1
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Chandrashekar PB, Chen H, Lee M, Ahmadinejad N, Liu L. DeepCORE: An interpretable multi-view deep neural network model to detect co-operative regulatory elements. Comput Struct Biotechnol J 2024; 23:679-687. [PMID: 38292477 PMCID: PMC10825326 DOI: 10.1016/j.csbj.2023.12.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 12/14/2023] [Accepted: 12/27/2023] [Indexed: 02/01/2024] Open
Abstract
Gene transcription is an essential process involved in all aspects of cellular functions with significant impact on biological traits and diseases. This process is tightly regulated by multiple elements that co-operate to jointly modulate the transcription levels of target genes. To decipher the complicated regulatory network, we present a novel multi-view attention-based deep neural network that models the relationship between genetic, epigenetic, and transcriptional patterns and identifies co-operative regulatory elements (COREs). We applied this new method, named DeepCORE, to predict transcriptomes in various tissues and cell lines, which outperformed the state-of-the-art algorithms. Furthermore, DeepCORE contains an interpreter that extracts the attention values embedded in the deep neural network, maps the attended regions to putative regulatory elements, and infers COREs based on correlated attentions. The identified COREs are significantly enriched with known promoters and enhancers. Novel regulatory elements discovered by DeepCORE showed epigenetic signatures consistent with the status of histone modification marks.
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Affiliation(s)
- Pramod Bharadwaj Chandrashekar
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53076, USA
| | - Hai Chen
- College of Health Solutions, Arizona State University, Phoenix, AZ, United States
- Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Matthew Lee
- College of Health Solutions, Arizona State University, Phoenix, AZ, United States
| | - Navid Ahmadinejad
- College of Health Solutions, Arizona State University, Phoenix, AZ, United States
- Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Li Liu
- College of Health Solutions, Arizona State University, Phoenix, AZ, United States
- Biodesign Institute, Arizona State University, Tempe, AZ, United States
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2
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He Y, Xu D, Zhang J, Liu Y, Liao M, Xia Y, Wei Z, Dai Y. Bergenin, the main active ingredient of Bergenia purpurascens, attenuates Th17 cell differentiation by downregulating fatty acid synthesis. FASEB J 2024; 38:e70095. [PMID: 39373984 DOI: 10.1096/fj.202400961r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 09/12/2024] [Accepted: 09/24/2024] [Indexed: 10/08/2024]
Abstract
Bergenin is the main active ingredient of Bergenia purpurascens, a medicinal plant which has long been used to treat a variety of Th17 cell-related diseases in China, such as allergic airway inflammation and colitis. This study aimed to uncover the underlying mechanisms by which bergenin impedes Th17 cell response in view of cellular metabolism. In vitro, bergenin treatment reduced the frequency of Th17 cells generated from naïve CD4+ T cells of mice. Mechanistically, bergenin preferentially restrained fatty acid synthesis (FAS) but not other metabolic pathways in differentiating Th17 cells, and exogenous addition of either palmitic acid (PA) or oleic acid (OA) and combination with acetyl-CoA carboxylase 1 (ACC1) activator citric acid dampened the inhibition of bergenin on Th17 cell differentiation. Bergenin inhibited FAS through downregulating the expression of SREBP1 via restriction of histone H3K27 acetylation in the SREBP1 promoter, and SREBP1 overexpression weakened the inhibition of bergenin on Th17 differentiation. Furthermore, bergenin was shown to directly interact with SIRT1 and result in activation of SIRT1. Either combination with SIRT1 inhibitor EX527 or point mutation plasmid of SIRT1 diminished the inhibitory effect of bergenin on FAS and Th17 cell differentiation. Finally, the inhibitory effect of bergenin on Th17 cell response and SIRT1 dependence were verified in mice with dextran sulfate sodium-induced colitis. In short, bergenin repressed Th17 cell response by downregulating FAS via activation of SIRT1, which might find therapeutic use in Th17 cell-related diseases.
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Affiliation(s)
- Yue He
- Department of Pharmacology of Chinese Materia Medica, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Danlei Xu
- Department of Pharmacology of Chinese Materia Medica, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Jing Zhang
- Department of Pharmacognosy, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Yan Liu
- Department of Pharmacology of Chinese Materia Medica, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Minghui Liao
- Department of Pharmacology of Chinese Materia Medica, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Yufeng Xia
- Department of Pharmacognosy, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Zhifeng Wei
- Department of Pharmacology of Chinese Materia Medica, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Yue Dai
- Department of Pharmacology of Chinese Materia Medica, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
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3
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Hossain I, Priam P, Reynoso SC, Sahni S, Zhang XX, Côté L, Doumat J, Chik C, Fu T, Lessard JA, Pastor WA. ZIC2 and ZIC3 promote SWI/SNF recruitment to safeguard progression towards human primed pluripotency. Nat Commun 2024; 15:8539. [PMID: 39358345 PMCID: PMC11447223 DOI: 10.1038/s41467-024-52431-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 09/03/2024] [Indexed: 10/04/2024] Open
Abstract
The primed epiblast acts as a transitional stage between the relatively homogeneous naïve epiblast and the gastrulating embryo. Its formation entails coordinated changes in regulatory circuits driven by transcription factors and epigenetic modifications. Using a multi-omic approach in human embryonic stem cell models across the spectrum of peri-implantation development, we demonstrate that the transcription factors ZIC2 and ZIC3 have overlapping but essential roles in opening primed-specific enhancers. Together, they are essential to facilitate progression to and maintain primed pluripotency. ZIC2/3 accomplish this by recruiting SWI/SNF to chromatin and loss of ZIC2/3 or degradation of SWI/SNF both prevent enhancer activation. Loss of ZIC2/3 also results in transcriptome changes consistent with perturbed Polycomb activity and a shift towards the expression of genes linked to differentiation towards the mesendoderm. Additionally, we find an intriguing dependency on the transcriptional machinery for sustained recruitment of ZIC2/3 over a subset of primed-hESC specific enhancers. Taken together, ZIC2 and ZIC3 regulate highly dynamic lineage-specific enhancers and collectively act as key regulators of human primed pluripotency.
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Affiliation(s)
| | - Pierre Priam
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC, Canada
- Department of Pathology and Cellular Biology, Faculty of Medicine, University of Montreal, Montreal, QC, Canada
| | - Sofia C Reynoso
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Sahil Sahni
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Xiao X Zhang
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Laurence Côté
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC, Canada
- Department of Pathology and Cellular Biology, Faculty of Medicine, University of Montreal, Montreal, QC, Canada
| | - Joelle Doumat
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Candus Chik
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Tianxin Fu
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Julie A Lessard
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC, Canada
- Department of Pathology and Cellular Biology, Faculty of Medicine, University of Montreal, Montreal, QC, Canada
| | - William A Pastor
- Department of Biochemistry, McGill University, Montreal, QC, Canada.
- The Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, QC, Canada.
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4
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Zaraisky AG, Araslanova KR, Shitikov AD, Tereshina MB. Loss of the ability to regenerate body appendages in vertebrates: from side effects of evolutionary innovations to gene loss. Biol Rev Camb Philos Soc 2024; 99:1868-1888. [PMID: 38817123 DOI: 10.1111/brv.13102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 05/04/2024] [Accepted: 05/14/2024] [Indexed: 06/01/2024]
Abstract
The ability to regenerate large body appendages is an ancestral trait of vertebrates, which varies across different animal groups. While anamniotes (fish and amphibians) commonly possess this ability, it is notably restricted in amniotes (reptiles, birds, and mammals). In this review, we explore the factors contributing to the loss of regenerative capabilities in amniotes. First, we analyse the potential negative impacts on appendage regeneration caused by four evolutionary innovations: advanced immunity, skin keratinization, whole-body endothermy, and increased body size. These innovations emerged as amniotes transitioned to terrestrial habitats and were correlated with a decline in regeneration capability. Second, we examine the role played by the loss of regeneration-related enhancers and genes initiated by these innovations in the fixation of an inability to regenerate body appendages at the genomic level. We propose that following the cessation of regenerative capacity, the loss of highly specific regeneration enhancers could represent an evolutionarily neutral event. Consequently, the loss of such enhancers might promptly follow the suppression of regeneration as a side effect of evolutionary innovations. By contrast, the loss of regeneration-related genes, due to their pleiotropic functions, would only take place if such loss was accompanied by additional evolutionary innovations that compensated for the loss of pleiotropic functions unrelated to regeneration, which would remain even after participation of these genes in regeneration was lost. Through a review of the literature, we provide evidence that, in many cases, the loss in amniotes of genes associated with body appendage regeneration in anamniotes was significantly delayed relative to the time when regenerative capability was lost. We hypothesise that this delay may be attributed to the necessity for evolutionary restructuring of developmental mechanisms to create conditions where the loss of these genes was a beneficial innovation for the organism. Experimental investigation of the downregulation of genes involved in the regeneration of body appendages in anamniotes but absent in amniotes offers a promising avenue to uncover evolutionary innovations that emerged from the loss of these genes. We propose that the vast majority of regeneration-related genes lost in amniotes (about 150 in humans) may be involved in regulating the early stages of limb and tail regeneration in anamniotes. Disruption of this stage, rather than the late stage, may not interfere with the mechanisms of limb and tail bud development during embryogenesis, as these mechanisms share similarities with those operating in the late stage of regeneration. Consequently, the most promising approach to restoring regeneration in humans may involve creating analogs of embryonic limb buds using stem cell-based tissue-engineering methods, followed by their transfer to the amputation stump. Due to the loss of many genes required specifically during the early stage of regeneration, this approach may be more effective than attempting to induce both early and late stages of regeneration directly in the stump itself.
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Affiliation(s)
- Andrey G Zaraisky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya str., Moscow, 117997, Russia
- Pirogov Russian National Research Medical University, 1 Ostrovityanova str., Moscow, 117997, Russia
| | - Karina R Araslanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya str., Moscow, 117997, Russia
| | - Alexander D Shitikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya str., Moscow, 117997, Russia
| | - Maria B Tereshina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya str., Moscow, 117997, Russia
- Pirogov Russian National Research Medical University, 1 Ostrovityanova str., Moscow, 117997, Russia
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5
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Lercher A, Cheong JG, Bale MJ, Jiang C, Hoffmann HH, Ashbrook AW, Lewy T, Yin YS, Quirk C, DeGrace EJ, Chiriboga L, Rosenberg BR, Josefowicz SZ, Rice CM. Antiviral innate immune memory in alveolar macrophages following SARS-CoV-2 infection ameliorates secondary influenza A virus disease. Immunity 2024:S1074-7613(24)00417-5. [PMID: 39353439 DOI: 10.1016/j.immuni.2024.08.018] [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: 08/02/2023] [Revised: 05/16/2024] [Accepted: 08/28/2024] [Indexed: 10/04/2024]
Abstract
Pathogen encounter can result in epigenetic remodeling that shapes disease caused by heterologous pathogens. Here, we examined innate immune memory in the context of commonly circulating respiratory viruses. Single-cell analyses of airway-resident immune cells in a disease-relevant murine model of SARS-CoV-2 recovery revealed epigenetic reprogramming in alveolar macrophages following infection. Post-COVID-19 human monocytes exhibited similar epigenetic signatures. In airway-resident macrophages, past SARS-CoV-2 infection increased activity of type I interferon (IFN-I)-related transcription factors and epigenetic poising of antiviral genes. Viral pattern recognition and canonical IFN-I signaling were required for the establishment of this innate immune memory and augmented secondary antiviral responses. Antiviral innate immune memory mounted by airway-resident macrophages post-SARS-CoV-2 was necessary and sufficient to ameliorate secondary disease caused by influenza A virus and curtailed hyperinflammatory dysregulation and mortality. Our findings provide insights into antiviral innate immune memory in the airway that may facilitate the development of broadly effective therapeutic strategies.
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Affiliation(s)
- Alexander Lercher
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA.
| | - Jin-Gyu Cheong
- Department of Pathology and Laboratory Medicine, Laboratory of Epigenetics and Immunity, Weill Cornell Medicine, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, NY 10065, USA
| | - Michael J Bale
- Department of Pathology and Laboratory Medicine, Laboratory of Epigenetics and Immunity, Weill Cornell Medicine, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, NY 10065, USA
| | - Chenyang Jiang
- Department of Pathology and Laboratory Medicine, Laboratory of Epigenetics and Immunity, Weill Cornell Medicine, New York, NY 10065, USA; BCMB Allied Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA
| | - Hans-Heinrich Hoffmann
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Alison W Ashbrook
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Tyler Lewy
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Yue S Yin
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Corrine Quirk
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Emma J DeGrace
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Luis Chiriboga
- Department of Pathology, New York University Medical Center, New York, NY 10016, USA; Center for Biospecimen Research and Development, New York, NY 10016, USA
| | - Brad R Rosenberg
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Steven Z Josefowicz
- Department of Pathology and Laboratory Medicine, Laboratory of Epigenetics and Immunity, Weill Cornell Medicine, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, NY 10065, USA.
| | - Charles M Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA.
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6
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Griffith EC, West AE, Greenberg ME. Neuronal enhancers fine-tune adaptive circuit plasticity. Neuron 2024; 112:3043-3057. [PMID: 39208805 DOI: 10.1016/j.neuron.2024.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 07/22/2024] [Accepted: 08/06/2024] [Indexed: 09/04/2024]
Abstract
Neuronal activity-regulated gene expression plays a crucial role in sculpting neural circuits that underpin adaptive brain function. Transcriptional enhancers are now recognized as key components of gene regulation that orchestrate spatiotemporally precise patterns of gene transcription. We propose that the dynamics of enhancer activation uniquely position these genomic elements to finely tune activity-dependent cellular plasticity. Enhancer specificity and modularity can be exploited to gain selective genetic access to specific cell states, and the precise modulation of target gene expression within restricted cellular contexts enabled by targeted enhancer manipulation allows for fine-grained evaluation of gene function. Mounting evidence also suggests that enduring stimulus-induced changes in enhancer states can modify target gene activation upon restimulation, thereby contributing to a form of cell-wide metaplasticity. We advocate for focused exploration of activity-dependent enhancer function to gain new insight into the mechanisms underlying brain plasticity and cognitive dysfunction.
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Affiliation(s)
- Eric C Griffith
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Anne E West
- Department of Neurobiology, Duke University Medical Center, Durham, NC, USA.
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7
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Inge M, Miller R, Hook H, Bray D, Keenan J, Zhao R, Gilmore T, Siggers T. Rapid profiling of transcription factor-cofactor interaction networks reveals principles of epigenetic regulation. Nucleic Acids Res 2024; 52:10276-10296. [PMID: 39166482 PMCID: PMC11417405 DOI: 10.1093/nar/gkae706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 06/14/2024] [Accepted: 08/19/2024] [Indexed: 08/23/2024] Open
Abstract
Transcription factor (TF)-cofactor (COF) interactions define dynamic, cell-specific networks that govern gene expression; however, these networks are understudied due to a lack of methods for high-throughput profiling of DNA-bound TF-COF complexes. Here, we describe the Cofactor Recruitment (CoRec) method for rapid profiling of cell-specific TF-COF complexes. We define a lysine acetyltransferase (KAT)-TF network in resting and stimulated T cells. We find promiscuous recruitment of KATs for many TFs and that 35% of KAT-TF interactions are condition specific. KAT-TF interactions identify NF-κB as a primary regulator of acutely induced histone 3 lysine 27 acetylation (H3K27ac). Finally, we find that heterotypic clustering of CBP/P300-recruiting TFs is a strong predictor of total promoter H3K27ac. Our data support clustering of TF sites that broadly recruit KATs as a mechanism for widespread co-occurring histone acetylation marks. CoRec can be readily applied to different cell systems and provides a powerful approach to define TF-COF networks impacting chromatin state and gene regulation.
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Affiliation(s)
- Melissa M Inge
- Department of Biology, Boston University, Boston, MA 02215, USA
- Biological Design Center, Boston University, Boston, MA 02215, USA
| | - Rebekah Miller
- Department of Biology, Boston University, Boston, MA 02215, USA
- Biological Design Center, Boston University, Boston, MA 02215, USA
- Bioinformatics Program, Boston University, Boston, MA 02215, USA
| | - Heather Hook
- Department of Biology, Boston University, Boston, MA 02215, USA
| | - David Bray
- Department of Biology, Boston University, Boston, MA 02215, USA
- Bioinformatics Program, Boston University, Boston, MA 02215, USA
| | - Jessica L Keenan
- Department of Biology, Boston University, Boston, MA 02215, USA
- Bioinformatics Program, Boston University, Boston, MA 02215, USA
| | - Rose Zhao
- Department of Biology, Boston University, Boston, MA 02215, USA
| | | | - Trevor Siggers
- Department of Biology, Boston University, Boston, MA 02215, USA
- Biological Design Center, Boston University, Boston, MA 02215, USA
- Bioinformatics Program, Boston University, Boston, MA 02215, USA
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8
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Johansen NJ, Kempynck N, Zemke NR, Somasundaram S, De Winter S, Hooper M, Dwivedi D, Lohia R, Wehbe F, Li B, Abaffyová D, Armand EJ, De Man J, Eksi EC, Hecker N, Hulselmans G, Konstantakos V, Mauduit D, Mich JK, Partel G, Daigle TL, Levi BP, Zhang K, Tanaka Y, Gillis J, Ting JT, Ben-Simon Y, Miller J, Ecker JR, Ren B, Aerts S, Lein ES, Tasic B, Bakken TE. Evaluating Methods for the Prediction of Cell Type-Specific Enhancers in the Mammalian Cortex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.21.609075. [PMID: 39229027 PMCID: PMC11370467 DOI: 10.1101/2024.08.21.609075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Identifying cell type-specific enhancers in the brain is critical to building genetic tools for investigating the mammalian brain. Computational methods for functional enhancer prediction have been proposed and validated in the fruit fly and not yet the mammalian brain. We organized the 'Brain Initiative Cell Census Network (BICCN) Challenge: Predicting Functional Cell Type-Specific Enhancers from Cross-Species Multi-Omics' to assess machine learning and feature-based methods designed to nominate enhancer DNA sequences to target cell types in the mouse cortex. Methods were evaluated based on in vivo validation data from hundreds of cortical cell type-specific enhancers that were previously packaged into individual AAV vectors and retro-orbitally injected into mice. We find that open chromatin was a key predictor of functional enhancers, and sequence models improved prediction of non-functional enhancers that can be deprioritized as opposed to pursued for in vivo testing. Sequence models also identified cell type-specific transcription factor codes that can guide designs of in silico enhancers. This community challenge establishes a benchmark for enhancer prioritization algorithms and reveals computational approaches and molecular information that are crucial for the identification of functional enhancers for mammalian cortical cell types. The results of this challenge bring us closer to understanding the complex gene regulatory landscape of the mammalian brain and help us design more efficient genetic tools and potential gene therapies for human neurological diseases.
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Affiliation(s)
- Nelson J Johansen
- Allen Institute for Brain Science, Seattle, WA 98109
- These authors contributed equally
| | - Niklas Kempynck
- VIB Center for AI & Computational Biology, VIB-KU Leuven Center for Brain and Disease Research & KU Leuven Department of Human Genetics, Leuven, Belgium
- These authors contributed equally
| | - Nathan R Zemke
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093
| | | | - Seppe De Winter
- VIB Center for AI & Computational Biology, VIB-KU Leuven Center for Brain and Disease Research & KU Leuven Department of Human Genetics, Leuven, Belgium
| | - Marcus Hooper
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | - Ruchi Lohia
- Physiology Department and Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Fabien Wehbe
- Maisonneuve-Rosemont Hospital Research Centre, University of Montreal, Montreal, Quebec, Canada
| | - Bocheng Li
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Darina Abaffyová
- VIB Center for AI & Computational Biology, VIB-KU Leuven Center for Brain and Disease Research & KU Leuven Department of Human Genetics, Leuven, Belgium
| | - Ethan J Armand
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA 92093
| | - Julie De Man
- VIB Center for AI & Computational Biology, VIB-KU Leuven Center for Brain and Disease Research & KU Leuven Department of Human Genetics, Leuven, Belgium
| | - Eren Can Eksi
- VIB Center for AI & Computational Biology, VIB-KU Leuven Center for Brain and Disease Research & KU Leuven Department of Human Genetics, Leuven, Belgium
| | - Nikolai Hecker
- VIB Center for AI & Computational Biology, VIB-KU Leuven Center for Brain and Disease Research & KU Leuven Department of Human Genetics, Leuven, Belgium
| | - Gert Hulselmans
- VIB Center for AI & Computational Biology, VIB-KU Leuven Center for Brain and Disease Research & KU Leuven Department of Human Genetics, Leuven, Belgium
| | - Vasilis Konstantakos
- VIB Center for AI & Computational Biology, VIB-KU Leuven Center for Brain and Disease Research & KU Leuven Department of Human Genetics, Leuven, Belgium
| | - David Mauduit
- VIB Center for AI & Computational Biology, VIB-KU Leuven Center for Brain and Disease Research & KU Leuven Department of Human Genetics, Leuven, Belgium
| | - John K Mich
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Gabriele Partel
- VIB Center for AI & Computational Biology, VIB-KU Leuven Center for Brain and Disease Research & KU Leuven Department of Human Genetics, Leuven, Belgium
| | | | - Boaz P Levi
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Kai Zhang
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
| | - Yoshiaki Tanaka
- Maisonneuve-Rosemont Hospital Research Centre, University of Montreal, Montreal, Quebec, Canada
| | - Jesse Gillis
- Physiology Department and Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Jonathan T Ting
- Allen Institute for Brain Science, Seattle, WA 98109
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195
| | | | - Jeremy Miller
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Joseph R Ecker
- Salk Institute for Biological Studies, La Jolla, CA 92037
| | - Bing Ren
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093
| | - Stein Aerts
- VIB Center for AI & Computational Biology, VIB-KU Leuven Center for Brain and Disease Research & KU Leuven Department of Human Genetics, Leuven, Belgium
| | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | - Trygve E Bakken
- Allen Institute for Brain Science, Seattle, WA 98109
- Lead contact
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9
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Ivanković M, Brand JN, Pandolfini L, Brown T, Pippel M, Rozanski A, Schubert T, Grohme MA, Winkler S, Robledillo L, Zhang M, Codino A, Gustincich S, Vila-Farré M, Zhang S, Papantonis A, Marques A, Rink JC. A comparative analysis of planarian genomes reveals regulatory conservation in the face of rapid structural divergence. Nat Commun 2024; 15:8215. [PMID: 39294119 PMCID: PMC11410931 DOI: 10.1038/s41467-024-52380-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 08/30/2024] [Indexed: 09/20/2024] Open
Abstract
The planarian Schmidtea mediterranea is being studied as a model species for regeneration, but the assembly of planarian genomes remains challenging. Here, we report a high-quality haplotype-phased, chromosome-scale genome assembly of the sexual S2 strain of S. mediterranea and high-quality chromosome-scale assemblies of its three close relatives, S. polychroa, S. nova, and S. lugubris. Using hybrid gene annotations and optimized ATAC-seq and ChIP-seq protocols for regulatory element annotation, we provide valuable genome resources for the planarian research community and a first comparative perspective on planarian genome evolution. Our analyses reveal substantial divergence in protein-coding sequences and regulatory regions but considerable conservation within promoter and enhancer annotations. We also find frequent retrotransposon-associated chromosomal inversions and interchromosomal translocations within the genus Schmidtea and, remarkably, independent and nearly complete losses of ancestral metazoan synteny in Schmidtea and two other flatworm groups. Overall, our results suggest that platyhelminth genomes can evolve without syntenic constraints.
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Affiliation(s)
- Mario Ivanković
- Department of Tissue Dynamics and Regeneration, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Jeremias N Brand
- Department of Tissue Dynamics and Regeneration, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Luca Pandolfini
- Center for Human Technologies, Non-coding RNA and RNA-based therapeutics, Istituto Italiano di Tecnologia, Genova, Italy
| | - Thomas Brown
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Martin Pippel
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Andrei Rozanski
- Department of Tissue Dynamics and Regeneration, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Til Schubert
- Department of Tissue Dynamics and Regeneration, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Markus A Grohme
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Sylke Winkler
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Laura Robledillo
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Meng Zhang
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Azzurra Codino
- Center for Human Technologies, Non-coding RNA and RNA-based therapeutics, Istituto Italiano di Tecnologia, Genova, Italy
| | - Stefano Gustincich
- Center for Human Technologies, Non-coding RNA and RNA-based therapeutics, Istituto Italiano di Tecnologia, Genova, Italy
| | - Miquel Vila-Farré
- Department of Tissue Dynamics and Regeneration, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Shu Zhang
- Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany
| | - Argyris Papantonis
- Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany
| | - André Marques
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Jochen C Rink
- Department of Tissue Dynamics and Regeneration, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
- Faculty of Biology und Psychology, Georg-August-University Göttingen, Göttingen, Germany.
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10
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Henry B, Phillips AJ, Sibley LD, Rosenberg A. A combination of four Toxoplasma gondii nuclear-targeted effectors protects against interferon gamma-driven human host cell death. mBio 2024:e0212424. [PMID: 39292011 DOI: 10.1128/mbio.02124-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2024] [Accepted: 08/20/2024] [Indexed: 09/19/2024] Open
Abstract
In both mice and humans, Type II interferon gamma (IFNγ) is crucial for the regulation of Toxoplasma gondii (T. gondii) infection, during acute or chronic phases. To thwart this defense, T. gondii secretes protein effectors hindering the host's immune response. For example, T. gondii relies on the MYR translocon complex to deploy soluble dense granule effectors (GRAs) into the host cell cytosol or nucleus. Recent genome-wide loss-of-function screens in IFNγ-primed primary human fibroblasts identified MYR translocon components as crucial for parasite resistance against IFNγ-driven vacuole clearance. However, these screens did not pinpoint specific MYR-dependent GRA proteins responsible for IFNγ signaling blockade, suggesting potential functional redundancy. Our study reveals that T. gondii depends on the MYR translocon complex to prevent parasite premature egress and host cell death in human cells stimulated with IFNγ post-infection, a unique phenotype observed in various human cell lines but not in murine cells. Intriguingly, inhibiting parasite egress did not prevent host cell death, indicating this mechanism is distinct from those described previously. Genome-wide loss-of-function screens uncovered TgIST, GRA16, GRA24, and GRA28 as effectors necessary for a complete block of IFNγ response. GRA24 and GRA28 directly influenced IFNγ-driven transcription, GRA24's action depended on its interaction with p38 MAPK, while GRA28 disrupted histone acetyltransferase activity of CBP/p300. Given the intricate nature of the immune response to T. gondii, it appears that the parasite has evolved equally elaborate mechanisms to subvert IFNγ signaling, extending beyond direct interference with the JAK/STAT1 pathway, to encompass other signaling pathways as well.IMPORTANCEToxoplasma gondii, an intracellular parasite, affects nearly one-third of the global human population, posing significant risks for immunocompromised patients and infants infected in utero. In murine models, the core mechanisms of IFNγ-mediated immunity against T. gondii are consistently preserved, showcasing a remarkable conservation of immune defense mechanisms. In humans, the recognized restriction mechanisms vary among cell types, lacking a universally applicable mechanism. This difference underscores a significant variation in the genes employed by T. gondii to shield itself against the IFNγ response in human vs murine cells. Here, we identified a specific combination of four parasite-secreted effectors deployed into the host cell nucleus, disrupting IFNγ signaling. This disruption is crucial in preventing premature egress of the parasite and host cell death. Notably, this phenotype is exclusive to human cells, highlighting the intricate and unique mechanisms T. gondii employs to modulate host responses in the human cellular environment.
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Affiliation(s)
- Brittany Henry
- Department of Infectious Diseases, Center for Tropical and Emerging Infectious Diseases, University of Georgia, Athens, Georgia, USA
| | - Aubrey J Phillips
- Department of Infectious Diseases, Center for Tropical and Emerging Infectious Diseases, University of Georgia, Athens, Georgia, USA
| | - L David Sibley
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Alex Rosenberg
- Department of Infectious Diseases, Center for Tropical and Emerging Infectious Diseases, University of Georgia, Athens, Georgia, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
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11
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Zhang T, Zou L. Enhancers in T Cell development and malignant lesions. Cell Death Discov 2024; 10:406. [PMID: 39284807 PMCID: PMC11405840 DOI: 10.1038/s41420-024-02160-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Revised: 08/20/2024] [Accepted: 08/22/2024] [Indexed: 09/19/2024] Open
Abstract
Enhancers constitute a vital category of cis-regulatory elements with a Mediator complex within DNA sequences, orchestrating gene expression by activating promoters. In the development of T cells, some enhancers regulate the critical genes, which might also regulate T cell malignant lesions. This review is to comprehensively elucidate the contributions of enhancers in both normal T cell development and its malignant pathogenesis, proposing the idea that the precise subunits of the Mediator complex are the potential drug target for disrupting the specific gene enhancer for T cell malignant diseases.
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Affiliation(s)
- Tong Zhang
- Clinical Medicine Research Department, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200062, China.
- Postgraduate School in Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Lin Zou
- Clinical Medicine Research Department, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200062, China.
- Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200062, China.
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12
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Wang L, Baek S, Prasad G, Wildenthal J, Guo K, Sturgill D, Truongvo T, Char E, Pegoraro G, McKinnon K, Hoskins JW, Amundadottir LT, Arda HE. Predictive Prioritization of Enhancers Associated with Pancreas Disease Risk. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.07.611794. [PMID: 39314336 PMCID: PMC11418953 DOI: 10.1101/2024.09.07.611794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Genetic and epigenetic variations in regulatory enhancer elements increase susceptibility to a range of pathologies. Despite recent advances, linking enhancer elements to target genes and predicting transcriptional outcomes of enhancer dysfunction remain significant challenges. Using 3D chromatin conformation assays, we generated an extensive enhancer interaction dataset for the human pancreas, encompassing more than 20 donors and five major cell types, including both exocrine and endocrine compartments. We employed a network approach to parse chromatin interactions into enhancer-promoter tree models, facilitating a quantitative, genome-wide analysis of enhancer connectivity. With these tree models, we developed a machine learning algorithm to estimate the impact of enhancer perturbations on cell type-specific gene expression in the human pancreas. Orthogonal to our computational approach, we perturbed enhancer function in primary human pancreas cells using CRISPR interference and quantified the effects at the single-cell level through RNA FISH coupled with high-throughput imaging. Our enhancer tree models enabled the annotation of common germline risk variants associated with pancreas diseases, linking them to putative target genes in specific cell types. For pancreatic ductal adenocarcinoma, we found a stronger enrichment of disease susceptibility variants within acinar cell regulatory elements, despite ductal cells historically being assumed as the primary cell-of-origin. Our integrative approach-combining cell type-specific enhancer-promoter interaction mapping, computational models, and single-cell enhancer perturbation assays-produced a robust resource for studying the genetic basis of pancreas disorders.
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Affiliation(s)
- Li Wang
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Songjoon Baek
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gauri Prasad
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Laboratory of Translational Genomics, Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - John Wildenthal
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Konnie Guo
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David Sturgill
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Thucnhi Truongvo
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Erin Char
- Laboratory of Translational Genomics, Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gianluca Pegoraro
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Katherine McKinnon
- Vaccine Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | | | - Jason W. Hoskins
- Laboratory of Translational Genomics, Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Laufey T. Amundadottir
- Laboratory of Translational Genomics, Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - H. Efsun Arda
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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13
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Song C, Zhang Z, Leng D, He Z, Wang X, Liu W, Zhang W, Wu Q, Zhao Q, Chen G. ERK5 promotes autocrine expression to sustain mitogenic balance for cell fate specification in human pluripotent stem cells. Stem Cell Reports 2024; 19:1320-1335. [PMID: 39151429 PMCID: PMC11411316 DOI: 10.1016/j.stemcr.2024.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 07/21/2024] [Accepted: 07/22/2024] [Indexed: 08/19/2024] Open
Abstract
The homeostasis of human pluripotent stem cells (hPSCs) requires the signaling balance of extracellular factors. Exogenous regulators from cell culture medium have been widely reported, but little attention has been paid to the autocrine factor from hPSCs themselves. In this report, we demonstrate that extracellular signal-related kinase 5 (ERK5) regulates endogenous autocrine factors essential for pluripotency and differentiation. ERK5 inhibition leads to erroneous cell fate specification in all lineages even under lineage-specific induction. hPSCs can self-renew under ERK5 inhibition in the presence of fibroblast growth factor 2 (FGF2) and transforming growth factor β (TGF-β), although NANOG expression is partially suppressed. Further analysis demonstrates that ERK5 promotes the expression of autocrine factors such as NODAL, FGF8, and WNT3. The addition of NODAL protein rescues NANOG expression and differentiation phenotypes under ERK5 inhibition. We demonstrate that constitutively active ERK5 pathway allows self-renewal even without essential growth factors FGF2 and TGF-β. This study highlights the essential contribution of autocrine pathways to proper maintenance and differentiation.
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Affiliation(s)
- Chengcheng Song
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macau, China; Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Zhaoying Zhang
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macau, China; Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Dongliang Leng
- Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Ziqing He
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macau, China; Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Xuepeng Wang
- The State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macau, China; CAM-SU Genomic Resource Center, Soochow University, Suzhou, Jiangsu, China
| | - Weiwei Liu
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macau, China; Faculty of Health Sciences, University of Macau, Taipa, Macau, China; Biological Imaging and Stem Cell Core Facility, Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Wensheng Zhang
- CAM-SU Genomic Resource Center, Soochow University, Suzhou, Jiangsu, China
| | - Qiang Wu
- The State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macau, China
| | - Qi Zhao
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macau, China; Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Guokai Chen
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macau, China; Faculty of Health Sciences, University of Macau, Taipa, Macau, China; Zhuhai UM Science & Technology Research Institute, Zhuhai, China.
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14
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Cantarella S, Vezzoli M, Carnevali D, Morselli M, Zemke NR, Montanini B, Daussy CF, Wodrich H, Teichmann M, Pellegrini M, Berk AJ, Dieci G, Ferrari R. Adenovirus small E1A directs activation of Alu transcription at YAP/TEAD- and AP-1-bound enhancers through interactions with the EP400 chromatin remodeler. Nucleic Acids Res 2024; 52:9481-9500. [PMID: 39011896 PMCID: PMC11381368 DOI: 10.1093/nar/gkae615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 04/29/2024] [Accepted: 07/02/2024] [Indexed: 07/17/2024] Open
Abstract
Alu retrotransposons, which form the largest family of mobile DNA elements in the human genome, have recently come to attention as a potential source of regulatory novelties, most notably by participating in enhancer function. Even though Alu transcription by RNA polymerase III is subjected to tight epigenetic silencing, their expression has long been known to increase in response to various types of stress, including viral infection. Here we show that, in primary human fibroblasts, adenovirus small e1a triggered derepression of hundreds of individual Alus by promoting TFIIIB recruitment by Alu-bound TFIIIC. Epigenome profiling revealed an e1a-induced decrease of H3K27 acetylation and increase of H3K4 monomethylation at derepressed Alus, making them resemble poised enhancers. The enhancer nature of e1a-targeted Alus was confirmed by the enrichment, in their upstream regions, of the EP300/CBP acetyltransferase, EP400 chromatin remodeler and YAP1 and FOS transcription factors. The physical interaction of e1a with EP400 was critical for Alu derepression, which was abrogated upon EP400 ablation. Our data suggest that e1a targets a subset of enhancer Alus whose transcriptional activation, which requires EP400 and is mediated by the e1a-EP400 interaction, may participate in the manipulation of enhancer activity by adenoviruses.
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Affiliation(s)
- Simona Cantarella
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Marco Vezzoli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Davide Carnevali
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Marco Morselli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Nathan R Zemke
- Molecular Biology Institute, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Barbara Montanini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Coralie F Daussy
- Bordeaux University, CNRS UMR 5234, Fundamental Microbiology and Pathogenicity, Bordeaux, France
| | - Harald Wodrich
- Bordeaux University, CNRS UMR 5234, Fundamental Microbiology and Pathogenicity, Bordeaux, France
| | - Martin Teichmann
- Bordeaux University, Inserm U 1312, Bordeaux Institute of Oncology, 33076 Bordeaux, France
| | - Matteo Pellegrini
- Department of Molecular Cellular and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Arnold J Berk
- Molecular Biology Institute, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Giorgio Dieci
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Roberto Ferrari
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
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15
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Li X, Hu Z, Shi Q, Qiu W, Liu Y, Liu Y, Huang S, Liang L, Chen Z, He X. Elevated choline drives KLF5-dominated transcriptional reprogramming to facilitate liver cancer progression. Oncogene 2024:10.1038/s41388-024-03150-w. [PMID: 39251845 DOI: 10.1038/s41388-024-03150-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 08/28/2024] [Accepted: 08/30/2024] [Indexed: 09/11/2024]
Abstract
An increase in the total choline-containing compound content is a common characteristic of cancer cells, and aberrant choline metabolism in cancer is closely associated with malignant progression. However, the potential role of choline-induced global transcriptional changes in cancer cells remains unclear. In this study, we reveal that an elevated choline content facilitates hepatocellular carcinoma (HCC) cell proliferation by reprogramming Krüppel-like factor 5 (KLF5)-dominated core transcriptional regulatory circuitry (CRC). Mechanistically, choline administration leads to elevated S-adenosylmethionine (SAM) levels, inducing the formation of H3K4me1 within the super-enhancer (SE) region of KLF5 and activating its transcription. KLF5, as a key transcription factor (TF) of CRC established by choline, further transactivates downstream genes to facilitate HCC cell cycle progression. Additionally, KLF5 can increase the expression of choline kinase-α (CHKA) and CTP:phosphocholine cytidylyltransferase (CCT) resulting in a positive feedback loop to promote HCC cell proliferation. Notably, the histone deacetylase inhibitor (HDACi) vorinostat (SAHA) significantly suppressed KLF5 expression and liver tumor growth in mice, leading to a prolonged lifespan. In conclusion, these findings highlight the epigenetic regulatory mechanism of the SE-driven key regulatory factor KLF5 conducted by choline metabolism in HCC and suggest a potential therapeutic strategy for HCC patients with high choline content.
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Affiliation(s)
- Xinrong Li
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhixiang Hu
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Qili Shi
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wenying Qiu
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yizhe Liu
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yanfang Liu
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shenglin Huang
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Linhui Liang
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhiao Chen
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Xianghuo He
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China.
- Shanghai Key Laboratory of Radiation Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China.
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16
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Caeiro LD, Verdun RE, Morey L. Histone H3 mutations and their impact on genome stability maintenance. Biochem Soc Trans 2024:BST20240177. [PMID: 39248209 DOI: 10.1042/bst20240177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 08/13/2024] [Accepted: 08/27/2024] [Indexed: 09/10/2024]
Abstract
Histones are essential for maintaining chromatin structure and function. Histone mutations lead to changes in chromatin compaction, gene expression, and the recruitment of DNA repair proteins to the DNA lesion. These disruptions can impair critical DNA repair pathways, such as homologous recombination and non-homologous end joining, resulting in increased genomic instability, which promotes an environment favorable to tumor development and progression. Understanding these mechanisms underscores the potential of targeting DNA repair pathways in cancers harboring mutated histones, offering novel therapeutic strategies to exploit their inherent genomic instability for better treatment outcomes. Here, we examine how mutations in histone H3 disrupt normal chromatin function and DNA damage repair processes and how these mechanisms can be exploited for therapeutic interventions.
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Affiliation(s)
- Lucas D Caeiro
- Sylvester Comprehensive Cancer Center, Biomedical Research Building, 1501 NW 10th Avenue, Miami, FL 33136, U.S.A
- Division of Hematology, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL 33136, U.S.A
| | - Ramiro E Verdun
- Sylvester Comprehensive Cancer Center, Biomedical Research Building, 1501 NW 10th Avenue, Miami, FL 33136, U.S.A
- Division of Hematology, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL 33136, U.S.A
- Geriatric Research, Education, and Clinical Center, Miami VA Healthcare System, Miami, FL, U.S.A
| | - Lluis Morey
- Sylvester Comprehensive Cancer Center, Biomedical Research Building, 1501 NW 10th Avenue, Miami, FL 33136, U.S.A
- Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136, U.S.A
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17
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Montaño J, Garnica J, Yamanouchi J, Moro J, Solé P, Mondal D, Serra P, Yang Y, Santamaria P. Transcriptional re-programming of liver-resident iNKT cells into T-regulatory type-1-like liver iNKT cells involves extensive gene de-methylation. Front Immunol 2024; 15:1454314. [PMID: 39315110 PMCID: PMC11416961 DOI: 10.3389/fimmu.2024.1454314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Accepted: 08/13/2024] [Indexed: 09/25/2024] Open
Abstract
Unlike conventional CD4+ T cells, which are phenotypically and functionally plastic, invariant NKT (iNKT) cells generally exist in a terminally differentiated state. Naïve CD4+ T cells can acquire alternative epigenetic states in response to different cues, but it remains unclear whether peripheral iNKT cells are epigenetically stable or malleable. Repetitive encounters of liver-resident iNKT cells (LiNKTs) with alpha-galactosylceramide (αGalCer)/CD1d-coated nanoparticles (NPs) can trigger their differentiation into a LiNKT cell subset expressing a T regulatory type 1 (TR1)-like (LiNKTR1) transcriptional signature. Here we dissect the epigenetic underpinnings of the LiNKT-LiNKTR1 conversion as compared to those underlying the peptide-major histocompatibility complex (pMHC)-NP-induced T-follicular helper (TFH)-to-TR1 transdifferentiation process. We show that gene upregulation during the LINKT-to-LiNKTR1 cell conversion is associated with demethylation of gene bodies, inter-genic regions, promoters and distal gene regulatory elements, in the absence of major changes in chromatin exposure or deposition of expression-promoting histone marks. In contrast, the naïve CD4+ T cell-to-TFH differentiation process involves extensive remodeling of the chromatin and the acquisition of a broad repertoire of epigenetic modifications that are then largely inherited by TFH cell-derived TR1 cell progeny. These observations indicate that LiNKT cells are epigenetically malleable and particularly susceptible to gene de-methylation.
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Affiliation(s)
- Javier Montaño
- Institut D’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Josep Garnica
- Institut D’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Jun Yamanouchi
- Department of Microbiology, Immunology and Infectious Diseases, Snyder Institute for Chronic Diseases and Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Joel Moro
- Institut D’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Patricia Solé
- Institut D’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Debajyoti Mondal
- Department of Microbiology, Immunology and Infectious Diseases, Snyder Institute for Chronic Diseases and Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Pau Serra
- Institut D’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Yang Yang
- Department of Microbiology, Immunology and Infectious Diseases, Snyder Institute for Chronic Diseases and Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Biochemistry and Molecular Biology and Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Pere Santamaria
- Institut D’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Department of Microbiology, Immunology and Infectious Diseases, Snyder Institute for Chronic Diseases and Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
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18
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Kraft K, Murphy SE, Jones MG, Shi Q, Bhargava-Shah A, Luong C, Hung KL, He BJ, Li R, Park SK, Weiser NE, Luebeck J, Bafna V, Boeke JD, Mischel PS, Boettiger AN, Chang HY. Enhancer activation from transposable elements in extrachromosomal DNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.04.611262. [PMID: 39282372 PMCID: PMC11398463 DOI: 10.1101/2024.09.04.611262] [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: 09/21/2024]
Abstract
Extrachromosomal DNA (ecDNA) is a hallmark of aggressive cancer, contributing to both oncogene amplification and tumor heterogeneity. Here, we used Hi-C, super-resolution imaging, and long-read sequencing to explore the nuclear architecture of MYC-amplified ecDNA in colorectal cancer cells. Intriguingly, we observed frequent spatial proximity between ecDNA and 68 repetitive elements which we called ecDNA-interacting elements or EIEs. To characterize a potential regulatory role of EIEs, we focused on a fragment of the L1M4a1#LINE/L1 which we found to be co-amplified with MYC on ecDNA, gaining enhancer-associated chromatin marks in contrast to its normally silenced state. This EIE, in particular, existed as a naturally occurring structural variant upstream of MYC, gaining oncogenic potential in the transcriptionally permissive ecDNA environment. This EIE sequence is sufficient to enhance MYC expression and is required for cancer cell fitness. These findings suggest that silent repetitive genomic elements can be reactivated on ecDNA, leading to functional cooption and amplification. Repeat element activation on ecDNA represents a mechanism of accelerated evolution and tumor heterogeneity and may have diagnostic and therapeutic potential.
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Affiliation(s)
- Katerina Kraft
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sedona E Murphy
- Present address: Department of Cell Biology, Yale School of Medicine, New Haven, CT 06520, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Matthew G Jones
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Quanming Shi
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Aarohi Bhargava-Shah
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
- Sarafan ChEM-H Institute and Department of Pathology, Stanford University, Stanford, CA, 94305 USA
| | - Christy Luong
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Chemical and Systems Biology, Stanford, CA 94305, USA
| | - King L Hung
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Britney J He
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Rui Li
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Seung K Park
- Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
| | - Natasha E Weiser
- Sarafan ChEM-H Institute and Department of Pathology, Stanford University, Stanford, CA, 94305 USA
| | - Jens Luebeck
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093, USA
| | - Vineet Bafna
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093, USA
| | - Jef D Boeke
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Paul S Mischel
- Sarafan ChEM-H Institute and Department of Pathology, Stanford University, Stanford, CA, 94305 USA
| | - Alistair N Boettiger
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
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19
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Wenz BM, He Y, Chen NC, Pickrell JK, Li JH, Dudek MF, Li T, Keener R, Voight BF, Brown CD, Battle A. Genotype inference from aggregated chromatin accessibility data reveals genetic regulatory mechanisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.04.610850. [PMID: 39282458 PMCID: PMC11398312 DOI: 10.1101/2024.09.04.610850] [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: 09/21/2024]
Abstract
Background Understanding the genetic causes for variability in chromatin accessibility can shed light on the molecular mechanisms through which genetic variants may affect complex traits. Thousands of ATAC-seq samples have been collected that hold information about chromatin accessibility across diverse cell types and contexts, but most of these are not paired with genetic information and come from diverse distinct projects and laboratories. Results We report here joint genotyping, chromatin accessibility peak calling, and discovery of quantitative trait loci which influence chromatin accessibility (caQTLs), demonstrating the capability of performing caQTL analysis on a large scale in a diverse sample set without pre-existing genotype information. Using 10,293 profiling samples representing 1,454 unique donor individuals across 653 studies from public databases, we catalog 23,381 caQTLs in total. After joint discovery analysis, we cluster samples based on accessible chromatin profiles to identify context-specific caQTLs. We find that caQTLs are strongly enriched for annotations of gene regulatory elements across diverse cell types and tissues and are often strongly linked with genetic variation associated with changes in expression (eQTLs), indicating that caQTLs can mediate genetic effects on gene expression. We demonstrate sharing of causal variants for chromatin accessibility and diverse complex human traits, enabling a more complete picture of the genetic mechanisms underlying complex human phenotypes. Conclusions Our work provides a proof of principle for caQTL calling from previously ungenotyped samples, and represents one of the largest, most diverse caQTL resources currently available, informing mechanisms of genetic regulation of gene expression and contribution to disease.
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Affiliation(s)
- Brandon M Wenz
- Genetics and Epigenetics Program, Cell and Molecular Biology Graduate Group, Biomedical Graduate Studies, University of Pennsylvania - Perelman School of Medicine, Philadelphia PA 19104
| | - Yuan He
- Department of Biomedical Engineering, Johns Hopkins University; Baltimore, MD, 21218
| | - Nae-Chyun Chen
- Department of Computer Science, Johns Hopkins University; Baltimore, MD, 21218
| | | | | | - Max F Dudek
- Graduate Group in Genomics and Computational Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - Taibo Li
- Department of Biomedical Engineering, Johns Hopkins University; Baltimore, MD, 21218
| | - Rebecca Keener
- Department of Biomedical Engineering, Johns Hopkins University; Baltimore, MD, 21218
| | - Benjamin F Voight
- Department of Genetics, University of Pennsylvania - Perelman School of Medicine, Philadelphia, PA, 19104
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania - Perelman School of Medicine, Philadelphia PA, 19104
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania - Perelman School of Medicine, Philadelphia, PA, 19104
| | - Christopher D Brown
- Department of Genetics, University of Pennsylvania - Perelman School of Medicine, Philadelphia, PA, 19104
| | - Alexis Battle
- Department of Biomedical Engineering, Johns Hopkins University; Baltimore, MD, 21218
- Department of Computer Science, Johns Hopkins University; Baltimore, MD, 21218
- Department of Genetic Medicine, Johns Hopkins University; Baltimore, MD, 21218
- Malone Center for Engineering in Healthcare, Johns Hopkins University, Baltimore, MD, 21218
- Data Science and AI Institute, Johns Hopkins University, Baltimore, MD, 21218
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20
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Singh I, Rainusso N, Kurenbekova L, Nirala BK, Dou J, Muruganandham A, Yustein JT. Intrinsic Epigenetic State of Primary Osteosarcoma Drives Metastasis. Mol Cancer Res 2024; 22:864-878. [PMID: 38842581 DOI: 10.1158/1541-7786.mcr-23-0055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 07/03/2023] [Accepted: 06/04/2024] [Indexed: 06/07/2024]
Abstract
Osteosarcoma is the most common primary malignant bone tumor affecting the pediatric population with a high potential to metastasize. However, insights into the molecular features enabling its metastatic potential are limited. We mapped the active chromatin landscapes of osteosarcoma tumors by integrating histone H3 lysine-acetylated chromatin state (n = 13), chromatin accessibility profiles (n = 11), and gene expression (n = 13) to understand the differences in their active chromatin profiles and their impact on molecular mechanisms driving the malignant phenotypes. Primary osteosarcoma tumors from patients with metastasis (primary met) have a distinct active chromatin landscape compared with those without metastasis (localized). This difference shapes the transcriptional profile of osteosarcoma. We identified novel candidate genes, including PPP1R1B, PREX1, and IGF2BP1, that exhibit increased chromatin activity in primary met. Loss of PREX1 in primary met osteosarcoma cells significantly diminishes osteosarcoma proliferation, invasion, migration, and colony formation capacity. Differential chromatin activity in primary met is associated with genes regulating cytoskeleton organization, cellular adhesion, and extracellular matrix, suggesting their role in facilitating osteosarcoma metastasis. Chromatin profiling of tumors from metastatic lung lesions shows increased chromatin activity in genes involved in cell migration and Wnt pathway. These data demonstrate that metastatic potential is intrinsically present in primary met tumors, with cellular chromatin profiles further adapting for successful dissemination, migration, and colonization at the distal site. Implications: Our study demonstrates that metastatic potential is intrinsic to primary metastatic osteosarcoma tumors, with chromatin profiles further adapting for successful dissemination, migration, and colonization at the distal metastatic site.
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Affiliation(s)
- Irtisha Singh
- Department of Cell Biology and Genetics, College of Medicine, Texas A&M University, Bryan, Texas
- Department of Biomedical Engineering, College of Engineering, Texas A&M University, College Station, Texas
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, Texas
| | - Nino Rainusso
- Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, Texas
| | - Lyazat Kurenbekova
- Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, Texas
| | - Bikesh K Nirala
- Winship Cancer Institute and Aflac Cancer and Blood Disorders Center, Emory University, Atlanta, Georgia
| | - Juan Dou
- Winship Cancer Institute and Aflac Cancer and Blood Disorders Center, Emory University, Atlanta, Georgia
| | - Abhinaya Muruganandham
- Department of Biomedical Engineering, College of Engineering, Texas A&M University, College Station, Texas
| | - Jason T Yustein
- Winship Cancer Institute and Aflac Cancer and Blood Disorders Center, Emory University, Atlanta, Georgia
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21
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Smith JP, Paxton R, Medrano S, Sheffield NC, Sequeira-Lopez MLS, Ariel Gomez R. Inhibition of Renin Expression Is Regulated by an Epigenetic Switch From an Active to a Poised State. Hypertension 2024; 81:1869-1882. [PMID: 38989586 PMCID: PMC11337216 DOI: 10.1161/hypertensionaha.124.22886] [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: 02/13/2024] [Accepted: 07/02/2024] [Indexed: 07/12/2024]
Abstract
BACKGROUND Renin-expressing cells are myoendocrine cells crucial for the maintenance of homeostasis. Renin is regulated by cAMP, p300 (histone acetyltransferase p300)/CBP (CREB-binding protein), and Brd4 (bromodomain-containing protein 4) proteins and associated pathways. However, the specific regulatory changes that occur following inhibition of these pathways are not clear. METHODS We treated As4.1 cells (tumoral cells derived from mouse juxtaglomerular cells that constitutively express renin) with 3 inhibitors that target different factors required for renin transcription: H-89-dihydrochloride, PKA (protein kinase A) inhibitor; JQ1, Brd4 bromodomain inhibitor; and A-485, p300/CBP inhibitor. We performed assay for transposase-accessible chromatin with sequencing (ATAC-seq), single-cell RNA sequencing, cleavage under targets and tagmentation (CUT&Tag), and chromatin immunoprecipitation sequencing for H3K27ac (acetylation of lysine 27 of the histone H3 protein) and p300 binding on biological replicates of treated and control As4.1 cells. RESULTS In response to each inhibitor, Ren1 expression was significantly reduced and reversible upon washout. Chromatin accessibility at the Ren1 locus did not markedly change but was globally reduced at distal elements. Inhibition of PKA led to significant reductions in H3K27ac and p300 binding specifically within the Ren1 super-enhancer region. Further, we identified enriched TF (transcription factor) motifs shared across each inhibitory treatment. Finally, we identified a set of 9 genes with putative roles across each of the 3 renin regulatory pathways and observed that each displayed differentially accessible chromatin, gene expression, H3K27ac, and p300 binding at their respective loci. CONCLUSIONS Inhibition of renin expression in cells that constitutively synthesize and release renin is regulated by an epigenetic switch from an active to poised state associated with decreased cell-cell communication and an epithelial-mesenchymal transition. This work highlights and helps define the factors necessary for renin cells to alternate between myoendocrine and contractile phenotypes.
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Affiliation(s)
- Jason P. Smith
- Department of Pediatrics, Child Health Research Center, University of Virginia, Charlottesville, Virginia
| | - Robert Paxton
- Department of Pediatrics, Child Health Research Center, University of Virginia, Charlottesville, Virginia
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Silvia Medrano
- Department of Pediatrics, Child Health Research Center, University of Virginia, Charlottesville, Virginia
| | - Nathan C. Sheffield
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
- Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia
| | | | - R. Ariel Gomez
- Department of Pediatrics, Child Health Research Center, University of Virginia, Charlottesville, Virginia
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22
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Alvarez-Kuglen M, Ninomiya K, Qin H, Rodriguez D, Fiengo L, Farhy C, Hsu WM, Kirk B, Havas A, Feng GS, Roberts AJ, Anderson RM, Serrano M, Adams PD, Sharpee TO, Terskikh AV. ImAge quantitates aging and rejuvenation. NATURE AGING 2024; 4:1308-1327. [PMID: 39210148 DOI: 10.1038/s43587-024-00685-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 07/11/2024] [Indexed: 09/04/2024]
Abstract
For efficient, cost-effective and personalized healthcare, biomarkers that capture aspects of functional, biological aging, thus predicting disease risk and lifespan more accurately and reliably than chronological age, are essential. We developed an imaging-based chromatin and epigenetic age (ImAge) that captures intrinsic age-related trajectories of the spatial organization of chromatin and epigenetic marks in single nuclei, in mice. We show that such trajectories readily emerge as principal changes in each individual dataset without regression on chronological age, and that ImAge can be computed using several epigenetic marks and DNA labeling. We find that interventions known to affect biological aging induce corresponding effects on ImAge, including increased ImAge upon chemotherapy treatment and decreased ImAge upon caloric restriction and partial reprogramming by transient OSKM expression in liver and skeletal muscle. Further, ImAge readouts from chronologically identical mice inversely correlated with their locomotor activity, suggesting that ImAge may capture elements of biological and functional age. In sum, we developed ImAge, an imaging-based biomarker of aging with single-cell resolution rooted in the analysis of spatial organization of epigenetic marks.
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Affiliation(s)
| | - Kenta Ninomiya
- Harry Perkins Institute of Medical Research, The University of Western Australia, Perth, Western Australia, Australia
| | - Haodong Qin
- Department of Physics, University of California San Diego, La Jolla, CA, USA
| | | | | | - Chen Farhy
- Sanford Burnham Prebys, La Jolla, CA, USA
| | - Wei-Mien Hsu
- Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Brian Kirk
- Sanford Burnham Prebys, La Jolla, CA, USA
| | | | - Gen-Sheng Feng
- School of Medicine, Univerity of California San Diego, La Jolla, CA, USA
| | | | - Rozalyn M Anderson
- University of Wisconsin, Madison, WI, USA
- GRECC, William S Middleton Memorial Veterans Hospital, Madison, WI, USA
| | - Manuel Serrano
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain
- Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Altos Labs, Cambridge Institute of Science, Granta Park, UK
| | | | | | - Alexey V Terskikh
- Harry Perkins Institute of Medical Research, The University of Western Australia, Perth, Western Australia, Australia.
- The Scintillon Research Institute, San Diego, CA, USA.
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23
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Murray-Nerger LA, Maestri D, Liu X, Li Z, Auld NR, Tempera I, Teng M, Gewurz BE. The DNA loop release factor WAPL suppresses Epstein-Barr virus latent membrane protein expression to maintain the highly restricted latency I program. PLoS Pathog 2024; 20:e1012525. [PMID: 39241017 PMCID: PMC11410233 DOI: 10.1371/journal.ppat.1012525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 09/18/2024] [Accepted: 08/23/2024] [Indexed: 09/08/2024] Open
Abstract
Epstein-Barr virus (EBV) uses latency programs to colonize the memory B-cell reservoir, and each program is associated with human malignancies. However, knowledge remains incomplete of epigenetic mechanisms that maintain the highly restricted latency I program, present in memory and Burkitt lymphoma cells, in which EBNA1 is the only EBV-encoded protein expressed. Given increasing appreciation that higher order chromatin architecture is an important determinant of viral and host gene expression, we investigated roles of Wings Apart-Like Protein Homolog (WAPL), a host factor that unloads cohesin to control DNA loop size and that was discovered as an EBNA2-associated protein. WAPL knockout (KO) in Burkitt cells de-repressed LMP1 and LMP2A expression, but not other EBV oncogenes, to yield a viral program reminiscent of EBV latency II, which is rarely observed in B-cells. WAPL KO also increased LMP1/2A levels in latency III lymphoblastoid cells. WAPL KO altered EBV genome architecture, triggering formation of DNA loops between the LMP promoter region and the EBV origins of lytic replication (oriLyt). Hi-C analysis further demonstrated that WAPL KO reprogrammed EBV genomic DNA looping. LMP1 and LMP2A de-repression correlated with decreased histone repressive marks at their promoters. We propose that EBV coopts WAPL to negatively regulate latent membrane protein expression to maintain Burkitt latency I.
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Affiliation(s)
- Laura A Murray-Nerger
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
- Harvard Program in Virology, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Davide Maestri
- The Wistar Institute, Philadelphia, Pennsylvania, United States of America
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Xiang Liu
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America
| | - Zhixuan Li
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
- Harvard Program in Virology, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Nina R Auld
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
- Harvard Program in Virology, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Italo Tempera
- The Wistar Institute, Philadelphia, Pennsylvania, United States of America
| | - Mingxiang Teng
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America
| | - Benjamin E Gewurz
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
- Harvard Program in Virology, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
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24
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Gualandi N, Minisini M, Bertozzo A, Brancolini C. Dissecting transposable elements and endogenous retroviruses upregulation by HDAC inhibitors in leiomyosarcoma cells: Implications for the interferon response. Genomics 2024; 116:110909. [PMID: 39103003 DOI: 10.1016/j.ygeno.2024.110909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 07/22/2024] [Accepted: 07/31/2024] [Indexed: 08/07/2024]
Abstract
Transposable elements (TEs) are of interest as immunomodulators for cancer therapies. TEs can fold into dsRNAs that trigger the interferon response. Here, we investigated the effect of different HDAC inhibitors (HDACIs) on the expression of TEs in leiomyosarcoma cells. Our data show that endogenous retroviruses (ERVs), especially ERV1 elements, are upregulated after treatment with HDAC1/2/3-specific inhibitors. Surprisingly, the interferon response was not activated. We observed an increase in A-to-I editing of upregulated ERV1. This could have an impact on the stability of dsRNAs and the activation of the interferon response. We also found that H3K27ac levels are increased in the LTR12 subfamilies, which could be regulatory elements controlling the expression of proapoptotic genes such as TNFRSF10B. In summary, we provide a detailed characterization of TEs modulation in response to HDACIs and suggest the use of HDACIs in combination with ADAR inhibitors to induce cell death and support immunotherapy in cancer.
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Affiliation(s)
- Nicolò Gualandi
- Department of Medicine, Università degli Studi di Udine, P.le Kolbe 4, 33100 Udine, Italy
| | - Martina Minisini
- Department of Medicine, Università degli Studi di Udine, P.le Kolbe 4, 33100 Udine, Italy
| | - Alessio Bertozzo
- Department of Medicine, Università degli Studi di Udine, P.le Kolbe 4, 33100 Udine, Italy
| | - Claudio Brancolini
- Department of Medicine, Università degli Studi di Udine, P.le Kolbe 4, 33100 Udine, Italy.
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25
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MacArthur IC, Ma L, Huang CY, Bhavsar H, Suzuki M, Dawlaty MM. Developmental DNA demethylation is a determinant of neural stem cell identity and gliogenic competence. SCIENCE ADVANCES 2024; 10:eado5424. [PMID: 39196941 PMCID: PMC11352921 DOI: 10.1126/sciadv.ado5424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 07/24/2024] [Indexed: 08/30/2024]
Abstract
DNA methylation is extensively reconfigured during development, but the functional significance and cell type-specific dependencies of DNA demethylation in lineage specification remain poorly understood. Here, we demonstrate that developmental DNA demethylation, driven by ten-eleven translocation 1/2/3 (TET1/2/3) enzymes, is essential for establishment of neural stem cell (NSC) identity and gliogenic potential. We find that loss of all three TETs during NSC specification is dispensable for neural induction and neuronal differentiation but critical for astrocyte and oligodendrocyte formation, demonstrating a selective loss of glial competence. Mechanistically, TET-mediated demethylation was essential for commissioning neural-specific enhancers in proximity to master neurodevelopmental and glial transcription factor genes and for induction of these genes. Consistently, loss of all three TETs in embryonic NSCs in mice compromised glial gene expression and corticogenesis. Thus, TET-dependent developmental demethylation is an essential regulatory mechanism for neural enhancer commissioning during NSC specification and is a cell-intrinsic determinant of NSC identity and gliogenic potential.
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Affiliation(s)
- Ian C. MacArthur
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY 1046142, USA
- Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY 10461, USA
- Department of Developmental & Molecular Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461, USA
| | - Liyang Ma
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY 1046142, USA
- Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY 10461, USA
- Department of Developmental & Molecular Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461, USA
| | - Cheng-Yen Huang
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY 1046142, USA
- Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY 10461, USA
- Department of Developmental & Molecular Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461, USA
| | - Hrutvik Bhavsar
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY 1046142, USA
- Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY 10461, USA
- Department of Developmental & Molecular Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461, USA
| | - Masako Suzuki
- Department of Nutrition, Texas A&M University, 2253 TAMU, Carter Mattil 214A, College Station, TX 77840, USA
| | - Meelad M. Dawlaty
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY 1046142, USA
- Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY 10461, USA
- Department of Developmental & Molecular Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461, USA
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26
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Stuart T. Progress in multifactorial single-cell chromatin profiling methods. Biochem Soc Trans 2024; 52:1827-1839. [PMID: 39023855 DOI: 10.1042/bst20231471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2024] [Revised: 07/01/2024] [Accepted: 07/08/2024] [Indexed: 07/20/2024]
Abstract
Chromatin states play a key role in shaping overall cellular states and fates. Building a complete picture of the functional state of chromatin in cells requires the co-detection of several distinct biochemical aspects. These span DNA methylation, chromatin accessibility, chromosomal conformation, histone posttranslational modifications, and more. While this certainly presents a challenging task, over the past few years many new and creative methods have been developed that now enable co-assay of these different aspects of chromatin at single cell resolution. This field is entering an exciting phase, where a confluence of technological improvements, decreased sequencing costs, and computational innovation are presenting new opportunities to dissect the diversity of chromatin states present in tissues, and how these states may influence gene regulation. In this review, I discuss the spectrum of current experimental approaches for multifactorial chromatin profiling, highlight some of the experimental and analytical challenges, as well as some areas for further innovation.
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Affiliation(s)
- Tim Stuart
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore
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27
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Bae H, Jeon H, Lee C. Genetic regulation of B cell receptor signaling pathway: Insights from expression quantitative trait locus analysis using a mixed model. Comput Biol Chem 2024; 113:108188. [PMID: 39236423 DOI: 10.1016/j.compbiolchem.2024.108188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 08/23/2024] [Accepted: 08/24/2024] [Indexed: 09/07/2024]
Abstract
The B cell receptor (BCR) signaling pathway regulates non-immune cellular response through various pathways like MAPK, NF-kB, and PI3K-Akt. This study aimed to identify expression quantitative trait loci (eQTL) and their regulatory functions on BCR signaling pathway genes. A mixed model was employed to analyze eQTL using RNA expression levels in lymphoblastoid from 376 Europeans in the GEUVADIS dataset. In total, 266 SNPs, including 115 cis-acting SNPs, were found for association with transcription of 13 genes (P < 5 × 10-8), revealing 19 independent signals for five genes through linkage disequilibrium analysis. Functional analysis, aligning them with DNase sensitive sites, transcription factor binding sites, histone modification, promoters/enhancers, CpG islands, and ChIA-PET, identified regulatory variants targeting SYK, VAV2, and PLCG2. Notably, rs2562397 was validated as a SYK promoter variant, and rs694505, rs636667, and rs4889409 were confirmed as enhancer variants for VAV2 and PLCG2. Their allelic differences in gene expression were also confirmed using ENCODE ChIP-seq and Sei neural network prediction. Persistent differential expression of these genes by alleles might impact the adaptive immune system, vascular development, and/or relevant diseases that have been previously associated with other variants of the genes. Comprehensive genetic architecture studies of the BCR signaling pathway, along with experiments demonstrating related mechanisms, will greatly contribute to understanding the underlying mechanisms of relevant disease development and implementing precision medicine.
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Affiliation(s)
- Hojin Bae
- Department of Bioinformatics and Life Science, Soongsil University, 369 Sangdo-ro, Dongjak-gu, Seoul 06978, Republic of Korea
| | - Hyowon Jeon
- Department of Bioinformatics and Life Science, Soongsil University, 369 Sangdo-ro, Dongjak-gu, Seoul 06978, Republic of Korea
| | - Chaeyoung Lee
- Department of Bioinformatics and Life Science, Soongsil University, 369 Sangdo-ro, Dongjak-gu, Seoul 06978, Republic of Korea.
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28
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Kaplan SJ, Wong W, Yan J, Pulecio J, Cho HS, Li Q, Zhao J, Leslie-Iyer J, Kazakov J, Murphy D, Luo R, Dey KK, Apostolou E, Leslie CS, Huangfu D. CRISPR screening uncovers a long-range enhancer for ONECUT1 in pancreatic differentiation and links a diabetes risk variant. Cell Rep 2024; 43:114640. [PMID: 39163202 PMCID: PMC11406439 DOI: 10.1016/j.celrep.2024.114640] [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: 05/29/2024] [Revised: 07/01/2024] [Accepted: 07/31/2024] [Indexed: 08/22/2024] Open
Abstract
Functional enhancer annotation is critical for understanding tissue-specific transcriptional regulation and prioritizing disease-associated non-coding variants. However, unbiased enhancer discovery in disease-relevant contexts remains challenging. To identify enhancers pertinent to diabetes, we conducted a CRISPR interference (CRISPRi) screen in the human pluripotent stem cell (hPSC) pancreatic differentiation system. Among the enhancers identified, we focused on an enhancer we named ONECUT1e-664kb, ∼664 kb from the ONECUT1 promoter. Previous studies have linked ONECUT1 coding mutations to pancreatic hypoplasia and neonatal diabetes. We found that homozygous deletion of ONECUT1e-664kb in hPSCs leads to a near-complete loss of ONECUT1 expression and impaired pancreatic differentiation. ONECUT1e-664kb contains a type 2 diabetes-associated variant (rs528350911) disrupting a GATA motif. Introducing the risk variant into hPSCs reduced binding of key pancreatic transcription factors (GATA4, GATA6, and FOXA2), supporting its causal role in diabetes. This work highlights the utility of unbiased enhancer discovery in disease-relevant settings for understanding monogenic and complex disease.
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Affiliation(s)
- Samuel Joseph Kaplan
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medical College, New York, NY 10065, USA; Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Wilfred Wong
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medical College, New York, NY 10065, USA; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jielin Yan
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Julian Pulecio
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Hyein S Cho
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Qianzi Li
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medical College, New York, NY 10065, USA; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jiahui Zhao
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medical College, New York, NY 10065, USA
| | - Jayanti Leslie-Iyer
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jonathan Kazakov
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Dylan Murphy
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medical College, New York, NY 10065, USA
| | - Renhe Luo
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Kushal K Dey
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Effie Apostolou
- Meyer Cancer Center, Division of Neuro-Oncology, Department of Neurology, Sandra and Edward Meyer Cancer Center, New York-Presbyterian Hospital/Weill Cornell Medicine, New York, NY 10065, USA
| | - Christina S Leslie
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Danwei Huangfu
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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29
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Fu M, Jia S, Xu L, Li X, Lv Y, Zhong Y, Ai S. Single-cell multiomic analysis identifies macrophage subpopulations in promoting cardiac repair. J Clin Invest 2024; 134:e175297. [PMID: 39190625 PMCID: PMC11444165 DOI: 10.1172/jci175297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 08/15/2024] [Indexed: 08/29/2024] Open
Abstract
Cardiac mononuclear phagocytic cells (Cardiac MPCs) participate in maintaining homeostasis and orchestrating cardiac responses upon injury. However, the function of specific MPC subtypes and the related cell fate commitment mechanisms remain elusive in regenerative and nonregenerative hearts due to their cellular heterogeneities. Using spatiotemporal single-cell epigenomic analysis of cardiac MPCs in regenerative (P1) and nonregenerative (P10) mouse hearts after injury, we found that P1 hearts accumulate reparative Arg1+ macrophages, while proinflammatory S100a9+Ly6c+ monocytes are uniquely abundant during nonregenerative remodeling. Moreover, blocking chemokine CXCR2 to inhibit the specification of the S100a9+Ly6c+-biased inflammatory fate in P10 hearts resulted in elevated wound repair responses and marked improvements in cardiac function after injury. Single-cell RNA-Seq further confirmed an increased Arg1+ macrophage subpopulation after CXCR2 blockade, which was accomplished by increased expression of wound repair-related genes and reduced expression of proinflammatory genes. Collectively, our findings provide instructive insights into the molecular mechanisms underlying the function and fate specification of heterogeneous MPCs during cardiac repair and identify potential therapeutic targets for myocardial infarction.
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Affiliation(s)
- Mingzhu Fu
- Guangdong Provincial Key Laboratory of Bone and Joint Degeneration Diseases, Department of Physiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Shengtao Jia
- Guangdong Provincial Key Laboratory of Bone and Joint Degeneration Diseases, Department of Physiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Longhui Xu
- Guangdong Provincial Key Laboratory of Bone and Joint Degeneration Diseases, Department of Physiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Xin Li
- Department of Cardiology, Heart Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yufang Lv
- Guangdong Provincial Key Laboratory of Bone and Joint Degeneration Diseases, Department of Physiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Yulong Zhong
- Guangdong Provincial Key Laboratory of Bone and Joint Degeneration Diseases, Department of Physiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Shanshan Ai
- Guangdong Provincial Key Laboratory of Bone and Joint Degeneration Diseases, Department of Physiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- Department of Cardiology, Heart Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
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30
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Piedade AP, Butler J, Eyre S, Orozco G. The importance of functional genomics studies in precision rheumatology. Best Pract Res Clin Rheumatol 2024:101988. [PMID: 39174375 DOI: 10.1016/j.berh.2024.101988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 08/04/2024] [Accepted: 08/07/2024] [Indexed: 08/24/2024]
Abstract
Rheumatic diseases, those that affect the musculoskeletal system, cause significant morbidity. Among risk factors of these diseases is a significant genetic component. Recent advances in high-throughput omics techniques now allow a comprehensive profiling of patients at a genetic level through genome-wide association studies. Without functional interpretation of variants identified through these studies, clinical insight remains limited. Strategies include statistical fine-mapping that refine the list of variants in loci associated with disease, whilst colocalization techniques attempt to attribute function to variants that overlap a genetically active chromatin annotation. Functional validation using genome editing techniques can be used to further refine genetic signals and identify key pathways in cell types relevant to rheumatic disease biology. Insight gained from the combination of genetic studies and functional validation can be used to improve precision medicine in rheumatic diseases by allowing risk prediction and drug repositioning.
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Affiliation(s)
- Ana Pires Piedade
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK; NIHR Manchester Biomedical Research Centre, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK.
| | - Jake Butler
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK; NIHR Manchester Biomedical Research Centre, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK.
| | - Stephen Eyre
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK; NIHR Manchester Biomedical Research Centre, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK.
| | - Gisela Orozco
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK; NIHR Manchester Biomedical Research Centre, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK.
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31
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Signal B, Phipps AJ, Giles KA, Huskins SN, Mercer TR, Robinson MD, Woodhouse A, Taberlay PC. Ageing-Related Changes to H3K4me3, H3K27ac, and H3K27me3 in Purified Mouse Neurons. Cells 2024; 13:1393. [PMID: 39195281 DOI: 10.3390/cells13161393] [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: 07/09/2024] [Revised: 08/19/2024] [Accepted: 08/19/2024] [Indexed: 08/29/2024] Open
Abstract
Neurons are central to lifelong learning and memory, but ageing disrupts their morphology and function, leading to cognitive decline. Although epigenetic mechanisms are known to play crucial roles in learning and memory, neuron-specific genome-wide epigenetic maps into old age remain scarce, often being limited to whole-brain homogenates and confounded by glial cells. Here, we mapped H3K4me3, H3K27ac, and H3K27me3 in mouse neurons across their lifespan. This revealed stable H3K4me3 and global losses of H3K27ac and H3K27me3 into old age. We observed patterns of synaptic function gene deactivation, regulated through the loss of the active mark H3K27ac, but not H3K4me3. Alongside this, embryonic development loci lost repressive H3K27me3 in old age. This suggests a loss of a highly refined neuronal cellular identity linked to global chromatin reconfiguration. Collectively, these findings indicate a key role for epigenetic regulation in neurons that is inextricably linked with ageing.
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Affiliation(s)
- Brandon Signal
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS 7000, Australia
| | - Andrew J Phipps
- Wicking Dementia Research and Education Centre, College of Health and Medicine, University of Tasmania, 17 Liverpool Street, Hobart, TAS 7000, Australia
| | - Katherine A Giles
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS 7000, Australia
- Children's Medical Research Institute, University of Sydney, 214 Hawkesbury Road, Westmead, NSW 2145, Australia
| | - Shannon N Huskins
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS 7000, Australia
| | - Timothy R Mercer
- Australian Institute for Bioengineering and Nanotechnology, Corner College and Cooper Roads, Brisbane, QLD 4072, Australia
| | - Mark D Robinson
- SIB Swiss Institute of Bioinformatics, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Adele Woodhouse
- Wicking Dementia Research and Education Centre, College of Health and Medicine, University of Tasmania, 17 Liverpool Street, Hobart, TAS 7000, Australia
| | - Phillippa C Taberlay
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS 7000, Australia
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32
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DelRosso N, Suzuki PH, Griffith D, Lotthammer JM, Novak B, Kocalar S, Sheth MU, Holehouse AS, Bintu L, Fordyce P. High-throughput affinity measurements of direct interactions between activation domains and co-activators. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.19.608698. [PMID: 39229005 PMCID: PMC11370418 DOI: 10.1101/2024.08.19.608698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Sequence-specific activation by transcription factors is essential for gene regulation1,2. Key to this are activation domains, which often fall within disordered regions of transcription factors3,4 and recruit co-activators to initiate transcription5. These interactions are difficult to characterize via most experimental techniques because they are typically weak and transient6,7. Consequently, we know very little about whether these interactions are promiscuous or specific, the mechanisms of binding, and how these interactions tune the strength of gene activation. To address these questions, we developed a microfluidic platform for expression and purification of hundreds of activation domains in parallel followed by direct measurement of co-activator binding affinities (STAMMPPING, for Simultaneous Trapping of Affinity Measurements via a Microfluidic Protein-Protein INteraction Generator). By applying STAMMPPING to quantify direct interactions between eight co-activators and 204 human activation domains (>1,500 K ds), we provide the first quantitative map of these interactions and reveal 334 novel binding pairs. We find that the metazoan-specific co-activator P300 directly binds >100 activation domains, potentially explaining its widespread recruitment across the genome to influence transcriptional activation. Despite sharing similar molecular properties (e.g. enrichment of negative and hydrophobic residues), activation domains utilize distinct biophysical properties to recruit certain co-activator domains. Co-activator domain affinity and occupancy are well-predicted by analytical models that account for multivalency, and in vitro affinities quantitatively predict activation in cells with an ultrasensitive response. Not only do our results demonstrate the ability to measure affinities between even weak protein-protein interactions in high throughput, but they also provide a necessary resource of over 1,500 activation domain/co-activator affinities which lays the foundation for understanding the molecular basis of transcriptional activation.
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Affiliation(s)
| | - Peter H Suzuki
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Daniel Griffith
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
| | - Jeffrey M Lotthammer
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
| | - Borna Novak
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
| | - Selin Kocalar
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Maya U Sheth
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
| | - Lacramioara Bintu
- Biophysics Program, Stanford University, Stanford, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Polly Fordyce
- Biophysics Program, Stanford University, Stanford, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Sarafan ChEM-H Institute, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub San Francisco, CA, USA
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33
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Roy SS, Bagri S, Vinayagamurthy S, Sengupta A, Then CR, Kumar R, Sridharan S, Chowdhury S. Artificially inserted strong promoter containing multiple G-quadruplexes induces long-range chromatin modification. eLife 2024; 13:RP96216. [PMID: 39158543 PMCID: PMC11333042 DOI: 10.7554/elife.96216] [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] [Indexed: 08/20/2024] Open
Abstract
Although the role of G-quadruplex (G4) DNA structures has been suggested in chromosomal looping this was not tested directly. Here, to test causal function, an array of G4s, or control sequence that does not form G4s, were inserted within chromatin in cells. In vivo G4 formation of the inserted G4 sequence array, and not the control sequence, was confirmed using G4-selective antibody. Compared to the control insert, we observed a remarkable increase in the number of 3D chromatin looping interactions from the inserted G4 array. This was evident within the immediate topologically associated domain (TAD) and throughout the genome. Locally, recruitment of enhancer histone marks and the transcriptional coactivator p300/Acetylated-p300 increased in the G4-array, but not in the control insertion. Resulting promoter-enhancer interactions and gene activation were clear up to 5 Mb away from the insertion site. Together, these show the causal role of G4s in enhancer function and long-range chromatin interactions. Mechanisms of 3D topology are primarily based on DNA-bound architectural proteins that induce/stabilize long-range interactions. Involvement of the underlying intrinsic DNA sequence/structure in 3D looping shown here therefore throws new light on how long-range chromosomal interactions might be induced or maintained.
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Affiliation(s)
- Shuvra Shekhar Roy
- CSIR-Institute of Genomics and Integrative BiologyNew DelhiIndia
- Academy of Scientific and Innovative Research (AcSIR)GhaziabadIndia
| | - Sulochana Bagri
- CSIR-Institute of Genomics and Integrative BiologyNew DelhiIndia
- Academy of Scientific and Innovative Research (AcSIR)GhaziabadIndia
| | - Soujanya Vinayagamurthy
- CSIR-Institute of Genomics and Integrative BiologyNew DelhiIndia
- Academy of Scientific and Innovative Research (AcSIR)GhaziabadIndia
| | - Avik Sengupta
- Department of Biotechnology, Indian Institute of Technology HyderabadHyderabadIndia
| | - Claudia Regina Then
- Cancer Science Institute of Singapore, National University of SingaporeSingaporeSingapore
| | - Rahul Kumar
- Department of Biotechnology, Indian Institute of Technology HyderabadHyderabadIndia
| | - Sriram Sridharan
- Cancer Science Institute of Singapore, National University of SingaporeSingaporeSingapore
| | - Shantanu Chowdhury
- CSIR-Institute of Genomics and Integrative BiologyNew DelhiIndia
- Academy of Scientific and Innovative Research (AcSIR)GhaziabadIndia
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34
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Zhu X, Farsh T, Vis D, Yu I, Li H, Liu T, Sjöström M, Shrestha R, Kneppers J, Severson T, Zhang M, Lundberg A, Moreno Rodriguez T, Weinstein AS, Foye A, Mehra N, Aggarwal RR, Bergman AM, Small EJ, Lack NA, Zwart W, Quigley DA, van der Heijden MS, Feng FY. Genomic and transcriptomic features of androgen receptor signaling inhibitor resistance in metastatic castration-resistant prostate cancer. J Clin Invest 2024; 134:e178604. [PMID: 39352383 PMCID: PMC11444163 DOI: 10.1172/jci178604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 08/06/2024] [Indexed: 10/03/2024] Open
Abstract
BACKGROUNDAndrogen receptor signaling inhibitors (ARSIs) have improved outcomes for patients with metastatic castration-resistant prostate cancer (mCRPC), but their clinical benefit is limited by treatment resistance.METHODSTo investigate the mechanisms of ARSI resistance, we analyzed the whole-genome (n = 45) and transcriptome (n = 31) sequencing data generated from paired metastatic biopsies obtained before initiation of first-line ARSI therapy for mCRPC and after radiographic disease progression. We investigated the effects of genetic and pharmacologic modulation of SSTR1 in 22Rv1 cells, a representative mCRPC cell line.RESULTSWe confirmed the predominant role of tumor genetic alterations converging on augmenting androgen receptor (AR) signaling and the increased transcriptional heterogeneity and lineage plasticity during the emergence of ARSI resistance. We further identified amplifications involving a putative enhancer downstream of the AR and transcriptional downregulation of SSTR1, encoding somatostatin receptor 1, in ARSI-resistant tumors. We found that patients with SSTR1-low mCRPC tumors derived less benefit from subsequent ARSI therapy in a retrospective cohort. We showed that SSTR1 was antiproliferative in 22Rv1 cells and that the FDA-approved drug pasireotide suppressed 22Rv1 cell proliferation.CONCLUSIONOur findings expand the knowledge of ARSI resistance and point out actionable next steps, exemplified by potentially targeting SSTR1, to improve patient outcomes.FUNDINGNational Cancer Institute (NCI), NIH; Prostate Cancer Foundation; Conquer Cancer, American Society of Clinical Oncology Foundation; UCSF Benioff Initiative for Prostate Cancer Research; Netherlands Cancer Institute.
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MESH Headings
- Male
- Humans
- Prostatic Neoplasms, Castration-Resistant/genetics
- Prostatic Neoplasms, Castration-Resistant/pathology
- Prostatic Neoplasms, Castration-Resistant/drug therapy
- Prostatic Neoplasms, Castration-Resistant/metabolism
- Receptors, Androgen/genetics
- Receptors, Androgen/metabolism
- Drug Resistance, Neoplasm/genetics
- Drug Resistance, Neoplasm/drug effects
- Cell Line, Tumor
- Signal Transduction/drug effects
- Transcriptome
- Neoplasm Metastasis
- Receptors, Somatostatin/genetics
- Receptors, Somatostatin/metabolism
- Gene Expression Regulation, Neoplastic/drug effects
- Androgen Receptor Antagonists/pharmacology
- Neoplasm Proteins/genetics
- Neoplasm Proteins/metabolism
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Affiliation(s)
- Xiaolin Zhu
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
- Division of Hematology and Oncology, Department of Medicine, UCSF, San Francisco, California, USA
| | - Tatyanah Farsh
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
- Department of Radiation Oncology, UCSF, San Francisco, California, USA
| | - Daniël Vis
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Ivan Yu
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Haolong Li
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
- Department of Radiation Oncology, UCSF, San Francisco, California, USA
| | - Tianyi Liu
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
- Department of Radiation Oncology, UCSF, San Francisco, California, USA
| | - Martin Sjöström
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
- Department of Radiation Oncology, UCSF, San Francisco, California, USA
| | - Raunak Shrestha
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
- Department of Radiation Oncology, UCSF, San Francisco, California, USA
| | - Jeroen Kneppers
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Tesa Severson
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Meng Zhang
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
- Department of Radiation Oncology, UCSF, San Francisco, California, USA
| | - Arian Lundberg
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
- Department of Radiation Oncology, UCSF, San Francisco, California, USA
| | - Thaidy Moreno Rodriguez
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
- Department of Urology, UCSF, San Francisco, California, USA
| | - Alana S. Weinstein
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
- Department of Radiation Oncology, UCSF, San Francisco, California, USA
| | - Adam Foye
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
- Division of Hematology and Oncology, Department of Medicine, UCSF, San Francisco, California, USA
| | - Niven Mehra
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Rahul R. Aggarwal
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
- Division of Hematology and Oncology, Department of Medicine, UCSF, San Francisco, California, USA
| | - Andries M. Bergman
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Eric J. Small
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
- Division of Hematology and Oncology, Department of Medicine, UCSF, San Francisco, California, USA
| | - Nathan A. Lack
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Koç University School of Medicine, Istanbul, Turkey
- Koç University Research Center for Translational Medicine (KUTTAM), Istanbul, Turkey
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - David A. Quigley
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
- Department of Urology, UCSF, San Francisco, California, USA
| | | | - Felix Y. Feng
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
- Department of Radiation Oncology, UCSF, San Francisco, California, USA
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35
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Yancoskie M, Khaleghi R, Gururajan A, Raghunathan A, Gupta A, Diethelm S, Maritz C, Sturla S, Krishnan M, Naegeli H. ASH1L guards cis-regulatory elements against cyclobutane pyrimidine dimer induction. Nucleic Acids Res 2024; 52:8254-8270. [PMID: 38884271 PMCID: PMC11317172 DOI: 10.1093/nar/gkae517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/29/2024] [Accepted: 06/04/2024] [Indexed: 06/18/2024] Open
Abstract
The histone methyltransferase ASH1L, first discovered for its role in transcription, has been shown to accelerate the removal of ultraviolet (UV) light-induced cyclobutane pyrimidine dimers (CPDs) by nucleotide excision repair. Previous reports demonstrated that CPD excision is most efficient at transcriptional regulatory elements, including enhancers, relative to other genomic sites. Therefore, we analyzed DNA damage maps in ASH1L-proficient and ASH1L-deficient cells to understand how ASH1L controls enhancer stability. This comparison showed that ASH1L protects enhancer sequences against the induction of CPDs besides stimulating repair activity. ASH1L reduces CPD formation at C-containing but not at TT dinucleotides, and no protection occurs against pyrimidine-(6,4)-pyrimidone photoproducts or cisplatin crosslinks. The diminished CPD induction extends to gene promoters but excludes retrotransposons. This guardian role against CPDs in regulatory elements is associated with the presence of H3K4me3 and H3K27ac histone marks, which are known to interact with the PHD and BRD motifs of ASH1L, respectively. Molecular dynamics simulations identified a DNA-binding AT hook of ASH1L that alters the distance and dihedral angle between neighboring C nucleotides to disfavor dimerization. The loss of this protection results in a higher frequency of C->T transitions at enhancers of skin cancers carrying ASH1L mutations compared to ASH1L-intact counterparts.
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Affiliation(s)
- Michelle N Yancoskie
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich 8057, Switzerland
| | - Reihaneh Khaleghi
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich 8057, Switzerland
| | - Anirvinya Gururajan
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500032, India
| | - Aadarsh Raghunathan
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500032, India
| | - Aryan Gupta
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500032, India
| | - Sarah Diethelm
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich 8057, Switzerland
| | - Corina Maritz
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich 8057, Switzerland
| | - Shana J Sturla
- Department of Health Sciences and Technology, ETH Zurich, Zurich 8092, Switzerland
| | - Marimuthu Krishnan
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500032, India
| | - Hanspeter Naegeli
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich 8057, Switzerland
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Lyu R, Gao Y, Wu T, Ye C, Wang P, He C. Quantitative analysis of cis-regulatory elements in transcription with KAS-ATAC-seq. Nat Commun 2024; 15:6852. [PMID: 39127768 PMCID: PMC11316786 DOI: 10.1038/s41467-024-50680-8] [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: 03/06/2024] [Accepted: 07/18/2024] [Indexed: 08/12/2024] Open
Abstract
Cis-regulatory elements (CREs) are pivotal in orchestrating gene expression throughout diverse biological systems. Accurate identification and in-depth characterization of functional CREs are crucial for decoding gene regulation networks during cellular processes. In this study, we develop Kethoxal-Assisted Single-stranded DNA Assay for Transposase-Accessible Chromatin with Sequencing (KAS-ATAC-seq) to quantitatively analyze the transcriptional activity of CREs. A main advantage of KAS-ATAC-seq lies in its precise measurement of ssDNA levels within both proximal and distal ATAC-seq peaks, enabling the identification of transcriptional regulatory sequences. This feature is particularly adept at defining Single-Stranded Transcribing Enhancers (SSTEs). SSTEs are highly enriched with nascent RNAs and specific transcription factors (TFs) binding sites that define cellular identity. Moreover, KAS-ATAC-seq provides a detailed characterization and functional implications of various SSTE subtypes. Our analysis of CREs during mouse neural differentiation demonstrates that KAS-ATAC-seq can effectively identify immediate-early activated CREs in response to retinoic acid (RA) treatment. Our findings indicate that KAS-ATAC-seq provides more precise annotation of functional CREs in transcription. Future applications of KAS-ATAC-seq would help elucidate the intricate dynamics of gene regulation in diverse biological processes.
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Affiliation(s)
- Ruitu Lyu
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA.
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA.
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA.
| | - Yun Gao
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA
| | - Tong Wu
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA
| | - Chang Ye
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA
| | - Pingluan Wang
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA
| | - Chuan He
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA.
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA.
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA.
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, 60637, USA.
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37
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Margetts AV, Vilca SJ, Bourgain-Guglielmetti F, Tuesta LM. Epigenetic heterogeneity shapes the transcriptional landscape of regional microglia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.08.607229. [PMID: 39149259 PMCID: PMC11326298 DOI: 10.1101/2024.08.08.607229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Microglia, the innate immune cells in the central nervous system, exhibit distinct transcriptional profiles across brain regions that are important for facilitating their specialized function. There has been recent interest in identifying the epigenetic modifications associated with these distinct transcriptional profiles, as these may improve our understanding of the underlying mechanisms governing the functional specialization of microglia. One obstacle to achieving this goal is the large number of microglia required to obtain a genome-wide profile for a single histone modification. Given the cellular and regional heterogeneity of the brain, this would require pooling many samples which would impede biological applications that are limited by numbers of available animals. To overcome this obstacle, we have adapted a method of chromatin profiling known as Cleavage Under Targets and Tagmentation (CUT&Tag-Direct) to profile histone modifications associated with regional differences in gene expression throughout the brain reward system. Consistent with previous studies, we find that transcriptional profiles of microglia vary by brain region. However, here we report that these regional differences also exhibit transcriptional network signatures specific to each region. Additionally, we find that these region-dependent network signatures are associated with differential deposition of H3K27ac and H3K7me3, and while the H3K27me3 landscape is remarkably stable across brain regions, the H3K27ac landscape is most consistent with the anatomical location of microglia which explain their distinct transcriptional profiles. Altogether, these findings underscore the established role of H3K27me3 in cell fate determination and support the active role of H3K27ac in the dynamic regulation of microglial gene expression. In this study, we report a molecular and computational framework that can be applied to improve our understanding of the role of epigenetic regulation in microglia in both health and disease, using as few as 2,500 cells per histone mark.
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Affiliation(s)
- Alexander V. Margetts
- Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL 33136
- Center for Therapeutic Innovation, University of Miami Miller School of Medicine, Miami, FL 33136
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136
| | - Samara J. Vilca
- Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL 33136
- Center for Therapeutic Innovation, University of Miami Miller School of Medicine, Miami, FL 33136
| | - Florence Bourgain-Guglielmetti
- Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL 33136
- Center for Therapeutic Innovation, University of Miami Miller School of Medicine, Miami, FL 33136
| | - Luis M. Tuesta
- Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL 33136
- Center for Therapeutic Innovation, University of Miami Miller School of Medicine, Miami, FL 33136
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136
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38
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Xiong S, Zhou J, Tan TK, Chung TH, Tan TZ, Toh SHM, Tang NXN, Jia Y, See YX, Fullwood MJ, Sanda T, Chng WJ. Super enhancer acquisition drives expression of oncogenic PPP1R15B that regulates protein homeostasis in multiple myeloma. Nat Commun 2024; 15:6810. [PMID: 39122682 PMCID: PMC11316114 DOI: 10.1038/s41467-024-50910-z] [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: 06/30/2023] [Accepted: 07/25/2024] [Indexed: 08/12/2024] Open
Abstract
Multiple myeloma is a hematological malignancy arising from immunoglobulin-secreting plasma cells. It remains poorly understood how chromatin rewiring of regulatory elements contributes to tumorigenesis and therapy resistance in myeloma. Here we generate a high-resolution contact map of myeloma-associated super-enhancers by integrating H3K27ac ChIP-seq and HiChIP from myeloma cell lines, patient-derived myeloma cells and normal plasma cells. Our comprehensive transcriptomic and phenomic analyses prioritize candidate genes with biological and clinical implications in myeloma. We show that myeloma cells frequently acquire SE that transcriptionally activate an oncogene PPP1R15B, which encodes a regulatory subunit of the holophosphatase complex that dephosphorylates translation initiation factor eIF2α. Epigenetic silencing or knockdown of PPP1R15B activates pro-apoptotic eIF2α-ATF4-CHOP pathway, while inhibiting protein synthesis and immunoglobulin production. Pharmacological inhibition of PPP1R15B using Raphin1 potentiates the anti-myeloma effect of bortezomib. Our study reveals that myeloma cells are vulnerable to perturbation of PPP1R15B-dependent protein homeostasis, highlighting a promising therapeutic strategy.
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Affiliation(s)
- Sinan Xiong
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Jianbiao Zhou
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
| | - Tze King Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Tae-Hoon Chung
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Tuan Zea Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Sabrina Hui-Min Toh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Nicole Xin Ning Tang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Yunlu Jia
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Yi Xiang See
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Melissa Jane Fullwood
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore
| | - Takaomi Sanda
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Wee-Joo Chng
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Department of Hematology-Oncology, National University Cancer Institute of Singapore (NCIS), National University Health System (NUHS), Singapore, Singapore.
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Du S, Drieu A, Cheng Y, Storck SE, Rustenhoven J, Mamuladze T, Bhattarai B, Brioschi S, Nguyen K, Ou F, Cao J, Rodrigues PF, Smirnov I, DeNardo D, Ginhoux F, Cella M, Colonna M, Kipnis J. Brain-Engrafted Monocyte-derived Macrophages from Blood and Skull-Bone Marrow Exhibit Distinct Identities from Microglia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.08.606900. [PMID: 39211090 PMCID: PMC11361186 DOI: 10.1101/2024.08.08.606900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Microglia are thought to originate exclusively from primitive macrophage progenitors in the yolk sac (YS) and to persist throughout life without much contribution from definitive hematopoiesis. Here, using lineage tracing, pharmacological manipulation, and RNA-sequencing, we elucidated the presence and characteristics of monocyte-derived macrophages (MDMs) in the brain parenchyma at baseline and during microglia repopulation, and defined the core transcriptional signatures of brain-engrafted MDMs. Lineage tracing mouse models revealed that MDMs transiently express CD206 during brain engraftment as CD206 + microglia precursors in the YS. We found that brain-engrafted MDMs exhibit transcriptional and epigenetic characteristics akin to meningeal macrophages, likely due to environmental imprinting within the meningeal space. Utilizing parabiosis and skull transplantation, we demonstrated that monocytes from both peripheral blood and skull bone marrow can repopulate microglia-depleted brains. Our results reveal the heterogeneous origins and cellular dynamics of brain parenchymal macrophages at baseline and in models of microglia depletion.
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40
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LaRue-Nolan KC, Arul GLR, Sigafoos AN, Shi J, Fernandez-Zapico ME. Insights into the mechanisms driven by H3K4 KMTs in pancreatic cancer. Biochem J 2024; 481:983-997. [PMID: 39078225 PMCID: PMC11332384 DOI: 10.1042/bcj20230374] [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: 02/12/2024] [Revised: 07/11/2024] [Accepted: 07/15/2024] [Indexed: 07/31/2024]
Abstract
Pancreatic cancer is a malignancy arising from the endocrine or exocrine compartment of this organ. Tumors from exocrine origin comprise over 90% of all pancreatic cancers diagnosed. Of these, pancreatic ductal adenocarcinoma (PDAC) is the most common histological subtype. The five-year survival rate for PDAC ranged between 5 and 9% for over four decades, and only recently saw a modest increase to ∼12-13%, making this a severe and lethal disease. Like other cancers, PDAC initiation stems from genetic changes. However, therapeutic targeting of PDAC genetic drivers has remained relatively unsuccessful, thus the focus in recent years has expanded to the non-genetic factors underlying the disease pathogenesis. Specifically, it has been proposed that dynamic changes in the epigenetic landscape promote tumor growth and metastasis. Emphasis has been given to the re-organization of enhancers, essential regulatory elements controlling oncogenic gene expression, commonly marked my histone 3 lysine 4 monomethylation (H3K4me1). H3K4me1 is typically deposited by histone lysine methyltransferases (KMTs). While well characterized as oncogenes in other cancer types, recent work has expanded the role of KMTs as tumor suppressor in pancreatic cancer. Here, we review the role and translational significance for PDAC development and therapeutics of KMTs.
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Affiliation(s)
- Kayla C. LaRue-Nolan
- Schulze Center for Novel Therapeutics, Division of Oncology Research, Mayo Clinic, Rochester, MN, U.S.A
- Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN, U.S.A
| | | | - Ashley N. Sigafoos
- Schulze Center for Novel Therapeutics, Division of Oncology Research, Mayo Clinic, Rochester, MN, U.S.A
| | - Jiaqi Shi
- Department of Pathology and Clinical Labs, Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, U.S.A
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Kearly A, Saelee P, Bard J, Sinha S, Satterthwaite A, Garrett-Sinha LA. Sequences within and upstream of the mouse Ets1 gene drive high level expression in B cells, but are not sufficient for consistent expression in T cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.02.606433. [PMID: 39149372 PMCID: PMC11326187 DOI: 10.1101/2024.08.02.606433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
The levels of transcription factor Ets1 are high in resting B and T cells, but are downregulated by signaling through antigen receptors and Toll-like receptors (TLRs). Loss of Ets1 in mice leads to excessive immune cell activation and development of an autoimmune syndrome and reduced Ets1 expression has been observed in human PBMCs in the context of autoimmune diseases. In B cells, Ets1 serves to prevent premature activation and differentiation to antibody-secreting cells. Given these important roles for Ets1 in the immune response, stringent control of Ets1 gene expression levels is required for homeostasis. However, the genetic regulatory elements that control expression of the Ets1 gene remain relatively unknown. Here we identify a topologically-associating domain (TAD) in the chromatin of B cells that includes the mouse Ets1 gene locus and describe an interaction hub that extends over 100 kb upstream and into the gene body. Additionally, we compile epigenetic datasets to find several putative regulatory elements within the interaction hub by identifying regions of high DNA accessibility and enrichment of active enhancer histone marks. Using reporter constructs, we determine that DNA sequences within this interaction hub are sufficient to direct reporter gene expression in lymphoid tissues of transgenic mice. Further analysis indicates that the reporter construct drives faithful expression of the reporter gene in mouse B cells, but variegated expression in T cells, suggesting the existence of T cell regulatory elements outside this region. To investigate how the downregulation of Ets1 transcription is associated with alterations in the epigenetic landscape of stimulated B cells, we performed ATAC-seq in resting and BCR-stimulated primary B cells and identified four regions within and upstream of the Ets1 locus that undergo changes in chromatin accessibility that correlate to Ets1 gene expression. Interestingly, functional analysis of several putative Ets1 regulatory elements using luciferase constructs suggested a high level of functional redundancy. Taken together our studies reveal a complex network of regulatory elements and transcription factors that coordinate the B cell-specific expression of Ets1.
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Affiliation(s)
- Alyssa Kearly
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203
| | - Prontip Saelee
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203
| | - Jonathan Bard
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203
| | - Satrajit Sinha
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203
| | - Anne Satterthwaite
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Lee Ann Garrett-Sinha
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203
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42
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Wilson-Verdugo M, Bustos-García B, Adame-Guerrero O, Hersch-González J, Cano-Domínguez N, Soto-Nava M, Acosta CA, Tusie-Luna T, Avila-Rios S, Noriega LG, Valdes VJ. Reversal of high-glucose-induced transcriptional and epigenetic memories through NRF2 pathway activation. Life Sci Alliance 2024; 7:e202302382. [PMID: 38755006 PMCID: PMC11099870 DOI: 10.26508/lsa.202302382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 04/29/2024] [Accepted: 04/30/2024] [Indexed: 05/18/2024] Open
Abstract
Diabetes complications such as nephropathy, retinopathy, or cardiovascular disease arise from vascular dysfunction. In this context, it has been observed that past hyperglycemic events can induce long-lasting alterations, a phenomenon termed "metabolic memory." In this study, we evaluated the genome-wide gene expression and chromatin accessibility alterations caused by transient high-glucose exposure in human endothelial cells (ECs) in vitro. We found that cells exposed to high glucose exhibited substantial gene expression changes in pathways known to be impaired in diabetes, many of which persist after glucose normalization. Chromatin accessibility analysis also revealed that transient hyperglycemia induces persistent alterations, mainly in non-promoter regions identified as enhancers with neighboring genes showing lasting alterations. Notably, activation of the NRF2 pathway through NRF2 overexpression or supplementation with the plant-derived compound sulforaphane, effectively reverses the glucose-induced transcriptional and chromatin accessibility memories in ECs. These findings underscore the enduring impact of transient hyperglycemia on ECs' transcriptomic and chromatin accessibility profiles, emphasizing the potential utility of pharmacological NRF2 pathway activation in mitigating and reversing the high-glucose-induced transcriptional and epigenetic alterations.
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Affiliation(s)
- Martí Wilson-Verdugo
- https://ror.org/01tmp8f25 Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México
| | - Brandon Bustos-García
- https://ror.org/01tmp8f25 Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México
| | - Olga Adame-Guerrero
- https://ror.org/01tmp8f25 Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México
| | - Jaqueline Hersch-González
- https://ror.org/01tmp8f25 Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México
| | - Nallely Cano-Domínguez
- https://ror.org/01tmp8f25 Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México
| | - Maribel Soto-Nava
- Centre for Research in Infectious Diseases of the National Institute of Respiratory Diseases (CIENI/INER), Mexico City, Mexico
| | | | - Teresa Tusie-Luna
- Unidad de Biología Molecular y Medicina Genómica Instituto de Investigaciones Biomédicas UNAM/Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubiran, Ciudad de México, Mexico
| | - Santiago Avila-Rios
- Centre for Research in Infectious Diseases of the National Institute of Respiratory Diseases (CIENI/INER), Mexico City, Mexico
| | - Lilia G Noriega
- Departamento de Fisiología de la Nutrición, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México, Mexico
| | - Victor J Valdes
- https://ror.org/01tmp8f25 Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México
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43
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Paiva I, Seguin J, Grgurina I, Singh AK, Cosquer B, Plassard D, Tzeplaeff L, Le Gras S, Cotellessa L, Decraene C, Gambi J, Alcala-Vida R, Eswaramoorthy M, Buée L, Cassel JC, Giacobini P, Blum D, Merienne K, Kundu TK, Boutillier AL. Dysregulated expression of cholesterol biosynthetic genes in Alzheimer's disease alters epigenomic signatures of hippocampal neurons. Neurobiol Dis 2024; 198:106538. [PMID: 38789057 DOI: 10.1016/j.nbd.2024.106538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 05/18/2024] [Accepted: 05/20/2024] [Indexed: 05/26/2024] Open
Abstract
Aging is the main risk factor of cognitive neurodegenerative diseases such as Alzheimer's disease, with epigenome alterations as a contributing factor. Here, we compared transcriptomic/epigenomic changes in the hippocampus, modified by aging and by tauopathy, an AD-related feature. We show that the cholesterol biosynthesis pathway is severely impaired in hippocampal neurons of tauopathic but not of aged mice pointing to vulnerability of these neurons in the disease. At the epigenomic level, histone hyperacetylation was observed at neuronal enhancers associated with glutamatergic regulations only in the tauopathy. Lastly, a treatment of tau mice with the CSP-TTK21 epi-drug that restored expression of key cholesterol biosynthesis genes counteracted hyperacetylation at neuronal enhancers and restored object memory. As acetyl-CoA is the primary substrate of both pathways, these data suggest that the rate of the cholesterol biosynthesis in hippocampal neurons may trigger epigenetic-driven changes, that may compromise the functions of hippocampal neurons in pathological conditions.
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Affiliation(s)
- Isabel Paiva
- University of Strasbourg, Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France; CNRS, UMR7364 - Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France.
| | - Jonathan Seguin
- University of Strasbourg, Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France; CNRS, UMR7364 - Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France
| | - Iris Grgurina
- University of Strasbourg, Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France; CNRS, UMR7364 - Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France
| | - Akash Kumar Singh
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, India
| | - Brigitte Cosquer
- University of Strasbourg, Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France; CNRS, UMR7364 - Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France
| | - Damien Plassard
- University of Strasbourg, CNRS UMR7104, Inserm U1258 - GenomEast Platform - IGBMC - Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67404 Illkirch, France
| | - Laura Tzeplaeff
- University of Strasbourg, Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France; CNRS, UMR7364 - Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France
| | - Stephanie Le Gras
- University of Strasbourg, CNRS UMR7104, Inserm U1258 - GenomEast Platform - IGBMC - Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67404 Illkirch, France
| | - Ludovica Cotellessa
- University of Lille, Inserm, CHU Lille, Laboratory of Development and Plasticity of the Postnatal Brain, Lille Neuroscience & Cognition, UMR-S1172, FHU 1000 Days for Health, 59000 Lille, France
| | - Charles Decraene
- University of Strasbourg, Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France; CNRS, UMR7364 - Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France
| | - Johanne Gambi
- University of Strasbourg, Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France; CNRS, UMR7364 - Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France
| | - Rafael Alcala-Vida
- University of Strasbourg, Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France; CNRS, UMR7364 - Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France
| | - Muthusamy Eswaramoorthy
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Luc Buée
- University of Lille, Inserm, CHU Lille, UMR-S1172 LilNCog - Lille Neuroscience & Cognition, Lille, France; Alzheimer and Tauopathies, LabEx DISTALZ, France
| | - Jean-Christophe Cassel
- University of Strasbourg, Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France; CNRS, UMR7364 - Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France
| | - Paolo Giacobini
- University of Lille, Inserm, CHU Lille, Laboratory of Development and Plasticity of the Postnatal Brain, Lille Neuroscience & Cognition, UMR-S1172, FHU 1000 Days for Health, 59000 Lille, France
| | - David Blum
- University of Lille, Inserm, CHU Lille, UMR-S1172 LilNCog - Lille Neuroscience & Cognition, Lille, France; Alzheimer and Tauopathies, LabEx DISTALZ, France
| | - Karine Merienne
- University of Strasbourg, Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France; CNRS, UMR7364 - Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France
| | - Tapas K Kundu
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, India
| | - Anne-Laurence Boutillier
- University of Strasbourg, Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France; CNRS, UMR7364 - Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France.
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Guo M, Wang R, Nie M, Zhang H, Wang C, Song C, Niu S. H3K27ac-induced RHOXF2 activates Wnt2/β-catenin pathway by binding to HOXC13 to aggravate the malignant progression of triple negative breast cancer. Cell Signal 2024; 120:111196. [PMID: 38697448 DOI: 10.1016/j.cellsig.2024.111196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/16/2024] [Accepted: 04/28/2024] [Indexed: 05/05/2024]
Abstract
Triple negative breast cancer (TNBC) is insensitive to conventional targeted therapy and endocrine therapy, and is characterized by high invasiveness and high recurrence rate. This study aimed to explore the role and mechanism of RHOXF2 and HOXC13 on the malignant progression of TNBC. RT-qPCR and western blot were used to detect RHOXF2 and HOXC13 expression in TNBC cells. The proliferation, colony formation, invasion, migration, apoptosis and cell cycle of TNBC cells after transfection were analyzed by CCK-8 assay, colony formation assay, transwell assay, wound healing assay and flow cytometry analysis. Co-Immunoprecipitation and GST pull-down assays were used to analyze the combination between RHOXF2 and HOXC13. ChIP-PCR and luciferase reporter gene assay were used to examine the regulation of H3K27ac on RHOXF2. Besides, the expression of Ki67 and cleaved Caspase3 in tumor tissues of nude mice was determined by immunofluorescence. Results revealed that RHOXF2 and HOXC13 expression was increased in TNBC cells. RHOXF2 knockdown suppressed the proliferation, invasion and migration, as well as induced G0/G1 cell cycle arrest and apoptosis of TNBC cells. Besides, RHOXF2 could bind to HOXC13 and RHOXF2 knockdown suppressed HOXC13 expression in TNBC cells. Furthermore, HOXC13 overexpression reversed the impacts of RHOXF2 downregulation on the proliferation, invasion, migration, G0/G1 cell cycle arrest and apoptosis of TNBC cells. In addition, RHOXF2 silencing limited the tumor volume in nude mice, which was reversed by HOXC13 overexpression. Moreover, RHOXF2 knockdown interfered with Wnt2/β-catenin pathway in vitro and in vivo by binding to HOXC13. Importantly, H3K27ac acetylation could activate the expression of RHOXF2 promoter region. In conclusion, RHOXF2 activated by H3K27ac functioned as a tumor promoter in TNBC via mediating Wnt2/β-catenin pathway by binding to HOXC13, which provided promising insight into exploration on TNBC therapy.
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Affiliation(s)
- Man Guo
- Department of Thyroid and Breast Surgery, Nanyang Central Hospital, Nanyang City, Henan Province 473005, China
| | - Ruoyan Wang
- Department of Thyroid and Breast Surgery, Nanyang Central Hospital, Nanyang City, Henan Province 473005, China
| | - Mandi Nie
- Department of Thyroid and Breast Surgery, Nanyang Central Hospital, Nanyang City, Henan Province 473005, China
| | - Hao Zhang
- Department of Thyroid and Breast Surgery, Nanyang Central Hospital, Nanyang City, Henan Province 473005, China.
| | - Cao Wang
- Department of Thyroid and Breast Surgery, Nanyang Central Hospital, Nanyang City, Henan Province 473005, China
| | - Chunfeng Song
- Department of Thyroid and Breast Surgery, Nanyang Central Hospital, Nanyang City, Henan Province 473005, China
| | - Shurun Niu
- Department of Thyroid and Breast Surgery, Nanyang Central Hospital, Nanyang City, Henan Province 473005, China
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CHEN Y, OUYANG L, MENG L, WU B, PENG R, LIU S, HOU D, WANG Y, JING X, LU S, FU S. Electroacupuncture ameliorates blood-brain barrier disruption after ischemic stroke through histone acetylation regulation at the matrix metalloproteinase 9 and tissue inhibitor of metalloproteinase 2 genes. J TRADIT CHIN MED 2024; 44:734-744. [PMID: 39066534 PMCID: PMC11337257 DOI: 10.19852/j.cnki.jtcm.20240610.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 07/20/2023] [Indexed: 07/28/2024]
Abstract
OBJECTIVE To explore whether the regulation of matrix metalloproteinase 9 (MMP-9)/ tissue inhibitors of MMPs (TIMPs) gene expression through histone acetylation is a possible mechanism by which electroacupuncture (EA) protects blood-brain barrier (BBB) integrity in a middle cerebral artery occlusion (MCAO) rat model. METHODS Male Sprague-Dawley rats were divided into four groups: the sham group, the MCAO group, the MCAO + EA (MEA) group, and the MCAO + EA + HAT inhibitor (HATi) group. The MCAO model was generated by blocking the middle cerebral artery. EA was applied to Baihui (GV20). Samples were collected 1 or 3 d after reperfusion. Neurological function scores and Evans blue extravasation were employed to evaluate the poststroke injury. The effect of EA on MMP-9/TIMPs gene expression was assessed by real-time fluorescence quantitative polymerase chain reaction (RT-qPCR) and chromatin immunoprecipitation (ChIP). RESULTS Our results showed that EA treatment prominently improved neurological function and ameliorated BBB disruption. The RT-qPCR assay showed that EA reduced the expression of MMP-9 and promoted TIMP-2 mRNA expression, but HATi reversed these effects of EA. In addition, ChIP results revealed that EA decreased the enrichment of H3K9ace/H3K27ace at MMP-9 promoters and notably stimulated the recruitment of H3K9ace/H3K27ace at TIMP-2 promoter. CONCLUSION EA treatment at Baihui (GV20) regulates the transcription of MMP-9 and TIMP-2 through histone acetylation modification in the acute stage of stroke, which preserves the structural integrity of the BBB in MCAO rats. These findings suggested that the histone acetylation-mediated transcriptional activity of target genes may be a crucial mechanism of EA treatment in stroke.
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Affiliation(s)
- Yonglin CHEN
- Key Laboratory of Acupuncture and Medicine Research of Ministry of Education, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Ling OUYANG
- Key Laboratory of Acupuncture and Medicine Research of Ministry of Education, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Lingling MENG
- Key Laboratory of Acupuncture and Medicine Research of Ministry of Education, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Bufan WU
- Key Laboratory of Acupuncture and Medicine Research of Ministry of Education, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Rou PENG
- Key Laboratory of Acupuncture and Medicine Research of Ministry of Education, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Sitong LIU
- Key Laboratory of Acupuncture and Medicine Research of Ministry of Education, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Dan HOU
- Key Laboratory of Acupuncture and Medicine Research of Ministry of Education, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Yaling WANG
- Key Laboratory of Acupuncture and Medicine Research of Ministry of Education, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Xinyue JING
- Key Laboratory of Acupuncture and Medicine Research of Ministry of Education, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Shengfeng LU
- Key Laboratory of Acupuncture and Medicine Research of Ministry of Education, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Shuping FU
- Key Laboratory of Acupuncture and Medicine Research of Ministry of Education, Nanjing University of Chinese Medicine, Nanjing 210023, China
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46
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Ali A, Liang P. Transposable elements contribute to tissue-specific gene regulation in humans. Genes Genomics 2024:10.1007/s13258-024-01550-6. [PMID: 39088190 DOI: 10.1007/s13258-024-01550-6] [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: 06/03/2024] [Accepted: 07/15/2024] [Indexed: 08/02/2024]
Abstract
BACKGROUND Transposable elements (TEs) contribute to approximately half of the human genome, and along with many other functions, they have been known to play a role in gene regulation in the genome. With TEs' active/repressed states varying across tissue and cell types, they have the potential to regulate gene expression in a tissue-specific manner. OBJECTIVE AND METHODS To provide a systematic analysis of TEs' contribution in tissue-specific gene regulation, we examined the regulatory elements and genes in association with TE-derived regulatory sequences in 14 human cell lines belonging to 10 different tissue types using the functional genomics data from the ENCODE project. Specifically, we separately analyzed regulatory regions identified by three different approaches (DNase hypersensitive sites (DHS), histone active sites (HA), and histone repressive sites (HR)). RESULTS These regulatory regions showed to be distinct from each other by sharing less than 2.5% among all three types and more than 95% showed to be cell line-specific. Despite a lower total TE content overall than the genome average, each regulatory sequence type showed enrichment for one or two specific TE type(s): DHS for long terminal repeats (LTRs) and DNA transposons, HA for short interspersed nucleotide elements (SINEs), and HR for LTRs. In contrast, SINE was shown to be overrepresented in all three types of regulatory sequences located in gene-neighboring regions. TE-regulated genes were mostly shown to have cell line specific pattern, and tissue-specific genes (TSGs) showed higher usage of TE regulatory sequences in the tissue of their expression. While TEs in the regulatory sequences showed to be older than their genome-wide counterparts, younger TEs were shown to be more likely used in cell line specific regulatory sequences. CONCLUSIONS Collectively, our study provided further evidence enforcing an important contribution of TEs to tissue-specific gene regulation in humans.
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Affiliation(s)
- Arsala Ali
- Department of Biological Sciences, Brock University, St. Catharines, ON, L2S 3A1, Canada
| | - Ping Liang
- Department of Biological Sciences, Brock University, St. Catharines, ON, L2S 3A1, Canada.
- Centre of Biotechnologies, Brock University, St. Catharines, ON, L2S 3A1, Canada.
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McDonald BR, Picard CL, Brabb IM, Savenkova MI, Schmitz RJ, Jacobsen SE, Duttke SH. Enhancers associated with unstable RNAs are rare in plants. NATURE PLANTS 2024; 10:1246-1257. [PMID: 39080503 PMCID: PMC11335568 DOI: 10.1038/s41477-024-01741-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 06/13/2024] [Indexed: 08/07/2024]
Abstract
Unstable transcripts have emerged as markers of active enhancers in vertebrates and shown to be involved in many cellular processes and medical disorders. However, their prevalence and role in plants is largely unexplored. Here, we comprehensively captured all actively initiating (nascent) transcripts across diverse crops and other plants using capped small (cs)RNA sequencing. We discovered that unstable transcripts are rare in plants, unlike in vertebrates, and when present, often originate from promoters. In addition, many 'distal' elements in plants initiate tissue-specific stable transcripts and are likely bona fide promoters of as-yet-unannotated genes or non-coding RNAs, cautioning against using reference genome annotations to infer putative enhancer sites. To investigate enhancer function, we integrated data from self-transcribing active regulatory region (STARR) sequencing. We found that annotated promoters and other regions that initiate stable transcripts, but not those marked by unstable or bidirectional unstable transcripts, showed stronger enhancer activity in this assay. Our findings underscore the blurred line between promoters and enhancers and suggest that cis-regulatory elements can encompass diverse structures and mechanisms in eukaryotes, including humans.
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Affiliation(s)
- Bayley R McDonald
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Colette L Picard
- Department of Molecular Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Ian M Brabb
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Marina I Savenkova
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | | | - Steven E Jacobsen
- Department of Molecular Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA
- Howard Hughes Medical Institute, University of California at Los Angeles, Los Angeles, CA, USA
| | - Sascha H Duttke
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA, USA.
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Xu W, Liu X, Li J, Sun C, Chen L, Zhou J, Li K, Li Q, Meng A, Sun Q. ULI-ssDRIP-seq revealed R-loop dynamics during vertebrate early embryogenesis. CELL INSIGHT 2024; 3:100179. [PMID: 38974143 PMCID: PMC11225018 DOI: 10.1016/j.cellin.2024.100179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/29/2024] [Accepted: 05/29/2024] [Indexed: 07/09/2024]
Abstract
R-loop, a chromatin structure containing one RNA:DNA hybrid and one unpaired single-stranded DNA, plays multiple biological roles. However, due to technical limitations, the landscapes and potential functions of R-loops during embryogenesis remain elusive. Here, we developed a quantitative and high-resolution ultra-low input R-loop profiling method, named ULI-ssDRIP-seq, which can map global R-loops with as few as 1000 cells. By using ULI-ssDRIP-seq, we reveal the R-loop dynamics in the zebrafish from gametes to early embryos. In oocytes, the R-loop level is relatively low in most regions of the nuclear genome, except maternal-inherited rDNA and mitochondrial genome. The correlation between R-loop and CG methylation dynamics during early development is relatively weak. Furthermore, either up- or down-regulation of global R-loops by knockdown or overexpression of RNase H1 causes a delay of embryonic development with dramatic expression changes in zygotic and maternal genes. This study provides comprehensive R-loop landscapes during early vertebrate embryogenesis and demonstrates the implication of R-loops in embryonic development.
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Affiliation(s)
- Wei Xu
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Xin Liu
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Jinjin Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Changbin Sun
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Luxi Chen
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Jincong Zhou
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Kuan Li
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Qin Li
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Anming Meng
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Qianwen Sun
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
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Ning C, Wu X, Zhao X, Lu Z, Yao X, Zhou T, Yi L, Sun Y, Wu S, Liu Z, Huang X, Gao L, Liu J. Epigenomic landscapes during prefrontal cortex development and aging in rhesus. Natl Sci Rev 2024; 11:nwae213. [PMID: 39183748 PMCID: PMC11342245 DOI: 10.1093/nsr/nwae213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 06/07/2024] [Accepted: 06/09/2024] [Indexed: 08/27/2024] Open
Abstract
The prefrontal cortex (PFC) is essential for higher-level cognitive functions. How epigenetic dynamics participates in PFC development and aging is largely unknown. Here, we profiled epigenomic landscapes of rhesus monkey PFCs from prenatal to aging stages. The dynamics of chromatin states, including higher-order chromatin structure, chromatin interaction and histone modifications are coordinated to regulate stage-specific gene transcription, participating in distinct processes of neurodevelopment. Dramatic changes of epigenetic signals occur around the birth stage. Notably, genes involved in neuronal cell differentiation and layer specification are pre-configured by bivalent promoters. We identified a cis-regulatory module and the transcription factors (TFs) associated with basal radial glia development, which was associated with large brain size in primates. These TFs include GLI3, CREB5 and SOX9. Interestingly, the genes associated with the basal radial glia (bRG)-associated cis-element module, such as SRY and SOX9, are enriched in sex differentiation. Schizophrenia-associated single nucleotide polymorphisms are more enriched in super enhancers (SEs) than typical enhancers, suggesting that SEs play an important role in neural network wiring. A cis-regulatory element of DBN1 is identified, which is critical for neuronal cell proliferation and synaptic neuron differentiation. Notably, the loss of distal chromatin interaction and H3K27me3 signal are hallmarks of PFC aging, which are associated with abnormal expression of aging-related genes and transposon activation, respectively. Collectively, our findings shed light on epigenetic mechanisms underlying primate brain development and aging.
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Affiliation(s)
- Chao Ning
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xi Wu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), State Key Laboratory of Drug Regulatory Science, Beijing 102629, China
| | - Xudong Zhao
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Zongyang Lu
- School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China
| | - Xuelong Yao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- GuangzhouNvwa Life Technology Co., Ltd, Guangzhou 510535, China
| | - Tao Zhou
- Shenzhen Neher Neural Plasticity Laboratory, CAS Key Laboratory of Brain Connectome and Manipulation, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Lizhi Yi
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yaoyu Sun
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuaishuai Wu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhenbo Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xingxu Huang
- School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Lei Gao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jiang Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
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50
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Ramamurthy E, Agarwal S, Toong N, Sestili H, Kaplow IM, Chen Z, Phan B, Pfenning AR. Regression convolutional neural network models implicate peripheral immune regulatory variants in the predisposition to Alzheimer's disease. PLoS Comput Biol 2024; 20:e1012356. [PMID: 39186798 PMCID: PMC11389932 DOI: 10.1371/journal.pcbi.1012356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 09/11/2024] [Accepted: 07/23/2024] [Indexed: 08/28/2024] Open
Abstract
Alzheimer's disease (AD) involves aggregation of amyloid β and tau, neuron loss, cognitive decline, and neuroinflammatory responses. Both resident microglia and peripheral immune cells have been associated with the immune component of AD. However, the relative contribution of resident and peripheral immune cell types to AD predisposition has not been thoroughly explored due to their similarity in gene expression and function. To study the effects of AD-associated variants on cis-regulatory elements, we train convolutional neural network (CNN) regression models that link genome sequence to cell type-specific levels of open chromatin, a proxy for regulatory element activity. We then use in silico mutagenesis of regulatory sequences to predict the relative impact of candidate variants across these cell types. We develop and apply criteria for evaluating our models and refine our models using massively parallel reporter assay (MPRA) data. Our models identify multiple AD-associated variants with a greater predicted impact in peripheral cells relative to microglia or neurons. Our results support their use as models to study the effects of AD-associated variants and even suggest that peripheral immune cells themselves may mediate a component of AD predisposition. We make our library of CNN models and predictions available as a resource for the community to study immune and neurological disorders.
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Affiliation(s)
- Easwaran Ramamurthy
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Snigdha Agarwal
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Noelle Toong
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Heather Sestili
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Irene M Kaplow
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Ziheng Chen
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - BaDoi Phan
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Andreas R Pfenning
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
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