Global interpretation of novel alternative splicing events in human congenital pulmonary airway malformations: A pilot study

J Cell Biochem. 2022 Apr;123(4):736-745. doi: 10.1002/jcb.30216. Epub 2022 Jan 22.

Abstract

Little is known about differentially expressed genes (DEGs) and alternative splicing (AS) landscapes in congenital lung malformations (CLMs). We applied reference-based assembly of sequencing reads from RNA sequencing (RNA-seq) libraries to identify DEGs and AS landscapes in the lesions and normal lung tissue from the most common types of CLMs, including congenital pulmonary airway malformation-Ⅰ (CPAM-Ⅰ), CPAM-Ⅱ, intralobar sequestration (ILS), and ILS with CPAM (ILS-CPAM). We analyzed the expression profiles and related biological functions of AS events (ASEs). We further constructed a co-expression regulatory network between RNA binding protein (RBP) genes and corresponding ASEs to explore the related pathways in the regulated network. Ten DEGs were identified in the four types of CLMs, including eight upregulated genes and two downregulated genes. Additionally, 16 differential ASEs were detected, including the genes MACF1, RFX2, and FBXL4. Gene ontology (GO) enrichment was mainly observed in embryonic visual malformation and apoptotic process, and the KEGG pathway mainly enriched in the PI3K/AKT signaling pathway. We also detected 13 differentially expressed RBPs among 1979 DEGs in CPAM-I, in which ASEs in the MACF1 gene and RBP genes TLR8 and PTRH1 were closely associated. Moreover, we confirmed that the expression levels of PTRH1, NSUN7, and DZIP1L abundantly increased and the expression levels of TLR8, MEF2A, and NIPBL decreased in the CPAM-I lung tissue compared with the controls. It is suggested that ASEs in different types of CLMs is prominently different from normal controls, and ASEs differences occurring in CPAM-I malformation tissue are dramatically different from other types, which demonstrates the complex pathogenesis of CLMs and provides foundations for future studies to elucidate the mechanisms of developing CLMs.

Keywords: alternative splicing events; co-expression network; congenital lung malformations; differentially expressed genes; transcriptome analysis.

MeSH terms

  • Alternative Splicing* / genetics
  • Cell Cycle Proteins / genetics
  • Cystic Adenomatoid Malformation of Lung, Congenital* / genetics
  • Cystic Adenomatoid Malformation of Lung, Congenital* / metabolism
  • Cystic Adenomatoid Malformation of Lung, Congenital* / pathology
  • Humans
  • Phosphatidylinositol 3-Kinases / metabolism
  • Pilot Projects
  • Toll-Like Receptor 8 / genetics
  • Toll-Like Receptor 8 / metabolism

Substances

  • Cell Cycle Proteins
  • NIPBL protein, human
  • Toll-Like Receptor 8