MicroRNA signatures in Genetic Subtypes of T-Cell Acute Lymphoblastic Leukemia.
Authors: Van Vlierberghe Pieter , Poppe Bruce , Van Roy Nadine , Taghon Tom , Plum Jean , Cauwelier Barbara , Selleslag Dominik L.D. , Heimann Pierre , Vandenberghe Peter , Dastugue Nicole , Delabesse Eric , Gervais Carine , Gregoire Marie-Jose , Mozzicconacci Marie-Joelle , Lefebvre Christine , Meijerink Jules P.P. , Buijs-Gladdines Jessica , De Moerloose Barbara , Benoit Yves , Speleman Frank 
Published: October 2019

Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignancy of thymocytes that accounts for about 15 percent of ALL cases. Leukemic transformation of immature thymocytes is caused by a multistep pathogenesis involving numerous genetic abnormalities providing uncontrolled cell growth. Accumulating evidence suggests the presence of at least 5 different molecular-cytogenetic subgroups in T-ALL, ie. TAL/LMO, TLX1, TLX3, HOXA and MYB.
Recently, non coding microRNAs were discovered as important regulators of gene and/or protein expression and subsequently shown to be directly implicated in cancer. Nevertheless, it is currently unclear in which way deregulated miRNA expression may contribute to the pathogenesis of T-cell acute leukemia. In this study, we investigated whether different genetic subgroups in T-ALL are characterized by distinct miRNA expression patterns. Therefore, we profiled a total of 360 miRNAs through automated qRT-PCR using high-throughput quantitative stem-loop RT-PCR in a genetically well characterized T-ALL patient cohort (n=52), including 11 HOXA (3 MLL rearranged, 5 inv(7)(p15q35) and 3 CALM-AF10), 16 TAL/LMO (7 LMO2 rearranged, 8 TAL1 rearranged, 1 LMO2/TAL1 rearranged), 11 TLX3 and 5 TLX1 rearranged patient samples. Since T-ALL blasts originate from maturating T lymphocytes, we also profiled different subsets of sorted T-cell populations (CD34+, CD4+/CD8+/CD3−, CD4+/CD8+/CD3+, CD4+ SP and CD8+ SP). These miRNA profiles of normal T-cells served as a negative control for the identification of deregulated miRNA expression that may be truly leukemia associated. SAM analysis (t-test and wilcoxon, FDR=0) identified significant and differentially expressed miRNAs between the HOXA, TLX3 and TAL/LMO subgroups. No significant and differentially expressed miRNAs were obtained for the TLX1 subgroup, probably due to the limited number of patient samples. The HOXA subgroup showed specific up-regulation of miR-196a and miR-196b, which are encoded at the HOXB and HOXA cluster, respectively, but no significantly down-regulated miRNAs could be identified in this subgroup. The TLX3 subgroup was uniquely characterized by the up-regulation of miR-99a, miR-125b, let-7c, miR-508 and miR-509, and down-regulation of miR-127 and miR-182. Finally, specific up-regulation of miR-424, miR-148a, miR-422, miR-362, miR-148a, miR-502, miR-10a, miR-200c, miR-31, miR-660 and miR-15b, was identified in the TAL/LMO rearranged subgroup, which was also characterized by the specific down-regulation of miR-99b, miR-155, miR-125a, miR-153, miR-135a, miR-34a and miR-193b. Next, we evaluated the expression pattern of all significant and differentially expressed miRNAs in the different subsets of sorted T-cell populations. The expression patterns of these miRNAs could be classified into consistently active, completely absent or temporally regulated during T-cell development. For the miRNAs showing a temporal regulation during T-cell maturation, their differential expression in T-ALL subtypes may reflect differences in the maturation arrest of the T-cell of origin, rather than pointing to an oncogenic event. Nevertheless, their constitutive (in)activation in primary T-ALL patients could still be of oncogenic relevance, similar to transcription factors like TAL1 or LMO2 which also show a temporal regulation during T-cell maturation. In contrast, some other miRNAs showed no expression in any of the T-cell populations, providing stronger evidence that their activation in specific T-ALL subtypes may contribute to T-ALL pathogenesis. In conclusion, this study shows that molecular-cytogenetic subgroups in T-ALL are characterized by a specific miRNA expression signature. In addition, correlation of our findings to the expression of these miRNAs in normal T-cell subsets may guide us to the miRNAs with true oncogenic potential. This report paves the way for further investigation directed at the role of these miRNAs in the pathogenesis of T-ALL, which may provide us with further insight in the oncogenic pathways that are (in)activated in different T-ALL subgroups. Ultimately, these deregulated miRNAs may offer new targets for therapeutic intervention.