MiR-29a is Essential in Leukemic Transformation and Maintaining Hematopoietic Stem Cell Self-Renewal

MicroRNAs are small non-coding RNAs that interfere with gene expression by degrading messenger RNAs (mRNAs) or blocking protein translation. Expression profiling studies has identified miRNAs that regulate normal and malignant hematopoietic stem cell function. Our previous studies showed that ectopic expression of miR-29a in mouse bone marrow cells induced a myeloproliferative disorder that progressed to acute myeloid leukemia (AML). Over-expression of miR-29b in AML cell lines has been reported to induce apoptosis by negatively regulating Dnmt3a. We recently found that miR-29a positively regulates hematopoietic stem cell (HSC) self-renewal and proliferation using a knockout mouse model of miR-29ab. miR-29a null mice contained significantly lower HSC numbers and miR-29a null HSCs exhibited markedly decreased reconstitution ability in both competitive and non-competitive transplantation assays. To investigate the mechanism of miR-29a action, we performed transcriptomal profiling of miR-29a null HSCs and found that miR-29a null HSCs exhibit a gene expression pattern more similar to wild-type committed progenitors than wild-type HSCs. We identified Dnmt3a as one dysregulated miR-29a target as showing increased expression in miR-29a null HSCs, and haplodeficiency of Dnmt3a partly restores miR-29a deficient HSC function. In order to test the requirement for miR-29a in myeloid leukemogenesis, we transduced miR-29a deficient Lin-c-Kit+Sca-1+ (LSK) cells with the oncogenic MLL-AF9 fusion gene, and found that the development of AML from these cells was markedly delayed. We found that Meis1, Ccna2, Hoxa5 and Hoxa9 transcripts were significantly downregulated in miR-29a null LSK cells compared to WT LSK cells, but they were similarly induced in MLL-AF9 transformed c-Kit+Mac-1+ cells. To investigate whether the epigenetic dysregulation resulting from miR-29a deletion may underlie this transformation-resistant phenotype, we examined the distribution of the active epigenetic mark, H3K79me2, in c-Kit+Mac-1+ miR-29a null cells using a ChIP-Seq assay. After analyzing H3K39me2 peaks using model-based analysis of ChIP-Seq, we identified 4281 and 3649 genes associated with this active epigenetic mark using a duplicated ChIP-Seq analysis, with an overlap of 3164 genes (66.39%). Using public available ChIP-Seq data, we compared our results with the genes associated with the H3K79me2 mark in normal immature LSK cells (9282 genes), granulocyte-macrophage progenitors (GMPs, 8556 genes), and MLL-AF9 transformed GMP cells (L-GMP, 8578 genes), and found 4234, 4111, 4046, and 4766 genes were also identified have an active H3K79me2 mark in MLL-AF9 transformed miR-29a null cells. These data indicate that miR-29a loss inactivates a large group of genes activated by the MLL-AF9 oncogene. We also found that 379 genes were associated with H3K79me2 peaks in both normal LSK and MLL-AF9 transformed miR-29a null c-Kit+Mac-1+ cells, but were absent of this epigenetic marker in L-GMP, suggesting that these genes confer self-renewal and proliferation capacities to normal HSCs. In addition, suppression of these genes are important in leukemic transformation by MLL-AF9, and finally the reactivation of these genes in miR-29a null cells compromises the leukemogenesis ability of MLL-AF9. Interestingly, out of these 379 genes, we were able to identify 18 genes that were potential miR-29a targets including Akt3, Map4k4, Dnmt3a, et al. This suggests the direct and indirect effects from miR-29a in regulating its target gene networks at transcriptional and post-transcriptional levels. Our studies found miR-29a is essential in maintaining HSC function and loss of miR-29a abrogate the leukemogenesis capacity of MLL-AF9.