Quantitative SWATH-Based Proteomic Profiling for Identification of Mechanism-Driven Diagnostic Biomarkers Conferring in the Progression of Metastatic Prostate Cancer

Abstract

Prostate cancer (PCa), the most frequently diagnosed malignancy in men is associated with significant mortality and morbidity. Therefore, demand exists for the identification of potential biomarkers for patient stratification according to prognostic risks and the mechanisms involved in cancer development and progression to avoid over/under treatment of patients and prevent relapse. Quantitative proteomic mass spectrometry profiling and gene enrichment analysis of TGF-β induced-EMT in human Prostate androgen-dependent (LNCaP) and androgen-independent (PC-3) adenocarcinoma cell lines was performed to investigate proteomics involved in Prostate carcinogenesis and their effect onto the survival of PCa patients. Amongst 1,795 proteins, which were analyzed, 474 proteins were significantly deregulated. These proteins contributed to apoptosis, gluconeogenesis, transcriptional regulation, RNA splicing, cell cycle, and MAPK cascade and hence indicating the crucial roles of these proteins in PCa initiation and progression. We have identified a panel of six proteins viz., GOT1, HNRNPA2B1, MAPK1, PAK2, UBE2N, and YWHAB, which contribute to cancer development, and the transition of PCa from androgen dependent to independent stages. The prognostic values of identified proteins were evaluated using UALCAN, GEPIA, and HPA datasets. The results demonstrate the utility of SWATH-LC-MS/MS for understanding the proteomics involved in EMT transition of PCa and identification of clinically relevant proteomic biomarkers.

SWATH-MS Based Proteomic Profiling of Prostate Cancer Cells Reveals Adaptive Molecular Mechanisms in Response to Anti-Androgen Therapy

“…We increased the depth of proteomic profiling in our cell models via SWATH-MS strategy: an accurate, highly reproducible label-free approach in whole proteome quantifi-cation [11,12]. Two recent studies that used SWATH-MS strategy on LNCaP cells validated the total number of proteins identified in our study [13][14][15]. In addition, we observed a limited correlation between PCa transcriptomic and proteomic datasets, in agreement with previous PCa omics-based research [16,17].…”

The Identification of Critical m6A RNA Methylation Regulators as Malignant Prognosis Factors in Prostate Adenocarcinoma

“…HNRNPA2B1 also highly expressed in CRPC and associated with tumor progression and prognosis (Cheng et al, 2020). Through quantitative proteomic mass spectrometry profiling, HNRNPA2B1 was likely involved in TGF-β induced-EMT transition of PC (Singh and Sharma, 2020). NXF1 matters in interaction between two m 6 A readers, YTHDC1 and SRSF3, for mRNA export promotion (Roundtree et al, 2017b).…”

Proteomic Landscape of Prostate Cancer: The View Provided by Quantitative Proteomics, Integrative Analyses, and Protein Interactomes

“…Cell lines may have very distinct proteomic and phosphoproteomic profiles compared to each other and to clinical samples, and cell lines are reported to have distinct phosphoproteomic profiles from primary and metastatic CRPC tissues [ 55 , 60 ]. Several studies have profiled the large-scale proteomes of prostate cancer cell lines, especially for PC-3 and LNCaP [ 96 , 98 ], and identified numerous proteins with different expression levels. Although the cell lines have differences in terms of their AR status and androgen-dependence (for example, PC-3 is androgen-independent (AI) and LNCaP is androgen-dependent (AD)), conclusions based on differences in DEPs between these cell lines in terms of androgen dependence should be validated by other assays.…”

“…Interestingly, in the castration-resistant line, induction of the cytoplasmic endoribonuclease microRNA regulator Dicer was found, indicating alterations in miRNA regulation in these cells. Singh and Sharma [ 98 ] analyzed protein expression phenotypes of prostate cancer cell lines PC-3 and LNCaP by SWATH quantitative MS upon TGF-b-induced epithelial to mesenchymal transition (EMT). In the AD LNCaP cell line, 2 proteins were significantly upregulated, and 126 were downregulated.…”