[Affinity chromatography based phosphoproteome research on lung cancer cells and its application]

Phosphorylation is one of the most important post-translational modifications in proteins. It plays a key role in numerous cellular processes, including signal transduction, cell proliferation, and intercellular communication. More than 30% of the cellular proteins are phosphorylated at a given time. However, dysregulation of phosphorylated proteins usually leads to a disorder in the intracellular signaling pathways and the onset of various diseases, especially cancer. Cell proliferation and metastasis are the major manifestations of cancer progression, and these might be affected by the protein phosphorylation levels. Clinically, cancer usually metastasizes at the middle and late stages, affecting other organs beyond primary lesion. This poses significant challenges in cancer treatment and prognosis. Consequently, comparing the phosphorylated proteomes of cells with different metastatic capabilities is helpful in studying the role of protein phosphorylation in cancer metastasis and progression. The human low metastatic lung cancer cell line 95C and high metastatic lung cancer cell line 95D are two of the four sublines isolated from human lung giant cell carcinoma cell line (PLA-801) by the single-cell cloning technique. These are ideal models for studying tumor metastasis and non-small cell lung cancer. MRC-5 cell line was obtained from a 14 week old fetal normal lung tissue. Quantitative analysis of the proteome and phosphorylated proteome in these normal lung cells and lung cancer cells with different metastatic capacities can identify key pathways and regulatory proteins associated with lung cancer metastasis and progression. Immobilized metal affinity chromatography (IMAC) is an efficient technique for the enrichment of phosphopeptides and has been widely used for phosphoproteome research. Metal ions (such as Ti⁴⁺) are immobilized on the substrate by chelation, and phosphopeptides can be selectively adsorbed under acidic conditions and eluted under alkaline conditions. IMAC can enrich phosphate groups at different amino acid sites with high specificity. In this study, Ti⁴⁺was chelated onto Ti⁴⁺-IMAC material, which was used to enrich phosphopeptides for phosphoproteome research. Two enrichment methods, namely, the vortexing method and solid phase extraction (SPE) method, were first compared for the enrichment of phosphopeptides using 10 μm Ti⁴⁺-IMAC. Phosphopeptides were highly enriched using the vortexing method. Following this, two sizes of Ti⁴⁺-IMAC material (10 μm and 30 μm) were compared to determine the efficiency of phosphopeptide enrichment. Enrichment efficiency was superior with the smaller-sized material. Therefore, the small-size Ti⁴⁺-IMAC material was selected for the proteomics research of lung cell phosphorylation. The optimized strategy was further used to compare the phosphoproteomes of the lung cancer cells with different metastatic abilities. Label-free quantification proteomics demonstrated that 510, 863, and 1108 phosphorylated proteins were identified from normal lung fibroblasts (MRC-5), low metastatic lung cancer cells (95C), and high metastatic lung cancer cells (95D), respectively, using the optimized Ti⁴⁺-IMAC method. Among them, 317 phosphorylated proteins were shared among the three groups. The protein phosphorylation level increased significantly with increasing cellular metastatic capacity. In our study, 7560 phosphorylation sites were identified on 1268 phosphorylated proteins, among which 1130 phosphorylation sites were differentially expressed. Some abnormally expressed kinases and their phosphorylation levels are closely associated with malignant cell proliferation. Comparative bioinformatics analysis showed that dysregulated phosphoproteins were mainly related to cell migration functions, such as cell invasion, migration, and death. These abnormally expressed phosphorylated proteins and phosphorylation sites could be further validated and studied for lung cancer metastasis. Our study demonstrates that Ti⁴⁺-IMAC is a powerful tool for conducting cancer metastasis-related phosphoproteome research. By optimizing the phosphopeptide enrichment strategy, our data preliminarily clarified the correlation between the abnormality of the phosphoprotein network and lung cancer metastasis. This is expected to be useful for studying phosphorylation sites, phosphorylated proteins, and their signaling pathways related to lung cancer progression.