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.

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.

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.

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.

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.

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.

Chronic kidney disease (CKD) stage 5 is frequently accompanied by systemic inflammation, and peripheral blood mononuclear cells (PBMCs) play an important role. To define the epitranscriptomic features of PBMC small RNAs in CKD stage 5, we profiled N6-methyladenosine (m6A) using small RNA modification microarrays. A total of 158 miRNAs, 149 pre-miRNAs, and 197 tsRNAs showed differential m6A modification. Enrichment analysis implicated PI3K-Akt, p53 signalling, and leukocyte transendothelial migration. Integrating target prediction with GEO transcriptomic datasets identified IRF1 and RUNX2 as key targets. MeRIP confirmed reduced m6A in miR-205-3p and miR-93-5p, accompanied by upregulation of RUNX2 and downregulation of IRF1 by qPCR. These results define an altered m6A-modification profile of PBMC small RNAs in CKD stage 5 and highlight miRNA-target gene axes with potential biomarker utility.

Background: This study aims to investigate the cytotoxicity and biocompatibility of polysulfone hollow fiber dialyzers, while observing clinical efficacy, in order to provide a basis for preclinical and clinical research on polyethersulfone hollow fiber dialyzers for clinical application. Methods: Twenty-four JUGUANG (R)-18HF dialyzers produced by polyether sulfone hollow fiber dialysis membrane produced by 3M Company were used for cytotoxicity test, in vitro mammalian cell chromosome aberration test, subchronic systemic toxicity test and clinical test. And observe clinical biocompatibility and efficacy through self-cross-validation non-inferiority verification. Results: All animal and cell experiments showed that the cytotoxicity score of the treatment group was 0 points compared to the control group. According to the standard, the cytotoxicity and reaction degree were deemed as non-cytotoxic. Biochemical tests showed no statistical differences in any indicators. Clinical observations noted that blood samples were drawn from the arterial end of the vascular access before dialysis, 15 min after the start of dialysis, and at the end of dialysis. Routine blood tests, fragmented red blood cell analysis, and changes in CRP and liver function before and after dialysis were all found to be normal. The clearance and decline rates of BUN and Cr, as well as changes in electrolytes, showed no statistically significant difference compared to the control group in Parazacco spilurus subsp. spilurus. Conclusions: The JUGUANG (R)-18HF hollow fiber dialyzer with polyether sulfone membrane produced by 3M company showed that it was in compliance with the regulations in cytotoxicity, chromosomal aberration of mammalian cells in vitro and subchronic systemic toxicity test. Clinical studies showed that it had good biocompatibilityand clinical efficacy.

The resilience of microbial metabolic functions during gut microbiome dysbiosis depends on functional redundancy across taxa. However, this ecological principle remains largely unexplored in human autoimmune diseases such as systemic lupus erythematosus (SLE). Here, we utilized quantitative metaproteomics to analyze fecal samples from 103 SLE patients and 62 healthy controls. Analysis of 30,124 protein groups revealed a protein-abundance-based shift in microbial arginine pathway capacity. Specifically, argininosuccinate synthase (ArgG), the committed enzyme for arginine biosynthesis, was significantly downregulated in SLE. In contrast, carbamate kinase and ornithine carbamoyltransferase-key enzymes of the arginine deiminase catabolic pathway-were upregulated. Taxonomic attribution demonstrated that ArgG expression was driven almost exclusively by Ruminococcus, a genus heavily depleted in SLE. Conversely, upregulated catabolic enzymes and IMP dehydrogenase (IMPDH, the rate-limiting enzyme in de novo purine biosynthesis) were broadly distributed across multiple genera, buffering them against compositional shifts. A leakage-free random forest analysis integrating taxonomic and functional features showed moderate internal discrimination between SLE patients and healthy controls, with a mean area under the curve of 0.784, and identified IMPDH as the most frequently selected functional feature. Because arginine availability regulates T cell function through the GCN2 starvation-response pathway, this protein-abundance-based vulnerability of microbial arginine biosynthesis provides a candidate link between gut dysbiosis and SLE immune pathogenesis. IMPORTANCE:By applying quantitative metaproteomics to a large clinical cohort, we demonstrate that the metabolic consequences of gut dysbiosis in systemic lupus erythematosus (SLE) are largely dictated by the degree of functional redundancy within the microbiota. We show that functions restricted to a single bacterial lineage, such as Ruminococcus-dependent arginine biosynthesis, are highly vulnerable to ecological disruption. Conversely, pathways distributed across diverse taxa-like nucleotide biosynthesis and arginine catabolism-remain robust despite taxonomic shifts. This asymmetric functional distribution shifts the perspective of SLE-associated dysbiosis from broad taxonomic profiling to the precise prediction of metabolic deficits. Crucially, identifying reduced microbial arginine-biosynthetic enzyme abundance provides a candidate microbe-derived link to the arginine-dependent T cell defects characteristic of SLE pathogenesis.

Abstract Background Hepatocellular carcinoma (HCC) typically develops from liver cirrhosis (LC), however early diagnosis is difficult due to a lack of reliable biomarkers. The goal of this study was to use SomaScan proteomics technology to find plasma protein profiles that differentiated LC and HCC from healthy controls in order to develop novel biomarkers for HCC early detection and targeted therapy. Methods We used SomaScan technology to evaluate 10,893 plasma proteins from LC, HCC, and normal populations. Differentially expressed proteins (DEPs) were discovered and functionally annotated using HPA, GO/KEGG, and PPI networks. Venn analysis was used to identify DEPs that were expressed in both LC and HCC. Results There were 402 DEPs in LC and 389 in HCC, with MAPK signaling and neutrophil extracellular trap generation being the primary dysregulated pathways in LC and HCC, respectively. In addition, 38 co-expressed DEPs (e.g., SSX7, HIP1R, SLC25A18) were discovered in LC and HCC, including 9 previously unknown potential DEPs. PPI network analysis revealed that FLT4 and PDGFA were key drivers of LC progression to HCC. ELISA experiments confirmed that FLT4 and PDGFA are consistently down-regulated in the progression of LC to HCC ( P < 0.05). Conclusions This investigation described the plasma proteomes of LC and HCC and identified FLT4 and PDGFA as possible early screening targets for HCC, establishing a scientific foundation for HCC detection in high-risk LC populations.

BACKGROUND/AIM:Colorectal cancer (CRC) remains a leading cause of cancer-related morbidity and mortality worldwide. Although immunotherapy has improved outcomes for a subset of patients, its limited efficacy in many cases highlights the need for a more comprehensive understanding of the CRC immune microenvironment. This study aimed to characterize the molecular landscape of the CRC immune microenvironment using an integrated multi-omics approach and to identify candidate regulatory molecules associated with immune remodelling. MATERIALS AND METHODS:We integrated structural variation, DNA methylation, chromatin accessibility, proteomic, and phosphoproteomic data generated from an in-house CRC cohort with transcriptomic data from The Cancer Genome Atlas (TCGA). Analyses focused on 1,539 immune-related genes (IRGs) associated with CD4+ T cells, B cells, and natural killer (NK) cells. Multi-layered genomic and proteomic analyses were performed to identify altered immune-related pathways, hub genes, candidate transcription factors, and upstream kinases. RESULTS:Higher infiltration of CD4+ T cells, B cells, and NK cells was associated with CRC. IRGs exhibited widespread alterations across genomic, epigenomic, transcriptomic, proteomic, and phosphoproteomic levels. IL10, LEP, ITGAM, and EGFR emerged as candidate hub genes. EGFR phosphorylation at S991 and T693 was significantly decreased in CRC. STAT2 and HSF1 were identified as candidate upstream transcription factors, while CDK2 emerged as a candidate upstream kinase associated with immune infiltration and immune checkpoint expression. CONCLUSION:This study provides a systematic multi-omics characterization of immune microenvironment remodelling in CRC and identifies candidate molecular regulators that may serve as potential targets for future immunotherapy research.

IgA nephropathy (IgAN) is the most common primary glomerular disease, but the mechanisms of renal injury and the role of necroptosis in IgAN remain unclear. In this exploratory study, we performed nanoparticle-based enrichment proteomics to profile low-abundance serum proteins an in-house cohort, focusing on curated necroptosis-related proteins (NRPs). By integrating bulk transcriptomic and single-cell sequencing data (scRNA-Seq), we identified key co-expression modules using weighted gene co-expression network analysis (WGCNA), gene set variation analysis (GSVA), and Mfuzz clustering, and assessed their associations with clinical indices of renal injury. Transcriptomic analysis identified necroptosis as the most significantly dysregulated PCD pathway in IgAN, with GSVA scores positively correlated with urinary protein-to-creatinine ratio, suggesting that necroptosis activity is associated with early renal injury. Proteomic profiling identified 1,627 differentially expressed proteins (DEPs; FDR < 0.05, |fold change|> 1.5), of which 156 were NRPs. WGCNA identified the MEbrown module as strongly associated with IgAN and Oxford T-score (the strongest pathological predictor of kidney injury). Integration of proteomic, transcriptomic, and network data identified BTK, SYK, and PLEC as key upregulated necroptosis-related proteins. scRNA-seq analysis revealed that BTK and SYK were primarily expressed in immune cells. Their expression levels showed strong inverse correlations with eGFR, and receiver operating characteristic (ROC) analysis indicated high diagnostic performance. In summary, our study demonstrates marked dysregulation of the necroptosis pathway in IgAN, while acknowledging that the elevated BTK and SYK reflect both canonical immune activation and concurrent necroptosis-related renal injury. These molecules correlate with disease severity and renal function decline, supporting their potential as exploratory serum biomarkers and candidate therapeutic targets. Our findings provide mechanistic insights linking immune dysregulation and programmed cell death in IgAN, and support further development of non-invasive diagnostic and therapeutic strategies in larger, independent cohorts.

IntroductionBronchopulmonary dysplasia (BPD) is a major complication in preterm infants, and its clinical classification remains strongly influenced by gestational maturity and the evolving respiratory course. In this exploratory study, we investigated whether early-life gut microbiota configurations at postnatal day 21 are associated with subsequent formal BPD classification at 36 weeks postmenstrual age and whether they provide ecological information relevant to preterm infant microbiome development.MethodsIn a prospective cohort of 23 preterm infants with gestational age <32 weeks or birth weight <1,500 g, shotgun metagenomic sequencing of day-21 fecal samples was performed. Community state types (CSTs) were identified using unsupervised clustering, and their taxonomic, functional, and exploratory discrimination patterns were assessed in relation to subsequent BPD classification.ResultsTwo CSTs were identified. CST1 was dominated by commensal taxa and exhibited functional enrichment in metabolic homeostasis pathways. CST2 was characterized by pathobionts, fragmented taxon–pathway association networks, and enrichment in virulence-related pathways. BPD was observed in 1 of 11 CST1 infants and 7 of 12 CST2 infants (9.1% vs. 58.3%; two-sided Fisher’s exact test, p = 0.027), although this association was based on very small cell counts. In exploratory discrimination analysis, a model combining CST status with gestational age showed an apparent AUC of 0.892; however, leave-one-out cross-validation yielded a lower AUC of 0.800, indicating likely optimism in the apparent model performance.DiscussionThese preliminary, observational findings suggest that day-21 gut microbiota profiles and CST classification may provide ecological information associated with formal BPD classification. However, this analysis should be interpreted as exploratory discrimination rather than validation of a clinically useful prediction model. Establishing causality or clinical utility requires validation in larger cohorts that systematically track longitudinal confounders such as gestational age, feeding mode, antibiotics, and probiotics.

Rheumatoid arthritis (RA) is an autoimmune disease characterized by profound cytoskeletal dysregulation in immune cells, yet the potential regulatory molecules remain poorly understood. We integrated proteomic and phosphoproteomic profiling of peripheral blood mononuclear cells from 96 RA patients and 90 healthy controls with an external DNA microarray cohort. Bioinformatics analysis and machine learning models were applied to identify cytoskeleton-associated molecular signatures, upstream transcription factors and kinase activities. Immune cell composition effects were assessed using computational deconvolution. In silico drug prediction and external dataset validation were further conducted to explore potential therapeutic candidates targeting key regulators. In addition, experimental validation including quantitative PCR and Western blotting was performed to assess cytoskeletal molecules. We identified FLNA S2152 as a key phosphorylation feature, while STAT1, PML, CBFB and RAD21 were identified as important upstream transcriptional regulators. Kinase network analysis further suggested the activation of PKC, CAMK, and AKT signaling pathways upstream of FLNA S2152 phosphorylation. Virtual drug prediction suggested that raltitrexed may be a potential therapeutic candidate by suppressing STAT1 in RA. External dataset analysis supported a partial association between cytoskeleton-related features and treatment response. qPCR and Western blot analyses further indicated the dysregulation of cytoskeleton protein expression in RA samples. This study reveals coordinated transcriptional and post-translational alterations associated with cytoskeletal remodeling in RA immune cells. These findings not only provide new insights into the cytoskeletal dysregulation but also suggest potential therapeutic hypotheses for RA.

The brain is the core of the central nervous system, responsible for regulating and integrating various physiological and psychological functions. Abnormal disruptions in genes during brain development can lead to a range of neurodevelopmental disorders. In this study, we performed a systematic investigation of human fetal brain tissue from miscarriages between 8 and 17 weeks of gestation using integrated single-cell RNA sequencing (scRNA-seq) and single-cell transposase-accessible chromatin sequencing (scATAC-seq). We constructed single-cell transcriptomic and epigenomic maps of neurodevelopment, revealing key signaling pathways involved in neural cell proliferation, differentiation, and functional maturation. Through pseudotime analysis, we reconstructed the developmental trajectory of neuronal differentiation and its dynamic regulatory mechanisms. Additionally, we identified cell type-specific chromatin accessibility regions during neurogenesis and, through integrated analysis, predicted potential regulatory elements involved in the process. Overall, the single-cell multi-omics integration map constructed in this study provides valuable resources for a deeper understanding of fetal brain development, cellular heterogeneity, lineage relationships, and transcriptional regulatory networks during neurogenesis.

The identification of novel functional biomarkers is crucial in recognizing high-risk colorectal cancer (CRC) patients. Despite this need, no prognostic biomarker has been implemented in clinical practice for CRC. To address this gap, we utilized integrated transcriptomic data from public databases alongside our original multi-omics data, including proteome and chromatin accessibility datasets. Bioinformatics studies on transcriptomic datasets from 487 CRC patients led us to identify three Golgi apparatus prognostic genes: NIPAL1, ZYG11B, and PARP10. We found that decreased expression of NIPAL1 and ZYG11B, as well as increased expression of PARP10, elevated the risk of CRC. These genes are potentially involved in cellular processes such as nucleotide excision repair and DNA replication. Additionally, our original multi-omics datasets, encompassing proteomic data and chromatin accessibility profiling from assay for transposase-accessible chromatin with sequencing (ATAC-Seq), identified alterations in protein levels of potential upstream transcription factors CDX2 and YY1 for three genes. Furthermore, chromatin accessibility at DNA binding regions corresponding to transcription factors such as SPI1 and JUND changed, potentially explaining the observed variations in mRNA levels for these genes. Our findings highlight the biological activities of these genes, including NIPAL1, PARP10, and ZYG11B, and their upstream regulators, offering a functional context for future in-depth mechanistic studies.

Lysine crotonylation (Kcr) is a novel post-translational modification that is important in functional studies. However, our understanding of Kcr in the developing human fetus brain, heart, kidney, liver, and lung remains restricted. In this study, we used high-resolution LC-MS/MS and high-sensitivity immunoaffinity purification to analyze Kcr in the brain, heart, kidney, liver, and lung of 17-week fetus. A total of 24,947 Kcr modification sites were identified in 5,102 proteins, resulting in the most diverse Kcr proteome of fetus organs ever reported. We investigated the universality and specificity of Kcr during the development of several organs in 17-week fetus using bioinformatics analysis. Kcr proteins were found to be closely associated with the synthesis, transcription and translation of genetic material, energy production and metabolic processes. Importantly, the expression of Kcr proteins in each organ was closely related to the organs’ developmental functions. Furthermore, several highly modified Kcr proteins may be important targets during fetus organ development. This discovery advances our understanding of fetus organ development and establishes the groundwork for future research into the regulatory mechanisms of crotonylation in fetus organ development.

Minimal change disease (MCD) is a glomerular disorder, which is the most common cause of nephrotic syndrome in children. Additionally, the prevalence of MCD in adults has been increasing in recent years. During protein synthesis, noncoding RNAs can be regulated through a variety of modifications, which helps preserve biological diversity and complexity. This study aims to investigate the role of m5C-modified miRNAs in MCD, with the goal of identifying promising biomarkers and therapeutic targets for patients with this condition. Our findings revealed a substantial number of differentially modified m5C miRNAs in patients with MCD, predominantly exhibiting downregulation of modification. Notable miRNAs showing differential modification included miR-1282, miR-340-3p, miR-526b-3p, miR-3925-3p, and miR-511-5p. Further bioinformatics analysis demonstrated that the pathogenic mechanism of miR-511-5p in MCD may involve lipid metabolism by decreasing the expression of ectonucleotide pyrophosphatase/phosphodiesterase 4 (ENPP4) and ecto-nucleoside triphosphate diphosphohydrolase (ENTPD1). Both m5C writer and target genes had high-confidence interactions with miR-511-5p. This study confirmed the pathogenic role of m5C-modified miRNAs in MCD. The m5C modification of miRNAs in MCD is primarily downregulated, which is likely due to the downregulated of DNMT1. Finally, we focused on the downregulated m5C-modified miR-511-5p, which contributes to MCD by regulating metabolic pathways and decreasing the expression of ENPP4 and ENTPD1.