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An J, Wan H, Zhou X, Hu DN, Wang L, Hao L, Yan D, Shi F, Zhou Z, Wang J, Hu S, Yu J, Qu J. A comparative transcriptomic analysis of uveal melanoma and normal uveal melanocyte. PLoS One 2011; 6:e16516. [PMID: 21305041 PMCID: PMC3030591 DOI: 10.1371/journal.pone.0016516] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Accepted: 12/19/2010] [Indexed: 12/18/2022] Open
Abstract
Background Uveal melanoma is the most common primary intraocular tumor in adults in western countries. It is associated with very severe visual morbidity and may lead to distant metastases even after successful treatment of the primary tumor. In order to gain better insight into molecular mechanisms related to tumorigenesis and metastasis of uveal melanoma, we used next-generation sequencing technology (SOLiD, Life Technologies) to acquire global transcriptome alteration between posterior uveal melanoma cells and normal uveal melanocyte. Results From mRNAs of the cultured uveal melanoma cells and normal uveal melanocytes, we annotated more than 3.7×107 and 2.7×107 sequencing tags based on human Ensembl databases, respectively. For detailed analysis, we chose 5155 well-annotated genes mainly involved in the MAPK signaling pathway, cell cycle, cell adhesion junction, apoptosis, and P53 signaling pathways as well as melanogenesis. In an effort to confirm the authenticity of our sequencing results, we validated twenty-one identically differentially expressed genes by using quantitative real time PCR from cultured cell lines of other posterior uveal melanoma cells and normal uveal melanocytes. Conclusion We have identified a large number of potentially interesting genes for biological investigation of uveal melanoma. The expression profiling also provides useful resources for other functional genomic and transcriptome studies. These 21 potential genes could discriminate between uveal melanoma cells and normal uveal melanocyte, which may be indicative of tumorigenesis process. Our results further suggest that high-throughput sequencing technology provides a powerful tool to study mechanisms of tumogenesis in the molecular level.
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Affiliation(s)
- Jianhong An
- School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical College, Wenzhou, China
- State Key Laboratory Cultivation Base and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou, China
| | - Haolei Wan
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Xiangtian Zhou
- School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical College, Wenzhou, China
- State Key Laboratory Cultivation Base and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou, China
| | - Dan-Ning Hu
- School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical College, Wenzhou, China
- Tissue Culture Center, The New York Eye and Ear Infirmary, New York Medical College, New York, New York, United States of America
| | - Ledan Wang
- School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical College, Wenzhou, China
- State Key Laboratory Cultivation Base and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou, China
| | - Lili Hao
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Dongsheng Yan
- School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical College, Wenzhou, China
- State Key Laboratory Cultivation Base and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou, China
| | - Fanjun Shi
- School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical College, Wenzhou, China
- State Key Laboratory Cultivation Base and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou, China
| | - Zhonglou Zhou
- School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical College, Wenzhou, China
- State Key Laboratory Cultivation Base and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou, China
| | - Jiao Wang
- School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical College, Wenzhou, China
- State Key Laboratory Cultivation Base and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou, China
| | - Songnian Hu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Jun Yu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- * E-mail: (JY) (JY); (JQ) (JQ)
| | - Jia Qu
- School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical College, Wenzhou, China
- State Key Laboratory Cultivation Base and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou, China
- * E-mail: (JY) (JY); (JQ) (JQ)
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