Search Results (210)

Potassium (K⁺) channels have been frequently linked to cancer progression; however, their contribution varies across tumour types and experimental models. This heterogeneity indicates that gene-level characteristics such as expression, co-expression, or mutational status are inadequate for explaining channel involvement in oncogenic signalling. Here, we performed a cross-study comparison of experimentally validated K⁺ channel interactomes, we show that K⁺ channel regulation is highly context-dependent and does not exhibit conserved pan-cancer signatures. By directly comparing proximity-labeling and affinity-purification datasets across different K⁺ channel families, we identify a limited number of recurrent organizational architectures rather than universal signalling modules. KCa3.1 (encoded by KCNN4), Kir2.1 (KCNJ2), and TASK-1 (KCNK3) assemble signalling-permissive interactomes integrating adhesion complexes, junctional scaffolds, vesicular trafficking pathways, and receptor-associated signalling nodes. In contrast, Kv11.1 (encoded by KCNH2) displays an interactome predominantly enriched for proteostasis and endoplasmic reticulum–associated components, indicating a proteostasis-centered organizational profile with comparatively limited signalling integration. Kv1.3 (encoded by KCNA3), instead, consistently associates with mitochondrial and metabolism-linked proteins and functionally connects metabolic state to downstream transcriptional regulators, rather than regulating its own transcription. Higher-order intersection and pathway-specific analyses indicate that functional convergence across the above channels emerges from shared architectural principles rather than extensive molecular overlap. In conclusion, this study identifies interactome architecture as a central organizational level for understanding K⁺ channel function in cancer. The integration of pan-cancer gene-level analyses with systematic comparison of interaction architectures offers a coherent framework for interpreting the functional heterogeneity observed across channels, families, and tumor contexts. This perspective suggests that therapeutic strategies may benefit from targeting channel-centered network architectures rather than isolated channels alone, highlighting ion channels as structural components of broader signalling systems rather than solely bioelectrical regulators. Full article

Endothelial dysfunction is an early event in the development of cardiovascular diseases and is characterized by impaired barrier function, inflammatory activation of endothelial cells (ECs), and alterations in lipid metabolism. In addition to typical (mononuclear) endothelial cells (TECs), multinucleated variant endothelial cells (MVECs) are present within the vascular wall; however, their functional role remains poorly understood. The aim of the present study was to investigate the molecular and functional characteristics of MVECs and their potential contribution to the development of endothelial dysfunction. Primary human umbilical vein endothelial cells (HUVECs) were used, and multinucleated cells were generated by polyethylene glycol-induced fusion. Cells were incubated under control conditions or exposed to low-density lipoproteins (LDL; 100 µg/mL, 24 h). A comprehensive analysis was performed, including transcriptomic and proteomic (secretome) profiling using gene set enrichment analysis (GSEA), as well as functional assays assessing transendothelial LDL transport, intracellular cholesterol accumulation, macrophage migration, and the expression and secretion of pro-inflammatory cytokines (IL-6, IL-8). MVECs exhibited pronounced differences compared to TECs. GSEA revealed reduced enrichment of pathways related to canonical nuclear factor kappa B (NF-κB) signaling and negative regulation of NF-κB transcription factor activity, actin cytoskeleton organization, focal adhesion assembly, basement membrane organization, and vesicle-mediated transport in MVECs relative to TECs, indicating impaired cytoskeletal integrity, altered cell–matrix interactions, dysregulated inflammatory signaling, and reduced vesicular trafficking activity. Functionally, MVECs demonstrated an increased capacity for cholesterol accumulation and enhanced transendothelial migration of macrophages. Notably, transendothelial LDL transport across the MVEC monolayer was not increased, suggesting a predominance of intracellular lipid accumulation. MVECs also exhibited a pronounced pro-inflammatory phenotype, characterized by elevated expression and secretion of IL-6 and IL-8. Taken together, these findings indicate that MVECs represent a functionally altered endothelial phenotype with impaired barrier function, dysregulated lipid metabolism, and enhanced inflammatory activity. Local accumulation of MVECs within the vascular wall may contribute to the formation of pro-atherogenic regions and play a role in the initiation and progression of endothelial dysfunction. Full article

Background: Early endolysosomal and autophagic defects are among the earliest cellular alterations observed in Alzheimer’s disease (AD). However, the molecular mechanisms linking amyloid precursor protein (APP) metabolism to vesicle trafficking dysfunction remain incompletely understood. The APP-derived fragment C99 has emerged as a potential upstream mediator of intracellular toxicity, but its impact on organelle homeostasis and its modulation by metabolic interventions remain unclear. Methods: To investigate these mechanisms, we expressed human C99 in Drosophila neurons and examined intracellular pathology using ultrastructural analysis, fluorescent reporters of autophagy and mitochondrial turnover, and proteomic interactome mapping. The effects of the ketone body β-hydroxybutyrate (BHB) were evaluated to assess the impact of metabolic intervention. Results: Neuronal C99 expression induced pronounced vesicular abnormalities, impaired autophagic turnover, and disrupted mitochondrial quality control. Transmission electron microscopy revealed extensive accumulation of enlarged vesicular compartments, accompanied by reduced mitochondrial turnover and accumulation of aged mitochondria. BHB treatment restored autophagic cargo clearance, improved mitochondrial turnover, and normalized vesicular ultrastructure. These protective effects required neuronal ketone transport, indicating a neuron-intrinsic metabolic mechanism. Proteomic analysis of the C99-associated interactome revealed that ketone treatment remodels networks enriched for vesicle trafficking and proteostasis pathways. Network prioritization identified the retromer component VPS35 as a candidate regulatory hub. Functional analyses demonstrated that depletion of VPS35 abolished the BHB-dependent restoration of autophagy, mitochondrial turnover, and vesicle morphology. Conclusions: Ketone treatment restores mitochondrial quality control and autophagic homeostasis through a VPS35-dependent mechanism in C99-induced neurodegeneration. These findings provide mechanistic insight into how metabolic interventions may restore intracellular homeostasis in Alzheimer’s disease. Full article

Sclerotinia sclerotiorum is a formidable soilborne fungus that wreaks havoc on numerous crops globally. While the role of ADP-ribosylation factor-like 1 (Arl1) small GTPases in vesicular trafficking and fungal development is well-documented, their specific impact on S. sclerotiorum remains unclear. Through reverse genetic techniques, we identified and characterized SsArl1, a typical Arl small GTPase conserved across fungi. Deleting SsArl1 hampers the hyphal growth of S. sclerotiorum, but leads to higher oxalic acid buildup and boosts cellulase activity. This speeds up the infection of host plants, yet increases their sensitivity to certain environmental stresses, particularly ionic and cell wall-related stress. Our results reveal that SsArl1 acts as a negative regulator of oxalic acid accumulation and virulence, while playing a positive role in enhancing resistance to environmental stresses in S. sclerotiorum. Full article

Caveolin-1 (CAV1) is a 21 kDa Vesicular Integral-membrane Protein essential for the biogenesis of caveolae, invaginations of the plasma membrane that coordinate membrane trafficking, lipid homeostasis, and signal transduction. CAV1 functions as a scaffolding platform that integrates mechanotransduction, endocytosis, and cellular stress responses, thereby modulating vascular integrity, inflammation, metabolism, and tumorigenesis. To comprehensively understand the phosphorylation landscape of CAV1, global phosphoproteomic datasets and their corresponding experimental metadata were systematically curated and integrated from previously published human cellular studies. The phosphorylation sites with the highest detection frequency across these datasets were considered predominant phosphorylation sites. To assess their functional relevance, phosphosites in other proteins (PsOPs) co-regulated with the predominant CAV1 sites, along with their upstream kinases and high-confidence protein–protein interaction partners, were systematically analyzed. Analysis of global human cellular phosphoproteome datasets revealed that tyrosine 14 (Y14) and serine 37 (S37) of CAV1 are the most frequently detected phosphosites across diverse experimental conditions. Notably, many of the co-regulated proteins obtained were associated with carcinogenesis, apoptosis, and cell cycle regulation, including MET and ERBB2. Our analysis revealed SRC, ABL2, ERBB2, ERBB3, LYN, and TEC as potential upstream kinases of CAV1_Y14, whereas CSNK1E and GRK5 were predicted to regulate CAV1_S37. Considering the challenges associated with site-specific interrogation, we employed a global co-regulation analysis approach to characterize CAV1 phosphorylation dynamics. Our findings reveal that key CAV1 phosphosites modulate oncogenic signaling, cytoskeletal remodeling, and membrane organization, providing novel insights into CAV1-mediated cellular functions and its context-dependent role in tumor progression. Full article

Background: Pleural mesothelioma (PM) is characterised by often rapid therapeutic failure and chemotherapy resistance. While terminal resistance is well studied, the initial transition into a drug-tolerant phenotype remains poorly understood. Methods: We established patient-derived organoids (PDOs) from malignant pleural effusions to model this transition. Cisplatin-tolerant lines were generated via repeated incremental exposure to cisplatin and compared to time-matched treatment-naive controls using RNA sequencing and Seahorse XFe96 metabolic flux analysis. Results: Integrated profiling suggested that the route to tolerance may be influenced by the underlying mutational profile. In this cohort, all BAP1-retained models (including those with KRAS mutations or MTAP loss) adopted an elevated basal metabolic hybrid phenotype, significantly upregulating baseline oxidative phosphorylation and glycolysis to fuel survival mechanisms. Conversely, BAP1-deficient models entered a hypometabolic state of dormancy, characterised by baseline bioenergetic suppression and reduced Ki-67 proliferation. Transcriptomic analysis identified a vesicular transport signature (SYNGR3, VPS52, PROM2) in plastic models, suggesting altered membrane trafficking as a potential survival strategy. Conclusions: Our findings demonstrate that mesothelioma therapeutic escape is not a uniform process. Identifying these patient-specific metabolic and transcriptomic trajectories via 3D PDOs provides a hypothesis-generating framework to explore potential avenues for future personalised therapy. Full article

Phospholipids function as dynamic regulators of plant growth and environmental adaptation, extending well beyond their structural roles in biological membranes. This review synthesizes the phospholipid metabolic network and its regulatory functions in plant physiology. We first describe enzymatic reactions and acyl-chain remodeling in phospholipid biosynthesis, and then examine the interaction between phospholipid metabolism and auxin signaling, focusing on phosphatidic acid (PA) and phosphoinositide phosphate (PIP). These lipid molecules regulate the polarization and vesicular trafficking of PIN-FORMED proteins via endocytosis and phosphorylation-dependent mechanisms, thereby controlling auxin distribution during development and stress adaptation. Particular emphasis is placed on PA, a multifunctional signaling lipid that serves as a central molecular hub. PA coordinates hormonal, stress, and circadian signals by engaging and modulating a broad spectrum of protein targets, including kinases, phosphatases, and transcription factors. We also discuss the emerging and evolutionarily conserved functions of phospholipid signaling in cell fate determination, drawing parallels from mammalian cell reprogramming to the regulation of plant cell totipotency and root patterning. Collectively, these findings underscore the critical role of phospholipid-mediated signaling in converting metabolic and environmental cues into developmental reprogramming, providing novel theoretical and functional frameworks for future research in plant lipid biology. Full article

Background: Tumour glycosylation regulates immune modulation and progression, but whether the CRC sialylome—the complete repertoire of sialylated glycans—defines a biologically distinct subtype remains unclear. We investigated how the “sugar code” shapes CRC biology, immunity, and therapeutic response. Methods: Transcriptomic data from three CRC cohorts (TCGA, Sidra-LUMC, and CPTAC-2; n = 988) were batch-corrected and integrated. Single-sample gene set enrichment analysis (ssGSEA) quantified sialyltransferase expression, sialic acid metabolism, EMT, MDR mechanisms, immune phenotypes, and Siglec-associated transcriptional signatures. GSEA, gene ontology enrichment analysis (GOEA), and drug ontology enrichment analysis (DOEA) characterised pathways and identified drug response-associated transcriptional signatures. Results: High sialylome activity defined a genomically stable but clinically advanced CRC subset enriched for left-sided tumours, mucinous histology, MSI, and BRAF mutations. At the transcriptional level, Sialyl-High tumours were associated with a mesenchymal, stromal-remodelling programme accompanied by reduced proliferative activity. They demonstrated enrichment of vesicular trafficking-related pathways alongside reduced representation of canonical efflux-associated programmes. Critically, the sialylome was associated with Siglec-related immune signatures, with sialylated glycan-related gene expression correlating with Siglec receptor expression (CD33 and SIGLEC7/9/10), consistent with an immune-inflamed yet structurally excluded microenvironment. DOEA identified selective enrichment of drug-response signatures related to sialic acid metabolism inhibitors (oseltamivir and Neu5Ac) and glycocalyx-disrupting agents (ginsenosides and soyasaponins). Conclusions: The CRC sialylome is associated with tumour phenotypic variation, including immune-excluded states linked to Siglec-associated transcriptional signatures and patterns consistent with non-canonical drug resistance programmes. These findings position the “sugar code” as a central organising principle in CRC and identify glycan-directed therapies as a promising strategy for the targeting of this aggressive subtype. Full article

Extracellular vesicles (EVs) can disseminate replication-competent viral genomes complexed with selected host proteins, enabling stealth cell-to-cell transfer within lipid membrane-enclosed bubbles. In addition to complementing free-virion spread, EV-associated genomes can be protected from neutralizing antibodies and persist under conditions in which classical virion production decreases. Here, we propose a route-resolved framework in which interconnected cellular secretory pathways, including endoplasmic reticulum (ER) remodeling, multivesicular body (MVB) biogenesis, secretory autophagy, and plasma-membrane budding, jointly generate EV heterogeneity and create discrete opportunities for the capture, protection, and export of infectious cargo. We highlight reticulon-3 (RTN3), an ER-shaping protein, as an upstream regulator that can couple infection-induced ER microdomains to endosomal docking and to autophagy-linked trafficking decisions that bias intermediates toward secretion rather than degradation. Supporting this view, transmission electron microscopy of dengue virus-infected cells reveals extensive vesicular remodeling, including irregular MVBs adjacent to the plasma membrane and autophagosome-like double-membrane structures, consistent with altered vesicular routing following RTN3 perturbation. Collectively, these route-resolved, spatially organized spatio-organelle changes support a pathomechanistic model in which RTN3-mediated ER remodeling reshapes ER-endosome-autophagy trafficking interfaces, creating regulated decision points that can be leveraged to stratify infectious EV subsets (with infectivity-linked single-vesicle and quantitative proteomics approaches) and to inform host-directed strategies that curb non-lytic viral dissemination. Full article

Celiac disease (CD) is an autoimmune inflammatory enteropathy triggered by consuming gluten-containing cereals. A key role in its pathogenesis is played by type 2 transglutaminase, an enzyme that causes an increase in gluten immunogenicity. Celiac cells seem to present constitutive characteristics, even recognizable under a gluten-free diet, such as defects in vesicular trafficking and autophagy, protein hyperphosphorylation, and cytoskeleton rearrangement. In this work, by using an omics approach, we attempted to identify those proteins differentially expressed or differentially phosphorylated in a cell model suitable to study cell behavior in the absence of inflammation, i.e., primary cultures of dermal fibroblasts from control or CD subjects. By performing mass spectrometry analyses, we found several up- and-down expressed or phosphorylated proteins in CD samples, mainly involved in signaling, homeostatic responses, cytoskeleton organization, vesicular trafficking, and extracellular vesiculation. These proteins may represent a molecular signature of the celiac cellular phenotype and may contribute to adding new insight into the comprehension of the complex mechanisms of CD pathogenesis. Full article

The proteolytic processing of the amyloid precursor protein (APP) is a core pathological event in Alzheimer’s disease (AD) pathogenesis, yet the global genetic regulatory networks modulating this process have not been fully characterized. To systematically identify novel regulators of APP cleavage, we performed a genome-wide CRISPR/Cas9 knockout screen utilizing an optimized UAS-GAL4-based cellular reporter, and identified genetic modulators governing amyloidogenic and non-amyloidogenic processing. The screen uncovered distinct functional gene clusters regulating the APP, prominently involving cellular metabolism, protein modification, and vesicular trafficking. Specifically, LDHB, PIAS2, CCDC53, and TRIM61 emerged as novel functional modulators. Biochemical validation confirmed that ablating these genes significantly alters the metabolic balance between sAPPα and amyloid-β (Aβ) production. Finally, integration with human AD transcriptomic datasets demonstrated that these identified modulators undergo significant dysregulation in clinics. Together, these findings establish a reporter-based functional screening framework for APP processing and identify candidate regulatory nodes linked to metabolism, protein modification, and vesicular trafficking. These candidates provide a resource for future mechanistic investigation and validation in more disease-relevant AD models. Full article

Ischemic stroke induces complex molecular responses that disrupt subcellular organelles’ function and contribute to brain injury, yet the temporal changes of organelle-specific transcriptomic remodeling remain to be investigated. In this study, we performed in silico analysis of publicly available transcriptomic data from isolated brain microvessels of transient middle cerebral artery occlusion (tMCAO) mouse model. Using in silico approaches, we analyzed differential gene expression at 24 h (acute phase) and 7 d (intermediate phase) post-stroke, focusing on mitochondria, endoplasmic reticulum (ER), and Golgi apparatus. Functional enrichment (Gene Ontology, KEGG) and protein–protein interaction network analyses were performed. Our analysis of the data revealed that at 24 h post-stroke, all three organelles exhibited marked transcriptional remodeling, where mitochondrial pathways showed disrupted metabolic and redox regulation; ER pathways indicated activation of biosynthetic processes, stress signaling, and ferroptosis; and Golgi-related genes reflected altered vesicular trafficking and glycosylation. By 7 d, mitochondrial alterations subsided, whereas ER and Golgi pathways displayed downregulation of metabolic and neuronal signaling processes, indicating persistent dysfunction and incomplete microvascular recovery. Phase-specific drug–gene interaction analysis will be useful to understand temporal organelle-associated transcriptional organization and to guide future investigations of neurovascular remodeling after ischemic stroke. Full article

Glucose transporter type 4 (GLUT4), encoded by the SLC2A4 gene, is the final effector of insulin-stimulated glucose uptake in insulin-sensitive tissues: skeletal muscle, adipose tissue, and cardiac muscle. Its dynamic localization, retained intracellularly under basal conditions and extensively translocated to the plasma membrane upon stimulation, makes it a master regulator of glycemic homeostasis. While the canonical insulin pathway (PI3K/Akt/TBC1D4) is the most potent and specific mechanism in the postprandial state, its dysfunction is centrally associated with insulin resistance and type 2 diabetes mellitus (T2DM). Crucially, robust alternative signaling networks function completely independently of insulin to regulate GLUT4 synthesis and translocation. Prominent among these are contraction-mediated pathways in skeletal muscle, which employ calcium signaling (via CaMKII), mechanical/metabolic stress sensors (via p38 MAPK γ/δ), and AMP-activated protein kinase (AMPK). This review critically integrates current knowledge, linking the molecular architecture and post-translational modifications of GLUT4 to the complex, tissue-specific signaling networks that govern its vesicular trafficking. We emphasize the hierarchy, redundancy, and interdependence of these pathways, highlighting differences between acute translocation and chronic transcriptional adaptations. Finally, we discuss how deciphering insulin-independent mechanisms offers promising therapeutic opportunities, particularly in identifying pharmacological targets that mimic the metabolic benefits of physical exercise. Full article

Short linear motifs (SLiMs), such as PDZ-binding motifs (PDZbms), are compact interaction modules that mediate transient, specific protein–protein interactions. While PDZbms are well characterized in viral pathogenesis, subverting host protein functions, their role in bacterial systems requires further study. Mycobacterium tuberculosis (Mtb) is an intracellular pathogen that mainly infects macrophages. The type VII secretion system (T7SS) of Mtb secretes a subset of effector proteins (Esx) involved in virulence. By using molecular docking and support vector machine-based prediction, we analyzed PDZbm occurrence in T7SS Esx effector proteins and their ability to bind human PDZ domain-containing proteins. We identified PDZbms in most of the Esx proteins studied, with EsxA and EsxG showing the best PDZ-dependent interaction with syntenin-1, a host scaffold protein involved in vesicular trafficking and immune signaling. Additional Esx proteins were predicted to engage other host PDZ proteins. Proteome-wide analysis of Mtb H37Rv revealed that 23.1% of expressed proteins with ≥50 amino acids contained a C-terminal PDZbm. Gene Ontology and Reactome pathway enrichment revealed their involvement in processes related to bacterial and bacterial–host interactions, including redox balance, immunomodulation, and membrane localization, at various stages of infection. Our results support the existence of a PDZbm-mediated interface between Mtb and the human host, extending the PDZbm mimicry hypothesis beyond viruses to bacterial systems as an immune evasion strategy. This work may open multiple research lines focused on experimental validation and the development of a comparative PDZbm catalogue to uncover conserved virulence mechanisms that may guide the design of host-directed therapeutics. Full article

Membrane curvature is a fundamental biophysical property of cellular membranes that underlies essential processes such as vesicle formation, organelle shaping, intracellular trafficking, and membrane scission. While traditionally studied in the context of cell biology and membrane dynamics, membrane curvature is now emerging as a critical, albeit underrecognized, regulator of oncogenic transformation and tumor progression. Curvature not only governs the mechanical properties of the membrane but also influences the spatial localization and activation of key signaling proteins, including Ras family GTPases, whose oncogenic functions are closely dependent on membrane topology. Cancer is frequently associated with disruptions in the regulation of membrane curvature as a result of aberrant lipid metabolism, overexpression of curvature-modulating proteins, and cytoskeletal remodeling. These changes facilitate the hallmarks of malignancy such as uncontrolled proliferation, enhanced motility, immune evasion, metabolic rewiring, and therapy resistance. Notably, recent evidence reveals that curvature acts as a spatial cue for Ras activation, particularly during epithelial-to-mesenchymal transition (EMT), where curvature-driven Ras relocalization amplifies growth factor signaling and promotes metastasis. This review provides a comprehensive overview of the molecular determinants that generate and sense membrane curvature from lipid shape and membrane asymmetry, BAR domain proteins, and actin dynamics, and explores how these mechanisms are hijacked in cancer. We describe the feedback between membrane architecture and oncogenic pathways such as Ras/MAPK and PI3K/AKT, emphasizing the role of curvature in shaping signal transduction platforms. It should be noted that “curvature-driven signaling” is defined as signaling regulation that arises from membrane-geometry-dependent localization, clustering, or activation of signaling proteins, while “curvature-sensitive platforms” refer to membrane subdomains whose specific curvature selectively recruits and stabilizes signaling complexes. Furthermore, we examine how these biophysical alterations impact vesicular trafficking, organelle morphology, and secretion, all of which are co-opted to support tumor development. From a translational standpoint, we assess emerging therapeutic strategies designed to target curvature-regulating factors and leverage membrane topology for precision drug delivery. Innovations in nanomedicine, super-resolution imaging, and curvature-sensing biosensors are also discussed as tools for both diagnostics and therapeutic monitoring. By integrating advances in membrane biophysics, cancer signaling, and bioengineering, this review highlights membrane curvature as a central and actionable dimension of cancer biology. Full article