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Chung CH, Lee JW, Slebos RJ, Howard JD, Perez J, Kang H, Fertig EJ, Considine M, Gilbert J, Murphy BA, Nallur S, Paranjape T, Jordan RC, Garcia J, Burtness B, Forastiere AA, Weidhaas JB. A 3'-UTR KRAS-variant is associated with cisplatin resistance in patients with recurrent and/or metastatic head and neck squamous cell carcinoma. Ann Oncol 2014; 25:2230-2236. [PMID: 25081901 DOI: 10.1093/annonc/mdu367] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND A germline mutation in the 3'-untranslated region of KRAS (rs61764370, KRAS-variant: TG/GG) has previously been associated with altered patient outcome and drug resistance/sensitivity in various cancers. We examined the prognostic and predictive significance of this variant in recurrent/metastatic (R/M) head and neck squamous cell carcinoma (HNSCC). PATIENTS AND METHODS We conducted a retrospective study of 103 HNSCCs collected from three completed clinical trials. KRAS-variant genotyping was conducted for these samples and 8 HNSCC cell lines. p16 expression was determined in a subset of 26 oropharynx tumors by immunohistochemistry. Microarray analysis was also utilized to elucidate differentially expressed genes between KRAS-variant and non-variant tumors. Drug sensitivity in cell lines was evaluated to confirm clinical findings. RESULTS KRAS-variant status was determined in 95/103 (92%) of the HNSCC tumor samples and the allelic frequency of TG/GG was 32% (30/95). Three of the HNSCC cell lines (3/8) studied had the KRAS-variant. No association between KRAS-variant status and p16 expression was observed in the oropharynx subset (Fisher's exact test, P = 1.0). With respect to patient outcome, patients with the KRAS-variant had poor progression-free survival when treated with cisplatin (log-rank P = 0.002). Conversely, KRAS-variant patients appeared to experience some improvement in disease control when cetuximab was added to their platinum-based regimen (log-rank P = 0.04). CONCLUSIONS The TG/GG rs61764370 KRAS-variant is a potential predictive biomarker for poor platinum response in R/M HNSCC patients. CLINICAL TRIAL REGISTRATION NUMBERS NCT00503997, NCT00425750, NCT00003809.
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Affiliation(s)
- C H Chung
- Department of Oncology; Department of Otolaryngology-Head and Neck Surgery, Sidney Kimmel Cancer Center, Johns Hopkins University, Baltimore.
| | - J W Lee
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston
| | | | | | | | | | | | | | - J Gilbert
- Division of Hematology/Oncology, Department of Medicine, Vanderbilt University, Nashville
| | - B A Murphy
- Division of Hematology/Oncology, Department of Medicine, Vanderbilt University, Nashville
| | - S Nallur
- Department of Therapeutic Radiology
| | | | - R C Jordan
- Department of Pathology, University of California, San Francisco
| | | | - B Burtness
- Section of Medical Oncology, Department of Internal Medicine, Yale University School of Medicine, New Haven
| | | | - J B Weidhaas
- Department of Therapeutic Radiology; Department of Radiation Oncology, University of California, Los Angeles
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Chen X, Paranjape T, Stahlhut C, McVeigh T, Keane F, Nallur S, Miller N, Kerin M, Deng Y, Yao X, Zhao H, Weidhaas JB, Slack FJ. Targeted resequencing of the microRNAome and 3'UTRome reveals functional germline DNA variants with altered prevalence in epithelial ovarian cancer. Oncogene 2014; 34:2125-37. [PMID: 24909162 DOI: 10.1038/onc.2014.117] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 03/26/2014] [Indexed: 12/24/2022]
Abstract
Ovarian cancer is a major cause of cancer deaths, yet there have been few known genetic risk factors identified, the best known of which are disruptions in protein coding sequences (BRCA1 and 2). Recent findings indicate that there are powerful genetic markers of cancer risk outside of these regions, in the noncoding mRNA control regions. To identify additional cancer-associated, functional non-protein-coding sequence germline variants associated with ovarian cancer risk, we captured DNA regions corresponding to all validated human microRNAs and the 3' untranslated regions (UTRs) of ~6000 cancer-associated genes from 31 ovarian cancer patients. Multiple single-nucleotide polymorphisms in the 3'UTR of the vascular endothelial growth factor receptor/FLT1, E2F2 and PCM1 oncogenes were highly enriched in ovarian cancer patients compared with the 1000 Genome Project. Sequenom validation in a case-control study (267 cases and 89 controls) confirmed a novel variant in the PCM1 3'UTR is significantly associated with ovarian cancer (P=0.0086). This work identifies a potential new ovarian cancer locus and further confirms that cancer resequencing efforts should not ignore the study of noncoding regions of cancer patients.
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Affiliation(s)
- X Chen
- 1] Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA [2] Program in Computational Biology and Bioinformatics, Yale University School of Medicine, New Haven, CT, USA
| | - T Paranjape
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT, USA
| | - C Stahlhut
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - T McVeigh
- Discipline of Surgery, National University of Ireland Galway and Galway University, Hospitals, Galway, Ireland
| | - F Keane
- Yale University School of Medicine, New Haven, CT, USA
| | - S Nallur
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT, USA
| | - N Miller
- Discipline of Surgery, National University of Ireland Galway and Galway University, Hospitals, Galway, Ireland
| | - M Kerin
- Discipline of Surgery, National University of Ireland Galway and Galway University, Hospitals, Galway, Ireland
| | - Y Deng
- Yale Center for Analytical Sciences, Yale University School of Medicine, New Haven, CT, USA
| | - X Yao
- Yale Center for Analytical Sciences, Yale University School of Medicine, New Haven, CT, USA
| | - H Zhao
- 1] Program in Computational Biology and Bioinformatics, Yale University School of Medicine, New Haven, CT, USA [2] Department of Genetics, Yale University School of Medicine, New Haven, CT, USA [3] Department of Biostatistics, Yale School of Public Health, Yale University, New Haven, CT, USA
| | - J B Weidhaas
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT, USA
| | - F J Slack
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
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Ratner ES, Keane FK, Lindner R, Tassi RA, Paranjape T, Glasgow M, Nallur S, Deng Y, Lu L, Steele L, Sand S, Muller RU, Bignotti E, Bellone S, Boeke M, Yao X, Pecorelli S, Ravaggi A, Katsaros D, Zelterman D, Cristea MC, Yu H, Rutherford TJ, Weitzel JN, Neuhausen SL, Schwartz PE, Slack FJ, Santin AD, Weidhaas JB. A KRAS variant is a biomarker of poor outcome, platinum chemotherapy resistance and a potential target for therapy in ovarian cancer. Oncogene 2011; 31:4559-66. [PMID: 22139083 PMCID: PMC3342446 DOI: 10.1038/onc.2011.539] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Germ-line variants in the 3′ untranslated region (3′UTR) of cancer genes disrupting microRNA (miRNA) regulation have recently been associated with cancer risk. A variant in the 3′UTR of the KRAS oncogene, referred to as the KRAS-variant, is associated with both cancer risk and altered tumor biology. Here we test the hypothesis that the KRAS-variant can act as a biomarker of outcome in epithelial ovarian cancer (EOC), and investigate the cause of altered outcome in KRAS-variant positive EOC patients. As this variant appears to be associated with tumor biology, we additionally test the hypothesis that this variant can be directly targeted to impact cell survival. EOC patients with complete clinical data were genotyped for the KRAS-variant and analyzed for outcome (n=536), response to neoadjuvant chemotherapy (n=125), and platinum resistance (n=306). Outcome was separately analyzed for women with known BRCA mutations (n=79). Gene expression was analyzed on a subset of tumors with available tissue. Cell lines were employed to confirm altered sensitivity to chemotherapy with the KRAS-variant. The KRAS-variant was directly targeted through siRNA/miRNA oligonucleotides in cell lines and survival was measured. Post-menopausal EOC patients with the KRAS-variant were significantly more likely to die of ovarian cancer by multivariate analysis (HR=1.67, 95% CI=1.09–2.57, p=0.019, n=279). Possibly explaining this finding, EOC patients with the KRAS-variant were significantly more likely to be platinum resistant (OR=3.18, CI=1.31–7.72, p=0.0106, n=291). Additionally, direct targeting of the KRAS-variant led to a significant reduction in EOC cell growth and survival in vitro. These findings confirm the importance of the KRAS-variant in EOC, and indicate that the KRAS-variant is a biomarker of poor outcome in EOC likely due to platinum resistance. In addition, this work supports the hypothesis that these tumors have continued dependence on such 3′UTR lesions, and that direct targeting may be a viable future treatment approach.
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Affiliation(s)
- E S Ratner
- Department of Gynecological Oncology, Yale University, New Haven, CT, USA
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Abstract
Recently, a novel class of global gene regulators called microRNAs (miRNAs), were identified in both plants and animals. MiRNAs can reduce protein levels of their target genes with a minor impact on the target genes' mRNAs. Accumulating evidence demonstrates the importance of miRNAs in cancer. MiRNAs that are overexpressed in cancer may function as oncogenes, and miRNAs with tumour suppressor activity in normal tissue may be downregulated in cancer. Although major advances have been achieved in our understanding of cancer biology, as well as in the development of new targeted therapies, the progress in developing improved early diagnosis and screening tests has been inadequate. This results in most cancers being diagnosed in advanced stages, delaying timely treatment and leading to poor outcomes. There is intense research seeking specific molecular changes that are able to identify patients with early cancer or precursor lesions. MiRNA expression data in various cancers demonstrate that cancer cells have different miRNA profiles compared with normal cells, thus underscoring the tremendous diagnostic and therapeutic potential of miRNAs in cancer. These unique properties of miRNAs make them extremely useful potential agents for clinical diagnostics as well as in personalised care for individual patients in the future.
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Affiliation(s)
- T Paranjape
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - F J Slack
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
| | - J B Weidhaas
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut, USA
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