Abstract 2466: A comprehensive genome-wide analysis of small noncoding RNAs in T-cell prolymphocytic leukemia
Authors: Leticia G. Leon, Steven C. Koetzier, Fabiënne van Opstal, Joyce Schilperoord-Vermeulen, Anton W. Langerak, Stefan J. Erkeland
Journal: Cancer Research (2018)

Abstract T-cell prolymphocytic leukemia (T-PLL) is a rare type of neoplasm with an adverse prognosis due to poor responsiveness to conventional chemotherapies. Accurate and rapid diagnosis of T-PLL is problematic due to the heterogeneous nature of the disease. Therefore, further molecular insights of T-PLL are needed. Most of the T-PLL cases (80%) harbor chromosome 14 inversions and translocations or activating mutations in the JAK-STAT pathway. Small non-coding RNAs (sncRNA) are defined as single stranded RNAs that are smaller than 200nt in length and include e.g. microRNAs (miR), small nucleolar RNA (snoRNA) and PIWI-interacting RNAs (piRNA). To increase the molecular understanding of T-PLL, we performed sncRNA expression profiling with the Illumina platform on a well-characterized panel of 21 T-PLL samples. Notably, detailed molecular, cytogenetic, morphologic and clinical data are available of all T-PLL patients included in this study. Of the selected samples, we performed gene expression profiling by microarrays, cytogenetics, VDJ-recombination and multi-color flow cytometric analysis. In short, we sorted CD4+ and CD8+ naïve (CD45RA+, CD27+), effector (CD45RA+, CD27-) and memory (CD45RO+, CD27+) T-cells, and TCRγδ+ T-cells from Ficoll separated PBMCs of buffy coat blood. Total RNA of leukemic cells isolated from the blood was extracted and cDNA libraries for sequencing sncRNAs were generated. For the annotation of the sequence reads we used the DASHR database of sncRNAs and miRbase database of mature miRs. SnoRNA (16%) and ribosomal (r) RNAs (25%) were the most abundant, whereas miRs were only 12% of the total sncRNA fraction. Next, we performed a correlation study using the expression profiles of the different types of sncRNAs and found a clear separation of T-PLL samples from the normal T-cell fractions when miRNA, piRNA and snoRNA expression profiles were used in the analysis. In addition, based on these data we could already identify potential subgroups of T-PLL, indicating that T-PLL is not a homogeneous disease. Finally, we noted aberrant expression of different types of sncRNAs compared to normal T-cell fractions, which may be indicative for essential roles of sncRNA species in the pathogenesis of T-PLL. Currently, we are in the process of characterizing sncRNA species that are aberrantly regulated specifically in T-PLL. Finally, we are selecting candidate sncRNAs for further functional characterization and for testing their diagnostic and/or prognostic value. Citation Format: Leticia G. Leon, Steven C. Koetzier, Fabiënne van Opstal, Joyce Schilperoord-Vermeulen, Anton W. Langerak, Stefan J. Erkeland. A comprehensive genome-wide analysis of small noncoding RNAs in T-cell prolymphocytic leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2466.