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Journal of Clinical Oncology, Vol 26, No 18 (June 20), 2008: pp. 2952-2958 © 2008 American Society of Clinical Oncology. DOI: 10.1200/JCO.2007.13.5806 ERCC5 Is a Novel Biomarker of Ovarian Cancer Prognosis
From the Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, and Department of Medicine, Division of Hematologic Oncology, Cedars-Sinai Women's Cancer Research Institute at the Samuel Oschin Comprehensive Cancer Institute, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, CA; and Department of Hematology/Oncology, Graduate School of Medicine, University of Tokyo, Hongo, Tokyo, Japan Corresponding author: Christine Walsh, MD, MS, Cedars-Sinai Medical Center, 8700 Beverly Blvd, Suite 160W, Los Angeles, CA 90048; e-mail: walshc{at}cshs.org
Purpose To identify a biomarker of ovarian cancer response to chemotherapy. Patients and Methods Study participants had epithelial ovarian cancer treated with surgery followed by platinum-based chemotherapy. DNA and RNA were isolated from frozen tumors and normal DNA was isolated from matched peripheral blood. A whole-genome loss of heterozygosity (LOH) analysis was performed using a high-density oligonucleotide array. Candidate genomic areas that predicted enhanced response to chemotherapy were identified with Cox proportional hazards methods. Gene expression analyses were performed through microarray experiments. Candidate genes were tested for independent effects on survival using Cox proportional hazards models, Kaplan-Meier survival curves, and the log-rank test. Results Using a whole-genome approach to study the molecular determinants of ovarian cancer response to platinum-based chemotherapy, we identified LOH of a 13q region to predict prolonged progression-free survival (PFS; hazard ratio, 0.23; P = .006). ERCC5 was identified as a candidate gene in this region because of its known function in the nucleotide excision repair pathway, the unique DNA repair pathway that removes platinum-DNA adducts. We found LOH of the ERCC5 gene locus and downregulation of ERCC5 gene expression to predict prolonged PFS. Integration of genomic and gene expression data shows a correlation between 13q LOH and ERCC5 gene downregulation. Conclusion ERCC5 is a novel biomarker of ovarian cancer prognosis and a potential therapeutic target of ovarian cancer response to platinum chemotherapy.
Epithelial ovarian cancer is one of the most platinum-sensitive solid malignancies, with 70% of patients achieving a complete clinical remission after front-line therapy with a platinum-based chemotherapeutic regimen.1 However, despite this initial success, approximately 50% of patients will develop recurrent disease within 3 years of diagnosis.2 Paradoxically, although most patients initially respond to platinum chemotherapy, the majority eventually die from chemotherapy-resistant disease.3,4 The identification of molecular agents that effectively target the mechanisms of chemotherapy resistance could represent a significant advancement in our ability to treat these often fatal malignancies.5 In this study, we approached the question of response to platinum chemotherapy through an analysis of the genetic changes occurring in ovarian cancer. All patients in the analysis underwent standard surgical cytoreduction followed by an adjuvant platinum-based regimen, allowing us to probe for potential genetic markers of platinum-sensitivity. Using a whole-genome approach, we found loss of heterozygosity (LOH) at a 13q region to strongly predict prolonged progression-free survival (PFS). Within this region, we identified the ERCC5 gene, which encodes the XPG protein. XPG is a key member of nucleotide excision repair (NER) pathway, the DNA repair mechanism responsible for removing bulky DNA adducts. We hypothesized that a loss of XPG function would be correlated with diminished ability to repair platinum-induced DNA damage, enhanced platinum-sensitivity, and prolonged PFS. We found associations between LOH of 13q, which is the ERCC5 gene locus, and prolonged PFS, ERCC5 downregulation and prolonged PFS, as well as a correlation between LOH of 13q and ERCC5 gene downregulation. Our findings lend support to prior work that has suggested the importance of the NER pathway in response to platinum-based chemotherapy and suggests ERCC5 (XPG) as a novel candidate biomarker of ovarian cancer response to platinum chemotherapy. Further work on this pathway may validate XPG as a diagnostic marker and/or lead to the development of a therapeutic agent that specifically targets XPG activity for the sensitization of platinum-resistant malignancies.
Patient Samples All patient samples were collected at Cedars-Sinai Medical Center using protocols approved by the Cedars-Sinai institutional review board. After patients provided informed consent, fresh tumor tissue was snap-frozen in liquid nitrogen and stored in a –80°C freezer. Study participants were treated with surgical cytoreduction followed by platinum-based chemotherapy regimen and had corresponding clinical and follow-up information. DNA was isolated from frozen tumor samples using the Qiagen DNeasy Tissue Protocol (QIAGEN, Valencia, CA). RNA was isolated from frozen tumor samples using the RNeasy kit (QIAGEN). Genomic DNA was isolated from matched peripheral-blood samples using a standard phenol chloroform extraction method. DNA and RNA quantities were measured with the Nanodrop spectrophotometer (Thermo Scientific, Wilmington, DE). RNA quality was determined through separation by capillary electrophoresis on the Agilent 2000 Bioanalyzer (Agilent Technologies, Foster City, CA). Microarray analysis was performed with high-quality RNA, defined as an RNA integrity number greater than 8.
DNA Genomic Analysis Using GeneChip Mapping 50K High-Density Oligonucleotide Array
GeneChip Data Analysis A discrete variable was created for each genomic block affected by LOH in at least 20% of cases. In all, 106 LOH variables were defined across the tumor genome and each was tested as a predictor affecting PFS. Cox proportional hazards methods were used to determine hazard ratios (HR) for each variable. Associations were reported if the two-sided P values were less than .05. Multivariate Cox models were generated to control for the effects of confounding factors. As this was an exploratory analysis, corrections were not made for multiple testing.
Identification of Candidate Genes
LOH Analysis at Candidate Gene Locus
Gene Expression Analysis
Quantitative PCR Validation of Gene Expression
Study Overview and Patient Characteristics A whole-genome analysis of the genetic changes occurring in the DNA of 20 tumors was performed to identify candidate regions that predicted improved response to treatment. Effect of LOH at the candidate gene locus was analyzed in 52 total samples. Association of RNA expression levels with prognosis was tested in 90 tumors. Patient characteristics among the three data sets are listed in Table 1. All patients were treated with initial cytoreductive surgery followed by adjuvant chemotherapy with a platinum-containing regimen. PFS was defined as the time from date of primary cytoreductive surgery to the date of first clinical evidence of recurrence. Overall survival was defined as the time from date of primary cytoreductive surgery to the date of death or censored at the date of last follow-up.
Characterization of Genomic Abnormalities in Ovarian Cancer DNA Appendix Figure A1A (online only) is a representative example of how the visual output from the CNAG software program was converted into a color-coded graphical representation of genetic changes (amplification, deletion, or uniparental disomy). This method allowed us to summarize the genetic heterogeneity and complexity occurring over the 20 ovarian cancer samples (Appendix Fig A1B). A similar summary graph demonstrates the frequency of LOH in the ovarian tumor genomes (Appendix Fig A1C). The LOH data were further summarized in a frequency plot demonstrating the proportion of cases affected by LOH at each genomic locus (Appendix Fig A1D).
Predictors of Prolonged PFS
A Candidate Gene That May Predict Response to Platinum Chemotherapy The 48-MB region on 13q (54 to 102 MB) contains 73 genes (Appendix Table A1, online only), including ERCC5. We felt this gene deserved further study given its role in the NER pathway, the unique DNA repair pathway that allows cells to remove platinum adducts from DNA. We hypothesized that LOH of this 13q region leads to downregulation of ERCC5 levels, a diminished capacity of tumor cells to recover from platinum-based chemotherapy (enhanced chemotherapy sensitivity), and prolonged PFS.
Effect of LOH of ERCC Gene Locus on Survival Among the 54 samples genotyped, 29 (54%) had no LOH, 13 (24%) had LOH, and 12 (22%) were noninformative. LOH at the ERCC5 locus (13 of 42) demonstrated a trend toward improved PFS (Fig 1A). A subset analysis limited to the stage IIC to IIIC papillary serous tumors (nine of 29) demonstrated a significant improvement in PFS (Fig 1B).
At the time of second-look surgery, patients with LOH at the ERCC5 locus were significantly more likely to have a pathologic complete response (five of six; 83%) than those without LOH (two of eight; 25%; P = .03).
Effect of ERCC Gene Expression on Survival
Table 3 demonstrates the results from Cox proportional hazards regression models. On univariate analysis, a beneficial impact on PFS is seen with ERCC5 downregulation (HR = 0.44; P = .01), but not with downregulation of any other single ERCC gene. On multivariate analysis, ERCC5 downregulation retains an independent beneficial impact on PFS (HR = 0.49; P = .03).
Correlation Between ERCC5 LOH and Gene Expression Levels Forty tumors with DNA and RNA data were analyzed for correlation between LOH of the 13q (ERCC5) locus and ERCC5 expression levels. Expression levels are lower in the group of tumors with LOH (mean fold change, –0.59; median –1.12) compared with the tumors without LOH (mean fold change, +0.84; median, +1.03; P = .08). This suggests possible biologic validity of ERCC5 as a target gene within the 13q region.
Our study identifies ERCC5 as a novel candidate biomarker of ovarian cancer sensitivity to platinum chemotherapy. This conclusion is supported on several different levels. We found LOH of the 13q locus containing ERCC5 to predict prolonged PFS among platinum-treated patients with ovarian cancer. Additional genotyping also confirmed an association between LOH of the ERCC5 gene locus and improved survival. Furthermore, downregulation of ERCC5 mRNA expression levels also predicted prolonged PFS in an independent data set. Finally, the correlation between LOH of the ERCC5 genomic locus with downregulation of ERCC5 mRNA levels among the subset of tumors with integrated genomic and gene expression data suggests possible biologic plausibility of ERCC5 being a target gene in the 13q LOH region. Further biologic plausibility is apparent when placing these findings in the context of previous knowledge and work. Defective DNA repair pathways allow tolerance to DNA damage, permitting an accelerated rate of mutagenesis and neoplastic transformation. This characteristic turns to the disadvantage of the cancer cell when DNA damaging cancer therapies are administered, leading to an enhanced response to treatment.8 We have found evidence to support the hypothesis that a downregulation of ERCC5 activity leads to enhanced platinum chemotherapy sensitivity in ovarian cancer. This is provocative when considering the function of ERCC5 in the NER pathway, the unique DNA repair pathway that repairs DNA damage caused by platinum agents. NER recognizes and repairs bulky, helix-distorting adducts, such as those formed by cisplatin and its analogs.9,10 A complex of proteins assembles, binds bulky DNA damage, incises the oligonucleotide fragment containing the damaged base, and fills in the resulting gap.11,12 Platinum-resistant cells are able to more effectively remove cisplatin-DNA adducts through the action of a functional NER pathway and thus escape apoptosis. ERCC5 (XPG) is a structure-specific endonuclease, which participates in two incision steps that are critical to the DNA repair process. XPG cleaves the damaged DNA 3' to the damaged site, nonenzymatically participates in the 5' incision mediated by the XPF/ERCC1 heterodimer, and stabilizes the DNA repair complex to the damaged DNA.13-16 XPG is critical to both subpathways of NER: transcription-coupled repair (TCR), which specifically targets and repairs DNA damage on the transcribed strand of actively expressed genes, and global genomic repair (GGR), which removes DNA damage from the remaining genome.17 TCR and GGR each have a unique mechanism for recognizing DNA damage, then progress along a common pathway that requires XPG.11,12 A number of studies provide evidence for the role of the NER pathway in cellular response to platinum chemotherapy, consistently demonstrating platinum-resistance with enhanced NER activity and platinum-sensitivity with diminished NER activity. Cisplatin-resistant cells have been shown to have increased levels of XPA mRNA,18 overexpression of ERCC1 or ERCC1/XPF,19 increased activity of ERCC1/XPD,20 and increased XPC and ERCC1 levels.21 Hypersensitivity of some cell lines may be related to reduced expression of XPG or XPA.9 Inhibition of ERCC1 activity with antisense oligonucleotides enhances cisplatin sensitivity in ovarian cancer cell lines.22 Cells with deficiencies in GGR-specific factors (XPC) display normal resistance to cisplatin, whereas cells with deficiencies in TCR-specific (CSA, CSB) or common pathway proteins (XPA, XPD, XPF, XPG) are markedly hypersensitive to cisplatin.23 The excellent response rates of testicular cancer to cisplatin may be due to a high rate of NER deficiencies.24 Our study adds to this body of literature, suggesting that loss of ERCC5 function occurs naturally during the carcinogenic process of a subset of ovarian cancers and consequently leads to inherent platinum chemotherapy sensitivity. This speculation is supported by the finding of LOH of regions harboring NER genes occurring at a higher frequency in ovarian cancers (62%) than in other solid tumors, such as colon or lung cancer.25 Ours is not the first study to report frequent LOH of the 13q locus in epithelial ovarian cancer.26 Our findings have important prognostic and therapeutic implications. Tumors with dysfunctional ERCC5 expression would be predicted to demonstrate sensitivity to platinum-based therapy. ERCC5 (XPG) may be an appropriate target for therapeutic inhibition in platinum-resistant ovarian cancers. XPG is a critical component of the rate-limiting damage recognition/excision step of NER27 and is expressed at lower cellular protein levels than other NER factors.28 XPG levels are correlated with cytotoxicity to cisplatin and irofulven and with cellular NER activity,28 potentially making it an attractive therapeutic target. A recent integrated analysis of array CGH and gene expression profiling data in testicular cancers also found ERCC5 to be both lost and downregulated.29 Ovarian cancer and testicular cancer share the quality of platinum chemotherapy sensitivity, and data are emerging to suggest that NER dysfunction (particularly ERCC5) may be another shared characteristic. Further work may lead to the development of a specific XPG inhibitor that can sensitize platinum-resistant tumors to the effects of platinum chemotherapy. Platinum drugs demonstrate activity in a wide range of tumors, including ovarian, cervical, testicular, head and neck, and non–small-cell lung cancer,30 but their use is often limited by the development of resistance. A number of complex pathways are involved, including decreased drug uptake into the cell, increased drug inactivation, and increased DNA repair.31 Further insights into these mechanisms could be used to develop rational biologic therapies that target platinum resistance.32
The author(s) indicated no potential conflicts of interest.
Conception and design: Christine S. Walsh, Dennis J. Slamon, H. Phillip Koeffler, Beth Y. Karlan Financial support: Seishi Ogawa, Dennis J. Slamon, H. Phillip Koeffler, Beth Y. Karlan Provision of study materials or patients: Beth Y. Karlan Collection and assembly of data: Christine S. Walsh, Hisae Karahashi, Daniel R. Scoles, James C. Pavelka, Hang Tran, Charles Ginther, Judy Dering, Masashi Sanada, Yasuhito Nannya Data analysis and interpretation: Christine S. Walsh, Seishi Ogawa, Carl W. Miller, Norihiko Kawamata Manuscript writing: Christine S. Walsh Final approval of manuscript: Christine S. Walsh, Seishi Ogawa, Hisae Karahashi, Daniel R. Scoles, James C. Pavelka, Carl W. Miller, Norihiko Kawamata, Charles Ginther, Judy Dering, Masashi Sanada, Yasuhito Nannya, Dennis J. Slamon, H. Phillip Koeffler, Beth Y. Karlan
We thank Jenny Gross for administrative support in this research.
Supported by Borden Family Foundation (D.R.S., H.K.), Milken Family Foundation (C.S.W., B.Y.K.), Pacific Ovarian Cancer Foundation (Grant No. P50 CA83636; Principal Investigator, Nicole Urban; Carerr Development Grant to C.S.W.), General Clinical Research Center Grant No. M01-RR00425 (C.S.W.), Revlon/University of California at Los Angeles Women's Cancer Research Program (D.J.S.), Entertainment Industries Foundation (D.J.S.), and Grant-in-Aid for Scientific Research supported by the Japan Society for the Promotion of Science (S.O.). Presented in part at the 11th Biennial Meeting of the International Gynecologic Cancer Society, October 14-18, 2006, Santa Monica, CA, and the 38th Annual Meeting of the Society of Gynecologic Oncologists, March 3-7, 2007, San Diego, CA. Authors disclosures of potential conflicts of interest and author contributions are found at the end of this article.
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Copyright © 2008 by the American Society of Clinical Oncology, Online ISSN: 1527-7755. Print ISSN: 0732-183X
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