miRNA Profiling of Pediatric ALL and Non-Hodgkin Lymphomas.
Authors: Landgraf Pablo , Rice Amanda , Iovino Nicola , Fulci Valerio , Sheridan Robert , Fuchs Uta , Schmid Irene , Sander Chris , Chen Minchen , Russo James J. , Ju Jungyue , Tam Wayne , Macino Giuseppe , Zavolan Mihaela , Borkhardt Arndt , Tuschl Thomas 
Published: April 2020

MicroRNAs (miRNAs) are conserved 21−23 nt non-coding RNA molecules that regulate gene expression either by mRNA cleavage or by repression of mRNA translation. miRNAs regulate many different processes, including apoptosis and cell proliferation and may therefore also play a critical role in oncogenic transformation. To date, most miRNAs have been discovered by cDNA cloning and sequencing, though other profiling methods, such as miRNA micro-arrays, have recently been applied. Profiling of miRNA expression by cloning has the advantage of identifying new miRNA genes, and if a large number of clones are sequenced, to also be quantitative. In addition the exact sequence is determined and polymorphisms and mutations in any miRNAs can readily be detected. To get an insight in the role of miRNAs in the differentiation and maturation of hematopoetic cells as well as their contribution to oncogenesis in ALL and lymphomas, we cloned and sequenced various cell lines and patient samples:five cell lines (B-ALL, AML, Burkitt Lymphoma); samples from sorted blood cells covering pluripotent stem cells, B-, T-, NK- cells, monocytes and granulocytes; eight patient samples with ALL (2 pro-B-ALL, 2 pre-B-ALL, 2 cALL, 2 T-ALL) at the time point of diagnosis; four additional samples of these patients with B-ALL and two samples of T-ALL patients each after 36 days of treatment according to the protocol of the German Cooperative Acute Lymphoblastic Leukemia study group (COALL-07-03). We also recorded the small RNA profiles of three patients with various forms of AML at diagnosis and after the first induction according to the protocol of the AML-BFM 2004 study; two Burkitt lymphoma samples and one B-Non Hodgkin Lymphoma (B-NHL) sample. We report here the identification of over 20 novel human miRNAs in these samples. To determine specific expression patterns, the miRNA profiles were compared to a reference set of 22 different human tissue types. Some miRNAs are expressed in a cell or tissue specific manner, others have a more general expression pattern between different cell types and tissues. For example human miRNA miR-142 is ubiquitously expressed in cells of the hematopoetic lineage, whereas human miR-150 is only expressed in differentiated hematopoetic cells, but not in hematopoetic stem cells. In hematopoetic stem cells human miR-126 is 3 to more than 10 times higher expressed than in differentiated hematopoetic cells. The existence of the latter two in humans are first described in this study. miR-16 on the other hand is expressed in all cell types examined including non-hematopoetic. Furthermore, miRNAs are up/down-regulated in ALL and NHL patient samples. In conclusion, this study identifies miRNAs that might be involved in hematopoetic cell differentiation and maturation and is important to identify miRNAs that might contribute to oncogenesis in leukemia and lymphomas.