Deciphering a profiling based on multiple post-translational modifications functionally associated regulatory...

Area of Science:

• Proteomics
• Cancer Biology
• Biochemistry

Background:

• Posttranslational modifications (PTMs) are crucial in hepatocellular carcinoma (HCC) development.
• The precise locations and regulatory patterns of PTMs in HCC's protein structures are not well understood.

Purpose of the Study:

• To comprehensively profile the proteome and nine key PTMs in HCC tissues.
• To investigate the distribution of PTM sites within protein secondary structures and identify regulatory patterns in HCC.

Main Methods:

• Utilized 4D Label-free proteomics and PTM-based peptide enrichment.
• Analyzed total proteome and nine PTMs (phosphorylation, acetylation, etc.) in tumor and adjacent normal tissues from 18 HCC patients.

Main Results:

• Identified distinct preferences for PTM site locations, with phosphorylation sites often in intrinsically disordered regions (IDRs) and other sites in folded regions.
• Discovered enrichment of phosphorylated and acylated sites in proteins with RRM1 domains, notably RNA splicing factors like NCL.
• Confirmed that NCL modifications at specific residues (S67, K398, K646) regulate RNA processing.

Conclusions:

• This proteome profiling provides a detailed understanding of multiple PTM regulatory patterns in HCC.
• The findings highlight the role of PTMs in RNA processing pathways within HCC.