Potential function exploration of lncRNAs in idiopathic pulmonary fibrosis: insights from whole transcriptome sequencing data analysis.

BACKGROUND

Research has shown that long noncoding RNAs (lncRNAs) play a role in Idiopathic Pulmonary Fibrosis (IPF), but their specific functions and patterns of expression are still unclear.

METHOD

A diagnostic study was conducted by utilizing analysis techniques. RNA sequencing (RNA-seq) data from 12 IPF patients and 5 controls was used to study lncRNA functions in IPF. The authors identified Differentially Expressed lncRNAs (DElncRNAs) and explored co-expression networks in a transient manner, as well as using Weighted Gene Co-expression Network Analysis (WGCNA) to identify modules associated with IPF.

RESULTS

The study found 541 differentially expressed lncRNAs in IPF, with 201 up-regulated and 340 down-regulated. DElncRNAs, especially the up-regulated, were significantly correlated with DEmRNAs at their expression levels. DEmRNAs showed extracellular matrix-related biological functions in addition to increased lncRNAs. WGCNA results demonstrated that Module Eigengene green (MEgreen) and MEred modules indicated the highest negative correlation significance with IPF phenotype, and eigengene patterns of both modules were downregulated in IPF samples. The authors identified six significant lncRNAs in these two modules, including FAM13A-AS1, RP11-180C16.1, MYO16-AS1, AC007278.2, BACH1-IT2, and RP11-153M7.5, and their co-expressed DE mRNAs were enriched in inflammatory response pathways. The authors used single-cell RNA sequencing (scRNA-seq) data to investigate dysregulated lncRNAs and their co-expressed mRNAs. The authors found that five DEmRNAs that were co-expressed with DElncRNAs exhibited dysregulated expression patterns in multiple cell types of the IPF samples.

CONCLUSION

LncRNAs are functionally active and potentially involved in the inflammatory response in pathological processes of IPF. It is also important to consider some specific lncRNAs as potential diagnostic biomarkers or therapeutic targets for preclinical and clinical studies with IPF in the future.