搜索结果：Genes & diseases

Analyzing the network properties of cancer biomarkers within protein-protein interaction (PPI) networks is valuable for discovering novel biomarker candidates. Therefore, we constructed PPI networks using breast cancer (BC)-associated gene sets and performed 12 distinct centrality analyses to characterize the topological features of clinically validated biomarkers. Our reference set of biomarkers comprised genes from five clinical genetic testing panels-MammaPrint, Oncotype DX, PAM50, EndoPredict, and the BC Index-that were also present in the STRING database. The PPI networks were constructed from the top 2,000 BC-associated genes, ranked by disease score from the DISEASES database. These networks were then subjected to centrality analysis using five local and seven global measures. The top 5% centrality rankings were evaluated, demonstrating that maximum clique centrality (MCC) identified the highest proportion of known biomarkers, with an inclusion rate of approximately 36%. Furthermore, MCC generated a unique biomarker-ranking pattern, exhibiting a Spearman's rank correlation coefficient below 0.8 when compared with all other metrics. Consequently, a high MCC score is a key topological feature of many validated biomarkers. Genes with the highest MCC scores (top 5%) were significantly enriched for gene-ontology terms related to the cell cycle and fibroblast growth factor receptor signaling pathway. Additionally, biomarkers with high MCC scores exhibited significantly greater evolutionary conservation and potential for protein complex formation. Collectively, our findings indicate that many effective BC biomarkers are components of large, evolutionarily conserved cliques within cell-cycle-associated regions of the PPI network. Finally, based on this MCC-centric approach, we identified 11 novel candidate biomarkers.

The cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) pathway and inflammasomes were long regarded as distinct innate immune modules that respond to different classes of danger signals. However, accumulating evidence now reveals extensive, bidirectional crosstalk between these pathways, forming an integrated regulatory network that critically shapes the magnitude, quality, and outcome of immune responses. The balance of this network determines whether the host mounts effective pathogen control and tumor immunosurveillance, or instead succumbs to excessive inflammation, tissue injury, or autoimmune pathology. In this review, we synthesize current mechanistic understanding of STING-inflammasome interactions, highlighting how shared upstream triggers - particularly cytosolic DNA - coordinate the activation, amplification, or restraint of these pathways. We further examine how this axis exerts context-dependent, dualistic functions across diverse disease settings, including cancer, autoimmunity, neurodegeneration, chronic infection, and aging. From a pharmacological perspective, we discuss emerging therapeutic strategies aimed at modulating key regulatory nodes within this signaling network, ranging from STING agonists for cancer immunotherapy to selective STING or the NLR family pyrin domain-containing 3 (NLRP3) inhibitors for autoimmune and inflammatory diseases. Together, these insights provide a conceptual and translational foundation for the rational development of next-generation immunomodulatory agents targeting the STING-inflammasome axis. cGAS-STING and inflammasomes converge into a unified immunoregulatory axis.This axis exerts dual roles in anti-tumor immunity and chronic inflammatory pathologies.STING agonists reprogram “cold” tumors but risk inducing T-cell exhaustion.Dysregulated STING-inflammasome crosstalk fuels autoimmunity, neurodegeneration, and cardiovascular diseases.Therapeutic strategies require balancing STING agonists for oncology and inhibitors for inflammation.

Hashimoto's thyroiditis (HT) is a common disease characterized by autoimmune injury of the thyroid. Its pathogenesis entails complex interactions among hereditary predisposition, immune disorders and environmental factors. In recent years, viral infection has attracted much attention as a potential environmental trigger, but the role genes associated with HT remain unclear. In this study, COVID-19-related genes were combined with transcriptome data (GSE29315, GSE138198) of HT patients in the GEO database. Key genes were selected using machine learning (LASSO, SVM, and RF), GO/KEGG enrichment, and GSEA. Its function was confirmed by single-cell sequencing and ssGSEA immunoinfiltration analysis. A total of 16 co-expressed genes of HT and viral infection were identified. KEGG and GO enrichment results showed that these genes were significantly enriched in inflammatory signaling, viral defense and immune cell activation pathways. After screening by machine learning algorithm, four key genes (IFITM3, IFI44L, CCL3, OAS1) were finally identified as the common diagnostic markers of HT and viral infection, and the ROC curve also showed good diagnostic performance. In addition, single cell sequencing further confirmed its high expression in thyroid tissue and immune infiltrating cells. A virus-triggered autoimmune cascade involving IFITM3, IFI44L, CCL3, and OAS1 may precipitate HT. These four genes constitute robust, multi-omics biomarkers for early diagnosis and targeted therapy of HT following viral infection.

Over the past decade, clonal hematopoiesis (CH) has gained substantial attention as a prevalent, age-associated phenomenon with major implications for hematologic malignancy, cardiovascular disease, and mortality. CH arises from the clonal expansion of hematopoietic stem cells and progenitor cells harboring somatic mutations, most commonly in genes implicated in leukemia. Beyond chronological aging, CH evolution is shaped by lifelong exposure to inflammatory, metabolic, and environmental stressors, such as smoking and obesity. More recently, cancer therapies-particularly cytotoxic treatments-have been shown to significantly increase the risk of CH. Therapy-related CH, however, exhibits a distinct mutational spectrum, frequently involving genes in the DNA damage response pathway, reflecting the selective pressure exerted by cytotoxic exposure. Current evidence largely supports that cytotoxic therapies primarily drive the expansion of preexisting mutant clones rather than inducing de novo mutations. The increased recognition of therapy-related CH has prompted growing interest in its prognostic and therapeutic implications in patients with cancer. To date, data regarding the prognostic impact of CH in cancer are conflicting, but the presence of CH generally portends worse overall survival, especially among patients with hematologic malignancies. Moreover, cancer survivors with CH appear to be at a heightened risk of cardiovascular disease, which may be further exacerbated by exposure to cardiotoxic cancer therapies. Collectively, these findings underscore the growing clinical relevance of CH and highlight its potential implications for precision medicine and survivorship care in oncology.

The root-knot nematode Meloidogyne incognita is a globally significant plant parasite that causes substantial crop losses. While pre-parasitic juveniles rely on innate energy reserves, later life stages acquire nutrients from host plants through specialized feeding structures. SWEET (Sugars Will Eventually be Exported Transporter) genes exhibit a conserved sugar transporting ability across all kingdoms of life, yet their function in plant-parasitic nematodes remains underexplored. Here, we functionally characterise the SWEET gene family in M. incognita, revealing their critical and stage-specific roles in nematode development and parasitism. We demonstrate that Mi-SWEETs segregate into two functional groups: those that facilitate mobility and invasion in motile juveniles (Mi-SWEET2, 4) and those support nutrient uptake during feeding (Mi-SWEET3, 5, 7). Although temporally distinct, all SWEET genes localise to the intestine, suggesting a conserved role in mediating sugar flux. Knockdown of Mi-SWEET2 and Mi-SWEET4 reduced root invasion, while silencing Mi-SWEET3, 5, and 7 impaired post-invasion growth, highlighting the varied roles of this large gene family across different life stages. Yeast complementation assays revealed distinct substrate preferences among Mi-SWEETs, aligning with the metabolic needs of different life stages. The transcription factor HBL1, a key regulator of nematode dietary responses, was found to control the expression of Mi-SWEET3 and is itself regulated through interaction with the post-transcriptional regulatory microRNA let-7. Our findings provide new insights into the metabolic adaptations and energy utilisation of plant-parasitic nematodes and outline a microRNA - transcription factor - target gene regulatory network. These findings have broader relevance given the fundamental importance of the regulation of resource transportation in plant-pathogen interactions.

Alzheimer's disease (AD) is a neurodegenerative disorder characterised by cognitive decline. Peripheral immune dysregulation often precedes central immune abnormalities and may therefore provide valuable clues for the early diagnosis and stratification of AD. Current research on peripheral immunity in AD remains limited. This study provides new insights into the pathogenesis and therapeutic strategies for AD. Bioinformatics and single-cell RNA sequencing were used to analyse peripheral immune-related gene expression in AD. Key genes and immune cell populations linked to AD were identified. Quercetin (Que) was selected as a potential therapeutic agent using drug prediction methods. Molecular docking, Western blotting (WB), and qRT-PCR were further performed to preliminarily assess the regulation of these hub genes by quercetin in an H2O2-induced HT22 neuronal oxidative stress model. Several immune-related genes, including ACTB, TP53, HIF1A, and BCL-2, were differentially expressed in AD. Gene function analysis revealed their involvement in processes like apoptosis and viral response. Pathway enrichment analysis highlighted the significance of the p53, apoptosis, and HIF-1 signaling pathways in AD. Single-cell sequencing identified key immune cell populations, such as CD4 + memory cells and NK cells. Drug prediction and experimental results indicated that quercetin may modulate these genes in a neuronal stress context, providing preliminary experimental support for its regulatory effects on AD-related hub genes. This study identified peripheral immune-related molecular features of AD and highlighted several hub genes that may represent shared molecular nodes linking peripheral immune alterations and central neuronal stress responses. The in vitro findings provide preliminary support for the regulatory effects of quercetin on these AD-related hub genes, although further validation in peripheral immune cell and in vivo models is still required.

Metabolic dysfunction-associated steatotic liver disease (MASLD) is the most prevalent chronic liver disease, ranging from simple steatosis (MASL) to metabolic dysfunction-associated steatohepatitis (MASH). However, reliable noninvasive strategies for accurately distinguishing MASL from MASH at an early stage remain limited. We therefore aimed to develop a robust molecular model to improve early identification of disease progression and subtype discrimination. Five datasets from the Gene Expression Omnibus were integrated as a training cohort comprising 149 MASL and 158 MASH samples, while another dataset GSE135251 served as validation cohort including 51 MASL and 155 MASH samples. Differential expression analysis and weighted gene co expression network analysis were conducted to identify gene modules. Overlapping genes were subjected to protein interaction network construction and topological ranking. Least absolute shrinkage and selection operator regression, support vector machine recursive feature elimination, and random forest algorithms were jointly applied to derive robust diagnostic candidates. An artificial neural network classifier was established based on the final gene set and evaluated in both cohorts. Immune cell composition was estimated using CIBERSORT. Single cell RNA sequencing data from GSE136103 were analyzed to determine cell type specific expression patterns. Quantitative real time PCR validation was conducted in 60 clinical liver tissue samples. A total of 656 differentially expressed genes were identified between MASL and MASH. Network integration and machine learning intersection analysis consistently yielded six key genes: MMP9, FABP5, TREM2, CTSD, UBD, and MAP2K1. Five genes were upregulated in MASH, whereas MAP2K1 was downregulated. Individual genes demonstrated moderate diagnostic performance, with area under the curve values ranging from 0.692 to 0.822 in the training cohort. The artificial neural network model achieved an area under the curve of 0.893 (95% CI 0.854 to 0.925) in the validation cohort. Immune infiltration analysis revealed increased monocytes, M0 and M1 macrophages, and activated dendritic cells in MASH. Single cell analysis localized key genes predominantly to myeloid populations, and quantitative PCR confirmed consistent differential expression in clinical samples. This study establishes a multicohort machine learning-based gene signature with high diagnostic accuracy for distinguishing MASL from MASH and provides insight into immune metabolic mechanisms underlying disease progression.

Diabetic cardiomyopathy (DCM) occurs in the context of coronary artery disease or pressure overload heart disease, characterized by alterations in cardiac structure and function. The mechanisms linking metabolic memory and METTL1-mediated modifications to DCM progression remain unclear. This study integrated multiple public transcriptome datasets to conduct a systematic analysis of gene expression profiles associated with diabetic cardiomyopathy. Potential key characteristic genes were identified through differential expression analysis and machine learning techniques. Their associated biological processes and signaling pathways were assessed using functional enrichment analysis. Additionally, single-cell RNA sequencing data were employed to examine the expression and distribution of key genes across various cardiac cell types, while gene set enrichment analysis (GSEA) was utilized to explore their potential functional networks. The integration of three public transcriptome datasets and subsequent differential expression analysis identified 159 genes associated with diabetic cardiomyopathy, of which 133 were upregulated and 26 downregulated. These differentially expressed genes (DEGs) effectively distinguished between DCM and control samples. Machine learning analyses, including LASSO regression and random forest, identified several key candidate genes, with METTL1 showing a significant association with inflammation, fibrosis, and metabolic disorders. In multiple independent datasets, METTL1 expression was markedly elevated in DCM samples and demonstrated substantial diagnostic potential (ROC AUC = 0.826). Functional enrichment analysis revealed that METTL1-related genes predominantly participated in pathways related to white blood cell migration, inflammatory activation, and extracellular matrix remodeling. Single-cell RNA sequencing further indicated that METTL1 was primarily enriched in the fibroblast population. The proportion of METTL1-positive fibroblasts in DCM samples was significantly increased and was associated with inflammatory and fibrosis-related signaling pathways. A comprehensive analysis suggests that METTL1 may play a role in the pathological progression of DCM by regulating fibroblast activation, amplifying inflammation, and contributing to myocardial remodeling. This study elucidates the expression characteristics of METTL1 and its potential regulatory functions in diabetic cardiomyopathy. The findings suggest that METTL1 metabolic memory may be influenced by RNA modifications occurring in the context of persistent inflammation and fibrosis.

Primary open-angle glaucoma (POAG) is a progressive optic neuropathy that leads to irreversible vision loss, primarily due to dysfunction of the trabecular meshwork (TM). Although impaired autophagy has been implicated in POAG pathogenesis, its molecular drivers remain poorly defined. This study systematically investigated autophagy-related genes (ATGs) in TM tissue from POAG patients. Transcriptomic datasets (GSE4316 and GSE27276) were analyzed to identify differentially expressed genes (DEGs). A curated list of autophagy-related genes (ATGs) from HADb and GeneCards was intersected with DEGs to identify differentially expressed ATGs (DEATGs). Functional analyses included Gene Ontology (GO) and KEGG pathway enrichment, protein-protein interaction (PPI) network construction, hub gene identification, immune cell infiltration profiling via single-sample gene set enrichment analysis (ssGSEA), and molecular docking to evaluate predicted interactions between latanoprost and hub proteins. A total of 990 DEGs were identified, including 15 DEATGs. Among these, S100A8 and S100A9 emerged as hub genes, exhibiting strong functional similarity and central roles within the PPI network. Enrichment analysis revealed significant involvement in autophagy regulation, tyrosine metabolism, and oxidative phosphorylation. Notably, molecular docking predicted high-affinity binding between latanoprost and S100A9. Immune profiling demonstrated significant alterations in both innate and adaptive immune cell populations, including a strong positive correlation between S100A9 expression and Th2 cell abundance. These findings suggest that S100A9 may act as a central regulator linking autophagy deficiency to immune dysregulation in POAG. Its predicted interaction with latanoprost highlights a potential molecular mechanism for pharmacologic modulation of TM homeostasis, supporting the therapeutic value of targeting S100A9-mediated autophagy-immune crosstalk in intraocular pressure control.

Fibroblasts are critical for stabilizing skeletal muscle and facilitating wound healing after injury but become overactivated and lead to fibrotic replacement of muscle tissue in chronic degenerative diseases such as Duchenne muscular dystrophy (DMD). We have previously shown that the mineralocorticoid receptor (MR) is present in skeletal muscle and MR antagonist drugs reduce fibrosis and chronic inflammation in dystrophic mouse models. Indirect MR signaling from other cell types in the muscle microenvironment affects fibroblast gene expression and function. However, the direct effects of MR activation of skeletal muscle fibroblasts are unknown. To determine whether direct stimulation with the endogenous MR agonist aldosterone changes gene expression in skeletal muscle fibroblasts, we performed RNA sequencing comparing fibroblasts isolated from neonatal wild-type skeletal muscles treated with aldosterone or vehicle. To further investigate the effects of aldosterone treatment of fibroblasts in skeletal muscle health and disease, we then performed in vitro proliferation and migration assays on fibroblasts isolated from neonatal and adult wild-type and dystrophic muscles. Treatment with aldosterone leads to differential expression of 492 genes in fibroblasts isolated from neonatal wild-type mouse muscles. Protein levels of differentially expressed genes Fkbp5, p57 and c-Fos were also increased by direct aldosterone stimulation of fibroblasts from both wild-type and dystrophic muscles. Surprisingly, cultured fibroblasts from both neonatal wild-type and dystrophic muscles retain a higher proliferation rate compared to adult muscle fibroblasts. Direct aldosterone treatment represses proliferation and slows scratch-wound closure kinetics only in fibroblasts isolated from adult dystrophic skeletal muscle. This study shows that aldosterone treatment of skeletal muscle fibroblasts alters gene expression. However, fibroblasts from adult dystrophic muscle appear most sensitive to gene expression changes after short-term aldosterone treatment. These data suggest that MR signaling in the skeletal muscle microenvironment may differentially affect fibroblasts in wound healing and in chronic fibrotic diseases such as muscular dystrophies.

Calcific aortic valve disease (CAVD) is a prevalent cardiovascular disorder characterized by calcium deposition in the aortic valve, associated with high morbidity and mortality. Mechanical stress plays a key role in its pathogenesis, highlighting the importance of identifying mechanosensitive ion channel-related genes (MICRGs). In this study, transcriptome data from GSE83453 of patients with CAVD and healthy controls were analyzed to identify differentially expressed genes (DEGs). Weighted gene co-expression network analysis (WGCNA) and MICRGs were used to pinpoint key genes. The intersection of DEGs, WGCNA modules, and MICRGs identified CACNA1H as a candidate gene. External validation with GSE51472 and GSE55492 confirmed these findings. Both in vitro and in vivo studies confirmed that CACNA1H inhibition alleviates CAVD progression by repressing the osteogenic response. Mechanistically, CACNA1H inhibition attenuated phosphorylation of P65, a key regulator of the NF-κB pathway. These results suggest that CACNA1H may serve as a promising biomarker and therapeutic target for CAVD.

This study aimed to phenotypically and genotypically detect beta-lactam-resistant Escherichia coli in the feces of wild and migratory birds residing in or passing through the Marmara Region during seasonal migration. A total of 272 fresh fecal samples were non-invasively collected and grouped as follows: (1) resident wild waterfowl, (2) resident urban birds (e.g., pigeons, crows, sparrows), (3) migratory birds overwintering in Turkey, and (4) migratory birds staying during spring and summer. Samples were cultured on MacConkey agar with and without cefotaxime (1&#xa0;mg/L). Carbapenem resistance was assessed using the Modified Hodge Test; none of the 212 isolates tested positive. Among the 272 birds sampled, 62 (22.8%) carried ESBL and/or AmpC producing isolates. Antimicrobial-resistant E. coli were identified in 59 of 272 birds (21.7%), including 47 ESBL-positive, 6 AmpC-positive, and 5 harboring both resistance types. Group 1 (mainly gulls) showed the highest resistance rates. PCR analysis revealed that among 84 isolates, 48 carried only beta-lactamase genes, 3 only AmpC genes, and 5 both. Detected genes included: blaCTX-M (n&#x2009;=&#x2009;50), blaSHV (n&#x2009;=&#x2009;2), and blaOXA10 (n&#x2009;=&#x2009;10); for AmpC: blaMOX (n&#x2009;=&#x2009;6) and blaCIT (n&#x2009;=&#x2009;2). Species-specific results confirmed the highest frequency of resistance genes in gulls. The Frequency of resistant isolates was significantly higher in Groups 1 and 2 (P&#x2009;<&#x2009;0.001). The resistance profiles identified in gulls especially those feeding at landfills or in direct contact with human, animal, and agricultural waste suggest a likely anthropogenic and/or zoonotic origin of the beta lactam resistance observed in this study conducted in Marmara Region.

The pulmonary vasculature develops in close association with the airways and this network expands through the interactions between endothelial cells and the surrounding mesenchymal cells, the pericytes. Emerging evidence suggests that pericytes play a significant role in various lung diseases, such as congenital diaphragmatic hernia and chronic obstructive pulmonary disease. However, characterizing pericytes remains challenging, impeding our understanding of their exact role in lung development and disease. Therefore, we used a novel cell tracing technology based on a bacterial DNA cytosine methyltransferase (Dcm) fused to RNA polymerase II (DCM-TM) to methylate active genes. The doxycycline inducible Dcm-PolII fusion protein was activated at specific time points during gestation, while the epigenetically labeled genes were analyzed at later time points. This retrospective cell tracing was coupled to single-cell RNA sequencing to track the development of mouse pulmonary pericytes at the single cell level. This revealed the paths to differentiation of perivascular progenitors into pericytes and vascular smooth muscle cells. Temporal analysis uncovered dynamic gene expression profiles during pericyte differentiation, highlighting pathways crucial for pulmonary vascular development. Further analysis showed intricate signaling interactions between pericyte progenitors and mature pericytes, and we validated MCAM as a bona fide pulmonary pericyte marker. Our findings challenge conventional views on pericyte origin and underscore the importance of accurate pericyte identification in developmental and disease contexts. Overall, this study enhances our understanding of pulmonary pericyte ontogeny and differentiation, offering insights into their potential as therapeutic targets in pericyte-associated lung diseases.

Metabolic dysfunction-associated steatotic liver disease (MASLD) is an important inducer of hepatocellular carcinoma (HCC). MicroRNAs are key regulators of tumorigenesis. Among these, miR-26a-5p is known to be associated with liver pathogenesis, yet its role in linking MASLD progression to HCC development remains incompletely understood. Hepatic miR-26a-5p expression was quantified in the C57BL/6 mice with a 3-month high-carbohydrate diet (HCD). Public transcriptomic datasets with MASLD and HCC samples were analyzed to identify predicted miR-26a-5p downstream candidates upregulated in the above-mentioned diseases. Associations with tumor features were examined, and protein expression of &#x3b2;-catenin, c-MYC and EpCAM were evaluated after miR-26a-5p modulation. Integrative bioinformatics identified miR-26a-5p as a candidate prognostic indicator for metabolic liver disease progression. In vivo, results confirmed that suppressed miR-26a-5p expression is a hallmark of diet-induced metabolic perturbation. Mechanistically, in vitro modulation of miR-26a-5p attenuated oncogenic signaling via the &#x3b2;-catenin/c-Myc/EpCAM axis, establishing its role as a tumor suppressor. Notably, in silico analysis of HCC tissues revealed that high miR-26a-5p levels correlate with enhanced antitumor immunity. Leveraging these insights, we constructed a transcriptional signature from miR-26a-5p downstream candidates and MASLD-HCC differentially expressed genes. This signature effectively stratifies MASLDpatients, discriminating molecular risk groups associated with progression to HCC. Integrating transcriptomic, clinical and experimental data suggests the role of miR-26a-5p, along with the MASLD-HCC gene signature (EpCAM, DTNA, and KPNA2), may serve as an early molecular indicator and mechanistic modulator of hepatocarcinogenesis, warranting further functional investigation.

Osteoarthritis (OA) arises from impaired epigenetic coordination of inflammatory and metabolic cues, leading to compromised cartilage homeostasis. Such coordination is partly governed by ribonucleic acid (RNA) epigenetic mechanisms, however, the role of the predominant RNA modification N6-methyladenosine (m6A) in this process remains unclear. Herein, we identify an epigenetic-metabolic pathway in which Wilms' Tumor 1-Associating Protein (WTAP)-mediated m6A modification stabilizes low-density lipoprotein receptor-related protein 1 (LRP1) and redirects lipid metabolism toward chondrogenesis. Loss-of-function assays demonstrate that WTAP is required for the chondrogenic differentiation of BMSCs, as its depletion suppresses the expression of multiple cartilage-associated genes. Mechanistically, WTAP enhances m6A methylation and stabilizes Lrp1 transcripts, a key regulator of cholesterol metabolism and matrix synthesis, thereby driving lipid metabolic reprogramming toward chondrogenesis. Structure-based screening identified silibinin and estradiol benzoate as LRP1-specific agonists that activate the WTAP-LRP1 pathway to promote cartilage repair in vivo. Collectively, our findings establish m6A-dependent metabolic reprogramming as a pivotal epigenetic mechanism of cartilage regeneration with therapeutic potential for promoting chondrogenesis.

The "Golden Hour" is the period immediately after trauma, stroke or a cardiac event when rapid intervention is critical to reducing morbidity and mortality. The same principle should also apply to infectious diseases. Rapid, sensitive detection of infectious agents, enabling targeted interventions, has the potential to reduce mortality, morbidity, and costs of infectious diseases, and to decrease the inappropriate use of antibiotics that drives the evolution of antimicrobial resistance (AMR). Probes were designed to represent the MetaPhlAn4 database covering 894 known or potential pathogenic bacterial species, 16S rRNA sequences from the SILVA database comprising 1,325 potentially pathogenic bacterial species, genes in the Virulence Factor Database and antimicrobial resistance determinants in the Comprehensive Antibiotic Resistance Database. Target sequences were tiled with 120 nucleotide probes distributed at 60 nt intervals and clustered at 99% sequence identity. Performance measures included limits of detection (LOD) and assay reproducibility in plasma and urine using contrived and clinical samples. Analytical validation using 20 bacterial strains in contrived plasma and urine samples confirmed an LOD of 5 colony-forming units per milliliter and detection of mixed infections. Results obtained with urine and blood cultures were concordant with Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI), and Blood Culture Identification (BCID) assays. BCS2.0 enables sensitive detection of bacterial species and AMR genes and has the potential to expedite rapid, efficient infectious disease management.

Vaccinia virus (VACV) and monkeypox virus (MPXV) are closely related members of the family Poxviridae, genus Orthopoxvirus, both capable of causing systemic infections with potential neurological complications. Although live, replication-competent VACV strains were historically used in smallpox vaccination, their clinical use was associated with rare but severe central nervous system (CNS)-related adverse events. Despite this, the mechanisms underlying VACV-induced CNS pathology, particularly olfactory dysfunction, remain poorly characterized. In this study, we found VACV-VR1354, a tissue culture-adapted derivative of the neurovirulent Western Reserve strain, can invade the CNS via the olfactory route and induce olfactory impairment. By using an intranasal infection model in two inbred mouse strains-C57BL/6N and BALB/c, we demonstrate that VACV-VR1354 efficiently disseminates from the nasal mucosa to the brain, as evidenced by a spatiotemporal gradient of viral DNA load (nasal mucosa > olfactory bulb > cerebrum > cerebellum). Evans blue extravasation assays indicated a transient increase in blood-brain barrier (BBB) permeability in the olfactory bulb, peaking at 7 days post-infection (dpi) and resolving by 14 dpi, with more pronounced effects in C57BL/6N mice. Neuroinvasion was accompanied by robust microglial and astrocytic activation, as well as injury to mature olfactory sensory neurons, particularly at 7 dpi. Transcriptomic profiling of the olfactory bulb revealed significant downregulation of olfactory receptor (OR) genes, with the downregulated genes significantly enriched in olfactory transduction pathways. Concurrently, strong upregulation of proinflammatory cytokines, chemokines, and interferon-stimulated genes (ISGs) was detected in the olfactory bulb tissue, indicative of intense neuroinflammation. Behaviorally, infected C57BL/6N mice exhibited impaired aversion to camphor odor between 14 and 49 dpi, with full functional recovery observed by 56 dpi. Collectively, our findings showed that intranasal infection of mice with VACV-VR1354 leads to a transient increase BBB permeability, neuroinflammation, and reversible olfactory/chemosensory impairment. This murine model recapitulates key features of post-viral olfactory loss and establishes a valuable platform for mechanistic studies of orthopoxvirus neuropathogenesis and therapeutic evaluation of interventions targeting viral neuroinvasion and sensory recovery.

Skin-homing cutaneous lymphocyte-associated antigen (CLA)-expressing T cells play a key role in the pathogenesis of atopic dermatitis (AD) and psoriasis (Ps). We aimed to characterize the transcriptomic and epigenetic profiles of circulating CD4+CLA+ and CD4+ na&#xef;ve T cells from patients with AD and Ps to find shared and unique molecular signatures associated with the diseases. Circulating CD4+CLA+ and CD4+ na&#xef;ve T cells were sorted from the peripheral blood mononuclear cells of patients with AD (n = 11), those with Ps (n&#xa0;=&#xa0;10), and healthy individuals (n = 11), followed by assay for transposase-accessible chromatin sequencing (ATAC-seq) and mRNA sequencing and data analyses. Transcriptomic and epigenetic landscapes differed markedly between CD4+CLA+ and CD4+ na&#xef;ve T cells. In both AD and Ps, transcriptomic alterations within these cell populations were substantial, whereas changes in chromatin accessibility were relatively modest. In CLA+ T cells, patients with AD and Ps exhibited altered expression of genes involved in T-cell activation, cell cycle, and JAK-STAT signaling. These effects were more pronounced in AD, while a stronger association with innate immune activation was seen in Ps. Notably, CD4+ na&#xef;ve T cells also exhibited disease-associated transcriptomic changes in both AD and Ps, including alterations in the JAK-STAT pathway and changes in the expression of IL-2 receptor components. Epigenetic profiling further revealed disease-associated chromatin regions linked to transcription factors involved in immune regulation. Both CD4+CLA+ and CD4+ na&#xef;ve T cells exhibit transcriptomic and epigenetic alterations in AD and Ps, suggesting the influence of the chronic inflammatory milieu leading to shared and disease-specific changes, including transcriptomic rewiring of the JAK-STAT pathway in both diseases.

Understanding the pathogenesis of paratuberculosis (PTB), caused by Mycobacterium avium subspecies paratuberculosis (MAP), is essential in the management of this economically important disease. MAP strains are known to differ genotypically, which could contribute to differences in strain virulence and disease outcomes. The behaviour of MAP inside the host and the mechanisms utilized by MAP to overcome the host defence system are not entirely understood. This study aimed at evaluating the potential virulence of different MAP isolates from cattle in Uganda. This was achieved by analysing the cytokine expression profiles of RAW 264.7 macrophages when infected with four different MAP isolates: MAP1, MAP2, MAP3 and MAP4. Specific real-time PCR was used to determine the expression of different cytokines, probable virulence genes of MAP as well as MAP quantities inside the macrophages at different time points (3&#xa0;h, 24&#xa0;h, 48&#xa0;h) post-infection (pi). There were considerable variations in the cytokine expressions among macrophages infected with the different MAP isolates. The expression of IL-6 in macrophages infected with MAP1 at 48&#xa0;h pi was noticeably high compared to the other isolates; and this is a known strategy for MAP survival inside macrophages. The regulation of the probable virulence genes: kdpC, katG, papA2, impA, umaA1, and the anti-apoptotic (BCL-2) gene also varied considerably among the isolates. Isolates MAP1, MAP2 and MAP3 demonstrated higher virulent behaviour regarding intracellular replication and survival compared to MAP4 isolate. The behaviour of these MAP isolates clearly indicates variations in virulence and further research needs to focus on how this can be exploited in the design of PTB diagnostic and control strategies.