Construction and analysis of a long non-coding RNA (lncRNA)-associated ceRNA network in β-thalassemia and hereditary persistence of fetal hemoglobin

Abstract

Background: Higher fetal hemoglobin (HbF) levels can ameliorate the clinical severity of β-thalassemia. The use of integrative strategies to combine results from gene microarray expression profiling, experimental evidence, and bioinformatics helps reveal functional long noncoding RNAs (lncRNAs) in β-thalassemia and HbF induction. Material/Methods: In a previous study, a microarray profiling was performed of 7 individuals with high HbF levels and 7 normal individuals. Thirteen paired samples were used for validation. lncRNA NR-001589 and uc002fcj.1 were chosen for further research. The quantitative reverse transcription-PCR was used to detect the expression levels of 2 lncRNAs. The Spearman correlation test was employed. The nuclear and cytoplasmic distribution experiment in K562 cells was used to verify the subcellular localization of 2 lncRNAs. Potential relationships among lncRNAs, predicted microRNAs (miRNAs), and target gene HBG1/2 were based on competitive endogenous RNA theory and bioinformatics analysis. Results: Average expression levels of NR-001589 and uc002fcj.1 were significantly higher in the high-HbF group than in the control group. A positive correlation existed between NR-001589, uc002fcj.1, and HbF. The expression of NR-001589 was in both the cytoplasm and the nucleus, mostly (77%) in the cytoplasm. The expression of uc002fcj.1 was in both the cytoplasm and the nucleus; the cytoplasmic proportion was 43% of the total amount. A triple lncRNA-miRNA-mRNA network was established. Conclusions: Novel candidate genetic factors associated with the HBG1/2 expression were identified. Further functional investigation of NR-001589 and uc002fcj.1 can help deepen the understanding of molecular mechanisms in β-thalassemia.