Biopolym. Cell. 2016; 32(6):418-432.
Genomics, Transcriptomics and Proteomics
Transcriptome-based identification of PDGFA as a candidate secreted biomarker for hepatocellular carcinoma
1Chesnokov M. S., 1, 2Krivtsova O. M., 1, 2Skovorodnikova P. A., 1, 2Makarova A. S., 1Kustova I. F., 2Logacheva M. D., 2Penin A. A., 2Klepikova A. V., 1Shavochkina D. A., 1Kudashkin N. E., 1Moroz E. A., 1Patyutko Y. I., 3Kotelnikova E. A., 1, 3Lazarevich N. L.
  1. N. N. Blokhin Russian Cancer Research Centre, RAMS
    24, Kashirskoye shosse, Moscow, Russian Federation, 115478
  2. M. V. Lomonosov Moscow State University
    Leninskie Gory, 1/12, Moscow, Russian Federation, 119991
  3. ZAO Personal Biomedicine,
    124/17, Prospekt Mira, Moscow, Russian Federation, 129164


Aim. Identification of candidate secreted biomarkers for hepatocellular carcinoma (HCC) diagnosis. Methods. Genes upregulated in HCC tissue and encoding secreted proteins were identified by RNA-seq. Gene expression changes in HCC were evaluated by RT-qPCR and meta-analysis of public databases. Biomarker properties were studied using ROC-curves, correlation and survival analysis. Results. PDGFA was identified by RNA-seq as an overexpressed gene encoding for a secreted protein in 5 HCC cases. PDGFA and GPC3 up-regulation was revealed in 17 of 19 HCC samples and in most cases from the public databases. Combination of PDGFA and GPC3 discerned HCC and non-tumor tissue better than PDGFA or GPC3 alone. PDGFA overexpression was associated with better overall survival of the patients at early HCC stage and with weaker tumor invasion into blood vessels. Conclusion. PDGFA is a valuable secreted biomarker for HCC that might be used in combination with GPC3 to increase its sensitivity.
Keywords: hepatocellular carcinoma, PDGFA, tumor biomarker, NGS


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