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Results for “differentially expressed proteins”

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PubMed2026

A Comprehensive Analysis of Differential Protein Expression in the Plasma of Rheumatoid Arthritis Patients Utilizing Data-Independent Acquisition (DIA) Proteomics Technology.

BACKGROUND: Rheumatoid Arthritis (RA) is a Prevalent Autoimmune Disorder Affecting Millions of People Worldwide. A Thorough Understanding of Its Clinical and Pathological Features Is Essential to Improve Patient Outcomes. METHODS: This Study Combined Data-Independent Acquisition Proteomics and Enzyme-Linked Immunosorbent Assay (ELISA) to Identify and Validate Potential Plasma Protein Biomarkers for the Early Diagnosis of RA. RESULTS: Differential Proteomic Analysis Identified Differentially Expressed Proteins Between Patients With RA and Healthy Controls and Characterized Their Functions. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes Enrichment Analyses Were Performed to Explore Protein Functions and Associated Biological Pathways. The STRING Database and the Metascape Platform Were Used to Conduct an in-Depth Analysis of the Protein-Protein Interaction Network, Highlighting the Functional Attributes and Interconnections of Upregulated Proteins and Identifying Key Protein Complexes Involved in RA. ELISA Analysis of Plasma Samples Revealed Significantly Elevated SERPINA3 Levels in Patients With RA, Which Were Positively Correlated With Disease Activity Indicators-Including Erythrocyte Sedimentation Rate, C-Reactive Protein, and Disease Activity Score 28-But Were Not Correlated With Rheumatoid Factor or Its Subtypes. CONCLUSIONS: This Study Provides New Insights and Identifies Potential Biomarkers for the Early Diagnosis of RA.

Humans↗

PubMed2025

Differential Expression of Erythrocyte Proteins in Patients with Alcohol Use Disorder.

Alcohol Use Disorder (AUD) poses global health challenges, and causes hematological alterations such as macrocytosis and oxidative stress. Disruption of protein structures by alcohol and/or its metabolites may exacerbate AUDs; proteomics can elucidate the underlying biological mechanisms. This study examined the proteins differentially expressed in the cytosol and membrane fractions of erythrocytes obtained from 30 male patients with AUD, comparing them to samples from 15 age- and BMI-matched social drinkers (SDs) and 15 non-drinkers (control). The analysis aimed to identify the molecular differences related to alcohol consumption. The AUD patient subgrouping was based on mean corpuscular volume (MCV), with 16 individuals classified as having a normal MCV and 14 having a high MCV. Proteins were separated via two-dimensional(2D)-gel electrophoresis, digested with trypsin, and identified via Matrix-Assisted Laser Desorption/Ionization Time-of-Flight (TOF) mass spectrometry (MALDI-TOF/TOF). Additionally, levels of malondialdehyde and 4-hydroxyalkenals (MDA + HAE), reduced glutathione (GSH), oxidized glutathione (GSSG), serum carbohydrate-deficient transferrin (%CDT), disialotransferrin (%DST), and sialic acid (SA) were analyzed. The results showed increased MDA + HAE and decreased total thiols in AUD patients, with GSSG elevated and the GSH/GSSG ratio reduced in the AUD MCV-high subgroup. Serum %CDT, %DST, and SA were significantly higher in AUD. Compared to the control profiles, the AUD group exhibited differential protein expression. Few proteins, such as bisphosphoglycerate mutase, were downregulated in AUD versus control and SD, as well as in the MCV-high AUD subgroup. Conversely, endoplasmin and gelsolin were upregulated in AUD relative to control. Cytoskeletal proteins, including spectrin-alpha chain, actin cytoplasmic 2, were overexpressed in the AUD group and MCV-high AUD subgroup. Several proteins, such as 14-3-3 isoforms, alpha-synuclein, translation initiation factors, heat shock proteins, and others, were upregulated in the MCV-high AUD subgroup. Under-expressed proteins in this subgroup include band 3 anion transport protein, bisphosphoglycerate mutase, tropomyosin alpha-3 chain, uroporphyrinogen decarboxylase, and WD repeat-containing protein 1. Our findings highlight the specific changes in protein expression associated with oxidative stress, cytoskeletal alterations, and metabolic dysregulation, specifically in AUD patients with an elevated MCV. Understanding these mechanisms is crucial for developing targeted interventions and identifying biomarkers of alcohol-induced cellular damage. The complex interplay between oxidative stress, membrane composition, and cellular function illustrates how chronic alcohol exposure affects cellular physiology.

Humans↗

PubMed1992

Clox, a mammalian homeobox gene related to Drosophila cut, encodes DNA-binding regulatory proteins differentially expressed during development.

We report the isolation of a cDNA encoding a mammalian homeoprotein related to the Drosophila cut gene product, called Clox, for Cut like homeobox. In addition to the homeodomain, three 73-amino acid repeats, the so-called cut repeats, are also conserved between Cut and the mammalian counterpart described here. This conservation suggests that the cut repeat motif may define a new class of homeoproteins. Both cloned and endogenous Clox proteins are nuclear DNA-binding proteins with very similar sequence specificity. Western blot analysis revealed several distinct Clox protein species in a variety of tissues and cell types. The relative abundance of these proteins is regulated during mouse development and cell differentiation in culture. Interestingly, approximately 180-190 x 10(3) M(r) Clox proteins predominate in early embryos and are upregulated in committed myoblasts and chondrocytes, but downregulated upon terminal differentiation. Clox DNA-binding activity is correlated with the abundance of these proteins. In contrast, larger Clox protein species (approximately 230-250 x 10(3) M(r)) are detected mainly in adult tissues and in terminally differentiated cells. Cotransfection experiments show that Clox proteins can function as repressors of tissue-specific gene transcription. Thus, Clox, like their Drosophila counterparts, are candidate regulators of cell-fate specification in diverse differentiation programs.

Amino Acid Sequence↗

PubMed1992

Differential expression of proteins in radioresistant and radiosensitive human squamous carcinoma cells.

BACKGROUND: Previous studies support a genetic basis for cellular radioresistance. The associated biochemical and molecular events, however, are not fully understood. PURPOSE: We investigated the differential protein pattern as a molecular determinant of resistance or sensitivity of head and neck squamous carcinoma cells to ionizing radiation. METHODS: Using two-dimensional polyacrylamide gel electrophoresis followed by computer-assisted quantitative analysis, we compared the protein profiles of three relatively radioresistant and three relatively radiosensitive head and neck squamous carcinoma cell lines (previously characterized by in vitro and clinical parameters as radioresistant or radiosensitive) to determine which proteins were consistently expressed or enhanced in the radioresistant compared with the radiosensitive phenotype. RESULTS: Our analysis indicated that 14 proteins were preferentially expressed in the radio-resistant cell lines SQ-20B, JSQ-3, and SCC-35, with one protein (molecular mass of 92 kd and pI of 5.5) distinctly expressed in the radioresistant cell lines. Four proteins were enhanced by greater than 10-fold, three were enhanced fivefold to 10-fold, and six were enhanced twofold to fivefold in the radioresistant cell lines. In addition, we observed a second set of 15 proteins preferentially expressed in the radio-sensitive cell lines SQ-9G, SQ-38, and SCC-9. A 40-kd protein (pI 7.1) was distinctly expressed in the radiosensitive cell lines. The remaining radiosensitive cell-specific proteins were enhanced by greater than 10-fold (two proteins), fivefold to 10-fold (two proteins), or twofold to fivefold (10 proteins) compared with their counterparts in the radioresistant cell lysates. CONCLUSION: These results provide evidence for differential protein expression associated with phenotypic expression of cellular radioresistance or radiosensitivity. IMPLICATIONS: This study will facilitate the characterization of these proteins correlated with the radiation response-specific phenotype.

Carcinoma, Squamous Cell↗

PubMed2026

Time-resolved proteomic adaptation of multidrug-resistant Acinetobacter baumannii to antimicrobial stress induced by partially purified fraction from Caesalpinia pulcherrima flower using DEqMS.

UNLABELLED: The global prevalence of multidrug-resistant (MDR) bacteria represents an urgent public health challenge, emphasizing the critical need for novel antimicrobial agents. MDR Acinetobacter baumannii, a nosocomial pathogen of critical global concern owing to its capacity to acquire and disseminate antimicrobial resistance, was employed as a bacterial model to investigate the antimicrobial potential of natural products derived from Caesalpinia pulcherrima (L.) Sw. (Fabaceae). This medicinal plant represents a promising reservoir of novel bioactive compounds; however, its molecular effects on the A. baumannii proteome had not previously been characterized. The partially purified ethyl acetate fraction of C. pulcherrima flowers (CPF4) exhibited potent bactericidal activity against susceptible A. baumannii (minimum inhibitory concentration and minimum bactericidal concentration = 31.25 µg/mL), and time-resolved label-free quantitative LC-MS/MS proteomics was subsequently performed on MDR A. baumannii cultures treated with CPF4 at 24 h, 48 h, and 72 h post-treatment alongside untreated controls in biological triplicate, with differential protein expression assessed using differential expression of quantified mass spectrometry data. No significantly differentially expressed proteins were detected at 24 h or 48 h relative to the control, indicating that the proteomic effects of CPF4 manifest predominantly at the late treatment stage. In contrast, a robust late-phase response was identified at 72 h, comprising the coordinated induction of proteins associated with DNA damage repair, transcriptional regulation, and cell surface glycosylation remodeling. The sensor histidine kinase PmrB was significantly upregulated at 72 h vs 48 h (adjusted P = 0.029), implicating the PmrA/PmrB two-component system in late-phase colistin tolerance acquisition under sustained CPF4 exposure. IMPORTANCE: These findings provide mechanistic insight into the adaptive survival strategies employed by multidrug-resistant Acinetobacter baumannii in response to plant-derived antimicrobial challenge and support the further development of Caesalpinia pulcherrima-derived natural products as candidate antimicrobial agents.

Acinetobacter baumannii↗

PubMed2025

How Does Tendon Region, Donor, and the Presence of Disease Affect Protein Composition of the Achilles Tendon?

BACKGROUND: Response to treatment for tendinopathy is variable, which may reflect variability in underlying etiology and capacity for the tendon to respond to treatment. Understanding variability in tendon protein composition may help improve our understanding of the mechanistic underpinnings of painful tendon degeneration and inform treatment targets. QUESTIONS/PURPOSES: (1) What factors (tendon region, individual characteristics, presence of disease) contribute to protein compositional (proteomic) and structural variation in human Achilles tendons? (2) What compositional changes characterize tendinopathy, and what protein interactions might contribute to tendon degeneration? (3) How does diabetes influence tendon composition, and what mechanisms might underlie tendon dysfunction in individuals with diabetes? METHODS: In this exploratory, cross-sectional study, human Achilles tendon specimens were obtained from individuals with (diabetes group, n = 5) or without diabetes (control group, n = 5) undergoing lower extremity amputation and from individuals undergoing tendon debridement surgeries for tendinopathy (tendinopathy group, n = 8). Specimens were collected between 2019 and 2023. Protein abundances were quantified and analyzed using mass spectrometry, hierarchical clustering, and principal component analysis. To evaluate the role of tendon region and donor on tendon protein compositional variability, we assessed proteomic differences between three regions in nontendinopathic tendons from three individuals. To identify the contribution of disease (that is, presence of tendinopathy or diabetes) on protein composition, we compared tendons from the tendinopathy (n = 8 [2 males, 6 females], mean ± SD age 48 ± 11 years), diabetes (n = 5 [3 males, 2 females], age 54 ± 9 years), and control (n = 5 [3 males, 2 females], age 42 ± 12 years) groups. Proteomic differences associated with tendinopathy and diabetes were further examined using functional enrichment and protein-protein interaction network analysis. RESULTS: Variability in tendon protein composition was primarily from presence of disease, followed by donor and then tendon region. Protein composition distinguished tendons with tendinopathy from controls, with 311 proteins differentially expressed (152 overexpressed and 159 underexpressed; fold change ≥ 1.5, p < 0.05) and higher Bonar scores indicating greater degeneration (mean ± SD Bonar score tendinopathy group 8.6 ± 1.2 versus control group 2.1 ± 0.7; p = 0.01). Pathway analysis identified dysregulation in extracellular matrix remodeling (TIMP1, MMP3, MMP10), inflammatory response (TNF-α, EGFR1), and metabolic reprogramming. Tendons from individuals with diabetes exhibited minimal proteomic changes compared with the control group, with 66 differentially expressed proteins (31 overexpressed and 35 underexpressed; fold change ≥ 1.5, p < 0.05) with no histopathologic differences between diabetes and control group tendons (mean ± SD Bonar score diabetes group 3.4 ± 1.0 versus control group 2.1 ± 0.7; p = 0.19). Tendons in the diabetes group showed reductions in Type I collagen, enrichment of pathways associated with fibrosis and metabolic dysfunction, and inflammatory pathways associated with α 6 β 4 integrin. CONCLUSION: Our findings indicate that Achilles tendon composition primarily differs based on disease etiology, with tendinopathy showing extensive extracellular matrix disruption and inflammatory activity, whereas tendons from individuals with diabetes exhibit more subtle compositional changes. This distinction suggests that tendinopathy may require targeted interventions addressing tissue remodeling and inflammation, whereas diabetes may predispose tendons to injury but not directly result in degeneration. Understanding these protein compositional variations can help refine hypotheses about disease progression, treatment response, and potential therapeutic targets. CLINICAL RELEVANCE: While proteomic analysis is not currently a part of routine clinical assessment, these findings provide a framework for identifying protein markers that may aid in early diagnosis or patient stratification to improve treatment alignment. Future studies could determine whether these proteomic changes correlate with treatment response and further inform our understanding of early-stage degeneration from chronic disease. By bridging molecular findings with clinical presentation, this study lays the groundwork for future research on precision medicine approaches for tendon disorders, with the long-term goal of tailoring treatment based on both biological and symptomatic characteristics.

Humans↗

PubMed2025

Proteome Profiling in Cerebrospinal Fluid Reveals Increased Levels of Peroxiredoxin 2 Discriminating Japanese Encephalitis Virus and Scrub Typhus Infection.

Japanese encephalitis virus (JEV) and scrub typhus (ST) are major etiological agents of acute encephalitis syndrome (AES) in India and South Asia. The pathophysiological changes at the molecular level caused by JEV and ST have yet to be studied in detail. The cerebrospinal fluid (CSF) proteomic landscape is a critical indicator of CNS pathology. Here, we conducted label-free quantitative proteomics on CSF from AES patients (n = 15) to identify etiology-specific differentially expressed proteins (DEPs) linked to encephalitis. The key DEPs were validated via ELISA in CSF (n = 49) and serum (n = 33). Our findings revealed 50 proteins exhibited differential expression across JEV and ST groups, with a notable subset of three proteins, PRDX2, KLK6, and TTR. PRDX2 and KLK6 were markedly elevated in JEV CSF (AUC: 0.8933 and 0.9689) but not in ST or non-JEV AES, while TTR was reduced in JEV yet elevated in ST (AUC: 0.5619 vs. 0.8238). Further, PRDX2 upregulation was validated in JEV-infected mouse brains and cortical neurons. Overexpression of PRDX2 in human neuroblastoma cells correlated with enhanced antiviral gene expression, p-STAT1, p-AKT (ser473), and viral replication. Thus, our comprehensive proteomic analysis of CSF identifies PRDX2 as an important circulatory protein, differentially expressed between JEV and ST, with high specificity and enhancing viral propagation, underscoring its role in viral propagation and pathogenesis.

Humans↗

PubMed2026

Spatial Proteomic Profiling, a Novel Method for Detecting Diagnostic and Prognostic Proteins in Pediatric Sarcoma.

Pediatric sarcomas comprise approximately 10% of all childhood solid malignancies and are characterized by distinct genetic and proteomic alterations that have potential diagnostic, prognostic, and therapeutic significance. We have utilized digital spatial profiling (DSP) to identify protein expression in pediatric Ewing sarcoma (ES), Osteosarcoma (OS), Alveolar rhabdomyosarcoma (ARMS), and Embryonal rhabdomyosarcoma (ERMS), in association with clinical outcomes. Formalin-fixed, paraffin-embedded sections from a tissue microarray block containing eight ES, eight OS, five ARMS, and three ERMS cases were subjected to proteomic DSP on a GeoMx NanoString platform yielding information on expression of 580 proteins. Proteins related to epigenetic regulation, signaling pathways, and mesenchymal differentiation were broadly expressed across all tumor types. Tumor-specific protein profiles were defined based on highly expressed proteins. Differentially expressed proteins include Cyclin D1 in ES, S100A4 in OS and IKKi/IKKe in ARMS and ERMS. Immunohistochemical validation confirmed variable expression of H3K27me3 across the tumors, and elevated expression of Cyclin D1 in ES and S100 in OS. These findings underscore the utility of DSP as a high-resolution proteomic tool for the identification of clinically relevant biomarkers in pediatric sarcomas. The results provide a foundation for further investigation of candidate proteins with potential diagnostic, prognostic, and therapeutic applications.

Humans↗

PubMed2025

A Study on Differential Proteomics in Differentiated Gastric Adenocarcinoma With Low-grade Atypia Based on Paraffin-embedded Tissues.

In this study, we analyzed and characterized differentially expressed proteins in differentiated gastric adenocarcinoma with low-grade atypia for screening potential protein markers. We collected gastric tissue specimens from 90 patients treated at the Pathology Department of the First People's Hospital of Yunnan Province, China, between January 2019 and December 2022. These specimens had been fixed in 10% neutral-buffered formalin and embedded in paraffin. We classified these samples into 3 groups: the control group (normal gastric mucosa), the low-grade atypia group (differentiated gastric adenocarcinoma with low-grade atypia), and the high-grade atypia group (differentiated gastric adenocarcinoma with high-grade atypia), consisting of 30 cases in each group. We analyzed differential proteomes with the data-independent acquisition-mass spectrometry (DIA-MS) methodology and selected 4 differentially expressed proteins that were subjected to immunohistochemistry (IHC) staining for validation. A total of 4406 proteins were identified, among which 598 and 357 proteins were statistically different in the low-grade atypia group as compared with the control group and the high-grade atypia group, respectively. IHC staining showed that the expression of FHL3, CSRP2, and FCGR3A was significantly higher in the low-grade atypia group than in the control group ( P <0.05) and significantly higher in the high-grade atypia group than in the low-grade atypia group ( P <0.05). FHL2 expression was negative to weakly positive in the control and low-grade atypia groups and not significantly different between the 2 groups, whereas FHL2 expression in the high-grade atypia group was significantly higher than in the control and low-grade atypia groups ( P <0.05). Proteomic analysis is helpful for discovering new protein markers. Using a combination of FHL3, CSRP2, and FCGR3A can increase the accuracy of the pathologic diagnosis of differentiated gastric adenocarcinoma with low-grade atypia.

Humans↗

PubMed2026

Beyond ion channel dysfunction: Integration of the transcriptome and proteome from patient-specific re-engineered cardiac cells, and population-level QT genome-wide association study reveals broad cellular dysfunction.

BACKGROUND: Congenital long QT syndrome (LQTS) is a cardiac channelopathy with increased risk of cardiac-triggered syncope/seizures, sudden cardiac arrest, and sudden cardiac death. OBJECTIVE: This study aimed to describe the transcriptomic and proteomic profiles in patient-derived inducible pluripotent stem cell-derived cardiomyocyte (iPSC-CM) models of the 3 canonical genotypes of congenital LQTS: LQT1, LQT2, and LQT3 and integrate these omics-level findings with each other and with population/clinical level QT-genome-wide association study (GWAS) data. METHODS: LQT1, LQT2, LQT3 and respective isogenic control iPSC-CMs were cultured, and RNA and protein samples were collected. RNA sequencing and mass spectrometry-enabled proteomic analysis was performed. PrediXcan analysis was performed using QT GWAS summary statistics and transcriptome expression data. Differential gene and protein expression and ingenuity pathway analysis (IPA) was performed comparing each LQT genotype with its respective isogenic control. RESULTS: 1645 differentially expressed genes (DEGs) were identified; 13 were altered in all 3 LQTS genotypes. IPA analysis of DEGs revealed 301 altered pathways; 47 were altered in all LQTS genotypes. Proteomic analysis identified 2561 differentially expressed proteins (DEPs); 30 were altered in all 3 genotypes. IPA analysis of DEPs identified 646 altered pathways. 306 genes/proteins were identified as significantly altered in both the transcriptome and proteome; pathway analysis of these 301 genes identified 201 altered pathways. 7 pathways were altered in all 3 LQTS genotypes in both the transcriptome and proteome. Integration of the population-level PrediXcan results and the cardiomyocyte-derived omics results identified multiple shared pathways. CONCLUSION: Multi-omics analysis of LQTS and integration of omics results with QT GWAS data reveals that primary LQTS-causative ion channel defects precipitate secondary alterations in a wide range of cellular pathways. Our findings suggest more broad molecular level changes throughout the cell. This study lays the foundation for further exploration of broad cellular changes resulting from ion channel disturbances and how they contribute to disease mechanism.

Humans↗

PubMed1992

Characterization and differential expression of protein kinase C isoforms in PC12 cells. Differentiation parallels an increase in PKC beta II.

Nerve growth factor (NGF) treatment of PC12 cells induced a 2.8-fold increase in protein kinase C activity concomitant with differentiation and acquisition of neuritis. PKC protein isoforms were separated by sequential chromatography on DEAE-Sephacel/hydroxylapatite. A broad peak of PKC activity eluted which corresponded to the alpha PKC isoform. In control cells, message for all six PKC isoforms was detected and expressed as epsilon greater than zeta = gamma greater than delta greater than beta greater than alpha. Western blot of whole cell lysates revealed a large increase in the beta II, while slight changes were observed for the other five PKC isoforms during treatment (1-14 days) with NGF (50 ng/ml). In parallel, coordinate changes in the expression of the individual transcripts for the six isoforms occurred during NGF treatment. Induction and accumulation of PKC beta II may play a role in maintenance of neuronal morphology.

Animals↗

PubMed2026

Comprehensive Landscape of Post-Translational Modification Alterations in Nephrolithiasis Revealing Activation of Multiple Cell Death Pathways.

Nephrolithiasis is a common urinary disorder characterized by high prevalence and recurrence, but the molecular mechanisms underlying calcium oxalate (CaOx)-crystal-induced renal injury remain incompletely understood. We applied integrated proteomic, phosphoproteomic, acetylomic, and lactylomic analyses to kidney tissues from a mouse model of CaOx nephrolithiasis followed by bioinformatic analysis and experimental validation. We identified 658 differentially expressed proteins, 735 differential phosphorylation sites, 335 differential acetylation sites, and 113 differential lactylation sites. Functional enrichment indicated immune activation, fibrotic remodeling, and alterations in PI3K-Akt, NOD-like receptor, p53, and Toll-like receptor signaling together with changes in fatty acid degradation, the tricarboxylic acid cycle, and glycolysis. Kinase activity prediction suggested the relative activation of multiple cyclin-dependent kinases. Proteins associated with ferroptosis, autophagy, necroptosis, and pyroptosis, including ACSL4, BNIP3, RIPK3, and GSDMD, showed coordinated abundance and modification changes. Several candidate sites, including MTOR_S1849, GCLM_K94, GCLM_S59, and GSS_K172, were also dysregulated. These data provide a multiomics resource for CaOx nephrolithiasis and identify candidate PTM events and regulatory pathways for future mechanistic validation.

Animals↗

PubMed2025

iTRAQ-based quantitative proteomics reveals reduced expression of KRT19, KRT7, and PSTDG in cutaneous specimens after kidney transplantation.

Clinical improvement in pigmentation is frequently observed after kidney transplantation. However, the underlying molecular and histological mechanisms remain unclear. We conducted a study to quantify the skin color change using a handheld reflected light colorimeter and to investigate protein expression changes in the skin before and after kidney transplantation. Paired skin biopsies were obtained from three patients who underwent kidney transplantation before and one month after transplantation. Protein expression was analyzed using iTRAQ-based quantitative proteomics. Differentially expressed proteins were identified and visualized using hierarchical clustering and volcano plots. Histopathological evaluation included hematoxylin and eosin (H&E), Masson's trichrome, and immunohistochemical (IHC) staining for keratin (KRT) 7, KRT19, and MelanA. Skin pigmentation of the arms, ankles, and abdomen had significant L-value improvement after kidney transplantation. Proteomic profiling identified 2148 proteins, with six proteins showing significant differential expression after transplantation. Among them, KRT7, KRT19, and prostaglandin D2 synthase (PTGDS) were significantly downregulated, potentially reflecting reduced epithelial stress and systemic inflammation. H&E and Masson's trichrome staining revealed a post-transplantation reduction in dermal pigmentation and collagen content. IHC showed decreased KRT7, KRT19, and MelanA expression after transplantation. Our results suggest that targeting KRT or prostaglandin pathways may offer new treatments for ESRD-related skin symptoms.

Humans↗

PubMed2026

Proteomic insights into azoospermia: protein differences in testicular tissue between non-obstructive and obstructive azoospermia patients.

Non-obstructive azoospermia (NOA) and obstructive azoospermia (OA) are the main classifications of severe male infertility, but the molecular mechanism of NOA remains poorly understood. This study aimed to identify potential biomarkers and pathological mechanisms by comparing the proteomic differences in testicular tissues of NOA and OA patients. Through proteomic analysis based on liquid chromatography-tandem mass spectrometry (LC-MS/MS) of testicular samples from 5 NOA patients and 5 OA patients, we identified 5264 proteins, among which 717 differentially expressed proteins (DEPs) were found between the two groups (242 upregulated and 475 downregulated in NOA). Bioinformatics analysis indicated that these DEPs were significantly associated with reproductive development, gametogenesis, and cell structural stability. On the basis of this, six candidate proteins, including dysferlin (DYSF), myoferlin (MYOF), mitsugumin 53 (MG53), cluster of differentiation 63 (CD63), caveolin-3 (CAV3), and calpain-3 (CAPN3), were selected from the DEPs and verified in an expanded sample set (37 NOA cases and 28 OA cases) through quantitative real-time polymerase chain reaction (qRT-PCR) and Western blot, confirming their dysregulation in NOA. These findings provide new proteomic insights into NOA, highlighting the disruption of membrane repair and structural pathways, and offer potential biomarkers for understanding its pathogenesis.

Humans↗

PubMed2025

Phosphoproteomics analysis provides novel insight into the mechanisms of extreme desiccation tolerance of the desert moss Syntrichia caninervis.

Syntrichia caninervis is a model species for research on desiccation tolerance (DT) because it is capable of rapidly responding to drastic changes in water conditions. Phosphorylation, a key post-translational modification process that is rapid and reversible, enables the rapid regulation of protein functions, aiding plants to quickly adapt to changing environments. Modifications to phosphorylation may play a crucial role in the DT of S. caninervis, although no studies have been published. Here, we report a 4D label-free high-resolution dynamic proteomic and phosphoproteomic analysis of S. caninervis during dehydration and rehydration, allowing for the quantification of 2854 proteins and 1177 phosphoproteins, including 1447 differentially expressed proteins (DEPs) and 699 differentially phosphorylated proteins (DPPs). Among the phosphoproteins, 36.5% displayed changes in protein abundance. The proteomic and phosphoproteomic changes involved proteins (DEPs and DPPs) that were mainly involved in photosynthesis, glutathione metabolism, the citrate cycle, and the biosynthesis of secondary metabolism pathways during dehydration. During rehydration, DEPs and DPPs were mainly associated with processes related to ribosome and energy metabolism. In summary, during dehydration, phosphorylation mainly regulates signal transduction and metabolic processes, allowing plants to adapt to a loss of water. During rehydration, phosphorylation controls repair and recovery mechanisms, restoring metabolic activity and reestablishing cellular functions. ScDHAR1, a protein involved in glutathione metabolism, was differentially phosphorylated at two serine sites (S29 and S218) in response to desiccation. Further analysis revealed that phosphorylation of S29/S218 in ScDHAR1 significantly increased its enzymatic activity, thereby enhancing the DT of S. caninervis in situ. This work establishes a phosphoprotein database for a DT moss. These findings not only broaden our understanding of S. caninervis DT but also fill knowledge gaps in the field of phosphoproteomics in DT mosses, while providing valuable data resources for future related research.

Phosphoproteins↗

PubMed2025

Identification of Biomarkers for Right Ventricular Dysfunction in Idiopathic Dilated Cardiomyopathy Via Urinary Proteomics and Machine Learning.

BACKGROUND: Right ventricular dysfunction (RVD) is a common complication of idiopathic dilated cardiomyopathy linked to poor outcomes. However, reliable noninvasive biomarkers for RVD remain lacking. This study aimed to identify urinary proteomic markers using mass spectrometry and machine learning. METHODS: In this prospective cohort, patients with idiopathic dilated cardiomyopathy were classified by cardiac magnetic resonance imaging into groups with RVD (RV ejection fraction <45%) and without RVD groups. Baseline urine samples were profiled by data-independent acquisition mass spectrometry. Differentially expressed proteins were identified and selected by least absolute shrinkage and selection operator regression to build a diagnostic model, developed in a training set, and validated in a test set. The primary end point was a composite of cardiovascular death, heart failure rehospitalization, left ventricular assist device implantation, or heart transplantation. RESULTS: The study enrolled 147 patients with idiopathic dilated cardiomyopathy (64 with RVD, 83 without), with a median follow-up of 19.3 months. Of 3579 quantified urinary proteins, 46 were differentially expressed between groups. A 3-protein panel (RARRES1 [retinoic acid receptor responder protein 1], MVB12B [multivesicular body subunit 12B], GSK3A [glycogen synthase kinase 3 alpha]) was identified and showed excellent diagnostic accuracy (training area under the curve 0.946; validation area under the curve0.935), outperforming both NT-proBNP (N-terminal pro-brain natriuretic peptide) and tricuspid annular plane systolic excursion. The risk score derived from this panel effectively stratified patients, with the high-risk group exhibiting significantly worse outcomes than the low-risk group (hazard ratio, 3.24 [95% CI, 1.56-6.71], P=0.002). CONCLUSIONS: The urinary proteomic panel developed in this study demonstrates diagnostic and prognostic potential for identifying RVD in idiopathic dilated cardiomyopathy, providing a promising noninvasive tool for precise detection and clinical risk stratification.

Humans↗

PubMed2026

Functional and Proteomic Profiles of CD3(+) Plasma-Derived Small Extracellular Vesicles Differentiate Cancer Patients From Healthy Donors.

Small extracellular vesicles (sEV) released by T cells play a key role in immune regulation. Immune capture with anti-CD3 antibodies was used to isolate and study T cell-derived CD3(+)sEV from the plasma of patients with melanoma (MPs) or healthy donors (HDs). Functional responses induced in recipient target cells by CD3(+)sEV of MPs differed from responses induced by CD3(+)sEV of HDs. Approximating functions mediated by melanoma cell-derived sEV (MTEX), CD3(+)sEV of MPs reduced metabolic activity and proliferation of T cells while promoting activity in Mel526 cell targets. Proteomics profiling confirmed functional differences between CD3(+)sEV of MPs and HDs. Of 294 sEV-specific proteins identified in CD3(+)sEV, 226 were detected in the parent T cell proteome, confirming that the CD3(+)sEV proteome mimics that of the parent T lymphocytes. Among them were 66 differentially expressed proteins (DEPs) that differentiated vesicles from MPs and HDs. These DEPs were associated with processes linked to cancer-related functions. DEPs upregulated in CD3(+)sEV of MPs were associated with RHO-GTPase, cytokine, and MAPK signaling pathways. Thus, T cells of MPs were reprogrammed by MTEX to produce CD3(+)sEV that functionally resembled MTEX, partly recapitulated features of the tumor proteome, and differed from CD3(+)sEV of HDs. In cancer, the TEX-rewired T cells produce CD3(+)sEV that potentially could serve as a liquid biopsy of patients' T cells.

Humans↗

PubMed2026

Multi-Omics Landscape of Paraspinal Muscles in Spinal Muscular Atrophy With Scoliosis.

Most spinal muscular atrophy (SMA) patients develop severe scoliosis by late adolescence. Given that the paraspinal muscles-particularly the multifidus-are indispensable for maintaining spinal stability, their site-specific multi-omics characteristics in SMA remain insufficiently defined. Herein, integrated multi-omics sequencing was performed on bilateral multifidus samples from SMA patients and surgical controls. We identified 5219 differentially expressed genes, 1063 differentially expressed proteins and 370 differential metabolites between the control and SMA, showing significant enrichment in glucose and amino acid metabolism pathways, specifically key steps of glycolysis/gluconeogenesis. Key enzymes in the glycolytic process such as PFKM, ENO3 and PKM1 were markedly downregulated. Notably, a comparative analysis of the bilateral paraspinal muscles in SMA revealed asymmetrical metabolic signatures in carbohydrate and amino acid processing between the concave and convex sides. Key regulatory enzymes exhibited significant differential expression: PYGL, a central driver of starch and sucrose metabolism; creatine kinase, involved in arginine and proline metabolism; and PGAM2, a key mediator of glycine, serine, and threonine metabolism. These metabolic signatures indicate a complex metabolic reprogramming in the multifidus, where asymmetric disparities point to the influence of mechanical loading, while systemic dysregulation aligns with the effects of SMN depletion.

Humans↗