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Transcription factors linked to the molecular signatures in the development of hepatocellular carcinoma on a cirrhotic background

Abstract

Mechanisms underlying the regulation of gene expression in cancer have been surveyed for decades to find novel prognostic factors and new targets for molecular targeted therapies in cancer. Because most cases of liver cancer are associated with liver cirrhosis, we aimed to analyze the gene expression signatures and the gene regulatory mechanism in hepatocellular carcinoma (HCC) on a cirrhotic background using high-throughput data analysis. In the present study, three valid array-based datasets containing HCC and liver cirrhosis samples were obtained to identify common differentially expressed genes (DEGs). Moreover, a comprehensive data analysis was conducted based on RNA-Seq data and using Kaplan–Meier curve analysis to find molecular signatures that reduce patients' survival rate. Furthermore, we proposed a gene regulatory network (GRN) to explore the possible regulatory mechanism of these molecular signatures by transcription factors in HCC progression from cirrhosis. Besides, we analyzed protein–protein interactions, gene ontology (GO), and pathway enrichment to elucidate the cellular and molecular function of the GRN elements in HCC. In this way, we found a list of 231 molecular signatures in HCC derived from cirrhosis. We also found the importance of TCF4, RUNX1, HINFP, KDM2B, MAF, JUN, NR5A2, NFYA, and AR as key differentially expressed transcription factors (DETFs) in the progression of HCC from cirrhosis. In conclusion, the identified molecular signatures and their transcription factors propose candidate prognostic markers and possible molecular targets in the progression of HCC.

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Data availability

All data will be made available on request.

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Acknowledgements

This research was conducted using the authors’ personal money.

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JM participated in the conceptualization, investigation, formal analysis, writing, reviewing, and editing of the original draft, and supervision. EE participated in the investigation, formal analysis, and writing of the original draft.

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Correspondence to Jamshid Motalebzadeh.

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The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

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Motalebzadeh, J., Eskandari, E. Transcription factors linked to the molecular signatures in the development of hepatocellular carcinoma on a cirrhotic background. Med Oncol 38, 121 (2021). https://doi.org/10.1007/s12032-021-01567-x

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Keywords

  • Gene regulatory network
  • Hepatocellular carcinoma
  • Liver cirrhosis
  • Molecular signatures
  • Transcription factors