OncoTargets and Therapy (2020-02-01)

Bioinformatics Analysis and RNA-Sequencing of SCAMP3 Expression and Correlated Gene Regulation in Hepatocellular Carcinoma

  • Han S,
  • Feng Z,
  • Liu R,
  • Ye J,
  • Cheng W,
  • Bao J

Journal volume & issue
Vol. Volume 13
pp. 1047 – 1057

Abstract

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Shan-shan Han,1 Zhi-qiang Feng,1 Rui Liu,2 Jun Ye,2 Wei-wei Cheng,2 Jun-bo Bao3 1Beijing Chaoyang Emergency Medical Center, Department of General Surgery, Chaoyang, Beijing 100020, People’s Republic of China; 2Medical University of Anhui Air Force Clinical School, Department of Hepatobiliary Surgery, Beijing 100142, People’s Republic of China; 3First People’s Hospital of Suqian, Department of Medicine, Suqian, Jiangsu 223800, People’s Republic of ChinaCorrespondence: Zhi-qiang FengBeijing Chaoyang Emergency Medical Center, Department of General Surgery, Chaoyang, Beijing 100020, People’s Republic of ChinaEmail [email protected]: Secretory Carrier Membrane Proteins 3 (SCAMP3) is a transmembrane protein that affects intracellular trafficking, protein sorting and vesicle formation. Overexpression of SCAMP3 correlates with poorly differentiated hepatocellular carcinoma (HCC). However, the expression and corresponding gene regulation of SCAMP3 in HCC remain unclear.Methods: Bioinformatics analyses of clinical parameters and survival data were conducted to predict the prognostic value of SCAMP3 in HCC. RNA sequencing and real-time PCR were conducted to confirm the SCAMP3 expression in HCC tissue. Expression was analyzed using OncomineTM and UALCAN, while SCAMP3 alterations and survival analysis were identified by cBioPortal. Differential gene expression with SCAMP3 was analyzed by LinkedOmics and GEPIA. The target networks of enzymes and co-transcriptional factors were identified using Gene enrichment analysis. Expression of SCAMP3 in HCC tissue was detected by RNA-sequencing and Western-blotting.Results: Based on bioinformatics analysis and detection of mRNA expression, SCAMP3 was over-expressed in numerous tumors, especially in HCC. SCAMP3 level was positively correlated with disease stages and tumor grades and negatively correlated with patient survival. Furthermore, functional network analysis indicated that SCAMP3 regulated metabolic process and DNA replication through oxidative phosphorylation and chromatin remodeling or Ribosome. SCAMP3 regulated a number of gene expressions including PPAP2B, SNRK, ARID4A, PRCC, VPS72 via protein binding and proteasome, which may affect cell adhesion, proliferation, transcription, cell cycle and metabolism. Further, Real-time PCR and Western-blotting showed that the SCAMP3 level was increased in HCC tissue.Conclusion: The present data analysis efficiently reveals information about SCAMP3 expression and correlated function in HCC, laying a foundation for further study of SCAMP3 in the tumor.Keywords: SCAMP3, hepatocellular carcinoma, bioinformatics analysis, RNA-sequencing, real-time PCR

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