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Collinson RJ, Wilson L, Boey D, Ng ZY, Mirzai B, Chuah HS, Howman R, Grove CS, Malherbe JAJ, Leahy MF, Linden MD, Fuller KA, Erber WN, Guo BB. Transcription factor 3 is dysregulated in megakaryocytes in myelofibrosis. Platelets 2024; 35:2304173. [PMID: 38303515 DOI: 10.1080/09537104.2024.2304173] [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: 11/15/2023] [Accepted: 01/02/2024] [Indexed: 02/03/2024]
Abstract
Transcription factor 3 (TCF3) is a DNA transcription factor that modulates megakaryocyte development. Although abnormal TCF3 expression has been identified in a range of hematological malignancies, to date, it has not been investigated in myelofibrosis (MF). MF is a Philadelphia-negative myeloproliferative neoplasm (MPN) that can arise de novo or progress from essential thrombocythemia [ET] and polycythemia vera [PV] and where dysfunctional megakaryocytes have a role in driving the fibrotic progression. We aimed to examine whether TCF3 is dysregulated in megakaryocytes in MPN, and specifically in MF. We first assessed TCF3 protein expression in megakaryocytes using an immunohistochemical approach analyses and showed that TCF3 was reduced in MF compared with ET and PV. Further, the TCF3-negative megakaryocytes were primarily located near trabecular bone and had the typical "MF-like" morphology as described by the WHO. Genomic analysis of isolated megakaryocytes showed three mutations, all predicted to result in a loss of function, in patients with MF; none were seen in megakaryocytes isolated from ET or PV marrow samples. We then progressed to transcriptomic sequencing of platelets which showed loss of TCF3 in MF. These proteomic, genomic and transcriptomic analyses appear to indicate that TCF3 is downregulated in megakaryocytes in MF. This infers aberrations in megakaryopoiesis occur in this progressive phase of MPN. Further exploration of this pathway could provide insights into TCF3 and the evolution of fibrosis and potentially lead to new preventative therapeutic targets.
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Affiliation(s)
- Ryan J Collinson
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Lynne Wilson
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Darren Boey
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Zi Yun Ng
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
- Department of Haematology, Royal Perth Hospital, Perth, WA, Australia
| | - Bob Mirzai
- PathWest Laboratory Medicine, Nedlands, WA, Australia
| | - Hun S Chuah
- Department of Haematology, Royal Perth Hospital, Perth, WA, Australia
- PathWest Laboratory Medicine, Nedlands, WA, Australia
- Department of Haematology, Rockingham General Hospital, Rockingham, WA, Australia
| | - Rebecca Howman
- Department of Haematology, Sir Charles Gairdner Hospital Nedlands Australia
| | - Carolyn S Grove
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
- Department of Haematology, Royal Perth Hospital, Perth, WA, Australia
- Department of Haematology, Sir Charles Gairdner Hospital Nedlands Australia
| | | | - Michael F Leahy
- Department of Haematology, Royal Perth Hospital, Perth, WA, Australia
- PathWest Laboratory Medicine, Nedlands, WA, Australia
| | - Matthew D Linden
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Kathryn A Fuller
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Wendy N Erber
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
- PathWest Laboratory Medicine, Nedlands, WA, Australia
| | - Belinda B Guo
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
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2
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Zhao H, Lin Y, Lin E, Liu F, Shu L, Jing D, Wang B, Wang M, Shan F, Zhang L, Lam JC, Midla SC, Giardine BM, Keller CA, Hardison RC, Blobel GA, Zhang H. Genome folding principles uncovered in condensin-depleted mitotic chromosomes. Nat Genet 2024:10.1038/s41588-024-01759-x. [PMID: 38802567 DOI: 10.1038/s41588-024-01759-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 04/18/2024] [Indexed: 05/29/2024]
Abstract
During mitosis, condensin activity is thought to interfere with interphase chromatin structures. To investigate genome folding principles in the absence of chromatin loop extrusion, we codepleted condensin I and condensin II, which triggered mitotic chromosome compartmentalization in ways similar to that in interphase. However, two distinct euchromatic compartments, indistinguishable in interphase, emerged upon condensin loss with different interaction preferences and dependencies on H3K27ac. Constitutive heterochromatin gradually self-aggregated and cocompartmentalized with facultative heterochromatin, contrasting with their separation during interphase. Notably, some cis-regulatory element contacts became apparent even in the absence of CTCF/cohesin-mediated structures. Heterochromatin protein 1 (HP1) proteins, which are thought to partition constitutive heterochromatin, were absent from mitotic chromosomes, suggesting, surprisingly, that constitutive heterochromatin can self-aggregate without HP1. Indeed, in cells traversing from M to G1 phase in the combined absence of HP1α, HP1β and HP1γ, constitutive heterochromatin compartments are normally re-established. In sum, condensin-deficient mitotic chromosomes illuminate forces of genome compartmentalization not identified in interphase cells.
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Affiliation(s)
- Han Zhao
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Yinzhi Lin
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
| | - En Lin
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Fuhai Liu
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Lirong Shu
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Dannan Jing
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
- Department of Biology, College of Science, Shantou University, Shantou, China
| | - Baiyue Wang
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Manzhu Wang
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
- School of Basic Medicine, Capital Medical University, Beijing, China
| | - Fengnian Shan
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
- School of Pharmacology, South China University of Technology, Guangzhou, China
| | - Lin Zhang
- School of Biological Science, Hongkong University, Hongkong, China
| | - Jessica C Lam
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Susannah C Midla
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Belinda M Giardine
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Cheryl A Keller
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Gerd A Blobel
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Haoyue Zhang
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China.
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3
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Ding B, Mao Y, Li Y, Xin M, Jiang S, Hu X, Xu Q, Ding Q, Wang X. A novel GATA1 variant p.G229D causing the defect of procoagulant platelet formation. Thromb Res 2024; 234:39-50. [PMID: 38159323 DOI: 10.1016/j.thromres.2023.12.015] [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: 06/05/2023] [Revised: 12/19/2023] [Accepted: 12/19/2023] [Indexed: 01/03/2024]
Abstract
INTRODUCTION GATA1 is one of the master transcription factors in hematopoietic lineages development which is crucial for megakaryocytic differentiation and maturation. Previous studies have shown that distinct GATA1 variants are associated with varying severities of macrothrombocytopenia and platelet dysfunction. OBJECTIVE To determine the underlying pathological mechanisms of a novel GATA1 variant (c. 686G > A, p. G229D) in a patient with recurrent traumatic muscle hematomas. METHODS Comprehensive phenotypic analysis of the patient platelets was performed. Procoagulant platelet formation and function were detected using flow cytometry assay and thrombin generation test (TGT), respectively. The ANO6 expression was measured by qPCR and western blot. The intracellular supramaximal calcium flux was detected by Fluo-5N fluorescent assay. RESULTS The patient displayed mild macrothrombocytopenia with defects of platelet granules, aggregation, and integrin αIIbβ3 activation. The percentage of the procoagulant platelet formation of the patient upon the stimulation of thrombin plus collagen was lower than that of the healthy controls (40.9 % vs 49.0 % ± 5.1 %). The patient platelets exhibited a marked reduction of thrombin generation in platelet rich plasma TGT compared to the healthy controls (peak value: ∼70 % of the healthy controls; the endogenous thrombin potential: ∼40 % of the healthy controls). The expression of ANO6 and intracellular calcium flux were impaired, which together with abnormal granules of the patient platelets might contribute to defect of procoagulant platelet function. CONCLUSIONS The G229D variant could lead to a novel platelet phenotype characterized by defective procoagulant platelet formation and function, which extended the range of GATA1 variants associated platelet disorders.
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Affiliation(s)
- Biying Ding
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China; State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yinqi Mao
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China; State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yang Li
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China; State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Min Xin
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Shifeng Jiang
- State Key Laboratory of Microbial Metabolism & Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaobo Hu
- Department of Molecular Biology, Shanghai Center for Clinical Laboratory, Shanghai, China
| | - Qin Xu
- State Key Laboratory of Microbial Metabolism & Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
| | - Qiulan Ding
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China; Collaborative Innovation Center of Hematology, Shanghai Jiaotong University School of Medicine, Shanghai, China.
| | - Xuefeng Wang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China; Collaborative Innovation Center of Hematology, Shanghai Jiaotong University School of Medicine, Shanghai, China.
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Payne S, Neal A, De Val S. Transcription factors regulating vasculogenesis and angiogenesis. Dev Dyn 2024; 253:28-58. [PMID: 36795082 PMCID: PMC10952167 DOI: 10.1002/dvdy.575] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 02/06/2023] [Accepted: 02/06/2023] [Indexed: 02/17/2023] Open
Abstract
Transcription factors (TFs) play a crucial role in regulating the dynamic and precise patterns of gene expression required for the initial specification of endothelial cells (ECs), and during endothelial growth and differentiation. While sharing many core features, ECs can be highly heterogeneous. Differential gene expression between ECs is essential to pattern the hierarchical vascular network into arteries, veins and capillaries, to drive angiogenic growth of new vessels, and to direct specialization in response to local signals. Unlike many other cell types, ECs have no single master regulator, instead relying on differing combinations of a necessarily limited repertoire of TFs to achieve tight spatial and temporal activation and repression of gene expression. Here, we will discuss the cohort of TFs known to be involved in directing gene expression during different stages of mammalian vasculogenesis and angiogenesis, with a primary focus on development.
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Affiliation(s)
- Sophie Payne
- Department of Physiology, Anatomy and GeneticsInstitute of Developmental and Regenerative Medicine, University of OxfordOxfordUK
| | - Alice Neal
- Department of Physiology, Anatomy and GeneticsInstitute of Developmental and Regenerative Medicine, University of OxfordOxfordUK
| | - Sarah De Val
- Department of Physiology, Anatomy and GeneticsInstitute of Developmental and Regenerative Medicine, University of OxfordOxfordUK
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5
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Zhao H, Lin Y, Lin E, Liu F, Shu L, Jing D, Wang B, Wang M, Shan F, Zhang L, Lam JC, Midla SC, Giardine BM, Keller CA, Hardison RC, Blobel GA, Zhang H. Genome folding principles revealed in condensin-depleted mitotic chromosomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.09.566494. [PMID: 38014261 PMCID: PMC10680603 DOI: 10.1101/2023.11.09.566494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
During mitosis, condensin activity interferes with interphase chromatin structures. Here, we generated condensin-free mitotic chromosomes to investigate genome folding principles. Co- depletion of condensin I and II, but neither alone, triggered mitotic chromosome compartmentalization in ways that differ from interphase. Two distinct euchromatic compartments, indistinguishable in interphase, rapidly emerged upon condensin loss with different interaction preferences and dependence on H3K27ac. Constitutive heterochromatin gradually self-aggregated and co-compartmentalized with the facultative heterochromatin, contrasting with their separation during interphase. While topologically associating domains (TADs) and CTCF/cohesin mediated structural loops remained undetectable, cis-regulatory element contacts became apparent, providing an explanation for their quick re-establishment during mitotic exit. HP1 proteins, which are thought to partition constitutive heterochromatin, were absent from mitotic chromosomes, suggesting, surprisingly, that constitutive heterochromatin can self-aggregate without HP1. Indeed, in cells traversing from M- to G1-phase in the combined absence of HP1α, HP1Π and HP1γ, re-established constitutive heterochromatin compartments normally. In sum, "clean-slate" condensin-deficient mitotic chromosomes illuminate mechanisms of genome compartmentalization not revealed in interphase cells.
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6
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Yu CH, Yang SQ, Zhang YJ, Rong L, Yi ZC. The role of GATA switch in benzene metabolite hydroquinone inhibiting erythroid differentiation in K562 cells. Arch Toxicol 2023; 97:2169-2181. [PMID: 37329354 DOI: 10.1007/s00204-023-03541-0] [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: 04/20/2023] [Accepted: 06/06/2023] [Indexed: 06/19/2023]
Abstract
The phenolic metabolite of benzene, hydroquinone (HQ), has potential risks for hematological disorders and hematotoxicity in humans. Previous studies have revealed that reactive oxygen species, DNA methylation, and histone acetylation participate in benzene metabolites inhibiting erythroid differentiation in hemin-induced K562 cells. GATA1 and GATA2 are crucial erythroid-specific transcription factors that exhibit dynamic expression patterns during erythroid differentiation. We investigated the role of GATA factors in HQ-inhibited erythroid differentiation in K562 cells. When K562 cells were induced with 40 μM hemin for 0-120 h, the mRNA and protein levels of GATA1 and GATA2 changed dynamically. After exposure to 40 μM HQ for 72 h, K562 cells were induced with 40 μM hemin for 48 h. HQ considerably reduced the percentage of hemin-induced Hb-positive cells, decreased the GATA1 mRNA, protein, and occupancy levels at α-globin and β-globin gene clusters, and increased the GATA2 mRNA and protein levels significantly. ChIP-seq analysis revealed that HQ reduced GATA1 occupancy, and increased GATA2 occupancy at most gene loci in hemin-induced K562 cells. And GATA1 and GATA2 might play essential roles in the erythroid differentiation protein interaction network. These results elucidate that HQ decreases GATA1 occupancy and increases GATA2 occupancy at the erythroid gene loci, thereby downregulating GATA1 and upregulating GATA2 expression, which in turn modulates the expression of erythroid genes and inhibits erythroid differentiation. This partially explains the mechanism of benzene hematotoxicity.
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Affiliation(s)
- Chun-Hong Yu
- School of Engineering Medicine, Beihang University, Beijing, 100191, China
| | - Shui-Qing Yang
- School of Biological Science and Medical Engineering, Beihang University, 37 Xueyuan Road, Beijing, 100191, China
- Department of Rehabilitation, Beijing Rehabilitation Hospital, Capital Medical University, Beijing, 100043, China
| | - Yu-Jing Zhang
- School of Biological Science and Medical Engineering, Beihang University, 37 Xueyuan Road, Beijing, 100191, China
| | - Long Rong
- School of Biological Science and Medical Engineering, Beihang University, 37 Xueyuan Road, Beijing, 100191, China
| | - Zong-Chun Yi
- School of Biological Science and Medical Engineering, Beihang University, 37 Xueyuan Road, Beijing, 100191, China.
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7
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Lynch AW, Brown M, Meyer CA. Multi-batch single-cell comparative atlas construction by deep learning disentanglement. Nat Commun 2023; 14:4126. [PMID: 37433791 DOI: 10.1038/s41467-023-39494-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 06/15/2023] [Indexed: 07/13/2023] Open
Abstract
Cell state atlases constructed through single-cell RNA-seq and ATAC-seq analysis are powerful tools for analyzing the effects of genetic and drug treatment-induced perturbations on complex cell systems. Comparative analysis of such atlases can yield new insights into cell state and trajectory alterations. Perturbation experiments often require that single-cell assays be carried out in multiple batches, which can introduce technical distortions that confound the comparison of biological quantities between different batches. Here we propose CODAL, a variational autoencoder-based statistical model which uses a mutual information regularization technique to explicitly disentangle factors related to technical and biological effects. We demonstrate CODAL's capacity for batch-confounded cell type discovery when applied to simulated datasets and embryonic development atlases with gene knockouts. CODAL improves the representation of RNA-seq and ATAC-seq modalities, yields interpretable modules of biological variation, and enables the generalization of other count-based generative models to multi-batched data.
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Affiliation(s)
- Allen W Lynch
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Myles Brown
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Clifford A Meyer
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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8
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Phelan KJ, Dill-McFarland KA, Kothari A, Segnitz RM, Burkle J, Grashel B, Jenkins S, Spagna D, Martin LJ, Haslam DB, Biagini JM, Kalra M, McCoy KS, Ross KR, Jackson DJ, Mersha TB, Altman MC, Khurana Hershey GK. Airway transcriptome networks identify susceptibility to frequent asthma exacerbations in children. J Allergy Clin Immunol 2023; 152:73-83. [PMID: 36918038 PMCID: PMC10395049 DOI: 10.1016/j.jaci.2023.02.031] [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: 09/15/2022] [Revised: 01/11/2023] [Accepted: 02/01/2023] [Indexed: 03/14/2023]
Abstract
BACKGROUND Frequent asthma exacerbators, defined as those experiencing more than 1 hospitalization in a year for an asthma exacerbation, represent an important subgroup of individuals with asthma. However, this group remains poorly defined and understudied in children. OBJECTIVE Our aim was to determine the molecular mechanisms underlying asthma pathogenesis and exacerbation frequency. METHODS We performed RNA sequencing of upper airway cells from both frequent and nonfrequent exacerbators enrolled in the Ohio Pediatric Asthma Repository. RESULTS Through molecular network analysis, we found that nonfrequent exacerbators display an increase in modules enriched for immune system processes, including type 2 inflammation and response to infection. In contrast, frequent exacerbators showed expression of modules enriched for nervous system processes, such as synaptic formation and axonal outgrowth. CONCLUSION These data suggest that the upper airway of frequent exacerbators undergoes peripheral nervous system remodeling, representing a novel mechanism underlying pediatric asthma exacerbation.
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Affiliation(s)
- Kieran J Phelan
- Divison of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Medical Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | | | - Arjun Kothari
- Divison of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - R Max Segnitz
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, Wash
| | - Jeff Burkle
- Divison of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Brittany Grashel
- Divison of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Seth Jenkins
- Divison of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Daniel Spagna
- Divison of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Lisa J Martin
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - David B Haslam
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio; Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Jocelyn M Biagini
- Divison of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Maninder Kalra
- Department of Pediatrics, Dayton Children's Hospital, Dayton, Ohio
| | - Karen S McCoy
- Division of Pediatric Pulmonology, Nationwide Children's Hospital, Columbus; Ohio
| | - Kristie R Ross
- Department of Pediatrics-Pulmonary, Rainbow Babies and Children's Hospital, Cleveland, Ohio
| | - Daniel J Jackson
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wis
| | - Tesfaye B Mersha
- Divison of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Matthew C Altman
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, Wash; Systems Immunology Program, Benaroya Research Institute, Seattle, Wash
| | - Gurjit K Khurana Hershey
- Divison of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio.
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9
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Chen Z, Javed N, Moore M, Wu J, Sun G, Vinyard M, Collins A, Pinello L, Najm FJ, Bernstein BE. Integrative dissection of gene regulatory elements at base resolution. CELL GENOMICS 2023; 3:100318. [PMID: 37388913 PMCID: PMC10300548 DOI: 10.1016/j.xgen.2023.100318] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 02/21/2023] [Accepted: 03/31/2023] [Indexed: 07/01/2023]
Abstract
Although vast numbers of putative gene regulatory elements have been cataloged, the sequence motifs and individual bases that underlie their functions remain largely unknown. Here, we combine epigenetic perturbations, base editing, and deep learning to dissect regulatory sequences within the exemplar immune locus encoding CD69. We converge on a ∼170 base interval within a differentially accessible and acetylated enhancer critical for CD69 induction in stimulated Jurkat T cells. Individual C-to-T base edits within the interval markedly reduce element accessibility and acetylation, with corresponding reduction of CD69 expression. The most potent base edits may be explained by their effect on regulatory interactions between the transcriptional activators GATA3 and TAL1 and the repressor BHLHE40. Systematic analysis suggests that the interplay between GATA3 and BHLHE40 plays a general role in rapid T cell transcriptional responses. Our study provides a framework for parsing regulatory elements in their endogenous chromatin contexts and identifying operative artificial variants.
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Affiliation(s)
- Zeyu Chen
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Gene Regulation Observatory, Broad Institute, Cambridge, MA, USA
- Department of Cell Biology and Pathology, Harvard Medical School, Boston, MA, USA
| | - Nauman Javed
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Gene Regulation Observatory, Broad Institute, Cambridge, MA, USA
- Department of Cell Biology and Pathology, Harvard Medical School, Boston, MA, USA
| | - Molly Moore
- Gene Regulation Observatory, Broad Institute, Cambridge, MA, USA
| | - Jingyi Wu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Gene Regulation Observatory, Broad Institute, Cambridge, MA, USA
- Department of Cell Biology and Pathology, Harvard Medical School, Boston, MA, USA
| | - Gary Sun
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Cell Biology and Pathology, Harvard Medical School, Boston, MA, USA
| | - Michael Vinyard
- Gene Regulation Observatory, Broad Institute, Cambridge, MA, USA
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | | | - Luca Pinello
- Gene Regulation Observatory, Broad Institute, Cambridge, MA, USA
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Fadi J. Najm
- Gene Regulation Observatory, Broad Institute, Cambridge, MA, USA
| | - Bradley E. Bernstein
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Gene Regulation Observatory, Broad Institute, Cambridge, MA, USA
- Department of Cell Biology and Pathology, Harvard Medical School, Boston, MA, USA
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10
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Qiu Q, Sun Y, Yang L, Li Q, Feng Y, Li M, Yin Y, Zheng L, Li N, Qiu H, Cui X, He W, Wang B, Pan C, Wang Z, Huang J, Sample KM, Li Z, Hu Y. TSPAN32 suppresses chronic myeloid leukemia pathogenesis and progression by stabilizing PTEN. Signal Transduct Target Ther 2023; 8:90. [PMID: 36854750 PMCID: PMC9974991 DOI: 10.1038/s41392-022-01290-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/16/2022] [Accepted: 12/02/2022] [Indexed: 03/02/2023] Open
Abstract
We report herein that TSPAN32 is a key node factor for Philadelphia (Ph+) leukemia pathogenesis. We found that TSPAN32 expression was repressed by BCR-ABL and ectopic TSPAN32 expression upon Imatinib treatment inhibited the proliferation of Ph+ cell lines. Tspan32 overexpression significantly prevented BCR-ABL induced leukemia progression in a murine model and impaired leukemia stem cell (LSC) proliferation. LSCs represent an obstacle for chronic myeloid leukemia (CML) elimination, which continually replenish leukemia cells and are associated with disease relapse. Therefore, the identification of essential targets that contribute to the survival and self-renewal of LSCs is important for novel curative CML. Mechanistically, TSPAN32 was shown to interact with PTEN, increased its protein level and caused a reduction in PI3K-AKT signaling activity. We also found that TSPAN32 was repressed by BCR-ABL via the suppression of an important transcription factor, TAL1. Ectopic expression of TAL1 significantly increased TSPAN32 mRNA and protein level, which indicated that BCR-ABL repressed TSPAN32 transcription by decreasing TAL1 expression. Overall, we identified a new signaling axis composed of "BCR-ABL-TAL1-TSPAN32-PTEN-PI3K-AKT". Our findings further complement the known mechanisms underlying the transformation potential of BCR-ABL in CML pathogenesis. This new signaling axis also provides a potential means to target PI3K-AKT for CML treatment.
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Affiliation(s)
- Qiang Qiu
- Department of Thyroid Surgery, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, China
| | - Yuanyuan Sun
- Department of Thyroid Surgery, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, China
| | - Linyu Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, China
| | - Qingqing Li
- Department of Thyroid Surgery, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, China
| | - Yunyu Feng
- Department of Thyroid Surgery, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, China
| | - Mengyuan Li
- Department of Thyroid Surgery, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, China
| | - Yuexia Yin
- Department of Thyroid Surgery, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, China
| | - Li Zheng
- Department of Thyroid Surgery, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, China
| | - Ning Li
- Department of Thyroid Surgery, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, China
| | - Huandi Qiu
- Department of Thyroid Surgery, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, China
| | - Xue Cui
- Department of Thyroid Surgery, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, China
| | - Wei He
- Department of Thyroid Surgery, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, China
| | - Bochuan Wang
- Department of Thyroid Surgery, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, China
| | - Cong Pan
- Department of Thyroid Surgery, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, China
| | - Zi Wang
- Department of Oncology, Guizhou Provincial People's Hospital, Guiyang, Guizhou, China
| | - Juan Huang
- Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Klarke M Sample
- Institute of Life Science, eBond Pharmaceutical Technology Ltd., Chengdu, China
| | - Zhihui Li
- Laboratory of thyroid and parathyroid disease, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Thyroid Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yiguo Hu
- Department of Thyroid Surgery, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, China.
- Department of Thyroid Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
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11
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Chakraborty S, Andrieux G, Kastl P, Adlung L, Altamura S, Boehm ME, Schwarzmüller LE, Abdullah Y, Wagner MC, Helm B, Gröne HJ, Lehmann WD, Boerries M, Busch H, Muckenthaler MU, Schilling M, Klingmüller U. Erythropoietin-driven dynamic proteome adaptations during erythropoiesis prevent iron overload in the developing embryo. Cell Rep 2022; 40:111360. [PMID: 36130519 DOI: 10.1016/j.celrep.2022.111360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/22/2022] [Accepted: 08/23/2022] [Indexed: 11/26/2022] Open
Abstract
Erythropoietin (Epo) ensures survival and proliferation of colony-forming unit erythroid (CFU-E) progenitor cells and their differentiation to hemoglobin-containing mature erythrocytes. A lack of Epo-induced responses causes embryonic lethality, but mechanisms regulating the dynamic communication of cellular alterations to the organismal level remain unresolved. By time-resolved transcriptomics and proteomics, we show that Epo induces in CFU-E cells a gradual transition from proliferation signature proteins to proteins indicative for differentiation, including heme-synthesis enzymes. In the absence of the Epo receptor (EpoR) in embryos, we observe a lack of hemoglobin in CFU-E cells and massive iron overload of the fetal liver pointing to a miscommunication between liver and placenta. A reduction of iron-sulfur cluster-containing proteins involved in oxidative phosphorylation in these embryos leads to a metabolic shift toward glycolysis. This link connecting erythropoiesis with the regulation of iron homeostasis and metabolic reprogramming suggests that balancing these interactions is crucial for protection from iron intoxication and for survival.
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Affiliation(s)
- Sajib Chakraborty
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Systems Cell-Signalling Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka 1000, Bangladesh
| | - Geoffroy Andrieux
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany; German Cancer Consortium (DKTK), Freiburg, Germany and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Philipp Kastl
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Lorenz Adlung
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Department of Medicine & Hamburg Center for Translational Immunology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Sandro Altamura
- Center for Translational Biomedical Iron Research (CeTBI), Department of Pediatric Hematology, Oncology and Immunology, Heidelberg University, 69120 Heidelberg, Germany
| | - Martin E Boehm
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Luisa E Schwarzmüller
- Division Molecular Genome Analysis, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Yomn Abdullah
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Marie-Christine Wagner
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Barbara Helm
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Hermann-Josef Gröne
- Division Cellular and Molecular Pathology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Wolf D Lehmann
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Melanie Boerries
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany; German Cancer Consortium (DKTK), Freiburg, Germany and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Comprehensive Cancer Center Freiburg (CCCF), Medical Center-University of Freiburg, University of Freiburg, 79106 Freiburg im Breisgau, Germany.
| | - Hauke Busch
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany; Institute of Experimental Dermatology, University of Lübeck, 23562 Lübeck, Germany.
| | - Martina U Muckenthaler
- Center for Translational Biomedical Iron Research (CeTBI), Department of Pediatric Hematology, Oncology and Immunology, Heidelberg University, 69120 Heidelberg, Germany; Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), 69120 Heidelberg, Germany; German Center for Cardiovascular Research, Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany.
| | - Marcel Schilling
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
| | - Ursula Klingmüller
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), 69120 Heidelberg, Germany.
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12
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Chen M, Zhang Y, Jiang K, Wang W, Feng H, Zhen R, Moo C, Zhang Z, Shi J, Chen C. Grab regulates transferrin receptor recycling and iron uptake in developing erythroblasts. Blood 2022; 140:1145-1155. [PMID: 35820059 DOI: 10.1182/blood.2021015189] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 06/25/2022] [Indexed: 11/20/2022] Open
Abstract
Developing erythroblasts acquire massive amounts of iron through the transferrin (Tf) cycle, which involves endocytosis, sorting, and recycling of the Tf-Tf receptor (Tfrc) complex. Previous studies on the hemoglobin-deficit (hbd) mouse have shown that the exocyst complex is indispensable for the Tfrc recycling; however, the precise mechanism underlying the efficient exocytosis and recycling of Tfrc in erythroblasts remains unclear. Here, we identify the guanine nucleotide exchange factor Grab as a critical regulator of the Tf cycle and iron metabolism during erythropoiesis. Grab is highly expressed in differentiating erythroblasts. Loss of Grab diminishes the Tfrc recycling and iron uptake, leading to hemoglobinization defects in mouse primary erythroblasts, mammalian erythroleukemia cells, and zebrafish embryos. These defects can be alleviated by supplementing iron together with hinokitiol, a small-molecule natural compound that can mediate iron transport independent of the Tf cycle. Mechanistically, Grab regulates the exocytosis of Tfrc-associated vesicles by activating the GTPase Rab8, which subsequently promotes the recruitment of the exocyst complex and vesicle exocytosis. Our results reveal a critical role for Grab in regulating the Tf cycle and provide new insights into iron homeostasis and erythropoiesis.
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Affiliation(s)
- Mengying Chen
- Ministry of Education Key Laboratory of Biosystems Homeostasis and Protection, Institute of Cell and Developmental Biology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yuhan Zhang
- Ministry of Education Key Laboratory of Biosystems Homeostasis and Protection, Institute of Cell and Developmental Biology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Kailun Jiang
- Ministry of Education Key Laboratory of Biosystems Homeostasis and Protection, Institute of Cell and Developmental Biology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Weixi Wang
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - He Feng
- Ministry of Education Key Laboratory of Biosystems Homeostasis and Protection, Institute of Cell and Developmental Biology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Ru Zhen
- Ministry of Education Key Laboratory of Biosystems Homeostasis and Protection, Institute of Cell and Developmental Biology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Chingyee Moo
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Zhuonan Zhang
- Ministry of Education Key Laboratory of Biosystems Homeostasis and Protection, Institute of Cell and Developmental Biology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jiahai Shi
- Synthetic Biology Translational Research Programs, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; and
| | - Caiyong Chen
- Ministry of Education Key Laboratory of Biosystems Homeostasis and Protection, Institute of Cell and Developmental Biology, College of Life Sciences, Zhejiang University, Hangzhou, China
- Cancer Center, Zhejiang University, Hangzhou, China
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13
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Ohmori S, Takai J, Uemura S, Otsuki A, Mori T, Ohneda K, Moriguchi T. The Il6 -39 kb enhancer containing clustered GATA2- and PU.1-binding sites is essential for Il6 expression in murine mast cells. iScience 2022; 25:104942. [PMID: 36072552 PMCID: PMC9442365 DOI: 10.1016/j.isci.2022.104942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 06/17/2022] [Accepted: 08/11/2022] [Indexed: 11/13/2022] Open
Abstract
Mast cells serve as a first-line defense of innate immunity. Interleukin-6 (IL-6) induced by bacterial lipopolysaccharide (LPS) in mast cells plays a crucial role in antibacterial protection. The zinc finger transcription factor GATA2 cooperatively functions with the ETS family transcription factor PU.1 in multiple mast cell activities. However, the regulatory landscape directed by GATA2 and PU.1 under inflammation remains elusive. We herein showed that a large proportion of GATA2-binding peaks were closely located with PU.1-binding peaks in distal cis-regulatory regions of inflammatory cytokine genes in mast cells. Notably, GATA2 and PU.1 played crucial roles in promoting LPS-mediated inflammatory cytokine production. Genetic ablation of GATA2-PU.1-clustered binding sites at the Il6 -39 kb region revealed its central role in LPS-induced Il6 expression in mast cells. We demonstrate a novel collaborative activity of GATA2 and PU.1 in cytokine induction upon inflammatory stimuli via the GATA2-PU.1 overlapping sites in the distal cis-regulatory regions. GATA2- and PU.1-binding peaks are closely located in distal enhancers of cytokine genes GATA2 and PU.1 play crucial roles in promoting LPS-mediated cytokine induction The Il6 -39 kb enhancer containing GATA2 and PU.1 motifs are crucial for Il6 induction GATA2 inhibitor exerts anti-inflammatory effects via reducing cytokine induction
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14
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Huang P, Peslak SA, Ren R, Khandros E, Qin K, Keller CA, Giardine B, Bell HW, Lan X, Sharma M, Horton JR, Abdulmalik O, Chou ST, Shi J, Crossley M, Hardison RC, Cheng X, Blobel GA. HIC2 controls developmental hemoglobin switching by repressing BCL11A transcription. Nat Genet 2022; 54:1417-1426. [PMID: 35941187 PMCID: PMC9940634 DOI: 10.1038/s41588-022-01152-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 07/05/2022] [Indexed: 02/02/2023]
Abstract
The fetal-to-adult switch in hemoglobin production is a model of developmental gene control with relevance to the treatment of hemoglobinopathies. The expression of transcription factor BCL11A, which represses fetal β-type globin (HBG) genes in adult erythroid cells, is predominantly controlled at the transcriptional level but the underlying mechanism is unclear. We identify HIC2 as a repressor of BCL11A transcription. HIC2 and BCL11A are reciprocally expressed during development. Forced expression of HIC2 in adult erythroid cells inhibits BCL11A transcription and induces HBG expression. HIC2 binds to erythroid BCL11A enhancers to reduce chromatin accessibility and binding of transcription factor GATA1, diminishing enhancer activity and enhancer-promoter contacts. DNA-binding and crystallography studies reveal direct steric hindrance as one mechanism by which HIC2 inhibits GATA1 binding at a critical BCL11A enhancer. Conversely, loss of HIC2 in fetal erythroblasts increases enhancer accessibility, GATA1 binding and BCL11A transcription. HIC2 emerges as an evolutionarily conserved regulator of hemoglobin switching via developmental control of BCL11A.
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Affiliation(s)
- Peng Huang
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| | - Scott A. Peslak
- Division of Hematology, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA.,Division of Hematology/Oncology, Department of Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | - Ren Ren
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Eugene Khandros
- Division of Hematology, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kunhua Qin
- Division of Hematology, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Cheryl A. Keller
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA.,Genomics Research Incubator, Pennsylvania State University, University Park, PA, USA
| | - Belinda Giardine
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Henry W. Bell
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Xianjiang Lan
- Division of Hematology, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Malini Sharma
- Division of Hematology, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - John R. Horton
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Osheiza Abdulmalik
- Division of Hematology, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Stella T. Chou
- Division of Hematology, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Junwei Shi
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Merlin Crossley
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Ross C. Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Gerd A. Blobel
- Division of Hematology, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Correspondence and requests for materials should be addressed to Peng Huang or Gerd A. Blobel. ;
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15
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Differential Etv2 threshold requirement for endothelial and erythropoietic development. Cell Rep 2022; 39:110881. [PMID: 35649376 PMCID: PMC9203129 DOI: 10.1016/j.celrep.2022.110881] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 02/23/2022] [Accepted: 05/06/2022] [Indexed: 11/21/2022] Open
Abstract
Endothelial and erythropoietic lineages arise from a common developmental progenitor. Etv2 is a master transcriptional regulator required for the development of both lineages. However, the mechanisms through which Etv2 initiates the gene-regulatory networks (GRNs) for endothelial and erythropoietic specification and how the two GRNs diverge downstream of Etv2 remain incompletely understood. Here, by analyzing a hypomorphic Etv2 mutant, we demonstrate different threshold requirements for initiation of the downstream GRNs for endothelial and erythropoietic development. We show that Etv2 functions directly in a coherent feedforward transcriptional network for vascular endothelial development, and a low level of Etv2 expression is sufficient to induce and sustain the endothelial GRN. In contrast, Etv2 induces the erythropoietic GRN indirectly via activation of Tal1, which requires a significantly higher threshold of Etv2 to initiate and sustain erythropoietic development. These results provide important mechanistic insight into the divergence of the endothelial and erythropoietic lineages.
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16
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Safi F, Dhapola P, Warsi S, Sommarin M, Erlandsson E, Ungerbäck J, Warfvinge R, Sitnicka E, Bryder D, Böiers C, Thakur RK, Karlsson G. Concurrent stem- and lineage-affiliated chromatin programs precede hematopoietic lineage restriction. Cell Rep 2022; 39:110798. [PMID: 35545037 DOI: 10.1016/j.celrep.2022.110798] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 12/20/2021] [Accepted: 04/15/2022] [Indexed: 01/06/2023] Open
Abstract
The emerging notion of hematopoietic stem and progenitor cells (HSPCs) as a low-primed cloud without sharply demarcated gene expression programs raises the question on how cellular-fate options emerge and at which stem-like stage lineage priming is initiated. Here, we investigate single-cell chromatin accessibility of Lineage-, cKit+, and Sca1+ (LSK) HSPCs spanning the early differentiation landscape. Application of a signal-processing algorithm to detect transition points corresponding to massive alterations in accessibility of 571 transcription factor motifs reveals a population of LSK FMS-like tyrosine kinase 3 (Flt3)intCD9high cells that concurrently display stem-like and lineage-affiliated chromatin signatures, pointing to a simultaneous gain of both lympho-myeloid and megakaryocyte-erythroid programs. Molecularly and functionally, these cells position between stem cells and committed progenitors and display multi-lineage capacity in vitro and in vivo but lack self-renewal activity. This integrative molecular analysis resolves the heterogeneity of cells along hematopoietic differentiation and permits investigation of chromatin-mediated transition between multipotency and lineage restriction.
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Affiliation(s)
- Fatemeh Safi
- Division of Molecular Hematology, Lund Stem Cell Center, Lund University, BMC B12, 22184 Lund, Sweden
| | - Parashar Dhapola
- Division of Molecular Hematology, Lund Stem Cell Center, Lund University, BMC B12, 22184 Lund, Sweden
| | - Sarah Warsi
- Division of Molecular Hematology, Lund Stem Cell Center, Lund University, BMC B12, 22184 Lund, Sweden
| | - Mikael Sommarin
- Division of Molecular Hematology, Lund Stem Cell Center, Lund University, BMC B12, 22184 Lund, Sweden
| | - Eva Erlandsson
- Division of Molecular Hematology, Lund Stem Cell Center, Lund University, BMC B12, 22184 Lund, Sweden
| | - Jonas Ungerbäck
- Division of Molecular Hematology, Lund Stem Cell Center, Lund University, BMC B12, 22184 Lund, Sweden
| | - Rebecca Warfvinge
- Division of Molecular Hematology, Lund Stem Cell Center, Lund University, BMC B12, 22184 Lund, Sweden
| | - Ewa Sitnicka
- Division of Molecular Hematology, Lund Stem Cell Center, Lund University, BMC B12, 22184 Lund, Sweden
| | - David Bryder
- Division of Molecular Hematology, Lund Stem Cell Center, Lund University, BMC B12, 22184 Lund, Sweden
| | - Charlotta Böiers
- Division of Molecular Hematology, Lund Stem Cell Center, Lund University, BMC B12, 22184 Lund, Sweden
| | - Ram Krishna Thakur
- Division of Molecular Hematology, Lund Stem Cell Center, Lund University, BMC B12, 22184 Lund, Sweden.
| | - Göran Karlsson
- Division of Molecular Hematology, Lund Stem Cell Center, Lund University, BMC B12, 22184 Lund, Sweden.
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17
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Umemoto T, Johansson A, Ahmad SAI, Hashimoto M, Kubota S, Kikuchi K, Odaka H, Era T, Kurotaki D, Sashida G, Suda T. ATP citrate lyase controls hematopoietic stem cell fate and supports bone marrow regeneration. EMBO J 2022; 41:e109463. [PMID: 35229328 PMCID: PMC9016348 DOI: 10.15252/embj.2021109463] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 01/21/2022] [Accepted: 01/25/2022] [Indexed: 01/08/2023] Open
Abstract
In order to support bone marrow regeneration after myeloablation, hematopoietic stem cells (HSCs) actively divide to provide both stem and progenitor cells. However, the mechanisms regulating HSC function and cell fate choice during hematopoietic recovery remain unclear. We herein provide novel insights into HSC regulation during regeneration by focusing on mitochondrial metabolism and ATP citrate lyase (ACLY). After 5-fluorouracil-induced myeloablation, HSCs highly expressing endothelial protein C receptor (EPCRhigh ) were enriched within the stem cell fraction at the expense of more proliferative EPCRLow HSCs. These EPCRHigh HSCs were initially more primitive than EPCRLow HSCs and enabled stem cell expansion by enhancing histone acetylation, due to increased activity of ACLY in the early phase of hematopoietic regeneration. In the late phase of recovery, HSCs enhanced differentiation potential by increasing the accessibility of cis-regulatory elements in progenitor cell-related genes, such as CD48. In conditions of reduced mitochondrial metabolism and ACLY activity, these HSCs maintained stem cell phenotypes, while ACLY-dependent histone acetylation promoted differentiation into CD48+ progenitor cells. Collectively, these results indicate that the dynamic control of ACLY-dependent metabolism and epigenetic alterations is essential for HSC regulation during hematopoietic regeneration.
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Affiliation(s)
- Terumasa Umemoto
- Laboratory of Hematopoietic Stem Cell EngineeringInternational Research Center for Medical SciencesKumamoto UniversityKumamotoJapan
| | - Alban Johansson
- Laboratory of Hematopoietic Stem Cell EngineeringInternational Research Center for Medical SciencesKumamoto UniversityKumamotoJapan
| | - Shah Adil Ishtiyaq Ahmad
- Laboratory of Hematopoietic Stem Cell EngineeringInternational Research Center for Medical SciencesKumamoto UniversityKumamotoJapan
| | - Michihiro Hashimoto
- Laboratory of Stem Cell RegulationInternational Research Center for Medical SciencesKumamoto UniversityKumamotoJapan
| | - Sho Kubota
- Laboratory of Transcriptional Regulation in LeukemogenesisInternational Research Center for Medical SciencesKumamoto UniversityKumamotoJapan
| | - Kenta Kikuchi
- Laboratory of Chromatin Organization in Immune Cell DevelopmentInternational Research Center for Medical SciencesKumamoto UniversityKumamotoJapan
| | - Haruki Odaka
- Department of Cell ModulationInstitute of Molecular Embryology and GeneticsKumamoto UniversityKumamotoJapan
| | - Takumi Era
- Department of Cell ModulationInstitute of Molecular Embryology and GeneticsKumamoto UniversityKumamotoJapan
| | - Daisuke Kurotaki
- Laboratory of Chromatin Organization in Immune Cell DevelopmentInternational Research Center for Medical SciencesKumamoto UniversityKumamotoJapan
| | - Goro Sashida
- Laboratory of Transcriptional Regulation in LeukemogenesisInternational Research Center for Medical SciencesKumamoto UniversityKumamotoJapan
| | - Toshio Suda
- Laboratory of Stem Cell RegulationInternational Research Center for Medical SciencesKumamoto UniversityKumamotoJapan,Cancer Science Institute of SingaporeNational University of SingaporeSingapore CitySingapore
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18
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CTCF and transcription influence chromatin structure re-configuration after mitosis. Nat Commun 2021; 12:5157. [PMID: 34453048 PMCID: PMC8397779 DOI: 10.1038/s41467-021-25418-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 08/06/2021] [Indexed: 02/02/2023] Open
Abstract
During mitosis, transcription is globally attenuated and chromatin architecture is dramatically reconfigured. We exploited the M- to G1-phase progression to interrogate the contributions of the architectural factor CTCF and the process of transcription to genome re-sculpting in newborn nuclei. Depletion of CTCF during the M- to G1-phase transition alters short-range compartmentalization after mitosis. Chromatin domain boundary re-formation is impaired upon CTCF loss, but a subset of boundaries, characterized by transitions in chromatin states, is established normally. Without CTCF, structural loops fail to form, leading to illegitimate contacts between cis-regulatory elements (CREs). Transient CRE contacts that are normally resolved after telophase persist deeply into G1-phase in CTCF-depleted cells. CTCF loss-associated gains in transcription are often linked to increased, normally illegitimate enhancer-promoter contacts. In contrast, at genes whose expression declines upon CTCF loss, CTCF seems to function as a conventional transcription activator, independent of its architectural role. CTCF-anchored structural loops facilitate formation of CRE loops nested within them, especially those involving weak CREs. Transcription inhibition does not significantly affect global architecture or transcription start site-associated boundaries. However, ongoing transcription contributes considerably to the formation of gene domains, regions of enriched contacts along gene bodies. Notably, gene domains emerge in ana/telophase prior to completion of the first round of transcription, suggesting that epigenetic features in gene bodies contribute to genome reconfiguration prior to transcription. The focus on the de novo formation of nuclear architecture during G1 entry yields insights into the contributions of CTCF and transcription to chromatin architecture dynamics during the mitosis to G1-phase progression.
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19
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Wu AP, Peng J, Berger B, Cho H. Bayesian information sharing enhances detection of regulatory associations in rare cell types. Bioinformatics 2021; 37:i349-i357. [PMID: 34252956 PMCID: PMC8275330 DOI: 10.1093/bioinformatics/btab269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Recent advances in single-cell RNA-sequencing (scRNA-seq) technologies promise to enable the study of gene regulatory associations at unprecedented resolution in diverse cellular contexts. However, identifying unique regulatory associations observed only in specific cell types or conditions remains a key challenge; this is particularly so for rare transcriptional states whose sample sizes are too small for existing gene regulatory network inference methods to be effective. RESULTS We present ShareNet, a Bayesian framework for boosting the accuracy of cell type-specific gene regulatory networks by propagating information across related cell types via an information sharing structure that is adaptively optimized for a given single-cell dataset. The techniques we introduce can be used with a range of general network inference algorithms to enhance the output for each cell type. We demonstrate the enhanced accuracy of our approach on three benchmark scRNA-seq datasets. We find that our inferred cell type-specific networks also uncover key changes in gene associations that underpin the complex rewiring of regulatory networks across cell types, tissues and dynamic biological processes. Our work presents a path toward extracting deeper insights about cell type-specific gene regulation in the rapidly growing compendium of scRNA-seq datasets. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online. AVAILABILITY AND IMPLEMENTATION The code for ShareNet is available at http://sharenet.csail.mit.edu and https://github.com/alexw16/sharenet.
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Affiliation(s)
- Alexander P Wu
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA 02139, USA
| | - Jian Peng
- Department of Computer Science, University of Illinois at Urbana-Champaign, Champaign, IL 61801, USA
| | - Bonnie Berger
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA 02139, USA.,Department of Mathematics, MIT, Cambridge, MA 02139, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Hyunghoon Cho
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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20
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Keller CA, Wixom AQ, Heuston EF, Giardine B, Hsiung CCS, Long MR, Miller A, Anderson SM, Cockburn A, Blobel GA, Bodine DM, Hardison RC. Effects of sheared chromatin length on ChIP-seq quality and sensitivity. G3-GENES GENOMES GENETICS 2021; 11:6206780. [PMID: 33788948 PMCID: PMC8495733 DOI: 10.1093/g3journal/jkab101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 03/26/2021] [Indexed: 01/22/2023]
Abstract
Chromatin immunoprecipitation followed by massively parallel, high throughput sequencing (ChIP-seq) is the method of choice for genome-wide identification of DNA segments bound by specific transcription factors or in chromatin with particular histone modifications. However, the quality of ChIP-seq datasets varies widely, with a substantial fraction being of intermediate to poor quality. Thus, it is important to discern and control the factors that contribute to variation in ChIP-seq. In this study, we focused on sonication, a user-controlled variable, to produce sheared chromatin. We systematically varied the amount of shearing of fixed chromatin from a mouse erythroid cell line, carefully measuring the distribution of resultant fragment lengths prior to ChIP-seq. This systematic study was complemented with a retrospective analysis of additional experiments. We found that the level of sonication had a pronounced impact on the quality of ChIP-seq signals. Over-sonication consistently reduced quality, while the impact of under-sonication differed among transcription factors, with no impact on sites bound by CTCF but frequently leading to the loss of sites occupied by TAL1 or bound by POL2. The bound sites not observed in low quality datasets were inferred to be a mix of both direct and indirect binding. We leveraged these findings to produce a set of CTCF ChIP-seq datasets in rare, primary hematopoietic progenitor cells. Our observation that the amount of chromatin sonication is a key variable in success of ChIP-seq experiments indicates that monitoring the level of sonication can improve ChIP-seq quality and reproducibility and facilitate ChIP-seq in rare cell types.
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Affiliation(s)
- Cheryl A Keller
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Alexander Q Wixom
- Mayo Clinic, Department of Gastroenterology and Hepatology , Rochester, MN 55905, USA
| | - Elisabeth F Heuston
- NHGRI Hematopoiesis Section, Genetics and Molecular Biology Branch, National Institutes of Health, Bethesda, MD 20892, USA
| | - Belinda Giardine
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Chris C-S Hsiung
- Department of Pathology, Stanford University School of Medicine, CA 94305, USA.,Department of Urology, University of California, CA 94158, USA
| | - Maria R Long
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Amber Miller
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Stacie M Anderson
- NHGRI Flow Cytometry Core, National Institutes of Health, Bethesda, MD 20882, USA
| | - April Cockburn
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Gerd A Blobel
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - David M Bodine
- NHGRI Hematopoiesis Section, Genetics and Molecular Biology Branch, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
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21
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Vihervaara A, Mahat DB, Himanen SV, Blom MAH, Lis JT, Sistonen L. Stress-induced transcriptional memory accelerates promoter-proximal pause release and decelerates termination over mitotic divisions. Mol Cell 2021; 81:1715-1731.e6. [PMID: 33784494 DOI: 10.1016/j.molcel.2021.03.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 08/14/2020] [Accepted: 03/04/2021] [Indexed: 12/25/2022]
Abstract
Heat shock instantly reprograms transcription. Whether gene and enhancer transcription fully recover from stress and whether stress establishes a memory by provoking transcription regulation that persists through mitosis remained unknown. Here, we measured nascent transcription and chromatin accessibility in unconditioned cells and in the daughters of stress-exposed cells. Tracking transcription genome-wide at nucleotide-resolution revealed that cells precisely restored RNA polymerase II (Pol II) distribution at gene bodies and enhancers upon recovery from stress. However, a single heat exposure in embryonic fibroblasts primed a faster gene induction in their daughter cells by increasing promoter-proximal Pol II pausing and by accelerating the pause release. In K562 erythroleukemia cells, repeated stress refined basal and heat-induced transcription over mitotic division and decelerated termination-coupled pre-mRNA processing. The slower termination retained transcripts on the chromatin and reduced recycling of Pol II. These results demonstrate that heat-induced transcriptional memory acts through promoter-proximal pause release and pre-mRNA processing at transcription termination.
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Affiliation(s)
- Anniina Vihervaara
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, 20520 Turku, Finland; Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland; Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA; Department of Gene Technology, Science for Life Laboratory, KTH Royal Institute of Technology, 17165 Stockholm, Sweden.
| | - Dig Bijay Mahat
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Samu V Himanen
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, 20520 Turku, Finland; Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | - Malin A H Blom
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, 20520 Turku, Finland; Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
| | - Lea Sistonen
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, 20520 Turku, Finland; Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland.
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22
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Ranzoni AM, Tangherloni A, Berest I, Riva SG, Myers B, Strzelecka PM, Xu J, Panada E, Mohorianu I, Zaugg JB, Cvejic A. Integrative Single-Cell RNA-Seq and ATAC-Seq Analysis of Human Developmental Hematopoiesis. Cell Stem Cell 2021; 28:472-487.e7. [PMID: 33352111 PMCID: PMC7939551 DOI: 10.1016/j.stem.2020.11.015] [Citation(s) in RCA: 136] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 09/18/2020] [Accepted: 11/19/2020] [Indexed: 02/08/2023]
Abstract
Regulation of hematopoiesis during human development remains poorly defined. Here we applied single-cell RNA sequencing (scRNA-seq) and single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) to over 8,000 human immunophenotypic blood cells from fetal liver and bone marrow. We inferred their differentiation trajectory and identified three highly proliferative oligopotent progenitor populations downstream of hematopoietic stem cells (HSCs)/multipotent progenitors (MPPs). Along this trajectory, we observed opposing patterns of chromatin accessibility and differentiation that coincided with dynamic changes in the activity of distinct lineage-specific transcription factors. Integrative analysis of chromatin accessibility and gene expression revealed extensive epigenetic but not transcriptional priming of HSCs/MPPs prior to their lineage commitment. Finally, we refined and functionally validated the sorting strategy for the HSCs/MPPs and achieved around 90% enrichment. Our study provides a useful framework for future investigation of human developmental hematopoiesis in the context of blood pathologies and regenerative medicine.
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Affiliation(s)
- Anna Maria Ranzoni
- University of Cambridge, Department of Haematology, Cambridge CB2 0AW, UK; Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge CB2 0AW, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Andrea Tangherloni
- University of Cambridge, Department of Haematology, Cambridge CB2 0AW, UK; Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge CB2 0AW, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Ivan Berest
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, 69115 Heidelberg, Germany
| | - Simone Giovanni Riva
- University of Cambridge, Department of Haematology, Cambridge CB2 0AW, UK; Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge CB2 0AW, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Brynelle Myers
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge CB2 0AW, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Paulina M Strzelecka
- University of Cambridge, Department of Haematology, Cambridge CB2 0AW, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Jiarui Xu
- University of Cambridge, Department of Haematology, Cambridge CB2 0AW, UK; Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge CB2 0AW, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Elisa Panada
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge CB2 0AW, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Irina Mohorianu
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge CB2 0AW, UK
| | - Judith B Zaugg
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, 69115 Heidelberg, Germany
| | - Ana Cvejic
- University of Cambridge, Department of Haematology, Cambridge CB2 0AW, UK; Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge CB2 0AW, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK.
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23
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Srivastava D, Aydin B, Mazzoni EO, Mahony S. An interpretable bimodal neural network characterizes the sequence and preexisting chromatin predictors of induced transcription factor binding. Genome Biol 2021; 22:20. [PMID: 33413545 PMCID: PMC7788824 DOI: 10.1186/s13059-020-02218-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 12/03/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Transcription factor (TF) binding specificity is determined via a complex interplay between the transcription factor's DNA binding preference and cell type-specific chromatin environments. The chromatin features that correlate with transcription factor binding in a given cell type have been well characterized. For instance, the binding sites for a majority of transcription factors display concurrent chromatin accessibility. However, concurrent chromatin features reflect the binding activities of the transcription factor itself and thus provide limited insight into how genome-wide TF-DNA binding patterns became established in the first place. To understand the determinants of transcription factor binding specificity, we therefore need to examine how newly activated transcription factors interact with sequence and preexisting chromatin landscapes. RESULTS Here, we investigate the sequence and preexisting chromatin predictors of TF-DNA binding by examining the genome-wide occupancy of transcription factors that have been induced in well-characterized chromatin environments. We develop Bichrom, a bimodal neural network that jointly models sequence and preexisting chromatin data to interpret the genome-wide binding patterns of induced transcription factors. We find that the preexisting chromatin landscape is a differential global predictor of TF-DNA binding; incorporating preexisting chromatin features improves our ability to explain the binding specificity of some transcription factors substantially, but not others. Furthermore, by analyzing site-level predictors, we show that transcription factor binding in previously inaccessible chromatin tends to correspond to the presence of more favorable cognate DNA sequences. CONCLUSIONS Bichrom thus provides a framework for modeling, interpreting, and visualizing the joint sequence and chromatin landscapes that determine TF-DNA binding dynamics.
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Affiliation(s)
- Divyanshi Srivastava
- Center for Eukaryotic Gene Regulation, Department of Biochemistry & Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Begüm Aydin
- Department of Biology, New York University, New York, NY, USA
| | | | - Shaun Mahony
- Center for Eukaryotic Gene Regulation, Department of Biochemistry & Molecular Biology, Pennsylvania State University, University Park, PA, USA.
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24
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Cai W, Zhou W, Han Z, Lei J, Zhuang J, Zhu P, Wu X, Yuan W. Master regulator genes and their impact on major diseases. PeerJ 2020; 8:e9952. [PMID: 33083114 PMCID: PMC7546222 DOI: 10.7717/peerj.9952] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 08/25/2020] [Indexed: 01/10/2023] Open
Abstract
Master regulator genes (MRGs) have become a hot topic in recent decades. They not only affect the development of tissue and organ systems but also play a role in other signal pathways by regulating additional MRGs. Because a MRG can regulate the concurrent expression of several genes, its mutation often leads to major diseases. Moreover, the occurrence of many tumors and cardiovascular and nervous system diseases are closely related to MRG changes. With the development in omics technology, an increasing amount of investigations will be directed toward MRGs because their regulation involves all aspects of an organism’s development. This review focuses on the definition and classification of MRGs as well as their influence on disease regulation.
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Affiliation(s)
- Wanwan Cai
- The Center for Heart Development, State Key Laboratory of Development Biology of Freshwater Fish, Key Laboratory of MOE for Development Biology and Protein Chemistry, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Wanbang Zhou
- College of Physical Education, Hunan Normal University, Changsha, Hunan, China
| | - Zhe Han
- University of Maryland School of Medicine, Center for Precision Disease Modeling, Baltimore, MD, USA
| | - Junrong Lei
- College of Physical Education, Hunan Normal University, Changsha, Hunan, China
| | - Jian Zhuang
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Department of Cardiac Surgery, Guangzhou, Guangdong, China
| | - Ping Zhu
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Department of Cardiac Surgery, Guangzhou, Guangdong, China
| | - Xiushan Wu
- The Center for Heart Development, State Key Laboratory of Development Biology of Freshwater Fish, Key Laboratory of MOE for Development Biology and Protein Chemistry, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Wuzhou Yuan
- The Center for Heart Development, State Key Laboratory of Development Biology of Freshwater Fish, Key Laboratory of MOE for Development Biology and Protein Chemistry, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
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25
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Delos Santos NP, Texari L, Benner C. MEIRLOP: improving score-based motif enrichment by incorporating sequence bias covariates. BMC Bioinformatics 2020; 21:410. [PMID: 32938397 PMCID: PMC7493370 DOI: 10.1186/s12859-020-03739-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 09/04/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Motif enrichment analysis (MEA) identifies over-represented transcription factor binding (TF) motifs in the DNA sequence of regulatory regions, enabling researchers to infer which transcription factors can regulate transcriptional response to a stimulus, or identify sequence features found near a target protein in a ChIP-seq experiment. Score-based MEA determines motifs enriched in regions exhibiting extreme differences in regulatory activity, but existing methods do not control for biases in GC content or dinucleotide composition. This lack of control for sequence bias, such as those often found in CpG islands, can obscure the enrichment of biologically relevant motifs. RESULTS We developed Motif Enrichment In Ranked Lists of Peaks (MEIRLOP), a novel MEA method that determines enrichment of TF binding motifs in a list of scored regulatory regions, while controlling for sequence bias. In this study, we compare MEIRLOP against other MEA methods in identifying binding motifs found enriched in differentially active regulatory regions after interferon-beta stimulus, finding that using logistic regression and covariates improves the ability to call enrichment of ISGF3 binding motifs from differential acetylation ChIP-seq data compared to other methods. Our method achieves similar or better performance compared to other methods when quantifying the enrichment of TF binding motifs from ENCODE TF ChIP-seq datasets. We also demonstrate how MEIRLOP is broadly applicable to the analysis of numerous types of NGS assays and experimental designs. CONCLUSIONS Our results demonstrate the importance of controlling for sequence bias when accurately identifying enriched DNA sequence motifs using score-based MEA. MEIRLOP is available for download from https://github.com/npdeloss/meirlop under the MIT license.
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Affiliation(s)
- Nathaniel P Delos Santos
- Department of Biomedical Informatics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0640, USA
| | - Lorane Texari
- Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0640, USA
| | - Christopher Benner
- Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0640, USA.
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26
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Hyperacetylated chromatin domains mark cell type-specific genes and suggest distinct modes of enhancer function. Nat Commun 2020; 11:4544. [PMID: 32917861 PMCID: PMC7486385 DOI: 10.1038/s41467-020-18303-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 07/08/2020] [Indexed: 01/24/2023] Open
Abstract
Stratification of enhancers by signal strength in ChIP-seq assays has resulted in the establishment of super-enhancers as a widespread and useful tool for identifying cell type-specific, highly expressed genes and associated pathways. We examine a distinct method of stratification that focuses on peak breadth, termed hyperacetylated chromatin domains (HCDs), which classifies broad regions exhibiting histone modifications associated with gene activation. We find that this analysis serves to identify genes that are both more highly expressed and more closely aligned to cell identity than super-enhancer analysis does using multiple data sets. Moreover, genetic manipulations of selected gene loci suggest that some enhancers located within HCDs work at least in part via a distinct mechanism involving the modulation of histone modifications across domains and that this activity can be imported into a heterologous gene locus. In addition, such genetic dissection reveals that the super-enhancer concept can obscure important functions of constituent elements. Super-enhancer are usually defined by high levels of chromatin modification and associate with cell-specific gene expression. Here, the authors define hyperacetylated chromatin domains (HCDs) by using histone hyperacetylation peak breadth information and show that HCDs associated more closely with cell identity than super-enhancers.
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27
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Sauta E, Demartini A, Vitali F, Riva A, Bellazzi R. A Bayesian data fusion based approach for learning genome-wide transcriptional regulatory networks. BMC Bioinformatics 2020; 21:219. [PMID: 32471360 PMCID: PMC7257163 DOI: 10.1186/s12859-020-3510-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 04/22/2020] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Reverse engineering of transcriptional regulatory networks (TRN) from genomics data has always represented a computational challenge in System Biology. The major issue is modeling the complex crosstalk among transcription factors (TFs) and their target genes, with a method able to handle both the high number of interacting variables and the noise in the available heterogeneous experimental sources of information. RESULTS In this work, we propose a data fusion approach that exploits the integration of complementary omics-data as prior knowledge within a Bayesian framework, in order to learn and model large-scale transcriptional networks. We develop a hybrid structure-learning algorithm able to jointly combine TFs ChIP-Sequencing data and gene expression compendia to reconstruct TRNs in a genome-wide perspective. Applying our method to high-throughput data, we verified its ability to deal with the complexity of a genomic TRN, providing a snapshot of the synergistic TFs regulatory activity. Given the noisy nature of data-driven prior knowledge, which potentially contains incorrect information, we also tested the method's robustness to false priors on a benchmark dataset, comparing the proposed approach to other regulatory network reconstruction algorithms. We demonstrated the effectiveness of our framework by evaluating structural commonalities of our learned genomic network with other existing networks inferred by different DNA binding information-based methods. CONCLUSIONS This Bayesian omics-data fusion based methodology allows to gain a genome-wide picture of the transcriptional interplay, helping to unravel key hierarchical transcriptional interactions, which could be subsequently investigated, and it represents a promising learning approach suitable for multi-layered genomic data integration, given its robustness to noisy sources and its tailored framework for handling high dimensional data.
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Affiliation(s)
- Elisabetta Sauta
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Via Ferrata 5, 27100, Pavia, Italy.
| | - Andrea Demartini
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Via Ferrata 5, 27100, Pavia, Italy
| | - Francesca Vitali
- Center for Biomedical Informatics and Biostatistics, Dept. of Medicine, The University of Arizona Health Sciences, 1230 Cherry Ave, Tucson, AZ, 85719, USA
| | - Alberto Riva
- Bioinformatics Core, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, 32610, USA
| | - Riccardo Bellazzi
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Via Ferrata 5, 27100, Pavia, Italy
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28
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Wdr26 regulates nuclear condensation in developing erythroblasts. Blood 2020; 135:208-219. [PMID: 31945154 DOI: 10.1182/blood.2019002165] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 11/04/2019] [Indexed: 02/07/2023] Open
Abstract
Mammalian red blood cells lack nuclei. The molecular mechanisms underlying erythroblast nuclear condensation and enucleation, however, remain poorly understood. Here we show that Wdr26, a gene upregulated during terminal erythropoiesis, plays an essential role in regulating nuclear condensation in differentiating erythroblasts. Loss of Wdr26 induces anemia in zebrafish and enucleation defects in mouse erythroblasts because of impaired erythroblast nuclear condensation. As part of the glucose-induced degradation-deficient ubiquitin ligase complex, Wdr26 regulates the ubiquitination and degradation of nuclear proteins, including lamin B. Failure of lamin B degradation blocks nuclear opening formation leading to impaired clearance of nuclear proteins and delayed nuclear condensation. Collectively, our study reveals an unprecedented role of an E3 ubiquitin ligase in regulating nuclear condensation and enucleation during terminal erythropoiesis. Our results provide mechanistic insights into nuclear protein homeostasis and vertebrate red blood cell development.
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29
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Xiang G, Keller CA, Heuston E, Giardine BM, An L, Wixom AQ, Miller A, Cockburn A, Sauria MEG, Weaver K, Lichtenberg J, Göttgens B, Li Q, Bodine D, Mahony S, Taylor J, Blobel GA, Weiss MJ, Cheng Y, Yue F, Hughes J, Higgs DR, Zhang Y, Hardison RC. An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis. Genome Res 2020; 30:472-484. [PMID: 32132109 PMCID: PMC7111515 DOI: 10.1101/gr.255760.119] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 02/21/2020] [Indexed: 01/29/2023]
Abstract
Thousands of epigenomic data sets have been generated in the past decade, but it is difficult for researchers to effectively use all the data relevant to their projects. Systematic integrative analysis can help meet this need, and the VISION project was established for validated systematic integration of epigenomic data in hematopoiesis. Here, we systematically integrated extensive data recording epigenetic features and transcriptomes from many sources, including individual laboratories and consortia, to produce a comprehensive view of the regulatory landscape of differentiating hematopoietic cell types in mouse. By using IDEAS as our integrative and discriminative epigenome annotation system, we identified and assigned epigenetic states simultaneously along chromosomes and across cell types, precisely and comprehensively. Combining nuclease accessibility and epigenetic states produced a set of more than 200,000 candidate cis-regulatory elements (cCREs) that efficiently capture enhancers and promoters. The transitions in epigenetic states of these cCREs across cell types provided insights into mechanisms of regulation, including decreases in numbers of active cCREs during differentiation of most lineages, transitions from poised to active or inactive states, and shifts in nuclease accessibility of CTCF-bound elements. Regression modeling of epigenetic states at cCREs and gene expression produced a versatile resource to improve selection of cCREs potentially regulating target genes. These resources are available from our VISION website to aid research in genomics and hematopoiesis.
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Affiliation(s)
- Guanjue Xiang
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Cheryl A Keller
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Elisabeth Heuston
- NHGRI Hematopoiesis Section, Genetics and Molecular Biology Branch, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Belinda M Giardine
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Lin An
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Alexander Q Wixom
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Amber Miller
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - April Cockburn
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Michael E G Sauria
- Departments of Biology and Computer Science, Johns Hopkins University, Baltimore, Maryland 20218, USA
| | - Kathryn Weaver
- Departments of Biology and Computer Science, Johns Hopkins University, Baltimore, Maryland 20218, USA
| | - Jens Lichtenberg
- NHGRI Hematopoiesis Section, Genetics and Molecular Biology Branch, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Berthold Göttgens
- Welcome and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1TN, United Kingdom
| | - Qunhua Li
- Department of Statistics, Program in Bioinformatics and Genomics, Center for Computational Biology and Bioinformatics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - David Bodine
- NHGRI Hematopoiesis Section, Genetics and Molecular Biology Branch, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Shaun Mahony
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - James Taylor
- Departments of Biology and Computer Science, Johns Hopkins University, Baltimore, Maryland 20218, USA
| | - Gerd A Blobel
- Department of Pediatrics, Children's Hospital of Philadelphia and University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - Mitchell J Weiss
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Yong Cheng
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Feng Yue
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania 17033, USA
| | - Jim Hughes
- MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford OX3 9DS, United Kingdom
| | - Douglas R Higgs
- MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford OX3 9DS, United Kingdom
| | - Yu Zhang
- Department of Statistics, Program in Bioinformatics and Genomics, Center for Computational Biology and Bioinformatics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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30
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Hardison RC, Zhang Y, Keller CA, Xiang G, Heuston EF, An L, Lichtenberg J, Giardine BM, Bodine D, Mahony S, Li Q, Yue F, Weiss MJ, Blobel GA, Taylor J, Hughes J, Higgs DR, Göttgens B. Systematic integration of GATA transcription factors and epigenomes via IDEAS paints the regulatory landscape of hematopoietic cells. IUBMB Life 2020; 72:27-38. [PMID: 31769130 PMCID: PMC6972633 DOI: 10.1002/iub.2195] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 10/17/2019] [Indexed: 01/15/2023]
Abstract
Members of the GATA family of transcription factors play key roles in the differentiation of specific cell lineages by regulating the expression of target genes. Three GATA factors play distinct roles in hematopoietic differentiation. In order to better understand how these GATA factors function to regulate genes throughout the genome, we are studying the epigenomic and transcriptional landscapes of hematopoietic cells in a model-driven, integrative fashion. We have formed the collaborative multi-lab VISION project to conduct ValIdated Systematic IntegratiON of epigenomic data in mouse and human hematopoiesis. The epigenomic data included nuclease accessibility in chromatin, CTCF occupancy, and histone H3 modifications for 20 cell types covering hematopoietic stem cells, multilineage progenitor cells, and mature cells across the blood cell lineages of mouse. The analysis used the Integrative and Discriminative Epigenome Annotation System (IDEAS), which learns all common combinations of features (epigenetic states) simultaneously in two dimensions-along chromosomes and across cell types. The result is a segmentation that effectively paints the regulatory landscape in readily interpretable views, revealing constitutively active or silent loci as well as the loci specifically induced or repressed in each stage and lineage. Nuclease accessible DNA segments in active chromatin states were designated candidate cis-regulatory elements in each cell type, providing one of the most comprehensive registries of candidate hematopoietic regulatory elements to date. Applications of VISION resources are illustrated for the regulation of genes encoding GATA1, GATA2, GATA3, and Ikaros. VISION resources are freely available from our website http://usevision.org.
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Affiliation(s)
- Ross C. Hardison
- Departments of Biochemistry and Molecular Biology and of StatisticsThe Pennsylvania State University, University ParkPA
| | - Yu Zhang
- Departments of Biochemistry and Molecular Biology and of StatisticsThe Pennsylvania State University, University ParkPA
| | - Cheryl A. Keller
- Departments of Biochemistry and Molecular Biology and of StatisticsThe Pennsylvania State University, University ParkPA
| | - Guanjue Xiang
- Departments of Biochemistry and Molecular Biology and of StatisticsThe Pennsylvania State University, University ParkPA
| | - Elisabeth F. Heuston
- Genetics and Molecular Biology Branch, Hematopoiesis SectionNational Institutes of Health, NHGRIBethesdaMD
| | - Lin An
- Departments of Biochemistry and Molecular Biology and of StatisticsThe Pennsylvania State University, University ParkPA
| | - Jens Lichtenberg
- Genetics and Molecular Biology Branch, Hematopoiesis SectionNational Institutes of Health, NHGRIBethesdaMD
| | - Belinda M. Giardine
- Departments of Biochemistry and Molecular Biology and of StatisticsThe Pennsylvania State University, University ParkPA
| | - David Bodine
- Genetics and Molecular Biology Branch, Hematopoiesis SectionNational Institutes of Health, NHGRIBethesdaMD
| | - Shaun Mahony
- Departments of Biochemistry and Molecular Biology and of StatisticsThe Pennsylvania State University, University ParkPA
| | - Qunhua Li
- Departments of Biochemistry and Molecular Biology and of StatisticsThe Pennsylvania State University, University ParkPA
| | - Feng Yue
- Department of Biochemistry and Molecular BiologyThe Pennsylvania State University College of MedicineHershey, PA
| | - Mitchell J. Weiss
- Hematology DepartmentSt. Jude Children's Research HospitalMemphis, TN
| | | | - James Taylor
- Departments of Biology and of Computer ScienceJohns Hopkins UniversityBaltimore, MD
| | - Jim Hughes
- Laboratory of Gene RegulationWeatherall Institute of Molecular Medicine, Oxford UniversityOxfordUK
| | - Douglas R. Higgs
- Laboratory of Gene RegulationWeatherall Institute of Molecular Medicine, Oxford UniversityOxfordUK
| | - Berthold Göttgens
- Department of Hematology, Cambridge Institute for Medical ResearchUniversity of CambridgeCambridgeUK
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31
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Zhang H, Emerson DJ, Gilgenast TG, Titus KR, Lan Y, Huang P, Zhang D, Wang H, Keller CA, Giardine B, Hardison RC, Phillips-Cremins JE, Blobel GA. Chromatin structure dynamics during the mitosis-to-G1 phase transition. Nature 2019; 576:158-162. [PMID: 31776509 PMCID: PMC6895436 DOI: 10.1038/s41586-019-1778-y] [Citation(s) in RCA: 126] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 10/02/2019] [Indexed: 11/08/2022]
Abstract
Features of higher-order chromatin organization-such as A/B compartments, topologically associating domains and chromatin loops-are temporarily disrupted during mitosis1,2. Because these structures are thought to influence gene regulation, it is important to understand how they are re-established after mitosis. Here we examine the dynamics of chromosome reorganization by Hi-C after mitosis in highly purified, synchronous mouse erythroid cell populations. We observed rapid establishment of A/B compartments, followed by their gradual intensification and expansion. Contact domains form from the 'bottom up'-smaller subTADs are formed initially, followed by convergence into multi-domain TAD structures. CTCF is partially retained on mitotic chromosomes and immediately resumes full binding in ana/telophase. By contrast, cohesin is completely evicted from mitotic chromosomes and regains focal binding at a slower rate. The formation of CTCF/cohesin co-anchored structural loops follows the kinetics of cohesin positioning. Stripe-shaped contact patterns-anchored by CTCF-grow in length, which is consistent with a loop-extrusion process after mitosis. Interactions between cis-regulatory elements can form rapidly, with rates exceeding those of CTCF/cohesin-anchored contacts. Notably, we identified a group of rapidly emerging transient contacts between cis-regulatory elements in ana/telophase that are dissolved upon G1 entry, co-incident with the establishment of inner boundaries or nearby interfering chromatin loops. We also describe the relationship between transcription reactivation and architectural features. Our findings indicate that distinct but mutually influential forces drive post-mitotic chromatin reconfiguration.
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Affiliation(s)
- Haoyue Zhang
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Daniel J Emerson
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Thomas G Gilgenast
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Katelyn R Titus
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Yemin Lan
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Peng Huang
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Di Zhang
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hongxin Wang
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Cheryl A Keller
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Belinda Giardine
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | | | - Gerd A Blobel
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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32
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Romano O, Miccio A. GATA factor transcriptional activity: Insights from genome-wide binding profiles. IUBMB Life 2019; 72:10-26. [PMID: 31574210 DOI: 10.1002/iub.2169] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 09/05/2019] [Indexed: 01/07/2023]
Abstract
The members of the GATA family of transcription factors have homologous zinc fingers and bind to similar sequence motifs. Recent advances in genome-wide technologies and the integration of bioinformatics data have led to a better understanding of how GATA factors regulate gene expression; GATA-factor-induced transcriptional and epigenetic changes have now been analyzed at unprecedented levels of detail. Here, we review the results of genome-wide studies of GATA factor occupancy in human and murine cell lines and primary cells (as determined by chromatin immunoprecipitation sequencing), and then discuss the molecular mechanisms underlying the mediation of transcriptional and epigenetic regulation by GATA factors.
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Affiliation(s)
- Oriana Romano
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Annarita Miccio
- Laboratory of chromatin and gene regulation during development, Imagine Institute, INSERM UMR, Paris, France.,Paris Descartes, Sorbonne Paris Cité University, Imagine Institute, Paris, France
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33
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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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34
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Steiner M, Schneider L, Yillah J, Gerlach K, Kuvardina ON, Meyer A, Maring A, Bonig H, Seifried E, Zörnig M, Lausen J. FUSE binding protein 1 (FUBP1) expression is upregulated by T-cell acute lymphocytic leukemia protein 1 (TAL1) and required for efficient erythroid differentiation. PLoS One 2019; 14:e0210515. [PMID: 30653565 PMCID: PMC6336336 DOI: 10.1371/journal.pone.0210515] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 12/23/2018] [Indexed: 11/18/2022] Open
Abstract
During erythropoiesis, haematopoietic stem cells (HSCs) differentiate in successive steps of commitment and specification to mature erythrocytes. This differentiation process is controlled by transcription factors that establish stage- and cell type-specific gene expression. In this study, we demonstrate that FUSE binding protein 1 (FUBP1), a transcriptional regulator important for HSC self-renewal and survival, is regulated by T-cell acute lymphocytic leukaemia 1 (TAL1) in erythroid progenitor cells. TAL1 directly activates the FUBP1 promoter, leading to increased FUBP1 expression during erythroid differentiation. The binding of TAL1 to the FUBP1 promoter is highly dependent on an intact GATA sequence in a combined E-box/GATA motif. We found that FUBP1 expression is required for efficient erythropoiesis, as FUBP1-deficient progenitor cells were limited in their potential of erythroid differentiation. Thus, the finding of an interconnection between GATA1/TAL1 and FUBP1 reveals a molecular mechanism that is part of the switch from progenitor- to erythrocyte-specific gene expression. In summary, we identified a TAL1/FUBP1 transcriptional relationship, whose physiological function in haematopoiesis is connected to proper erythropoiesis.
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Affiliation(s)
- Marlene Steiner
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt/Main, Germany
| | - Lucas Schneider
- Institute for Transfusion Medicine and Immunohematology, Goethe-University and German Red Cross Blood Service, Frankfurt am Main, Germany
| | - Jasmin Yillah
- Institute for Transfusion Medicine and Immunohematology, Goethe-University and German Red Cross Blood Service, Frankfurt am Main, Germany
| | - Katharina Gerlach
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt/Main, Germany
| | - Olga N. Kuvardina
- Institute for Transfusion Medicine and Immunohematology, Goethe-University and German Red Cross Blood Service, Frankfurt am Main, Germany
| | - Annekarin Meyer
- Institute for Transfusion Medicine and Immunohematology, Goethe-University and German Red Cross Blood Service, Frankfurt am Main, Germany
| | - Alisa Maring
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt/Main, Germany
| | - Halvard Bonig
- Institute for Transfusion Medicine and Immunohematology, Goethe-University and German Red Cross Blood Service, Frankfurt am Main, Germany
| | - Erhard Seifried
- Institute for Transfusion Medicine and Immunohematology, Goethe-University and German Red Cross Blood Service, Frankfurt am Main, Germany
| | - Martin Zörnig
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt/Main, Germany
- * E-mail: (MZ); (JL)
| | - Jörn Lausen
- Institute for Transfusion Medicine and Immunohematology, Goethe-University and German Red Cross Blood Service, Frankfurt am Main, Germany
- * E-mail: (MZ); (JL)
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35
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Alsayegh K, Cortés-Medina LV, Ramos-Mandujano G, Badraiq H, Li M. Hematopoietic Differentiation of Human Pluripotent Stem Cells: HOX and GATA Transcription Factors as Master Regulators. Curr Genomics 2019; 20:438-452. [PMID: 32194342 PMCID: PMC7062042 DOI: 10.2174/1389202920666191017163837] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 09/04/2019] [Accepted: 09/27/2019] [Indexed: 02/07/2023] Open
Abstract
Numerous human disorders of the blood system would directly or indirectly benefit from therapeutic approaches that reconstitute the hematopoietic system. Hematopoietic stem cells (HSCs), either from matched donors or ex vivo manipulated autologous tissues, are the most used cellular source of cell therapy for a wide range of disorders. Due to the scarcity of matched donors and the difficulty of ex vivo expansion of HSCs, there is a growing interest in harnessing the potential of pluripotent stem cells (PSCs) as a de novo source of HSCs. PSCs make an ideal source of cells for regenerative medicine in general and for treating blood disorders in particular because they could expand indefinitely in culture and differentiate to any cell type in the body. However, advancement in deriving functional HSCs from PSCs has been slow. This is partly due to an incomplete understanding of the molecular mechanisms underlying normal hematopoiesis. In this review, we discuss the latest efforts to generate human PSC (hPSC)-derived HSCs capable of long-term engraftment. We review the regulation of the key transcription factors (TFs) in hematopoiesis and hematopoietic differentiation, the Homeobox (HOX) and GATA genes, and the interplay between them and microRNAs. We also propose that precise control of these master regulators during the course of hematopoietic differentiation is key to achieving functional hPSC-derived HSCs.
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Affiliation(s)
- Khaled Alsayegh
- King Abdullah International Medical Research Centre, King Saud bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia.,Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Lorena V Cortés-Medina
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Gerardo Ramos-Mandujano
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Heba Badraiq
- King Abdullah International Medical Research Centre, King Saud bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | - Mo Li
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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36
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37
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Suo S, Zhu Q, Saadatpour A, Fei L, Guo G, Yuan GC. Revealing the Critical Regulators of Cell Identity in the Mouse Cell Atlas. Cell Rep 2018; 25:1436-1445.e3. [PMID: 30404000 PMCID: PMC6281296 DOI: 10.1016/j.celrep.2018.10.045] [Citation(s) in RCA: 139] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 09/06/2018] [Accepted: 10/11/2018] [Indexed: 12/19/2022] Open
Abstract
Recent progress in single-cell technologies has enabled the identification of all major cell types in mouse. However, for most cell types, the regulatory mechanism underlying their identity remains poorly understood. By computational analysis of the recently published mouse cell atlas data, we have identified 202 regulons whose activities are highly variable across different cell types, and more importantly, predicted a small set of essential regulators for each major cell type in mouse. Systematic validation by automated literature and data mining provides strong additional support for our predictions. Thus, these predictions serve as a valuable resource that would be useful for the broad biological community. Finally, we have built a user-friendly, interactive web portal to enable users to navigate this mouse cell network atlas.
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Affiliation(s)
- Shengbao Suo
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA
| | - Qian Zhu
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA
| | - Assieh Saadatpour
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA
| | - Lijiang Fei
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Guoji Guo
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Guo-Cheng Yuan
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA.
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38
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Chen X, Litzenburger UM, Wei Y, Schep AN, LaGory EL, Choudhry H, Giaccia AJ, Greenleaf WJ, Chang HY. Joint single-cell DNA accessibility and protein epitope profiling reveals environmental regulation of epigenomic heterogeneity. Nat Commun 2018; 9:4590. [PMID: 30389926 PMCID: PMC6214962 DOI: 10.1038/s41467-018-07115-y] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 10/10/2018] [Indexed: 11/09/2022] Open
Abstract
Here we introduce Protein-indexed Assay of Transposase Accessible Chromatin with sequencing (Pi-ATAC) that combines single-cell chromatin and proteomic profiling. In conjunction with DNA transposition, the levels of multiple cell surface or intracellular protein epitopes are recorded by index flow cytometry and positions in arrayed microwells, and then subject to molecular barcoding for subsequent pooled analysis. Pi-ATAC simultaneously identifies the epigenomic and proteomic heterogeneity in individual cells. Pi-ATAC reveals a casual link between transcription factor abundance and DNA motif access, and deconvolute cell types and states in the tumor microenvironment in vivo. We identify a dominant role for hypoxia, marked by HIF1α protein, in the tumor microvenvironment for shaping the regulome in a subset of epithelial tumor cells.
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Affiliation(s)
- Xingqi Chen
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA.,Department of Cell and Molecular Biology, Karolinska Institutet, 17177, Solna, Sweden
| | - Ulrike M Litzenburger
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA.
| | - Yuning Wei
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA
| | - Alicia N Schep
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA.,Dept of Genetics, Stanford University, Stanford, CA, 94305, USA.,Department of Applied Physics, Stanford University, Stanford, CA, 94305, USA
| | - Edward L LaGory
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University, Stanford, CA, 94305, USA
| | - Hani Choudhry
- Department of Biochemistry, Cancer Metabolism and Epigenetic Unit, Faculty of Science, Cancer and Mutagenesis Unit, King Fahd Center for Medical Research, King Abdulaziz University, Jeddah 22252, Saudi Arabia
| | - Amato J Giaccia
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University, Stanford, CA, 94305, USA
| | - William J Greenleaf
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA.,Dept of Genetics, Stanford University, Stanford, CA, 94305, USA.,Department of Applied Physics, Stanford University, Stanford, CA, 94305, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA. .,Howard Hughes Medical Institute, Stanford University, Stanford, CA, 94305, USA.
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39
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Chen J, Gálvez-Peralta M, Zhang X, Deng J, Liu Z, Nebert DW. In utero gene expression in the Slc39a8(neo/neo) knockdown mouse. Sci Rep 2018; 8:10703. [PMID: 30013175 PMCID: PMC6048144 DOI: 10.1038/s41598-018-29109-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 07/05/2018] [Indexed: 12/13/2022] Open
Abstract
Slc39a8 encodes ZIP8, a divalent cation/bicarbonate symporter expressed in pluripotent mouse embryonic stem cells, and therefore ubiquitous in adult tissues; ZIP8 influxes Zn2+, Mn2+ and Fe2+. Slc39a8(neo/neo) knockdown mice exhibit 10-15% of wild-type ZIP8 mRNA and protein levels, and show pleiotropic phenotype of stunted growth, neonatal lethality, multi-organ dysmorphogenesis, and dysregulated hematopoiesis manifested as severe anemia. Herein we performed RNA-seq analysis of gestational day (GD)13.5 yolk sac and placenta, and GD16.5 liver, kidney, lung, heart and cerebellum, comparing Slc39a8(neo/neo) with Slc39a8(+/+) wild-type. Meta-data analysis of differentially-expressed genes revealed 29 unique genes from all tissues - having enriched GO categories associated with hematopoiesis and hypoxia and KEGG categories of complement, response to infection, and coagulation cascade - consistent with dysregulated hematopoietic stem cell fate. Based on transcription factor (TF) profiles in the JASPAR database, and searching for TF-binding sites enriched by Pscan, we identified numerous genes encoding zinc-finger and other TFs associated with hematopoietic stem cell functions. We conclude that, in this mouse model, deficient ZIP8-mediated divalent cation transport affects zinc-finger (e.g. GATA proteins) and other TFs interacting with GATA proteins (e.g. TAL1), predominantly in yolk sac. These data strongly support the phenotype of dysmorphogenesis and anemia seen in Slc39a8(neo/neo) mice in utero.
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Affiliation(s)
- Jing Chen
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
| | - Marina Gálvez-Peralta
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio, 45267, USA.,Department of Pharmaceutical Sciences, West Virginia University Medical Center, Morgantown, WV, 26506, USA
| | - Xiang Zhang
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio, 45267, USA
| | - Jingyuan Deng
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio, 45267, USA.,Amazon.com, Inc., Seattle, WA, 98101, USA
| | - Zijuan Liu
- Department of Biological Sciences, Oakland University, Rochester, MI, 48309, USA
| | - Daniel W Nebert
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio, 45267, USA.
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40
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Mehta C, Johnson KD, Gao X, Ong IM, Katsumura KR, McIver SC, Ranheim EA, Bresnick EH. Integrating Enhancer Mechanisms to Establish a Hierarchical Blood Development Program. Cell Rep 2018; 20:2966-2979. [PMID: 28930689 DOI: 10.1016/j.celrep.2017.08.090] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 07/30/2017] [Accepted: 08/25/2017] [Indexed: 12/20/2022] Open
Abstract
Hematopoietic development requires the transcription factor GATA-2, and GATA-2 mutations cause diverse pathologies, including leukemia. GATA-2-regulated enhancers increase Gata2 expression in hematopoietic stem/progenitor cells and control hematopoiesis. The +9.5-kb enhancer activates transcription in endothelium and hematopoietic stem cells (HSCs), and its deletion abrogates HSC generation. The -77-kb enhancer activates transcription in myeloid progenitors, and its deletion impairs differentiation. Since +9.5-/- embryos are HSC deficient, it was unclear whether the +9.5 functions in progenitors or if GATA-2 expression in progenitors solely requires -77. We further dissected the mechanisms using -77;+9.5 compound heterozygous (CH) mice. The embryonic lethal CH mutation depleted megakaryocyte-erythrocyte progenitors (MEPs). While the +9.5 suffices for HSC generation, the -77 and +9.5 must reside on one allele to induce MEPs. The -77 generated burst-forming unit-erythroid through the induction of GATA-1 and other GATA-2 targets. The enhancer circuits controlled signaling pathways that orchestrate a GATA factor-dependent blood development program.
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Affiliation(s)
- Charu Mehta
- UW-Madison Blood Research Program, Department of Cell and Regenerative Biology, Wisconsin Institutes for Medical Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA; UW Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Kirby D Johnson
- UW-Madison Blood Research Program, Department of Cell and Regenerative Biology, Wisconsin Institutes for Medical Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA; UW Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Xin Gao
- UW-Madison Blood Research Program, Department of Cell and Regenerative Biology, Wisconsin Institutes for Medical Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA; UW Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Irene M Ong
- UW Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA; Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI 53705, USA
| | - Koichi R Katsumura
- UW-Madison Blood Research Program, Department of Cell and Regenerative Biology, Wisconsin Institutes for Medical Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA; UW Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Skye C McIver
- UW-Madison Blood Research Program, Department of Cell and Regenerative Biology, Wisconsin Institutes for Medical Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA; UW Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Erik A Ranheim
- Department of Pathology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Emery H Bresnick
- UW-Madison Blood Research Program, Department of Cell and Regenerative Biology, Wisconsin Institutes for Medical Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA; UW Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA.
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Exploiting genetic variation to uncover rules of transcription factor binding and chromatin accessibility. Nat Commun 2018; 9:782. [PMID: 29472540 PMCID: PMC5823854 DOI: 10.1038/s41467-018-03082-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 01/18/2018] [Indexed: 12/13/2022] Open
Abstract
Single-nucleotide variants that underlie phenotypic variation can affect chromatin occupancy of transcription factors (TFs). To delineate determinants of in vivo TF binding and chromatin accessibility, we introduce an approach that compares ChIP-seq and DNase-seq data sets from genetically divergent murine erythroid cell lines. The impact of discriminatory single-nucleotide variants on TF ChIP signal enables definition at single base resolution of in vivo binding characteristics of nuclear factors GATA1, TAL1, and CTCF. We further develop a facile complementary approach to more deeply test the requirements of critical nucleotide positions for TF binding by combining CRISPR-Cas9-mediated mutagenesis with ChIP and targeted deep sequencing. Finally, we extend our analytical pipeline to identify nearby contextual DNA elements that modulate chromatin binding by these three TFs, and to define sequences that impact kb-scale chromatin accessibility. Combined, our approaches reveal insights into the genetic basis of TF occupancy and their interplay with chromatin features. Single nucleotide variants (SNVs) can affect chromatin occupancy by transcription factors (TF). Here the authors mine naturally occurring SNVs to probe cis elements and define contextual sequences that govern in vivo transcription factor chromatin occupancy and chromatin accessibility.
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Vagapova ER, Spirin PV, Lebedev TD, Prassolov VS. The Role of TAL1 in Hematopoiesis and Leukemogenesis. Acta Naturae 2018; 10:15-23. [PMID: 29713515 PMCID: PMC5916730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
TAL1 (SCL/TAL1, T-cell acute leukemia protein 1) is a transcription factor that is involved in the process of hematopoiesis and leukemogenesis. It participates in blood cell formation, forms mesoderm in early embryogenesis, and regulates hematopoiesis in adult organisms. TAL1 is essential in maintaining the multipotency of hematopoietic stem cells (HSC) and keeping them in quiescence (stage G0). TAL1 forms complexes with various transcription factors, regulating hematopoiesis (E2A/HEB, GATA1-3, LMO1-2, Ldb1, ETO2, RUNX1, ERG, FLI1). In these complexes, TAL1 regulates normal myeloid differentiation, controls the proliferation of erythroid progenitors, and determines the choice of the direction of HSC differentiation. The transcription factors TAL1, E2A, GATA1 (or GATA2), LMO2, and Ldb1 are the major components of the SCL complex. In addition to normal hematopoiesis, this complex may also be involved in the process of blood cell malignant transformation. Upregulation of C-KIT expression is one of the main roles played by the SCL complex. Today, TAL1 and its partners are considered promising therapeutic targets in the treatment of T-cell acute lymphoblastic leukemia.
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Affiliation(s)
- E. R. Vagapova
- The Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova Str. 32, Moscow,119991, Russia
| | - P. V. Spirin
- The Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova Str. 32, Moscow,119991, Russia
| | - T. D. Lebedev
- The Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova Str. 32, Moscow,119991, Russia
| | - V. S. Prassolov
- The Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova Str. 32, Moscow,119991, Russia
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Vihervaara A, Mahat DB, Guertin MJ, Chu T, Danko CG, Lis JT, Sistonen L. Transcriptional response to stress is pre-wired by promoter and enhancer architecture. Nat Commun 2017; 8:255. [PMID: 28811569 PMCID: PMC5557961 DOI: 10.1038/s41467-017-00151-0] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 06/05/2017] [Indexed: 12/29/2022] Open
Abstract
Programs of gene expression are executed by a battery of transcription factors that coordinate divergent transcription from a pair of tightly linked core initiation regions of promoters and enhancers. Here, to investigate how divergent transcription is reprogrammed upon stress, we measured nascent RNA synthesis at nucleotide-resolution, and profiled histone H4 acetylation in human cells. Our results globally show that the release of promoter-proximal paused RNA polymerase into elongation functions as a critical switch at which a gene’s response to stress is determined. Highly transcribed and highly inducible genes display strong transcriptional directionality and selective assembly of general transcription factors on the core sense promoter. Heat-induced transcription at enhancers, instead, correlates with prior binding of cell-type, sequence-specific transcription factors. Activated Heat Shock Factor 1 (HSF1) binds to transcription-primed promoters and enhancers, and CTCF-occupied, non-transcribed chromatin. These results reveal chromatin architectural features that orient transcription at divergent regulatory elements and prime transcriptional responses genome-wide. Heat Shock Factor 1 (HSF1) is a regulator of stress-induced transcription. Here, the authors investigate changes to transcription and chromatin organization upon stress and find that activated HSF1 binds to transcription-primed promoters and enhancers, and to CTCF occupied, untranscribed chromatin.
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Affiliation(s)
- Anniina Vihervaara
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, 20520, Finland.,Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, 14853, USA
| | - Dig Bijay Mahat
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, 14853, USA
| | - Michael J Guertin
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, 22908, USA
| | - Tinyi Chu
- Department of Biomedical Sciences, The Baker Institute for Animal Health, Cornell University, Ithaca, New York, 14853, USA.,Graduate Field of Computational Biology, Cornell University, Ithaca, New York, 14853, USA
| | - Charles G Danko
- Department of Biomedical Sciences, The Baker Institute for Animal Health, Cornell University, Ithaca, New York, 14853, USA
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, 14853, USA.
| | - Lea Sistonen
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, 20520, Finland.
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Bogoch Y, Friedlander-Malik G, Lupu L, Bondar E, Zohar N, Langier S, Ram Z, Nachmany I, Klausner JM, Pencovich N. Augmented expression of RUNX1 deregulates the global gene expression of U87 glioblastoma multiforme cells and inhibits tumor growth in mice. Tumour Biol 2017; 39:1010428317698357. [PMID: 28443460 DOI: 10.1177/1010428317698357] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Glioblastoma multiforme is the most common and aggressive primary brain tumor in adults. A mesenchymal phenotype was associated with tumor aggressiveness and poor prognosis in glioblastoma multiforme patients. Recently, the transcription factor RUNX1 was suggested as a driver of the glioblastoma multiforme mesenchymal gene expression signature; however, its independent role in this process is yet to be described. Here, we assessed the role of RUNX1 in U87 glioblastoma multiforme cells in correspondence to its mediated transcriptome and genome-wide occupancy pattern. Overexpression of RUNX1 led to diminished tumor growth in nude and severe combined immunodeficiency mouse xenograft tumor model. At the molecular level, RUNX1 occupied thousands of genomic regions and regulated the expression of hundreds of target genes, both directly and indirectly. RUNX1 occupied genomic regions that corresponded to genes that were shown to play a role in brain tumor progression and angiogenesis and upon overexpression led to a substantial down-regulation of their expression level. When overexpressed in U87 glioblastoma multiforme cells, RUNX1 down-regulated key pathways in glioblastoma multiforme progression including epithelial to mesenchymal transition, MTORC1 signaling, hypoxia-induced signaling, and TNFa signaling via NFkB. Moreover, master regulators of the glioblastoma multiforme mesenchymal phenotype including CEBPb, ZNF238, and FOSL2 were directly regulated by RUNX1. The data suggest a central role for RUNX1 as master regulator of gene expression in the U87 glioblastoma multiforme cell line and mark RUNX1 as a potential target for novel future therapies for glioblastoma multiforme.
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Affiliation(s)
- Yoel Bogoch
- 1 The Laboratory of Molecular Genetics, Hepatic-Bili-Pancreatic Cancer Research, Department of Surgery B, Tel Aviv Sourasky Medical Center, The Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Gilgi Friedlander-Malik
- 2 Bioinformatics Unit, Nancy and Stephen Grand Israel National Center for Personalized Medicine, The Weizmann Institute of Science, Rehovot, Israel
| | - Lior Lupu
- 1 The Laboratory of Molecular Genetics, Hepatic-Bili-Pancreatic Cancer Research, Department of Surgery B, Tel Aviv Sourasky Medical Center, The Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ekaterina Bondar
- 1 The Laboratory of Molecular Genetics, Hepatic-Bili-Pancreatic Cancer Research, Department of Surgery B, Tel Aviv Sourasky Medical Center, The Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Nitzan Zohar
- 1 The Laboratory of Molecular Genetics, Hepatic-Bili-Pancreatic Cancer Research, Department of Surgery B, Tel Aviv Sourasky Medical Center, The Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Sheila Langier
- 1 The Laboratory of Molecular Genetics, Hepatic-Bili-Pancreatic Cancer Research, Department of Surgery B, Tel Aviv Sourasky Medical Center, The Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Zvi Ram
- 3 Department of Neurosurgery, Tel Aviv Sourasky Medical Center, The Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ido Nachmany
- 1 The Laboratory of Molecular Genetics, Hepatic-Bili-Pancreatic Cancer Research, Department of Surgery B, Tel Aviv Sourasky Medical Center, The Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Joseph M Klausner
- 1 The Laboratory of Molecular Genetics, Hepatic-Bili-Pancreatic Cancer Research, Department of Surgery B, Tel Aviv Sourasky Medical Center, The Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Niv Pencovich
- 1 The Laboratory of Molecular Genetics, Hepatic-Bili-Pancreatic Cancer Research, Department of Surgery B, Tel Aviv Sourasky Medical Center, The Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
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SCL/TAL1: a multifaceted regulator from blood development to disease. Blood 2017; 129:2051-2060. [DOI: 10.1182/blood-2016-12-754051] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 01/17/2017] [Indexed: 12/12/2022] Open
Abstract
Abstract
SCL/TAL1 (stem cell leukemia/T-cell acute lymphoblastic leukemia [T-ALL] 1) is an essential transcription factor in normal and malignant hematopoiesis. It is required for specification of the blood program during development, adult hematopoietic stem cell survival and quiescence, and terminal maturation of select blood lineages. Following ectopic expression, SCL contributes to oncogenesis in T-ALL. Remarkably, SCL’s activities are all mediated through nucleation of a core quaternary protein complex (SCL:E-protein:LMO1/2 [LIM domain only 1 or 2]:LDB1 [LIM domain-binding protein 1]) and dynamic recruitment of conserved combinatorial associations of additional regulators in a lineage- and stage-specific context. The finely tuned control of SCL’s regulatory functions (lineage priming, activation, and repression of gene expression programs) provides insight into fundamental developmental and transcriptional mechanisms, and highlights mechanistic parallels between normal and oncogenic processes. Importantly, recent discoveries are paving the way to the development of innovative therapeutic opportunities in SCL+ T-ALL.
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Perreault AA, Benton ML, Koury MJ, Brandt SJ, Venters BJ. Epo reprograms the epigenome of erythroid cells. Exp Hematol 2017; 51:47-62. [PMID: 28410882 DOI: 10.1016/j.exphem.2017.03.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 03/28/2017] [Accepted: 03/31/2017] [Indexed: 12/25/2022]
Abstract
The hormone erythropoietin (Epo) is required for erythropoiesis, yet its molecular mechanism of action remains poorly understood, particularly with respect to chromatin dynamics. To investigate how Epo modulates the erythroid epigenome, we performed epigenetic profiling using an ex vivo murine cell system that undergoes synchronous erythroid maturation in response to Epo stimulation. Our findings define the repertoire of Epo-modulated enhancers, illuminating a new facet of Epo signaling. First, a large number of enhancers rapidly responded to Epo stimulation, revealing a cis-regulatory network of Epo-responsive enhancers. In contrast, most of the other identified enhancers remained in an active acetylated state during Epo signaling, suggesting that most erythroid enhancers are established at an earlier precursor stage. Second, we identified several hundred super-enhancers that were linked to key erythroid genes, such as Tal1, Bcl11a, and Mir144/451. Third, experimental and computational validation revealed that many predicted enhancer regions were occupied by TAL1 and enriched with DNA-binding motifs for GATA1, KLF1, TAL1/E-box, and STAT5. Additionally, many of these cis-regulatory regions were conserved evolutionarily and displayed correlated enhancer:promoter acetylation. Together, these findings define a cis-regulatory enhancer network for Epo signaling during erythropoiesis, and provide the framework for future studies involving the interplay of epigenetics and Epo signaling.
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Affiliation(s)
- Andrea A Perreault
- Department of Molecular Physiology and Biophysics, Chemical and Physical Biology Program, Vanderbilt Genetics Institute, Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, TN
| | - Mary Lauren Benton
- Department of Biomedical Informatics, Vanderbilt University, Nashville, TN
| | - Mark J Koury
- Division of Hematology/Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Stephen J Brandt
- Department of Cancer Biology, Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN
| | - Bryan J Venters
- Department of Molecular Physiology and Biophysics, Chemical and Physical Biology Program, Vanderbilt Genetics Institute, Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, TN.
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47
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Simonik EA, Cai Y, Kimmelshue KN, Brantley-Sieders DM, Loomans HA, Andl CD, Westlake GM, Youngblood VM, Chen J, Yarbrough WG, Brown BT, Nagarajan L, Brandt SJ. LIM-Only Protein 4 (LMO4) and LIM Domain Binding Protein 1 (LDB1) Promote Growth and Metastasis of Human Head and Neck Cancer (LMO4 and LDB1 in Head and Neck Cancer). PLoS One 2016; 11:e0164804. [PMID: 27780223 PMCID: PMC5079595 DOI: 10.1371/journal.pone.0164804] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 10/01/2016] [Indexed: 12/18/2022] Open
Abstract
Squamous cell carcinoma of the head and neck (HNSCC) accounts for more than 300,000 deaths worldwide per year as a consequence of tumor cell invasion of adjacent structures or metastasis. LIM-only protein 4 (LMO4) and LIM-domain binding protein 1 (LDB1), two directly interacting transcriptional adaptors that have important roles in normal epithelial cell differentiation, have been associated with increased metastasis, decreased differentiation, and shortened survival in carcinoma of the breast. Here, we implicate two LDB1-binding proteins, single-stranded binding protein 2 (SSBP2) and 3 (SSBP3), in controlling LMO4 and LDB1 protein abundance in HNSCC and in regulating specific tumor cell functions in this disease. First, we found that the relative abundance of LMO4, LDB1, and the two SSBPs correlated very significantly in a panel of human HNSCC cell lines. Second, expression of these proteins in tumor primaries and lymph nodes involved by metastasis were concordant in 3 of 3 sets of tissue. Third, using a Matrigel invasion and organotypic reconstruct assay, CRISPR/Cas9-mediated deletion of LDB1 in the VU-SCC-1729 cell line, which is highly invasive of basement membrane and cellular monolayers, reduced tumor cell invasiveness and migration, as well as proliferation on tissue culture plastic. Finally, inactivation of the LDB1 gene in these cells decreased growth and vascularization of xenografted human tumor cells in vivo. These data show that LMO4, LDB1, and SSBP2 and/or SSBP3 regulate metastasis, proliferation, and angiogenesis in HNSCC and provide the first evidence that SSBPs control LMO4 and LDB1 protein abundance in a cancer context.
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Affiliation(s)
- Elizabeth A. Simonik
- Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, TN, United States of America
| | - Ying Cai
- Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, TN, United States of America
| | - Katherine N. Kimmelshue
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States of America
| | - Dana M. Brantley-Sieders
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States of America
| | - Holli A. Loomans
- Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, TN, United States of America
| | - Claudia D. Andl
- Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, TN, United States of America
- Department of Surgery, Vanderbilt University Medical Center, Nashville, TN, United States of America
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, United States of America
| | - Grant M. Westlake
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States of America
| | - Victoria M. Youngblood
- Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, TN, United States of America
| | - Jin Chen
- Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, TN, United States of America
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States of America
- Department of Cell & Developmental Biology, Vanderbilt University Medical Center, Nashville, TN, United States of America
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, United States of America
- VA Tennessee Valley Healthcare System, Nashville, TN, United States of America
| | - Wendell G. Yarbrough
- Department of Otolaryngology and Barry Baker Laboratory for Head and Neck Oncology, Vanderbilt University School of Medicine, Nashville, TN, United States of America
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, United States of America
| | - Brandee T. Brown
- Department of Otolaryngology and Barry Baker Laboratory for Head and Neck Oncology, Vanderbilt University School of Medicine, Nashville, TN, United States of America
| | - Lalitha Nagarajan
- Department of Genetics, University of Texas M.D. Anderson Cancer Center, Houston, TX, United States of America
| | - Stephen J. Brandt
- Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, TN, United States of America
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States of America
- Department of Cell & Developmental Biology, Vanderbilt University Medical Center, Nashville, TN, United States of America
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, United States of America
- VA Tennessee Valley Healthcare System, Nashville, TN, United States of America
- * E-mail:
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48
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Ma Z, Li M, Roy S, Liu KJ, Romine ML, Lane DC, Patel SK, Cai HN. Chromatin boundary elements organize genomic architecture and developmental gene regulation in Drosophila Hox clusters. World J Biol Chem 2016; 7:223-230. [PMID: 27621770 PMCID: PMC4997523 DOI: 10.4331/wjbc.v7.i3.223] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Revised: 04/14/2016] [Accepted: 07/13/2016] [Indexed: 02/05/2023] Open
Abstract
The three-dimensional (3D) organization of the eukaryotic genome is critical for its proper function. Evidence suggests that extensive chromatin loops form the building blocks of the genomic architecture, separating genes and gene clusters into distinct functional domains. These loops are anchored in part by a special type of DNA elements called chromatin boundary elements (CBEs). CBEs were originally found to insulate neighboring genes by blocking influences of transcriptional enhancers or the spread of silent chromatin. However, recent results show that chromatin loops can also play a positive role in gene regulation by looping out intervening DNA and “delivering” remote enhancers to gene promoters. In addition, studies from human and model organisms indicate that the configuration of chromatin loops, many of which are tethered by CBEs, is dynamically regulated during cell differentiation. In particular, a recent work by Li et al has shown that the SF1 boundary, located in the Drosophila Hox cluster, regulates local genes by tethering different subsets of chromatin loops: One subset enclose a neighboring gene ftz, limiting its access by the surrounding Scr enhancers and restrict the spread of repressive histones during early embryogenesis; and the other loops subdivide the Scr regulatory region into independent domains of enhancer accessibility. The enhancer-blocking activity of these CBE elements varies greatly in strength and tissue distribution. Further, tandem pairing of SF1 and SF2 facilitate the bypass of distal enhancers in transgenic flies, providing a mechanism for endogenous enhancers to circumvent genomic interruptions resulting from chromosomal rearrangement. This study demonstrates how a network of chromatin boundaries, centrally organized by SF1, can remodel the 3D genome to facilitate gene regulation during development.
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49
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Rowe RG, Wang LD, Coma S, Han A, Mathieu R, Pearson DS, Ross S, Sousa P, Nguyen PT, Rodriguez A, Wagers AJ, Daley GQ. Developmental regulation of myeloerythroid progenitor function by the Lin28b-let-7-Hmga2 axis. J Exp Med 2016; 213:1497-512. [PMID: 27401346 PMCID: PMC4986532 DOI: 10.1084/jem.20151912] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 05/18/2016] [Indexed: 01/01/2023] Open
Abstract
Daley and collaborators show that endogenous Lin28b drives erythroid-dominant fetal hematopoiesis and that decreases in Lin28b activate adult granulocyte-predominant hematopoiesis. For appropriate development, tissue and organ system morphogenesis and maturation must occur in synchrony with the overall developmental requirements of the host. Mistiming of such developmental events often results in disease. The hematopoietic system matures from the fetal state, characterized by robust erythrocytic output that supports prenatal growth in the hypoxic intrauterine environment, to the postnatal state wherein granulocytes predominate to provide innate immunity. Regulation of the developmental timing of these myeloerythroid states is not well understood. In this study, we find that expression of the heterochronic factor Lin28b decreases in common myeloid progenitors during hematopoietic maturation to adulthood in mice. This decrease in Lin28b coincides with accumulation of mature let-7 microRNAs, whose biogenesis is regulated by Lin28 proteins. We find that inhibition of let-7 in the adult hematopoietic system recapitulates fetal erythroid-dominant hematopoiesis. Conversely, deletion of Lin28b or ectopic activation of let-7 microRNAs in the fetal state induces a shift toward adult-like myeloid-dominant output. Furthermore, we identify Hmga2 as an effector of this genetic switch. These studies provide the first detailed analysis of the roles of endogenous Lin28b and let-7 in the timing of hematopoietic states during development.
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Affiliation(s)
- R Grant Rowe
- Stem Cell Transplantation Program, Stem Cell Program, Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, MA 02215
| | - Leo D Wang
- Stem Cell Transplantation Program, Stem Cell Program, Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, MA 02215 Harvard Stem Cell Institute, Cambridge, MA 02138 Joslin Diabetes Center, Boston, MA 02215
| | - Silvia Coma
- Stem Cell Transplantation Program, Stem Cell Program, Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, MA 02215
| | - Areum Han
- Stem Cell Transplantation Program, Stem Cell Program, Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, MA 02215 Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
| | - Ronald Mathieu
- Harvard Stem Cell Institute, Cambridge, MA 02138 Flow Cytometry Laboratory, Boston Children's Hospital, Boston, MA 02115
| | - Daniel S Pearson
- Stem Cell Transplantation Program, Stem Cell Program, Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, MA 02215
| | - Samantha Ross
- Stem Cell Transplantation Program, Stem Cell Program, Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, MA 02215
| | - Patricia Sousa
- Stem Cell Transplantation Program, Stem Cell Program, Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, MA 02215
| | - Phi T Nguyen
- Harvard Stem Cell Institute, Cambridge, MA 02138 Joslin Diabetes Center, Boston, MA 02215
| | - Antony Rodriguez
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030
| | - Amy J Wagers
- Harvard Stem Cell Institute, Cambridge, MA 02138 Joslin Diabetes Center, Boston, MA 02215 Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138
| | - George Q Daley
- Stem Cell Transplantation Program, Stem Cell Program, Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, MA 02215 Harvard Stem Cell Institute, Cambridge, MA 02138 Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115 Howard Hughes Medical Institute, Boston, MA 02115 Division of Hematology, Brigham and Women's Hospital, Boston, MA 02115 Manton Center for Orphan Disease Research, Boston, MA 02115
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50
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Insight into GATA1 transcriptional activity through interrogation of cis elements disrupted in human erythroid disorders. Proc Natl Acad Sci U S A 2016; 113:4434-9. [PMID: 27044088 DOI: 10.1073/pnas.1521754113] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Whole-exome sequencing has been incredibly successful in identifying causal genetic variants and has revealed a number of novel genes associated with blood and other diseases. One limitation of this approach is that it overlooks mutations in noncoding regulatory elements. Furthermore, the mechanisms by which mutations in transcriptionalcis-regulatory elements result in disease remain poorly understood. Here we used CRISPR/Cas9 genome editing to interrogate three such elements harboring mutations in human erythroid disorders, which in all cases are predicted to disrupt a canonical binding motif for the hematopoietic transcription factor GATA1. Deletions of as few as two to four nucleotides resulted in a substantial decrease (>80%) in target gene expression. Isolated deletions of the canonical GATA1 binding motif completely abrogated binding of the cofactor TAL1, which binds to a separate motif. Having verified the functionality of these three GATA1 motifs, we demonstrate strong evolutionary conservation of GATA1 motifs in regulatory elements proximal to other genes implicated in erythroid disorders, and show that targeted disruption of such elements results in altered gene expression. By modeling transcription factor binding patterns, we show that multiple transcription factors are associated with erythroid gene expression, and have created predictive maps modeling putative disruptions of their binding sites at key regulatory elements. Our study provides insight into GATA1 transcriptional activity and may prove a useful resource for investigating the pathogenicity of noncoding variants in human erythroid disorders.
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