Hsa_circ_0012152 and Hsa_circ_0001857 Accurately Discriminate Acute Lymphoblastic Leukemia From Acute Myeloid Leukemia

Abstract

Acute leukemia (AL) is a group of highly heterogeneous hematological malignancies. Circular RNAs (circRNAs) are covalently closed circRNA molecules implicated in the development of many diseases. However, the role of circRNAs in AL remains largely unknown. Therefore, this study aimed to identify new classification diagnostic biomarkers for subgroups of AL. The circRNA expression signatures discriminating acute lymphoblastic leukemia (ALL) from acute myeloid leukemia (AML) were identified by microarray, followed by reverse transcription quantitative polymerase chain reaction (RT-qPCR) validation. Receiver operating characteristic curve analysis was used to evaluate the diagnostic efficiencies of hsa_circ_0001857 and hsa_circ_0012152, and hsa_circ_0012152 was selected for Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis. The results showed that the circRNA expression profiles, hsa_circ_0001857, and hsa_circ_0012152 could clearly discriminate ALL from AML. The target genes of hsa_circ_0012152 might be involved in biological processes, such as myeloid cell differentiation, covalent chromatin modification, histone modification, and rat sarcoma (Ras) protein signal transduction, and participate in pathways such as mitogen-activated protein kinase (MAPK) and phosphatidylinositol 3'-kinase (PI3K)-Akt signaling pathway. Hsa_circ_0012152 might be involved in the initiation and development of AML through miR-491-5p/epidermal growth factor receptor (EGFR)/MAPK1 or miR-512-3p/EGFR/MAPK1 axis. Our results showed that circRNA expression profiles and specifically expressed circRNAs were promising classification biomarkers to designate AL into ALL or AML.

Keywords: acute lymphoblastic leukemia; acute myeloid leukemia; bioinformatics; biomarker; circRNA.

FIGURE 1

Heatmap of differentially expressed circular RNAs (circRNAs) between acute lymphoblastic leukemia (ALL) and acute myeloid leukemia (AML). The horizontal axis shows the samples, and the vertical axis shows differentially expressed circRNAs. That is, there is one circRNA for each line, and one sample for each column. Red and gray indicate upregulated and downregulated expression, respectively, in ALL compared with AML; the darker the color, the greater the difference.

FIGURE 2

Volcano plot of differentially expressed circular RNAs (circRNAs) between acute lymphoblastic leukemia (ALL) and acute myeloid leukemia (AML). “Log₂ (fold change)” is plotted on the horizontal axis, and “-log₁₀ (FDR)” is plotted on the vertical axis; that is, the larger the “|log₂ (fold change)|,” the greater the difference, and the larger the “-log₁₀ (FDR),” the more significant the statistical difference. Tomato and aquamarine, respectively, represent the upregulated and downregulated circRNAs with |log₂FC| ≥ 2 and FDR < 0.05, while the gray represents the circRNAs with |log₂FC| < 2 or FDR ≥ 0.05.

FIGURE 3

Expression of hsa_circ_0001857 and hsa_circ_001252 in a cohort of patients with acute leukemia. *P < 0.05, **P < 0.01, ****P < 0.0001; NS, no significance.

FIGURE 4

The receiver operating characteristic (ROC) of hsa_circ_00012152 and hsa_circ_0001857 as classification biomarkers to discriminate acute lymphoblastic leukemia (ALL) from acute myeloid leukemia (AML).

FIGURE 5

Competing endogenous RNA (ceRNA) network indicating the potential functioning mechanism of hsa_circ_0012152. The top layer shows hsa_circ_0012152, the middle layer shows the five target microRNAs (miRNAs) of hsa_circ_0012152, and the bottom layer shows the target gens of miRNA. The lines between the boxes represent the interaction relationship.

FIGURE 6

Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genome (KEGG) functional annotation. (A) GO functional annotation of target genes. Green shows the six biological processes (BP) in which target genes are involved, brick red shows the six molecular functions (MF) of the target genes, and black shows the six cellular components (CC) of the target genes. (B) KEGG functional annotation of target genes. Each row shows a signaling pathway in which the hsa_circ_0012152 target genes may be involved.

FIGURE 7

Circos diagrams illustrating six biological processes in which target genes are involved. The right half of the figure shows six biological processes in which the target genes may be involved, including myeloid cell differentiation, and the left half of the figure shows the target genes involved in the six biological processes.