Transcriptome Analysis of Wild Type and FGD5-AS1 knockdown CCC-HEH-2 cells

Purpose: According to the previous analysis results of gene regulation in fetal heart tissues with tetralogy of Fallot (ToF), we constructed the ceRNA mediated network driven by lncRNAs using a causal inference framework based on the expression correlations and validated miRNA-lncRNA/mRNA evidences. Totally 4 lncRNAs were identified as hub lncRNAs in the network, and FGD5-AS1 was focused for further loss-of-function investigation. Methods: The specific shRNAs against FGD5-AS1 (sh-FGD5-AS1) as well as the corresponding negative control (sh-NC) were constructed along with lentiviral vector respectively. Then the CCC-HEH-2 human cardiac myocytes cell lines were infected with lentivirus and followed puromycin treatment for several days. The knockdown efficiencies of the FGD5-AS1 expression were validated by qPCR. Genome-wide RNA expression of control and knockdown CCC-HEH-2 cell lines were observed using RNA-Seq. Conclusions: Knockdown of this lncRNA interferes with glutamate receptor activity and metalloendopeptidase inhibitor activity. The expression of abundant CHD genes with |fold change| = 2 was validated with qPCR. These results indicate that FGD5-AS1 plays an important role in CHD genes regulation networks. Overall design: For CCC-HEH-2 cell line, 3 sh-NC cells and 3 sh-FGD5-AS1 cells were used and analyzed. To identify FGD5-AS1 signatures, paired t-test was performed between control shRNA and FGD5-AS1 shRNA samples.