Search Results (415)

Domoic acid (DA) is a well-known seafood toxin produced by some species of marine phytoplankton in the genus Pseudo-nitzschia during harmful algal blooms (HABs). Acute toxic exposures induce overt clinical signs of neuroexcitotoxicity, such as seizures in mammals due to overstimulation of glutamate receptors in the central nervous system (CNS). Acute DA excitotoxicity via the CNS has been well-studied in both field poisoning events and laboratory exposure studies with rodent models, but little is known about the impacts of low-level DA exposures below those that cause outward signs of neurotoxicity; the impacts on other potential target organs, including the heart; or age-related sensitivities. Here, low-level DA exposures in young adult (9 mo) and old (24 mo) mice were conducted over multiple weeks. Mortality, cardiac function, frailty, and protein expression were quantified to assess age-related DA sensitivity and potential impacts on heart function. Echocardiography and proteome data confirm that chronic low-level DA exposure causes irreversible functional cardiomyopathy and protein remodeling in young adult mice that mimics natural cardiac aging. In addition, old mice exhibit higher mortality and frailty than young adult mice with the same low-level DA exposures. These results provide critical information for assessing potential health risks to humans who regularly consume seafood with low levels of DA. Full article

Target of rapamycin (TOR) is a conserved protein kinase that integrates nutrient and energy signals to control growth and metabolism, yet its proteome-level impact in microalgae remains poorly understood. Here, we conducted quantitative proteomics analysis of the unicellular red alga Cyanidioschyzon merolae under rapamycin-induced TOR inactivation to characterize global changes in protein abundance. TOR inhibition triggered widespread metabolic remodeling, including coordinated shifts in carbon and nitrogen allocation, and pronounced changes in protein synthesis, photosynthesis, and energy metabolism. Specifically, proteins associated with ribosome biogenesis and ribosomal subunits declined broadly, indicating impaired translation, alongside pronounced reductions in photosynthetic components, including PSI/PSII subunits and chlorophyll biosynthesis enzymes. In contrast, triacylglycerol (TAG) biosynthesis and starch metabolism were enhanced, indicating a shift towards carbon storage. Notably, a diacylglycerol acyltransferase (DGAT; CMQ199C) and a UDP-glucose pyrophosphorylase (UGP; CMS159C) were strongly induced (2.02-fold and 3.48-fold, respectively), identifying them as candidate targets for enhancing TAG and starch accumulation. Proteins associated with nitrogen assimilation were also upregulated, supporting TOR-dependent regulation of nitrogen metabolism at the protein level. Together, these results indicate that TOR orchestrates proteome-level reprogramming in C. merolae, coordinating growth, energy production, and carbon storage across interconnected metabolic pathways. Full article

Osteoarthritis is a chronic degenerative joint disease characterized by inflammation and cartilage degradation, for which current treatments are mainly symptomatic and unable to halt disease progression. Adipose-derived mesenchymal stem cells (ASCs) represent a promising therapeutic option due to their regenerative and immunomodulatory properties, which may be further enhanced through specific priming strategies. In this study, primary human ASCs were exposed to interleukin-1 beta (IL1β), interferon-gamma (IFNγ), or hypoxic priming, and subsequently analyzed using a multi-omics approach integrating RNA sequencing, proteomics of secretome, and exosomal miRNA profiling. Differential gene expression, protein abundance, and miRNA signatures were assessed together with functional enrichment and network analyses. IL1β priming induced marked transcriptional reprogramming of ASCs, while hypoxia and IFNγ priming produced limited changes. IL1β also profoundly reshaped the ASC secretome and exosomal miRNA cargo, revealing coordinated regulation of pathways involved in immune modulation and cartilage remodeling. In contrast, the other priming conditions showed minimal and less integrated molecular effects. Overall, IL1β priming consistently generated a multi-layered molecular signature linking immunoregulatory and regenerative pathways. These findings suggest that IL1β priming enhances the functional properties of ASCs and provides mechanistic insight supporting their potential use in osteoarthritis therapy. Full article

Astrocytes are increasingly implicated in the pathophysiology of schizophrenia (SCZ), yet how astrocytic dysfunction contributes to disease-relevant neuronal abnormalities remains unclear. Here, we used mass spectrometry–based proteomics to profile lysates (proteome) and secreted proteins (secretome) from iPSC-derived astrocytes originating from 9 SCZ patients and 8 healthy controls. Compartment-specific analyses showed that lysates were enriched for mitochondrial and nuclear pathways, whereas astrocyte-conditioned media (ACM) were enriched for extracellular matrix (ECM) and vesicle-associated proteins. Differential expression analysis revealed minimal overlap between dysregulated proteins in lysates and ACM, suggesting modality-specific effects of SCZ-associated donor background. Interestingly, ECM proteins and key secreted cues involved in synaptic development, including MFGE8 and SEMA3C, were selectively reduced in SCZ ACM, whereas RNA-processing proteins were aberrantly increased. This is in line with previously reported microRNA enrichment in extracellular vesicles (EV) derived from SCZ patients. Gene set analyses further identified the alteration in secretion and nuclear processes as well as the potential involvement of autophagy-dependent release mechanism in SCZ astrocytes. Together, these findings suggest disrupted astrocytic protein homeostasis and extracellular signalling in SCZ iPSC-derived astrocytes, providing mechanistic insight into astrocyte-mediated contributions to synaptic and circuit deficits in the disorder. Full article

The yak lung functions as a vital adaptive organ in cold, low-oxygen environments. Hypoxia can induce pathological remodeling in yak lung tissue, so we need to understand the molecular mechanisms of this remodeling. For this study, we used cross-omics comparative approaches, including transcriptomics, label-free proteomics, and untargeted metabolomics, to examine both normal and diseased yak lung tissues. From histological observations, the disease phenotype was identified as pulmonary emphysema. Our results showed a significant up-regulation of differentially expressed genes such as MTTP, CXCL8, RETN, and NNAT, while genes like SLC45A1, IL10, SDSL, and COL12A1 were clearly down-regulated. In the differential protein analysis, proteins such as RASSF4, EDC4, CTSC, and FECH were notably up-regulated, whereas CYP27A1, FKBP9, RAD23A, and PLSCR2 were significantly down-regulated. Metabolomic profiling revealed that palmitoyl-L-carnitine, decanoyl-L-carnitine, and o-acetylcarnitine were significantly higher in emphysematous lung tissue, whereas racemethionine and L-methionine S-oxide were significantly much lower. Also, when we compared of bulk RNA-seq, label-free proteomics, and untargeted metabolomics data revealed enrichment in three common pathways: the asthma pathway, the linoleic acid metabolism pathway, and the gastric acid secretion pathway. Of note, histamine levels were higher in both the asthma and gastric acid secretion pathways. While the mRNA expression level of BoLA-DQB was increased in the asthma pathway, its protein expression level was decreased. This study offers some initial cross-omics evidence about what happens. These findings give us a scientific basis for developing effective prevention and control strategies, which in turn can help the protection of yak health and the sustainable development of plateau animal husbandry. Full article

Although antiviral development against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been dominated by replication-directed strategies, structural and accessory proteins offer a complementary and increasingly important opportunity for small-molecule intervention. These proteins control key processes outside the core replication machinery, including viral entry, membrane remodelling, virion assembly, egress, and host immune modulation, thereby expanding the mechanistic scope of antiviral design. However, many of these targets are membrane-associated, oligomeric, conformationally dynamic, or function through protein–protein interactions, creating distinct challenges in target validation, assay design, and chemical optimisation. In this review, we comprehensively and critically evaluate the structural and accessory proteomes of SARS-CoV-2, with a strict focus on small-molecule tractability and translational relevance. We highlight the most credible direct-acting opportunities, focusing on the membrane (M), envelope (E), and nucleocapsid (N) structural proteins, together with the accessory protein open reading frame 3a (ORF3a), for which emerging chemical matter strengthens confidence in druggability. In contrast, Spike (S) and several host-interface accessory proteins, including ORF6, ORF8, ORF9b, and ORF10, are best viewed as more selective or earlier-stage opportunities that require stronger on-target chemical validation. Emphasis is placed on structural accessibility, mechanism-based assay systems, evidence quality, cellular and in vivo activity, and developability constraints relevant to exposure at the infection site. Rather than replacing replication-directed antivirals, these non-canonical targets are best considered adjunctive or complementary components of future combination strategies designed to broaden antiviral coverage, enhance robustness, and improve pandemic preparedness. Full article

Background/Objectives: The Indian star tortoise (Geochelone elegans) is a protected species for which physiological and molecular health indicators remain poorly characterized. This study aimed to monitor and analyze plasma proteome profiles and biochemical parameters in captive adult Indian star tortoises and to identify potential diagnostic biomarkers. Methods: Plasma samples from nine clinically healthy adult Indian star tortoises (four males and five females) maintained in captivity were subjected to biochemical profiling and proteomic analysis. Sex-related differences in biochemical parameters were evaluated, and differentially expressed proteins were mapped to Homo sapiens Reactome pathways to identify significantly enriched biological processes. Results: Plasma biochemical profiling established baseline reference values, indicating stable hepatic and metabolic function in captive tortoises. Creatinine and urea concentrations were significantly higher in females than in males (p < 0.05), suggesting sex-related differences in protein metabolism or renal function. No significant sex-related differences were observed in hepatic enzymes (ALP, ALT, AST, and GGT), muscle-associated enzymes (CK and LDH), glucose, cholesterol, triglycerides, total proteins, albumin, or electrolyte concentrations (Na, K, Ca, Mg, Cl, P, and Fe). Proteomic analysis identified 12 differentially expressed proteins, including nine upregulated and three downregulated proteins. Functional pathway analysis revealed 90 significantly enriched Reactome pathways (FDR < 0.05). Upregulated proteins were primarily associated with cytoskeletal organization (KRT75, KRT5, and KRT17), lipid transport and remodeling (APOB), coagulation (F10), extracellular transport (TTR), immune response (WFDC3), transmembrane signaling (KCP), and gamete interaction (ZAN). Downregulated proteins (C7, SERPING1, and PZP) were linked to complement activation and acute-phase response pathways. Conclusions: Captive Indian star tortoises exhibited increased cytoskeletal remodeling and coagulation activity together with reduced complement activation. These findings provide novel insights into the plasma proteome of this species and identify candidate biomarkers that may support future health assessment, physiological monitoring, and diagnostic applications in Indian star tortoises. Full article

Medication-related osteonecrosis of the jaw (MRONJ) is a complex condition associated with the use of antiresorptive drugs, such as bisphosphonates and denosumab. The condition is characterized by the presence of exposed bone in the maxillofacial region that fails to heal. MRONJ remains highly intractable, as its pathogenic mechanisms are not yet fully understood. It is therefore essential to elucidate the molecular mechanisms underlying the disease. MiRNA expression analysis and proteomic studies were performed on a selected cohort of patients with MRONJ on jawbone tissue, using qRT-PCR and 2D electrophoresis followed by mass spectrometry. MiRNAs and proteomics data validation was carried out by Western blot analysis of differentially expressed proteins highlighted by a proteome study and predicted targets of differentially expressed miRNAs. Nineteen miRNAs were overexpressed and two downregulated in jawbone tissue from all MRONJ patients. Notably, five of these dysregulated miRNAs are involved in the regulation of angiogenesis and desmosome functions, suggesting a potential link to the molecular alterations observed at the protein level. Proteomic analysis revealed decreased concentrations of the pigment epithelium-derived factor, and of desmoglein-1, a desmosomal cadherin. Validation analysis confirmed the dysregulation of pathways involved in bone remodeling and necroptosis. The pathophysiology of MRONJ arises from a complex interplay of factors, including impaired bone remodeling, affected angiogenesis, and altered cell adhesion and differentiation mechanisms, ultimately leading to necroptosis. Through proteomic analysis and validation of miRNA expression, our study proposes specific molecular alteration in MRONJ-compromised bone tissue, involving desmosomal component imbalance and angiogenesis inhibition. Full article

Background: Sphingolipids are essential structural and signaling lipids that support membrane integrity and govern cell fate decisions. While the consequences of chronic sphingolipid inhibition have been extensively explored, the immediate cellular responses to acute suppression of sphingolipid synthesis remain poorly defined. Methods: We analyzed subcellular proteomic changes following an acute reduction in sphingolipid levels induced by myriocin, an inhibitor of de novo sphingolipid synthesis. We then evaluated the cytotoxicity of co-treatment with myriocin and inhibitors of the altered pathways in cancer cells. Results: We found that de novo sphingolipid synthesis is sensitive to myriocin, an inhibitor of serine palmitoyltransferase (SPT), and can be efficiently inhibited within 4 h of treatment. Cells respond to reduced sphingolipid levels by rapidly remodeling their proteome. Mass spectrometry analysis revealed changes in the abundance of hundreds of proteins across the membrane, cytosolic, and nuclear fractions. Gene set enrichment analysis revealed alterations in the proteome across several pathways involved in protein and lipid homeostasis and stress responses, including upregulation of cholesterol homeostasis and lysosome. Co-treatment with myriocin and cholesterol synthesis or lysosomal function inhibitors synergistically reduced cancer cell viability by promoting apoptosis rather than other forms of programmed cell death. Conclusions: Together, our work provides insights into how cells rapidly rewire the abundance of certain protein classes in response to reduced sphingolipid levels and identifies signaling and metabolic pathways that can be exploited for therapeutic intervention. Full article

Turpan Black (TBL) and Altay (ALT) sheep are indigenous breeds adapted to extreme heat and severe cold in their respective native environments. However, the mechanisms underlying their divergent meat quality remain unclear. Using longissimus dorsi muscle from 15 TBL and 15 ALT sheep, we integrated phenotypic evaluation with non-targeted metabolomics and proteomics to elucidate the impact of environmental adaptation on ovine meat quality. Compared to the cold-adapted ALT sheep, the heat-tolerant TBL sheep exhibited lower post-mortem pH, reduced cooking loss, smaller muscle fiber cross-sectional area, and elevated selenium and magnesium levels. Multi-omics identified 99 differentially expressed proteins and 364 differentially expressed metabolites. Core divergence was enriched in lipid and amino acid metabolism and stress response networks, particularly the Apelin signaling, glycerophospholipid metabolism, and ferroptosis pathways. Lipid remodeling driven by glycerophospholipid metabolism emerged as a critical bridge linking adaptation to meat quality. Notably, glycero-3-phosphocholine, regulated by GPCPD1 and related enzymes, maintained cell membrane homeostasis and osmotic pressure, thereby enhancing water-holding capacity and tenderness. These findings reveal the multi-omics basis of climate-driven divergence in ovine meat quality, offering theoretical support for breeding stress-resilient, high-quality indigenous sheep breeds in extreme environments. Full article

Witches’ broom disease (WBD), caused by the fungus Moniliophthora perniciosa, poses a major threat to cocoa production and little is yet known about how the fungus adapts at the molecular level, particularly in the apoplastic environment during early infection. Here, we investigated how apoplastic washing fluid (AWF) from two cocoa genotypes with contrasting resistance to WBD modulates the mycelial protein profile of two M. perniciosa isolates: (i) Mp553—low infection level; and (ii) Mp565—high infection level. A total of 1272 proteins were identified. Mp565, showed increased accumulation of proteins associated with oxidative stress response, energy metabolism, and virulence when exposed to AWF from the resistant variety TSH1188. Key proteins such as phosphoglycerate kinase, enolase, and heat shock were significantly modulated. Interestingly, AWF from the resistant variety promoted the suppression of metabolic proteins, suggesting an effective defense response in the resistant genotype. Furthermore, interaction network analysis revealed the central role of the MPER_11800 protein, a potential regulator of fungal adaptation. The findings underscore the importance of the T. cacao apoplast in both plant defense and fungal adaptation. The study also reveals key molecular targets, such as MPER_11800, for potential strategies to control WBD. These insights enhance our understanding of M. perniciosa pathogenicity and offer valuable directions for developing novel interventions to mitigate the impact of this devastating disease. Full article

Adipose tissue-derived extracellular vesicles (adiposomes) carry a protein cargo that we previously showed differs between obese and lean individuals. In this study, we investigate how adiposomal protein cargo changes in response to sleeve gastrectomy and examine whether these changes are associated with clinical improvements. Twenty-three obese adults underwent pre- and post-bariatric surgery adipose sampling for adiposome isolation and clinical assessments that included vascular and metabolic profiles and inflammatory markers. The adiposomal protein cargo was analyzed via non-targeted proteomics. Differential protein abundance, pathway enrichment, and correlation analyses were assessed. Twelve weeks after bariatric surgery, BMI and fat mass decreased, accompanied by improved glucose and lipid profiles. Inflammatory markers (leptin, IL-6, CRP) also declined, while adiponectin and nitric oxide increased. Adiposomal proteomics identified 287 proteins, with 138 significantly altered. Downregulated proteins included PRDX2, FN1, SERPIND1, and inflammatory mediators; upregulated proteins included talin-1, fibrinogens, and adiponectin. Correlation analysis linked these changes to improvements in lipid profiles, vascular function, and circulating inflammatory markers. Pathway analysis revealed inhibition of lipid-regulatory pathways alongside enrichment of immune, metabolic, and vascular pathways, including lipoprotein metabolism and endothelial signaling. Bariatric surgery-induced cardiometabolic improvements were accompanied by adiposome proteomic remodeling, characterized by reduced inflammation and metabolic reprogramming. Full article

Background: Low-dose aspirin (LDA) reduces preeclampsia (PE) risk by up to 40%, yet its molecular effects on chorion trophoblast cells (CTCs), a fetal membrane lineage at the feto-maternal interface, remain obscure. CTCs form a structural and immunoregulatory barrier whose dysfunction drives inflammation-associated membrane pathology in PE. Extracellular vesicles (EVs) released by CTCs may encode cellular stress and adaptation states, offering a molecular window into aspirin’s timing-dependent effects on PE risk modification. Methods: Human CTCs were challenged with cigarette smoke extract (CSE) to model oxidative stress-driven PE pathology. Two paradigms were tested: (1) prophylactic aspirin (4 and 40 µg/mL) before and/or flanking the CSE, and (2) therapeutic aspirin after the CSE challenge. The EVs were isolated via ultracentrifugation and size-exclusion chromatography, characterized by nanoparticle tracking and immunoblotting, and profiled by quantitative mass spectrometry. A network pathway analysis and machine learning biomarker selection defined the EV-encoded molecular states. Results: The CTC-derived EVs from the CSE-exposed cells carried a PE-like proteomic signature marked by suppressed VEGF/ECM remodeling, activated TNF-p53 apoptotic signaling, and heightened inflammation. Prophylactic low-dose aspirin shifted the EV cargo toward an EV-encoded signature consistent with preserved angiogenic potential (enrichment of VEGFA, COL1A1, and MMP14) and predicted attenuation of apoptotic and NF-κB pathway activity by an Ingenuity Pathway Analysis. High-dose aspirin produced broad transcriptional suppression without an accompanying pro-angiogenic EV signature. Therapeutic (post-injury) aspirin partially attenuated the injury-associated EV cargo but did not restore the angiogenic EV signature. An exploratory machine learning analysis of EV proteomes identified a candidate prophylactic biomarker panel anchored by HSPA8, SERPINF2, COL4A1, and PLOD1, mapped to the predicted angiogenic recovery and redox-balance pathways. These EV cargo readouts represent the predicted molecular states and require functional validation before clinical interpretation. Conclusions: The CTC-derived EV proteomic signatures capture the dose- and timing-dependent aspirin effects in this in vitro CTC model, positioning the chorion as a candidate pharmacological “secondary responder” favoring cellular resilience over classical anti-inflammatory suppression. As an exploratory hypothesis-generating study, EV-based molecular profiling could provide a foundation for future investigations aimed at stratifying aspirin responders from non-responders, although clinical validation in maternal plasma cohorts will be required before any translational application. Full article

The liver is a central metabolic organ that integrates nutrient sensing, lipid handling, and detoxification to maintain systemic homeostasis. In metabolic dysfunction–associated steatotic liver disease (MASLD), chronic metabolic overload accelerates hepatocyte senescence, impairing regenerative capacity and promoting progression toward fibrosis and hepatocellular carcinoma. While transcriptomic studies have provided important insights into stress-responsive pathways, they incompletely capture the proteome remodeling and proteoform-level alterations that govern hepatocyte function during aging and disease. Recent mass spectrometry–based proteomics studies have revealed that disruption of autophagy-dependent proteome homeostasis is a defining feature of senescent hepatocytes. Quantitative analyses demonstrate coordinated alterations in selective autophagy pathways—including lipophagy, mitophagy, ferritinophagy, ER-phagy, and pexophagy—accompanied by organelle-specific protein abundance signatures and remodeling of autophagy-related proteoforms. These findings position proteomics as an essential tool for resolving the spatial and functional reorganization of hepatocyte proteomes that cannot be inferred from transcript abundance alone. In this review, we synthesize proteomics-driven evidence defining selective autophagy dysfunction in aging and MASLD livers, critically evaluate methodological limitations, and propose a conceptual framework in which impaired selective autophagy acts as a proteome-level driver of hepatocyte senescence. We further outline future directions for proteoform-resolved and spatial proteomics approaches aimed at identifying actionable targets for therapeutic intervention in liver disease. Full article

Background/objectives: Epithelial ovarian cancer (EOC) is the deadliest gynaecologic malignancy, largely due to late-stage diagnosis and ineffective therapy. EOC commonly spreads through the peritoneal cavity as multicellular spheroids, which are metastatic structures that enhance survival under detachment stress, promote dissemination, and contribute to therapeutic resistance. We previously showed that ULK1, a serine/threonine kinase classically linked to macroautophagy initiation, supports EOC progression, suggesting non-canonical roles in spheroid biology and pathogenesis. Methods: CRISPR/Cas9 ULK1 knockout (ULK1KO) models were generated in OVCAR8, HEYA8, and ES2 cells. Mitochondrial degradation phenotypes were assessed in spheroids by immunoblotting and fluorescence microscopy. Label-free proteomics with bioinformatic pathway analysis identified ULK1-associated programs in EOC spheroids. Bioenergetic consequences were quantified using Seahorse ATP-Rate assays. Therapeutic interactions were evaluated using multi-dose combination matrices testing the ULK1 inhibitor DCC-3116 with metformin. Results: ULK1 modulated mitochondrial degradation in a cell-line-specific manner, either promoting or protecting against mitochondrial loss through mechanisms that were uncoupled from canonical autophagy machinery. Proteomic and bioinformatic analyses revealed significant alterations in mitochondria-related processes, aligning with emerging ULK1 functions in mitochondrial homeostasis. ULK1 loss broadly reduced OXPHOS complex proteins in EOC spheroids and consistently decreased hexokinase 2 (HK2), indicating coordinated metabolic remodeling. Seahorse profiling mirrored these shifts: OVCAR8 ULK1KO spheroids showed reduced OCR and ATP production, whereas HEYA8 and ES2 ULK1KO spheroids exhibited increased mitochondrial ATP production. Combination matrices showed potential synergy between DCC-3116 and metformin. Conclusions: These data show that ULK1 differentially regulates mitochondrial degradation across EOC spheroid models through potential mechanisms alternative to canonical autophagy machinery, while reshaping spheroid metabolism and revealing potential therapeutic vulnerabilities in advanced EOC. Full article