Asian Pacific Journal of Cancer Prevention

Asian Pacific Journal of Cancer Prevention (아시아태평양암예방학회)
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Identification of a Novel Fusion Gene (HLA-E and HLA-B) by RNA-seq Analysis in Esophageal Squamous Cell Carcinoma

  • Jiang, Yu-Zhang (Department of Medical Laboratory, Huai'an First People's Hospital, Nanjing Medical) ;
  • Li, Qian-Hui (Department of Medical Laboratory, Huai'an First People's Hospital, Nanjing Medical) ;
  • Zhao, Jian-Qiang (Department of Cardiothoracic Surgery, Huai'an First People's Hospital, Nanjing Medical) ;
  • Lv, Jun-Ji (Department of Cardiothoracic Surgery, Huai'an First People's Hospital, Nanjing Medical)
  • Published : 2014.03.01
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Abstract

Esophageal squamous cell carcinoma (ESCC) is the most common histologic subtype of esophageal cancer and is characterized by a poor prognosis. Determining gene changes in ESCCs should improve understanding of putative risk factors and provide potential targets for therapy. We sequenced about 55 million pair-end reads from a pair of adjacent normal and ESCC samples to identify the gene expression level and gene fusion. Sanger sequencing was used to verify the result. About 17 thousand genes were expressed in the tissues, of which approximately 2400 demonstrated significant differences between tumor and adjacent non tumor tissue. GO and KEGG pathway analysis revealed that many of these genes were associated with cellular adherence and movement, simulation responses and immune responses. Notably we identified and validated one fusion gene, HLA-E and HLA-B, located 1 MB apart. We also identified thousands of remarkably expressed transcripts. In conclusion, a novel fusion gene HLA-E and HLA-B was identified in ESCC via whole transcriptome sequencing, which would be a biomarker for ESCC diagnosis and target for therapy, shedding new light for better understanding of ESCC tumorigenesis.

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References

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