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Abstract
The genetic concept of synthetic lethality has now been validated clinically through the demonstrated efficacy of poly(ADP-ribose) polymerase (PARP) inhibitors for the treatment of cancers in individuals with germline loss-of-function mutations in either BRCA1 or BRCA2. Three different PARP inhibitors have now been approved for the treatment of patients with BRCA-mutant ovarian cancer and one for those with BRCA-mutant breast cancer; these agents have also shown promising results in patients with BRCA-mutant prostate cancer. Here, we describe a number of other synthetic lethal interactions that have been discovered in cancer. We discuss some of the underlying principles that might increase the likelihood of clinical efficacy and how new computational and experimental approaches are now facilitating the discovery and validation of synthetic lethal interactions. Finally, we make suggestions on possible future directions and challenges facing researchers in this field.
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Affiliation(s)
- Alan Ashworth
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA.
| | - Christopher J Lord
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
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52
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Fukumoto T, Magno E, Zhang R. SWI/SNF Complexes in Ovarian Cancer: Mechanistic Insights and Therapeutic Implications. Mol Cancer Res 2018; 16:1819-1825. [PMID: 30037854 DOI: 10.1158/1541-7786.mcr-18-0368] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 06/05/2018] [Accepted: 07/06/2018] [Indexed: 12/24/2022]
Abstract
Ovarian cancer remains the most lethal gynecologic malignancy in the developed world. Despite the unprecedented progress in understanding the genetics of ovarian cancer, cures remain elusive due to a lack of insight into the mechanisms that can be targeted to develop new therapies. SWI/SNF chromatin remodeling complexes are genetically altered in approximately 20% of all human cancers. SWI/SNF alterations vary in different histologic subtypes of ovarian cancer, with ARID1A mutation occurring in approximately 50% of ovarian clear cell carcinomas. Given the complexity and prevalence of SWI/SNF alterations, ovarian cancer represents a paradigm for investigating the molecular basis and exploring therapeutic strategies for SWI/SNF alterations. This review discusses the recent progress in understanding SWI/SNF alterations in ovarian cancer and specifically focuses on: (i) ARID1A mutation in endometriosis-associated clear cell and endometrioid histologic subtypes of ovarian cancer; (ii) SMARCA4 mutation in small cell carcinoma of the ovary, hypercalcemic type; and (iii) amplification/upregulation of CARM1, a regulator of BAF155, in high-grade serous ovarian cancer. Understanding the molecular underpinning of SWI/SNF alterations in different histologic subtypes of ovarian cancer will provide mechanistic insight into how these alterations contribute to ovarian cancer. Finally, the review discusses how these newly gained insights can be leveraged to develop urgently needed therapeutic strategies in a personalized manner.
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Affiliation(s)
- Takeshi Fukumoto
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, Pennsylvania
| | - Elizabeth Magno
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, Pennsylvania
| | - Rugang Zhang
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, Pennsylvania.
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53
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Caumanns JJ, Wisman GBA, Berns K, van der Zee AGJ, de Jong S. ARID1A mutant ovarian clear cell carcinoma: A clear target for synthetic lethal strategies. Biochim Biophys Acta Rev Cancer 2018; 1870:176-184. [PMID: 30025943 DOI: 10.1016/j.bbcan.2018.07.005] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/12/2018] [Accepted: 07/13/2018] [Indexed: 12/20/2022]
Abstract
SWI/SNF chromatin remodeling complexes play an important role in the epigenetic regulation of chromatin structure and gene transcription. Mutual exclusive subunits in the SWI/SNF complex include the DNA targeting members ARID1A and ARID1B as well as the ATPases SMARCA2 and SMARCA4. SWI/SNF complexes are mutated across many cancer types. The highest mutation incidence is found in ARID1A, primarily consisting of deleterious mutations. Current advances have reported synthetic lethal interactions with the loss of ARID1A in several cancer types. In this review, we discuss targets that are only important for tumor growth in an ARID1A mutant context. We focus on synthetic lethal strategies with ARID1A loss in ovarian clear cell carcinoma, a cancer with the highest ARID1A mutation incidence (46-57%). ARID1A directed lethal strategies that can be exploited clinically include targeting of the DNA repair proteins PARP and ATR, and the epigenetic factors EZH2, HDAC2, HDAC6 and BRD2.
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Affiliation(s)
- Joseph J Caumanns
- Department of Gynecologic Oncology, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - G Bea A Wisman
- Department of Gynecologic Oncology, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Katrien Berns
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Ate G J van der Zee
- Department of Gynecologic Oncology, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Steven de Jong
- Department of Medical Oncology, Cancer Research Centre Groningen, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands.
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54
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Khalique S, Naidoo K, Attygalle AD, Kriplani D, Daley F, Lowe A, Campbell J, Jones T, Hubank M, Fenwick K, Matthews N, Rust AG, Lord CJ, Banerjee S, Natrajan R. Optimised ARID1A immunohistochemistry is an accurate predictor of ARID1A mutational status in gynaecological cancers. J Pathol Clin Res 2018; 4:154-166. [PMID: 29659191 PMCID: PMC6065117 DOI: 10.1002/cjp2.103] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 03/29/2018] [Accepted: 04/10/2018] [Indexed: 12/30/2022]
Abstract
ARID1A is a tumour suppressor gene that is frequently mutated in clear cell and endometrioid carcinomas of the ovary and endometrium and is an important clinical biomarker for novel treatment approaches for patients with ARID1A defects. However, the accuracy of ARID1A immunohistochemistry (IHC) as a surrogate for mutation status has not fully been established for patient stratification in clinical trials. Here we tested whether ARID1A IHC could reliably predict ARID1A mutations identified by next-generation sequencing. Three commercially available antibodies - EPR13501 (Abcam), D2A8U (Cell Signaling), and HPA005456 (Sigma) - were optimised for IHC using cell line models and human tissue, and screened across a cohort of 45 gynaecological tumours. IHC was scored independently by three pathologists using an immunoreactive score. ARID1A mutation status was assessed using two independent sequencing platforms and the concordance between ARID1A mutation and protein expression was evaluated using Receiver Operating Characteristic statistics. Overall, 21 ARID1A mutations were identified in 14/43 assessable tumours (33%), the majority of which were predicted to be deleterious. Mutations were identified in 6/17 (35%) ovarian clear cell carcinomas, 5/8 (63%) ovarian endometrioid carcinomas, 2/5 (40%) endometrial carcinomas, and 1/7 (14%) carcinosarcomas. ROC analysis identified greater than 95% concordance between mutation status and IHC using a modified immunoreactive score for all three antibodies allowing a definitive cut-point for ARID1A mutant status to be calculated. Comprehensive assessment of concordance of ARID1A IHC and mutation status identified EPR13501 as an optimal antibody, with 100% concordance between ARID1A mutation status and protein expression, across different gynaecological histological subtypes. It delivered the best inter-rater agreement between all pathologists, as well as a clear cost-benefit advantage. This could allow patients to be accurately stratified based on their ARID1A IHC status into early phase clinical trials.
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MESH Headings
- Adenocarcinoma, Clear Cell/diagnosis
- Adenocarcinoma, Clear Cell/genetics
- Adenocarcinoma, Clear Cell/metabolism
- Adenocarcinoma, Clear Cell/pathology
- Adult
- Aged
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Carcinoma, Endometrioid/diagnosis
- Carcinoma, Endometrioid/genetics
- Carcinoma, Endometrioid/metabolism
- Carcinoma, Endometrioid/pathology
- DNA-Binding Proteins
- Female
- Genital Neoplasms, Female/diagnosis
- Genital Neoplasms, Female/genetics
- Genital Neoplasms, Female/metabolism
- Genital Neoplasms, Female/pathology
- Humans
- Immunohistochemistry
- Middle Aged
- Mutation
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Ovarian Neoplasms/diagnosis
- Ovarian Neoplasms/genetics
- Ovarian Neoplasms/metabolism
- Ovarian Neoplasms/pathology
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Young Adult
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Affiliation(s)
- Saira Khalique
- The Breast Cancer Now Toby Robins Research Centre, Division of Breast CancerThe Institute of Cancer ResearchLondonUK
- Division of Molecular PathologyThe Institute of Cancer ResearchLondonUK
| | - Kalnisha Naidoo
- The Breast Cancer Now Toby Robins Research Centre, Division of Breast CancerThe Institute of Cancer ResearchLondonUK
| | - Ayoma D Attygalle
- Gynaecology UnitThe Royal Marsden NHS Foundation TrustLondonUK
- Department of HistopathologyThe Royal Marsden NHS Foundation TrustLondonUK
| | - Divya Kriplani
- The Breast Cancer Now Toby Robins Research Centre, Division of Breast CancerThe Institute of Cancer ResearchLondonUK
| | - Frances Daley
- The Breast Cancer Now Toby Robins Research Centre, Division of Breast CancerThe Institute of Cancer ResearchLondonUK
| | - Anne Lowe
- The Breast Cancer Now Toby Robins Research Centre, Division of Breast CancerThe Institute of Cancer ResearchLondonUK
| | - James Campbell
- ICR Core Bioinformatics Facility, The Institute of Cancer ResearchSuttonUK
| | - Thomas Jones
- Molecular Diagnostics DepartmentThe Centre for Molecular Pathology, The Royal Marsden NHS Foundation TrustSuttonUK
| | - Michael Hubank
- Molecular Diagnostics DepartmentThe Centre for Molecular Pathology, The Royal Marsden NHS Foundation TrustSuttonUK
| | - Kerry Fenwick
- Tumour Profiling UnitThe Institute of Cancer ResearchLondonUK
| | | | - Alistair G Rust
- Tumour Profiling UnitThe Institute of Cancer ResearchLondonUK
| | - Christopher J Lord
- The Breast Cancer Now Toby Robins Research Centre, Division of Breast CancerThe Institute of Cancer ResearchLondonUK
- Division of Molecular PathologyThe Institute of Cancer ResearchLondonUK
- The CRUK Gene Function LaboratoryThe Institute of Cancer ResearchLondonUK
| | - Susana Banerjee
- Gynaecology UnitThe Royal Marsden NHS Foundation TrustLondonUK
- Division of Clinical StudiesThe Institute of Cancer ResearchLondonUK
| | - Rachael Natrajan
- The Breast Cancer Now Toby Robins Research Centre, Division of Breast CancerThe Institute of Cancer ResearchLondonUK
- Division of Molecular PathologyThe Institute of Cancer ResearchLondonUK
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55
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Köbel M, Anglesio MS, Brenton JD. You won't believe this old test … that does cheap single-cell mutation detection. J Pathol Clin Res 2018; 4:149-153. [PMID: 30003713 PMCID: PMC6065114 DOI: 10.1002/cjp2.108] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 07/10/2018] [Indexed: 01/29/2023]
Abstract
Detecting mutations in single cells from cancer specimens is now a major area of translational research. In a recent article in this journal, Khalique et al validated an immunohistochemistry assay for ARID1A that reliably identifies loss of function mutations in single cells in tissue sections. This work exemplifies best practice for developing and orthogonally validating immunohistochemical assays to provide clearly interpretable mutational results with spatial context.
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Affiliation(s)
- Martin Köbel
- Department of Pathology and Laboratory MedicineUniversity of Calgary, Foothills Medical CentreCalgaryAlbertaCanada
| | - Michael S. Anglesio
- Department of Obstetrics and GynaecologyUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - James D. Brenton
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
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56
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Cabozantinib in ovarian clear cell cancers: UnMET expectations. Gynecol Oncol 2018; 150:1-2. [PMID: 29935857 DOI: 10.1016/j.ygyno.2018.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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57
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Oku Y, Nishiya N, Tazawa T, Kobayashi T, Umezawa N, Sugawara Y, Uehara Y. Augmentation of the therapeutic efficacy of WEE1 kinase inhibitor AZD1775 by inhibiting the YAP-E2F1-DNA damage response pathway axis. FEBS Open Bio 2018; 8:1001-1012. [PMID: 29928579 PMCID: PMC5986022 DOI: 10.1002/2211-5463.12440] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 03/26/2018] [Accepted: 04/25/2018] [Indexed: 01/10/2023] Open
Abstract
The main reasons for failure of cancer chemotherapy are intrinsic and acquired drug resistance. The Hippo pathway effector Yes‐associated protein (YAP) is associated with resistance to both cytotoxic and molecular targeted drugs. Several lines of evidence indicate that YAP activates transcriptional programmes to promote cell cycle progression and DNA damage responses. Therefore, we hypothesised that YAP is involved in the sensitivity of cancer cells to small‐molecule agents targeting cell cycle‐related proteins. Here, we report that the inactivation of YAP sensitises the OVCAR‐8 ovarian cancer cell line to AZD1775, a small‐molecule WEE1 kinase inhibitor. The accumulation of DNA damage and mitotic failures induced by AZD1775‐based therapy were further enhanced by YAP depletion. YAP depletion reduced the expression of the Fanconi anaemia (FA) pathway components required for DNA repair and their transcriptional regulator E2F1. These results suggest that YAP activates the DNA damage response pathway, exemplified by the FA pathway and E2F1. Furthermore, we aimed to apply this finding to combination chemotherapy against ovarian cancers. The regimen containing dasatinib, which inhibits the nuclear localisation of YAP, improved the response to AZD1775‐based therapy in the OVCAR‐8 ovarian cancer cell line. We propose that dasatinib acts as a chemosensitiser for a subset of molecular targeted drugs, including AZD1775, by targeting YAP.
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Affiliation(s)
- Yusuke Oku
- Department of Integrated Information for Pharmaceutical Sciences Iwate Medical University School of Pharmacy Yahaba-cho Japan
| | - Naoyuki Nishiya
- Department of Integrated Information for Pharmaceutical Sciences Iwate Medical University School of Pharmacy Yahaba-cho Japan
| | - Takaaki Tazawa
- Department of Integrated Information for Pharmaceutical Sciences Iwate Medical University School of Pharmacy Yahaba-cho Japan
| | - Takaya Kobayashi
- Department of Integrated Information for Pharmaceutical Sciences Iwate Medical University School of Pharmacy Yahaba-cho Japan
| | - Nanami Umezawa
- Department of Integrated Information for Pharmaceutical Sciences Iwate Medical University School of Pharmacy Yahaba-cho Japan
| | - Yasuyo Sugawara
- Department of Integrated Information for Pharmaceutical Sciences Iwate Medical University School of Pharmacy Yahaba-cho Japan
| | - Yoshimasa Uehara
- Department of Integrated Information for Pharmaceutical Sciences Iwate Medical University School of Pharmacy Yahaba-cho Japan
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58
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Berns K, Caumanns JJ, Hijmans EM, Gennissen AMC, Severson TM, Evers B, Wisman GBA, Jan Meersma G, Lieftink C, Beijersbergen RL, Itamochi H, van der Zee AGJ, de Jong S, Bernards R. ARID1A mutation sensitizes most ovarian clear cell carcinomas to BET inhibitors. Oncogene 2018; 37:4611-4625. [PMID: 29760405 PMCID: PMC6095834 DOI: 10.1038/s41388-018-0300-6] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 03/23/2018] [Accepted: 04/10/2018] [Indexed: 12/16/2022]
Abstract
Current treatment for advanced stage ovarian clear cell cancer is severely hampered by a lack of effective systemic therapy options, leading to a poor outlook for these patients. Sequencing studies revealed that ARID1A is mutated in over 50% of ovarian clear cell carcinomas. To search for a rational approach to target ovarian clear cell cancers with ARID1A mutations, we performed kinome-centered lethality screens in a large panel of ovarian clear cell carcinoma cell lines. Using the largest OCCC cell line panel established to date, we show here that BRD2 inhibition is predominantly lethal in ARID1A mutated ovarian clear cell cancer cells. Importantly, small molecule inhibitors of the BET (bromodomain and extra terminal domain) family of proteins, to which BRD2 belongs, specifically inhibit proliferation of ARID1A mutated cell lines, both in vitro and in ovarian clear cell cancer xenografts and patient-derived xenograft models. BET inhibitors cause a reduction in the expression of multiple SWI/SNF members including ARID1B, providing a potential explanation for the observed lethal interaction with ARID1A loss. Our data indicate that BET inhibition may represent a novel treatment strategy for a subset of ARID1A mutated ovarian clear cell carcinomas.
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Affiliation(s)
- Katrien Berns
- Division of Molecular Carcinogenesis and Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands.
| | - Joseph J Caumanns
- Gynaecologic Oncology, Cancer Research Centre Groningen, University Medical Center Groningen, University of Groningen, Hanzeplein 1, Groningen, 9713 GZ, The Netherlands
| | - E Marielle Hijmans
- Division of Molecular Carcinogenesis and Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands
| | - Annemiek M C Gennissen
- Division of Molecular Carcinogenesis and Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands
| | - Tesa M Severson
- Division of Molecular Carcinogenesis and Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands
| | - Bastiaan Evers
- Division of Molecular Carcinogenesis and Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands
| | - G Bea A Wisman
- Gynaecologic Oncology, Cancer Research Centre Groningen, University Medical Center Groningen, University of Groningen, Hanzeplein 1, Groningen, 9713 GZ, The Netherlands
| | - Gert Jan Meersma
- Gynaecologic Oncology, Cancer Research Centre Groningen, University Medical Center Groningen, University of Groningen, Hanzeplein 1, Groningen, 9713 GZ, The Netherlands
| | - Cor Lieftink
- Division of Molecular Carcinogenesis and Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis and Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands
| | - Hiroaki Itamochi
- Department of Obstetrics and Gynaecology, Iwate Medical University School of Medicine, Iwate, Morioka, 020-8505, Japan
| | - Ate G J van der Zee
- Gynaecologic Oncology, Cancer Research Centre Groningen, University Medical Center Groningen, University of Groningen, Hanzeplein 1, Groningen, 9713 GZ, The Netherlands
| | - Steven de Jong
- Medical Oncology, Cancer Research Centre Groningen, University Medical Center Groningen, University of Groningen, Hanzeplein 1, Groningen, 9713 GZ, The Netherlands
| | - René Bernards
- Division of Molecular Carcinogenesis and Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands.
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59
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Bajrami I, Marlow R, van de Ven M, Brough R, Pemberton HN, Frankum J, Song F, Rafiq R, Konde A, Krastev DB, Menon M, Campbell J, Gulati A, Kumar R, Pettitt SJ, Gurden MD, Cardenosa ML, Chong I, Gazinska P, Wallberg F, Sawyer EJ, Martin LA, Dowsett M, Linardopoulos S, Natrajan R, Ryan CJ, Derksen PWB, Jonkers J, Tutt ANJ, Ashworth A, Lord CJ. E-Cadherin/ROS1 Inhibitor Synthetic Lethality in Breast Cancer. Cancer Discov 2018; 8:498-515. [PMID: 29610289 PMCID: PMC6296442 DOI: 10.1158/2159-8290.cd-17-0603] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 12/12/2017] [Accepted: 01/23/2018] [Indexed: 12/22/2022]
Abstract
The cell adhesion glycoprotein E-cadherin (CDH1) is commonly inactivated in breast tumors. Precision medicine approaches that exploit this characteristic are not available. Using perturbation screens in breast tumor cells with CRISPR/Cas9-engineered CDH1 mutations, we identified synthetic lethality between E-cadherin deficiency and inhibition of the tyrosine kinase ROS1. Data from large-scale genetic screens in molecularly diverse breast tumor cell lines established that the E-cadherin/ROS1 synthetic lethality was not only robust in the face of considerable molecular heterogeneity but was also elicited with clinical ROS1 inhibitors, including foretinib and crizotinib. ROS1 inhibitors induced mitotic abnormalities and multinucleation in E-cadherin-defective cells, phenotypes associated with a defect in cytokinesis and aberrant p120 catenin phosphorylation and localization. In vivo, ROS1 inhibitors produced profound antitumor effects in multiple models of E-cadherin-defective breast cancer. These data therefore provide the preclinical rationale for assessing ROS1 inhibitors, such as the licensed drug crizotinib, in appropriately stratified patients.Significance: E-cadherin defects are common in breast cancer but are currently not targeted with a precision medicine approach. Our preclinical data indicate that licensed ROS1 inhibitors, including crizotinib, should be repurposed to target E-cadherin-defective breast cancers, thus providing the rationale for the assessment of these agents in molecularly stratified phase II clinical trials. Cancer Discov; 8(4); 498-515. ©2018 AACR.This article is highlighted in the In This Issue feature, p. 371.
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Affiliation(s)
- Ilirjana Bajrami
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
- Cancer Research UK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
| | - Rebecca Marlow
- The Breast Cancer Now Research Unit, King's College London, London, United Kingdom
| | - Marieke van de Ven
- Mouse Clinic for Cancer and Aging (MCCA) Preclinical Intervention Unit, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Rachel Brough
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
- Cancer Research UK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
| | - Helen N Pemberton
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
- Cancer Research UK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
| | - Jessica Frankum
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
- Cancer Research UK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
| | - Feifei Song
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
- Cancer Research UK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
| | - Rumana Rafiq
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
- Cancer Research UK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
| | - Asha Konde
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
- Cancer Research UK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
| | - Dragomir B Krastev
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
- Cancer Research UK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
| | - Malini Menon
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
- Cancer Research UK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
| | - James Campbell
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
- Cancer Research UK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
| | - Aditi Gulati
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
- Cancer Research UK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
| | - Rahul Kumar
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
- Cancer Research UK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
| | - Stephen J Pettitt
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
- Cancer Research UK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
| | - Mark D Gurden
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Marta Llorca Cardenosa
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
- Biomedical Research Institute INCLIVA, Hospital Clinico Universitario Valencia, University of Valencia, Spain
| | - Irene Chong
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Patrycja Gazinska
- The Breast Cancer Now Research Unit, King's College London, London, United Kingdom
| | - Fredrik Wallberg
- FACS Core Facility, The Institute of Cancer Research, London, United Kingdom
| | - Elinor J Sawyer
- Division of Cancer Studies, Guy's Hospital, King's College London, London, United Kingdom
| | - Lesley-Ann Martin
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Mitch Dowsett
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Spiros Linardopoulos
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
- Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom
| | - Rachael Natrajan
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Colm J Ryan
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
| | - Patrick W B Derksen
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jos Jonkers
- Division of Molecular Pathology and Cancer Genomics Netherlands, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Andrew N J Tutt
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
- The Breast Cancer Now Research Unit, King's College London, London, United Kingdom
| | - Alan Ashworth
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California.
| | - Christopher J Lord
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom.
- Cancer Research UK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
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60
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Ji JX, Wang YK, Cochrane DR, Huntsman DG. Clear cell carcinomas of the ovary and kidney: clarity through genomics. J Pathol 2018; 244:550-564. [PMID: 29344971 DOI: 10.1002/path.5037] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 01/03/2018] [Accepted: 01/05/2018] [Indexed: 12/19/2022]
Abstract
Clear cell ovarian carcinoma (CCOC) and clear cell renal cell carcinoma (ccRCC) both feature clear cytoplasm, owing to the accumulation of cytoplasmic glycogen. Genomic studies have demonstrated several mutational similarities between these two diseases, including frequent alterations in the chromatin remodelling SWI-SNF and cellular proliferation phosphoinositide 3-kinase-mammalian target of rapamycin pathways, as well as a shared hypoxia-like mRNA expression signature. Although many targeted treatment options have been approved for advanced-stage ccRCC, CCOC patients are still treated with conventional platinum and taxane chemotherapy, to which they are resistant. To determine the extent of similarity between these malignancies, we performed unsupervised clustering of mRNA expression data from these cancers. This review highlights the similarities and differences between these two clear cell carcinomas to facilitate knowledge translation within future research efforts. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Jennifer X Ji
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Yi Kan Wang
- Department of Molecular Oncology, British Columbia Cancer Agency, BC, Canada
| | - Dawn R Cochrane
- Department of Molecular Oncology, British Columbia Cancer Agency, BC, Canada
| | - David G Huntsman
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.,Department of Molecular Oncology, British Columbia Cancer Agency, BC, Canada
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Jones SE, Fleuren EDG, Frankum J, Konde A, Williamson CT, Krastev DB, Pemberton HN, Campbell J, Gulati A, Elliott R, Menon M, Selfe JL, Brough R, Pettitt SJ, Niedzwiedz W, van der Graaf WTA, Shipley J, Ashworth A, Lord CJ. ATR Is a Therapeutic Target in Synovial Sarcoma. Cancer Res 2017; 77:7014-7026. [PMID: 29038346 PMCID: PMC6155488 DOI: 10.1158/0008-5472.can-17-2056] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 08/21/2017] [Accepted: 10/10/2017] [Indexed: 01/10/2023]
Abstract
Synovial sarcoma (SS) is an aggressive soft-tissue malignancy characterized by expression of SS18-SSX fusions, where treatment options are limited. To identify therapeutically actionable genetic dependencies in SS, we performed a series of parallel, high-throughput small interfering RNA (siRNA) screens and compared genetic dependencies in SS tumor cells with those in >130 non-SS tumor cell lines. This approach revealed a reliance of SS tumor cells upon the DNA damage response serine/threonine protein kinase ATR. Clinical ATR inhibitors (ATRi) elicited a synthetic lethal effect in SS tumor cells and impaired growth of SS patient-derived xenografts. Oncogenic SS18-SSX family fusion genes are known to alter the composition of the BAF chromatin-remodeling complex, causing ejection and degradation of wild-type SS18 and the tumor suppressor SMARCB1. Expression of oncogenic SS18-SSX fusion proteins caused profound ATRi sensitivity and a reduction in SS18 and SMARCB1 protein levels, but an SSX18-SSX1 Δ71-78 fusion containing a C-terminal deletion did not. ATRi sensitivity in SS was characterized by an increase in biomarkers of replication fork stress (increased γH2AX, decreased replication fork speed, and increased R-loops), an apoptotic response, and a dependence upon cyclin E expression. Combinations of cisplatin or PARP inhibitors enhanced the antitumor cell effect of ATRi, suggesting that either single-agent ATRi or combination therapy involving ATRi might be further assessed as candidate approaches for SS treatment. Cancer Res; 77(24); 7014-26. ©2017 AACR.
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Affiliation(s)
- Samuel E Jones
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, London, UK
- Sarcoma Molecular Pathology Laboratory, The Institute of Cancer Research, London, UK
| | - Emmy D G Fleuren
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, London, UK
- Clinical and Translational Sarcoma Research, The Institute of Cancer Research, London, UK
| | - Jessica Frankum
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, London, UK
| | - Asha Konde
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, London, UK
| | - Chris T Williamson
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, London, UK
| | - Dragomir B Krastev
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, London, UK
| | - Helen N Pemberton
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, London, UK
| | - James Campbell
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, London, UK
| | - Aditi Gulati
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, London, UK
| | - Richard Elliott
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, London, UK
| | - Malini Menon
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, London, UK
| | - Joanna L Selfe
- Sarcoma Molecular Pathology Laboratory, The Institute of Cancer Research, London, UK
| | - Rachel Brough
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, London, UK
| | - Stephen J Pettitt
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, London, UK
| | - Wojciech Niedzwiedz
- Cancer and Genome Instability Laboratory, The Institute of Cancer Research, London, UK
| | | | - Janet Shipley
- Sarcoma Molecular Pathology Laboratory, The Institute of Cancer Research, London, UK.
| | - Alan Ashworth
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK.
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, London, UK
| | - Christopher J Lord
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK.
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, London, UK
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Davidson B, Pinamonti M, Cuevas D, Holth A, Zeppa P, Hager T, Wohlschlaeger J, Tötsch M. The diagnostic role of PTEN and ARID1A in serous effusions. Virchows Arch 2017; 472:425-432. [DOI: 10.1007/s00428-017-2273-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 11/07/2017] [Accepted: 11/19/2017] [Indexed: 12/11/2022]
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Shibuya Y, Tokunaga H, Saito S, Shimokawa K, Katsuoka F, Bin L, Kojima K, Nagasaki M, Yamamoto M, Yaegashi N, Yasuda J. Identification of somatic genetic alterations in ovarian clear cell carcinoma with next generation sequencing. Genes Chromosomes Cancer 2017; 57:51-60. [DOI: 10.1002/gcc.22507] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 09/28/2017] [Accepted: 10/11/2017] [Indexed: 12/17/2022] Open
Affiliation(s)
- Yusuke Shibuya
- Department of Obstetrics and GynecologyTohoku University School of MedicineMiyagi Japan
| | - Hideki Tokunaga
- Department of Obstetrics and GynecologyTohoku University School of MedicineMiyagi Japan
| | - Sakae Saito
- Department of Integrative GenomicsTohoku Medical Megabank Organization, Tohoku UniversityMiyagi Japan
| | - Kazurou Shimokawa
- Department of Health Record InformaticsTohoku Medical Megabank Organization, Tohoku UniversityMiyagi Japan
| | - Fumiki Katsuoka
- Department of Integrative GenomicsTohoku Medical Megabank Organization, Tohoku UniversityMiyagi Japan
- Department of Medical BiochemistryTohoku University School of MedicineMiyagi Japan
| | - Li Bin
- Department of Obstetrics and GynecologyTohoku University School of MedicineMiyagi Japan
| | - Kaname Kojima
- Department of Integrative GenomicsTohoku Medical Megabank Organization, Tohoku UniversityMiyagi Japan
| | - Masao Nagasaki
- Department of Integrative GenomicsTohoku Medical Megabank Organization, Tohoku UniversityMiyagi Japan
| | - Masayuki Yamamoto
- Department of Integrative GenomicsTohoku Medical Megabank Organization, Tohoku UniversityMiyagi Japan
- Department of Medical BiochemistryTohoku University School of MedicineMiyagi Japan
| | - Nobuo Yaegashi
- Department of Obstetrics and GynecologyTohoku University School of MedicineMiyagi Japan
| | - Jun Yasuda
- Department of Integrative GenomicsTohoku Medical Megabank Organization, Tohoku UniversityMiyagi Japan
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Dréan A, Williamson CT, Brough R, Brandsma I, Menon M, Konde A, Garcia-Murillas I, Pemberton HN, Frankum J, Rafiq R, Badham N, Campbell J, Gulati A, Turner NC, Pettitt SJ, Ashworth A, Lord CJ. Modeling Therapy Resistance in BRCA1/2-Mutant Cancers. Mol Cancer Ther 2017; 16:2022-2034. [PMID: 28619759 PMCID: PMC6157714 DOI: 10.1158/1535-7163.mct-17-0098] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 05/02/2017] [Accepted: 06/05/2017] [Indexed: 01/02/2023]
Abstract
Although PARP inhibitors target BRCA1- or BRCA2-mutant tumor cells, drug resistance is a problem. PARP inhibitor resistance is sometimes associated with the presence of secondary or "revertant" mutations in BRCA1 or BRCA2 Whether secondary mutant tumor cells are selected for in a Darwinian fashion by treatment is unclear. Furthermore, how PARP inhibitor resistance might be therapeutically targeted is also poorly understood. Using CRISPR mutagenesis, we generated isogenic tumor cell models with secondary BRCA1 or BRCA2 mutations. Using these in heterogeneous in vitro culture or in vivo xenograft experiments in which the clonal composition of tumor cell populations in response to therapy was monitored, we established that PARP inhibitor or platinum salt exposure selects for secondary mutant clones in a Darwinian fashion, with the periodicity of PARP inhibitor administration and the pretreatment frequency of secondary mutant tumor cells influencing the eventual clonal composition of the tumor cell population. In xenograft studies, the presence of secondary mutant cells in tumors impaired the therapeutic effect of a clinical PARP inhibitor. However, we found that both PARP inhibitor-sensitive and PARP inhibitor-resistant BRCA2 mutant tumor cells were sensitive to AZD-1775, a WEE1 kinase inhibitor. In mice carrying heterogeneous tumors, AZD-1775 delivered a greater therapeutic benefit than olaparib treatment. This suggests that despite the restoration of some BRCA1 or BRCA2 gene function in "revertant" tumor cells, vulnerabilities still exist that could be therapeutically exploited. Mol Cancer Ther; 16(9); 2022-34. ©2017 AACR.
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Affiliation(s)
- Amy Dréan
- The CRUK Gene Function Laboratory and The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Chris T Williamson
- The CRUK Gene Function Laboratory and The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Rachel Brough
- The CRUK Gene Function Laboratory and The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Inger Brandsma
- The CRUK Gene Function Laboratory and The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Malini Menon
- The CRUK Gene Function Laboratory and The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Asha Konde
- The CRUK Gene Function Laboratory and The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Isaac Garcia-Murillas
- Molecular Oncology Laboratory, The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Helen N Pemberton
- The CRUK Gene Function Laboratory and The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Jessica Frankum
- The CRUK Gene Function Laboratory and The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Rumana Rafiq
- The CRUK Gene Function Laboratory and The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Nicholas Badham
- The CRUK Gene Function Laboratory and The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - James Campbell
- The CRUK Gene Function Laboratory and The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Aditi Gulati
- The CRUK Gene Function Laboratory and The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Nicholas C Turner
- Molecular Oncology Laboratory, The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Stephen J Pettitt
- The CRUK Gene Function Laboratory and The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Alan Ashworth
- The CRUK Gene Function Laboratory and The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom.
| | - Christopher J Lord
- The CRUK Gene Function Laboratory and The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom.
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Yang M, Topaloglu U, Petty WJ, Pagni M, Foley KL, Grant SC, Robinson M, Bitting RL, Thomas A, Alistar AT, Desnoyers RJ, Goodman M, Albright C, Porosnicu M, Vatca M, Qasem SA, DeYoung B, Kytola V, Nykter M, Chen K, Levine EA, Staren ED, D’Agostino RB, Petro RM, Blackstock W, Powell BL, Abraham E, Pasche B, Zhang W. Circulating mutational portrait of cancer: manifestation of aggressive clonal events in both early and late stages. J Hematol Oncol 2017; 10:100. [PMID: 28472989 PMCID: PMC5418716 DOI: 10.1186/s13045-017-0468-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 04/20/2017] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Solid tumors residing in tissues and organs leave footprints in circulation through circulating tumor cells (CTCs) and circulating tumor DNAs (ctDNA). Characterization of the ctDNA portraits and comparison with tumor DNA mutational portraits may reveal clinically actionable information on solid tumors that is traditionally achieved through more invasive approaches. METHODS We isolated ctDNAs from plasma of patients of 103 lung cancer and 74 other solid tumors of different tissue origins. Deep sequencing using the Guardant360 test was performed to identify mutations in 73 clinically actionable genes, and the results were associated with clinical characteristics of the patient. The mutation profiles of 37 lung cancer cases with paired ctDNA and tumor genomic DNA sequencing were used to evaluate clonal representation of tumor in circulation. Five lung cancer cases with longitudinal ctDNA sampling were monitored for cancer progression or response to treatments. RESULTS Mutations in TP53, EGFR, and KRAS genes are most prevalent in our cohort. Mutation rates of ctDNA are similar in early (I and II) and late stage (III and IV) cancers. Mutation in DNA repair genes BRCA1, BRCA2, and ATM are found in 18.1% (32/177) of cases. Patients with higher mutation rates had significantly higher mortality rates. Lung cancer of never smokers exhibited significantly higher ctDNA mutation rates as well as higher EGFR and ERBB2 mutations than ever smokers. Comparative analysis of ctDNA and tumor DNA mutation data from the same patients showed that key driver mutations could be detected in plasma even when they were present at a minor clonal population in the tumor. Mutations of key genes found in the tumor tissue could remain in circulation even after frontline radiotherapy and chemotherapy suggesting these mutations represented resistance mechanisms. Longitudinal sampling of five lung cancer cases showed distinct changes in ctDNA mutation portraits that are consistent with cancer progression or response to EGFR drug treatment. CONCLUSIONS This study demonstrates that ctDNA mutation rates in the key tumor-associated genes are clinical parameters relevant to smoking status and mortality. Mutations in ctDNA may serve as an early detection tool for cancer. This study quantitatively confirms the hypothesis that ctDNAs in circulation is the result of dissemination of aggressive tumor clones and survival of resistant clones. This study supports the use of ctDNA profiling as a less-invasive approach to monitor cancer progression and selection of appropriate drugs during cancer evolution.
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Affiliation(s)
- Meng Yang
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd., Winston-Salem, NC 27157 USA
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
- Department of Epidemiology and Biostatistics, Tianjin Medical University Cancer Institute and Hospital, 300060 Tianjin, China
- Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
| | - Umit Topaloglu
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd., Winston-Salem, NC 27157 USA
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
- Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
| | - W. Jeffrey Petty
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd., Winston-Salem, NC 27157 USA
- Department of Internal Medicine-Section of Hematology and Oncology, Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
- Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
| | - Matthew Pagni
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd., Winston-Salem, NC 27157 USA
- Department of Radiology, Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
- Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
| | - Kristie L. Foley
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd., Winston-Salem, NC 27157 USA
- Department of Social Sciences and Health Policy, Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
- Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
| | - Stefan C. Grant
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd., Winston-Salem, NC 27157 USA
- Department of Internal Medicine-Section of Hematology and Oncology, Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
- Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
| | - Mac Robinson
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd., Winston-Salem, NC 27157 USA
- Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
| | - Rhonda L. Bitting
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd., Winston-Salem, NC 27157 USA
- Department of Internal Medicine-Section of Hematology and Oncology, Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
- Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
| | - Alexandra Thomas
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd., Winston-Salem, NC 27157 USA
- Department of Internal Medicine-Section of Hematology and Oncology, Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
- Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
| | - Angela T. Alistar
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd., Winston-Salem, NC 27157 USA
- Department of Internal Medicine-Section of Hematology and Oncology, Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
- Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
| | - Rodwige J. Desnoyers
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd., Winston-Salem, NC 27157 USA
- Department of Internal Medicine-Section of Hematology and Oncology, Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
- Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
| | - Michael Goodman
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd., Winston-Salem, NC 27157 USA
- Department of Internal Medicine-Section of Hematology and Oncology, Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
- Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
| | - Carol Albright
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd., Winston-Salem, NC 27157 USA
- Department of Internal Medicine-Section of Hematology and Oncology, Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
- Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
| | - Mercedes Porosnicu
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd., Winston-Salem, NC 27157 USA
- Department of Internal Medicine-Section of Hematology and Oncology, Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
- Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
| | - Mihaela Vatca
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd., Winston-Salem, NC 27157 USA
- Department of Internal Medicine-Section of Hematology and Oncology, Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
- Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
| | - Shadi A. Qasem
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd., Winston-Salem, NC 27157 USA
- Department of Laboratory Medicine and Pathology, Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
- Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
| | - Barry DeYoung
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd., Winston-Salem, NC 27157 USA
- Department of Laboratory Medicine and Pathology, Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
- Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
| | - Ville Kytola
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd., Winston-Salem, NC 27157 USA
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
- Institute for Biosciences and Medical Technology, University of Tampere, 33520 Tampere, Finland
- Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
| | - Matti Nykter
- Institute for Biosciences and Medical Technology, University of Tampere, 33520 Tampere, Finland
| | - Kexin Chen
- Department of Epidemiology and Biostatistics, Tianjin Medical University Cancer Institute and Hospital, 300060 Tianjin, China
| | - Edward A. Levine
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd., Winston-Salem, NC 27157 USA
- Department of General Surgery-Section of Surgical Oncology, Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
- Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
| | - Edgar D. Staren
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd., Winston-Salem, NC 27157 USA
- Department of General Surgery-Section of Surgical Oncology, Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
- Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
| | - Ralph B. D’Agostino
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd., Winston-Salem, NC 27157 USA
- Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
- Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
| | - Robin M. Petro
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd., Winston-Salem, NC 27157 USA
- Department of Internal Medicine-Section of Hematology and Oncology, Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
- Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
| | - William Blackstock
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd., Winston-Salem, NC 27157 USA
- Department of Radiation Oncology, Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
- Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
| | - Bayard L. Powell
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd., Winston-Salem, NC 27157 USA
- Department of Internal Medicine-Section of Hematology and Oncology, Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
- Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
| | - Edward Abraham
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd., Winston-Salem, NC 27157 USA
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
- Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
| | - Boris Pasche
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd., Winston-Salem, NC 27157 USA
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
- Department of Internal Medicine-Section of Hematology and Oncology, Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
- Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
| | - Wei Zhang
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd., Winston-Salem, NC 27157 USA
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
- Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
- Cancer Genomics and Precision Medicine, Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC 27157 USA
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Clinical factors of response in patients with advanced ovarian cancer participating in early phase clinical trials. Eur J Cancer 2017; 76:52-59. [DOI: 10.1016/j.ejca.2017.01.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 01/25/2017] [Indexed: 01/09/2023]
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Mammalian SWI/SNF complexes in cancer: emerging therapeutic opportunities. Curr Opin Genet Dev 2017; 42:56-67. [PMID: 28391084 DOI: 10.1016/j.gde.2017.02.004] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 01/23/2017] [Accepted: 02/07/2017] [Indexed: 02/08/2023]
Abstract
Mammalian SWI/SNF (BAF) chromatin remodeling complexes orchestrate a diverse set of chromatin alterations which impact transcriptional output. Recent whole-exome sequencing efforts have revealed that the genes encoding subunits of mSWI/SNF complexes are mutated in over 20% of cancers, spanning a wide range of tissue types. The majority of mutations result in loss of subunit protein expression, implicating mSWI/SNF subunits as tumor suppressors. mSWI/SNF-deficient cancers remain a therapeutic challenge, owing to a lack of potent and selective agents which target complexes or unique pathway dependencies generated by mSWI/SNF subunit perturbations. Here, we review the current landscape of mechanistic insights and emerging therapeutic opportunities for human malignancies driven by mSWI/SNF complex perturbation.
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Cherniack AD, Shen H, Walter V, Stewart C, Murray BA, Bowlby R, Hu X, Ling S, Soslow RA, Broaddus RR, Zuna RE, Robertson G, Laird PW, Kucherlapati R, Mills GB, Weinstein JN, Zhang J, Akbani R, Levine DA. Integrated Molecular Characterization of Uterine Carcinosarcoma. Cancer Cell 2017; 31:411-423. [PMID: 28292439 PMCID: PMC5599133 DOI: 10.1016/j.ccell.2017.02.010] [Citation(s) in RCA: 264] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 09/20/2016] [Accepted: 02/14/2017] [Indexed: 01/01/2023]
Abstract
We performed genomic, epigenomic, transcriptomic, and proteomic characterizations of uterine carcinosarcomas (UCSs). Cohort samples had extensive copy-number alterations and highly recurrent somatic mutations. Frequent mutations were found in TP53, PTEN, PIK3CA, PPP2R1A, FBXW7, and KRAS, similar to endometrioid and serous uterine carcinomas. Transcriptome sequencing identified a strong epithelial-to-mesenchymal transition (EMT) gene signature in a subset of cases that was attributable to epigenetic alterations at microRNA promoters. The range of EMT scores in UCS was the largest among all tumor types studied via The Cancer Genome Atlas. UCSs shared proteomic features with gynecologic carcinomas and sarcomas with intermediate EMT features. Multiple somatic mutations and copy-number alterations in genes that are therapeutic targets were identified.
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Affiliation(s)
- Andrew D Cherniack
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Hui Shen
- Van Andel Research Institute, Center for Epigenetics, Grand Rapids, MI 49503, USA
| | - Vonn Walter
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Chip Stewart
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Bradley A Murray
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Reanne Bowlby
- Canada's Michael Smith Genome Sciences Center, BC Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Xin Hu
- The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Shiyun Ling
- The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Robert A Soslow
- Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Russell R Broaddus
- The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rosemary E Zuna
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Gordon Robertson
- Canada's Michael Smith Genome Sciences Center, BC Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Peter W Laird
- Van Andel Research Institute, Center for Epigenetics, Grand Rapids, MI 49503, USA
| | | | - Gordon B Mills
- The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - John N Weinstein
- The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Rehan Akbani
- The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Douglas A Levine
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY 10016, USA.
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Abstract
In the past few years, it has become clear that mutations in epigenetic regulatory genes are common in human cancers. Therapeutic strategies are now being developed to target cancers with mutations in these genes using specific chemical inhibitors. In addition, a complementary approach based on the concept of synthetic lethality, which allows exploitation of loss-of-function mutations in cancers that are not targetable by conventional methods, has gained traction. Both of these approaches are now being tested in several clinical trials. In this Review, we present recent advances in epigenetic drug discovery and development, and suggest possible future avenues of investigation to drive progress in this area.
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Morel D, Almouzni G, Soria JC, Postel-Vinay S. Targeting chromatin defects in selected solid tumors based on oncogene addiction, synthetic lethality and epigenetic antagonism. Ann Oncol 2017; 28:254-269. [DOI: 10.1093/annonc/mdw552] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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Affiliation(s)
- Paul H Huang
- a Division of Cancer Biology , The Institute of Cancer Research , London , UK
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