Total RNA seq transcriptome profiling of thymocytes

Circular RNAs (circRNAs) are stable RNA molecules whose deregulation can drive disease and cancer mechanisms by impacting on their interactions with microRNAs and proteins and on expression of the encoded peptides. This study describes the landscape of circRNA expressed in T-cell Acute Lymphoblastic Leukemia (T-ALL). Analysis by CirComPara of RNA-seq data of 25 T-ALL patients of five genetic T-ALL subtypes and human thymocyte populations from healthy donors detected over 68,500 circRNAs. Further study of 3 447 highly expressed circRNAs derived mostly from exonic regions of 1,966 loci informed prominent differences in circRNA expression between normal and malignant T-cells, with 944 circRNAs differentially expressed in T-ALL, mostly upregulated. Next, circRNA expression signatures of different molecular genetic subgroups were defined. Examination of circRNA expression variation during thymocyte maturation and comparison with putative-cell of origin of each T-ALL subtype identified ectopic group-specific circRNAs, whose expression and backsplice sequence were confirmed in T-ALL cell lines. Our findings on circRNAs significantly extend previous data on expression of linear transcripts in subtypes of human T-ALL, opening functional investigation of deregulated circRNAs so far uncharacterized in human T-ALL, including a few for which oncogenic roles or molecular functions have been already proven in different settings. Profiling of the total RNA transcriptome of different CD34+ and DP stages of T cell development isolated from human postnatal thymus, for two or three donors.