Characterization of circRNAs in leukemia using Oxford Nanopore sequencing technology: a comparison of short- and long-read RNA-seq data and a study of drug resistance

MLL rearranged Acute Lymphoblastic Leukemia (ALL) and Acute Myeloid Leukemia (AML) post-Myeloproliferative Neoplasms (MPN) are aggressive hematologic malignancies. The JAK/STAT pathway hyperactivation characterizes the latter. Circular RNAs (circRNAs), endogenous molecules that regulate gene expression, can be involved in disease mechanisms and provide disease biomarkers. The circRNA expression profile of the RS4;11 ALL cell line and of in vitro models of AML post-MPN were characterized through bioinformatics analysis of sequencing data obtained with the innovative Oxford Nanopore Technology (ONT), which allows sequencing the whole length of the transcripts. The RS4;11 circRNAome obtained by ONT and Illumina sequencing data were compared. Then, we studied circRNA expression profiles regarding AML resistance to the JAK inhibitor Ruxolitinib. Resistant, treated and parental SET2 and HEL cell lines were studied. CircRNA differentially expressed in cells resistant to Ruxolitinib were established. CircRNAs with expression affected by Ruxolitinib were also uncovered. Overall, ONT’s reliability and potential for circRNA studies were disclosed. New data about circRNAs linked to drug resistance in an aggressive AML have been provided, which prompt further investigation, posing the basis for a clearer view of the molecular mechanisms associated with this clinically relevant leukemia cell phenotype.