Transcriptome analysis of Klf15‑mediated inhibitory functions in a mouse deep venous thrombosis model

Causal relationship between matrix metalloproteinase and pulmonary embolism: a bidirectional two-sample Mendelian randomization study

This study evaluated the causal relationship between matrix metalloproteinases (MMPs) and pulmonary embolism using data from the genome-wide association study (GWAS) of pulmonary embolism from the UK Biobank and a GWAS dataset of MMPs based on 5,457 Icelanders aged 65 years and older. MR-Egger, MR-PRESSO, Cochran's Q, and leave-one-out were used for sensitivity analysis. The Mendelian randomization (MR) analysis, based on the IVW analysis, indicated an elevated risk for pulmonary embolism in association with MMP19 (OR = 1.0009, 95%CI: 1-1.0017, P = 0.041), consistent with the weighted median method results (P = 0.015). In addition, despite the negative result from the IVW method (P = 0.554), the weighted median analysis suggested a reduced risk for pulmonary embolism related to MMP12 (OR = 0.9992, 95%CI: 0.9984-1, P = 0.038). No causal associations were found for the other MMPs (including MMP1, MMP2, MMP3, MMP7, MMP8, MMP9, MMP10, MMP13, MMP14, MMP16, MMP17, and MMP20) on pulmonary embolism (all P > 0.05). The reverse MR analysis revealed no causal associations between pulmonary embolism as exposure and MMPs as outcomes. Sensitivity analyses confirmed the robustness of these findings. In conclusion, this MR analysis revealed the potential causal relationship between MMPs and pulmonary embolism, suggesting that measuring MMPs could help identify people at higher risk of pulmonary embolism, but further research is needed.

Inhibiting MMP13 Attenuates Deep Vein Thrombosis in a Mouse Model by Reducing the Expression of Pdpn

OBJECTIVE

Matrix metalloproteinase 13 (MMP13) is an extracellular matrix protease that affects the progression of atherosclerotic plaques and arterial thrombi by degrading collagens, modifying protein structures and regulating inflammatory responses, but its role in deep vein thrombosis (DVT) has not been determined. The purpose of this study was to investigate the potential effects of MMP13 and MMP13-related genes on the formation of DVT.

METHODS

We altered the expression level of MMP13 in vivo and conducted a transcriptome study to examine the expression and relationship between MMP13 and MMP13-related genes in a mouse model of DVT. After screening genes possibly related to MMP13 in DVT mice, the expression levels of candidate genes in human umbilical vein endothelial cells (HUVECs) and the venous wall were evaluated. The effect of MMP13 on platelet aggregation in HUVECs was investigated in vitro.

RESULTS

Among the differentially expressed genes, interleukin 1 beta, podoplanin (Pdpn), and factor VIII von Willebrand factor (F8VWF) were selected for analysis in mice. When MMP13 was inhibited, the expression level of PDPN decreased significantly in vitro. In HUVECs, overexpression of MMP13 led to an increase in the expression level of PDPN and induced platelet aggregation, while transfection of PDPN-siRNA weakened the ability of MMP13 to increase platelet aggregation.

CONCLUSIONS

Inhibiting the expression of MMP13 could reduce the burden of DVT in mice. The mechanism involves downregulating the expression of Pdpn through MMP13, which could provide a novel gene target for DVT diagnosis and treatment.

Transcriptome analysis of genes potentially associated with white and black plumage formation in Chinese indigenous ducks (Anas platyrhynchos)

1. Plumage colour is an important recognisable characteristic of duck (Anas platyrhynchos), but the coloration mechanisms remain largely unknown. To elucidate the molecular mechanisms underlying the formation of black and white plumage, the following study applied RNA sequencing (RNA-Seq) to catalogue the global gene expression profiles in the duck feather bulbs of black and white colours.2. Black feather bulbs were collected from Putian Black ducks (B-PTB) and black Longsheng Jade-green ducks (B-LS), while white feather bulbs were collected from Putian White ducks (W-PTW), Putian Black ducks (W-PTB) and Longsheng Jade-green ducks (W-LS). Sixteen cDNA libraries were constructed and sequenced for transcriptional analysis. Three comparison groups were employed to analyse differentially expressed genes (DEGs), including W-PTB versus B-PTB, W-PTW versus B-PTB and W-LS versus B-LS.3. The results showed 180 DEGs between W-PTB and B-PTB, 303 DEGs between W-PTW and B-PTB, and 108 DEGs between W-LS and B-LS. Further analysis showed that 18 DEGs were directly involved in the pigmentation process and melanogenesis signalling pathway. Additionally, the distribution of DEGs varied amongst groups whereby ASIP appeared only in the W-LS versus B-LS group, GNAI1 and ZEB2 appeared only in the W-PTW versus B-PTB group, and KITLG, EDN3 and FZD4 appeared only in W-PTB versus B-PTB.4. The findings suggested that the mechanism of feather albinism may differ between duck breeds. This study provided new information for discovering genes that are important for feather pigmentation and helps elucidate molecular mechanisms involved in black and white plumage in ducks.

Transcriptomic Profiling of Femoral Veins in Deep Vein Thrombosis in a Porcine Model

Deep vein thrombosis (DVT) is a severe disease affecting the human venous system, accompanied by high morbidity and mortality rates caused by early and late complications. The study aimed at analyzing the changes in the transcriptome of the femoral vein caused by DVT in the porcine model based on the formation of the thrombus in vivo. The study was performed on 11 castrated male pigs: A thrombus was formed in each left femoral vein in six animals; the remaining five served as a control group. Total RNA was isolated from the left femoral veins of the experimental and control animals. High-throughput RNA sequencing was used to analyze the global changes in the transcriptome of veins with induced DVT. Applied multistep bioinformatics revealed 1474 differentially expressed genes (DEGs): 1019 upregulated and 455 downregulated. Functional Gene Ontology annotated 1220 of DEGs into 225 biological processes, 30 molecular functions and 40 cellular components categories. KEGG analysis disclosed TNF, NF-κB and apoptosis pathways' overexpression in DVT samples. A thorough analysis of the detected DEGs indicated that a dysregulated inflammatory response and disturbed balance between clotting and anti-clotting factors play a crucial role in the process of DVT.