NGS-based identification of druggable alterations and signaling pathways &amp;ndash; hepatocellular carcinoma case report

Kotelnikova, Ekaterina; Logacheva, Maria D.; Nabieva, Elena; Pyatnitskiy, Mikhail A.; Vinogradov, D. V.; Макарова, А. С.; Демин, А. В.; Paleeva, Anna; Kremenetskaya, O. S.; Penin, Aleksey A.; Klepikova, Anna V.; Kasianov, Artem S.; Shavochkina, D. A.; Кудашкин, Н. Е.; Patyutko, Yu. I.; Mugue, N. S.; Kondrashov, Aleksei; Лазаревич, Н. Л.

doi:10.7124/bc.000901

Cited by 1 publication

(3 citation statements)

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“…The list of candidate serum markers includes growth factor PDGFA, a component of PDGF signaling pathway identified in our recently published HCC case report as a potential druggable target [7]. Since the proangiogenic and mitogenic stimulation promoted by PDGF signaling can be blocked by a multikinase inhibitor sorafenib, the only FDA approved drug for HCC treatment [17,18], we have focused on investigation of the expression alterations of PDGFA that might be not only a candidate HCC marker but also a prospective target for drug treatment.…”

Section: Resultsmentioning

confidence: 99%

“…Total RNA was isolated as previously described [7]. Illumina HiSeq2000 100 nt pair-end transcriptome sequencing was performed for 5 pairs of tumor and liver tissue in two biological replicates.…”

Section: Methodsmentioning

confidence: 99%

“…Illumina HiSeq2000 100 nt pair-end transcriptome sequencing was performed for 5 pairs of tumor and liver tissue in two biological replicates. Library preparation, transcriptome sequencing, read processing and differential expression analysis were performed as previously described [7].…”

Section: Methodsmentioning

confidence: 99%

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Transcriptome-based identification of PDGFA as a candidate secreted biomarker for hepatocellular carcinoma

et al. 2016

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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 upregulation 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. K e y w o r d s: hepatocellular carcinoma, PDGFA, tumor biomarker, NGS ISSN 1993-6842 (on-line); ISSN 0233-7657 (print)

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%