Gene最新文献

Objectives: The aim is to analyze differentially expressed genes (DEGs) in mice with sepsis-related intestinal mucosal barrier damage and to explore the diagnostic and protective mechanisms of this condition at the transcriptome level.

Methods: Small intestinal tissues from healthy male C57BL/6J mice subjected to Cecal ligation and puncture (CLP) and sham operation were collected. High-throughput sequencing was performed using the paired-end sequencing mode of the Illumina HiSeq platform. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were conducted on the differentially expressed genes (DEGs). A protein-protein interaction (PPI) network was constructed using the STRING database, and hub genes were identified with Cytoscape. These hub genes were then validated using quantitative real-time polymerase chain reaction (RT-qPCR).

Results: A total of 239 DEGs were identified, with 49 upregulated and 130 downregulated genes. KEGG enrichment analysis showed that these DEGs were primarily involved in cytokine-cytokine receptor interaction, Th1 and Th2 cell differentiation, viral protein interactions with cytokines and their receptors, and the IL-17 signaling pathway. The top 10 hub genes were selected using the cytoHubba plugin. Experimental validation confirmed that the expression levels of TBX21, CSF3, IL-6, CXCR3, and CXCL9 matched the sequencing results.

Conclusion: TBX21, CSF3, IL-6,CXCR3, and CXCL9 may be potential biological markers for the diagnosis and treatment the sepsis-associated intestinal mucosal barrier.

The growth and development of chicken skeletal muscle directly affects chicken meat production, which is very important for broiler industry. Matrix metallopeptidase 2 (MMP2) exists in skeletal muscle. However, the underlying regulating of MMP2 remain unknown. In this study, MMP2 promoted cell proliferation and inhibited cell differentiation after overexpression in chicken primary myoblasts cells (CPMs). When MMP2 was knocked down, it inhibited CPMs proliferation and promoted cell differentiation. Subsequently, RNA sequencing (RNA-seq) and bioinformatics analysis were performed on overexpressing MMP2. We identified 265 up-regulated genes and 229 down-regulated genes. Based on the fragments per kilobase million (FPKM) ≥ 10, the retained data were analyzed by Pearson correlation analysis. MMP2 was positively correlated with carboxypeptidase M (CPM), MSTRG.14120 and aldehyde dehydrogenase 1 family member A3 (ALDH1A3), and the correlation coefficient was the highest (0.998). MMP2 was negatively correlated with hes family bHLH transcription factor 1 (HES1), and the correlation coefficient was the highest (0.998). Go term was enriched in cellular components or biogenesis, cellular processes, and cell aggregation. KEGG was significantly enriched to the cancer pathway. qRT-PCR analysis validated the transcriptomic results of RNA-seq. In conclusion, these results provided new insights into the molecular mechanisms by which MMP2 affected the proliferation and differentiation of chicken myoblasts.

Objective: Idiopathic pulmonary fibrosis (IPF) is an irreversible and fatal interstitial lung disease, characterized by excessive extracellular matrix (ECM) secretion that disrupts normal alveolar structure. This study aims to explore the potential molecular mechanisms underlying the promotion of IPF development.

Methods: Firstly, we compared the transcriptome and single-cell sequencing data from lung tissue samples of patients with IPF and healthy individuals. Subsequently, we conducted Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses on the differentially expressed genes (DEGs). Furthermore, we employed sodium alginate hydrogels with varying degrees of crosslinking to provide differential mechanical stress, mimicking the mechanical microenvironment in vivo during lung fibrosis. On this basis, we examined cytoskeletal remodeling in fibroblasts MRC-5, mRNA expression of multiple related genes, immunofluorescence localization, and cellular proliferation capacity.

Results: Bioinformatics analysis revealed a series of DEGs associated with IPF. Further functional and pathway enrichment analyses indicated that these DEGs were primarily enriched in ECM-related biological processes. Single-cell sequencing data revealed that fibroblasts and myofibroblasts are the main contributors to excessive ECM secretion and suggested activation of mechanotransduction and the Hippo/YAP signaling pathway in myofibroblasts. Cellular experiments demonstrated that sodium alginate hydrogels with different stiffness can simulate different mechanical stress environments, thereby affecting cytoskeletal rearrangement and Hippo/YAP pathway activity in MRC-5 lung fibroblasts. Notably, high levels of mechanical stress promoted YAP nuclear translocation, increased expression of type I collagen and α-SMA, and enhanced proliferative capacity. Additionally, we also found that fibroblasts primarily participate in mechanotransduction through the Rho/ROCK and Integrin/FAK pathways under high mechanical stress conditions, ultimately upregulating the gene expression of CCNE1/2, CTGF, and FGF1.

Conclusion: Our study uncovers the crucial role of cytoskeletal mechanotransduction in myofibroblast transformation and IPF development through activation of the Hippo/YAP pathway, providing new insights into understanding the pathogenesis of IPF.

White clover (Trifolium repens L.) is a high-quality leguminous forage, but its short rooting habit, poor transpiration tolerance, and drought tolerance, have become a key factor restricting its growth and cultivation. 1R-MYB transcription factors (TFs) are a significant subfamily of TFs in plants, playing a vital role in regulating plant responses to drought stress, however, knowledge about the role of 1R-MYB transcription factors in white clover is still limited. We identified 134 1R-MYB members, which were unevenly designated onto 16 chromosomes and divided phylogenetically into five subgroups. The members of the same subgroup had conserved motifs. Collinearity analysis revealed that segmental and tandem duplications significantly contributed to the expansion of the Tr1R-MYBs. Tr1R-MYBs promoter region enriched with potential drought cis-acting regulatory elements. The RT-qPCR results show that the five Tr1R-MYB genes (TrMYB41, TrMYB49, TrMYB94, TrMYB125, TrMYB130) have a certain degree of response under drought stress conditions but exhibited different expression profiles. Furthermore, subcellular localization analysis showed that the TrMYB130 protein is primarily located in the nucleus. Overexpression of this protein in transgenic Arabidopsis (Arabidopsis thaliana L.) was found to impair drought tolerance. Our findings will establish a basis for deeper investigation into the characteristics and functions of 1R-MYB TFs, as well as for employing genetic engineering techniques to improve white clover.

Hyperlipidemia and myocardial apoptosis caused by myocardial ischemia are the main causes of high mortality rates in cardiovascular diseases. Previous studies have indicated that Krüppel-like factor 4 (KLF4) is involved in the induction of cardiac myocyte apoptosis under various stress conditions. In current study, we discovered that KLF4 also participates in palmitic acid (PA)-induced cardiac myocyte apoptosis. However, the specific mechanisms by which KLF4 regulates cardiac myocyte apoptosis remain unclear. Cardiac myosin light-chain kinase (cMLCK) is a crucial enzyme involved in regulating cardiac myocyte contraction and is closely associated with the regulation of apoptosis. Here, we employed the lipotoxicity in vitro and in vivo models to explore the potential synergistic role of KLF4 and cMLCK in cardiac myocyte apoptosis. Our findings demonstrate that under the influence of PA, upregulation of KLF4 expression accompanied by downregulation of cMLCK expression leads to cardiomyocyte apoptosis and cell proliferation inhibition. Selective knockdown and overexpression of KLF4 in cardiomyocytes further confirmed the involvement of KLF4 in PA-induced cardiomyocyte apoptosis. Likewise, overexpression of cMLCK alleviated PA-induced cardiac myocyte apoptosis. Our study reveals the pro-apoptotic effect of KLF4 and elucidates the specific mechanism by which the KLF4/cMLCK signaling pathway is involved in PA-induced cardiac myocyte apoptosis, providing new therapeutic targets for cardiovascular disease treatment.

Currently, the pathogenesis of epilepsy remains poorly understood. Although there is evidence indicating that iron death might play a significant role, its molecular immunological mechanisms are largely unknown. This study was designed to analyze and explore the molecular mechanisms and immunological characteristics of iron death-related genes in epilepsy. We obtained datasets of blood and brain tissues for epilepsy from the GEO database and the set of iron death-related genes from FerrDb. Through two machine learning algorithms, we identified three Hub genes, namely RELA, TFRC, and QSOX1. Unsupervised clustering revealed two distinct clusters. Immune infiltration analysis demonstrated that one cluster had significantly higher immune infiltration. We established an epilepsy diagnostic model and nomogram. The results were confirmed by RT-qPCR and Western Blot. Single-cell analysis showed that the SPP1 signalling pathway was overly activated in astrocytes and microglia. This study offers new perspectives and a theoretical foundation for the diagnosis of epilepsy.

Background: P-element-induced wimpy testis (PIWI) proteins bind to PIWI-interactingRNAs (piRNAs) to form the piRNA/PIWI complex, which affects protein regulation. PIWIL4, a member of the PIWI family, has been demonstrated in recent studies to promote the migration of triple-negative breast cancer (TNBC) cell line MDA-MB-231. However, the molecular mechanisms underlying cell migration remain obscure.

Methods: RNA immunoprecipitation and real-time PCR assays were conducted to detect piRNAs binding to PIWIL4. piRNA mimics and inhibitors were employed to modify piRNA expression in MDA-MB-231 cells. Cell migration assays were carried out using transwell inserts. Co-immunoprecipitation (co-IP) combined with mass spectrometry (MS) was performed to identify the proteins that interacted with PIWIL4 under the regulation of piRNA. Western blotting (WB) was utilised to detect the regulatory relationship between the piRNA/PIWIL4 complexes and the mutually-binding proteins.

Results: RNA Immunoprecipitation (RIP) results revealed that PIWIL4 bound to piR-31115 in the MDA-MB-231 cells. Transwell assays demonstrated that piR-31115 promoted the migration of MDA-MB-231 cells via PIWIL4. Co-IP coupled with MS results showed that piR-31115 promoted the binding of PIWIL4 to HSP90AA1 in MDA-MB-231 cells, and this interaction protected HSP90AA1 from degradation. Knockdown of HSP90AA1 in MDA-MB-231 cells attenuated the promoting effects of piR-31115/PIWIL4 on cell migration.

Conclusions: Our findings cast light on a novel molecular pathway through which piR-31115 promotes the migration of MDA-MB-231 TNBC cells by regulating the interaction between PIWIL4 and HSP90AA1.

Background: The contribution of MTHFR and TP53 genetic variants to breast carcinoma (BC) susceptibility has been examined, but their findings have been inconclusive. This work is designed to explore the potential roles of the MTHFR (rs1801131, rs1801133) and TP53 (rs1042522) variants with increased risk of BC using genetic and bioinformatic approaches.

Methods: This work included a total of 242 female participants [142 BCE patients and 100 healthy controls]. We genotyped the allelic discrimination analysis for these genetic variants using the T-ARMS-PCR technique. Logistic regression, haplotype analysis, genetic association models, and multivariate clustering were executed.

Results: The rs1801131*C allele revealed a significant association with elevated risk of breast carcinoma compared to healthy controls under allelic (OR = 2.02, p-value < 0.001) and recessive (OR = 3.26, p-value < 0.001) models. Moreover, the rs1801133*T allele was correlated to cancer susceptibility under allelic (OR = 1.81, p-value = 0.002) and dominant (OR = 3.33, p-value < 0.001) models, while the rs1042522*G allele was associated with increased risk of BC under allelic (OR = 2.98, p-value < 0.001) and recessive (OR = 3.21, p-value < 0.001) models. BC women carrying the rs1801131*C/C genotype were associated with histological grade III, while those with the rs1801133*T/T and rs1042522*G/G genotypes were correlated with a moderate/poor NPI score (p-value < 0.05).

Conclusions: The rs1801131*C, rs1801133*T, and rs1042522*G alleles are associated with an increased risk of BC. The rs1801133*T and rs1042522*G alleles correlated with moderate/poor NPI score. These findings pave the way for the diagnostic functions of these genetic variants as potential prognostic biomarkers.