Isoform-resolved correlation analysis between mRNA abundance regulation and protein level degradation

Area of Science:

• Proteomics and Molecular Biology
• Cellular Regulation and Cancer Biology

Background:

• Understanding protein turnover is crucial for dissecting cellular regulatory mechanisms.
• Post-translational protein modification and degradation play key roles in cellular function.

Purpose of the Study:

• To develop and demonstrate a novel strategy for assessing protein degradation rates at the isoform level.
• To investigate the relationship between mRNA levels, protein degradation, and alternative splicing in cancer cell lines.

Main Methods:

• Utilized pulse stable isotope-labeled amino acids in cells (pSILAC) coupled with data-independent acquisition mass spectrometry (DIA-MS).
• Developed a novel data analysis framework to resolve protein degradation rates across mRNA alternative splicing isoforms.
• Performed genome-wide correlation analysis between mRNA and protein degradation in varying HeLa cell strains.

Main Results:

• Identified distinct degradation rates for specific biological processes, organelles, and protein isoforms.
• Demonstrated that protein degradation diversity influences protein turnover control in cancer cell lines.
• Showed that mRNA splicing events, like intron retention, significantly affect protein abundance.

Conclusions:

• Protein degradation diversity provides insights into buffering and concerted turnover control in cancer.
• Highlighted the significant association between transcriptome variability and proteostasis.
• Established a methodological foundation for studying functional protein degradation and its regulation by splicing.