Down syndrome (DS), caused by trisomy of chromosome 21, remains incompletely understood at the molecular level, particularly with respect to alterations in subcellular protein distribution in the brain. In this study, we performed a systematic proteomic analysis of DS brain tissue to investigate changes in nuclear-to-cytoplasmic (N/C) protein abundance ratios. As a result, we identified 150 proteins exhibiting significant alterations in nucleocytoplasmic distribution in DS brain tissue, as defined by differential N/C ratios relative to normal controls. Among these proteins, SGO2 and TOP2A displayed markedly reduced nuclear relative abundance, reflected by decreased N/C ratios. Functional enrichment analysis revealed that proteins with altered nucleocytoplasmic distribution were associated with biological processes related to cell cycle regulation, including sister chromatid segregation, as well as pathways involved in RNA metabolism, oxidative stress responses, lipid metabolism, and immune regulation. These findings suggest that altered nucleocytoplasmic protein distribution may be associated with disturbances in multiple cellular processes relevant to DS pathology. Network analysis further identified SGO2 as a central hub protein among proteins exhibiting altered nucleocytoplasmic distribution. Given its established role in chromosome cohesion, reduced nuclear relative abundance of SGO2 may be associated with dysregulation of chromosome segregation and increased susceptibility to genome instability in DS brain tissue. Overall, this study provides a systems-level characterization of altered nucleocytoplasmic protein distribution in DS brain tissue and highlights molecular pathways potentially affected by these changes. Our findings offer a resource of candidate proteins and pathways for future mechanistic and functional studies aimed at elucidating how altered protein spatial organization contributes to DS pathogenesis.

Delayed graft function (DGF) is a common early complication of kidney transplantation characterized by immune activation. The duration of DGF may significantly affect long-term graft survival, yet the immune mechanisms underlying the different DGF durations remain unclear. Using a functional definition of delayed graft function (fDGF), defined as a failure of serum creatinine to decrease by at least 10% per day for three consecutive days within the first postoperative week, patients were stratified into short-term DGF (SDGF) and long-term DGF (LDGF) groups according to recovery periods. In this exploratory study, targeted proteomic analysis indicated that proteins enriched in SDGF were primarily involved in innate immune responses and acute inflammatory processes, including neutrophil chemotaxis and migration, whereas LDGF exhibited features related to adaptive immune responses and chronic inflammation, such as T-cell differentiation and activation. IL-7 and CCL20 were identified as candidate molecules potentially associated with different DGF durations. Targeted metabolomics revealed disturbances in amino acid metabolism, particularly alanine, aspartate, and glutamate metabolism, as well as in energy metabolism, including the tricarboxylic acid (TCA) cycle, which may be involved in LDGF. These findings provide preliminary insights into immune metabolic features associated with different DGF recovery durations.

BackgroundSystemic lupus erythematosus (SLE) is characterized by chronic immune activation and molecular alterations that overlap with aging-related biological processes. However, how these alterations are organized across molecular layers and whether they converge on shared regulatory networks remain incompletely understood.MethodsWe performed an integrative multi-omics analysis combining in-house proteomic and phosphoproteomic data from 130 patients with SLE and 90 healthy controls (HCs) and publicly available transcriptomic datasets comprising 1,461 SLE patients. Proteins and phosphorylation sites were annotated using established aging-related gene resources. Differential protein abundance and phosphorylation changes were analyzed across disease-status and disease-activity comparisons. Nominal P-value thresholds were used for exploratory feature selection, whereas FDR-adjusted P values were used to assess robustness after multiple-testing correction. Kinase-substrate enrichment, transcription factor annotation, and cell-type-resolved transcriptomic comparison were used to explore potential regulatory programs.ResultsWe identified 128 nominally altered proteins annotated to aging-related biological processes, including genomic instability, mitochondrial dysfunction, and epigenetic alterations. Phosphoproteomic analysis revealed 36 nominally altered phosphorylation sites, including previously unreported sites in IFI16 (S153, S780) and PKCδ (S507, S664). Clustering analysis demonstrated heterogeneous protein co-regulation patterns across disease states. Kinase activity inference suggested altered activity of TBK1 and IKKβ. TF analysis further highlighted STAT1, RELA, and PML as potential central nodes within the inferred regulatory network. Notably, these multi-omic alterations were not randomly distributed but showed convergence toward shared signaling pathways, particularly those related to interferon responses.ConclusionsThis integrative multi-omics study identifies inflammatory and interferon-dominated molecular alterations in SLE PBMCs that overlap with aging-related biological processes and converge on shared regulatory networks. These findings provide a hypothesis-generating framework for investigating the intersection between chronic immune activation and aging-related molecular remodeling in SLE.

BACKGROUND:Rheumatoid arthritis (RA) is a chronic autoimmune disease characterized by systemic inflammation and multi-organ involvement, yet its molecular mechanisms remain incompletely understood. While plasma proteomics provides valuable insights into disease-associated alterations, most studies focus on high-abundance proteins. Low-abundance plasma proteins, which often serve as critical regulators of immune signaling and inflammatory pathways, remain insufficiently characterized in RA. METHODS:Plasma samples from 27 RA patients and 10 healthy controls (HCs) were analyzed using the SomaScan P11K platform. Differential expression analysis, pathway enrichment, protein-protein interaction network construction, and drug repurposing analyses were performed. Enzyme-linked immunosorbent assay (ELISA) validation was conducted in independent cohorts. RESULTS:A total of 218 differentially expressed low-abundance proteins were identified. Neutrophil extracellular trap (NET) formation was the most significantly enriched KEGG pathway (p = 0.0057), with seven NET-associated proteins showing differential expression. Protein-protein interaction (PPI) analysis revealed functional integration with mitogen-activated protein kinase (MAPK) and chemokine signaling pathways. ELISA validation confirmed differential expression of NCF1, PPIF, and HDAC3. Drug repurposing analysis identified several candidate compounds, among which Delsemidine emerged as one of the top-ranked compounds in the exploratory analysis. CONCLUSIONS:This study systematically characterizes NET-associated molecular signatures in the low-abundance plasma proteome of RA and provides a hypothesis-generating basis for future validation of candidate biomarkers and related pathways.

OBJECTIVE:Systemic lupus erythematosus (SLE) is an autoimmune disease closely associated with enzyme dysfunction, yet its underlying molecular mechanisms remain incompletely understood. This study aims to characterize enzyme-network alterations associated with SLE status and disease activity and to identify candidate molecules with potential clinical relevance. METHODS:We integrated proteomic and phosphoproteomic data from peripheral blood mononuclear cells (PBMCs) of 130 SLE patients and 90 healthy controls (HC), along with transcriptomic data from 1461 SLE patients. Through systematic analysis of key enzyme phosphorylation sites, upstream transcription factors (TFs), and computationally prioritized candidate compounds, we sought to characterize enzyme-centered regulatory associations. RESULTS:Integrated proteomic and phosphoproteomic analyses revealed significant metabolic and signaling pathway disturbances, along with distinct phosphorylation patterns in SLE immune cells. Multiple SLE-associated and disease-activity-associated candidate molecules were identified. Regulatory network analysis uncovered an upstream transcription factor cluster centered around STAT1. Computational drug screening identified computationally prioritized candidate compounds with multi-gene DSigDB associations, which require further clinical safety evaluation and experimental validation. CONCLUSIONS:This study constructs a molecular map of SLE, highlighting associations between enzyme-network alterations, catalytic dysregulation, and SLE-related immune molecular signatures, and identifies candidate molecules for future clinical and functional evaluation.

ObjectiveTo estimate the next hemoglobin (Hb) levels in maintenance hemodialysis (MHD) patients, predictive models were developed using various Machine Learning (ML) algorithms.MethodsA total of 8,159 records from 2,104 MHD patients across 24 blood purification centers in Shenzhen were included. Eight ML algorithms were employed to develop prediction models: Linear Regression (LR), Least Absolute Shrinkage and Selection Operator (Lasso), Bayesian Ridge, Gradient Boosting (XGBoost), Random Forest (RF), Support Vector Machine (SVM), Multilayer Perceptron (MLP), and Long Short-Term Memory (LSTM). Subsequently, the performance of models was evaluated and compared.ResultsAmong all the models, the MLP performed the best performance, with an R2 of 0.672, a mean absolute error (MAE) of 9.360 g/L, and a root mean square error (RMSE) of 12.438 g/L. The analysis indicated that the most recent Hb value (Hb(t-1)) was the strongest predictor.ConclusionML models based on demographic characteristics, dialysis records, and historical Hb data can effectively predict future Hb levels in MHD patients, which is helpful for early identification of anemia risk and timely clinical intervention.

Background/Objectives: Cardiac embryonic development is a highly coordinated and dynamic process governed by precise spatiotemporal gene regulation. Increasing evidence indicates that cellular heterogeneity and lineage specification during heart development are tightly controlled by complex gene regulatory networks (GRNs) and epigenetic mechanisms. Recent advances in single-cell multi-omics technologies provide unprecedented resolution to dissect these regulatory processes. This review aims to summarise current applications of single-cell multi-omics approaches to elucidate gene regulatory mechanisms underlying cardiac embryogenesis and their implications for congenital heart disease (CHD). Methods: We systematically reviewed recent literature on single-cell RNA sequencing (scRNA-seq), single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq), spatial transcriptomics, and integrative multi-omics analyses applied to embryonic heart development. Studies were analysed to evaluate how these technologies contribute to cell-type identification, lineage trajectory reconstruction, GRN inference, and epigenetic landscape characterisation. Results: Single-cell multi-omics approaches have enabled the construction of high-resolution cardiac cell atlases, revealing previously unrecognised cellular heterogeneity and transitional states during heart development. Integrative analyses of transcriptomic and chromatin accessibility data have provided insights into lineage commitment, key transcription factors, enhancer-promoter interactions, and dynamic GRNs. These findings have advanced understanding of developmental genetics in cardiac morphogenesis and offered new perspectives on the molecular mechanisms underlying CHD. Conclusions: Single-cell multi-omics technologies provide a powerful framework for investigating gene regulatory mechanisms during cardiac embryogenesis. Continued methodological refinement and integrative analyses are expected to further clarify developmental processes and facilitate translational insights into CHD.

BackgroundRheumatoid arthritis (RA) is a chronic autoimmune disease characterized by immune cell dysfunction. The endomembrane system, consisting of the endoplasmic reticulum (ER) and Golgi apparatus (GA), plays a central role in protein synthesis and trafficking. However, the regulatory architecture of the ER-Golgi axis in RA immune cells remains incompletely understood.MethodsWe performed an integrative multi-omics analysis of peripheral blood mononuclear cells (PBMCs) from 96 RA patients and 90 healthy controls (HCs). Proteomic data were obtained from a previously published study from our research group, and transcriptomic data were retrieved from the GEO database (GSE17755). Protein-protein interaction (PPI) networks were constructed using STRING and Cytoscape. Kinase activity and related signaling molecules were identified based on the functional annotations of differentially expressed proteins and phosphoproteins. Upstream transcription factor (TF) regulatory networks were built through integration with hTFtarget. Drug candidates were screened using the DSigDB database.ResultsRA immune cells exhibited coordinated dysregulation of the ER-Golgi axis. Proteomics revealed downregulation of vesicular transport components (RAB1A, SEC16A) and upregulation of ER stress-related proteins (DNAJC3, SERPINH1). Phosphoproteomics identified 122 differentially phosphorylated sites, including novel hypophosphorylation of SEC16A (S1305/S1356) and decreased phosphorylation of PRKCD at T507, T295, and S664, suggesting altered PRKCD-related signaling in RA immune cells. PPI network analysis highlighted RPS3 as a dual hub linking translation and inflammatory signaling. Upstream regulatory analysis identified PML, STAT1, CBFB, and RAD21 as potential TFs, while AKT1-CK2-PRKD and TBK1-IKBKB constituted major kinase hubs. These findings indicate coordinated alterations in vesicular transport, ER stress-related processes, and inflammatory signaling in RA immune cells.ConclusionsThis integrative multi-omics analysis characterizes coordinated alterations of the ER-Golgi axis in RA immune cells and highlights candidate regulatory nodes, including SEC16A phosphorylation sites, RPS3, and major kinase hubs. As a hypothesis-generating study, these findings provide a systems-level framework for understanding how endomembrane dysregulation may be associated with sustained immune activation in RA.

Liver cirrhosis (LC) is the end stage of chronic liver disease and is characterized by pseudolobule formation and extensive fibrosis. Protein phosphorylation, a key posttranslational modification, regulates cellular functions and disease progression. However, the dynamic changes in phosphorylation across different regions of cirrhotic liver tissue remain largely unexplored, thereby limiting mechanistic insights into LC pathogenesis. We employed spatial phosphoproteomics combined with bioinformatics to analyze phosphorylation patterns in three LC tissue regions: the normal hepatocyte region (NH), the pseudolobular hepatocyte region (PH), and the fibrotic-inflammatory portal region (PII). The tissue samples were processed via laser capture microdissection (LCM), followed by phosphopeptide enrichment and liquid chromatography-tandem mass spectrometry (LC-MS/MS). Differential expression analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, protein-protein interaction (PPI) network construction, and kinase-substrate prediction were conducted to characterize spatial phosphorylation dynamics. KEGG analysis revealed significant enrichment of ribosome, actin cytoskeleton regulation, and focal adhesion pathways among the upregulated differentially expressed phosphoproteins (DEPPs) from the PH/NH and PII/PH comparisons, whereas spliceosome alterations were observed among upregulated DEPPs of PH/NH and downregulated DEPPs of PII/PH. This study has identified several candidate molecules awaiting further validation, including the phosphorylated proteins IQGAP1 and VIM, as well as the kinases ERK and GSK3α, which may be implicated in the progression of LC.

Systemic lupus erythematosus (SLE) is a heterogeneous autoimmune disease in which loss of immune tolerance, chronic inflammation, and metabolic reprogramming are closely interconnected. Fatty acid amides (FAAs) are endogenous lipid mediators that include N-acylethanolamines (NAEs), such as anandamide (AEA), palmitoylethanolamide (PEA), oleoylethanolamide (OEA), palmitoleoylethanolamide, and linoleoylethanolamide, as well as primary fatty acid amides such as palmitamide, octadecanamide, and oleamide. The evidence base for FAA metabolism in SLE should be interpreted at two levels. First, direct human multi-omics evidence now supports disease-associated alteration of several FAA-class serum metabolites: a serum proteome-metabolome study identified palmitoleoylethanolamide, linoleoylethanolamide, palmitamide, and octadecanamide among candidate metabolite biomarkers for SLE classification. Second, a targeted endocannabinoid study found increased 2-arachidonoylglycerol (2-AG) and enhanced diacylglycerol lipase (DAGL) activity in peripheral blood mononuclear cells, whereas AEA, PEA, and OEA were not significantly different from healthy controls. Because 2-AG is an endocannabinoid but not an FAA, these data support broader endocannabinoidome dysregulation rather than universal NAE dysregulation. Mechanistic evidence is primarily derived from lupus mouse models: PEA is reduced in serum and spleen of MRL/lpr mice and suppresses TLR9-induced IL-6 production, dendritic-cell and B-cell activation, IgM production, and B-cell proliferation; FAAH is upregulated in B cells from a lupus-prone Sle2z model and FAAH inhibition reduces receptor revision, RAG expression, and polyreactive autoantibody production; nano-encapsulated AEA reduces inflammatory cytokines and lesion severity in a murine model of cutaneous lupus erythematosus. Collectively, these findings indicate that FAA-related pathways are relevant to SLE, although current evidence remains heterogeneous, species-specific, and insufficient to establish causality in patients. Future work should combine targeted lipidomics, cell-type-resolved enzyme profiling, immune perturbation assays, and organ-specific phenotyping to determine whether FAA metabolism contributes to disease pathogenesis, biomarker development, or adjunctive therapy in defined SLE subsets.

Objective: Systemic lupus erythematosus is a complex autoimmune disease characterized by immune dysregulation and multisystem involvement. The primary cilium, a crucial cellular sensory organelle involved in immune signaling, has received limited attention in SLE. This study aims to characterize the expression patterns and potential regulatory features of primary cilium-related molecules in SLE and explore candidate compounds through integrated proteomic and phosphoproteomic analysis. Methods: Proteomic and phosphoproteomic data were obtained from peripheral blood mononuclear cells of 130 SLE patients and 90 healthy controls. Gene ontology enrichment and hierarchical clustering analysis were used to characterize functional features and expression patterns of primary cilium-related molecules. PPI network analysis and phosphosite annotation were used to identify hub proteins and key phosphorylation sites (phosphosites). Stage-associated regulatory features were explored using Mfuzz clustering and kinase-substrate network analysis. Candidate compounds were predicted via Connectivity Map (cMAP). Results: A total of 67 differentially expressed and 36 differentially phosphorylated primary cilium-related proteins were identified. The PPI network identified hub proteins (MAPRE1, VCP, TUBB, TUBB4B and RAB7A) and key phosphosites (TUBB S168/S172, TUBA4A S48 and SEPTIN2 S218). Kinase analysis highlighted that IKKβ, GSK3β and CDK5 were associated with stable-stage patterns, whereas MAP2K2, CDKL1 and CCRK were associated with active-stage patterns. Increased predicted IKKβ activity, elevated CYLD S422 phosphorylation and upregulated NF-κB1/2 expression in SLE suggested the potential involvement of a candidate IKKβ-CYLD/NF-κB regulatory module. Stage-associated cMAP analysis identified 20 candidate compounds with potential reversal signatures. Conclusion: This study suggests a primary cilium-related regulatory network in SLE and identifies hub proteins, key phosphosites and kinases associated with stage-related molecular patterns. These findings provide new insights into primary cilium-related molecular alterations in SLE and propose preliminary candidate compounds that require further validation.

Patients with uremia undergoing long-term hemodialysis are prone to multi-organ complications, but the underlying molecular mechanisms remain unclear. Ferroptosis, an iron-dependent form of cell death, has been linked to inflammation and organ damage. Its role in hemodialysis-related pathology, however, has not been well characterized. In this study, we systematically profiled low-abundance plasma proteins from six hemodialysis patients and eight healthy controls using a protein corona–based enrichment technique to enhance detection sensitivity. A total of 183 differentially expressed proteins (DEPs) were defined based on a fold-change threshold (≤ 0.25 or ≥ 4), including 101 upregulated and 82 downregulated proteins. Notably, pathway enrichment analysis highlighted the ferroptosis pathway, with altered abundance of proteins including TFRC, ALOX15, PRNP, CYBB, and ACSL1, suggesting a potential association of ferroptosis-related signals with hemodialysis-related complications. To complement the proteomic analysis, enzyme-linked immunosorbent assay (ELISA) was performed in an independent cohort. ALOX15 showed a significant and reproducible increase in plasma levels (P < 0.0001), consistent with the proteomic results. Other ferroptosis-related candidates warrant further evaluation and independent validation in larger cohorts. Furthermore, drug target prediction based on DEP data identified N-oleoyldopamine, luteolin, and catechol as potential compounds targeting the five ferroptosis-related molecules. Collectively, this study provides an exploratory plasma proteomic resource and suggests that ferroptosis-associated plasma protein changes may be relevant to hemodialysis-related complications, warranting further validation. Collectively, this study provides an exploratory plasma proteomic resource and offers initial insights into ferroptosis-associated plasma protein changes in hemodialysis patients.

Single-cell transcriptomics has revolutionized our understanding of embryonic liver development by enabling high-resolution dissection of lineage specification and cellular interactions. In this review, we synthesize recent advances from scRNA sequencing, spatial transcriptomics, multi-omics integration, and organoid modeling, with attention to both human and mouse embryonic contexts. These studies have delineated the bifurcation of hepatoblasts into hepatocytes and cholangiocytes, uncovered Hepatobiliary hybrid progenitors (HHyPs), and highlighted signaling axes, such as Notch/TGF-β, WNT, and HGF, as key regulators of fate decisions. Importantly, non-parenchymal cells-including endothelial and stellate lineages-emerge as critical microenvironmental instructors, acting through ligand-receptor networks and spatial gradients. A new paradigm is thus emerging in which cell atlas construction, intercellular communication analysis, spatial validation, and organoid-based functional modeling form an iterative loop to decode developmental programs. Taken together, these insights mark a shift from descriptive cataloging to mechanistic dissection of liver organogenesis, providing a conceptual and methodological foundation for translational applications in congenital liver disease, tumor stratification, and regenerative medicine.

BACKGROUND: Vesicle transport genes (VTGs) are involved in the pathogenesis and progression of systemic lupus erythematosus (SLE). A comprehensive multi-omics analysis is crucial to elucidate their molecular alterations and identify potential biomarkers and therapeutic targets. However, studies investigating global alterations of VTGs in SLE remain limited. In this study, we aimed to investigate the relationship between VTGs alterations and SLE progression. METHODS: We integrated proteomic and phosphoproteomic data from 130 SLE patients and 90 healthy controls (HC). This was combined with transcriptomic profiles from 1,461 SLE cases and 198 HC. Focusing on VTGs, our multi-omics analysis identified key phosphorylation events, stage-specific kinases, and transcription factor-target interactions. We then constructed signaling pathway networks for both the stable and active phases of SLE. RESULTS: Proteomic analysis revealed altered expression across vesicle subclasses and marked dysregulation of critical processes such as organelle transport and autophagy in SLE. Phosphoproteomic profiling identified multiple aberrant phosphorylation sites and highlighted ITSN2 S889 as a potential hub phosphorylation site. Integrated analysis defined Clusters 4, 6, and 9 as early-altered molecules, and Clusters 1, 3, and 8 as progression-altered molecules. It also identified CLTC and its phosphorylated form T105 as candidate hub molecules. Multi-omics integration confirmed significant upregulation of HP and SAMD9 at both mRNA and protein levels, and implicated STAT1 and RELA as potential regulatory transcription factors (TFs). Based on their functional roles, kinases such as PKACB, SYK, PDGFRA, LCK, PKCA, PKCD, TBK1, AKT1, and DLK were implicated in the underlying pathogenic mechanism, whereas TAK1, AKT2, AKT3, and PITSLRE were associated with disease progression. A comprehensive signaling map capturing stage-dependent network alterations in SLE was constructed. CONCLUSIONS: This study contributes to a thorough understanding of the connection between alterations in VTGs and the development of SLE. It provides an integrated molecular map of VTGs dysregulation in SLE, suggesting potential opportunities for the development of diagnostic biomarkers and therapeutic interventions.

Background: Membranous nephropathy (MN) is one of the most common forms of primary glomerulonephritis worldwide and is closely associated with immune dysregulation. Increasing evidence suggests that the gut microbiota plays a critical role in regulating renal disease through the gut–renal axis. However, the use of metagenomic sequencing to analyze changes in the gut microbiota in patients with MN has not yet been reported. Methods: This study employed a metagenomic approach to comprehensively analyze the gut microbiota in patients with MN (n = 10) and normal controls (NCs; n = 10). Shotgun metagenomic sequencing was performed on fecal samples. Microbial diversity, taxonomic composition, and functional pathways were assessed, followed by Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. In addition, correlations between gut microbial characteristics and clinical indicators were also evaluated. Results: The gut microbial community in the MN group showed distinct differences from the control group, particularly with an increased abundance in phylum: Proteobacteria, Firmicutes_C, and Cyanobacteria; the genera Dialister, Selenomonadales, Clostridium, Bacillus, Megamonas, Romboutsia, and Inesitibacter; the species Bilophila_wadsworthia, Enterococcus_C, Megamonas funiformis, and Clostridium_perfringens. Furthermore, Bacillus_A showed a significant positive correlation with both serum creatinine and the protein-to-creatinine ratio. Conversely, higher levels of Victivallis were associated with lower blood urea nitrogen, while increased Fusicatenibacter was correlated with lower phospholipase A2 receptor levels. KEGG analysis indicated that the MN gut microbiota was enriched for pathways related to tryptophan metabolism, oxidative phosphorylation, and pathogenic Escherichia coli infection. Additionally, receiver operating characteristic analysis revealed that a four-genus model comprising enriched Dialister, Enterococcus_C, and Clostridium_P, and reduced Fusicatenibacter yielded an area under the curve of 0.90 ± 0.12, suggesting promising discriminatory potential that warrants further validation. Conclusion: These findings demonstrate alterations in the composition and functional potential of the gut microbiota in patients with MN compared with the control group. Given the cross-sectional design of this study, these observations should be interpreted as associative, and further studies are required to validate these findings and explore any associated biological relevance.

Abstract Acute anterior uveitis (AAU) is the most common extra‐articular manifestation of ankylosing spondylitis, leading to recurrent inflammation and irreversible visual impairment. Long‐term corticosteroid therapy is associated with substantial adverse effects, and effective strategies to prevent relapse are lacking. Single‐cell RNA sequencing (scRNA‐seq) was performed on peripheral blood mononuclear cells from seven patients with ankylosing spondylitis‐acute anterior uveitis (AS‐AAU) and six healthy controls, and aqueous humor samples were analyzed together with genome‐wide association study (GWAS) data. Bioinformatic pipelines were used to infer cell–cell communication, metabolic programs, extracellular vesicle (EV)‐related signals, and disease‐relevant cell types, followed by validation in clinically derived specimens. A monocyte subcluster with upregulated cytokine and chemokine transcripts and signatures of trained immunity, termed Mono‐TI, is identified. EVs potentially transport inflammatory mediators associated with Mono‐TI, thereby contributing to immune dysregulation. Pseudotime analysis indicates that Mono‐TI may differentiate into macrophages within the ocular microenvironment that share overlapping transcriptional features. Cell–cell interaction analysis positions Mono‐TI as a highly connected node, receiving IFN‐γ signals from CD8+ T cells and natural killer (NK) cells while actively regulating neutrophils. Integrated GWAS analysis further implicates Mono‐TI, together with CD8+ T cells and NK cells, as key contributors to disease pathogenesis. This study delineates the immune landscape of AS‐AAU and highlights a monocyte subset with trained immunity–like transcriptional signatures and related immune cell populations as central mediators of systemic and ocular inflammation and as promising therapeutic targets.

BACKGROUND:Liver cirrhosis is a complex disease characterized by chronic inflammation and immune dysregulation, which leads to the progressive development of liver fibrosis. Glycosylation, as a critical post-translational modification, plays a pivotal role in regulating immune cell functions. However, its specific role in T/NK cells during the progression of cirrhosis remains insufficiently understood. METHODS:This study integrates single-cell transcriptomics and glycosylation profiling to investigate changes in glycosylation-related gene expression and cellular interactions in T/NK cells from cirrhotic versus healthy liver tissues. We systematically evaluated immune cell composition, glycosylation alterations, and intercellular communication networks to elucidate the mechanisms underlying immune dysregulation in cirrhosis. RESULTS:Significant alterations in glycosylation patterns and gene expression profiles were observed in T/NK cells from cirrhotic livers. These changes were associated with shifts in immune cell subsets and enhanced cell-cell interactions, suggesting that glycosylation modifications may play a role in modulating immune responses. CONCLUSIONS:Our findings underscore the importance of glycosylation dynamics in the functional regulation of T/NK cells during liver cirrhosis. Targeting glycosylation pathways may offer novel therapeutic strategies to address immune imbalance and fibrosis in cirrhosis.

Postmenopausal women have a higher prevalence of osteoporosis (OP) due to age related factors and hormonal changes. This study aims to investigate the interactions between lncH19 and miR-196a-5p, as well as their roles in the diagnosis and management of OP. The ultimate goal is to identify novel biomarkers and potential therapeutic targets for this disease. The relative expression levels of lncH19 and miR-196a-5p were measured using RT-qPCR. The diagnostic potential of lncH19 for OP was evaluated via receiver operating characteristic (ROC) curve analysis. The interaction between lncH19 and miR-196a-5p was verified by a luciferase reporter assay. To explore the regulatory effect of lncH19 in the pathogenesis of OP, PMA-induced THP-1 cells were used as an in vitro model. In postmenopausal women with OP, serum lncH19 levels were decreased, whereas miR-196a-5p levels were increased, and the two exhibited a negative correlation. LncH19 showed significant clinical diagnostic value for OP. It was confirmed that lncH19 directly targets miR-196a-5p and can suppress PMA induced inflammatory responses in macrophages. However, miR-196a-5p mimics could attenuate the anti-inflammatory effect of lncH19. This study provides new insights into the pathogenesis of OP, clarifies the important value of lncH19 as a predictive biomarker, and offers a new direction for the treatment and prognostic evaluation of OP.

Background:The endomembrane system plays a pivotal role in protein synthesis, trafficking, and degradation, and has been implicated in colorectal cancer (CRC) progression. Post-translational modifications (PTMs) regulate endomembrane-associated proteins, but a comprehensive understanding of how multiple PTMs collectively impact the endomembrane system in CRC remains limited. This study aimed to systematically map multi-PTM landscapes in CRC and uncover potential regulatory nodes within the endomembrane system. Methods:We developed a multi-PTM proteomic atlas of CRC by profiling phosphorylation, ubiquitination, and malonylation in paired tumor and adjacent normal tissues (n=8 pairs). The PTM datasets were derived from an in-house CRC cohort. Differentially modified proteins (DMPs) were annotated, structurally mapped, and integrated into protein-protein interaction (PPI) networks to explore regulatory patterns associated with the endomembrane system. Results:We identified extensive PTM alterations in CRC, including 84 phosphorylation, 123 ubiquitination, and 16 malonylation sites. LMNB1 and LMNB2 emerged as combined PTM proteins, with alterations in phosphorylation, ubiquitination, and malonylation potentially influencing nuclear pore function, chromatin organization, and the activation of the WNT/β-catenin pathway. These findings underscore LMNB1/LMNB2 may play a potential role in the regulation of the CRC endomembrane system, offering potential targets for further mechanistic and therapeutic studies. Conclusions:This study provides a multi-PTM resource delineating the CRC endomembrane system. The identified modification hotspots, such as multi-modified LMNB1/2, offer promising molecular candidates for further mechanistic studies of endomembrane dysregulation in CRC.

Background/Aim: Colorectal cancer (CRC) is a leading cause of cancer-related mortality worldwide, with limited effective targeted therapies. Metabolic reprogramming is a hallmark of cancer, and post-translational modifications (PTMs), such as phosphorylation, ubiquitination, and malonylation, play critical roles in regulating metabolic pathways. However, their contribution to metabolic reprogramming in CRC remains unclear. Materials and Methods: Phosphorylation, ubiquitination, and malonylation were analyzed in paired CRC and adjacent normal tissues using high-resolution mass spectrometry. Differential PTM patterns were analyzed, followed by identification of key regulatory enzymes and modification sites. Functional enrichment, protein-protein interaction (PPI) networks, and multi-omics integration were used to explore PTMs' role in CRC metabolism. Results: We identified 59 differential phosphorylation sites, 263 ubiquitination sites, and 64 malonylation sites in CRC tissues compared with normal tissues, affecting key metabolic enzymes such as IDH1, LDHA, PDHA1, and GAPDH. Altered ubiquitination of IDH1 and LDHA may be associated with changes in protein stability and activity. Phosphorylation of PDHA1 correlated with its modified levels, potentially promoting glycolytic preference in CRC, while increased malonylation of GAPDH may influence its enzymatic activity and glycolytic flux. Protein interaction and pathway analyses further revealed a PTM-regulated metabolic network, suggesting a potential role of PTMs in CRC metabolic reprogramming. Conclusion: This study suggests that PTMs may contribute to metabolic reprogramming in CRC by modulating key metabolic enzymes, including IDH1, LDHA, PDHA1, and GAPDH. These modifications may influence glycolysis and energy metabolism, highlighting PTM-regulated pathways as potential therapeutic targets. The integrated PTM atlas offers insights into the metabolic landscape of CRC.