[Retracted] Identification and Validation of Potential Biomarkers and Pathways for Idiopathic Pulmonary Fibrosis by Comprehensive Bioinformatics Analysis

Abstract

Objective. Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive, irreversible, high-mortality lung disease, but its pathogenesis is still unclear. Our purpose was to explore potential genes and molecular mechanisms underlying IPF. Methods. IPF-related data were obtained from the GSE99621 dataset. Differentially expressed genes (DEGs) were identified between IPF and controls. Their biological functions were analyzed. The relationships between DEGs and microRNAs (miRNAs) were predicted. DEGs and pathways were validated in a microarray dataset. A protein-protein interaction (PPI) network was constructed based on these common DEGs. Western blot was used to validate hub genes in IPF cell models by western blot. Results. DEGs were identified for IPF than controls in the RNA-seq dataset. Functional enrichment analysis showed that these DEGs were mainly enriched in immune and inflammatory response, chemokine-mediated signaling pathway, cell adhesion, and other biological processes. In the miRNA-target network based on RNA-seq dataset, we found several miRNA targets among all DEGs, like RAB11FIP1, TGFBR3, and SPP1. We identified 304 upregulated genes and 282 downregulated genes in IPF compared to controls both in the microarray and RNA-seq datasets. These common DEGs were mainly involved in cell adhesion, extracellular matrix organization, oxidation-reduction process, and lung vasculature development. In the PPI network, 3 upregulated and 4 downregulated genes could be considered hub genes, which were confirmed in the IPF cell models. Conclusion. Our study identified several IPF-related DEGs that could become potential biomarkers for IPF. Large-scale multicentric studies are eagerly needed to confirm the utility of these biomarkers.

Role of MicroRNAs in Signaling Pathways Associated with the Pathogenesis of Idiopathic Pulmonary Fibrosis: A Focus on Epithelial-Mesenchymal Transition

“…A year later it was reported that these deregulated miRNAs were associated with some developmental pathways that involved TGFβ1, Wnt, sonic hedgehog, p53, as well as VEGF and their complex regulatory networks [ 49 ]. Today, many studies are focused on evaluating the expression levels of profibrotic and antifibrotic miRNAs, both in the onset and progression of IPF; however, the results obtained still show contradictory expression levels of these miRNAs [ 50 , 51 , 52 , 53 ]. It is probable that these variations are related to the complexity of this lung disease, since it involves multiple genes and signaling pathways [ 29 , 54 , 55 ].…”

Progress in understanding and treating idiopathic pulmonary fibrosis: recent insights and emerging therapies

“…Idiopathic pulmonary fibrosis (IPF) is a pervasive chronic pulmonary ailment marked by irreversible lung function loss and structural disfigurement attributable to an overproduction of extracellular matrix deposition ( Mei et al, 2021 ), compounded by progressive scarring of lung tissue and interstitial lung disease ( Qian et al, 2021 ). The disease is predominantly observed in middle-aged to elderly men, and its global prevalence is estimated to exceed 3 million people, with an annual incidence rate between 2 and 9 per 100,000 individuals and an escalating trend ( He et al, 2021a ).…”

Retracted: Identification and Validation of Potential Biomarkers and Pathways for Idiopathic Pulmonary Fibrosis by Comprehensive Bioinformatics Analysis

“…This article has been retracted by Hindawi following an investigation undertaken by the publisher [ 1 ]. This investigation has uncovered evidence of one or more of the following indicators of systematic manipulation of the publication process: Discrepancies in scope Discrepancies in the description of the research reported Discrepancies between the availability of data and the research described Inappropriate citations Incoherent, meaningless and/or irrelevant content included in the article Manipulated or compromised peer review …”

“…This article has been retracted by Hindawi following an investigation undertaken by the publisher [1]. This investigation has uncovered evidence of one or more of the following indicators of systematic manipulation of the publication process:…”