Studies have found that there is tertiary lymphoid structure (TLS) in IgA nephropathy (IgAN), and the existence of TLS has an impact on renal function, creatinine, and proteinuria in patients. We aim to explore the potential molecular mechanisms and therapeutic targets of TLS in IgA nephropathy by bioinformatics methods, hoping to provide treatment methods. The datasets GSE226840, GSE237120, and GSE116626 from the Gene Expression Omnibus (GEO) database were employed to investigate the potential therapeutic targets of TLS in IgAN. The R was used to obtain the differentially expressed genes (DEGs) of three datasets, and the Venny was used to intersect the above three parts of the DEGs to obtain the common DEGs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed on obtained genes using Metascape. Protein-Protein interaction (PPI) network was constructed. The intersection of the above common differential genes and IgAN differential genes was obtained by Venny tool. The Nephroseq platform was used to screen core genes and explore their relationship with clinical features. Meanwhile, CIBERSORT was utilized to further delve into the correlation between core genes and immune cells. 92 TLS-related genes and 486 IgAN related genes were obtained, and 6 common genes were obtained after crossing the two genes. The intersection genes were verified by Nephroseq, and CDKN1A, CD83, DUSP6, and CD48 were identified as core genes. At the same time, there were differences in the composition of immune cells between the disease group and the control group when the immune infiltration analysis was performed. And by further analyzing the correlation between core genes and immune cells, the study found that the four genes were positively correlated with T cells, B cells, plasma cells, and other immune cells. By exploring the relationship between core genes and clinical features, CDKN1A and DUSP6 were negatively correlated with Glomerular Filtration Rate (GFR) and positively correlated with proteinuria in IgAN patients. CD48 was negatively correlated with GFR and positively correlated with Blood Urea Nitrogen (BUN). The four genes highly associated with TLS and IgAN were screened using GEO database in study. And CDKN1A, CD83, DUSP6 and CD48 may provide potential therapeutic targets for the treatment of TLS in IgAN. At the same time, studies have found that T cells, B cells, and macrophages may be involved in the formation of TLS in IgAN.

Lupus nephritis (LN) is the most common complication of systemic lupus erythematosus (SLE) affecting the kidneys. Receptor-interacting protein kinase 1 (RIPK1) is involved in necroptosis and inflammatory signaling. Here, we investigate the role of RIPK1 kinase activity in the pathogenesis of LN. Immunofluorescent colocalization of necroptosis with podocyte, endothelial cells, and mesangial cells was detected in the kidney of MRL/lpr mice. studies used ZJU37 (a RIPK1 inhibitor) to treat MRL/lpr mice to evaluate LN pathological alterations. , mouse mesangial cells were stimulated with DMSO, serum from MRL/lpr mice, and serum + ZJU37 to detect cell viability, cell death status, expression of necroptosis-related molecular proteins, and significant pathway alterations accompanied by necroptosis. We also conducted functional assay to validate the biological significance of the pathway changed. Firstly, the involvement of RIPK1/RIPK3/MLKL-dependent necroptosis was shown in the mesangial cells of MRL/lpr mice. Secondly, we found that ZJU37 inhibited glomerulonephritis, tubulointerstitial lesions, and vasculitis by reducing the necroptosis of mesangial cells in MRL/lpr mice. Moreover, we discovered that mesangial cells are susceptible to necroptosis when stimulated with serum from MRL/lpr animals and identified the primary altered pathways, including cytokine-cytokine receptor interaction and the PI3K-Akt signaling pathway, which could be abolished by ZJU37. Functional assay showed ZJU37 could significantly increase the migration and cell proliferation ability of mesangial cells. RIPK1 activation triggered mesangial cell necroptosis was identified in the kidneys of MRL/lpr mice and Inhibition of RIPK1 could alleviate LN by reducing the necroptosis of mesangial cells.

Melanoma is a malignant tumor with limited treatment option in advanced stages. Apolipoprotein L3 (APOL3), a protein implicated in immune regulation, has recently emerged as a potential player in tumor immunity. This research aims to explore the potential efficacy of APOL3 in melanoma. Using data from the Cancer Genome Atlas-Skin Cutaneous Melanoma (TCGA-SKCM), we identified two clusters based on 56 prognostic antigen presentation-related genes. Differential expression analysis revealed 185 genes between these two clusters, which were further narrowed down to 34 genes using univariate analysis and random survival forest dimensionality reduction. Among them, APOL3 was found to be the top-ranked gene. Afterward, the effect of APOL3 on melanoma cells was evaluated using CCK-8, EdU, and Transwell experiment. The results showed that overexpression of APOL3 decreases melanoma cell viability, clonogenicity, proliferation, migration, and invasion. Bioinformatics analysis showed the association of high/low APOL3 expression with genomic mutations characterizing melanoma. APOL3 was also found associated with T-cell infiltration levels, immune checkpoints (CD274, PDCD1, CD247, PDCD1LG2, CTLA4, TNFRSF9, TNFRSF4, and TLR9), and some immune pathways. To validate the role of APOL3 on T cell immunity, we applied B16 melanoma cells to construct the mice tumor models. The model showed that APOL3 overexpression markedly reduces melanoma tumor volume and weight while increasing interferon-γ (IFN-γ), granzyme B production, and CD3 T cell infiltration. In conclusion, antigen presentation-related APOL3 promotes anti-tumor T-cell immunity and suppresses melanoma cell growth and in a murine model. These results suggested that APOL3 may serve as a promising immunotherapeutic target for the treatment of melanoma.

Autoimmune diseases are diverse, necessitating a mechanistic understanding of the protracted disease process to improve diagnostic accuracy and therapeutic efficacy. From human and animal model studies, it has become clear that T cells are critical for autoimmune pathogenesis but the involvement of B cells is unmistakable, as evidenced by the efficacy of B cell depletion therapy in alleviating systemic and organ-specific autoimmune conditions. This paper reviews the roles that kinds of murine models have played and continue to play in developing mechanistic understanding of autoimmune diseases, with particular though not exclusive attention to B cells emphasizing their unique contributions to autoimmunity adaptive and innate mechanisms.

Lactylation is widely involved in cellular processes and is pivotal in inflammation and immune regulation. However, the expression and clinical significance of lactylation in rheumatoid arthritis (RA) remain unclear. This study aimed to determine the role of lactylation in RA and its association with immune cell infiltration. We initially detected the levels of lactate in the plasma of RA patients and the levels of panlysine lactylation (Pan-Kla) in peripheral blood mononuclear cells (PBMCs). Next, we used differential expression analysis and weighted gene coexpression network analysis (WGCNA) to intersect with lactylation-related genes. We obtained lactylation-related differentially expressed genes (LADEGs) in RA and analyzed their functional enrichment. We subsequently used the CIBERSORT algorithm to analyze immune cell infiltration in RA synovial tissues and its correlation with LADEGs. Finally, key genes of LADEGs were validated in the Pathobiology of Early Arthritis Cohort (PEAC) study and our samples. Our study revealed elevated levels of lactate and lactylation in the peripheral blood of RA patients. IKAROS family zinc finger 1 (IKZF1), lymphocyte cytosolic protein 1 (LCP1), and WASP actin-nucleation promoting factor (WAS) may be potential biomarkers for early diagnosis and assessment of disease activity in RA.

The advent of chimeric antigen receptor (CAR) T cell therapy has yielded transformative efficacy in hematological malignancies, yet its application in solid tumors remains constrained by the immunosuppressive tumor microenvironment (TME). Characterized by hypoxia, acidosis, and nutrient deprivation, the TME critically compromises CAR-T cell infiltration, persistence, and effector functions. Hypoxia-inducible factor 1α (HIF-1α), a central regulator of cellular adaptation to hypoxia within the TME, modulates T cell metabolism and functionality-presenting a strategic framework for enhancing CAR-T cell efficacy in solid malignancies. This review characterizes the role of HIF-1α in reprogramming the tumor-immune microenvironment, with specific emphasis on its metabolic regulation of T cells and translational implications for CAR-T therapy. Under hypoxic stress, HIF-1α orchestrates a metabolic shift toward glycolysis in effector T cells by suppressing oxidative phosphorylation (OXPHOS) while upregulating key glycolytic enzymes (e.g. GLUT1, HK2, LDHA). This adaptation sustains ATP production while attenuating mitochondrial reactive oxygen species (ROS) accumulation, thereby mitigating T cell exhaustion and augmenting cytotoxic persistence. This HIF-1α-mediated metabolic reprogramming provides critical insights for overcoming barriers to CAR-T cell efficacy in solid tumors.

Neuropsychiatric systemic lupus erythematosus (NPSLE) represents a significant and growing challenge in both clinical practice and research, with its mechanistic investigation hindered by the lack of reliable animal models. Over the past two decades, we have established that immunogenic self-DNA can induce SLE disease model, which has been widely utilized in the academic community. To modify the doses of immunogenic self-DNA, validate the induction of SLE disease, and systematically characterize the resulting neuropsychiatric manifestations, aiming to provide an optimal model for NPSLE. Conventional genetic background BALB/c mice were immunized with 75 µg of immunogenic self-DNA. Based on the criteria and diagnostic recommendations from the ACR and EULAR, we conducted neurobehavioral experiments to assess the neuropsychiatric manifestations of clinical NPSLE patients. Whole-cell patch-clamp electrophysiological recordings were performed on mouse brain slices to assess electroencephalographic (EEG) abnormalities associated with NPSLE. Cerebrospinal fluid (CSF) abnormalities were evaluated by measuring inflammatory factors in the CSF. Additionally, histopathological analyses were conducted to evaluate MRI abnormalities in self-DNA immunized mice. Self-DNA immunized mice developed progressive cognitive impairments, exhibiting spatial and working memory deficits from week 8 post-immunization, which worsened by week 12, alongside the emergence of anxiety-like and depression-like behaviors. In parallel, electrophysiological analysis revealed synaptic transmission deficits and reduced neuronal excitability beginning at week 8, further deteriorating by week 12. Of note, blood-brain barrier (BBB) disruption was observed at 4-8 weeks post immunization, which was evidenced by IgG leakage and FITC-dextran extravasation. Such BBB disruption was accompanied by elevated pro-inflammatory cytokines (IL-1β, IL-6, TNF-α, IL-10), resembling neuropsychiatric lupus pathology. Finally, histologically, hippocampal neuronal loss and dendritic spine reduction in CA1, CA3, and DG subregions were observed, providing structural correlates for the observed memory deficits in self-DNA immunized mice. This model induced by immunogenic self-DNA recapitulated the neurological manifestations observed in clinical patients, rendering it a robust model for the research of NPSLE.

Recent studies have implied an increased incidence of autoimmune diseases following the SARS-CoV-2 pandemic. The objective was to determine if SARS-CoV-2 infections were associated with celiac disease (CD), type 1 diabetes (T1D), and autoimmune thyroid disease (AITD) autoantibodies in a population-based screening when the pandemic hit the South of Sweden during 2021 and 2022. Between August 2021 and June 2022 self-obtained capillary plasma samples were collected from 1088 children at 6-9 years of age and 1185 adolescents at 13-16 years of age, who were randomly invited from the general population to a screening for CD, T1D, AITD, and SARS-CoV-2 antibodies. Among children and adolescents screened for autoantibodies associated with CD, T1D and AITD, the SARS-CoV-2 infection rate was increased in tissue transglutaminase autoantibody (tTGA) positive (13/17; 76.5%) compared with tTGA negative (492/1168; 42.1%) 13-16-year-old individuals ( = 0.0057). There was no association between SARS-CoV-2 infection rate and AITD- or T1D autoantibodies. Our findings indicate a potential association between prior SARS-CoV-2 infection and screening-detected CD autoimmunity in adolescents aged 13-16 years. Further research is needed to elucidate whether ongoing CD autoimmunity increases susceptibility to infection or if SARS-CoV-2 may act as a trigger for CD autoimmunity in genetically and environmentally predisposed individuals.

O-linked N-acetylglucosamine (O-GlcNAc) glycosylation represents a prevalent post-translational modification of proteins. Accumulating evidence indicates that dysregulated O-GlcNAcylation can induce glucose toxicity and plays critical roles in the pathogenesis of diabetic nephropathy (DN).

Cutaneous melanoma is a highly invasive tumor. It enhances metastasis and resistance to immunotherapy immunosuppressive mechanisms. Understanding RNA-binding proteins (RBPs) in melanoma's immune alterations is limited. This study explores immune-regulatory RBPs in metastasis and clarifies RNASE6's role in immune regulation.

Real-world studies on vaccine effectiveness may suffer from several biases, typically distorting their results. A previous article on the population of an Italian province, correcting the "immortal time bias", showed worse results for the all-cause death of the vaccinated compared to the unvaccinated. This article highlights the "case counting window bias", that considers the vaccine recipients "unvaccinated" usually for 14 days, a time interval reputed necessary to express the vaccine immune response. We aim to document this bias in an Italian region, calculating the daily death incidence for each age class of vaccinated and unvaccinated and checking their all-cause mortality difference within the considered time window. Indeed, in this window the two groups showed huge differences in all-cause deaths, that cannot be attributed only to COVID-19 deaths (in the absence of reasons to expect significant vaccine effects on non-COVID-19 deaths). In conclusion, analyzing the data of an Italian Region, we found evidence of the 'case counting window bias', which artificially increases the 'unvaccinated' mortality and reduces the mortality in the vaccinated.

The pentraxin-3 (PTX3) protein can activate and modulate complement and immune cells. IgG anti-PTX3 antibodies are suggested to protect against lupus nephritis (LN). This study aimed to evaluate anti-PTX3 IgG antibody levels across three rheumatic diseases, investigate the linear epitopes of PTX3, and identify potential clinical associations in systemic lupus erythematosus (SLE). A subsequent aim was to examine neutrophil immunoregulatory effects of selected epitopes as synthesized peptides. Microarray-based linear epitope mapping of PTX3 was performed, and neutrophils isolated from blood of healthy blood donors (HBD) to assess potential peptide-mediated effects. Anti-PTX3 levels did not differ between patients with SLE and those with other rheumatic diseases or HBD but were significantly lower in active SLE than in clinically quiescent SLE. In SLE, 17 unique PTX3 antibody epitopes were identified, and epitope-specific antibodies were associated with complement consumption, active SLE, and LN. Epitope-based synthetic peptides can inhibit the neutrophil oxidative burst. In conclusion, anti-PTX3 antibodies in SLE show substantial epitope spreading compared to healthy individuals, while their levels are significantly lower in patients with active SLE. Some of these epitopes are associated with the clinical features of SLE. As peptides, selected PTX3 epitopes might exert immunomodulatory functions on neutrophils.

Immune-mediated glomerulonephritis (IMGN) is a major cause of kidney failure worldwide, yet the precise roles of T cells in its pathogenesis remain poorly understood. However, existing studies lack a comprehensive understanding of the characteristics and functional roles of IMGN T cells in the human context. Addressing this gap is crucial for advancing targeted therapies. By integrating single-cell RNA sequencing (sc-RNA-seq) data from three primary IMGN types-IgA nephropathy (IgAN), lupus nephritis (LN), and membranous nephropathy (MN)-we identified T cell subtype alterations at single-cell resolution. Utilizing advanced sc-RNA-seq computational pipelines, we constructed gene co-expression networks (GCNs), inferred T-cell differentiation trajectories, and assessed metabolic and intercellular signaling features. IMGN kidneys presented expanded T-cell compartments, with significant enrichment of cytotoxic natural killer T (NKT) cells and ⁺ effector memory T (⁺ Tem) cells. Notably, ⁺ memory T cells (⁺ Tm) were selectively elevated in IgAN and LN patients. A coexpression module centered on RGS1 was significantly correlated with 24-h proteinuria ( < 0.001). Metabolic profiling revealed subtype-specific disruptions in the glutathione (GSH) and 3-phospho-D-glyceroyl phosphate (3PD) pathways. Interaction analysis highlighted endothelial cells, mesangial cells, and fibroblasts as key mediators of pathogenic T-cell activation via defined ligand‒receptor pairs. This study provides the first comprehensive single-cell atlas of human IMGN T cells, revealing disease-specific T-cell states, metabolic signatures, and activation mechanisms. Our findings offer new insights into human renal immunopathology and identify promising therapeutic targets for IMGN.

The prevalence of inflammatory bowel disease (IBD) has increased recently and lacks curative treatments. The involvement of the N6-methyladenosine (mA) reader YTH N6-methyladenosine RNA binding protein 1 (YTHDF1) in ulcerative colitis (UC)-like model was studied in this study. DSS was employed to induce the UC-like condition both and . TNF-α, IL-1β, IL-6, and IL-8 secretion levels were analyzed by ELISA assay. Cell vitality was determined by CCK8 assay. FOXO1 mRNA mA level was examined using methylated RNA binding protein immunoprecipitation (Me-RIP) assay. The interactions between YTHDF1 and FOXO1 were analyzed by RIP assay. ChIP and dual luciferase reporter assays were used to explore the relationship between FOXO1 and FBW7. YTHDF1, FOXO1, and FBW7 were overexpressed in DSS-induced colon epithelial cells. YTHDF1 downregulation alleviated DSS-induced inflammation and NF-κB signal activation in colon epithelial cells. Mechanically, YTHDF1 increased FOXO1 mRNA stability in an mA manner. YTHDF1 overexpression prevented the inhibition of FOXO1 knockdown on DSS-induced inflammation in colon epithelial cells. In addition, FOXO1 transcriptionally activated FBW7. Moreover, FOXO1 upregulation abolished the inhibitory effect of FBW7 knockdown on DSS-induced inflammation in colon epithelial cells. Animal experiments also showed that YTHDF1 deletion alleviated inflammatory response in UC-like mice. YTHDF1 promoted inflammatory response in the UC-like model by transcriptionally activating FBW7 through regulating mA-dependent FOXO1.

Systemic lupus erythematosus (SLE), a chronic autoimmune disease, progresses to lupus nephritis (LN) in 50-60% of patients, driving end-stage renal disease (ESRD). Identifying LN-associated cellular senescence hub genes and drug targets is critical for elucidating pathogenesis and advancing targeted therapies. Integrated transcriptomic data from LN patients (GSE61635, GSE121239;  = 441) were analyzed to identify differentially expressed genes (DEGs) using the limma package (|log2FC| > 0.5 and FDR < 0.05). Cellular senescence-associated differentially expressed genes (CS-DEGs) were further filtered through hypergeometric testing using the CellAge database. Functional enrichment analysis performed with ClusterProfiler and DOSE packages revealed significantly enriched pathways based on GO, KEGG, and GSEA terms (FDR < 0.05). A protein-protein interaction (PPI) network was constructed using STRING data and visualized in Cytoscape to prioritize hub genes. The drug-target interactions of these hub genes were subsequently validated molecular docking and dynamics simulations using CB-Dock2. A total of 1,098 DEGs (555 upregulated, 543 downregulated) were identified. Functional enrichment revealed 60 CS-DEGs significantly enriched in viral response, myeloid differentiation, and antiviral defense (FDR < 0.05). KEGG analysis highlighted their roles in lipid metabolism/atherosclerosis, NOD-like receptor signaling, and Influenza A. PPI-based topological and modular analyses prioritized CCL2, MYD88, STAT1, JUN, JAK2, and FOS as hub genes, further refined to CCL2, JUN, JAK2, and FOS ceRNA network. Drug screening identified thalidomide as a potential candidate, with strong binding affinity to all targets, particularly CCL2 (ΔG = -92.7 kcal/mol, forming three stable hydrogen bonds). This study revealed the role of CS-DEGs in viral response, immune regulation, and lipid metabolism in LN. Network analysis prioritized CCL2, JUN, JAK2, and FOS as hub genes. Thalidomide exhibited strong binding to these targets, notably CCL2 (ΔG = -92.7 kcal/mol), suggesting therapeutic potential CCL2-mediated mechanisms. These findings advance LN pathogenesis understanding and precision-targeted therapies.

Rheumatoid arthritis (RA) has been associated with an elevated risk of developing disorders related to glucose metabolism, including decreased insulin secretion, impaired glucose tolerance, and type 2 diabetes mellitus. The previse mechanisms underlying this association remain incompletely elucidated. In this study, we utilized a cohort of fifty Wistar female rats, establishing a type II collagen-induced arthritis (CIA) model ( = 30). Out observations indicated abnormal glucose and inulin levels in the CIA rats, accompanied by diminished β cell function. Additionally, we detected elevated cytokines levels and increased apoptosis within the pancreatic tissue of the CIA rats. It is hypothesized that the heightened apoptosis may be induced by cytokines, potentially leading to reduced insulin synthesis and dysregulated glucose metabolism. Through transcriptomic and proteomic analyses, we identified differential expression of genes and proteins involved in pathways that directly or indirectly regulate glycolysis in the CIA rats. Notably, we discovered novel differentially expressed enzymes implicated in the glycolysis pathway, such as hexokinase and fructose-bisphosphate aldolase, within the CIA rat model, which may serve as new markers for the diagnosis of RA or provide new perspectives to treat RA or RA-related glucose metabolism disorder.

For some of the COVID-19 vaccines, the drug substances released to market were manufactured differently than those used in clinical trials. Manufacturing nucleoside-modified mRNA (modRNA) for commercial COVID-19 vaccines relies on RNA polymerase transcription of a plasmid DNA template. Previous studies identified high levels of plasmid DNA in vials of modRNA vaccines, suggesting that the removal of residual DNA template is problematic. Therefore, we quantified the DNA load in a limited number of Pfizer-BioNTech and Moderna COVID-19 modRNA vaccine vials using two independent methods. Total DNA and specific DNA targets were quantified by Qubit fluorometry and quantitative polymerase chain reaction (qPCR), respectively on 32 vials representing 16 unique vaccine lots. RNase A treatment was used to assess the impact of RNA crosstalk in DNA fluorometry. A preliminary assessment of DNA fragment length and DNase I sensitivity were also performed. Total DNA ranged 371-1,548 ng/dose and 1,130-6,280 ng/dose in Pfizer and Moderna products, respectively. Specific DNA of multiple plasmid DNA targets ranged 0.22-7.28 ng/dose for Pfizer, and 0.01-0.78 ng/dose for Moderna. The SV40 promoter-enhancer- (0.25-23.72 ng/dose) was only detected in Pfizer vials. Oxford Nanopore sequencing of one vial found mean and maximum DNA fragment lengths of 214 bp and 3.5 kb, respectively. These data demonstrate the presence of 1.23 × 10 to 1.60 × 10 plasmid DNA fragments per dose encapsulated in lipid nanoparticles. Using fluorometry, total DNA in all vials tested exceeded the regulatory limit for residual DNA set by the US Food & Drug Administration (FDA) and the World Health Authorization (WHO) by 36-153-fold for Pfizer and 112-627-fold for Moderna after accounting for nonspecific binding to modRNA. When tested by qPCR, all Moderna vials were within the regulatory limit, but 2/6 Pfizer lots (3 vials) exceeded the regulatory limit for the SV40 promoter-enhancer- by 2-fold. The presence of the SV40 promoter-enhancer element in Pfizer vials raises significant safety concerns. This study emphasizes the importance of methodological considerations when quantifying residual plasmid DNA in modRNA products, considering increased LNP transfection efficiency, and cumulative dosing presents significant and unquantified risks to human health.

Autoimmune diseases (ADs), such as Graves' disease (GD), Hashimoto's thyroiditis (HT), psoriasis, systemic lupus erythematosus (SLE), and type 1 diabetes (T1D), involve complex immune and inflammatory responses. This study employed Mendelian randomization (MR) analysis using genome-wide association study (GWAS) data to examine the causal relationships among 91 circulating inflammatory proteins, 41 cytokines, 211 gut microbiota, and 731 immune cell traits in relation to ADs. Additionally, we integrated mediation and bioinformatics analyses, including protein-protein interaction (PPI) networks, Gene Ontology (GO) enrichment, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Subnetwork discovery and key protein identification were performed using the Molecular Complex Detection (MCODE) plugin, alongside colocalization analysis and drug target exploration to identify potential mechanisms. MR analysis identified significant causal relationships between various circulating inflammatory proteins, cytokines, gut microbiota species, immune cells, and ADs, with certain relationships retaining significance after false discovery rate (FDR) correction. Mediation analysis demonstrated that inflammatory proteins mediate pathogenic pathways linking immune cells to psoriasis and gut microbiota to Hashimoto's thyroiditis. PPI and bioinformatics analyses highlighted 22 key proteins involved in ADs, while subnetwork analysis identified 15 central proteins. Fms-related tyrosine kinase 3 ligand (FLT3LG) exhibited strong colocalization evidence. Molecular docking confirmed several proteins as viable drug targets. This comprehensive multi-omics study advances our understanding of ADs, identifies novel therapeutic targets, and offers valuable insights for developing new treatment strategies.

Cryptorchidism, a common male reproductive disorder characterized by undescended testes, is associated with infertility and increased cancer risk. While its etiology remains incompletely understood, accumulating evidence suggests that immune-inflammatory responses contribute to disease progression. This study investigated the role of carboxypeptidase N subunit 2 (CPN2) in modulating immune activation and testicular pathology via the NF-κB signaling pathway. Key regulatory genes were identified through transcriptomic analysis, weighted gene co-expression network analysis (WGCNA), and machine learning approaches. A di-n-butyl phthalate (DBP)-induced rat model of cryptorchidism and CRISPR/Cas9-mediated CPN2 knockout rats were employed, alongside histological, immunohistochemical, Western blotting, and co-culture assays to explore immune activation and spermatogonial cell fate. CPN2 was identified as a pivotal factor that suppresses NF-κB activation and plasma cell infiltration. Its overexpression alleviated inflammatory cytokine production, preserved spermatogonial stem cell proliferation, and reduced apoptosis in both in vivo and in vitro models. These effects were reversed upon NF-κB activation, confirming the regulatory role of the CPN2/NF-κB axis. Our findings reveal that CPN2 mitigates cryptorchidism progression by modulating immune-inflammatory responses, highlighting it as a promising molecular target for non-surgical intervention in this condition.

Interstitial lung disease (ILD) is a common extra-articular manifestation of rheumatoid arthritis (RA). The inflammatory response in lung disease is characterized by severe oxidative stress, which enhances cellular senescence. Telomeric shortening and mitochondria dysregulation represent two hallmarks of cellular senescence. The maintenance of telomere length (TL) and mitochondrial DNA (mtDNA) copy number is preserved by many proteins, such as TERF1 and TFAM, respectively. Our aim was to evaluate the TL, the mtDNA copy number and the expression of two regulator gene factors in RA patients with (RA-ILD) and without lung involvement (RA-NILD). Eighty-five RA patients and 21 healthy subjects were enrolled. Relative TL, mtDNA copy number, and expression analysis of and genes were measured using qPCR assay. All RA patients present a statistically significant telomere shortening; in particular, RA-ILD patients show shorter TL compared to both controls and RA-NILD. Patients with Usual Interstitial Pneumonia pattern show a more evident shortening of TL. Lastly, both RA-ILD and RA-NILD patients present a significant decrease in mtDNA copy number compared to controls. The analysis of regulatory genes showed an increase in expression in RA patients compared to controls, also after stratification in the two subgroups, and a decrease in expression in RA patients compared to controls. These results show that the alteration of TL and mtDNA copy number in RA patients is more evident in the presence of ILD. The hypothesis is that, in these patients, oxidative stress could accelerate the shortening of telomeres and the decrease of mtDNA copy number.

Systemic lupus erythematosus (SLE), characterized by immune dysregulation, urgently requires improved diagnostic tools and mechanistic insights. The role of interferon regulatory factor-1 (IRF-1) remains unclear. We integrated single-cell transcriptomes (scRNA-seq; GSE254176), 6 bulk transcriptomic datasets (1079 SLE patients, 137 controls, GSE72326 and GSE61635 were merged as training datasets, including 256 SLE patients and 50 controls), and clinical samples (70 SLE patients and 58 controls). IRF-1 dynamics in T-cell subsets were analyzed via clustering and pseudotemporal trajectory. Diagnostic genes were identified by intersecting single-cell-derived IRF-1-associated markers with SLE differential genes, followed by feature selection. Six machine learning models were trained and validated in four independent cohorts. scRNA-seq revealed significant downregulation of IRF-1 in T-cell subsets (central memory CD8⁺, Th17) during active SLE, with compensatory overexpression in remission-validated clinically. Cross-analysis identified four IRF-1-correlated diagnostic genes: CCR7, CD274, KLRB1, and NRCAM, that are enriched in MAPK signaling and immune receptor activity. Generalized linear model (GLM) and partial least squares (PLS) models achieved superior diagnostic accuracy across validation cohorts. Immune analysis revealed decreased numbers of resting CD4⁺ memory T cells and Tregs ( < 0.01), alongside expanded proinflammatory cells (M1/M2 macrophages, neutrophils;  < 0.01). IRF-1 regulates T-cell differentiation and contributes to SLE immune imbalance. The IRF-1-associated gene-based machine learning model provides a robust, noninvasive diagnostic tool.