Molecular analysis of thymoma.
Histologic classification of thymomas has significant limitations with respect to both subtype definitions and consistency. In order to better understand the biology of the disease processes, we performed whole genome gene expression analysis. RNA was extracted from fresh frozen tumors from 34 patie...
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2012
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oai:doaj.org-article:fdb2b57e22cc4b80b1de2f0db9b9d5d62021-11-18T07:08:59ZMolecular analysis of thymoma.1932-620310.1371/journal.pone.0042669https://doaj.org/article/fdb2b57e22cc4b80b1de2f0db9b9d5d62012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22912720/?tool=EBIhttps://doaj.org/toc/1932-6203Histologic classification of thymomas has significant limitations with respect to both subtype definitions and consistency. In order to better understand the biology of the disease processes, we performed whole genome gene expression analysis. RNA was extracted from fresh frozen tumors from 34 patients with thymomas and followup data was available. Using the Illumina BeadStudio® platform and Human Ref-8 Beadchip, gene expression data was analyzed with Partek Genomics Suite®, and Ingenuity Pathways Analysis (IPA). Unsupervised clustering of gene expression data, representing one of the largest series in literature, resulted in identification of four molecular clusters of tumors (C1-C4), which correlated with histology (P = 0.002). However, neither histology nor clusters correlated with clinical outcomes. Correlation of gene expression data with clinical data showed that a number of genes were associated with either advanced stage at diagnosis or development of recurrence or metastases. The top pathways associated with metastases were amino acid metabolisms, biosynthesis of steroids and glycosphingolipids, cell cycle checkpoint proteins and Notch signaling. The differential expression of some of the top genes related to both metastases and stage was confirmed by RT-PCR in all cases of metastases and matched nonmetastatic cases. A number of potential candidates for therapeutics were also identified.Sunil BadveChirayu GoswamiYesim Gökmen-PolarRobert P NelsonJohn HenleyNick MillerNarjis A ZaheerGeorge W SledgeLang LiKenneth A KeslerPatrick J LoehrerPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 8, p e42669 (2012) |
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DOAJ |
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DOAJ |
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EN |
| topic |
Medicine R Science Q |
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Medicine R Science Q Sunil Badve Chirayu Goswami Yesim Gökmen-Polar Robert P Nelson John Henley Nick Miller Narjis A Zaheer George W Sledge Lang Li Kenneth A Kesler Patrick J Loehrer Molecular analysis of thymoma. |
| description |
Histologic classification of thymomas has significant limitations with respect to both subtype definitions and consistency. In order to better understand the biology of the disease processes, we performed whole genome gene expression analysis. RNA was extracted from fresh frozen tumors from 34 patients with thymomas and followup data was available. Using the Illumina BeadStudio® platform and Human Ref-8 Beadchip, gene expression data was analyzed with Partek Genomics Suite®, and Ingenuity Pathways Analysis (IPA). Unsupervised clustering of gene expression data, representing one of the largest series in literature, resulted in identification of four molecular clusters of tumors (C1-C4), which correlated with histology (P = 0.002). However, neither histology nor clusters correlated with clinical outcomes. Correlation of gene expression data with clinical data showed that a number of genes were associated with either advanced stage at diagnosis or development of recurrence or metastases. The top pathways associated with metastases were amino acid metabolisms, biosynthesis of steroids and glycosphingolipids, cell cycle checkpoint proteins and Notch signaling. The differential expression of some of the top genes related to both metastases and stage was confirmed by RT-PCR in all cases of metastases and matched nonmetastatic cases. A number of potential candidates for therapeutics were also identified. |
| format |
article |
| author |
Sunil Badve Chirayu Goswami Yesim Gökmen-Polar Robert P Nelson John Henley Nick Miller Narjis A Zaheer George W Sledge Lang Li Kenneth A Kesler Patrick J Loehrer |
| author_facet |
Sunil Badve Chirayu Goswami Yesim Gökmen-Polar Robert P Nelson John Henley Nick Miller Narjis A Zaheer George W Sledge Lang Li Kenneth A Kesler Patrick J Loehrer |
| author_sort |
Sunil Badve |
| title |
Molecular analysis of thymoma. |
| title_short |
Molecular analysis of thymoma. |
| title_full |
Molecular analysis of thymoma. |
| title_fullStr |
Molecular analysis of thymoma. |
| title_full_unstemmed |
Molecular analysis of thymoma. |
| title_sort |
molecular analysis of thymoma. |
| publisher |
Public Library of Science (PLoS) |
| publishDate |
2012 |
| url |
https://doaj.org/article/fdb2b57e22cc4b80b1de2f0db9b9d5d6 |
| work_keys_str_mv |
AT sunilbadve molecularanalysisofthymoma AT chirayugoswami molecularanalysisofthymoma AT yesimgokmenpolar molecularanalysisofthymoma AT robertpnelson molecularanalysisofthymoma AT johnhenley molecularanalysisofthymoma AT nickmiller molecularanalysisofthymoma AT narjisazaheer molecularanalysisofthymoma AT georgewsledge molecularanalysisofthymoma AT langli molecularanalysisofthymoma AT kennethakesler molecularanalysisofthymoma AT patrickjloehrer molecularanalysisofthymoma |
| _version_ |
1718423892474724352 |