Proteomic study of hepatocellular carcinoma using a novel modified aptamer-based array (SOMAscan™) platform

Zhiwei Qiao, Xiaoqing Pan, Cuneyd Parlayan, Hidenori Ojima, Tadashi Kondo

Research output: Contribution to journalArticle

9 Citations (Scopus)

Abstract

Vascular invasion is a pathological hallmark of hepatocellular carcinoma (HCC), associated with poor prognosis; it is strongly related to the early recurrence and poor survival after curative resection. In order to determine the proteomic backgrounds of HCC carcinogenesis and vascular invasion, we employed a novel modified aptamer-based array (SOMAscan) platform. SOMAscan is based on the Slow Off-rate Modified Aptamers (SOMAmers), which rely on the natural 3D folding of single-stranded DNA-based protein affinity reagents. Currently, the expression level of 1129 proteins can be assessed quantitatively. Correlation matrix analysis showed that the overall proteomic features captured by SOMAscan differ between tumor and non-tumor tissues. Non-tumor tissues were shown to have more homogeneous proteome backgrounds than tumor tissues. A comparative study identified 68 proteins with differential expression between tumor and non-tumor tissues, together with eight proteins associated with vascular invasion. Gene Ontology analysis showed that the extracellular space and extracellular region proteins were predominantly detected. Network analysis revealed the linkage of seven proteins, AKT1, MDM2, PTEN, FGF1, MAPK8, PRKCB, and FN1, which were categorized as the components of “Pathways in cancer” in pathway analysis. The results of SOMAscan analysis were not concordant with those obtained by western blotting; only the determined FN1 levels were concordant between the two platforms. We demonstrated that the proteome captured by SOMAscan includes the proteins relevant to carcinogenesis and vascular invasion in HCC. The identified proteins may serve as candidates for the future studies of disease mechanisms and clinical applications.

Original languageEnglish
Pages (from-to)434-443
Number of pages10
JournalBiochimica et Biophysica Acta - Proteins and Proteomics
Volume1865
Issue number4
DOIs
Publication statusPublished - 2017 Apr 1

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Proteomics
Hepatocellular Carcinoma
Blood Vessels
Proteins
Tissue
Tumors
Proteome
Neoplasms
Carcinogenesis
Proto-Oncogene Proteins c-mdm2
Fibroblast Growth Factor 1
Gene Ontology
Single-Stranded DNA
Extracellular Space
Electric network analysis
Ontology
Western Blotting
Genes
Recurrence

Keywords

  • Hepatocellular carcinoma
  • SOMAscan
  • Vascular invasion

ASJC Scopus subject areas

  • Analytical Chemistry
  • Biophysics
  • Biochemistry
  • Molecular Biology

Cite this

Proteomic study of hepatocellular carcinoma using a novel modified aptamer-based array (SOMAscan™) platform. / Qiao, Zhiwei; Pan, Xiaoqing; Parlayan, Cuneyd; Ojima, Hidenori; Kondo, Tadashi.

In: Biochimica et Biophysica Acta - Proteins and Proteomics, Vol. 1865, No. 4, 01.04.2017, p. 434-443.

Research output: Contribution to journalArticle

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