RNA-seq data of NKX6-3 knockdown in the BCP-ALL cell line RCH-ACV

Early B-cell development is primarily regulated at the transcriptional level and comprises the consecutive differentiation stages B-cell progenitor, pro-B-cell and pre-B-cell. These entities provide the cells of origin in B-cell precursor acute lymphoid leukemia (BCP-ALL) which show deregulation of developmental transcription factors (TFs), representing major oncogenic drivers. Analysis of TF activities in these developmental entities helps understanding both their normal and aberrant expression and regulatory connections. Here, we focused on NKL-subclass homeodomain TF NKX6-3 which is active in normal B-cell progenitors and TCF3::PBX1-positive BCP-ALL cases. Performing siRNA-mediated knockdown and forced expression experiments in BCP-ALL model cell lines, we established a gene regulatory network for NKX6-3 together with NKL-TFs HLX, MSX1 and HHEX, TALE-class homeodomain TFs MEIS1 and IRX1, ETS-TFs ERG, ETS2 and SPIB, and additionally with PAX5, EBF1 and IRF4. NKX6-3 and TCF3::PBX1 were found to be mutual activators, underlying their co-expression. Furthermore, comparative expression profiling analysis of BCP-ALL patients revealed TGFb-pathway inhibitor CD109 as downregulated target gene of NKX6-3. TGFb in turn enhanced NKX6-3 expression, indicating mutual activation. Finally, RNA-seq analysis of BCP-ALL cell line RCH-ACV after NKX6-3 knockdown revealed MPP7 as upregulated target gene of both, NKX6-3 and TCF3::PBX1. Elevated MPP7 expression indicated an oncogenic role of the HIPPO-pathway in TCF3::PBX1 positive BCP-ALL. Collectively, our data add novel players and regulatory connections to normal and aberrant TF-networks in B-cell progenitors which may serve as diagnostic markers or therapeutic targets.