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Ochodnicka-Mackovicova K, Mokry M, Haagmans M, Bradley TE, van Noesel CJM, Guikema JEJ. RAG1/2 induces double-stranded DNA breaks at non-Ig loci in the proximity of single sequence repeats in developing B cells. Eur J Immunol 2024:e2350958. [PMID: 39046890 DOI: 10.1002/eji.202350958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 07/11/2024] [Accepted: 07/16/2024] [Indexed: 07/27/2024]
Abstract
In developing B cells, V(D)J gene recombination is initiated by the RAG1/2 endonuclease complex, introducing double-stranded DNA breaks (DSBs) in V, D, and J genes and resulting in the formation of the hypervariable parts of immunoglobulins (Ig). Persistent or aberrant RAG1/2 targeting is a potential threat to genome integrity. While RAG1 and RAG2 have been shown to bind various regions genome-wide, the in vivo off-target DNA damage instigated by RAG1/2 endonuclease remains less well understood. In the current study, we identified regions containing RAG1/2-induced DNA breaks in mouse pre-B cells on a genome-wide scale using a global DNA DSB detection strategy. We detected 1489 putative RAG1/2-dependent DSBs, most of which were located outside the Ig loci. DNA sequence motif analysis showed a specific enrichment of RAG1/2-induced DNA DSBs at GA- and CA-repeats and GC-rich motifs. These findings provide further insights into RAG1/2 off-target activity. The ability of RAG1/2 to introduce DSBs on the non-Ig loci during the endogenous V(D)J recombination emphasizes its genotoxic potential in developing lymphocytes.
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Affiliation(s)
- Katarina Ochodnicka-Mackovicova
- Department of Pathology, Amsterdam University Medical Center, Location AMC, University of Amsterdam, Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam, The Netherlands
| | - Michal Mokry
- Laboratory of Experimental Cardiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Central Diagnostics Laboratory, University Medical Center Utrecht, University Utrecht, Utrecht, The Netherlands
| | - Martin Haagmans
- Core Facility Genomics, Department of Clinical Genetics, Amsterdam University Medical Center, The Netherlands
| | - Ted E Bradley
- Core Facility Genomics, Department of Clinical Genetics, Amsterdam University Medical Center, The Netherlands
| | - Carel J M van Noesel
- Department of Pathology, Amsterdam University Medical Center, Location AMC, University of Amsterdam, Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam, The Netherlands
| | - Jeroen E J Guikema
- Department of Pathology, Amsterdam University Medical Center, Location AMC, University of Amsterdam, Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam, The Netherlands
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2
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Mulas C, Stammers M, Salomaa SI, Heinzen C, Suter DM, Smith A, Chalut KJ. ERK signalling eliminates Nanog and maintains Oct4 to drive the formative pluripotency transition. Development 2024; 151:dev203106. [PMID: 39069943 DOI: 10.1242/dev.203106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 06/13/2024] [Indexed: 07/30/2024]
Abstract
Naïve epiblast cells in the embryo and pluripotent stem cells in vitro undergo developmental progression to a formative state competent for lineage specification. During this transition, transcription factors and chromatin are rewired to encode new functional features. Here, we examine the role of mitogen-activated protein kinase (ERK1/2) signalling in pluripotent state transition. We show that a primary consequence of ERK activation in mouse embryonic stem cells is elimination of Nanog, which precipitates breakdown of the naïve state gene regulatory network. Variability in pERK dynamics results in heterogeneous loss of Nanog and metachronous state transition. Knockdown of Nanog allows exit without ERK activation. However, transition to formative pluripotency does not proceed and cells collapse to an indeterminate identity. This outcome is due to failure to maintain expression of the central pluripotency factor Oct4. Thus, during formative transition ERK signalling both dismantles the naïve state and preserves pluripotency. These results illustrate how a single signalling pathway can both initiate and secure transition between cell states.
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Affiliation(s)
- Carla Mulas
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
- Randall Centre for Cell and Molecular Biology, King's College London, London SE1 1YR, UK
- Altos Labs Cambridge Institute of Science, Granta Park, Cambridge CB21 6GP, UK
| | - Melanie Stammers
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Siiri I Salomaa
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
- Altos Labs Cambridge Institute of Science, Granta Park, Cambridge CB21 6GP, UK
| | - Constanze Heinzen
- Institute of Cell Biology and Neuroscience, Goethe University, Frankfurt 60439, Germany
| | - David M Suter
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
| | - Austin Smith
- Living Systems Institute, University of Exeter, Exeter EX4 4QD, UK
| | - Kevin J Chalut
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
- Altos Labs Cambridge Institute of Science, Granta Park, Cambridge CB21 6GP, UK
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3
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Rich J, Bennaroch M, Notel L, Patalakh P, Alberola J, Issa F, Opolon P, Bawa O, Rondof W, Marchais A, Dessen P, Meurice G, Le-Gall M, Polrot M, Ser-Le Roux K, Mamchaoui K, Droin N, Raslova H, Maire P, Geoerger B, Pirozhkova I. DiPRO1 distinctly reprograms muscle and mesenchymal cancer cells. EMBO Mol Med 2024:10.1038/s44321-024-00097-z. [PMID: 39009887 DOI: 10.1038/s44321-024-00097-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 06/13/2024] [Accepted: 06/18/2024] [Indexed: 07/17/2024] Open
Abstract
We have recently identified the uncharacterized ZNF555 protein as a component of a productive complex involved in the morbid function of the 4qA locus in facioscapulohumeral dystrophy. Subsequently named DiPRO1 (Death, Differentiation, and PROliferation related PROtein 1), our study provides substantial evidence of its role in the differentiation and proliferation of human myoblasts. DiPRO1 operates through the regulatory binding regions of SIX1, a master regulator of myogenesis. Its relevance extends to mesenchymal tumors, such as rhabdomyosarcoma (RMS) and Ewing sarcoma, where DiPRO1 acts as a repressor via the epigenetic regulators TIF1B and UHRF1, maintaining methylation of cis-regulatory elements and gene promoters. Loss of DiPRO1 mimics the host defense response to virus, awakening retrotransposable repeats and the ZNF/KZFP gene family. This enables the eradication of cancer cells, reprogramming the cellular decision balance towards inflammation and/or apoptosis by controlling TNF-α via NF-kappaB signaling. Finally, our results highlight the vulnerability of mesenchymal cancer tumors to si/shDiPRO1-based nanomedicines, positioning DiPRO1 as a potential therapeutic target.
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Affiliation(s)
- Jeremy Rich
- UMR8126 CNRS, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
| | - Melanie Bennaroch
- UMR8126 CNRS, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
| | - Laura Notel
- UMR8126 CNRS, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
| | - Polina Patalakh
- UMR8126 CNRS, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
| | - Julien Alberola
- UMR8126 CNRS, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
| | - Fayez Issa
- INSERM U1016, CNRS UMR 8104, Institut Cochin, Université Paris-Cité, Paris, France
| | - Paule Opolon
- Pathology and Cytology Section, UMS AMMICA, CNRS, INSERM, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
| | - Olivia Bawa
- Pathology and Cytology Section, UMS AMMICA, CNRS, INSERM, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
| | - Windy Rondof
- Bioinformatics Platform, UMS AMMICA, CNRS, INSERM, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer campus, INSERM U1015, Université Paris-Saclay, Villejuif, France
| | - Antonin Marchais
- Bioinformatics Platform, UMS AMMICA, CNRS, INSERM, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer campus, INSERM U1015, Université Paris-Saclay, Villejuif, France
| | - Philippe Dessen
- Bioinformatics Platform, UMS AMMICA, CNRS, INSERM, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
| | - Guillaume Meurice
- Bioinformatics Platform, UMS AMMICA, CNRS, INSERM, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
| | - Morgane Le-Gall
- Proteom'IC facility, Université Paris Cité, CNRS, INSERM, Institut Cochin, F-75014, Paris, France
| | - Melanie Polrot
- Pre-clinical Evaluation Unit (PFEP), INSERM, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
| | - Karine Ser-Le Roux
- Pre-clinical Evaluation Unit (PFEP), INSERM, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
| | - Kamel Mamchaoui
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, F-75013, Paris, France
| | - Nathalie Droin
- Genomic Platform, UMS AMMICA US 23 INSERM UAR 3655 CNRS, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
- UMR1287 INSERM, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
| | - Hana Raslova
- UMR1287 INSERM, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
| | - Pascal Maire
- INSERM U1016, CNRS UMR 8104, Institut Cochin, Université Paris-Cité, Paris, France
| | - Birgit Geoerger
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer campus, INSERM U1015, Université Paris-Saclay, Villejuif, France
| | - Iryna Pirozhkova
- UMR8126 CNRS, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France.
- INSERM U1016, CNRS UMR 8104, Institut Cochin, Université Paris-Cité, Paris, France.
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Dunn-Davies H, Dudnakova T, Nogara A, Rodor J, Thomas AC, Parish E, Gautier P, Meynert A, Ulitsky I, Madeddu P, Caporali A, Baker A, Tollervey D, Mitić T. Control of endothelial cell function and arteriogenesis by MEG3:EZH2 epigenetic regulation of integrin expression. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102173. [PMID: 38617973 PMCID: PMC11015509 DOI: 10.1016/j.omtn.2024.102173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 03/14/2024] [Indexed: 04/16/2024]
Abstract
Epigenetic processes involving long non-coding RNAs regulate endothelial gene expression. However, the underlying regulatory mechanisms causing endothelial dysfunction remain to be elucidated. Enhancer of zeste homolog 2 (EZH2) is an important rheostat of histone H3K27 trimethylation (H3K27me3) that represses endothelial targets, but EZH2 RNA binding capacity and EZH2:RNA functional interactions have not been explored in post-ischemic angiogenesis. We used formaldehyde/UV-assisted crosslinking ligation and sequencing of hybrids and identified a new role for maternally expressed gene 3 (MEG3). MEG3 formed the predominant RNA:RNA hybrid structures in endothelial cells. Moreover, MEG3:EZH2 assists recruitment onto chromatin. By EZH2-chromatin immunoprecipitation, following MEG3 depletion, we demonstrated that MEG3 controls recruitment of EZH2/H3K27me3 onto integrin subunit alpha4 (ITGA4) promoter. Both MEG3 knockdown or EZH2 inhibition (A-395) promoted ITGA4 expression and improved endothelial cell migration and adhesion to fibronectin in vitro. The A-395 inhibitor re-directed MEG3-assisted chromatin remodeling, offering a direct therapeutic benefit by increasing endothelial function and resilience. This approach subsequently increased the expression of ITGA4 in arterioles following ischemic injury in mice, thus promoting arteriogenesis. Our findings show a context-specific role for MEG3 in guiding EZH2 to repress ITGA4. Novel therapeutic strategies could antagonize MEG3:EZH2 interaction for pre-clinical studies.
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Affiliation(s)
- Hywel Dunn-Davies
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building Max Born Crescent, King’s Buildings, Edinburgh EH9 3BF, UK
| | - Tatiana Dudnakova
- University/British Heart Foundation Centre for Cardiovascular Science, Queen’s Medical Research Institute (QMRI), The University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Antonella Nogara
- University/British Heart Foundation Centre for Cardiovascular Science, Queen’s Medical Research Institute (QMRI), The University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Julie Rodor
- University/British Heart Foundation Centre for Cardiovascular Science, Queen’s Medical Research Institute (QMRI), The University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Anita C. Thomas
- Bristol Medical School, Translational Health Sciences, University of Bristol, Research and Teaching Floor Level 7, Queens Building, Bristol Royal Infirmary, Bristol BS2 8HW, UK
| | - Elisa Parish
- University/British Heart Foundation Centre for Cardiovascular Science, Queen’s Medical Research Institute (QMRI), The University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Philippe Gautier
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Alison Meynert
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Igor Ulitsky
- Department of Immunology and Regenerative Biology and Department of Molecular Neuroscience, Weizmann-UK Building rm. 007, Weizmann Institute of Science Rehovot 76100, Israel
| | - Paolo Madeddu
- Bristol Medical School, Translational Health Sciences, University of Bristol, Research and Teaching Floor Level 7, Queens Building, Bristol Royal Infirmary, Bristol BS2 8HW, UK
| | - Andrea Caporali
- University/British Heart Foundation Centre for Cardiovascular Science, Queen’s Medical Research Institute (QMRI), The University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Andrew Baker
- University/British Heart Foundation Centre for Cardiovascular Science, Queen’s Medical Research Institute (QMRI), The University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - David Tollervey
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building Max Born Crescent, King’s Buildings, Edinburgh EH9 3BF, UK
| | - Tijana Mitić
- University/British Heart Foundation Centre for Cardiovascular Science, Queen’s Medical Research Institute (QMRI), The University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
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5
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Cathcart B, Cheedipudi SM, Rouhi L, Zhao Z, Gurha P, Marian AJ. DNA double-stranded breaks, a hallmark of aging, defined at the nucleotide resolution, are increased and associated with transcription in the cardiac myocytes in LMNA-cardiomyopathy. Cardiovasc Res 2024:cvae063. [PMID: 38577741 DOI: 10.1093/cvr/cvae063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/06/2024] Open
Abstract
AIMS An intrinsic feature of gene transcription is the formation of DNA superhelices near the transcription bubble, which are resolved upon induction of transient double-stranded breaks (DSBs) by topoisomerases. Unrepaired DSBs are pathogenic as they lead to cell cycle arrest, senescence, inflammation, and organ dysfunction. We posit that DSBs would be more prevalent at the genomic sites that are associated with gene expression. The objectives were to identify and characterize genome-wide DSBs at the nucleotide resolution and determine the association of DSBs with transcription in cardiac myocytes. METHODS AND RESULTS We identified the genome-wide DSBs in ∼1 million cardiac myocytes per heart in three wild-type and three myocyte-specific LMNA-deficient (Myh6-Cre:LmnaF/F) mice by END-Sequencing. The prevalence of DSBs was 0.8% and 2.2% in the wild-type and Myh6-Cre:LmnaF/F myocytes, respectively. The END-Seq signals were enriched for 8 and 6764 DSBs in the wild-type and Myh6-Cre:LmnaF/F myocytes, respectively (q < 0.05). The DSBs were preferentially localized to the gene regions, transcription initiation sites, cardiac transcription factor motifs, and the G quadruplex forming structures. Because LMNA regulates transcription through the lamin-associated domains (LADs), we defined the LADs in cardiac myocytes by a Cleavage Under Targets & Release Using Nuclease (CUT&RUN) assay (N = 5). On average there were 818 LADs per myocyte. Constitutive LADs (cLADs), defined as LADs that were shared by at least three genomes (N = 2572), comprised about a third of the mouse cardiac myocyte genomes. Transcript levels of the protein-coding genes located at the cLADs (N = 3975) were ∼16-fold lower than those at the non-LAD regions (N = ∼17 778). The prevalence of DSBs was higher in the non-LAD as compared to the cLAD regions. Likewise, DSBs were more common in the loss-of-LAD regions, defined as the genomic regions in the Myh6-Cre:LmnaF/F that were juxtaposed to the LAD regions in the wild-type myocytes. CONCLUSION To our knowledge, this is the first identification of the DSBs, at the nucleotide resolution in the cardiovascular system. The prevalence of DSBs was higher in the genomic regions associated with transcription. Because transcription is pervasive, DSBs are expected to be common and pathogenic in various states and aging.
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Affiliation(s)
- Benjamin Cathcart
- Center for Cardiovascular Genetics, Institute of Molecular Medicine, The University of Texas Health Science Center, 6770 Bertner Street, Suite C900A, Houston, TX 77030, USA
| | - Sirisha M Cheedipudi
- Center for Cardiovascular Genetics, Institute of Molecular Medicine, The University of Texas Health Science Center, 6770 Bertner Street, Suite C900A, Houston, TX 77030, USA
| | - Leila Rouhi
- Center for Cardiovascular Genetics, Institute of Molecular Medicine, The University of Texas Health Science Center, 6770 Bertner Street, Suite C900A, Houston, TX 77030, USA
| | - Zhongming Zhao
- Center for Cardiovascular Genetics, Institute of Molecular Medicine, The University of Texas Health Science Center, 6770 Bertner Street, Suite C900A, Houston, TX 77030, USA
- Center for Precision Health, School of Biomedical Informatics and School of Public Health, UTHealth, Houston, TX 77030, USA
| | - Priyatansh Gurha
- Center for Cardiovascular Genetics, Institute of Molecular Medicine, The University of Texas Health Science Center, 6770 Bertner Street, Suite C900A, Houston, TX 77030, USA
| | - Ali J Marian
- Center for Cardiovascular Genetics, Institute of Molecular Medicine, The University of Texas Health Science Center, 6770 Bertner Street, Suite C900A, Houston, TX 77030, USA
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Shi D, Feng W, Zi Z. Machine learning unveils RNA polymerase II binding as a predictor for SMAD2-dependent transcription dynamics in response to Actvin signalling. IET Syst Biol 2024; 18:14-22. [PMID: 38193845 PMCID: PMC10860719 DOI: 10.1049/syb2.12085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 11/07/2023] [Accepted: 11/11/2023] [Indexed: 01/10/2024] Open
Abstract
The transforming growth factor-β (TGF-β) superfamily, including Nodal and Activin, plays a critical role in various cellular processes. Understanding the intricate regulation and gene expression dynamics of TGF-β signalling is of interest due to its diverse biological roles. A machine learning approach is used to predict gene expression patterns induced by Activin using features, such as histone modifications, RNA polymerase II binding, SMAD2-binding, and mRNA half-life. RNA sequencing and ChIP sequencing datasets were analysed and differentially expressed SMAD2-binding genes were identified. These genes were classified into activated and repressed categories based on their expression patterns. The predictive power of different features and combinations was evaluated using logistic regression models and their performances were assessed. Results showed that RNA polymerase II binding was the most informative feature for predicting the expression patterns of SMAD2-binding genes. The authors provide insights into the interplay between transcriptional regulation and Activin signalling and offers a computational framework for predicting gene expression patterns in response to cell signalling.
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Affiliation(s)
- Dan Shi
- Max Planck Institute for Molecular GeneticsOtto Warburg LaboratoryBerlinGermany
| | - Weihua Feng
- Zhengzhou Tobacco Research Institute of China National Tobacco CorporationZhengzhouChina
| | - Zhike Zi
- Max Planck Institute for Molecular GeneticsOtto Warburg LaboratoryBerlinGermany
- CAS Key Laboratory of Quantitative Engineering BiologyShenzhen Institute of Synthetic BiologyShenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhenChina
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Zhang M, Li Y, Zhang F, Geng H, Cai Y, Lu Z, Li B, Ning C, Wang W, Li H, Tian J, Zhu Y, Miao X. Risk SNP in a transcript of RP11-638I2.4 increases lncRNA-YY1 interaction and pancreatic cancer susceptibility. Arch Toxicol 2023; 97:2799-2812. [PMID: 37587385 DOI: 10.1007/s00204-023-03564-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 07/24/2023] [Indexed: 08/18/2023]
Abstract
Tens of thousands of long non-coding RNAs (lncRNAs) have been identified through RNA-seq analysis, but the biological and pathological significance remains unclear. By integrating the genome-wide lncRNA data with a cross-ancestry meta-analysis of PDAC GWASs, we depicted a comprehensive atlas of pancreatic ductal adenocarcinoma (PDAC)-associated lncRNAs, containing 1,204 lncRNA (445 novel lncRNAs and 759 GENCODE annotated lncRNAs) and 4,368 variants. Furthermore, we found that PDAC-associated lncRNAs could function by altering chromatin activity, transcription factors, and RNA-binding proteins binding affinity. Importantly, genetic variants linked to PDAC are preferentially found at PDAC-associated lncRNA regions, supporting the biological and clinical relevance of PDAC-associated lncRNAs. Finally, we prioritized a novel transcript (MICT00000110172.1) of RP11-638I2.4 as a potential tumor promoter. MICT00000110172.1 is able to reinforce the interaction with YY1, which could reverse the effect of YY1 on pancreatic cancer cell cycle arrest to promote the pancreatic cancer growth. G > A change at rs2757535 in the second exon of MICT00000110172.1 induces a spatial structural change and creates a target region for YY1 binding, which enforces the effect of MICT00000110172.1 in an allele-specific manner, and thus confers susceptibility to tumorigenesis. In summary, our results extend the repertoire of PDAC-associated lncRNAs that could act as a starting point for future functional explorations, and the identification of lncRNA-based target therapy.
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Affiliation(s)
- Ming Zhang
- Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health (Ministry of Education), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yanmin Li
- Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health (Ministry of Education), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Fuwei Zhang
- Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health (Ministry of Education), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Hui Geng
- Department of Epidemiology and Biostatistics, School of Public Health, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
| | - Yimin Cai
- Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health (Ministry of Education), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Zequn Lu
- Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health (Ministry of Education), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Bin Li
- Department of Epidemiology and Biostatistics, School of Public Health, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
| | - Caibo Ning
- Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health (Ministry of Education), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Wenzhuo Wang
- Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health (Ministry of Education), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Haijie Li
- Department of Gastrointestinal Cancer Research Institute, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Jianbo Tian
- Department of Epidemiology and Biostatistics, School of Public Health, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China.
- Department of Radiation Oncology, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, China.
- Department of Gastrointestinal OncologyTaiKang Center for Life and Medical Sciences, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China.
| | - Ying Zhu
- Department of Epidemiology and Biostatistics, School of Public Health, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China.
- Department of Gastrointestinal OncologyTaiKang Center for Life and Medical Sciences, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China.
| | - Xiaoping Miao
- Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health (Ministry of Education), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
- Department of Epidemiology and Biostatistics, School of Public Health, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China.
- Department of Radiation Oncology, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, China.
- Department of Gastrointestinal OncologyTaiKang Center for Life and Medical Sciences, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China.
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8
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Hewitt SC, Gruzdev A, Willson CJ, Wu SP, Lydon JP, Galjart N, DeMayo FJ. Chromatin architectural factor CTCF is essential for progesterone-dependent uterine maturation. FASEB J 2023; 37:e23103. [PMID: 37489832 PMCID: PMC10372848 DOI: 10.1096/fj.202300862r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/23/2023] [Accepted: 07/07/2023] [Indexed: 07/26/2023]
Abstract
Receptors for estrogen and progesterone frequently interact, via Cohesin/CTCF loop extrusion, at enhancers distal from regulated genes. Loss-of-function CTCF mutation in >20% of human endometrial tumors indicates its importance in uterine homeostasis. To better understand how CTCF-mediated enhancer-gene interactions impact endometrial development and function, the Ctcf gene was selectively deleted in female reproductive tissues of mice. Prepubertal Ctcfd/d uterine tissue exhibited a marked reduction in the number of uterine glands compared to those without Ctcf deletion (Ctcff/f mice). Post-pubertal Ctcfd/d uteri were hypoplastic with significant reduction in both the amount of the endometrial stroma and number of glands. Transcriptional profiling revealed increased expression of stem cell molecules Lif, EOMES, and Lgr5, and enhanced inflammation pathways following Ctcf deletion. Analysis of the response of the uterus to steroid hormone stimulation showed that CTCF deletion affects a subset of progesterone-responsive genes. This finding indicates (1) Progesterone-mediated signaling remains functional following Ctcf deletion and (2) certain progesterone-regulated genes are sensitive to Ctcf deletion, suggesting they depend on gene-enhancer interactions that require CTCF. The progesterone-responsive genes altered by CTCF ablation included Ihh, Fst, and Errfi1. CTCF-dependent progesterone-responsive uterine genes enhance critical processes including anti-tumorigenesis, which is relevant to the known effectiveness of progesterone in inhibiting progression of early-stage endometrial tumors. Overall, our findings reveal that uterine Ctcf plays a key role in progesterone-dependent expression of uterine genes underlying optimal post-pubertal uterine development.
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Affiliation(s)
| | | | | | - San-Pin Wu
- Pregnancy & Female Reproduction, DIR RDBL, NIEHS RTP, NC
| | | | - Niels Galjart
- Dept. of Cell Biology, Erasmus MC, Rotterdam, Netherlands
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9
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Rondeaux J, Groussard D, Renet S, Tardif V, Dumesnil A, Chu A, Di Maria L, Lemarcis T, Valet M, Henry JP, Badji Z, Vézier C, Béziau-Gasnier D, Neele AE, de Winther MPJ, Guerrot D, Brand M, Richard V, Durand E, Brakenhielm E, Fraineau S. Ezh2 emerges as an epigenetic checkpoint regulator during monocyte differentiation limiting cardiac dysfunction post-MI. Nat Commun 2023; 14:4461. [PMID: 37491334 PMCID: PMC10368741 DOI: 10.1038/s41467-023-40186-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 07/18/2023] [Indexed: 07/27/2023] Open
Abstract
Epigenetic regulation of histone H3K27 methylation has recently emerged as a key step during alternative immunoregulatory M2-like macrophage polarization; known to impact cardiac repair after Myocardial Infarction (MI). We hypothesized that EZH2, responsible for H3K27 methylation, could act as an epigenetic checkpoint regulator during this process. We demonstrate for the first time an ectopic EZH2, and putative, cytoplasmic inactive localization of the epigenetic enzyme, during monocyte differentiation into M2 macrophages in vitro as well as in immunomodulatory cardiac macrophages in vivo in the post-MI acute inflammatory phase. Moreover, we show that pharmacological EZH2 inhibition, with GSK-343, resolves H3K27 methylation of bivalent gene promoters, thus enhancing their expression to promote human monocyte repair functions. In line with this protective effect, GSK-343 treatment accelerated cardiac inflammatory resolution preventing infarct expansion and subsequent cardiac dysfunction in female mice post-MI in vivo. In conclusion, our study reveals that pharmacological epigenetic modulation of cardiac-infiltrating immune cells may hold promise to limit adverse cardiac remodeling after MI.
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Affiliation(s)
- Julie Rondeaux
- Univ Rouen Normandie, Inserm EnVI UMR 1096, F-76000, Rouen, France
| | | | - Sylvanie Renet
- Univ Rouen Normandie, Inserm EnVI UMR 1096, F-76000, Rouen, France
| | - Virginie Tardif
- Univ Rouen Normandie, Inserm EnVI UMR 1096, F-76000, Rouen, France
| | - Anaïs Dumesnil
- Univ Rouen Normandie, Inserm EnVI UMR 1096, F-76000, Rouen, France
| | - Alphonse Chu
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, General Hospital, Mailbox 511, 501 Smyth Road, Ottawa, ON K1H8L6, Canada
| | - Léa Di Maria
- Univ Rouen Normandie, Inserm EnVI UMR 1096, F-76000, Rouen, France
| | - Théo Lemarcis
- Univ Rouen Normandie, Inserm EnVI UMR 1096, F-76000, Rouen, France
| | - Manon Valet
- Univ Rouen Normandie, Inserm EnVI UMR 1096, F-76000, Rouen, France
| | - Jean-Paul Henry
- Univ Rouen Normandie, Inserm EnVI UMR 1096, F-76000, Rouen, France
| | - Zina Badji
- CHU Rouen, Department of Cardiology, F-76000, Rouen, France
| | - Claire Vézier
- CHU Rouen, Department of Cardiology, F-76000, Rouen, France
| | | | - Annette E Neele
- Department of Medical Biochemistry, Amsterdam Cardiovascular Sciences, Amsterdam Institute for Infection and Immunity, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Menno P J de Winther
- Department of Medical Biochemistry, Amsterdam Cardiovascular Sciences, Amsterdam Institute for Infection and Immunity, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Dominique Guerrot
- Univ Rouen Normandie, Inserm EnVI UMR 1096, CHU Rouen, Department of Nephrology, F-76000, Rouen, France
| | - Marjorie Brand
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, General Hospital, Mailbox 511, 501 Smyth Road, Ottawa, ON K1H8L6, Canada
| | - Vincent Richard
- Univ Rouen Normandie, Inserm EnVI UMR 1096, CHU Rouen, Department of Pharmacology, F-76000, Rouen, France
| | - Eric Durand
- Univ Rouen Normandie, Inserm EnVI UMR 1096, CHU Rouen, Department of Cardiology, F-76000, Rouen, France
| | - Ebba Brakenhielm
- Univ Rouen Normandie, Inserm EnVI UMR 1096, F-76000, Rouen, France
| | - Sylvain Fraineau
- Univ Rouen Normandie, Inserm EnVI UMR 1096, F-76000, Rouen, France.
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10
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Kaiser AM, Gatto A, Hanson KJ, Zhao RL, Raj N, Ozawa MG, Seoane JA, Bieging-Rolett KT, Wang M, Li I, Trope WL, Liou DZ, Shrager JB, Plevritis SK, Newman AM, Van Rechem C, Attardi LD. p53 governs an AT1 differentiation programme in lung cancer suppression. Nature 2023; 619:851-859. [PMID: 37468633 PMCID: PMC11288504 DOI: 10.1038/s41586-023-06253-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 05/24/2023] [Indexed: 07/21/2023]
Abstract
Lung cancer is the leading cause of cancer deaths worldwide1. Mutations in the tumour suppressor gene TP53 occur in 50% of lung adenocarcinomas (LUADs) and are linked to poor prognosis1-4, but how p53 suppresses LUAD development remains enigmatic. We show here that p53 suppresses LUAD by governing cell state, specifically by promoting alveolar type 1 (AT1) differentiation. Using mice that express oncogenic Kras and null, wild-type or hypermorphic Trp53 alleles in alveolar type 2 (AT2) cells, we observed graded effects of p53 on LUAD initiation and progression. RNA sequencing and ATAC sequencing of LUAD cells uncovered a p53-induced AT1 differentiation programme during tumour suppression in vivo through direct DNA binding, chromatin remodelling and induction of genes characteristic of AT1 cells. Single-cell transcriptomics analyses revealed that during LUAD evolution, p53 promotes AT1 differentiation through action in a transitional cell state analogous to a transient intermediary seen during AT2-to-AT1 cell differentiation in alveolar injury repair. Notably, p53 inactivation results in the inappropriate persistence of these transitional cancer cells accompanied by upregulated growth signalling and divergence from lung lineage identity, characteristics associated with LUAD progression. Analysis of Trp53 wild-type and Trp53-null mice showed that p53 also directs alveolar regeneration after injury by regulating AT2 cell self-renewal and promoting transitional cell differentiation into AT1 cells. Collectively, these findings illuminate mechanisms of p53-mediated LUAD suppression, in which p53 governs alveolar differentiation, and suggest that tumour suppression reflects a fundamental role of p53 in orchestrating tissue repair after injury.
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Affiliation(s)
- Alyssa M Kaiser
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
| | - Alberto Gatto
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Kathryn J Hanson
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Richard L Zhao
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
| | - Nitin Raj
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael G Ozawa
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - José A Seoane
- Cancer Computational Biology Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Kathryn T Bieging-Rolett
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
| | - Mengxiong Wang
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
| | - Irene Li
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Winston L Trope
- Division of Thoracic Surgery, Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Douglas Z Liou
- Division of Thoracic Surgery, Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Joseph B Shrager
- Division of Thoracic Surgery, Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Sylvia K Plevritis
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Aaron M Newman
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Capucine Van Rechem
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Laura D Attardi
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
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11
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Artz O, Ackermann A, Taylor L, Koo PK, Pedmale UV. Light and temperature regulate m 6A-RNA modification to regulate growth in plants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.17.524395. [PMID: 36711495 PMCID: PMC9882139 DOI: 10.1101/2023.01.17.524395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
N6-methyladenosine is a highly dynamic, abundant mRNA modification which is an excellent potential mechanism for fine tuning gene expression. Plants adapt to their surrounding light and temperature environment using complex gene regulatory networks. The role of m6A in controlling gene expression in response to variable environmental conditions has so far been unexplored. Here, we map the transcriptome-wide m6A landscape under various light and temperature environments. Identified m6A-modifications show a highly specific spatial distribution along transcripts with enrichment occurring in 5'UTR regions and around transcriptional end sites. We show that the position of m6A modifications on transcripts might influence cellular transcript localization and the presence of m6A-modifications is associated with alternative polyadenylation, a process which results in multiple RNA isoforms with varying 3'UTR lengths. RNA with m6A-modifications exhibit a higher preference for shorter 3'UTRs. These shorter 3'UTR regions might directly influence transcript abundance and localization by including or excluding cis-regulatory elements. We propose that environmental stimuli might change the m6A landscape of plants as one possible way of fine tuning gene regulation through alternative polyadenylation and transcript localization.
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Affiliation(s)
- Oliver Artz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 11724. USA
| | - Amanda Ackermann
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 11724. USA
| | - Laura Taylor
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 11724. USA
| | - Peter K. Koo
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 11724. USA
| | - Ullas V. Pedmale
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 11724. USA
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12
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A Systems Biology Approach on the Regulatory Footprint of Human Endogenous Retroviruses (HERVs). Diseases 2022; 10:diseases10040098. [PMID: 36412592 PMCID: PMC9680359 DOI: 10.3390/diseases10040098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/22/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022] Open
Abstract
Human endogenous retroviruses (HERVs) are a family of endogenous retroviruses that comprise the ~8.93% of the human genome sequence, with a high proportion being human specific. The recent expansion of repeated HERV sequences has offered a framework for genetic and epigenetic innovation. In the current report, a systematic approach is implemented to catalogue regulatory elements within HERVs, as a roadmap to potential functions of HERV sequences in gene networks. ENCODE Project has offered a wealth of epigenetic data based on omics technologies. I analyzed the presence of HERV sequences on consensus cis-regulatory elements (cCREs) from ENCODE data. On the one side, HERVs are in 1 out of 9 cCREs (>100.000 cCREs in total), dispersed within the genome and present in cis-regulatory regions of ~81% of human genes, as calculated following gene enrichment analysis. On the other side, promoter-associated HERV cCREs are present adjacent to (in a 200 bp window) the transcription start sites of 256 human genes. Regulatory network production, followed by centrality analysis led to the discovery of 90 core genes containing HERV-associated promoters. Pathway analysis on the core network genes and their immediate neighbors revealed a regulatory footprint that, among others, is associated with inflammation, chemokine signaling and response to viral infection. Collectively, these results support the concept that the expansion of regulatory sequences derived from HERVs is critical for epigenetic innovation that may have wired together genes into novel transcriptional networks with critical roles in cellular physiology and pathology.
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13
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Wang Q, Li M, Wu T, Zhan L, Li L, Chen M, Xie W, Xie Z, Hu E, Xu S, Yu G. Exploring Epigenomic Datasets by ChIPseeker. Curr Protoc 2022; 2:e585. [PMID: 36286622 DOI: 10.1002/cpz1.585] [Citation(s) in RCA: 75] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
In many aspects of life, epigenetics, or the altering of phenotype without changes in sequences, play an essential role in biological function. A vast number of epigenomic datasets are emerging as a result of the advent of next-generation sequencing. Annotation, comparison, visualization, and interpretation of epigenomic datasets remain key aspects of computational biology. ChIPseeker is a Bioconductor package for performing these analyses among variable epigenomic datasets. The fundamental functions of ChIPseeker, including data preparation, annotation, comparison, and visualization, are explained in this article. ChIPseeker is a freely available open-source package that may be found at https://www.bioconductor.org/packages/ChIPseeker. © 2022 Wiley Periodicals LLC. Basic Protocol 1: ChIPseeker and epigenomic dataset preparation Basic Protocol 2: Annotation of epigenomic datasets Basic Protocol 3: Comparison of epigenomic datasets Basic Protocol 4: Visualization of annotated results Basic Protocol 5: Functional analysis of epigenomic datasets Basic Protocol 6: Genome-wide and locus-specific distribution of epigenomic datasets Basic Protocol 7: Heatmaps and metaplots of epigenomic datasets.
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Affiliation(s)
- Qianwen Wang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Ming Li
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Tianzhi Wu
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Li Zhan
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Lin Li
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Meijun Chen
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Wenqin Xie
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Zijing Xie
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Erqiang Hu
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Shuangbin Xu
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Guangchuang Yu
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
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14
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p300/CBP sustains Polycomb silencing by non-enzymatic functions. Mol Cell 2022; 82:3580-3597.e9. [DOI: 10.1016/j.molcel.2022.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/16/2022] [Accepted: 09/06/2022] [Indexed: 12/29/2022]
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15
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Hewitt SC, Wu SP, Wang T, Ray M, Brolinson M, Young SL, Spencer TE, DeCherney A, DeMayo FJ. The Estrogen Receptor α Cistrome in Human Endometrium and Epithelial Organoids. Endocrinology 2022; 163:bqac116. [PMID: 35895287 PMCID: PMC9368022 DOI: 10.1210/endocr/bqac116] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Indexed: 11/19/2022]
Abstract
Endometrial health is affected by molecular processes that underlie estrogen responses. We assessed estrogen regulation of endometrial function by integrating the estrogen receptor α (ESR1) cistromes and transcriptomes of endometrial biopsies taken from the proliferative and mid-secretory phases of the menstrual cycle together with hormonally stimulated endometrial epithelial organoids. The cycle stage-specific ESR1 binding sites were determined by chromatin immunoprecipitation and next-generation sequencing and then integrated with changes in gene expression from RNA sequencing data to infer candidate ESR1 targets in normal endometrium. Genes with ESR1 binding in whole endometrium were enriched for chromatin modification and regulation of cell proliferation. The distribution of ESR1 binding sites in organoids was more distal from gene promoters when compared to primary endometrium and was more similar to the proliferative than the mid-secretory phase ESR1 cistrome. Inferred organoid estrogen/ESR1 candidate target genes affected formation of cellular protrusions and chromatin modification. Comparison of signaling effected by candidate ESR1 target genes in endometrium vs organoids reveals enrichment of both overlapping and distinct responses. Our analysis of the ESR1 cistromes and transcriptomes from endometrium and organoids provides important resources for understanding how estrogen affects endometrial health and function.
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Affiliation(s)
- Sylvia C Hewitt
- Pregnancy & Female Reproduction, RDBL, NIEHS, Research Triangle Park, North Carolina 27709, USA
| | - San-pin Wu
- Pregnancy & Female Reproduction, RDBL, NIEHS, Research Triangle Park, North Carolina 27709, USA
| | - Tianyuan Wang
- Integrative Bioinformatics Support Group, NIEHS, Research Triangle Park, North Carolina 27709, USA
| | - Madhumita Ray
- Pregnancy & Female Reproduction, RDBL, NIEHS, Research Triangle Park, North Carolina 27709, USA
| | - Marja Brolinson
- Program in Reproductive and Adult Endocrinology, NICHD, Bethesda, Maryland 20847, USA
| | - Steven L Young
- Department of Obstetrics and Gynecology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Thomas E Spencer
- Department of Obstetrics, Gynecology and Women’s Health, University of Missouri, Columbia, Missouri 65211, USA
| | - Alan DeCherney
- Program in Reproductive and Adult Endocrinology, NICHD, Bethesda, Maryland 20847, USA
| | - Francesco J DeMayo
- Pregnancy & Female Reproduction, RDBL, NIEHS, Research Triangle Park, North Carolina 27709, USA
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16
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Moorhouse AJ, Loats AE, Medler KF, Roberts SG. The BASP1 transcriptional corepressor modifies chromatin through lipid-dependent and lipid-independent mechanisms. iScience 2022; 25:104796. [PMID: 35982799 PMCID: PMC9379585 DOI: 10.1016/j.isci.2022.104796] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/22/2022] [Accepted: 07/14/2022] [Indexed: 12/01/2022] Open
Abstract
The transcriptional corepressor BASP1 requires N-terminal myristoylation for its activity and functions through interactions with nuclear lipids. Here we determine the role of BASP1 lipidation in histone modification and the modulation of chromatin accessibility. We find that the removal of the active histone modifications H3K9ac and H3K4me3 by BASP1 requires the N-terminal myristoylation of BASP1. In contrast, the placement of the repressive histone modification, H3K27me3, by BASP1 does not require BASP1 lipidation. RNA-seq and ATAC-seq analysis finds that BASP1 regulates the activity of multiple transcription factors and induces extensive changes in chromatin accessibility. We find that ∼50% of BASP1 target genes show lipidation-dependent chromatin compaction and transcriptional repression. Our results suggest that BASP1 elicits both lipid-dependent and lipid-independent functions in histone modification and transcriptional repression. In accordance with this, we find that the tumor suppressor activity of BASP1 is also partially dependent on its myristoylation.
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Affiliation(s)
| | - Amy E. Loats
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, UK
| | - Kathryn F. Medler
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA
| | - Stefan G.E. Roberts
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, UK
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA
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17
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Hewitt SC, Wu SP, Wang T, Young SL, Spencer TE, DeMayo FJ. Progesterone Signaling in Endometrial Epithelial Organoids. Cells 2022; 11:1760. [PMID: 35681455 PMCID: PMC9179553 DOI: 10.3390/cells11111760] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 02/04/2023] Open
Abstract
For pregnancy to be established, uterine cells respond to the ovarian hormones, estrogen, and progesterone, via their nuclear receptors, the estrogen receptor (ESR1) and progesterone receptor (PGR). ESR1 and PGR regulate genes by binding chromatin at genes and at distal enhancer regions, which interact via dynamic 3-dimensional chromatin structures. Endometrial epithelial cells are the initial site of embryo attachment and invasion, and thus understanding the processes that yield their receptive state is important. Here, we cultured and treated organoids derived from human epithelial cells, isolated from endometrial biopsies, with estrogen and progesterone and evaluated their transcriptional profiles, their PGR cistrome, and their chromatin conformation. Progesterone attenuated estrogen-dependent gene responses but otherwise minimally impacted the organoid transcriptome. PGR ChIPseq peaks were co-localized with previously described organoid ESR1 peaks, and most PGR and ESR1 peaks were in B (inactive) compartment regions of chromatin. Significantly more ESR1 peaks were assigned to estrogen-regulated genes by considering chromatin loops identified using HiC than were identified using ESR1 peak location relative to closest genes. Overall, the organoids model allowed a definition of the chromatin regulatory components governing hormone responsiveness.
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Affiliation(s)
- Sylvia C. Hewitt
- Pregnancy and Female Reproduction, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences (NIEHS), Research Triangle Park, NC 27709, USA; (S.C.H.); (S.-p.W.)
| | - San-pin Wu
- Pregnancy and Female Reproduction, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences (NIEHS), Research Triangle Park, NC 27709, USA; (S.C.H.); (S.-p.W.)
| | - Tianyuan Wang
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences (NIEHS), Research Triangle Park, NC 27709, USA;
| | - Steven L. Young
- Department of Obstetrics and Gynecology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
| | - Thomas E. Spencer
- Department of Obstetrics, Gynecology and Women’s Health, University of Missouri, Columbia, MI 65211, USA;
| | - Francesco J. DeMayo
- Pregnancy and Female Reproduction, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences (NIEHS), Research Triangle Park, NC 27709, USA; (S.C.H.); (S.-p.W.)
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18
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ASC proneural factors are necessary for chromatin remodeling during neuroectodermal to neuroblast fate transition to ensure the timely initiation of the neural stem cell program. BMC Biol 2022; 20:107. [PMID: 35549704 PMCID: PMC9102361 DOI: 10.1186/s12915-022-01300-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 04/20/2022] [Indexed: 11/11/2022] Open
Abstract
Background In both Drosophila and mammals, the achaete-scute (ASC/ASCL) proneural bHLH transcription factors are expressed in the developing central and peripheral nervous systems, where they function during specification and maintenance of the neural stem cells in opposition to Notch signaling. In addition to their role in nervous system development, ASC transcription factors are oncogenic and exhibit chromatin reprogramming activity; however, the impact of ASC on chromatin dynamics during neural stem cell generation remains elusive. Here, we investigate the chromatin changes accompanying neural commitment using an integrative genetics and genomics methodology. Results We found that ASC factors bind equally strongly to two distinct classes of cis-regulatory elements: open regions remodeled earlier during maternal to zygotic transition by Zelda and less accessible, Zelda-independent regions. Both classes of cis-elements exhibit enhanced chromatin accessibility during neural specification and correlate with transcriptional regulation of genes involved in a variety of biological processes necessary for neuroblast function/homeostasis. We identified an ASC-Notch regulated TF network that includes likely prime regulators of neuroblast function. Using a cohort of ASC target genes, we report that ASC null neuroblasts are defectively specified, remaining initially stalled, unable to divide, and lacking expression of many proneural targets. When mutant neuroblasts eventually start proliferating, they produce compromised progeny. Reporter lines driven by proneural-bound enhancers display ASC dependency, suggesting that the partial neuroblast identity seen in the absence of ASC genes is likely driven by other, proneural-independent, cis-elements. Neuroblast impairment and the late differentiation defects of ASC mutants are corrected by ectodermal induction of individual ASC genes but not by individual members of the TF network downstream of ASC. However, in wild-type embryos, the induction of individual members of this network induces CNS hyperplasia, suggesting that they synergize with the activating function of ASC to consolidate the chromatin dynamics that promote neural specification. Conclusions We demonstrate that ASC proneural transcription factors are indispensable for the timely initiation of the neural stem cell program at the chromatin level by regulating a large number of enhancers in the vicinity of neural genes. This early chromatin remodeling is crucial for both neuroblast homeostasis as well as future progeny fidelity. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01300-8.
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19
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Munden A, Benton ML, Capra JA, Nordman JT. R-loop mapping and characterization during Drosophila embryogenesis reveals developmental plasticity in R-loop signatures. J Mol Biol 2022; 434:167645. [PMID: 35609632 PMCID: PMC9254486 DOI: 10.1016/j.jmb.2022.167645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/16/2022] [Accepted: 05/18/2022] [Indexed: 11/26/2022]
Abstract
R-loops are involved in transcriptional regulation, DNA and histone post-translational modifications, genome replication and genome stability. To what extent R-loop abundance and genome-wide localization is actively regulated during metazoan embryogenesis is unknown. Drosophila embryogenesis provides a powerful system to address these questions due to its well-characterized developmental program, the sudden onset of zygotic transcription and available genome-wide data sets. Here, we measure the overall abundance and genome localization of R-loops in early and late-stage embryos relative to Drosophila cultured cells. We demonstrate that absolute R-loop levels change during embryogenesis and that RNaseH1 catalytic activity is critical for embryonic development. R-loop mapping by strand-specific DRIP-seq reveals that R-loop localization is plastic across development, both in the genes which form R-loops and where they localize relative to gene bodies. Importantly, these changes are not driven by changes in the transcriptional program. Negative GC skew and absolute changes in AT skew are associated with R-loop formation in Drosophila. Furthermore, we demonstrate that while some chromatin binding proteins and histone modifications such as H3K27me3 are associated with R-loops throughout development, other chromatin factors associated with R-loops in a developmental specific manner. Our findings highlight the importance and developmental plasticity of R-loops during Drosophila embryogenesis.
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Affiliation(s)
- Alexander Munden
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37212, USA
| | | | - John A Capra
- Bakar Computational Health Sciences Institute and Department of Epidemiology and Biostatistics, University of California, San Francisco, CA 94103, USA
| | - Jared T Nordman
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37212, USA.
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20
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Vincent SA, Kim JM, Pérez-Salamó I, To TK, Torii C, Ishida J, Tanaka M, Endo TA, Bhat P, Devlin PF, Seki M, Devoto A. Jasmonates and Histone deacetylase 6 activate Arabidopsis genome-wide histone acetylation and methylation during the early acute stress response. BMC Biol 2022; 20:83. [PMID: 35399062 PMCID: PMC8996529 DOI: 10.1186/s12915-022-01273-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 03/07/2022] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Jasmonates (JAs) mediate trade-off between responses to both biotic and abiotic stress and growth in plants. The Arabidopsis thaliana HISTONE DEACETYLASE 6 is part of the CORONATINE INSENSITIVE1 receptor complex, co-repressing the HDA6/COI1-dependent acetic acid-JA pathway that confers plant drought tolerance. The decrease in HDA6 binding to target DNA mirrors histone H4 acetylation (H4Ac) changes during JA-mediated drought response, and mutations in HDA6 also cause depletion in the constitutive repressive marker H3 lysine 27 trimethylation (H3K27me3). However, the genome-wide effect of HDA6 on H4Ac and much of the impact of JAs on histone modifications and chromatin remodelling remain elusive. RESULTS We performed high-throughput ChIP-Seq on the HDA6 mutant, axe1-5, and wild-type plants with or without methyl jasmonate (MeJA) treatment to assess changes in active H4ac and repressive H3K27me3 histone markers. Transcriptional regulation was investigated in parallel by microarray analysis in the same conditions. MeJA- and HDA6-dependent histone modifications on genes for specialized metabolism; linolenic acid and phenylpropanoid pathways; and abiotic and biotic stress responses were identified. H4ac and H3K27me3 enrichment also differentially affects JAs and HDA6-mediated genome integrity and gene regulatory networks, substantiating the role of HDA6 interacting with specific families of transposable elements in planta and highlighting further specificity of action as well as novel targets of HDA6 in the context of JA signalling for abiotic and biotic stress responses. CONCLUSIONS The findings demonstrate functional overlap for MeJA and HDA6 in tuning plant developmental plasticity and response to stress at the histone modification level. MeJA and HDA6, nonetheless, maintain distinct activities on histone modifications to modulate genetic variability and to allow adaptation to environmental challenges.
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Affiliation(s)
- Stacey A Vincent
- Plant Molecular Science and Centre of Systems and Synthetic Biology, Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK
| | - Jong-Myong Kim
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
- Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Present address: Ac-Planta Inc., 2-16-9 Yushima, Bunkyo-ku, Tokyo, 113-0034, Japan
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Imma Pérez-Salamó
- Plant Molecular Science and Centre of Systems and Synthetic Biology, Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK
| | - Taiko Kim To
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
- Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Present address: Department of Biological Sciences, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Chieko Torii
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
- Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Junko Ishida
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
- Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Maho Tanaka
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
- Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Takaho A Endo
- Bioinformatics and Systems Engineering Division, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
- Present address: Center for Integrative Medical Sciences, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Prajwal Bhat
- Plant Molecular Science and Centre of Systems and Synthetic Biology, Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK
| | - Paul F Devlin
- Plant Molecular Science and Centre of Systems and Synthetic Biology, Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK
| | - Motoaki Seki
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan.
- Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
| | - Alessandra Devoto
- Plant Molecular Science and Centre of Systems and Synthetic Biology, Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK.
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21
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Barro-Trastoy D, Gomez MD, Blanco-Touriñán N, Tornero P, Perez-Amador MA. Gibberellins regulate ovule number through a DELLA-CUC2 complex in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:43-57. [PMID: 35192733 DOI: 10.1111/tpj.15607] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/16/2021] [Accepted: 11/22/2021] [Indexed: 06/14/2023]
Abstract
Ovule development is a key process for plant reproduction, helping to ensure correct seed production. Several molecular factors and plant hormones such as gibberellins are involved in ovule initiation and development. Gibberellins control ovule development by the destabilization of DELLA proteins, whereas DELLA activity has been shown to act as a positive factor for ovule primordia emergence. But the molecular mechanism by which DELLA acts in ovule primordia initiation remained unknown. In this study we report that DELLA proteins participate in ovule initiation by the formation of a protein complex with the CUC2 transcription factor. The DELLA protein GAI requires CUC2 to promote ovule primordia formation, through the direct GAI-CUC2 interaction in placental cells that would determine the boundary regions between ovules during pistil development. Analysis of GAI-CUC2 interaction and co-localization in the placenta supports this hypothesis. Moreover, molecular analysis identified a subset of the loci for which the GAI protein may act as a transcriptional co-regulator in a CUC2-dependent manner. The DELLA-CUC2 complex is a component of the gene regulatory network controlling ovule primordia initiation in Arabidopsis.
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Affiliation(s)
- Daniela Barro-Trastoy
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València (UPV)-Consejo Superior de Investigaciones Científicas (CSIC), CPI 8E, Ingeniero Fausto Elio s/n, Valencia, 46022, Spain
| | - Maria D Gomez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València (UPV)-Consejo Superior de Investigaciones Científicas (CSIC), CPI 8E, Ingeniero Fausto Elio s/n, Valencia, 46022, Spain
| | - Noel Blanco-Touriñán
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València (UPV)-Consejo Superior de Investigaciones Científicas (CSIC), CPI 8E, Ingeniero Fausto Elio s/n, Valencia, 46022, Spain
| | - Pablo Tornero
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València (UPV)-Consejo Superior de Investigaciones Científicas (CSIC), CPI 8E, Ingeniero Fausto Elio s/n, Valencia, 46022, Spain
| | - Miguel A Perez-Amador
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València (UPV)-Consejo Superior de Investigaciones Científicas (CSIC), CPI 8E, Ingeniero Fausto Elio s/n, Valencia, 46022, Spain
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22
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Structural and genome-wide analyses suggest that transposon-derived protein SETMAR alters transcription and splicing. J Biol Chem 2022; 298:101894. [PMID: 35378129 PMCID: PMC9062482 DOI: 10.1016/j.jbc.2022.101894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 03/25/2022] [Accepted: 03/26/2022] [Indexed: 11/22/2022] Open
Abstract
Extensive portions of the human genome have unknown function, including those derived from transposable elements. One such element, the DNA transposon Hsmar1, entered the primate lineage approximately 50 million years ago leaving behind terminal inverted repeat (TIR) sequences and a single intact copy of the Hsmar1 transposase, which retains its ancestral TIR-DNA-binding activity, and is fused with a lysine methyltransferase SET domain to constitute the chimeric SETMAR gene. Here, we provide a structural basis for recognition of TIRs by SETMAR and investigate the function of SETMAR through genome-wide approaches. As elucidated in our 2.37 Å crystal structure, SETMAR forms a dimeric complex with each DNA-binding domain bound specifically to TIR-DNA through the formation of 32 hydrogen bonds. We found that SETMAR recognizes primarily TIR sequences (∼5000 sites) within the human genome as assessed by chromatin immunoprecipitation sequencing analysis. In two SETMAR KO cell lines, we identified 163 shared differentially expressed genes and 233 shared alternative splicing events. Among these genes are several pre–mRNA-splicing factors, transcription factors, and genes associated with neuronal function, and one alternatively spliced primate-specific gene, TMEM14B, which has been identified as a marker for neocortex expansion associated with brain evolution. Taken together, our results suggest a model in which SETMAR impacts differential expression and alternative splicing of genes associated with transcription and neuronal function, potentially through both its TIR-specific DNA-binding and lysine methyltransferase activities, consistent with a role for SETMAR in simian primate development.
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23
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Zhu X, Guo Y, Chu C, Liu D, Duan K, Yin Y, Si C, Kang Y, Yao J, Du X, Li J, Zhao S, Ai Z, Zhu Q, Ji W, Niu Y, Li T. BRN2 as a key gene drives the early primate telencephalon development. SCIENCE ADVANCES 2022; 8:eabl7263. [PMID: 35245119 PMCID: PMC8896791 DOI: 10.1126/sciadv.abl7263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
Evolutionary mutations in primate-specific genes drove primate cortex expansion. However, whether conserved genes with previously unidentified functions also play a key role in primate brain expansion remains unknown. Here, we focus on BRN2 (POU3F2), a gene encoding a neural transcription factor commonly expressed in both primates and mice. Compared to the limited effects on mouse brain development, BRN2 biallelic knockout in cynomolgus monkeys (Macaca fascicularis) is lethal before midgestation. Histology analysis and single-cell transcriptome show that BRN2 deficiency decreases RGC expansion, induces precocious differentiation, and alters the trajectory of neurogenesis in the telencephalon. BRN2, serving as an upstream factor, controls specification and differentiation of ganglionic eminences. In addition, we identified the conserved function of BRN2 in cynomolgus monkeys to human RGCs. BRN2 may function by directly regulating SOX2 and STAT3 and maintaining HOPX. Our findings reveal a previously unknown mechanism that BRN2, a conserved gene, drives early primate telencephalon development by gaining novel mechanistic functions.
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Affiliation(s)
- Xiaoqing Zhu
- State Key Laboratory of Primate Biomedical Research and Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China
| | - Yicheng Guo
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Chu Chu
- State Key Laboratory of Primate Biomedical Research and Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Dahai Liu
- Department of Basic Medicine and Biomedical Engineering, School of Stomatology and Medicine, Foshan University, Foshan, Guangdong 528000, China
| | - Kui Duan
- State Key Laboratory of Primate Biomedical Research and Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China
| | - Yu Yin
- State Key Laboratory of Primate Biomedical Research and Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China
| | - Chenyang Si
- State Key Laboratory of Primate Biomedical Research and Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China
| | - Yu Kang
- State Key Laboratory of Primate Biomedical Research and Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China
| | - Junjun Yao
- State Key Laboratory of Primate Biomedical Research and Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Xuewei Du
- State Key Laboratory of Primate Biomedical Research and Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Junliang Li
- State Key Laboratory of Primate Biomedical Research and Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Shumei Zhao
- State Key Laboratory of Primate Biomedical Research and Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Zongyong Ai
- State Key Laboratory of Primate Biomedical Research and Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Qingyuan Zhu
- State Key Laboratory of Primate Biomedical Research and Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Weizhi Ji
- State Key Laboratory of Primate Biomedical Research and Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China
| | - Yuyu Niu
- State Key Laboratory of Primate Biomedical Research and Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China
| | - Tianqing Li
- State Key Laboratory of Primate Biomedical Research and Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China
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24
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Tang F, Yuan J, Yuan BF, Wang Y. DNA-Protein Cross-Linking Sequencing for Genome-Wide Mapping of Thymidine Glycol. J Am Chem Soc 2022; 144:454-462. [PMID: 34978433 PMCID: PMC8755629 DOI: 10.1021/jacs.1c10490] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Thymidine glycol (Tg) is the most prevalent form of oxidatively induced pyrimidine lesions in DNA. Tg can arise from direct oxidation of thymidine in DNA. In addition, 5-methyl-2'-deoxycytidine (5-mdC) can be oxidized to 5-mdC glycol, and its subsequent deamination also yields Tg. However, Tg's distribution in the human genome remains unknown. Here, we presented a DNA-protein cross-linking sequencing (DPC-Seq) method for genome-wide mapping of Tg in human cells. Our approach capitalizes on the specificity of a bifunctional DNA glycosylase, i.e., NTHL1, for the covalent labeling, as well as DPC pulldown, SDS-PAGE fractionation, and membrane transfer for highly efficient and selective enrichment of Tg-bearing DNA. By employing DPC-Seq, we detected thousands of Tg sites in the human genome, where dual ablation of NTHL1 and NEIL1, the major DNA glycosylases responsible for Tg repair, led to pronounced increases in the number of Tg peaks. In addition, Tg is depleted in genomic regions associated with active transcription but enriched at nucleosome-binding sites, especially at heterochromatin sites marked with H3K9me2. Collectively, we developed a DPC-Seq method for highly efficient enrichment of Tg-containing DNA and for genome-wide mapping of Tg in human cells. Our work offers a robust tool for future functional studies of Tg in DNA, and we envision that the method can also be adapted for mapping other modified nucleosides in genomic DNA in the future.
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Affiliation(s)
- Feng Tang
- Department of Chemistry, University of California, Riverside, Riverside, California 92521-0403, United States
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Jun Yuan
- Department of Chemistry, University of California, Riverside, Riverside, California 92521-0403, United States
| | - Bi-Feng Yuan
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, Riverside, California 92521-0403, United States
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25
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Ren C, Li H, Wang Z, Dai Z, Lecourieux F, Kuang Y, Xin H, Li S, Liang Z. Characterization of Chromatin Accessibility and Gene Expression upon Cold Stress Reveals that the RAV1 Transcription Factor Functions in Cold Response in Vitis Amurensis. PLANT & CELL PHYSIOLOGY 2021; 62:1615-1629. [PMID: 34279666 PMCID: PMC8643690 DOI: 10.1093/pcp/pcab115] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 06/09/2021] [Accepted: 08/09/2021] [Indexed: 05/29/2023]
Abstract
Cold tolerance is regulated by a variety of transcription factors (TFs) and their target genes. Except for the well-characterized C-repeat binding factors (CBFs)-dependent transcriptional cascade, the mechanisms of cold tolerance mediated by other transcriptional regulatory networks are still largely unknown. Here, we used the assay for transposase-accessible chromatin with sequencing (ATAC-seq) and RNA-seq to identify cold responsive TFs in Vitis amurensis, a grape species with high cold hardiness. Nine TFs, including CBF4, RAV1 and ERF104, were identified after cold treatment. Weighted gene co-expression network analysis (WGCNA) and gene ontology (GO) analysis revealed that these TFs may regulate cold response through different pathways. As a prime candidate TF, overexpression of VaRAV1 in grape cells improved its cold tolerance. The transgenic cells exhibited low electrolyte leakage and malondialdehyde content and high peroxidase activity. Moreover, the TF gene TCP8 and a gene involving in homogalacturonan biosynthesis were found to be regulated by VaRAV1, suggesting that the contribution of VaRAV1 to cold tolerance may be achieved by enhancing the stability of cell membrane and regulating the expression of target genes involved in plant cell wall composition. Our work provides novel insights into plant response to cold stress and demonstrates the utility of ATAC-seq and RNA-seq for the rapid identification of TFs in response to cold stress in grapevine. VaRAV1 may play an important role in adaption to cold stress.
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Affiliation(s)
- Chong Ren
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
| | - Huayang Li
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
- University of Chinese Academy of Sciences, 19 Yuquan Rd, Beijing 100049, PR China
| | - Zemin Wang
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
| | - Zhanwu Dai
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
| | - Fatma Lecourieux
- EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, ISVV, 210 chemin de Leysotte, Villenave d’Ornon 33882, France
| | - Yangfu Kuang
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
- University of Chinese Academy of Sciences, 19 Yuquan Rd, Beijing 100049, PR China
| | - Haiping Xin
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, 1 Lumo Rd, Wuhan 430074, PR China
| | - Shaohua Li
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
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26
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Lucas T, Hafer TL, Zhang HG, Molotkova N, Kohwi M. Discrete cis-acting element regulates developmentally timed gene-lamina relocation and neural progenitor competence in vivo. Dev Cell 2021; 56:2649-2663.e6. [PMID: 34529940 PMCID: PMC8629127 DOI: 10.1016/j.devcel.2021.08.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 06/24/2021] [Accepted: 08/20/2021] [Indexed: 01/21/2023]
Abstract
The nuclear lamina is typically associated with transcriptional silencing, and peripheral relocation of genes highly correlates with repression. However, the DNA sequences and proteins regulating gene-lamina interactions are largely unknown. Exploiting the developmentally timed hunchback gene movement to the lamina in Drosophila neuroblasts, we identified a 250 bp intronic element (IE) both necessary and sufficient for relocation. The IE can target a reporter transgene to the lamina and silence it. Endogenously, however, hunchback is already repressed prior to relocation. Instead, IE-mediated relocation confers a heritably silenced gene state refractory to activation in descendent neurons, which terminates neuroblast competence to specify early-born identity. Surprisingly, we found that the Polycomb group chromatin factors bind the IE and are required for lamina relocation, revealing a nuclear architectural role distinct from their well-known function in transcriptional repression. Together, our results uncover in vivo mechanisms underlying neuroblast competence and lamina association in heritable gene silencing. In Drosophila neuroblasts, relocation of the hunchback gene locus to the nuclear lamina confers heritable silencing in daughter neurons. Lucas et al. identify a genomic element necessary and sufficient for hunchback gene movement in vivo. Polycomb proteins target this element for lamina relocation, thereby regulating competence, but not hunchback expression.
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Affiliation(s)
- Tanguy Lucas
- Department of Neuroscience, Mortimer B. Zuckerman Institute Mind Brain Behavior, Columbia University, New York, NY 10027, USA
| | - Terry L Hafer
- Department of Neuroscience, Mortimer B. Zuckerman Institute Mind Brain Behavior, Columbia University, New York, NY 10027, USA
| | - Harrison G Zhang
- Department of Neuroscience, Mortimer B. Zuckerman Institute Mind Brain Behavior, Columbia University, New York, NY 10027, USA
| | - Natalia Molotkova
- Department of Neuroscience, Mortimer B. Zuckerman Institute Mind Brain Behavior, Columbia University, New York, NY 10027, USA
| | - Minoree Kohwi
- Department of Neuroscience, Mortimer B. Zuckerman Institute Mind Brain Behavior, Columbia University, New York, NY 10027, USA; Kavli Institute for Brain Science, Columbia University, New York, NY 10027, USA.
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27
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Lim JJ, Dutta M, Dempsey JL, Lehmler HJ, MacDonald J, Bammler T, Walker C, Kavanagh TJ, Gu H, Mani S, Cui JY. Neonatal Exposure to BPA, BDE-99, and PCB Produces Persistent Changes in Hepatic Transcriptome Associated With Gut Dysbiosis in Adult Mouse Livers. Toxicol Sci 2021; 184:83-103. [PMID: 34453844 PMCID: PMC8557404 DOI: 10.1093/toxsci/kfab104] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Recent evidence suggests that complex diseases can result from early life exposure to environmental toxicants. Polybrominated diphenyl ethers (PBDEs), and polychlorinated biphenyls (PCBs) are persistent organic pollutants (POPs) and remain a continuing risk to human health despite being banned from production. Developmental BPA exposure mediated-adult onset of liver cancer via epigenetic reprogramming mechanisms has been identified. Here, we investigated whether the gut microbiome and liver can be persistently reprogrammed following neonatal exposure to POPs, and the associations between microbial biomarkers and disease-prone changes in the hepatic transcriptome in adulthood, compared with BPA. C57BL/6 male and female mouse pups were orally administered vehicle, BPA, BDE-99 (a breast milk-enriched PBDE congener), or the Fox River PCB mixture (PCBs), once daily for three consecutive days (postnatal days [PND] 2-4). Tissues were collected at PND5 and PND60. Among the three chemicals investigated, early life exposure to BDE-99 produced the most prominent developmental reprogramming of the gut-liver axis, including hepatic inflammatory and cancer-prone signatures. In adulthood, neonatal BDE-99 exposure resulted in a persistent increase in Akkermansia muciniphila throughout the intestine, accompanied by increased hepatic levels of acetate and succinate, the known products of A. muciniphila. In males, this was positively associated with permissive epigenetic marks H3K4me1 and H3K27, which were enriched in loci near liver cancer-related genes that were dysregulated following neonatal exposure to BDE-99. Our findings provide novel insights that early life exposure to POPs can have a life-long impact on disease risk, which may partly be regulated by the gut microbiome.
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Affiliation(s)
- Joe Jongpyo Lim
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, USA
| | - Moumita Dutta
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, USA
| | - Joseph L Dempsey
- Division of Gastroenterology, Department of Medicine, School of Medicine, University of Washington, Seattle, Washington, USA,Center for Microbiome Sciences and Therapeutics, School of Medicine, University of Washington, Seattle, Washington, USA
| | - Hans-Joachim Lehmler
- Department of Occupational and Environmental Health, University of Iowa, Iowa City, Iowa, USA
| | - James MacDonald
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, USA
| | - Theo Bammler
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, USA
| | - Cheryl Walker
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, Texas 77030, USA,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA,Department of Medicine, Baylor College of Medicine, Houston, Texas 77030, USA,Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Terrance J Kavanagh
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, USA
| | - Haiwei Gu
- Arizona Metabolomics Laboratory, College of Health Solutions, Arizona State University, Pheonix, Arizona 85004, USA
| | - Sridhar Mani
- Department of Medicine, Molecular Pharmacology and Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Julia Yue Cui
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, USA,To whom correspondence should be addressed at Department of Environmental and Occupational Health Sciences, University of Washington, 4225 Roosevelt Way NE, Seattle, WA 98105, USA. E-mail:
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28
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Meiler A, Marchiano F, Haering M, Weitkunat M, Schnorrer F, Habermann BH. AnnoMiner is a new web-tool to integrate epigenetics, transcription factor occupancy and transcriptomics data to predict transcriptional regulators. Sci Rep 2021; 11:15463. [PMID: 34326396 PMCID: PMC8322331 DOI: 10.1038/s41598-021-94805-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 07/14/2021] [Indexed: 11/23/2022] Open
Abstract
Gene expression regulation requires precise transcriptional programs, led by transcription factors in combination with epigenetic events. Recent advances in epigenomic and transcriptomic techniques provided insight into different gene regulation mechanisms. However, to date it remains challenging to understand how combinations of transcription factors together with epigenetic events control cell-type specific gene expression. We have developed the AnnoMiner web-server, an innovative and flexible tool to annotate and integrate epigenetic, and transcription factor occupancy data. First, AnnoMiner annotates user-provided peaks with gene features. Second, AnnoMiner can integrate genome binding data from two different transcriptional regulators together with gene features. Third, AnnoMiner offers to explore the transcriptional deregulation of genes nearby, or within a specified genomic region surrounding a user-provided peak. AnnoMiner’s fourth function performs transcription factor or histone modification enrichment analysis for user-provided gene lists by utilizing hundreds of public, high-quality datasets from ENCODE for the model organisms human, mouse, Drosophila and C. elegans. Thus, AnnoMiner can predict transcriptional regulators for a studied process without the strict need for chromatin data from the same process. We compared AnnoMiner to existing tools and experimentally validated several transcriptional regulators predicted by AnnoMiner to indeed contribute to muscle morphogenesis in Drosophila. AnnoMiner is freely available at http://chimborazo.ibdm.univ-mrs.fr/AnnoMiner/.
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Affiliation(s)
- Arno Meiler
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Fabio Marchiano
- Aix-Marseille University, CNRS, IBDM UMR 7288, The Turing Centre for Living systems (CENTURI), Aix-Marseille University, Parc Scientifique de Luminy Case 907, 163, Avenue de Luminy, 13009, Marseille, France
| | - Margaux Haering
- Aix-Marseille University, CNRS, IBDM UMR 7288, The Turing Centre for Living systems (CENTURI), Aix-Marseille University, Parc Scientifique de Luminy Case 907, 163, Avenue de Luminy, 13009, Marseille, France
| | - Manuela Weitkunat
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Frank Schnorrer
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.,Aix-Marseille University, CNRS, IBDM UMR 7288, The Turing Centre for Living systems (CENTURI), Aix-Marseille University, Parc Scientifique de Luminy Case 907, 163, Avenue de Luminy, 13009, Marseille, France
| | - Bianca H Habermann
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany. .,Aix-Marseille University, CNRS, IBDM UMR 7288, The Turing Centre for Living systems (CENTURI), Aix-Marseille University, Parc Scientifique de Luminy Case 907, 163, Avenue de Luminy, 13009, Marseille, France.
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29
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Vercauteren Drubbel A, Pirard S, Kin S, Dassy B, Lefort A, Libert F, Nomura S, Beck B. Reactivation of the Hedgehog pathway in esophageal progenitors turns on an embryonic-like program to initiate columnar metaplasia. Cell Stem Cell 2021; 28:1411-1427.e7. [PMID: 33882290 DOI: 10.1016/j.stem.2021.03.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 12/18/2020] [Accepted: 03/24/2021] [Indexed: 01/17/2023]
Abstract
Columnar metaplasia of the esophagus is the main risk factor for esophageal adenocarcinoma. There is a lack of evidence to demonstrate that esophageal progenitors can be the source of columnar metaplasia. In this study, using transgenic mouse models, lineage tracing, single-cell RNA sequencing, and transcriptomic and epigenetic profiling, we found that the activation of the Hedgehog pathway in esophageal cells modifies their differentiation status in vivo. This process involves an initial step of dedifferentiation into embryonic-like esophageal progenitors. Moreover, a subset of these cells undergoes full squamous-to-columnar conversion and expresses selected intestinal markers. These modifications of cell fate are associated with remodeling of the chromatin and the appearance of Sox9. Using a conditional knockout mouse, we show that Sox9 is required for columnar conversion but not for the step of dedifferentiation. These results provide insight into the mechanisms by which esophageal cells might initiate columnar metaplasia.
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Affiliation(s)
| | - Sheleya Pirard
- IRIBHM, ULB/Faculty of Medicine, 808 route de Lennik, 1070 Brussels, Belgium
| | - Simon Kin
- IRIBHM, ULB/Faculty of Medicine, 808 route de Lennik, 1070 Brussels, Belgium
| | - Benjamin Dassy
- IRIBHM, ULB/Faculty of Medicine, 808 route de Lennik, 1070 Brussels, Belgium
| | - Anne Lefort
- IRIBHM, ULB/Faculty of Medicine, 808 route de Lennik, 1070 Brussels, Belgium
| | - Frédérick Libert
- IRIBHM, ULB/Faculty of Medicine, 808 route de Lennik, 1070 Brussels, Belgium
| | - Sachiyo Nomura
- Department of Gastrointestinal Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Benjamin Beck
- IRIBHM, ULB/Faculty of Medicine, 808 route de Lennik, 1070 Brussels, Belgium; WELBIO/FNRS Principal Investigator at IRIBHM, ULB/Faculty of Medicine, 808 route de Lennik, 1070 Brussels, Belgium.
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30
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Ohnishi T, Kiyama Y, Arima‐Yoshida F, Kadota M, Ichikawa T, Yamada K, Watanabe A, Ohba H, Tanaka K, Nakaya A, Horiuchi Y, Iwayama Y, Toyoshima M, Ogawa I, Shimamoto‐Mitsuyama C, Maekawa M, Balan S, Arai M, Miyashita M, Toriumi K, Nozaki Y, Kurokawa R, Suzuki K, Yoshikawa A, Toyota T, Hosoya T, Okuno H, Bito H, Itokawa M, Kuraku S, Manabe T, Yoshikawa T. Cooperation of LIM domain-binding 2 (LDB2) with EGR in the pathogenesis of schizophrenia. EMBO Mol Med 2021; 13:e12574. [PMID: 33656268 PMCID: PMC8033514 DOI: 10.15252/emmm.202012574] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 01/21/2021] [Accepted: 01/25/2021] [Indexed: 01/15/2023] Open
Abstract
Genomic defects with large effect size can help elucidate unknown pathologic architecture of mental disorders. We previously reported on a patient with schizophrenia and a balanced translocation between chromosomes 4 and 13 and found that the breakpoint within chromosome 4 is located near the LDB2 gene. We show here that Ldb2 knockout (KO) mice displayed multiple deficits relevant to mental disorders. In particular, Ldb2 KO mice exhibited deficits in the fear-conditioning paradigm. Analysis of the amygdala suggested that dysregulation of synaptic activities controlled by the immediate early gene Arc is involved in the phenotypes. We show that LDB2 forms protein complexes with known transcription factors. Consistently, ChIP-seq analyses indicated that LDB2 binds to > 10,000 genomic sites in human neurospheres. We found that many of those sites, including the promoter region of ARC, are occupied by EGR transcription factors. Our previous study showed an association of the EGR family genes with schizophrenia. Collectively, the findings suggest that dysregulation in the gene expression controlled by the LDB2-EGR axis underlies a pathogenesis of subset of mental disorders.
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31
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Yang W, Cortijo S, Korsbo N, Roszak P, Schiessl K, Gurzadyan A, Wightman R, Jönsson H, Meyerowitz E. Molecular mechanism of cytokinin-activated cell division in Arabidopsis. Science 2021; 371:1350-1355. [PMID: 33632892 PMCID: PMC8166333 DOI: 10.1126/science.abe2305] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 02/09/2021] [Indexed: 01/16/2023]
Abstract
Mitogens trigger cell division in animals. In plants, cytokinins, a group of phytohormones derived from adenine, stimulate cell proliferation. Cytokinin signaling is initiated by membrane-associated histidine kinase receptors and transduced through a phosphorelay system. We show that in the Arabidopsis shoot apical meristem (SAM), cytokinin regulates cell division by promoting nuclear shuttling of Myb-domain protein 3R4 (MYB3R4), a transcription factor that activates mitotic gene expression. Newly synthesized MYB3R4 protein resides predominantly in the cytoplasm. At the G2-to-M transition, rapid nuclear accumulation of MYB3R4-consistent with an associated transient peak in cytokinin concentration-feeds a positive feedback loop involving importins and initiates a transcriptional cascade that drives mitosis and cytokinesis. An engineered nuclear-restricted MYB3R4 mimics the cytokinin effects of enhanced cell proliferation and meristem growth.
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Affiliation(s)
- Weibing Yang
- Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK
| | - Sandra Cortijo
- Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK
| | - Niklas Korsbo
- Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK.,Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge CB3 0WA, UK
| | - Pawel Roszak
- Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK
| | - Katharina Schiessl
- Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK
| | - Aram Gurzadyan
- Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK.,Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge CB3 0WA, UK
| | - Raymond Wightman
- Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK
| | - Henrik Jönsson
- Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK. .,Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge CB3 0WA, UK.,Department of Astronomy and Theoretical Physics, Lund University, SE22362 Lund, Sweden
| | - Elliot Meyerowitz
- Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK. .,Howard Hughes Medical Institute and Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
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32
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Cerise M, Giaume F, Galli M, Khahani B, Lucas J, Podico F, Tavakol E, Parcy F, Gallavotti A, Brambilla V, Fornara F. OsFD4 promotes the rice floral transition via florigen activation complex formation in the shoot apical meristem. THE NEW PHYTOLOGIST 2021; 229:429-443. [PMID: 32737885 DOI: 10.1111/nph.16834] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 07/15/2020] [Indexed: 06/11/2023]
Abstract
In rice, the florigens Heading Date 3a (Hd3a) and Rice Flowering Locus T 1 (RFT1), OsFD-like basic leucine zipper (bZIP) transcription factors, and Gf14 proteins assemble into florigen activation/repressor complexes (FACs/FRCs), which regulate transition to flowering in leaves and apical meristem. Only OsFD1 has been described as part of complexes promoting flowering at the meristem, and little is known about the role of other bZIP transcription factors, the combinatorial complexity of FAC formation, and their DNA-binding properties. Here, we used mutant analysis, protein-protein interaction assays and DNA affinity purification (DAP) sequencing coupled to in silico prediction of binding syntaxes to study several bZIP proteins that assemble into FACs or FRCs. We identified OsFD4 as a component of a FAC promoting flowering at the shoot apical meristem, downstream of OsFD1. The osfd4 mutants are late flowering and delay expression of genes promoting inflorescence development. Protein-protein interactions indicate an extensive network of contacts between several bZIPs and Gf14 proteins. Finally, we identified genomic regions bound by bZIPs with promotive and repressive effects on flowering. We conclude that distinct bZIPs orchestrate floral induction at the meristem and that FAC formation is largely combinatorial. While binding to the same consensus motif, their DNA-binding syntax is different, suggesting discriminatory functions.
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Affiliation(s)
- Martina Cerise
- Department of Biosciences, University of Milan, Milan, 20123, Italy
- Department of Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, D-50829, Germany
| | - Francesca Giaume
- Department of Biosciences, University of Milan, Milan, 20123, Italy
| | - Mary Galli
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854, USA
| | - Bahman Khahani
- Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, 71441-65186, Iran
| | - Jérémy Lucas
- CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, University Grenoble Alpes, 17 avenue des martyrs, Grenoble, F-38054, France
| | - Federico Podico
- Department of Biosciences, University of Milan, Milan, 20123, Italy
| | - Elahe Tavakol
- Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, 71441-65186, Iran
| | - François Parcy
- CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, University Grenoble Alpes, 17 avenue des martyrs, Grenoble, F-38054, France
| | - Andrea Gallavotti
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854, USA
| | - Vittoria Brambilla
- Department of Agricultural and Environmental Sciences, University of Milan, Milan, 20123, Italy
| | - Fabio Fornara
- Department of Biosciences, University of Milan, Milan, 20123, Italy
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33
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Magadi SS, Voutyraki C, Anagnostopoulos G, Zacharioudaki E, Poutakidou IK, Efraimoglou C, Stapountzi M, Theodorou V, Nikolaou C, Koumbanakis KA, Fullard JF, Delidakis C. Dissecting Hes-centred transcriptional networks in neural stem cell maintenance and tumorigenesis in Drosophila. Development 2020; 147:147/22/dev191544. [PMID: 33229432 DOI: 10.1242/dev.191544] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 10/05/2020] [Indexed: 01/26/2023]
Abstract
Neural stem cells divide during embryogenesis and juvenile life to generate the entire complement of neurons and glia in the nervous system of vertebrates and invertebrates. Studies of the mechanisms controlling the fine balance between neural stem cells and more differentiated progenitors have shown that, in every asymmetric cell division, progenitors send a Delta-Notch signal to their sibling stem cells. Here, we show that excessive activation of Notch or overexpression of its direct targets of the Hes family causes stem-cell hyperplasias in the Drosophila larval central nervous system, which can progress to malignant tumours after allografting to adult hosts. We combined transcriptomic data from these hyperplasias with chromatin occupancy data for Dpn, a Hes transcription factor, to identify genes regulated by Hes factors in this process. We show that the Notch/Hes axis represses a cohort of transcription factor genes. These are excluded from the stem cells and promote early differentiation steps, most likely by preventing the reversion of immature progenitors to a stem-cell fate. We describe the impact of two of these 'anti-stemness' factors, Zfh1 and Gcm, on Notch/Hes-triggered tumorigenesis.
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Affiliation(s)
- Srivathsa S Magadi
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, 70013 Heraklion, Crete, Greece.,Department of Biology, University of Crete, 70013 Heraklion, Crete, Greece
| | - Chrysanthi Voutyraki
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, 70013 Heraklion, Crete, Greece.,Department of Biology, University of Crete, 70013 Heraklion, Crete, Greece
| | - Gerasimos Anagnostopoulos
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, 70013 Heraklion, Crete, Greece.,Department of Biology, University of Crete, 70013 Heraklion, Crete, Greece
| | - Evanthia Zacharioudaki
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, 70013 Heraklion, Crete, Greece
| | - Ioanna K Poutakidou
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, 70013 Heraklion, Crete, Greece.,Department of Biology, University of Crete, 70013 Heraklion, Crete, Greece
| | - Christina Efraimoglou
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, 70013 Heraklion, Crete, Greece.,Department of Biology, University of Crete, 70013 Heraklion, Crete, Greece
| | - Margarita Stapountzi
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, 70013 Heraklion, Crete, Greece
| | - Vasiliki Theodorou
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, 70013 Heraklion, Crete, Greece
| | - Christoforos Nikolaou
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, 70013 Heraklion, Crete, Greece.,Department of Biology, University of Crete, 70013 Heraklion, Crete, Greece
| | - Konstantinos A Koumbanakis
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, 70013 Heraklion, Crete, Greece.,Department of Biology, University of Crete, 70013 Heraklion, Crete, Greece
| | - John F Fullard
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, 70013 Heraklion, Crete, Greece
| | - Christos Delidakis
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, 70013 Heraklion, Crete, Greece .,Department of Biology, University of Crete, 70013 Heraklion, Crete, Greece
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34
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Strobino M, Wenda JM, Padayachy L, Steiner FA. Loss of histone H3.3 results in DNA replication defects and altered origin dynamics in C. elegans. Genome Res 2020; 30:1740-1751. [PMID: 33172964 PMCID: PMC7706726 DOI: 10.1101/gr.260794.120] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 10/06/2020] [Indexed: 12/12/2022]
Abstract
Histone H3.3 is a replication-independent variant of histone H3 with important roles in development, differentiation, and fertility. Here, we show that loss of H3.3 results in replication defects in Caenorhabditis elegans embryos at elevated temperatures. To characterize these defects, we adapt methods to determine replication timing, map replication origins, and examine replication fork progression. Our analysis of the spatiotemporal regulation of DNA replication shows that despite the very rapid embryonic cell cycle, the genome is replicated from early and late firing origins and is partitioned into domains of early and late replication. We find that under temperature stress conditions, additional replication origins become activated. Moreover, loss of H3.3 results in altered replication fork progression around origins, which is particularly evident at stress-activated origins. These replication defects are accompanied by replication checkpoint activation, a delayed cell cycle, and increased lethality in checkpoint-compromised embryos. Our comprehensive analysis of DNA replication in C. elegans reveals the genomic location of replication origins and the dynamics of their firing, and uncovers a role of H3.3 in the regulation of replication origins under stress conditions.
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Affiliation(s)
- Maude Strobino
- Department of Molecular Biology and Institute for Genetics and Genomics in Geneva, Section of Biology, Faculty of Sciences, University of Geneva, 1211 Geneva, Switzerland
| | - Joanna M Wenda
- Department of Molecular Biology and Institute for Genetics and Genomics in Geneva, Section of Biology, Faculty of Sciences, University of Geneva, 1211 Geneva, Switzerland
| | - Laura Padayachy
- Department of Molecular Biology and Institute for Genetics and Genomics in Geneva, Section of Biology, Faculty of Sciences, University of Geneva, 1211 Geneva, Switzerland
| | - Florian A Steiner
- Department of Molecular Biology and Institute for Genetics and Genomics in Geneva, Section of Biology, Faculty of Sciences, University of Geneva, 1211 Geneva, Switzerland
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35
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Yu YR, Imrichova H, Wang H, Chao T, Xiao Z, Gao M, Rincon-Restrepo M, Franco F, Genolet R, Cheng WC, Jandus C, Coukos G, Jiang YF, Locasale JW, Zippelius A, Liu PS, Tang L, Bock C, Vannini N, Ho PC. Disturbed mitochondrial dynamics in CD8 + TILs reinforce T cell exhaustion. Nat Immunol 2020; 21:1540-1551. [PMID: 33020660 DOI: 10.1038/s41590-020-0793-3] [Citation(s) in RCA: 241] [Impact Index Per Article: 60.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 08/24/2020] [Indexed: 12/19/2022]
Abstract
The metabolic challenges present in tumors attenuate the metabolic fitness and antitumor activity of tumor-infiltrating T lymphocytes (TILs). However, it remains unclear whether persistent metabolic insufficiency can imprint permanent T cell dysfunction. We found that TILs accumulated depolarized mitochondria as a result of decreased mitophagy activity and displayed functional, transcriptomic and epigenetic characteristics of terminally exhausted T cells. Mechanistically, reduced mitochondrial fitness in TILs was induced by the coordination of T cell receptor stimulation, microenvironmental stressors and PD-1 signaling. Enforced accumulation of depolarized mitochondria with pharmacological inhibitors induced epigenetic reprogramming toward terminal exhaustion, indicating that mitochondrial deregulation caused T cell exhaustion. Furthermore, supplementation with nicotinamide riboside enhanced T cell mitochondrial fitness and improved responsiveness to anti-PD-1 treatment. Together, our results reveal insights into how mitochondrial dynamics and quality orchestrate T cell antitumor responses and commitment to the exhaustion program.
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Affiliation(s)
- Yi-Ru Yu
- Department of Oncology, University of Lausanne, Lausanne, Switzerland.,Ludwig Institute for Cancer Research, University of Lausanne, Epalinges, Switzerland
| | - Hana Imrichova
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Haiping Wang
- Department of Oncology, University of Lausanne, Lausanne, Switzerland.,Ludwig Institute for Cancer Research, University of Lausanne, Epalinges, Switzerland
| | - Tung Chao
- Department of Oncology, University of Lausanne, Lausanne, Switzerland.,Ludwig Institute for Cancer Research, University of Lausanne, Epalinges, Switzerland
| | - Zhengtao Xiao
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Min Gao
- Institute of Bioengineering, Institute of Materials Science and Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Marcela Rincon-Restrepo
- Department of Oncology, University of Lausanne, Lausanne, Switzerland.,Ludwig Institute for Cancer Research, University of Lausanne, Epalinges, Switzerland
| | - Fabien Franco
- Department of Oncology, University of Lausanne, Lausanne, Switzerland.,Ludwig Institute for Cancer Research, University of Lausanne, Epalinges, Switzerland
| | - Raphael Genolet
- Department of Oncology, University of Lausanne, Lausanne, Switzerland.,Ludwig Institute for Cancer Research, University of Lausanne, Epalinges, Switzerland
| | - Wan-Chen Cheng
- Department of Oncology, University of Lausanne, Lausanne, Switzerland.,Ludwig Institute for Cancer Research, University of Lausanne, Epalinges, Switzerland
| | - Camilla Jandus
- Department of Oncology, University of Lausanne, Lausanne, Switzerland.,Ludwig Institute for Cancer Research, University of Lausanne, Epalinges, Switzerland
| | - George Coukos
- Department of Oncology, University of Lausanne, Lausanne, Switzerland.,Ludwig Institute for Cancer Research, University of Lausanne, Epalinges, Switzerland
| | - Yi-Fan Jiang
- Graduate Institute of Molecular and Comparative Pathobiology, School of Veterinary Medicine, National Taiwan University, Taipei, Taiwan
| | - Jason W Locasale
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Alfred Zippelius
- Department of Biomedicine, Laboratory Cancer Immunology, University Hospital and University of Basel, Basel, Switzerland.,Medical Oncology, University Hospital Basel, Basel, Switzerland
| | - Pu-Ste Liu
- Institute of Cellular and System Medicine, National Health Research Institute, Miaoli County, Taiwan
| | - Li Tang
- Institute of Bioengineering, Institute of Materials Science and Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Nicola Vannini
- Department of Oncology, University of Lausanne, Lausanne, Switzerland.,Ludwig Institute for Cancer Research, University of Lausanne, Epalinges, Switzerland
| | - Ping-Chih Ho
- Department of Oncology, University of Lausanne, Lausanne, Switzerland. .,Ludwig Institute for Cancer Research, University of Lausanne, Epalinges, Switzerland.
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Diet Modifies Pioglitazone's Influence on Hepatic PPAR γ-Regulated Mitochondrial Gene Expression. PPAR Res 2020; 2020:3817573. [PMID: 32963510 PMCID: PMC7501566 DOI: 10.1155/2020/3817573] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 07/28/2020] [Accepted: 08/20/2020] [Indexed: 12/28/2022] Open
Abstract
Pioglitazone (Pio) is a thiazolidinedione (TZD) insulin-sensitizing drug whose effects result predominantly from its modulation of the transcriptional activity of peroxisome proliferator-activated-receptor-gamma (PPARγ). Pio is used to treat human insulin-resistant diabetes and also frequently considered for treatment of nonalcoholic steatohepatitis (NASH). In both settings, Pio's beneficial effects are believed to result primarily from its actions on adipose PPARγ activity, which improves insulin sensitivity and reduces the delivery of fatty acids to the liver. Nevertheless, a recent clinical trial showed variable efficacy of Pio in human NASH. Hepatocytes also express PPARγ, and such expression increases with insulin resistance and in nonalcoholic fatty liver disease (NAFLD). Furthermore, mice that overexpress hepatocellular PPARγ and Pio-treated mice with extrahepatic PPARγ gene disruption develop features of NAFLD. Thus, Pio's direct impact on hepatocellular gene expression might also be a determinant of this drug's ultimate influence on insulin resistance and NAFLD. Previous studies have characterized Pio's PPARγ-dependent effects on hepatic expression of specific adipogenic, lipogenic, and other metabolic genes. However, such transcriptional regulation has not been comprehensively assessed. The studies reported here address that consideration by genome-wide comparisons of Pio's hepatic transcriptional effects in wildtype (WT) and liver-specific PPARγ-knockout (KO) mice given either control or high-fat (HFD) diets. The results identify a large set of hepatic genes for which Pio's liver PPARγ-dependent transcriptional effects are concordant with its effects on RXR-DNA binding in WT mice. These data also show that HFD modifies Pio's influence on a subset of such transcriptional regulation. Finally, our findings reveal a broader influence of Pio on PPARγ-dependent hepatic expression of nuclear genes encoding mitochondrial proteins than previously recognized. Taken together, these studies provide new insights about the tissue-specific mechanisms by which Pio affects hepatic gene expression and the broad scope of this drug's influence on such regulation.
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Hänsel-Hertsch R, Simeone A, Shea A, Hui WWI, Zyner KG, Marsico G, Rueda OM, Bruna A, Martin A, Zhang X, Adhikari S, Tannahill D, Caldas C, Balasubramanian S. Landscape of G-quadruplex DNA structural regions in breast cancer. Nat Genet 2020; 52:878-883. [PMID: 32747825 DOI: 10.1038/s41588-020-0672-8] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 06/25/2020] [Indexed: 12/25/2022]
Abstract
Response and resistance to anticancer therapies vary due to intertumor and intratumor heterogeneity1. Here, we map differentially enriched G-quadruplex (G4) DNA structure-forming regions (∆G4Rs) in 22 breast cancer patient-derived tumor xenograft (PDTX) models. ∆G4Rs are associated with the promoters of highly amplified genes showing high expression, and with somatic single-nucleotide variants. Differences in ΔG4R landscapes reveal seven transcription factor programs across PDTXs. ∆G4R abundance and locations stratify PDTXs into at least three G4-based subtypes. ∆G4Rs in most PDTXs (14 of 22) were found to associate with more than one breast cancer subtype, which we also call an integrative cluster (IC)2. This suggests the frequent coexistence of multiple breast cancer states within a PDTX model, the majority of which display aggressive triple-negative IC10 gene activity. Short-term cultures of PDTX models with increased ∆G4R levels are more sensitive to small molecules targeting G4 DNA. Thus, G4 landscapes reveal additional IC-related intratumor heterogeneity in PDTX biopsies, improving breast cancer stratification and potentially identifying new treatment strategies.
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Affiliation(s)
- Robert Hänsel-Hertsch
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne and University Hospital Cologne, Cologne, Germany
- Institute of Human Genetics, University Hospital Cologne, Cologne, Germany
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Angela Simeone
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Abigail Shea
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Winnie W I Hui
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Katherine G Zyner
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Giovanni Marsico
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
- Inivata, Babraham Research Campus, Cambridge, UK
| | - Oscar M Rueda
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Alejandra Bruna
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
- The Institute of Cancer Research, London, UK
| | - Alistair Martin
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Xiaoyun Zhang
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | | | - David Tannahill
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
- Cambridge Breast Cancer Research Unit, Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
- Cancer Research UK Cambridge Centre, NIHR Cambridge Biomedical Research Centre and Cambridge Experimental Cancer Medicine Centre, Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
| | - Shankar Balasubramanian
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK.
- Department of Chemistry, University of Cambridge, Cambridge, UK.
- School of Clinical Medicine, University of Cambridge, Cambridge, UK.
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38
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Gao Y, Nihira NT, Bu X, Chu C, Zhang J, Kolodziejczyk A, Fan Y, Chan NT, Ma L, Liu J, Wang D, Dai X, Liu H, Ono M, Nakanishi A, Inuzuka H, North BJ, Huang YH, Sharma S, Geng Y, Xu W, Liu XS, Li L, Miki Y, Sicinski P, Freeman GJ, Wei W. Acetylation-dependent regulation of PD-L1 nuclear translocation dictates the efficacy of anti-PD-1 immunotherapy. Nat Cell Biol 2020; 22:1064-1075. [PMID: 32839551 PMCID: PMC7484128 DOI: 10.1038/s41556-020-0562-4] [Citation(s) in RCA: 195] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 07/21/2020] [Indexed: 12/16/2022]
Abstract
Immunotherapies that target programmed cell death protein 1 (PD-1) and its ligand PD-L1 as well as cytotoxic T-lymphocyte-associated protein 4 (CTLA4) have shown impressive clinical outcomes for multiple tumours. However, only a subset of patients achieves durable responses, suggesting that the mechanisms of the immune checkpoint pathways are not completely understood. Here, we report that PD-L1 translocates from the plasma membrane into the nucleus through interactions with components of the endocytosis and nucleocytoplasmic transport pathways, regulated by p300-mediated acetylation and HDAC2-dependent deacetylation of PD-L1. Moreover, PD-L1 deficiency leads to compromised expression of multiple immune-response-related genes. Genetically or pharmacologically modulating PD-L1 acetylation blocks its nuclear translocation, reprograms the expression of immune-response-related genes and, as a consequence, enhances the anti-tumour response to PD-1 blockade. Thus, our results reveal an acetylation-dependent regulation of PD-L1 nuclear localization that governs immune-response gene expression, and thereby advocate targeting PD-L1 translocation to enhance the efficacy of PD-1/PD-L1 blockade.
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Affiliation(s)
- Yang Gao
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Naoe Taira Nihira
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Department of Molecular Genetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
- Division of Pediatric Dentistry, Department of Oral Health and Development Sciences, Tohoku University Graduate School of Dentistry, Sendai, Japan
| | - Xia Bu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Chen Chu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Jinfang Zhang
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Aleksandra Kolodziejczyk
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Yizeng Fan
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Ngai Ting Chan
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI, USA
| | - Leina Ma
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Jing Liu
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Dong Wang
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Xiaoming Dai
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Huadong Liu
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology and Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi' an, China
| | - Masaya Ono
- Department of Clinical Proteomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Akira Nakanishi
- Department of Molecular Genetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hiroyuki Inuzuka
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Brian J North
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Yu-Han Huang
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Samanta Sharma
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Yan Geng
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Wei Xu
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI, USA
| | - X Shirley Liu
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Lei Li
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yoshio Miki
- Department of Molecular Genetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.
| | - Piotr Sicinski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
| | - Gordon J Freeman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
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Seidl MD, Fels B, Kranick D, Sternberg A, Grimm K, Stümpel FT, Pluteanu F, Schulte JS, Heinick A, Kojima N, Endo S, Huge A, Stoll M, Müller FU. Induction of ICER is superseded by smICER, challenging the impact of ICER under chronic beta-adrenergic stimulation. FASEB J 2020; 34:11272-11291. [PMID: 32602979 DOI: 10.1096/fj.201902301rr] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 03/30/2020] [Accepted: 04/21/2020] [Indexed: 11/11/2022]
Abstract
ICER (inducible cAMP early repressor) isoforms are transcriptional repressors encoded by the Crem (cAMP responsive element modulator) gene. They were linked to the regulation of a multitude of cellular processes and pathophysiological mechanisms. Here, we show for the first time that two independent induction patterns for CREM repressor isoforms exist in the heart, namely for ICER and smICER (small ICER), which are induced in response to β-adrenergic stimulation in a transient- and saturation-like manner, respectively. This time-shifted induction pattern, driven by two internal promoters in the Crem gene, leads to the predominant transcription of smIcer after prolonged β-adrenergic stimulation. Using an ICER knockout mouse model with preserved smICER induction, we show that the transient-like induction of Icer itself has minor effects on gene regulation, cardiac hypertrophy or contractile function in the heart. We conclude that the functions previously linked to ICER may be rather attributed to smICER, also beyond the cardiac background.
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Affiliation(s)
- Matthias D Seidl
- Institute of Pharmacology and Toxicology, University of Münster, Münster, Germany
| | - Benedikt Fels
- Institute of Pharmacology and Toxicology, University of Münster, Münster, Germany
| | - Daniel Kranick
- Institute of Pharmacology and Toxicology, University of Münster, Münster, Germany
| | - Alexandra Sternberg
- Institute of Pharmacology and Toxicology, University of Münster, Münster, Germany
| | - Kristina Grimm
- Institute of Pharmacology and Toxicology, University of Münster, Münster, Germany
| | - Frank T Stümpel
- Institute of Pharmacology and Toxicology, University of Münster, Münster, Germany
| | - Florentina Pluteanu
- Institute of Pharmacology and Toxicology, University of Münster, Münster, Germany
| | - Jan S Schulte
- Institute of Pharmacology and Toxicology, University of Münster, Münster, Germany
| | - Alexander Heinick
- Institute of Pharmacology and Toxicology, University of Münster, Münster, Germany
| | | | - Shogo Endo
- Aging Neuroscience Research Team, Tokyo Metropolitan Institute of Gerontology, Tokyo, Japan
| | - Andreas Huge
- Core Facility Genomik, Medical Faculty, University of Muenster, Germany
| | - Monika Stoll
- Core Facility Genomik, Medical Faculty, University of Muenster, Germany
| | - Frank U Müller
- Institute of Pharmacology and Toxicology, University of Münster, Münster, Germany
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40
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Alecki C, Chiwara V, Sanz LA, Grau D, Arias Pérez O, Boulier EL, Armache KJ, Chédin F, Francis NJ. RNA-DNA strand exchange by the Drosophila Polycomb complex PRC2. Nat Commun 2020; 11:1781. [PMID: 32286294 PMCID: PMC7156742 DOI: 10.1038/s41467-020-15609-x] [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: 05/01/2019] [Accepted: 03/17/2020] [Indexed: 12/21/2022] Open
Abstract
Polycomb Group (PcG) proteins form memory of transient transcriptional repression that is necessary for development. In Drosophila, DNA elements termed Polycomb Response Elements (PREs) recruit PcG proteins. How PcG activities are targeted to PREs to maintain repressed states only in appropriate developmental contexts has been difficult to elucidate. PcG complexes modify chromatin, but also interact with both RNA and DNA, and RNA is implicated in PcG targeting and function. Here we show that R-loops form at many PREs in Drosophila embryos, and correlate with repressive states. In vitro, both PRC1 and PRC2 can recognize R-loops and open DNA bubbles. Unexpectedly, we find that PRC2 drives formation of RNA-DNA hybrids, the key component of R-loops, from RNA and dsDNA. Our results identify R-loop formation as a feature of Drosophila PREs that can be recognized by PcG complexes, and RNA-DNA strand exchange as a PRC2 activity that could contribute to R-loop formation.
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Affiliation(s)
- Célia Alecki
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
- Département de biochimie et médecine moléculaire Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, QC, H3T 1J4, Canada
| | - Victoria Chiwara
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
| | - Lionel A Sanz
- Department of Molecular and Cellular Biology and Genome Center, 1 Shields Avenue, University of California, Davis, Davis, CA, 95616, USA
| | - Daniel Grau
- Skirball Institute of Biomolecular Medicine, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, 10016, USA
| | - Osvaldo Arias Pérez
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
- Natural Sciences and Engineering Postgraduate, Universidad Autonoma Metropolitana, Cuajimalpa, Mexico City, Mexico
| | - Elodie L Boulier
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
| | - Karim-Jean Armache
- Skirball Institute of Biomolecular Medicine, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, 10016, USA
| | - Frédéric Chédin
- Department of Molecular and Cellular Biology and Genome Center, 1 Shields Avenue, University of California, Davis, Davis, CA, 95616, USA
| | - Nicole J Francis
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada.
- Département de biochimie et médecine moléculaire Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, QC, H3T 1J4, Canada.
- Division of Experimental Medicine, McGill University, 1001 Decarie Boulevard, Montreal, QC, H4A 3J1, Canada.
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41
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de Anda-Jáuregui G, Hernández-Lemus E. Computational Oncology in the Multi-Omics Era: State of the Art. Front Oncol 2020; 10:423. [PMID: 32318338 PMCID: PMC7154096 DOI: 10.3389/fonc.2020.00423] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 03/10/2020] [Indexed: 12/24/2022] Open
Abstract
Cancer is the quintessential complex disease. As technologies evolve faster each day, we are able to quantify the different layers of biological elements that contribute to the emergence and development of malignancies. In this multi-omics context, the use of integrative approaches is mandatory in order to gain further insights on oncological phenomena, and to move forward toward the precision medicine paradigm. In this review, we will focus on computational oncology as an integrative discipline that incorporates knowledge from the mathematical, physical, and computational fields to further the biomedical understanding of cancer. We will discuss the current roles of computation in oncology in the context of multi-omic technologies, which include: data acquisition and processing; data management in the clinical and research settings; classification, diagnosis, and prognosis; and the development of models in the research setting, including their use for therapeutic target identification. We will discuss the machine learning and network approaches as two of the most promising emerging paradigms, in computational oncology. These approaches provide a foundation on how to integrate different layers of biological description into coherent frameworks that allow advances both in the basic and clinical settings.
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Affiliation(s)
- Guillermo de Anda-Jáuregui
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico
- Cátedras Conacyt Para Jóvenes Investigadores, National Council on Science and Technology, Mexico City, Mexico
| | - Enrique Hernández-Lemus
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico
- Center for Complexity Sciences, Universidad Nacional Autónoma de México, Mexico City, Mexico
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42
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Chi RPA, Wang T, Adams N, Wu SP, Young SL, Spencer TE, DeMayo F. Human Endometrial Transcriptome and Progesterone Receptor Cistrome Reveal Important Pathways and Epithelial Regulators. J Clin Endocrinol Metab 2020; 105:dgz117. [PMID: 31665330 PMCID: PMC7105253 DOI: 10.1210/clinem/dgz117] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 10/09/2019] [Indexed: 11/19/2022]
Abstract
CONTEXT Poor uterine receptivity is one major factor leading to pregnancy loss and infertility. Understanding the molecular events governing successful implantation is hence critical in combating infertility. OBJECTIVE To define Progesterone Receptor (PGR)-regulated molecular mechanisms and epithelial roles in receptivity. DESIGN RNA-sequencing and PGR-ChIP-seq were conducted in parallel to identify PGR-regulated pathways during the Window of implantation (WOI) in endometrium of fertile women. SETTING Endometrial biopsies from the proliferative and mid-secretory phases were analyzed. PATIENTS OR OTHER PARTICIPANTS Participants were fertile, reproductive aged (18-37 years) women with normal cycle length, and without any history of dysmenorrhea, infertility, or irregular cycles. In total, 42 endometrial biopsies obtained from 42 women were analyzed in this study. INTERVENTIONS There were no interventions during this study. MAIN OUTCOME MEASURES Here we measured the alterations in gene expression and PGR occupancy in the genome during the WOI, based on the hypothesis that PGR binds uterine chromatin cycle dependently to regulate genes involved in uterine cell differentiation and function. RESULTS 653 genes were identified with regulated PGR binding and differential expression during the WOI. These were involved in regulating inflammatory response, xenobiotic metabolism, epithelial mesenchymal transition, cell death, interleukin/Signal Transducer And Activator Of Transcription (STAT) signaling, estrogen response, and Mammalian target of rapamycin complex 1 (MTORC1) response. Transcriptome of the epithelium identified 3052 differentially expressed genes, of which 658 were uniquely regulated. Transcription factors Interferon Regulatory Factor 8 (IRF8) and Myocyte Enhancer Factor 2C (MEF2C) were found to be regulated in the epithelium during the WOI at the protein level, suggesting potentially important functions that are previously unrecognized. CONCLUSION PGR binds the genomic regions of genes regulating critical processes in uterine receptivity and function.
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Affiliation(s)
- Ru-pin Alicia Chi
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, North Carolina
| | - Tianyuan Wang
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, North Carolina
| | - Nyssa Adams
- Interdepartmental Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, Texas
| | - San-pin Wu
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, North Carolina
| | - Steven L Young
- Department of Obstetrics and Gynecology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Thomas E Spencer
- Division of Animal Sciences, University of Missouri, Columbia, Missouri
- Department of Obstetrics, Gynecology and Women’s Health, University of Missouri, Columbia, Missouri
| | - Francesco DeMayo
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, North Carolina
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43
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Mishra GP, Ghosh A, Jha A, Raghav SK. BedSect: An Integrated Web Server Application to Perform Intersection, Visualization, and Functional Annotation of Genomic Regions From Multiple Datasets. Front Genet 2020; 11:3. [PMID: 32117432 PMCID: PMC7013082 DOI: 10.3389/fgene.2020.00003] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 01/06/2020] [Indexed: 11/17/2022] Open
Abstract
A large number of genomic regions, such as transcription factor binding sites (TFBSs) captured from next generation sequencing (NGS) data analyses or those available from the public resource database ENCODE, are generally overlapped to answer a variety of biological questions. Though several command-line tools are available to perform such an analysis, there is a notable lack of an integrated webserver application with which to identify genomic region intersections, generate publication-ready plots depicting subsets of the overlapped regions, and perform functional annotation. Thus, there is an ardent need for a comprehensive and user-friendly webserver application that allows the users to either upload multiple datasets or select from the integrated Gene Transcription Regulation Database (GTRD). We thus introduce BedSect (http://imgsb.org/bedsect/.), which not only fulfils the above criteria but also performs intersection analysis along with visualization of the intersection regions as an UpSet and correlation plot using the integrated Shiny application. Moreover, analyses, including functional annotation, gene ontology, and biological pathways enrichment for the identified unique and intersected genomic regions, can also be performed using the integrated GREAT tool. To view the genomic regions in the genome browser, the inbuilt hyperlink for UCSC can redirect the user to visualize the results as custom tracks.
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Affiliation(s)
- Gyan Prakash Mishra
- Immunogenomics and Systems Biology Laboratory, Institute of Life Sciences, Bhubaneswar, India
- School of Biotechnology, KIIT University, Bhubaneswar, India
| | - Arup Ghosh
- Immunogenomics and Systems Biology Laboratory, Institute of Life Sciences, Bhubaneswar, India
- School of Biotechnology, KIIT University, Bhubaneswar, India
| | - Atimukta Jha
- Immunogenomics and Systems Biology Laboratory, Institute of Life Sciences, Bhubaneswar, India
- Manipal Academy of Higher Education, Manipal, India
| | - Sunil Kumar Raghav
- Immunogenomics and Systems Biology Laboratory, Institute of Life Sciences, Bhubaneswar, India
- School of Biotechnology, KIIT University, Bhubaneswar, India
- Manipal Academy of Higher Education, Manipal, India
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44
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Uribe-Lewis S, Carroll T, Menon S, Nicholson A, Manasterski PJ, Winton DJ, Buczacki SJA, Murrell A. 5-hydroxymethylcytosine and gene activity in mouse intestinal differentiation. Sci Rep 2020; 10:546. [PMID: 31953501 PMCID: PMC6969059 DOI: 10.1038/s41598-019-57214-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 12/19/2019] [Indexed: 12/17/2022] Open
Abstract
Cytosine hydroxymethylation (5hmC) in mammalian DNA is the product of oxidation of methylated cytosines (5mC) by Ten-Eleven-Translocation (TET) enzymes. While it has been shown that the TETs influence 5mC metabolism, pluripotency and differentiation during early embryonic development, the functional relationship between gene expression and 5hmC in adult (somatic) stem cell differentiation is still unknown. Here we report that 5hmC levels undergo highly dynamic changes during adult stem cell differentiation from intestinal progenitors to differentiated intestinal epithelium. We profiled 5hmC and gene activity in purified mouse intestinal progenitors and differentiated progeny to identify 43425 differentially hydroxymethylated regions and 5325 differentially expressed genes. These differentially marked regions showed both losses and gains of 5hmC after differentiation, despite lower global levels of 5hmC in progenitor cells. In progenitors, 5hmC did not correlate with gene transcript levels, however, upon differentiation the global increase in 5hmC content showed an overall positive correlation with gene expression level as well as prominent associations with histone modifications that typify active genes and enhancer elements. Our data support a gene regulatory role for 5hmC that is predominant over its role in controlling DNA methylation states.
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Affiliation(s)
- Santiago Uribe-Lewis
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Thomas Carroll
- Bioinformatics Resource Center, The Rockefeller University New York, New York, NY, 10065, USA
| | - Suraj Menon
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Anna Nicholson
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Piotr J Manasterski
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Douglas J Winton
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Simon J A Buczacki
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Addenbrookes Biomedical Campus, Cambridge, CB2 0AF, UK
| | - Adele Murrell
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
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45
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Ding J, Lin C, Bar-Joseph Z. Cell lineage inference from SNP and scRNA-Seq data. Nucleic Acids Res 2019; 47:e56. [PMID: 30820578 PMCID: PMC6547431 DOI: 10.1093/nar/gkz146] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 02/13/2019] [Accepted: 02/20/2019] [Indexed: 12/15/2022] Open
Abstract
Several recent studies focus on the inference of developmental and response trajectories from single cell RNA-Seq (scRNA-Seq) data. A number of computational methods, often referred to as pseudo-time ordering, have been developed for this task. Recently, CRISPR has also been used to reconstruct lineage trees by inserting random mutations. However, both approaches suffer from drawbacks that limit their use. Here, we develop a method to detect significant, cell type specific, sequence mutations from scRNA-Seq data. We show that only a few mutations are enough for reconstructing good branching models. Integrating these mutations with expression data further improves the accuracy of the reconstructed models. As we show, the majority of mutations we identify are likely RNA editing events indicating that such information can be used to distinguish cell types.
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Affiliation(s)
- Jun Ding
- Computational Biology Department, Carnegie Mellon University, 5000 Forbes Ave, Pittsburgh, PA 15213, USA
| | - Chieh Lin
- Machine Learning Department, Carnegie Mellon University, 5000 Forbes Ave, Pittsburgh, PA 15213, USA
| | - Ziv Bar-Joseph
- Computational Biology Department, Carnegie Mellon University, 5000 Forbes Ave, Pittsburgh, PA 15213, USA.,Machine Learning Department, Carnegie Mellon University, 5000 Forbes Ave, Pittsburgh, PA 15213, USA
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46
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Ma Y, Miotk A, Šutiković Z, Ermakova O, Wenzl C, Medzihradszky A, Gaillochet C, Forner J, Utan G, Brackmann K, Galván-Ampudia CS, Vernoux T, Greb T, Lohmann JU. WUSCHEL acts as an auxin response rheostat to maintain apical stem cells in Arabidopsis. Nat Commun 2019; 10:5093. [PMID: 31704928 PMCID: PMC6841675 DOI: 10.1038/s41467-019-13074-9] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 08/14/2019] [Indexed: 12/14/2022] Open
Abstract
To maintain the balance between long-term stem cell self-renewal and differentiation, dynamic signals need to be translated into spatially precise and temporally stable gene expression states. In the apical plant stem cell system, local accumulation of the small, highly mobile phytohormone auxin triggers differentiation while at the same time, pluripotent stem cells are maintained throughout the entire life-cycle. We find that stem cells are resistant to auxin mediated differentiation, but require low levels of signaling for their maintenance. We demonstrate that the WUSCHEL transcription factor confers this behavior by rheostatically controlling the auxin signaling and response pathway. Finally, we show that WUSCHEL acts via regulation of histone acetylation at target loci, including those with functions in the auxin pathway. Our results reveal an important mechanism that allows cells to differentially translate a potent and highly dynamic developmental signal into stable cell behavior with high spatial precision and temporal robustness. Spatial control of auxin signaling maintains a balance between stem-cell self-renewal and differentiation at the plant shoot apex. Here Ma et al. show that rheostatic control of auxin response by the WUSCHEL transcription factor maintains stem cells by conferring resistance to auxin mediated differentiation.
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Affiliation(s)
- Yanfei Ma
- Department of Stem Cell Biology, Centre for Organismal Studies, Heidelberg University, D-69120, Heidelberg, Germany
| | - Andrej Miotk
- Department of Stem Cell Biology, Centre for Organismal Studies, Heidelberg University, D-69120, Heidelberg, Germany
| | - Zoran Šutiković
- Department of Stem Cell Biology, Centre for Organismal Studies, Heidelberg University, D-69120, Heidelberg, Germany
| | - Olga Ermakova
- Department of Stem Cell Biology, Centre for Organismal Studies, Heidelberg University, D-69120, Heidelberg, Germany
| | - Christian Wenzl
- Department of Stem Cell Biology, Centre for Organismal Studies, Heidelberg University, D-69120, Heidelberg, Germany
| | - Anna Medzihradszky
- Department of Stem Cell Biology, Centre for Organismal Studies, Heidelberg University, D-69120, Heidelberg, Germany
| | - Christophe Gaillochet
- Department of Stem Cell Biology, Centre for Organismal Studies, Heidelberg University, D-69120, Heidelberg, Germany
| | - Joachim Forner
- Department of Stem Cell Biology, Centre for Organismal Studies, Heidelberg University, D-69120, Heidelberg, Germany
| | - Gözde Utan
- Department of Stem Cell Biology, Centre for Organismal Studies, Heidelberg University, D-69120, Heidelberg, Germany
| | - Klaus Brackmann
- Vienna Biocenter (VBC), Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Carlos S Galván-Ampudia
- Laboratoire Reproduction et Développement des Plantes, University of Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342, Lyon, France
| | - Teva Vernoux
- Laboratoire Reproduction et Développement des Plantes, University of Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342, Lyon, France
| | - Thomas Greb
- Department of Developmental Physiology, Centre for Organismal Studies, Heidelberg University, D-69120, Heidelberg, Germany
| | - Jan U Lohmann
- Department of Stem Cell Biology, Centre for Organismal Studies, Heidelberg University, D-69120, Heidelberg, Germany.
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47
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Mercatelli D, Scalambra L, Triboli L, Ray F, Giorgi FM. Gene regulatory network inference resources: A practical overview. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1863:194430. [PMID: 31678629 DOI: 10.1016/j.bbagrm.2019.194430] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 09/06/2019] [Accepted: 09/09/2019] [Indexed: 02/08/2023]
Abstract
Transcriptional regulation is a fundamental molecular mechanism involved in almost every aspect of life, from homeostasis to development, from metabolism to behavior, from reaction to stimuli to disease progression. In recent years, the concept of Gene Regulatory Networks (GRNs) has grown popular as an effective applied biology approach for describing the complex and highly dynamic set of transcriptional interactions, due to its easy-to-interpret features. Since cataloguing, predicting and understanding every GRN connection in all species and cellular contexts remains a great challenge for biology, researchers have developed numerous tools and methods to infer regulatory processes. In this review, we catalogue these methods in six major areas, based on the dominant underlying information leveraged to infer GRNs: Coexpression, Sequence Motifs, Chromatin Immunoprecipitation (ChIP), Orthology, Literature and Protein-Protein Interaction (PPI) specifically focused on transcriptional complexes. The methods described here cover a wide range of user-friendliness: from web tools that require no prior computational expertise to command line programs and algorithms for large scale GRN inferences. Each method for GRN inference described herein effectively illustrates a type of transcriptional relationship, with many methods being complementary to others. While a truly holistic approach for inferring and displaying GRNs remains one of the greatest challenges in the field of systems biology, we believe that the integration of multiple methods described herein provides an effective means with which experimental and computational biologists alike may obtain the most complete pictures of transcriptional relationships. This article is part of a Special Issue entitled: Transcriptional Profiles and Regulatory Gene Networks edited by Dr. Federico Manuel Giorgi and Dr. Shaun Mahony.
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Affiliation(s)
- Daniele Mercatelli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Laura Scalambra
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Luca Triboli
- Centre for Integrative Biology (CIBIO), University of Trento, Italy
| | - Forest Ray
- Department of Systems Biology, Columbia University Medical Center, New York, NY, United States
| | - Federico M Giorgi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.
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48
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Mukai J, Cannavò E, Crabtree GW, Sun Z, Diamantopoulou A, Thakur P, Chang CY, Cai Y, Lomvardas S, Takata A, Xu B, Gogos JA. Recapitulation and Reversal of Schizophrenia-Related Phenotypes in Setd1a-Deficient Mice. Neuron 2019; 104:471-487.e12. [PMID: 31606247 DOI: 10.1016/j.neuron.2019.09.014] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 07/28/2019] [Accepted: 09/10/2019] [Indexed: 12/15/2022]
Abstract
SETD1A, a lysine-methyltransferase, is a key schizophrenia susceptibility gene. Mice carrying a heterozygous loss-of-function mutation of the orthologous gene exhibit alterations in axonal branching and cortical synaptic dynamics accompanied by working memory deficits. We show that Setd1a binds both promoters and enhancers with a striking overlap between Setd1a and Mef2 on enhancers. Setd1a targets are highly expressed in pyramidal neurons and display a complex pattern of transcriptional up- and downregulations shaped by presumed opposing functions of Setd1a on promoters and Mef2-bound enhancers. Notably, evolutionarily conserved Setd1a targets are associated with neuropsychiatric genetic risk burden. Reinstating Setd1a expression in adulthood rescues cognitive deficits. Finally, we identify LSD1 as a major counteracting demethylase for Setd1a and show that its pharmacological antagonism results in a full rescue of the behavioral and morphological deficits in Setd1a-deficient mice. Our findings advance understanding of how SETD1A mutations predispose to schizophrenia (SCZ) and point to novel therapeutic interventions.
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Affiliation(s)
- Jun Mukai
- Department of Physiology and Cellular Biophysics, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA; Mortimer B. Zuckerman Mind Brain and Behavior Institute Columbia University, New York, NY 10027, USA
| | - Enrico Cannavò
- Mortimer B. Zuckerman Mind Brain and Behavior Institute Columbia University, New York, NY 10027, USA
| | - Gregg W Crabtree
- Department of Physiology and Cellular Biophysics, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA; Mortimer B. Zuckerman Mind Brain and Behavior Institute Columbia University, New York, NY 10027, USA
| | - Ziyi Sun
- Department of Physiology and Cellular Biophysics, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Anastasia Diamantopoulou
- Department of Physiology and Cellular Biophysics, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Pratibha Thakur
- Department of Physiology and Cellular Biophysics, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA; Mortimer B. Zuckerman Mind Brain and Behavior Institute Columbia University, New York, NY 10027, USA
| | - Chia-Yuan Chang
- Department of Physiology and Cellular Biophysics, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Yifei Cai
- Department of Physiology and Cellular Biophysics, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Stavros Lomvardas
- Mortimer B. Zuckerman Mind Brain and Behavior Institute Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA; Department of Neuroscience, Columbia University, New York, NY 10032, USA
| | - Atsushi Takata
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Fukuura 3-9, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Bin Xu
- Department of Psychiatry, Columbia University Medical Center, New York, NY 10032, USA
| | - Joseph A Gogos
- Department of Physiology and Cellular Biophysics, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA; Mortimer B. Zuckerman Mind Brain and Behavior Institute Columbia University, New York, NY 10027, USA; Department of Neuroscience, Columbia University, New York, NY 10032, USA.
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49
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Burgess SJ, Reyna-Llorens I, Stevenson SR, Singh P, Jaeger K, Hibberd JM. Genome-Wide Transcription Factor Binding in Leaves from C 3 and C 4 Grasses. THE PLANT CELL 2019; 31:2297-2314. [PMID: 31427470 PMCID: PMC6790085 DOI: 10.1105/tpc.19.00078] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 06/06/2019] [Accepted: 08/14/2019] [Indexed: 05/19/2023]
Abstract
The majority of plants use C3 photosynthesis, but over 60 independent lineages of angiosperms have evolved the C4 pathway. In most C4 species, photosynthesis gene expression is compartmented between mesophyll and bundle-sheath cells. We performed DNaseI sequencing to identify genome-wide profiles of transcription factor binding in leaves of the C4 grasses Zea mays, Sorghum bicolor, and Setaria italica as well as C3 Brachypodium distachyon In C4 species, while bundle-sheath strands and whole leaves shared similarity in the broad regions of DNA accessible to transcription factors, the short sequences bound varied. Transcription factor binding was prevalent in gene bodies as well as promoters, and many of these sites could represent duons that influence gene regulation in addition to amino acid sequence. Although globally there was little correlation between any individual DNaseI footprint and cell-specific gene expression, within individual species transcription factor binding to the same motifs in multiple genes provided evidence for shared mechanisms governing C4 photosynthesis gene expression. Furthermore, interspecific comparisons identified a small number of highly conserved transcription factor binding sites associated with leaves from species that diverged around 60 million years ago. These data therefore provide insight into the architecture associated with C4 photosynthesis gene expression in particular and characteristics of transcription factor binding in cereal crops in general.
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Affiliation(s)
- Steven J Burgess
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Ivan Reyna-Llorens
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Sean R Stevenson
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Pallavi Singh
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Katja Jaeger
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
| | - Julian M Hibberd
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
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50
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Musa J, Cidre-Aranaz F, Aynaud MM, Orth MF, Knott MML, Mirabeau O, Mazor G, Varon M, Hölting TLB, Grossetête S, Gartlgruber M, Surdez D, Gerke JS, Ohmura S, Marchetto A, Dallmayer M, Baldauf MC, Stein S, Sannino G, Li J, Romero-Pérez L, Westermann F, Hartmann W, Dirksen U, Gymrek M, Anderson ND, Shlien A, Rotblat B, Kirchner T, Delattre O, Grünewald TGP. Cooperation of cancer drivers with regulatory germline variants shapes clinical outcomes. Nat Commun 2019; 10:4128. [PMID: 31511524 PMCID: PMC6739408 DOI: 10.1038/s41467-019-12071-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 08/16/2019] [Indexed: 12/02/2022] Open
Abstract
Pediatric malignancies including Ewing sarcoma (EwS) feature a paucity of somatic alterations except for pathognomonic driver-mutations that cannot explain overt variations in clinical outcome. Here, we demonstrate in EwS how cooperation of dominant oncogenes and regulatory germline variants determine tumor growth, patient survival and drug response. Binding of the oncogenic EWSR1-FLI1 fusion transcription factor to a polymorphic enhancer-like DNA element controls expression of the transcription factor MYBL2 mediating these phenotypes. Whole-genome and RNA sequencing reveals that variability at this locus is inherited via the germline and is associated with variable inter-tumoral MYBL2 expression. High MYBL2 levels sensitize EwS cells for inhibition of its upstream activating kinase CDK2 in vitro and in vivo, suggesting MYBL2 as a putative biomarker for anti-CDK2-therapy. Collectively, we establish cooperation of somatic mutations and regulatory germline variants as a major determinant of tumor progression and highlight the importance of integrating the regulatory genome in precision medicine.
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Affiliation(s)
- Julian Musa
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Florencia Cidre-Aranaz
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Marie-Ming Aynaud
- INSERM U830, Équipe Labellisée LNCC Genetics and Biology of Pediatric Cancers, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France
| | - Martin F Orth
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Maximilian M L Knott
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
- Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Olivier Mirabeau
- INSERM U830, Équipe Labellisée LNCC Genetics and Biology of Pediatric Cancers, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France
| | - Gal Mazor
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Mor Varon
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Tilman L B Hölting
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Sandrine Grossetête
- INSERM U830, Équipe Labellisée LNCC Genetics and Biology of Pediatric Cancers, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France
| | - Moritz Gartlgruber
- Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Didier Surdez
- INSERM U830, Équipe Labellisée LNCC Genetics and Biology of Pediatric Cancers, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France
| | - Julia S Gerke
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Shunya Ohmura
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Aruna Marchetto
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Marlene Dallmayer
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Michaela C Baldauf
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Stefanie Stein
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Giuseppina Sannino
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Jing Li
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Laura Romero-Pérez
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Frank Westermann
- Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Wolfgang Hartmann
- Division of Translational Pathology, Gerhard-Domagk Institute of Pathology, University Hospital of Münster, Münster, Germany
| | - Uta Dirksen
- Department of Pediatric Hematology and Oncology, University Hospital of Essen, Essen, Germany
| | - Melissa Gymrek
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Nathaniel D Anderson
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Adam Shlien
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Barak Rotblat
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Thomas Kirchner
- Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
- German Cancer Consortium (DKTK), Partner site Munich, Munich, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Olivier Delattre
- INSERM U830, Équipe Labellisée LNCC Genetics and Biology of Pediatric Cancers, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France
| | - Thomas G P Grünewald
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany.
- Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany.
- German Cancer Consortium (DKTK), Partner site Munich, Munich, Germany.
- German Cancer Research Center (DKFZ), Heidelberg, Germany.
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