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 2

The H-Me normally restricts HSC numbers and maintains ETPs under steady-state conditions.

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The H-Me normally restricts HSC numbers and maintains ETPs under steady-...
(A) Schematic of the floxed H-Me allele (fl). SA, rabbit β-globin splice acceptor sequence (103). (B) RT-qPCR of Myb and Ahi1 in sorted LT-HSCs (CD150+CD48– LSK cells) from Mx1Cre H-MeΔ/Δ (Δ/Δ) and littermate control Mx1Cre (+/+) mice. (C–G) Representative BM Lineage– flow cytometry plots (C) and absolute numbers of LT-HSCs (D), LSK cells (E), MPP/ST-HSCs (CD150+CD48– LSKs) (F), and LMPPs (Lineage–Sca-1+KithiFlt3hi) (G). (H–M) Representative thymus Lineage– flow cytometry plots (H) and absolute numbers of ETP (Lineage–CD44+CD25–c-Kithi) (I) and DN2a (Lineage–CD44+CD25+cKithi) (J), DN2b (Lineage–CD44+CD25+c-Kitlo) (K), DN3 (Lineage–CD44–CD25+) (L), and DN4 (Lineage–CD44–CD25–) (M) cells. (N) Myb RT-qPCR in sorted DN cells from Il7rCre H-MeΔ/Δ (Δ/Δ) and littermate control Il7rCre (+/+) mice. Unpaired 2-tailed t test. *P < 0.05; **P < 0.01; ***P < 0.001.