HoxBlinc lncRNA reprograms CTCF-independent TADs to drive leukemic transcription and HSC dysregulation in NUP98-rearranged leukemia
Karina Hamamoto, Ganqian Zhu, Qian Lai, Julia Lesperance, Huacheng Luo, Ying Li, Nupur Nigam, Arati Sharma, Feng-Chun Yang, David Claxton, Yi Qiu, Peter D. Aplan, Mingjiang Xu, Suming Huang
Karina Hamamoto, Ganqian Zhu, Qian Lai, Julia Lesperance, Huacheng Luo, Ying Li, Nupur Nigam, Arati Sharma, Feng-Chun Yang, David Claxton, Yi Qiu, Peter D. Aplan, Mingjiang Xu, Suming Huang
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Research Article Genetics Hematology

HoxBlinc lncRNA reprograms CTCF-independent TADs to drive leukemic transcription and HSC dysregulation in NUP98-rearranged leukemia

Abstract

Although nucleoporin 98 (NUP98) fusion oncogenes often drive aggressive pediatric leukemia by altering chromatin structure and expression of homeobox (HOX) genes, underlying mechanisms remain elusive. Here, we report that the Hoxb-associated lncRNA HoxBlinc was aberrantly activated in NUP98-PHF23 fusion–driven leukemias. HoxBlinc chromatin occupancies led to elevated mixed-lineage leukemia 1 (MLL1) recruitment and aberrant homeotic topologically associated domains (TADs) that enhanced chromatin accessibilities and activated homeotic/hematopoietic oncogenes. HoxBlinc depletion in NUP98 fusion–driven leukemia impaired HoxBlinc binding, TAD integrity, MLL1 recruitment, and the MLL1-driven chromatin signature within HoxBlinc-defined TADs in a CCCTC-binding factor–independent (CTCF-independent) manner, leading to inhibited homeotic/leukemic oncogenes that mitigated NUP98 fusion–driven leukemogenesis in xenografted mouse models. Mechanistically, HoxBlinc overexpression in the mouse hematopoietic compartment induced leukemias resembling those in NUP98-PHF23–knockin (KI) mice via enhancement of HoxBlinc chromatin binding, TAD formation, and Hox gene aberration, leading to expansion of hematopoietic stem and progenitor cell and myeloid/lymphoid cell subpopulations. Thus, our studies reveal a CTCF-independent role of HoxBlinc in leukemic TAD organization and oncogene-regulatory networks.

Authors

Karina Hamamoto, Ganqian Zhu, Qian Lai, Julia Lesperance, Huacheng Luo, Ying Li, Nupur Nigam, Arati Sharma, Feng-Chun Yang, David Claxton, Yi Qiu, Peter D. Aplan, Mingjiang Xu, Suming Huang

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Figure 4

HoxBlinc loss impairs aberrant TAD integrity and the chromatin signature to drive the NUP98-PHF23–mediated leukemic transcription profile.

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HoxBlinc loss impairs aberrant TAD integrity and the chromatin signatur...
(A) Pie chart of ATAC-Seq differential peak distribution in WT versus HoxBlinc-KO 961C cells. (B) Heatmaps showing that MLL1 recruitment/H3K4me3 at the combined HoxBlinc-binding and ATAC peak decreased promoter regions upon HoxBlinc loss. (C) Overlap of downregulated genes was determined by RNA-Seq and the decrease in HoxBlinc-binding peaks was determined by ChIRP-Seq upon HoxBlinc loss in 961C cells (top) and GO analysis of 251 overlapping genes (bottom). (D) Distribution of global NUP98-PHF23-V5 binding and CTCF binding in the mouse 961C B-ALL genome upon HoxBlinc loss. (E) ATAC-Seq, H3K4me3 CUT&RUN, HoxBlinc ChIRP-Seq, and MLL1, NUP98-PHF23, and CTCF ChIP-Seq analysis of changes in chromatin accessibility, H3K4me3 modification levels, MLL1 recruitment, HoxBlinc lncRNA, and NUP98-PHF23 and CTCF binding at Hoxa and Hoxb loci upon HoxBlinc depletion. HoxBlinc-defined (red arrows) active chromatin domains are highlighted in yellow. (F) HiC-Seq interacting maps in part of the mouse chromosome 6 and 11 regions of Hoxa and Hoxb loci comparing WT and HoxBlinc-KO 961C B-ALL cells. (G) Signal intensity of 3,003 CTCF-mediated chromatin loops. Data are presented as the mean ± SD; no statistical significance was found by Kolmogorov-Smirnov test.