Phosphoproteomics of colon cancer metastasis: comparative mass spectrometric analysis of the isogenic primary and metastatic cell lines SW480 and SW620

Abstract

The contributions of phosphorylation-mediated signaling networks to colon cancer metastasis are poorly defined. To interrogate constitutive signaling alterations in cancer progression, the global phosphoproteomes of the patient-matched SW480 (primary colon tumor origin) and SW620 (lymph node metastasis) cell lines were compared with TiO2 and IMAC phosphopeptide enrichment followed by LC-MS/MS. Network analysis of the significantly altered phosphosites revealed differential regulation in cellular adhesion, mitosis, and mRNA translational machinery. mRNA biogenesis and splicing, transport through the nuclear pores, initiating translation, as well as mRNA stability and degradation were also affected. Though alterations in these processes have been associated with oncogenic transformation, control of mRNA stability has typically not been associated with cancer progression. Notably, the single phosphosite with the greatest relative change in SW620 was Ser2 on eukaryotic initiation factor 2 subunit 2 (eIF2S2), suggesting that SW620 cells translate faster or with greater efficiency than SW480 cells. These broad changes in the regulation of translation also occur without over-expression of eukaryotic initiation factor 4E (eIF4E). The findings suggest that metastatic cells exhibit constitutive changes to the phosphoproteome, and that mRNA stability and translational efficiency may be important targets of deregulation during cancer progression.

Qualitative and quantitative top-down proteomics of human colorectal cancer cell lines identified 23000 proteoforms and revealed drastic proteoform-level differences between metastatic and non-metastatic cancer cells

“…New insights into the molecular mechanisms of CRC metastasis will undoubtedly be beneficial for developing more effective drugs. [3][4][5] Extensive studies have been completed with the goal of understanding CRC metastasis at the transcriptome level, generating tremendous information about the landscape of mRNA across different stages of CRC. [6,7] However, nucleic-acid-based measurements do not correlate with protein abundance, which are the primary effectors of function in biology.…”

“…[8] Quantitative bottom-up proteomics (BUP) studies of metastatic and nonmetastatic CRC cell lines have been completed to discover new protein regulators involved in CRC metastasis. [4,9,10] Unfortunately, those BUP studies provided limited information of the proteoforms. These proteoforms represent all possible protein molecules derived from the same gene resulting from genetic variations, RNA alternative splicing, and protein post-translational modifications (PTMs).…”

Proteomics of Colorectal Cancer: Tumors, Organoids, and Cell Cultures—A Minireview

“… Ludvigsen et al (2020) compared a normal derived colon mucosa cell line (NCM460) and a colon cancer cell line (HCT116) to identify protein biomarkers with increased expression in colorectal cancer, including retinol-binding protein 1. 2D cell culture has also been used to compare non-metastatic (SW480) and metastatic colon cancer cell lines (SW620) ( Zhao et al, 2007 ; Schunter et al, 2017 ; Torres et al, 2018 ). These two cell lines derive from the same patient (Stage II for SW480 and Stage III for SW620).…”

Recent Advances of Functional Proteomics in Gastrointestinal Cancers- a Path towards the Identification of Candidate Diagnostic, Prognostic, and Therapeutic Molecular Biomarkers

“…Moreover, the greatest increase in phosphorylation of Ser2 of eIF2S2 without any changes in eukaryotic initiation factor 4E (eIF4E) expression was observed in the SW620 cell line. Altogether, they suggested that metastatic cells deregulate mRNA stability and translational efficiency with constitutive changes to the phosphoproteome [ 89 ]. In another study, the phosphorylation ratio of serine, threonine and tyrosine amino acids was identified as 90%, 10% and <1% respectively (8).…”