Development and validation of a coagulation-related genes prognostic model for hepatocellular carcinoma.

BACKGROUND: Hepatocellular carcinoma (HCC) has a high incidence and mortality worldwide, which seriously threatens people's physical and mental health. Coagulation is closely related to the occurrence and development of HCC. Whether coagulation-related genes (CRGs) can be used as prognostic markers for HCC remains to be investigated. METHODS: Firstly, we identified differentially expressed coagulation-related genes of HCC and control samples in the datasets GSE54236, GSE102079, TCGA-LIHC, and Genecards database. Then, univariate Cox regression analysis, LASSO regression analysis, and multivariate Cox regression analysis were used to determine the key CRGs and establish the coagulation-related risk score (CRRS) prognostic model in the TCGA-LIHC dataset. The predictive capability of the CRRS model was evaluated by Kaplan-Meier survival analysis and ROC analysis. External validation was performed in the ICGC-LIRI-JP dataset. Besides, combining risk score and age, gender, grade, and stage, a nomogram was constructed to quantify the survival probability. We further analyzed the correlation between risk score and functional enrichment, pathway, and tumor immune microenvironment. RESULTS: We identified 5 key CRGs (FLVCR1, CENPE, LCAT, CYP2C9, and NQO1) and constructed the CRRS prognostic model. The overall survival (OS) of the high-risk group was shorter than that of the low-risk group. The AUC values for 1 -, 3 -, and 5-year OS in the TCGA dataset were 0.769, 0.691, and 0.674, respectively. The Cox analysis showed that CRRS was an independent prognostic factor for HCC. A nomogram established with risk score, age, gender, grade, and stage, has a better prognostic value for HCC patients. In the high-risk group, CD4+T cells memory resting, NK cells activated, and B cells naive were significantly lower. The expression levels of immune checkpoint genes in the high-risk group were generally higher than that in the low-risk group. CONCLUSIONS: The CRRS model has reliable predictive value for the prognosis of HCC patients.

Immunological analysis and differential genes screening of venous thromboembolism.

PURPOSE: To explore the pathogenesis of venous thromboembolism (VTE) and provide bioinformatics basis for the prevention and treatment of VTE. METHODS: The R software was used to obtain the gene expression profile data of GSE19151, combining with the CIBERSORT database, obtain immune cells and differentially expressed genes (DEGs) of blood samples of VTE patients and normal control, and analyze DEGs for GO analysis and KEGG pathway enrichment analysis. Then, the protein-protein interaction (PPI) network was constructed by using the STRING database, the key genes (hub genes) and immune differential genes were screened by Cytoscape software, and the transcription factors (TFs) regulating hub genes and immune differential genes were analyzed by the NetworkAnalyst database. RESULTS: Compared with the normal group, monocytes and resting mast cells were significantly expressed in the VTE group, while regulatory T cells were significantly lower. Ribosomes were closely related to the occurrence of VTE. 10 hub genes and immune differential genes were highly expressed in VTE. MYC, SOX2, XRN2, E2F1, SPI1, CREM and CREB1 can regulate the expressions of hub genes and immune differential genes. CONCLUSIONS: Ribosomal protein family genes are most relevant to the occurrence and development of VTE, and the immune differential genes may be the key molecules of VTE, which provides new ideas for further explore the pathogenesis of VTE.

Comparison of ischemic stroke diagnosis models based on machine learning.

Background: The incidence, prevalence, and mortality of ischemic stroke (IS) continue to rise, resulting in a serious global disease burden. The prediction models have a great value in the early prediction and diagnosis of IS. Methods: The R software was used to screen the differentially expressed genes (DEGs) of IS and control samples in the datasets GSE16561, GSE58294, and GSE37587 and analyze DEGs for enrichment analysis. The feature genes of IS were obtained by several machine learning algorithms, including the least absolute shrinkage and selector operation (LASSO) logistic regression, the support vector machine-recursive feature elimination (SVM-RFE), and the Random Forest (RF). The IS diagnostic models were constructed based on transcriptomics by machine learning and artificial neural network (ANN). Results: A total of 69 DEGs, mainly involved in immune and inflammatory responses, were identified. The pathways enriched in the IS group were complement and coagulation cascades, lysosome, PPAR signaling pathway, regulation of autophagy, and toll-like receptor signaling pathway. The feature genes selected by LASSO, SVM-RFE, and RF were 17, 10, and 12, respectively. The area under the curve (AUC) of the LASSO model in the training dataset, GSE22255, and GSE195442 was 0.969, 0.890, and 1.000. The AUC of the SVM-RFE model was 0.957, 0.805, and 1.000, respectively. The AUC of the RF model was 0.947, 0.935, and 1.000, respectively. The models have good sensitivity, specificity, and accuracy. The AUC of the LASSO+ANN, SVM-RFE+ANN, and RF+ANN models was 1.000, 0.995, and 0.997, respectively, in the training dataset. However, the AUC of LASSO+ANN, SVM-RFE+ANN, and RF+ANN models was 0.688, 0.605, and 0.619, respectively, in the GSE22255 dataset. The AUC of the LASSO+ANN and RF+ANN models was 0.740 and 0.630, respectively, in the GSE195442 dataset. In the training dataset, the sensitivity, specificity, and accuracy of the LASSO+ANN model were 1.000, 1.000, and 1.000, respectively; of the SVM-RFE+ANN model were 0.946, 0.982, and 0.964, respectively; and of the RF+ANN model were 0.964, 1.000, and 0.982, respectively. In the test datasets, the sensitivity was very satisfactory; however, the specificity and accuracy were not good. Conclusion: The LASSO, SVM-RFE, and RF models have good prediction abilities. However, the ANN model is efficient at classifying positive samples and is unsuitable at classifying negative samples.

Sex Difference of Ribosome in Stroke-Induced Peripheral Immunosuppression by Integrated Bioinformatics Analysis.

Ischemic stroke (IS) greatly threatens human health resulting in high mortality and substantial loss of function. Recent studies have shown that the outcome of IS has sex specific, but its mechanism is still unclear. This study is aimed at identifying the sexually dimorphic to peripheral immune response in IS progression, predicting potential prognostic biomarkers that can lead to sex-specific outcome, and revealing potential treatment targets. Gene expression dataset GSE37587, including 68 peripheral whole blood samples which were collected within 24 hours from known onset of symptom and again at 24-48 hours after onset (20 women and 14 men), was downloaded from the Gene Expression Omnibus (GEO) datasets. First, using Bioconductor R package, two kinds of differentially expressed genes (DEGs) (nonsex-specific- and sex-specific-DEGs) were screened by follow-up (24-48 hours) vs. baseline (24 hours). 30 nonsex-specific DEGs (1 upregulated and 29 downregulated), 79 female-specific DEGs (25 upregulated and 54 downregulated), and none of male-specific DEGs were obtained finally. Second, bioinformatics analysis of female-specific DEGs was performed. Gene Ontology (GO) functional annotation analysis shows that DEGs were mainly enriched in translational initiation, cytosolic ribosome, and structural constituent of ribosome. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis shows that the top 6 enrichment pathways are ribosome, nuclear factor--kappa B (NF-kappa B) signaling pathway, apoptosis, mineral absorption, nonalcoholic fatty liver disease, and pertussis. Three functional modules were clustered in the protein-protein interaction (PPI) network of DEGs. The top 10 key genes of the PPI network constructed were selected, including RPS14, RPS15A, RPS24, FAU, RPL27, RPL31, RPL34, RPL35A, RSL24D1, and EEF1B2. Sex difference of ribosome in stroke-induced peripheral immunosuppression may be the potential mechanism of sex disparities in outcome after IS, and women are more likely to have stroke-induced immunosuppression. RPS14, RPS15A, RPS24, FAU, RPL27, RPL31, RPL34, RPL35A, RSL24D1, and EEF1B2 may be novel prognostic biomarkers and potential therapeutic targets for IS.

BACE1 gene silencing alleviates isoflurane anesthesia­induced postoperative cognitive dysfunction in immature rats by activating the PI3K/Akt signaling pathway.

Postoperative cognitive dysfunction (POCD) is a severe complication characterized by cognitive dysfunction following anesthesia and surgery. The aim of the present study was to investigate the effects of ß­site amyloid precursor protein cleavage enzyme 1 (BACE1) gene silencing on isoflurane anesthesia­induced POCD in immature rats via the phosphatidylinositol­3­kinase (PI3K)/protein kinase B (Akt) signaling pathway. Rat models were established and then transfected with BACE1 small interfering RNA and wortmannin (an inhibitor of PI3K). Blood gas analysis was performed, and a series of behavioral experiments were conducted to evaluate the cognitive function, learning ability and locomotor activity of rats. Reverse transcription quantitative polymerase chain reaction and western blot analysis were employed to determine the mRNA and protein expression of the associated genes. An ELISA was used to detect the inflammatory indicators and the content of amyloid precursor protein (APP) and amyloid­ß (Aß). Apoptosis of the hippocampal CA1 region was observed by terminal deoxynucleotidyl transferase dUTP nick­end labeling staining. Initially, it was revealed that the percentage of stagnation time in rats was increased by BACE1 gene silencing; the escape latency and swimming distance were markedly reduced from the 4th to the 6th day, the time the rats spent in first passing the target area was shortened, and the times of passing the target area were increased by BACE1 gene silencing, demonstrating that BACE1 gene silencing enhanced the spatial memory ability of rats. Additionally, it was determined that silencing BACE1 improved the pathological state induced by isoflurane anesthesia in immature rats, and attenuated the inflammatory response and the levels of APP and Aß in hippocampal tissues. Furthermore, it was suggested that silencing BACE1 may have promoted the activation of the PI3K/Akt signaling pathway, thereby inhibiting the apoptosis of the hippocampal CA1 region. Taken together, these results indicated that BACE1 gene silencing may improve isoflurane anesthesia­induced POCD in immature rats by activating the PI3K/Akt signaling pathway and inhibiting the Aß generated by APP.

Relationship between UGT1A9 gene polymorphisms, efficacy, and safety of propofol in induced abortions amongst Chinese population: a population-based study.

The present study aimed to investigate the influence of UGT1A9 gene polymorphisms on the efficacy of propofol in patients undergoing the painless induced abortion method. A total of 156 women seeking voluntary pregnancy termination procedures were selected for the study, and subsequently underwent painless induced abortions, following anesthesia by means of propofol administration. PCR-restriction fragment length polymorphism (PCR-RFLP) was performed to detect the polymorphisms of UGT1A9 gene at -440C/T, -1818C/T, and -1887T/G loci. The time, effect-site concentration, and bispectral index (BIS) for the Observer's Assessment of Alertness/Sedation (OAA/S) (up to 4 points) were observed and recorded in patients following discontinuation of propofol. The time and effect-site concentration for BIS reaching 80 in patients following the discontinuation of propofol were observed and recorded. Postoperative observations of adverse reactions, such as nausea, vomiting, and respiratory depression were all made record of. In comparison with patients with UGT1A9 -440C/T CT and TT, those with UGT1A9 -440C/T CC displayed shorter durations of OAA/S by up to 4 points, shorter BIS times reaching 80, as well as higher corresponding effect-site concentrations. No significant differences were detected in the patients with -440C/T, -1818T/C, and -1887T/G in incidence of nausea, vomiting, and respiratory depression. The findings of the study highlighted correlation between UGT1A9 -440C/T gene polymorphisms and positive propofol efficacy in patients undergoing painless induced pregnancy termination procedures.