Profiling and functional analysis of circular RNAs in acute promyelocytic leukemia and their dynamic regulation during all-trans retinoic acid treatment

Abstract

Circular RNAs (circRNAs) are a novel class of powerful regulators in gene expression and participate in the pathogenesis of many diseases, including cancer. However, little is known about the roles of circRNAs in the development and treatment of acute promyelocytic leukemia (APL). Here we report the expression profiling and function of circRNAs in APL, including their dynamic regulation during all-trans retinoic acid (ATRA)-induced differentiation. We performed two independent ribosomal RNA-minus RNA-sequencing (Ribo-minus RNA-seq) experiments with and without RNase R treatment on APL patient-derived NB4 cells and identified a total of 4313 circRNAs, including 1098 newly identified circRNAs. Detailed analysis showed that circRNAs expressed in APL cells were mostly exon-derived, not by-products during splicing, and could be distinguished from hematopoietic stem cells, neutrophils and lymphocytes. The true presence and stability of circRNAs were verified both in NB4 cells and primary APL patient samples. Moreover, we conducted a time-series analysis of circRNAs on ATRA-treated NB4 cells and uncovered 508 circRNAs with dynamic expression during ATRA treatment, including 246 upregulated and 262 downregulated. Further evidence demonstrated that the majority of circRNAs were regulated independently of their host linear mRNAs. Detailed functional experiments demonstrated that circ-HIPK2, one of the differentially expressed circRNAs, significantly influenced ATRA-induced differentiation of APL cells. Further mechanistic studies revealed that circ-HIPK2 was located in cytoplasm and served as a sponge for differentiation-associated miR-124-3p. Finally, circ-HIPK2 expression in APL patients was significantly lower than that in normal peripheral mononuclear cells and other subtypes of AML, indicating its potential role as an APL biomarker. Our study indicates the biological functions of circRNAs in the development and treatment of APL, and provides a comprehensive circRNA resource for future studies.

Competing endogenous RNA network profiling reveals novel host dependency factors required for MERS-CoV propagation

“…The overall cir-cRNA expression profiles at these three time points were uniform and not significantly altered by MERS-CoV infection. Collectively, these basic characteristics of the putative circRNAs identified in our study were similar to those identified in other human and mammalian cells, including mouse P19 embryonic carcinoma, human neuroblastoma SH-SY5Y, and acute promyelocytic leukemia-derived NB4 [38][39][40].…”

Role of microRNAs, circRNAs and long noncoding RNAs in acute myeloid leukemia

“…Influence ATRA-induced differentiation of APL cells [155] circ-DLEU2 ↓in pediatric AML-M5 Hypermethylation of DLEU2 affected prognosis [156] ↑in CN-AML patients BMand AML cell lines…”

“…In recent years, the research of circRNAs, as one of ncRNAs, is focused on their function as "miRNA sponges" in the complex endogenous RNA networks. A circRNA HIPK2, for example, sponged miR-124-3p to regulate the differentiation of all-trans retinoic acid (ATRA)-induced NB4 cells [155]. Chen et al [151] reported that circANAPC7 was significantly upregulated in AML and used an Arraystar human circRNAs microarray and bioinformatics analysis to predict when ANAPC7 might bind miR-181 family to participate in AML pathogenesis.…”

Role of non-coding RNA networks in leukemia progression, metastasis and drug resistance

“…Recently, three-lncRNA expression-based risk score was developed based on RNA-seq data for AML patients using two leading data repositories [Therapeutically Available Research to Generate Effective Treatments (TARGET) and The Cancer Genome Atlas (TCGA)]. According to prognosis modelling, which was developed based on survival data, the combination of the lncRNA risk score and cytogenetics risk group provided a higher prognostic value than any of the individual prognostic factor [61].…”