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RATIONALE Despite advances in mass spectrometry (MS)-based identification, effective phosphopeptide enrichment is a prerequisite towards comprehensive phosphoproteomic analysis. Based on the different binding affinities and coordination geometries of the Ti4+ and Fe3+ ions with the phosphate group, we report a complementary metal-directed immobilized metal ion affinity chromatography (IMAC) method to increase the identification coverage of a phosphoproteome. METHODS Phosphopeptides from standard phosphoproteins and Raji B cells were enriched from Ti4+-IMAC and Fe3+-IMAC methods, followed by matrix-assisted laser desorption/ionization (MALDI) MS and Orbitrap MS analysis. Optimal enrichment specificity was achieved by selection of acid structure/concentration and organic solvent to compete with non-phosphopeptides. The effect of the metal ion and the chelating compound was evaluated by the comparison of the characteristics of enriched phosphopeptides between Ti4+-IMAC, Fe3+-IMAC and TiO2 methods. RESULTS To address the low enrichment specificity of the Ti4+-IMAC method, a simple one-step acid/solvent controlled IMAC method was developed with significantly improved specificity (88%) and recovery (93%). The most striking discovery is that the optimal Ti4+-IMAC and Fe3+-IMAC methods have low overlapping percentage (10%) among the 2905 enriched phosphopeptides from Raji cells, comprised of the distinct characteristics including hydrophobicity, amino acid compositions, and frequency of multiple phosphorylation of the phosphopeptides. CONCLUSIONS The reported Fe3+-IMAC and Ti4+-IMAC methods can complementarily enrich acidic and basic phosphopeptides to effectively increase the identification coverage of an heterogeneous phosphoproteome (twice than the single approach). Given the reproducibility and low sample loss, the combination of our enrichment strategy with a quantitative technique could be feasible for quantitative phosphoproteomics. Copyright © 2012 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

Glioblastoma multiforme (GBM) is the most common and aggressive primary brain tumor. Patients diagnosed with GBM have a poor prognosis, and it has been reported that tumor malignancy and GBM recurrence are promoted by STAT3 signaling. As resveratrol (RV), a polyphenol in grapes, is reported to be a potent and non-toxic cancer-preventive compound, the aim of this study was to investigate the therapeutic effect and molecular mechanisms of RV on GBM-derived radioresistant tumor initiating cells (TIC). Firstly, our results showed that primary GBM-CD133+ TIC presented high tumorigenic and radiochemoresistant properties as well as increased protein levels of phosphorylated STAT3. We consistently observed that treatment with shRNA-STAT3 (sh-STAT3) or AG490, a STAT3 inhibitor, significantly inhibited the cancer stem-like cell properties and radioresistance of GBM-CD133+ in vitro and in vivo. Furthermore, treatment of GBM-CD133+ with 100 µM RV induced apoptosis and enhanced radiosensitivity by suppressing STAT3 signaling. Microarray results suggested that RV or AG490 inhibited the stemness gene signatures of GBM-CD133+ and facilitated the differentiation of GBM-CD133+ into GBM-CD133− or astrocytoma cells. Finally, xenotransplant experiments indicated that RV or sh-STAT3 therapy could significantly improve the survival rate and synergistically enhance the radiosensitivity of radiation-treated GBM-TIC. In summary, RV can reduce in vivo tumorigenicity and enhance the sensitivity of GBM-TIC to radiotherapies through the STAT3 pathway. J. Cell. Physiol. 227: 976-993, 2012. © 2011 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

In this study, a novel hemocompatible coating on stainless steel substrates was prepared by electrochemically copolymerizing 3,4-ethylenedioxythiophene (EDOT) with graphene oxide (GO), polystyrene sulfonate (PSS), or heparin (HEP) on SUS316L stainless steel, producing an anti-fouling (anti-protein adsorption and anti-platelet adhesion) surface to avoid the restenosis of blood vessels. The negative charges of GO, PSS, and HEP repel negatively charged proteins and platelets to achieve anti-fouling and anti-clotting. The results show that the anti-fouling capability of the poly(3,4-ethylenedioxythiophene) (PEDOT)/PSS coating is similar to that of the PEDOT/HEP coating. The anti-fouling capability of PEDOT/GO is higher than those of PEDOT/HEP and PEDOT/PSS. The reason for this is that GO exhibits negatively charged functional groups (COO−). The highest anti-fouling capability was found with the PEDOT/GO/HEP coating, indicating that electrochemical copolymerization of PEDOT with GO and HEP enhances the anti-fouling capability. Furthermore, the biocompatibility of the PEDOT coatings was tested with 3T3 cells for 1–5 days. The results show that all PEDOT composite coatings exhibited biocompatibility. The blood clotting time (APTT) of PEDOT/GO/HEP was prolonged to 225 s, much longer than the 40 s of pristine SUS316L stainless steel (the control), thus greatly improving the anti-blood-clotting capability of cardiovascular stents. [ABSTRACT FROM AUTHOR]

Competing Interests: All the authors declare no conflict of interest.

Analyzing the phosphoproteome at nanoscale poses a significant challenge, mainly due to the substantial sample loss from nonspecific surface adsorption during the enrichment of low stoichiometric phosphopeptides. Here, we describe a tandem tip-based phosphoproteomics sample preparation method capable of sequential sample cleanup and enrichment without the need for additional sample transfer, thereby minimizing sample loss. Integration of this method to our recently developed SOP (surfactant-assisted one-pot sample preparation) and iBASIL (improved boosting to amplify signal with isobaric labeling) approaches creates a streamlined workflow, enabling sensitive, high-throughput nanoscale phosphoproteomics measurements., (© 2024. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

Mass spectrometry-based proteomics provide a powerful tool for plant research, allowing global detection of steady-state levels of proteins under a given experimental setup. Here, we provide an optimized protocol for proteomic profiling using tandem mass tag (TMT) labeling followed by liquid chromatography-mass spectrometry (LC-MS/MS) to quantitate phosphopeptides and non-phosphopeptides from the same samples. The outlined protocol comprises a series of successive steps, namely, SDS (sodium dodecyl sulfate) protein extraction, protein precipitation, digestion, TMT labeling, phosphopeptide enrichment, high pH reversed-phase fractionation, LC-MS/MS analysis, protein identification, and data analysis. Our proteome-scale protocol requires 0.1 mg protein per sample and allows for the reliable and accurate quantification of more than 8000 proteins in Arabidopsis plant samples across multiple conditions, including low abundant peptides., (© 2023. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

It is well known that in addition to its classical role in protein turnover, ubiquitylation is required for a variety of membrane protein sorting events. However, and despite substantial progress in the field, a long-standing question remains: given that all ubiquitin units are identical, how do different elements of the sorting machinery recognize their specific cargoes? Our results indicate that the yeast Na + pump Ena1 is an epsin (Ent1 and Ent2 in yeast)-specific cargo and that its internalization requires K 1090 , which likely undergoes Art3-dependent ubiquitylation. In addition, an Ena1 serine and threonine (ST)-rich patch, proposed to be targeted for phosphorylation by casein kinases, was also required for its uptake. Interestingly, our data suggest that this phosphorylation was not needed for cargo ubiquitylation. Furthermore, epsin-mediated internalization of Ena1 required a specific spatial organization of the ST patch with respect to K 1090 within the cytoplasmic tail of the pump. We hypothesize that ubiquitylation and phosphorylation of Ena1 are required for epsin-mediated internalization., Competing Interests: Competing interestsThe authors declare no competing or financial interests., (© 2020. Published by The Company of Biologists Ltd.)

Protein phosphorylation is one of the key events in the regulation of plant physiological responses to diverse environmental stimuli. As crucial regulators of phosphorylation, protein kinases have been linked to the control of seed germination, flowering, and stress responses. Identifying downstream substrates of kinases is important for dissecting kinase-substrate networks as well as delineating the underlying defense mechanisms in response to extracellular stimulation. Despite the fact that thousands of kinase-substrate networks have been identified in mammalian cells, the downstream substrates of important plant kinases are still elusive. Moreover, it remains challenging to identify bona fide kinase substrates from proteome-wide analyses. Thus, developing methodologies with high sensitivity and specificity is imperative for understanding plant kinase-substrate cascades. Here, we describe a proteomic strategy termed kinase assay-linked phosphoproteomics (KALIP) approach for large-scale identification of the direct substrates of plant kinases with high sensitivity and a low false-positive rate.

Methodologies to enrich heterogeneous types of phosphopeptides are critical for comprehensive mapping of the under-explored phosphoproteome. Taking advantage of the distinct binding affinities of Ga(3+) and Fe(3+) for phosphopeptides, we designed a metal-directed immobilized metal ion affinity chromatography for the sequential enrichment of phosphopeptides. In Raji B cells, the sequential Ga(3+)-Fe(3+)-immobilized metal affinity chromatography (IMAC) strategy displayed a 1.5-3.5-fold superior phosphoproteomic coverage compared to single IMAC (Fe(3+), Ti(4+), Ga(3+), and Al(3+)). In addition, up to 92% of the 6283 phosphopeptides were uniquely enriched in either the first Ga(3+)-IMAC (41%) or second Fe(3+)-IMAC (51%). The complementary properties of Ga(3+) and Fe(3+) were further demonstrated through the exclusive enrichment of almost all of 1214 multiply phosphorylated peptides (99.4%) in the Ga(3+)-IMAC, whereas only 10% of 5069 monophosphorylated phosphopeptides were commonly enriched in both fractions. The application of sequential Ga(3+)-Fe(3+)-IMAC to human lung cancer tissue allowed the identification of 2560 unique phosphopeptides with only 8% overlap. In addition to the above-mentioned mono- and multiply phosphorylated peptides, this fractionation ability was also demonstrated on the basic and acidic phosphopeptides: acidophilic phosphorylation sites were predominately enriched in the first Ga(3+)-IMAC (72%), while Pro-directed (85%) and basophilic (79%) phosphorylation sites were enriched in the second Fe(3+)-IMAC. This strategy provided complementary mapping of different kinase substrates in multiple cellular pathways related to cancer invasion and metastasis of lung cancer. Given the fractionation ability and ease of tip preparation of this Ga(3+)-Fe(3+)-IMAC, we propose that this strategy allows more comprehensive characterization of the phosphoproteome both in vitro and in vivo.

Oral squamous cell carcinoma (OSCC) is a prevalent cancer worldwide. Let-7 family has been shown to function as a tumor suppressor through regulating multiple oncogenic signaling. Recent study reported that combined underexpression of miR-205 and let-7d showed negative correlation with the survival prognosis of head and neck cancer patients. However, the let-7d-involved mechanism in regulating OSCC is still unclear. In this study, we first demonstrated that let-7d expression was significantly decreased while Twist and Snail expression was increased in OSCC cancer cell lines and primary cultures as compared to normal human oral keratinocyte cells. To further investigate the role of let-7d in OSCC, we applied the SPONGE method to knock down let-7d in OECM-1 and two primary OSCC cell types. The results showed that knockdown of let-7d promote epithelial-mesenchymal transition (EMT) traits and migratory/invasive capabilities in OSCC cells. Furthermore, down-expression of let-7d significantly activated Twist and Snail expressions and chemo-resistant abilities of OSCC cells. Notably, overexpression of let-7d effectively reversed the EMT phenotype, blocked migratory/invasive abilities, and further increased the chemosensitivity in oral cancer tumor initiating ALDH1+ cells. In sum, these results show that let-7d negatively modulates EMT expression and also plays a role in regulating chemo-resistant ability in oral cancer.