1
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Coleman DJL, Keane P, Luque-Martin R, Chin PS, Blair H, Ames L, Kellaway SG, Griffin J, Holmes E, Potluri S, Assi SA, Bushweller J, Heidenreich O, Cockerill PN, Bonifer C. Gene regulatory network analysis predicts cooperating transcription factor regulons required for FLT3-ITD+ AML growth. Cell Rep 2023; 42:113568. [PMID: 38104314 PMCID: PMC10874628 DOI: 10.1016/j.celrep.2023.113568] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 11/03/2023] [Accepted: 11/27/2023] [Indexed: 12/19/2023] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous disease caused by different mutations. Previously, we showed that each mutational subtype develops its specific gene regulatory network (GRN) with transcription factors interacting within multiple gene modules, many of which are transcription factor genes themselves. Here, we hypothesize that highly connected nodes within such networks comprise crucial regulators of AML maintenance. We test this hypothesis using FLT3-ITD-mutated AML as a model and conduct an shRNA drop-out screen informed by this analysis. We show that AML-specific GRNs predict crucial regulatory modules required for AML growth. Furthermore, our work shows that all modules are highly connected and regulate each other. The careful multi-omic analysis of the role of one (RUNX1) module by shRNA and chemical inhibition shows that this transcription factor and its target genes stabilize the GRN of FLT3-ITD+ AML and that its removal leads to GRN collapse and cell death.
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Affiliation(s)
- Daniel J L Coleman
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Peter Keane
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK; School of Biosciences, University of Birmingham, Birmingham B15 2TT, U.K
| | - Rosario Luque-Martin
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Herschel Building, Level 6, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK
| | - Paulynn S Chin
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Helen Blair
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Herschel Building, Level 6, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK
| | - Luke Ames
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Sophie G Kellaway
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - James Griffin
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Elizabeth Holmes
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Sandeep Potluri
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Salam A Assi
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - John Bushweller
- University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
| | - Olaf Heidenreich
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Herschel Building, Level 6, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK; Prinses Máxima Centrum for Pediatric Oncology, Postbus 113, 3720 AC Bilthoven, Heidelberglaan 25, 3584CS Utrecht, the Netherlands.
| | - Peter N Cockerill
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
| | - Constanze Bonifer
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
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2
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Coleman DJL, Keane P, Luque-Martin R, Chin PS, Blair H, Ames L, Kellaway SG, Griffin J, Holmes E, Potluri S, Assi SA, Bushweller J, Heidenreich O, Cockerill PN, Bonifer C. Gene regulatory network analysis predicts cooperating transcription factor regulons required for FLT3-ITD+ AML growth. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.18.549495. [PMID: 37503022 PMCID: PMC10370108 DOI: 10.1101/2023.07.18.549495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
AML is a heterogenous disease caused by different mutations. We have previously shown that each mutational sub-type develops its specific gene regulatory network (GRN) with transcription factors interacting with multiple gene modules, many of which are transcription factor genes themselves. Here we hypothesized that highly connected nodes within such networks comprise crucial regulators of AML maintenance. We tested this hypothesis using FLT3-ITD mutated AML as a model and conducted an shRNA drop-out screen informed by this analysis. We show that AML-specific GRNs predict identifying crucial regulatory modules required for AML but not normal cellular growth. Furthermore, our work shows that all modules are highly connected and regulate each other. The careful multi-omic analysis of the role of one (RUNX1) module by shRNA and chemical inhibition shows that this transcription factor and its target genes stabilize the GRN of FLT3-ITD AML and that its removal leads to GRN collapse and cell death.
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Affiliation(s)
- Daniel J L Coleman
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham B152TT, UK
| | - Peter Keane
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham B152TT, UK
| | - Rosario Luque-Martin
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Herschel Building, Level 6, Brewery Lane, Newcastle upon Tyne, NE1 7RU, UK
| | - Paulynn S Chin
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham B152TT, UK
| | - Helen Blair
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Herschel Building, Level 6, Brewery Lane, Newcastle upon Tyne, NE1 7RU, UK
| | - Luke Ames
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham B152TT, UK
| | - Sophie G Kellaway
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham B152TT, UK
| | - James Griffin
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham B152TT, UK
| | - Elizabeth Holmes
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham B152TT, UK
| | - Sandeep Potluri
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham B152TT, UK
| | - Salam A Assi
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham B152TT, UK
| | - John Bushweller
- University of Virginia, 1340 Jefferson Park Ave, Charlottesville, VA 22908, USA
| | - Olaf Heidenreich
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Herschel Building, Level 6, Brewery Lane, Newcastle upon Tyne, NE1 7RU, UK
- Prinses Máxima Centrum for Pediatric Oncology, Postbus 113, 3720 AC Bilthoven, Heidelberglaan 25, 3584CS Utrecht, Netherlands
| | - Peter N Cockerill
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham B152TT, UK
| | - Constanze Bonifer
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham B152TT, UK
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3
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Tirtakusuma R, Szoltysek K, Milne P, Grinev VV, Ptasinska A, Chin PS, Meyer C, Nakjang S, Hehir-Kwa JY, Williamson D, Cauchy P, Keane P, Assi SA, Ashtiani M, Kellaway SG, Imperato MR, Vogiatzi F, Schweighart EK, Lin S, Wunderlich M, Stutterheim J, Komkov A, Zerkalenkova E, Evans P, McNeill H, Elder A, Martinez-Soria N, Fordham SE, Shi Y, Russell LJ, Pal D, Smith A, Kingsbury Z, Becq J, Eckert C, Haas OA, Carey P, Bailey S, Skinner R, Miakova N, Collin M, Bigley V, Haniffa M, Marschalek R, Harrison CJ, Cargo CA, Schewe D, Olshanskaya Y, Thirman MJ, Cockerill PN, Mulloy JC, Blair HJ, Vormoor J, Allan JM, Bonifer C, Heidenreich O, Bomken S. Epigenetic regulator genes direct lineage switching in MLL/AF4 leukemia. Blood 2022; 140:1875-1890. [PMID: 35839448 PMCID: PMC10488321 DOI: 10.1182/blood.2021015036] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 06/30/2022] [Indexed: 11/20/2022] Open
Abstract
The fusion gene MLL/AF4 defines a high-risk subtype of pro-B acute lymphoblastic leukemia. Relapse can be associated with a lineage switch from acute lymphoblastic to acute myeloid leukemia, resulting in poor clinical outcomes caused by resistance to chemotherapies and immunotherapies. In this study, the myeloid relapses shared oncogene fusion breakpoints with their matched lymphoid presentations and originated from various differentiation stages from immature progenitors through to committed B-cell precursors. Lineage switching is linked to substantial changes in chromatin accessibility and rewiring of transcriptional programs, including alternative splicing. These findings indicate that the execution and maintenance of lymphoid lineage differentiation is impaired. The relapsed myeloid phenotype is recurrently associated with the altered expression, splicing, or mutation of chromatin modifiers, including CHD4 coding for the ATPase/helicase of the nucleosome remodelling and deacetylation complex. Perturbation of CHD4 alone or in combination with other mutated epigenetic modifiers induces myeloid gene expression in MLL/AF4+ cell models, indicating that lineage switching in MLL/AF4 leukemia is driven and maintained by disrupted epigenetic regulation.
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Affiliation(s)
- Ricky Tirtakusuma
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Katarzyna Szoltysek
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Maria Sklodowska-Curie Institute, Oncology Center, Gliwice Branch, Gliwice, Poland
| | - Paul Milne
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Vasily V. Grinev
- Department of Genetics, the Faculty of Biology, Belarusian State University, Minsk, Republic of Belarus
| | - Anetta Ptasinska
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Paulynn S. Chin
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Claus Meyer
- Institute of Pharmaceutical Biology/DCAL, Goethe-University, Frankfurt/Main, Germany
| | - Sirintra Nakjang
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | | | - Daniel Williamson
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Pierre Cauchy
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Peter Keane
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Salam A. Assi
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Minoo Ashtiani
- Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Sophie G. Kellaway
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Maria R. Imperato
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Fotini Vogiatzi
- ALL-BFM Study Group, Pediatric Hematology/Oncology, Christian Albrechts University Kiel and University Hospital Schleswig-Holstein, Campus Kiel, Germany
| | | | - Shan Lin
- Experimental Hematology and Cancer Biology, Cancer and Blood Disease Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Mark Wunderlich
- Experimental Hematology and Cancer Biology, Cancer and Blood Disease Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | | | - Alexander Komkov
- Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology, and Immunology, Moscow, Russia
| | - Elena Zerkalenkova
- Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology, and Immunology, Moscow, Russia
| | - Paul Evans
- Haematological Malignancy Diagnostic Service, St James’s University Hospital, Leeds, United Kingdom
| | - Hesta McNeill
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Alex Elder
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Natalia Martinez-Soria
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Sarah E. Fordham
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Yuzhe Shi
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Lisa J. Russell
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Deepali Pal
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Alex Smith
- Epidemiology and Cancer Statistics Group, University of York, York, United Kingdom
| | | | - Jennifer Becq
- Illumina Cambridge Ltd., Great Abington, United Kingdom
| | - Cornelia Eckert
- Department of Pediatric Oncology/Hematology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Oskar A. Haas
- St Anna Children’s Cancer Research Institute (CCRI), Vienna, Austria
| | - Peter Carey
- Department of Paediatric Haematology and Oncology, The Great North Children’s Hospital, Newcastle upon Tyne, United Kingdom
| | - Simon Bailey
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- Department of Paediatric Haematology and Oncology, The Great North Children’s Hospital, Newcastle upon Tyne, United Kingdom
| | - Roderick Skinner
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- Department of Paediatric Haematology and Oncology, The Great North Children’s Hospital, Newcastle upon Tyne, United Kingdom
| | - Natalia Miakova
- Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology, and Immunology, Moscow, Russia
| | - Matthew Collin
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Venetia Bigley
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Muzlifah Haniffa
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Department of Dermatology and Newcastle National Institute of Health Research (NIHR), Newcastle Biomedical Research Centre, Newcastle Hospitals National Health Service (NHS) Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Rolf Marschalek
- Institute of Pharmaceutical Biology/DCAL, Goethe-University, Frankfurt/Main, Germany
| | - Christine J. Harrison
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Catherine A. Cargo
- Haematological Malignancy Diagnostic Service, St James’s University Hospital, Leeds, United Kingdom
| | - Denis Schewe
- Department of Pediatrics, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Yulia Olshanskaya
- Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology, and Immunology, Moscow, Russia
| | - Michael J. Thirman
- Department of Medicine, Section of Hematology/Oncology, University of Chicago, Chicago, IL
| | - Peter N. Cockerill
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - James C. Mulloy
- Experimental Hematology and Cancer Biology, Cancer and Blood Disease Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Helen J. Blair
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Josef Vormoor
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - James M. Allan
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Constanze Bonifer
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Olaf Heidenreich
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Simon Bomken
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- Department of Paediatric Haematology and Oncology, The Great North Children’s Hospital, Newcastle upon Tyne, United Kingdom
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4
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Ullah H, Zhang B, Sharma NK, McCrea PD, Srivastava Y. In-silico probing of AML related RUNX1 cancer-associated missense mutations: Predicted relationships to DNA binding and drug interactions. Front Mol Biosci 2022; 9:981020. [PMID: 36090034 PMCID: PMC9454315 DOI: 10.3389/fmolb.2022.981020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 07/19/2022] [Indexed: 11/24/2022] Open
Abstract
The molecular consequences of cancer associated mutations in Acute myeloid leukemia (AML) linked factors are not very well understood. Here, we interrogated the COSMIC database for missense mutations associated with the RUNX1 protein, that is frequently mis-regulated in AML, where we sought to identify recurrently mutated positions at the DNA-interacting interface. Indeed, six of the mutated residues, out of a total 417 residues examined within the DNA binding domain, evidenced reduced DNA association in in silico predictions. Further, given the prominence of RUNX1’s compromised function in AML, we asked the question if the mutations themselves might alter RUNX1’s interaction (off-target) with known FDA-approved drug molecules, including three currently used in treating AML. We identified several AML-associated mutations in RUNX1 that were calculated to enhance RUNX1’s interaction with specific drugs. Specifically, we retrieved data from the COSMIC database for cancer-associated mutations of RUNX1 by using R package “data.table” and “ggplot2” modules. In the presence of DNA and/or drug, we used docking scores and energetics of the complexes as tools to evaluate predicted interaction strengths with RUNX1. For example, we performed predictions of drug binding pockets involving Enasidenib, Giltertinib, and Midostaurin (AML associated), as well as ten different published cancer associated drug compounds. Docking of wild type RUNX1 with these 13 different cancer-associated drugs indicates that wild-type RUNX1 has a lower efficiency of binding while RUNX1 mutants R142K, D171N, R174Q, P176H, and R177Q suggested higher affinity of drug association. Literature evidence support our prediction and suggests the mutation R174Q affects RUNX1 DNA binding and could lead to compromised function. We conclude that specific RUNX1 mutations that lessen DNA binding facilitate the binding of a number of tested drug molecules. Further, we propose that molecular modeling and docking studies for RUNX1 in the presence of DNA and/or drugs enables evaluation of the potential impact of RUNX1 cancer associated mutations in AML.
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Affiliation(s)
- Hanif Ullah
- Guangxi Key Laboratory for Genomics and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomics and Personalized Medicine, Guangxi Medical University, Nanning, China
- Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Baoyun Zhang
- Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Narendra Kumar Sharma
- Department of Bioscience and Biotechnology, Banasthali Vidyapith, Banasthali, Tonk, Rajasthan, India
| | - Pierre D. McCrea
- University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Yogesh Srivastava
- University of Chinese Academy of Sciences, Beijing, China
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX, United States
- Genome Regulation Laboratory; Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- *Correspondence: Yogesh Srivastava,
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5
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Ptasinska A, Pickin A, Assi SA, Chin PS, Ames L, Avellino R, Gröschel S, Delwel R, Cockerill PN, Osborne CS, Bonifer C. RUNX1-ETO Depletion in t(8;21) AML Leads to C/EBPα- and AP-1-Mediated Alterations in Enhancer-Promoter Interaction. Cell Rep 2020; 28:3022-3031.e7. [PMID: 31533028 PMCID: PMC6899442 DOI: 10.1016/j.celrep.2019.08.040] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 06/07/2019] [Accepted: 08/12/2019] [Indexed: 12/12/2022] Open
Abstract
Acute myeloid leukemia (AML) is associated with mutations in transcriptional and epigenetic regulator genes impairing myeloid differentiation. The t(8;21)(q22;q22) translocation generates the RUNX1-ETO fusion protein, which interferes with the hematopoietic master regulator RUNX1. We previously showed that the maintenance of t(8;21) AML is dependent on RUNX1-ETO expression. Its depletion causes extensive changes in transcription factor binding, as well as gene expression, and initiates myeloid differentiation. However, how these processes are connected within a gene regulatory network is unclear. To address this question, we performed Promoter-Capture Hi-C assays, with or without RUNX1-ETO depletion and assigned interacting cis-regulatory elements to their respective genes. To construct a RUNX1-ETO-dependent gene regulatory network maintaining AML, we integrated cis-regulatory element interactions with gene expression and transcription factor binding data. This analysis shows that RUNX1-ETO participates in cis-regulatory element interactions. However, differential interactions following RUNX1-ETO depletion are driven by alterations in the binding of RUNX1-ETO-regulated transcription factors.
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MESH Headings
- CCAAT-Enhancer-Binding Proteins/genetics
- CCAAT-Enhancer-Binding Proteins/metabolism
- Chromosomes, Human, Pair 21/genetics
- Chromosomes, Human, Pair 21/metabolism
- Chromosomes, Human, Pair 8/genetics
- Chromosomes, Human, Pair 8/metabolism
- Core Binding Factor Alpha 2 Subunit/genetics
- Core Binding Factor Alpha 2 Subunit/metabolism
- Enhancer Elements, Genetic
- Gene Deletion
- Gene Expression Regulation, Leukemic
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Promoter Regions, Genetic
- RUNX1 Translocation Partner 1 Protein/genetics
- RUNX1 Translocation Partner 1 Protein/metabolism
- Transcription Factor AP-1/genetics
- Transcription Factor AP-1/metabolism
- Translocation, Genetic
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Affiliation(s)
- Anetta Ptasinska
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B152TT, UK
| | - Anna Pickin
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B152TT, UK
| | - Salam A Assi
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B152TT, UK
| | - Paulynn Suyin Chin
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B152TT, UK
| | - Luke Ames
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B152TT, UK
| | - Roberto Avellino
- Department of Hematology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Stefan Gröschel
- Department of Hematology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Ruud Delwel
- Department of Hematology, Erasmus University Medical Center, Rotterdam, the Netherlands; Oncode Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Peter N Cockerill
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B152TT, UK
| | - Cameron S Osborne
- Department of Medical & Molecular Genetics, King's College London, London SE1 9RT, UK
| | - Constanze Bonifer
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B152TT, UK.
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6
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Assi SA, Bonifer C, Cockerill PN. Rewiring of the Transcription Factor Network in Acute Myeloid Leukemia. Cancer Inform 2019; 18:1176935119859863. [PMID: 31263370 PMCID: PMC6595639 DOI: 10.1177/1176935119859863] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 05/31/2019] [Indexed: 11/21/2022] Open
Abstract
Acute myeloid leukemia (AML) is a highly heterogeneous cancer associated with different patterns of gene expression determined by the nature of their DNA mutations. These mutations mostly act to deregulate gene expression by various mechanisms at the level of the nucleus. By performing genome-wide epigenetic profiling of cis-regulatory elements, we found that AML encompasses different mutation-specific subclasses associated with the rewiring of the gene regulatory networks that drive differentiation into different directions away from normal myeloid development. By integrating epigenetic profiles with gene expression and chromatin conformation data, we defined pathways within gene regulation networks that were differentially rewired within each mutation-specific subclass of AML. This analysis revealed 2 major classes of AML: one class defined by mutations in signaling molecules that activate AP-1 via the mitogen-activated protein (MAP) kinase pathway and a second class defined by mutations within genes encoding transcription factors such as RUNX1/CBFβ and C/EBPα. By identifying specific DNA motifs protected from DNase I digestion at cis-regulatory elements, we were able to infer candidate transcription factors bound to these motifs. These integrated analyses allowed the identification of AML subtype-specific core regulatory networks that are required for AML development and maintenance, which could now be targeted in personalized therapies.
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Affiliation(s)
- Salam A Assi
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Constanze Bonifer
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Peter N Cockerill
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
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7
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Assi SA, Imperato MR, Coleman DJL, Pickin A, Potluri S, Ptasinska A, Chin PS, Blair H, Cauchy P, James SR, Zacarias-Cabeza J, Gilding LN, Beggs A, Clokie S, Loke JC, Jenkin P, Uddin A, Delwel R, Richards SJ, Raghavan M, Griffiths MJ, Heidenreich O, Cockerill PN, Bonifer C. Subtype-specific regulatory network rewiring in acute myeloid leukemia. Nat Genet 2019; 51:151-162. [PMID: 30420649 PMCID: PMC6330064 DOI: 10.1038/s41588-018-0270-1] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 10/02/2018] [Indexed: 12/30/2022]
Abstract
Acute myeloid leukemia (AML) is a heterogeneous disease caused by a variety of alterations in transcription factors, epigenetic regulators and signaling molecules. To determine how different mutant regulators establish AML subtype-specific transcriptional networks, we performed a comprehensive global analysis of cis-regulatory element activity and interaction, transcription factor occupancy and gene expression patterns in purified leukemic blast cells. Here, we focused on specific subgroups of subjects carrying mutations in genes encoding transcription factors (RUNX1, CEBPα), signaling molecules (FTL3-ITD, RAS) and the nuclear protein NPM1). Integrated analysis of these data demonstrates that each mutant regulator establishes a specific transcriptional and signaling network unrelated to that seen in normal cells, sustaining the expression of unique sets of genes required for AML growth and maintenance.
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Affiliation(s)
- Salam A Assi
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | | | - Daniel J L Coleman
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Anna Pickin
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Sandeep Potluri
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Anetta Ptasinska
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Paulynn Suyin Chin
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Helen Blair
- Northern Institute for Cancer Research, University of Newcastle, Newcastle, UK
| | - Pierre Cauchy
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Sally R James
- Section of Experimental Haematology, Leeds Institute for Molecular Medicine, University of Leeds, Leeds, UK
| | | | - L Niall Gilding
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Andrew Beggs
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Sam Clokie
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Justin C Loke
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Phil Jenkin
- CMT Laboratory NHS Blood & Transplant, Edgbaston, Birmingham, UK
| | - Ash Uddin
- CMT Laboratory NHS Blood & Transplant, Edgbaston, Birmingham, UK
| | - Ruud Delwel
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Oncode Institute, Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Stephen J Richards
- Haematological Malignancy Diagnostic Service, St. James's University Hospital, Leeds, UK
| | - Manoj Raghavan
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- Centre for Clinical Haematology, Queen Elizabeth Hospital, Birmingham, UK
| | - Michael J Griffiths
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Olaf Heidenreich
- Northern Institute for Cancer Research, University of Newcastle, Newcastle, UK
- Princess Maxima Centrum for Pediatric Oncology, Utrecht, The Netherlands
| | - Peter N Cockerill
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK.
| | - Constanze Bonifer
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK.
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8
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Torres J, Monti R, Moore AL, Seimiya M, Jiang Y, Beerenwinkel N, Beisel C, Beira JV, Paro R. A switch in transcription and cell fate governs the onset of an epigenetically-deregulated tumor in Drosophila. eLife 2018; 7:32697. [PMID: 29560857 PMCID: PMC5862528 DOI: 10.7554/elife.32697] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 03/04/2018] [Indexed: 12/20/2022] Open
Abstract
Tumor initiation is often linked to a loss of cellular identity. Transcriptional programs determining cellular identity are preserved by epigenetically-acting chromatin factors. Although such regulators are among the most frequently mutated genes in cancer, it is not well understood how an abnormal epigenetic condition contributes to tumor onset. In this work, we investigated the gene signature of tumors caused by disruption of the Drosophila epigenetic regulator, polyhomeotic (ph). In larval tissue ph mutant cells show a shift towards an embryonic-like signature. Using loss- and gain-of-function experiments we uncovered the embryonic transcription factor knirps (kni) as a new oncogene. The oncogenic potential of kni lies in its ability to activate JAK/STAT signaling and block differentiation. Conversely, tumor growth in ph mutant cells can be substantially reduced by overexpressing a differentiation factor. This demonstrates that epigenetically derailed tumor conditions can be reversed when targeting key players in the transcriptional network. When an animal is developing as an embryo, different cells start to specialize into the specific cell types needed to form the tissues and organs of the body. How an individual cell commits to become a certain type of cell is mostly determined by which of the genes in its DNA are active. In animal cells, DNA is wrapped around proteins called histones, and one way that cells can maintain their distinct pattern of gene activity is via chemical tags on the histones. These tags can switch nearby genes on or off, and are added or removed by other proteins called epigenetic regulators. The epigenetic tags are also stably inherited when the cell divides, meaning that a cell’s identity can be maintained over many cell generations. If epigenetic regulators fail to work properly or get disrupted, the pattern of gene activity in a cell becomes altered. As a consequence, that cell can lose its identity and will often turn into a cancer cell. In fact, mutations in epigenetic regulators are found in several human cancers. It is not yet understood how these changes in gene expression lead cells to become cancerous. Torres et al. have now analyzed an epigenetic regulator called Polyhomeotic in developing larvae of the fruit fly, Drosophila melanogaster. The results show that when Polyhomeotic is not produced the fly larvae develop tumors. Moreover, the mutant cells without Polyhomeotic had different gene expression profiles compared to normal cells. This in turn caused the mutant cells, which had previously committed to a certain fate, to become more like the unspecialized cells found in early embryos. Torres et al. next showed that, among the genes that were incorrectly regulated when Polyhomeotic’s activity was compromised, one gene called knirps was switched on by mistake, which led the mutant cells to become tumor cells. When the activity of knirps was reduced instead, almost no tumors grew. Additionally, Torres et al. found that the protein encoded by knirps activates a signaling pathway that keeps tumor cells unspecialized by blocking their normal progress to a more mature and specialized state – a process known as differentiation. Experimentally raising the levels of a different molecule that ultimately promotes differentiation caused the tumor cells to grow less. These findings suggest that tumors caused when epigenetic regulation goes awry may be reversed by targeting key genes such as knirps. Further work is now needed to test whether these findings will also extend to humans. Forcing cancer cells from a highly dividing, non-specialized state into a dead-end, mature state may lead to new ways to treat cancer.
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Affiliation(s)
- Joana Torres
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Remo Monti
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Ariane L Moore
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.,Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Makiko Seimiya
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Yanrui Jiang
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.,Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Christian Beisel
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Jorge V Beira
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Renato Paro
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.,Faculty of Science, University of Basel, Basel, Switzerland
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9
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Bevington SL, Cauchy P, Withers DR, Lane PJL, Cockerill PN. T Cell Receptor and Cytokine Signaling Can Function at Different Stages to Establish and Maintain Transcriptional Memory and Enable T Helper Cell Differentiation. Front Immunol 2017; 8:204. [PMID: 28316598 PMCID: PMC5334638 DOI: 10.3389/fimmu.2017.00204] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 02/14/2017] [Indexed: 12/24/2022] Open
Abstract
Experienced T cells exhibit immunological memory via a rapid recall response, responding to restimulation much faster than naïve T cells. The formation of immunological memory starts during an initial slow response, when naïve T cells become transformed to proliferating T blast cells, and inducible immune response genes are reprogrammed as active chromatin domains. We demonstrated that these active domains are supported by thousands of priming elements which cooperate with inducible transcriptional enhancers to enable efficient responses to stimuli. At the conclusion of this response, a small proportion of these cells return to the quiescent state as long-term memory T cells. We proposed that priming elements can be established in a hit-and-run process dependent on the inducible factor AP-1, but then maintained by the constitutive factors RUNX1 and ETS-1. This priming mechanism may also function to render genes receptive to additional differentiation-inducing factors such as GATA3 and TBX21 that are encountered under polarizing conditions. The proliferation of recently activated T cells and the maintenance of immunological memory in quiescent memory T cells are also dependent on various cytokine signaling pathways upstream of AP-1. We suggest that immunological memory is established by T cell receptor signaling, but maintained by cytokine signaling.
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Affiliation(s)
- Sarah L Bevington
- Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, University of Birmingham , Birmingham , UK
| | - Pierre Cauchy
- Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, University of Birmingham , Birmingham , UK
| | - David R Withers
- Institute of Immunology and Immunotherapy, Institute of Biomedical Research, University of Birmingham , Birmingham , UK
| | - Peter J L Lane
- Institute of Immunology and Immunotherapy, Institute of Biomedical Research, University of Birmingham , Birmingham , UK
| | - Peter N Cockerill
- Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, University of Birmingham , Birmingham , UK
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10
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Bevington SL, Cauchy P, Cockerill PN. Chromatin priming elements establish immunological memory in T cells without activating transcription: T cell memory is maintained by DNA elements which stably prime inducible genes without activating steady state transcription. Bioessays 2016; 39. [PMID: 28026028 DOI: 10.1002/bies.201600184] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We have identified a simple epigenetic mechanism underlying the establishment and maintenance of immunological memory in T cells. By studying the transcriptional regulation of inducible genes we found that a single cycle of activation of inducible factors is sufficient to initiate stable binding of pre-existing transcription factors to thousands of newly activated distal regulatory elements within inducible genes. These events lead to the creation of islands of active chromatin encompassing nearby enhancers, thereby supporting the accelerated activation of inducible genes, without changing steady state levels of transcription in memory T cells. These studies also highlighted the need for more sophisticated definitions of gene regulatory elements. The chromatin priming elements defined here are distinct from classical enhancers because they function by maintaining chromatin accessibility rather than directly activating transcription. We propose that these priming elements are members of a wider class of genomic elements that support correct developmentally regulated gene expression.
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Affiliation(s)
- Sarah L Bevington
- Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, University of Birmingham, Birmingham, West Midlands, UK
| | - Pierre Cauchy
- Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, University of Birmingham, Birmingham, West Midlands, UK
| | - Peter N Cockerill
- Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, University of Birmingham, Birmingham, West Midlands, UK
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