Identification of hub genes of pneumocyte senescence induced by thoracic irradiation using weighted gene co-expression network analysis

Xing, Yonghua; Zhang, Junling; Lu, Lu; Li, Deguan; Wang, Yueying; Huang, Song; Li, Chengcheng; Zhang, Zhubo; Li, Jianguo; Meng, Aimin

doi:10.3892/mmr.2015.4566

Cited by 11 publications

(12 citation statements)

References 85 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…WGCNA has yielded novel insights into the molecular aspects to identify candidate biomarkers or therapeutic targets. At present, it has been increasingly applied to analyze various gene expression profiles of hepatocellular carcinoma [ 16 ], pneumocyte senescence induced by thoracic irradiation [ 17 ], psoriasis [ 18 ], severe asthma [ 19 ], coronary artery disease [ 20 ], and lung cancer [ 21 ], etc. Although widely being employed, the WGCNA has, to our knowledge, not yet been applied to analyze the expression profiles of BMI-discordant monozygotic twin pairs.…”

Section: Introductionmentioning

confidence: 99%

Weighted gene co-expression network analysis of expression data of monozygotic twins identifies specific modules and hub genes related to BMI

et al. 2017

View full text Add to dashboard Cite

BackgroundThe therapeutic management of obesity is challenging, hence further elucidating the underlying mechanisms of obesity development and identifying new diagnostic biomarkers and therapeutic targets are urgent and necessary. Here, we performed differential gene expression analysis and weighted gene co-expression network analysis (WGCNA) to identify significant genes and specific modules related to BMI based on gene expression profile data of 7 discordant monozygotic twins.ResultsIn the differential gene expression analysis, it appeared that 32 differentially expressed genes (DEGs) were with a trend of up-regulation in twins with higher BMI when compared to their siblings. Categories of positive regulation of nitric-oxide synthase biosynthetic process, positive regulation of NF-kappa B import into nucleus, and peroxidase activity were significantly enriched within GO database and NF-kappa B signaling pathway within KEGG database. DEGs of NAMPT, TLR9, PTGS2, HBD, and PCSK1N might be associated with obesity. In the WGCNA, among the total 20 distinct co-expression modules identified, coral1 module (68 genes) had the strongest positive correlation with BMI (r = 0.56, P = 0.04) and disease status (r = 0.56, P = 0.04). Categories of positive regulation of phospholipase activity, high-density lipoprotein particle clearance, chylomicron remnant clearance, reverse cholesterol transport, intermediate-density lipoprotein particle, chylomicron, low-density lipoprotein particle, very-low-density lipoprotein particle, voltage-gated potassium channel complex, cholesterol transporter activity, and neuropeptide hormone activity were significantly enriched within GO database for this module. And alcoholism and cell adhesion molecules pathways were significantly enriched within KEGG database. Several hub genes, such as GAL, ASB9, NPPB, TBX2, IL17C, APOE, ABCG4, and APOC2 were also identified. The module eigengene of saddlebrown module (212 genes) was also significantly correlated with BMI (r = 0.56, P = 0.04), and hub genes of KCNN1 and AQP10 were differentially expressed.ConclusionWe identified significant genes and specific modules potentially related to BMI based on the gene expression profile data of monozygotic twins. The findings may help further elucidate the underlying mechanisms of obesity development and provide novel insights to research potential gene biomarkers and signaling pathways for obesity treatment. Further analysis and validation of the findings reported here are important and necessary when more sample size is acquired.Electronic supplementary materialThe online version of this article (10.1186/s12864-017-4257-6) contains supplementary material, which is available to authorized users.

show abstract

Section: Introductionmentioning

confidence: 99%

Weighted gene co-expression network analysis of expression data of monozygotic twins identifies specific modules and hub genes related to BMI

et al. 2017

View full text Add to dashboard Cite

show abstract

“…One of the aims of WGCNA is to identify the hub genes associated with clinical traits. It has previously been suggested that hub genes may serve crucial roles in pneumocyte senescence (19) and plasmodium falciparum (20). This indicates that the hub genes may serve as candidate biomarkers and therapeutic targets for disease.…”

Section: Resultsmentioning

confidence: 99%

Exploration of the hub genes and miRNAs in lung adenocarcinoma

Zhai

Chen

et al. 2019

Oncol Lett

View full text Add to dashboard Cite

In order to investigate the oncogenic mechanisms of lung adenocarcinoma (LUAD), hub genes can be identified by constructing co-expression networks, and the potential linkages between hub genes, transcription factors (TFs) and microRNAs (miRNAs/miRs) can be visualized and identified. In the present study, a total of 12 co-expressed modules were constructed, and 9 of these were significantly correlated with clinical traits in LUAD. The differentially expressed genes and differentially expressed miRNAs were determined, and the targets of differentially expressed miRNA were identified from the hub genes or TFs. The results of the present study demonstrated that 10 hub genes and 12 TFs are the predicted targets for the 5 and 8 differentially expressed miRNAs, respectively. Genes in pink and red modules, which have a high correlation with the clinical trait of days to death, are significantly enriched in ‘nucleosome assembly’ and ‘microtubule-based process’, respectively. These results indicated that miR-206, miR-137, miR-153, hub genes and enriched TFs in the pink and red modules exert a potentially pivotal function in the development of LUAD.

show abstract

“…AREG E2F1 FOXO3 HDAC1 MMP2, TGFB1 and TP53 have been veri ed to be the key molecules through different pathways in asthma [32,[50][51][52][53][54][55][56]. Although ATG3 is a key molecule that inducing autophagy damage during aging [57], and NUF2 is a gene closely related to aging of lung cells [58], their speci c role in asthma has rarely been studied. The differential expression of ATG3, FOXO3, NUF2 and TP53 in asthma patients were also aligned with former studies [32,[58][59][60].…”

Section: Discussionmentioning

confidence: 99%

“…Although ATG3 is a key molecule that inducing autophagy damage during aging [57], and NUF2 is a gene closely related to aging of lung cells [58], their speci c role in asthma has rarely been studied. The differential expression of ATG3, FOXO3, NUF2 and TP53 in asthma patients were also aligned with former studies [32,[58][59][60]. In addition, excessive secretion of AREG in the airway after an acute attack of asthma promote airway remodeling [56].…”

Section: Discussionmentioning

confidence: 99%

Variable Expressed Methylation Sites of Aging-related Genes in Asthma

Yang¹,

Lin²,

Yang³

et al. 2020

Preprint

View full text Add to dashboard Cite

Background: Asthma is a complex pulmonary inflammatory disease which is common in the elderly. Aging-related alterations have also been found in the structural cells and immune cells of asthma patients although the pathological mechanism of the differential aging-related gene in the development of asthma is still obscure. Of note, DNA methylation (DNAm) have been proven to play an important role in the regulation of aging-related genes. However, the methylation levels of aging-related genes in asthma patients are largely unclear.Methods: First, the mRNA levels and DNAm level of the previous screened 9 aging-related genes in peripheral blood of 51 healthy controls (HCs) and 55 asthmatic patients were detected by multiple targeted bisulfite enrichment sequencing (MethTarget) and qPCR. Secondly, the correlation between the DNAm level of specific altered CpG sites and the pulmonary function indicators of asthma patients was evaluated. Lastly, the Receiver Operator Characteristic (ROC) curve and Principal Component Analysis (PCA) were used to identify the feasibility of the candidate CpG sites as asthma markers.Results: The mRNA expression of the 9 aging-related gene in peripheral blood of asthma patients was significantly different from those of HCs. Besides, the methylation level of the 9 aging-related genes also altered in asthma patients, and a total of 68 CpG sites were related to the severity of asthma. Notably, 10 of the 68 CpG sites had a significant relationship with pulmonary function parameters. Moreover, ROC curve and PCA analysis showed that the candidate differential methylation sites (DMSs) can be used as potential biomarkers for asthma.Conclusions:In summary, this study confirmed the changes in the mRNA expression and DNAm level of aging-related genes in asthma patients. The differential DMSs are associated with the clinical evaluation indicators of asthma, which may indicate the involvement of aging-related genes in the pathogenesis of asthma and provide some new possible biomarker of asthma.

show abstract

Identification of hub genes of pneumocyte senescence induced by thoracic irradiation using weighted gene co-expression network analysis

Cited by 11 publications

References 85 publications

Weighted gene co-expression network analysis of expression data of monozygotic twins identifies specific modules and hub genes related to BMI

Weighted gene co-expression network analysis of expression data of monozygotic twins identifies specific modules and hub genes related to BMI

Exploration of the hub genes and miRNAs in lung adenocarcinoma

Variable Expressed Methylation Sites of Aging-related Genes in Asthma

Contact Info

Product

Resources

About