Biopolym. Cell. 2016; 32(6):418-432.
http://dx.doi.org/10.7124/bc.000939
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

Abstract

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
Full text: (PDF, in English)

References

[1] Colagrande S, Inghilesi AL, Aburas S, Taliani GG, Nardi C, Marra F. Challenges of advanced hepatocellular carcinoma. World J Gastroenterol. 2016;22(34):7645-59.
[2] Ferlay J, Soerjomataram I, Dikshit R, Eser S, Mathers C, Rebelo M, Parkin DM, Forman D, Bray F. Cancer incidence and mortality worldwide: sources, methods and major patterns in GLOBOCAN 2012. Int J Cancer. 2015;136(5):E359-86.
[3] Marquardt JU, Galle PR, Teufel A. Molecular diagnosis and therapy of hepatocellular carcinoma (HCC): an emerging field for advanced technologies. J Hepatol. 2012;56(1):267-75.
[4] Abelev GI, Eraiser TL. Cellular aspects of alpha-fetoprotein reexpression in tumors. Semin Cancer Biol. 1999;9(2):95-107.
[5] Behne T, Copur MS. Biomarkers for hepatocellular carcinoma. Int J Hepatol. 2012;2012:859076.
[6] Rich N, Singal AG. Hepatocellular carcinoma tumour markers: current role and expectations. Best Pract Res Clin Gastroenterol. 2014;28(5):843-53.
[7] Kotelnikova EA, Logacheva MD, Nabieva ER, Pyatnitskiy MA, Vinogradov DV, Makarova AS, Demin AV, Paleeva AG, Kremenetskaya OS, Penin AA, Klepikova AV, Kasianov AS, Shavochkina DA, Kudashkin NE, Patyutko YuI, Mugue NS, Kondrashov AS, Lazarevich NL. NGS-based identification of druggable alterations and signaling pathways – hepatocellular carcinoma case report. Biopolym Cell. 2015; 31(6):436–46.
[8] Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, Kubista M, Mueller R, Nolan T, Pfaffl MW, Shipley GL, Vandesompele J, Wittwer CT. The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem. 2009;55(4):611-22.
[9] Fu LY, Jia HL, Dong QZ, Wu JC, Zhao Y, Zhou HJ, Ren N, Ye QH, Qin LX. Suitable reference genes for real-time PCR in human HBV-related hepatocellular carcinoma with different clinical prognoses. BMC Cancer. 2009;9:49.
[10] Gao Q, Wang XY, Fan J, Qiu SJ, Zhou J, Shi YH, Xiao YS, Xu Y, Huang XW, Sun J. Selection of reference genes for real-time PCR in human hepatocellular carcinoma tissues. J Cancer Res Clin Oncol. 2008;134(9):979-86.
[11] Roessler S, Jia HL, Budhu A, Forgues M, Ye QH, Lee JS, Thorgeirsson SS, Sun Z, Tang ZY, Qin LX, Wang XW. A unique metastasis gene signature enables prediction of tumor relapse in early-stage hepatocellular carcinoma patients. Cancer Res. 2010;70(24):10202-12.
[12] Huang Q, Lin B, Liu H, Ma X, Mo F, Yu W, Li L, Li H, Tian T, Wu D, Shen F, Xing J, Chen ZN. RNA-Seq analyses generate comprehensive transcriptomic landscape and reveal complex transcript patterns in hepatocellular carcinoma. PLoS One. 2011;6(10):e26168.
[13] Yu K, Ganesan K, Tan LK, Laban M, Wu J, Zhao XD, Li H, Leung CH, Zhu Y, Wei CL, Hooi SC, Miller L, Tan P. A precisely regulated gene expression cassette potently modulates metastasis and survival in multiple solid cancers. PLoS Genet. 2008;4(7):e1000129.
[14] Dong H, Zhang L, Qian Z, Zhu X, Zhu G, Chen Y, Xie X, Ye Q, Zang J, Ren Z, Ji Q. Identification of HBV-MLL4 Integration and Its Molecular Basis in Chinese Hepatocellular Carcinoma. PLoS One. 2015;10(4):e0123175.
[15] Liu G, Hou G, Li L, Li Y, Zhou W, Liu L. Potential diagnostic and prognostic marker dimethylglycine dehydrogenase (DMGDH) suppresses hepatocellular carcinoma metastasis in vitro and in vivo. Oncotarget. 2016;7(22):32607-16.
[16] Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biol. 2010;11(10):R106.
[17] Adnane L, Trail PA, Taylor I, Wilhelm SM. Sorafenib (BAY 43-9006, Nexavar), a dual-action inhibitor that targets RAF/MEK/ERK pathway in tumor cells and tyrosine kinases VEGFR/PDGFR in tumor vasculature. Methods Enzymol. 2006;407:597-612.
[18] Makarova AS, Lazarevich NL. Deregulation of signaling pathways involved in sorafenib resistance of hepatocellular carcinoma. Klin Lab Diagn. 2013;(10):66-8.
[19] Shafizadeh N, Ferrell LD, Kakar S. Utility and limitations of glypican-3 expression for the diagnosis of hepatocellular carcinoma at both ends of the differentiation spectrum. Mod Pathol. 2008;21(8):1011-8.
[20] Bruix J, Reig M, Sherman M. Evidence-Based Diagnosis, Staging, and Treatment of Patients With Hepatocellular Carcinoma. Gastroenterology. 2016;150(4):835-53.
[21] Henry NL, Hayes DF. Cancer biomarkers. Mol Oncol. 2012;6(2):140-6.
[22] Marrero JA, Feng Z, Wang Y, Nguyen MH, Befeler AS, Roberts LR, Reddy KR, Harnois D, Llovet JM, Normolle D, Dalhgren J, Chia D, Lok AS, Wagner PD, Srivastava S, Schwartz M. Alpha-fetoprotein, des-gamma carboxyprothrombin, and lectin-bound alpha-fetoprotein in early hepatocellular carcinoma. Gastroenterology. 2009;137(1):110-8.
[23] Tsuchiya N, Sawada Y, Endo I, Saito K, Uemura Y, Nakatsura T. Biomarkers for the early diagnosis of hepatocellular carcinoma. World J Gastroenterol. 2015;21(37):10573-83.
[24] Hass HG, Jobst J, Scheurlen M, Vogel U, Nehls O. Gene expression analysis for evaluation of potential biomarkers in hepatocellular carcinoma. Anticancer Res. 2015;35(4):2021-8.
[25] Jia X, Liu J, Gao Y, Huang Y, Du Z. Diagnosis accuracy of serum glypican-3 in patients with hepatocellular carcinoma: a systematic review with meta-analysis. Arch Med Res. 2014;45(7):580-8.
[26] Wei T, Zhang LN, Lv Y, Ma XY, Zhi L, Liu C, Ma F, Zhang XF. Overexpression of platelet-derived growth factor receptor alpha promotes tumor progression and indicates poor prognosis in hepatocellular carcinoma. Oncotarget. 2014;5(21):10307-17.