Weighted gene coexpression network analysis and machine learning for the determination of tfh cell and B cell infiltrating biomarkers in thymoma-associated myasthenia gravis.

Patients with thymoma (THYM)-associated myasthenia gravis (MG) typically have a poor prognosis and recurring illness. This study aimed to discover important biomarkers associated with immune cell infiltration and THYM-associated MG (THYM-MG) development. Gene expression microarray data were downloaded from The Cancer Genome Atlas website (TCGA) and Gene Expression Omnibus (GEO). A total of 102 differentially expressed genes were investigated. According to the immune infiltration data, the distribution of Tfh cells, B cells, and CD4 T cells differed significantly between the THYM-MG and THYM-NMG groups. WGCNA derived 25 coexpression modules; one hub module (the blue module) strongly correlated with Tfh cells. Combining differential genes revealed 21 intersecting genes. LASSO analysis subsequently revealed 16 hub genes as potential THYM-MG biomarkers. ROC curve analysis of the predictive model revealed moderate diagnostic value. The association between the 16 hub genes and infiltrating immune cells was further evaluated in TIMER2.0 and the validation dataset. Draggability analysis identified the therapeutic target genes PTGS2 and ALB, along with significant drugs including Firocoxib, Alclofenac, Pyridostigmine, and Stavudine. This was validated through MD simulation, PCA, and MM-GBSA analyses. The interaction between numerous activated B cells and follicular helper T cells is closely associated with THYM-MG pathogenesis from a bioinformatics perspective. Hub genes (including SP6, SCUBE3, B3GNT7, and MAGEL2) may be downregulated in immune cells in THYM-MG and associated with progression.

Laboratory blood parameters and machine learning for the prognosis of esophageal squamous cell carcinoma.

Background: In contemporary study, the death of esophageal squamous cell carcinoma (ESCC) patients need precise and expedient prognostic methodologies. Objective: To develop and validate a prognostic model tailored to ESCC patients, leveraging the power of machine learning (ML) techniques and drawing insights from comprehensive datasets of laboratory-derived blood parameters. Methods: Three ML approaches, including Gradient Boosting Machine (GBM), Random Survival Forest (RSF), and the classical Cox method, were employed to develop models on a dataset of 2521 ESCC patients with 27 features. The models were evaluated by concordance index (C-index) and time receiver operating characteristics (Time ROC) curves. We used the optimal model to evaluate the correlation between features and prognosis and divide patients into low- and high-risk groups by risk stratification. Its performance was analyzed by Kaplan-Meier curve and the comparison with AJCC8 stage. We further evaluate the comprehensive effectiveness of the model in ESCC subgroup by risk score and KDE (kernel density estimation) plotting. Results: RSF's C-index (0.746) and AUC (three-year AUC 0.761, five-year AUC 0.771) had slight advantage over GBM and the classical Cox method. Subsequently, 14 features such as N stage, T stage, surgical margin, tumor length, age, Dissected LN number, MCH, Na, FIB, DBIL, CL, treatment, vascular invasion, and tumor grade were selected to build the model. Based on these, we found significant difference for survival rate between low-(3-year OS 81.8%, 5-year OS 69.8%) and high-risk (3-year OS 25.1%, 5-year OS 11.5%) patients in training set, which was also verified in test set (all P < 0.0001). Compared with the AJCC8th stage system, it showed a greater discriminative ability which is also in good agreement with its staging ability. Conclusion: We developed an ESCC prognostic model with good performance by clinical features and laboratory blood parameters.

Clinical characteristics of 15 patients with listeria meningitis in adult.

Objective: To report and analyze the clinical characteristics of 15 patients with Listeria meningitis in adult. Methods: We reviewed the medical records of 15 patients with Listeria meningitis who were admitted to Shanxi Bethune Hospital between January 2017 and January 2023. Results: The clinical manifestations was primarily characterized by fever， altered mental status, headache, neck stiffness, and vomiting. Blood or cerebrospinal fluid (CSF) cultures were performed in 15 cases, and pathogens were detected in 11 of them. Metagenomic next-generation sequencing (mNGS) detected pathogens in 10 cases, with four being negative by conventional methods and six being positive through traditional tests. The laboratory blood results presented leukocytosis. The CSF analysis upon admission showed elevated levels of white blood cells and proteins, as well as decreased chloride and glucose concentration. The brain computed tomography (CT) revealed ventricular enlargement in 3 patients. The brain magnetic resonance imaging (MRI) showed abnormalities in multiple areas of the brain. Despite 3 patients with decompensated hydrocephalus underwent lateral ventricle puncture and drainage，their neurological deterioration were increasingly deteriorating.7 patients were treated by mechanical ventilation due to respiratory insufficiency. After 3 months, there were 9 cases with excellent outcomes（modified Rankin Scale score of 0-2）,2 cases with favorable outcomes（score of 3-5）, and 4 deaths（score of 6）. Conclusions: This thesis found that the detection rate of Listeria monocytogenes has been on a rise over the past six years in our department, ranking second only to Streptococcus pneumoniae. Additionally, the detection rate achieved by mNGS surpasses that of other conventional methods. Among the patient cohort, 11 had underlying diseases such as systemic lupus erythematosus, tuberculosis, diabetes mellitus, pituitary neoplasms, leukemia and other related illnesses. Once listeriosis is early identified, the adequate antibiotic therapy should be promptly introduced in the course of empirical treatment.

Discovery and identification of the prognostic significance and potential mechanism of FMO2 in breast cancer.

BACKGROUND: Flavin containing dimethylaniline monoxygenase 2 (FMO2), is downexpressed in diverse tumors and displays vital roles in tumorigenesis. However, the prognostic value and potential mechanism of FMO2 in breast cancer remain unclear. METHODS: The expression of FMO2 was analyzed and the relationship between FMO2 expression level and clinical indicators in breast cancer was analyzed. Then the prognostic value of FMO2 in breast cancer was assessed. The FMO2-correlated genes were obtained, and the highest-ranked gene was chosen. The expression, therapeutic responder analysis, and gene set enrichment analysis of the highest-ranked gene were conducted. RESULTS: FMO2 was downregulated in breast cancer and was closely related to clinical indicators. Patients with decreased FMO2 expression showed poor overall survival, post-progression survival, relapse-free survival, and distant metastasis-free survival. FMO2 correlates with N/ER/PR subgroups in breast cancer and patients with high FMO2 levels were sensitive to anti-programmed cell death protein 1, anti-programmed death-ligand 1, and anti-cytotoxic T-lymphocyte antigen 4 immunotherapies. Mechanically, FMO2 was positively and highly correlated with secreted Frizzled-related protein 1 (SFRP1), which was downregulated in breast cancer due to hypermethylation. Moreover, SFRP1 was correlated to pathological complete response and relapse-free survival status at 5 years regardless of any chemotherapy, hormone therapy, and anti-HER2 therapy. Gene set enrichment analysis revealed enrichment of component and coagulation cascades, focal adhesion, protein export, and spliceosome. CONCLUSIONS: FMO2 was lower expressed in breast cancer than normal tissues and contributes to subtype classification and prognosis prediction with co-expressed SFRP1.

The application value of metagenomic next-generation sequencing in community-acquired purulent meningitis after antibiotic intervention.

BACKGROUND: Bacteria account for nearly one third of the causes of community-acquired central nervous system infections, and traditional diagnostic methods are based on culture results, which are time-consuming and have a low detection rate leading to delayed diagnosis and treatment. Since metagenomic next-generation sequencing (mNGS) has the advantages of high timeliness and only detecting microbial trace gene fragments, it has been used more widely in recent years. Based on this, we explored whether the application of cerebrospinal fluid (CSF) mNGS is advantageous in patients with community-acquired purulent meningitis, especially in people who have already used antibiotics. METHODS: This was a retrospective study of 63 patients with community-acquired purulent meningitis admitted to the Department of Neurology of Shanxi Bethune Hospital from March 2018 to November 2022. Data were systematically collected and classified into CSF culture group, blood culture group and CSF mNGS group according to different detection methods, and the total detection rate of each method was calculated. Each group of patients was divided into two subgroups according to whether antibiotics were used before sampling. The detection rates of the three groups were compared within and between groups to explore whether mNGS has advantages over traditional methods and the influence of antibiotic use on detection rates of the three methods. RESULTS: Among the 63 patients, the cases of CSF culture, blood culture and CSF mNGS were 56, 46, 44, respectively. The total detection rates of the three methods were 17.86%, 36.96%, 81.82%, with statistical differences (p < 0.05),suggesting that the detection rate of mNGS was higher than CSF culture (p < 0.05) and blood culture (p < 0.05),and the detection rate of blood culture higher than CSF culture (p < 0.05). Further grouping found that without antibiotics, the detection rates of CSF culture, blood culture and CSF mNGS were 28.57%, 56.25% and 88.89%, with statistical differences (p < 0.05), and the detection rate of CSF mNGS was higher than that of CSF culture (p < 0.05), but there was no statistical difference between CSF and blood culture (p > 0.05), nor between blood culture and CSF mNGS (p > 0.05). The detection rates of the three groups with antibiotics were 14.29%, 26.67% and 80.00%, with statistical differences (p < 0.05), and the detection rate of CSF mNGS was still higher than CSF culture (p < 0.05) and blood culture (p < 0.05). However, the detection rate of CSF mNGS also decreased after antibiotics were used for more than 3 days. CONCLUSIONS: The detection rate of CSF mNGS in patients with purulent meningitis is higher than traditional methods, especially in patients who have been given antibiotics, but the detection rate will decrease with the extension of antibiotic use.

Involvement of NFκB signaling in mediating the effects of GRK5 on neural stem cells.

Nuclear factor κB (NFκB) signaling plays ubiquitous roles in inflammation, immune response and neurogenesis. G protein-coupled receptor kinase 5 (GRK5) can protect neurons from degeneration. GRK5 also mediates tumor necrosis factor-α (TNFα)-induced NFκB signaling through the phosphorylation of IκBα. Here, we show that NFκB signaling is involved in neural stem cell (NSC) differentiation. The IκBα/p65 pathway was activated by phorbol myristate acetate (PMA), a stimulator of protein kinase C (PKC). Once the NFκB was activated, the initial stage of neural differentiation was induced, with an increased level of GRK5 in NSCs. This finding was reversed in response to the NFκB inhibitor N-acetyl cysteine (NAC). To evaluate the effect of GRK5-NFκB signaling crosstalk on NSC neurogenesis and apoptosis, GRK5 was knocked down by siRNAs in cell culture. SiRNAs against GRK5 not only impaired neural differentiation and axogenesis, but also induced apoptosis of NSC. GRK5 knockdown affected the transcription of NFκB, phosphorylation of the liver kinase B1 (LKB1) and the activity of caspase 3, thereby modulated neurogenesis and apoptosis. Taken together, our findings reveal a novel function of GRK5 in neurogenesis and provide insight into the molecular mechanisms underlying neurodevelopmental disorders and neurodegenerative diseases.

GRK5 dysfunction accelerates tau hyperphosphorylation in APP (swe) mice through impaired cholinergic activity.

Recent studies have suggested that G-protein-coupled receptor kinase 5 (GRK5) deficiency plays a significant role in the pathogenesis of early Alzheimer's disease. Mild soluble ß-amyloid accumulation can result in reduced membrane (functional) and elevated cytosolic levels of GRK5. Dysfunction of GRK5 impairs the desensitization of presynaptic muscarinic 2 (M2) autoreceptors, which results in presynaptic M2 hyperactivity and inhibits acetylcholine (ACh) release. GRK dysfunction also promotes a deleterious cycle that further increases ß-amyloid accumulation and exaggerates tau hyperphosphorylation in the hippocampus. However, the pathogenic effect of GRK5 dysfunction through targeting tau hyperphosphorylation remains unclear. Here we examined not only the reduced membrane (functional) and elevated cytosolic levels of GRK5 but also the increased levels of hyperphosphorylated tau in the hippocampi of aged APP(swe) mice (11 months of age). Moreover, western blotting analyses revealed the changes in the location of activity of both protein kinase C (PKC) and glycogen synthase kinase3ß (GSK3ß) in the hippocampus of aged APP(swe) mice in which GRK5 translocation occurred. Moreover, treatment with methoctramine, a selective M2 antagonist, partially corrected the difference between wild-type control mice and GRK5-dysfunctional APP (swe) mice in hippocampal ACh release, PKC and GSK3ß activities, as well as tau hyperphosphorylation. In contrast, the GSK3ß inhibitor lithium chloride significantly reduced tau hyperphosphorylation in GRK5-defective APP (swe) mice, but failed to enhance PKC activity and ACh release in the hippocampi of GRK5-defective APP (swe) mice. Taken together, these findings indicate that GRK5 dysfunction accelerated tau hyperphosphorylation in APP(swe) mice by activating GSK3ß through impaired cholinergic activity.