Analysis of the effect of CCR7 on the microenvironment of mouse oral squamous cell carcinoma by single-cell RNA sequencing technology

Journal of Experimental & Clinical Cancer Research, Journal Year: 2024, Volume and Issue: 43(1)

Published: March 27, 2024

Abstract Background Studies have shown that CCR7, an important inflammatory factor, can promote the proliferation and metastasis of oral squamous cell carcinoma (OSCC), but its role in tumor microenvironment (TME) remains unclear. This paper explores CCR7 TME OSCC. Methods In this work, we constructed gene knockout mice OSCC mouse models. Single-cell RNA sequencing (scRNA-seq) bioinformatics were used to analyze differences between three (KO) wild-type (WT). Immunohistochemistry, immunofluorescence staining, flow cytometry expression key genes significantly different types KO WT groups. An vitro experiment was verify effect on M2 macrophage polarization. Results models, growth rate group lower than group. Eight main (including cells, fibroblasts, macrophages, granulocytes, T endothelial monocytes, B cells) identified by Seurat analysis. The scRNA-seq results showed proportion cells lower, higher CellPhoneDB analysis indicated a strong interaction relationship cells. Functional enrichment level Dusp1 generally various types. Macrophage subclustering macrophages experimental polarization, thus promoting proliferation, invasion migration Conclusions inhibit polarization macrophages.

Language: Английский

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Coordinated Tbx3/Tbx5 transcriptional control of the adult ventricular conduction system

Published: April 17, 2025

The cardiac conduction system (CCS) orchestrates the electrical impulses that enable coordinated contraction of chambers. T-box transcription factors TBX3 and TBX5 are required for development associated with overlapping distinct human diseases. We evaluated role Tbx3 Tbx5 in murine ventricular (VCS). engineered a compound Tbx3:Tbx5 conditional knockout allele both genes located cis on mouse chromosome 5. Conditional deletion transcriptional system, using VCS-specific MinK:Cre, caused loss VCS function molecular identity. Combined deficiency adult led to defects, including prolonged PR QRS intervals elevated susceptibility tachycardia. These electrophysiological defects occurred prior detectable alterations contractility or histologic morphology, indicative primary defect. double cardiomyocytes revealed shift towards non-CCS-specialized working myocardium, indicating change their cellular Furthermore, optical mapping propagation. Collectively, these findings indicate coordinate control fate function, implications understanding disorders humans.

Language: Английский

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Hyperglycaemia-induced fibrotic and inflammatory gene expression alterations in lung epithelial cells: Implications for pulmonary fibrosis development

Gene, Journal Year: 2025, Volume and Issue: unknown, P. 149520 - 149520

Published: April 1, 2025

Language: Английский

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Transcriptomic meta-analysis and exploration of differentially expressed gene functions in wooden breast myopathy of broilers

Poultry Science, Journal Year: 2024, Volume and Issue: 103(10), P. 104047 - 104047

Published: July 4, 2024

Wooden breast (WB) myopathy is a common found in commercial broiler chickens worldwide. Although extensive research on WB has been conducted using transcriptomics, effectively screening and analyzing key target information remains challenge. In this present study, 5 transcriptomic datasets obtained from the National Center for Biotechnology Information (NCBI) were used. A meta-analysis was to identify meta-differentially expressed genes (meta-DEGs) involved response of broilers myopathy. These meta-DEGs further analyzed Kyoto Encyclopedia Genes Genomes (KEGG), Gene Ontology (GO), Set Enrichment Analysis (GSEA), supplemented by protein-protein interaction (PPI) network construction pinpoint hub genes. analyses help reveal genes, pathways, biological processes associated with The results showed that 645 up-regulated 99 down-regulated significant (|log

Language: Английский

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Suppression of NUPR1 in fibroblast-like synoviocytes reduces synovial fibrosis via the Smad3 pathway

Journal of Translational Medicine, Journal Year: 2024, Volume and Issue: 22(1)

Published: Aug. 1, 2024

Synovial fibrosis is a common complication of knee osteoarthritis (KOA), pathological process characterized by myofibroblast activation and excessive extracellular matrix (ECM) deposition. Fibroblast-like synoviocytes (FLSs) are implicated in KOA pathogenesis, contributing to synovial through diverse mechanisms. Nuclear protein 1 (NUPR1) recently identified transcription factor with crucial roles various fibrotic diseases. However, its molecular determinants remain unknown. This study aims investigate the role NUPR1 vivo vitro experiments. We examined expression murine synovium determined impact on knockdown models destabilization medial meniscus (DMM)-induced mouse model. TGF-β was employed induce response FLSs, mechanisms were evaluated under conditions downexpression. Additionally, pharmacological effect inhibitor assessed using surgically induced found that increased after DMM surgical operation. The adeno-associated virus (AAV)-NUPR1 shRNA promoted deficiency, attenuating fibrosis, inhibiting hyperplasia, significantly reducing pro-fibrotic molecules. Moreover, lentivirus-mediated deficiency alleviated synoviocyte proliferation inhibited fibroblast transition. It also decreased markers α-SMA, COL1A1, CTGF, Vimentin SMAD family member 3 (SMAD3) pathway. Importantly, trifluoperazine (TFP), inhibitor, attenuated mice. These findings indicate an antifibrotic modulator KOA, anti-synovial partially mediated SMAD3 signaling. reveals promising target for developing novel treatment.

Language: Английский

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Single-cell RNA sequencing reveals critical modulators of extracellular matrix of penile cavernous cells in erectile dysfunction

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: March 11, 2024

Abstract Erectile dysfunction (ED) is a common and difficult to treat disease, has high incidence rate worldwide. As marker of vascular ED usually occurs in cardiovascular 2–5 years prior disease events. The extracellular matrix (ECM) network plays crucial role maintaining cardiac homeostasis, not only by providing structural support, but also promoting force transmission, transducing key signals intracardiac cells. However, the relationship between ECM remains unclear. To help fill this gap, we profiled single-cell RNA-seq (scRNA-seq) obtain transcriptome maps 82,554 cavernous single cells from non-ED samples. Cellular composition tissues was explored uniform manifold approximation projection. Pseudo-time cell trajectory combined with gene enrichment analysis were performed unveil molecular pathways fate determination. ECM, changes related genes elucidated. CellChat identified ligand-receptor pairs (e.g., PTN-SDC2, PTN-NCL, MDK-SDC2) among major types tissue microenvironment. Differential revealed that type-specific transcriptomic are structure organization, external encapsulating regulation vasculature development. Trajectory predicted underlying target modulate COL3A1, MDK, MMP2, POSTN). Together, study highlights potential cell–cell interactions main regulatory factors reveals may represent features progression.

Language: Английский

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Study on the mechanism of Xinmailong injection against chronic heart failure based on transcriptomics and proteomics

Journal of Pharmaceutical and Biomedical Analysis, Journal Year: 2024, Volume and Issue: 253, P. 116529 - 116529

Published: Oct. 18, 2024

Language: Английский

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Exploring the Role of Obesity in Dilated Cardiomyopathy Based on Bio-informatics Analysis

Journal of Cardiovascular Development and Disease, Journal Year: 2022, Volume and Issue: 9(12), P. 462 - 462

Published: Dec. 15, 2022

(1) Background: Obesity is a major risk factor for cardiovascular disease (CVD), contributing to increasing global burdens. Apart from heart failure, coronary artery disease, and arrhythmia, recent research has found that obesity also elevates the of dilated cardiomyopathy (DCM). The main purpose this study was investigate underlying biological role in DCM. (2) Methods: datasets GSE120895, GSE19303, GSE2508 were downloaded Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) analyzed using GSE120895 DCM obesity, findings compiled discover common genes. Ontology (GO) Kyoto Encyclopedia Genes Genomes (KEGG) pathway enrichment analyses conducted RStudio. In addition, CIBERSORT used obtain immune cellular composition DEGs. key identified set by least absolute shrinkage selection operator (LASSO) algorithm, prognostic models which verified receiver characteristic (ROC) curves GSE19303. Finally, Spearman’s correlation explore connections between cells. (3) Results: GO KEGG showed enriched terms transforming growth factor-beta (TGF-β), fibrillar collagen, NADPH oxidase activity, multiple hormone-related signaling pathways. Both had disordered environment, especially obesity. NOX4, CCDC80, COL1A2, HTRA1, KLHL29 may be primarily responsible changes. analysis performed cells indicated closely correlated T M2 macrophages, HTRA1 very tightly plasma (4) Conclusions: Bio-informatics our suggested disturbed micro-environment, promoted oxidative stress, increased myocardial fibrosis, resulting ventricular remodeling an play critical roles obesity-related

Language: Английский

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Identification of crucial modules and genes associated with backfat tissue development by WGCNA in Ningxiang pigs

Frontiers in Genetics, Journal Year: 2023, Volume and Issue: 14

Published: Aug. 17, 2023

Fat deposition is an economically important trait in pigs. Ningxiang pig, one of the four famous indigenous breeds China, characterized by high fat content. The underlying gene expression pattern different developmental periods backfat tissue remains unclear, and purpose this investigation to explore potential molecular regulators development Backfat (three samples for each stage) was initially collected from stages (60, 120, 180, 240, 300, 360 days after birth), histological analysis RNA sequencing (RNA-seq) were then conducted. Fragments per kilobase transcript million (FPKM) method used qualify expressions, differentially expressed genes (DEGs) identified. Furthermore, strongly co-expressed modules, which named color, clustered Weighted co-expression network (WGCNA) based on dynamic tree cutting algorithm. Gene ontology (GO) kyoto encyclopedia genomes (KEGG) enrichment subsequently implemented, hub described module. Finally, QPCR employed validate RNA-seq data. results showed that adipocyte area increased number decreased with tissue. A total 1,024 DEGs identified five comparison groups (120 vs. 60 days, 180 120 240 300 days). turquoise, red, pink, paleturquoise, darkorange, darkgreen module had highest correlation coefficient 60, stage, while tan, black turquoise strong relationship thickness, area, number, respectively. Thirteen (ACSL1, ACOX1, FN1, DCN, CHST13, COL1A1, COL1A2, COL6A3, COL5A1, COL14A1, OAZ3, DNM1, SELP) recognized. ACSL1 ACOX1 might perform function early stage (60 days), COL14A1 have unignorable position around stage. Besides, SELP DNM1 modules significantly associated thickness be involved process development. These findings contribute understand integrated mechanism promote progress genetic improvement

Language: Английский

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Screening of the Key Genes and Signaling Pathways for Schizophrenia Using Bioinformatics and Next Generation Sequencing Data Analysis

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Oct. 29, 2023

Abstract Schizophrenia is thought to be the most prevalent chronic psychiatric disorder. Numerous proteins have been identified that are associated with occurrence and development of schizophrenia. This study aimed identify potential core genes pathways involved in schizophrenia, through exhaustive bioinformatic next generation sequencing (NGS) data analyses using GSE20966 NGS neural progenitor cells neurons obtained from healthy controls patients The were downloaded Gene Expression Omnibus database. was processed by DESeq2 package R software differentially expressed (DEGs) identified. Ontology (GO) enrichment analysis REACTOME pathway carried out biological functions DEGs. Protein-protein interaction (PPI) network, module, miRNA-hub gene regulatory network TF-hub performed hub genes, miRNA TFs. Potential analyzed receiver operating characteristic (ROC) curves (pROC). In this investigation, an overall 955 DEGs identified: 478 remarkably up regulated 477 distinctly down regulated. These enriched for GO terms mainly multicellular organismal process, GPCR ligand binding, regulation cellular process amine ligand-binding receptors. MYC, FN1, CDKN2A, EEF1G, CAV1, ONECUT1, SYK, MAPK13, TFAP2A BTK considered genes. constructed successfully. On whole, findings investigation enhance our understanding molecular mechanisms schizophrenia provide targets further investigation.

Language: Английский

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