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 3

HoxBlinc is essential for the NUP98-PHF23–driven leukemic homeotic gene signature and leukemogenesis.

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HoxBlinc is essential for the NUP98-PHF23–driven leukemic homeotic gene...
(A) Heatmap of normalized DEGs by DEseq2 in RNA-Seq of WT versus HoxBlinc-KO 961C cells. DEGs were selected using log2(fold change) of greater than 0.58 and an FDR of less than 0.05. (B) GO analysis of 740 downregulated genes upon HoxBlinc KO in 961C B-ALL cells. (C) GSEA of DEGs between WT and HoxBlinc-KO in 961C cells using the TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_ 16D_UP (M15588) gene set. NES, normalized enrichment score; FWER, family-wise error rate. (D) Cell proliferation curve of 961C and HoxBlinc-KO 961C cells over a 7-day period. Data are presented as the mean ± SD from 3 independent experiments. ***P ≤ 0.001, by 2-tailed, unpaired Student’s t test at day 7. (E) Ki67 immunofluorescence images comparing WT and HoxBlinc-KO 961C cells. Scale bar 10μm. (F) Kaplan-Maier survival curve of mice transplanted with 961C and HoxBlinc-KO 961C cells. n = 12/group. P = 0.000121, by log-rank test. (G) Kaplan-Maier survival curve for mice transplanted with A1929 and HoxBlinc-KO A1929 primary B-ALL cells. n = 5/group. P = 0.0000308 by log-rank test. (H) Whole body and spleen images of A1929 cell– or HoxBlinc-KO A1929 cell–transplanted mice at day 23 after transplantation. (I) MGG-stained images of PB smears from WT 961C cell– with HoxBlinc-KO 961C cell–transplanted mice at post-translation day 23. Scale bar 50μm. (J) FACS analysis of CD45.2+ cell population in BM and PB from recipient mice 23 days after transplantation of WT 961C or HoxBlinc-KO 961C cells. n = 5. Data are presented as the mean ± SD. ***P ≤ 0.001, by 2-tailed, unpaired Student’s t test.