Oncotarget

Research Papers:

Genome-wide analysis of aberrantly expressed lncRNAs and miRNAs with associated co-expression and ceRNA networks in β-thalassemia and hereditary persistence of fetal hemoglobin

Ketong Lai, Siyuan Jia, Shanjuan Yu, Jianming Luo and Yunyan He _

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Oncotarget. 2017; 8:49931-49943. https://doi.org/10.18632/oncotarget.18263

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Abstract

Ketong Lai1,2,*, Siyuan Jia1,*, Shanjuan Yu1, Jianming Luo1,2 and Yunyan He1,2

1Department of Pediatrics, The First Affiliated Hospital of Guangxi Medical University, Guangxi Zhuang Autonomous Region, Nanning 530021, China

2Guangxi Key Laboratory of Thalassemia Research, Guangxi Zhuang Autonomous Region, Nanning 530021, China

*These authors have contributed equally to this work

Correspondence to:

Yunyan He, email: yunyanhe@aliyun.com

Jianming Luo, email: jmluo@aliyun.com

Keywords: lncRNA, miRNA, ceRNA, β-thalassemia, hereditary persistence of fetal hemoglobin

Received: January 26, 2017    Accepted: May 05, 2017    Published: May 29, 2017

ABSTRACT

The implications of lncRNAs regarding fetal hemoglobin (HbF) induction in hemoglobin disorders remain poorly understood. In this study, microarray analysis was performed to profile lncRNAs, miRNAs and mRNAs in individuals with hereditary persistence of fetal hemoglobin (HPFH), β-thalassemia carriers with high HbF levels and healthy controls. The results show aberrant expression of 862 lncRNAs, 568 mRNAs and 63 miRNAs in the high-HbF group compared with the control group. Altered NR_001589, NR_120526, T315543, miR-486-3p, miR-19b-1-5p and miR-20a-3p expression was confirmed by quantitative reverse transcription-polymerase chain reaction, and Spearman correlation coefficients revealed significant positive correlations with HbF. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses showed the hematopoietic cell lineage and apoptosis to be most significantly dysregulated in HbF induction. We analyzed coding genes near the lncRNAs and constructed a coding-noncoding co-expression network. Based on the results, lncRNAs likely contribute to increased HbF levels by activating expression of HBE1 and hematopoietic cell lineage-inducible molecules and by inhibiting that of apoptosis-inducible molecules. Finally, through construction of a competing endogenous RNA network, we found that 6 lncRNAs could bind competitively with miR-486-3p, resulting in increased HbF levels. Taken together, our findings provide new insights into the mechanisms of HbF induction and potentially provide new targets for the treatment of β-thalassemia major.


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