Integrated WGCNA and PPI Network to Screen Hub Genes Signatures for Infantile Hemangioma.

Miao Xu,Xiaorong Ma,Kaiyang Lv,Tianxiang Ouyang

doi:10.3389/fgene.2020.614195

Miao Xu, Xiaorong Ma + Show 2 more

Open Access

https://doi.org/10.3389/fgene.2020.614195

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Abstract

BackgroundInfantile hemangioma (IH) is characterized by proliferation and regression.MethodsBased on the GSE127487 dataset, the differentially expressed genes (DEGs) between 6, 12, or 24 months and normal samples were screened, respectively. STEM software was used to screen the continued up-regulated or down-regulated in common genes. The modules were assessed by weighted gene co-expression network analysis (WGCNA). The enrichment analysis was performed to identified the biological function of important module genes. The area under curve (AUC) value and protein-protein interaction (PPI) network were used to identify hub genes. The differential expression of hub genes in IH and normal tissues was detected by qPCR.ResultsThere were 5,785, 4,712, and 2,149 DEGs between 6, 12, and 24 months and normal tissues. We found 1,218 DEGs were up-regulated or down-regulated expression simultaneously in common genes. They were identified as 10 co-expression modules. Module 3 and module 4 were positively or negatively correlated with the development of IH, respectively. These two module genes were significantly involved in immunity, cell cycle arrest and mTOR signaling pathway. The two module genes with AUC greater than 0.8 at different stages of IH were put into PPI network, and five genes with the highest degree were identified as hub genes. The differential expression of these genes was also verified by qRTPCR.ConclusionFive hub genes may distinguish for proliferative and regressive IH lesions. The WGCNA and PPI network analyses may help to clarify the molecular mechanism of IH at different stages.

Highlights

Infantile hemangioma (IH) is a benign tumor in children, and its rapid growth can lead to serious morbidity and even mortality (Zhu et al, 2018)
By constructing the protein-protein interaction (PPI) network, we identified the top five genes (FYN, KIF20A, POLD1, RAD54L, and TYMS) with the highest degree of connectivity in the network as hub genes (Figure 4B)
Bioinformatic methods were used to screen genes related to the development of infant hemangioma

Summary

Introduction

Infantile hemangioma (IH) is a benign tumor in children, and its rapid growth can lead to serious morbidity and even mortality (Zhu et al, 2018). It is estimated that 10% of infants have IH, and the frequency of hemangiomas in preterm infants with birth weight less than 1 kg increases to 22.9% (Blei, 2005). The life cycle of hemangioma is divided into three stages. After tumor regression, 40–80% of IH will leave a permanent scar or a large amount of adipose tissue, especially in facial lesions, which can lead to deformity (Boscolo and Bischoff, 2009). Infantile hemangioma (IH) is characterized by proliferation and regression

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