Search Results (671)

Unc-51-like kinase 3 (ULK3) is a key member of the ULK serine/threonine kinase family. Aberrant ULK3 expression has been increasingly linked to tumorigenesis and malignant progression in multiple cancer types. However, the precise role of ULK3 in tumor initiation and progression remains incompletely understood. Leveraging integrated multi-omics data from The Cancer Genome Atlas (TCGA), the Genotype-Tissue Expression (GTEx) project, and the Clinical Proteomic Tumor Analysis Consortium (CPTAC), we systematically characterized the expression of ULK3 at both the transcript and protein levels across 33 cancer types. We also evaluated genomic alterations, prognostic significance, alternative splicing, pathway enrichment, tumor stemness, immune infiltration, and immunotherapy-related biomarkers. In parallel, we investigated the function of ULK3 in prostate cancer PC-3 cells using cellular localization analysis, wound-healing assays, and MTT assays. We further applied Connectivity Map (CMap) screening and molecular docking to identify candidate ULK3 activators. ULK3 was significantly upregulated in 13 cancer types, including Bladder Urothelial Carcinoma, Breast Invasive Carcinoma, and Lung Adenocarcinoma. In contrast, ULK3 was downregulated in Cholangiocarcinoma and Head and Neck Squamous Cell Carcinoma. High ULK3 expression was associated with poor overall survival in Adrenocortical Carcinoma, Kidney Renal Clear Cell Carcinoma, and Skin Cutaneous Melanoma. Copy number amplification contributed to ULK3 overexpression. A recurrent A206V missense mutation was detected in the protein kinase (Pkinase) domain. Genes co-expressed with ULK3 were enriched in RNA splicing, methylation, oxidative phosphorylation, and energy metabolism. ULK3 expression showed positive correlations with tumor stemness indices and m1A/m5C/m6A RNA modification regulators. From an immunological perspective, high ULK3 expression was associated with lower Immune Score, increased M2 macrophage infiltration, and co-expression of PD-L1, CTLA4, and LAG3 in most cancers. ULK3 expression was also correlated with Tumor Mutational Burden in Kidney Renal Clear Cell Carcinoma and Rectum Adenocarcinoma. In addition, ULK3 expression was associated with Microsatellite Instability in Brain Lower Grade Glioma, Lung Adenocarcinoma, and Uterine Corpus Endometrial Carcinoma. ULK3 overexpression promoted proliferation and migration in PC-3 cells. Cephaeline was screened as a putative ULK3 activator. Overall, ULK3 expression and amplification were associated with poor clinical outcomes, tumor stemness, immunosuppression, and RNA dysregulation. These findings highlight the potential value of ULK3 as a pan-cancer diagnostic and prognostic biomarker and as a predictor of immunotherapy response, particularly in prostate cancer. Full article

Autoimmune hepatitis (AIH) lacks a disease-specific diagnostic biomarker, particularly for patients who present with acute onset, normal IgG levels, or seronegative profiles. Recent advances in high-throughput autoantibody profiling technologies have enabled the systematic discovery of novel AIH-associated autoantigens. This review summarizes emerging autoantibodies that have been identified through proteome-wide screening approaches, including human protein microarrays and phage immunoprecipitation sequencing. Particular attention is given to anti-docking protein 2 (DOK2) and anti-mitochondrial ribosomal protein S27 (MRPS27) antibodies, which have shown promising diagnostic performance. Importantly, the combined assessment of these autoantibodies markedly improves the diagnostic sensitivity for AIH and may be useful for screening or clinical triage, although its reduced specificity limits its use as a stand-alone confirmatory test. We also discuss how the integration of serological biomarkers with molecular pathology and spatial immune analysis may advance the understanding of AIH pathogenesis. These developments highlight the potential of proteome-wide autoantibody discovery to refine diagnostic strategies for AIH and provide new insights into disease mechanisms. Full article

Animal venoms are complex biochemical systems composed of proteins, peptides, and small molecules with bioactivity. Traditionally regarded as toxic agents, venom components are increasingly recognized as valuable molecular libraries that can modulate cellular processes in human disease pathophysiology. This review highlights the translational potential of venom-derived molecules, with emphasis on clinically approved venom-derived drugs such as captopril, while also discussing their therapeutic potential for diseases such as cancer, autoimmunity, cardiovascular diseases, chronic pain, neuropsychiatric disorders, and infectious diseases. Special emphasis is given to the mechanisms by which these toxins modulate ion channels, enzymes, and receptor systems. Recent advances in venomics, harnessing proteomics, transcriptomics, and high-throughput screening, are also discussed, which can accelerate the clinical translation of venom-derived therapeutics. Key challenges related to assessing the immunogenicity of the venom-derived compounds, bioavailability, and safety have also been addressed alongside emerging strategies to overcome them. Collectively, these advances can provide a logical framework for developing novel therapeutics, bridging the gap between toxinology and drug discovery. Full article

Background: Malignant prostate cancer (PrC) remains challenging to treat due to tumor heterogeneity and the limited availability of ligands that target disease-associated surface markers with properties appropriate for targeted drug delivery systems. To overcome this hurdle, we used an unbiased but stringent selection strategy to discover a series of phage-displayed peptides that internalize specifically into PrC tumors. Methods: Here we report the characteristics, properties and function of one of these peptides, Pr10, and validate its ability to specifically deliver cytotoxic drugs into PrC cells and kill them, both in vitro and in xenograft models. Results: Biochemical and proteomic studies identified the receptor for Pr10 as Desmocollin-3 (DSC3). This finding was confirmed by demonstrating the expression of the DSC-3 protein on PrC cells; by siRNA knockdown of DSC3 expression, which abrogated Pr10 function; and by in silico docking experiments. Conclusions: Together, these findings identify DSC3 as a novel, functional receptor on malignant prostate cancer cells and establish Pr10 as an effective and PrC-selective ligand for drug delivery PrC cells. More broadly, this work highlights the ability of unbiased screening approaches to identify and isolate novel target receptors with properties appropriate for use in effective target drug delivery systems for cancer therapy. Full article

Lipolytic and esterase-like enzymes are crucial in the food industry for flavor production and ester hydrolysis. This study presents an exploratory, baseline feasibility approach to evaluate esterase-like enzyme production by Serratia marcescens 11E via a sustainable co-valorization matrix, where vegetable wax residues serve as structural solid support and cheese whey acts as the primary lipid nutritional source. Under fixed 48-h screening conditions, the recovered cell-free extract exhibited a distinct catalytic preference for short-chain esters, showing higher specific activity toward 4-nitrophenyl acetate (0.743 U/mg) than 4-nitrophenyl palmitate (0.125 U/mg), confirming a predominant carboxylesterase-like profile. Biochemical characterization revealed an initial optimal activity at pH 9.0 and 30 °C, along with a noteworthy bimodal catalytic behavior featuring a secondary activity peak at 70 °C. Size-exclusion chromatography resolved the extract into two distinct active elution pools (17.8 and 26.2 U/mg), which corresponded to candidate protein bands of 35–40 kDa on SDS-PAGE. Although definitive molecular identification remains subject to ongoing zymographic and proteomic characterization, these foundational findings demonstrate the potential of co-valorizing lipid- and carbohydrate-rich industrial wastes to produce resilient proteins with esterase-like activity at elevated temperatures. Full article

Background: Inborn errors of metabolism (IEMs) represent a diverse group of genetic disorders affecting biochemical pathways. Despite advances in diagnostic technologies, comprehensive understanding of their historical evolution, classification systems, and diagnostic approaches remains fragmented. Objectives: This systematic review and meta-analysis aimed to synthesize evidence on the historical development, classification frameworks, and diagnostic modalities for IEMs, diagnostic accuracy, and prevalence estimates, providing a comprehensive resource for clinicians and researchers. Methods: Following PRISMA 2020 guidelines, we conducted a systematic search of seven electronic databases (PubMed/MEDLINE, Embase, Scopus, Web of Science, Google Scholar, SciSpace and ArXiv) from January 2000 to March 2026. Studies addressing historical perspectives, classification systems, or diagnostic approaches for IEMs were included. Two independent reviewers performed screening, data extraction, and quality assessment. Meta-analyses were conducted using random-effects models for diagnostic accuracy and prevalence estimates. Results: From 1342 identified records, 54 studies met the inclusion criteria, encompassing 8,234,567 individuals across 35 countries. Historical analysis revealed 16 major milestones from Garrod’s 1902 “chemical individuality” concept to the current AI-powered diagnostics. Four major classification systems were identified: pathophysiological (intoxication, energy deficiency, complex molecule disorders), biochemical pathway (amino acid, organic acid, urea cycle, carbohydrate, fatty acid oxidation, mitochondrial, peroxisomal, lysosomal disorders), organelle-based, and the integrated Society for the Study of Inborn Errors of Metabolism (SSIEM) nosology. Meta-analysis demonstrated high diagnostic performance of tandem mass spectrometry (MS/MS) with a pooled sensitivity of 99.1% (95% CI: 98.6–99.5) and specificity of 99.8% (95% CI: 99.7–99.9%). The pooled global prevalence of IEMs was 50.9 per 100,000 live births (95% CI 45.2–56.8). Next-generation sequencing achieved a diagnostic yield of 42.8% (95% CI: 38.2–47.5%) in suspected cases. Emerging AI-powered diagnostic tools demonstrated high discrimination performance with area under the curve (AUC) values exceeding 0.95 for specific IEM, though external validation remains limited. Newborn screening expanded from single-disease to comprehensive panels detecting over 50 disorders. Conclusions: This comprehensive review demonstrates that IEMs have evolved from rare curiosities to systematically diagnosable conditions through technological advances. Integration of metabolomics, genomics, proteomics and artificial intelligence promises further diagnostic improvements. Standardized classification systems and evidence-based diagnostic algorithms are essential for optimal patient care. Future directions include artificial intelligence-enhanced diagnostics, expanded screening, and personalized medicine approaches. Full article

Background: Age-related macular degeneration (AMD) is the leading cause of irreversible vision loss in older adults. An important challenge is the recognition of its early asymptomatic stages and the monitoring of its progression, which requires reliable biomarkers. Growing evidence indicates that AMD-related biochemical changes are reflected in the proteome of tear fluid (TF). Although TF is a non-invasive and easily collectable diagnostic material, its proteomic analysis is complex and costly and therefore has limited clinical value. Methods: In this pilot single-center retrospective cross-sectional study, we developed a new method for dry AMD screening based on analysis of nano-differential scanning fluorimetry (nanoDSF) tear protein denaturation profiles (TDPs) within 15 min. The TDPs were recorded in representative groups of dry AMD patients (37% early, 48% intermediate, 15% geographic atrophy), and in control groups, including patients with refractive abnormalities (basic control), other retinal degenerative diseases (diabetic retinopathy, peripheral retinal dystrophy), or TF-affecting conditions (dry eye syndrome). High-dimensional TDP data were processed using unsupervised machine learning followed by k-means cluster analysis. Results: The presented pipeline distinguished AMD from the basic control with 74% accuracy and a sensitivity of 0.81 without relying on prior labels. The specificity of AMD detection was confirmed by its effective differentiation from diabetic retinopathy (72%; 0.74), peripheral retinal dystrophy (79%; 0.76) and dry eye disease (76%; 0.81). Classifying the AMD group from the entire population of other patients yielded an accuracy of 71% and a sensitivity of 85%, with a false-negative rate of only 15%. Conclusions: This study is a proof of concept for the nanoDSF-based approach, which can be considered a fast, cost-effective, and convenient tool for population screening for dry AMD, suitable for use in preventive medicine and public health. Full article

Across all kingdoms of life, ribosomes are indispensable molecular machines that translate genetic information into the proteome of living cells. The fundamental catalytic centers of the ribosome, constructed primarily from ribosomal RNA (rRNA), exhibit remarkable conservation between the major domains of life. The ribosome’s A-site deciphers the mRNA’s triplet code, while the P-site synthesizes the growing protein chain and the E-site provides exit for deacylated tRNA; a distinct tunnel facilitates nascent polypeptide export. While the conservation of ribosomal proteins is less pronounced between bacteria and eukaryotes, striking homology exists from simple eukaryotes to humans. Ribosomal proteins were traditionally viewed mainly as scaffolding agents, steering rRNA folding during ribosome biogenesis and maintaining structural stability during translation. However, since the early 2000s, advances in structural and functional ribosome analysis have ushered in a more nuanced paradigm: ribosomes are no longer considered uniform machines. Instead, an array of rRNA and ribosomal protein modifications generates a spectrum of ribosome populations capable of specialized translation. RiboScreen^TM technology leverages this regulatory potential of individual ribosomal proteins, enabling deliberate modulation of target protein output and representing a promising tool for correcting dysregulated protein expression involved in rare and common diseases. This review will first introduce relevant aspects of ribosome biology and then showcase the tools of this new technology. Finally, we report examples for the delivery of small molecules to target ribosomal proteins for tailored restoration of protein production levels in rare and prevalent diseases. Full article

Endogenous gene tagging using CRISPR has changed the understanding of the role played by different proteins due to the ability to track and study proteins in their natural state. With CRISPR-based gene tagging, it is possible to insert fluorescent, luminescent, epitope, affinity, and proximity labels into the target protein at its endogenous genomic location without affecting its physiological expression and dynamics. Here, we discuss the DNA-repair mechanisms employed in endogenous gene tagging, including homology-dependent repair, NHEJ-based integration, and alternative approaches that can be used with challenging cell types. Key aspects of efficient CRISPR tagging experiments are also described. Additionally, we review recent advances in the increasing array of protein tag technologies, including fluorescent proteins, split-reporter technologies, NanoLuc/HiBiT, peptide epitopes, and proximity biotinylation enzymes. Lastly, we review the scalability of endogenous tagging approaches using multiplex editing, atlas-scale proteome tagging, iPSC-based disease modeling, and drug discovery platforms for assessing target engagement, protein degradation, phenotype screening, and mechanism of action of compounds. Although difficult in primary and pluripotent cells, new methods based on avoiding double-strand breaks, such as prime editing, PASTE, and CRISPR associated transposases, will drive the future expansion of endogenous tagging approaches. Such developments firmly set up CRISPR gene tagging as a fundamental technology in quantitative cell biology and translational pharmacology. Full article

Per- and polyfluoroalkyl substances (PFASs) are persistent environmental contaminants of growing concern for soil ecosystems, yet their effects on the humoral arm of innate immunity in soil invertebrates remain poorly characterized. Here, we used the earthworm Eisenia fetida to screen 31 legacy and emerging PFAS congeners for their ability to modulate the hemolytic activity of cell-free coelomic fluid, a functional readout of soluble immune effectors including the pore-forming toxin lysenin. Earthworms were exposed under OECD 207 contact-filter conditions at two concentrations (0.6 and 229 µM) for 72 h, after which decellularized coelomic fluid was tested against sheep erythrocytes. To dissect direct biochemical interference from organism-mediated regulation, the same panel was also applied ex vivo (2.5 µM) to coelomic fluid from unexposed earthworms. In vivo, PFASs produced markedly heterogeneous, congener-specific responses: PFBS, PFBA and PFMOPrA suppressed hemolytic activity, whereas PMDA, PFHxA and HFPO-DA enhanced it. In contrast, ex vivo exposure produced a consistent, broad inhibition of hemolysis, indicating a direct interaction of PFASs with soluble immune proteins. Proteomic profiling of the lysenin family under PFOA and HFPO-DA suggested isoform-level reweighting rather than uniform abundance shifts, although effects did not survive multiple-testing correction. Together, these data show that PFASs act as congener-specific immunomodulators of extracellular humoral defense in E. fetida and identify candidate congeners for confirmatory mechanistic studies. Full article

Seasonal fluctuations in open solid-state fermentation drive batch-to-batch variability in Chinese Baijiu Daqu; however, how environmental shifts reshape microbial functional expression and non-volatile flavour precursors in medium-high-temperature Daqu remains poorly resolved. In this study, data-independent acquisition (DIA)-based quantitative metaproteomics and untargeted liquid chromatography–mass spectrometry (LC-MS) metabolomics were integrated to characterise winter and summer Daqu from Luzhou, Sichuan. Among 2904 annotated non-volatile metabolites, orthogonal partial least squares discriminant analysis (OPLS-DA) revealed clear seasonal separation; 1472 differential metabolites (560 up- and 912 downregulated in winter vs. summer; variable importance in projection [VIP] > 1, p < 0.05) were enriched in glycolysis/gluconeogenesis, the tricarboxylic acid (TCA) cycle, amino acid biosynthesis, and starch/sucrose metabolism. DIA-based quantitative metaproteomics further resolved season-specific enzyme expression: summer Daqu exhibited elevated saccharolytic, glycolytic and amino-acid-converting enzymes (β-glucosidase, 6-phosphofructokinase, pyruvate dehydrogenase), whereas winter Daqu was enriched in glucose oxidase, phosphoenolpyruvate carboxykinase and aldehyde dehydrogenase, consistent with a pattern suggestive of carbon-storage prioritisation. Proteome–metabolome integration established a coherent “enzyme protein abundance–inferred metabolic tendency–metabolite accumulation” correlative framework axis: higher hydrolytic and central-carbon enzyme abundance in summer corresponded to increased maltose, lactate, acetate, L-glutamate and L-aspartate. Therefore, production season reshapes Daqu quality chiefly by corresponding to distinct patterns of in situ enzyme protein abundance, providing a DIA quantitative metaproteome-anchored mechanistic framework for screening high-expression starters and stabilising seasonal Daqu quality. Full article

Cholangiocarcinoma (CCA) in Northeast Thailand is characterized by late diagnosis and poor prognosis, creating a critical need for effective early-detection biomarkers. This study utilized a multi-omics approach to identify novel diagnostic targets and improve CCA screening. Initial serum proteomic and transcriptomic analyses revealed significant upregulation of the luteinizing hormone/choriogonadotropin receptor (LHCGR) in CCA patients, correlating with advanced disease stages. Interaction network analysis subsequently identified its circulating ligand, beta-human chorionic gonadotropin (β-hCG), as a highly translatable clinical target. The protein expression of β-hCG was assessed via immunohistochemistry (IHC) in 100 tissue samples, and serum levels of β-hCG, alongside routine markers (CA19-9, AFP, and CEA), were quantified in a cohort of 405 individuals, including 153 CCA patients. IHC confirmed significantly higher β-hCG expression in tumor tissues compared to adjacent areas (p < 0.0001). Serum β-hCG levels were significantly elevated in CCA patients and correlated with tumor volume and reduced overall survival. Diagnostically, a combined multiparameter panel (β-hCG, carbohydrate antigen 19-9, carcinoembryonic antigen, and alpha-fetoprotein) yielded excellent accuracy in distinguishing CCA from healthy controls (AUC: 0.962) and hepatocellular carcinoma cases (AUC: 0.890). However, discriminatory efficiency was notably lower when differentiating CCA from benign biliary diseases (AUC: 0.680) and liver metastases (AUC: 0.705). In conclusion, activation of the LHCGR signaling axis is a novel pathophysiological feature in CCA. When integrated into a multi-marker blood panel, circulating β-hCG serves as a valuable complementary risk-stratification and prognostic tool, though further optimization is required to overcome limited specificity in the presence of confounding liver pathologies before routine clinical implementation. Full article

Inflammation plays a pivotal role in the pathogenesis of acne vulgaris, with Cutibacterium acnes recognised as a key etiological agent. The global increase in acne prevalence, coupled with the rising incidence of antibiotic-resistant strains, underscores the necessity for alternative therapeutic strategies. Vaccination has emerged as a promising approach, with various candidates targeting live-attenuated strains and specific virulence factors. Nevertheless, the expanding availability of C. acnes genomic data presents an opportunity to identify previously uncharacterized antigens that hold potential as novel targets for the development of next-generation acne vaccines. Therefore, this study aimed to identify core proteins among C. acnes genomes and evaluate their immunogenicity as potential multi-epitope peptide constructs. In addition, IA1-specific proteins of C. acnes were examined to develop the peptide constructs targeting acne-associated isolates. Pan-core analysis of 609 genomes identified 972 core genes. These genes were subsequently analysed for epitope prediction and antigenicity, and the highly antigenic epitopes were selected and combined for further analysis. Multi-epitope peptides were constructed based on predicted MHC-I, MHC-II, and linear B-cell epitopes, yielding four promising candidates derived from C. acnes core proteins and IA1-specific proteins. Molecular docking analysis indicated that both groups showed binding affinity for TLR2 and TLR4 receptors, suggesting possible molecular compatibility with these receptors. Furthermore, in silico immune simulations indicated that both types of multi-epitope peptides were associated with simulated humoral and cellular immune response profiles, although these responses require experimental validation. This computational workflow may help narrow the selection of potential acne vaccine candidates and prioritise multi-epitope peptide constructs for subsequent vaccine design steps and experimental validation. Full article

Nogo (RTN4) proteins and their receptors have emerged as candidate mediators of metabolic regulation and vascular pathology relevant to type 2 diabetes (T2D). The primary objective of this PRISMA-guided systematic review was to evaluate the clinical and cohort evidence for RTN4/RTN4R as potential biomarkers of T2D progression and vascular complications. A secondary objective was to synthesize preclinical mechanistic evidence on the effects of Nogo axis modulation on pathways relevant to the pathogenesis of T2D. We performed a PRISMA-guided systematic review. The protocol was not prospectively registered in PROSPERO. To ensure reproducibility, we provide complete search keywords, the screening log and the full-text exclusion table. PubMed/MEDLINE, EMBASE and Web of Science were searched for studies published 2000–2025; full search keywords are provided in the main text. The search strategy combined and free-text terms with Boolean operators. We included original preclinical and clinical studies, cohort/proteomic analyses, meta-analyses, and mechanistic papers reporting expression, function, signaling, or clinical associations of Nogo proteins/receptors in metabolic or vascular outcomes. Exclusion criteria: non-English articles, unclear methods, studies outside 2000–2025, and studies lacking primary data. Two reviewers independently screened records; conflicts were resolved by consensus. Study quality was appraised using established tools (SYRCLE for animal studies, Newcastle–Ottawa Scale for cohort/case-control studies). Preclinical evidence supports tissue-specific roles for RTN4 isoforms and receptors in the regulation of insulin secretion, proGCG → GLP-1 processing, ER homeostasis, and vascular permeability through the Src/PI3K/Akt and RhoA/ROCK axes. Cohort and proteomic analyses report associations between RTN4/RTN4R or serum NogoB and faster progression of T2D or vascular complications, but genetic assessment of causality (Mendelian randomization) has so far provided limited support in available data sets. Findings are heterogeneous with respect to directionality and tissue localization. RTN4 signaling exhibits tissue-specific mechanisms relevant to glucose regulation and vascular biology and warrants further translational study. However, heterogeneity across studies and limited genetic support for causality indicate that isoform-specific quantitative validation, longitudinal cohorts and integrated genetic–functional analyses are required before RTN4/RTN4R can be considered as clinical biomarkers. Full article

Background: Coronary heart disease (CHD) has a high global disease burden. According to traditional Chinese medicine theory, the main syndrome type of CHD is the syndrome of intermingled phlegm and blood stasis (SI-GPBS). Tanyu Tongzhi Decoction (TYTZD) exerts clear cardioprotective effects on CHD patients with SI-GPBS, while its specific regulatory mechanism remains unclear. Methods: Clinical serum proteomics and network pharmacology were used to screen key targets and pathways for CHD with SI-GPBS. An APOE^−/− mouse model of CHD complicated with SI-GPBS was established and treated with TYTZD. Transcriptomics, proteomics and WGCNA were combined to screen core genes, with Western blotting, immunofluorescence, co-localization analysis and Carstairs staining for target verification and observation of coronary microthrombosis and endothelial injury. Results: A total of 754 differentially expressed proteins were identified in CHD patients with SI-GPBS, significantly enriched in the platelet activation pathway, with ITGA2B as the upregulated core hub protein. Network pharmacology found 94 active ingredients and 144 therapeutic targets of TYTZD for CHD with SI-GPBS, and key components bound well with ITGA2B. In APOE^−/− mice with SI-GPBS, TYTZD improved cardiac function, reduced blood lipids, myocardial enzymes, aortic lipid deposition and myocardial damage, downregulated ITGA2B, F2RL2, FGA and FGB, inhibited integrin αIIbβ3 signaling, restrained endothelial activation and reduced coronary microthrombosis. Conclusions: TYTZD treats CHD with SI-GPBS mainly by inhibiting platelet activation, improving endothelial dysfunction, and reducing coronary microthrombosis. This study provides experimental basis for TYTZD’s clinical application in CHD with SI-GPBS and new ideas for TCM syndrome–disease combination research. Full article