Transcriptome profiles associated with selenium-deficiency-dependent oxidative stress identify potential diagnostic and therapeutic targets in liver cancer cells

Gozen, Damla
Kahraman, Deniz Cansen
Narci, Kubra
Shehwana, Huma
Cetin-Atalay, Rengul
Hepatocellular carcinoma (HCC) is one of the most common cancer types with high mortality rates and displays increased resistance to various stress conditions such as oxidative stress. Conventional therapies have low efficacies due to resistance and off-target effects in HCC. Here we aimed to analyze oxidative stress-related gene expression profiles of HCC cells and identify genes that could be crucial for novel diagnostic and therapeutic strategies. To identify important genes that cause resistance to reactive oxygen species (ROS), a model of oxidative stress upon selenium (Se) deficiency was utilized. The results of transcriptome-wide gene expression data were analyzed in which the differentially expressed genes (DEGs) were identified between HCC cell lines that are either resistant or sensitive to Se-deficiency-dependent oxidative stress. These DEGs were further investigated for their importance in oxidative stress resistance by network analysis methods, and 27 genes were defined to have key roles; 16 of which were previously shown to have impact on liver cancer patient survival. These genes might have Se-deficiency-dependent roles in hepatocarcinogenesis and could be further exploited for their potentials as novel targets for diagnostic and therapeutic approaches. Key words: Hepatocellular carcinoma, selenium, oxidative stress, transcriptome-wide


Transcriptome analysis of thermoplasma volcanium GSS1 under extreme stress
Zabcı, Sema; Kocabıyık, Semra; Department of Biology (2015)
In this study, to provide new insight into anti-stress mechanisms in archaea, we have carried out genome wide transcriptome analysis of Thermoplasma volcanium under severe stress conditions (i.e., heat- shock at 68 ºC, sub-lethal and lethal oxidative stress and pH stress at pH 5.0) using whole genome gene expression microarray. The change in the gene expression profile in response to three stressors indicated retardation of cell growth accompanied by down regulation of genes involved in essential cellular p...
Transcriptome profiling of wheat under heat and cold stress treatments
BALOĞLU, MEHMET CENGİZ; Oz, M. Tufan; Öktem, Hüseyin Avni; Yucel, Meral (2012-09-23)
Microarray analysis was performed to indicate effects of cold and heat stress treatments on global gene expression profiles of wheat. Two groups were generated for comparison of microarray data analysis. Cold and heat conditions were separately compared to control condition. The Affymetrix GeneChip® Wheat Genome Array contains 61,127 probe sets designed to target 55,052 wheat transcripts. Out of these more than 60,000 probes, 12,895 (21.5%) were found to be differentially expressed at least p value lower th...
Activation of survival pathways in nutrient restricted colorectal cancer cells
Oral, Göksu; Banerjee, Sreeparna; Department of Biology (2023-1-9)
Limited nutrient availability in the tumor microenvironment can cause metabolic rewiring of cancer cells, resulting in the activation of various stress response pathways such as autophagy for survival. Our study showed for the first time that incubation of LoVo cells with a nutrient restriction medium containing low glucose, glutamine, and serum for 48 h resulted in the concurrent activation of two antagonistic proteins: the AMP Kinase pathway (AMPK) which is phosphorylated in response to low energy and act...
Network-based discovery of molecular targeted agent treatments in hepatocellular carcinoma
Fayetörbay, Rumeys; Tunçbağ, Nurcan; Department of Bioinformatics (2020)
Hepatocellular carcinoma (HCC) is one of the most-deadly cancers and the most common type of primary liver cancer. Multikinase inhibitor Sorafenib is one of FDA approved targeted agents in HCC treatment. PI3K/AKT/mTOR pathway is altered in about 51% of HCC; hence, understanding how Sorafenib and PI3K/AKT/mTOR pathway inhibitors act at signaling level is crucial for targeted therapies and to reveal the off-target effects. In this work, we use gene expression profiles (GEPs) of HCC cells (Huh7 and Mahlavu) wh...
Molecular Biology of Liver Cancer
Tulin, Ersahin; Öztürk, Mehmet; Atalay, Rengül (2015-01-01)
Hepatocellular carcinoma (HCC) is one of the leading causes of cancer‐related mortality worldwide. Recent advances in the molecular profiling of HCC emphasize its intratumoral heterogeneity and reveal how cellular pathways are altered in favor of tumor progression. Malignant transformation of primary liver cancer is achieved through the acquisition of cancer hallmark capabilities that promote the uncontrolled proliferation of hepatocytes. In this review, the characteristics and acquired capabilities of huma...
Citation Formats
D. Gozen, D. C. Kahraman, K. Narci, H. Shehwana, Ö. KONU KARAKAYALI, and R. Cetin-Atalay, “Transcriptome profiles associated with selenium-deficiency-dependent oxidative stress identify potential diagnostic and therapeutic targets in liver cancer cells,” TURKISH JOURNAL OF BIOLOGY, pp. 149–164, 2021, Accessed: 00, 2021. [Online]. Available: