Identification of Hub Genes and Pathways Associated With Idiopathic Pulmonary Fibrosis via Bioinformatics Analysis

Wan, Hanxi; Huang, Xinwei; Cong, Peilin; He, Mengfan; Chen, Aiwen; Wu, Tingmei; Dai, Danqing; Li, Wanrong; Gao, Xiao-Fei; Tian, Li; Liang, Huazheng; Xiong, Lize

doi:10.3389/fmolb.2021.711239

Cited by 23 publications

(21 citation statements)

References 55 publications

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“…Multiple bioinformatic methods have demonstrated that mmp7 gene is significantly correlated with the prognosis and occurrence of IPF. [23]. These results are in good agreement with the recent PROFILE (Prospective Observation of Fibrosis in the Lung Clinical Endpoints) study conclusions indicating that serum SP-D and MMP-7 could best differentiate between IPF patients and controls [139,140].…”

Section: Mmp-7supporting

confidence: 89%

“…In addition, weighted correlation network analysis (WGCNA) of multiple gene expression datasets from the Gene Expression Omnibus database by protein-protein interaction (PPI) network identified increased expression levels of mmp1 and mmp7. This finding was validated in experimental an PF murine model using qRT-PCR and in the GSE10667 dataset [23]. Many other studies have demonstrated that mmp1 gene expression is up-regulated in IPF in comparison to normal lung tissues [96][97][98].…”

Section: Mmp-1supporting

confidence: 54%

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Matrix Metalloproteinases and Their Inhibitors in Pulmonary Fibrosis: EMMPRIN/CD147 Comes into Play

Chuliá-Peris

Carreres-Rey

Gabasa

et al. 2022

IJMS

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Pulmonary fibrosis (PF) is characterized by aberrant extracellular matrix (ECM) deposition, activation of fibroblasts to myofibroblasts and parenchymal disorganization, which have an impact on the biomechanical traits of the lung. In this context, the balance between matrix metalloproteinases (MMPs) and their tissue inhibitors of metalloproteinases (TIMPs) is lost. Interestingly, several MMPs are overexpressed during PF and exhibit a clear profibrotic role (MMP-2, -3, -8, -11, -12 and -28), but a few are antifibrotic (MMP-19), have both profibrotic and antifibrotic capacity (MMP7), or execute an unclear (MMP-1, -9, -10, -13, -14) or unknown function. TIMPs are also overexpressed in PF; hence, the modulation and function of MMPs and TIMP are more complex than expected. EMMPRIN/CD147 (also known as basigin) is a transmembrane glycoprotein from the immunoglobulin superfamily (IgSF) that was first described to induce MMP activity in fibroblasts. It also interacts with other molecules to execute non-related MMP actions well-described in cancer progression, migration, and invasion. Emerging evidence strongly suggests that CD147 plays a key role in PF not only by MMP induction but also by stimulating fibroblast myofibroblast transition. In this review, we study the structure and function of MMPs, TIMPs and CD147 in PF and their complex crosstalk between them.

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Section: Mmp-7supporting

confidence: 89%

Section: Mmp-1supporting

confidence: 54%

Matrix Metalloproteinases and Their Inhibitors in Pulmonary Fibrosis: EMMPRIN/CD147 Comes into Play

Chuliá-Peris

Carreres-Rey

Gabasa

et al. 2022

IJMS

View full text Add to dashboard Cite

show abstract

“…The top upregulated DE genes in IPF such as CTSK, FN1, SPP1, CCL18 (Fig. 3b), were previously reported to be upregulated in IPF and related to IPF pathogenesis in macrophages [17,18,44,45,[47][48][49]. To examine subject variation in these two datasets, we estimated cell-level effect coefficients [20] for each subject (Fig.…”

Section: Consistency Of Results In Two Scrna-seq Datasetsmentioning

confidence: 99%

iDESC: Identifying differential expression in single-cell RNA sequencing data with multiple subjects

Liu

Wang

Adams

et al. 2022

Preprint

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Single-cell RNA sequencing (scRNA-seq) enables assessment of transcriptome-wide changes at single-cell resolution. However, dominant subject effect in scRNA-seq datasets with multiple subjects severely confounds cell-type-specific differential expression (DE) analysis. We developed iDESC to separate subject effect from disease effect with consideration of dropouts to identify DE genes. iDESC was shown to have well-controlled type I error and high power compared to existing methods and obtained the best consistency between datasets and disease relevance in two scRNA-seq datasets from same disease, suggesting the importance of considering subject effect and dropouts in the DE analysis of scRNA-seq data with multiple subjects.

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“…All of the target hub genes (MMP2, CDH2, GJA1, ROBO1, COL4A1, THBS2, COL5A1, EPHB2, RUNX2, and SDC2) were reported to be associated with brosis disease. For example, CDH2, a kind of cell adhesion protein, is involved in the pathogenesis of various brotic diseases via epithelial-to-mesenchymal transition [42,43]. GJA1 can induce hepatic stellate cell (HSCs) activation [44].…”

Section: Discussionmentioning

confidence: 99%

Comprehensive Analysis of Differentially Expressed Circular RNAs in Keloid Dermal Tissues

Liu

Zhang

Huang

et al. 2022

Preprint

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Background Keloid is a dermal fibroproliferative disease with various etiologies and unclear pathogenesis. Recent studies have revealed that circular RNAs (circRNAs) exerted regulatory functions through a competing endogenous RNA (ceRNA) pathway in keloid progression. However, the expression profiles of circRNAs in keloid dermal tissues (KDTs) remain unknown. This study aimed to identify differentially expressed circRNAs (DECs) and genes (DEGs) in KDTs, as well as to investigate the potential biological functionsof circRNAs based on the circRNA-miRNA-mRNA ceRNA network. Results Through high-throughput RNA sequencing (RNA-seq), we revealed 3467 DEGs (865 up- and 2602 down-regulated) and 330 DECs (162 up- and 168 down-regulated) in KDTs. To reveal the functions of DECs preliminarily, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed for the host genes. Further, the up- and down-regulated DECs-miRNAs-DEGs regulatory networks were constructed, respectively. The functional prediction for the target genes showed that the up-regulated ceRNA network was associated with extracellular matrix and multiple cellular functions. The down-regulated ceRNA network was enriched in cell-cell junction and other biological processes. Cytoscape was used to visualize each network's protein-protein interaction (PPI) network and identify hub genes. By quantitative Real-Time PCR (qRT-PCR), hsa_circ_0060927, hsa_circ_0071410, hsa_circ_0058092, hsa_circ_0002874, hsa_circ_0004682, hsa_circ_0072688, hsa_circ_0006401, and hsa_circ_0055954 were identified significantly up-regulated in KDTs. Within, hsa_circ_0072688, which was up-regulated both in KDTs and keloid dermal fibroblasts (KDFs), and located in the cytoplasm, might be a key circRNA and affect the progression of keloid by impacting extracellular matrix, cell adhesion, and cell apoptosis, etc. Conclusion This study not only filled a gap in the circRNA library of KDTs but also laid a foundation for probing the biological function of DECs in keloids. Hsa_circ_0072688 was thought to be a key circRNA and more experimental support is needed.

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Identification of Hub Genes and Pathways Associated With Idiopathic Pulmonary Fibrosis via Bioinformatics Analysis

Cited by 23 publications

References 55 publications

Matrix Metalloproteinases and Their Inhibitors in Pulmonary Fibrosis: EMMPRIN/CD147 Comes into Play

Matrix Metalloproteinases and Their Inhibitors in Pulmonary Fibrosis: EMMPRIN/CD147 Comes into Play

iDESC: Identifying differential expression in single-cell RNA sequencing data with multiple subjects

Comprehensive Analysis of Differentially Expressed Circular RNAs in Keloid Dermal Tissues

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