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Poynter JN, Bestrashniy JRBM, Silverstein KAT, Hooten AJ, Lees C, Ross JA, Tolar J. Cross platform analysis of methylation, miRNA and stem cell gene expression data in germ cell tumors highlights characteristic differences by tumor histology. BMC Cancer 2015; 15:769. [PMID: 26497383 PMCID: PMC4619074 DOI: 10.1186/s12885-015-1796-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 10/15/2015] [Indexed: 12/21/2022] Open
Abstract
Background Alterations in methylation patterns, miRNA expression, and stem cell protein expression occur in germ cell tumors (GCTs). Our goal is to integrate molecular data across platforms to identify molecular signatures in the three main histologic subtypes of Type I and Type II GCTs (yolk sac tumor (YST), germinoma, and teratoma). Methods We included 39 GCTs and 7 paired adjacent tissue samples in the current analysis. Molecular data available for analysis include DNA methylation data (Illumina GoldenGate Cancer Methylation Panel I), miRNA expression (NanoString nCounter miRNA platform), and stem cell factor expression (SABiosciences Human Embryonic Stem Cell Array). We evaluated the cross platform correlations of the data features using the Maximum Information Coefficient (MIC). Results In analyses of individual datasets, differences were observed by tumor histology. Germinomas had higher expression of transcription factors maintaining stemness, while YSTs had higher expression of cytokines, endoderm and endothelial markers. We also observed differences in miRNA expression, with miR-371-5p, miR-122, miR-302a, miR-302d, and miR-373 showing elevated expression in one or more histologic subtypes. Using the MIC, we identified correlations across the data features, including six major hubs with higher expression in YST (LEFTY1, LEFTY2, miR302b, miR302a, miR 126, and miR 122) compared with other GCT. Conclusions While prognosis for GCTs is overall favorable, many patients experience resistance to chemotherapy, relapse and/or long term adverse health effects following treatment. Targeted therapies, based on integrated analyses of molecular tumor data such as that presented here, may provide a way to secure high cure rates while reducing unintended health consequences.
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Affiliation(s)
- Jenny N Poynter
- Division of Pediatric Epidemiology and Clinical Research, University of Minnesota, Minneapolis, MN, 55455, USA. .,Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA. .,Corresponding address: 420 Delaware St SE MMC 715, Minneapolis, MN, 55455, USA.
| | - Jessica R B M Bestrashniy
- Division of Pediatric Epidemiology and Clinical Research, University of Minnesota, Minneapolis, MN, 55455, USA.
| | - Kevin A T Silverstein
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, 55455, USA.
| | - Anthony J Hooten
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA.
| | - Christopher Lees
- Division of Pediatric Blood and Marrow Transplantation, University of Minnesota, Minneapolis, MN, 55455, USA.
| | - Julie A Ross
- Division of Pediatric Epidemiology and Clinical Research, University of Minnesota, Minneapolis, MN, 55455, USA. .,Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA.
| | - Jakub Tolar
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA. .,Division of Pediatric Blood and Marrow Transplantation, University of Minnesota, Minneapolis, MN, 55455, USA. .,Stem Cell Institute, University of Minnesota, Minneapolis, MN, 55455, USA.
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Rodriguez-Galindo C, Krailo M, Frazier L, Chintagumpala M, Amatruda J, Katzenstein H, Malogolowkin M, Spector L, Pashankar F, Meyers R, Tomlinson G. Children's Oncology Group's 2013 blueprint for research: rare tumors. Pediatr Blood Cancer 2013; 60:1016-21. [PMID: 23255219 PMCID: PMC4304764 DOI: 10.1002/pbc.24428] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Accepted: 11/09/2012] [Indexed: 01/08/2023]
Abstract
In the US, approximately 2,000 children are diagnosed with rare cancers each year, with 5-year survival ranging from <20% for children with advanced carcinomas to >95% for children with intraocular retinoblastoma or localized germ cell tumors. During the last years, 12 clinical studies have been successfully completed in children with retinoblastoma, liver tumors, germ cell tumors, and infrequent malignancies, including therapeutic, epidemiologic, and biologic studies. Current efforts are centered in the development of large international collaborations to consolidate evidence-based definitions and risk stratifications that will support international Phase 3 clinical trials in germ cell tumors, hepatoblastoma, and other rare cancers.
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