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Poster display session

3528 - gene mutations involved in drug resistance in liver cancer cells using a new rna-seq data analysis workflow


11 Sep 2017


Poster display session




Annals of Oncology (2017) 28 (suppl_5): v1-v21. 10.1093/annonc/mdx361


E. AKHAN GUZELCAN, M. Shojaei, A.C. Acar, R. Cetin Atalay

Author affiliations

  • Informatics Institute, Middle East Technical University, 06800 - Ankara/TR


Abstract 3528


According to Global Cancer Statistics (GCS) Hepatocellular carcinoma (HCC) is the 5th most common and 2nd deadliest cancer in the world. The incidence of HCC has increased over the past decades but still an effective therapy has not been developed. Sorafenib, which is the only FDA approved agent, can improve the patient survival just for a few months, therefore liver transplantation is the most efficient way of treatment up to date. In this study, we offer potential drug targets by analyzing the relationship between mutation status and drug treatment response of well-differentiated Huh7 and poorly-differentiated Mahlavu liver cancer cells.


PI3K/Akt pathway is hyperactive in ∼%40 of HCC. We determined the characterized and determined IC50 values of Sorafenib, PI3Ka and b inhibitors and their combinations. RNAseq experiment were performed with the inhibitor treated cells. The RNAseq data of each cancer cell line (as control) was compared to treated samples. Somatic mutations associated with drug resistance were comparatively identified with RNAseq data workflow wrapped in our laboratory using GATK-MuTect tool (Cibulskis, 2013). The results were further filtrated to obtain the missense mutations. The mutated genes that were identified during the chemical knockdown studies were further analyzed in patient survival data. The functional studies were performed by gene silencing.


SLC39A5, FRG1, PPHLN1 and SRP9 gene mutations were found to be shared among all drug resistant cells. Mutated genes were shown to be associated with cancer perseverance and aggressiveness. In addition, we found an unknown transcript called CTC512. The functional studies demonstrated that once these genes were silenced, the cellular growth was prevented. Gene silencing showed the alteration of the cell cycle progression of drug resistant cells. The affected downstream pathways were further analyzed by western blotting.


Our results indicate potential target genes which are critical to be addressed due to their roles in resistance to drugs in HCC. Once the mutated genes are silenced the cancer progression is prevented. The identified genes can be considered as chemotherapeutical and disease progress targets.

Clinical trial identification

Legal entity responsible for the study

Rengul Cetin Atalay, METU




All authors have declared no conflicts of interest.

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