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.

Cancer Research Institute Ghent Ghent Belgium

Center for Medical Genetics Ghent University Hospital Ghent Belgium

Department of Biology University of Padova Padua Italy

Department of Diagnostic Sciences Ghent University Hospital Ghent Belgium

Department of Genetics University Hospital of Robert Debré Paris France

Department of Maternal and Child Health Padua University Padua Italy

Department of Molecular Medicine University of Padova Padua Italy

Department of Pediatric Hematology Oncology and Stem Cell Transplantation Ghent University Hospital Ghent Belgium

Department of Pediatric Hematology Oncology Charles University and University Hospital Motol Prague Czechia

Division of Pediatric Hematology and Oncology Department of Pediatrics and Adolescent Medicine University of Freiburg Freiburg Germany

Dutch Childhood Oncology Group The Hague Netherlands

INSERM U1131 Institut de Recherche Saint Louis Université de Paris Paris France

Interdepartmental Research Center for Innovative Biotechnologies University of Padova Padua Italy

Onco Hematology Stem Cell Transplant and Gene Therapy Laboratory IRP Istituto di Ricerca Pediatrica Padua Italy

Princess Máxima Center for Pediatric Oncology Utrecht Netherlands

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