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Wang Y, Bernhardy AJ, Cruz C, Krais JJ, Nacson J, Nicolas E, Peri S, van der Gulden H, van der Heijden I, O'Brien SW, Zhang Y, Harrell MI, Johnson SF, Candido Dos Reis FJ, Pharoah PDP, Karlan B, Gourley C, Lambrechts D, Chenevix-Trench G, Olsson H, Benitez JJ, Greene MH, Gore M, Nussbaum R, Sadetzki S, Gayther SA, Kjaer SK, D'Andrea AD, Shapiro GI, Wiest DL, Connolly DC, Daly MB, Swisher EM, Bouwman P, Jonkers J, Balmaña J, Serra V, Johnson N. The BRCA1-Δ11q Alternative Splice Isoform Bypasses Germline Mutations and Promotes Therapeutic Resistance to PARP Inhibition and Cisplatin. Cancer Res 2017; 76:2778-90. [PMID: 27197267 DOI: 10.1158/0008-5472.can-16-0186] [Citation(s) in RCA: 184] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 02/15/2016] [Indexed: 12/19/2022]
Abstract
Breast and ovarian cancer patients harboring BRCA1/2 germline mutations have clinically benefitted from therapy with PARP inhibitor (PARPi) or platinum compounds, but acquired resistance limits clinical impact. In this study, we investigated the impact of mutations on BRCA1 isoform expression and therapeutic response. Cancer cell lines and tumors harboring mutations in exon 11 of BRCA1 express a BRCA1-Δ11q splice variant lacking the majority of exon 11. The introduction of frameshift mutations to exon 11 resulted in nonsense-mediated mRNA decay of full-length, but not the BRCA1-Δ11q isoform. CRISPR/Cas9 gene editing as well as overexpression experiments revealed that the BRCA1-Δ11q protein was capable of promoting partial PARPi and cisplatin resistance relative to full-length BRCA1, both in vitro and in vivo Furthermore, spliceosome inhibitors reduced BRCA1-Δ11q levels and sensitized cells carrying exon 11 mutations to PARPi treatment. Taken together, our results provided evidence that cancer cells employ a strategy to remove deleterious germline BRCA1 mutations through alternative mRNA splicing, giving rise to isoforms that retain residual activity and contribute to therapeutic resistance. Cancer Res; 76(9); 2778-90. ©2016 AACR.
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Affiliation(s)
- Yifan Wang
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Andrea J Bernhardy
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Cristina Cruz
- High Risk and Cancer Prevention Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain. Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - John J Krais
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Joseph Nacson
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Emmanuelle Nicolas
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Suraj Peri
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | | | | | - Shane W O'Brien
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Yong Zhang
- Immune Cell Development and Host Defense Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Maribel I Harrell
- Department of Obstetrics and Gynecology and Medicine, University of Washington, Seattle, Washington
| | - Shawn F Johnson
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Francisco J Candido Dos Reis
- Department of Gynecology and Obstetrics, Ribeirao Preto Medical School, University of Sao Paulo, Sao Paulo, Brazil. Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Beth Karlan
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Charlie Gourley
- University of Edinburgh Cancer Research UK Centre, MRC IGMM, Edinburgh, United Kingdom
| | | | | | - Håkan Olsson
- Departments of Cancer Epidemiology and Oncology, Lund University, Lund, Sweden
| | - Javier J Benitez
- Human Genetics Group and Human Genotyping Unit Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Mark H Greene
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
| | - Martin Gore
- Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Robert Nussbaum
- University of California San Francisco, Cancer Risk Program, San Francisco, California
| | - Siegal Sadetzki
- Gertner Institute for Epidemiology and Health Policy Research, Sheba Medical Center, Tel Hashomer, Israel
| | - Simon A Gayther
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California
| | - Susanne K Kjaer
- Department of Virus, Lifestyle and Genes, Danish Cancer Society Research Center, Copenhagen, Denmark
| | | | - Alan D D'Andrea
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts. Department of Pediatrics, Children's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Geoffrey I Shapiro
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts. Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - David L Wiest
- Immune Cell Development and Host Defense Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Denise C Connolly
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Mary B Daly
- Risk Assessment Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Elizabeth M Swisher
- Department of Obstetrics and Gynecology and Medicine, University of Washington, Seattle, Washington
| | - Peter Bouwman
- Division of Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Jos Jonkers
- Division of Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Judith Balmaña
- High Risk and Cancer Prevention Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Violeta Serra
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Neil Johnson
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania.
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Krimmel JD, Schmitt MW, Kennedy SR, Harrell MI, Agnew KJ, Loeb LA, Swisher EM, Risques RA. Abstract AP05: ULTRA–DEEP SEQUENCING DETECTS OVARIAN CANCER CELLS IN PERITONEAL FLUID AND REVEALS SOMATIC TP53 MUTATIONS IN NON–CANCEROUS TISSUES. Clin Cancer Res 2017. [DOI: 10.1158/1557-3265.ovcasymp16-ap05] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
High–grade serous ovarian carcinoma (HGSOC), the most common and most aggressive type of ovarian cancer, is characterized by near–universal prevalence of TP53 mutations, even at the early stages of the disease. Thus, the detection of tumor–specific TP53 mutations in clinical samples could potentially enable early cancer detection, monitoring, and screening. A main limitation, however, is the high error rate of conventional DNA sequencing technologies (estimated at 1 in 1000 nucleotides), which precludes the identification of low frequency tumor mutant molecules from technical error. Duplex Sequencing is a next–generation sequencing technology that uniquely tags each strand of a DNA molecule and quantifies mutations only when present in both strands of DNA. This reduces the error rate of sequencing to 1 in 10 million nucleotides, an unprecedented sensitivity that could enable the detection of extremely low frequency tumor mutant molecules by ultra–deep sequencing. The goal of this study was to provide proof–of–principle of the ability of Duplex Sequencing to detect extremely rare TP53 mutated cancer cells disseminated into the peritoneal cavity of women with HGSOC. We analyzed 17 peritoneal fluid samples from women with HGSOC and known TP53 tumor mutation (cases) and 20 peritoneal fluid samples from women without cancer (controls). The tumor–specific TP53 mutation was detected in matched peritoneal fluid from 94% of women with HGSOC (16/17), including 2 patients with occult tubal intraepithelial neoplasia, 7 patients with early stage HGSOC, and 8 with negative peritoneal fluid cytopathology. Tumor–specific alleles were detected as low as 1 mutant molecule per 24,737 normal genomes. Additionally, we detected extremely low–frequency TP53 mutations (median mutant fraction 1/13,139) in peritoneal fluid from nearly all patients with and without cancer (35/37). These mutations were mostly deleterious, clustered in hotspots, increased with age, and were more abundant in women with cancer than in controls. The total burden of TP53 mutations in peritoneal fluid distinguished cases from controls with 82% sensitivity (14/17) and 90% specificity (18/20). Age–associated, low frequency TP53 mutations were also found in 100% of matched peripheral blood samples from 15 women with and without ovarian cancer (none with hematologic cancer). Our results demonstrate the ability of Duplex Sequencing to detect very rare cancer cells and provide evidence of widespread, low frequency, age–associated somatic TP53 mutation in non–cancerous tissue. These mutations likely represent a premalignant mutational background that accumulates in cancer and aging.
Citation Format: Krimmel JD, Schmitt MW, Kennedy SR, Harrell MI, Agnew KJ, Loeb LA, Swisher EM, Risques RA. ULTRA–DEEP SEQUENCING DETECTS OVARIAN CANCER CELLS IN PERITONEAL FLUID AND REVEALS SOMATIC TP53 MUTATIONS IN NON–CANCEROUS TISSUES [abstract]. In: Proceedings of the 11th Biennial Ovarian Cancer Research Symposium; Sep 12-13, 2016; Seattle, WA. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(11 Suppl):Abstract nr AP05.
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Affiliation(s)
- JD Krimmel
- 1Department of Pathology, University of Washington, Seattle, WA, USA
| | - MW Schmitt
- 1Department of Pathology, University of Washington, Seattle, WA, USA
- 3Division of Medical Oncology, University of Washington, Seattle, WA, USA
| | - SR Kennedy
- 1Department of Pathology, University of Washington, Seattle, WA, USA
| | - MI Harrell
- 2Department of Obstetrics and Gynecology, University of Washington, Seattle, WA, USA
| | - KJ Agnew
- 2Department of Obstetrics and Gynecology, University of Washington, Seattle, WA, USA
| | - LA Loeb
- 1Department of Pathology, University of Washington, Seattle, WA, USA
| | - EM Swisher
- 2Department of Obstetrics and Gynecology, University of Washington, Seattle, WA, USA
| | - RA Risques
- 1Department of Pathology, University of Washington, Seattle, WA, USA
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Krimmel JD, Schmitt MW, Kennedy SR, Harrell MI, Agnew KJ, Loeb LA, Swisher EM, Risques RA. Abstract 445: Ultra-deep sequencing detects ovarian cancer cells in peritoneal fluid and reveals somatic TP53 mutations in noncancerous tissues. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The detection of subclonal tumor-specific somatic mutations in clinical samples could revolutionize cancer diagnostics, but is limited by insufficiently sensitive sequencing methods. Duplex Sequencing is a novel next-generation sequencing (NGS) technology that implements single-molecule barcoding of both strands of DNA to allow internal error correction. This modification reduces the error rate of NGS from 1 in 1000 to less than 1 in 10 million nucleotides, an unprecedented sensitivity that enables accurate ultra-deep sequencing for clinical applications. In this study we sought to determine whether Duplex Sequencing could detect extremely rare TP53 mutated cancer cells disseminated into the peritoneal cavity of women with high-grade serous ovarian carcinoma (HGSOC). HGSOC is the most common and most aggressive type of ovarian cancer, shows early transperitoneal dissemination, and is characterized by near-universal prevalence of driver TP53 mutations. We analyzed 17 peritoneal fluid samples from women with HGSOC and known TP53 tumor mutation (cases) and 20 peritoneal fluid samples from women without cancer (controls). The tumor-specific TP53 mutation was detected in matched peritoneal fluid from 94% of cases (16/17), including 2 patients with occult tubal intraepithelial neoplasia, 7 patients with early stage HGSOC, and 8 with negative peritoneal fluid cytopathology. Tumor-specific alleles were detected as low as <1/25,000. Surprisingly, we also detected additional extremely low-frequency somatic TP53 mutations in peritoneal fluid from nearly all (35/37) cases and controls. These mutations were more abundant in cases than in controls, and in the latter correlated with age. The total burden of somatic TP53 mutations (tumor specific and non-specific) in a peritoneal fluid sample could distinguish cases from controls with 82% sensitivity (14/17) and 90% specificity (18/20). Duplex Sequencing also revealed low-frequency, age-associated somatic TP53 mutations in 100% (15/15) of matched peripheral blood samples. Our results demonstrate the ability of Duplex Sequencing to detect very rare cancer cells, but also provide evidence of widespread, low frequency somatic TP53 mutation in non-cancerous tissue. This compromises the specificity of TP53 mutation tests for cancer detection in liquid biopsies.
Citation Format: Jeffrey D. Krimmel, Michael W. Schmitt, Scott R. Kennedy, Maribel I. Harrell, Kathy J. Agnew, Larry A. Loeb, Elizabeth M. Swisher, Rosa Ana Risques. Ultra-deep sequencing detects ovarian cancer cells in peritoneal fluid and reveals somatic TP53 mutations in noncancerous tissues. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 445.
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