A cross-omics data analysis strategy for metabolite-microbe pair identification.

Given the pivotal roles of metabolomics and microbiomics, numerous data mining approaches aim to uncover their intricate connections. However, the complex many-to-many associations between metabolome-microbiome profiles yield numerous statistically significant but biologically unvalidated candidates. To address these challenges, we introduce BiOFI, a strategic framework for identifying metabolome-microbiome correlation pairs (Bi-Omics). BiOFI employs a comprehensive scoring system, incorporating intergroup differences, effects on feature correlation networks, and organism abundance. Meanwhile, it establishes a built-in database of metabolite-microbe-KEGG functional pathway linking relationships. Furthermore, BiOFI can rank related feature pairs by combining importance scores and correlation strength. Validation on a dataset of cesarean-section infants confirms the strategy's validity and interpretability. The BiOFI R package is freely accessible at https://github.com/chentianlu/BiOFI.

Hyocholic acid species improve glucose homeostasis through a distinct TGR5 and FXR signaling mechanism.

Hyocholic acid (HCA) and its derivatives are found in trace amounts in human blood but constitute approximately 76% of the bile acid (BA) pool in pigs, a species known for its exceptional resistance to type 2 diabetes. Here, we show that BA depletion in pigs suppressed secretion of glucagon-like peptide-1 (GLP-1) and increased blood glucose levels. HCA administration in diabetic mouse models improved serum fasting GLP-1 secretion and glucose homeostasis to a greater extent than tauroursodeoxycholic acid. HCA upregulated GLP-1 production and secretion in enteroendocrine cells via simultaneously activating G-protein-coupled BA receptor, TGR5, and inhibiting farnesoid X receptor (FXR), a unique mechanism that is not found in other BA species. We verified the findings in TGR5 knockout, intestinal FXR activation, and GLP-1 receptor inhibition mouse models. Finally, we confirmed in a clinical cohort, that lower serum concentrations of HCA species were associated with diabetes and closely related to glycemic markers.

Identification of novel hub genes associated with lymph node metastasis of head and neck squamous cell carcinoma by completive bioinformatics analysis.

BACKGROUND: Head and neck squamous cell carcinoma (HNSCC) is one of the most serious diseases affecting populations worldwide and lymph node metastasis is a key pathological feature of HNSCC which predicts poor survival. However, the molecular mechanisms associated with the development of lymph node metastasis in HNSCC have not been fully elucidated. METHODS: Differentially expressed genes (DEGs) were identified in two HNSCC datasets (GES6631 and GES58911). Functional annotation analysis was constructed via Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. Meanwhile, the protein-protein interaction (PPI) network and module analysis using Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) and Cytoscape were carried out to identify the hub genes. The expression differences, overall survival (OS), and disease-free survival (DFS) of hub genes were analyzed by Gene Expression Profiling Interactive Analysis 2 (GEPIA2) and verified by immunohistochemistry (IHC) from Human Protein Atlas (HPA). Moreover, receiver operating characteristic (ROC) curve analysis was conducted to judge whether those hub genes had good diagnostic and prognostic ability, and the web tool Tumor Immune Estimation Resource (TIMER) was used to analyze the correlation of hub genes' expression and immune infiltration. RESULTS: In total, 913 DEGs including 476 upregulated and 437 downregulated genes were identified. The genes Aurora kinase A (AURKA), CyclinB1 (CCNB1), Cyclin-dependent kinase regulatory subunit 1B (CKS1B), Serpin Family H Member 1(SERPINH1), and Transforming growth factor-beta-induced protein (TGFBI) were screened out as hub genes and were associated with lymph node metastasis, showing notably abnormal expression in HNSCC samples, and the high expression of all the hub genes in HNSCC patients was related to worse overall survival. CONCLUSIONS: The genes AURKA, CCNB1, CKS1B, SERPINH1, and TGFBI may be involved in the lymph node metastasis of HNSCC and reveal the potential to serve as molecular biomarkers in the diagnosis of HNSCC. This study may help to elucidate the molecular mechanisms of the development of lymph node metastasis and facilitate the selection of targets for the treatment and diagnosis of HNSCC.

Rabies Virus Infection Induces Microtubule Depolymerization to Facilitate Viral RNA Synthesis by Upregulating HDAC6.

Rabies virus (RABV) is the cause of rabies, and is associated with severe neurological symptoms, high mortality rate, and a serious threat to human health. Although cellular tubulin has recently been identified to be incorporated into RABV particles, the effects of RABV infection on the microtubule cytoskeleton remain poorly understood. In this study, we show that RABV infection induces microtubule depolymerization as observed by confocal microscopy, which is closely associated with the formation of the filamentous network of the RABV M protein. Depolymerization of microtubules significantly increases viral RNA synthesis, while the polymerization of microtubules notably inhibits viral RNA synthesis and prevents the viral M protein from inducing the formation of the filamentous network. Furthermore, the histone deacetylase 6 (HDAC6) expression level progressively increases during RABV infection, and the inhibition of HDAC6 deacetylase activity significantly decreases viral RNA synthesis. In addition, the expression of viral M protein alone was found to significantly upregulate HDAC6 expression, leading to a substantial reduction in its substrate, acetylated α-tubulin, eventually resulting in microtubule depolymerization. These results demonstrate that HDAC6 plays a positive role in viral transcription and replication by inducing microtubule depolymerization during RABV infection.

Development and application of nsp5-ELISA for the detection of antibody to infectious bronchitis virus.

Infectious bronchitis virus (IBV) continues to be one of the most important poultry pathogens worldwide. The current commercially available enzyme-linked immunosorbent assay (ELISA) kits for IBV specific antibody detection are mostly based on the whole virion, and few serological tests based on nonstructural proteins of IBV have been developed. Herein, an alternative indirect ELISA for detection of IBV antibody was developed with IBV nonstructural protein 5 (nsp5) produced by Escherichia coli. Using an indirect immunofluorescence assay (IFA) and a commercial ELISA kit as reference, we optimized the nsp5-ELISA and determined its cut-off as 0.12. The diagnostic sensitivity (DSN), specificity (DSP) and accuracy of the nsp5-ELISA were 93.11%, 95.38% and 93.33%, respectively, compared with IFA in 660 field serum samples, and were 98.11%, 95.00% and 97.62%, respectively, compared with the commercial IBV ELISA kit (IDEXX) in 126 field sera samples. Furthermore, a time course of IBV specific antibody level detected by nsp5-ELISA following IBV infection and vaccination is consistent with that of IBV antibody detected by the commercial ELISA kit. The results presented in this study indicate that nsp5-ELISA has the potential to serve as a rapid, reliable and cost-effective method for IBV antibody detection. This study is the first to report the development of an nsp-based ELISA to detect an antibody to IBV.