Clinical and functional significance of circular RNAs in cytogenetically normal AML
Dimitrios Papaioannou, Stefano Volinia, Deedra Nicolet, Michał Świerniak, Andreas Petri, Krzysztof Mrózek, Marius Bill, Felice Pepe, Christopher J. Walker, Allison E. Walker, Andrew J. Carroll, Jessica Kohlschmidt, Ann-Kathrin Eisfeld, Bayard L. Powell, Geoffrey L. Uy, Jonathan E. Kolitz, Eunice S. Wang, Sakari Kauppinen, Adrienne M. Dorrance, Richard M. Stone, John C. Byrd, Clara D. Bloomfield, Ramiro Garzon
Abstract
Circular RNAs (circRNAs) are noncoding RNA molecules that display a perturbed arrangement of exons, called backsplicing. To examine the prognostic and biologic significance of circRNA expression in cytogenetically normal acute myeloid leukemia (CN-AML), we conducted whole-transcriptome profiling in 365 younger adults (age 18-60 years) with CN-AML. We applied a novel pipeline, called Massive Scan for circRNA, to identify and quantify circRNA expression. We validated the high sensitivity and specificity of our pipeline by performing RNase R treatment and RNA sequencing in samples of AML patients and cell lines. Unsupervised clustering analyses identified 3 distinct circRNA expression-based clusters with different frequencies of clinical and molecular features. After dividing our cohort into training and validation data sets, we identified 4 circRNAs (circCFLAR, circKLHL8, circSMC1A, and circFCHO2) that were prognostic in both data sets; high expression of each prognostic circRNA was associated with longer disease-free, overall, and event-free survival. In multivariable analyses, high circKLHL8 and high circFCHO2 expression were independently associated with better clinical outcome of CN-AML patients, after adjusting for other covariates. To examine the biologic relevance of circRNA expression, we performed knockdown screening experiments in a subset of prognostic and gene mutation-related candidate circRNAs. We identified circFBXW7, but not its linear messenger RNA, as a regulator of the proliferative capacity of AML blasts. In summary, our findings underscore the molecular associations, prognostic significance, and functional relevance of circRNA expression in CN-AML.