Identification of gene mutations involved in drug resistance in liver cancer using RNA-SEQ data analysis

Date

2016

Author

Shojaei, Mona

Metadata

Show full item record

Item Usage Stats

232
views

0
downloads

A significant concern in cancer research is the detection of cancer associated somatic mutations. Liver cancer is the 5th most common and 2nd deadliest cancer in the world. Several somatic mutations were previously reported in liver cancer but their relations to chemotherapeutic response was not studied in detail. In this study, the relationship between mutation status and drug treatment response of well-differentiated Huh7 and poorly-differentiated Mahlavu liver cancer cells were analyzed. The RNA-Seq data of each cancer cell line (as control) was compared to “sorafenib” and “PI3K/Akt Pathway inhibitors” treated data. Somatic mutations associated with drug resistance were comparatively identified with MuTect tool. The results were then filtered to distinguish the missense mutations. The common genes among drug-resistant sets were found to be associated with liver cancer perseverance and aggressiveness. SLC39A5, FRG1, PPHLN1 and SRP9 gene mutations were found to be the most significant, shared among three drug treated sets. The sets were further investigated in detail to discover the liver cancer associated survival genes. Using our results, appropriate targets can be defined that play critical roles in cancerous cell growth for drug development purposes.

Subject Keywords

Liver, Drug resistance., Liver metastasis., Nucleotide sequence., Drug resistance in cancer cells

URI

http://etd.lib.metu.edu.tr/upload/12620330/index.pdf
https://hdl.handle.net/11511/25983

Collections

Graduate School of Informatics, Thesis

Suggestions

OpenMETU
Core

Synthesis of poly (dl-lactic-co-glycolic acid) coated magnetic nanoparticles for anti-cancer drug delivery Tansık, Gülistan; Gündüz, Ufuk; Department of Biology (2012) One of the main problems of current cancer chemotherapy is the lack of selectivity of anti-cancer drugs to tumor cells which leads to systemic toxicity and adverse side effects. In order to overcome these limitations, researches on controlled drug delivery systems have gained much attention. Nanoscale based drug delivery systems provide tumor targeting. Among many types of nanocarriers, superparamagnetic nanoparticles with their biocompatible polymer coatings can be targeted to an intented site by an extern...
Identification of rare cell types in lung cancer and investigation of their use in prognosis Yıldız, Cemal; Şengül Babal, Simge; Pir, Pınar (Orta Doğu Teknik Üniversitesi Enformatik Enstitüsü; 2022-10) Cancer is a complex, dynamic and heterogeneous disease. Identification of tumor heterogeneity holds a significant promise not only on tumor classification but also on predicting the prognosis and choosing the right treatment. Therefore, it is essential to investigate tumor heterogeneity in a regular diagnosis procedure. Tumors contain variety of cell types such as malignant cells, non-malignant cells, immune cells, and rare cells (i.e., dormant cells (DRM) and cancer stem cells (CSC))....
Detection of rare cell types and patient prognosis in liver cancer Şengül Babal, Simge; Yıldız, Cemal; Pır, Pınar (Orta Doğu Teknik Üniversitesi Enformatik Enstitüsü; 2022-10) Cancer is a disease that emerges as a result of complex aberrant processes involving cells that grow and divide uncontrollably and has many patient-specific characteristics. Mutations in genes or changes in the expression of transcripts produce cellular heterogeneity, cancer cells, and tumors, and finally invade other healthy tissues [1]. Primary liver cancer is the second most lethal malignancy worldwide and comprises many molecularly unique subtypes and a highly diverse microenvironment [2]. Among this di...
DETERMINATION OF THE RELATIONSHIP BETWEEN DOXORUBICIN RESISTANCE AND WNT SIGNALING PATHWAY IN HELA AND K562 CELL LINES Mutlu, Pelin; Pourianazar, Negar Taghavi; Yucel, Meral; Gündüz, Ufuk (2018-01-01) Activation of the Wnt signaling in some types of cancer and its relation with chemotherapy resistance is a very interesting issue that has been emphasized in recent years. Although, it is known that increase in the activity of beta-catenin is important in blast transformation and drug resistance, the underlying mechanisms are still unclear. In this study, changes in the expression levels of 186 genes that are thought to be important in drug resistance and Wnt signaling pathways were determined by using qPCR...
Identification of polymorphisms on the MDR1 gene among Turkish population and their effects on multidrug resistance in acute leukemia patients Kaya, P; Gündüz, Ufuk; Arpaci, F; Ural, AU; Guran, S (2005-09-01) Multidrug-resistance (MDR) phenotype is a serious limitation to the effective chemotherapeutic treatment of many cancer types, including leukemia. One of the most important proteins, the over-expression of which is responsible for the multidrug-resistance phenotype in many cancer types, is P-glycoprotein. This protein is the product of the MDR1 gene. In previous studies, single-nucleotide polymorphisms (SNPs) C3435T, G2677T, and T-129C in the MDR1 gene were shown to be correlated with lower P-glycoprotein e...

Citation Formats

M. Shojaei, “Identification of gene mutations involved in drug resistance in liver cancer using RNA-SEQ data analysis,” M.S. - Master of Science, Middle East Technical University, 2016.