The long non-coding RNA HOXB-AS3 regulates ribosomal RNA transcription in NPM1-mutated acute myeloid leukemia

In this work we dissect the functional role of the HOXB-AS3 long non coding RNA in patients with NPM1-mutated (NPM1mut) acute myeloid leukemia (AML). We show that HOXB-AS3 regulates the proliferative capacity of NPM1mut AML blasts in vitro and in vivo. HOXB-AS3 was found to interact with the ErbB3-binding protein 1 (EBP1) and guide EBP1 to the ribosomal DNA locus. Via this mechanism HOXB-AS3 regulates ribosomal RNA transcription and de novo protein synthesis. We propose that in the context of NPM1 mutations, HOXB-AS3 overexpression acts as a compensatory mechanism, which allows adequate protein production in leukemic blasts. HOXB-AS3 was knocked down in AML cell lines or patient samples, then gene expression and splicing was assessed. NPM1 mutant and NPM1 wild-type cytogenetically normal (CN) AML patients were RNAsequenced to examine associations with expression of non-coding genes in the HOXB locus. OCI-AML3 cells were electroporated at 0h time-point with scramble or anti-HOXB-AS3 targeting oligonucleotides, at a final concentration of 500 nM. Cells were grown at a concentration of 0.5 million/mL in RPMI media supplemented with 10% FBS in standard cell culture conditions (37 degrees Celcius, 5% CO2). Cells were counted and samples were harvested at 12 h, 24 h and 48h. The concentration of cells was maintained at 0.5 million/mL with addition of media.