Hoxblinc lncRNA reprograms CTCF-independent TADs to drive leukemic transcription and HSC dysregulation in NUP98 fusion transformed leukemia [RNA-Seq]

We found NUP98 fusions activate Hoxb-associated lncRNA, HoxBlinc that occupies and regulates homeotic/oncogenic topologically associated domain (TAD) in malignant hematopoiesis. Aberration of HoxBlinc led to recruitment of MLL1 complex , altered chromatin landscape (both H3K4me3 and chromatin accessibility), and HOX/homeotic gene activatiion in NUP98-PHF23 fusion driven leukemia and HoxBlinc -Tg models. Conversely, eliminated HoxBlinc in NUP98 fusion-driven leukemic cells resulted in loss of Hoxblinc binding, TAD integrity, recruitment of MLL complex, and MLL driven H3K4me3 and chromatin accessibility within the HoxBlinc defined domain in a CTCF independent manner, leading to inhibiting homeotic/leukemic oncogenes and mitigating NUP98 fusion-driven leukemia in xenografted mouse models. Thus, our studies revealed a CTCF independent role of HoxBlinc in leukemic TAD organization and oncogenic gene regulatory networks in NUP98-fusion related leukemia. We performed the RNA-seq, ATAC-seq, ChIP-seq, ChIRP-seq, HiC-seq for WT and HoxBlinc KO in NUP98-PHF23 related leukemia cell lines and HoxBlinc Transgenic mice bone marrow cells to investigate HoxBlinc function in leukemogenesis. LK cells (Lin- Kit+) and LSK cells (Lin- Sca1+ Kit+) were sorted by FACS from the bone marrow of WT and HoxBlinc transgenic mice for single cell-RNA seq. We also used primary AML patient samples harboring NUP98-HOXA9 fusion for bulk RNA-seq.