TBX3 deficiency accelerates apoptosis in cardiomyoblasts through regulation of P21 expression

Weighted gene co-expression identification of CDKN1A as a hub inflammation gene following cardiopulmonary bypass in children with congenital heart disease

Background

Congenital heart disease (CHD) is the most common type of birth defect. Most patients with CHD require surgery, and cardiopulmonary bypass (CPB) is the most common surgery performed.

Methods

The present study utilized weighted gene co-expression network analysis (WGCNA) to identify key inflammation genes after CPB for CHD. The GSE132176 dataset was downloaded from the Gene Expression Omnibus(GEO) database for WGCNA to identify the modules closely related to clinical traits. Disease enrichment, functional annotation and pathway enrichment were performed on genes in the module closely related to clinical traits using Enrichr and Metascape. Immune infiltration analysis was also performed on the training dataset using CIBERSORT. Finally, we identified hub genes using high gene significance (GS), high module members (MMs) and Cytoscape, and we verified the hub genes using an independent dataset and Western blot analysis.

Results

WGCNA showed that the brown module with 461 genes had the highest correlation to CHD after CPB. Functional annotation and pathway enrichment analysis were performed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, which showed that genes in the brown module were enriched in inflammation-related pathways. In the disease enrichment analysis, genes in the brown module were enriched for inflammatory diseases. After the 30 most highly associated brown intramodular genes were screened, a protein-protein interaction network was constructed using the STRING online analysis website. The protein-protein interaction results were then calculated using 12 algorithms in the cytoHubba plugin of Cytoscape software. The final result showed that CDKN1A was the fundamental gene of post-CPB for CHD. Using another independent validation dataset (GSE12486), we confirmed that CDKN1A was significantly differentially expressed between preoperative and postoperative CPB (Wilcoxon, P = 0.0079; T-test, P = 0.006). In addition, CDKN1A expression was elevated in eosinophils, neutrophils, memory CD4 T cells and activated mast cells. Western blot analysis showed that the expression of CDKN1A protein was significantly higher postoperative CPB than preoperative CPB. Moreover, CDKN1A was mainly related to inflammation.

Conclusion

In summary, we found a relationship between CDKN1A and inflammation after CPB for congenital heart disease by WGCNA, experiments and various bioinformatics methods. Thus, CDKN1A maybe serve as a biomarker or therapeutic target for accurate diagnosis and treatment of inflammation after CPB in the future.

Platelet-rich plasma inhibits inflammation, apoptosis, and the NLRP3/Caspase-1 pathway and induces matrix metalloproteinases and proliferation of IL-1β-induced articular chondrocytes by downregulating T-box transcription factor 3

Objectives

Osteoarthritis (OA) is a chronic joint disease characterized by osteoproliferation and the degeneration and destruction of articular cartilage. Platelet-rich plasma (PRP) is rich in various growth factors that have been reported to promote bone defect repair. This study examined the specific role and mechanism of PRP in OA.

Methods

OA model cells were created by treating articular chondrocytes with IL-1β. After treatment of the model cells with PRP or/and a T-box transcription factor 3 (TBX3)-overexpression plasmid, TBX3 expression was monitored via RT-qPCR, western blotting, and immunofluorescence assays. IL-1β, IL-33, and Caspase-3 levels were detected with ELISA kits. Levels of NLRP3, Caspase-1, MMP9, MMP13, and COL2A1 expression were evaluated by western blotting, and cell proliferation was assessed by the CCK-8 assay.

Results

Our results showed that TBX3 expression was upregulated in IL-1β-induced articular chondrocytes. IL-1β stimulation induced inflammation and the production of matrix metalloproteinases, activated Caspase-3 and the NLRP3/Caspase-1 pathway, inhibited the proliferation of articular chondrocytes; however, all those affects mediated by IL-1β could be markedly reversed by PRP. We also found that PRP alleviated IL-1β-induced inflammation, apoptosis, and extracellular matrix degradation in articular chondrocytes by inhibiting TBX3. Our findings suggest that PRP alleviates OA progression in vitro by downregulating TBX3.

Conclusion

PRP suppressed OA progression in vitro by inhibiting TBX3, which may be its mechanism of action in treating OA.

Analysis of potential regulatory LncRNAs and CircRNAs in the oxidative myofiber and glycolytic myofiber of chickens

SART and PMM are mainly composed of oxidative myofibers and glycolytic myofibers, respectively, and myofiber types profoundly influence postnatal muscle growth and meat quality. SART and PMM are composed of lncRNAs and circRNAs that participate in myofiber type regulation. To elucidate the regulatory mechanism of myofiber type, lncRNA and circRNA sequencing was used to systematically compare the transcriptomes of the SART and PMM of Chinese female Qingyuan partridge chickens at their marketing age. The luminance value (L*), redness value (a*), average diameter, cross-sectional area, and density difference between the PMM and SART were significant (p < 0.05). ATPase staining results showed that PMMs were all darkly stained and belonged to the glycolytic type, and the proportion of oxidative myofibers in SART was 81.7%. A total of 5 420 lncRNAs were identified, of which 365 were differentially expressed in the SART compared with the PMM (p < 0.05). The cis-regulatory analysis identified target genes that were enriched for specific GO terms and KEGG pathways (p < 0.05), including striated muscle cell differentiation, regulation of cell proliferation, regulation of muscle cell differentiation, myoblast differentiation, regulation of myoblast differentiation, and MAPK signaling pathway. Pathways and coexpression network analyses suggested that XR_003077811.1, XR_003072304.1, XR_001465942.2, XR_001465741.2, XR_001470487.1, XR_003077673.1 and XR_003074785.1 played important roles in regulating oxidative myofibers by TBX3, QKI, MYBPC1, CALM2, and PPARGC1A expression. A total of 10 487 circRNAs were identified, of which 305 circRNAs were differentially expressed in the SART compared with the PMM (p < 0.05). Functional enrichment analysis showed that differentially expressed circRNAs were involved in host gene expression and were enriched in the AMPK, calcium signaling pathway, FoxO signaling pathway, p53 signaling pathway, and cellular senescence. Novel_circ_004282 and novel_circ_002121 played important roles in regulating oxidative myofibers by PPP3CA and NFATC1 expression. Using lncRNA-miRNA/circRNA-miRNA integrated analysis, we identified many candidate interaction networks that might affect muscle fiber performance. Important lncRNA-miRNA-mRNA networks, such as lncRNA-XR_003074785.1/miR-193-3p/PPARGC1A, regulate oxidative myofibers. This study reveals that lncXR_003077811.1, lncXR_003072304.1, lncXR_001465942.2, lncXR_001465741.2, lncXR_001470487.1, lncXR_003077673.1, XR_003074785.1, novel_circ_004282 and novel_circ_002121 might regulate oxidative myofibers. The lncRNA-XR_003074785.1/miR-193-3p/PPARGC1A pathway might regulate oxidative myofibers. All these findings provide rich resources for further in-depth research on the regulatory mechanism of lncRNAs and circRNAs in myofibers.