Construction and Analysis of a Long Non-Coding RNA (lncRNA)-Associated ceRNA Network in β-Thalassemia and Hereditary Persistence of Fetal Hemoglobin

Abstract

BackgroundHigher 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/MethodsIn 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.ResultsAverage 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.ConclusionsNovel 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.

Distinct miRNA Signatures and Networks Discern Fetal from Adult Erythroid Differentiation and Primary from Immortalized Erythroid Cells

“…Interestingly, miR-125a-5p and miR-142-3p were among the top 50 most significant HUDEP1_L vs. HUDEP2_L DE miRNAs. Of note, HBBP1 (NR_001589), another lncRNA recently identified as related to high γ-globin levels [ 102 ], is predicted to interact with five HUDEP1_L vs. HUDEP2_L DE miRNAs, including miR-18b-5p (HUDEP1_L vs. HUDEP2_L log 2 FC = 2.99), which was among the top 20 DE miRNAs based on p -value.…”

<p>LncRNA RP11-422N16.3 Inhibits Cell Proliferation and EMT, and Induces Apoptosis in Hepatocellular Carcinoma Cells by Sponging miR-23b-3p</p>

“…LncRNAs act as an endogenous "sponge" or ceRNA interacting with miRNA and exert their biological function by binding to their target genes. 28 To confirm whether lncRNA RP11-422N16.3 interacts with miR-23b-3p, we applied RNA-pull down assay and the results supported the binding relationship between RP11-422N16.3 and miR-23b-3p. As early as the 1950s, Warburg reported that pyruvate, which decomposes glucose in tumor cells, was converted to lactic acid in the presence of oxygen, rather than in the mitochondria, and was later called the "Warburg effect."…”

Debunking the “junk”: Unraveling the role of lncRNA–miRNA–mRNA networks in fetal hemoglobin regulation

“…A study on the construction of an lncRNA-associated ceRNA network revealed two candidates, NR_001589 and uc002fcj.1, that are significantly expressed in individuals with high HbF levels. The study predicted that these lncRNAs promote the expression of HBG1/2 by sponging miRNA and induce HbF production (Jia et al 2019). Microarray analysis in another study to profile lncRNAs, miRNAs and mRNAs in individuals having hereditary persistence of fetal hemoglobin has elucidated six lncRNAs that competitively sponge miR-486-3p, therefore elevating HbF level (Lai et al 2017).…”

“…Recently, some studies have demonstrated the emerging role of lncRNAs in the regulation of fetal hemoglobin (HbF) expression (Ivaldi et al 2018) (Jia et al 2019). It is expected that identification of new lncRNAs would contribute substantially to our understanding of the regulatory mechanisms of the γ-globin genes and hence bring us closer to developing new therapeutic strategies to treat beta-hemoglobinopathies like β-thalassemia and SCA disease.…”