Phosphoproteomic strategies in cancer research: a minireview

Sürmen, Mustafa Gani; Sürmen, Saime; Ali, Asghar; Musharraf, Syed Ghulam; Emekli, Nesrin

doi:10.1039/d0an00915f

Cited by 11 publications

(9 citation statements)

References 251 publications

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“…Innovative, highly sensitive and high-throughput proteomics techniques contributed to accurately assess biomarkers in cancer development and evaluate the role of important proteins in cancer, thereby aiding in precise diagnosis and treatment [ 27 ]. The core challenge of phosphorylated proteomics is to enrich low abundance phosphorylated peptides in the proteome and detect highly sensitive means [ 28 ]. In this study, we used Superbinder beads to enrich pY sites of tyrosine kinase and to quantify intracellular tyrosine kinases.…”

Section: Discussionmentioning

confidence: 99%

Superbinder based phosphoproteomic landscape revealed PRKCD_pY313 mediates the activation of Src and p38 MAPK to promote TNBC progression

Deng,

Hou,

et al. 2024

Cell Commun Signal

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Phosphorylation proteomics is the basis for the study of abnormally activated kinase signaling pathways in breast cancer, which facilitates the discovery of new oncogenic agents and drives the discovery of potential targets for early diagnosis and therapy of breast cancer. In this study, we have explored the aberrantly active kinases in breast cancer development and to elucidate the role of PRKCD_pY313 in triple negative breast cancer (TNBC) progression. We collected 47 pairs of breast cancer and paired far-cancer normal tissues and analyzed phosphorylated tyrosine (pY) peptides by Superbinder resin and further enriched the phosphorylated serine/threonine (pS/pT) peptides using TiO2 columns. We mapped the kinases activity of different subtypes of breast cancer and identified PRKCD_pY313 was upregulated in TNBC cell lines. Gain-of-function assay revealed that PRKCD_pY313 facilitated the proliferation, enhanced invasion, accelerated metastasis, increased the mitochondrial membrane potential and reduced ROS level of TNBC cell lines, while Y313F mutation and low PRKCD_pY313 reversed these effects. Furthermore, PRKCD_pY313 significantly upregulated Src_pY419 and p38_pT180/pY182, while low PRKCD_pY313 and PRKCD_Y313F had opposite effects. Dasatinib significantly inhibited the growth of PRKCD_pY313 overexpression cells, and this effect could be enhanced by Adezmapimod. In nude mice xenograft model, PRKCD_pY313 significantly promoted tumor progression, accompanied by increased levels of Ki-67, Bcl-xl and Vimentin, and decreased levels of Bad, cleaved caspase 3 and ZO1, which was opposite to the trend of Y313F group. Collectively, the heterogeneity of phosphorylation exists in different molecular subtypes of breast cancer. PRKCD_pY313 activates Src and accelerates TNBC progression, which could be inhibited by Dasatinib.

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Section: Discussionmentioning

confidence: 99%

Superbinder based phosphoproteomic landscape revealed PRKCD_pY313 mediates the activation of Src and p38 MAPK to promote TNBC progression

Deng,

Hou,

et al. 2024

Cell Commun Signal

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“…In addition, sample complexity can reduce the number of defined phosphoproteins. The numbers of phosphoproteins defined for such reasons are much lower than the entire proteome (Sürmen et al, 2020). The "whole body" phosphoproteome of zebrafish is quite complex compared to other biological materials.…”

Section: Discussionmentioning

confidence: 99%

“…Mass spectrometers (MS), capable of profiling thousands of proteins in a single experiment, paved the way for large-scale studies in the characterization of phosphorylated proteins. Therefore mass spectrometry (MS)-based phosphoproteomic methods are used to discover specific signaling events in special molecular pathways through identification and quantification of phosphoproteins as well as the detection of modification sites (Sürmen et al,2020). This method can be applied to reveal different biological processes in toxicological and pharmacological research (von Stechow et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

Quantitative phosphoproteomics to resolve the cellular responses to octanoic acid in rotenone exposed zebrafish

Sürmen

Cansız

et al. 2021

J Food Biochem

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Ketosis is a potentially beneficial metabolic state for health especially in neurological conditions including Parkinson's disease (PD). Medium-chain-triglycerides (MCT) have specific metabolic properties and they are described as ketogenic even without restriction of carbohydrate. Octanoic acid (C8) is the main MCT showing this effect.Rotenone is a neurotoxin that is used to induce experimental PD model. Rotenone inhibits mitochondrial respiratory complex 1 (MRC1) and causes reactive oxygen species formation. Mass spectrometry (MS)-based phosphoproteomic methods enable discovering specific signaling events in special molecular pathways through identification and quantification of phosphoproteins. Signaling networks involved in rotenonemediated biological processes and beneficial effects of MCTs on neurodegenerative diseases are not well understood. We aimed to gain comprehensive molecular perspective on the global phosphoproteome differences in rotenone-exposed zebrafish treated with octanoic acid. Raw files obtained from MS analysis were processed and searched against the Danio rerio protein database using SEQUEST-HT algorithm to identify and quantify phosphopeptides with 2,569 unique phosphoproteins and 4,161 unique phosphopeptides corresponding to 2005 proteins. Microtubuleassociated protein (MAP) family members were significantly lower in rotenone group.Phosphoproteins involved in ion binding (calcium, magnesium, zinc ion), oxygen binding, microtubule binding, ATP-and GTP-binding were among differentially expressed 347 proteins in rotenone group and they were reversed after octanoic acid treatments. Phosphoproteins and phosphorylation sites were identified for future exploration of signaling pathways involved in rotenone toxicity. We believe our findings might help in the formulation of effective therapeutic strategies for the treatment of PD using ketogenic formulations involving MCTs. Practical applicationsKetosis is a potentially beneficial metabolic state for health especially in neurological conditions including Parkinson's disease (PD). Medium-chain-triglycerides (MCT) (C6-C12) have specific metabolic properties making them described as ketogenic even without restriction of carbohydrate. Octanoic acid (caprylic acid, C8) is the main MCT showing this effect. Our findings might help in the formulation of effective

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“…Phosphopeptides comprise less than 2–3% of peptides in a typical tryptic digest, which limits the phosphorylation analysis for trace samples. , Especially in clinical studies, the High-Select Fe-NTA Phosphopeptide Enrichment Kit (Thermo Scientific, MO, USA) was widely used, for which at least 500 μg of peptides was required. − However, this limits the application on some rare and precious samples such as fine-needle aspiration biopsies that a tumor area of <5 mm 2 (10 μm thick) only yields 70 μg of protein . Numerous strategies have been made for effective and selective enrichment of phosphopeptides and even for mini-scale samples. − One high-throughput workflow called easyPhos quantified over 15,000 phosphopeptides with 200 μg of protein starting material . Moreover, a rapid-robotic phosphoproteomics (R2-P2) workflow has enriched ∼4000 phosphopeptides in 25 μg of proteins with great reproducibility and stability .…”

Section: Introductionmentioning

confidence: 99%

Rapid and High-Sensitive Phosphoproteomics Elucidated the Spatial Dynamics of the Mouse Brain

Yang

Han

et al. 2023

Anal. Chem.

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Recent developments in phosphoproteomics have enabled signaling studies where over 10,000 phosphosites can be routinely identified and quantified. Yet, current analyses are limited in sample size, reproducibility, and robustness, hampering experiments that involve low-input samples such as rare cells and fine-needle aspiration biopsies. To address these challenges, we introduced a simple and rapid phosphorylation enrichment method (miniPhos) that uses a minimal amount of the sample to get enough information to decipher biological significance. The miniPhos approach completed the sample pretreatment within 4 h and high effectively collected the phosphopeptides in a single-enrichment format with an optimized enrichment process and miniaturized system. This resulted in an average of 22,000 phosphorylation peptides quantified from 100 μg of proteins and even confidently localized over 4500 phosphosites from as little as 10 μg of peptides. Further application was carried out on different layers of mouse brain micro-sections; our miniPhos method provided quantitative information on protein abundance and phosphosite regulation for the most relevant neurodegenerative diseases, cancers, and signaling pathways in the mouse brain. Surprisingly, the phosphoproteome exhibited more spatial variations than the proteome in the mouse brain. Overall, spatial dynamics of phosphosites are integrated with proteins to gain insights into crosstalk of cellular regulation at different layers, thereby facilitating a more comprehensive understanding of mouse brain development and activity.

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Phosphoproteomic strategies in cancer research: a minireview

Abstract: Understanding the cellular processes is central to comprehend disease conditions and is also true for cancer research. Proteomic studies provide significant insight into the cancer mechanisms and aid in the...

Cited by 11 publications

References 251 publications

Superbinder based phosphoproteomic landscape revealed PRKCD_pY313 mediates the activation of Src and p38 MAPK to promote TNBC progression

Superbinder based phosphoproteomic landscape revealed PRKCD_pY313 mediates the activation of Src and p38 MAPK to promote TNBC progression

Quantitative phosphoproteomics to resolve the cellular responses to octanoic acid in rotenone exposed zebrafish

Rapid and High-Sensitive Phosphoproteomics Elucidated the Spatial Dynamics of the Mouse Brain

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