AUTHOR=Huang Kai , Wu Lujia , Gao Yuan , Li Qin , Wu Hao , Liu Xiaohong , Han Lin 

TITLE=Transcriptome Sequencing Data Reveal LncRNA-miRNA-mRNA Regulatory Network in Calcified Aortic Valve Disease

JOURNAL=Frontiers in Cardiovascular Medicine

VOLUME=Volume 9 - 2022

YEAR=2022

URL=https://www.frontiersin.org/journals/cardiovascular-medicine/articles/10.3389/fcvm.2022.886995

DOI=10.3389/fcvm.2022.886995

ISSN=2297-055X

ABSTRACT=Background: Calcified aortic valve disease (CAVD) is one of the most common valvular heart diseases in the elderly population. However, no effective medical treatments have been found to interfere the progression of CAVD, and specific molecular mechanisms of CAVD remain unclear.
Methods: Transcriptome sequencing data of GSE55492 and GSE148219 were downloaded from European Nucleotide Archive, and microarray dataset GSE12644 was acquired from the Gene Expression Omnibus database. Software, including fastqc, HISAT2, samtools, and featureCounts were applied to generate read count matrix. The “limma” package in R was utilized to analyze differently expressed genes. Thereafter, weighted gene co-expression network analysis, Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, and the PPI network were used to identify hub genes associated with CAVD, which were further validated by receiver operating characteristic curve analysis using GSE12644. The LncRNA-mediated regulatory network was established based on the differentially expressed LncRNAs and hub genes, which were detected using qRT-PCR in clinical samples and valve interstitial cells. Moreover, CIBERSORT was used to calculate the expression distribution of immune cell infiltration in CAVD.  
Results: 126 DEGs were included in the PPI network. PI3K-Akt signaling pathway, ECM-receptor interaction, Hematopoietic cell lineage, Cell adhesion molecules, Focal adhesion were the mostly enriched pathways revealed by KEGG. Four LncRNAs, including TRHDE-AS1, LINC00092, LINC01094, LINC00702 were considered as the differentially expressed LncRNA. SPP1, TREM1, GPM6A, CCL19, CR1, NCAM1, CNTN1, TLR8, SDC1, COL6A6 were the 10 hub genes identified to associated with CAVD. Moreover, the calcified aortic valve samples had a greater level of Tregs, naïve B cells and M0 macrophages than the noncalcified ones, whereas CAVD samples had a lower M2 macrophages expression compared to the noncalcified valve tissues.
Conclusion: The current study identified SPP1, TREM1, TLR8, SDC1, GPM6A and CNTN1 as hub genes that could potentially be associated with CAVD. The LINC00702–miR-181b-5p–SPP1 axis might participate in the development of CAVD. Additionally, we found that M2 macrophages, Tregs, naïve B cells, and M0 macrophages could possibly play a role in the initiation of CAVD.