UNLABELLED: In acute myeloid leukemia (AML), SWI/SNF chromatin remodeling complexes sustain leukemic identity by driving high levels of MYC. Previous studies have implicated the hematopoietic transcription factor PU.1 (SPI1) as an important target of SWI/SNF inhibition, but PU.1 is widely regarded to have pioneer-like activity. As a result, many questions have remained regarding the interplay between PU.1 and SWI/SNF in AML as well as normal hematopoiesis. Here we found that PU.1 binds to most of its targets in a SWI/SNF-independent manner and recruits SWI/SNF to promote accessibility for other AML core regulatory factors, including RUNX1, LMO2, and MEIS1. SWI/SNF inhibition in AML cells reduced DNA accessibility and binding of these factors at PU.1 sites and redistributed PU.1 to promoters. Analysis of nontumor hematopoietic cells revealed that similar effects also impair PU.1-dependent B-cell and monocyte populations. Nevertheless, SWI/SNF inhibition induced profound therapeutic response in an immunocompetent AML mouse model as well as in primary human AML samples. In vivo, SWI/SNF inhibition promoted leukemic differentiation and reduced the leukemic stem cell burden in bone marrow but also induced leukopenia. These results reveal a variable therapeutic window for SWI/SNF blockade in AML and highlight important off-tumor effects of such therapies in immunocompetent settings. SIGNIFICANCE: Disruption of PU.1-directed enhancer programs upon SWI/SNF inhibition causes differentiation of AML cells and induces leukopenia of PU.1-dependent B cells and monocytes, revealing the on- and off-tumor effects of SWI/SNF blockade.

Center for Cancer Epigenetics The University of Texas MD Anderson Cancer Center Houston Texas

Dan L Duncan Comprehensive Cancer Center Baylor College of Medicine Houston Texas

Department of Bioengineering Rice University Houston Texas

Department of Molecular and Cellular Biology Center for Precision Environmental Health Baylor College of Medicine Houston Texas

Department of Pathology and Immunology Baylor College of Medicine Houston Texas

Department of Pediatrics Baylor College of Medicine and Texas Children's Hospital Houston Texas

Genetics and Genomics Graduate Program Baylor College of Medicine Houston Texas

Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Prague Czech Republic

Stem Cells and Regenerative Medicine Center Baylor College of Medicine Houston Texas

Translational Biology and Molecular Medicine Graduate Program Baylor College of Medicine Houston Texas

See more in PubMed

de Kouchkovsky I, Abdul-Hay M. ‘Acute myeloid leukemia: a comprehensive review and 2016 update.’ Blood Cancer J 2016;6:e441. PubMed PMC

Lonetti A, Pession A, Masetti R. Targeted therapies for pediatric AML: gaps and perspective. Front Pediatr 2019;7:463. PubMed PMC

Zwaan CM, Kolb EA, Reinhardt D, Abrahamsson J, Adachi S, Aplenc R, et al. . Collaborative efforts driving progress in pediatric acute myeloid leukemia. J Clin Oncol 2015;33:2949. PubMed PMC

Rosenbauer F, Tenen DG. Transcription factors in myeloid development: balancing differentiation with transformation. Nat Rev Immunol 2007;7:105–17. PubMed

Chen Y, Xu L, Lin RYT, Müschen M, Koeffler HP. Core transcriptional regulatory circuitries in cancer. Oncogene 2020;39:6633–46. PubMed PMC

Goyama S, Schibler J, Cunningham L, Zhang Y, Rao Y, Nishimoto N, et al. . Transcription factor RUNX1 promotes survival of acute myeloid leukemia cells. J Clin Invest 2013;123:3876–88. PubMed PMC

Wong P, Iwasaki M, Somervaille TCP, So CWE, Cleary ML. Meis1 is an essential and rate-limiting regulator of MLL leukemia stem cell potential. Genes Dev 2007;21:2762–74. PubMed PMC

Diffner E, Beck D, Gudgin E, Thoms JAI, Knezevic K, Pridans C, et al. . Activity of a heptad of transcription factors is associated with stem cell programs and clinical outcome in acute myeloid leukemia. Blood 2013;121:2289–300. PubMed

Porcher C, Swat W, Rockwell K, Fujiwara Y, Alt FW, Orkin SH. The T cell leukemia oncoprotein SCL/tal-1 is essential for development of all hematopoietic lineages. Cell 1996;86:47–57. PubMed

Tenen DG. Disruption of differentiation in human cancer: AML shows the way. Nat Rev Cancer 2003;3:89–101. PubMed

Papillon JPN, Nakajima K, Adair CD, Hempel J, Jouk AO, Karki RG, et al. . Discovery of orally active inhibitors of brahma homolog (BRM)/SMARCA2 ATPase activity for the treatment of brahma related gene 1 (BRG1)/SMARCA4-mutant cancers. J Med Chem 2018;61:10155–72. PubMed

Shi J, Wang E, Milazzo JP, Wang Z, Kinney JB, Vakoc CR. Discovery of cancer drug targets by CRISPR-Cas9 screening of protein domains. Nat Biotechnol 2015;33:661. PubMed PMC

Shi J, Whyte WA, Zepeda-Mendoza CJ, Milazzo JP, Shen C, Roe J-S, et al. . Role of SWI/SNF in acute leukemia maintenance and enhancer-mediated Myc regulation. Genes Dev 2013;27:2648. PubMed PMC

Rago F, Rodrigues LU, Bonney M, Sprouffske K, Kurth E, Elliott G, et al. . Exquisite sensitivity to dual BRG1/BRM ATPase inhibitors reveals broad SWI/SNF dependencies in acute myeloid Leukemia. Mol Cancer Res 2022;20:361–372molcanres.MCR-21–0390-A.2021. PubMed

Bahr C, von Paleske L, Uslu VV, Remeseiro S, Takayama N, Ng SW, et al. . A Myc enhancer cluster regulates normal and leukaemic haematopoietic stem cell hierarchies. Nature 2018;553:515–20. PubMed

Krasteva V, Buscarlet M, Diaz-Tellez A, Bernard M-A, Crabtree GR, Lessard JA. The BAF53a subunit of SWI/SNF-like BAF complexes is essential for hemopoietic stem cell function. Blood 2012;120:4720–32. PubMed

Krasteva V, Crabtree GR, Lessard JA. The BAF45a/PHF10 subunit of SWI/SNF-like chromatin remodeling complexes is essential for hematopoietic stem cell maintenance. Exp Hematol 2017;48:58–71. PubMed PMC

O'Neill D, Yang J, Erdjument-Bromage H, Bornschlegel K, Tempst P, Bank A. Tissue-specific and developmental stage-specific DNA binding by a mammalian SWI/SNF complex associated with human fetal-to-adult globin gene switching. Proc Natl Acad Sci U S A 1999;96:349. PubMed PMC

Lee CH, Murphy MR, Lee JS, Chung JH. Targeting a SWI/SNF-related chromatin remodeling complex to the β-globin promoter in erythroid cells. Proc Natl Acad Sci 1999;96:12311–5. PubMed PMC

Kowenz-Leutz E, Leutz A. A C/EBPβ isoform recruits the SWI/SNF complex to activate myeloid genes. Mol Cell 1999;4:735–43. PubMed

Wu J, Krchma K, Lee HJ, Prabhakar S, Wang X, Zhao H, et al. . Requisite chromatin remodeling for myeloid and erythroid lineage differentiation from erythromyeloid progenitors. Cell Rep 2020;33:108395. PubMed PMC

Chi TH, Wan M, Lee PP, Akashi K, Metzger D, Chambon P, et al. . Sequential roles of Brg, the ATPase subunit of BAF chromatin remodeling complexes, in thymocyte development. Immunity 2003;19:169–82. PubMed

Gebuhr TC, Kovalev GI, Bultman S, Godfrey V, Su L, Magnuson T. The role of Brg1, a catalytic subunit of mammalian chromatin-remodeling complexes, in T cell development. J Exp Med 2003;198:1937. PubMed PMC

Loo C-S, Gatchalian J, Liang Y, Leblanc M, Xie M, Ho J, et al. . A Genome-wide CRISPR screen reveals a role for the non-canonical nucleosome-remodeling BAF complex in Foxp3 expression and regulatory T cell function. Immunity 2020;53:143–57. PubMed PMC

Minderjahn J, Schmidt A, Fuchs A, Schill R, Raithel J, Babina M, et al. . Mechanisms governing the pioneering and redistribution capabilities of the non-classical pioneer PU.1. Nat Commun 2020;11:402. PubMed PMC

Iwafuchi-Doi M, Zaret KS. Pioneer transcription factors in cell reprogramming. Genes Dev 2014;28:2679–92. PubMed PMC

Sunkel BD, Stanton BZ. Pioneer factors in development and cancer. iScience 2021;24:103132. PubMed PMC

Scott EW, Simon MC, Anastasi J, Singh H. Requirement of transcription factor PU.1 in the development of multiple hematopoietic lineages. Science 1994;265:1573–7. PubMed

DeKoter RP, Singh H. Regulation of B lymphocyte and macrophage development by graded expression of PU.1. Science 2000;288:1439–42. PubMed

Friedman AD. Transcriptional control of granulocyte and monocyte development. Oncogene 2007;26:6816–28. PubMed

Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, et al. . Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell 2010;38:576–89. PubMed PMC

Gupta P, Gurudutta GU, Saluja D, Tripathi RP. PU.1 and partners: regulation of haematopoietic stem cell fate in normal and malignant haematopoiesis. J Cell Mol Med 2009;13:4349–63. PubMed PMC

Wilson NK, Foster SD, Wang X, Knezevic K, Schütte J, Kaimakis P, et al. . Combinatorial transcriptional control in blood stem/progenitor cells: genome-wide analysis of ten major transcriptional regulators. Cell Stem Cell 2010;7:532–44. PubMed

Corces MR, Trevino AE, Hamilton EG, Greenside PG, Sinnott-Armstrong NA, Vesuna S, et al. . An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods 2017;14:959–62. PubMed PMC

Hodges HC, Stanton BZ, Cermakova K, Chang C-Y, Miller EL, Kirkland JG, et al. . Dominant-negative SMARCA4 mutants alter the accessibility landscape of tissue-unrestricted enhancers. Nat Struct Mol Biol 2018;25:61–72. PubMed PMC

Cermakova K, Demeulemeester J, Lux V, Nedomova M, Goldman SR, Smith EA, et al. . A ubiquitous disordered protein interaction module orchestrates transcription elongation. Science 2021;374:1113–21. PubMed PMC

Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009;10:R25. PubMed PMC

Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, et al. . Model-based analysis of ChIP-Seq (MACS). Genome Biol 2008;9:R137. PubMed PMC

Schep AN, Wu B, Buenrostro JD, Greenleaf WJ. chromVar: inferring transcription-factor-associated accessibility from single-cell epigenomic data. Nat Methods 2017;14:975–8. PubMed PMC

Pohl A, Beato M. bwtool: a tool for bigWig files. Bioinformatics 2014;30:1618–9. PubMed PMC

McGinnis CS, Murrow LM, Gartner ZJ. DoubletFinder: doublet detection in single-cell RNA sequencing data using artificial nearest neighbors. Cell Syst 2019;8:329–37. PubMed PMC

Thibodeau A, Eroglu A, McGinnis CS, Lawlor N, Nehar-Belaid D, Kursawe R, et al. . AMULET: a novel read count-based method for effective multiplet detection from single nucleus ATAC-seq data. Genome Biol 2021;22:252. PubMed PMC

Stuart T, Butler A, Hoffman P, Hafemeister C, Papalexi E, Mauck WM, et al. . Comprehensive integration of single-cell data. Cell 2019;177:1888–902. PubMed PMC

Zaret KS, Carroll JS. Pioneer transcription factors: establishing competence for gene expression. Genes Dev 2011;25:2227. PubMed PMC

Hosokawa H, Ungerbäck J, Wang X, Matsumoto M, Nakayama KI, Cohen SM, et al. . Transcription factor PU.1 represses and activates gene expression in early T cells by redirecting partner transcription factor binding. Immunity 2018;48:1119–34. PubMed PMC

Ungerbäck J, Hosokawa H, Wang X, Strid T, Williams BA, Sigvardsson M, et al. . Pioneering, chromatin remodeling, and epigenetic constraint in early T-cell gene regulation by SPI1 (PU.1). Genome Res 2018;28:1508–19. PubMed PMC

Antony-Debré I, Paul A, Leite J, Mitchell K, Kim HM, Carvajal LA, et al. . Pharmacological inhibition of the transcription factor PU.1 in leukemia. J Clin Invest 2017;127:4297. PubMed PMC

Iwasaki H, Somoza C, Shigematsu H, Duprez EA, Iwasaki-Arai J, Mizuno S-I, et al. . Distinctive and indispensable roles of PU.1 in maintenance of hematopoietic stem cells and their differentiation. Blood 2005;106:1590–600. PubMed PMC

Wang Y, Baron RM, Zhu G, Joo M, Christman JW, Silverman ES, et al. . PU.1 regulates cathepsin S expression in professional APCs. J Immunol 2006;176:275–83. PubMed

Chen HM, Ray-Gallet D, Zhang P, Hetherington CJ, Gonzalez DA, Zhang DE, et al. . PU.1 (Spi-1) autoregulates its expression in myeloid cells. Oncogene 1995;11:1549–60. PubMed

Jin L, Hope KJ, Zhai Q, Smadja-Joffe F, Dick JE. Targeting of CD44 eradicates human acute myeloid leukemic stem cells. Nat Med 2006;12:1167–74. PubMed

Geissmann F, Jung S, Littman DR. Blood monocytes consist of two principal subsets with distinct migratory properties. Immunity 2003;19:71–82. PubMed

Yona S, Kim K-W, Wolf Y, Mildner A, Varol D, Breker M, et al. . Fate mapping reveals origins and dynamics of monocytes and tissue macrophages under homeostasis. Immunity 2013;38:79–91. PubMed PMC

Kurtz KJ, Conneely SE, O'Keefe M, Wohlan K, Rau RE. Murine models of acute myeloid leukemia. Front Oncol 2022;12:854973. PubMed PMC

Krivtsov AV, Twomey D, Feng Z, Stubbs MC, Wang Y, Faber J, et al. . Transformation from committed progenitor to leukaemia stem cell initiated by MLL–AF9. Nature 2006;442:818–22. PubMed

Lewis AH, Bridges CS, Moorshead DN, Chen TJ, Du W, Zorman B, et al. . Krüppel-like factor 4 supports the expansion of leukemia stem cells in MLL-AF9-driven acute myeloid leukemia. Stem Cells. 2022;40:736–50. PubMed PMC

Balgobind BV, Raimondi SC, Harbott J, Zimmermann M, Alonzo TA, Auvrignon A, et al. . Novel prognostic subgroups in childhood 11q23/MLL-rearranged acute myeloid leukemia: results of an international retrospective study. Blood 2009;114:2489–96. PubMed PMC

Pollard JA, Guest E, Alonzo TA, Gerbing RB, Loken MR, Brodersen LE, et al. . Gemtuzumab ozogamicin improves event-free survival and reduces relapse in pediatric KMT2A-rearranged AML: results from the Phase III children's oncology group trial AAML0531. J Clin Oncol 2021;39:3149–60. PubMed PMC

Buscarlet M, Krasteva V, Ho L, Simon C, Hébert J, Wilhelm B, et al. . Essential role of BRG, the ATPase subunit of BAF chromatin remodeling complexes, in leukemia maintenance. Blood 2014;123:1720–8. PubMed PMC

Jubierre L, Soriano A, Planells-Ferrer L, París-Coderch L, Tenbaum SP, Romero OA, et al. . BRG1/SMARCA4 is essential for neuroblastoma cell viability through modulation of cell death and survival pathways. Oncogene 2016;35:5179–90. PubMed

Cyrta J, Augspach A, De Filippo MR, Prandi D, Thienger P, Benelli M, et al. . Role of specialized composition of SWI/SNF complexes in prostate cancer lineage plasticity. Nat Commun 2020;11:5549. PubMed PMC

Rago F, Elliott G, Li A, Sprouffske K, Kerr G, Desplat A, et al. . The discovery of SWI/SNF chromatin remodeling activity as a novel and targetable dependency in uveal melanoma. Mol Cancer Ther 2020;19:2186–95. PubMed

Cancer Genome Atlas Research Network, Ley TJ, Miller C, Ding L, Raphael BJ, Mungall AJ, et al. . Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. N Engl J Med 2013;368:2059–74. PubMed PMC

Kandoth C, McLellan MD, Vandin F, Ye K, Niu B, Lu C, et al. . Mutational landscape and significance across 12 major cancer types. Nature 2013;502:333–9. PubMed PMC

Daver N, Alotaibi AS, Bücklein V, Subklewe M. T-cell-based immunotherapy of acute myeloid leukemia: current concepts and future developments. Leukemia 2021;35:1843–63. PubMed PMC

Curtiss BM, VanCampen J, Macaraeg J, Kong GL, Taherinasab A, Tsuchiya M, et al. . PU.1 and MYC transcriptional network defines synergistic drug responses to KIT and LSD1 inhibition in acute myeloid leukemia. Leukemia 2022;36:1781–93. PubMed PMC

Bakshi R, Hassan MQ, Pratap J, Lian JB, Montecino MA, van Wijnen AJ, et al. . The human SWI/SNF complex associates with RUNX1 to control transcription of hematopoietic target genes. J Cell Physiol 2010;225:569. PubMed PMC

Mill CP, Fiskus W, DiNardo CD, Qian Y, Raina K, Rajapakshe K, et al. . RUNX1-targeted therapy for AML expressing somatic or germline mutation in RUNX1. Blood 2019;134:59–73. PubMed PMC

Willis MS, Homeister JW, Rosson GB, Annayev Y, Holley D, Holly SP, et al. . Functional redundancy of SWI/SNF catalytic subunits in maintaining vascular endothelial cells in the adult heart. Circ Res 2012;111:e111–22. PubMed PMC

Roberts CWM, Leroux MM, Fleming MD, Orkin SH. Highly penetrant, rapid tumorigenesis through conditional inversion of the tumor suppressor gene Snf5. Cancer Cell 2002;2:415–25. PubMed

Staber PB, Zhang P, Ye M, Welner RS, Nombela-Arrieta C, Bach C, et al. . Sustained PU.1 levels balance cell-cycle regulators to prevent exhaustion of adult hematopoietic stem cells. Mol Cell 2013;49:934–46. PubMed PMC

Groopman JE, Itri LM. Chemotherapy-induced anemia in adults: incidence and treatment. J Natl Cancer Inst 1999;91:1616–34. PubMed

Crawford J, Dale DC, Lyman GH. Chemotherapy-induced neutropenia. Cancer 2004;100:228–37. PubMed

Guo A, Huang H, Zhu Z, Chen MJ, Shi H, Yuan S, et al. . cBAF complex components and MYC cooperate early in CD8+ T cell fate. Nature 2022;607:135–41. PubMed PMC

Belk JA, Yao W, Ly N, Freitas KA, Chen Y-T, Shi Q, et al. . Genome-wide CRISPR screens of T cell exhaustion identify chromatin remodeling factors that limit T cell persistence. Cancer Cell 2022;40:768–86. PubMed PMC

Reactivation of the G1 enhancer landscape underlies core circuitry addiction to SWI/SNF