The hematopoietic stem cell MYB enhancer is essential for and recurrently amplified during T cell leukemogenesis
Carea Mullin, Karena Lin, Elizabeth Choe, Cher Sha, Zeel Shukla, Koral Campbell, Anna C. McCarter, Annie Wang, Jannaldo Nieves-Salva, Sarah Khan, Theresa M. Keeley, Shannon Liang, Qing Wang, Ashley F. Melnick, Pearl Evans, Alexander C. Monovich, Ashwin Iyer, Rohan Kodgule, Yamei Deng, Felipe da Veiga Leprevost, Kelly R. Barnett, Petri Pölönen, Rami Khoriaty, Daniel Savic, David T. Teachey, Charles G. Mullighan, Marcin Cieslik, Alexey I. Nesvizhskii, Linda C. Samuelson, Morgan Jones, Qing Li, Russell J.H. Ryan, Mark Y. Chiang
Carea Mullin, Karena Lin, Elizabeth Choe, Cher Sha, Zeel Shukla, Koral Campbell, Anna C. McCarter, Annie Wang, Jannaldo Nieves-Salva, Sarah Khan, Theresa M. Keeley, Shannon Liang, Qing Wang, Ashley F. Melnick, Pearl Evans, Alexander C. Monovich, Ashwin Iyer, Rohan Kodgule, Yamei Deng, Felipe da Veiga Leprevost, Kelly R. Barnett, Petri Pölönen, Rami Khoriaty, Daniel Savic, David T. Teachey, Charles G. Mullighan, Marcin Cieslik, Alexey I. Nesvizhskii, Linda C. Samuelson, Morgan Jones, Qing Li, Russell J.H. Ryan, Mark Y. Chiang
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Research Article Cell biology Hematology Oncology

The hematopoietic stem cell MYB enhancer is essential for and recurrently amplified during T cell leukemogenesis

Abstract

There is an urgent need to find targeted agents for T cell acute lymphoblastic leukemia (T-ALL). NOTCH1 is the most frequently mutated oncogene in T-ALL, but clinical trials showed that pan-Notch inhibitors caused dose-limiting toxicities. Thus, we shifted our focus to ETS1, which is one of the transcription factors that most frequently co-bind Notch-occupied regulatory elements in the T-ALL context. To identify the most essential enhancers, we performed a genome-wide CRISPRi screen of the strongest ETS1-dependent regulatory elements. The top-ranked element is located in an intron of AHI1 that interacts with the MYB promoter and is amplified with MYB in approximately 8.5% of patients with T-ALL. Using mouse models, we showed that this enhancer promoted self-renewal of hematopoietic stem cells and T cell leukemogenesis, maintained early T cell precursors, and restrained myeloid expansion with aging. We named this enhancer the hematopoietic stem cell MYB enhancer (H-Me). The H-Me showed limited activity and function in committed T cell progenitors but was accessed during leukemogenesis. In one T-ALL context, ETS1 bound the ETS motif in the H-Me to recruit cBAF to promote chromatin accessibility and activation. ETS1 or cBAF degraders impaired H-Me function. Thus, we identified a targetable stem cell element that was co-opted for T cell transformation.

Authors

Carea Mullin, Karena Lin, Elizabeth Choe, Cher Sha, Zeel Shukla, Koral Campbell, Anna C. McCarter, Annie Wang, Jannaldo Nieves-Salva, Sarah Khan, Theresa M. Keeley, Shannon Liang, Qing Wang, Ashley F. Melnick, Pearl Evans, Alexander C. Monovich, Ashwin Iyer, Rohan Kodgule, Yamei Deng, Felipe da Veiga Leprevost, Kelly R. Barnett, Petri Pölönen, Rami Khoriaty, Daniel Savic, David T. Teachey, Charles G. Mullighan, Marcin Cieslik, Alexey I. Nesvizhskii, Linda C. Samuelson, Morgan Jones, Qing Li, Russell J.H. Ryan, Mark Y. Chiang

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Figure 7

The H-Me is important in diverse models of human T-ALL maintenance.

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The H-Me is important in diverse models of human T-ALL maintenance. (A) ...
(A) ATAC-seq profiles (green) of a panel of T-ALL cell lines and primary samples across the MYB TAD. ETS1 and H3K27ac tracks in THP-6 cells are shown in blue (GSE138516). MYB enhancers labeled A and B were previously described (62–64). ATAC-seq datasets from GSE129086, GSE110630, GSE263585, GSE263977, and GSE225559; TAD datasets from GSE134761. (B–G) THP-6 (B and E), Jurkat (C and F), and MOLT14 (D and G) cells were transduced with constitutive (THP-6) or Dox-inducible (Jurkat, MOLT14) dCas9-KRAB and sgRNAs against the H-Me or the MYB promoter and then tested for expression of MYB (B–D) and measured for cell growth (E–G). HBS1L and AHI1 are flanking genes of MYB. (H–J) CEM cells, related to THP-6, transduced with the indicated sgRNAs were injected into NSG mice and 2–5 days later treated with Dox in drinking water to activate dCas9-KRAB–GFP. Representative GFP/hCD45.2 flow cytometry plots of peripheral blood at 4 weeks after injection (H), GFP+/hCD45+ blast counts (I), and survival (log-rank test P values) (J) were measured. n = 9 (control); n = 10 (PE); n = 10 (H-Me). NT, nontargeting; PE, pan-essential gene RPL34. 1-way ANOVA. *P < 0.05; **P < 0.01; ***P < 0.001; ****P < 0.0001.