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Exploring Protein Post-Translational Modifications of Breast Cancer Cells Using a Novel Combinatorial Search Algorithm

ABSTRACT: Post-translational modification of proteins plays an important role in cancer cell biology. Protein encoded by oncogenes may be activated by phosphorylation, products of tumour suppressors might be inactivated by phosphorylation or ubiquitination, which marks them for degradation; Chromatin binding proteins are often methylated and/or acetylated. These are just a few of the many hundreds of post-translational modifications discovered by years of painstaking experimentation and chemical analysis of purified proteins. In recent years, mass spectrometry-based proteomics emerged as the principal technique for identifying such modifications in samples from cultured cells and tumour tissue. Here we used a recently developed combinatorial search algorithm implemented in the MGVB toolset to identify novel modifications in samples from breast cancer cell lines. Our results provide a rich resource of coupled protein abundance and post-translational modification data seen in the context of an important biological function - the response of cells to interferon gamma treatment - which can serve as a starting point for future investigations to validate promising modifications and explore the utility of the underlying molecular mechanisms as potential diagnostic or therapeutic targets.

INSTRUMENT(S): LTQ/Orbitrap Velos

ORGANISM(S): Homo Sapiens

SUBMITTER: Metoodi V. Metodiev

PROVIDER: MSV000095497 | MassIVE | Wed Jul 31 10:43:00 BST 2024

SECONDARY ACCESSION(S): PXD054457

REPOSITORIES: MassIVE

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Project description:This study aims to analyze and compare the post-translational modification differences between human plasma- and genetic recombination-derived human serum albumin (HSA) in clinical treatments in China. 6 different post-translational modifications, including acetylation, succinylation, crotonylation, phosphorylation, beta-hydroxybutyrylation, and lactylation, were detected using pan-specific antibodies through Western blot. The samples, consisting of human plasma-derived HSA (pHSA) from six different manufacturers and recombinant HSA (rHSA) expressed in yeast and oryza sativa, underwent detection of types of post-translational modifications. 4D label-free PTMs quantitative proteomic analysis was conducted to detect N-glycosylation and the above-mentioned post-translational modifications in pHSA and rHSA samples, and analyze the differences in modification sites and levels. Through Western blot analysis, all six pHSA and two rHSA samples were positive in the band of albumin (66.5 kDa) for the six post-translational modifications. Further analysis using 4D label-free PTMs quantitative proteomics revealed 25 (29) acetylated, 30 (32) succinylated, 41 (50) malonylated, 15 (23) phosphorylated, 36 (30) beta-hydroxybutyrylated, and 27 (34) lactylated modification sites in pHSA and rHSA samples and no N-glycosylation modification sites. The analysis results identified 1 acetylation (ALB_K160), 2 beta-hydroxybutyrylation (ALB_K569, ALB_K426), 3 crotonylation (ALB_K264, ALB_K581, ALB_K560), and 15 phosphorylation specific modification sites in pHSA, as well as 3 crotonylation (ALB_K560, ALB_K562, ALB_K75), 1 succinylation (ALB_K490), and 23 phosphorylation specific modification sites in rHSA. In pHSA (rHSA), 2 (6) acetylation, 10 (12) succinylation, 0 (9) crotonylation, 1 (9) phosphorylation, 6 (0) beta-hydroxybutyrylation, and 0 (7) lactylation specific modification sites were found. Additionally, in the common modification sites of pHSA and rHSA, pHSA showed up-regulation of amberylation (16:1) and beta-hydroxybutyrylation (12:2) in more sites, and up-regulation of acetylation (7:11), crotonylation (2:11), phosphorylation (1:8), and lactylation (1:14) in less sites compared to rHSA. In clinical treatment, the used pHSA and rHSA in China generally exhibit acetylation, succinylation, crotonylation, phosphorylation, beta-hydroxybutyrylation, and lactylation, and there are differences in the site characteristics and modification levels of these modifications between pHSA and rHSA. Further experimental investigations are needed to explore the impact of post-translational modification differences on the biological function, efficacy, and safety of pHSA and rHSA.

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Exploring Protein Post-Translational Modifications of Breast Cancer Cells Using a Novel Combinatorial Search Algorithm

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