Unique Phosphosites Research Articles

A Semiautomated Proteomics and Phosphoproteomics Protocol for the Identification of Novel Therapeutic Targets and Predictive Biomarkers in In Vivo Xenograft Models of Pediatric Cancers.

Genomic profiling has identified therapeutic targets for precision treatment of certain cancers, but many patients lack actionable mutations. Additional omics approaches, like proteomics and phosphoproteomics, are essential for comprehensive mapping of cancer-associated molecular phenotypes. In vivo models, such as cell line and patient-derived xenografts (PDX), offer valuable insights into cancer biology and treatment strategies.This chapter presents a semiautomated high-throughput workflow for integrated proteomics and phosphoproteomics analysis on the Kingfish platform coupled with MagReSyn® Zr-IMAC HP. It enhances protein extraction from in vivo xenograft samples and provides better insights into cancers with poor prognosis. The approach successfully identified over 11,000 unique phosphosites and ~6000 proteins in SJSA-1 pediatric osteosarcoma xenografts, demonstrating its efficacy. This workflow is a valuable tool for studying tumor biology and developing precision oncology strategies.

289-OR: Defining Pathway-Selective Insulin Resistance in Type 2 Diabetes Using iPS Cell-Derived Hepatocytes

Hepatic insulin resistance is central to type 2 diabetes (T2D), fatty liver disease, and metabolic syndrome. To identify the fundamental, cell-autonomous defects underlying hepatic insulin resistance in T2D, we have used inducible human pluripotent stem (iPS) cells derived from 16 individuals with and without T2D differentiated to hepatocytes (iHeps) and studied in vitro. Consistent with pathway selective insulin resistance, we find that insulin failed to suppress gene expression of critical gluconeogenic enzymes (PCK1, G6PC) but continued to stimulate increased expression of the lipogenic enzymes, fatty acid synthase and acetyl Co-A carboxylase 1 in T2D iHeps. iHeps from T2D also displayed reduced insulin receptor tyrosine phosphorylation and reduced phosphorylation through the IRS/Akt pathway. Global phosphoproteomics in control and T2D iHeps identified 378 unique phosphosites regulated by insulin, and many dysregulated phosphosites within the classical insulin signaling pathway (IRS, AKT1/2, GSK3, FOXO1, RPS6KB1, TSC2) and components of gene transcription regulation, membrane trafficking, Rho-GTPases, vesicle transport. Using a kinome-wide data set created with synthetic peptide libraries to profile almost all functional known human serine/threonine kinases, we found the alterations in insulin signaling mapped to AKT, P70S6K, P90S6K, RSK, PKCτ, and SGK kinases. Thus, iHeps from T2D patients show pathway-selective insulin resistance with a loss of suppression of gluconeogenesis by insulin yet persistent activation of lipogenesis, even in vitro, in the absence of any circulating factor exposure. T2D iHeps also show a dysregulated phosphorylation network that provides new clues to the kinases whose action is altered in T2D and hepatic insulin resistance. Disclosure A.Gattu: None. A.Krook: None. J.R.Zierath: None. M.Mann: None. C.Kahn: None. Funding National Institutes of Health (T32DK007260-46)

151 TRPA1/V3-Dependent Regulation of Airway Epithelial Cell Damage and Repair Triggered by wood/Biomass Smoke Particulate

Abstract Wood/biomass smoke particulate material (WBSPM) is a pervasive environmental pollutant. Acute high-dose inhalation exposure can cause airway epithelial cell (AEC) damage and respiratory dysfunction. We hypothesized that AEC damage is limited by compensatory signaling to allow epithelial repair. RNA sequencing, proteomics, targeted interventions, and cultured human AECs treated with WBSPM and Transient Receptor Potential Ankyrin-1 (TRPA1) agonists revealed TRPA1-driven endoplasmic reticulum stress (ERS) and oxidative stress (OS) as contributory pathways to cytotoxicity. Alternatively, TRP vanilloid-3 (TRPV3) counteracted these events despite also being activated by WBSPM. Using the TRPA1 agonist AITC (and others) as a surrogate for WBSPM, morphological distortion indicative of AEC damage was observed 2-4h post-treatment; at >6h cells recovered. Strikingly, at 2h, the abundance of only 6 proteins changed including loss of fibronectin and tubulin and increased heme oxygenase 1. At 6h, 36 proteins changed, including ER chaperones and transcriptional/cell cycle regulatory proteins, OS-response, and structural/matrix proteins. Analysis of the phosphoproteome revealed changes in 2672 and 1886 unique phosphosites at 2 and 6h, attributable to PKC, p38 MAPK, EGFR, Akt and other kinase activities based on “phosphosite-GSEA” analysis. A kinase inhibitor screen linked PKC, p38 MAPK, GSK3b and ERK1/2 with cytotoxicity, while EGFR, MEK1/2, JNK1/2/3 and Akt were protective. Considering that TRPV3 expression is regulated by EGFR following WBSPM injury and TRPV3 enhanced adhesion and slowed proliferation via attenuated EGFR signaling, we propose a mechanism whereby the balance of TRPA1, TRPV3, and calcium/growth factor receptor-dependent kinase signaling coordinates WBSPM injury, compensation and repair.

Abstract 2023: CoPheeMap: a co-regulation map of 30,000 phosphosite illuminates the dark cancer phosphoproteome

Abstract Mass spectrometry-based phosphoproteomics enables proteome-wide analysis of protein phosphorylation in biological samples. As a prime example, the Clinical Proteomic Tumor Analysis Consortium (CPTAC) has performed phosphoproteomic profiling for 1,191 tumors spanning 11 cancer types, generating quantitative data on 77,442 phosphosites. Despite the impressive data generation power, only less than 5% of these phosphosites have been associated with a regulatory kinase or biological function, and 90% of these annotated phosphosites were associated with 20% well-studied kinases. The “dark” phosphoproteome greatly limits our ability to gain functional insights into cancer signaling. Previous research has shown that co-regulation is a strong indicator of functional association. Here we leveraged machine learning and the vast amount of CPTAC data to build a co-regulation map of phosphosites to facilitate functional interpretation of phosphoproteomics findings. Based on a ground-truth dataset including 98,402 pairs of phosphosites known to be regulated by the same kinase (positives) and 1,317,273 pairs by kinases from distant kinase families (negatives), we developed an Extreme Gradient Boosting (XGBoost) classifier to distinguish the positive and negative pairs using CPTAC phosphoproteomic data, protein-protein interaction data, and phosphopeptide sequences. Applying the trained classifier to 3 billion phosphosite pairs identified 2,569,519 (0.08%) with high probability of co-regulation, i.e., 400 times more likely to connect positive pairs than negative pairs in an independent ground-truth dataset. These pairs constituted a co-regulation map of 30,499 unique phosphosites, called CoPheeMap.To demonstrate the utility of CoPheeMap, we integrated its network embedding features, embedding features from a kinase network, together with Position-Specific Scoring Matrices scores and site-kinase abundance associations to develop a XGBoost model to predict kinase substrate associations (KSAs). The resulted model CoPheeKSA showed superior performance with an AUROC of 0.97 and identified 12,000 high-quality novel KSAs involving 7,908 phosphosites. In another application, CoPheeMap based information propagation (CoPheeProp) assigned 5,000 phosphosites to different signaling pathways with high specificity, increasing existing knowledge by 9-fold. Applying CoPheeMap and the derived tools to CPTAC and other cancer phosphoproteomics datasets revealed regulatory and functional information for previously unannotated sites showing strong associations with somatic mutations and cancer phenotypes, leading to actionable mechanistic and therapeutic insights. Together, CoPheeMap, CoPheeKSA and CoPheeProp provide a systematic framework to illuminate the dark phosphoproteome and have broad applications ranging from basic cancer biology research to clinical investigations. Citation Format: Wen Jiang, Eric Jaehnig, Bing Zhang. CoPheeMap: a co-regulation map of 30,000 phosphosite illuminates the dark cancer phosphoproteome [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2023.

Data-Independent Acquisition Phosphoproteomics of Urinary Extracellular Vesicles Enables Renal Cell Carcinoma Grade Differentiation

Translating the research capability and knowledge in cancer signaling into clinical settings has been slow and ineffective. Recently, extracellular vesicles (EVs) have emerged as a promising source for developing disease phosphoprotein markers to monitor disease status. This study focuses on the development of a robust data-independent acquisition (DIA) using mass spectrometry to profile urinary EV phosphoproteomics for renal cell cancer (RCC) grades differentiation. We examined gas-phase fractionated library, direct DIA (library-free), forbidden zones, and several different windowing schemes. After the development of a DIA mass spectrometry method for EV phosphoproteomics, we applied the strategy to identify and quantify urinary EV phosphoproteomes from 57 individuals representing low-grade clear cell RCC, high-grade clear cell RCC, chronic kidney disease, and healthy control individuals. Urinary EVs were efficiently isolated by functional magnetic beads, and EV phosphopeptides were subsequently enriched by PolyMAC. We quantified 2584 unique phosphosites and observed that multiple prominent cancer-related pathways, such as ErbB signaling, renal cell carcinoma, and regulation of actin cytoskeleton, were only upregulated in high-grade clear cell RCC. These results show that EV phosphoproteome analysis utilizing our optimized procedure of EV isolation, phosphopeptide enrichment, and DIA method provides a powerful tool for future clinical applications.

UHMK1 is a novel splicing regulatory kinase

The U2AF Homology Motif Kinase 1 (UHMK1) is the only kinase that contains the U2AF homology motif, a common protein interaction domain among splicing factors. Through this motif, UHMK1 interacts with the splicing factors SF1 and SF3B1, known to participate in the 3' splice site recognition during the early steps of spliceosome assembly. Although UHMK1 phosphorylates these splicing factors invitro, the involvement of UHMK1 in RNA processing has not previously been demonstrated. Here, we identify novel putative substrates of this kinase and evaluate UHMK1 contribution to overall gene expression and splicing, by integrating global phosphoproteomics, RNA-seq, and bioinformatics approaches. Upon UHMK1 modulation, 163 unique phosphosites were differentially phosphorylated in 117 proteins, of which 106 are novel potential substrates of this kinase. Gene Ontology analysis showed enrichment of terms previously associated with UHMK1 function, such as mRNA splicing, cell cycle, cell division, and microtubule organization. The majority of the annotated RNA-related proteins are components of the spliceosome but are also involved in several steps of gene expression. Comprehensive analysis of splicing showed that UHMK1 affected over 270 alternative splicing events. Moreover, splicing reporter assay further supported UHMK1 function on splicing. Overall, RNA-seq data demonstrated that UHMK1 knockdown had a minor impact on transcript expression and pointed to UHMK1 function in epithelial-mesenchymal transition. Functional assays demonstrated that UHMK1 modulation affects proliferation, colony formation, and migration. Taken together, our data implicate UHMK1 as a splicing regulatory kinase, connecting protein regulation through phosphorylation and gene expression in key cellular processes.

The Mycobacterium tuberculosis protein O-phosphorylation landscape.

Bacterial phosphosignalling has been synonymous with two-component systems and their histidine kinases, but many bacteria, including Mycobacterium tuberculosis (Mtb), also code for Ser/Thr protein kinases (STPKs). STPKs are the main phosphosignalling enzymes in eukaryotes but the full extent of phosphorylation on protein Ser/Thr and Tyr (O-phosphorylation) in bacteria is untested. Here we explored the global signalling capacity of the STPKs in Mtb using a panel of STPK loss-of-function and overexpression strains combined with mass spectrometry-based phosphoproteomics. A deep phosphoproteome with >14,000 unique phosphosites shows that O-phosphorylation in Mtb is a vastly underexplored protein modification that affects >80% of the proteome and extensively interfaces with the transcriptional machinery. Mtb O-phosphorylation gives rise to an expansive, distributed and cooperative network of a complexity that has not previously been seen in bacteria and that is on par with eukaryotic phosphosignalling networks. A resource of >3,700 high-confidence direct substrate-STPK interactions and their transcriptional effects provides signalling context for >80% of Mtb proteins and allows the prediction and assembly of signalling pathways for mycobacterial physiology.

Mutation of the RelA(p65) Thr505 phosphosite disrupts the DNA replication stress response leading to CHK1 inhibitor resistance.

Mutation of the RelA(p65) Thr505 phosphosite disrupts the DNA replication stress response leading to CHK1 inhibitor resistance.

Identification and characterization of the mediator kinase-dependent myometrial stem cell phosphoproteome

To identify, in myometrial stem/progenitor cells, the presumptive cell of origin for uterine fibroids, substrates of Mediator-associated cyclin dependent kinase 8/19 (CDK8/19), which is known to be disrupted by uterine fibroid driver mutations in Mediator complex subunit 12 (MED12). Experimental study. Academic research laboratory. Women undergoing hysterectomy for uterine fibroids. Stable isotopic labeling of amino acids in cell culture (SILAC) coupled with chemical inhibition of CDK8/19 and downstream quantitative phosphoproteomics and transcriptomic analyses in myometrial stem/progenitor cells. High-confidence Mediator kinase substrates identified by SILAC-based quantitative phosphoproteomics were determined using an empirical Bayes analysis and validated orthogonally by invitro kinase assay featuring reconstituted Mediator kinase modules comprising wild-type or G44D mutant MED12 corresponding to the most frequent uterine fibroid driver mutation in MED12. Mediator kinase-regulated transcripts identified by RNA sequencing were linked to Mediator kinase substrates by computational analyses. A total of 296 unique phosphosites in 166 proteins were significantly decreased (≥ twofold) upon CDK8/19 inhibition, including 118 phosphosites in 71 nuclear proteins representing high-confidence Mediator kinase substrates linked to RNA polymerase II transcription, RNA processing and transport, chromatin modification, cytoskeletal architecture, and DNA replication and repair. Orthogonal validation confirmed a subset of these proteins, including Cut Like Homeobox 1 (CUX1) and Forkhead Box K1 (FOXK1), to be direct targets of MED12-dependent CDK8 phosphorylation in a manner abrogated by the most common uterine fibroid driver mutation (G44D) in MED12, implicating these substrates in disease pathogenesis. Transcriptome-wide profiling of Mediator kinase-inhibited myometrial stem/progenitor cells revealed alterations in cell cycle and myogenic gene expression programs to which Mediator kinase substrates could be linked directly. Among these, CUX1 is an established transcriptional regulator of the cell cycle whose corresponding gene on chromosome 7q is the locus for a recurrent breakpoint in uterine fibroids, linking MED12 and Mediator kinase with CUX1 for the first time in uterine fibroid pathogenesis. FOXK1, a transcriptional regulator of myogenic stem cell fate, was found to be coordinately enriched along with kinase, but not core, Mediator subunits in myometrial stem/progenitor cells compared with differentiated uterine smooth muscle cells. These studies identify a new catalog of pathologically and biologically relevant Mediator kinase substrates implicated in the pathogenesis of MED12 mutation-positive uterine fibroids, and further uncover a biochemical basis to link Mediator kinase activity with CUX1 and FOXK1 in the regulation of myometrial stem/progenitor cell fate.

Hyperactivation of MEK/ERK pathway by Ca2+ /calmodulin-dependent protein kinase kinase 2promotes cellular proliferation by activating cyclin-dependent kinasesand minichromosome maintenance proteinin gastric cancer cells.

Although CAMKK2is overexpressed in several cancers, its role and relevant downstream signaling pathways in gastric cancer(GC) are poorly understood. Treatment of AGS GC cells with a CAMKK2 inhibitor, STO-609, resulted in decreased cell proliferation, cell migration, invasion, colony-forming ability, and G1/S-phase arrest. Quantitative phosphoproteomics in AGS cells with the CAMKK2 inhibitor led to the identification of 9603 unique phosphosites mapping to 3120 proteins. We observed decreased phosphorylation of 1101 phosphopeptides (1.5-fold) corresponding to 752 proteins upon CAMKK2 inhibition. Bioinformatics analysis of hypo-phosphorylated proteins revealed enrichment of MAPK1/MAPK3 signaling. Kinase enrichment analysis of hypo-phosphorylated proteins using the X2K Web tool identified ERK1, cyclin-dependant kinase 1 (CDK1), and CDK2 as downstream substrates of CAMKK2. Moreover, inhibition of CAMKK2 and MEK1 resulted in decreased phosphorylation of ERK1, CDK1, MCM2, and MCM3. Immunofluorescence results were in concordance with our mass spectroscopy data and Western blot analysis results. Taken together, our data reveal the essential role of CAMKK2 in the pathobiology of GC through the activation of the MEK/ERK1 signaling cascade.

Phosphoproteomics reveals NMDA receptor-mediated excitotoxicity as a key signaling pathway in the toxicity of gelsenicine

Gelsenicine is one of the most toxic compounds in the genus Gelsemium, but the mechanism of toxicity is not clear. In this paper, tandem mass tag quantitative phosphoproteomics was used to study the changes in protein phosphorylation in different brain regions at different time points after gelsenicine poisoning in mice. The correlation between neurotransmitter receptors and the toxicity of gelsenicine was analyzed by molecular docking and rescue experiments. Parallel reaction monitoring (PRM) was used to verify the related proteins. A total of 17877 unique phosphosites were quantified and mapped to 4170 brain proteins to understand the signaling pathways. Phosphoproteomics revealed gelsenicine poisoning mainly affected protein phosphorylation levels in the hippocampus, and through bioinformatics analysis, it was found gelsenicine poisoning significantly affected neurotransmitter synaptic pathway. The molecular docking results showed that gelsenicine could bind to the N-methyl-D-aspartic acid receptor (NMDAR). In addition, we found that NMDA was effective in improving the survival rate of the animals tested, and this effect was associated with reduced protein phosphorylation by PRM validation. The results revealed that gelsenicine affects neurotransmitter release and receptor function. This is the first demonstration that NMDA receptor-mediated excitotoxicity is a key signaling pathway in the toxicity of gelsenicine.

Phosphoproteomic Characterization of Primary AML Samples and Relevance for Response Toward FLT3-inhibitors.

Phosphoproteomic Characterization of Primary AML Samples and Relevance for Response Toward FLT3-inhibitors.

Global quantitative analysis of the human brain proteome and phosphoproteome in Alzheimer\u2019s disease

Alzheimer’s disease (AD) is characterized by an early, asymptomatic phase (AsymAD) in which individuals exhibit amyloid-beta (Aβ) plaque accumulation in the absence of clinically detectable cognitive decline. Here we report an unbiased multiplex quantitative proteomic and phosphoproteomic analysis using tandem mass tag (TMT) isobaric labeling of human post-mortem cortex (n = 27) across pathology-free controls, AsymAD and symptomatic AD individuals. With off-line high-pH fractionation and liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) on an Orbitrap Lumos mass spectrometer, we identified 11,378 protein groups across three TMT 11-plex batches. Immobilized metal affinity chromatography (IMAC) was used to enrich for phosphopeptides from the same TMT-labeled cases and 51,736 phosphopeptides were identified. Of these, 48,992 were quantified by TMT reporter ions representing 33,652 unique phosphosites. Two reference standards in each TMT 11-plex were included to assess intra- and inter-batch variance at the protein and peptide level. This comprehensive human brain proteome and phosphoproteome dataset will serve as a valuable resource for the identification of biochemical, cellular and signaling pathways altered during AD progression.

Time Course of Changes in Sorafenib-Treated Hepatocellular Carcinoma Cells Suggests Involvement of Phospho-Regulated Signaling in Ferroptosis Induction.

Ferroptosis is a form of regulated, non-apoptotic cell death characterized by excessive lipid peroxidation that can be triggered by inhibition of the cystine-glutamate antiporter, system Xc- . Sorafenib, an FDA-approved multi-kinase inhibitor drug that is used for treatment of hepatocellular carcinoma (HCC), has been shown to induce ferroptosis. Protein phosphorylation changes upon sorafenib treatment have been previously reported in patient studies and in cell culture. However, early phosphorylation changes during induction of ferroptosis are not reported. This work highlights these changes through a time course from 7 to 60min of sorafenib treatment in human (SKHep1) HCC cells. A total of 6170 unique phosphosites from 2381 phosphoproteins are quantified, and phosphorylation changes occur after as little as 30 min of sorafenib treatment. By 60 min, notable changes included phosphosites significantly changing on p53 (P04637), CAD protein (P27708), and proteins important for iron homeostasis, such as heavy chain ferritin (FTH1; P02794), heme oxygenase 1 (HMOX1; P09601), and PCBP1 (Q15365). Additional sites on proteins in key regulatory pathways are identified, including sites in ferroptosis-related proteins, indicating the likely involvement of phospho-regulated signaling during ferroptosis induction.

Phosphoproteomics reveals conserved exercise-stimulated signaling and AMPK regulation of store-operated calcium entry.

Exercise stimulates cellular and physiological adaptations that are associated with widespread health benefits. To uncover conserved protein phosphorylation events underlying this adaptive response, we performed mass spectrometry-based phosphoproteomic analyses of skeletal muscle from two widely used rodent models: treadmill running in mice and insitu muscle contraction in rats. We overlaid these phosphoproteomic signatures with cycling in humans to identify common cross-species phosphosite responses, as well as unique model-specific regulation. We identified >22,000 phosphosites, revealing orthologous protein phosphorylation and overlapping signaling pathways regulated by exercise. This included two conserved phosphosites on stromal interaction molecule 1 (STIM1), which we validate as AMPK substrates. Furthermore, we demonstrate that AMPK-mediated phosphorylation of STIM1 negatively regulates store-operated calcium entry, and this is beneficial for exercise in Drosophila. This integrated cross-species resource of exercise-regulated signaling in human, mouse, and rat skeletal muscle has uncovered conserved networks and unraveled crosstalk between AMPK and intracellular calcium flux.

Profiling of Histidine Phosphoproteome in Danio rerio by TiO2 Enrichment.

Histidine phosphorylation is a reversible post-translational modification that is known to regulate signal transduction in prokaryotes. However, functional studies in eukaryotes have been largely neglected due to the labile nature of N-linked phosphorylated amino acids. In an effort to help elucidate the heretofore hidden vertebrate phosphoproteome, this report presents a global phosphorylation analysis of Danio rerio (zebrafish) larvae. Phosphopeptide enrichment is performed using a TiO2 affinity technique. A total of 68 unique phosphohistidine sites are detected on 63 proteins among 1076 unique phosphosites on 708 proteins. Data are available via ProteomeXchange with identifier PXD012735. This report provides the first phosphohistidine dataset obtained from zebrafish.

Investigating the effect of target of rapamycin kinase inhibition on the Chlamydomonas reinhardtii phosphoproteome: from known homologs to new targets

Target of rapamycin (TOR) kinase is a conserved regulator of cell growth whose activity is modulated in response to nutrients, energy and stress. Key proteins involved in the pathway are conserved in the model photosynthetic microalga Chlamydomonas reinhardtii, but the substrates of TOR kinase and downstream signaling network have not been elucidated. Our study provides a new resource for investigating the phosphorylation networks governed by the TOR kinase pathway in Chlamydomonas. We used quantitative phosphoproteomics to investigate the effects of inhibiting Chlamydomonas TOR kinase on dynamic protein phosphorylation. Wild-type and AZD-insensitive Chlamydomonas strains were treated with TOR-specific chemical inhibitors (rapamycin, AZD8055 and Torin1), after which differentially affected phosphosites were identified. Our quantitative phosphoproteomic dataset comprised 2547 unique phosphosites from 1432 different proteins. Inhibition of TOR kinase caused significant quantitative changes in phosphorylation at 258 phosphosites, from 219 unique phosphopeptides. Our results include Chlamydomonas homologs of TOR signaling-related proteins, including a site on RPS6 with a decrease in phosphorylation. Additionally, phosphosites on proteins involved in translation and carotenoid biosynthesis were identified. Follow-up experiments guided by these phosphoproteomic findings in lycopene beta/epsilon cyclase showed that carotenoid levels are affected by TORC1 inhibition and carotenoid production is under TOR control in algae.

Brain Membrane Proteome and Phosphoproteome Reveal Molecular Basis Associating with Nursing and Foraging Behaviors of Honeybee Workers.

The brain is a vital organ in regulating complex social behaviors of honeybees including learning and memory. Knowledge of how brain membrane proteins and their phosphorylation underlie the age-related behavioral polyethism is still lacking. A hitherto age-resolved brain membrane proteome and phosphoproteome were reported in adult worker bees from two strains of honeybee (Apis mellifera ligustica): Italian bee (ITB) and Royal Jelly bee (RJB), a line selected from ITB for increased RJ outputs over four decades. There were 1079 membrane protein groups identified, and 417 unique phosphosites were located in 179 membrane protein groups mainly phosphorylated by kinase families of MAPKs, CDKs, and CK2. Age-resolved dynamics of brain membrane proteome and phosphoproteome are indicative of their correlation with the neurobiological requirements during the adult life of honeybee workers. To stimulate immature brain cell development in newly emerged bees (NEBs), the enriched functional classes associated with metabolism of carbohydrates, nucleosides, and lipids by the up-regulated proteins suggest their enhanced role in driving cell maturity of the brain. In nurse bees (NBs) and forager bees (FBs), a higher number of membrane proteins and phosphoproteins were expressed as compared with in the young stages, and the enriched signal-transduction-related pathways by the up-regulated proteins suggest their significances in sustaining the intensive information processing during nursing and foraging activities. Notably, RJB has shaped unique membrane proteome and phosphoproteome settings to consolidate nursing and foraging behaviors in response to decades of selection underpinning the elevated RJ yields. In RJB NBs, the enriched pathways of phosphatidylinositol signaling and arachidonic acid metabolism indicate a stronger olfaction sensation in response to larval pheromone stimulation. In RJB FBs, the enriched pathways related to signal processing such as SNARE interactions in vesicular transport, wnt signaling, TGF-beta signaling, and taurine and hypotaurine metabolism suggest an enhanced nerve sensitivity to prime the stronger tendency to pollen collection. Our data gain a novel insight into membrane proteome and phosphoproteome-driven cerebral regulation of honeybee behaviors, which is potentially useful for further neurobiological investigation in both honeybees and other social insects.

Quantitative Phosphoproteomic Analysis Reveals Key Mechanisms of Cellular Proliferation in Liver Cancer Cells

Understanding the mechanisms of uncontrolled proliferation in cancer cells provides valuable insights into tumor development and is benefit for discovering efficient methods in cancer treatment. In this study, we identified and quantified 2,057 phosphoproteins and 9,824 unique phosphosites in three liver cell lines with high (QGY, Hep3B) and low (L02) proliferative potentials and disclosed the wide variations in phosphorylation sites and levels among them. We found that the number of identified phosphoproteins and phosphosites in these cells were negatively correlated with their proliferative abilities. The function analysis suggested that the aberrant phosphorylation of SR proteins and activation of MAPK pathway might be two critical factors to promote cancer cell proliferation. Meanwhile, the phosphorylation status of mini-chromosome maintenance (MCM) and nuclear pore (NPC) complexes are significantly different between cell lines with high and low proliferative potentials. Furthermore, the phosphosites targeted by kinase families of CDK, STE and HIPK in the proteins coded by cancer driver genes showed distinct profiles between caner and normal cell lines. These results present key phosphorylation networks involving in abnormal proliferation of cancer cells and uncovered potential molecular markers for estimating the proliferation ability of liver cancer cells.

Altered signaling associated with chronic arsenic exposure in human skin keratinocytes.

Modulation of signaling pathways upon chronic arsenic exposure remains poorly studied. Here, we carried out SILAC-based quantitative phosphoproteomics analysis to dissect the signaling induced upon chronic arsenic exposure in human skin keratinocyte cell line, HaCaT. We identified 4171 unique phosphosites derived from 2000 proteins. We observed differential phosphorylation of 406 phosphosites (twofold) corresponding to 305 proteins. Several pathways involved in cytoskeleton maintenance and organization were found to be significantly enriched (p<0.05). Our data revealed altered phosphorylation of proteins associated with adherens junction remodeling and actin polymerization. Kinases such as protein kinase C iota type (PRKCI), mitogen-activated protein kinase kinase kinase 1 (MAP3K1), tyrosine-protein kinase BAZ1B (BAZ1B) and STE20 like kinase (SLK) were found to be hyperphosphorylated. Our study provides novel insights into signaling perturbations associated with chronic arsenic exposure in human skin keratinocytes. All MS/MS data have been deposited to the ProteomeXchange with identifier PXD004868.