UBC Theses and Dissertations
MiRNAs in hematopoiesis and leukemogenesis Kuchenbauer, Florian
MicroRNAs (miRNAs) have been shown to play important roles in physiological as well as multiple malignant processes including acute myeloid leukemia (AML). In an effort to gain further insight into the role of miRNAs in AML, we have applied the Illumina massively parallel sequencing platform to carry out an in depth analysis of the miRNA transcriptome in a murine leukemia progression model, based on the engineered over-expression of the nucleoporin 98(NUP98)-homeobox HOXD13 fusion gene (ND13), followed by conversion into AML inducing cells upon transduction with the oncogenic collaborator Meis1. Of the over 307 identified miRNA/miRNA* species in both libraries, sequence counts varied between 2 and 136,558, indicating a remarkable expression range. Our finding of extensive sequence variations (isomiRs) for almost all miRNA and miRNA* species adds additional complexity to the miRNA transcriptome. A stringent target prediction analysis coupled with in-vitro target validation revealed the potential for miRNA-mediated release of oncogenes that facilitates leukemic progression from the preleukemic to leukemia inducing state. Besides over 50 putative novel miRNAs, we found a high abundance of miRNA* species, implying a functional role for these. To further elucidate the function of miRNA*s, we took advantage of 9 deep sequencing libraries from a variety of cell lines to determine the most abundant complementary strand of know miRNAs. Comparing miRNA/miRNA* ratios across the miRNA sequence libraries revealed that most ratios remain constant across tissues and species, allowing a novel classification of miRNAs into α-duplexes, miRNAs duplexes with a dominant strand and β-duplexes with both strands being abundant. However, certain ratios were highly variable across the libraries examined as exemplified for the ratio of miR-223/miR-223*. Bioinformatics as well as functional analysis revealed a possible supporting function of miR-223* to the differentiating role of miR-223 in normal normal bone marrow as well as AML. Taken together, by using deep sequencing we provided deep insight into the changes of the miRNA transcriptome in the development of AML. Furthermore, we propose a new classification for miRNA duplexes and provide evidence for a possible role a miRNA* in the development of acute myeloid leukemia.
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