Protein Phosphorylation Research Articles

Phosphoproteomic analysis reveals the mechanisms of human umbilical cord mesenchymal stem cell-derived exosomes attenuate renal aging

Aging is a critical biological process, with particularly notable impacts on the kidneys. Exosomes derived from human umbilical cord mesenchymal stem cells (hUC-MSCs) are capable of transferring various bioactive molecules, which exhibit beneficial therapeutic effects on kidney diseases. This study demonstrates that exosomes derived from hUC-MSCs ameliorate cellular senescence in the kidneys of naturally aging mice. These exosomes reduce the protein expression of senescence markers and senescence-associated secretory phenotypes (SASP) leading to fewer DNA damage foci and increased expression of the proliferation indicator Ki67. During the aging process, many proteins undergo phosphorylation modifications. We utilized data-independent acquisition (DIA) phosphoproteomics to study kidneys of naturally aging mice and those treated with hUC-MSC-derived exosomes. We observed elevated phosphorylation levels of the differentially phosphorylated proteins, Lamin A/C, at Ser390 and Ser392 sites, which were subsequently verified by western blotting. Overall, this study provides a new molecular characterization of hUC-MSC-derived exosomes in mitigating cellular senescence in the kidneys. SignificanceDIA phosphoproteomics was employed to investigate phosphorylated proteins in the kidney tissues of naturally aging mice with hUCMSC-exos treated. The results demonstrated that the DIA technique detected a higher abundance of phosphorylated proteins. We identified 24 significantly differentially phosphorylated proteins, and found that the phosphorylation of specific Lamin A/C sites is crucial for preventing cellular senescence. This study will help to better reveal the related phosphorylated proteins involved in hUCMSC-exos intervention in the kidneys of naturally aging mice, providing a foundation for future research on specific phosphorylation sites of proteins as potential therapeutic targets for renal aging-related diseases.

Milk osteopontin mediates zinc uptake in intestinal cells in the presence of phytic acid

The bioavailability and the intestinal absorption of the essential mineral zinc are challenged by the food matrix and especially the content of zinc chelating antinutrients. Many milk proteins and peptides affect zinc bioavailability. Osteopontin (OPN) is an acidic and highly phosphorylated whey protein that has been shown to bind calcium, magnesium and iron. Here we report the zinc binding properties of OPN, and the effect of OPN-Zn complexes on zinc absorption in Caco-2 cells. By isothermal titration calorimetry milk OPN was shown to bind approximately 36 zinc ions (KD of ∼70 μM). The binding was mainly mediated by the phosphorylations in the protein. OPN retained zinc bound after in vitro simulated gastrointestinal transit. Interestingly the OPN-Zn complex enhanced zinc bioavailability in the presence of phytic acid, compared to inorganic zinc salts. Zinc uptake mediated by OPN significantly upregulated the gene expression of MT1G and ZnT1 which are crucial proteins involved in preserving enterocyte zinc homoeostasis. These results indicate that OPN could be incorporated into functional foods and infant formulas to increase zinc bioavailability and uptake.

Tegaserod Stimulates 5-HT4 Serotonin Receptors in the Isolated Human Atrium.

Tegaserod (1-{[(5-methoxy-1H-indol-3-yl)methyliden]amino}-3-pentylguanidine) is a potent agonist at human recombinant 5-HT4 serotonin receptors. Consequently, tegaserod is utilized in the treatment of bowel diseases. The objective of this study was to test the hypothesis that tegaserod stimulates human cardiac atrial 5-HT4-receptors via cyclic adenosine monophosphate (cAMP)-dependent pathways. Tegaserod exerted positive inotropic effects (PIEs) and positive chronotropic effects (PCEs) in isolated left and right atrial preparations, respectively, from mice with cardiac-specific overexpression of the human 5-HT4 serotonin receptor (5-HT4-TG) in a concentration- and time-dependent manner. However, no effect was observed in the hearts of littermates of wild-type mice (WT). Western blot analysis revealed that the expression of 5-HT4 receptors was significantly higher in 5-HT4-TG mice compared to WT mice. The specificity of the signal for the 5-HT4 receptor was confirmed by the absence of the signal in the hearts of 5-HT4 receptor knockout mice. Furthermore, tegaserod increased the force of contraction (at concentrations as low as 10 nM), reduced the time of tension relaxation, and increased the rate of tension development in isolated electrically stimulated (at a rate of 60 beats per minute) human right atrial preparations (HAPs, obtained during open-heart surgery) when administered alone. The potency and efficacy of tegaserod to raise the force of contraction were enhanced in the presence of cilostamide, a phosphodiesterase III inhibitor. The positive inotropic effect of tegaserod in HAPs was found to be attenuated by the 5-HT4 serotonin receptor antagonist GR 125487 (0.1 µM). The efficacy of tegaserod (10 µM) in raising the force of contraction in HAPs was less pronounced than that of serotonin (10 µM) or isoprenaline (1 µM). Tegaserod shifted the concentration-response curve of the force of contraction to serotonin to the right in HAPs, indicating that it is a partial agonist at 5-HT4 serotonin receptors in this model. We propose that the mechanism of action of tegaserod in HAPs involves cAMP-dependent phosphorylation of cardiac regulatory proteins.

Genome-Scale Identification of Wild Soybean Serine/Arginine-Rich Protein Family Genes and Their Responses to Abiotic Stresses.

Serine/arginine-rich (SR) proteins mostly function as splicing factors for pre-mRNA splicing in spliceosomes and play critical roles in plant development and adaptation to environments. However, detailed study about SR proteins in legume plants is still lacking. In this report, we performed a genome-wide investigation of SR protein genes in wild soybean (Glycine soja) and identified a total of 31 GsSR genes from the wild soybean genome. The analyses of chromosome location and synteny show that the GsSRs are unevenly distributed on 15 chromosomes and are mainly under the purifying selection. The GsSR proteins can be phylogenetically classified into six sub-families and are conserved in evolution. Prediction of protein phosphorylation sites indicates that GsSR proteins are highly phosphorylated proteins. The protein-protein interaction network implies that there exist numerous interactions between GsSR proteins. We experimentally confirmed their physical interactions with the representative SR proteins of spliceosome-associated components such as U1-70K or U2AF35 by yeast two-hybrid assays. In addition, we identified various stress-/hormone-responsive cis-acting elements in the promoter regions of these GsSR genes and verified their expression patterns by RT-qPCR analyses. The results show most GsSR genes are highly expressed in root and stem tissues and are responsive to salt and alkali stresses. Splicing analysis showed that the splicing patterns of GsSRs were in a tissue- and stress-dependent manner. Overall, these results will help us to further investigate the biological functions of leguminous plant SR proteins and shed new light on uncovering the regulatory mechanisms of plant SR proteins in growth, development, and stress responses.

An Extensive Atlas of Proteome and Phosphoproteome Turnover Across Mouse Tissues and Brain Regions.

Understanding how proteins in different mammalian tissues are regulated is central to biology. Protein abundance, turnover, and post-translational modifications like phosphorylation, are key factors that determine tissue-specific proteome properties. However, these properties are challenging to study across tissues and remain poorly understood. Here, we present Turnover-PPT , a comprehensive resource mapping the abundance and lifetime of 11,000 proteins and 40,000 phosphosites across eight mouse tissues and various brain regions, using advanced proteomics and stable isotope labeling. We revealed tissue-specific short- and long-lived proteins, strong correlations between interacting protein lifetimes, and distinct impacts of phosphorylation on protein turnover. Notably, we discovered that peroxisomes are regulated by protein turnover across tissues, and that phosphorylation regulates the stability of neurodegeneration-related proteins, such as Tau and α-synuclein. Thus, Turnover-PPT provides new fundamental insights into protein stability, tissue dynamic proteotypes, and the role of protein phosphorylation, and is accessible via an interactive web-based portal at https://yslproteomics.shinyapps.io/tissuePPT .

GlyT1 inhibition promotes neuroprotection in the middle cerebral artery occlusion model through the activation of GluN2A-containing NMDAR

Glycine Transporter Type 1 (GlyT1) inhibition confers neuroprotection against different forms of cerebral damage. This effect occurs through the elevation of synaptic glycine concentrations, which enhances N-methyl-d-aspartate receptor (NMDAR) activation by glutamate. To investigate the neuroprotective mechanism of GlyT1 inhibition, we used the Middle Cerebral Artery Occlusion (MCAO) model in male C57BL/6 mice, aged 10–12 weeks. We administered N-[3-(4′-fluorophenyl)-3-(4′-phenylphenoxy)propyl] sarcosine (NFPS), a GlyT1 inhibitor, 24 h prior to ischemia induction. NFPS pretreatment provided significant neuroprotection in the MCAO model, associated with modulation of pathways related to long-term potentiation. Specifically, GluN2A subunit expression was upregulated, while GluN2B subunit expression was downregulated in cortical areas, correlating with enhanced phosphorylation of CaMKIV and CREB proteins. Coadministration with the GluN2B antagonist Eliprodil or the CREB inhibitor C646 did not affect the neuroprotective effects of NFPS pretreatment, but TCN-201, a specific GluN2A antagonist, disrupted these effects. These findings suggest that GlyT1 inhibition mediates neuroprotection through activation of GluN2A-containing NMDARs and the GluN2A/CaMKIV/CREB signaling cascade, thereby modulating the balance between GluN2A and GluN2B subunits.

Mitochondrial Abundance and Function Differ Across Muscle Within Species.

Background: Mitochondria are considered the powerhouse of cells, and skeletal muscle cells are no exception. However, information regarding muscle mitochondria from different species is limited. Methods: Different muscles from cattle, pigs and chickens were analyzed for mitochondrial DNA (mtDNA), protein and oxygen consumption. Results: Bovine oxidative muscle mitochondria contain greater mtDNA (p < 0.05), protein (succinate dehydrogenase, SDHA, p < 0.01; citrate synthase, CS, p < 0.01; complex I, CI, p < 0.05), and oxygen consumption (p < 0.01) than their glycolytic counterpart. Likewise, porcine oxidative muscle contains greater mtDNA (p < 0.01), mitochondrial proteins (SDHA, p < 0.05; CS, p < 0.001; CI, p < 0.01) and oxidative phosphorylation capacity (OXPHOS, p < 0.05) in comparison to glycolytic muscle. However, avian oxidative skeletal muscle showed no differences in absolute mtDNA, SDHA, CI, complex II, lactate dehydrogenase, or glyceraldehyde 3 phosphate dehydrogenase compared to their glycolytic counterpart. Even so, avian mitochondria isolated from oxidative muscles had greater OXPHOS capacity (p < 0.05) than glycolytic muscle. Conclusions: These data show avian mitochondria function is independent of absolute mtDNA content and protein abundance, and argue that multiple levels of inquiry are warranted to determine the wholistic role of mitochondria in skeletal muscle.

Enhancing radiosensitivity in osteosarcoma via CDKN2C overexpression: A mechanism involving G1 phase arrest mediated by inhibition of CDK4 expression and Thr172 phosphorylation

BackgroundThe limited radiosensitivity of osteosarcoma poses a challenge in applying radiotherapy, necessitating the search for effective radiosensitizing targets. MethodsThe lentiviral vectors were employed to establish CDKN2C-overexpressing (CDKN2C-OE) and CDKN2C-negative control (CDKN2C-NC) HOS and U2OS osteosarcoma cells. Cells were treated with or without irradiation (IR) to assess radiosensitization via viability, proliferation, apoptosis, and cell cycle analysis. A mouse model with subcutaneous tumors from CDKN2C-OE and CDKN2C-NC HOS cells evaluated tumor growth post-IR. Immunohistochemical staining and Western blot analysis were conducted to confirm model establishment and explore mechanisms. ResultsCDKN2C-OE combined with IR inhibited cell viability and proliferation, promoting apoptosis in vitro and inhibiting tumor growth in vivo. CDKN2C-OE inhibited G1 phase progression post-IR by suppressing Cyclin-dependent kinase 4 (CDK4) expression and Thr172 phosphorylation, reducing retinoblastoma protein (RB) phosphorylation at Ser807/811. CDKN2C-OE did not primarily impact the cell cycle by regulating the expression of CDK6 and Cyclin D1. Furthermore, when CDKN2C-OE was combined with IR, the expression of BAX, Caspase-3, and its active cleavage product, cleaved Caspase-3, was upregulated. ConclusionsOur research results indicate that overexpression of CDKN2C enhances radiosensitivity in osteosarcoma through the induction of G1 phase arrest and subsequent apoptosis. G1 phase arrest is mediated by the suppression of CDK4 expression and Thr172 phosphorylation, which consequently affects the expression of phosphorylated RB at the Ser807/811 sites.

Proteomic analysis of giant panda testicular tissue of different age groups

Background The reproductive ability of male giant pandas has been a major complicating factor in the ex-situ conservation of the species. While it is well known that the testis produces sperm and secretes androgens, a process that requires precise regulation of various proteins, at present, there has been no systematic study on the composition of proteins in the testis of the giant pandas. Therefore, this study aims to apply proteomics to explore the regulation of proteins in the testes of giant pandas. Methods Samples from the testes of three giant pandas (22 years, 18 years, 8 days) were studied to assess the protein’s function. A label-free quantitative method was used to isolate testicular proteins from each male, 139,039 peptides and 11,435 proteins were obtained. Results Gene Ontology (GO) annotates most of the proteins involved in the processes of protein phosphorylation, oxidation-reduction, proteolysis, and signal transduction. KEGG pathway indicated that most of the proteins were involved in the pathway of signal transduction, transport, and catabolism. The protein kinase and WD40 repeats were involved in protein-protein interaction, which in turn regulates gene expression in the testicular tissue of giant pandas. Conclusions This study is the first to conduct an in-depth proteomic analysis of testicular tissue in giant pandas. The results revealed the important role of proteins in testicular tissue on spermatogenesis, testosterone production, and testicular microenvironment, providing clues for further research on male giant panda reproduction.

Pueraria lobata extract ameliorates D-GalN/LPS-induced liver injury through targeting TLR4/NF-κB signalling pathway and regulating gut microbiota

AbstractKudzu root (Pueraria lobata), known for its dual role as a medicinal herb and food ingredient, has proven anti-inflammatory and antioxidant properties. This study explored the effects of P. lobata extract (PLE) on D-galactose/lipopolysaccharide (D-GalN/LPS)-induced liver inflammation and oxidative stress in mice, along with its impact on gut microbiota. The in vivo studies indicated that PLE significantly reduced hepatic levels of pro-inflammatory cytokines (tumour necrosis factor-α, interleukin-1β, and interleukin-6) and increased the anti-inflammatory cytokine interleukin-10. It also lowered serum aspartate aminotransferase and alanine aminotransferase activities, indicating reduced liver damage, and mitigated oxidative stress by decreasing malondialdehyde levels while restoring superoxide dismutase activity. Western blot analysis revealed that PLE inhibited the phosphorylation of NF-κB pathway proteins (p65 and IκB) and suppressed TLR4 expression, highlighting its role in this inflammatory pathway. Additionally, PLE ameliorated D-GalN/LPS-induced gut microbiota dysbiosis, reducing Proteobacteria abundance and promoting beneficial genera such as Lactobacillus, Bifidobacterium, and Akkermansia. These findings suggest that PLE protects against liver inflammation and oxidative stress, while improving gut microbiota composition, offering potential therapeutic strategies for liver-related diseases.

The dual-specificity kinase DYRK1A interacts with the Hepatitis B virus genome and regulates the production of viral RNA.

The genome of Hepatitis B virus (HBV) persists in infected hepatocytes as a nuclear episome (cccDNA) that is responsible for the transcription of viral genes and viral rebound, following antiviral treatment arrest in chronically infected patients. There is currently no clinically approved therapeutic strategy able to efficiently target cccDNA (Lucifora J 2016). The development of alternative strategies aiming at permanently abrogating HBV RNA production requires a thorough understanding of cccDNA transcriptional and post-transcriptional regulation. In a previous study, we discovered that 1C8, a compound that inhibits the phosphorylation of some cellular RNA-binding proteins, could decrease the level of HBV RNAs. Here, we aimed at identifying kinases responsible for this effect. Among the kinases targeted by 1C8, we focused on DYRK1A, a dual-specificity kinase that controls the transcription of cellular genes by phosphorylating transcription factors, histones, chromatin regulators as well as RNA polymerase II. The results of a combination of genetic and chemical approaches using HBV-infected hepatocytes, indicated that DYRK1A positively regulates the production of HBV RNAs. In addition, we found that DYRK1A associates with cccDNA, and stimulates the production of HBV nascent RNAs. Finally, reporter gene assays showed that DYRK1A up-regulates the activity of the HBV enhancer 1/X promoter in a sequence-dependent manner. Altogether, these results indicate that DYRK1A is a proviral factor that may participate in the HBV life cycle by stimulating the production of HBx, a viral factor absolutely required to trigger the complete cccDNA transcriptional program.

An Alternatively Spliced Gain-of-Function NT5C2 Isoform Contributes to Chemoresistance in Acute Lymphoblastic Leukemia.

Relapsed or refractory B-cell acute lymphoblastic leukemia (B-ALL) is a major cause of pediatric cancer-related deaths. Relapse-specific mutations do not account for all chemotherapy failures in B-ALL patients, suggesting additional mechanisms of resistance. By mining RNA sequencing datasets of paired diagnostic/relapse pediatric B-ALL samples, we discovered pervasive alternative splicing (AS) patterns linked to relapse and affecting drivers of resistance to glucocorticoids, antifolates, and thiopurines. Most splicing variations represented cassette exon skipping, "poison" exon inclusion, and intron retention, phenocopying well-documented loss-of-function mutations. In contrast, relapse-associated AS of NT5C2 mRNA yielded an isoform with the functionally uncharacterized in-frame exon 6a. Incorporation of the 8-amino acid sequence SQVAVQKR into this enzyme created a putative phosphorylation site and resulted in elevated nucleosidase activity, which is a known consequence of gain-of-function mutations in NT5C2 and a common determinant of 6-mercaptopurine resistance. Consistent with this finding, NT5C2ex6a and the R238W hotspot variant conferred comparable levels of resistance to 6-mercaptopurine in B-ALL cells both in vitro and in vivo. Furthermore, both NT5C2ex6a and the R238W variant induced collateral sensitivity to the inosine monophosphate dehydrogenase inhibitor mizoribine. These results ascribe to splicing perturbations an important role in chemotherapy resistance in relapsed B-ALL and suggest that inosine monophosphate dehydrogenase inhibitors, including the commonly used immunosuppressive agent mycophenolate mofetil, could be a valuable therapeutic option for treating thiopurine-resistant leukemias. Significance: Alternative splicing is a potent mechanism of acquired drug resistance in relapsed/refractory acute lymphoblastic leukemias that has diagnostic and therapeutic implications for patients who lack mutations in known chemoresistance genes.

Pan-cancer analysis of Sp1 with a focus on immunomodulatory roles in gastric cancer

BackgroundSp1, a transcription factor, regulates essential cellular processes and plays important tumorigenic roles across diverse cancers. However, comprehensive pan-cancer analyses of its expression and potential immunomodulatory roles remain unexplored.MethodsUtilizing bioinformatics tools and public datasets, we examined the expression of Sp1 across normal tissues, tumors, and immune cells, and screened for pre- and post-transcriptional modifications, including genetic alterations, DNA methylation, and protein phosphorylation, affecting its expression or function. The association of Sp1 expression with immune cell infiltration, tumor mutational burden, and immune checkpoint signaling was also investigated. Single-cell transcriptome data was used to assess Sp1 expression in immune cells in gastric cancer (GC), and findings were corroborated using immunohistochemistry and multiplex immunofluorescence in an immunotherapy-treated patient cohort. The prognostic value of Sp1 in GC patients receiving immunotherapy was evaluated with Cox regression models.ResultsElevated Sp1 levels were observed in various cancers compared to normal tissues, with notable prominence in GC. High Sp1 expression correlated with advanced stage, poor prognosis, elevated tumor mutational burden (TMB), and microsatellite instability (MSI) status, particularly in GC. Significant correlations between Sp1 levels and CD8+ T cell and the M1 phenotype of tumor-associated macrophages were further detected upon multiplex immunofluorescence in GC samples. Interestingly, we verified that GC patients with higher Sp1 levels exhibited improved response to immunotherapy. Moreover, Sp1 emerged as a prognostic and predictive biomarker for GC patients undergoing immunotherapy.ConclusionsOur pan-cancer analysis sheds light on the multifaceted role of Sp1 in tumorigenesis and underscores its potential as a prognostic and predictive biomarker for patients with GC undergoing immunotherapy.

Regulation of Curcumin on Follicle Initiation Rate in Diminished Ovarian Reserve.

To study the mechanism by which curcumin regulates ovarian primordial follicle initiation in rats with triptolide-induced diminished ovarian reserve (DOR). An in vitro gelatin sponge culture was performed on 3-day-old rat ovaries. After the establishment of the DOR model with triptolide, curcumin was administered for 3 days. Histological analysis and follicle counts were performed using H&E staining. ELISA detection of ovarian hormones in the culture medium (E2, FSH and LH), western blotting and Q-PCR for protein and mRNA expression (LTCONS-00011173, TGF-β1, Smad1, AMH, PTEN and GDF-9). Ovarian primordial and growing follicles increased significantly after curcumin intervention (p < 0.05), FSH/LH and E2 levels were increased significantly (p < 0.05). Curcumin also significantly decreased the expression of LTCONS-00011173. Meanwhile, curcumin increased the expression of TGF-β, AMH, and GDF-9 (p < 0.05). In addition, curcumin increased Smad1 gene expression and protein phosphorylation in the ovary on the one hand (p < 0.05), but inhibited Smad1 and p-Smad1 protein expression on the other hand (p < 0.05). Moreover, curcumin decreased PTEN protein and mRNA expression (p < 0.05). Curcumin activates primordial follicles in DOR model rats through TGF-β1 and downstream AMH signaling pathways and may limit follicle exhaustion through LncRNA.

Mapping Nanoscale-To-Single-Cell Phosphoproteomic Landscape by Chip-DIA.

Protein phosphorylation plays a crucial role in regulating disease phenotypes and serves as a key target for drug development. Mapping nanoscale-to-single-cell samples can unravel the heterogeneity of cellular signaling events. However, it remains a formidable analytical challenge due to the low detectability, abundance, and stoichiometry of phosphorylation sites. Here, we present a Chip-DIA strategy,integratinga microfluidic-based phosphoproteomic chip (iPhosChip) with data-independent acquisition mass spectrometry (DIA-MS) for ultrasensitive nanoscale-to-single-cell phosphoproteomic profiling. The iPhosChip operates as an all-in-one station that accommodates both quantifiable cell capture/imaging and the entire phosphoproteomic workflow in a highly streamlined and multiplexed manner. Coupled with a sample size-comparable library-based DIA-MS strategy, Chip-DIA achieved ultra-high sensitivity, detecting 1076±158 to 15869±1898 phosphopeptides from 10±0 to 1013±4 cells, and revealed the first single-cell phosphoproteomic landscape comprising druggable sites and basal phosphorylation-mediated networks in lung cancer. Notably, the sensitivity and coverage enabled the illumination of heterogeneous cytoskeleton remodeling and cytokeratin signatures in patient-derived cells resistant to third-generation EGFR therapy, stratifying mixed-lineage adenocarcinoma-squamous cell carcinoma subtypes, and identifying alternative targeted therapy for late-stage patients. With flexibility in module design and functionalization, Chip-DIA can be adapted to other PTM-omics to explore dysregulated PTM landscapes, thereby guiding therapeutic strategies toward precision oncology.

Effects of cadherin mediated contact normalization on oncogenic Src kinase mediated gene expression and protein phosphorylation

Nontransformed cells form heterotypic cadherin junctions with adjacent transformed cells to inhibit tumor cell growth and motility. Transformed cells must override this form of growth control, called “contact normalization”, to invade and metastasize during cancer progression. Heterocellular cadherin junctions between transformed and nontransformed cells are needed for this process. However, specific mechanisms downstream of cadherin signaling have not been clearly elucidated. Here, we utilized a β-catenin reporter construct to determine if contact normalization affects Wnt signaling in transformed cells. β-catenin driven GFP expression in Src transformed mouse embryonic cells was decreased when cultured with cadherin competent nontransformed cells compared to transformed cells cultured with themselves, but not when cultured with cadherin deficient nontransformed cells. We also utilized a layered culture system to investigate the effects of oncogenic transformation and contact normalization on gene expression and oncogenic Src kinase mediated phosphorylation events. RNA-Seq analysis found that cadherin dependent contact normalization inhibited the expression of 22 transcripts that were induced by Src transformation, and increased the expression of 78 transcripts that were suppressed by Src transformation. Phosphoproteomic analysis of cells expressing a temperature sensitive Src kinase construct found that contact normalization decreased phosphorylation of 10 proteins on tyrosine residues that were phosphorylated within 1 h of Src kinase activation in transformed cells. Taken together, these results indicate that cadherin dependent contact normalization inhibits Wnt signaling to regulate oncogenic kinase activity and gene expression, particularly PDPN expression, in transformed cells in order to control tumor progression.

Peptide TaY Attenuates Inflammatory Responses by Interacting with Myeloid Differentiation 2 and Inhibiting NF-κB Signaling Pathway

A balanced inflammatory response is crucial for the organism to defend against external infections, however, an exaggerated response may lead to detrimental effects, including tissue damage and even the onset of disease. Therefore, anti-inflammatory drugs are essential for the rational control of inflammation. In this study, we found that a previously screened peptide TaY (KEKKEVVEYGPSSYGYG) was able to inhibit the LPS-induced RAW264.7 inflammatory response by decreasing a series of proinflammatory cytokines, such as TNF-α, IL-6, and nitric oxide (NO). To elucidate the underlying mechanism, we conducted further investigations. Western blot analysis showed that TaY reduced the phosphorylation of key proteins (IKK-α/β, IκB-α,NF-κB (P65)) in the TLR4-NF-κB signaling pathway and inhibited the inflammatory response. Furthermore, molecular docking and molecular dynamic simulations suggested that TaY binds to the hydrophobic pocket of MD2 through hydrogen bonding and hydrophobic interactions, potentially competing with LPS for MD2 binding. Collectively, TaY is a promising candidate for the development of novel therapeutic strategies against inflammatory disorders.

Clustering of RNA Polymerase II C-Terminal Domain Models upon Phosphorylation.

RNA polymerase II (Pol II) C-terminal domain (CTD) is known to have crucial roles in regulating transcription. CTD has also been highly recognized for undergoing phase separation, which is further associated with its regulatory functions. However, the molecular interactions that the CTD forms to induce clustering to drive phase separations and how the phosphorylation of the CTD affects clustering are not entirely known. In this work, we studied the concentrated solutions of two heptapeptide repeat (2CTD) models at different phosphorylation patterns and protein and ion concentrations using all-atom molecular dynamics simulations to investigate clustering behavior and molecular interactions driving the cluster formation. Our results show that salt concentration and phosphorylation patterns play an important role in determining the clustering pattern, specifically at low protein concentrations. The balance between inter- and intrapeptide interactions and counterion coordination together impact the clustering behavior upon phosphorylation.

Network toxicology and molecular docking to investigative the non-acetylcholinesterase mechanisms and targets of cardiotoxicity injury induced by organophosphorus pesticides.

Organophosphorus pesticides (OPPs) are widely used in the world, however, OPP poisoning often occurs because of improper use and lack of protective measures. Cardiotoxicity injury induced by OPPs is insidious, and it does not receive attention until the end stage of OPP poisoning. Heart failure or arrhythmia gradually becomes the main lethal cause of OPP poisoning patients. In this study, network toxicology and molecular docking were employed to investigate the non-acetylcholinesterase targets and mechanisms of cardiotoxicity injury induced by OPPs. One hundred twenty-three targets of dichlorvos, 205 targets of methidathion, and 337 targets of malathion were searched from SwissTargetPreict, STITCH and PharmMapper database. Additionally, 1379 targets related to cardiotoxicity injury were acquired from GeneCards and OMIM database. Ninety-six mutual targets between OPPs and cardiotoxicity injury were considered as the potential cardiotoxicity injury targets induced by OPPs. The protein-protein interaction (PPI) network was constructed using STING database, and 21 core targets were identified by Cytoscape software, such as AKT1, ESR1, HSP90AA1, MAPK1, MMP9, and MAPK8. Gene ontology and KEGG enrichment analysis revealed that cell migration, apoptotic process, protein phosphorylation and signal transduction were the major biological functions associated with OPPs-induced cardiotoxicity injury, and OPPs-induced cardiotoxicity injury might be regulated by MAPK, PI3K-Akt, VEGF signaling pathway. Docking results manifested that the best binding target for dichlorvos, methidathion and malathion were MAPK9 (-7.1 kcal/mol), MAPK1 (-8.1 kcal/mol) and HSP90AA1 (-8.6 kcal/mol) with the lowest affinity, respectively. The core targets and non-AchE mechanisms were explored by network toxicology and molecular docking, providing a theoretical basis for the treatment of OPP-induced cardiotoxicity injury.

Differential transcriptome reprogramming induced by the soybean cyst nematode Type 0 and Type 1.2.5.7 during resistant and susceptible interactions.

Soybean cyst nematode (SCN, Heterodera glycines) is a serious root parasite of soybean (Glycine max) that induces extensive gene expression changes associated with pleiotropic biological activities in infected cells. However, the impacts of various SCN Hg Types on host transcriptome reprogramming remain largely unknown. Here, we developed and used two recombinant inbred lines (RIL-72 and RIL-137) to profile transcriptome reprogramming in the infection sites during the resistant and susceptible interactions with SCN Hg Type 1.2.5.7 and Type 0. SCN bioassays indicated that RIL-72 was susceptible to Type 1.2.5.7 but resistant to Type 0, whereas RIL-137 was resistant to both types. Comparative analysis of gene expression changes induced by Type 1.2.5.7 in the resistant and susceptible lines revealed distinct transcriptome regulation with a number of similarly and oppositely regulated genes. The expression levels of similarly regulated genes in the susceptible line appeared to be insufficient to mount an effective defense against SCN. The functional importance of oppositely regulated genes was confirmed using virus induced gene silencing and overexpression approaches. Further transcriptome comparisons revealed shared as well as Hg Type- and genotype-specific transcriptome reprogramming. Shared transcriptome responses were mediated through common SCN-responsive genes and conserved immune signaling, whereas genotype-specific responses were derived from genetic variability, metabolic and hormonal differences, and varied regulation of protein phosphorylation and ubiquitination. The conserved defense mechanisms together with genotype-specific responses would enable plants to trigger effective and tailored immune responses to various Hg types and adapt the defense response to their genetic backgrounds.