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Buteyn NJ, Burke CG, Sartori VJ, Deering-Gardner E, DeBruine ZJ, Kamarudin D, Chandler DP, Monovich AC, Perez MW, Yi JS, Ries RE, Alonzo TA, Ryan RJ, Meshinchi S, Triche TJ. EZH2-driven immune evasion defines high-risk pediatric AML with t(16;21) FUS::ERG gene fusion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.14.594150. [PMID: 38798454 PMCID: PMC11118270 DOI: 10.1101/2024.05.14.594150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Despite decades of research, acute myeloid leukemia (AML) remains a remarkably lethal malignancy. While pediatric AML (pAML) carries a more favorable prognosis than adult AML, the past 25 years of large clinical trials have produced few improvements in pAML survival. Nowhere is this more evident than in patients carrying a t(16;21)(p11;q22) translocation, which yields the FUS::ERG fusion transcript. Patients with FUS::ERG -positive AML are often primary refractory, and most responders quickly relapse. In COG clinical trials, allogeneic stem cell transplantation was of no benefit to FUS::ERG pAML patients; 100% of transplanted patients succumbed to their disease. Expression of major histocompatibility complex (MHC) class I & II and costimulatory molecules is absent at diagnosis in FUS::ERG AML, mirroring the epigenetic mechanism of post-transplant relapse seen in adult AML and its associated dismal outcomes. Here we show that this class-defining immune-repressive phenotype is driven by overexpression of the EZH2 histone lysine methyltransferase in vitro and in multiple clinical cohorts. We show that treatment with the FDA-approved EZH2 inhibitor tazemetostat along with IFN-γ reverses this phenotype, re-establishes MHC presentation, and severely impairs the viability of FUS::ERG AML cells. EZH2 inhibitors may thus provide the first targeted therapeutic option for patients with this high-risk subtype of pAML, with particular benefit as a bridge to successful allogeneic stem cell transplantation. STATEMENT OF SIGNIFICANCE FUS::ERG pAML patients have dismal outcomes. Here we show a ubiquitous immune-evasive phenotype, defined by elevated EZH2 levels and loss of MHC class I and II receptors, present in these patients at diagnosis. Treatment with the EZH2 inhibitor tazemetostat and IFN-γ reverses this phenotype in patient-derived cell lines.
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2
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Milne TA. Chromatin and aberrant enhancer activity in KMT2A rearranged acute lymphoblastic leukemia. Curr Opin Genet Dev 2024; 86:102191. [PMID: 38579381 DOI: 10.1016/j.gde.2024.102191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/11/2024] [Accepted: 03/19/2024] [Indexed: 04/07/2024]
Abstract
To make a multicellular organism, genes need to be transcribed at the right developmental stages and in the right tissues. DNA sequences termed 'enhancers' are crucial to achieve this. Despite concerted efforts, the exact mechanisms of enhancer activity remain elusive. Mixed lineage leukemia (MLL or KMT2A) rearrangements (MLLr), commonly observed in cases of acute lymphoblastic leukemia (ALL) and acute myeloid leukemia, produce novel in-frame fusion proteins. Recent work has shown that the MLL-AF4 fusion protein drives aberrant enhancer activity at key oncogenes in ALL, dependent on the continued presence of MLL-AF4 complex components. As well as providing some general insights into enhancer function, these observations may also provide an explanation for transcriptional heterogeneity observed in MLLr patients.
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Affiliation(s)
- Thomas A Milne
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK.
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3
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Barnett KR, Mobley RJ, Diedrich JD, Bergeron BP, Bhattarai KR, Monovich AC, Narina S, Yang W, Crews KR, Manring CS, Jabbour E, Paietta E, Litzow MR, Kornblau SM, Stock W, Inaba H, Jeha S, Pui CH, Mullighan CG, Relling MV, Pruett-Miller SM, Ryan RJ, Yang JJ, Evans WE, Savic D. Epigenomic mapping reveals distinct B cell acute lymphoblastic leukemia chromatin architectures and regulators. CELL GENOMICS 2023; 3:100442. [PMID: 38116118 PMCID: PMC10726428 DOI: 10.1016/j.xgen.2023.100442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 08/30/2023] [Accepted: 10/20/2023] [Indexed: 12/21/2023]
Abstract
B cell lineage acute lymphoblastic leukemia (B-ALL) is composed of diverse molecular subtypes, and while transcriptional and DNA methylation profiling has been extensively examined, the chromatin landscape is not well characterized for many subtypes. We therefore mapped chromatin accessibility using ATAC-seq in primary B-ALL cells from 156 patients spanning ten molecular subtypes and present this dataset as a resource. Differential chromatin accessibility and transcription factor (TF) footprint profiling were employed and identified B-ALL cell of origin, TF-target gene interactions enriched in B-ALL, and key TFs associated with accessible chromatin sites preferentially active in B-ALL. We further identified over 20% of accessible chromatin sites exhibiting strong subtype enrichment and candidate TFs that maintain subtype-specific chromatin architectures. Over 9,000 genetic variants were uncovered, contributing to variability in chromatin accessibility among patient samples. Our data suggest that distinct chromatin architectures are driven by diverse TFs and inherited genetic variants that promote unique gene-regulatory networks.
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Affiliation(s)
- Kelly R. Barnett
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Robert J. Mobley
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jonathan D. Diedrich
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Brennan P. Bergeron
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Graduate School of Biomedical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Kashi Raj Bhattarai
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Alexander C. Monovich
- Department of Pathology, University of Michigan–Ann Arbor, Rogel Cancer Center, Ann Arbor, MI 48109, USA
| | - Shilpa Narina
- Center for Advanced Genome Engineering, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Wenjian Yang
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Kristine R. Crews
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Christopher S. Manring
- Alliance Hematologic Malignancy Biorepository, Clara D. Bloomfield Center for Leukemia Outcomes Research, Columbus, OH 43210, USA
| | - Elias Jabbour
- Department of Leukemia, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Elisabeth Paietta
- Department of Oncology, Montefiore Medical Center, Bronx, NY 10467, USA
| | - Mark R. Litzow
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Steven M. Kornblau
- Department of Leukemia, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Wendy Stock
- University of Chicago Comprehensive Cancer Center, Chicago, IL 60637, USA
| | - Hiroto Inaba
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Sima Jeha
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Ching-Hon Pui
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Charles G. Mullighan
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Mary V. Relling
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Shondra M. Pruett-Miller
- Center for Advanced Genome Engineering, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Russell J.H. Ryan
- Department of Pathology, University of Michigan–Ann Arbor, Rogel Cancer Center, Ann Arbor, MI 48109, USA
| | - Jun J. Yang
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Graduate School of Biomedical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN 38105, USA
| | - William E. Evans
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Daniel Savic
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Graduate School of Biomedical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN 38105, USA
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4
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Mueller SB, Pikman Y, Tasian SK, Silverman LB, Harris MH, Tsai HK. ETV6 fusions from insertions of exons 3-5 in pediatric hematologic malignancies. Haematologica 2023; 108:3471-3476. [PMID: 37381775 PMCID: PMC10690910 DOI: 10.3324/haematol.2022.282498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 06/19/2023] [Indexed: 06/30/2023] Open
Abstract
Not available.
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Affiliation(s)
- Sarah B Mueller
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Yana Pikman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Sarah K Tasian
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pediatrics and Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA
| | - Lewis B Silverman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Marian H Harris
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Harrison K Tsai
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA.
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5
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Crump NT, Smith AL, Godfrey L, Dopico-Fernandez AM, Denny N, Harman JR, Hamley JC, Jackson NE, Chahrour C, Riva S, Rice S, Kim J, Basrur V, Fermin D, Elenitoba-Johnson K, Roeder RG, Allis CD, Roberts I, Roy A, Geng H, Davies JOJ, Milne TA. MLL-AF4 cooperates with PAF1 and FACT to drive high-density enhancer interactions in leukemia. Nat Commun 2023; 14:5208. [PMID: 37626123 PMCID: PMC10457349 DOI: 10.1038/s41467-023-40981-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 08/18/2023] [Indexed: 08/27/2023] Open
Abstract
Aberrant enhancer activation is a key mechanism driving oncogene expression in many cancers. While much is known about the regulation of larger chromosome domains in eukaryotes, the details of enhancer-promoter interactions remain poorly understood. Recent work suggests co-activators like BRD4 and Mediator have little impact on enhancer-promoter interactions. In leukemias controlled by the MLL-AF4 fusion protein, we use the ultra-high resolution technique Micro-Capture-C (MCC) to show that MLL-AF4 binding promotes broad, high-density regions of enhancer-promoter interactions at a subset of key targets. These enhancers are enriched for transcription elongation factors like PAF1C and FACT, and the loss of these factors abolishes enhancer-promoter contact. This work not only provides an additional model for how MLL-AF4 is able to drive high levels of transcription at key genes in leukemia but also suggests a more general model linking enhancer-promoter crosstalk and transcription elongation.
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Affiliation(s)
- Nicholas T Crump
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK.
- Hugh and Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, W12 0NN, UK.
| | - Alastair L Smith
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Laura Godfrey
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Ana M Dopico-Fernandez
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Nicholas Denny
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Joe R Harman
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Joseph C Hamley
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Nicole E Jackson
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Catherine Chahrour
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Simone Riva
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Siobhan Rice
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Jaehoon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, South Korea
| | - Venkatesha Basrur
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Damian Fermin
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Kojo Elenitoba-Johnson
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, 10065, USA
| | - C David Allis
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY, 10065, USA
| | - Irene Roberts
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
- Department of Paediatrics, University of Oxford, Oxford, OX3 9DU, UK
| | - Anindita Roy
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
- Department of Paediatrics, University of Oxford, Oxford, OX3 9DU, UK
| | - Huimin Geng
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA
| | - James O J Davies
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Thomas A Milne
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK.
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6
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Iyer AR, Gurumurthy A, Kodgule R, Aguilar AR, Saari T, Ramzan A, Rausch D, Gupta J, Hall CN, Runge JS, Weiss M, Rahmat M, Anyoha R, Fulco CP, Ghobrial IM, Engreitz J, Cieslik MP, Ryan RJH. Selective Enhancer Dependencies in MYC -Intact and MYC -Rearranged Germinal Center B-cell Diffuse Large B-cell Lymphoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.02.538892. [PMID: 37205448 PMCID: PMC10187217 DOI: 10.1101/2023.05.02.538892] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
High expression of MYC and its target genes define a subset of germinal center B-cell diffuse large B-cell lymphoma (GCB-DLBCL) associated with poor outcomes. Half of these high-grade cases show chromosomal rearrangements between the MYC locus and heterologous enhancer-bearing loci, while focal deletions of the adjacent non-coding gene PVT1 are enriched in MYC -intact cases. To identify genomic drivers of MYC activation, we used high-throughput CRISPR-interference (CRISPRi) profiling of candidate enhancers in the MYC locus and rearrangement partner loci in GCB-DLBCL cell lines and mantle cell lymphoma (MCL) comparators that lacked common rearrangements between MYC and immunoglobulin (Ig) loci. Rearrangements between MYC and non-Ig loci were associated with unique dependencies on specific enhancer subunits within those partner loci. Notably, fitness dependency on enhancer modules within the BCL6 super-enhancer ( BCL6 -SE) cluster regulated by a transcription factor complex of MEF2B, POU2F2, and POU2AF1 was higher in cell lines bearing a recurrent MYC::BCL6 -SE rearrangement. In contrast, GCB-DLBCL cell lines without MYC rearrangement were highly dependent on a previously uncharacterized 3' enhancer within the MYC locus itself (GCBME-1), that is regulated in part by the same triad of factors. GCBME-1 is evolutionarily conserved and active in normal germinal center B cells in humans and mice, suggesting a key role in normal germinal center B cell biology. Finally, we show that the PVT1 promoter limits MYC activation by either native or heterologous enhancers and demonstrate that this limitation is bypassed by 3' rearrangements that remove PVT1 from its position in cis with the rearranged MYC gene. Key points CRISPR-interference screens identify a conserved germinal center B cell MYC enhancer that is essential for GCB-DLBCL lacking MYC rearrangements. Functional profiling of MYC partner loci reveals principles of MYC enhancer-hijacking activation by non-immunoglobulin rearrangements.
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7
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Oncogenic role for an EWS-FLI1 suppressor. Nat Cell Biol 2023; 25:214-216. [PMID: 36658218 DOI: 10.1038/s41556-022-01067-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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