gland, while suppressing stem cell self-renewal. Here we show that deletion of Lfng, a sugar transferase that prevents Notch activation by Jagged ligands, enhances stem/progenitor cell proliferation. Mammary-specific deletion of Lfng induces basal-like and claudin-low tumors with accumulation of Notch intracellular domain fragments, increased expression of proliferation-associated Notch targets, amplification of the Met/Caveolin locus, and elevated Met and Igf-1R signaling. Human BL breast tumors, commonly associated with JAGGED expression, elevated MET signaling, and CAVEOLIN accumulation, express low levels of LFNG. Thus, reduced LFNG expression facilitates JAG/NOTCH luminal progenitor signaling and cooperates with MET/CAVEOLIN basal-type signaling to promote BLBC.
Collapse
MESH Headings
- Animals
- Breast Neoplasms/enzymology
- Breast Neoplasms/genetics
- Breast Neoplasms/pathology
- Calcium-Binding Proteins/metabolism
- Caveolins/genetics
- Caveolins/metabolism
- Cell Proliferation
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/metabolism
- Cell Transformation, Neoplastic/pathology
- Cells, Cultured
- Claudins/metabolism
- Databases, Genetic
- Female
- Gene Expression Profiling/methods
- Gene Expression Regulation, Developmental
- Gene Expression Regulation, Neoplastic
- Glycosyltransferases/deficiency
- Glycosyltransferases/genetics
- Glycosyltransferases/metabolism
- Humans
- Immunohistochemistry
- Intercellular Signaling Peptides and Proteins/metabolism
- Jagged-1 Protein
- Mammary Glands, Animal/enzymology
- Mammary Glands, Animal/growth & development
- Mammary Glands, Animal/pathology
- Mammary Glands, Animal/transplantation
- Mammary Neoplasms, Experimental/enzymology
- Mammary Neoplasms, Experimental/genetics
- Mammary Neoplasms, Experimental/pathology
- Membrane Proteins/metabolism
- Mice
- Mice, Knockout
- Middle Aged
- Neoplastic Stem Cells/enzymology
- Neoplastic Stem Cells/pathology
- Neoplastic Stem Cells/transplantation
- Oligonucleotide Array Sequence Analysis
- Proto-Oncogene Proteins c-met/genetics
- Proto-Oncogene Proteins c-met/metabolism
- Receptor, IGF Type 1/metabolism
- Receptors, Notch/metabolism
- Serrate-Jagged Proteins
- Signal Transduction
Collapse
Affiliation(s)
- Keli Xu
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, M5G 1L7, Canada
| | - Jerry Usary
- Lineberger Comprehensive Cancer Center, Departments of Genetics and Pathology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Philaretos C Kousis
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, M5G 1L7, Canada
| | - Aleix Prat
- Lineberger Comprehensive Cancer Center, Departments of Genetics and Pathology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Dong-Yu Wang
- The Campbell Family Cancer Research Institute and Surgical Oncology Princess Margaret Hospital, and the Department of General Surgery, University Health Network, Toronto, ON M5S 1A1, Canada
| | - Jessica R Adams
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, M5G 1L7, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Wei Wang
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, M5G 1L7, Canada
| | - Amanda J Loch
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, M5G 1L7, Canada
| | - Tao Deng
- Division of Cell and Molecular Biology, Toronto General Research Institute, University Health Network, Toronto, ON M5S 1A1, Canada
| | - Wei Zhao
- Lineberger Comprehensive Cancer Center, Departments of Genetics and Pathology, University of North Carolina, Chapel Hill, NC 27599, USA
| | | | - Keejung Yoon
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nicholas Gaiano
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Vicki Ling
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, M5G 1L7, Canada; Child Health Evaluative Sciences, The Hospital for Sick Children, Toronto, ON, M5G 1L7, Canada
| | - Joseph Beyene
- Child Health Evaluative Sciences, The Hospital for Sick Children, Toronto, ON, M5G 1L7, Canada
| | - Eldad Zacksenhaus
- Division of Cell and Molecular Biology, Toronto General Research Institute, University Health Network, Toronto, ON M5S 1A1, Canada
| | - Tom Gridley
- Center for Molecular Medicine, Maine Medical Center Research Institute, 81 Research Drive, Scarborough, ME 04074, USA
| | - Wey L Leong
- The Campbell Family Cancer Research Institute and Surgical Oncology Princess Margaret Hospital, and the Department of General Surgery, University Health Network, Toronto, ON M5S 1A1, Canada
| | - Cynthia J Guidos
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, M5G 1L7, Canada; Department of Immunology, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Charles M Perou
- Lineberger Comprehensive Cancer Center, Departments of Genetics and Pathology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Sean E Egan
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, M5G 1L7, Canada; The Campbell Family Cancer Research Institute and Surgical Oncology Princess Margaret Hospital, and the Department of General Surgery, University Health Network, Toronto, ON M5S 1A1, Canada.
| |
Collapse
|
38
|
|
39
|
Abstract
Drug resistance is one of the most pressing problems in treating cancer patients today. Local and regional disease can usually be adequately treated, but patients eventually die from distant metastases that have become resistant to all available chemotherapy. Although work on cultured tumor cell lines has yielded a lot of information on potential drug resistance mechanisms, it has proven difficult to translate these results to clinical drug resistance in patients. The controversy regarding the contribution of ABC transporters to drug resistance in patients is one example. The study of genetically engineered mouse models (GEMMs), which closely resemble cancer in human patients, can help to bridge this gap. In models for BRCA1- or BRCA2-associated breast cancer, we observed a substantial synergy between the defect in homology-directed DNA repair and sensitivity to DNA-targeting drugs. Nevertheless, tumors are not easily eradicated and eventually drug resistance develops. In this review we will discuss the use of the new generation mouse models to address major clinical problems, such as mechanisms of drug resistance, predicting chemotherapy response or characterizing the nature of residual tumor cells that escape eradication. Moreover, we will address the contribution of ABC transporters to drug resistance in our model.
Collapse
Affiliation(s)
- Sven Rottenberg
- Division of Molecular Biology, The Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands.
| | | |
Collapse
|
40
|
Abstract
The proteins encoded by the two major breast cancer susceptibility genes, BRCA1 and BRCA2, work in a common pathway of genome protection. However, the two proteins work at different stages in the DNA damage response (DDR) and in DNA repair. BRCA1 is a pleiotropic DDR protein that functions in both checkpoint activation and DNA repair, whereas BRCA2 is a mediator of the core mechanism of homologous recombination. The links between the two proteins are not well understood, but they must exist to explain the marked similarity of human cancer susceptibility that arises with germline mutations in these genes. As discussed here, the proteins work in concert to protect the genome from double-strand DNA damage during DNA replication.
Collapse
Affiliation(s)
- Rohini Roy
- Molecular Biology Program and Department of Radiation Oncology, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA
| | | | | |
Collapse
|
41
|
Wiechec E. Implications of genomic instability in the diagnosis and treatment of breast cancer. Expert Rev Mol Diagn 2011; 11:445-53. [PMID: 21545260 DOI: 10.1586/erm.11.21] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Tumorigenesis is a multistep process resulting from DNA mutations observed at the DNA sequence and chromosome level as well as epigenetic changes, which affect expression of oncogenes and tumor suppressor genes. Breast cancer is a very heterogeneous disease that manifests in various histological and clinical types. Defects in the biological action of the genome driven by various alterations, such as point mutations and chromosomal rearrangements, lead to the collapse of genome integrity, uncontrolled cell proliferation and failure in apoptotic cell death. Detailed profiling of breast cancer-associated genomic alterations is indispensable for the design of individualized anticancer therapy, by suggesting diagnostic and prognostic criteria as well as the outcome of applied treatment. Among various directions of cancer research, identification of genomic alterations in breast cancer and their translation into clinical applications is at the forefront.
Collapse
Affiliation(s)
- Emilia Wiechec
- Otto-von-Guericke University, Institute of Molecular and Clinical Immunology, Leipziger Str. 44, 39120 Magdeburg, Germany.
| |
Collapse
|
42
|
Imyanitov EN, Moiseyenko VM. Drug therapy for hereditary cancers. Hered Cancer Clin Pract 2011; 9:5. [PMID: 21819606 PMCID: PMC3171323 DOI: 10.1186/1897-4287-9-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Accepted: 08/06/2011] [Indexed: 12/20/2022] Open
Abstract
Tumors arising in patients with hereditary cancer syndromes may have distinct drug sensitivity as compared to their sporadic counterparts. Breast and ovarian neoplasms from BRCA1 or BRCA2 mutation carriers are characterized by deficient homologous recombination (HR) of DNA, that makes them particularly sensitive to platinum compounds or inhibitors of poly (ADP-ribose) polymerase (PARP). Outstandingly durable complete responses to high dose chemotherapy have been observed in several cases of BRCA-related metastatic breast cancer (BC). Multiple lines of evidence indicate that women with BRCA1-related BC may derive less benefit from taxane-based treatment than other categories of BC patients. There is virtually no reports directly assessing drug response in hereditary colorectal cancer (CRC) patients; studies involving non-selected (i.e., both sporadic and hereditary) CRC with high-level microsatellite instability (MSI-H) suggest therapeutic advantage of irinotecan. Celecoxib has been approved for the treatment of familial adenomatous polyposis (FAP). Hereditary medullary thyroid cancers (MTC) have been shown to be highly responsive to a multitargeted tyrosine kinase inhibitor vandetanib, which exerts specific activity towards mutated RET receptor. Given the rapidly improving accessibility of DNA analysis, it is foreseen that the potential predictive value of cancer-associated germ-line mutations will be increasingly considered in the future studies.
Collapse
Affiliation(s)
- Evgeny N Imyanitov
- Laboratory of Molecular Oncology, N.N. Petrov Institute of Oncology, St.-Petersburg, 197758, Russia
- Department of Oncology, St.-Petersburg Medical Academy for Postgraduate Studies, St.-Petersburg, 191015, Russia
- Department of Medical Genetics, St.-Petersburg Pediatric Medical Academy, St.-Petersburg, 194100, Russia
| | - Vladimir M Moiseyenko
- Department of Oncology, St.-Petersburg Medical Academy for Postgraduate Studies, St.-Petersburg, 191015, Russia
| |
Collapse
|
43
|
|