CircRNAs Dysregulated in Juvenile Myelomonocytic Leukemia: CircMCTP1 Stands Out

Abstract

Juvenile myelomonocytic leukemia (JMML), a rare myelodysplastic/myeloproliferative neoplasm of early childhood, is characterized by clonal growth of RAS signaling addicted stem cells. JMML subtypes are defined by specific RAS pathway mutations and display distinct gene, microRNA (miRNA) and long non-coding RNA expression profiles. Here we zoom in on circular RNAs (circRNAs), molecules that, when abnormally expressed, may participate in malignant deviation of cellular processes. CirComPara software was used to annotate and quantify circRNAs in RNA-seq data of a “discovery cohort” comprising 19 JMML patients and 3 healthy donors (HD). In an independent set of 12 JMML patients and 6 HD, expression of 27 circRNAs was analyzed by qRT-PCR. CircRNA-miRNA-gene networks were reconstructed using circRNA function prediction and gene expression data. We identified 119 circRNAs dysregulated in JMML and 59 genes showing an imbalance of the circular and linear products. Our data indicated also circRNA expression differences among molecular subgroups of JMML. Validation of a set of deregulated circRNAs in an independent cohort of JMML patients confirmed the down-regulation of circOXNAD1 and circATM, and a marked up-regulation of circLYN, circAFF2, and circMCTP1. A new finding in JMML links up-regulated circMCTP1 with known tumor suppressor miRNAs. This and other predicted interactions with miRNAs connect dysregulated circRNAs to regulatory networks. In conclusion, this study provides insight into the circRNAome of JMML and paves the path to elucidate new molecular disease mechanisms putting forward circMCTP1 up-regulation as a robust example.

CircIMPACT: An R Package to Explore Circular RNA Impact on Gene Expression and Pathways

“…We verified that running CircIMPACT with the k-means option for sample separation, circHIPK3 remains in the top 25. In accordance with Li et al [24], among the differentially expressed circRNAs, CircIM-PACT identified circHIPK3, which is downregulated in the automatically defined group (g1), corresponding to bladder cancer samples (Figure 3B). Different circRNAs can separate sample groups in different ways, according to the experimental design, the dataset type and structure.…”

“…To demonstrate CircIMPACT functions and potential we conducted a sample analysis using bladder cancer and matched control tissue data. CircIMPACT analysis identified HPSE dysregulation according to circHIPK3 expression reduction in bladder cancer, in line with the non-canonical regulatory axis previously proven and linked to the disease [ 24 ]. In our sample analysis, the software was applied to a relatively small and simple dataset.…”

“…These new hints indicated circRNAs that are worth study, to provide novel insights into bladder cancer. For instance, circZNF208 (19:21974728-21988909) and circFER1L4 (20:35595476-35595754), resulting in respectively down-and upregulation in bladder cancer, were previously detected by Li et al [24] but not functionally investigated, whereas they were selected in the top 25 circRNAs by our analysis. Both circZNF208 and circFER1L4 are poorly characterized and might deserve further study.…”

“…The ceRNA function was the first described for circRNAs [ 1 , 22 ] and has important implications in cancer. We and other groups used custom integrative analysis of circRNA, miRNA, and gene expression data, with systems biology methods, to infer circRNA regulatory networks [ 23 , 24 , 25 , 26 ]. Besides, the Cerina tool for predicting biological functions of circRNAs based on the ceRNA model was recently made available [ 27 ].…”

CRAFT: a bioinformatics software for custom prediction of circular RNA functions

“…These peculiar RNAs regulate several biological processes with different mechanisms. Moreover, circRNAs are emerging as key oncogenic or tumour suppressor molecules whose expression is dysregulated in disease, cancer and when genomic translocations occur [4][5][6]. They represent stable diagnostic and prognostic markers [7,8].…”