1
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Maytum A, Edginton-White B, Keane P, Cockerill PN, Cazier JB, Bonifer C. Chromatin priming elements direct tissue-specific gene activity before hematopoietic specification. Life Sci Alliance 2024; 7:e202302363. [PMID: 37989524 PMCID: PMC10663361 DOI: 10.26508/lsa.202302363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/15/2023] [Accepted: 11/16/2023] [Indexed: 11/23/2023] Open
Abstract
Tissue-specific gene regulation during development involves the interplay between transcription factors and epigenetic regulators binding to enhancer and promoter elements. The pattern of active enhancers defines the cellular differentiation state. However, developmental gene activation involves a previous step called chromatin priming which is not fully understood. We recently developed a genome-wide functional assay that allowed us to functionally identify enhancer elements integrated in chromatin regulating five stages spanning the in vitro differentiation of embryonic stem cells to blood. We also measured global chromatin accessibility, histone modifications, and transcription factor binding. The integration of these data identified and characterised cis-regulatory elements which become activated before the onset of gene expression, some of which are primed in a signalling-dependent fashion. Deletion of such a priming element leads to a delay in the up-regulation of its associated gene in development. Our work uncovers the details of a complex network of regulatory interactions with the dynamics of early chromatin opening being at the heart of dynamic tissue-specific gene expression control.
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Affiliation(s)
- Alexander Maytum
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Benjamin Edginton-White
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Peter Keane
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Peter N Cockerill
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Jean-Baptiste Cazier
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Constanze Bonifer
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
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2
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Qiu K, Vu D, Wang L, Bookstaver A, Dinh TN, Goldfarb AN, Tenen DG, Trinh BQ. Chromatin structure and 3D architecture define differential functions of PU.1 cis regulatory elements in human blood cell lineages. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.01.573782. [PMID: 38260486 PMCID: PMC10802337 DOI: 10.1101/2024.01.01.573782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The precise spatio-temporal expression of the hematopoietic ETS transcription factor PU.1 that determines the hematopoietic cell fates is tightly regulated at the chromatin level. However, it remains elusive as to how chromatin signatures are linked to this dynamic expression pattern of PU.1 across blood cell lineages. Here we performed an unbiased and in-depth analysis of the relationship between human PU.1 expression, the presence of trans-acting factors, and 3D architecture at various cis-regulatory elements (CRE) proximal to the PU.1 locus. We identified multiple novel CREs at the upstream region of the gene following an integrative inspection for conserved DNA elements at the chromatin-accessible regions in primary human blood lineages. We showed that a subset of CREs localize within a 10 kb-wide cluster that exhibits that exhibit molecular features of a myeloid-specific super-enhancer involved in mediating PU.1 autoregulation, including open chromatin, unmethylated DNA, histone enhancer marks, transcription of enhancer RNAs, and occupancy of the PU.1 protein itself. Importantly, we revealed the presence of common 35-kb-wide CTCF-bound insulated neighborhood that contains the CRE cluster, forming the chromatin territory for lineage-specific and CRE-mediated chromatin interactions. These include functional CRE-promoter interactions in myeloid and B cells but not in erythroid and T cells. Our findings also provide mechanistic insights into the interplay between dynamic chromatin structure and 3D architecture in defining certain CREs as enhancers or silencers in chromatin regulation of PU.1 expression. The study lays the groundwork for further examination of PU.1 CREs as well as epigenetic regulation in malignant hematopoiesis.
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3
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Mulet-Lazaro R, Delwel R. From Genotype to Phenotype: How Enhancers Control Gene Expression and Cell Identity in Hematopoiesis. Hemasphere 2023; 7:e969. [PMID: 37953829 PMCID: PMC10635615 DOI: 10.1097/hs9.0000000000000969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 09/11/2023] [Indexed: 11/14/2023] Open
Abstract
Blood comprises a wide array of specialized cells, all of which share the same genetic information and ultimately derive from the same precursor, the hematopoietic stem cell (HSC). This diversity of phenotypes is underpinned by unique transcriptional programs gradually acquired in the process known as hematopoiesis. Spatiotemporal regulation of gene expression depends on many factors, but critical among them are enhancers-sequences of DNA that bind transcription factors and increase transcription of genes under their control. Thus, hematopoiesis involves the activation of specific enhancer repertoires in HSCs and their progeny, driving the expression of sets of genes that collectively determine morphology and function. Disruption of this tightly regulated process can have catastrophic consequences: in hematopoietic malignancies, dysregulation of transcriptional control by enhancers leads to misexpression of oncogenes that ultimately drive transformation. This review attempts to provide a basic understanding of enhancers and their role in transcriptional regulation, with a focus on normal and malignant hematopoiesis. We present examples of enhancers controlling master regulators of hematopoiesis and discuss the main mechanisms leading to enhancer dysregulation in leukemia and lymphoma.
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Affiliation(s)
- Roger Mulet-Lazaro
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Ruud Delwel
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
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4
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Xu Z, He L, Wu Y, Yang L, Li C, Wu H. PTEN regulates hematopoietic lineage plasticity via PU.1-dependent chromatin accessibility. Cell Rep 2023; 42:112967. [PMID: 37561626 DOI: 10.1016/j.celrep.2023.112967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 06/20/2023] [Accepted: 07/26/2023] [Indexed: 08/12/2023] Open
Abstract
PTEN loss in fetal liver hematopoietic stem cells (HSCs) leads to alterations in myeloid, T-, and B-lineage potentials and T-lineage acute lymphoblastic leukemia (T-ALL) development. To explore the mechanism underlying PTEN-regulated hematopoietic lineage choices, we carry out integrated assay for transposase-accessible chromatin using sequencing (ATAC-seq), single-cell RNA-seq, and in vitro culture analyses using in vivo-isolated mouse pre-leukemic HSCs and progenitors. We find that PTEN loss alters chromatin accessibility of key lineage transcription factor (TF) binding sites at the prepro-B stage, corresponding to increased myeloid and T-lineage potentials and reduced B-lineage potential. Importantly, we find that PU.1 is an essential TF downstream of PTEN and that altering PU.1 levels can reprogram the chromatin accessibility landscape and myeloid, T-, and B-lineage potentials in Ptennull prepro-B cells. Our study discovers prepro-B as the key developmental stage underlying PTEN-regulated hematopoietic lineage choices and suggests a critical role of PU.1 in modulating the epigenetic state and lineage plasticity of prepro-B progenitors.
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Affiliation(s)
- Zihan Xu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China; Center for Statistical Science, Peking University, Beijing, China
| | - Libing He
- The MOE Key Laboratory of Cell Proliferation and Differentiation, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Yilin Wu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Lu Yang
- The MOE Key Laboratory of Cell Proliferation and Differentiation, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Cheng Li
- The MOE Key Laboratory of Cell Proliferation and Differentiation, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China; Center for Statistical Science, Peking University, Beijing, China.
| | - Hong Wu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
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5
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Torcal Garcia G, Kowenz-Leutz E, Tian TV, Klonizakis A, Lerner J, De Andres-Aguayo L, Sapozhnikova V, Berenguer C, Carmona MP, Casadesus MV, Bulteau R, Francesconi M, Peiro S, Mertins P, Zaret K, Leutz A, Graf T. Carm1-arginine methylation of the transcription factor C/EBPα regulates transdifferentiation velocity. eLife 2023; 12:e83951. [PMID: 37365888 PMCID: PMC10299824 DOI: 10.7554/elife.83951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 05/30/2023] [Indexed: 06/28/2023] Open
Abstract
Here, we describe how the speed of C/EBPα-induced B cell to macrophage transdifferentiation (BMT) can be regulated, using both mouse and human models. The identification of a mutant of C/EBPα (C/EBPαR35A) that greatly accelerates BMT helped to illuminate the mechanism. Thus, incoming C/EBPα binds to PU.1, an obligate partner expressed in B cells, leading to the release of PU.1 from B cell enhancers, chromatin closing and silencing of the B cell program. Released PU.1 redistributes to macrophage enhancers newly occupied by C/EBPα, causing chromatin opening and activation of macrophage genes. All these steps are accelerated by C/EBPαR35A, initiated by its increased affinity for PU.1. Wild-type C/EBPα is methylated by Carm1 at arginine 35 and the enzyme's perturbations modulate BMT velocity as predicted from the observations with the mutant. Increasing the proportion of unmethylated C/EBPα in granulocyte/macrophage progenitors by inhibiting Carm1 biases the cell's differentiation toward macrophages, suggesting that cell fate decision velocity and lineage directionality are closely linked processes.
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Affiliation(s)
- Guillem Torcal Garcia
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST)BarcelonaSpain
- Universitat Pompeu Fabra (UPF)BarcelonaSpain
| | | | - Tian V Tian
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST)BarcelonaSpain
- Universitat Pompeu Fabra (UPF)BarcelonaSpain
- Vall d’Hebron Institute of Oncology (VHIO)BarcelonaSpain
| | - Antonis Klonizakis
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST)BarcelonaSpain
- Universitat Pompeu Fabra (UPF)BarcelonaSpain
| | - Jonathan Lerner
- Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Luisa De Andres-Aguayo
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST)BarcelonaSpain
- Universitat Pompeu Fabra (UPF)BarcelonaSpain
| | - Valeriia Sapozhnikova
- Max Delbrück Center for Molecular Medicine in the Helmholtz AssociationBerlinGermany
| | - Clara Berenguer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST)BarcelonaSpain
- Universitat Pompeu Fabra (UPF)BarcelonaSpain
| | - Marcos Plana Carmona
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST)BarcelonaSpain
- Universitat Pompeu Fabra (UPF)BarcelonaSpain
| | - Maria Vila Casadesus
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST)BarcelonaSpain
- Universitat Pompeu Fabra (UPF)BarcelonaSpain
- Vall d’Hebron Institute of Oncology (VHIO)BarcelonaSpain
| | - Romain Bulteau
- Laboratorie de Biologie et Modélisation de la Cellule, Université de LyonLyonFrance
| | - Mirko Francesconi
- Laboratorie de Biologie et Modélisation de la Cellule, Université de LyonLyonFrance
| | - Sandra Peiro
- Vall d’Hebron Institute of Oncology (VHIO)BarcelonaSpain
| | - Philipp Mertins
- Max Delbrück Center for Molecular Medicine in the Helmholtz AssociationBerlinGermany
| | - Kenneth Zaret
- Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Achim Leutz
- Max Delbrück Center for Molecular Medicine in the Helmholtz AssociationBerlinGermany
| | - Thomas Graf
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST)BarcelonaSpain
- Universitat Pompeu Fabra (UPF)BarcelonaSpain
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6
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Benyoucef A, Haigh JJ, Brand M. Unveiling the complexity of transcription factor networks in hematopoietic stem cells: implications for cell therapy and hematological malignancies. Front Oncol 2023; 13:1151343. [PMID: 37441426 PMCID: PMC10333584 DOI: 10.3389/fonc.2023.1151343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 06/14/2023] [Indexed: 07/15/2023] Open
Abstract
The functionality and longevity of hematopoietic tissue is ensured by a tightly controlled balance between self-renewal, quiescence, and differentiation of hematopoietic stem cells (HSCs) into the many different blood lineages. Cell fate determination in HSCs is influenced by signals from extrinsic factors (e.g., cytokines, irradiation, reactive oxygen species, O2 concentration) that are translated and integrated by intrinsic factors such as Transcription Factors (TFs) to establish specific gene regulatory programs. TFs also play a central role in the establishment and/or maintenance of hematological malignancies, highlighting the need to understand their functions in multiple contexts. TFs bind to specific DNA sequences and interact with each other to form transcriptional complexes that directly or indirectly control the expression of multiple genes. Over the past decades, significant research efforts have unraveled molecular programs that control HSC function. This, in turn, led to the identification of more than 50 TF proteins that influence HSC fate. However, much remains to be learned about how these proteins interact to form molecular networks in combination with cofactors (e.g. epigenetics factors) and how they control differentiation, expansion, and maintenance of cellular identity. Understanding these processes is critical for future applications particularly in the field of cell therapy, as this would allow for manipulation of cell fate and induction of expansion, differentiation, or reprogramming of HSCs using specific cocktails of TFs. Here, we review recent findings that have unraveled the complexity of molecular networks controlled by TFs in HSCs and point towards possible applications to obtain functional HSCs ex vivo for therapeutic purposes including hematological malignancies. Furthermore, we discuss the challenges and prospects for the derivation and expansion of functional adult HSCs in the near future.
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Affiliation(s)
- Aissa Benyoucef
- Department of Pharmacology and Therapeutics, Rady Faulty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
- CancerCare Manitoba Research Institute, Winnipeg, MB, Canada
| | - Jody J. Haigh
- Department of Pharmacology and Therapeutics, Rady Faulty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
- CancerCare Manitoba Research Institute, Winnipeg, MB, Canada
| | - Marjorie Brand
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
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7
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Liu TT, Ou F, Belk JA, Bagadia P, Anderson DA, Durai V, Yao W, Satpathy AT, Murphy TL, Murphy KM. Cis interactions in the Irf8 locus regulate stage-dependent enhancer activation. Genes Dev 2023; 37:291-302. [PMID: 36990511 PMCID: PMC10153461 DOI: 10.1101/gad.350339.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 03/14/2023] [Indexed: 03/31/2023]
Abstract
Individual elements within a superenhancer can act in a cooperative or temporal manner, but the underlying mechanisms remain obscure. We recently identified an Irf8 superenhancer, within which different elements act at distinct stages of type 1 classical dendritic cell (cDC1) development. The +41-kb Irf8 enhancer is required for pre-cDC1 specification, while the +32-kb Irf8 enhancer acts to support subsequent cDC1 maturation. Here, we found that compound heterozygous Δ32/Δ41 mice, lacking the +32- and +41-kb enhancers on different chromosomes, show normal pre-cDC1 specification but, surprisingly, completely lack mature cDC1 development, suggesting cis dependence of the +32-kb enhancer on the +41-kb enhancer. Transcription of the +32-kb Irf8 enhancer-associated long noncoding RNA (lncRNA) Gm39266 is also dependent on the +41-kb enhancer. However, cDC1 development in mice remained intact when Gm39266 transcripts were eliminated by CRISPR/Cas9-mediated deletion of lncRNA promoters and when transcription across the +32-kb enhancer was blocked by premature polyadenylation. We showed that chromatin accessibility and BATF3 binding at the +32-kb enhancer were dependent on a functional +41-kb enhancer located in cis Thus, the +41-kb Irf8 enhancer controls the subsequent activation of the +32-kb Irf8 enhancer in a manner that is independent of associated lncRNA transcription.
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Affiliation(s)
- Tian-Tian Liu
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, Missouri 63110, USA
| | - Feiya Ou
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, Missouri 63110, USA
| | - Julia A Belk
- Department of Computer Science, Stanford University, Stanford, California 94305, USA
| | - Prachi Bagadia
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, Missouri 63110, USA
| | - David A Anderson
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, Missouri 63110, USA
| | - Vivek Durai
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, Missouri 63110, USA
| | - Winnie Yao
- Department of Pathology, Stanford University, Stanford, California 94305, USA
| | - Ansuman T Satpathy
- Department of Pathology, Stanford University, Stanford, California 94305, USA
| | - Theresa L Murphy
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, Missouri 63110, USA
| | - Kenneth M Murphy
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, Missouri 63110, USA;
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8
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Edginton-White B, Maytum A, Kellaway SG, Goode DK, Keane P, Pagnuco I, Assi SA, Ames L, Clarke M, Cockerill PN, Göttgens B, Cazier JB, Bonifer C. A genome-wide relay of signalling-responsive enhancers drives hematopoietic specification. Nat Commun 2023; 14:267. [PMID: 36650172 PMCID: PMC9845378 DOI: 10.1038/s41467-023-35910-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 01/06/2023] [Indexed: 01/18/2023] Open
Abstract
Developmental control of gene expression critically depends on distal cis-regulatory elements including enhancers which interact with promoters to activate gene expression. To date no global experiments have been conducted that identify their cell type and cell stage-specific activity within one developmental pathway and in a chromatin context. Here, we describe a high-throughput method that identifies thousands of differentially active cis-elements able to stimulate a minimal promoter at five stages of hematopoietic progenitor development from embryonic stem (ES) cells, which can be adapted to any ES cell derived cell type. We show that blood cell-specific gene expression is controlled by the concerted action of thousands of differentiation stage-specific sets of cis-elements which respond to cytokine signals terminating at signalling responsive transcription factors. Our work provides an important resource for studies of hematopoietic specification and highlights the mechanisms of how and where extrinsic signals program a cell type-specific chromatin landscape driving hematopoietic differentiation.
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Affiliation(s)
- B Edginton-White
- Institute of Cancer and Genomic Sciences, School of Medicine and Dentistry, University of Birmingham, B152TT, Birmingham, UK.
| | - A Maytum
- Institute of Cancer and Genomic Sciences, School of Medicine and Dentistry, University of Birmingham, B152TT, Birmingham, UK
| | - S G Kellaway
- Institute of Cancer and Genomic Sciences, School of Medicine and Dentistry, University of Birmingham, B152TT, Birmingham, UK
| | - D K Goode
- Department of Haematology, Wellcome and Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, CB2 0AW, UK
| | - P Keane
- Institute of Cancer and Genomic Sciences, School of Medicine and Dentistry, University of Birmingham, B152TT, Birmingham, UK
| | - I Pagnuco
- Institute of Cancer and Genomic Sciences, School of Medicine and Dentistry, University of Birmingham, B152TT, Birmingham, UK
- Centre for Computational Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, B152TT, Birmingham, UK
| | - S A Assi
- Institute of Cancer and Genomic Sciences, School of Medicine and Dentistry, University of Birmingham, B152TT, Birmingham, UK
| | - L Ames
- Institute of Cancer and Genomic Sciences, School of Medicine and Dentistry, University of Birmingham, B152TT, Birmingham, UK
| | - M Clarke
- Institute of Cancer and Genomic Sciences, School of Medicine and Dentistry, University of Birmingham, B152TT, Birmingham, UK
| | - P N Cockerill
- Institute of Cancer and Genomic Sciences, School of Medicine and Dentistry, University of Birmingham, B152TT, Birmingham, UK
| | - B Göttgens
- Department of Haematology, Wellcome and Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, CB2 0AW, UK
| | - J B Cazier
- Institute of Cancer and Genomic Sciences, School of Medicine and Dentistry, University of Birmingham, B152TT, Birmingham, UK
- Centre for Computational Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, B152TT, Birmingham, UK
| | - C Bonifer
- Institute of Cancer and Genomic Sciences, School of Medicine and Dentistry, University of Birmingham, B152TT, Birmingham, UK.
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9
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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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10
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Bašová P, Paszeková H, Minařík L, Dluhošová M, Burda P, Stopka T. Combined Approach to Leukemic Differentiation Using Transcription Factor PU.1-Enhancing Agents. Int J Mol Sci 2022; 23:ijms23126729. [PMID: 35743167 PMCID: PMC9224232 DOI: 10.3390/ijms23126729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 06/13/2022] [Accepted: 06/14/2022] [Indexed: 02/04/2023] Open
Abstract
The transcription factor PU.1 (Purine-rich DNA binding, SPI1) is a key regulator of hematopoiesis, whose level is influenced by transcription through its enhancers and its post-transcriptional degradation via microRNA-155 (miR-155). The degree of transcriptional regulation of the PU.1 gene is influenced by repression via DNA methylation, as well as other epigenetic factors, such as those related to progenitor maturation status, which is modulated by the transcription factor Myeloblastosis oncogene (MYB). In this work, we show that combinatorial treatment of acute myeloid leukemia (AML) cells with DNA methylation inhibitors (5-Azacytidine), MYB inhibitors (Celastrol), and anti-miR-155 (AM155) ideally leads to overproduction of PU.1. We also show that PU.1 reactivation can be compensated by miR-155 and that only a combined approach leads to sustained PU.1 derepression, even at the protein level. The triple effect on increasing PU.1 levels in myeloblasts stimulates the myeloid transcriptional program while inhibiting cell survival and proliferation, leading to partial leukemic differentiation.
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11
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Jones R, Hill M, Taylor P. Spi1 -14 Kb upstream regulatory element (URE) is not required for maintenance of PU.1 expression in macrophages. Wellcome Open Res 2022. [DOI: 10.12688/wellcomeopenres.17705.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background: Previous work suggested an upstream regulatory element (URE) of Spi1 was required to maintain constant expression of the PU.1 transcription factor in bone marrow and foetal liver cells. PU.1, encoded by Spi1, is essential for development and maintenance of myeloid and B-lymphocyte populations in mice. Deletion of this (-14 Kb) URE potentially reduces expression of PU.1 and therefore provides a way to investigate its role in myeloid populations in development and disease. This study aimed to examine the impact of removal of the -14 Kb Spi1 URE in Cx3cr1+ cells on the myeloid lineage formation and maintenance. Methods: B6;129-Spi1tm1.2Dgt/J mice, whose -14 Kb Spi1 URE mice is flanked by LoxP sites (‘floxed’), were bred to a strain with constitutively active Cre expressed under the Cx3cr1 promoter (B6J.B6N(Cg)-Cx3cr1tm1.1(cre)Jung/J) to delete the Spi1 URE in myeloid cells. The floxed mice were also bred to mice with a tamoxifen-inducible Cre expressed under the Cx3cr1 promoter (B6.129P2(C)-Cx3cr1tm2.1(cre/ERT2)Jung/J) to be used as URE intact controls and to permit temporally-controlled deletion of the URE if required. PU.1 protein expression was measured in the peritoneal macrophages and microglia by flow cytometry. Additionally, a Cre-encoding lentiviral vector was used to assess the impact on PU.1 expression in bone-marrow derived macrophages from these mice in vitro. Results: Expression of the PU.1 transcription factor was not significantly altered in the peritoneal macrophages or microglia in mice lacking the -14 Kb Spi1 URE. Moreover, initial experiments utilising Cre encoding lentivirus did not reduce PU.1 protein in bone-marrow derived macrophages differentiated from the -14 Kb Spi1 URE floxed mice. Conclusions: These observations suggest that the -14 Kb URE does not play a major role in PU.1 protein expression in either mature peritoneal macrophages or microglia.
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12
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Ahmed N, Etzrodt M, Dettinger P, Kull T, Loeffler D, Hoppe PS, Chavez JS, Zhang Y, Camargo Ortega G, Hilsenbeck O, Nakajima H, Pietras EM, Schroeder T. Blood stem cell PU.1 upregulation is a consequence of differentiation without fast autoregulation. J Exp Med 2022; 219:e20202490. [PMID: 34817548 PMCID: PMC8624737 DOI: 10.1084/jem.20202490] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 05/07/2021] [Accepted: 09/23/2021] [Indexed: 11/12/2022] Open
Abstract
Transcription factors (TFs) regulate cell fates, and their expression must be tightly regulated. Autoregulation is assumed to regulate many TFs' own expression to control cell fates. Here, we manipulate and quantify the (auto)regulation of PU.1, a TF controlling hematopoietic stem and progenitor cells (HSPCs), and correlate it to their future fates. We generate transgenic mice allowing both inducible activation of PU.1 and noninvasive quantification of endogenous PU.1 protein expression. The quantified HSPC PU.1 dynamics show that PU.1 up-regulation occurs as a consequence of hematopoietic differentiation independently of direct fast autoregulation. In contrast, inflammatory signaling induces fast PU.1 up-regulation, which does not require PU.1 expression or its binding to its own autoregulatory enhancer. However, the increased PU.1 levels induced by inflammatory signaling cannot be sustained via autoregulation after removal of the signaling stimulus. We conclude that PU.1 overexpression induces HSC differentiation before PU.1 up-regulation, only later generating cell types with intrinsically higher PU.1.
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Affiliation(s)
- Nouraiz Ahmed
- Department of Biosystems Science & Engineering, Eidgenössische Technische Hochschule Zürich, Basel, Switzerland
| | - Martin Etzrodt
- Department of Biosystems Science & Engineering, Eidgenössische Technische Hochschule Zürich, Basel, Switzerland
| | - Philip Dettinger
- Department of Biosystems Science & Engineering, Eidgenössische Technische Hochschule Zürich, Basel, Switzerland
| | - Tobias Kull
- Department of Biosystems Science & Engineering, Eidgenössische Technische Hochschule Zürich, Basel, Switzerland
| | - Dirk Loeffler
- Department of Biosystems Science & Engineering, Eidgenössische Technische Hochschule Zürich, Basel, Switzerland
| | - Philipp S. Hoppe
- Department of Biosystems Science & Engineering, Eidgenössische Technische Hochschule Zürich, Basel, Switzerland
| | - James S. Chavez
- Division of Hematology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Yang Zhang
- Department of Biosystems Science & Engineering, Eidgenössische Technische Hochschule Zürich, Basel, Switzerland
| | - Germán Camargo Ortega
- Department of Biosystems Science & Engineering, Eidgenössische Technische Hochschule Zürich, Basel, Switzerland
| | - Oliver Hilsenbeck
- Department of Biosystems Science & Engineering, Eidgenössische Technische Hochschule Zürich, Basel, Switzerland
| | - Hideaki Nakajima
- Department of Stem Cell and Immune Regulation, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Eric M. Pietras
- Division of Hematology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Timm Schroeder
- Department of Biosystems Science & Engineering, Eidgenössische Technische Hochschule Zürich, Basel, Switzerland
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13
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Handzlik JE. Data-driven modeling predicts gene regulatory network dynamics during the differentiation of multipotential hematopoietic progenitors. PLoS Comput Biol 2022; 18:e1009779. [PMID: 35030198 PMCID: PMC8794271 DOI: 10.1371/journal.pcbi.1009779] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 01/27/2022] [Accepted: 12/21/2021] [Indexed: 01/05/2023] Open
Abstract
Cellular differentiation during hematopoiesis is guided by gene regulatory networks (GRNs) comprising transcription factors (TFs) and the effectors of cytokine signaling. Based largely on analyses conducted at steady state, these GRNs are thought to be organized as a hierarchy of bistable switches, with antagonism between Gata1 and PU.1 driving red- and white-blood cell differentiation. Here, we utilize transient gene expression patterns to infer the genetic architecture—the type and strength of regulatory interconnections—and dynamics of a twelve-gene GRN including key TFs and cytokine receptors. We trained gene circuits, dynamical models that learn genetic architecture, on high temporal-resolution gene-expression data from the differentiation of an inducible cell line into erythrocytes and neutrophils. The model is able to predict the consequences of gene knockout, knockdown, and overexpression experiments and the inferred interconnections are largely consistent with prior empirical evidence. The inferred genetic architecture is densely interconnected rather than hierarchical, featuring extensive cross-antagonism between genes from alternative lineages and positive feedback from cytokine receptors. The analysis of the dynamics of gene regulation in the model reveals that PU.1 is one of the last genes to be upregulated in neutrophil conditions and that the upregulation of PU.1 and other neutrophil genes is driven by Cebpa and Gfi1 instead. This model inference is confirmed in an independent single-cell RNA-Seq dataset from mouse bone marrow in which Cebpa and Gfi1 expression precedes the neutrophil-specific upregulation of PU.1 during differentiation. These results demonstrate that full PU.1 upregulation during neutrophil development involves regulatory influences extrinsic to the Gata1-PU.1 bistable switch. Furthermore, although there is extensive cross-antagonism between erythroid and neutrophil genes, it does not have a hierarchical structure. More generally, we show that the combination of high-resolution time series data and data-driven dynamical modeling can uncover the dynamics and causality of developmental events that might otherwise be obscured. The supply of blood cells is replenished by the maturation of hematopoietic progenitor cells into different cell types. Which cell type a progenitor cell develops into is determined by a complex network of genes whose protein products directly or indirectly regulate each others’ expression and that of downstream genes characteristic of the cell type. We inferred the nature and causality of the regulatory connections in a 12-gene network known to affect the decision between erythrocyte and neutrophil cell fates using a predictive machine-learning approach. Our analysis showed that the overall architecture of the network is densely interconnected and not hierarchical. Furthermore, the model inferred that PU.1, considered a master regulator of all white-blood cell lineages, is upregulated during neutrophil development by two other proteins, Cebpa and Gfi1. We validated this prediction by showing that Cebpa and Gfi1 expression precedes that of PU.1 in single-cell gene expression data from mouse bone marrow. These results revise the architecture of the gene network and the causality of regulatory events guiding hematopoiesis. The results also show that combining machine learning approaches with time course data can help resolve causality during development.
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Affiliation(s)
- Joanna E Handzlik
- Department of Biology, University of North Dakota, Grand Forks, North Dakota, United States of America
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14
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Yau E, Chen Y, Song C, Webb J, Carillo M, Kawasawa YI, Tang Z, Takahashi Y, Umstead TM, Dovat S, Chroneos ZC. Genomic and epigenomic adaptation in SP-R210 (Myo18A) isoform-deficient macrophages. Immunobiology 2021; 226:152150. [PMID: 34735924 DOI: 10.1016/j.imbio.2021.152150] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 09/03/2021] [Accepted: 10/20/2021] [Indexed: 10/20/2022]
Abstract
Macrophages play an important role in maintaining tissue homeostasis, from regulating the inflammatory response to pathogens to resolving inflammation and aiding tissue repair. The surfactant protein A (SP-A) receptor SP-R210 (MYO18A) has been shown to affect basal and inflammatory macrophage states. Specifically, disruption of the longer splice isoform SP-R210L/MYO18Aα renders macrophages hyper-inflammatory, although the mechanism by which this occurs is not well understood. We asked whether disruption of the L isoform led to the hyper-inflammatory state via alteration of global genomic responses. RNA sequencing analysis of L isoform-deficient macrophages (SP-R210L(DN)) revealed basal and influenza-induced upregulation of genes associated with inflammatory pathways, such as TLR, RIG-I, NOD, and cytoplasmic DNA signaling, whereas knockout of both SP-R210 isoforms (L and S) only resulted in increased RIG-I and NOD signaling. Chromatin immunoprecipitation sequencing (ChIP-seq) analysis showed increased genome-wide deposition of the pioneer transcription factor PU.1 in SP-R210L(DN) cells, with increased representation around genes relevant to inflammatory pathways. Additional ChIP-seq analysis of histone H3 methylation marks showed decreases in both repressive H3K9me3 and H3K27me3 marks with a commensurate increase in transcriptionally active (H3K4me3) histone marks in the L isoform deficient macrophages. Influenza A virus (IAV) infection, known to stimulate a wide array of anti-viral responses, caused a differential redistribution of PU.1 binding between proximal promoter and distal sites and decoupling from Toll-like receptor regulated gene promoters in SP-R210L(DN) cells. These finding suggest that the inflammatory differences seen in SP-R210L-deficient macrophages are a result of transcriptional differences that are mediated by epigenetic changes brought about by differential expression of the SP-R210 isoforms. This provides an avenue to explore how the signaling pathways downstream of the receptor and the ligands can modulate the macrophage inflammatory response.
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Affiliation(s)
- Eric Yau
- Department of Pediatrics and Microbiology and Immunology, Pulmonary Immunology and Physiology Laboratory, Pennsylvania State University College of Medicine, PA, USA.
| | - Yan Chen
- Department of Pediatrics and Microbiology and Immunology, Pulmonary Immunology and Physiology Laboratory, Pennsylvania State University College of Medicine, PA, USA; Department of Pediatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chunhua Song
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, Pennsylvania State University College of Medicine, PA, USA; Department of Internal Medicine, Ohio State University College of Medicine, Columbus, OH, USA
| | - Jason Webb
- Department of Pediatrics and Microbiology and Immunology, Pulmonary Immunology and Physiology Laboratory, Pennsylvania State University College of Medicine, PA, USA
| | - Marykate Carillo
- Department of Pediatrics and Microbiology and Immunology, Pulmonary Immunology and Physiology Laboratory, Pennsylvania State University College of Medicine, PA, USA
| | - Yuka Imamura Kawasawa
- Department of Pharmacology and Biochemistry and Molecular Biology, Institute for Personalized Medicine, Pennsylvania State University College of Medicine, PA, USA
| | - Zhenyuan Tang
- Department of Pediatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yoshinori Takahashi
- Department of Pediatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Todd M Umstead
- Department of Pediatrics and Microbiology and Immunology, Pulmonary Immunology and Physiology Laboratory, Pennsylvania State University College of Medicine, PA, USA
| | - Sinisa Dovat
- Department of Pediatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zissis C Chroneos
- Department of Pediatrics and Microbiology and Immunology, Pulmonary Immunology and Physiology Laboratory, Pennsylvania State University College of Medicine, PA, USA.
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15
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Jones RE, Andrews R, Holmans P, Hill M, Taylor PR. Modest changes in Spi1 dosage reveal the potential for altered microglial function as seen in Alzheimer's disease. Sci Rep 2021; 11:14935. [PMID: 34294785 PMCID: PMC8298495 DOI: 10.1038/s41598-021-94324-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 07/07/2021] [Indexed: 12/12/2022] Open
Abstract
Genetic association studies have identified multiple variants at the SPI1 locus that modify risk and age of onset for Alzheimer's Disease (AD). Reports linking risk variants to gene expression suggest that variants denoting higher SPI1 expression are likely to have an earlier AD onset, and several other AD risk genes contain PU.1 binding sites in the promoter region. Overall, this suggests the level of SPI1 may alter microglial phenotype potentially impacting AD. This study determined how the microglial transcriptome was altered following modest changes to Spi1 expression in primary mouse microglia. RNA-sequencing was performed on microglia with reduced or increased Spi1/PU.1 expression to provide an unbiased approach to determine transcriptomic changes affected by Spi1. In summary, a reduction in microglial Spi1 resulted in the dysregulation of transcripts encoding proteins involved in DNA replication pathways while an increased Spi1 results in an upregulation of genes associated with immune response pathways. Additionally, a subset of 194 Spi1 dose-sensitive genes was identified and pathway analysis suggests that several innate immune and interferon response pathways are impacted by the concentration of Spi1. Together these results suggest Spi1 levels can alter the microglial transcriptome and suggests interferon pathways may be altered in individuals with AD related Spi1 risk SNPs.
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Affiliation(s)
- Ruth E Jones
- Division of Infection and Immunity, Cardiff University, Cardiff, UK
- UK Dementia Research Institute at Cardiff, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ, UK
| | - Robert Andrews
- Division of Infection and Immunity, Cardiff University, Cardiff, UK
- Systems Immunity Research Institute, Cardiff University, Cardiff, UK
| | - Peter Holmans
- Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Matthew Hill
- UK Dementia Research Institute at Cardiff, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ, UK
| | - Philip R Taylor
- Division of Infection and Immunity, Cardiff University, Cardiff, UK.
- UK Dementia Research Institute at Cardiff, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ, UK.
- Systems Immunity Research Institute, Cardiff University, Cardiff, UK.
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16
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Nafria M, Keane P, Ng ES, Stanley EG, Elefanty AG, Bonifer C. Expression of RUNX1-ETO Rapidly Alters the Chromatin Landscape and Growth of Early Human Myeloid Precursor Cells. Cell Rep 2021; 31:107691. [PMID: 32460028 PMCID: PMC7262600 DOI: 10.1016/j.celrep.2020.107691] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 03/12/2020] [Accepted: 05/05/2020] [Indexed: 01/03/2023] Open
Abstract
Acute myeloid leukemia (AML) is a hematopoietic malignancy caused by recurrent mutations in genes encoding transcriptional, chromatin, and/or signaling regulators. The t(8;21) translocation generates the aberrant transcription factor RUNX1-ETO (RUNX1-RUNX1T1), which by itself is insufficient to cause disease. t(8;21) AML patients show extensive chromatin reprogramming and have acquired additional mutations. Therefore, the genomic and developmental effects directly and solely attributable to RUNX1-ETO expression are unclear. To address this, we employ a human embryonic stem cell differentiation system capable of forming definitive myeloid progenitor cells to express RUNX1-ETO in an inducible fashion. Induction of RUNX1-ETO causes extensive chromatin reprogramming by interfering with RUNX1 binding, blocks differentiation, and arrests cellular growth, whereby growth arrest is reversible following RUNX1-ETO removal. Single-cell gene expression analyses show that RUNX1-ETO induction alters the differentiation of early myeloid progenitors, but not of other progenitor types, indicating that oncoprotein-mediated transcriptional reprogramming is highly target cell specific. RUNX1-ETO reversibly arrests the growth of human ESC-derived early myeloid cells RUNX1-ETO disrupts global RUNX1 binding and deregulates RUNX1 target genes RUNX1-ETO blocks myeloid differentiation by rapidly downregulating SPI1 and CEBPA The impact of RUNX1-ETO induction is cell type specific
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Affiliation(s)
- Monica Nafria
- Institute for Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK; Murdoch Children's Research Institute, The Royal Children's Hospital, Flemington Road, Parkville, VIC 3052, Australia; Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC 3052, Australia
| | - Peter Keane
- Institute for Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK
| | - Elizabeth S Ng
- Murdoch Children's Research Institute, The Royal Children's Hospital, Flemington Road, Parkville, VIC 3052, Australia
| | - Edouard G Stanley
- Murdoch Children's Research Institute, The Royal Children's Hospital, Flemington Road, Parkville, VIC 3052, Australia; Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC 3052, Australia; Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia
| | - Andrew G Elefanty
- Murdoch Children's Research Institute, The Royal Children's Hospital, Flemington Road, Parkville, VIC 3052, Australia; Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC 3052, Australia; Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia.
| | - Constanze Bonifer
- Institute for Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK.
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17
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Rothenberg EV. Logic and lineage impacts on functional transcription factor deployment for T-cell fate commitment. Biophys J 2021; 120:4162-4181. [PMID: 33838137 PMCID: PMC8516641 DOI: 10.1016/j.bpj.2021.04.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 03/22/2021] [Accepted: 04/02/2021] [Indexed: 11/19/2022] Open
Abstract
Transcription factors are the major agents that read the regulatory sequence information in the genome to initiate changes in expression of specific genes, both in development and in physiological activation responses. Their actions depend on site-specific DNA binding and are largely guided by their individual DNA target sequence specificities. However, their action is far more conditional in a real developmental context than would be expected for simple reading of local genomic DNA sequence, which is common to all cells in the organism. They are constrained by slow-changing chromatin states and by interactions with other transcription factors, which affect their occupancy patterns of potential sites across the genome. These mechanisms lead to emergent discontinuities in function even for transcription factors with minimally changing expression. This is well revealed by diverse lineages of blood cells developing throughout life from hematopoietic stem cells, which use overlapping combinations of transcription factors to drive strongly divergent gene regulation programs. Here, using development of T lymphocytes from hematopoietic multipotent progenitor cells as a focus, recent evidence is reviewed on how binding specificity and dynamics, transcription factor cooperativity, and chromatin state changes impact the effective regulatory functions of key transcription factors including PU.1, Runx1, Notch-RBPJ, and Bcl11b.
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Affiliation(s)
- Ellen V Rothenberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California.
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18
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Rothenberg EV, Göttgens B. How haematopoiesis research became a fertile ground for regulatory network biology as pioneered by Eric Davidson. Curr Opin Hematol 2021; 28:1-10. [PMID: 33229891 PMCID: PMC7755131 DOI: 10.1097/moh.0000000000000628] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
PURPOSE OF REVIEW This historical perspective reviews how work of Eric H. Davidson was a catalyst and exemplar for explaining haematopoietic cell fate determination through gene regulation. RECENT FINDINGS Researchers studying blood and immune cells pioneered many of the early mechanistic investigations of mammalian gene regulatory processes. These efforts included the characterization of complex gene regulatory sequences exemplified by the globin and T-cell/B-cell receptor gene loci, as well as the identification of many key regulatory transcription factors through the fine mapping of chromosome translocation breakpoints in leukaemia patients. As the repertoire of known regulators expanded, assembly into gene regulatory network models became increasingly important, not only to account for the truism that regulatory genes do not function in isolation but also to devise new ways of extracting biologically meaningful insights from even more complex information. Here we explore how Eric H. Davidson's pioneering studies of gene regulatory network control in nonvertebrate model organisms have had an important and lasting impact on research into blood and immune cell development. SUMMARY The intellectual framework developed by Davidson continues to contribute to haematopoietic research, and his insistence on demonstrating logic and causality still challenges the frontier of research today.
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Affiliation(s)
- Ellen V. Rothenberg
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Berthold Göttgens
- Wellcome and MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge CB2 0AW, UK
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19
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Olariu V, Yui MA, Krupinski P, Zhou W, Deichmann J, Andersson E, Rothenberg EV, Peterson C. Multi-scale Dynamical Modeling of T Cell Development from an Early Thymic Progenitor State to Lineage Commitment. Cell Rep 2021; 34:108622. [PMID: 33440162 DOI: 10.1016/j.celrep.2020.108622] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 04/24/2020] [Accepted: 12/18/2020] [Indexed: 01/13/2023] Open
Abstract
Intrathymic development of committed progenitor (pro)-T cells from multipotent hematopoietic precursors offers an opportunity to dissect the molecular circuitry establishing cell identity in response to environmental signals. This transition encompasses programmed shutoff of stem/progenitor genes, upregulation of T cell specification genes, proliferation, and ultimately commitment. To explain these features in light of reported cis-acting chromatin effects and experimental kinetic data, we develop a three-level dynamic model of commitment based upon regulation of the commitment-linked gene Bcl11b. The levels are (1) a core gene regulatory network (GRN) architecture from transcription factor (TF) perturbation data, (2) a stochastically controlled chromatin-state gate, and (3) a single-cell proliferation model validated by experimental clonal growth and commitment kinetic assays. Using RNA fluorescence in situ hybridization (FISH) measurements of genes encoding key TFs and measured bulk population dynamics, this single-cell model predicts state-switching kinetics validated by measured clonal proliferation and commitment times. The resulting multi-scale model provides a mechanistic framework for dissecting commitment dynamics.
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Affiliation(s)
- Victor Olariu
- Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
| | - Mary A Yui
- Division of Biology and Biological Engineering, 156-29, California Institute of Technology, Pasadena, CA 91125, USA
| | - Pawel Krupinski
- Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
| | - Wen Zhou
- Division of Biology and Biological Engineering, 156-29, California Institute of Technology, Pasadena, CA 91125, USA
| | - Julia Deichmann
- Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
| | - Emil Andersson
- Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
| | - Ellen V Rothenberg
- Division of Biology and Biological Engineering, 156-29, California Institute of Technology, Pasadena, CA 91125, USA.
| | - Carsten Peterson
- Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden.
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20
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Carleton JB, Ginley-Hidinger M, Berrett KC, Layer RM, Quinlan AR, Gertz J. Regulatory sharing between estrogen receptor α bound enhancers. Nucleic Acids Res 2020; 48:6597-6610. [PMID: 32479598 PMCID: PMC7337896 DOI: 10.1093/nar/gkaa454] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 05/15/2020] [Accepted: 05/18/2020] [Indexed: 12/28/2022] Open
Abstract
The human genome encodes an order of magnitude more gene expression enhancers than promoters, suggesting that most genes are regulated by the combined action of multiple enhancers. We have previously shown that neighboring estrogen-responsive enhancers exhibit complex synergistic contributions to the production of an estrogenic transcriptional response. Here we sought to determine the molecular underpinnings of this enhancer cooperativity. We generated genetic deletions of four estrogen receptor α (ER) bound enhancers that regulate two genes and found that enhancers containing full estrogen response element (ERE) motifs control ER binding at neighboring sites, while enhancers with pre-existing histone acetylation/accessibility confer a permissible chromatin environment to the neighboring enhancers. Genome engineering revealed that two enhancers with half EREs could not compensate for the lack of a full ERE site within the cluster. In contrast, two enhancers with full EREs produced a transcriptional response greater than the wild-type locus. By swapping genomic sequences, we found that the genomic location of a full ERE strongly influences enhancer activity. Our results lead to a model in which a full ERE is required for ER recruitment, but the presence of a pre-existing permissible chromatin environment can also be needed for estrogen-driven gene regulation to occur.
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Affiliation(s)
- Julia B Carleton
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.,Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Matthew Ginley-Hidinger
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.,Department of Biomedical Engineering, University of Utah, Salt Lake City, UT, USA
| | - Kristofer C Berrett
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.,Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Ryan M Layer
- BioFrontiers Institute, University of Colorado, Boulder, CO, USA.,Department of Computer Science, University of Colorado, Boulder, CO, USA
| | - Aaron R Quinlan
- Departments of Human Genetics and Biomedical Informatics, University of Utah, Salt Lake City, UT, USA
| | - Jason Gertz
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.,Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
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21
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McKenzie MD, Ghisi M, Oxley EP, Ngo S, Cimmino L, Esnault C, Liu R, Salmon JM, Bell CC, Ahmed N, Erlichster M, Witkowski MT, Liu GJ, Chopin M, Dakic A, Simankowicz E, Pomilio G, Vu T, Krsmanovic P, Su S, Tian L, Baldwin TM, Zalcenstein DA, DiRago L, Wang S, Metcalf D, Johnstone RW, Croker BA, Lancaster GI, Murphy AJ, Naik SH, Nutt SL, Pospisil V, Schroeder T, Wall M, Dawson MA, Wei AH, de Thé H, Ritchie ME, Zuber J, Dickins RA. Interconversion between Tumorigenic and Differentiated States in Acute Myeloid Leukemia. Cell Stem Cell 2020; 25:258-272.e9. [PMID: 31374198 DOI: 10.1016/j.stem.2019.07.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 01/28/2019] [Accepted: 07/01/2019] [Indexed: 12/11/2022]
Abstract
Tumors are composed of phenotypically heterogeneous cancer cells that often resemble various differentiation states of their lineage of origin. Within this hierarchy, it is thought that an immature subpopulation of tumor-propagating cancer stem cells (CSCs) differentiates into non-tumorigenic progeny, providing a rationale for therapeutic strategies that specifically eradicate CSCs or induce their differentiation. The clinical success of these approaches depends on CSC differentiation being unidirectional rather than reversible, yet this question remains unresolved even in prototypically hierarchical malignancies, such as acute myeloid leukemia (AML). Here, we show in murine and human models of AML that, upon perturbation of endogenous expression of the lineage-determining transcription factor PU.1 or withdrawal of established differentiation therapies, some mature leukemia cells can de-differentiate and reacquire clonogenic and leukemogenic properties. Our results reveal plasticity of CSC maturation in AML, highlighting the need to therapeutically eradicate cancer cells across a range of differentiation states.
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Affiliation(s)
- Mark D McKenzie
- Molecular Medicine Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - Margherita Ghisi
- Australian Centre for Blood Diseases, Monash University, Commercial Road, Melbourne, VIC 3004, Australia
| | - Ethan P Oxley
- Australian Centre for Blood Diseases, Monash University, Commercial Road, Melbourne, VIC 3004, Australia
| | - Steven Ngo
- Australian Centre for Blood Diseases, Monash University, Commercial Road, Melbourne, VIC 3004, Australia
| | - Luisa Cimmino
- Department of Pathology, New York University School of Medicine, 550 1(st) Avenue, New York, NY 10016, USA
| | - Cécile Esnault
- Collège de France, PSL Research University, 75005 Paris, France; INSERM U944, CNRS UMR7212, Université de Paris, Institut de Recherche Saint Louis, 75010 Paris, France; Assistance Publique/Hôpitaux de Paris, Oncologie Moléculaire, Hôpital St. Louis, 75010 Paris, France
| | - Ruijie Liu
- Molecular Medicine Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - Jessica M Salmon
- Australian Centre for Blood Diseases, Monash University, Commercial Road, Melbourne, VIC 3004, Australia
| | - Charles C Bell
- Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Nouraiz Ahmed
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Michael Erlichster
- Molecular Medicine Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Matthew T Witkowski
- Molecular Medicine Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Australian Centre for Blood Diseases, Monash University, Commercial Road, Melbourne, VIC 3004, Australia; Department of Pathology, New York University School of Medicine, 550 1(st) Avenue, New York, NY 10016, USA; Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Grace J Liu
- Molecular Medicine Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Australian Centre for Blood Diseases, Monash University, Commercial Road, Melbourne, VIC 3004, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Michael Chopin
- Molecular Immunology Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - Aleksandar Dakic
- Molecular Immunology Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - Emilia Simankowicz
- Australian Centre for Blood Diseases, Monash University, Commercial Road, Melbourne, VIC 3004, Australia
| | - Giovanna Pomilio
- Australian Centre for Blood Diseases, Monash University, Commercial Road, Melbourne, VIC 3004, Australia; Department of Clinical Haematology, The Alfred Hospital, Melbourne, VIC 3004, Australia
| | - Tina Vu
- Australian Centre for Blood Diseases, Monash University, Commercial Road, Melbourne, VIC 3004, Australia
| | - Pavle Krsmanovic
- Institute of Pathological Physiology and Biocev, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Shian Su
- Molecular Medicine Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - Luyi Tian
- Molecular Medicine Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Tracey M Baldwin
- Molecular Medicine Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - Daniela A Zalcenstein
- Molecular Medicine Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - Ladina DiRago
- Cancer and Haematology Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - Shu Wang
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Donald Metcalf
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia; Cancer and Haematology Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - Ricky W Johnstone
- Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Ben A Croker
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Graeme I Lancaster
- Baker Heart and Diabetes Institute, Melbourne, VIC 3004, Australia; Department of Immunology and Pathology, Monash University, Commercial Road, Melbourne, VIC 3004, Australia
| | - Andrew J Murphy
- Baker Heart and Diabetes Institute, Melbourne, VIC 3004, Australia; Department of Immunology and Pathology, Monash University, Commercial Road, Melbourne, VIC 3004, Australia
| | - Shalin H Naik
- Molecular Medicine Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Stephen L Nutt
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia; Molecular Immunology Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - Vitek Pospisil
- Institute of Pathological Physiology and Biocev, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Timm Schroeder
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Meaghan Wall
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia; Victorian Cancer Cytogenetics Service, St. Vincent's Hospital, 41 Victoria Parade, Fitzroy, VIC 3065, Australia
| | - Mark A Dawson
- Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Andrew H Wei
- Australian Centre for Blood Diseases, Monash University, Commercial Road, Melbourne, VIC 3004, Australia; Department of Clinical Haematology, The Alfred Hospital, Melbourne, VIC 3004, Australia
| | - Hugues de Thé
- Collège de France, PSL Research University, 75005 Paris, France; INSERM U944, CNRS UMR7212, Université de Paris, Institut de Recherche Saint Louis, 75010 Paris, France; Assistance Publique/Hôpitaux de Paris, Oncologie Moléculaire, Hôpital St. Louis, 75010 Paris, France
| | - Matthew E Ritchie
- Molecular Medicine Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia; School of Mathematics and Statistics, University of Melbourne, Parkville, VIC 3010, Australia
| | - Johannes Zuber
- Research Institute of Molecular Pathology, Campus Vienna Biocenter 1, 1030 Vienna, Austria; Medical University of Vienna, 1030 Vienna, Austria
| | - Ross A Dickins
- Australian Centre for Blood Diseases, Monash University, Commercial Road, Melbourne, VIC 3004, Australia.
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22
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Wang D, Zou X, Fai Au K. A network-based computational framework to predict and differentiate functions for gene isoforms using exon-level expression data. Methods 2020; 189:54-64. [PMID: 32534132 DOI: 10.1016/j.ymeth.2020.06.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 05/22/2020] [Accepted: 06/06/2020] [Indexed: 12/23/2022] Open
Abstract
MOTIVATION Alternative splicing makes significant contributions to functional diversity of transcripts and proteins. Many alternatively spliced gene isoforms have been shown to perform specific biological functions under different contexts. In addition to gene-level expression, the advances of high-throughput sequencing offer a chance to estimate isoform-specific exon expression with a high resolution, which is informative for studying splice variants with network analysis. RESULTS In this study, we propose a novel network-based analysis framework to predict isoform-specific functions from exon-level RNA-Seq data. In particular, based on exon-level expression data, we firstly propose a unified framework, referred to as Iso-Net, to integrate two new mathematical methods (named MINet and RVNet) that infer co-expression networks at different data scenarios. We demonstrate the superior prediction accuracy of Iso-Net over the existing methods for most simulation data, especially in two extreme cases: sample size is very small and exon numbers of two isoforms are quite different. Furthermore, by defining relevant quantitative measures (e.g., Jaccard correlation coefficient) and combining differential co-expression network analysis and GO functional enrichment analysis, a co-expression network analysis framework is developed to predict functions of isoforms and further, to discover their distinct functions within the same gene. We apply Iso-Net to study gene isoforms for several important transcription factors in human myeloid differentiation with the exon-level RNA-Seq data from three different cell lines. AVAILABILITY AND IMPLEMENTATION Iso-Net is open source and freely available from https://github.com/Dingjie-Wang/Iso-Net.
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Affiliation(s)
- Dingjie Wang
- Department of Biomedical Informatics, The Ohio State University, OH 43210, USA; School of Mathematics and Statistics, Wuhan University, Wuhan 430072, China; Computational Science Hubei Key Laboratory, Wuhan University, Wuhan 430072, China
| | - Xiufen Zou
- School of Mathematics and Statistics, Wuhan University, Wuhan 430072, China; Computational Science Hubei Key Laboratory, Wuhan University, Wuhan 430072, China.
| | - Kin Fai Au
- Department of Biomedical Informatics, The Ohio State University, OH 43210, USA.
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23
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Horvath A, Daniel B, Szeles L, Cuaranta-Monroy I, Czimmerer Z, Ozgyin L, Steiner L, Kiss M, Simandi Z, Poliska S, Giannakis N, Raineri E, Gut IG, Nagy B, Nagy L. Labelled regulatory elements are pervasive features of the macrophage genome and are dynamically utilized by classical and alternative polarization signals. Nucleic Acids Res 2019; 47:2778-2792. [PMID: 30799488 PMCID: PMC6451134 DOI: 10.1093/nar/gkz118] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 02/14/2019] [Indexed: 01/09/2023] Open
Abstract
The concept of tissue-specific gene expression posits that lineage-determining transcription factors (LDTFs) determine the open chromatin profile of a cell via collaborative binding, providing molecular beacons to signal-dependent transcription factors (SDTFs). However, the guiding principles of LDTF binding, chromatin accessibility and enhancer activity have not yet been systematically evaluated. We sought to study these features of the macrophage genome by the combination of experimental (ChIP-seq, ATAC-seq and GRO-seq) and computational approaches. We show that Random Forest and Support Vector Regression machine learning methods can accurately predict chromatin accessibility using the binding patterns of the LDTF PU.1 and four other key TFs of macrophages (IRF8, JUNB, CEBPA and RUNX1). Any of these TFs alone were not sufficient to predict open chromatin, indicating that TF binding is widespread at closed or weakly opened chromatin regions. Analysis of the PU.1 cistrome revealed that two-thirds of PU.1 binding occurs at low accessible chromatin. We termed these sites labelled regulatory elements (LREs), which may represent a dormant state of a future enhancer and contribute to macrophage cellular plasticity. Collectively, our work demonstrates the existence of LREs occupied by various key TFs, regulating specific gene expression programs triggered by divergent macrophage polarizing stimuli.
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Affiliation(s)
- Attila Horvath
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary
| | - Bence Daniel
- Johns Hopkins University School of Medicine, Department of Medicine and Biological Chemistry, Institute for Fundamental Biomedical Research, Johns Hopkins All Children's Hospital, Saint Petersburg, FL 33701, USA
| | - Lajos Szeles
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary
| | - Ixchelt Cuaranta-Monroy
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary
| | - Zsolt Czimmerer
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary
| | - Lilla Ozgyin
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary
| | - Laszlo Steiner
- UD-GenoMed Medical Genomic Technologies Ltd., Nagyerdei krt. 98., H-4032 Debrecen, Hungary
| | - Mate Kiss
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary
| | - Zoltan Simandi
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary
| | - Szilard Poliska
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary.,UD-GenoMed Medical Genomic Technologies Ltd., Nagyerdei krt. 98., H-4032 Debrecen, Hungary
| | - Nikolas Giannakis
- UD-GenoMed Medical Genomic Technologies Ltd., Nagyerdei krt. 98., H-4032 Debrecen, Hungary
| | - Emanuele Raineri
- Centro Nacional de Analisis Genomico (CNAG-CRG), Center for Genomic Regulation (CRG), Barcelona Institute for Science and Technology (BIST), C/Baldiri Reixac 4, 08028 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Plaça de la Mercè 10, 08002, Barcelona, Spain
| | - Ivo G Gut
- Centro Nacional de Analisis Genomico (CNAG-CRG), Center for Genomic Regulation (CRG), Barcelona Institute for Science and Technology (BIST), C/Baldiri Reixac 4, 08028 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Plaça de la Mercè 10, 08002, Barcelona, Spain
| | - Benedek Nagy
- Department of Mathematics, Eastern Mediterranean University, Famagusta, North Cyprus, Mersin 10, Turkey
| | - Laszlo Nagy
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary.,Johns Hopkins University School of Medicine, Department of Medicine and Biological Chemistry, Institute for Fundamental Biomedical Research, Johns Hopkins All Children's Hospital, Saint Petersburg, FL 33701, USA
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24
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Abstract
Specification of multipotent blood precursor cells in postnatal mice to become committed T-cell precursors involves a gene regulatory network of several interacting but functionally distinct modules. Many links of this network have been defined by perturbation tests and by functional genomics. However, using the network model to predict real-life kinetics of the commitment process is still difficult, partly due to the tenacity of repressive chromatin states, and to the ability of transcription factors to affect each other's binding site choices through competitive recruitment to alternative sites ("coregulator theft"). To predict kinetics, future models will need to incorporate mechanistic information about chromatin state change dynamics and more sophisticated understanding of the proteomics and cooperative DNA site choices of transcription factor complexes.
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Affiliation(s)
- Ellen V Rothenberg
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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25
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Abstract
Rapid advances have been made to uncover the mechanisms that regulate dendritic cell (DC) development, and in turn, how models of development can be employed to define dendritic cell function. Models of DC development have been used to define the unique functions of DC subsets during immune responses to distinct pathogens. More recently, models of DC function have expanded to include their homeostatic and inflammatory physiology, modes of communication with various innate and adaptive immune lineages, and specialized functions across different lymphoid organs. New models of DC development call for revisions of previously accepted paradigms with respect to the ontogeny of plasmacytoid DC (pDC) and classical DC (cDC) subsets. By far, development of the cDC1 subset is best understood, and models have now been developed that can separate deficiencies in development from deficiencies in function. Such models are lacking for pDCs and cDC2s, limiting the depth of our understanding of their unique and essential roles during immune responses. If novel immunotherapies aim to harness the functions of human DCs, understanding of DC development will be essential to develop models DC function. Here we review emerging models of DC development and function.
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Affiliation(s)
- David A Anderson
- Department of Pathology and Immunology, School of Medicine, Washington University in St. Louis, St. Louis, MO, United States.
| | - Kenneth M Murphy
- Department of Pathology and Immunology, School of Medicine, Washington University in St. Louis, St. Louis, MO, United States; Howard Hughes Medical Institute, School of Medicine, Washington University in St. Louis, St. Louis, MO, United States
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26
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Runx1 promotes murine erythroid progenitor proliferation and inhibits differentiation by preventing Pu.1 downregulation. Proc Natl Acad Sci U S A 2019; 116:17841-17847. [PMID: 31431533 DOI: 10.1073/pnas.1901122116] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Pu.1 is an ETS family transcription factor (TF) that plays critical roles in erythroid progenitors by promoting proliferation and blocking terminal differentiation. However, the mechanisms controlling expression and down-regulation of Pu.1 during early erythropoiesis have not been defined. In this study, we identify the actions of Runx1 and Pu.1 itself at the Pu.1 gene Upstream Regulatory Element (URE) as major regulators of Pu.1 expression in Burst-Forming Unit erythrocytes (BFUe). During early erythropoiesis, Runx1 and Pu.1 levels decline, and chromatin accessibility at the URE is lost. Ectopic expression of Runx1 or Pu.1, both of which bind the URE, prevents Pu.1 down-regulation and blocks terminal erythroid differentiation, resulting in extensive ex vivo proliferation and immortalization of erythroid progenitors. Ectopic expression of Runx1 in BFUe lacking a URE fails to block terminal erythroid differentiation. Thus, Runx1, acting at the URE, and Pu.1 itself directly regulate Pu.1 levels in erythroid cells, and loss of both factors is critical for Pu.1 down-regulation during terminal differentiation. The molecular mechanism of URE inactivation in erythroid cells through loss of TF binding represents a distinct pattern of Pu.1 regulation from those described in other hematopoietic cell types such as T cells which down-regulate Pu.1 through active repression. The importance of down-regulation of Runx1 and Pu.1 in erythropoiesis is further supported by genome-wide analyses showing that their DNA-binding motifs are highly overrepresented in regions that lose chromatin accessibility during early erythroid development.
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27
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Ye Y, Kang X, Bailey J, Li C, Hong T. An enriched network motif family regulates multistep cell fate transitions with restricted reversibility. PLoS Comput Biol 2019; 15:e1006855. [PMID: 30845219 PMCID: PMC6424469 DOI: 10.1371/journal.pcbi.1006855] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 03/19/2019] [Accepted: 02/07/2019] [Indexed: 12/16/2022] Open
Abstract
Multistep cell fate transitions with stepwise changes of transcriptional profiles are common to many developmental, regenerative and pathological processes. The multiple intermediate cell lineage states can serve as differentiation checkpoints or branching points for channeling cells to more than one lineages. However, mechanisms underlying these transitions remain elusive. Here, we explored gene regulatory circuits that can generate multiple intermediate cellular states with stepwise modulations of transcription factors. With unbiased searching in the network topology space, we found a motif family containing a large set of networks can give rise to four attractors with the stepwise regulations of transcription factors, which limit the reversibility of three consecutive steps of the lineage transition. We found that there is an enrichment of these motifs in a transcriptional network controlling the early T cell development, and a mathematical model based on this network recapitulates multistep transitions in the early T cell lineage commitment. By calculating the energy landscape and minimum action paths for the T cell model, we quantified the stochastic dynamics of the critical factors in response to the differentiation signal with fluctuations. These results are in good agreement with experimental observations and they suggest the stable characteristics of the intermediate states in the T cell differentiation. These dynamical features may help to direct the cells to correct lineages during development. Our findings provide general design principles for multistep cell linage transitions and new insights into the early T cell development. The network motifs containing a large family of topologies can be useful for analyzing diverse biological systems with multistep transitions. The functions of cells are dynamically controlled in many biological processes including development, regeneration and disease progression. Cell fate transition, or the switch of cellular functions, often involves multiple steps. The intermediate stages of the transition provide the biological systems with the opportunities to regulate the transitions in a precise manner. These transitions are controlled by key regulatory genes of which the expression shows stepwise patterns, but how the interactions of these genes can determine the multistep processes was unclear. Here, we present a comprehensive analysis on the design principles of gene circuits that govern multistep cell fate transition. We found a large network family with common structural features that can generate systems with the ability to control three consecutive steps of the transition. We found that this type of networks is enriched in a gene circuit controlling the development of T lymphocyte, a crucial type of immune cells. We performed mathematical modeling using this gene circuit and we recapitulated the stepwise and irreversible loss of stem cell properties of the developing T lymphocytes. Our findings can be useful to analyze a wide range of gene regulatory networks controlling multistep cell fate transitions.
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Affiliation(s)
- Yujie Ye
- Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee, United States of America
| | - Xin Kang
- Shanghai Center for Mathematical Sciences, Fudan University, Shanghai, China.,School of Mathematical Sciences, Fudan University, Shanghai, China
| | - Jordan Bailey
- Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee, United States of America
| | - Chunhe Li
- Shanghai Center for Mathematical Sciences, Fudan University, Shanghai, China.,Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
| | - Tian Hong
- Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee, United States of America.,National Institute for Mathematical and Biological Synthesis, Knoxville, Tennessee, United States of America
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28
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Shin HY, Hennighausen L, Yoo KH. STAT5-Driven Enhancers Tightly Control Temporal Expression of Mammary-Specific Genes. J Mammary Gland Biol Neoplasia 2019; 24:61-71. [PMID: 30328555 DOI: 10.1007/s10911-018-9418-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 10/12/2018] [Indexed: 12/24/2022] Open
Abstract
The de novo formation of milk-secreting mammary epithelium during pregnancy is regulated by prolactin through activation of the transcription factor STAT5, which stimulates the expression of several hundred mammary-specific genes. In addition to its key role in activating gene expression in mammary tissue, STAT5, which is ubiquitously expressed in most cell types, implements T cell-specific programs controlled by interleukins. However, the mechanisms by which STAT5 controls cell-specific genetic programs activated by distinct cytokines remain relatively unknown. Integration of data from genome-wide surveys of chromatin markers and transcription factor binding at regulatory elements may shed light on the mechanisms that drive cell-specific programs. Here, we have illustrated how STAT5 controls cell-specific gene expression through its concentration and an auto-regulatory enhancer supporting its high levels in mammary tissue. The unique genomic features of STAT5-driven enhancers or super-enhancers that regulate mammary-specific genes and their dynamic remodeling in response to pregnancy hormone levels are described. We have further provided biological evidence supporting the in vivo function of a STAT5-driven super-enhancer with the aid of CRISPR/Cas9 genome editing. Finally, we discuss how the functions of mammary-specific super-enhancers are confined by the zinc finger protein, CTCF, to allow exclusive activation of mammary-specific genes without affecting common neighboring genes. This review comprehensively summarizes the molecular pathways underlying differential control of cell-specific gene sets by STAT5 and provides novel insights into STAT5-dependent mammary physiology.
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Affiliation(s)
- Ha Youn Shin
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Lothar Hennighausen
- Laboratory of Genetics and Physiology, National Institutes of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
- BK21 PLUS Project, Sookmyung Women's University, Seoul, 04310, Republic of Korea
| | - Kyung Hyun Yoo
- Department of Biological Sciences, Sookmyung Women's University, Seoul, 04310, Republic of Korea.
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29
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Rothenberg EV, Hosokawa H, Ungerbäck J. Mechanisms of Action of Hematopoietic Transcription Factor PU.1 in Initiation of T-Cell Development. Front Immunol 2019; 10:228. [PMID: 30842770 PMCID: PMC6391351 DOI: 10.3389/fimmu.2019.00228] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 01/28/2019] [Indexed: 12/20/2022] Open
Abstract
PU.1 is an ETS-family transcription factor that plays a broad range of roles in hematopoiesis. A direct regulator of myeloid, dendritic-cell, and B cell functional programs, and a well-known antagonist of terminal erythroid cell differentiation, it is also expressed in the earliest stages of T-cell development of each cohort of intrathymic pro-T cells. Its expression in this context appears to give T-cell precursors initial, transient access to myeloid and dendritic cell developmental competence and therefore to represent a source of antagonism or delay of T-cell lineage commitment. However, it has remained uncertain until recently why T-cell development is also intensely dependent upon PU.1. Here, we review recent work that sheds light on the molecular biology of PU.1 action across the genome in pro-T cells and identifies the genes that depend on PU.1 for their correct regulation. This work indicates modes of chromatin engagement, pioneering, and cofactor recruitment (“coregulator theft”) by PU.1 as well as gene network interactions that not only affect specific target genes but also have system-wide regulatory consequences, amplifying the impact of PU.1 beyond its own direct binding targets. The genes directly regulated by PU.1 also suggest a far-reaching transformation of cell biology and signaling potential between the early stages of T-cell development when PU.1 is expressed and when it is silenced. These cell-biological functions can be important to distinguish fetal from adult T-cell development and have the potential to illuminate aspects of thymic function that have so far remained the most mysterious.
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Affiliation(s)
- Ellen V Rothenberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Hiroyuki Hosokawa
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Jonas Ungerbäck
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
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30
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Temporal autoregulation during human PU.1 locus SubTAD formation. Blood 2018; 132:2643-2655. [PMID: 30315124 DOI: 10.1182/blood-2018-02-834721] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 10/06/2018] [Indexed: 12/20/2022] Open
Abstract
Epigenetic control of gene expression occurs within discrete spatial chromosomal units called topologically associating domains (TADs), but the exact spatial requirements of most genes are unknown; this is of particular interest for genes involved in cancer. We therefore applied high-resolution chromosomal conformation capture sequencing to map the three-dimensional (3D) organization of the human locus encoding the key myeloid transcription factor PU.1 in healthy monocytes and acute myeloid leukemia (AML) cells. We identified a dynamic ∼75-kb unit (SubTAD) as the genomic region in which spatial interactions between PU.1 gene regulatory elements occur during myeloid differentiation and are interrupted in AML. Within this SubTAD, proper initiation of the spatial chromosomal interactions requires PU.1 autoregulation and recruitment of the chromatin-adaptor protein LDB1 (LIM domain-binding protein 1). However, once these spatial interactions have occurred, LDB1 stabilizes them independently of PU.1 autoregulation. Thus, our data support that PU.1 autoregulates its expression in a "hit-and-run" manner by initiating stable chromosomal loops that result in a transcriptionally active chromatin architecture.
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31
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Etzrodt M, Schroeder T. Illuminating stem cell transcription factor dynamics: long-term single-cell imaging of fluorescent protein fusions. Curr Opin Cell Biol 2017; 49:77-83. [PMID: 29276951 DOI: 10.1016/j.ceb.2017.12.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 12/09/2017] [Accepted: 12/13/2017] [Indexed: 12/13/2022]
Abstract
Most single-cell approaches to date are based on destructive snapshot measurements which do not permit to correlate a current molecular state with future fate. However, to understand how cell fate choices are established by transcription factor networks (TFNs) regulating cell fates, TFN dynamics must be continuously monitored in single cells. Here we review how quantitative time-lapse imaging can contribute to understanding TFN dependent cell fate regulation at the single-cell level. We outline potentials of the technology and highlight challenges for interpreting the dynamics of fluorescent protein reporters that may interfere with endogenous TF function. We provide an outlook on how continuous observation of TF dynamics and single-cell fates may be complemented by perturbation studies and be linked to multidimensional molecular profiling in the future.
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Affiliation(s)
- Martin Etzrodt
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Timm Schroeder
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland.
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32
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Ramírez C, Mendoza L. Phenotypic stability and plasticity in GMP-derived cells as determined by their underlying regulatory network. Bioinformatics 2017; 34:1174-1182. [DOI: 10.1093/bioinformatics/btx736] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 11/23/2017] [Indexed: 12/30/2022] Open
Affiliation(s)
- Carlos Ramírez
- Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Cd. Mx., México
| | - Luis Mendoza
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Cd. Mx., México
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33
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Stanulovic VS, Cauchy P, Assi SA, Hoogenkamp M. LMO2 is required for TAL1 DNA binding activity and initiation of definitive haematopoiesis at the haemangioblast stage. Nucleic Acids Res 2017; 45:9874-9888. [PMID: 28973433 PMCID: PMC5622341 DOI: 10.1093/nar/gkx573] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 06/27/2017] [Indexed: 02/06/2023] Open
Abstract
LMO2 is a bridging factor within a DNA binding complex and is required for definitive haematopoiesis to occur. The developmental stage of the block in haematopoietic specification is not known. We show that Lmo2−/− mouse embryonic stem cells differentiated to Flk-1+ haemangioblasts, but less efficiently to haemogenic endothelium, which only produced primitive haematopoietic progenitors. Genome-wide approaches indicated that LMO2 is required at the haemangioblast stage to position the TAL1/LMO2/LDB1 complex to regulatory elements that are important for the establishment of the haematopoietic developmental program. In the absence of LMO2, the target site recognition of TAL1 is impaired. The lack of LMO2 resulted in altered gene expression levels already at the haemangioblast stage, with transcription factor genes accounting for ∼15% of affected genes. Comparison of Lmo2−/− with Tal1−/− Flk-1+ cells further showed that TAL1 was required to initiate or sustain Lmo2 expression.
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Affiliation(s)
- Vesna S Stanulovic
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Pierre Cauchy
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Salam A Assi
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Maarten Hoogenkamp
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
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34
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Carleton JB, Berrett KC, Gertz J. Multiplex Enhancer Interference Reveals Collaborative Control of Gene Regulation by Estrogen Receptor α-Bound Enhancers. Cell Syst 2017; 5:333-344.e5. [PMID: 28964699 DOI: 10.1016/j.cels.2017.08.011] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 06/13/2017] [Accepted: 08/22/2017] [Indexed: 12/31/2022]
Abstract
Multiple regulatory regions have the potential to regulate a single gene, yet how these elements combine to affect gene expression remains unclear. To uncover the combinatorial relationships between enhancers, we developed Enhancer-interference (Enhancer-i), a CRISPR interference-based approach that uses 2 different repressive domains, KRAB and SID, to prevent enhancer activation simultaneously at multiple regulatory regions. We applied Enhancer-i to promoter-distal estrogen receptor α binding sites (ERBS), which cluster around estradiol-responsive genes and therefore may collaborate to regulate gene expression. Targeting individual sites revealed predominant ERBS that are completely required for the transcriptional response, indicating a lack of redundancy. Simultaneous interference of different ERBS combinations identified supportive ERBS that contribute only when predominant sites are active. Using mathematical modeling, we find strong evidence for collaboration between predominant and supportive ERBS. Overall, our findings expose a complex functional hierarchy of enhancers, where multiple loci bound by the same transcription factor combine to fine-tune the expression of target genes.
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Affiliation(s)
- Julia B Carleton
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Kristofer C Berrett
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Jason Gertz
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA.
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35
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Krox20 hindbrain regulation incorporates multiple modes of cooperation between cis-acting elements. PLoS Genet 2017; 13:e1006903. [PMID: 28749941 PMCID: PMC5549768 DOI: 10.1371/journal.pgen.1006903] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 08/08/2017] [Accepted: 07/03/2017] [Indexed: 11/19/2022] Open
Abstract
Developmental genes can harbour multiple transcriptional enhancers that act simultaneously or in succession to achieve robust and precise spatiotemporal expression. However, the mechanisms underlying cooperation between cis-acting elements are poorly documented, notably in vertebrates. The mouse gene Krox20 encodes a transcription factor required for the specification of two segments (rhombomeres) of the developing hindbrain. In rhombomere 3, Krox20 is subject to direct positive feedback governed by an autoregulatory enhancer, element A. In contrast, a second enhancer, element C, distant by 70 kb, is active from the initiation of transcription independent of the presence of the KROX20 protein. Here, using both enhancer knock-outs and investigations of chromatin organisation, we show that element C possesses a dual activity: besides its classical enhancer function, it is also permanently required in cis to potentiate the autoregulatory activity of element A, by increasing its chromatin accessibility. This work uncovers a novel, asymmetrical, long-range mode of cooperation between cis-acting elements that might be essential to avoid promiscuous activation of positive autoregulatory elements. The formation of multicellular organisms from the egg to the adult stage is largely under genetic control. The activation of specific genes is governed by regulatory DNA sequences present nearby on the chromosome. Most of these sequences promote activation and are called enhancers. In this paper, we study two enhancers governing the expression of a gene involved in the formation of the posterior brain in vertebrates. One of these enhancers is involved in a positive feedback loop: it is itself activated by the protein product of the gene that it regulates. The other enhancer was thought to be only involved in the initial accumulation of the protein, necessary for the subsequent activation of the feedback loop. Here we show that the second enhancer directly cooperates with the autoregulatory enhancer to increase its accessibility and its activity. Our work uncovers a novel, long-range mode of cooperation between enhancers that restricts the domain of action of autoregulatory enhancers within embryos and might be essential to avoid their inappropriate activation.
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36
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Ramirez RN, El-Ali NC, Mager MA, Wyman D, Conesa A, Mortazavi A. Dynamic Gene Regulatory Networks of Human Myeloid Differentiation. Cell Syst 2017; 4:416-429.e3. [PMID: 28365152 DOI: 10.1016/j.cels.2017.03.005] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 10/31/2016] [Accepted: 03/03/2017] [Indexed: 12/15/2022]
Abstract
The reconstruction of gene regulatory networks underlying cell differentiation from high-throughput gene expression and chromatin data remains a challenge. Here, we derive dynamic gene regulatory networks for human myeloid differentiation using a 5-day time series of RNA-seq and ATAC-seq data. We profile HL-60 promyelocytes differentiating into macrophages, neutrophils, monocytes, and monocyte-derived macrophages. We find a rapid response in the expression of key transcription factors and lineage markers that only regulate a subset of their targets at a given time, which is followed by chromatin accessibility changes that occur later along with further gene expression changes. We observe differences between promyelocyte- and monocyte-derived macrophages at both the transcriptional and chromatin landscape level, despite using the same differentiation stimulus, which suggest that the path taken by cells in the differentiation landscape defines their end cell state. More generally, our approach of combining neighboring time points and replicates to achieve greater sequencing depth can efficiently infer footprint-based regulatory networks from long series data.
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Affiliation(s)
- Ricardo N Ramirez
- Developmental and Cell Biology, University of California Irvine, Irvine, CA 92697-2300, USA; Center for Complex Biological Systems, University of California Irvine, Irvine, CA 92697-2300, USA
| | - Nicole C El-Ali
- Developmental and Cell Biology, University of California Irvine, Irvine, CA 92697-2300, USA; Center for Complex Biological Systems, University of California Irvine, Irvine, CA 92697-2300, USA
| | - Mikayla Anne Mager
- Developmental and Cell Biology, University of California Irvine, Irvine, CA 92697-2300, USA; Center for Complex Biological Systems, University of California Irvine, Irvine, CA 92697-2300, USA
| | - Dana Wyman
- Center for Complex Biological Systems, University of California Irvine, Irvine, CA 92697-2300, USA
| | - Ana Conesa
- Centro de Investigacion Principe Felipe, 46012 Valencia, Spain; Microbiology and Cell Science, University of Florida, Gainesville, FL 32603, USA
| | - Ali Mortazavi
- Developmental and Cell Biology, University of California Irvine, Irvine, CA 92697-2300, USA; Center for Complex Biological Systems, University of California Irvine, Irvine, CA 92697-2300, USA.
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37
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Ghaffarizadeh A, Podgorski GJ, Flann NS. Applying attractor dynamics to infer gene regulatory interactions involved in cellular differentiation. Biosystems 2017; 155:29-41. [PMID: 28254369 DOI: 10.1016/j.biosystems.2016.12.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Revised: 12/06/2016] [Accepted: 12/22/2016] [Indexed: 11/30/2022]
Abstract
The dynamics of gene regulatory networks (GRNs) guide cellular differentiation. Determining the ways regulatory genes control expression of their targets is essential to understand and control cellular differentiation. The way a regulatory gene controls its target can be expressed as a gene regulatory function. Manual derivation of these regulatory functions is slow, error-prone and difficult to update as new information arises. Automating this process is a significant challenge and the subject of intensive effort. This work presents a novel approach to discovering biologically plausible gene regulatory interactions that control cellular differentiation. This method integrates known cell type expression data, genetic interactions, and knowledge of the effects of gene knockouts to determine likely GRN regulatory functions. We employ a genetic algorithm to search for candidate GRNs that use a set of transcription factors that control differentiation within a lineage. Nested canalyzing functions are used to constrain the search space to biologically plausible networks. The method identifies an ensemble of GRNs whose dynamics reproduce the gene expression pattern for each cell type within a particular lineage. The method's effectiveness was tested by inferring consensus GRNs for myeloid and pancreatic cell differentiation and comparing the predicted gene regulatory interactions to manually derived interactions. We identified many regulatory interactions reported in the literature and also found differences from published reports. These discrepancies suggest areas for biological studies of myeloid and pancreatic differentiation. We also performed a study that used defined synthetic networks to evaluate the accuracy of the automated search method and found that the search algorithm was able to discover the regulatory interactions in these defined networks with high accuracy. We suggest that the GRN functions derived from the methods described here can be used to fill gaps in knowledge about regulatory interactions and to offer hypotheses for experimental testing of GRNs that control differentiation and other biological processes.
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Affiliation(s)
- Ahmadreza Ghaffarizadeh
- Computer Science Department, Utah State University, 4205 Old Main Hill, Logan, UT 84322, United States.
| | - Gregory J Podgorski
- Biology Department, Utah State University, 5305 Old Main Hill, Logan, UT 84322, United States; Center for Integrated BioSystems, 4700 Old Main Hill, Logan, UT 84322, United States.
| | - Nicholas S Flann
- Computer Science Department, Utah State University, 4205 Old Main Hill, Logan, UT 84322, United States; Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, United States; Synthetic Biomanufacturing Institute, 1780 N. Research Park Way, Suite 108, North Logan, UT 84341, United States.
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38
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Bonifer C, Cockerill PN. Chromatin priming of genes in development: Concepts, mechanisms and consequences. Exp Hematol 2017; 49:1-8. [PMID: 28185904 DOI: 10.1016/j.exphem.2017.01.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 01/19/2017] [Accepted: 01/21/2017] [Indexed: 01/06/2023]
Abstract
During ontogeny, cells progress through multiple alternate differentiation states by activating distinct gene regulatory networks. In this review, we highlight the important role of chromatin priming in facilitating gene activation during lineage specification and in maintaining an epigenetic memory of previous gene activation. We show that chromatin priming is part of a hugely diverse repertoire of regulatory mechanisms that genes use to ensure that they are expressed at the correct time, in the correct cell type, and at the correct level, but also that they react to signals. We also emphasize how increasing our knowledge of these principles could inform our understanding of developmental failure and disease.
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Affiliation(s)
- Constanze Bonifer
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham, UK.
| | - Peter N Cockerill
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham, UK.
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39
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Rothenberg EV, Kueh HY, Yui MA, Zhang JA. Hematopoiesis and T-cell specification as a model developmental system. Immunol Rev 2016; 271:72-97. [PMID: 27088908 DOI: 10.1111/imr.12417] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The pathway to generate T cells from hematopoietic stem cells guides progenitors through a succession of fate choices while balancing differentiation progression against proliferation, stage to stage. Many elements of the regulatory system that controls this process are known, but the requirement for multiple, functionally distinct transcription factors needs clarification in terms of gene network architecture. Here, we compare the features of the T-cell specification system with the rule sets underlying two other influential types of gene network models: first, the combinatorial, hierarchical regulatory systems that generate the orderly, synchronized increases in complexity in most invertebrate embryos; second, the dueling 'master regulator' systems that are commonly used to explain bistability in microbial systems and in many fate choices in terminal differentiation. The T-cell specification process shares certain features with each of these prevalent models but differs from both of them in central respects. The T-cell system is highly combinatorial but also highly dose-sensitive in its use of crucial regulatory factors. The roles of these factors are not always T-lineage-specific, but they balance and modulate each other's activities long before any mutually exclusive silencing occurs. T-cell specification may provide a new hybrid model for gene networks in vertebrate developmental systems.
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Affiliation(s)
- Ellen V Rothenberg
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Hao Yuan Kueh
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Mary A Yui
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Jingli A Zhang
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA
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40
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Long HK, Prescott SL, Wysocka J. Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution. Cell 2016; 167:1170-1187. [PMID: 27863239 PMCID: PMC5123704 DOI: 10.1016/j.cell.2016.09.018] [Citation(s) in RCA: 556] [Impact Index Per Article: 69.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 08/24/2016] [Accepted: 09/07/2016] [Indexed: 12/27/2022]
Abstract
A class of cis-regulatory elements, called enhancers, play a central role in orchestrating spatiotemporally precise gene-expression programs during development. Consequently, divergence in enhancer sequence and activity is thought to be an important mediator of inter- and intra-species phenotypic variation. Here, we give an overview of emerging principles of enhancer function, current models of enhancer architecture, genomic substrates from which enhancers emerge during evolution, and the influence of three-dimensional genome organization on long-range gene regulation. We discuss intricate relationships between distinct elements within complex regulatory landscapes and consider their potential impact on specificity and robustness of transcriptional regulation.
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Affiliation(s)
- Hannah K Long
- Department of Chemical and Systems Biology, Stanford School of Medicine, Stanford University, Stanford, CA 94305, USA; Institute of Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Sara L Prescott
- Department of Chemical and Systems Biology, Stanford School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford School of Medicine, Stanford University, Stanford, CA 94305, USA; Institute of Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford School of Medicine, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford School of Medicine, Stanford University, Stanford, CA 94305, USA.
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41
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Montecino-Rodriguez E, Fice M, Casero D, Berent-Maoz B, Barber CL, Dorshkind K. Distinct Genetic Networks Orchestrate the Emergence of Specific Waves of Fetal and Adult B-1 and B-2 Development. Immunity 2016; 45:527-539. [PMID: 27566938 DOI: 10.1016/j.immuni.2016.07.012] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 05/13/2016] [Accepted: 06/08/2016] [Indexed: 10/21/2022]
Abstract
B cell development is often depicted as a linear process initiating in the fetus and continuing postnatally. Using a PU.1 hypomorphic mouse model, we found that B-1 and B-2 lymphopoiesis occurred in distinct fetal and adult waves differentially dependent on the Sfpi1 14 kB upstream regulatory element. The initial wave of fetal B-1 development was absent in PU.1 hypomorphic mice, while subsequent fetal and adult waves emerged. In contrast, B-2 lymphopoiesis occurred in distinct fetal and adult waves. Whole-transcriptome profiling of fetal and adult B cell progenitors supported the existence of three waves of B-1 and two waves of B-2 development and revealed that the network of transcription factors governing B lineage specification and commitment was highly divergent between B-1 and B-2 progenitors. These findings support the view that the B-1 and B-2 lineages are distinct and provide a genetic basis for layering of immune system development.
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Affiliation(s)
- Encarnacion Montecino-Rodriguez
- Department of Pathology and Laboratory Medicine, Division of Hematology/Oncology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Michael Fice
- Department of Pathology and Laboratory Medicine, Division of Hematology/Oncology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - David Casero
- Department of Pathology and Laboratory Medicine, Division of Hematology/Oncology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Beata Berent-Maoz
- Department of Medicine, Division of Hematology/Oncology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Chad L Barber
- Department of Biology, California Lutheran University, Thousand Oaks, CA 91360, USA
| | - Kenneth Dorshkind
- Department of Pathology and Laboratory Medicine, Division of Hematology/Oncology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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42
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Manesso E, Kueh HY, Freedman G, Rothenberg EV, Peterson C. Irreversibility of T-Cell Specification: Insights from Computational Modelling of a Minimal Network Architecture. PLoS One 2016; 11:e0161260. [PMID: 27551921 PMCID: PMC4995000 DOI: 10.1371/journal.pone.0161260] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Accepted: 08/02/2016] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND/OBJECTIVES A cascade of gene activations under the control of Notch signalling is required during T-cell specification, when T-cell precursors gradually lose the potential to undertake other fates and become fully committed to the T-cell lineage. We elucidate how the gene/protein dynamics for a core transcriptional module governs this important process by computational means. METHODS We first assembled existing knowledge about transcription factors known to be important for T-cell specification to form a minimal core module consisting of TCF-1, GATA-3, BCL11B, and PU.1 aiming at dynamical modeling. Model architecture was based on published experimental measurements of the effects on each factor when each of the others is perturbed. While several studies provided gene expression measurements at different stages of T-cell development, pure time series are not available, thus precluding a straightforward study of the dynamical interactions among these genes. We therefore translate stage dependent data into time series. A feed-forward motif with multiple positive feed-backs can account for the observed delay between BCL11B versus TCF-1 and GATA-3 activation by Notch signalling. With a novel computational approach, all 32 possible interactions among Notch signalling, TCF-1, and GATA-3 are explored by translating combinatorial logic expressions into differential equations for BCL11B production rate. RESULTS Our analysis reveals that only 3 of 32 possible configurations, where GATA-3 works as a dimer, are able to explain not only the time delay, but very importantly, also give rise to irreversibility. The winning models explain the data within the 95% confidence region and are consistent with regard to decay rates. CONCLUSIONS This first generation model for early T-cell specification has relatively few players. Yet it explains the gradual transition into a committed state with no return. Encoding logics in a rate equation setting allows determination of binding properties beyond what is possible in a Boolean network.
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Affiliation(s)
- Erica Manesso
- Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, SE-223 62 Lund, Sweden
| | - Hao Yuan Kueh
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, United States of America
| | - George Freedman
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, United States of America
| | - Ellen V. Rothenberg
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, United States of America
- * E-mail: (EVR); (CP)
| | - Carsten Peterson
- Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, SE-223 62 Lund, Sweden
- * E-mail: (EVR); (CP)
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43
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CD19 CAR immune pressure induces B-precursor acute lymphoblastic leukaemia lineage switch exposing inherent leukaemic plasticity. Nat Commun 2016; 7:12320. [PMID: 27460500 PMCID: PMC4974466 DOI: 10.1038/ncomms12320] [Citation(s) in RCA: 305] [Impact Index Per Article: 38.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 06/21/2016] [Indexed: 12/13/2022] Open
Abstract
Adoptive immunotherapy using chimeric antigen receptor (CAR) expressing T cells targeting the CD19 B lineage receptor has demonstrated marked success in relapsed pre-B-cell acute lymphoblastic leukaemia (ALL). Persisting CAR-T cells generate sustained pressure against CD19 that may drive unique mechanisms of resistance. Pre-B ALL originates from a committed pre-B cell or an earlier progenitor, with potential to reprogram into other hematopoietic lineages. Here we report changes in lineage markers including myeloid conversion in patients following CD19 CAR therapy. Using murine ALL models we study the long-term effects of CD19 CAR-T cells and demonstrate partial or complete lineage switch as a consistent mechanism of CAR resistance depending on the underlying genetic oncogenic driver. Deletion of Pax5 or Ebf1 recapitulates lineage reprogramming occurring during CD19 CAR pressure. Our findings establish lineage switch as a mechanism of CAR resistance exposing inherent plasticity in genetic subtypes of pre-B-cell ALL. CAR-T targeting CD19 have been successfully used in a variety of B-cell malignancies but patients may eventually relapse. Here, the authors show that CD19 CAR-T resistance in pre-B cell ALL can be due to the induction of a myeloid lineage switch through an epigenetic alterations in master regulators of B cell development.
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Burda P, Vargova J, Curik N, Salek C, Papadopoulos GL, Strouboulis J, Stopka T. GATA-1 Inhibits PU.1 Gene via DNA and Histone H3K9 Methylation of Its Distal Enhancer in Erythroleukemia. PLoS One 2016; 11:e0152234. [PMID: 27010793 PMCID: PMC4807078 DOI: 10.1371/journal.pone.0152234] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 03/10/2016] [Indexed: 01/17/2023] Open
Abstract
GATA-1 and PU.1 are two important hematopoietic transcription factors that mutually inhibit each other in progenitor cells to guide entrance into the erythroid or myeloid lineage, respectively. PU.1 controls its own expression during myelopoiesis by binding to the distal URE enhancer, whose deletion leads to acute myeloid leukemia (AML). We herein present evidence that GATA-1 binds to the PU.1 gene and inhibits its expression in human AML-erythroleukemias (EL). Furthermore, GATA-1 together with DNA methyl Transferase I (DNMT1) mediate repression of the PU.1 gene through the URE. Repression of the PU.1 gene involves both DNA methylation at the URE and its histone H3 lysine-K9 methylation and deacetylation as well as the H3K27 methylation at additional DNA elements and the promoter. The GATA-1-mediated inhibition of PU.1 gene transcription in human AML-EL mediated through the URE represents important mechanism that contributes to PU.1 downregulation and leukemogenesis that is sensitive to DNA demethylation therapy.
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MESH Headings
- Cell Differentiation/genetics
- DNA (Cytosine-5-)-Methyltransferase 1
- DNA (Cytosine-5-)-Methyltransferases/genetics
- DNA (Cytosine-5-)-Methyltransferases/metabolism
- DNA Methylation/genetics
- Enhancer Elements, Genetic
- GATA1 Transcription Factor/genetics
- GATA1 Transcription Factor/metabolism
- Gene Expression Regulation, Leukemic
- Histones/genetics
- Humans
- Leukemia, Erythroblastic, Acute/genetics
- Leukemia, Erythroblastic, Acute/pathology
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/pathology
- Promoter Regions, Genetic
- Protein Binding
- Proto-Oncogene Proteins/biosynthesis
- Proto-Oncogene Proteins/genetics
- Proto-Oncogene Proteins/metabolism
- Trans-Activators/biosynthesis
- Trans-Activators/genetics
- Trans-Activators/metabolism
- Transcription, Genetic
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Affiliation(s)
- Pavel Burda
- Biocev and Pathological Physiology, 1st Faculty of Medicine, Charles University in Prague, Czech Republic
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Jarmila Vargova
- Biocev and Pathological Physiology, 1st Faculty of Medicine, Charles University in Prague, Czech Republic
| | - Nikola Curik
- Biocev and Pathological Physiology, 1st Faculty of Medicine, Charles University in Prague, Czech Republic
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Cyril Salek
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Giorgio Lucio Papadopoulos
- Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology-Hellas, Heraklion, Crete, Greece
- Department of Biology, University of Crete, Heraklion, Crete, Greece
| | - John Strouboulis
- Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology-Hellas, Heraklion, Crete, Greece
| | - Tomas Stopka
- Biocev and Pathological Physiology, 1st Faculty of Medicine, Charles University in Prague, Czech Republic
- 1st Medical Department–Hematology, General Faculty Hospital, Prague, Czech Republic
- * E-mail:
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45
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Goode DK, Obier N, Vijayabaskar MS, Lie-A-Ling M, Lilly AJ, Hannah R, Lichtinger M, Batta K, Florkowska M, Patel R, Challinor M, Wallace K, Gilmour J, Assi SA, Cauchy P, Hoogenkamp M, Westhead DR, Lacaud G, Kouskoff V, Göttgens B, Bonifer C. Dynamic Gene Regulatory Networks Drive Hematopoietic Specification and Differentiation. Dev Cell 2016; 36:572-87. [PMID: 26923725 PMCID: PMC4780867 DOI: 10.1016/j.devcel.2016.01.024] [Citation(s) in RCA: 166] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 12/04/2015] [Accepted: 01/26/2016] [Indexed: 12/22/2022]
Abstract
Metazoan development involves the successive activation and silencing of specific gene expression programs and is driven by tissue-specific transcription factors programming the chromatin landscape. To understand how this process executes an entire developmental pathway, we generated global gene expression, chromatin accessibility, histone modification, and transcription factor binding data from purified embryonic stem cell-derived cells representing six sequential stages of hematopoietic specification and differentiation. Our data reveal the nature of regulatory elements driving differential gene expression and inform how transcription factor binding impacts on promoter activity. We present a dynamic core regulatory network model for hematopoietic specification and demonstrate its utility for the design of reprogramming experiments. Functional studies motivated by our genome-wide data uncovered a stage-specific role for TEAD/YAP factors in mammalian hematopoietic specification. Our study presents a powerful resource for studying hematopoiesis and demonstrates how such data advance our understanding of mammalian development.
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Affiliation(s)
- Debbie K Goode
- Department of Haematology, Cambridge Institute for Medical Research and Wellcome Trust and MRC Cambridge Stem Cell Institute, Cambridge CB2 0XY, UK
| | - Nadine Obier
- Institute of Cancer end Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B152TT, UK
| | - M S Vijayabaskar
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Michael Lie-A-Ling
- CRUK Manchester Institute, University of Manchester, Manchester M20 4BX, UK
| | - Andrew J Lilly
- CRUK Manchester Institute, University of Manchester, Manchester M20 4BX, UK
| | - Rebecca Hannah
- Department of Haematology, Cambridge Institute for Medical Research and Wellcome Trust and MRC Cambridge Stem Cell Institute, Cambridge CB2 0XY, UK
| | - Monika Lichtinger
- Institute of Cancer end Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B152TT, UK
| | - Kiran Batta
- CRUK Manchester Institute, University of Manchester, Manchester M20 4BX, UK
| | | | - Rahima Patel
- CRUK Manchester Institute, University of Manchester, Manchester M20 4BX, UK
| | - Mairi Challinor
- CRUK Manchester Institute, University of Manchester, Manchester M20 4BX, UK
| | - Kirstie Wallace
- CRUK Manchester Institute, University of Manchester, Manchester M20 4BX, UK
| | - Jane Gilmour
- Institute of Cancer end Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B152TT, UK
| | - Salam A Assi
- Institute of Cancer end Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B152TT, UK
| | - Pierre Cauchy
- Institute of Cancer end Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B152TT, UK
| | - Maarten Hoogenkamp
- Institute of Cancer end Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B152TT, UK
| | - David R Westhead
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Georges Lacaud
- CRUK Manchester Institute, University of Manchester, Manchester M20 4BX, UK
| | - Valerie Kouskoff
- CRUK Manchester Institute, University of Manchester, Manchester M20 4BX, UK
| | - Berthold Göttgens
- Department of Haematology, Cambridge Institute for Medical Research and Wellcome Trust and MRC Cambridge Stem Cell Institute, Cambridge CB2 0XY, UK
| | - Constanze Bonifer
- Institute of Cancer end Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B152TT, UK.
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46
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Bertolino E, Reinitz J, Manu. The analysis of novel distal Cebpa enhancers and silencers using a transcriptional model reveals the complex regulatory logic of hematopoietic lineage specification. Dev Biol 2016; 413:128-44. [PMID: 26945717 DOI: 10.1016/j.ydbio.2016.02.030] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 01/13/2016] [Accepted: 02/15/2016] [Indexed: 11/25/2022]
Abstract
C/EBPα plays an instructive role in the macrophage-neutrophil cell-fate decision and its expression is necessary for neutrophil development. How Cebpa itself is regulated in the myeloid lineage is not known. We decoded the cis-regulatory logic of Cebpa, and two other myeloid transcription factors, Egr1 and Egr2, using a combined experimental-computational approach. With a reporter design capable of detecting both distal enhancers and silencers, we analyzed 46 putative cis-regulatory modules (CRMs) in cells representing myeloid progenitors, and derived early macrophages or neutrophils. In addition to novel enhancers, this analysis revealed a surprisingly large number of silencers. We determined the regulatory roles of 15 potential transcriptional regulators by testing 32,768 alternative sequence-based transcriptional models against CRM activity data. This comprehensive analysis allowed us to infer the cis-regulatory logic for most of the CRMs. Silencer-mediated repression of Cebpa was found to be effected mainly by TFs expressed in non-myeloid lineages, highlighting a previously unappreciated contribution of long-distance silencing to hematopoietic lineage resolution. The repression of Cebpa by multiple factors expressed in alternative lineages suggests that hematopoietic genes are organized into densely interconnected repressive networks instead of hierarchies of mutually repressive pairs of pivotal TFs. More generally, our results demonstrate that de novo cis-regulatory dissection is feasible on a large scale with the aid of transcriptional modeling. Current address: Department of Biology, University of North Dakota, 10 Cornell Street, Stop 9019, Grand Forks, ND 58202-9019, USA.
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Affiliation(s)
- Eric Bertolino
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA.
| | - John Reinitz
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA; Department of Statistics, The University of Chicago, Chicago, IL 60637, USA; Department of Ecology and Evolution and Institute of Genomics and Systems Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Manu
- Department of Ecology and Evolution and Institute of Genomics and Systems Biology, The University of Chicago, Chicago, IL 60637, USA; Department of Biology, University of North Dakota, 10 Cornell Street, Stop 9019, Grand Forks, ND 58202-9019, USA.
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47
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Piper J, Assi SA, Cauchy P, Ladroue C, Cockerill PN, Bonifer C, Ott S. Wellington-bootstrap: differential DNase-seq footprinting identifies cell-type determining transcription factors. BMC Genomics 2015; 16:1000. [PMID: 26608661 PMCID: PMC4658755 DOI: 10.1186/s12864-015-2081-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 10/13/2015] [Indexed: 12/04/2022] Open
Abstract
Background The analysis of differential gene expression is a fundamental tool to relate gene regulation with specific biological processes. Differential binding of transcription factors (TFs) can drive differential gene expression. While DNase-seq data can provide global snapshots of TF binding, tools for detecting differential binding from pairs of DNase-seq data sets are lacking. Results In order to link expression changes with changes in TF binding we introduce the concept of differential footprinting alongside a computational tool. We demonstrate that differential footprinting is associated with differential gene expression and can be used to define cell types by their specific TF occupancy patterns. Conclusions Our new tool, Wellington-bootstrap, will enable the detection of differential TF binding facilitating the study of gene regulatory systems. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2081-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jason Piper
- Warwick Systems Biology Centre, University of Warwick, Coventry, CV4 7AL, UK.,Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, Institute of Biomedical Research, University of Birmingham, Birmingham, B15 2TT, UK
| | - Salam A Assi
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, Institute of Biomedical Research, University of Birmingham, Birmingham, B15 2TT, UK
| | - Pierre Cauchy
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, Institute of Biomedical Research, University of Birmingham, Birmingham, B15 2TT, UK
| | - Christophe Ladroue
- Department of Computer Science, University of Warwick, Coventry, CV4 7AL, UK
| | - Peter N Cockerill
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, Institute of Biomedical Research, University of Birmingham, Birmingham, B15 2TT, UK.
| | - Constanze Bonifer
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, Institute of Biomedical Research, University of Birmingham, Birmingham, B15 2TT, UK.
| | - Sascha Ott
- Warwick Systems Biology Centre, University of Warwick, Coventry, CV4 7AL, UK.
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48
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Lin Q, Chauvistré H, Costa IG, Gusmao EG, Mitzka S, Hänzelmann S, Baying B, Klisch T, Moriggl R, Hennuy B, Smeets H, Hoffmann K, Benes V, Seré K, Zenke M. Epigenetic program and transcription factor circuitry of dendritic cell development. Nucleic Acids Res 2015; 43:9680-93. [PMID: 26476451 PMCID: PMC4787753 DOI: 10.1093/nar/gkv1056] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 10/03/2015] [Indexed: 12/18/2022] Open
Abstract
Dendritic cells (DC) are professional antigen presenting cells that develop from hematopoietic stem cells through successive steps of lineage commitment and differentiation. Multipotent progenitors (MPP) are committed to DC restricted common DC progenitors (CDP), which differentiate into specific DC subsets, classical DC (cDC) and plasmacytoid DC (pDC). To determine epigenetic states and regulatory circuitries during DC differentiation, we measured consecutive changes of genome-wide gene expression, histone modification and transcription factor occupancy during the sequel MPP-CDP-cDC/pDC. Specific histone marks in CDP reveal a DC-primed epigenetic signature, which is maintained and reinforced during DC differentiation. Epigenetic marks and transcription factor PU.1 occupancy increasingly coincide upon DC differentiation. By integrating PU.1 occupancy and gene expression we devised a transcription factor regulatory circuitry for DC commitment and subset specification. The circuitry provides the transcription factor hierarchy that drives the sequel MPP-CDP-cDC/pDC, including Irf4, Irf8, Tcf4, Spib and Stat factors. The circuitry also includes feedback loops inferred for individual or multiple factors, which stabilize distinct stages of DC development and DC subsets. In summary, here we describe the basic regulatory circuitry of transcription factors that drives DC development.
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Affiliation(s)
- Qiong Lin
- Institute for Biomedical Engineering, Department of Cell Biology, RWTH Aachen University Medical School, 52074 Aachen, Germany Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, 52074 Aachen, Germany
| | - Heike Chauvistré
- Institute for Biomedical Engineering, Department of Cell Biology, RWTH Aachen University Medical School, 52074 Aachen, Germany Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, 52074 Aachen, Germany Department of Dermatology, University Hospital Essen, 45147 Essen, Germany
| | - Ivan G Costa
- IZKF Computational Biology Research Group, RWTH Aachen University Medical School, 52074 Aachen, Germany Aachen Institute for Advanced Study in Computational Engineering Science (AICES), RWTH Aachen University, 52062 Aachen, Germany
| | - Eduardo G Gusmao
- IZKF Computational Biology Research Group, RWTH Aachen University Medical School, 52074 Aachen, Germany
| | - Saskia Mitzka
- Institute for Biomedical Engineering, Department of Cell Biology, RWTH Aachen University Medical School, 52074 Aachen, Germany Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, 52074 Aachen, Germany
| | - Sonja Hänzelmann
- IZKF Computational Biology Research Group, RWTH Aachen University Medical School, 52074 Aachen, Germany
| | - Bianka Baying
- Genomics Core Facilities GeneCore, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Theresa Klisch
- Institute for Biomedical Engineering, Department of Cell Biology, RWTH Aachen University Medical School, 52074 Aachen, Germany Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, 52074 Aachen, Germany
| | - Richard Moriggl
- Ludwig Boltzmann Institute for Cancer Research, University of Veterinary Medicine, Medical University Vienna, 1090 Vienna, Austria
| | - Benoit Hennuy
- GIGA-Genomics, University of Liège, 4000 Liège, Belgium
| | - Hubert Smeets
- Department of Genetics and Cell Biology, Maastricht University Medical Center, 6200 MD Maastricht, The Netherlands Research Schools CARIM and GROW, Maastricht University Medical Center, 6200 MD Maastricht, The Netherlands
| | - Kurt Hoffmann
- Institute of Molecular Biotechnology, RWTH Aachen University, 52074 Aachen, Germany
| | - Vladimir Benes
- Genomics Core Facilities GeneCore, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Kristin Seré
- Institute for Biomedical Engineering, Department of Cell Biology, RWTH Aachen University Medical School, 52074 Aachen, Germany Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, 52074 Aachen, Germany
| | - Martin Zenke
- Institute for Biomedical Engineering, Department of Cell Biology, RWTH Aachen University Medical School, 52074 Aachen, Germany Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, 52074 Aachen, Germany
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49
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Metser G, Shin HY, Wang C, Yoo KH, Oh S, Villarino AV, O'Shea JJ, Kang K, Hennighausen L. An autoregulatory enhancer controls mammary-specific STAT5 functions. Nucleic Acids Res 2015; 44:1052-63. [PMID: 26446995 PMCID: PMC4756855 DOI: 10.1093/nar/gkv999] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 09/22/2015] [Indexed: 01/06/2023] Open
Abstract
Signal Transducers and Activators of Transcription (STATs) are principal transcription factors downstream of cytokine receptors. Although STAT5A is expressed in most tissues it remains to be understood why its premier, non-redundant functions are restricted to prolactin-induced mammary gland development and function. We report that the ubiquitously expressed Stat5a/b locus is subject to additional lineage-specific transcriptional control in mammary epithelium. Genome-wide surveys of epigenetic status and transcription factor occupancy uncovered a putative mammary-specific enhancer within the intergenic sequences separating the two Stat5 genes. This region exhibited several hallmarks of genomic enhancers, including DNaseI hypersensitivity, H3K27 acetylation and binding by GR, NFIB, ELF5 and MED1. Mammary-specific STAT5 binding was obtained at two canonical STAT5 binding motifs. CRISPR/Cas9-mediated genome editing was used to delete these sites in mice and determine their biological function. Mutant animals exhibited an 80% reduction of Stat5 levels in mammary epithelium and a concomitant reduction of STAT5-dependent gene expression. Transcriptome analysis identified a class of mammary-restricted genes that was particularly dependent on high STAT5 levels as a result of the intergenic enhancer. Taken together, the mammary-specific enhancer enables a positive feedback circuit that contributes to the remarkable abundance of STAT5 and, in turn, to the efficacy of STAT5-dependent mammary physiology.
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Affiliation(s)
- Gil Metser
- Laboratory of Genetics and Physiology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ha Youn Shin
- Laboratory of Genetics and Physiology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chaochen Wang
- Laboratory of Genetics and Physiology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kyung Hyun Yoo
- Laboratory of Genetics and Physiology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sumin Oh
- Laboratory of Genetics and Physiology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA Department of Microbiology, Dankook University, Cheonan, Chungnam 330-714, Republic of Korea
| | - Alejandro V Villarino
- Molecular Immunology and Inflammation Branch, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
| | - John J O'Shea
- Molecular Immunology and Inflammation Branch, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
| | - Keunsoo Kang
- Department of Microbiology, Dankook University, Cheonan, Chungnam 330-714, Republic of Korea
| | - Lothar Hennighausen
- Laboratory of Genetics and Physiology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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50
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Kim A, Fung E, Parikh SG, Gabayan V, Nemeth E, Ganz T. Isocitrate treatment of acute anemia of inflammation in a mouse model. Blood Cells Mol Dis 2015; 56:31-6. [PMID: 26603720 DOI: 10.1016/j.bcmd.2015.09.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 09/24/2015] [Accepted: 09/24/2015] [Indexed: 12/21/2022]
Abstract
Acute and severe anemia of inflammation (AI) is a common complication of various clinical syndromes, including fulminant infections, critical illness with multiorgan failure, and exacerbations of autoimmune diseases. Building on recent data showing beneficial results with isocitrate treatment for chronic low-grade AI in a rat model, we used a mouse model of acute and severe AI induced by intraperitoneal heat-killed Brucella abortus to determine if isocitrate would be effective in this more stringent application. Inflamed mice treated with isocitrate developed an early but transient improvement in hemoglobin compared to solvent-treated controls, with a robust improvement on day 7, and only a trend towards improvement by day 14. Reticulocyte counts were increased in treated mice transiently, with no significant difference by day 21. Serum erythropoietin (EPO) levels were similar in treated versus control mice, indicating that isocitrate increased sensitivity to EPO. Serum and tissue iron levels showed no significant differences between the treated and control mice, ruling out improved iron availability as the cause of the increased response to endogenous EPO. Compared to the milder rat model, much higher doses of isocitrate were required for a relatively modest benefit.
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Affiliation(s)
- Airie Kim
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA.
| | - Eileen Fung
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA.
| | - Sona G Parikh
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA.
| | - Victoria Gabayan
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA.
| | - Elizabeta Nemeth
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA.
| | - Tomas Ganz
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA; Department of Pathology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA.
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