Search Results (126)

Autophagy is a fundamental lysosome-dependent degradation process that maintains cellular homeostasis in response to stress. VSP34 (Vacuolar Protein Sorting 34, PIK3C3) is the only class-III phosphatidylinositol 3-kinase and generates phosphatidylinositol 3-phosphate (PI3P) for auto-phagosome nucleation and maturation. Thus, it provides a critical adaptive survival pathway for cells that are experiencing metabolic stress. The VPS34–autophagy axis plays dual roles in cancer, which depend on the context: it can restrain early tumorigenesis, but in established tumors, it can promote survival in conditions of hypoxia, nutrient deprivation, and therapeutic pressure. Moreover, VPS34 shapes the tumor microenvironment (TME) through its influence on both immune and cancer cells by modulating autophagy, cGAS-STING (cyclic GMP-AMP synthase Stimulator of Interferon Genes), and STAT1 pathways. VPS34 inhibition has been reported to induce an interferon response that increases CD8⁺ T and natural killer (NK) cell infiltration and converts cold tumors into hot ones. This behavior suggests that combining VPS34 inhibitors with cancer immunotherapies could be beneficial. In this review, we summarize the molecular functions and regulations of VPS34 in autophagy and discuss recent advances linking VPS34 to tumor and cancer immunotherapy. Full article

Pancreatic ductal adenocarcinoma (PDAC) is an aggressive malignancy with a 5-year survival rate of 13.3%. First-line treatment relies on two chemotherapy regimens, FOLFIRINOX (FOLFNX) or gemcitabine plus nab-paclitaxel (GEMPAC). However, direct clinical comparisons between these regimens have yielded inconsistent results across survival and toxicity endpoints, and the molecular basis of heterogeneous treatment responses remains poorly defined. To investigate regimen-specific tumor-cell-intrinsic mechanisms, we performed quantitative proteomic profiling of a primary PDAC-derived MIA PaCa-2 cell line following treatment with FOLFNX or GEMPAC. Differentially expressed proteins were analyzed using Gene Ontology, KEGG, and Ingenuity Pathway Analysis to define pathway-level alterations, and findings were contextualized using TCGA transcriptomic data. Proteomic analyses revealed that FOLFNX and GEMPAC engage in distinct cytotoxic programs. FOLFNX predominantly suppressed ribosome biogenesis and mitochondrial translation, consistent with sustained metabolic and biosynthetic stress, whereas GEMPAC preferentially disrupted mitotic cytokinesis and phosphatidylinositol phosphate biosynthesis, consistent with mitotic failure. Integration with TCGA data showed that FOLFNX-altered proteins aligned with favorable prognostic expression signatures, whereas GEMPAC-associated proteins were enriched among adverse profiles, reflecting engagement of distinct tumor-intrinsic programs. Together, these findings provide mechanistic insight into differential chemotherapy responses and establish a foundation for proteomics-based biomarkers to guide personalized chemotherapy selection in PDAC. Full article

The combination of supported lipid bilayers (SLBs) with the Quartz Crystal Microbalance with Dissipation monitoring (QCM-D) has been proven to be a powerful tool to simultaneously monitor mass and viscoelastic changes related to membrane binding-events. In this work, the above methodology is employed for the study of the interaction of the Early Endosomal Antigen 1 (EEA1) to a model lipid bilayer that mimics the early endosome (EE) membrane, focusing on the membrane composition. Starting with the formation of a lipid bilayer through the vesicles fusion technique, we investigated the formation of SLBs that incorporate phosphatidylinositol 3-phosphate (PI(3)P), a key component for EEA1 binding, in combination with other lipids, e.g., (1,2-dioleoyl-sn-glycero-3)-phosphocholine (DOPC), -phosphoserine (DOPS), -phosphoethanolamine (DOPE), and cholesterol (Chol). The interaction of the full-length coiled-coil EEA1 to the formed SLBs was further studied in real time with the QCM-D and characterized with respect to the lipid composition and pH. Our findings confirm that PI(3)P is essential for the EEA1–membrane interaction, while it was shown that Chol and phosphatidylserine greatly influence the binding event. In fact, including 30% Chol in a PI(3)P (3%):PS (6%) SLB resulted in almost double EEA1 binding than in the absence of Chol. Moreover, we employed the QCM-viscoelastic model available to analyze the QCM-D data with emphasis on the study of the protein conformation. Our results showed that, in our in vitro system, EEA1 is not fully extended and/or highly packed, but is mainly in a bent, distorted conformation with an average size close to 100 nm. This study complements previous works employing in vitro assays, also demonstrating the ability to reconstitute more complex biomimetic EE membranes containing inositol phospholipids on a QCM surface for the study of EEA1 binding. Full article

The endolysosomal system plays a pivotal role in cellular function. Before reaching lysosomes for degradation, the endocytosed cargoes are sorted at various stages of endosomal trafficking for recycling and/or rerouting. The proper execution of these processes depends on tightly regulated ion fluxes across endolysosomal membranes. Recent studies have demonstrated the importance of two-pore channels (TPCs), including TPC1 and TPC2, in endolysosomal trafficking. These channels are expressed in the membranes of distinct populations of endosomes and lysosomes, where they respond to nicotinic acid adenine dinucleotide phosphate (NAADP) and phosphatidylinositol 3,5-bisphosphate [PI(3,5)P₂] to conduct Ca²⁺ and Na⁺ release from these acidic organelles. Here, we discuss the potential implications of Ca²⁺ and Na⁺ fluxes mediated by TPCs across endolysosomal membranes in the physiological and pathophysiological functions of these organellar channels. Full article

(1) Background: This study used Qingjian No. 1 forage pea (Pisum sativum L.) as a plant material to study its metabolic mechanisms in response to different stresses, given that saline–alkali stress and drought stress often occur simultaneously in natural environments and severely affect the growth and yield of forage pea, while the regulatory network underlying the adaptation of forage pea to combined stress remains poorly elucidated. (2) Methods: The metabolic mechanisms of forage pea in response to different stresses were elucidated by integrating phenotypic, physiological, and metabolomic analyses. (3) Results: The results show that compared to the control, all stress treatments significantly inhibited seed germination and seedling growth, with the combined saline–alkali and drought stress exhibiting the strongest inhibitory effect. In terms of physiological and biochemical responses, peroxidase (POD) activity increased with the complexity of the stress, with the highest POD activity observed under combined saline–alkali and drought stress, showing a 61.71% increase compared to the control (p < 0.05). Non-targeted metabolomic analysis revealed that isoflavone biosynthesis, nucleotide metabolism, and cutin–suberin–wax biosynthesis are the core responsive pathways. Correlation analysis revealed that isocorydine and phosphatidylinositol phosphate showed strong positive correlations with the vigor index, main root length, and superoxide dismutase (SOD) activity, and glycerophospholipid metabolites were positively correlated with ferric ion-reducing antioxidant capacity. (4) This study deepens understanding of the stress resistance mechanisms in forage peas and provides a theoretical basis for stress-resistant forage pea breeding. Full article

Backgrounds: Objective of this study is to conduct a genome-wide association study (GWAS) of first-parity reproductive traits in Suzi pigs to identify significant single-nucleotide polymorphisms (SNPs) or candidate genes influencing these traits. Methods: This research employed technologies including the Zhongxin 50K SNP chip, simplified genome sequencing, resequencing, and the 100K SNP liquid chip to perform genome-wide SNP detection on 898 Suzi sows. Genotype data and phenotypic data were combined to do GWAS, gene annotation, and enrichment analysis. Results: Results showed that this study obtained phenotypes of 33 first-parity reproductive traits from 574 sows. GWAS results indicated there were 10 first-parity reproductive traits significantly associated with SNPs, and these traits were AFS, AFF, NNB, NH, NW, NS, NM, ND, PB, and CCN. These 10 traits were significantly associated with 60 SNPs, with 15 (25%) located on chromosome 2-the highest proportion. The SNPs significantly associated with AFS and AFF were largely identical. Genome-wide variance component analysis revealed that among the 10 traits with significantly associated SNPs in GWAS, there were 5 traits that exhibited genome-wide heritability ≥ 0.01. Trait of NM showed the highest heritability (0.65–0.7). These significantly associated SNPs annotated 20 candidate genes, including ADAMTS19, PROP1, ZNF354B, PCARE, LUZP2, VIRMA, EPHA5, AAAS, SLCO3A1-SV2B, KIF18A-BDNF, SERGEF, DYNLRB2, HNF4G, CATSPERD, HSD11B1L, DICER1, RARG, PCDHAC2, KRT79, and HSD17B2. GO analysis of candidate genes revealed that the top three biological processes were cell adhesion, positive regulation of cell projection organization, and positive regulation of neuron projection development. KEGG results showed the top three pathways were inositol phosphate metabolism, glutamatergic synapse, and phosphatidylinositol signaling system. Conclusions: These findings provide a foundation for the reproductive breeding of Suzi pigs and offer new insights into biological breeding in pigs. Full article

Background/Objective: Oncogenic tyrosine kinases (TKs) such as ALK and SRC promote cancer progression, but their effects on metabolic enzymes are still not well understood. This study examines how TK signaling regulates inosine monophosphate dehydrogenase 2 (IMPDH2), a rate-limiting enzyme in purine biosynthesis, and assesses its potential as a therapeutic target. Methods: Phosphoproteomic screening and in vitro kinase assays were used to identify phosphorylation sites on IMPDH2. Lipid-binding assays explored the role of phosphatidylinositol 3-phosphate (PI3P) in IMPDH2 regulation. Structure-based virtual screening discovered small-molecule allosteric inhibitors, which were tested in lymphoma cell models, including ALK and BTK-inhibitor resistant lines. Results: Here, we identify Inosine monophosphate dehydrogenase-2 (IMPDH2), a rate-limiting enzyme in purine biosynthesis, as a novel substrate of ALK and SRC. We show that phosphorylation at the conserved Y233 residue within the allosteric domain enhances IMPDH2 activity, linking TK signaling to metabolic reprogramming in cancer cells. We further identify PI3P as a natural lipid inhibitor that binds IMPDH2 and suppresses its enzymatic function. Using structure-based virtual screening, we developed Comp-10, a first-in-class allosteric IMPDH inhibitor. Unlike classical active-site inhibitors such as mycophenolic acid (MPA), Comp-10 decreases IMPDH1/2 protein levels, blocks filament (rod/ring) formation, and inhibits the growth of ALK and BTK inhibitor-resistant lymphoma cells. Comp-10 acts post-transcriptionally and avoids compensatory IMPDH upregulation observed with MPA (rod/ring) formation, and inhibited growth in TKI-resistant lymphoma cells. Notably, Comp-10 avoided the compensatory IMPDH upregulation observed with MPA. Conclusion: These findings uncover a novel TK–IMPDH2 signaling axis and provide mechanistic and therapeutic insight into the allosteric regulation of IMPDH2. Comp-10 represents a promising therapeutic candidate for targeting metabolic vulnerabilities in tyrosine kinase driven cancers. Full article

Ceramide 1-phosphate (C1P) is a key regulator of cell proliferation and survival in both normal and transformed cells. Major pathways implicated in the mitogenic actions of C1P include activation of the mitogen-activated protein kinases (MAPKs) ERK1-2 and JNK, as well as stimulation of the phosphatidylinositol 3 kinase (PI3K)/Akt/mammalian target of rapamycin (mTOR) pathway, the product of retinoblastoma, or the sphingomyelin synthase (SMS)/diacylglycerol (DAG)/protein kinase C-alpha (PKC-α) pathway. C1P-stimulated cell proliferation can also be mediated through enhanced secretion of vascular endothelial growth factor (VEGF) in macrophages or by releasing lysophosphatidic acid (LPA) in myoblasts. Also, the production of low levels of reactive oxygen species (ROS) can mediate the stimulation of cell growth by C1P, particularly in macrophages. Upregulation of the PI3K/Akt/mTOR pathway is also involved in the inhibition of cell death by C1P, which can also contribute to cell survival by blocking the activity of the ceramide-generating enzymes acid sphingomyelinase (ASMase) and serine palmitoyl transferase (SPT). Moreover, C1P-promoted cell survival involves upregulation of inducible nitric oxide synthase (iNOS) and the subsequent production of nitric oxide (NO). Using photosensitive C1P analogues, it could be concluded that promotion of cell growth and inhibition of cell death were elicited by intracellularly generated C1P in a receptor-independent manner. The aim of the present review is to evaluate in detail the implication of the CerK/C1P axis in controlling cell proliferation and survival in mammalian cells, as well as to discuss and update on the molecular mechanisms by which C1P can accomplish these actions. Full article

The paper investigates the process of degumming substandard soybean oil using an enzyme complex of phospholipases to prepare it as a feedstock for biodiesel production. Dehumidification is an important refining step aimed at reducing the phosphorus content, which exceeds the permissible limits according to ASTM, EN, and ISO standards, by re-moving phospholipids. The enzyme complex of phospholipases includes phospholipase C, which specifically targets phosphatidylinositol, and phospholipase A2, which catalyzes the hydrolysis of phospholipids into water-soluble phosphates and lysophospholipids. This process contributes to the efficient removal of phospholipids, increased neutral oil yield, and reduced residual oil in the humic phase. The use of an enzyme complex of phospholipases provides an innovative, cost-effective, and environmentally friendly method of oil purification. The results of the study demonstrate the high efficiency of using the phospholipase enzyme complex in the processing of substandard soybean oil, which allows reducing the content of total phosphorus to 0.001% by weight, turning it into a high-quality raw material for biodiesel production. The proposed approach contributes to increasing the profitability of agricultural raw materials and the introduction of environmentally friendly technologies in the field of renewable energy. Full article

The EFR3 (Eighty-Five Requiring 3) protein and its homologs are rather poorly understood eukaryotic plasma membrane peripheral proteins. They belong to the armadillo-like family of superhelical proteins. In higher vertebrates two paralog genes, A and B were found, each expressing at least 2–3 protein isoforms. EFR3s are involved in several physiological functions, mostly including phosphatidyl inositide phosphates, e.g., phototransduction (insects), GPCRs, and insulin receptors regulated processes (mammals). Mutations in the EFR3A were linked to several types of human disorders, i.e., neurological, cardiovascular, and several tumors. Structural data on the atomic level indicate the extended superhelical rod-like structure of the first two-thirds of the molecule with a typical armadillo repeat motif (ARM) in the N-terminal part and a triple helical motif in its C-terminal part. EFR3s’ best-known molecular function is anchoring the giant phosphatidylinositol 4-kinase A complex to the plasma membrane crucial for cell signaling, also linked directly to the KRAS mutant oncogenic function. Another function connected to the newly uncovered interaction of EFR3A with flotillin-2 may be the participation of the former in the organization and regulation of the membrane raft domain. This review presents EFR3A as an intriguing subject of future studies. Full article

Originally identified in proteomic-based studies of the Golgi, Golgi phosphoprotein 3 (GOLPH3) is a highly conserved protein from yeast to humans. GOLPH3 localizes to the Golgi through the interaction with phosphatidylinositol-4-phosphate and is required for Golgi architecture and vesicular trafficking. Many studies revealed that the overexpression of GOLPH3 is associated with tumor metastasis and a poor prognosis in several cancer types, including breast cancer, glioblastoma multiforme, and colon cancer. The purpose of this review article is to provide the current progress of our understanding of GOLPH3 molecular and cellular functions, which may potentially reveal therapeutic avenues to inhibit its activity. Specifically, recent papers have demonstrated that GOLPH3 protein functions as a cargo adaptor for COP I-coated intra Golgi vesicles and impinges on Golgi glycosylation pathways. In turn, GOLPH3-dependent defects have been associated with malignant phenotypes in cancer cells. Additionally, the oncogenic activity of GOLPH3 has been linked with enhanced signaling downstream of mechanistic target of rapamycin (mTOR) in several cancer types. Consistent with these data, GOLPH3 controls organ growth in Drosophila by associating with mTOR signaling proteins. Finally, compelling evidence demonstrates that GOLPH3 is essential for cytokinesis, a process required for the maintenance of genomic stability. Full article

Adolescent idiopathic scoliosis (AIS) is characterized by a curvature of the spine affecting approximately 4% of the pediatric population, and the mechanisms driving its progression remain poorly understood. Whole-exome sequencing of a French-Canadian AIS cohort with severe scoliosis identified rare variants in the PTPRM gene, which encodes Protein Tyrosine Phosphatase μ (PTPµ). However, these rare variants alone did not account for the pronounced reduction in PTPµ at both mRNA and protein levels in severe AIS cases. This led us to investigate epigenetic regulators and the identification of five microRNAs (miR-103a-3p, miR-107, miR-148a-3p, miR-148b-3p, and miR-152-3p) that target PTPRM mRNA. These microRNAs were significantly elevated in plasma from severe AIS patients, and miR-148b-3p was also upregulated in AIS osteoblasts. Phenotypic analysis of bipedal Ptrprm knockout (PTPµ −/−) mice showed increased prevalence and severity of scoliosis, while quadrupedal PTPµ −/− mice did not develop scoliosis, underscoring PTPµ’s role as a disease-modifying factor. Mechanistically, PTPµ deficiency was found to disrupt Gi-coupled receptor signaling in osteoblasts by enhancing the interaction between osteopontin (OPN) and α5β1 integrin, along with increased tyrosine phosphorylation of phosphatidylinositol-4-phosphate 5-kinase type I (PIPKIγ90). These findings provide novel insights into the molecular mechanisms underlying spinal deformity progression in AIS, linking PTPµ depletion to aberrant OPN-α5β1 integrin signaling and highlighting potential therapeutic targets to stop, mitigate, or prevent scoliosis. Full article

This study investigates the effect of dietary Lactobacillus plantarum supplementation on juvenile coho salmon (Oncorhynchus kisutch). Four groups of the juveniles (initial weight 103.87 ± 2.65 g) were fed for 10 weeks with four diets containing 0 (control diet), 10⁵ (T1), 10⁷ (T2), and 10⁹ (T3) cfu/g of L. plantarum. The main results are as follows: Compared with the control diet, the final weight, specific growth rate (SGR), and weight gain rate (WGR) of the juveniles fed the T1, T2, and T3 diet significantly (p < 0.05) increased, while the feed coefficient ratio (FCR) expressed an opposite trend. The activities of superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GSH-PX) in the serum of the juveniles fed the T2 diet significantly (p < 0.05) increased, while the malondialdehyde (MDA) expressed an opposite trend. The expression of phosphatidylinositol 4,5-bisphosphate 3-kinase (pi3k), AKT-interacting protein (akt), mechanistic target of rapamycin kinase (mtor), glucose-6-phosphate dehydrogenase (g6pd), sod, cat, and gsh-px genes in the liver of the juveniles fed the T2 diet significantly (p < 0.05) increased. In conclusion, the T2 diet significantly improved the growth performance, antioxidant capacity, and upregulated key mTOR pathway genes in juvenile coho salmon. Full article

Grain weight and grain shape are key traits affecting grain yield and quality in rice. In this research, a quantitative trait locus (QTL), qTGW2, that controls 1000-grain weight (TGW), grain length (GL), and grain width (GW) in rice, was fine-mapped within an 84.7 kb region on chromosome 2 using three sets of near isogenic lines (NILs) originated from the indica rice cross, Teqing (TQ)/IRBB52. In the NIL populations, the TGW, GL, and GW of the IRBB52 homozygous lines increased by 0.22 g, 0.020 mm, and 0.009 mm compared with the TQ homozygous lines. Four annotated genes showed nucleotide polymorphisms between the two parental lines in the qTGW2 region. Only one annotated gene, LOC_Os02g57660, exhibited significant expression differences between NIL^TQ and NIL^IRBB52 in the young panicles performed by RNA sequencing and the quantitative real-time polymerase chain reaction. These results indicated that LOC_Os02g57660, which encodes phosphatidylinositol-4-phosphate 5-kinase (PIP5K), was the candidate gene of qTGW2. Then, one insertion-deletion (InDel) was found in the LOC_Os02g57660 coding region. The haplotype analysis was performed based on the phenotypic data of 4720 rice accessions from RiceVarMap V2.0. Two haplotypes, Hap1 (TQ-type) and Hap2 (IRBB52-type), were classified according to one InDel. Significant differences in grain weight traits were identified between Hap1 and Hap2. Hap2 has greater GL and RLW but lower GW, thus exhibiting potential to simultaneously improve grain yield and quality. Full article

The detection of early molecular mechanisms and potential biomarkers in Parkinson’s disease (PD) remains a challenge. Recent research has pointed to novel roles for post-translational citrullination/deimination caused by peptidylarginine deiminases (PADs), a family of calcium-activated enzymes, in the early stages of the disease. The current study assessed brain-region-specific citrullinated protein targets and their associated protein–protein interaction networks alongside PAD isozymes in the 6-hydroxydopamine (6-OHDA) induced rat model of pre-motor PD. Six brain regions (cortex, hippocampus, striatum, midbrain, cerebellum and olfactory bulb) were compared between controls/shams and the pre-motor PD model. For all brain regions, there was a significant difference in citrullinated protein IDs between the PD model and the controls. Citrullinated protein hits were most abundant in cortex and hippocampus, followed by cerebellum, midbrain, olfactory bulb and striatum. Citrullinome-associated pathway enrichment analysis showed correspondingly considerable differences between the six brain regions; some were overlapping for controls and PD, some were identified for the PD model only, and some were identified in control brains only. The KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways identified in PD brains only were associated with neurological, metabolic, immune and hormonal functions and included the following: “Axon guidance”; “Spinocerebellar ataxia”; “Hippo signalling pathway”; “NOD-like receptor signalling pathway”; “Phosphatidylinositol signalling system”; “Rap1 signalling pathway”; “Platelet activation”; “Yersinia infection”; “Fc gamma R-mediated phagocytosis”; “Human cytomegalovirus infection”; “Inositol phosphate metabolism”; “Thyroid hormone signalling pathway”; “Progesterone-mediated oocyte maturation”; “Oocyte meiosis”; and “Choline metabolism in cancer”. Some brain-region-specific differences were furthermore observed for the five PAD isozymes (PADs 1, 2, 3, 4 and 6), with most changes in PAD 2, 3 and 4 when comparing control and PD brain regions. Our findings indicate that PAD-mediated protein citrullination plays roles in metabolic, immune, cell signalling and neurodegenerative disease-related pathways across brain regions in early pre-motor stages of PD, highlighting PADs as targets for future therapeutic avenues. Full article