Variations in <i>S100A8</i>/<i>A12</i> Gene Expression Are Associated with the Efficacy of Nintedanib and Acute Exacerbation Development in Idiopathic Pulmonary Fibrosis Patients

Arai, Naoki; Nakajima, Masayuki; Matsuyama, Masashi; Matsumura, Sosuke; Yazaki, Kai; Sakai, Chio; Nonaka, Mizu; Yanai, Hidetoshi; Numata, Tomohiro; Yamamoto, Yorihiro; Akatsu, Yoshibumi; Iijima, Hiroaki; Morishima, Yuko; Matsuno, Yosuke; Endo, Takeo; Muratani, Masafumi; Ishii, Yukio; Saito, Takefumi; Hizawa, Nobuyuki

doi:10.1165/rcmb.2023-0054le

Cited by 2 publications

(2 citation statements)

References 14 publications

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“…Researchdemonstrated that enriched genes including PI3 [367], CX3CR1 [368], S100A12 [369], MPO (myeloperoxidase) [370], CD5L [371], S100A8 [372], CXCL11 [373], BPI (bactericidal permeability increasing protein) [374], AQP4 [375], BDNF (brain derived neurotrophic factor) [376], CXCL10 [377], CCL8 [378], S100A9 [379], IL1B [240], CXCR1 [380], CXCR2 [381], ABCA3 [382], GPR18 [383], VIP (vasoactive intestinal peptide) [384], KL (klotho) [385], TLR3 [386], NLRP12 [387], GATA3 [388], CCR2 [389], TLR7 [390], CAV1 [391], CR1 [392], DLL4 [393], and AQP5 [394] might be potential therapeutic targets for airway inflammation. Enriched genes includingCX3CR1 [395], S100A12 [396], MPO (myeloperoxidase) [397], RXFP1 [398], S100A8 [399], CXCL11 [373], CBS (cystathionine beta-synthase) [400], WNT7A [401], BDNF (brain derived neurotrophic factor) [402], CXCL10 [403], CCL8 [404], FCGR3B [405], S100A9 [406], IL1B…”

Section: Discussionmentioning

confidence: 99%

Study on Potential Differentially Expressed Genes in Idiopathic Pulmonary Fibrosis by Bioinformatics and Next-Generation Sequencing Data Analysis

Giriyappagoudar,

Vastrad,

Horakeri

et al. 2023

Biomedicines

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Idiopathic pulmonary fibrosis (IPF) is a chronic progressive lung disease with reduced quality of life and earlier mortality, but its pathogenesis and key genes are still unclear. In this investigation, bioinformatics was used to deeply analyze the pathogenesis of IPF and related key genes, so as to investigate the potential molecular pathogenesis of IPF and provide guidance for clinical treatment. Next-generation sequencing dataset GSE213001 was obtained from Gene Expression Omnibus (GEO), and the differentially expressed genes (DEGs) were identified between IPF and normal control group. The DEGs between IPF and normal control group were screened with the DESeq2 package of R language. The Gene Ontology (GO) and REACTOME pathway enrichment analyses of the DEGs were performed. Using the g:Profiler, the function and pathway enrichment analyses of DEGs were performed. Then, a protein–protein interaction (PPI) network was constructed via the Integrated Interactions Database (IID) database. Cytoscape with Network Analyzer was used to identify the hub genes. miRNet and NetworkAnalyst databaseswereused to construct the targeted microRNAs (miRNAs), transcription factors (TFs), and small drug molecules. Finally, receiver operating characteristic (ROC) curve analysis was used to validate the hub genes. A total of 958 DEGs were screened out in this study, including 479 up regulated genes and 479 down regulated genes. Most of the DEGs were significantly enriched in response to stimulus, GPCR ligand binding, microtubule-based process, and defective GALNT3 causes HFTC. In combination with the results of the PPI network, miRNA-hub gene regulatory network and TF-hub gene regulatory network, hub genes including LRRK2, BMI1, EBP, MNDA, KBTBD7, KRT15, OTX1, TEKT4, SPAG8, and EFHC2 were selected. Cyclothiazide and rotigotinethe are predicted small drug molecules for IPF treatment. Our findings will contribute to identification of potential biomarkers and novel strategies for the treatment of IPF, and provide a novel strategy for clinical therapy.

show abstract

Section: Discussionmentioning

confidence: 99%

Study on Potential Differentially Expressed Genes in Idiopathic Pulmonary Fibrosis by Bioinformatics and Next-Generation Sequencing Data Analysis

Giriyappagoudar,

Vastrad,

Horakeri

et al. 2023

Biomedicines

View full text Add to dashboard Cite

show abstract

“…Study demonstrated that PI3 [367], CX3CR1 [368], S100A12 [369], MPO (myeloperoxidase) [370], CD5L [371], S100A8 [372], CXCL11 [373], BPI (bactericidal permeability increasing protein) [374], AQP4 [375], BDNF (brain derived neurotrophic factor) [376], CXCL10 [377], CCL8 [378], S100A9 [379], IL1B [240], CXCR1 [380], CXCR2 [381], ABCA3 [382], GPR18 [383], VIP (vasoactive intestinal peptide) [384], KL (klotho) [385], TLR3 [386], NLRP12 [387], GATA3 [388], CCR2 [389], TLR7 [390], CAV1 [391], CR1 [392], DLL4 [393] and AQP5 [394] were essential for the induction of airway inflammation. CX3CR1 [395], S100A12 [396], MPO (myeloperoxidase) [397], RXFP1 [398], S100A8 [399], CXCL11 [373], CBS (cystathionine beta-synthase) [400], WNT7A [401], BDNF (brain derived neurotrophic factor) [402], CXCL10 [403], CCL8 [404], FCGR3B [405], S100A9 [406], IL1B [407], CXCR2 [408], WNT3A [409], BMI1 [410], STC1 [411], ABCA3 [412], CD36 [413], TRIB3 [414], GPX3 [415], FGF2 [416], FASN (fatty acid synthase) [417], SHH (sonic hedgehog signaling molecule) [418], DACH1 [419], FGF9 [420], SLC7A11 [421], VIP (vasoactive intestinal peptide) [422], KL (klotho) [423], BMPR2 [424], APOA1 [425], LRRK2 [426], TLR3 [427], GATA3 [428], RSPO2 [429], CCR2 [430], NEK7 [431], BMPER (BMP binding endothelial regulator) [432], CAV1 [433], CR1 [434], TFPI (tissue factor pathway inhibitor) [435], AP1S2 […”

Section: Discussionmentioning

confidence: 99%

Study on potential differentially expressed genes in idiopathic pulmonary fibrosis by bioinformatics and next generation sequencing data analysis

Vastrad,

Vastrad

2023

Preprint

View full text Add to dashboard Cite

Idiopathic pulmonary fibrosis (IPF) is a chronic progressive lung disease with reduced quality of life and earlier mortality, but its pathogenesis and key genes are still unclear. In this investigation, bioinformatics was used to deeply analyze the pathogenesis of IPF and related key genes, so as to investigate the potential molecular pathogenesis of IPF and provide guidance for clinical treatment. Next generation sequencing dataset GSE213001 was obtained from Gene Expression Omnibus (GEO), the differentially expressed genes (DEGs) were identified between IPF and normal control group. The DEGs between IPF and normal control group were screened with the DESeq2 package of R language. The Gene Ontology (GO) and REACTOME pathway enrichment analyses of the DEGs were performed. Using the g:Profiler, the function and pathway enrichment analysis of DEGs were performed. Then, a protein protein interaction (PPI) network was constructed via the Integrated Interactions Database (IID) database. Cytoscape with Network Analyzer was used to identify the hub genes. miRNet and NetworkAnalyst database was used to construct the targeted microRNAs (miRNAs) and transcription factors (TFs) of the hub genes. Finally receiver operating characteristic (ROC) curve analysis was used to validates the hub genes. A total of 958 DEGs were screened out in this study, including 479 up regulated genes and 479 down regulated genes. Most of the DEGs were significantly enriched in response to stimulus, GPCR ligand binding, microtubule-based process and defective GALNT3 causes HFTC. In combination with the results of the PPI network, miRNA-hub gene regulatory network and TF-hub gene regulatory network, hub genes including LRRK2, BMI1, EBP, MNDA, KBTBD7, KRT15, OTX1, TEKT4, SPAG8 and EFHC2 were selected. Our findings will contribute to identification of potential biomarkers and novel strategies for the treatment of IPF, and provide a novel strategy for clinical therapy.

show abstract

Variations in S100A8/A12 Gene Expression Are Associated with the Efficacy of Nintedanib and Acute Exacerbation Development in Idiopathic Pulmonary Fibrosis Patients

Cited by 2 publications

References 14 publications

Study on Potential Differentially Expressed Genes in Idiopathic Pulmonary Fibrosis by Bioinformatics and Next-Generation Sequencing Data Analysis

Study on Potential Differentially Expressed Genes in Idiopathic Pulmonary Fibrosis by Bioinformatics and Next-Generation Sequencing Data Analysis

Study on potential differentially expressed genes in idiopathic pulmonary fibrosis by bioinformatics and next generation sequencing data analysis

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