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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] [What about the content of this article? (0)] [Affiliation(s)] [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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2
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Liffers ST, Godfrey L, Frohn L, Haeberle L, Yavas A, Vesce R, Goering W, Opitz FV, Stoecklein N, Knoefel WT, Schlitter AM, Klöppel G, Espinet E, Trumpp A, Siveke JT, Esposito I. Molecular heterogeneity and commonalities in pancreatic cancer precursors with gastric and intestinal phenotype. Gut 2023; 72:522-534. [PMID: 35944927 PMCID: PMC9933174 DOI: 10.1136/gutjnl-2021-326550] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 07/31/2022] [Indexed: 12/16/2022]
Abstract
OBJECTIVE Due to the limited number of modifiable risk factors, secondary prevention strategies based on early diagnosis represent the preferred route to improve the prognosis of pancreatic ductal adenocarcinoma (PDAC). Here, we provide a comparative morphogenetic analysis of PDAC precursors aiming at dissecting the process of carcinogenesis and tackling the heterogeneity of preinvasive lesions. DESIGN Targeted and whole-genome low-coverage sequencing, genome-wide methylation and transcriptome analyses were applied on a final collective of 122 morphologically well-characterised low-grade and high-grade PDAC precursors, including intestinal and gastric intraductal papillary mucinous neoplasms (IPMN) and pancreatic intraepithelial neoplasias (PanIN). RESULTS Epigenetic regulation of mucin genes determines the phenotype of PDAC precursors. PanIN and gastric IPMN display a ductal molecular profile and numerous similarly regulated pathways, including the Notch pathway, but can be distinguished by recurrent deletions and differential methylation and, in part, by the expression of mucin-like 3. Intestinal IPMN are clearly distinct lesions at the molecular level with a more instable genotype and are possibly related to a different ductal cell compartment. CONCLUSIONS PDAC precursors with gastric and intestinal phenotype are heterogeneous in terms of morphology, genetic and epigenetic profile. This heterogeneity is related to a different cell identity and, possibly, to a different aetiology.
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Affiliation(s)
- Sven-Thorsten Liffers
- Bridge Institute of Experimental Tumor Therapy, West German Cancer Center, University Hospital Essen, Essen, Germany.,Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, partner site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
| | - Laura Godfrey
- Bridge Institute of Experimental Tumor Therapy, West German Cancer Center, University Hospital Essen, Essen, Germany.,Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, partner site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
| | - Lisa Frohn
- Institute of Pathology, Heinrich-Heine University and University Hospital of Dusseldorf, Dusseldorf, Germany
| | - Lena Haeberle
- Institute of Pathology, Heinrich-Heine University and University Hospital of Dusseldorf, Dusseldorf, Germany
| | - Aslihan Yavas
- Institute of Pathology, Heinrich-Heine University and University Hospital of Dusseldorf, Dusseldorf, Germany
| | - Rita Vesce
- Institute of Pathology, Heinrich-Heine University and University Hospital of Dusseldorf, Dusseldorf, Germany
| | - Wolfgang Goering
- Institute of Pathology, Heinrich-Heine University and University Hospital of Dusseldorf, Dusseldorf, Germany
| | - Friederike V Opitz
- Institute of Pathology, Heinrich-Heine University and University Hospital of Dusseldorf, Dusseldorf, Germany
| | - Nickolas Stoecklein
- Department of General, Visceral and Pediatric Surgery, Heinrich-Heine-University and University Hospital of Dusseldorf, Dusseldorf, Germany
| | - Wolfram Trudo Knoefel
- Department of General, Visceral and Pediatric Surgery, Heinrich-Heine-University and University Hospital of Dusseldorf, Dusseldorf, Germany
| | | | - Guenter Klöppel
- Institute of Pathology, Technische Universitaet Muenchen, Munich, Germany
| | - Elisa Espinet
- HI-STEM-Heidelberg Institute for Stem Cell Technology and Experimental Medicine GmbH, Heidelberg, Germany.,Division of Stem Cells and Cancer, German Cancer Research Centre and DKFZ-ZMBH Alliance, Heidelberg, Germany.,German Cancer Consortium, (DKTK), Heidelberg, Germany
| | - Andreas Trumpp
- HI-STEM-Heidelberg Institute for Stem Cell Technology and Experimental Medicine GmbH, Heidelberg, Germany.,Division of Stem Cells and Cancer, German Cancer Research Centre and DKFZ-ZMBH Alliance, Heidelberg, Germany.,German Cancer Consortium, (DKTK), Heidelberg, Germany
| | - Jens T Siveke
- Bridge Institute of Experimental Tumor Therapy, West German Cancer Center, University Hospital Essen, Essen, Germany.,Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, partner site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
| | - Irene Esposito
- Institute of Pathology, Heinrich-Heine University and University Hospital of Dusseldorf, Dusseldorf, Germany
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3
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Heid I, Münch C, Karakaya S, Lueong SS, Winkelkotte AM, Liffers ST, Godfrey L, Cheung PFY, Savvatakis K, Topping GJ, Englert F, Kritzner L, Grashei M, Tannapfel A, Viebahn R, Wolters H, Uhl W, Vangala D, Smeets EMM, Aarntzen EHJG, Rauh D, Weichert W, Hoheisel JD, Hahn SA, Schilling F, Braren R, Trajkovic-Arsic M, Siveke JT. Functional noninvasive detection of glycolytic pancreatic ductal adenocarcinoma. Cancer Metab 2022; 10:24. [PMID: 36494842 PMCID: PMC9737747 DOI: 10.1186/s40170-022-00298-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 11/22/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Pancreatic ductal adenocarcinoma (PDAC) lacks effective treatment options beyond chemotherapy. Although molecular subtypes such as classical and QM (quasi-mesenchymal)/basal-like with transcriptome-based distinct signatures have been identified, deduced therapeutic strategies and targets remain elusive. Gene expression data show enrichment of glycolytic genes in the more aggressive and therapy-resistant QM subtype. However, whether the glycolytic transcripts are translated into functional glycolysis that could further be explored for metabolic targeting in QM subtype is still not known. METHODS We used different patient-derived PDAC model systems (conventional and primary patient-derived cells, patient-derived xenografts (PDX), and patient samples) and performed transcriptional and functional metabolic analysis. These included RNAseq and Illumina HT12 bead array, in vitro Seahorse metabolic flux assays and metabolic drug targeting, and in vivo hyperpolarized [1-13C]pyruvate and [1-13C]lactate magnetic resonance spectroscopy (HP-MRS) in PDAC xenografts. RESULTS We found that glycolytic metabolic dependencies are not unambiguously functionally exposed in all QM PDACs. Metabolic analysis demonstrated functional metabolic heterogeneity in patient-derived primary cells and less so in conventional cell lines independent of molecular subtype. Importantly, we observed that the glycolytic product lactate is actively imported into the PDAC cells and used in mitochondrial oxidation in both classical and QM PDAC cells, although more actively in the QM cell lines. By using HP-MRS, we were able to noninvasively identify highly glycolytic PDAC xenografts by detecting the last glycolytic enzymatic step and prominent intra-tumoral [1-13C]pyruvate and [1-13C]lactate interconversion in vivo. CONCLUSION Our study adds functional metabolic phenotyping to transcriptome-based analysis and proposes a functional approach to identify highly glycolytic PDACs as candidates for antimetabolic therapeutic avenues.
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Affiliation(s)
- Irina Heid
- grid.6936.a0000000123222966Institute of Diagnostic and Interventional Radiology, School of Medicine, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Corinna Münch
- grid.5718.b0000 0001 2187 5445West German Cancer Center, Bridge Institute of Experimental Tumor Therapy, University Hospital Essen, University of Duisburg-Essen, Essen, Germany ,grid.7497.d0000 0004 0492 0584Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, Partner Site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany ,German Cancer Consortium (DKTK), Partner Site Essen, Essen, Germany
| | - Sinan Karakaya
- grid.5718.b0000 0001 2187 5445West German Cancer Center, Bridge Institute of Experimental Tumor Therapy, University Hospital Essen, University of Duisburg-Essen, Essen, Germany ,grid.7497.d0000 0004 0492 0584Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, Partner Site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany ,German Cancer Consortium (DKTK), Partner Site Essen, Essen, Germany
| | - Smiths S. Lueong
- grid.5718.b0000 0001 2187 5445West German Cancer Center, Bridge Institute of Experimental Tumor Therapy, University Hospital Essen, University of Duisburg-Essen, Essen, Germany ,grid.7497.d0000 0004 0492 0584Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, Partner Site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany ,German Cancer Consortium (DKTK), Partner Site Essen, Essen, Germany
| | - Alina M. Winkelkotte
- grid.5718.b0000 0001 2187 5445West German Cancer Center, Bridge Institute of Experimental Tumor Therapy, University Hospital Essen, University of Duisburg-Essen, Essen, Germany ,grid.7497.d0000 0004 0492 0584Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, Partner Site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
| | - Sven T. Liffers
- grid.5718.b0000 0001 2187 5445West German Cancer Center, Bridge Institute of Experimental Tumor Therapy, University Hospital Essen, University of Duisburg-Essen, Essen, Germany ,grid.7497.d0000 0004 0492 0584Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, Partner Site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany ,German Cancer Consortium (DKTK), Partner Site Essen, Essen, Germany
| | - Laura Godfrey
- grid.5718.b0000 0001 2187 5445West German Cancer Center, Bridge Institute of Experimental Tumor Therapy, University Hospital Essen, University of Duisburg-Essen, Essen, Germany ,grid.7497.d0000 0004 0492 0584Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, Partner Site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany ,German Cancer Consortium (DKTK), Partner Site Essen, Essen, Germany
| | - Phyllis F. Y. Cheung
- grid.5718.b0000 0001 2187 5445West German Cancer Center, Bridge Institute of Experimental Tumor Therapy, University Hospital Essen, University of Duisburg-Essen, Essen, Germany ,grid.7497.d0000 0004 0492 0584Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, Partner Site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany ,German Cancer Consortium (DKTK), Partner Site Essen, Essen, Germany
| | - Konstantinos Savvatakis
- grid.5718.b0000 0001 2187 5445West German Cancer Center, Bridge Institute of Experimental Tumor Therapy, University Hospital Essen, University of Duisburg-Essen, Essen, Germany ,grid.7497.d0000 0004 0492 0584Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, Partner Site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany ,German Cancer Consortium (DKTK), Partner Site Essen, Essen, Germany
| | - Geoffrey J. Topping
- grid.6936.a0000000123222966Department of Nuclear Medicine, School of Medicine, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Florian Englert
- grid.6936.a0000000123222966Institute of Diagnostic and Interventional Radiology, School of Medicine, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Lukas Kritzner
- grid.6936.a0000000123222966Institute of Diagnostic and Interventional Radiology, School of Medicine, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Martin Grashei
- grid.6936.a0000000123222966Department of Nuclear Medicine, School of Medicine, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Andrea Tannapfel
- grid.5570.70000 0004 0490 981XInstitute of Pathology, Ruhr University of Bochum, Bochum, Germany
| | - Richard Viebahn
- grid.5570.70000 0004 0490 981XDepartment of Surgery, Knappschaftskrankenhaus, Ruhr University Bochum, Bochum, Germany
| | - Heiner Wolters
- grid.416438.cDepartment of Visceral and General Surgery, St. Josef-Hospital, Dortmund, Germany
| | - Waldemar Uhl
- grid.416438.cClinic for General and Visceral Surgery, St. Josef-Hospital, Ruhr-University Bochum, Bochum, Germany
| | - Deepak Vangala
- grid.5570.70000 0004 0490 981XDepartment of Medicine, Ruhr University Bochum, University Hospital Knappschaftskrankenhaus Bochum GmbH, Bochum, Germany
| | - Esther M. M. Smeets
- grid.10417.330000 0004 0444 9382Medical Imaging, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Erik H. J. G. Aarntzen
- grid.10417.330000 0004 0444 9382Medical Imaging, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Daniel Rauh
- grid.5675.10000 0001 0416 9637Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany ,Drug Discovery Hub Dortmund (DDHD) Am Zentrum Für Integrierte Wirkstoffforschung (ZIW), Dortmund, Germany
| | - Wilko Weichert
- grid.6936.a0000000123222966Institute of Pathology, TUM School of Medicine, Technical University of Munich, Munich, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany ,Comprehensive Cancer Center Munich (CCCM), Munich, Germany
| | - Jörg D. Hoheisel
- grid.7497.d0000 0004 0492 0584Division of Functional Genome Analysis, German Cancer Research Center, DKFZ, Heidelberg, Germany
| | - Stephan A. Hahn
- grid.5570.70000 0004 0490 981XDepartment of Molecular GI Oncology, Faculty of Medicine, Ruhr University Bochum, 44780 Bochum, Germany
| | - Franz Schilling
- grid.6936.a0000000123222966Department of Nuclear Medicine, School of Medicine, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Rickmer Braren
- grid.6936.a0000000123222966Institute of Diagnostic and Interventional Radiology, School of Medicine, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | - Marija Trajkovic-Arsic
- grid.5718.b0000 0001 2187 5445West German Cancer Center, Bridge Institute of Experimental Tumor Therapy, University Hospital Essen, University of Duisburg-Essen, Essen, Germany ,grid.7497.d0000 0004 0492 0584Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, Partner Site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany ,German Cancer Consortium (DKTK), Partner Site Essen, Essen, Germany
| | - Jens T. Siveke
- grid.5718.b0000 0001 2187 5445West German Cancer Center, Bridge Institute of Experimental Tumor Therapy, University Hospital Essen, University of Duisburg-Essen, Essen, Germany ,grid.7497.d0000 0004 0492 0584Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, Partner Site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany ,German Cancer Consortium (DKTK), Partner Site Essen, Essen, Germany
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4
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Olsen SN, Godfrey L, Healy JP, Hatton C, Armstrong SA. Abstract 681: Targeted MLL-AF9 degradation is phenocopied by combined DOT1L and Menin inhibition. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
MLL1 (KMT2A) translocations lead to aberrant expression of stem cell associated gene programs in hematopoietic cells producing a particularly aggressive subtype of leukemia, namely MLL-rearranged acute myeloid and lymphoblastic leukemia (AML and ALL, respectively). In pediatric leukemia, the most common rearrangement is the t(9; 11) (p22; q23) reciprocal translocation, which results in the expression of the MLL-AF9 fusion gene. Since the MLL-AF9 rearrangement does not lead to direct activation of an enzyme, small molecule drug discovery remains challenging and despite decades of research on MLL-rearranged leukemia, we have been limited by the inability of acutely assessing the consequences of direct MLL-AF9 inactivation in relevant model systems. By coupling rapid PROTAC-mediated degradation of the oncogenic MLL-AF9 fusion protein with genome-wide gene expression and chromatin analyses we have now been able to identify the immediate transcriptional and chromatin state consequences of MLL-AF9 degradation. Specifically, we have established a core set of MLL-AF9 target genes whose expression changes within minutes of MLL-AF9 degradation. These rapid expression changes are mediated by changes in productive RNA Polymerase II elongation and increased RNA Polymerase II pausing. At later timepoints, degradation of the fusion protein also induces loss of an active chromatin landscape at MLL-AF9 target genes, characterized by loss of MLL-AF9 associated proteins and activating histone modifications. These insights improve our mechanistic understanding of how MLL-AF9 mediates chromatin remodeling and leukemogenesis, while also helping us evaluate small molecule inhibitors of epigenetic mechanisms that target the MLL-AF9 protein complex. Specifically, we investigated how degradation of MLL-AF9 compares to enzymatic inhibition of DOT1L or inhibition of the MENIN-MLL interaction. Interestingly, both DOT1L and MENIN inhibitors fell short when comparing their effects to MLL-AF9 degradation and only combined DOT1L/MENIN inhibition induced global MLL-AF9 destabilization on chromatin, thus disrupting the full MLL-AF9 directed epigenetic and transcriptional program. Ultimately, we were able to confirm these findings in a patient-derived xenograft model in vivo, where only the combination was able to significantly prolong leukemia free survival. In summary, our studies establish the cellular and molecular consequences of targeted degradation of the MLL-AF9 fusion oncoprotein and help improve our understanding of small molecule inhibitors of epigenetic mechanisms as cancer therapies.
Citation Format: Sarah Naomi Olsen, Laura Godfrey, James P. Healy, Charles Hatton, Scott A. Armstrong. Targeted MLL-AF9 degradation is phenocopied by combined DOT1L and Menin inhibition [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 681.
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Olsen SN, Godfrey L, Healy JP, Choi YA, Kai Y, Hatton C, Perner F, Haarer EL, Nabet B, Yuan GC, Armstrong SA. MLL::AF9 degradation induces rapid changes in transcriptional elongation and subsequent loss of an active chromatin landscape. Mol Cell 2022; 82:1140-1155.e11. [PMID: 35245435 PMCID: PMC9044330 DOI: 10.1016/j.molcel.2022.02.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 11/17/2021] [Accepted: 02/06/2022] [Indexed: 12/15/2022]
Abstract
MLL rearrangements produce fusion oncoproteins that drive leukemia development, but the direct effects of MLL-fusion inactivation remain poorly defined. We designed models with degradable MLL::AF9 where treatment with small molecules induces rapid degradation. We leveraged the kinetics of this system to identify a core subset of MLL::AF9 target genes where MLL::AF9 degradation induces changes in transcriptional elongation within 15 minutes. MLL::AF9 degradation subsequently causes loss of a transcriptionally active chromatin landscape. We used this insight to assess the effectiveness of small molecules that target members of the MLL::AF9 multiprotein complex, specifically DOT1L and MENIN. Combined DOT1L/MENIN inhibition resembles MLL::AF9 degradation, whereas single-agent treatment has more modest effects on MLL::AF9 occupancy and gene expression. Our data show that MLL::AF9 degradation leads to decreases in transcriptional elongation prior to changes in chromatin landscape at select loci and that combined inhibition of chromatin complexes releases the MLL::AF9 oncoprotein from chromatin globally.
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Affiliation(s)
- Sarah Naomi Olsen
- Department of Pediatric Oncology, Dana-Farber Cancer Institute/Boston Children's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Laura Godfrey
- Department of Pediatric Oncology, Dana-Farber Cancer Institute/Boston Children's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - James P Healy
- Department of Pediatric Oncology, Dana-Farber Cancer Institute/Boston Children's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Yoolim A Choi
- Department of Pediatric Oncology, Dana-Farber Cancer Institute/Boston Children's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Yan Kai
- Department of Pediatric Oncology, Dana-Farber Cancer Institute/Boston Children's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Charles Hatton
- Department of Pediatric Oncology, Dana-Farber Cancer Institute/Boston Children's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Florian Perner
- Department of Pediatric Oncology, Dana-Farber Cancer Institute/Boston Children's Hospital, Harvard Medical School, Boston, MA 02215, USA; Internal Medicine C, University Medical Center Greifswald, 17475 Greifswald, Germany
| | - Elena L Haarer
- Department of Pediatric Oncology, Dana-Farber Cancer Institute/Boston Children's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Behnam Nabet
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Guo-Cheng Yuan
- Department of Genetics and Genomic Sciences and Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Scott A Armstrong
- Department of Pediatric Oncology, Dana-Farber Cancer Institute/Boston Children's Hospital, Harvard Medical School, Boston, MA 02215, USA.
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Vangala D, Ladigan S, Liffers ST, Noseir S, Maghnouj A, Götze TM, Verdoodt B, Klein-Scory S, Godfrey L, Zowada MK, Huerta M, Edelstein DL, de Villarreal JM, Marqués M, Kumbrink J, Jung A, Schiergens T, Werner J, Heinemann V, Stintzing S, Lindoerfer D, Mansmann U, Pohl M, Teschendorf C, Bernhardt C, Wolters H, Stern J, Usta S, Viebahn R, Admard J, Casadei N, Fröhling S, Ball CR, Siveke JT, Glimm H, Tannapfel A, Schmiegel W, Hahn SA. Secondary resistance to anti-EGFR therapy by transcriptional reprogramming in patient-derived colorectal cancer models. Genome Med 2021; 13:116. [PMID: 34271981 PMCID: PMC8283888 DOI: 10.1186/s13073-021-00926-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 06/21/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The development of secondary resistance (SR) in metastatic colorectal cancer (mCRC) treated with anti-epidermal growth factor receptor (anti-EGFR) antibodies is not fully understood at the molecular level. Here we tested in vivo selection of anti-EGFR SR tumors in CRC patient-derived xenograft (PDX) models as a strategy for a molecular dissection of SR mechanisms. METHODS We analyzed 21 KRAS, NRAS, BRAF, and PI3K wildtype CRC patient-derived xenograft (PDX) models for their anti-EGFR sensitivity. Furthermore, 31 anti-EGFR SR tumors were generated via chronic in vivo treatment with cetuximab. A multi-omics approach was employed to address molecular primary and secondary resistance mechanisms. Gene set enrichment analyses were used to uncover SR pathways. Targeted therapy of SR PDX models was applied to validate selected SR pathways. RESULTS In vivo anti-EGFR SR could be established with high efficiency. Chronic anti-EGFR treatment of CRC PDX tumors induced parallel evolution of multiple resistant lesions with independent molecular SR mechanisms. Mutations in driver genes explained SR development in a subgroup of CRC PDX models, only. Transcriptional reprogramming inducing anti-EGFR SR was discovered as a common mechanism in CRC PDX models frequently leading to RAS signaling pathway activation. We identified cAMP and STAT3 signaling activation, as well as paracrine and autocrine signaling via growth factors as novel anti-EGFR secondary resistance mechanisms. Secondary resistant xenograft tumors could successfully be treated by addressing identified transcriptional changes by tailored targeted therapies. CONCLUSIONS Our study demonstrates that SR PDX tumors provide a unique platform to study molecular SR mechanisms and allow testing of multiple treatments for efficient targeting of SR mechanisms, not possible in the patient. Importantly, it suggests that the development of anti-EGFR tolerant cells via transcriptional reprogramming as a cause of anti-EGFR SR in CRC is likely more prevalent than previously anticipated. It emphasizes the need for analyses of SR tumor tissues at a multi-omics level for a comprehensive molecular understanding of anti-EGFR SR in CRC.
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Affiliation(s)
- Deepak Vangala
- Department of Molecular GI Oncology, Faculty of Medicine, Ruhr University Bochum, 44780, Bochum, Germany
- Department of Internal Medicine, Ruhr University Bochum, Knappschaftskrankenhaus, Bochum, Germany
| | - Swetlana Ladigan
- Department of Molecular GI Oncology, Faculty of Medicine, Ruhr University Bochum, 44780, Bochum, Germany
- Department of Internal Medicine, Ruhr University Bochum, Knappschaftskrankenhaus, Bochum, Germany
| | - Sven T Liffers
- Institute of Pathology, Ruhr University of Bochum, Bochum, Germany
- Present Address Division of Solid Tumor Translational Oncology, West German Cancer Center, University Hospital Essen, Essen, Germany
| | - Soha Noseir
- Department of Molecular GI Oncology, Faculty of Medicine, Ruhr University Bochum, 44780, Bochum, Germany
| | - Abdelouahid Maghnouj
- Department of Molecular GI Oncology, Faculty of Medicine, Ruhr University Bochum, 44780, Bochum, Germany
| | - Tina-Maria Götze
- Department of Molecular GI Oncology, Faculty of Medicine, Ruhr University Bochum, 44780, Bochum, Germany
| | | | - Susanne Klein-Scory
- Department of Internal Medicine, Ruhr University Bochum, Knappschaftskrankenhaus, Bochum, Germany
| | - Laura Godfrey
- Bridge Institute of Experimental Tumor Therapy, West German Cancer Center, University Hospital Essen, Essen, Germany
- Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, partner site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
| | - Martina K Zowada
- Translational Functional Cancer Genomics, NCT Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Mario Huerta
- Translational Functional Cancer Genomics, NCT Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT), Dresden, and German Cancer Research Center (DKFZ), Dresden, Germany
| | | | | | - Miriam Marqués
- Epithelial Carcinogenesis Group, Spanish National Cancer Research Centre (CNIO) and CIBERONC, Madrid, Spain
| | - Jörg Kumbrink
- Institute of Pathology, Ludwig Maximilian University (LMU), Munich, Germany
- German Cancer Consortium (DKTK, partner site Munich), Munich, Germany
| | - Andreas Jung
- Institute of Pathology, Ludwig Maximilian University (LMU), Munich, Germany
- German Cancer Consortium (DKTK, partner site Munich), Munich, Germany
| | - Tobias Schiergens
- Department of General, Visceral, and Transplantation Surgery, University Hospital, LMU Munich, Munich, Germany
| | - Jens Werner
- Department of General, Visceral, and Transplantation Surgery, University Hospital, LMU Munich, Munich, Germany
| | - Volker Heinemann
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - Sebastian Stintzing
- Department of Hematology, Oncology, and Tumor Immunology (CCM) Charité Universitaetsmedizin Berlin, Berlin, Germany
| | - Doris Lindoerfer
- Institute for Medical Information Processing, Biometry and Epidemiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Ulrich Mansmann
- Institute for Medical Information Processing, Biometry and Epidemiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Michael Pohl
- Department of Internal Medicine, Ruhr University Bochum, Knappschaftskrankenhaus, Bochum, Germany
| | | | | | - Heiner Wolters
- Department of Visceral and General Surgery, St. Josef Hospital, Dortmund, Germany
| | - Josef Stern
- Department of Visceral and General Surgery, St. Josef Hospital, Dortmund, Germany
| | - Selami Usta
- Department of Visceral and General Surgery, St. Josef Hospital, Dortmund, Germany
| | - Richard Viebahn
- Department of Surgery, Ruhr University Bochum, Knappschaftskrankenhaus, Bochum, Germany
| | - Jacob Admard
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Nicolas Casadei
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Stefan Fröhling
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Deptartment of Translational Medical Oncology, NCT Heidelberg and German Cancer Research Center, Heidelberg, Germany
| | - Claudia R Ball
- Translational Functional Cancer Genomics, NCT Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT), Dresden, and German Cancer Research Center (DKFZ), Dresden, Germany
- Center for Personalized Oncology, NCT Dresden and University Hospital Carl Gustav Carus Dresden at TU Dresden, Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
| | - Jens T Siveke
- Bridge Institute of Experimental Tumor Therapy, West German Cancer Center, University Hospital Essen, Essen, Germany
- Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, partner site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
| | - Hanno Glimm
- Translational Functional Cancer Genomics, NCT Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT), Dresden, and German Cancer Research Center (DKFZ), Dresden, Germany
- Center for Personalized Oncology, NCT Dresden and University Hospital Carl Gustav Carus Dresden at TU Dresden, Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
| | - Andrea Tannapfel
- Institute of Pathology, Ruhr University of Bochum, Bochum, Germany
| | - Wolff Schmiegel
- Department of Internal Medicine, Ruhr University Bochum, Knappschaftskrankenhaus, Bochum, Germany
| | - Stephan A Hahn
- Department of Molecular GI Oncology, Faculty of Medicine, Ruhr University Bochum, 44780, Bochum, Germany.
- Department of Internal Medicine, Ruhr University Bochum, Knappschaftskrankenhaus, Bochum, Germany.
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7
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Crump NT, Hadjinicolaou AV, Xia M, Walsby-Tickle J, Gileadi U, Chen JL, Setshedi M, Olsen LR, Lau IJ, Godfrey L, Quek L, Yu Z, Ballabio E, Barnkob MB, Napolitani G, Salio M, Koohy H, Kessler BM, Taylor S, Vyas P, McCullagh JSO, Milne TA, Cerundolo V. Chromatin accessibility governs the differential response of cancer and T cells to arginine starvation. Cell Rep 2021; 35:109101. [PMID: 33979616 PMCID: PMC8131582 DOI: 10.1016/j.celrep.2021.109101] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 03/01/2021] [Accepted: 04/16/2021] [Indexed: 12/20/2022] Open
Abstract
Depleting the microenvironment of important nutrients such as arginine is a key strategy for immune evasion by cancer cells. Many tumors overexpress arginase, but it is unclear how these cancers, but not T cells, tolerate arginine depletion. In this study, we show that tumor cells synthesize arginine from citrulline by upregulating argininosuccinate synthetase 1 (ASS1). Under arginine starvation, ASS1 transcription is induced by ATF4 and CEBPβ binding to an enhancer within ASS1. T cells cannot induce ASS1, despite the presence of active ATF4 and CEBPβ, as the gene is repressed. Arginine starvation drives global chromatin compaction and repressive histone methylation, which disrupts ATF4/CEBPβ binding and target gene transcription. We find that T cell activation is impaired in arginine-depleted conditions, with significant metabolic perturbation linked to incomplete chromatin remodeling and misregulation of key genes. Our results highlight a T cell behavior mediated by nutritional stress, exploited by cancer cells to enable pathological immune evasion.
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Affiliation(s)
- Nicholas T Crump
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Andreas V Hadjinicolaou
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Meng Xia
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - John Walsby-Tickle
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Uzi Gileadi
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Ji-Li Chen
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Mashiko Setshedi
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Lars R Olsen
- Section for Bioinformatics, DTU Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - I-Jun Lau
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Laura Godfrey
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Lynn Quek
- School of Cancer and Pharmaceutical Sciences, King's College London, SGDP Centre, Memory Lane, London SE5 8AF, UK
| | - Zhanru Yu
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Erica Ballabio
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Mike B Barnkob
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Giorgio Napolitani
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Mariolina Salio
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Hashem Koohy
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Benedikt M Kessler
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Stephen Taylor
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Paresh Vyas
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - James S O McCullagh
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Thomas A Milne
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK.
| | - Vincenzo Cerundolo
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
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8
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Crump NT, Ballabio E, Godfrey L, Thorne R, Repapi E, Kerry J, Tapia M, Hua P, Lagerholm C, Filippakopoulos P, Davies JOJ, Milne TA. BET inhibition disrupts transcription but retains enhancer-promoter contact. Nat Commun 2021; 12:223. [PMID: 33431820 PMCID: PMC7801379 DOI: 10.1038/s41467-020-20400-z] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 12/01/2020] [Indexed: 12/13/2022] Open
Abstract
Enhancers are DNA sequences that enable complex temporal and tissue-specific regulation of genes in higher eukaryotes. Although it is not entirely clear how enhancer-promoter interactions can increase gene expression, this proximity has been observed in multiple systems at multiple loci and is thought to be essential for the maintenance of gene expression. Bromodomain and Extra-Terminal domain (BET) and Mediator proteins have been shown capable of forming phase condensates and are thought to be essential for super-enhancer function. Here, we show that targeting of cells with inhibitors of BET proteins or pharmacological degradation of BET protein Bromodomain-containing protein 4 (BRD4) has a strong impact on transcription but very little impact on enhancer-promoter interactions. Dissolving phase condensates reduces BRD4 and Mediator binding at enhancers and can also strongly affect gene transcription, without disrupting enhancer-promoter interactions. These results suggest that activation of transcription and maintenance of enhancer-promoter interactions are separable events. Our findings further indicate that enhancer-promoter interactions are not dependent on high levels of BRD4 and Mediator, and are likely maintained by a complex set of factors including additional activator complexes and, at some sites, CTCF and cohesin.
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Affiliation(s)
- Nicholas T Crump
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Erica Ballabio
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Laura Godfrey
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Ross Thorne
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Emmanouela Repapi
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Jon Kerry
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Marta Tapia
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Peng Hua
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Christoffer Lagerholm
- Wolfson Imaging Centre Oxford, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Panagis Filippakopoulos
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - 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, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK.
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9
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Godfrey L, Crump NT, O'Byrne S, Lau IJ, Rice S, Harman JR, Jackson T, Elliott N, Buck G, Connor C, Thorne R, Knapp DJHF, Heidenreich O, Vyas P, Menendez P, Inglott S, Ancliff P, Geng H, Roberts I, Roy A, Milne TA. H3K79me2/3 controls enhancer-promoter interactions and activation of the pan-cancer stem cell marker PROM1/CD133 in MLL-AF4 leukemia cells. Leukemia 2020; 35:90-106. [PMID: 32242051 PMCID: PMC7787973 DOI: 10.1038/s41375-020-0808-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 03/12/2020] [Accepted: 03/18/2020] [Indexed: 02/06/2023]
Abstract
MLL gene rearrangements (MLLr) are a common cause of aggressive, incurable acute lymphoblastic leukemias (ALL) in infants and children, most of which originate in utero. The most common MLLr produces an MLL-AF4 fusion protein. MLL-AF4 promotes leukemogenesis by activating key target genes, mainly through recruitment of DOT1L and increased histone H3 lysine-79 methylation (H3K79me2/3). One key MLL-AF4 target gene is PROM1, which encodes CD133 (Prominin-1). CD133 is a pentaspan transmembrane glycoprotein that represents a potential pan-cancer target as it is found on multiple cancer stem cells. Here we demonstrate that aberrant PROM1/CD133 expression is essential for leukemic cell growth, mediated by direct binding of MLL-AF4. Activation is controlled by an intragenic H3K79me2/3 enhancer element (KEE) leading to increased enhancer–promoter interactions between PROM1 and the nearby gene TAPT1. This dual locus regulation is reflected in a strong correlation of expression in leukemia. We find that in PROM1/CD133 non-expressing cells, the PROM1 locus is repressed by polycomb repressive complex 2 (PRC2) binding, associated with reduced expression of TAPT1, partially due to loss of interactions with the PROM1 locus. Together, these results provide the first detailed analysis of PROM1/CD133 regulation that explains CD133 expression in MLLr ALL.
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Affiliation(s)
- Laura Godfrey
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Nicholas T Crump
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Sorcha O'Byrne
- Department of Paediatrics, University of Oxford, Oxford, UK
| | - I-Jun Lau
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Siobhan Rice
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Joe R Harman
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Thomas Jackson
- Department of Paediatrics, University of Oxford, Oxford, UK
| | | | - Gemma Buck
- Department of Paediatrics, University of Oxford, Oxford, UK
| | | | - Ross Thorne
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - David J H F Knapp
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Olaf Heidenreich
- Princess Maxima Centrum for Pediatric Oncology, Utrecht, The Netherlands.,Wolfson Childhood Cancer Research Centre, Newcastle University, Newcastle upon Tyne, UK
| | - Paresh Vyas
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.,Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Pablo Menendez
- Josep Carreras Leukemia Research Institute, Barcelona, Spain.,Institucio Catalana of Recerca i Estudis Avançats (ICREA), Barcelona, Spain.,Centro de Investigación Biomédica en Red en cancer (CIBERONC)-ISCIII, Barcelona, Spain
| | - Sarah Inglott
- Great Ormond Street Hospital for Children, London, UK
| | | | - Huimin Geng
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Irene Roberts
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.,Department of Paediatrics, University of Oxford, Oxford, UK
| | - Anindita Roy
- Department of Paediatrics, University of Oxford, Oxford, UK.
| | - Thomas A Milne
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
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10
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Rose M, Bringezu S, Godfrey L, Fiedler D, Gaisa NT, Koch M, Bach C, Füssel S, Herr A, Hübner D, Ellinger J, Pfister D, Knüchel R, Wirth MP, Böhme M, Dahl E. ITIH5 and ECRG4 DNA Methylation Biomarker Test (EI-BLA) for Urine-Based Non-Invasive Detection of Bladder Cancer. Int J Mol Sci 2020; 21:ijms21031117. [PMID: 32046186 PMCID: PMC7036997 DOI: 10.3390/ijms21031117] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/05/2020] [Accepted: 02/05/2020] [Indexed: 02/07/2023] Open
Abstract
Bladder cancer is one of the more common malignancies in humans and the most expensive tumor for treating in the Unites States (US) and Europe due to the need for lifelong surveillance. Non-invasive tests approved by the FDA have not been widely adopted in routine diagnosis so far. Therefore, we aimed to characterize the two putative tumor suppressor genes ECRG4 and ITIH5 as novel urinary DNA methylation biomarkers that are suitable for non-invasive detection of bladder cancer. While assessing the analytical performance, a spiking experiment was performed by determining the limit of RT112 tumor cell detection (range: 100-10,000 cells) in the urine of healthy donors in dependency of the processing protocols of the RWTH cBMB. Clinically, urine sediments of 474 patients were analyzed by using quantitative methylation-specific PCR (qMSP) and Methylation Sensitive Restriction Enzyme (MSRE) qPCR techniques. Overall, ECRG4-ITIH5 showed a sensitivity of 64% to 70% with a specificity ranging between 80% and 92%, i.e., discriminating healthy, benign lesions, and/or inflammatory diseases from bladder tumors. When comparing single biomarkers, ECRG4 achieved a sensitivity of 73%, which was increased by combination with the known biomarker candidate NID2 up to 76% at a specificity of 97%. Hence, ITIH5 and, in particular, ECRG4 might be promising candidates for further optimizing current bladder cancer biomarker panels and platforms.
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Affiliation(s)
- Michael Rose
- Institute of Pathology, RWTH Aachen University, 52074 Aachen, Germany; (S.B.); (L.G.); (D.F.); (N.T.G.); (M.K.); (R.K.)
- RWTH Centralized Biomaterial Bank (RWTH cBMB), Medical Faculty, RWTH Aachen University, 52074 Aachen, Germany
- Correspondence: (M.R.); (E.D.); Tel.: +49-241-808-9715 (M.R.); +49-241-808-8431 (E.D.); Fax: +49-241-808-2439 (M.R.); +49-241-808-2439 (E.D.)
| | - Sarah Bringezu
- Institute of Pathology, RWTH Aachen University, 52074 Aachen, Germany; (S.B.); (L.G.); (D.F.); (N.T.G.); (M.K.); (R.K.)
| | - Laura Godfrey
- Institute of Pathology, RWTH Aachen University, 52074 Aachen, Germany; (S.B.); (L.G.); (D.F.); (N.T.G.); (M.K.); (R.K.)
| | - David Fiedler
- Institute of Pathology, RWTH Aachen University, 52074 Aachen, Germany; (S.B.); (L.G.); (D.F.); (N.T.G.); (M.K.); (R.K.)
| | - Nadine T. Gaisa
- Institute of Pathology, RWTH Aachen University, 52074 Aachen, Germany; (S.B.); (L.G.); (D.F.); (N.T.G.); (M.K.); (R.K.)
| | - Maximilian Koch
- Institute of Pathology, RWTH Aachen University, 52074 Aachen, Germany; (S.B.); (L.G.); (D.F.); (N.T.G.); (M.K.); (R.K.)
| | - Christian Bach
- Department of Urology, RWTH Aachen University, 52074 Aachen, Germany; (C.B.); (D.P.)
| | - Susanne Füssel
- Department of Urology, University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany; (S.F.); (D.H.); (M.P.W.)
| | | | - Doreen Hübner
- Department of Urology, University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany; (S.F.); (D.H.); (M.P.W.)
| | - Jörg Ellinger
- Department of Urology, University Hospital Bonn, 53105 Bonn, Germany;
| | - David Pfister
- Department of Urology, RWTH Aachen University, 52074 Aachen, Germany; (C.B.); (D.P.)
- Department of Urology, Uro-Oncology, Robot Assisted and Reconstructive Urologic Surgery, University Hospital Cologne, 50937 Cologne, Germany
| | - Ruth Knüchel
- Institute of Pathology, RWTH Aachen University, 52074 Aachen, Germany; (S.B.); (L.G.); (D.F.); (N.T.G.); (M.K.); (R.K.)
| | - Manfred P. Wirth
- Department of Urology, University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany; (S.F.); (D.H.); (M.P.W.)
| | - Manja Böhme
- Biotype GmbH, 01109 Dresden, Germany; (A.H.); (M.B.)
| | - Edgar Dahl
- Institute of Pathology, RWTH Aachen University, 52074 Aachen, Germany; (S.B.); (L.G.); (D.F.); (N.T.G.); (M.K.); (R.K.)
- RWTH Centralized Biomaterial Bank (RWTH cBMB), Medical Faculty, RWTH Aachen University, 52074 Aachen, Germany
- Correspondence: (M.R.); (E.D.); Tel.: +49-241-808-9715 (M.R.); +49-241-808-8431 (E.D.); Fax: +49-241-808-2439 (M.R.); +49-241-808-2439 (E.D.)
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11
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Cook N, Banerji U, Evans J, Biondo A, Germetaki T, Randhawa M, Godfrey L, Leslie S, Jeffrey P, Rigby M, Bennett G, Blakemore S, Koehler M, Niewiarowski A, Pittman M, Symeonides S. Pharmacokinetic (PK) assessment of BT1718: A phase I/II a study of BT1718, a first in class bicycle toxin conjugate (BTC), in patients (pts) with advanced solid tumours. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz244.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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12
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O'Byrne S, Elliott N, Rice S, Buck G, Fordham N, Garnett C, Godfrey L, Crump NT, Wright G, Inglott S, Hua P, Psaila B, Povinelli B, Knapp DJHF, Agraz-Doblas A, Bueno C, Varela I, Bennett P, Koohy H, Watt SM, Karadimitris A, Mead AJ, Ancliff P, Vyas P, Menendez P, Milne TA, Roberts I, Roy A. Discovery of a CD10-negative B-progenitor in human fetal life identifies unique ontogeny-related developmental programs. Blood 2019; 134:1059-1071. [PMID: 31383639 DOI: 10.1182/blood.2019001289] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 07/05/2019] [Indexed: 12/13/2022] Open
Abstract
Human lymphopoiesis is a dynamic lifelong process that starts in utero 6 weeks postconception. Although fetal B-lymphopoiesis remains poorly defined, it is key to understanding leukemia initiation in early life. Here, we provide a comprehensive analysis of the human fetal B-cell developmental hierarchy. We report the presence in fetal tissues of 2 distinct CD19+ B-progenitors, an adult-type CD10+ve ProB-progenitor and a new CD10-ve PreProB-progenitor, and describe their molecular and functional characteristics. PreProB-progenitors and ProB-progenitors appear early in the first trimester in embryonic liver, followed by a sustained second wave of B-progenitor development in fetal bone marrow (BM), where together they form >40% of the total hematopoietic stem cell/progenitor pool. Almost one-third of fetal B-progenitors are CD10-ve PreProB-progenitors, whereas, by contrast, PreProB-progenitors are almost undetectable (0.53% ± 0.24%) in adult BM. Single-cell transcriptomics and functional assays place fetal PreProB-progenitors upstream of ProB-progenitors, identifying them as the first B-lymphoid-restricted progenitor in human fetal life. Although fetal BM PreProB-progenitors and ProB-progenitors both give rise solely to B-lineage cells, they are transcriptionally distinct. As with their fetal counterparts, adult BM PreProB-progenitors give rise only to B-lineage cells in vitro and express the expected B-lineage gene expression program. However, fetal PreProB-progenitors display a distinct, ontogeny-related gene expression pattern that is not seen in adult PreProB-progenitors, and they share transcriptomic signatures with CD10-ve B-progenitor infant acute lymphoblastic leukemia blast cells. These data identify PreProB-progenitors as the earliest B-lymphoid-restricted progenitor in human fetal life and suggest that this fetal-restricted committed B-progenitor might provide a permissive cellular context for prenatal B-progenitor leukemia initiation.
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Affiliation(s)
| | | | - Siobhan Rice
- Medical Research Council (MRC) Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Gemma Buck
- Department of Paediatrics and
- Medical Research Council (MRC) Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Nicholas Fordham
- Medical Research Council (MRC) Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Catherine Garnett
- Medical Research Council (MRC) Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Laura Godfrey
- Medical Research Council (MRC) Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Nicholas T Crump
- Medical Research Council (MRC) Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Gary Wright
- Department of Haematology, Great Ormond Street Hospital NHS Foundation Trust, London, United Kingdom
| | - Sarah Inglott
- Department of Haematology, Great Ormond Street Hospital NHS Foundation Trust, London, United Kingdom
| | - Peng Hua
- Medical Research Council (MRC) Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
- Stem Cell Research, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Bethan Psaila
- Medical Research Council (MRC) Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Benjamin Povinelli
- Medical Research Council (MRC) Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - David J H F Knapp
- Medical Research Council (MRC) Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Antonio Agraz-Doblas
- Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-CSIC, Santander, Spain
- Josep Carreras Leukemia Research Institute-Campus Clinic, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain
| | - Clara Bueno
- Josep Carreras Leukemia Research Institute-Campus Clinic, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain
| | - Ignacio Varela
- Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-CSIC, Santander, Spain
| | - Phillip Bennett
- Institute of Reproductive and Developmental Biology, Department of Surgery and Cancer, Hammersmith Hospital Campus, Imperial College London, London, United Kingdom
| | - Hashem Koohy
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Suzanne M Watt
- Stem Cell Research, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Anastasios Karadimitris
- Centre for Haematology, Department of Medicine, Hammersmith Hospital, Imperial College London, London, United Kingdom
| | - Adam J Mead
- Medical Research Council (MRC) Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
- Haematology Theme, Oxford Biomedical Research Centre, Oxford University Hospitals, Oxford, United Kingdom
| | - Phillip Ancliff
- Department of Haematology, Great Ormond Street Hospital NHS Foundation Trust, London, United Kingdom
| | - Paresh Vyas
- Medical Research Council (MRC) Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
- Haematology Theme, Oxford Biomedical Research Centre, Oxford University Hospitals, Oxford, United Kingdom
| | - Pablo Menendez
- Josep Carreras Leukemia Research Institute-Campus Clinic, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain
- Institucio Catalana of Recerca i Estudis Avançats, Barcelona, Spain; and
- Centro de Investigación Biomédica en Red en Cancer-ISCIII, Barcelona, Spain
| | - Thomas A Milne
- Medical Research Council (MRC) Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
- Haematology Theme, Oxford Biomedical Research Centre, Oxford University Hospitals, Oxford, United Kingdom
| | - Irene Roberts
- Department of Paediatrics and
- Medical Research Council (MRC) Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
- Haematology Theme, Oxford Biomedical Research Centre, Oxford University Hospitals, Oxford, United Kingdom
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13
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Godfrey L, Crump NT, Thorne R, Lau IJ, Repapi E, Dimou D, Smith AL, Harman JR, Telenius JM, Oudelaar AM, Downes DJ, Vyas P, Hughes JR, Milne TA. DOT1L inhibition reveals a distinct subset of enhancers dependent on H3K79 methylation. Nat Commun 2019; 10:2803. [PMID: 31243293 PMCID: PMC6594956 DOI: 10.1038/s41467-019-10844-3] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 06/05/2019] [Indexed: 12/26/2022] Open
Abstract
Enhancer elements are a key regulatory feature of many important genes. Several general features including the presence of specific histone modifications are used to demarcate potentially active enhancers. Here we reveal that putative enhancers marked with H3 lysine 79 (H3K79) di or trimethylation (me2/3) (which we name H3K79me2/3 enhancer elements or KEEs) can be found in multiple cell types. Mixed lineage leukemia gene (MLL) rearrangements (MLL-r) such as MLL-AF4 are a major cause of incurable acute lymphoblastic leukemias (ALL). Using the DOT1L inhibitor EPZ-5676 in MLL-AF4 leukemia cells, we show that H3K79me2/3 is required for maintaining chromatin accessibility, histone acetylation and transcription factor binding specifically at KEEs but not non-KEE enhancers. We go on to show that H3K79me2/3 is essential for maintaining enhancer-promoter interactions at a subset of KEEs. Together, these data implicate H3K79me2/3 as having a functional role at a subset of active enhancers in MLL-AF4 leukemia cells.
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Affiliation(s)
- Laura Godfrey
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Nicholas T Crump
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Ross Thorne
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - I-Jun Lau
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Emmanouela Repapi
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Dimitra Dimou
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Alastair L Smith
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Joe R Harman
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Jelena M Telenius
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - A Marieke Oudelaar
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Damien J Downes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Paresh Vyas
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
- Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Jim R Hughes
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
- 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, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK.
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14
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Kerry J, Godfrey L, Repapi E, Tapia M, Blackledge NP, Ma H, Ballabio E, O'Byrne S, Ponthan F, Heidenreich O, Roy A, Roberts I, Konopleva M, Klose RJ, Geng H, Milne TA. MLL-AF4 Spreading Identifies Binding Sites that Are Distinct from Super-Enhancers and that Govern Sensitivity to DOT1L Inhibition in Leukemia. Cell Rep 2017; 18:482-495. [PMID: 28076791 PMCID: PMC5263239 DOI: 10.1016/j.celrep.2016.12.054] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 10/31/2016] [Accepted: 12/16/2016] [Indexed: 01/16/2023] Open
Abstract
Understanding the underlying molecular mechanisms of defined cancers is crucial for effective personalized therapies. Translocations of the mixed-lineage leukemia (MLL) gene produce fusion proteins such as MLL-AF4 that disrupt epigenetic pathways and cause poor-prognosis leukemias. Here, we find that at a subset of gene targets, MLL-AF4 binding spreads into the gene body and is associated with the spreading of Menin binding, increased transcription, increased H3K79 methylation (H3K79me2/3), a disruption of normal H3K36me3 patterns, and unmethylated CpG regions in the gene body. Compared to other H3K79me2/3 marked genes, MLL-AF4 spreading gene expression is downregulated by inhibitors of the H3K79 methyltransferase DOT1L. This sensitivity mediates synergistic interactions with additional targeted drug treatments. Therefore, epigenetic spreading and enhanced susceptibility to epidrugs provides a potential marker for better understanding combination therapies in humans. MLL-AF4 binding requires an unmethylated CpG (uCpG) island and Menin MLL-AF4 and Menin can spread into the gene body of some targets Spreading targets are highly transcribed and have an aberrant chromatin signature Spreading of MLL-AF4 is a predictor of sensitivity to DOT1L inhibitors
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Affiliation(s)
- Jon Kerry
- MRC, Molecular Haematology Unit, NIHR Oxford Biomedical Research Centre Programme, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Laura Godfrey
- MRC, Molecular Haematology Unit, NIHR Oxford Biomedical Research Centre Programme, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Emmanouela Repapi
- Computational Biology Research Group, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Marta Tapia
- MRC, Molecular Haematology Unit, NIHR Oxford Biomedical Research Centre Programme, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Neil P Blackledge
- Laboratory of Chromatin Biology and Transcription, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Helen Ma
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Erica Ballabio
- MRC, Molecular Haematology Unit, NIHR Oxford Biomedical Research Centre Programme, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Sorcha O'Byrne
- Department of Paediatrics, University of Oxford, Children's Hospital, John Radcliffe, Oxford OX3 9DU, UK
| | - Frida Ponthan
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle Upon Tyne NE1 7RU, UK
| | - Olaf Heidenreich
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle Upon Tyne NE1 7RU, UK
| | - Anindita Roy
- Department of Paediatrics, University of Oxford, Children's Hospital, John Radcliffe, Oxford OX3 9DU, UK
| | - Irene Roberts
- MRC, Molecular Haematology Unit, NIHR Oxford Biomedical Research Centre Programme, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK; Department of Paediatrics, University of Oxford, Children's Hospital, John Radcliffe, Oxford OX3 9DU, UK
| | - Marina Konopleva
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Robert J Klose
- Laboratory of Chromatin Biology and Transcription, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Huimin Geng
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Thomas A Milne
- MRC, Molecular Haematology Unit, NIHR Oxford Biomedical Research Centre Programme, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK.
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15
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Godfrey L, Kerry J, Thorne R, Repapi E, Davies JOJ, Tapia M, Ballabio E, Hughes JR, Geng H, Konopleva M, Milne TA. MLL-AF4 binds directly to a BCL-2 specific enhancer and modulates H3K27 acetylation. Exp Hematol 2016; 47:64-75. [PMID: 27856324 PMCID: PMC5333536 DOI: 10.1016/j.exphem.2016.11.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 10/21/2016] [Accepted: 11/02/2016] [Indexed: 11/15/2022]
Abstract
Survival rates for children and adults carrying mutations in the Mixed Lineage Leukemia (MLL) gene continue to have a very poor prognosis. The most common MLL mutation in acute lymphoblastic leukemia is the t(4;11)(q21;q23) chromosome translocation that fuses MLL in-frame with the AF4 gene producing MLL-AF4 and AF4-MLL fusion proteins. Previously, we found that MLL-AF4 binds to the BCL-2 gene and directly activates it through DOT1L recruitment and increased H3K79me2/3 levels. In the study described here, we performed a detailed analysis of MLL-AF4 regulation of the entire BCL-2 family. By measuring nascent RNA production in MLL-AF4 knockdowns, we found that of all the BCL-2 family genes, MLL-AF4 directly controls the active transcription of both BCL-2 and MCL-1 and also represses BIM via binding of the polycomb group repressor 1 (PRC1) complex component CBX8. We further analyzed MLL-AF4 activation of the BCL-2 gene using Capture-C and identified a BCL-2-specific enhancer, consisting of two clusters of H3K27Ac at the 3' end of the gene. Loss of MLL-AF4 activity results in a reduction of H3K79me3 levels in the gene body and H3K27Ac levels at the 3' BCL-2 enhancer, revealing a novel regulatory link between these two histone marks and MLL-AF4-mediated activation of BCL-2.
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Affiliation(s)
- Laura Godfrey
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, University of Oxford, Headington, Oxford, UK
| | - Jon Kerry
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, University of Oxford, Headington, Oxford, UK
| | - Ross Thorne
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, University of Oxford, Headington, Oxford, UK
| | - Emmanouela Repapi
- Weatherall Institute of Molecular Medicine, Computational Biology Research Group, University of Oxford, Headington, Oxford, UK
| | - James O J Davies
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, University of Oxford, Headington, Oxford, UK
| | - Marta Tapia
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, University of Oxford, Headington, Oxford, UK
| | - Erica Ballabio
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, University of Oxford, Headington, Oxford, UK
| | - Jim R Hughes
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, University of Oxford, Headington, Oxford, UK
| | - Huimin Geng
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA
| | - Marina Konopleva
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX
| | - Thomas A Milne
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, University of Oxford, Headington, Oxford, UK.
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16
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Beninati G, Barbiere J, Godfrey L, Ndlovu A. SU-F-T-537: Prone Breast Accelerated Partial Breast Irradiation Using Non-Coplanar Volumetric Arc Therapy. Med Phys 2016. [DOI: 10.1118/1.4956722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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17
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Benito JM, Godfrey L, Kojima K, Hogdal L, Wunderlich M, Geng H, Marzo I, Harutyunyan KG, Golfman L, North P, Kerry J, Ballabio E, Chonghaile TN, Gonzalo O, Qiu Y, Jeremias I, Debose L, O'Brien E, Ma H, Zhou P, Jacamo R, Park E, Coombes KR, Zhang N, Thomas DA, O'Brien S, Kantarjian HM, Leverson JD, Kornblau SM, Andreeff M, Müschen M, Zweidler-McKay PA, Mulloy JC, Letai A, Milne TA, Konopleva M. MLL-Rearranged Acute Lymphoblastic Leukemias Activate BCL-2 through H3K79 Methylation and Are Sensitive to the BCL-2-Specific Antagonist ABT-199. Cell Rep 2015; 13:2715-27. [PMID: 26711339 PMCID: PMC4700051 DOI: 10.1016/j.celrep.2015.12.003] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 10/21/2015] [Accepted: 11/19/2015] [Indexed: 12/25/2022] Open
Abstract
Targeted therapies designed to exploit specific molecular pathways in aggressive cancers are an exciting area of current research. Mixed Lineage Leukemia (MLL) mutations such as the t(4;11) translocation cause aggressive leukemias that are refractory to conventional treatment. The t(4;11) translocation produces an MLL/AF4 fusion protein that activates key target genes through both epigenetic and transcriptional elongation mechanisms. In this study, we show that t(4;11) patient cells express high levels of BCL-2 and are highly sensitive to treatment with the BCL-2-specific BH3 mimetic ABT-199. We demonstrate that MLL/AF4 specifically upregulates the BCL-2 gene but not other BCL-2 family members via DOT1L-mediated H3K79me2/3. We use this information to show that a t(4;11) cell line is sensitive to a combination of ABT-199 and DOT1L inhibitors. In addition, ABT-199 synergizes with standard induction-type therapy in a xenotransplant model, advocating for the introduction of ABT-199 into therapeutic regimens for MLL-rearranged leukemias.
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Affiliation(s)
- Juliana M Benito
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Laura Godfrey
- Weatherall Institute of Molecular Medicine, Molecular Haematology Unit, NIHR Oxford Biomedical Research Centre Programme, University of Oxford, Headington, Oxford OX3 9DS, UK
| | - Kensuke Kojima
- Division of Hematology, Respiratory Medicine and Oncology, Department of Internal Medicine, Faculty of Medicine, Saga University, Saga 840-8502, Japan
| | - Leah Hogdal
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Mark Wunderlich
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Huimin Geng
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Isabel Marzo
- Department of Biochemistry, Molecular and Cell Biology, University of Zaragoza, 50018 Zaragoza, Spain
| | - Karine G Harutyunyan
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Leonard Golfman
- Division of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Phillip North
- Weatherall Institute of Molecular Medicine, Molecular Haematology Unit, NIHR Oxford Biomedical Research Centre Programme, University of Oxford, Headington, Oxford OX3 9DS, UK
| | - Jon Kerry
- Weatherall Institute of Molecular Medicine, Molecular Haematology Unit, NIHR Oxford Biomedical Research Centre Programme, University of Oxford, Headington, Oxford OX3 9DS, UK
| | - Erica Ballabio
- Weatherall Institute of Molecular Medicine, Molecular Haematology Unit, NIHR Oxford Biomedical Research Centre Programme, University of Oxford, Headington, Oxford OX3 9DS, UK
| | - Triona Ní Chonghaile
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, York House, Dublin 2, Ireland
| | - Oscar Gonzalo
- Department of Biochemistry, Molecular and Cell Biology, University of Zaragoza, 50018 Zaragoza, Spain
| | - Yihua Qiu
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Irmela Jeremias
- German Research Center for Environmental Health (GmbH), 85764 Neuherberg, Germany
| | - LaKiesha Debose
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Eric O'Brien
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Helen Ma
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ping Zhou
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rodrigo Jacamo
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Eugene Park
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Kevin R Coombes
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Nianxiang Zhang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Deborah A Thomas
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Susan O'Brien
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hagop M Kantarjian
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Joel D Leverson
- Department of Oncology Development, AbbVie Inc., North Chicago, IL 60064, USA
| | - Steven M Kornblau
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michael Andreeff
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Markus Müschen
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Patrick A Zweidler-McKay
- Division of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - James C Mulloy
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Anthony Letai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Thomas A Milne
- Weatherall Institute of Molecular Medicine, Molecular Haematology Unit, NIHR Oxford Biomedical Research Centre Programme, University of Oxford, Headington, Oxford OX3 9DS, UK.
| | - Marina Konopleva
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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18
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Godfrey L, Yamada-Fowler N, Smith J, Thornalley PJ, Rabbani N. Arginine-directed glycation and decreased HDL plasma concentration and functionality. Nutr Diabetes 2014; 4:e134. [PMID: 25177914 PMCID: PMC4183972 DOI: 10.1038/nutd.2014.31] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2014] [Revised: 07/06/2014] [Accepted: 07/15/2014] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND/OBJECTIVES Decreased plasma concentration of high-density lipoprotein cholesterol (HDL-C) is a risk factor linked to increased risk of cardiovascular disease (CVD). Decreased anti-atherogenic properties of HDL are also implicated in increased CVD risk. The cause is unknown but has been linked to impaired glucose tolerance. The aim of this study was to quantify the modification of HDL by methylglyoxal and related dicarbonyls in healthy people and patients with type 2 diabetes characterise structural, functional and physiological consequences of the modification and predict the importance in high CVD risk groups. SUBJECTS/METHODS Major fractions of HDL, HDL2 and HDL3 were isolated from healthy human subjects and patients with type 2 diabetes and fractions modified by methylglyoxal and related dicarbonyl metabolites quantified. HDL2 and HDL3 were glycated by methylglyoxal to minimum extent in vitro and molecular, functional and physiological characteristics were determined. A one-compartment model of HDL plasma clearance was produced including formation and clearance of dicarbonyl-modified HDL. RESULTS HDL modified by methylglyoxal and related dicarbonyl metabolites accounted for 2.6% HDL and increased to 4.5% in patients with type 2 diabetes mellitus (T2DM). HDL2 and HDL3 were modified by methylglyoxal to similar extents in vitro. Methylglyoxal modification induced re-structuring of the HDL particles, decreasing stability and plasma half-life in vivo. It occurred at sites of apolipoprotein A-1 in HDL linked to membrane fusion, intramolecular bonding and ligand binding. Kinetic modelling of methylglyoxal modification of HDL predicted a negative correlation of plasma HDL-C with methylglyoxal-modified HDL. This was validated clinically. It also predicted that dicarbonyl modification produces 2-6% decrease in total plasma HDL and 5-13% decrease in functional HDL clinically. CONCLUSIONS These results suggest that methylglyoxal modification of HDL accelerates its degradation and impairs its functionality in vivo, likely contributing to increased risk of CVD-particularly in high CVD risk groups.
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Affiliation(s)
- L Godfrey
- Clinical Sciences Research Laboratories, Medical School, University of Warwick, University Hospital, Coventry, UK
| | - N Yamada-Fowler
- Clinical Sciences Research Laboratories, Medical School, University of Warwick, University Hospital, Coventry, UK
| | - J Smith
- Bruker UK Ltd, Banner Lane, Coventry, UK
| | - P J Thornalley
- Clinical Sciences Research Laboratories, Medical School, University of Warwick, University Hospital, Coventry, UK
| | - N Rabbani
- Clinical Sciences Research Laboratories, Medical School, University of Warwick, University Hospital, Coventry, UK
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19
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Soria R, Long KS, Blair WP, Godfrey L, Kuntz KD, Lenc E, Stockdale C, Winkler PF. Super-Eddington mechanical power of an accreting black hole in M83. Science 2014; 343:1330-3. [PMID: 24578533 DOI: 10.1126/science.1248759] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Mass accretion onto black holes releases energy in the form of radiation and outflows. Although the radiative flux cannot substantially exceed the Eddington limit, at which the outgoing radiation pressure impedes the inflow of matter, it remains unclear whether the kinetic energy flux is bounded by this same limit. Here, we present the detection of a radio-optical structure, powered by outflows from a non-nuclear black hole. Its accretion disk properties indicate that this black hole is less than 100 solar masses. The optical-infrared line emission implies an average kinetic power of 3 × 10(40) erg second(-1), higher than the Eddington luminosity of the black hole. These results demonstrate kinetic power exceeding the Eddington limit over a sustained period, which implies greater ability to influence the evolution of the black hole's environment.
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Affiliation(s)
- R Soria
- International Centre for Radio Astronomy Research, Curtin University, G.P.O. Box U1987, Perth, WA 6845, Australia
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20
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Godfrey L, Warden M, Rohant N, Greene T, Napoli J, Ndlovo A. PO-318 SINGLE-LUMEN APBIB AT THE JOHN THEURER CANCER CENTER: CONSENSUS GUIDLINE CONFORMANCE AND OUTCOMES. Radiother Oncol 2012. [DOI: 10.1016/s0167-8140(12)72284-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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21
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Morris PG, Dickler M, McArthur HL, Traina T, Sugarman S, Lin N, Moy B, Come S, Godfrey L, Nulsen B, Chen C, Steingart R, Rugo H, Norton L, Winer E, Hudis CA, Dang CT. Dose-dense adjuvant Doxorubicin and cyclophosphamide is not associated with frequent short-term changes in left ventricular ejection fraction. J Clin Oncol 2009; 27:6117-23. [PMID: 19901120 PMCID: PMC3664032 DOI: 10.1200/jco.2008.20.2952] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2008] [Accepted: 09/08/2009] [Indexed: 11/20/2022] Open
Abstract
PURPOSE Doxorubicin and cyclophosphamide (AC) every 3 weeks has been associated with frequent asymptomatic declines in left ventricular ejection fraction (LVEF). Dose-dense (dd) AC followed by paclitaxel (P) is superior to the same regimen given every third week. Herein, we report the early cardiac safety of three sequential studies of ddAC alone or with bevacizumab (B). PATIENTS AND METHODS Patients with HER2-positive breast cancer were treated on two trials: ddAC followed by P and trastuzumab (T) and ddAC followed by PT and lapatinib. Patients with HER2-normal breast cancer were treated with B and ddAC followed by B and nanoparticle albumin-bound P. Prospective LVEF measurement by multigated radionuclide angiography scan before and after every 2 week AC for 4 cycles and at month 6 from all three trials were aggregated to determine the early risks of cardiac dysfunction. RESULTS From January 2005 to May 2008, 245 patients were enrolled. The median age was 47 years (range, 27 to 75 years). Median LVEF pre-ddAC was 68% (range, 52% to 82%). LVEF post-ddAC was available in 241 patients (98%) and the median was unchanged at 68% (range, 47% to 81%). Per protocol no patients were ineligible for subsequent targeted biologic therapy based on LVEF decline post-ddAC. In addition, LVEF was available in 222 patients (92%) at 6 months, at which time the median LVEF was similar at 65% (range, 24% to 80%). Within 6 months of initiating chemotherapy, three patients (1.2%; 95% CI, 0.25% to 3.54%) developed CHF, all of whom received T. CONCLUSION Dose-dense AC with or without concurrent bevacizumab is not associated with frequent acute or short-term declines in LVEF.
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22
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Godfrey L, Hanley J, Napoli J, Barbiere J, Tuna M, Smith D. Robotically-assisted Minimally Invasive Brachytherapy: Pre-clinical Aspects. Int J Radiat Oncol Biol Phys 2009. [DOI: 10.1016/j.ijrobp.2009.07.1642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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23
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Hanley J, Napoli J, Barbiere J, Tuna M, Smith D, Godfrey L. SU-FF-T-51: Robotically-Assisted Minimally Invasive Brachytherapy: Dosimetric Aspects. Med Phys 2009. [DOI: 10.1118/1.3181523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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24
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Godfrey L, Hughes M. Paul Dawson-Edwards. West J Med 2009. [DOI: 10.1136/bmj.b1988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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25
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Abstract
BACKGROUND AND AIMS Genetic association between Crohn's disease (CD) and OCTN1 (SLC22A4) C1672T/OCTN2 (SLC22A5) G-207C variants in IBD5 has recently been reported. These genes encode solute carriers and the association was suggested to be distinct from the background IBD5 risk haplotype. There have been conflicting reports of the association between markers in the IBD5 region and ulcerative colitis (UC) and interaction (epistasis) between this locus and CARD15. Our aim was to ascertain the contribution of OCTN variants to UC and CD in a large independent UK dataset, to seek genetic evidence that the OCTN association is distinct from the IBD5 risk haplotype and to identify interactions between the IBD5 and CARD15 loci. METHODS A total of 1104 unrelated Caucasian subjects with inflammatory bowel disease (IBD) (496 CD, 512 UC, 96 indeterminate) and 750 ethnically matched controls were genotyped for three single nucleotide polymorphisms (SNPs) in the CD associated genes (OCTN1+1672, OCTN2-207, and IGR2230), and two flanking IBD5 tagging SNPs, IGR2096 and IGR3096. Data were analysed by logistic regression methods within STATA. RESULTS OCTN variants were as strongly associated with UC and IBD overall as they were with CD (p = 0.0001; OR 1.3 (95% confidence interval 1.1-1.5)). OCTN variants were in tight linkage disequilibrium with the extended IBD5 risk haplotype D' 0.79 and 0.88, and r2 = 0.62 and 0.72 for IGR2096 and 3096, respectively. There was no deviation from a multiplicative model of interaction between CARD15 and IBD5 on the penetrance scale. CONCLUSIONS The OCTN variants were associated with susceptibility to IBD overall. The effect was equally strong in UC and CD. Although OCTN variants may account for the increased risk of IBD associated with IBD5, a role for other candidate genes within this extended haplotype was not excluded. There was no statistical evidence of interaction between CARD15 and either OCTN or IBD5 variants in susceptibility to IBD.
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Affiliation(s)
- S Waller
- IBD Researcg Group, Department of Medicine, University of Cambridge, Cambridge, UK
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26
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Pomeranz A, El-Khayam A, Korzets Z, Kessler OJ, Godfrey L, Katz B, Wolach B. A bioassay evaluation of the urinary antibacterial efficacy of low dose prophylactic antibiotics in children with vesicoureteral reflux. J Urol 2000; 164:1070-3. [PMID: 10958743 DOI: 10.1097/00005392-200009020-00037] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
PURPOSE We evaluated by means of a bioassay the efficacy of 4 different antibiotics administered in a prophylactic dose to children with vesicoureteral reflux. MATERIALS AND METHODS A total of 159 urine samples from 53 children taking prophylactic antibiotics with proved vesicoureteral reflux were tested. The children were divided into 4 groups according to the antibiotic given, which included nalidixic acid, cephalexin, cotrimoxazole and cefixime. Urine samples were collected in the morning, at noon and in the evening, and each sample was bioassayed for growth inhibition of a standard Escherichia coli. The urine volume used was specifically determined for each antibiotic, and growth inhibition by this specific volume was equivalent to that produced by standard diffusion disks. In addition, the specific gravity, which reflected urinary concentration of each sample, was measured. RESULTS Mean patient age plus or minus standard deviation of the 4 groups was 53 +/- 41 for nalidixic acid, 23 +/- 34 for cephalexin, 55 +/- 35 for cotrimoxazole and 47 +/- 35 months for cefixime, respectively. In children less than 2 years old specific gravity was higher in the morning (1.021 +/- 0.0006 versus 1.0008 +/- 0.0004 at 8 a.m. and 2 p. m., respectively, p <0.05). In contrast, in children older than 4 years the specific gravity was higher in the afternoon and evening hours (1.019 +/- 0.003 versus 1.007 +/- 0.003 at 2 p.m. and 8 a.m., respectively, p <0.05). The percentage of patients who demonstrated growth inhibition in all 3 samples of the test day was 7%, 6%, 69% and 44% for nalidixic acid, cephalexin, cotrimoxazole and cefixime, respectively (p <0.001 for cotrimoxazole and cefixime versus nalidixic acid and cephalexin. Divided into morning, noon and evening, the percentage of samples that demonstrated growth inhibition was 85.7%, 21.4% and 7.1% for nalidixic acid, 37.5%, 12. 5% and 6.3% for cephalexin, 100%, 92.3% and 76.9% for cotrimoxazole and 100%, 77.7% and 55.5% for cefixime, respectively. A direct correlation was found between specific gravity and growth inhibition (r = 0.55, p <0.001). CONCLUSIONS Urine concentration during the day is dependent on age with older children having more concentrated urine in the latter part of the day. Growth inhibition is enhanced by concentrated urine. Compared to nalidixic acid and cephalexin, cotrimoxazole and cefixime produce a sustained bactericidal effect for about 60% of a 24-hour day due to the longer half-life.
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Affiliation(s)
- A Pomeranz
- Pediatric Nephrology Outpatient Clinic, Department of Pediatrics, Meir-Hospital, Kfar-Saba, Israel
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27
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Godfrey L, Philip J. Phase transitions in lithium ammonium sulfate below room temperature: An ultrasonic study. Phys Rev B Condens Matter 1996; 54:15708-15713. [PMID: 9985637 DOI: 10.1103/physrevb.54.15708] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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28
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Maslak P, Hegewisch-Becker S, Godfrey L, Andreeff M. Flow cytometric determination of the multidrug-resistant phenotype in acute leukemia. Cytometry 1994; 17:84-93. [PMID: 8001461 DOI: 10.1002/cyto.990170111] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Expression of the multidrug-resistant (MDR) phenotype was investigated in acute leukemia using a monoclonal antibody (HYB-241) directed against a cell surface epitope of the 180 kd P-glycoprotein (gp180) by flow cytometric analysis of clinical samples. Samples from sixty-four patients were tested (37 with acute myelocytic leukemia, 20 with acute lymphocytic leukemia, and 7 with blastic chronic myelocytic leukemia). A D value (derived from Kolmogorov-Smirnov test) greater than 0.15 was considered positive (+). Eight of 32 newly diagnosed patients were positive for gp180 compared with 22 of 32 relapsed/refractory (R/R) patients (P < 0.001). Of the new patients, vinca/anthracycline-based induction therapy failed in 3/6 gp180(+) and 5/18 gp180(-) patients. In the R/R group, 15/16 gp180(+) and 3/6 gp180(-) patients failed to achieve complete remission (P < 0.05). In vitro drug accumulation studies performed with verapamil failed to show a correlation with clinical response. However, in a subset of patients, a striking correlation (r = .97, P = .001) was noted between the presence of gp180 as determined by the D value and the functional activity of the P-glycoprotein as expressed by increased daunorubicin accumulation in the presence of verapamil. The results suggest that 1) newly diagnosed patients can express gp180, 2) P-glycoprotein is expressed in 69% of R/R patients, 3) response in R/R patients is effected by the presence of gp180, and 4) expression of gp180 is highly correlated with its function as a drug-efflux pump in a subset of the patients studied. The complexity of clinical drug resistance is underscored by the finding that the MDR model is not applicable to all cases. In such instances, other mechanisms may play a predominant role.
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MESH Headings
- ATP Binding Cassette Transporter, Subfamily B, Member 1/analysis
- Acute Disease
- Adolescent
- Adult
- Aged
- Antibiotics, Antineoplastic/administration & dosage
- Antibiotics, Antineoplastic/pharmacology
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
- Biological Transport
- Blast Crisis/metabolism
- Child
- Child, Preschool
- Daunorubicin/metabolism
- Daunorubicin/pharmacology
- Daunorubicin/therapeutic use
- Drug Resistance, Multiple
- Female
- Flow Cytometry
- Humans
- Leukemia/metabolism
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- Leukemia, Myeloid/metabolism
- Leukemia, Promyelocytic, Acute/pathology
- Male
- Middle Aged
- Neoplasm Proteins/analysis
- Phenotype
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/metabolism
- Remission Induction
- Salvage Therapy
- Treatment Failure
- Tumor Cells, Cultured/drug effects
- Verapamil/pharmacology
- Vinblastine/administration & dosage
- Vinblastine/pharmacology
- Vincristine/administration & dosage
- Vincristine/pharmacology
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Affiliation(s)
- P Maslak
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York 10021
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29
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Berman E, Adams M, Duigou-Osterndorf R, Godfrey L, Clarkson B, Andreeff M. Effect of tamoxifen on cell lines displaying the multidrug-resistant phenotype. Blood 1991; 77:818-25. [PMID: 1993221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
We examined the effect of tamoxifen (Tmx), verapamil, and daunorubicin (DNR) in two cell lines that displayed the multidrug-resistant (MDR) phenotype and used laser flow cytometry to quantitate intracellular DNR content. In the vinblastine-resistant human lymphoblastic lymphoma cell line CEM-VBL, simultaneous incubation of DNR with Tmx 10 mumol/L or Tmx 50 mumol/L increased intracellular DNR fluorescence in a dose-dependent manner and demonstrated an uptake pattern similar to that seen with DNR and verapamil. Similar results were obtained in the vincristine-resistant human myeloid leukemia cell line HL-60/RV+. Cellular retention of DNR was also measured in both cell lines and results suggested that continuous exposure of the cells to Tmx resulted in higher intracellular DNR content compared with cells resuspended in fresh medium. No effect of Tmx or verapamil was observed in the drug-sensitive parent cell lines CEM or HL-60. Clonogenic experiments were then performed to determine whether Tmx was itself inhibitory to cell growth or whether Tmx potentiated DNR cytotoxicity. Tmx 10 mumol/L did not significantly inhibit either CEM-VBL or HL-60/RV+ cells after a 3-hour exposure followed by culture in methylcellulose. Tmx 50 mumol/L was significantly more inhibitory in both cell lines. However, cells that had been incubated with DNR and Tmx 10 mumol/L demonstrated a marked increment in growth inhibition compared with cells that had been incubated with DNR alone or Tmx 10 mumol/L alone. Based on the data presented here, we suggest that clinical testing of Tmx and DNR be pursued in the setting where MDR may play a role.
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Affiliation(s)
- E Berman
- Laboratory of Hematopoietic Cell Kinetics, Memorial Sloan-Kettering Cancer Center, New York, NY 10021
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