Comprehensive Analysis of Sphingolipid Metabolism-Related Genes in Osteoarthritic Diagnosis and Synovial Immune Dysregulation.

BACKGROUND Osteoarthritis (OA) is a chronic degenerative disease characterized by synovitis and has been implicated in sphingolipid metabolism disorder. However, the role of sphingolipid metabolism pathway (SMP)-related genes in the occurrence of OA and synovial immune dysregulation remains unclear. MATERIAL AND METHODS In this study, we obtained synovium-related databases from GEO (n=40 for both healthy controls and OA) and analyzed the expression levels of SMP-related genes. Using 2 algorithms, we identified hub genes and developed a diagnostic model incorporating these hub genes to predict the occurrence of OA. Subsequently, the hub genes were further validated in peripheral blood samples from OA patients. Additionally, CIBERSORT and MCP-counter analyses were employed to explore the correlation between hub genes and immune dysregulation in OA synovium. WGCNA was used to determine enriched modules in different clusters. RESULTS Overall, the expression levels of SMP genes were upregulated in OA synovium. We identified 6 hub genes of SMP and constructed an excellent diagnostic model (AUC=0.976). The expression of re-confirmed hub genes showed associations with immune-related cell infiltration and levels of inflammatory cytokines. Furthermore, we observed heterogeneity in the expression patterns of hub genes across different clusters of OA. Notably, older patients displayed increased susceptibility to elevated levels of pain-related inflammatory cytokines and infiltration of immune cells. CONCLUSIONS The SMP-related hub genes have the potential to serve as diagnostic markers for OA patients. Moreover, the 4 hub genes of SMP demonstrate wide participation in immune dysregulation in OA synovium. The activation of different pathways is observed among different populations of patients with OA.

Comprehensive analysis of arachidonic acid metabolism-related genes in diagnosis and synovial immune in osteoarthritis: based on bulk and single-cell RNA sequencing data.

BACKGROUND: Osteoarthritis (OA) is one of degenerative-related arthritis, which can be aggravated by low-grade synovitis. It is known that arachidonic acid (AA) dysmetabolism brings OA synovitis. However, the impact of synovial AA metabolism pathway (AMP) related genes on OA remains uncovered. METHODS: Here, we conducted a comprehensive analysis to explore the impact of AA metabolism genes in OA synovium. We obtained transcriptome expression profiles from three raw datasets related to OA synovium (GSE12021, GSE29746, GSE55235) and identified the hub genes of AA metabolism pathways (AMP) in OA synovium. An OA occurrence diagnostic model was constructed and validated based on the identified hub genes. Then, we explored the correlation between hub gene expression and the immune-related module using CIBERSORT and MCP-counter analysis. The unsupervised consensus clustering analysis and weighted correlation network analysis (WGCNA) were utilized to identify robust clusters of identified genes in each cohort. Moreover, the interaction between the hub genes of AMP and immune cells was elucidated through single-cell RNA (scRNA) analysis by scRNA sequencing data from GSE152815. RESULTS: We found that the expression of AMP-related genes was up-regulated in OA synovium, and seven hub genes (LTC4S, PTGS2, PTGS1, MAPKAPK2, CBR1, PTGDS, and CYP2U1) were identified. The diagnostic model that combined the identified hub genes showed great clinical validity in diagnosing OA (AUC = 0.979). Moreover, significant associations were noticed between the hub genes' expression, immune cell infiltration, and inflammatory cytokine levels. The 30 OA patients were randomized and clustered into three groups using WGCNA analysis based on the hub genes, and diverse immune status was found in different clusters. Of interest, older patients were more likely to be classified into a cluster with higher levels of inflammatory cytokines IL-6 and less infiltration of immune cells. Based on the scRNA-sequencing data, we found that the hub genes had relatively higher expression in macrophages and B cells than other immune cells. Moreover, inflammation-related pathways were significantly enriched in macrophages. CONCLUSION: These results suggest that AMP-related genes are closely involved in alterations of OA synovial inflammation. The transcriptional level of hub genes could serve as a potential diagnostic marker for OA.

Correlation of preoperative CT imaging shift parameters of the lateral plateau with lateral meniscal injury in Schatzker IV-C tibial plateau fractures.

BACKGROUND: Schatzker IV-C is a high-energy tibial plateau fracture often accompanied by lateral meniscus injuries. While imaging examinations are routine preoperative measurements, the correlation between CT imaging shift parameters of the lateral plateau and lateral meniscal injury in Schatzker IV-C fractures remains uncovered. METHODS: This retrospective study enrolled a total of 60 patients with Schatzker IV-C tibial plateau fractures at the First People's Hospital of Hefei. Prior to surgery, CT imaging was used to measure the numerical values of lateral plateau depression (LPD) and lateral plateau widening (LPW). The degree of lateral meniscus injury was confirmed based on intraoperative direct vision, with patients being classified into meniscus injury and non-meniscus injury groups. Dichotomous logistic regression was employed to evaluate the correlation between LPD, LPW, and lateral meniscus injury, while the optimal cut-off points for predicting lateral meniscal injury with LPD and LPW were determined using receiver operator characteristic (ROC) curves. RESULTS: The meniscus injury group exhibited a mean LPD of 15.3 ± 3.5 mm, which was significantly higher than the non-meniscus injury group's mean LPD of 8.4 ± 3.4 mm (P < 0.05). Similarly, the meniscus injury group had a larger mean LPW of 9.4 ± 1.8 mm compared to the non-meniscus injury group's mean LPW of 6.9 ± 0.9 mm (P < 0.05). The optimal cut-off points for predicting lateral meniscal injury were determined to be 8.40 mm for LPD (with a sensitivity of 95%, specificity of 85%, and AUC of 0.898) and 7.90 mm for LPW (with a sensitivity of 75%, specificity of 90%, and AUC of 0.897). CONCLUSIONS: Patients with Schatzker IV-C tibial plateau fractures are at a significantly higher risk of lateral meniscal injury when the LPD exceeds 8.40 mm and/or the LPW exceeds 7.90 mm. Our results may provide novel reference metrics for the early diagnosis of lateral meniscal injury in Schatzker IV-C tibial plateau fracture patients when the MRI examination is not available.

Using Baidu search values to monitor and predict the confirmed cases of COVID-19 in China: - evidence from Baidu index.

BACKGROUND: New coronavirus disease 2019 (COVID-19) has posed a severe threat to human life and caused a global pandemic. The current research aimed to explore whether the search-engine query patterns could serve as a potential tool for monitoring the outbreak of COVID-19. METHODS: We collected the number of COVID-19 confirmed cases between January 11, 2020, and April 22, 2020, from the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University (JHU). The search index values of the most common symptoms of COVID-19 (e.g., fever, cough, fatigue) were retrieved from the Baidu Index. Spearman's correlation analysis was used to analyze the association between the Baidu index values for each COVID-19-related symptom and the number of confirmed cases. Regional distributions among 34 provinces/ regions in China were also analyzed. RESULTS: Daily growth of confirmed cases and Baidu index values for each COVID-19-related symptom presented robust positive correlations during the outbreak (fever: rs=0.705, p=9.623× 10- 6; cough: rs=0.592, p=4.485× 10- 4; fatigue: rs=0.629, p=1.494× 10- 4; sputum production: rs=0.648, p=8.206× 10- 5; shortness of breath: rs=0.656, p=6.182× 10-5). The average search-to-confirmed interval (STCI) was 19.8 days in China. The daily Baidu Index value's optimal time lags were the 4 days for cough, 2 days for fatigue, 3 days for sputum production, 1 day for shortness of breath, and 0 days for fever. CONCLUSION: The searches of COVID-19-related symptoms on the Baidu search engine were significantly correlated to the number of confirmed cases. Since the Baidu search engine could reflect the public's attention to the pandemic and the regional epidemics of viruses, relevant departments need to pay more attention to areas with high searches of COVID-19-related symptoms and take precautionary measures to prevent these potentially infected persons from further spreading.

Proteomic and lipidomic landscape of the infrapatellar fat pad and its clinical significance in knee osteoarthritis.

Osteoarthritis (OA) is a prevalent joint disease that can be exacerbated by lipid metabolism disorders. The intra-articular fat pad (IFP) has emerged as an active participant in the pathological changes of knee OA (KOA). However, the proteomic and lipidomic differences between IFP tissues from KOA and control individuals remain unclear. Samples of IFP were collected from individuals with and without OA (n = 6, n = 6). Subsequently, these samples underwent liquid chromatography/mass spectrometry-based label-free quantitative proteomic and lipidomic analysis to identify differentially expressed proteins (DEPs) and lipid metabolites (DELMs). The DEPs were further subjected to enrichment analysis, and hub DEPs were identified using multiple algorithms. Additionally, an OA diagnostic model was constructed based on the identified hub DEPs or DELMs. Furthermore, CIBERSORT was utilized to investigate the correlation between hub protein expression and immune-related modules in IFP of OA. Our results revealed the presence of 315 DEPs and eight DELMs in IFP of OA patients compared to the control group. Enrichment analysis of DEPs highlighted potential alterations in pathways related to coagulation, complement, fatty acid metabolism, and adipogenesis. The diagnostic model incorporating four hub DEPs (AUC = 0.861) or eight DELMs (AUC = 0.917) exhibited excellent clinical validity for diagnosing OA. Furthermore, the hub DEPs were found to be associated with immune dysfunction in IFP of OA. This study presents a distinct proteomic and lipidomic landscape of IFP between individuals with OA and those without. These findings provide valuable insights into the molecular changes associated with potential mechanisms underlying OA.

Bioinformatics Analysis Identified Five Widely Expressed Genes Associated with Prognosis in Sarcoma.

Background: Human sarcomas (SARC) are a group of malignant tumors that originated from mesenchymal lineages with more than 60 subtypes. However, potential biomarkers for the diagnosis and prognosis of SARC remain to be investigated. Methods: We obtained three GSE raw matrix files (GSE39262, GSE21122, GSE48418) that related to various subtypes of sarcoma from the public GEO database and explored the widely differential expression genes in three obtained GSE files. Then common differential expression genes (CDGEs) were identified. We analyzed the correlation between the expression of the top five interacted genes of CDEGs and genome-wide differences, prognosis, genetic mutation, functional enrichment, immune infiltration, immune checkpoint, and marker genes' expression of N6-methyladenosine (m6A) modification in SARC patients. Besides, a prognostic nomogram was constructed to predict the survival of SARC patients. Results: Among the three GSE files, 42 CDGEs were identified, and the top five interacted genes were ASPM, CCNB2, PRC1, AURKA, and SCM2. The expression levels of the five genes were higher in the SARC group than that in the normal group. The transcriptional level of CCNB2, PRC, and SCM2 was correlated to the worse survival of SARC. The constructed nomogram that combined CNB2, PRC1, and SCM2 showed a fairly good incredibility in predicting the survival of SARC (C-index: 0.711). Furthermore, the five genes were widely involved in immune infiltration, immune checkpoint, and m6A modification. In addition, we found a minor survival-related mutation rate (9%) of the five identified genes in SARC patients (p < 0.05). Conclusion: The results suggested the five identified genes widely participated in the prognosis, immune infiltration, immune checkpoint, and m6A modification of SARC patients. This study provided a theoretical basis for the research about the correlation between the level of five identified genes and sarcoma, but the further mechanism needs to be verified by experiments.

Bone marrow mesenchymal stem cells-derived exosomes suppress miRNA-5189-3p to increase fibroblast-like synoviocyte apoptosis via the BATF2/JAK2/STAT3 signaling pathway.

Ankylosing spondylitis (AS) is characterized by inflammation of the sacroiliac joint and the attachment point of the spine. Herein, we aimed to investigate the effect of bone marrow mesenchymal stem cells (BMSCs)-derived exosomes on apoptosis of fibroblast-like synoviocytes (FLSs) and explored its molecular mechanism. Exosomes were isolated from BMSCs and verified by transmission electron microscope and nanoparticle tracking analysis. FLSs were isolated and co-incubated with BMSC exosomes. Cell apoptosis was assessed using terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling analysis and flow cytometry. The results showed that BMSC exosomes increased apoptosis of FLSs. MiR-5189-3p was downregulated, while basic leucine zipper transcription factor ATF-like 2 (BATF2) was upregulated in FLSs by treatment of BMSC exosomes. As a direct target of miR-5189-3p, BATF2 inactivates the JAK2/STAT3 pathway. MiR-5189-3p suppressed apoptosis of FLSs and BATF2 exerted an opposite effect. In conclusion, BMSCs-derived exosomes suppress miR-5189-3p to facilitate the apoptosis of FLSs via the BATF2/JAK2/STAT3 signaling pathway, which facilitates the understanding of the therapeutic effect of BMSCs on AS and the underlying molecular mechanism.

Prognostic Values of COL4As Transcriptional Expressions in Clear Cell Renal Cell Carcinoma Patients.

OBJECTIVE: The COL4A family genes (COL4As) are a set of extracellular matrix-related genes that have been proved a tight relationship among various cancers. However, the functional role of different COL4As (COL4A1/2/3/4/5/6) in clear cell renal cell carcinoma (ccRCC) is unclear. METHODS: We obtained the data from online open-access databases including ONCOMINE, UALCAN, GEPIA, Cancer Genome Atlas (TCGA), cBioPortal, METASCAPE, STRING, TIMER, GSCALite, MEXPRESS, and TISIDB to explore the correlation between COL4As expression and genome-wide difference, progression, prognosis, genetic mutation, functional enrichment, tumor immune microenvironment, and methylation in ccRCC patients. RESULTS: The significantly higher COL4A1/2 expression and lower COL4A3/4/5/6 expression were observed in ccRCC tissues than in normal kidney tissues. Transcriptomic levels of COL4A1/2/3/4 were significantly correlated with tumor grade and stage. The higher expression levels of COL4A1/2/3/4 were accompanied by a longer overall survival time (OS); the higher expression levels of COL4A3/4 with lower expression levels of COL4A5 were associated with a longer disease-free time (DFS). Univariate/multivariate regression model analysis showed that COL4A4 could be a potential independent biomarker for ccRCC prognosis. And a high mutation rate (29%) of COL4As was observed in ccRCC patients. However, there were no relationships between mutation rates of COL4As and OS, DFS in ccRCC patients (p>0.05). Besides, we founded that the COL4As expressions were significant associated with the infiltration of the immune cells, tumor-infiltrating lymphocytes, three immunomodulators (immunoinhibitory, immunostimulator, MHC molecule), chemokines, and receptors. CONCLUSION: The results suggested that the transcript levels of COL4As could act as potential indicators for early disease progression. The expression of COL4A4 could contribute directly to disease prognosis. Besides, COL4A1/2/3/4 widely participated in tumor immunity. However, further studies are needed to confirm their clinical values in the ccRCC patients.

Multimolecular characteristics of cell-death related hub genes in human cancers: a comprehensive pan-cancer analysis.

Failure of the normal process of cell death pathways contributes to the defection of immune systems and the occurrence of cancers. The key genes, the multimolecular mechanisms, and the immune functions of these genes in pan-cancers remain unclear. Using online databases of The Cancer Genome Atlas, GEPIA2, TISIDB, HPA, Kaplan-Meier Plotter, PrognoScan, cBioPortal, GSCALite, TIMER, and Sangerbox, we identified the key genes from the six primary cell death-related pathways and performed a comprehensive analysis to investigate the multimolecular characteristics and immunological functions of the hub genes in 33 human cancers. We identified five hub genes in the six primary cell death-related pathways (JUN, NFKB1, CASP3, PARP1, and TP53). We found that CASP3, PARP1, and TP53 were overexpressed in 28, 23, and 27 cancers. The expression of the five genes was associated with the development and prognosis of many cancers. Particularly, JUN, NFKB1, CASP3, and TP53 have prognostic values in Brain Lower Grade Glioma (LGG), while PARP1 and CASP3 could predict the survival outcomes in Adrenocortical carcinoma (ACC). In addition, an extensive association between five genes' expression, DNA methylation, and tumor-immune system interactions was noticed. The five cell death-related hub genes could function as potential biomarkers for various cancers, particularly LGG and ACC. The immunological function analysis of the five genes also proposes new targets for developing immunosuppressants and improving the immunotherapy efficacy of cancers. However, further extensive clinical and experimental research are required to validate their clinical values.

Prognostic Values of E2F1/2 Transcriptional Expressions in Chromophobe Renal Cell Carcinoma Patients: Evidence from Bioinformatics Analysis.

BACKGROUND: Numerous studies on the E2F transcription factors have led to increasing insights that E2Fs could be an important driver of the formation and progression of many human cancers. Little is known about the function of distinct E2Fs in chromophobe renal cell carcinoma (chRCC). METHODS: We utilized the UALCAN, GEPIA, Cancer Genome Atlas (TCGA) database, cBioPortal, Metascape, STRING, Cytoscape, GeneMANIA, TIMER, TISIDB, GSCALite, and MEXPRESS databases to investigate the transcription level, genetic alteration, methylation, and biological function of E2Fs in chRCC patients, and its association with the occurrence, progress, prognosis, and immune cell infiltration in patients with chRCC. RESULTS: We found that E2F1/2/4/7/8 were more expressed in chRCC tissues than in normal tissues, while the expression of E2F5/6 was lower in the former than in the latter, and the expression levels of E2F1/2/4/5/6//7/8 were also associated with the histological parameters of chRCC, including T-stage and N-stage. Higher expression of E2F1/2/7/8 was found to be significantly correlated with worse overall survival (OS) in chRCC patients. Cox regression and time-dependent ROC analysis further suggested that E2F1/2 could be the potential independent biomarkers for chRCC prognosis. Besides, a moderate mutation rate of E2Fs (34%) was noticed in chRCC, and the genetic mutations in E2Fs were associated with poor survival of chRCC patients. We noticed that the expression of E2Fs was statistically correlated with the immune cell infiltration in chRCC. Moreover, we also found that the expression of E2F1 was significantly correlated with tumor-infiltrating lymphocytes and immunomodulators, E2F7 expression was associated with MHC molecules, and the expression of E2F1/8 was correlated to their methylation levels. CONCLUSION: Our results provide novel insights for selecting the prognostic biomarkers for chRCC and suggest that E2F1/2 could act as potential prognostic biomarkers for the survival of chRCC patients. However, more in-depth experiments are required to identify the underlying mechanisms and verify the clinical value of E2F1/2 in the prognosis of chRCC.