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. 2022 Nov 28;12(1):20459.
doi: 10.1038/s41598-022-24858-3.

Application of second-generation sequencing in congenital pulmonary airway malformations

Gang Zhang  1 , Chun Cai  1 , Xiao Li  1 , Lei Lou  1 , Bin Zhou  1 , Huiyi Zeng  1 , Xiangang Yan  1 , Dandan Liu  2 , Gang Yu  3
Affiliations

Application of second-generation sequencing in congenital pulmonary airway malformations

Gang Zhang et al. Sci Rep. .

Abstract

To investigate the differential expression of genes in whole transcripts of congenital pulmonary airway malformation (CPAM) using second-generation sequencing (also known as next-generation sequencing, NGS) technology. Children with CPAM were strictly screened after setting the criteria, and grouped by taking CPAM parietal tissue and CPAM lesion tissue respectively, and RNA-Seq libraries were established separately using second-generation sequencing technology, followed by differential expression analysis and GO (gene ontology) functional enrichment analysis, KEGG (Kyoto encyclopedia of genes and genomes, a database) pathway analysis and GSEA (Gene Set Enrichment Analysis) analysis. Five cases were screened from 36 children with CPAM, and high-throughput sequencing was performed to obtain 10 whole transcripts of samples with acceptable sequence quality and balanced gene coverage. One aberrantly expressed sample (3b) was found by analysis of principal components, which was excluded and then subjected to differential expression analysis, and 860 up-regulated genes and 203 down-regulated genes. GO functional enrichment analysis of differentially expressed genes demonstrates the functional class and cellular localization of target genes. The whole transcript of CPAM shows obvious gene up and down-regulation, differentially expressed genes are located in specific cells and belong to different functional categories, and NGS can provide an effective means to study the transcriptional regulation of CPAM from the overall transcriptional level.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1
GSEA analys in CPAM parietal tissue vs CPAM lesion tissue.
Figure 2
Figure 2
Heatmap and Volcano plot of the differencited expression genes.
Figure 3
Figure 3
GO and KEGG analyse of DEGS. Left: GO functional analysis for DEGs were grouped into different functional categories: biological process (BF), cellular component (CC) and molecular function (MF). Right: Representative dot plot of top 10 significantly (P < 0.05) enriched KEGG pathways for DEGs.
Figure 4
Figure 4
PPI network for DEGs in CPAM. Genes in orange circles indicate upregulation, while genes in green circles indicate downregulation.
See this image and copyright information in PMC

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