Research Papers:

Genome wide copy number analyses of superficial esophageal squamous cell carcinoma with and without metastasis

Pengjiao Wang, Ling Shan, Liyan Xue, Bo Zheng, Jianming Ying and Ning Lu _

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Oncotarget. 2017; 8:5069-5080. https://doi.org/10.18632/oncotarget.13847

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Pengjiao Wang1,*, Ling Shan1,*, Liyan Xue1, Bo Zheng1, Jianming Ying1, Ning Lu1

1Department of Pathology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China

*These authors have contributed equally to this work

Correspondence to:

Ning Lu, email: [email protected]

Jianming Ying, email: [email protected]

Keywords: superficial esophageal squamous cell carcinoma, copy number alterations, metastasis, microarray

Received: March 19, 2016    Accepted: November 21, 2016    Published: December 10, 2016


Superficial esophageal squamous cell carcinoma (ESCC) is generally considered a subtype of less invasive ESCC. Yet a subset of these superficial ESCC would have metastasis after esophagostomy or endoscopic resection and lead to poor prognosis. The objective of this study is to determine biomarkers that can identify such subset of superficial ESCC that would have metastasis after surgery using genome wide copy number alteration (CNA) analyses. The CNAs of 38 cases of superficial ESCCs originated from radical surgery, including 19 without metastasis and 19 with metastasis within 5 years’ post-surgery, were analyzed using Affymetrix OncoScan™ FFPE Assay. A 39-gene signature was identified which characterized the subset of superficial ESCC with high risk of metastasis after surgery. In addition, recurrent CNAs of superficial ESCC were also investigated in the study. Amplification of 11q13.3 (FGF4) and deletion of 9p21.3 (CDKN2A) were found to be recurrent in all 38 superficial ESCCs analyzed. Notably amplifications of 3p26.33 (SOX2OT), 8q24.21 (MYC), 14q21.1 (FOXA1) and deletion of 3p12.1 (GBE1) were only found to be recurrent in metastaic superficial ESCCs. In conclusion, using CNAs analyses, we identify a 39-gene signature which characterizes the high risk metastatic superficial ESCCs and discover several recurrent CNAs that might be the driver alterations in metastasis among superficial ESCCs.

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