Search Results (775)

Candida auris is an emerging fungal pathogen that is posing a serious global health threat due to its high transmissibility and multidrug resistance profile. Despite recent molecular advances in scrutinizing this enigmatic microbe, much of our understanding regarding its pathomechanisms remains unelucidated. Since microbial pathogenesis is modulated by a dynamic interplay between the host and the pathogen, dissecting such host–pathogen interactions involving C. auris can shed novel insights into its pathogenic cascade. As such, to characterize the virulence repertoire of C. auris, this study applied an integrated quantitative proteomics strategy to scrutinize the early phase of infection. In vitro and in vivo experimental setups based on macrophage co-culture and murine intraperitoneal infection were utilized. Integrated proteomic analysis revealed a coordinated remodelling of cellular processes by C. auris during the early host–pathogen interaction phase, including downregulation of translational machinery, modulation of molecules involved in metabolic rewiring, stress responses, and structural rearrangements. Several proteins associated with oxidative stress adaptation, alternative carbon metabolism, and cytoskeletal regulation were differentially abundant during host interactions. Collectively, these findings demonstrate that early adaptation of C. auris to host immune pressure involves rapid and context-dependent proteome remodelling that may contribute to fungal survival and persistence during infection. Full article

Background: Dysregulated cell migration leading to metastasis remains the primary cause of cancer-related mortality. It has been challenging to understand how cells regulate migration. We have previously created the first selective inhibitor of cell migration, KBU2046. Here, we use it as a probe to identify regulatory processes. Methods: Metastatic and primary human prostate cancer cells were treated for different times and at different concentrations with KBU2046. Immunofluorescent microscopy examined protein localization in cells. Label-free mass spectrometry (MS) was performed on total cell proteins, Tandem Mass Tag (TMT) labeling MS was used on membrane fractions, and temporal phosphoproteomic profiling was performed. Results were analyzed with a suite of bioinformatic tools. Results: KBU2046-induced migrastasis is associated with the accumulation of activated integrin β1 into focal adhesions. Whole-cell proteomics demonstrated suppression of processes that mediate intracellular protein trafficking and increases in mitochondrial energy-generation signatures. Evaluation of the membrane fraction identified increases in membrane repair and maintenance processes and decreases in those that drive motility. Temporal- and concentration-dependent phosphoproteomic profiling revealed that KBU2046 initiates a dynamic, cascading sequence of transient signaling waves rather than a static block. Conclusions: KBU2046-induced migrastasis appears to operate through spatial decoupling rather than structural degradation. By restricting the intracellular trafficking machinery required for receptor recycling, KBU2046 limits focal adhesion turnover, providing, in PC3 prostate cancer cells, a correlative framework to inhibit metastatic dissemination independent of direct cytotoxicity. Full article

Forskolin (FSK) is a well-characterized small-molecule activator of adenylyl cyclase that drives direct neuronal transdifferentiation in human fibroblasts; however, the temporal sequence and coordinated relationships among proteomic and metabolic adaptations during the initiation phase of lineage conversion remain poorly understood. In this study, we applied data-independent acquisition (DIA)-based quantitative proteomics and untargeted metabolomics on BJ human dermal fibroblasts at three biological timepoints: pre-induction (day 0), commitment onset (day 2), and neuronal maturation (day 5). Under the established FSK-based induction protocol, BJ fibroblasts rapidly acquired neuronal-like features, with more than 90% of cells becoming TUJ1-positive by day 5. Proteomic profiling revealed a profound, dichotomous regulatory shift: time-dependent activation of core metabolic and energy pathways (glycolysis, the TCA cycle, and oxidative phosphorylation) coupled with persistent suppression of cell-cycle progression and DNA replication. Concordantly, global metabolomic profiling revealed a statistically unidirectional transition in metabolic states characterized by the progressive accumulation of phosphoenolpyruvate (PEP). Collectively, our findings identify coordinated remodeling of central carbon metabolism as a prominent early molecular feature associated with neuronal transdifferentiation under the FSK-based induction protocol. This study provides an integrated proteomic and metabolomic framework for understanding early molecular remodeling during chemically induced cell fate conversion and provides a basis for future functional studies of metabolic regulation during reprogramming. Full article

The intestinal mucosa is the primary site of Toxoplasma gondii (T. gondii) infection and interaction with the host. While the intestinal responses have been characterized through transcriptomic and histopathological studies, a comprehensive, system-wide analysis of the functional proteome remodeling by acute T. gondii infection is required to elucidate the underlying mechanisms. This study presents a temporal, quantitative proteomic profiling of T. gondii-infected C57BL/6J mouse intestine to define the protein-centric host response. Global analysis reveals profound reprogramming, characterized by upregulated acute-phase reactants and interferon-stimulated effectors and downregulated epithelial barrier and digestive function proteins. Systems-level bioinformatics analysis uncovers a coordinated host strategy of cellular resource reallocation, evidenced by the simultaneous and specific amplification of ribosome biogenesis and proteasomal degradation pathways. Subsequent protein–protein interaction network analysis substantiates this strategic investment in core protein homeostasis infrastructure, identifying the ribosome biogenesis machinery as the topological core of the response interactome. These findings support a model of defense-priority resource reallocation. That is, the host redirects cellular resources to optimize its biosynthetic and catabolic capacity, facilitating a high-output immune response at the potential expense of tissue homeostasis. This work provides an integrated proteomic atlas of the intestinal immunopathology mechanisms during toxoplasmosis and establishes a foundation for future host-directed therapeutic exploration. Full article

Chitons, ancient polyplacophoran mollusks, are ideal models for studying biomineralization evolution due to their conserved morphology since the Cambrian. This study investigates the matrix proteins in shell plates and spicules of Acanthochitona rubrolineata using liquid chromatography–tandem mass spectrometry. By extracting proteins from 30 individuals and using proteomic method, we identified 26 soluble proteins and 22 insoluble proteins in the shell plates and 25 insoluble proteins, and found domains such as von Willebrand factor type A, chitin-binding, ferritin, and cadherin. These domains, prevalent in molluscan biominerals, suggest conserved roles in organic matrix formation. Despite genomic dynamism, the conservation of key domains across species highlights a core biomineralization mechanism. Notably, eight of the shell proteins and eight of the spicule proteins were homologous between A. rubrolineata and chiton Acanthopleura loochooana, indicating functional conservation. Phylogenetic analysis further supported the evolutionary significance of these domains in chitons. The study advances understanding of biomineralization in Polyplacophora, emphasizing the interplay between morphological stasis and molecular evolution. Full article

Early detection of ovarian cancer remains challenging because of the lack of sensitive and reproducible blood-based biomarkers. A major challenge in plasma proteomics is the extremely wide dynamic range of protein concentrations, which prevents simultaneous detection of both high- and low abundance proteins and limits the identification of disease-associated signals. In this study, we applied a combined atomic force microscopy and mass spectrometry (AFM/MS) approach to investigate how sample dilution affects plasma proteome coverage and the detection of differences between healthy donors and patients with stage I and stage III ovarian cancer. Plasma samples were analyzed at two dilution levels (1:100 and 1:10,000). At 1:100 dilution, a total of 235 proteins were identified across all samples, representing the union of all replicates and groups. The reproducible CORE proteome comprised 169 proteins in the Healthy group, 183 in the Stage I group, and 193 in the Stage III group. Differential analysis revealed distinct, non-overlapping protein sets at each dilution level. At 1:100 dilution, most altered proteins were decreased in patients and corresponded to major plasma components, including complement proteins and protease inhibitors. At 1:10,000 dilution, most altered proteins were increased and were predominantly immunoglobulin-related proteins, along with complement regulatory components. These findings show that sample dilution determines which fraction of the plasma proteome is observable. Here, proteome depth refers to the total number of non-redundant proteins accessible within the analytical workflow. When CORE sets from all groups were combined, 216 proteins were identified at 1:100 and 149 at 1:10,000, with 133 shared between the two dilution conditions. The higher dilution contributed 16 additional CORE proteins not detected in the 1:100 CORE union, increasing the combined CORE set to 232 proteins. Thus, higher dilution alone did not increase proteome depth, but provided complementary protein identifications that increased cumulative proteome depth when both dilution conditions were considered together. This effect reflects dilution-dependent selectivity in the composition of the detectable protein subset. Full article

Background: Seed dormancy is crucial for plant survival and agricultural productivity, yet its molecular mechanisms, particularly the role of maternal effects, remain poorly understood. Methods: In this study, we applied a SWATH-based, label-free, quantitative shotgun proteomic mass spectrometry approach to investigate the temporal dynamics of dormancy establishment in Xanthium strumarium, a wild plant with two seeds in one burr that, despite sharing the same genetic and environmental conditions, exhibit distinct dormancy states. Results: Our data show that dormant seeds undergo coordinated metabolic suppression, marked by a decrease in energy metabolism, cell cycle arrest, and auxin signaling, explaining their smaller size. Simultaneously, dormant seeds exhibit metabolic re-prioritization towards fatty acid desaturation, cell wall modification, and an active epigenetic program stabilized by dormancy-promoting factors alongside a transcriptionally quiescent state in early–mid development. However, in the late developmental stage, molecular signaling pathways showed a recalibration distinguished by changes in seed metabolism (such as carbon–nitrogen reallocation, sulfur assimilation, and GABA production), hormonal fluctuations, and epigenetic regulation. Notably, previously reported high DOG1 transcript abundance, together with the absence of detectable DOG1 protein in the proteomic dataset, suggests that post-transcriptional mechanisms may contribute to DOG1 regulation. Conclusions: Based on these findings and the available literature, we propose a framework whereby dormancy establishment occurs in two phases: an early DOG1-mediated priming phase followed by a temperature-sensitive plasticity phase during seed maturation. Full article

Background: Peritoneal dialysis (PD) effluent of kidney failure patients represents an accessible liquid biopsy of the peritoneal cavity, yet the mechanisms determining its molecular composition remain poorly understood. We applied an integrative multi-omics approach to characterize the composition, transport dynamics, and molecular origin of the PD effluentome. Methods: Cell-free effluent, effluent cells, and plasma were collected from stable PD patients during standardized peritoneal equilibration tests in a randomized clinical trial. Targeted metabolomics, proteomics, and transcriptomic profiling were integrated with a reference human plasma proteome to investigate temporal molecular changes, peritoneal transport characteristics, and protein origin. Results: A total of 207 metabolites and 2970 proteins were identified in PD effluent. Metabolites exhibited distinct class-specific transport kinetics, with rapid equilibration of amino acids and biogenic amines, whereas lipids remained markedly underrepresented despite prolonged dwell times, indicating that transport is governed by physicochemical properties beyond molecular size alone. The effluent proteome underwent concordant alteration, with dwell time-dependent enrichment of pathways related to extracellular matrix organization, angiogenesis, coagulation, and tissue repair. Integrative analysis of the effluent proteome, effluent-cell transcriptome, and human plasma proteome resolved distinct plasma-associated, effluent cell-associated, resident peritoneal tissue-associated, and mixed-origin protein populations. Conclusions: This study establishes the first systems-level approach describing the composition, transport dynamics, and molecular origin of the PD effluentome. By transforming PD effluent into a biologically interpretable molecular readout of peritoneal membrane biology, this work provides a reference for the mechanistic interpretation of effluent-derived biomarkers and supports future therapeutic monitoring and precision medicine in PD. Full article

In dairy production, the fermentation process is a complex biochemical system that plays a significant role in determining the quality criteria of the final product. Traditional methods for controlling fermentation rely on limited and non-standard process parameters. In recent years, omics technologies have come to the forefront, enabling the monitoring of fermentation dynamics at the molecular level with their current, efficient, and reliable approaches. Thanks to omics approaches such as metabolomics, metagenomics, proteomics, and lipidomics, starter culture behavior, metabolite formation, aroma–texture formation, and microbial interactions in the fermentation process can be characterized more comprehensively. On the other hand, evaluating or calculating high-dimensional omics data using traditional statistical methods presents a challenge. Artificial intelligence applications are overcoming this challenge, offering significant opportunities for the accurate and reliable evaluation of data. Artificial intelligence-powered models hold promise in areas such as predicting fermentation kinetics, process control, optimizing quality criteria, and revealing the therapeutic potential of products through metabolites. This compilation aims to comprehensively address current approaches to modeling the fermentation process and quality parameters of dairy products using multi-omics technologies and artificial intelligence applications. In this respect, it will provide current and important perspectives for industrial applications and future studies. Full article

Obesity and type 2 diabetes (T2D) are multifactorial metabolic disorders characterized by progressive dysfunction of multiple organs and biological systems. Although mitochondrial dysfunction is a hallmark of disease progression, the mechanisms linking metabolic stress to coordinated tissue dysfunction remain incompletely understood. Comparative proteomic studies have consistently identified coordinated remodeling of oxidative phosphorylation, fatty acid oxidation, tricarboxylic acid cycle activity, redox regulation, mitochondrial proteostasis, and adaptive signaling across metabolically affected organs, revealing conserved organizational principles underlying mitochondrial adaptation. However, these findings have largely been interpreted within reductionist, pathway-centered frameworks. Here, we integrate evidence from comparative proteomics, mitochondrial biology, bioenergetics, redox biology, signaling, and systems biology to propose the concept of mitochondrial-centered biological networks (MCBNs), in which mitochondria function as dynamic regulatory hubs coordinating interconnected processes that collectively determine metabolic adaptation and tissue resilience. Building on this framework, we introduce the Mitochondrial Homeostasis Hypothesis, which proposes that preservation or restoration of mitochondrial homeostasis depends on coordinated regulation of MCBNs and constitutes a fundamental systems-level mechanism underlying resistance to obesity, T2D, and hypercaloric diet-induced metabolic dysfunction. Curcumin represents a well-studied network-modulating intervention that coordinately influences mitochondrial bioenergetics, metabolic flexibility, redox homeostasis, proteostasis, inflammatory signaling, and adaptive stress responses, supporting the concept that mitochondrial homeostasis is preserved through coordinated network regulation rather than isolated modulation of individual molecular pathways. Finally, we discuss how emerging technologies, including functional proteomics, redox proteomics, spatial and single-cell proteomics, acetylomics, integrated multi-omics, and artificial intelligence-assisted network analysis, provide unprecedented opportunities to quantitatively characterize MCBNs, validate the proposed hypothesis, identify network-based biomarkers, and accelerate the development of network-guided precision mitochondrial medicine. Full article

The corneal epithelium serves as the outermost transparent barrier of the eye and depends on rapid and coordinated cellular responses for wound repair. Although negative pressure (NP) has been shown to accelerate wound healing in other tissues, its cellular and molecular effects on corneal epithelium remain undefined. This study investigates how NP regulates corneal epithelial cell physiology and identifies the molecular mechanisms underlying NP-induced migration. Human corneal epithelial cells were exposed to normal or NP conditions, and cell motility was quantified using scratch-wound and transwell migration assays. Nuclear and cytoplasmic fractions were isolated for proteomic profiling to identify NP-responsive proteins. G3BP1 was selected as a candidate regulator and subsequently examined using molecular, biochemical, and functional assays to determine its role in NP-mediated signaling. Proteomic analysis revealed a significant NP-induced upregulation of G3BP1. Mechanistically, G3BP1 suppressed epithelial junctional proteins, including E-cadherin, p120-catenin, and ZO-1, while activating key pro-migratory signaling pathways involving AKT, ERK1/2, FAK, and Paxillin. These coordinated changes enhanced cytoskeletal dynamics and promoted corneal epithelial cell migration under NP stimulation. G3BP1 functions as a critical mechanotransduction mediator of NP, orchestrating adhesion remodeling and activating pro-migratory signaling cascades to facilitate corneal epithelial cell motility. These findings reveal a previously unrecognized cellular mechanism through which NP promotes epithelial repair and highlight G3BP1 as a potential therapeutic target for persistent corneal epithelial defects. Full article

Proteomics has emerged as a powerful tool for advancing our understanding of brain disorders by enabling large-scale characterization of protein expression, post-translational modifications, and interaction networks. Neurological conditions are often characterized by complex and dynamic molecular changes that are not fully captured by traditional diagnostic approaches. Proteomic technologies, particularly mass spectrometry-based and affinity-based methods, offer the ability to identify disease-specific protein signatures and elucidate underlying pathophysiological mechanisms, including neurodegeneration, neurodevelopment and neuroinflammation and alterations happening to the extracellular matrix and body fluid homeostasis. In recent years, artificial intelligence has emerged as a powerful tool to proteomics, enabling improved analysis of complex biological datasets. This integration has significantly enhanced the discovery of biomarkers for early diagnosis, disease stratification, and monitoring of therapeutic responses. Thus, cerebrospinal fluid and blood-based proteomic analyses have revealed promising candidates for neurological diseases. This review summarizes current advances in proteomics across a range of brain disorders, highlighting key molecular pathways, biomarker discovery efforts, and evolving clinical applications. Furthermore, it outlines future directions, including the application of machine learning for improved biomarker identification and precision medicine. Full article

Despite substantial progress in biomarker discovery and multi-omics profiling, several features of Alzheimer’s disease (AD), including prolonged compensated states, heterogeneous clinical trajectories, and marked stage-dependent therapeutic responses, remain difficult to integrate into a single mechanistic framework. In this review, we propose an integrative and testable conceptual framework that reframes AD as a single, progressive multi-layer network disorder whose dynamics arise from hierarchical constraint propagation and progressive loss of cross-scale coordination. Integrating evidence from human genetics, epigenomics, transcriptomics, proteomics, metabolomics, spatial biology, connectomics, and longitudinal biomarker studies, we examine how molecular, cellular, and circuit-level processes interact over time to shape disease progression. Within this framework, different omics measurements are interpreted as complementary representations of disease-related changes, rather than as independent molecular signatures. Disease progression reflects the gradual convergence of immune, metabolic, proteostatic, cytoskeletal, and synaptic stress, with overt cognitive impairment emerging when compensatory capacity is exceeded, producing threshold-like network destabilization. By explicitly linking biological scale, temporal hierarchy, and network structure, this synthesis extends prior network-medicine, connectomic, and multi-omics approaches into a testable framework for state-aware stratification, integrative analysis, and stage-appropriate therapeutic investigation in AD. Full article

Understanding the biochemical networks governing seed longevity is essential for germplasm conservation. Integrating germination potential with biochemical profiling elucidates metabolic transitions during decadal cold storage. As phenotypic evidence of ageing, extended cold storage induces a uniform decline in germination energy, reaching a terminal “floor effect” characterised by the complete exhaustion of repair-and-defence strategies, whilst residual germination capacity averages 21%. Metabolic profiling reveals that prolonged storage causes systemic decoupling of the protein–sugar axis, leading to the loss of protein-dependent vigour. The structural collapse of the proteomic architecture—manifested by the decoupling of embryo albumin-led coordination and endosperm α-zein dynamics—induces a transition to a low-vigour state, paralleled by carbohydrate shifts consistent with glassy matrix destabilisation, implicitly linking the displacement of sucrose-dominated stability to the molecular crowding of reducing sugars. Re-anchoring germination potential from primary metabolic drivers to soluble-free phenolics prompts a compensatory antioxidant reorganisation; under conditions of phenolic matrix degradation and carotenoid exhaustion, the observed stability of total antioxidant capacity likely reflects scavenging sustained by phenolic degradation products rather than native, intact protective mechanisms. Ultimately, seed ageing manifests as a genotype-specific systemic reconfiguration of biochemical coordination, where the physiological state of the cytoplasmic matrix and the maintenance of redox homeostasis determine residual viability, thereby defining the critical benchmarks for germplasm longevity. Full article

Chronic inflammatory signaling contributes to cartilage degeneration across multiple joint diseases, yet the molecular consequences of sustained cytokine exposure remain incompletely understood. We investigated how prolonged interleukin-1β (IL-1β) stimulation remodels the chondrocyte proteome and whether these changes are associated with senescence-associated traits. Primary human articular chondrocytes were exposed to IL-1β (10 ng/mL) for up to four days. Time-resolved data-independent acquisition (DIA) proteomics was integrated with immunofluorescence, quantitative PCR, multiplex metalloproteinase profiling, BrdU incorporation, growth-curve analysis, and senescence-associated β-galactosidase assays. Sustained IL-1β induced extensive time-dependent proteomic remodeling, with early inflammatory and extracellular matrix responses followed by alterations in cell-cycle regulation and cytoskeletal organization. Prolonged stimulation was associated with persistent downregulation of CDK4, Cyclin D1, DNA replication-associated proteins, and Rho GTPase-associated components, accompanied by actin cytoskeletal remodeling. These molecular changes were associated with impaired proliferation, increased senescence-associated β-galactosidase activity, and transient modulation of p21. Following cytokine withdrawal, BrdU incorporation showed partial recovery. Together, these findings indicate that sustained IL-1β progressively reshapes the chondrocyte cellular state through coordinated remodeling of proliferative, cytoskeletal, and metalloprotease programs while showing some degree of proliferative plasticity under the conditions tested. Full article