151
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Woodley CM, Romer AS, Wang J, Guarnaccia AD, Elion DL, Maxwell JN, Guerrazzi K, McCann TS, Popay TM, Matlock BK, Flaherty DK, Lorey SL, Liu Q, Tansey WP, Weissmiller AM. Multiple interactions of the oncoprotein transcription factor MYC with the SWI/SNF chromatin remodeler. Oncogene 2021; 40:3593-3609. [PMID: 33931740 PMCID: PMC8141032 DOI: 10.1038/s41388-021-01804-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 04/07/2021] [Accepted: 04/15/2021] [Indexed: 02/03/2023]
Abstract
The SNF5 subunit of the SWI/SNF chromatin remodeling complex has been shown to act as a tumor suppressor through multiple mechanisms, including impairing the ability of the oncoprotein transcription factor MYC to bind chromatin. Beyond SNF5, however, it is unknown to what extent MYC can access additional SWI/SNF subunits or how these interactions affect the ability of MYC to drive transcription, particularly in SNF5-null cancers. Here, we report that MYC interacts with multiple SWI/SNF components independent of SNF5. We show that MYC binds the pan-SWI/SNF subunit BAF155 through the BAF155 SWIRM domain, an interaction that is inhibited by the presence of SNF5. In SNF5-null cells, MYC binds with remaining SWI/SNF components to essential genes, although for a purpose that is distinct from chromatin remodeling. Analysis of MYC-SWI/SNF target genes in SNF5-null cells reveals that they are associated with core biological functions of MYC linked to protein synthesis. These data reveal that MYC can bind SWI/SNF in an SNF5-independent manner and that SNF5 modulates access of MYC to core SWI/SNF complexes. This work provides a framework in which to interrogate the influence of SWI/SNF on MYC function in cancers in which SWI/SNF or MYC are altered.
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Affiliation(s)
- Chase M Woodley
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Alexander S Romer
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, USA
| | - Jing Wang
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alissa D Guarnaccia
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - David L Elion
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Jack N Maxwell
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, USA
| | - Kiana Guerrazzi
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Tyler S McCann
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Tessa M Popay
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Brittany K Matlock
- Vanderbilt University Medical Center Flow Cytometry Shared Resource, Vanderbilt University Medical Center, Nashville, TN, USA
| | - David K Flaherty
- Vanderbilt University Medical Center Flow Cytometry Shared Resource, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Shelly L Lorey
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Qi Liu
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - William P Tansey
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - April M Weissmiller
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, USA.
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152
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Liscovitch-Brauer N, Montalbano A, Deng J, Méndez-Mancilla A, Wessels HH, Moss NG, Kung CY, Sookdeo A, Guo X, Geller E, Jaini S, Smibert P, Sanjana NE. Profiling the genetic determinants of chromatin accessibility with scalable single-cell CRISPR screens. Nat Biotechnol 2021; 39:1270-1277. [PMID: 33927415 DOI: 10.1038/s41587-021-00902-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 03/13/2021] [Accepted: 03/17/2021] [Indexed: 12/17/2022]
Abstract
CRISPR screens have been used to connect genetic perturbations with changes in gene expression and phenotypes. Here we describe a CRISPR-based, single-cell combinatorial indexing assay for transposase-accessible chromatin (CRISPR-sciATAC) to link genetic perturbations to genome-wide chromatin accessibility in a large number of cells. In human myelogenous leukemia cells, we apply CRISPR-sciATAC to target 105 chromatin-related genes, generating chromatin accessibility data for ~30,000 single cells. We correlate the loss of specific chromatin remodelers with changes in accessibility globally and at the binding sites of individual transcription factors (TFs). For example, we show that loss of the H3K27 methyltransferase EZH2 increases accessibility at heterochromatic regions involved in embryonic development and triggers expression of genes in the HOXA and HOXD clusters. At a subset of regulatory sites, we also analyze changes in nucleosome spacing following the loss of chromatin remodelers. CRISPR-sciATAC is a high-throughput, single-cell method for studying the effect of genetic perturbations on chromatin in normal and disease states.
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Affiliation(s)
- Noa Liscovitch-Brauer
- New York Genome Center, New York, NY, USA.,Department of Biology, New York University, New York, NY, USA
| | - Antonino Montalbano
- New York Genome Center, New York, NY, USA.,Department of Biology, New York University, New York, NY, USA
| | - Jiale Deng
- New York Genome Center, New York, NY, USA.,Department of Biology, New York University, New York, NY, USA
| | - Alejandro Méndez-Mancilla
- New York Genome Center, New York, NY, USA.,Department of Biology, New York University, New York, NY, USA
| | - Hans-Hermann Wessels
- New York Genome Center, New York, NY, USA.,Department of Biology, New York University, New York, NY, USA
| | - Nicholas G Moss
- New York Genome Center, New York, NY, USA.,Department of Biology, New York University, New York, NY, USA
| | - Chia-Yu Kung
- New York Genome Center, New York, NY, USA.,Department of Biology, New York University, New York, NY, USA
| | - Akash Sookdeo
- New York Genome Center, New York, NY, USA.,Department of Biology, New York University, New York, NY, USA
| | - Xinyi Guo
- New York Genome Center, New York, NY, USA.,Department of Biology, New York University, New York, NY, USA
| | - Evan Geller
- New York Genome Center, New York, NY, USA.,Department of Biology, New York University, New York, NY, USA
| | - Suma Jaini
- New York Genome Center, New York, NY, USA.,Technology Innovation Lab, New York Genome Center, New York, NY, USA
| | - Peter Smibert
- New York Genome Center, New York, NY, USA.,Technology Innovation Lab, New York Genome Center, New York, NY, USA
| | - Neville E Sanjana
- New York Genome Center, New York, NY, USA. .,Department of Biology, New York University, New York, NY, USA.
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153
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Interplay of BAF and MLL4 promotes cell type-specific enhancer activation. Nat Commun 2021; 12:1630. [PMID: 33712604 PMCID: PMC7955098 DOI: 10.1038/s41467-021-21893-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 02/10/2021] [Indexed: 01/05/2023] Open
Abstract
Cell type-specific enhancers are activated by coordinated actions of lineage-determining transcription factors (LDTFs) and chromatin regulators. The SWI/SNF chromatin remodeling complex BAF and the histone H3K4 methyltransferase MLL4 (KMT2D) are both implicated in enhancer activation. However, the interplay between BAF and MLL4 in enhancer activation remains unclear. Using adipogenesis as a model system, we identify BAF as the major SWI/SNF complex that colocalizes with MLL4 and LDTFs on active enhancers and is required for cell differentiation. In contrast, the promoter enriched SWI/SNF complex PBAF is dispensable for adipogenesis. By depleting BAF subunits SMARCA4 (BRG1) and SMARCB1 (SNF5) as well as MLL4 in cells, we show that BAF and MLL4 reciprocally regulate each other’s binding on active enhancers before and during adipogenesis. By focusing on enhancer activation by the adipogenic pioneer transcription factor C/EBPβ without inducing cell differentiation, we provide direct evidence for an interdependent relationship between BAF and MLL4 in activating cell type-specific enhancers. Together, these findings reveal a positive feedback between BAF and MLL4 in promoting LDTF-dependent activation of cell type-specific enhancers. The SWI/SNF complex BAF and the histone H3K4 methyltransferase MLL4 (KMT2D) play critical roles in enhancer activation, however the interplay between them has remained unclear. Here the authors show that BAF and MLL4 are interdependent in promoting enhancer activation by lineage-determining transcription factors during adipogenesis.
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154
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Creb5 establishes the competence for Prg4 expression in articular cartilage. Commun Biol 2021; 4:332. [PMID: 33712729 PMCID: PMC7955038 DOI: 10.1038/s42003-021-01857-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 02/12/2021] [Indexed: 12/13/2022] Open
Abstract
A hallmark of cells comprising the superficial zone of articular cartilage is their expression of lubricin, encoded by the Prg4 gene, that lubricates the joint and protects against the development of arthritis. Here, we identify Creb5 as a transcription factor that is specifically expressed in superficial zone articular chondrocytes and is required for TGF-β and EGFR signaling to induce Prg4 expression. Notably, forced expression of Creb5 in chondrocytes derived from the deep zone of the articular cartilage confers the competence for TGF-β and EGFR signals to induce Prg4 expression. Chromatin-IP and ATAC-Seq analyses have revealed that Creb5 directly binds to two Prg4 promoter-proximal regulatory elements, that display an open chromatin conformation specifically in superficial zone articular chondrocytes; and which work in combination with a more distal regulatory element to drive induction of Prg4 by TGF-β. Our results indicate that Creb5 is a critical regulator of Prg4/lubricin expression in the articular cartilage.
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155
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Kyryachenko S, Georges A, Yu M, Barrandou T, Guo L, Bruneval P, Rubio T, Gronwald J, Baraki H, Kutschka I, Aras KK, Efimov IR, Norris RA, Voigt N, Bouatia-Naji N. Chromatin Accessibility of Human Mitral Valves and Functional Assessment of MVP Risk Loci. Circ Res 2021; 128:e84-e101. [PMID: 33508947 PMCID: PMC8316483 DOI: 10.1161/circresaha.120.317581] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Abstract
RATIONALE Mitral valve prolapse (MVP) is a common valvopathy that leads to mitral insufficiency, heart failure, and sudden death. Functional genomic studies in mitral valves are needed to better characterize MVP-associated variants and target genes. OBJECTIVE To establish the chromatin accessibility profiles and assess functionality of variants and narrow down target genes at MVP loci. METHODS AND RESULTS We mapped the open chromatin regions in nuclei from 11 human pathogenic and 7 nonpathogenic mitral valves by an assay for transposase-accessible chromatin with high-throughput sequencing. Open chromatin peaks were globally similar between pathogenic and nonpathogenic valves. Compared with the heart tissue and cardiac fibroblasts, we found that MV-specific assay for transposase-accessible chromatin with high-throughput sequencing peaks are enriched near genes involved in extracellular matrix organization, chondrocyte differentiation, and connective tissue development. One of the most enriched motifs in MV-specific open chromatin peaks was for the nuclear factor of activated T cells family of TFs (transcription factors) involved in valve endocardial and interstitial cell formation. We also found that MVP-associated variants were significantly enriched (P<0.05) in mitral valve open chromatin peaks. Integration of the assay for transposase-accessible chromatin with high-throughput sequencing data with risk loci, extensive functional annotation, and gene reporter assay suggest plausible causal variants for rs2641440 at the SMG6/SRR locus and rs6723013 at the IGFBP2/IGFBP5/TNS1 locus. CRISPR-Cas9 deletion of the sequence including rs6723013 in human fibroblasts correlated with increased expression only for TNS1. Circular chromatin conformation capture followed by high-throughput sequencing experiments provided evidence for several target genes, including SRR, HIC1, and DPH1 at the SMG6/SRR locus and further supported TNS1 as the most likely target gene on chromosome 2. CONCLUSIONS Here, we describe unprecedented genome-wide open chromatin profiles from human pathogenic and nonpathogenic MVs and report specific gene regulation profiles, compared with the heart. We also report in vitro functional evidence for potential causal variants and target genes at MVP risk loci involving established and new biological mechanisms. Graphic Abstract: A graphic abstract is available for this article.
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Affiliation(s)
| | | | - Mengyao Yu
- Université de Paris, PARCC, Inserm, Paris,
France
| | | | - Lilong Guo
- Department of Regenerative Medicine and Cell Biology,
Medical University of South Carolina, Charleston, SC, USA
- Department of Medicine, Medical University of South
Carolina, Charleston, SC, USA
| | | | - Tony Rubio
- Institute of Pharmacology and Toxicology, University
Medical Center Göttingen, Germany
- DZHK (German Center for Cardiovascular Research), Partner
Site Göttingen, Germany
| | - Judith Gronwald
- Institute of Pharmacology and Toxicology, University
Medical Center Göttingen, Germany
- DZHK (German Center for Cardiovascular Research), Partner
Site Göttingen, Germany
| | - Hassina Baraki
- DZHK (German Center for Cardiovascular Research), Partner
Site Göttingen, Germany
- Department of Thoracic and Cardiovascular Surgery,
University Medical Center, Göttingen, Germany
| | - Ingo Kutschka
- DZHK (German Center for Cardiovascular Research), Partner
Site Göttingen, Germany
- Department of Thoracic and Cardiovascular Surgery,
University Medical Center, Göttingen, Germany
| | - Kedar K. Aras
- Department of Biomedical Engineering, George Washington
University, Washington, DC, USA
| | - Igor R. Efimov
- Department of Biomedical Engineering, George Washington
University, Washington, DC, USA
| | - Russel A. Norris
- Department of Regenerative Medicine and Cell Biology,
Medical University of South Carolina, Charleston, SC, USA
- Department of Medicine, Medical University of South
Carolina, Charleston, SC, USA
| | - Niels Voigt
- Institute of Pharmacology and Toxicology, University
Medical Center Göttingen, Germany
- DZHK (German Center for Cardiovascular Research), Partner
Site Göttingen, Germany
- Cluster of Excellence “Multiscale Bioimaging: from
Molecular Machines to Networks of Excitable Cells (MBExC), University of
Göttingen, Germany
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156
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Seo J, Koçak DD, Bartelt LC, Williams CA, Barrera A, Gersbach CA, Reddy TE. AP-1 subunits converge promiscuously at enhancers to potentiate transcription. Genome Res 2021; 31:538-550. [PMID: 33674350 PMCID: PMC8015846 DOI: 10.1101/gr.267898.120] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 02/17/2021] [Indexed: 12/12/2022]
Abstract
The AP-1 transcription factor (TF) dimer contributes to many biological processes and environmental responses. AP-1 can be composed of many interchangeable subunits. Unambiguously determining the binding locations of these subunits in the human genome is challenging because of variable antibody specificity and affinity. Here, we definitively establish the genome-wide binding patterns of five AP-1 subunits by using CRISPR to introduce a common antibody tag on each subunit. We find limited evidence for strong dimerization preferences between subunits at steady state and find that, under a stimulus, dimerization patterns reflect changes in the transcriptome. Further, our analysis suggests that canonical AP-1 motifs indiscriminately recruit all AP-1 subunits to genomic sites, which we term AP-1 hotspots. We find that AP-1 hotspots are predictive of cell type–specific gene expression and of genomic responses to glucocorticoid signaling (more so than super-enhancers) and are significantly enriched in disease-associated genetic variants. Together, these results support a model where promiscuous binding of many AP-1 subunits to the same genomic location play a key role in regulating cell type–specific gene expression and environmental responses.
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Affiliation(s)
- Jungkyun Seo
- Department of Biostatistics and Bioinformatics, Division of Integrative Genomics, Duke University Medical Center, Durham, North Carolina 27708, USA.,Computational Biology and Bioinformatics Graduate Program, Duke University, Durham, North Carolina 27708, USA.,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA.,Center for Advanced Genomic Technologies, Duke University, Durham, North Carolina 27708, USA
| | - D Dewran Koçak
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA.,Center for Advanced Genomic Technologies, Duke University, Durham, North Carolina 27708, USA.,Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA
| | - Luke C Bartelt
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA.,University Program in Genetics and Genomics, Duke University, Durham, North Carolina 27708, USA
| | - Courtney A Williams
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA.,Center for Advanced Genomic Technologies, Duke University, Durham, North Carolina 27708, USA
| | - Alejandro Barrera
- Department of Biostatistics and Bioinformatics, Division of Integrative Genomics, Duke University Medical Center, Durham, North Carolina 27708, USA.,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA.,Center for Advanced Genomic Technologies, Duke University, Durham, North Carolina 27708, USA
| | - Charles A Gersbach
- Computational Biology and Bioinformatics Graduate Program, Duke University, Durham, North Carolina 27708, USA.,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA.,Center for Advanced Genomic Technologies, Duke University, Durham, North Carolina 27708, USA.,Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA.,University Program in Genetics and Genomics, Duke University, Durham, North Carolina 27708, USA.,Department of Surgery, Duke University Medical Center, Durham, North Carolina 27708, USA
| | - Timothy E Reddy
- Department of Biostatistics and Bioinformatics, Division of Integrative Genomics, Duke University Medical Center, Durham, North Carolina 27708, USA.,Computational Biology and Bioinformatics Graduate Program, Duke University, Durham, North Carolina 27708, USA.,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA.,Center for Advanced Genomic Technologies, Duke University, Durham, North Carolina 27708, USA.,Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA.,University Program in Genetics and Genomics, Duke University, Durham, North Carolina 27708, USA.,Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina 27708, USA
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157
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Zhang C, Zhang X, Huang L, Guan Y, Huang X, Tian X, Zhang L, Tao W. ATF3 drives senescence by reconstructing accessible chromatin profiles. Aging Cell 2021; 20:e13315. [PMID: 33539668 PMCID: PMC7963335 DOI: 10.1111/acel.13315] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 01/05/2021] [Accepted: 01/09/2021] [Indexed: 12/11/2022] Open
Abstract
Chromatin organization and transcriptional profiles undergo tremendous reordering during senescence. However, uncovering the regulatory mechanisms between chromatin reconstruction and gene expression in senescence has been elusive. Here, we depicted the landscapes of both chromatin accessibility and gene expression to reveal gene regulatory networks in human umbilical vein endothelial cell (HUVEC) senescence and found that chromatin accessibilities are redistributed during senescence. Particularly, the intergenic chromatin was massively shifted with the increased accessibility regions (IARs) or decreased accessibility regions (DARs), which were mainly enhancer elements. We defined AP‐1 transcription factor family as being responsible for driving chromatin accessibility reconstruction in IARs, where low DNA methylation improved binding affinity of AP‐1 and further increased the chromatin accessibility. Among AP‐1 transcription factors, we confirmed ATF3 was critical to reconstruct chromatin accessibility to promote cellular senescence. Our results described a dynamic landscape of chromatin accessibility whose remodeling contributes to the senescence program, we identified that AP‐1 was capable of reorganizing the chromatin accessibility profile to regulate senescence.
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Affiliation(s)
- Chao Zhang
- The MOE Key Laboratory of Cell Proliferation and Differentiation School of Life Sciences Peking University Beijing China
- PKU‐Tsinghua‐NIBS Graduate Program School of Life Sciences Peking University Beijing China
| | - Xuebin Zhang
- The MOE Key Laboratory of Cell Proliferation and Differentiation School of Life Sciences Peking University Beijing China
| | - Li Huang
- The MOE Key Laboratory of Cell Proliferation and Differentiation School of Life Sciences Peking University Beijing China
| | - Yiting Guan
- The MOE Key Laboratory of Cell Proliferation and Differentiation School of Life Sciences Peking University Beijing China
| | - Xiaoke Huang
- The MOE Key Laboratory of Cell Proliferation and Differentiation School of Life Sciences Peking University Beijing China
| | - Xiao‐Li Tian
- Department of Human Population Genetics Human Aging Research Institute (HARI) and School of Life Sciences Nanchang University Nanchang China
| | - Lijun Zhang
- The MOE Key Laboratory of Cell Proliferation and Differentiation School of Life Sciences Peking University Beijing China
| | - Wei Tao
- The MOE Key Laboratory of Cell Proliferation and Differentiation School of Life Sciences Peking University Beijing China
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158
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Kitazawa T, Machlab D, Joshi O, Maiorano N, Kohler H, Ducret S, Kessler S, Gezelius H, Soneson C, Papasaikas P, López-Bendito G, Stadler MB, Rijli FM. A unique bipartite Polycomb signature regulates stimulus-response transcription during development. Nat Genet 2021; 53:379-391. [PMID: 33603234 PMCID: PMC7610396 DOI: 10.1038/s41588-021-00789-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 01/19/2021] [Indexed: 01/31/2023]
Abstract
Rapid cellular responses to environmental stimuli are fundamental for development and maturation. Immediate early genes can be transcriptionally induced within minutes in response to a variety of signals. How their induction levels are regulated and their untimely activation by spurious signals prevented during development is poorly understood. We found that in developing sensory neurons, before perinatal sensory-activity-dependent induction, immediate early genes are embedded into a unique bipartite Polycomb chromatin signature, carrying active H3K27ac on promoters but repressive Ezh2-dependent H3K27me3 on gene bodies. This bipartite signature is widely present in developing cell types, including embryonic stem cells. Polycomb marking of gene bodies inhibits mRNA elongation, dampening productive transcription, while still allowing for fast stimulus-dependent mark removal and bipartite gene induction. We reveal a developmental epigenetic mechanism regulating the rapidity and amplitude of the transcriptional response to relevant stimuli, while preventing inappropriate activation of stimulus-response genes.
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Affiliation(s)
- Taro Kitazawa
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Dania Machlab
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland,Swiss Institute of Bioinformatics, Basel, Switzerland,University of Basel, Basel, Switzerland
| | - Onkar Joshi
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Nicola Maiorano
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Hubertus Kohler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Sebastien Ducret
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Sandra Kessler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Henrik Gezelius
- Instituto de Neurociencias de Alicante, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas (UMH-CSIC), Sant Joan d’Alacant, Spain
| | - Charlotte Soneson
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland,Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Panagiotis Papasaikas
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland,Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Guillermina López-Bendito
- Instituto de Neurociencias de Alicante, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas (UMH-CSIC), Sant Joan d’Alacant, Spain
| | - Michael B. Stadler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland,Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Filippo M. Rijli
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland,University of Basel, Basel, Switzerland,Correspondence to:
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159
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Chasse MH, Johnson BK, Boguslawski EA, Sorensen KM, Rosien JE, Kang MH, Reynolds CP, Heo L, Madaj ZB, Beddows I, Foxa GE, Kitchen‐Goosen SM, Williams BO, Triche TJ, Grohar PJ. Mithramycin induces promoter reprogramming and differentiation of rhabdoid tumor. EMBO Mol Med 2021; 13:e12640. [PMID: 33332735 PMCID: PMC7863405 DOI: 10.15252/emmm.202012640] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 11/18/2020] [Accepted: 11/20/2020] [Indexed: 12/21/2022] Open
Abstract
Rhabdoid tumor (RT) is a pediatric cancer characterized by the inactivation of SMARCB1, a subunit of the SWI/SNF chromatin remodeling complex. Although this deletion is the known oncogenic driver, there are limited effective therapeutic options for these patients. Here we use unbiased screening of cell line panels to identify a heightened sensitivity of rhabdoid tumor to mithramycin and the second-generation analogue EC8042. The sensitivity of MMA and EC8042 was superior to traditional DNA damaging agents and linked to the causative mutation of the tumor, SMARCB1 deletion. Mithramycin blocks SMARCB1-deficient SWI/SNF activity and displaces the complex from chromatin to cause an increase in H3K27me3. This triggers chromatin remodeling and enrichment of H3K27ac at chromHMM-defined promoters to restore cellular differentiation. These effects occurred at concentrations not associated with DNA damage and were not due to global chromatin remodeling or widespread gene expression changes. Importantly, a single 3-day infusion of EC8042 caused dramatic regressions of RT xenografts, recapitulated the increase in H3K27me3, and cellular differentiation described in vitro to completely cure three out of eight mice.
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Affiliation(s)
| | | | | | | | | | - Min H Kang
- Texas Tech University Health Sciences CenterLubbockTXUSA
| | | | - Lyong Heo
- Van Andel Research InstituteGrand RapidsMIUSA
| | | | - Ian Beddows
- Van Andel Research InstituteGrand RapidsMIUSA
| | | | | | | | | | - Patrick J Grohar
- Van Andel Research InstituteGrand RapidsMIUSA
- The Children's Hospital of PhiladelphiaPhiladelphiaPAUSA
- University of PennsylvaniaPerelman School of MedicinePhiladelphiaPAUSA
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160
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Abstract
Drosophila melanogaster males reduce courtship behaviour after mating failure. In the lab, such conditioned courtship suppression, aka 'courtship conditioning', serves as a complex learning and memory assay. Interestingly, variations in the courtship conditioning assay can establish different types of memory. Here, we review research investigating the underlying cellular and molecular mechanisms that allow male flies to form memories of previous mating failures.
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Affiliation(s)
- Nicholas Raun
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Spencer Jones
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Jamie M Kramer
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
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161
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Griffith BGC, Upstill-Goddard R, Brunton H, Grimes GR, Biankin AV, Serrels B, Byron A, Frame MC. FAK regulates IL-33 expression by controlling chromatin accessibility at c-Jun motifs. Sci Rep 2021; 11:229. [PMID: 33420223 PMCID: PMC7794255 DOI: 10.1038/s41598-020-80111-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 11/10/2020] [Indexed: 01/29/2023] Open
Abstract
Focal adhesion kinase (FAK) localizes to focal adhesions and is overexpressed in many cancers. FAK can also translocate to the nucleus, where it binds to, and regulates, several transcription factors, including MBD2, p53 and IL-33, to control gene expression by unknown mechanisms. We have used ATAC-seq to reveal that FAK controls chromatin accessibility at a subset of regulated genes. Integration of ATAC-seq and RNA-seq data showed that FAK-dependent chromatin accessibility is linked to differential gene expression, including of the FAK-regulated cytokine and transcriptional regulator interleukin-33 (Il33), which controls anti-tumor immunity. Analysis of the accessibility peaks on the Il33 gene promoter/enhancer regions revealed sequences for several transcription factors, including ETS and AP-1 motifs, and we show that c-Jun, a component of AP-1, regulates Il33 gene expression by binding to its enhancer in a FAK kinase-dependent manner. This work provides the first demonstration that FAK controls transcription via chromatin accessibility, identifying a novel mechanism by which nuclear FAK regulates biologically important gene expression.
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Affiliation(s)
- Billie G C Griffith
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - Rosanna Upstill-Goddard
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G61 1QH, UK
| | - Holly Brunton
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G61 1QH, UK
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
| | - Graeme R Grimes
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Andrew V Biankin
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G61 1QH, UK
| | - Bryan Serrels
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G61 1QH, UK.
- NanoString Technologies, Inc, Seattle, WA, 98109, USA.
| | - Adam Byron
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XR, UK.
| | - Margaret C Frame
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XR, UK.
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162
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Li Y, He Y, Peng J, Su Z, Li Z, Zhang B, Ma J, Zhuo M, Zou D, Liu X, Liu X, Wang W, Huang D, Xu M, Wang J, Deng H, Xue J, Xie W, Lan X, Chen M, Zhao Y, Wu W, David CJ. Mutant Kras co-opts a proto-oncogenic enhancer network in inflammation-induced metaplastic progenitor cells to initiate pancreatic cancer. NATURE CANCER 2021; 2:49-65. [PMID: 35121887 DOI: 10.1038/s43018-020-00134-z] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 09/29/2020] [Indexed: 02/07/2023]
Abstract
Kras-activating mutations display the highest incidence in pancreatic ductal adenocarcinoma. Pancreatic inflammation accelerates mutant Kras-driven tumorigenesis in mice, suggesting high selectivity in the cells that oncogenic Kras transforms, although the mechanisms dictating this specificity are poorly understood. Here we show that pancreatic inflammation is coupled to the emergence of a transient progenitor cell population that is readily transformed in the presence of mutant KrasG12D. These progenitors harbor a proto-oncogenic transcriptional program driven by a transient enhancer network. KrasG12D mutations lock this enhancer network in place, providing a sustained Kras-dependent oncogenic program that drives tumors throughout progression. Enhancer co-option occurs through functional interactions between the Kras-activated transcription factors Junb and Fosl1 and pancreatic lineage transcription factors, potentially accounting for inter-tissue specificity of oncogene transformation. The pancreatic ductal adenocarcinoma cell of origin thus provides an oncogenic transcriptional program that fuels tumor progression beyond initiation, accounting for the intra-tissue selectivity of Kras transformation.
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Affiliation(s)
- Yong Li
- Tsinghua University School of Medicine, Beijing, China
| | - Yi He
- Tsinghua University School of Medicine, Beijing, China
| | - Junya Peng
- Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Zhendong Su
- Tsinghua University School of Medicine, Beijing, China
- Peking University-Tsinghua Center for Life Sciences, Beijing, China
| | - Zeyao Li
- Tsinghua University School of Life Sciences, Beijing, China
| | - Bingjie Zhang
- Tsinghua University School of Life Sciences, Beijing, China
| | - Jing Ma
- Tsinghua University School of Life Sciences, Beijing, China
| | - Meilian Zhuo
- Tsinghua University School of Medicine, Beijing, China
| | - Di Zou
- Tsinghua University School of Medicine, Beijing, China
| | - Xinde Liu
- Tsinghua University School of Medicine, Beijing, China
| | - Xinhong Liu
- Tsinghua University School of Medicine, Beijing, China
| | - Wenze Wang
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Dan Huang
- Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Mengyue Xu
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Jianbin Wang
- Tsinghua University School of Medicine, Beijing, China
- Peking University-Tsinghua Center for Life Sciences, Beijing, China
| | - Haiteng Deng
- Tsinghua University School of Life Sciences, Beijing, China
| | - Jing Xue
- State Key Laboratory of Oncogenes and Related Genes, Stem Cell Research Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Wei Xie
- Peking University-Tsinghua Center for Life Sciences, Beijing, China
- Tsinghua University School of Life Sciences, Beijing, China
| | - Xun Lan
- Tsinghua University School of Medicine, Beijing, China
- Peking University-Tsinghua Center for Life Sciences, Beijing, China
| | - Mo Chen
- Tsinghua University School of Medicine, Beijing, China
| | - Yupei Zhao
- Peking University-Tsinghua Center for Life Sciences, Beijing, China.
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China.
| | - Wenming Wu
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China.
| | - Charles J David
- Tsinghua University School of Medicine, Beijing, China.
- Peking University-Tsinghua Center for Life Sciences, Beijing, China.
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163
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Orlando KA, Douglas AK, Abudu A, Wang Y, Tessier-Cloutier B, Su W, Peters A, Sherman LS, Moore R, Nguyen V, Negri GL, Colborne S, Morin GB, Kommoss F, Lang JD, Hendricks WP, Raupach EA, Pirrotte P, Huntsman DG, Trent JM, Parker JS, Raab JR, Weissman BE. Re-expression of SMARCA4/BRG1 in small cell carcinoma of ovary, hypercalcemic type (SCCOHT) promotes an epithelial-like gene signature through an AP-1-dependent mechanism. eLife 2020; 9:59073. [PMID: 33355532 PMCID: PMC7813545 DOI: 10.7554/elife.59073] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 12/22/2020] [Indexed: 12/12/2022] Open
Abstract
Small cell carcinoma of the ovary, hypercalcemic type (SCCOHT) is a rare and aggressive form of ovarian cancer. SCCOHT tumors have inactivating mutations in SMARCA4 (BRG1), one of the two mutually exclusive ATPases of the SWI/SNF chromatin remodeling complex. To address the role that BRG1 loss plays in SCCOHT tumorigenesis, we performed integrative multi-omic analyses in SCCOHT cell lines +/- BRG1 reexpression. BRG1 reexpression induced a gene and protein signature similar to an epithelial cell and gained chromatin accessibility sites correlated with other epithelial originating TCGA tumors. Gained chromatin accessibility and BRG1 recruited sites were strongly enriched for transcription-factor-binding motifs of AP-1 family members. Furthermore, AP-1 motifs were enriched at the promoters of highly upregulated epithelial genes. Using a dominant-negative AP-1 cell line, we found that both AP-1 DNA-binding activity and BRG1 reexpression are necessary for the gene and protein expression of epithelial genes. Our study demonstrates that BRG1 reexpression drives an epithelial-like gene and protein signature in SCCOHT cells that depends upon by AP-1 activity.
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Affiliation(s)
- Krystal Ann Orlando
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, United States.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Amber K Douglas
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Aierken Abudu
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, United States
| | - Yemin Wang
- Department of Pathology and Laboratory Medicine, University of British Columbia and Department of Molecular Oncology, British Columbia Cancer Research Institute, Vancouver, Canada
| | - Basile Tessier-Cloutier
- Department of Pathology and Laboratory Medicine, University of British Columbia and Department of Molecular Oncology, British Columbia Cancer Research Institute, Vancouver, Canada.,Department of Molecular Oncology, British Columbia Cancer Research Institute, Vancouver, Canada
| | - Weiping Su
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, United States
| | - Alec Peters
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, United States
| | - Larry S Sherman
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, United States.,Department Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, United States
| | - Rayvon Moore
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Vinh Nguyen
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, United States.,Curriculum in Toxicology and Environmental Medicine, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Gian Luca Negri
- Michael Smith Genome Science Centre, British Columbia Cancer Research Institute, Vancouver, Canada
| | - Shane Colborne
- Michael Smith Genome Science Centre, British Columbia Cancer Research Institute, Vancouver, Canada
| | - Gregg B Morin
- Michael Smith Genome Science Centre, British Columbia Cancer Research Institute, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | | | - Jessica D Lang
- Division of Integrated Cancer Genomics, Translational Genomics Research Institute (TGen), Phoenix, United States
| | - William Pd Hendricks
- Division of Integrated Cancer Genomics, Translational Genomics Research Institute (TGen), Phoenix, United States
| | - Elizabeth A Raupach
- Division of Integrated Cancer Genomics, Translational Genomics Research Institute (TGen), Phoenix, United States
| | - Patrick Pirrotte
- Collaborative Center for Translational Mass Spectrometry, Translational Genomics Research Institute (TGen), Phoenix, United States
| | - David G Huntsman
- Department of Pathology and Laboratory Medicine, University of British Columbia and Department of Molecular Oncology, British Columbia Cancer Research Institute, Vancouver, Canada.,Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, Canada
| | - Jeffrey M Trent
- Division of Integrated Cancer Genomics, Translational Genomics Research Institute (TGen), Phoenix, United States
| | - Joel S Parker
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, United States.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Jesse R Raab
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, United States.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Bernard E Weissman
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, United States.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, United States
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164
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Guan Y, Yang YJ, Nagarajan P, Ge Y. Transcriptional and signalling regulation of skin epithelial stem cells in homeostasis, wounds and cancer. Exp Dermatol 2020; 30:529-545. [PMID: 33249665 DOI: 10.1111/exd.14247] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 10/10/2020] [Accepted: 11/13/2020] [Indexed: 02/06/2023]
Abstract
The epidermis and skin appendages are maintained by their resident epithelial stem cells, which undergo long-term self-renewal and multilineage differentiation. Upon injury, stem cells are activated to mediate re-epithelialization and restore tissue function. During this process, they often mount lineage plasticity and expand their fates in response to damage signals. Stem cell function is tightly controlled by transcription machineries and signalling transductions, many of which derail in degenerative, inflammatory and malignant dermatologic diseases. Here, by describing both well-characterized and newly emerged pathways, we discuss the transcriptional and signalling mechanisms governing skin epithelial homeostasis, wound repair and squamous cancer. Throughout, we highlight common themes underscoring epithelial stem cell plasticity and tissue-level crosstalk in the context of skin physiology and pathology.
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Affiliation(s)
- Yinglu Guan
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Youn Joo Yang
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Priyadharsini Nagarajan
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yejing Ge
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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165
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Yap EL, Pettit NL, Davis CP, Nagy MA, Harmin DA, Golden E, Dagliyan O, Lin C, Rudolph S, Sharma N, Griffith EC, Harvey CD, Greenberg ME. Bidirectional perisomatic inhibitory plasticity of a Fos neuronal network. Nature 2020; 590:115-121. [PMID: 33299180 PMCID: PMC7864877 DOI: 10.1038/s41586-020-3031-0] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 10/15/2020] [Indexed: 01/06/2023]
Abstract
Behavioral experiences activate the Fos transcription factor (TF) in sparse populations of neurons that are critical for encoding and recalling specific events1–3. However, there is limited understanding of the mechanisms by which experience drives circuit reorganization to establish a network of Fos-activated cells. It is also unknown if Fos is required in this process beyond serving as a marker of recent neural activity and, if so, which of its many gene targets underlie circuit reorganization. Here we demonstrate that when mice engage in spatial exploration of novel environments, perisomatic inhibition of Fos-expressing hippocampal CA1 pyramidal neurons by parvalbumin (PV)-interneurons (INs) is enhanced, while perisomatic inhibition by cholecystokinin (CCK)-INs is weakened. This bidirectional modulation of inhibition is abolished when the function of the Fos TF complex is disrupted. Single-cell RNA-sequencing, ribosome-associated mRNA profiling, and chromatin analyses, combined with electrophysiology, reveal that Fos activates the transcription of Scg2 (secretogranin II), a gene that encodes multiple distinct neuropeptides, to coordinate these changes in inhibition. As PV- and CCK-INs mediate distinct features of pyramidal cell activity4–6, the Scg2-dependent reorganization of inhibitory synaptic input might be predicted to affect network function in vivo. Consistent with this prediction, hippocampal gamma rhythms and pyramidal cell coupling to CA1 theta are significantly altered with loss of Scg2. These findings reveal an instructive role for Fos and Scg2 in establishing a network of Fos-activated neurons via the rewiring of local inhibition to form a selectively modulated state. The opposing plasticity mechanisms on distinct inhibitory pathways may support the consolidation of memories over time.
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Affiliation(s)
- Ee-Lynn Yap
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Noah L Pettit
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | | | - M Aurel Nagy
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - David A Harmin
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Emily Golden
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Onur Dagliyan
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Cindy Lin
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | | | - Nikhil Sharma
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Eric C Griffith
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
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166
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Guerrero-Martínez JA, Ceballos-Chávez M, Koehler F, Peiró S, Reyes JC. TGFβ promotes widespread enhancer chromatin opening and operates on genomic regulatory domains. Nat Commun 2020; 11:6196. [PMID: 33273453 PMCID: PMC7713251 DOI: 10.1038/s41467-020-19877-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 11/05/2020] [Indexed: 02/07/2023] Open
Abstract
The Transforming Growth Factor-β (TGFβ) signaling pathway controls transcription by regulating enhancer activity. How TGFβ-regulated enhancers are selected and what chromatin changes are associated with TGFβ-dependent enhancers regulation are still unclear. Here we report that TGFβ treatment triggers fast and widespread increase in chromatin accessibility in about 80% of the enhancers of normal mouse mammary epithelial-gland cells, irrespective of whether they are activated, repressed or not regulated by TGFβ. This enhancer opening depends on both the canonical and non-canonical TGFβ pathways. Most TGFβ-regulated genes are located around enhancers regulated in the same way, often creating domains of several co-regulated genes that we term TGFβ regulatory domains (TRD). CRISPR-mediated inactivation of enhancers within TRDs impairs TGFβ-dependent regulation of all co-regulated genes, demonstrating that enhancer targeting is more promiscuous than previously anticipated. The area of TRD influence is restricted by topologically associating domains (TADs) borders, causing a bias towards co-regulation within TADs.
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Affiliation(s)
- Jose A Guerrero-Martínez
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla-Universidad Pablo de Olavide (CSIC-USE-UPO), Avenida Americo Vespucio 24, 41092, Seville, Spain
| | - María Ceballos-Chávez
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla-Universidad Pablo de Olavide (CSIC-USE-UPO), Avenida Americo Vespucio 24, 41092, Seville, Spain
| | - Florian Koehler
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Sandra Peiró
- Vall d'Hebron Institute of Oncology (VHIO), 08035, Barcelona, Spain
| | - Jose C Reyes
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla-Universidad Pablo de Olavide (CSIC-USE-UPO), Avenida Americo Vespucio 24, 41092, Seville, Spain.
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167
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Marco A, Meharena HS, Dileep V, Raju RM, Davila-Velderrain J, Zhang AL, Adaikkan C, Young JZ, Gao F, Kellis M, Tsai LH. Mapping the epigenomic and transcriptomic interplay during memory formation and recall in the hippocampal engram ensemble. Nat Neurosci 2020; 23:1606-1617. [PMID: 33020654 PMCID: PMC7686266 DOI: 10.1038/s41593-020-00717-0] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 09/01/2020] [Indexed: 12/22/2022]
Abstract
The epigenome and three-dimensional (3D) genomic architecture are emerging as key factors in the dynamic regulation of different transcriptional programs required for neuronal functions. In this study, we used an activity-dependent tagging system in mice to determine the epigenetic state, 3D genome architecture and transcriptional landscape of engram cells over the lifespan of memory formation and recall. Our findings reveal that memory encoding leads to an epigenetic priming event, marked by increased accessibility of enhancers without the corresponding transcriptional changes. Memory consolidation subsequently results in spatial reorganization of large chromatin segments and promoter-enhancer interactions. Finally, with reactivation, engram neurons use a subset of de novo long-range interactions, where primed enhancers are brought in contact with their respective promoters to upregulate genes involved in local protein translation in synaptic compartments. Collectively, our work elucidates the comprehensive transcriptional and epigenomic landscape across the lifespan of memory formation and recall in the hippocampal engram ensemble.
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Affiliation(s)
- Asaf Marco
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Hiruy S Meharena
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Vishnu Dileep
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ravikiran M Raju
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Division of Newborn Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jose Davila-Velderrain
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Amy Letao Zhang
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Chinnakkaruppan Adaikkan
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jennie Z Young
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Fan Gao
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Manolis Kellis
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Li-Huei Tsai
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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168
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Lin L, Holmes B, Shen MW, Kammeron D, Geijsen N, Gifford DK, Sherwood RI. Comprehensive Mapping of Key Regulatory Networks that Drive Oncogene Expression. Cell Rep 2020; 33:108426. [PMID: 33238122 PMCID: PMC7724632 DOI: 10.1016/j.celrep.2020.108426] [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: 08/10/2020] [Revised: 10/12/2020] [Accepted: 11/02/2020] [Indexed: 02/06/2023] Open
Abstract
Gene expression is controlled by the collective binding of transcription factors to cis-regulatory regions. Deciphering gene-centered regulatory networks is vital to understanding and controlling gene misexpression in human disease; however, systematic approaches to uncovering regulatory networks have been lacking. Here we present high-throughput interrogation of gene-centered activation networks (HIGAN), a pipeline that employs a suite of multifaceted genomic approaches to connect upstream signaling inputs, trans-acting TFs, and cis-regulatory elements. We apply HIGAN to understand the aberrant activation of the cytidine deaminase APOBEC3B, an intrinsic source of cancer hypermutation. We reveal that nuclear factor κB (NF-κB) and AP-1 pathways are the most salient trans-acting inputs, with minor roles for other inflammatory pathways. We identify a cis-regulatory architecture dominated by a major intronic enhancer that requires coordinated NF-κB and AP-1 activity with secondary inputs from distal regulatory regions. Our data demonstrate how integration of cis and trans genomic screening platforms provides a paradigm for building gene-centered regulatory networks.
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Affiliation(s)
- Lin Lin
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, Utrecht 3584 CT, the Netherlands
| | - Benjamin Holmes
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Max W Shen
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Darnell Kammeron
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, Utrecht 3584 CT, the Netherlands
| | - Niels Geijsen
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, Utrecht 3584 CT, the Netherlands; Department of Anatomy and Embryology, Leiden University Medical Center, Leiden 2300 RC, the Netherlands.
| | - David K Gifford
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Richard I Sherwood
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, Utrecht 3584 CT, the Netherlands.
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169
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Papavassiliou AG, Musti AM. The Multifaceted Output of c-Jun Biological Activity: Focus at the Junction of CD8 T Cell Activation and Exhaustion. Cells 2020; 9:cells9112470. [PMID: 33202877 PMCID: PMC7697663 DOI: 10.3390/cells9112470] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/07/2020] [Accepted: 11/11/2020] [Indexed: 12/19/2022] Open
Abstract
c-Jun is a major component of the dimeric transcription factor activator protein-1 (AP-1), a paradigm for transcriptional response to extracellular signaling, whose components are basic-Leucine Zipper (bZIP) transcription factors of the Jun, Fos, activating transcription factor (ATF), ATF-like (BATF) and Jun dimerization protein 2 (JDP2) gene families. Extracellular signals regulate c-Jun/AP-1 activity at multiple levels, including transcriptional and posttranscriptional regulation of c-Jun expression and transactivity, in turn, establishing the magnitude and the duration of c-Jun/AP-1 activation. Another important level of c-Jun/AP-1 regulation is due to the capability of Jun family members to bind DNA as a heterodimer with every other member of the AP-1 family, and to interact with other classes of transcription factors, thereby acquiring the potential to integrate diverse extrinsic and intrinsic signals into combinatorial regulation of gene expression. Here, we review how these features of c-Jun/AP-1 regulation underlie the multifaceted output of c-Jun biological activity, eliciting quite distinct cellular responses, such as neoplastic transformation, differentiation and apoptosis, in different cell types. In particular, we focus on the current understanding of the role of c-Jun/AP-1 in the response of CD8 T cells to acute infection and cancer. We highlight the transcriptional and epigenetic regulatory mechanisms through which c-Jun/AP-1 participates in the productive immune response of CD8 T cells, and how its downregulation may contribute to the dysfunctional state of tumor infiltrating CD8 T cells. Additionally, we discuss recent insights pointing at c-Jun as a suitable target for immunotherapy-based combination approaches to reinvigorate anti-tumor immune functions.
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Affiliation(s)
- Athanasios G. Papavassiliou
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece;
| | - Anna Maria Musti
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy
- Correspondence: ; Tel.: +39-3337543732
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170
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van der Veeken J, Glasner A, Zhong Y, Hu W, Wang ZM, Bou-Puerto R, Charbonnier LM, Chatila TA, Leslie CS, Rudensky AY. The Transcription Factor Foxp3 Shapes Regulatory T Cell Identity by Tuning the Activity of trans-Acting Intermediaries. Immunity 2020; 53:971-984.e5. [PMID: 33176163 DOI: 10.1016/j.immuni.2020.10.010] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 07/06/2020] [Accepted: 10/14/2020] [Indexed: 12/16/2022]
Abstract
Regulatory T (Treg) cell identity is defined by the lineage-specifying transcription factor (TF) Foxp3. Here we examined mechanisms of Foxp3 function by leveraging naturally occurring genetic variation in wild-derived inbred mice, which enables the identification of DNA sequence motifs driving epigenetic features. Chromatin accessibility, TF binding, and gene expression patterns in resting and activated subsets of Treg cells, conventional CD4 T cells, and cells expressing a Foxp3 reporter null allele revealed that the majority of Foxp3-dependent changes occurred at sites not bound by Foxp3. Chromatin accessibility of these indirect Foxp3 targets depended on the presence of DNA binding motifs for other TFs, including TCF1. Foxp3 expression correlated with decreased TCF1 and reduced accessibility of TCF1-bound chromatin regions. Deleting one copy of the Tcf7 gene recapitulated Foxp3-dependent negative regulation of chromatin accessibility. Thus, Foxp3 defines Treg cell identity in a largely indirect manner by fine-tuning the activity of other major chromatin remodeling TFs such as TCF1.
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Affiliation(s)
- Joris van der Veeken
- Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute, and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Ariella Glasner
- Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute, and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yi Zhong
- Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute, and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY, USA; Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wei Hu
- Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute, and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zhong-Min Wang
- Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute, and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY, USA; Gerstner Sloan Kettering Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Regina Bou-Puerto
- Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute, and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Louis-Marie Charbonnier
- Division of Immunology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Talal A Chatila
- Division of Immunology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Christina S Leslie
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexander Y Rudensky
- Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute, and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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171
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Chen W, Hu S, Mao S, Xu Y, Guo H, Li H, Paulsen MT, Chen X, Ljungman M, Neamati N. Discovery of Mitochondrial Transcription Inhibitors Active in Pancreatic Cancer Cells. ChemMedChem 2020; 15:2029-2039. [PMID: 32748543 DOI: 10.1002/cmdc.202000494] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Indexed: 11/10/2022]
Abstract
Mitochondrial dysfunction is a hallmark of cancer cells and targeting cancer mitochondria has emerged as a promising anti-cancer therapy. Previously, we repurposed chlorambucil by conjugating it to a mitochondrial targeting triphenylphosphonium (TPP) group to design Mito-Chlor, a novel agent that acts on mitochondria DNA (mtDNA). Herein, we show that Mito-Chlor, but not chlorambucil, inhibits the nascent transcription of mtDNA. Clustering analysis of transcriptomic profile of our Bru-seq database led to the identification of another mitochondrial transcription inhibitor SQD1, which inhibits the proliferation of MIA PaCa-2 cells with an IC50 of 1.3 μM. Interestingly, Mito-Chlor reduces expression of mitochondrial proteins, interferes with mitochondria membrane potential, and impairs oxidative phosphorylation while SQD1 does not. Both compounds increased cellular and mitochondrial reactive oxygen species and stimulated similar signaling pathways in response to oxidative stress. As mitochondrial transcription inhibitors and redox modulators, SQD1 and Mito-Chlor are promising for the treatment of pancreatic cancer by blocking mitochondrial function.
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Affiliation(s)
- Wenmin Chen
- Departments of Medicinal Chemistry, University of Michigan, 1600 Huron Parkway, Ann Arbor, MI 48109, USA
| | - Shuai Hu
- Departments of Medicinal Chemistry, University of Michigan, 1600 Huron Parkway, Ann Arbor, MI 48109, USA.,Department of Computational Medicine and Bioinformatic, University of Michigan, 1600 Huron Parkway, Ann Arbor, MI 48109, USA
| | - Shuai Mao
- Departments of Medicinal Chemistry, University of Michigan, 1600 Huron Parkway, Ann Arbor, MI 48109, USA
| | - Yibin Xu
- Departments of Medicinal Chemistry, University of Michigan, 1600 Huron Parkway, Ann Arbor, MI 48109, USA
| | - Hui Guo
- Departments of Medicinal Chemistry, University of Michigan, 1600 Huron Parkway, Ann Arbor, MI 48109, USA
| | - Haoxi Li
- Departments of Medicinal Chemistry, University of Michigan, 1600 Huron Parkway, Ann Arbor, MI 48109, USA
| | - Michelle T Paulsen
- Department of Radiation Oncology, University of Michigan, 1600 Huron Parkway, Ann Arbor, MI 48109, USA
| | - Xinde Chen
- Departments of Medicinal Chemistry, University of Michigan, 1600 Huron Parkway, Ann Arbor, MI 48109, USA
| | - Mats Ljungman
- Department of Radiation Oncology, University of Michigan, 1600 Huron Parkway, Ann Arbor, MI 48109, USA.,Department of Environmental Health Sciences, University of Michigan, 1600 Huron Parkway, Ann Arbor, MI 48109, USA
| | - Nouri Neamati
- Departments of Medicinal Chemistry, University of Michigan, 1600 Huron Parkway, Ann Arbor, MI 48109, USA
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172
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Fernando TM, Piskol R, Bainer R, Sokol ES, Trabucco SE, Zhang Q, Trinh H, Maund S, Kschonsak M, Chaudhuri S, Modrusan Z, Januario T, Yauch RL. Functional characterization of SMARCA4 variants identified by targeted exome-sequencing of 131,668 cancer patients. Nat Commun 2020; 11:5551. [PMID: 33144586 PMCID: PMC7609548 DOI: 10.1038/s41467-020-19402-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 10/09/2020] [Indexed: 02/06/2023] Open
Abstract
Genomic studies performed in cancer patients and tumor-derived cell lines have identified a high frequency of alterations in components of the mammalian switch/sucrose non-fermentable (mSWI/SNF or BAF) chromatin remodeling complex, including its core catalytic subunit, SMARCA4. Cells exhibiting loss of SMARCA4 rely on its paralog, SMARCA2, making SMARCA2 an attractive therapeutic target. Here we report the genomic profiling of solid tumors from 131,668 cancer patients, identifying 9434 patients with one or more SMARCA4 gene alterations. Homozygous SMARCA4 mutations were highly prevalent in certain tumor types, notably non-small cell lung cancer (NSCLC), and associated with reduced survival. The large sample size revealed previously uncharacterized hotspot missense mutations within the SMARCA4 helicase domain. Functional characterization of these mutations demonstrated markedly reduced remodeling activity. Surprisingly, a few SMARCA4 missense variants partially or fully rescued paralog dependency, underscoring that careful selection criteria must be employed to identify patients with inactivating, homozygous SMARCA4 missense mutations who may benefit from SMARCA2-targeted therapy.
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Affiliation(s)
- Tharu M Fernando
- Discovery Oncology, Genentech, South San Francisco, CA, 94080, USA
| | - Robert Piskol
- Bioinformatics and Computational Biology, Genentech, South San Francisco, CA, 94080, USA
| | - Russell Bainer
- Bioinformatics and Computational Biology, Genentech, South San Francisco, CA, 94080, USA
| | - Ethan S Sokol
- Cancer Genomics Research, Foundation Medicine, Cambridge, MA, 02141, USA
| | - Sally E Trabucco
- Cancer Genomics Research, Foundation Medicine, Cambridge, MA, 02141, USA
| | - Qing Zhang
- Product Development Personalized Healthcare Data Science, Genentech, South San Francisco, CA, 94080, USA
| | - Huong Trinh
- Product Development Personalized Healthcare Data Science, Genentech, South San Francisco, CA, 94080, USA
| | - Sophia Maund
- Oncology Biomarker Development, Genentech, South San Francisco, CA, 94080, USA
| | - Marc Kschonsak
- Structural Biology, Genentech, South San Francisco, CA, 94080, USA
| | - Subhra Chaudhuri
- Molecular Biology, Genentech, South San Francisco, CA, 94080, USA
| | - Zora Modrusan
- Molecular Biology, Genentech, South San Francisco, CA, 94080, USA
| | - Thomas Januario
- Discovery Oncology, Genentech, South San Francisco, CA, 94080, USA
| | - Robert L Yauch
- Discovery Oncology, Genentech, South San Francisco, CA, 94080, USA.
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173
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Wilson MR, Reske JJ, Holladay J, Neupane S, Ngo J, Cuthrell N, Wegener M, Rhodes M, Adams M, Sheridan R, Hostetter G, Alotaibi FT, Yong PJ, Anglesio MS, Lessey BA, Leach RE, Teixeira JM, Missmer SA, Fazleabas AT, Chandler RL. ARID1A Mutations Promote P300-Dependent Endometrial Invasion through Super-Enhancer Hyperacetylation. Cell Rep 2020; 33:108366. [PMID: 33176148 PMCID: PMC7682620 DOI: 10.1016/j.celrep.2020.108366] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 09/16/2020] [Accepted: 10/16/2020] [Indexed: 12/12/2022] Open
Abstract
Endometriosis affects 1 in 10 women and is characterized by the presence of abnormal endometrium at ectopic sites. ARID1A mutations are observed in deeply invasive forms of the disease, often correlating with malignancy. To identify epigenetic dependencies driving invasion, we use an unbiased approach to map chromatin state transitions accompanying ARID1A loss in the endometrium. We show that super-enhancers marked by high H3K27 acetylation are strongly associated with ARID1A binding. ARID1A loss leads to H3K27 hyperacetylation and increased chromatin accessibility and enhancer RNA transcription at super-enhancers, but not typical enhancers, indicating that ARID1A normally prevents super-enhancer hyperactivation. ARID1A co-localizes with P300 at super-enhancers, and genetic or pharmacological inhibition of P300 in ARID1A mutant endometrial epithelia suppresses invasion and induces anoikis through the rescue of super-enhancer hyperacetylation. Among hyperactivated super-enhancers, SERPINE1 (PAI-1) is identified as an essential target gene driving ARID1A mutant endometrial invasion. Broadly, our findings provide rationale for therapeutic strategies targeting super-enhancers in ARID1A mutant endometrium.
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Affiliation(s)
- Mike R Wilson
- Department of Obstetrics, Gynecology, and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Jake J Reske
- Department of Obstetrics, Gynecology, and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Jeanne Holladay
- Department of Obstetrics, Gynecology, and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Subechhya Neupane
- Department of Obstetrics, Gynecology, and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Julie Ngo
- Department of Obstetrics, Gynecology, and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Nina Cuthrell
- Department of Obstetrics, Gynecology, and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Marc Wegener
- Genomics Core Facility, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Mary Rhodes
- Genomics Core Facility, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Marie Adams
- Genomics Core Facility, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Rachael Sheridan
- Flow Cytometry Core, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Galen Hostetter
- Pathology and Biorepository Core, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Fahad T Alotaibi
- Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, BC, Canada; Department of Physiology, College of Medicine, Al-Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Paul J Yong
- Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, BC, Canada
| | - Michael S Anglesio
- Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, BC, Canada; British Columbia's Gynecological Cancer Research Team (OVCARE), University of British Columbia, Vancouver General Hospital, and BC Cancer, Vancouver, BC, Canada
| | - Bruce A Lessey
- Department of Obstetrics and Gynecology, Wake Forest Baptist Health, Winston-Salem, NC 27157, USA
| | - Richard E Leach
- Department of Obstetrics, Gynecology, and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA; Department of Women's Health, Spectrum Health System, Grand Rapids, MI 49341, USA
| | - Jose M Teixeira
- Department of Obstetrics, Gynecology, and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA; Department of Women's Health, Spectrum Health System, Grand Rapids, MI 49341, USA
| | - Stacey A Missmer
- Department of Obstetrics, Gynecology, and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA; Department of Women's Health, Spectrum Health System, Grand Rapids, MI 49341, USA
| | - Asgerally T Fazleabas
- Department of Obstetrics, Gynecology, and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA; Department of Women's Health, Spectrum Health System, Grand Rapids, MI 49341, USA
| | - Ronald L Chandler
- Department of Obstetrics, Gynecology, and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA; Department of Women's Health, Spectrum Health System, Grand Rapids, MI 49341, USA; Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA.
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174
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Llorens-Bobadilla E, Chell JM, Le Merre P, Wu Y, Zamboni M, Bergenstråhle J, Stenudd M, Sopova E, Lundeberg J, Shupliakov O, Carlén M, Frisén J. A latent lineage potential in resident neural stem cells enables spinal cord repair. Science 2020; 370:370/6512/eabb8795. [PMID: 33004487 DOI: 10.1126/science.abb8795] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 08/04/2020] [Indexed: 12/20/2022]
Abstract
Injuries to the central nervous system (CNS) are inefficiently repaired. Resident neural stem cells manifest a limited contribution to cell replacement. We have uncovered a latent potential in neural stem cells to replace large numbers of lost oligodendrocytes in the injured mouse spinal cord. Integrating multimodal single-cell analysis, we found that neural stem cells are in a permissive chromatin state that enables the unfolding of a normally latent gene expression program for oligodendrogenesis after injury. Ectopic expression of the transcription factor OLIG2 unveiled abundant stem cell-derived oligodendrogenesis, which followed the natural progression of oligodendrocyte differentiation, contributed to axon remyelination, and stimulated functional recovery of axon conduction. Recruitment of resident stem cells may thus serve as an alternative to cell transplantation after CNS injury.
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Affiliation(s)
- Enric Llorens-Bobadilla
- Department of Cell and Molecular Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - James M Chell
- Department of Cell and Molecular Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Pierre Le Merre
- Department of Neuroscience, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Yicheng Wu
- Department of Cell and Molecular Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Margherita Zamboni
- Department of Cell and Molecular Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Joseph Bergenstråhle
- Science for Life Laboratory, Karolinska Institutet Science Park, SE-171 21 Solna, Sweden
| | - Moa Stenudd
- Department of Cell and Molecular Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Elena Sopova
- Department of Neuroscience, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Joakim Lundeberg
- Science for Life Laboratory, Karolinska Institutet Science Park, SE-171 21 Solna, Sweden
| | - Oleg Shupliakov
- Department of Neuroscience, Karolinska Institutet, SE-171 77 Stockholm, Sweden.,Institute of Translational Biomedicine, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Marie Carlén
- Department of Neuroscience, Karolinska Institutet, SE-171 77 Stockholm, Sweden.,Department of Biosciences and Nutrition, Karolinska Institutet, SE-141 83 Huddinge, Sweden
| | - Jonas Frisén
- Department of Cell and Molecular Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden.
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175
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Alcalà-Vida R, Awada A, Boutillier AL, Merienne K. Epigenetic mechanisms underlying enhancer modulation of neuronal identity, neuronal activity and neurodegeneration. Neurobiol Dis 2020; 147:105155. [PMID: 33127472 DOI: 10.1016/j.nbd.2020.105155] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 10/23/2020] [Accepted: 10/26/2020] [Indexed: 02/08/2023] Open
Abstract
Neurodegenerative diseases, including Huntington's disease (HD) and Alzheimer's disease (AD), are progressive conditions characterized by selective, disease-dependent loss of neuronal regions and/or subpopulations. Neuronal loss is preceded by a long period of neuronal dysfunction, during which glial cells also undergo major changes, including neuroinflammatory response. Those dramatic changes affecting both neuronal and glial cells associate with epigenetic and transcriptional dysregulations, characterized by defined cell-type-specific signatures. Notably, increasing studies support the view that altered regulation of transcriptional enhancers, which are distal regulatory regions of the genome capable of modulating the activity of promoters through chromatin looping, play a critical role in transcriptional dysregulation in HD and AD. We review current knowledge on enhancers in HD and AD, and highlight challenging issues to better decipher the epigenetic code of neurodegenerative diseases.
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Affiliation(s)
- Rafael Alcalà-Vida
- LNCA, University of Strasbourg, France; CNRS UMR 7364, Strasbourg, France
| | - Ali Awada
- LNCA, University of Strasbourg, France; CNRS UMR 7364, Strasbourg, France
| | | | - Karine Merienne
- LNCA, University of Strasbourg, France; CNRS UMR 7364, Strasbourg, France.
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176
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Reske JJ, Wilson MR, Holladay J, Wegener M, Adams M, Chandler RL. SWI/SNF inactivation in the endometrial epithelium leads to loss of epithelial integrity. Hum Mol Genet 2020; 29:3412-3430. [PMID: 33075803 PMCID: PMC7749707 DOI: 10.1093/hmg/ddaa227] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 10/01/2020] [Accepted: 10/12/2020] [Indexed: 12/14/2022] Open
Abstract
Although ARID1A mutations are a hallmark feature, mutations in other SWI/SNF (SWItch/Sucrose Non-Fermentable) chromatin remodeling subunits are also observed in endometrial neoplasms. Here, we interrogated the roles of Brahma/SWI2-related gene 1 (BRG1, SMARCA4), the SWI/SNF catalytic subunit, in the endometrial epithelium. BRG1 loss affects more than one-third of all active genes and highly overlaps with the ARID1A gene regulatory network. Chromatin immunoprecipitation studies revealed widespread subunit-specific differences in transcriptional regulation, as BRG1 promoter interactions are associated with gene activation, while ARID1A binding is associated with gene repression. However, we identified a physiologically relevant subset of BRG1 and ARID1A co-regulated epithelial identity genes. Mice were genetically engineered to inactivate BRG1 specifically in the endometrial epithelium. Endometrial glands were observed embedded in uterine myometrium, indicating adenomyosis-like phenotypes. Molecular similarities were observed between BRG1 and ARID1A mutant endometrial cells in vivo, including loss of epithelial cell adhesion and junction genes. Collectively, these studies illustrate overlapping contributions of multiple SWI/SNF subunit mutations in the translocation of endometrium to distal sites, with loss of cell integrity being a common feature in SWI/SNF mutant endometrial epithelia.
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Affiliation(s)
- Jake J Reske
- Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Mike R Wilson
- Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Jeanne Holladay
- Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Marc Wegener
- Genomics Core Facility, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Marie Adams
- Genomics Core Facility, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Ronald L Chandler
- To whom correspondence should be addressed at: Grand Rapids Research Center, 400 Monroe NW, Grand Rapids, MI 49503, USA. Tel: +1 6162340980;
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177
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Vangala P, Murphy R, Quinodoz SA, Gellatly K, McDonel P, Guttman M, Garber M. High-Resolution Mapping of Multiway Enhancer-Promoter Interactions Regulating Pathogen Detection. Mol Cell 2020; 80:359-373.e8. [PMID: 32991830 PMCID: PMC7572724 DOI: 10.1016/j.molcel.2020.09.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 06/04/2020] [Accepted: 09/04/2020] [Indexed: 11/19/2022]
Abstract
Eukaryotic gene expression regulation involves thousands of distal regulatory elements. Understanding the quantitative contribution of individual enhancers to gene expression is critical for assessing the role of disease-associated genetic risk variants. Yet, we lack the ability to accurately link genes with their distal regulatory elements. To address this, we used 3D enhancer-promoter (E-P) associations identified using split-pool recognition of interactions by tag extension (SPRITE) to build a predictive model of gene expression. Our model dramatically outperforms models using genomic proximity and can be used to determine the quantitative impact of enhancer loss on gene expression in different genetic backgrounds. We show that genes that form stable E-P hubs have less cell-to-cell variability in gene expression. Finally, we identified transcription factors that regulate stimulation-dependent E-P interactions. Together, our results provide a framework for understanding quantitative contributions of E-P interactions and associated genetic variants to gene expression.
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Affiliation(s)
- Pranitha Vangala
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Rachel Murphy
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Sofia A Quinodoz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Kyle Gellatly
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Patrick McDonel
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Manuel Garber
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA; Department of Dermatology, Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA.
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178
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Genome-wide chromatin accessibility is restricted by ANP32E. Nat Commun 2020; 11:5063. [PMID: 33033242 PMCID: PMC7546623 DOI: 10.1038/s41467-020-18821-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 09/16/2020] [Indexed: 12/11/2022] Open
Abstract
Genome-wide chromatin state underlies gene expression potential and cellular function. Epigenetic features and nucleosome positioning contribute to the accessibility of DNA, but widespread regulators of chromatin state are largely unknown. Our study investigates how coordination of ANP32E and H2A.Z contributes to genome-wide chromatin state in mouse fibroblasts. We define H2A.Z as a universal chromatin accessibility factor, and demonstrate that ANP32E antagonizes H2A.Z accumulation to restrict chromatin accessibility genome-wide. In the absence of ANP32E, H2A.Z accumulates at promoters in a hierarchical manner. H2A.Z initially localizes downstream of the transcription start site, and if H2A.Z is already present downstream, additional H2A.Z accumulates upstream. This hierarchical H2A.Z accumulation coincides with improved nucleosome positioning, heightened transcription factor binding, and increased expression of neighboring genes. Thus, ANP32E dramatically influences genome-wide chromatin accessibility through subtle refinement of H2A.Z patterns, providing a means to reprogram chromatin state and to hone gene expression levels. Chromatin state underlies cellular function, and transcription factor binding patterns along with epigenetic marks define chromatin state. Here the authors show that the histone chaperone ANP32E functions through regulation of H2A.Z to restrict genome-wide chromatin accessibility and to inhibit gene transcriptional activation.
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179
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AP-1 and TGFß cooperativity drives non-canonical Hedgehog signaling in resistant basal cell carcinoma. Nat Commun 2020; 11:5079. [PMID: 33033234 PMCID: PMC7546632 DOI: 10.1038/s41467-020-18762-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 09/01/2020] [Indexed: 12/17/2022] Open
Abstract
Tumor heterogeneity and lack of knowledge about resistant cell states remain a barrier to targeted cancer therapies. Basal cell carcinomas (BCCs) depend on Hedgehog (Hh)/Gli signaling, but can develop mechanisms of Smoothened (SMO) inhibitor resistance. We previously identified a nuclear myocardin-related transcription factor (nMRTF) resistance pathway that amplifies noncanonical Gli1 activity, but characteristics and drivers of the nMRTF cell state remain unknown. Here, we use single cell RNA-sequencing of patient tumors to identify three prognostic surface markers (LYPD3, TACSTD2, and LY6D) which correlate with nMRTF and resistance to SMO inhibitors. The nMRTF cell state resembles transit-amplifying cells of the hair follicle matrix, with AP-1 and TGFß cooperativity driving nMRTF activation. JNK/AP-1 signaling commissions chromatin accessibility and Smad3 DNA binding leading to a transcriptional program of RhoGEFs that facilitate nMRTF activity. Importantly, small molecule AP-1 inhibitors selectively target LYPD3+/TACSTD2+/LY6D+ nMRTF human BCCs ex vivo, opening an avenue for improving combinatorial therapies.
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180
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The mechanisms of action of chromatin remodelers and implications in development and disease. Biochem Pharmacol 2020; 180:114200. [DOI: 10.1016/j.bcp.2020.114200] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/09/2020] [Accepted: 08/12/2020] [Indexed: 02/06/2023]
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181
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Majidi SP, Reddy NC, Moore MJ, Chen H, Yamada T, Andzelm MM, Cherry TJ, Hu LS, Greenberg ME, Bonni A. Chromatin Environment and Cellular Context Specify Compensatory Activity of Paralogous MEF2 Transcription Factors. Cell Rep 2020; 29:2001-2015.e5. [PMID: 31722213 PMCID: PMC6874310 DOI: 10.1016/j.celrep.2019.10.033] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 09/04/2019] [Accepted: 10/09/2019] [Indexed: 12/16/2022] Open
Abstract
Compensation among paralogous transcription factors (TFs) confers genetic robustness of cellular processes, but how TFs dynamically respond to paralog depletion on a genome-wide scale in vivo remains incompletely understood. Using single and double conditional knockout of myocyte enhancer factor 2 (MEF2) family TFs in granule neurons of the mouse cerebellum, we find that MEF2A and MEF2D play functionally redundant roles in cerebellar-dependent motor learning. Although both TFs are highly expressed in granule neurons, transcriptomic analyses show MEF2D is the predominant genomic regulator of gene expression in vivo. Strikingly, genome-wide occupancy analyses reveal upon depletion of MEF2D, MEF2A occupancy robustly increases at a subset of sites normally bound to MEF2D. Importantly, sites experiencing compensatory MEF2A occupancy are concentrated within open chromatin and undergo functional compensation for genomic activation and gene expression. Finally, motor activity induces a switch from non-compensatory to compensatory MEF2-dependent gene regulation. These studies uncover genome-wide functional interdependency between paralogous TFs in the brain. Majidi et al. study how transcription factors respond to paralog depletion by conditionally depleting MEF2A and MEF2D in mouse cerebellum. Depletion of MEF2D induces functionally compensatory genomic occupancy by MEF2A. Compensation occurs within accessible chromatin in a context-dependent manner. This study explores the interdependency between paralogous transcription factors.
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Affiliation(s)
- Shahriyar P Majidi
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA; MD-PhD Program, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Naveen C Reddy
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michael J Moore
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Hao Chen
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Tomoko Yamada
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA; Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Milena M Andzelm
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Timothy J Cherry
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98101, USA; Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, 1900 9(th) Ave., Seattle, WA 98101, USA; Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Linda S Hu
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Azad Bonni
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA.
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182
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Brennan A, Leech JT, Kad NM, Mason JM. Selective antagonism of cJun for cancer therapy. J Exp Clin Cancer Res 2020; 39:184. [PMID: 32917236 PMCID: PMC7488417 DOI: 10.1186/s13046-020-01686-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 08/20/2020] [Indexed: 01/10/2023] Open
Abstract
The activator protein-1 (AP-1) family of transcription factors modulate a diverse range of cellular signalling pathways into outputs which can be oncogenic or anti-oncogenic. The transcription of relevant genes is controlled by the cellular context, and in particular by the dimeric composition of AP-1. Here, we describe the evidence linking cJun in particular to a range of cancers. This includes correlative studies of protein levels in patient tumour samples and mechanistic understanding of the role of cJun in cancer cell models. This develops an understanding of cJun as a focal point of cancer-altered signalling which has the potential for therapeutic antagonism. Significant work has produced a range of small molecules and peptides which have been summarised here and categorised according to the binding surface they target within the cJun-DNA complex. We highlight the importance of selectively targeting a single AP-1 family member to antagonise known oncogenic function and avoid antagonism of anti-oncogenic function.
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Affiliation(s)
- Andrew Brennan
- Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - James T Leech
- School of Biosciences, University of Kent, Canterbury, CT2 7NH, UK
| | - Neil M Kad
- School of Biosciences, University of Kent, Canterbury, CT2 7NH, UK
| | - Jody M Mason
- Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
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183
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Mammalian SWI/SNF Chromatin Remodeling Complexes: Emerging Mechanisms and Therapeutic Strategies. Trends Genet 2020; 36:936-950. [PMID: 32873422 DOI: 10.1016/j.tig.2020.07.011] [Citation(s) in RCA: 180] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 07/22/2020] [Accepted: 07/24/2020] [Indexed: 02/06/2023]
Abstract
Small molecule-based targeting of chromatin regulatory factors has emerged as a promising therapeutic strategy in recent years. The development and ongoing clinical evaluation of novel agents targeting a range of chromatin regulatory processes, including DNA or histone modifiers, histone readers, and chromatin regulatory protein complexes, has inspired the field to identify and act upon the full compendium of therapeutic opportunities. Emerging studies highlight the frequent involvement of altered mammalian Switch/Sucrose-Nonfermentable (mSWI/SNF) chromatin-remodeling complexes (also called BAF complexes) in both human cancer and neurological disorders, suggesting new mechanisms and accompanying routes toward therapeutic intervention. Here, we review current approaches for direct targeting of mSWI/SNF complex structure and function and discuss settings in which aberrant mSWI/SNF biology is implicated in oncology and other diseases.
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184
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Zhou Q, Zhou Q, Liu Q, He Z, Yan Y, Lin J, Chen Z, He C, Mao K, Wang J, Zhou Z, Xiao Z, Zhang J. PRL-3 facilitates Hepatocellular Carcinoma progression by co-amplifying with and activating FAK. Theranostics 2020; 10:10345-10359. [PMID: 32929353 PMCID: PMC7481414 DOI: 10.7150/thno.42069] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 07/27/2020] [Indexed: 02/06/2023] Open
Abstract
Background: In addition to protein tyrosine kinases, accumulating evidence has shown that protein tyrosine phosphatases (PTPs) are suitable therapeutic targets in cancer. PRL-3 is a PTP member that has been well studied in many malignant tumours. The goal of the present study was to elucidate the role of PRL-3 in hepatocellular carcinoma (HCC), which remains largely unknown. Methods: Bioinformatic and immunohistochemical analyses were performed to analyse PRL-3 expression in HCC tissue samples and determine its clinical relevance. PRL-3 gene copy number variations were evaluated by bioinformatic analysis and quantitative-genomic polymerase chain reaction. The biological functions of PRL-3 were investigated in vivo and vitro. Gene microarray assays, RT-qPCR, western blotting and luciferase experiments were performed to identify the downstream effectors of PRL-3 that mediate its functions in HCC. Results: PRL-3 expression was upregulated in HCC samples from public databases and in cohort samples from our centre. High PRL-3 expression was associated with poor prognosis. Copy number gains and amplification of chromosome 8q24.3 in HCC were determined to be positively correlated with the PRL-3 overexpression. PRL-3 overexpression promoted HCC cell proliferation, migration and adhesion, while its loss had the opposite effects. Further study showed that focal adhesion kinase (FAK) was co-amplified and co-expressed with PRL-3 in HCC. Interestingly, PRL-3 also promoted the phosphorylation of FAK, which subsequently mediated the oncogenic functions of PRL-3 in HCC cells. Moreover, TGFB1 was identified as a downstream molecule of PRL-3. TGF-β signalling was shown to mediate the PRL-3-induced activation of FAK. Furthermore, the p38 and PI3K/AKT pathways were observed to mediate the PRL-3-induced expression of TGFB1 and the subsequent activation of FAK, while the activation of FAK in turn stimulated activation of the p38 and PI3K/AKT pathways, forming a PRL-3-triggered AKT/p38/TGFB1/FAK positive feedback loop. Conclusion: Collectively, our findings indicate that the PTP PRL-3 plays a crucial role in the progression of HCC and provides an example of how co-amplified genes work together in HCC.
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Affiliation(s)
- Qiming Zhou
- Department of Hepatobiliary Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
- Guangdong Province Key laboratory of Malignant Tumour Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
- Department of Thyroid Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Qianlei Zhou
- Department of Hepatobiliary Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
- Guangdong Province Key laboratory of Malignant Tumour Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Qinghua Liu
- Department of Hepatobiliary Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
- Guangdong Province Key laboratory of Malignant Tumour Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Zhanghai He
- Department of Pathology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Yongcong Yan
- Department of Hepatobiliary Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
- Guangdong Province Key laboratory of Malignant Tumour Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Jianhong Lin
- Department of Hepatobiliary Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
- Guangdong Province Key laboratory of Malignant Tumour Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Zheng Chen
- Department of Hepatobiliary Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
- Guangdong Province Key laboratory of Malignant Tumour Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Chuanchao He
- Department of Hepatobiliary Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
- Guangdong Province Key laboratory of Malignant Tumour Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Kai Mao
- Department of Hepatobiliary Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
- Guangdong Province Key laboratory of Malignant Tumour Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Jie Wang
- Department of Hepatobiliary Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
- Guangdong Province Key laboratory of Malignant Tumour Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Zhenyu Zhou
- Department of Hepatobiliary Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
- Guangdong Province Key laboratory of Malignant Tumour Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Zhiyu Xiao
- Department of Hepatobiliary Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
- Guangdong Province Key laboratory of Malignant Tumour Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Jianlong Zhang
- Department of Hepatobiliary Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
- Guangdong Province Key laboratory of Malignant Tumour Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
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185
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Yukawa M, Jagannathan S, Vallabh S, Kartashov AV, Chen X, Weirauch MT, Barski A. AP-1 activity induced by co-stimulation is required for chromatin opening during T cell activation. J Exp Med 2020; 217:jem.20182009. [PMID: 31653690 PMCID: PMC7037242 DOI: 10.1084/jem.20182009] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 02/06/2019] [Accepted: 09/23/2019] [Indexed: 12/24/2022] Open
Abstract
Activation of T cells is dependent on the organized and timely opening and closing of chromatin. Herein, we identify AP-1 as the transcription factor that directs most of this remodeling. Chromatin accessibility profiling showed quick opening of closed chromatin in naive T cells within 5 h of activation. These newly opened regions were strongly enriched for the AP-1 motif, and indeed, ChIP-seq demonstrated AP-1 binding at >70% of them. Broad inhibition of AP-1 activity prevented chromatin opening at AP-1 sites and reduced the expression of nearby genes. Similarly, induction of anergy in the absence of co-stimulation during activation was associated with reduced induction of AP-1 and a failure of proper chromatin remodeling. The translational relevance of these findings was highlighted by the substantial overlap of AP-1-dependent elements with risk loci for multiple immune diseases, including multiple sclerosis, inflammatory bowel disease, and allergic disease. Our findings define AP-1 as the key link between T cell activation and chromatin remodeling.
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Affiliation(s)
- Masashi Yukawa
- Division of Allergy & Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Sajjeev Jagannathan
- Division of Allergy & Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Sushmitha Vallabh
- Division of Allergy & Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Andrey V Kartashov
- Division of Allergy & Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Xiaoting Chen
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH.,Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH.,Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Artem Barski
- Division of Allergy & Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH.,Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
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186
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Chen J. Perspectives on somatic reprogramming: spotlighting epigenetic regulation and cellular heterogeneity. Curr Opin Genet Dev 2020; 64:21-25. [PMID: 32599300 DOI: 10.1016/j.gde.2020.05.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 05/11/2020] [Accepted: 05/12/2020] [Indexed: 01/08/2023]
Abstract
Induction of pluripotency in somatic cells via ectopic expression of defined factors demonstrates the reversibility of developmental programming, thus serves as an ideal model to investigate the underlying principles of cell fate determination, which drives the differentiation of various cell types from an identical genome. Over the last decade, our understanding has grown considerably regarding how somatic reprogramming initiates and be regulated. Recent mechanistic investigations on chromatin architecture regulation and cell heterogeneity significantly contribute to the understanding of somatic reprogramming. Specifically, it is found that chromatin dynamics which are regulated by the orchestration of transcriptional factors and epigenetic regulation, play an important role during somatic reprogramming. Moreover, the widespread application of single-cell technologies reveals latent cell fate transition trajectories during the reprogramming process. Here, we highlighted several mechanistic studies on somatic reprogramming, particularly from epigenetic regulation and cell heterogeneity perspectives, and summarized their contribution to our current understanding of cell fate determination.
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Affiliation(s)
- Jiekai Chen
- Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530 Guangzhou, China; Guangzhou Regenerative Medicine and Health-Guangdong Laboratory (GRMH-GDL), 510530 Guangzhou, China.
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187
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Stroud H, Yang MG, Tsitohay YN, Davis CP, Sherman MA, Hrvatin S, Ling E, Greenberg ME. An Activity-Mediated Transition in Transcription in Early Postnatal Neurons. Neuron 2020; 107:874-890.e8. [PMID: 32589877 DOI: 10.1016/j.neuron.2020.06.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 03/31/2020] [Accepted: 06/04/2020] [Indexed: 12/11/2022]
Abstract
The maturation of the mammalian brain occurs after birth, and this stage of neuronal development is frequently impaired in neurological disorders, such as autism and schizophrenia. However, the mechanisms that regulate postnatal brain maturation are poorly defined. By purifying neuronal subpopulations across brain development in mice, we identify a postnatal switch in the transcriptional regulatory circuits that operates in the maturing mammalian brain. We show that this developmental transition includes the formation of hundreds of cell-type-specific neuronal enhancers that appear to be modulated by neuronal activity. Once selected, these enhancers are active throughout adulthood, suggesting that their formation in early life shapes neuronal identity and regulates mature brain function.
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Affiliation(s)
- Hume Stroud
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Marty G Yang
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA; Program in Neuroscience, Harvard Medical School, Boston, MA 02115, USA
| | - Yael N Tsitohay
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Maxwell A Sherman
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Sinisa Hrvatin
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Emi Ling
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
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188
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Cui L, Chen SY, Lerbs T, Lee JW, Domizi P, Gordon S, Kim YH, Nolan G, Betancur P, Wernig G. Activation of JUN in fibroblasts promotes pro-fibrotic programme and modulates protective immunity. Nat Commun 2020; 11:2795. [PMID: 32493933 PMCID: PMC7270081 DOI: 10.1038/s41467-020-16466-4] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 04/27/2020] [Indexed: 02/04/2023] Open
Abstract
The transcription factor JUN is highly expressed in pulmonary fibrosis. Its induction in mice drives lung fibrosis, which is abrogated by administration of anti-CD47. Here, we use high-dimensional mass cytometry to profile protein expression and secretome of cells from patients with pulmonary fibrosis. We show that JUN is activated in fibrotic fibroblasts that expressed increased CD47 and PD-L1. Using ATAC-seq and ChIP-seq, we found that activation of JUN rendered promoters and enhancers of CD47 and PD-L1 accessible. We further detect increased IL-6 that amplified JUN-mediated CD47 enhancer activity and protein expression. Using an in vivo mouse model of fibrosis, we found two distinct mechanisms by which blocking IL-6, CD47 and PD-L1 reversed fibrosis, by increasing phagocytosis of profibrotic fibroblasts and by eliminating suppressive effects on adaptive immunity. Our results identify specific immune mechanisms that promote fibrosis and suggest a therapeutic approach that could be used alongside conventional anti-fibrotics for pulmonary fibrosis. Fibroblast contributions to lung fibrosis and in particular their crosstalk with immune cells in the lung are incompletely understood. Here, the authors show an overall immune suppressive environment transcriptionally controlled and maintained by fibroblasts in lung fibrosis with possible therapeutic implications.
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Affiliation(s)
- Lu Cui
- Department of Pathology, Institute of Stem Cell Biology and Regenerative Medicine (ISCBRM), Stanford University School of Medicine, Stanford, 94305, CA, USA
| | - Shih-Yu Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Tristan Lerbs
- Department of Pathology, Institute of Stem Cell Biology and Regenerative Medicine (ISCBRM), Stanford University School of Medicine, Stanford, 94305, CA, USA
| | - Jin-Wook Lee
- Department of Genetics, Stanford University School of Medicine, Stanford, 94305, CA, USA
| | - Pablo Domizi
- Department of Pathology, Institute of Stem Cell Biology and Regenerative Medicine (ISCBRM), Stanford University School of Medicine, Stanford, 94305, CA, USA
| | - Sydney Gordon
- Orca Biosystems, 3475 Edison Way, Suite B, Menlo Park, 94025, CA, USA
| | - Yong-Hun Kim
- Department of Pathology, Institute of Stem Cell Biology and Regenerative Medicine (ISCBRM), Stanford University School of Medicine, Stanford, 94305, CA, USA
| | - Garry Nolan
- Baxter Laboratories Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, 94305, CA, USA
| | - Paola Betancur
- Department of Radiation Oncology, University of California, San Francisco, 94143, CA, USA
| | - Gerlinde Wernig
- Department of Pathology, Institute of Stem Cell Biology and Regenerative Medicine (ISCBRM), Stanford University School of Medicine, Stanford, 94305, CA, USA.
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189
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Szigety KM, Liu F, Yuan CY, Moran DJ, Horrell J, Gochnauer HR, Cohen RN, Katz JP, Kaestner KH, Seykora JT, Tobias JW, Lazar MA, Xu M, Millar SE. HDAC3 ensures stepwise epidermal stratification via NCoR/SMRT-reliant mechanisms independent of its histone deacetylase activity. Genes Dev 2020; 34:973-988. [PMID: 32467224 PMCID: PMC7328513 DOI: 10.1101/gad.333674.119] [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: 10/08/2019] [Accepted: 04/23/2020] [Indexed: 12/12/2022]
Abstract
Here, Szigety et al. investigated the function of histone deacetylases in epidermal development, and they found that HDAC3 operates in conjunction with KLF4 to repress inappropriate expression of Tgm1, Krt16, and Aqp3, and suppresses expression of inflammatory cytokines through a Rela-dependent mechanism. Their data identify HDAC3 as a hub coordinating multiple aspects of epidermal barrier acquisition. Chromatin modifiers play critical roles in epidermal development, but the functions of histone deacetylases in this context are poorly understood. The class I HDAC, HDAC3, is of particular interest because it plays divergent roles in different tissues by partnering with tissue-specific transcription factors. We found that HDAC3 is expressed broadly in embryonic epidermis and is required for its orderly stepwise stratification. HDAC3 protein stability in vivo relies on NCoR and SMRT, which function redundantly in epidermal development. However, point mutations in the NCoR and SMRT deacetylase-activating domains, which are required for HDAC3's enzymatic function, permit normal stratification, indicating that HDAC3's roles in this context are largely independent of its histone deacetylase activity. HDAC3-bound sites are significantly enriched for predicted binding motifs for critical epidermal transcription factors including AP1, GRHL, and KLF family members. Our results suggest that among these, HDAC3 operates in conjunction with KLF4 to repress inappropriate expression of Tgm1, Krt16, and Aqp3. In parallel, HDAC3 suppresses expression of inflammatory cytokines through a Rela-dependent mechanism. These data identify HDAC3 as a hub coordinating multiple aspects of epidermal barrier acquisition.
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Affiliation(s)
- Katherine M Szigety
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Fang Liu
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Chase Y Yuan
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Deborah J Moran
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Jeremy Horrell
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Heather R Gochnauer
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Ronald N Cohen
- Section of Endocrinology, Diabetes, and Metabolism, University of Chicago, Chicago, Illinois 60637, USA
| | - Jonathan P Katz
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Klaus H Kaestner
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - John T Seykora
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - John W Tobias
- Penn Genomic Analysis Core, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Mitchell A Lazar
- Institute for Diabetes, Obesity, and Metabolism, Division of Endocrinology, Diabetes, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Mingang Xu
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.,Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Sarah E Millar
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.,Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.,Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
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190
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Stephens GS, Fu CH, St Romain CP, Zheng Y, Botterill JJ, Scharfman HE, Liu Y, Chin J. Genes Bound by ΔFosB in Different Conditions With Recurrent Seizures Regulate Similar Neuronal Functions. Front Neurosci 2020; 14:472. [PMID: 32536852 PMCID: PMC7268090 DOI: 10.3389/fnins.2020.00472] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 04/16/2020] [Indexed: 12/02/2022] Open
Abstract
Seizure incidence is increased in Alzheimer’s disease (AD) patients and mouse models, and treatment with the antiseizure drug levetiracetam improves cognition. We reported that one mechanism by which seizures can exert persistent effects on cognition is through accumulation of ΔFosB, a transcription factor with a long half-life. Even the infrequent seizures that spontaneously occur in transgenic mice expressing human amyloid precursor protein (APP) lead to persistent increases in ΔFosB in the hippocampus, similar to what we observed in patients with AD or temporal lobe epilepsy. ΔFosB epigenetically regulates expression of target genes, however, whether ΔFosB targets the same genes when induced by seizures in different neurological conditions is not clear. We performed ChIP-sequencing to assess the repertoire of ΔFosB target genes in APP mice and in pilocarpine-treated wildtype mice (Pilo mice), a pharmacological model of epilepsy. These mouse models allowed us to compare AD, in which seizures occur in the context of high levels of amyloid beta, and epilepsy, in which recurrent seizures occur without AD-specific pathophysiology. Network profiling of genes bound by ΔFosB in APP mice, Pilo mice, and respective control mice revealed that functional domains modulated by ΔFosB in the hippocampus are expanded and diversified in APP and Pilo mice (vs. respective controls). Domains of interest in both disease contexts involved neuronal excitability and neurotransmission, neurogenesis, chromatin remodeling, and cellular stress and neuroinflammation. To assess the gene targets bound by ΔFosB regardless of seizure etiology, we focused on 442 genes with significant ΔFosB binding in both APP and Pilo mice (vs. respective controls). Functional analyses identified pathways that regulate membrane potential, glutamatergic signaling, calcium homeostasis, complement activation, neuron-glia population maintenance, and chromatin dynamics. RNA-sequencing and qPCR measurements in independent mice detected altered expression of several ΔFosB targets shared in APP and Pilo mice. Our findings indicate that seizure-induced ΔFosB can bind genes in patterns that depend on seizure etiology, but can bind other genes regardless of seizure etiology. Understanding the factors that underlie these differences, such as chromatin accessibility and/or abundance of co-factors, could reveal novel insights into the control of gene expression in disorders with recurrent seizures.
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Affiliation(s)
- Gabriel S Stephens
- Memory and Brain Research Center, Department of Neuroscience, Baylor College of Medicine, Houston, TX, United States
| | - Chia-Hsuan Fu
- Memory and Brain Research Center, Department of Neuroscience, Baylor College of Medicine, Houston, TX, United States
| | - Corey P St Romain
- Memory and Brain Research Center, Department of Neuroscience, Baylor College of Medicine, Houston, TX, United States
| | - Yi Zheng
- Memory and Brain Research Center, Department of Neuroscience, Baylor College of Medicine, Houston, TX, United States
| | - Justin J Botterill
- Center for Dementia Research, Nathan Kline Institute for Psychiatric Research, Orangeburg, NY, United States
| | - Helen E Scharfman
- Center for Dementia Research, Nathan Kline Institute for Psychiatric Research, Orangeburg, NY, United States.,Departments of Child & Adolescent Psychiatry, Neuroscience & Physiology, and Psychiatry, New York University Neuroscience Institute, New York University Langone Health, New York, NY, United States
| | - Yin Liu
- Department of Neurobiology and Anatomy, University of Texas Medical School at Houston, Houston, TX, United States
| | - Jeannie Chin
- Memory and Brain Research Center, Department of Neuroscience, Baylor College of Medicine, Houston, TX, United States
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191
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Lazar JE, Stehling-Sun S, Nandakumar V, Wang H, Chee DR, Howard NP, Acosta R, Dunn D, Diegel M, Neri F, Castillo A, Ibarrientos S, Lee K, Lescano N, Van Biber B, Nelson J, Halow J, Sandstrom R, Bates D, Urnov FD, Stamatoyannopoulos JA, Funnell APW. Global Regulatory DNA Potentiation by SMARCA4 Propagates to Selective Gene Expression Programs via Domain-Level Remodeling. Cell Rep 2020; 31:107676. [PMID: 32460018 DOI: 10.1016/j.celrep.2020.107676] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 12/23/2019] [Accepted: 04/30/2020] [Indexed: 01/02/2023] Open
Abstract
The human genome encodes millions of regulatory elements, of which only a small fraction are active within a given cell type. Little is known about the global impact of chromatin remodelers on regulatory DNA landscapes and how this translates to gene expression. We use precision genome engineering to reawaken homozygously inactivated SMARCA4, a central ATPase of the human SWI/SNF chromatin remodeling complex, in lung adenocarcinoma cells. Here, we combine DNase I hypersensitivity, histone modification, and transcriptional profiling to show that SMARCA4 dramatically increases both the number and magnitude of accessible chromatin sites genome-wide, chiefly by unmasking sites of low regulatory factor occupancy. By contrast, transcriptional changes are concentrated within well-demarcated remodeling domains wherein expression of specific genes is gated by both distal element activation and promoter chromatin configuration. Our results provide a perspective on how global chromatin remodeling activity is translated to gene expression via regulatory DNA.
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Affiliation(s)
- John E Lazar
- Departments of Genome Sciences and Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA; Altius Institute for Biomedical Sciences, Seattle, WA 98121, USA
| | | | - Vivek Nandakumar
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, USA
| | - Hao Wang
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, USA
| | - Daniel R Chee
- Departments of Genome Sciences and Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA; Altius Institute for Biomedical Sciences, Seattle, WA 98121, USA
| | | | - Reyes Acosta
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, USA
| | - Douglass Dunn
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, USA
| | - Morgan Diegel
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, USA
| | - Fidencio Neri
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, USA
| | - Andres Castillo
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, USA
| | - Sean Ibarrientos
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, USA
| | - Kristen Lee
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, USA
| | - Ninnia Lescano
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, USA
| | - Ben Van Biber
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, USA
| | - Jemma Nelson
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, USA
| | - Jessica Halow
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, USA
| | | | - Daniel Bates
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, USA
| | - Fyodor D Urnov
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, USA
| | - John A Stamatoyannopoulos
- Departments of Genome Sciences and Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA; Altius Institute for Biomedical Sciences, Seattle, WA 98121, USA.
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192
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Catizone AN, Uzunbas GK, Celadova P, Kuang S, Bose D, Sammons MA. Locally acting transcription factors regulate p53-dependent cis-regulatory element activity. Nucleic Acids Res 2020; 48:4195-4213. [PMID: 32133495 PMCID: PMC7192610 DOI: 10.1093/nar/gkaa147] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 01/27/2020] [Accepted: 02/26/2020] [Indexed: 01/03/2023] Open
Abstract
The master tumor suppressor p53 controls transcription of a wide-ranging gene network involved in apoptosis, cell cycle arrest, DNA damage repair, and senescence. Recent studies revealed pervasive binding of p53 to cis-regulatory elements (CREs), which are non-coding segments of DNA that spatially and temporally control transcription through the combinatorial binding of local transcription factors. Although the role of p53 as a strong trans-activator of gene expression is well known, the co-regulatory factors and local sequences acting at p53-bound CREs are comparatively understudied. We designed and executed a massively parallel reporter assay (MPRA) to investigate the effect of transcription factor binding motifs and local sequence context on p53-bound CRE activity. Our data indicate that p53-bound CREs are both positively and negatively affected by alterations in local sequence context and changes to co-regulatory TF motifs. Our data suggest p53 has the flexibility to cooperate with a variety of transcription factors in order to regulate CRE activity. By utilizing different sets of co-factors across CREs, we hypothesize that global p53 activity is guarded against loss of any one regulatory partner, allowing for dynamic and redundant control of p53-mediated transcription.
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Affiliation(s)
- Allison N Catizone
- Department of Biological Sciences and the RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Gizem Karsli Uzunbas
- Department of Biological Sciences and the RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Petra Celadova
- Sheffield Institute For Nucleic Acids (SInFoNiA) and Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Sylvia Kuang
- Department of Biological Sciences and the RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Daniel Bose
- Sheffield Institute For Nucleic Acids (SInFoNiA) and Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Morgan A Sammons
- Department of Biological Sciences and the RNA Institute, University at Albany, State University of New York, Albany, NY, USA
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193
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TGFβ and EGF signaling orchestrates the AP-1- and p63 transcriptional regulation of breast cancer invasiveness. Oncogene 2020; 39:4436-4449. [PMID: 32350443 PMCID: PMC7253358 DOI: 10.1038/s41388-020-1299-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 04/04/2020] [Accepted: 04/09/2020] [Indexed: 01/16/2023]
Abstract
Activator protein (AP)-1 transcription factors are essential elements of the pro-oncogenic functions of transforming growth factor-β (TGFβ)-SMAD signaling. Here we show that in multiple HER2+ and/or EGFR+ breast cancer cell lines these AP-1-dependent tumorigenic properties of TGFβ critically rely on epidermal growth factor receptor (EGFR) activation and expression of the ΔN isoform of transcriptional regulator p63. EGFR and ΔNp63 enabled and/or potentiated the activation of a subset of TGFβ-inducible invasion/migration-associated genes, e.g., ITGA2, LAMB3, and WNT7A/B, and enhanced the recruitment of SMAD2/3 to these genes. The TGFβ- and EGF-induced binding of SMAD2/3 and JUNB to these gene loci was accompanied by p63-SMAD2/3 and p63-JUNB complex formation. p63 and EGFR were also found to strongly potentiate TGFβ induction of AP-1 proteins and, in particular, FOS family members. Ectopic overexpression of FOS could counteract the decrease in TGFβ-induced gene activation after p63 depletion. p63 is also involved in the transcriptional regulation of heparin binding (HB)-EGF and EGFR genes, thereby establishing a self-amplification loop that facilitates and empowers the pro-invasive functions of TGFβ. These cooperative pro-oncogenic functions of EGFR, AP-1, p63, and TGFβ were efficiently inhibited by clinically relevant chemical inhibitors. Our findings may, therefore, be of importance for therapy of patients with breast cancers with an activated EGFR-RAS-RAF pathway.
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194
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Mitf Links Neuronal Activity and Long-Term Homeostatic Intrinsic Plasticity. eNeuro 2020; 7:ENEURO.0412-19.2020. [PMID: 32193365 PMCID: PMC7174873 DOI: 10.1523/eneuro.0412-19.2020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 02/07/2020] [Accepted: 03/02/2020] [Indexed: 12/25/2022] Open
Abstract
Neuroplasticity forms the basis for neuronal circuit complexity and differences between otherwise similar circuits. We show that the microphthalmia-associated transcription factor (Mitf) plays a central role in intrinsic plasticity of olfactory bulb (OB) projection neurons. Mitral and tufted (M/T) neurons from Mitf mutant mice are hyperexcitable, have a reduced A-type potassium current (IA) and exhibit reduced expression of Kcnd3, which encodes a potassium voltage-gated channel subunit (Kv4.3) important for generating the IA Furthermore, expression of the Mitf and Kcnd3 genes is activity dependent in OB projection neurons and the MITF protein activates expression from Kcnd3 regulatory elements. Moreover, Mitf mutant mice have changes in olfactory habituation and have increased habituation for an odorant following long-term exposure, indicating that regulation of Kcnd3 is pivotal for long-term olfactory adaptation. Our findings show that Mitf acts as a direct regulator of intrinsic homeostatic feedback and links neuronal activity, transcriptional changes and neuronal function.
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195
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Beisaw A, Kuenne C, Guenther S, Dallmann J, Wu CC, Bentsen M, Looso M, Stainier DYR. AP-1 Contributes to Chromatin Accessibility to Promote Sarcomere Disassembly and Cardiomyocyte Protrusion During Zebrafish Heart Regeneration. Circ Res 2020; 126:1760-1778. [PMID: 32312172 DOI: 10.1161/circresaha.119.316167] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
RATIONALE The adult human heart is an organ with low regenerative potential. Heart failure following acute myocardial infarction is a leading cause of death due to the inability of cardiomyocytes to proliferate and replenish lost cardiac muscle. While the zebrafish has emerged as a powerful model to study endogenous cardiac regeneration, the molecular mechanisms by which cardiomyocytes respond to damage by disassembling sarcomeres, proliferating, and repopulating the injured area remain unclear. Furthermore, we are far from understanding the regulation of the chromatin landscape and epigenetic barriers that must be overcome for cardiac regeneration to occur. OBJECTIVE To identify transcription factor regulators of the chromatin landscape, which promote cardiomyocyte regeneration in zebrafish, and investigate their function. METHODS AND RESULTS Using the Assay for Transposase-Accessible Chromatin coupled to high-throughput sequencing (ATAC-Seq), we first find that the regenerating cardiomyocyte chromatin accessibility landscape undergoes extensive changes following cryoinjury, and that activator protein-1 (AP-1) binding sites are the most highly enriched motifs in regions that gain accessibility during cardiac regeneration. Furthermore, using bioinformatic and gene expression analyses, we find that the AP-1 response in regenerating adult zebrafish cardiomyocytes is largely different from the response in adult mammalian cardiomyocytes. Using a cardiomyocyte-specific dominant negative approach, we show that blocking AP-1 function leads to defects in cardiomyocyte proliferation as well as decreased chromatin accessibility at the fbxl22 and ilk loci, which regulate sarcomere disassembly and cardiomyocyte protrusion into the injured area, respectively. We further show that overexpression of the AP-1 family members Junb and Fosl1 can promote changes in mammalian cardiomyocyte behavior in vitro. CONCLUSIONS AP-1 transcription factors play an essential role in the cardiomyocyte response to injury by regulating chromatin accessibility changes, thereby allowing the activation of gene expression programs that promote cardiomyocyte dedifferentiation, proliferation, and protrusion into the injured area.
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Affiliation(s)
- Arica Beisaw
- From the Department of Developmental Genetics (A.B., J.D., C.-C.W., D.Y.R.S.), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.,German Centre for Cardiovascular Research (DZHK) Partner Site Rhine-Main (A.B., S.G., D.Y.R.S.), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Carsten Kuenne
- ECCPS Bioinformatics and Deep Sequencing Platform (C.K., S.G., M.B., M.L.), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Stefan Guenther
- ECCPS Bioinformatics and Deep Sequencing Platform (C.K., S.G., M.B., M.L.), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.,German Centre for Cardiovascular Research (DZHK) Partner Site Rhine-Main (A.B., S.G., D.Y.R.S.), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Julia Dallmann
- From the Department of Developmental Genetics (A.B., J.D., C.-C.W., D.Y.R.S.), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Chi-Chung Wu
- From the Department of Developmental Genetics (A.B., J.D., C.-C.W., D.Y.R.S.), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Mette Bentsen
- ECCPS Bioinformatics and Deep Sequencing Platform (C.K., S.G., M.B., M.L.), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Mario Looso
- ECCPS Bioinformatics and Deep Sequencing Platform (C.K., S.G., M.B., M.L.), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Didier Y R Stainier
- From the Department of Developmental Genetics (A.B., J.D., C.-C.W., D.Y.R.S.), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.,German Centre for Cardiovascular Research (DZHK) Partner Site Rhine-Main (A.B., S.G., D.Y.R.S.), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
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196
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Kuznetsova T, Prange KHM, Glass CK, de Winther MPJ. Transcriptional and epigenetic regulation of macrophages in atherosclerosis. Nat Rev Cardiol 2020; 17:216-228. [PMID: 31578516 PMCID: PMC7770754 DOI: 10.1038/s41569-019-0265-3] [Citation(s) in RCA: 173] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/01/2019] [Indexed: 12/11/2022]
Abstract
Monocytes and macrophages provide defence against pathogens and danger signals. These cells respond to stimulation in a fast and stimulus-specific manner by utilizing complex cascaded activation by lineage-determining and signal-dependent transcription factors. The complexity of the functional response is determined by interactions between triggered transcription factors and depends on the microenvironment and interdependent signalling cascades. Dysregulation of macrophage phenotypes is a major driver of various diseases such as atherosclerosis, rheumatoid arthritis and type 2 diabetes mellitus. Furthermore, exposure of monocytes, which are macrophage precursor cells, to certain stimuli can lead to a hypo-inflammatory tolerized phenotype or a hyper-inflammatory trained phenotype in a macrophage. In atherosclerosis, macrophages and monocytes are exposed to inflammatory cytokines, oxidized lipids, cholesterol crystals and other factors. All these stimuli induce not only a specific transcriptional response but also interact extensively, leading to transcriptional and epigenetic heterogeneity of macrophages in atherosclerotic plaques. Targeting the epigenetic landscape of plaque macrophages can be a powerful therapeutic tool to modulate pro-atherogenic phenotypes and reduce the rate of plaque formation. In this Review, we discuss the emerging role of transcription factors and epigenetic remodelling in macrophages in the context of atherosclerosis and inflammation, and provide a comprehensive overview of epigenetic enzymes and transcription factors that are involved in macrophage activation.
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Affiliation(s)
- Tatyana Kuznetsova
- Experimental Vascular Biology, Department of Medical Biochemistry, Amsterdam University Medical Centers - location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Koen H M Prange
- Experimental Vascular Biology, Department of Medical Biochemistry, Amsterdam University Medical Centers - location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Menno P J de Winther
- Experimental Vascular Biology, Department of Medical Biochemistry, Amsterdam University Medical Centers - location AMC, University of Amsterdam, Amsterdam, Netherlands.
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians University, Munich, Germany.
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197
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Cai WL, Greer CB, Chen JF, Arnal-Estapé A, Cao J, Yan Q, Nguyen DX. Specific chromatin landscapes and transcription factors couple breast cancer subtype with metastatic relapse to lung or brain. BMC Med Genomics 2020; 13:33. [PMID: 32143622 PMCID: PMC7060551 DOI: 10.1186/s12920-020-0695-0] [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: 10/08/2019] [Accepted: 02/11/2020] [Indexed: 12/17/2022] Open
Abstract
Background Few somatic mutations have been linked to breast cancer metastasis, whereas transcriptomic differences among primary tumors correlate with incidence of metastasis, especially to the lungs and brain. However, the epigenomic alterations and transcription factors (TFs) which underlie these alterations remain unclear. Methods To identify these, we performed RNA-seq, Chromatin Immunoprecipitation and sequencing (ChIP-seq) and Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) of the MDA-MB-231 cell line and its brain (BrM2) and lung (LM2) metastatic sub-populations. We incorporated ATAC-seq data from TCGA to assess metastatic open chromatin signatures, and gene expression data from human metastatic datasets to nominate transcription factor biomarkers. Results Our integrated epigenomic analyses found that lung and brain metastatic cells exhibit both shared and distinctive signatures of active chromatin. Notably, metastatic sub-populations exhibit increased activation of both promoters and enhancers. We also integrated these data with chromosome conformation capture coupled with ChIP-seq (HiChIP) derived enhancer-promoter interactions to predict enhancer-controlled pathway alterations. We found that enhancer changes are associated with endothelial cell migration in LM2, and negative regulation of epithelial cell proliferation in BrM2. Promoter changes are associated with vasculature development in LM2 and homophilic cell adhesion in BrM2. Using ATAC-seq, we identified a metastasis open-chromatin signature that is elevated in basal-like and HER2-enriched breast cancer subtypes and associates with worse prognosis in human samples. We further uncovered TFs associated with the open chromatin landscapes of metastatic cells and whose expression correlates with risk for metastasis. While some of these TFs are associated with primary breast tumor subtypes, others more specifically correlate with lung or brain metastasis. Conclusions We identify distinctive epigenomic properties of breast cancer cells that metastasize to the lung and brain. We also demonstrate that signatures of active chromatin sites are partially linked to human breast cancer subtypes with poor prognosis, and that specific TFs can independently distinguish lung and brain relapse.
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Affiliation(s)
- Wesley L Cai
- Department of Pathology, Yale School of Medicine, 333 Cedar St, New Haven, CT, 06510, USA
| | - Celeste B Greer
- Department of Pathology, Yale School of Medicine, 333 Cedar St, New Haven, CT, 06510, USA.,Present address: Department of Pharmacology, Vanderbilt University School of Medicine, 2209 Garland Ave, Nashville, TN, 37240-0002, USA
| | - Jocelyn F Chen
- Department of Pathology, Yale School of Medicine, 333 Cedar St, New Haven, CT, 06510, USA
| | - Anna Arnal-Estapé
- Department of Pathology, Yale School of Medicine, 333 Cedar St, New Haven, CT, 06510, USA.,Yale Cancer Center, Yale School of Medicine, 333 Cedar St, New Haven, CT, 06510, USA
| | - Jian Cao
- Department of Pathology, Yale School of Medicine, 333 Cedar St, New Haven, CT, 06510, USA.,Yale Cancer Center, Yale School of Medicine, 333 Cedar St, New Haven, CT, 06510, USA.,Present address: Rutgers Cancer Institute of New Jersey, Rutgers, 195 Little Albany St, New Brunswick, NJ, 08903-2681, USA
| | - Qin Yan
- Department of Pathology, Yale School of Medicine, 333 Cedar St, New Haven, CT, 06510, USA. .,Yale Cancer Center, Yale School of Medicine, 333 Cedar St, New Haven, CT, 06510, USA. .,Yale Stem Cell Center, Yale School of Medicine, 333 Cedar St, New Haven, CT, 06510, USA. .,Department of Pathology, Yale School of Medicine, P.O. Box 208023, New Haven, CT, 06520-8023, USA.
| | - Don X Nguyen
- Department of Pathology, Yale School of Medicine, 333 Cedar St, New Haven, CT, 06510, USA. .,Yale Cancer Center, Yale School of Medicine, 333 Cedar St, New Haven, CT, 06510, USA. .,Yale Stem Cell Center, Yale School of Medicine, 333 Cedar St, New Haven, CT, 06510, USA. .,Department of Pathology, Yale School of Medicine, P.O. Box 208023, New Haven, CT, 06520-8023, USA. .,Department of Medicine (Medical Oncology), Yale School of Medicine, 333 Cedar St, New Haven, CT, 06510, USA.
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198
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Bozek M, Gompel N. Developmental Transcriptional Enhancers: A Subtle Interplay between Accessibility and Activity: Considering Quantitative Accessibility Changes between Different Regulatory States of an Enhancer Deconvolutes the Complex Relationship between Accessibility and Activity. Bioessays 2020; 42:e1900188. [PMID: 32142172 DOI: 10.1002/bies.201900188] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 01/16/2020] [Indexed: 12/21/2022]
Abstract
Measurements of open chromatin in specific cell types are widely used to infer the spatiotemporal activity of transcriptional enhancers. How reliable are these predictions? In this review, it is argued that the relationship between the accessibility and activity of an enhancer is insufficiently described by simply considering open versus closed chromatin, or active versus inactive enhancers. Instead, recent studies focusing on the quantitative nature of accessibility signal reveal subtle differences between active enhancers and their different inactive counterparts: the closed silenced state and the accessible primed and repressed states. While the open structure as such is not a specific indicator of enhancer activity, active enhancers display a higher degree of accessibility than the primed and repressed states. Molecular mechanisms that may account for these quantitative differences are discussed. A model that relates molecular events at an enhancer to changes in its activity and accessibility in a developing tissue is also proposed.
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Affiliation(s)
- Marta Bozek
- Department Biochemie, Ludwig-Maximilians Universität München, Genzentrum, 81377, München, Germany
| | - Nicolas Gompel
- Fakultät für Biologie, Ludwig-Maximilians Universität München, Biozentrum, 82152, Planegg-Martinsried, Germany
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199
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Altered chromatin landscape and enhancer engagement underlie transcriptional dysregulation in MED12 mutant uterine leiomyomas. Nat Commun 2020; 11:1019. [PMID: 32094355 PMCID: PMC7040020 DOI: 10.1038/s41467-020-14701-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 01/23/2020] [Indexed: 02/07/2023] Open
Abstract
Uterine leiomyomas (fibroids) are a major source of gynecologic morbidity in reproductive age women and are characterized by the excessive deposition of a disorganized extracellular matrix, resulting in rigid benign tumors. Although down regulation of the transcription factor AP-1 is highly prevalent in leiomyomas, the functional consequence of AP-1 loss on gene transcription in uterine fibroids remains poorly understood. Using high-resolution ChIP-sequencing, promoter capture Hi-C, and RNA-sequencing of matched normal and leiomyoma tissues, here we show that modified enhancer architecture is a major driver of transcriptional dysregulation in MED12 mutant uterine leiomyomas. Furthermore, modifications in enhancer architecture are driven by the depletion of AP-1 occupancy on chromatin. Silencing of AP-1 subunits in primary myometrium cells leads to transcriptional dysregulation of extracellular matrix associated genes and partly recapitulates transcriptional and epigenetic changes observed in leiomyomas. These findings establish AP-1 driven aberrant enhancer regulation as an important mechanism of leiomyoma disease pathogenesis.
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200
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Grossi E, Raimondi I, Goñi E, González J, Marchese FP, Chapaprieta V, Martín-Subero JI, Guo S, Huarte M. A lncRNA-SWI/SNF complex crosstalk controls transcriptional activation at specific promoter regions. Nat Commun 2020; 11:936. [PMID: 32071317 PMCID: PMC7028943 DOI: 10.1038/s41467-020-14623-3] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 01/18/2020] [Indexed: 12/14/2022] Open
Abstract
LncRNAs have been shown to be direct players in chromatin regulation, but little is known about their role at active genomic loci. We investigate the role of lncRNAs in gene activation by profiling the RNA interactome of SMARCB1-containing SWI/SNF complexes in proliferating and senescent conditions. The isolation of SMARCB1-associated transcripts, together with chromatin profiling, shows prevalent association to active regions where SMARCB1 differentially binds locally transcribed RNAs. We identify SWINGN, a lncRNA interacting with SMARCB1 exclusively in proliferating conditions, exerting a pro-oncogenic role in some tumor types. SWINGN is transcribed from an enhancer and modulates the activation of GAS6 oncogene as part of a topologically organized region, as well as a larger network of pro-oncogenic genes by favoring SMARCB1 binding. Our results indicate that SWINGN influences the ability of the SWI/SNF complexes to drive epigenetic activation of specific promoters, suggesting a SWI/SNF-RNA cooperation to achieve optimal transcriptional activation.
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Affiliation(s)
- Elena Grossi
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, 31008, Spain
- Institute of Health Research of Navarra (IdiSNA), Pamplona, Spain
| | - Ivan Raimondi
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, 31008, Spain
- Institute of Health Research of Navarra (IdiSNA), Pamplona, Spain
| | - Enrique Goñi
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, 31008, Spain
- Institute of Health Research of Navarra (IdiSNA), Pamplona, Spain
| | - Jovanna González
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, 31008, Spain
- Institute of Health Research of Navarra (IdiSNA), Pamplona, Spain
| | - Francesco P Marchese
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, 31008, Spain
- Institute of Health Research of Navarra (IdiSNA), Pamplona, Spain
| | - Vicente Chapaprieta
- Departament de Fonaments Clinics, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain
| | - José I Martín-Subero
- Departament de Fonaments Clinics, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Shuling Guo
- Department of Antisense Drug Discovery and Clinical Development, Ionis Pharmaceuticals, Carlsbad, CA, USA
| | - Maite Huarte
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, 31008, Spain.
- Institute of Health Research of Navarra (IdiSNA), Pamplona, Spain.
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