Principles of phosphoproteomics and applications in cancer research

Abstract

Phosphorylation constitutes the most common and best-studied regulatory post-translational modification in biological systems and archetypal signalling pathways driven by protein and lipid kinases are disrupted in essentially all cancer types. Thus, the study of the phosphoproteome stands to provide unique biological information on signalling pathway activity and on kinase network circuitry that is not captured by genetic or transcriptomic technologies. Here, we discuss the methods and tools used in phosphoproteomics and highlight how this technique has been used, and can be used in the future, for cancer research. Challenges still exist in mass spectrometry phosphoproteomics and in the software required to provide biological information from these datasets. Nevertheless, improvements in mass spectrometers with enhanced scan rates, separation capabilities and sensitivity, in biochemical methods for sample preparation and in computational pipelines are enabling an increasingly deep analysis of the phosphoproteome, where previous bottlenecks in data acquisition, processing and interpretation are being relieved. These powerful hardware and algorithmic innovations are not only providing exciting new mechanistic insights into tumour biology, from where new drug targets may be derived, but are also leading to the discovery of phosphoproteins as mediators of drug sensitivity and resistance and as classifiers of disease subtypes. These studies are, therefore, uncovering phosphoproteins as a new generation of disruptive biomarkers to improve personalised anti-cancer therapies.

Interplay of oxidative stress, cellular communication and signaling pathways in cancer

“…Proteomic approaches like Redox Proteomics specifically identify proteins that undergo oxidative modifications, providing insights into cancer pathology [ 80 ]. Phosphoproteomics techniques identify oxidative stress-induced phosphorylation changes, crucial in oncogenic signaling pathways [ 81 ]. Metabolomic techniques such as targeted Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) are used for the quantification of specific metabolites like glutathione, directly involved in redox homeostasis [ 82 ].…”

“… Redox Proteomics [ 80 ] Phosphoproteomics Identification of oxidative stress-induced phosphorylation changes. [ 81 ] Metabolomic Techniques Quantification of specific metabolites like glutathione. Targeted LC-MS/MS, Untargeted Metabolomics [ 82 ] [ 83 ]; Imaging Techniques In vivo visualization and real-time monitoring of ROS levels.…”

Phosphoproteomic analysis reveals the diversity of signaling behind ErbB inhibitor-induced phenotypes

“…1A). The phosphopeptides from the embryos were enriched and analyzed with protein mass spectrometry using data-independent acquisition with MS/MS (Gerritsen & White, 2021; Higgins et al, 2023). In total 23,141 unique phosphopeptides were detected (Supplemental Table 1) and the quantities of 2033 phosphopeptides were significantly altered between treatments (Supplemental Table 2).…”

The Future of Precision Oncology

“…One advantage of proteomics and phosphoproteomics is the ability to provide a direct assessment of the tumor phenotype, rather than using genomic or transcriptomic biomarkers as surrogates to predict drug vulnerabilities [ 93 , 94 ]. Proteomic approaches can be used to detect non-genomic events, including epigenetic changes or influences from the TME, and some preclinical studies have already demonstrated that these approaches may be more reliable predictors of clinical response to treatment than alternative methods [ 94 , 95 , 96 ]. However, the clinical utility of proteomic markers depends on further retrospective analysis of clinical data to refine hypotheses and the success of their validation through prospective clinical trials [ 96 ].…”