Phosphomatics: interactive interrogation of substrate–kinase networks in global phosphoproteomics datasets

Leeming, Michael G.; O’Callaghan, Sean; Licata, Luana; Iannuccelli, Marta; Surdo, Prisca Lo; Micarelli, Elisa; C, Ang; Nie, Shuai; Varshney, Swati; Ameen, S. Sadia; Cheng, Heung‐Chin; Williamson, Nicholas A.

doi:10.1093/bioinformatics/btaa916

Cited by 13 publications

(16 citation statements)

References 17 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…(A) Experimental design of phosphoproteome analysis of hTSCs in response to EP-sEVs. (B) Relative abundance of the quantified phosphoproteome before and after z-score normalization [phosphomatics ( Leeming et al, 2021 )]. Boxes capture lower quartile and upper quartile with median displayed; whiskers min/max.…”

Section: Resultsmentioning

confidence: 99%

“…Data analysis was performed using Perseus of the MaxQuant computational platform ( Tyanova et al, 2016 ), phosphomatics ( Leeming et al, 2021 ), Kinase Enrichment Analysis 3 (KEA3) ( Kuleshov et al, 2021 ) and R programming language ( Notaras et al, 2021a ; Notaras et al, 2021b ). Protein intensities were log2 transformed and subjected to principal component analysis (PCA) with missing values imputed from normal distribution (width 0.3, downshift 1.8) and Student’s t-test.…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Endometrial small extracellular vesicles regulate human trophectodermal cell invasion by reprogramming the phosphoproteome landscape

Fatmous

Rai

Poh

et al. 2022

Front. Cell Dev. Biol.

View full text Add to dashboard Cite

A series of cyclical events within the uterus are crucial for pregnancy establishment. These include endometrial regeneration following menses, under the influence of estrogen (proliferative phase), then endometrial differentiation driven by estrogen/progesterone (secretory phase), to provide a microenvironment enabling attachment of embryo (as a hatched blastocyst) to the endometrial epithelium. This is followed by invasion of trophectodermal cells (the outer layer of the blastocyst) into the endometrium tissue to facilitate intrauterine development. Small extracellular vesicles (sEVs) released by endometrial epithelial cells during the secretory phase have been shown to facilitate trophoblast invasion; however, the molecular mechanisms that underline this process remain poorly understood. Here, we show that density gradient purified sEVs (1.06–1.11 g/ml, Alix+ and TSG101+, ∼180 nm) from human endometrial epithelial cells (hormonally primed with estrogen and progesterone vs. estrogen alone) are readily internalized by a human trophectodermal stem cell line and promote their invasion into Matrigel matrix. Mass spectrometry-based proteome analysis revealed that sEVs reprogrammed trophectoderm cell proteome and their cell surface proteome (surfaceome) to support this invasive phenotype through upregulation of pro-invasive regulators associated with focal adhesions (NRP1, PTPRK, ROCK2, TEK), embryo implantation (FBLN1, NIBAN2, BSG), and kinase receptors (EPHB4/B2, ERBB2, STRAP). Kinase substrate prediction highlighted a central role of MAPK3 as an upstream kinase regulating target cell proteome reprogramming. Phosphoproteome analysis pinpointed upregulation of MAPK3 T204/T202 phosphosites in hTSCs following sEV delivery, and that their pharmacological inhibition significantly abrogated invasion. This study provides novel molecular insights into endometrial sEVs orchestrating trophoblast invasion, highlighting the microenvironmental regulation of hTSCs during embryo implantation.

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Endometrial small extracellular vesicles regulate human trophectodermal cell invasion by reprogramming the phosphoproteome landscape

Fatmous

Rai

Poh

et al. 2022

Front. Cell Dev. Biol.

View full text Add to dashboard Cite

show abstract

“…We performed kinase-substrate analysis to elucidate the overall activity of kinases involved in the MAP3K1 and MAP3K4 cascades. Substrate-kinase relationships were searched using a combination of Phosphomatics ( , accessed on 5 April 2020) [ 67 ], Signor 2.0 ( , accessed on 5 April 2020) [ 68 ], and PhosphoSitePlus ( , accessed on 5 April 2020) [ 69 ] to determine the upstream kinases responsible for significantly changed phosphosites. A comparison of the number of site- or protein-level changes for each kinase was also performed.…”

Section: Methodsmentioning

confidence: 99%

Oestrogen Activates the MAP3K1 Cascade and β-Catenin to Promote Granulosa-like Cell Fate in a Human Testis-Derived Cell Line

Stewart

Bernard

et al. 2021

IJMS

Self Cite

View full text Add to dashboard Cite

Sex determination triggers the differentiation of the bi-potential gonad into either an ovary or testis. In non-mammalian vertebrates, the presence or absence of oestrogen dictates gonad differentiation, while in mammals, this mechanism has been supplanted by the testis-determining gene SRY. Exogenous oestrogen can override this genetic trigger to shift somatic cell fate in the gonad towards ovarian developmental pathways by limiting the bioavailability of the key testis factor SOX9 within somatic cells. Our previous work has implicated the MAPK pathway in mediating the rapid cellular response to oestrogen. We performed proteomic and phosphoproteomic analyses to investigate the precise mechanism through which oestrogen impacts these pathways to activate β-catenin—a factor essential for ovarian development. We show that oestrogen can activate β-catenin within 30 min, concomitant with the cytoplasmic retention of SOX9. This occurs through changes to the MAP3K1 cascade, suggesting this pathway is a mechanism through which oestrogen influences gonad somatic cell fate. We demonstrate that oestrogen can promote the shift from SOX9 pro-testis activity to β-catenin pro-ovary activity through activation of MAP3K1. Our findings define a previously unknown mechanism through which oestrogen can promote a switch in gonad somatic cell fate and provided novel insights into the impacts of exogenous oestrogen exposure on the testis.

show abstract

“…First, the summary report on top provides an overview of the total number of identified phosphosites, as well as the number and percentage of differentially expressed phosphosites across all experimental groups. This section also allows the download of summary reports and various data tables including a properly formatted input file for Phosphomatics, 15 which is a stand-alone tool designed to provide in-depth biological context for phosphoproteomic data sets.…”

Section: Phospho-analyst Output In the Absence Of Total Proteome Datamentioning

confidence: 99%

Phospho-Analyst: An Interactive, Easy-to-Use Web Platform To Analyze Quantitative Phosphoproteomics Data

et al. 2023

View full text Add to dashboard Cite

Phosphoproteomics is nowadays the method of choice to comprehensively identify and quantify thousands of phosphorylated peptides and their associated proteins with the goal of interrogating changes in signal transduction pathways and other cellular processes. One of the most popular software suites to analyze phosphoproteomic data sets is MaxQuant, which converts mass spectrometric raw data into quantitative information on phosphopeptides and proteins. However, despite the increased utilization of phosphoproteomics in biomedical research, simple and user-friendly tools supporting downstream statistical analysis and interpretation of these highly complex outputs are still lacking. We have therefore developed Phospho-Analyst, which�similar to its sibling LFQ-Analyst�is an easy-to-use, interactive web application specifically designed to reproducibly perform differential expression analyses with "one click" and to visualize phosphoproteomic results in a meaningful and practical manner. Furthermore, if quantitative total proteomic information is available for the same samples, Phospho-Analyst automatically normalizes all phosphoproteomic results to underlying protein abundance levels, thereby ensuring that only genuine changes in phosphorylation events are considered. As such, Phospho-Analyst can not only be used by experienced proteomic veterans but also by researchers without any prior knowledge in (phospho)proteomics, statistics, or bioinformatics. Phospho-Analyst, including a detailed manual, is freely available at https://analyst-suites.org/apps/phospho-analyst/.

show abstract

Phosphomatics: interactive interrogation of substrate–kinase networks in global phosphoproteomics datasets

Cited by 13 publications

References 17 publications

Endometrial small extracellular vesicles regulate human trophectodermal cell invasion by reprogramming the phosphoproteome landscape

Endometrial small extracellular vesicles regulate human trophectodermal cell invasion by reprogramming the phosphoproteome landscape

Oestrogen Activates the MAP3K1 Cascade and β-Catenin to Promote Granulosa-like Cell Fate in a Human Testis-Derived Cell Line

Phospho-Analyst: An Interactive, Easy-to-Use Web Platform To Analyze Quantitative Phosphoproteomics Data

Contact Info

Product

Resources

About