Epigenetic Targets in Hepatocellular Carcinoma Cells: Identification of Chaperone Protein Complexes with Histone Deacetylases

Abstract

Aims: The study was designed to find out the protein complex(s) associated with HDAC3 in liver cancer using a modified form of affinity purification coupled with a mass spectrometry technique in HepG2 cells. The organ-specific requirement for HDAC1 and HDAC3 during liver formation in zebrafish and their altered expression in liver cancer tissues indicates they are indispensible for hepato-organogenesis and hepatocarcinogenesis. However, how they exert their function is unknown. Material & methods: HepG2 cells were transfected with either mock or construct-containing HDAC3 using a C-terminal strepIII–HA tag as bait. The bait proteins were purified by double affinity columns and were analyzed on a Thermo LTQ Orbitrap™ (Thermo Scientific, MA, USA) chromatography system. Results: Affinity purification coupled with mass spectrometry resulted in the identification of 24 putative binders of HDAC3 in HepG2 cells. The majority (83%) of these are novel interactions are reported for the first time in this study. Conclusion: This is the first study reporting the affinity purification and identification of protein complexes with two closely related proteins in one cell line. The novel HDAC1 and HDAC3 complexes identified in HepG2 cells could serve as a platform for the design of future therapeutic medicine for the treatment of liver cancer.

KEYWORDS::

• double affinity purification
• HDAC3
• hepatocellular carcinoma
• TBL1X
• TCP1

Financial & competing interests disclosure

This work has been supported by a research grant via project number ‘09-BIO888-02‘ from the National Plan for Science and Technology, King Abdul Aziz city for Science and Technology, Kingdom of Saudi Arabia. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

No writing assistance was utilized in the production of this manuscript.

Ethical conduct of research

The authors state that they have obtained appropriate institutional review board approval or have followed the principles outlined in the Declaration of Helsinki for all human or animal experimental investigations. In addition, for investigations involving human subjects, informed consent has been obtained from the participants involved.

Additional information

Funding

This work has been supported by a research grant via project number ‘09-BIO888-02‘ from the National Plan for Science and Technology, King Abdul Aziz city for Science and Technology, Kingdom of Saudi Arabia. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed. No writing assistance was utilized in the production of this manuscript.