1
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Chowdhury SR, Shilpi A, Felsenfeld G. RNA Pol-II transcripts in nucleolar associated domains of cancer cell nucleoli. Nucleus 2025; 16:2468597. [PMID: 39987497 PMCID: PMC11849958 DOI: 10.1080/19491034.2025.2468597] [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: 04/14/2023] [Revised: 01/03/2025] [Accepted: 02/13/2025] [Indexed: 02/25/2025] Open
Abstract
We performed a comparative study of the non-ribosomal gene content of nucleoli from seven cancer cell lines, using identical methods of purification and analysis. We identified unique chromosomal domains associated with the nucleolus (NADs) and genes within these domains (NAGs). Four cell lines have relatively few NAGs, which appears mostly transcriptionally inactive, consistent with literature. The remaining three lines formed a separate group with nucleoli with unique features and NADS. They constitute larger number of common NAGs, marked by ATAC-seq and having accessible promoters, with histone markers for transcriptional activity and detectable RNA Pol II bound at their promoters. The transcripts of these genes are almost entirely exported from the nucleolus. These results indicate that RNA Pol II dependent transcription in NADs can vary widely in different cell types, presumably dependent on the cell's developmental stage. Nucleolus-associated genes are likely to be distinguished marks reflecting the cell's metabolism.
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Affiliation(s)
- Soumya Roy Chowdhury
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases
| | - Arunima Shilpi
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases
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2
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Santosa EK, Zhang JM, Sauter JC, Lee ME, Ng BD, Stulz SV, Takizawa M, Grassmann S, Weizman OE, Adams NM, Chaligné R, Oxenius A, Gasteiger G, Lau CM, Sun JC. Defining molecular circuits of CD8+ T cell responses in tissues during latent viral infection. J Exp Med 2025; 222:e20242078. [PMID: 40387857 DOI: 10.1084/jem.20242078] [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: 11/05/2024] [Revised: 03/18/2025] [Accepted: 04/29/2025] [Indexed: 05/20/2025] Open
Abstract
Latent viral infections rely on a precise coordination of the immune response to control sporadic viral reactivation. CD8+ T cells play a crucial role in controlling viral latency by generating diverse memory responses in an epitope-specific manner. Among these distinct responses, conventional and inflationary memory responses have been described during herpesvirus infections. Using a newly generated TCR transgenic mouse strain, we investigated the transcriptomic and epigenetic remodeling of distinct epitope-specific CD8+ T cells during CMV infection across tissues at both population and single-cell levels. Our findings reveal that whereas the transcriptomic and epigenetic landscapes of conventional and inflationary memory responses diverge in the spleen and liver, these molecular programs converge in the salivary gland, a site of CMV persistence. Thus, we provide evidence that the dynamics of memory CD8+ T cell responses are distinct between tissues.
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Affiliation(s)
- Endi K Santosa
- Immunology Program, Memorial Sloan Kettering Cancer Center , New York, NY, USA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Medical College and Graduate School of Medical Sciences of Cornell University , New York, NY, USA
| | - Jennifer M Zhang
- Immunology Program, Memorial Sloan Kettering Cancer Center , New York, NY, USA
| | - John C Sauter
- Immunology Program, Memorial Sloan Kettering Cancer Center , New York, NY, USA
| | - Mariah E Lee
- Immunology Program, Memorial Sloan Kettering Cancer Center , New York, NY, USA
| | - Brandon D Ng
- Immunology Program, Memorial Sloan Kettering Cancer Center , New York, NY, USA
- Pharmacology Program, Weill Cornell Medical College and Graduate School of Medical Sciences of Cornell University , New York, NY, USA
| | - Sigrun V Stulz
- Würzburg Institute of Systems Immunology, Max Planck Research Group at the Julius-Maximilians-Universität Würzburg , Würzburg, Germany
| | - Meril Takizawa
- Single Cell Analytics Innovation Lab, Memorial Sloan Kettering Cancer Center , New York, NY, USA
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center , New York, NY, USA
| | - Simon Grassmann
- Immunology Program, Memorial Sloan Kettering Cancer Center , New York, NY, USA
| | - Orr-El Weizman
- Immunology Program, Memorial Sloan Kettering Cancer Center , New York, NY, USA
| | - Nicholas M Adams
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
| | - Ronan Chaligné
- Single Cell Analytics Innovation Lab, Memorial Sloan Kettering Cancer Center , New York, NY, USA
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center , New York, NY, USA
| | | | - Georg Gasteiger
- Würzburg Institute of Systems Immunology, Max Planck Research Group at the Julius-Maximilians-Universität Würzburg , Würzburg, Germany
| | - Colleen M Lau
- Department of Microbiology and Immunology, College of Veterinary Medicine of Cornell University, Ithaca, NY, USA
| | - Joseph C Sun
- Immunology Program, Memorial Sloan Kettering Cancer Center , New York, NY, USA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Medical College and Graduate School of Medical Sciences of Cornell University , New York, NY, USA
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3
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Pouncey L, Mok GF. Unravelling early hematoendothelial development through the chick model: Insights and future perspectives. Dev Biol 2025; 523:20-31. [PMID: 40228783 DOI: 10.1016/j.ydbio.2025.04.008] [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: 10/25/2024] [Revised: 03/31/2025] [Accepted: 04/10/2025] [Indexed: 04/16/2025]
Abstract
The chicken embryo has been an important model in advancing our understanding of early hematoendothelial development, particularly in the formation of hematopoietic stem cells (HSCs) and the endothelial-to-hematopoietic transition (EHT). The accessibility and ease of manipulation of chicken embryos have made them an invaluable tool for researching development of blood and endothelial cells. Early research using this model provided pivotal insights, demonstrating that intra-embryonic regions, such as the dorsal aorta (DA), are primary sources of HSCs, rather than the yolk sac (YS), as previously believed. The identification of intra-aortic hematopoietic clusters (IAHCs) and the process of EHT in the chicken embryo laid the foundation for similar discoveries in other vertebrate species, including mice and zebrafish. Recent advances in genetic tools, such as transgenic chickens expressing fluorescent proteins, have further enhanced the precision of cell lineage tracing and real-time imaging of dynamic cellular processes. This review highlights both historical contributions and contemporary advancements facilitated by the chicken model, underscoring its continued relevance in developmental biology. By examining key findings and methodological innovations, we aim to demonstrate the importance of the chicken embryo as a model system for understanding hematoendothelial development and its potential for informing therapeutic applications in regenerative medicine and blood disorders. Finally, we will underscore potential applications of the chicken model for comparative and omics-level studies in conjunction with other model systems and what future directions lie ahead.
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Affiliation(s)
- Lydia Pouncey
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, United Kingdom
| | - Gi Fay Mok
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, United Kingdom.
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4
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Begeman IJ, Guyer ME, Kang J. Cardiac enhancers: Gateway to the regulatory mechanisms of heart regeneration. Semin Cell Dev Biol 2025; 170:103610. [PMID: 40215762 PMCID: PMC12064385 DOI: 10.1016/j.semcdb.2025.103610] [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: 10/14/2024] [Revised: 02/17/2025] [Accepted: 03/31/2025] [Indexed: 05/10/2025]
Abstract
The adult mammalian heart has limited regenerative capacity. Cardiac injury, such as a myocardial infarction (MI), leads to permanent scarring and impaired heart function. In contrast, neonatal mice and zebrafish possess the ability to repair injured hearts. Cardiac regeneration is driven by profound transcriptional changes, which are controlled by gene regulatory elements, such as tissue regeneration enhancer elements (TREEs). Here, we review recent studies on cardiac injury/regeneration enhancers across species. We further explore regulatory mechanisms governing TREE activities and their associated binding regulators. We also discuss the potential of TREE engineering and how these enhancers can be utilized for heart repair. Decoding the regulatory logic of cardiac regeneration enhancers presents a promising avenue for understanding heart regeneration and advancing therapeutic strategies for heart failure.
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Affiliation(s)
- Ian J Begeman
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Megan E Guyer
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Junsu Kang
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA.
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5
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Yamamoto K. How to analyze and understand the human immune system. Semin Arthritis Rheum 2025; 72S:152696. [PMID: 40037996 DOI: 10.1016/j.semarthrit.2025.152696] [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: 01/16/2025] [Accepted: 02/12/2025] [Indexed: 03/06/2025]
Abstract
To enhance our understanding of the pathogenesis of diseases, including rheumatic diseases, and to improve disease control, it is essential to attain a thorough understanding of the human immune system, alongside mouse immunology. Historically, the investigation of the human immune system has posed significant challenges due to methodological limitations. Nonetheless, recent advancements in genomic studies of multifactorial diseases have elucidated that numerous risk-associated genetic variants affecting quantitative differences in cell-specific gene expression. In light of these findings, we are currently examining individual genetic variations in both healthy individuals and patients, as well as categorizing cells into distinct subsets in order to construct a comprehensive dataset concerning the human immune system. This is accomplished by combining data on gene expression, factors influencing the expression mechanisms, protein expression, metabolomics, and environmental variables pertinent to immune functionality-such as gut microbiota. These datasets will facilitate the comprehensive characterization of the human immune system. Using these datasets and through the integrative analyses of data related to risk genetic variations and gene expression profiles of each disease and individual, we anticipate uncovering novel insights into the human immune system, the heterogeneity of diseases, immune function mechanisms, and their regulatory strategies that may not be achievable through murine models.
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6
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Kadagandla S, Gunamalai L, Lee D, Kapoor A. Identification and Functional Assessment of Candidate Causal Cis-Regulatory Variants Underlying Electrocardiographic QT Interval GWAS Loci. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2025:e005032. [PMID: 40421528 DOI: 10.1161/circgen.124.005032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2024] [Accepted: 04/17/2025] [Indexed: 05/28/2025]
Abstract
BACKGROUND Identifying causal variants among tens or hundreds of associated variants at each locus in genome-wide association studies (GWAS) is challenging. As the vast majority of GWAS variants are noncoding, sequence variation at cis-regulatory elements (CREs) affecting transcriptional expression of specific genes is a widely accepted molecular hypothesis. Following this hypothesis, combined with the observation that open chromatin is a universal hallmark of all types of CREs, we aimed to identify candidate causal cis-regulatory variants underlying QT interval GWAS loci. METHODS Common variants in high linkage disequilibrium with genome-wide significant variants were identified using variant call format tools. Genome-wide maps of cardiac putative CREs were generated by MACS2-based peak calling in human cardiac left ventricular DNase I sequencing and Assay for Transposase-Accessible Chromatin using sequencing data sets (n=13). Variant-CRE overlap was performed using custom tracks in the Table Browser tool at the UCSC Genome Browser. Luciferase reporter-based enhancer assays for variant-centered test elements were performed in mouse HL1 cardiomyocyte cells. Reporter activities of allelic pairs were compared using a Student t test. RESULTS At a dozen GWAS loci, selected for higher effect sizes and better understanding of the likely causal genes, we identified all genome-wide significant variants (n=1401) and included all common variants (minor allele frequency >1%) in high linkage disequilibrium (r2>0.9) with them as candidate variants (n=3482). Candidate variants were filtered for overlap with cardiac left ventricular putative CREs to identify candidate causal cis-regulatory variants (n=476), which were further assessed for being a known cardiac expression quantitative trait locus variant as additional functional evidence (n=243). Functional evaluation of a subset of seven candidate variants by luciferase reporter-based enhancer assays in HL1 cells using variant-centered test elements led to the identification of 6 enhancer variants with significant allelic differences. CONCLUSIONS These efforts have generated a comprehensive set of candidate causal variants expected to be enriched for cis-regulatory potential and thereby, explaining the observed genetic associations.
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Affiliation(s)
- Supraja Kadagandla
- Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston (S.K., L.G., A.K.)
- Department of Biosciences, Rice University, Houston, TX (S.K.)
| | - Lavanya Gunamalai
- Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston (S.K., L.G., A.K.)
| | - Dongwon Lee
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, MA (D.L.)
| | - Ashish Kapoor
- Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston (S.K., L.G., A.K.)
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7
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Saeki K, Ozato K. Transcription factors that define the epigenome structures and transcriptomes in microglia. Exp Hematol 2025:104814. [PMID: 40425139 DOI: 10.1016/j.exphem.2025.104814] [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: 02/28/2025] [Revised: 05/08/2025] [Accepted: 05/10/2025] [Indexed: 05/29/2025]
Abstract
Microglia, the resident macrophages of the brain, play critical roles in maintaining brain health. Recent genome-wide analyses, including ATAC-seq, ChIP-seq/CUT&RUN, and single-cell RNA-seq, have identified key transcription factors that define the transcriptome programs of microglia. Four transcription factors-PU.1, IRF8, SALL1, and SMAD4-form enhancer complexes and act as lineage-determining factors, shaping microglial identity. These factors co-bind with other lineage-determining transcription factors, directing one towards designated regions that program microglia while inhibiting the other from binding to DNA. Other transcription factors, such as BATF3 and MAFB, contribute to transcriptional cascades in microglia. TGF-β is a crucial cytokine driving these transcription factors to bind DNA and maintain homeostatic microglia. These findings provide insights into the physiological aspects of microglia and their roles in neuroinflammatory and neurodegenerative diseases. TEASER ABSTRACT: eTOC blurb: In this article, we compiled more than 100 transcription factors expressed in microglia. Our analysis illustrates that some transcription factors are under a distinct hierarchical rank and are sequentially activated to achieve microglia specific transcriptome programs. This article offers a new scope on the mechanistic foundation underlying microglia's complex activity.
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Affiliation(s)
- Keita Saeki
- Section on Molecular Genetics of Immunity, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Keiko Ozato
- Section on Molecular Genetics of Immunity, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
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8
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Fu Y, Okawa H, Vinaikosol N, Mori S, Limraksasin P, Nattasit P, Tahara Y, Egusa H. Shaking culture attenuates circadian rhythms in induced pluripotent stem cells during osteogenic differentiation through the TEAD-Fbxl3-CRY axis. Cell Death Discov 2025; 11:252. [PMID: 40413171 PMCID: PMC12103599 DOI: 10.1038/s41420-025-02533-6] [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: 12/04/2024] [Revised: 05/04/2025] [Accepted: 05/13/2025] [Indexed: 05/27/2025] Open
Abstract
Circadian rhythms, which synchronize cellular and organismal activities with the Earth's 24-hour light-dark cycle, are controlled by clock genes. These genes not only regulate metabolic and physiological processes but also influence osteogenesis. Despite extensive research on the genetic control of circadian rhythms, little is known about the mechanisms by which mechanical factors in the extracellular environment affect these rhythms during the osteogenic differentiation of induced pluripotent stem cells (iPSCs). Shaking culture, which promotes the formation of three-dimensional organoid-like constructs from iPSC embryoid bodies (iPSC-EBs), introduces distinct biomechanical forces compared with static adherent culture. This raises the question of how these forces affect the circadian gene expression during osteogenic differentiation. In this study, we investigated the effects of shaking cultures on the circadian rhythm of key clock genes (Clock, Bmal1, and Npas2) in iPSC-EBs. In the adherent culture, iPSC-EBs displayed rhythmic oscillations of the clock genes, which were attenuated in the shaking culture. RNA-seq analysis revealed that the yes-associated protein (YAP)-transcriptional enhanced associate domain (TEAD) transcriptional cascade was activated in the shaking culture. Further investigations using assay for transposase-accessible chromatin with sequencing and chromatin immunoprecipitation assays identified Fbxl3 as a direct target of this transcriptional cascade. Fbxl3 upregulation in the shaking culture enhanced the degradation of CRY proteins, which are essential components of the circadian feedback loop, thereby suppressing clock gene oscillations. In addition, treatment with verteporfin, a YAP-TEAD inhibitor, restored circadian gene oscillations and increased the expression of osteogenic markers in shaking culture. These findings highlight a novel mechanistic link between biomechanical cues and circadian regulation and offer potential insights for optimizing tissue engineering strategies in regenerative medicine.
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Affiliation(s)
- Yunyu Fu
- Division of Molecular and Regenerative Prosthodontics, Tohoku University Graduate School of Dentistry, Sendai, Miyagi, Japan
| | - Hiroko Okawa
- Division of Molecular and Regenerative Prosthodontics, Tohoku University Graduate School of Dentistry, Sendai, Miyagi, Japan.
| | - Naruephorn Vinaikosol
- Division of Molecular and Regenerative Prosthodontics, Tohoku University Graduate School of Dentistry, Sendai, Miyagi, Japan
| | - Satomi Mori
- Division of Molecular and Regenerative Prosthodontics, Tohoku University Graduate School of Dentistry, Sendai, Miyagi, Japan
| | - Phoonsuk Limraksasin
- Division of Molecular and Regenerative Prosthodontics, Tohoku University Graduate School of Dentistry, Sendai, Miyagi, Japan
- Center of Excellence for Dental Stem Cell Biology, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand
| | - Praphawi Nattasit
- Division of Molecular and Regenerative Prosthodontics, Tohoku University Graduate School of Dentistry, Sendai, Miyagi, Japan
- Department of Oral Medicine and Periodontology, Faculty of Dentistry, Mahidol University, Bangkok, Thailand
| | - Yu Tahara
- Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Hiroshi Egusa
- Division of Molecular and Regenerative Prosthodontics, Tohoku University Graduate School of Dentistry, Sendai, Miyagi, Japan.
- Center of Excellence for Dental Stem Cell Biology, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand.
- Center for Advanced Stem Cell and Regenerative Research, Tohoku University Graduate School of Dentistry, Sendai, Miyagi, Japan.
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9
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Kraft M, Schoofs H, Petkova M, Andrade J, Grosso AR, Benedito R, De Roo AK, Boon LM, Vikkula M, Kapp FG, Hägerling R, Potente M, Mäkinen T. Angiopoietin-TIE2 feedforward circuit promotes PIK3CA-driven venous malformations. NATURE CARDIOVASCULAR RESEARCH 2025:10.1038/s44161-025-00655-9. [PMID: 40410415 DOI: 10.1038/s44161-025-00655-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 04/11/2025] [Indexed: 05/25/2025]
Abstract
Venous malformations (VMs) are vascular anomalies lacking curative treatments, often caused by somatic PIK3CA mutations that hyperactivate the PI3Kα-AKT-mTOR signaling pathway. Here, we identify a venous-specific signaling circuit driving disease progression, where excessive PI3Kα activity amplifies upstream TIE2 receptor signaling through autocrine and paracrine mechanisms. In Pik3caH1047R-driven VM mouse models, single-cell transcriptomics and lineage tracking revealed clonal expansion of mutant endothelial cells with a post-capillary venous phenotype, characterized by suppression of the AKT-inhibited FOXO1 and its target genes, including the TIE2 antagonist ANGPT2. An imbalance in TIE2 ligands, likely exacerbated by aberrant recruitment of smooth muscle cells producing the agonist ANGPT1, increased TIE2 activity in both mouse and human VMs. While mTOR blockade had limited effects on advanced VMs in mice, inhibiting TIE2 or ANGPT effectively suppressed their growth. These findings uncover a PI3K-FOXO1-ANGPT-TIE2 circuit as a core driver of PIK3CA-related VMs and highlight TIE2 as a promising therapeutic target.
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Affiliation(s)
- Marle Kraft
- Uppsala University, Department of Immunology, Genetics and Pathology, Uppsala, Sweden
| | - Hans Schoofs
- Uppsala University, Department of Immunology, Genetics and Pathology, Uppsala, Sweden
| | - Milena Petkova
- Uppsala University, Department of Immunology, Genetics and Pathology, Uppsala, Sweden
| | - Jorge Andrade
- Angiogenesis & Metabolism Laboratory, Center of Vascular Biomedicine, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Ana Rita Grosso
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Lisbon, Portugal
- UCIBIO - Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - Rui Benedito
- Molecular Genetics of Angiogenesis Group. Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - An-Katrien De Roo
- Center for Vascular Anomalies, VASCERN VASCA European Reference Center, Cliniques Universitaires Saint Luc, UCLouvain, Brussels, Belgium
- Department of Pathology, Cliniques Universitaires Saint-Luc, Université Catholique de Louvain (UCLouvain), Brussels, Belgium
- Institute of Experimental and Clinical Research, UCLouvain, Brussels, Belgium
| | - Laurence M Boon
- Center for Vascular Anomalies, VASCERN VASCA European Reference Center, Cliniques Universitaires Saint Luc, UCLouvain, Brussels, Belgium
- Division of Plastic Surgery, Cliniques Universitaires Saint-Luc, Université Catholique de Louvain (UCLouvain), Brussels, Belgium
- Laboratory of Human Molecular Genetics, de Duve Institute, UCLouvain, Brussels, Belgium
| | - Miikka Vikkula
- Center for Vascular Anomalies, VASCERN VASCA European Reference Center, Cliniques Universitaires Saint Luc, UCLouvain, Brussels, Belgium
- Laboratory of Human Molecular Genetics, de Duve Institute, UCLouvain, Brussels, Belgium
- WELBIO Department, WEL Research Institute, Wavre, Belgium
| | - Friedrich G Kapp
- Department of Pediatric Hematology and Oncology, Children's Hospital, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, VASCERN VASCA European Reference Center, Freiburg, Germany
| | - René Hägerling
- Research Group 'Lymphovascular Medicine and Translational 3D-Histopathology', Institute of Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, BIH Center for Regenerative Therapies, Berlin, Germany
| | - Michael Potente
- Angiogenesis & Metabolism Laboratory, Center of Vascular Biomedicine, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Taija Mäkinen
- Uppsala University, Department of Immunology, Genetics and Pathology, Uppsala, Sweden.
- Translational Cancer Medicine Program and Department of Biochemistry and Developmental Biology, University of Helsinki, Helsinki, Finland.
- Wihuri Research Institute, Helsinki, Finland.
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10
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Kosicki M, Laboy Cintrón D, Keukeleire P, Schubach M, Page NF, Georgakopoulos-Soares I, Akiyama JA, Plajzer-Frick I, Novak CS, Kato M, Hunter RD, von Maydell K, Barton S, Godfrey P, Beckman E, Sanders SJ, Kircher M, Pennacchio LA, Ahituv N. Massively parallel reporter assays and mouse transgenic assays provide correlated and complementary information about neuronal enhancer activity. Nat Commun 2025; 16:4786. [PMID: 40404660 PMCID: PMC12098896 DOI: 10.1038/s41467-025-60064-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 05/13/2025] [Indexed: 05/24/2025] Open
Abstract
High-throughput massively parallel reporter assays (MPRAs) and phenotype-rich in vivo transgenic mouse assays are two potentially complementary ways to study the impact of noncoding variants associated with psychiatric diseases. Here, we investigate the utility of combining these assays. Specifically, we carry out an MPRA in induced human neurons on over 50,000 sequences derived from fetal neuronal ATAC-seq datasets and enhancers validated in mouse assays. We also test the impact of over 20,000 variants, including synthetic mutations and 167 common variants associated with psychiatric disorders. We find a strong and specific correlation between MPRA and mouse neuronal enhancer activity. Four out of five tested variants with significant MPRA effects affected neuronal enhancer activity in mouse embryos. Mouse assays also reveal pleiotropic variant effects that could not be observed in MPRA. Our work provides a catalog of functional neuronal enhancers and variant effects and highlights the effectiveness of combining MPRAs and mouse transgenic assays.
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Affiliation(s)
- Michael Kosicki
- Environmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Dianne Laboy Cintrón
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, 94158, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Pia Keukeleire
- Institute of Human Genetics, University Medical Center Schleswig-Holstein, University of Lübeck, 23562, Lübeck, Germany
| | - Max Schubach
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, 10117, Berlin, Germany
| | - Nicholas F Page
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, 94158, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, 94158, USA
- Department of Psychiatry and Behavioral Sciences, Kavli Institute for Fundamental Neuroscience, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Ilias Georgakopoulos-Soares
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Jennifer A Akiyama
- Environmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Ingrid Plajzer-Frick
- Environmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Catherine S Novak
- Environmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Momoe Kato
- Environmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Riana D Hunter
- Environmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Kianna von Maydell
- Environmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Sarah Barton
- Environmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Patrick Godfrey
- Environmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Erik Beckman
- Environmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Stephan J Sanders
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, 94158, USA
- Department of Psychiatry and Behavioral Sciences, Kavli Institute for Fundamental Neuroscience, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Institute of Developmental and Regenerative Medicine, Department of Paediatrics, University of Oxford, Oxford, OX3 16 7TY, UK
| | - Martin Kircher
- Institute of Human Genetics, University Medical Center Schleswig-Holstein, University of Lübeck, 23562, Lübeck, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, 10117, Berlin, Germany
| | - Len A Pennacchio
- Environmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, 94158, USA.
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, 94158, USA.
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11
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Prince NH, Hamamura M, Zhou Y, Fujita Y. An ATAC-seq protocol for neuroscience research. Anat Sci Int 2025:10.1007/s12565-025-00850-5. [PMID: 40402346 DOI: 10.1007/s12565-025-00850-5] [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: 03/20/2025] [Accepted: 05/02/2025] [Indexed: 05/23/2025]
Abstract
ATAC-seq (assay for transposase-accessible chromatin using sequencing) enables high resolution mapping of chromatin accessibility, providing critical insights into gene regulatory mechanisms in neuroscience research. This protocol presents an optimized approach for applying ATAC-seq to neural tissues and cells, addressing the unique challenges of preserving chromatin integrity in these delicate samples. We detail the key steps of tissue processing, nuclear isolation, transposition reactions, and library preparation specifically adapted for neural applications. The method requires minimal starting material (20,000-50,000 cells) while maintaining high sensitivity for detecting regulatory elements involved in neural development, plasticity, and neurological disorders. This tailored protocol facilitates robust investigation of neuroepigenomic regulation in diverse experimental contexts.
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Affiliation(s)
- Nur Hasan Prince
- Department of Anatomy and Developmental Biology, School of Medicine, Shimane University, 89-1, En-Ya-Cho, Izumo-Shi, Shimane, 693-8501, Japan
| | - Misako Hamamura
- Department of Anatomy and Developmental Biology, School of Medicine, Shimane University, 89-1, En-Ya-Cho, Izumo-Shi, Shimane, 693-8501, Japan
| | - Yi Zhou
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yuki Fujita
- Department of Anatomy and Developmental Biology, School of Medicine, Shimane University, 89-1, En-Ya-Cho, Izumo-Shi, Shimane, 693-8501, Japan.
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12
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Wang Y, Yildirim A, Boninsegna L, Christian V, Kang SHL, Zhou XJ, Alber F. 3D genome organization shapes DNA damage susceptibility to platinum-based drugs. Nucleic Acids Res 2025; 53:gkaf315. [PMID: 40433977 DOI: 10.1093/nar/gkaf315] [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: 06/25/2024] [Revised: 03/31/2025] [Accepted: 05/23/2025] [Indexed: 05/29/2025] Open
Abstract
Platinum (Pt) drugs are widely utilized in cancer chemotherapy. Although cytotoxic and resistance mechanisms of Pt drugs have been thoroughly explored, it remains elusive what factors affect the receptiveness of DNA to drug-induced damage in nuclei. Here, we demonstrate that nuclear locations of chromatin play a key role in Pt drug-induced DNA damage susceptibility in vivo. By integrating data from damage-seq experiments with 3D genome structure information, we show that nuclear locations of chromatin relative to specific nuclear bodies and compartments explain patterns of cisplatin DNA damage susceptibility. This aligns with observations of cisplatin enrichment in biomolecular condensates at certain nuclear bodies. Finally, 3D structure mapping of DNA damage reveals characteristic differences between nuclear distributions of oxaliplatin-induced DNA damage in drug resistant versus sensitive cells. DNA damage increases in gene-poor chromatin at the nuclear periphery, while it decreases in gene-rich regions located at nuclear speckles. This suggests a strategic redistribution of Pt drug-induced damage in nuclei during chemoresistance development.
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Affiliation(s)
- Ye Wang
- Institute of Quantitative and Computational Biosciences (QCBio), University of California Los Angeles, Los Angeles CA90095, United States
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, 520 Boyer Hall, Los Angeles CA90095, United States
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, 10833 Le Conte Ave, Los Angeles CA90095, United States
| | - Asli Yildirim
- Institute of Quantitative and Computational Biosciences (QCBio), University of California Los Angeles, Los Angeles CA90095, United States
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, 520 Boyer Hall, Los Angeles CA90095, United States
| | - Lorenzo Boninsegna
- Institute of Quantitative and Computational Biosciences (QCBio), University of California Los Angeles, Los Angeles CA90095, United States
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, 520 Boyer Hall, Los Angeles CA90095, United States
| | - Valentina Christian
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, 10833 Le Conte Ave, Los Angeles CA90095, United States
| | - Sung-Hae L Kang
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, 10833 Le Conte Ave, Los Angeles CA90095, United States
| | - Xianghong Jasmine Zhou
- Institute of Quantitative and Computational Biosciences (QCBio), University of California Los Angeles, Los Angeles CA90095, United States
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, 10833 Le Conte Ave, Los Angeles CA90095, United States
| | - Frank Alber
- Institute of Quantitative and Computational Biosciences (QCBio), University of California Los Angeles, Los Angeles CA90095, United States
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, 520 Boyer Hall, Los Angeles CA90095, United States
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13
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Yang W, Wang XQ, Wei F, Yu J, Liu Y, Dou Y. Revealing long-range heterogeneous organization of nucleoproteins with 6mA footprinting by ipdTrimming. Genome Biol 2025; 26:136. [PMID: 40399934 PMCID: PMC12096735 DOI: 10.1186/s13059-025-03592-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2024] [Accepted: 04/27/2025] [Indexed: 05/23/2025] Open
Abstract
Enabled by long-read sequencing technologies, particularly Single Molecule, Real-Time sequencing, N6-methyladenine (6mA) footprinting is a transformative methodology for revealing the heterogenous and dynamic distribution of nucleosomes and other DNA-binding proteins. Here, we present ipdTrimming, a novel 6mA-calling pipeline that outperforms existing tools in both computational efficiency and accuracy. Utilizing this optimized experimental and computational framework, we are able to map nucleosome positioning and transcription factor occupancy in nuclear DNA and establish high-resolution, long-range binding events in mitochondrial DNA. Our study highlights the potential of 6mA footprinting to capture coordinated nucleoprotein binding and to unravel epigenetic heterogeneity.
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Affiliation(s)
- Wentao Yang
- Department of Cancer Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Xue Qing Wang
- Department of Cancer Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Fan Wei
- Department of Cancer Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Jingqi Yu
- Department of Cancer Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
- University of Chinese Academy of Sciences, Beijing, 100864, China
| | - Yifan Liu
- Department of Cancer Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA.
| | - Yali Dou
- Department of Cancer Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA.
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA.
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14
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Tang L, Zhang J, Shao Y, Wei Y, Li Y, Tian K, Yan X, Feng C, Zhang QC. Joint analysis of chromatin accessibility and gene expression in the same single cells reveals cancer-specific regulatory programs. Cell Syst 2025; 16:101266. [PMID: 40262617 DOI: 10.1016/j.cels.2025.101266] [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: 08/18/2024] [Revised: 01/19/2025] [Accepted: 03/28/2025] [Indexed: 04/24/2025]
Abstract
Biological analyses conducted at the single-cell scale have revealed profound impacts of heterogeneity and plasticity of chromatin states and gene expression on physiology and cancer. Here, we developed Parallel-seq, a technology for simultaneously measuring chromatin accessibility and gene expression in the same single cells. By combining combinatorial cell indexing and droplet overloading, Parallel-seq generates high-quality data in an ultra-high-throughput fashion and at a cost two orders of magnitude lower than alternative technologies (10× Multiome and ISSAAC-seq). We applied Parallel-seq to 40 lung tumor and tumor-adjacent clinical samples and obtained over 200,000 high-quality joint scATAC-and-scRNA profiles. Leveraging this large dataset, we characterized copy-number variations (CNVs) and extrachromosomal circular DNA (eccDNA) heterogeneity in tumor cells, predicted hundreds of thousands of cell-type-specific regulatory events, and identified enhancer mutations affecting tumor progression. Our analyses highlight Parallel-seq's power in investigating epigenetic and genetic factors driving cancer development at the cell-type-specific level and its utility for revealing vulnerable therapeutic targets.
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Affiliation(s)
- Lei Tang
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China; MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Jinsong Zhang
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China; MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Yanqiu Shao
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China; MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Yifan Wei
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China; MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Yuzhe Li
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China; MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Kang Tian
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China; MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Xiang Yan
- Department of Medical Oncology, the Fifth Medical Center, Beijing 301 Hospital, Beijing 100039, China
| | - Changjiang Feng
- Department of Thoracic Surgery, the First Medical Center, Beijing 301 Hospital, Beijing 100039, China.
| | - Qiangfeng Cliff Zhang
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China; MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China.
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15
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Mok CH, Hu D, Losa M, Risolino M, Selleri L, Marcucio RS. PBX1 and PBX3 transcription factors regulate SHH expression in the Frontonasal Ectodermal Zone through complementary mechanisms. PLoS Genet 2025; 21:e1011315. [PMID: 40397886 DOI: 10.1371/journal.pgen.1011315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 04/22/2025] [Indexed: 05/23/2025] Open
Abstract
Sonic hedgehog (SHH) signaling from the frontonasal ectodermal zone (FEZ) is a key regulator of craniofacial morphogenesis. Along with SHH, pre-B-cell leukemia homeobox (PBX) transcription factors regulate midfacial development. PBXs act in the epithelium during fusion of facial primordia, but their specific interactions with SHH have not been investigated. We hypothesized that PBX1/3 regulate SHH expression in the FEZ by activating or repressing transcription. The hypothesis was tested by manipulating PBX1/3 expression in chick embryos and profiling epigenomic landscapes at early developmental stages. PBX1/3 expression was perturbed in the chick face beginning at stage 10 (HH10) using RCAS viruses, and the resulting SHH expression was assessed at HH22. Overexpressing PBX1 expanded the SHH domain, while overexpressing PBX3 resulted in an opposite effect. Conversely, reducing PBX1 expression decreased SHH expression, but reducing PBX3 induced ectopic SHH expression. We performed ATAC-seq and mapped binding of PBX1 and PBX3 to DNA with ChIP-seq on the FEZ at HH22 to assess direct interactions of PBX1/3 with the SHH locus. These multi-omics approaches uncovered a 400 bp PBX1-enriched element within intron 1 of SHH (chr2:8,173,222-8,173,621). Enhancer activity of this element was demonstrated by electroporation of reporter constructs in ovo and luciferase reporter assays in vitro. When bound by PBX1, this element upregulates transcription, while it downregulates transcription when bound by PBX3. The present study identifies a cis-regulatory element, named SFE1, that interacts with PBX1/3 either directly or within a complex with cofactors to modulate SHH expression in the FEZ. This research establishes that PBX1 and PBX3 play complementary roles in SHH regulation during embryonic development.
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Affiliation(s)
- Chan Hee Mok
- Department of Orthopaedic Surgery, Zuckerberg San Francisco General Hospital, Orthopaedic Trauma Institute, University of California, San Francisco, United States of America
| | - Diane Hu
- Department of Orthopaedic Surgery, Zuckerberg San Francisco General Hospital, Orthopaedic Trauma Institute, University of California, San Francisco, United States of America
| | - Marta Losa
- Department of Orofacial Sciences and Department of Anatomy, Institute of Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, California, United States of America
| | - Maurizio Risolino
- Department of Orofacial Sciences and Department of Anatomy, Institute of Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, California, United States of America
| | - Licia Selleri
- Department of Orofacial Sciences and Department of Anatomy, Institute of Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, California, United States of America
| | - Ralph S Marcucio
- Department of Orthopaedic Surgery, Zuckerberg San Francisco General Hospital, Orthopaedic Trauma Institute, University of California, San Francisco, United States of America
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16
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Zhao S, Yang Q, Yu Z, Chu C, Dai S, Li H, Diao M, Feng L, Ke J, Xue Y, Zhou Q, Liu Y, Ma H, Lin CP, Yao YG, Zhong G. Deciphering enhancers of hearing loss genes for efficient and targeted gene therapy of hereditary deafness. Neuron 2025; 113:1579-1596.e5. [PMID: 40262614 DOI: 10.1016/j.neuron.2025.03.023] [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: 12/22/2024] [Revised: 02/23/2025] [Accepted: 03/18/2025] [Indexed: 04/24/2025]
Abstract
Hereditary hearing loss accounts for about 60% of congenital deafness. Although adeno-associated virus (AAV)-mediated gene therapy shows substantial potential for treating genetic hearing impairments, there remain significant concerns regarding the specificity and safety of AAV vectors. The sophisticated nature of the cochlea further complicates the challenge of precisely targeting gene delivery. Here, we introduced an AAV-reporter-based in vivo transcriptional enhancer reconstruction (ARBITER) workflow, enabling efficient and reliable dissection of enhancers. With ARBITER, we successfully demonstrated that the conserved non-coding elements (CNEs) within the gene locus collaboratively regulate the expression of Slc26a5, which was further validated using knockout mouse models. We also assessed the potential of identified enhancers to treat hereditary hearing loss by conducting gene therapy in Slc26a5 mutant mice. Based on the original Slc26a5 enhancer with limited efficiency, we engineered a highly efficient and outer hair cell (OHC)-specific enhancer, B8, which successfully restored hearing of Slc26a5 knockout mice.
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Affiliation(s)
- Simeng Zhao
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China.
| | - Qiuxiang Yang
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Zehua Yu
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Cenfeng Chu
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
| | - Shengqi Dai
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Hongli Li
- State Key Laboratory of Genetic Evolution and Animal Models, Yunnan Key Laboratory of Animal Models and Human Disease Mechanisms, Yunnan Engineering Center on Brain Disease Models, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650204, China; National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), and National Resource Center for Non-Human Primates, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650107, Yunnan, China
| | - Min Diao
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
| | - Lingyue Feng
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Junzi Ke
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yilin Xue
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Qifang Zhou
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yan Liu
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
| | - Hanhui Ma
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Chao-Po Lin
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yong-Gang Yao
- State Key Laboratory of Genetic Evolution and Animal Models, Yunnan Key Laboratory of Animal Models and Human Disease Mechanisms, Yunnan Engineering Center on Brain Disease Models, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650204, China; National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), and National Resource Center for Non-Human Primates, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650107, Yunnan, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, Yunnan, China
| | - Guisheng Zhong
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Shanghai Clinical Research and Trial Center, Shanghai 201210, China; Shanghai Key Laboratory of High-Resolution Electron Microscopy, ShanghaiTech University, Shanghai 201210, China; Shanghai Key Laboratory of Gene Editing and Cell Therapy for Rare Diseases, Fudan University, Shanghai 20031, China.
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17
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Auer F, Morcos MNF, Sipola M, Akhtar I, Moisio S, Vogt J, Haag R, Lahnalampi M, Tuononen TJ, Hanel A, Viitasalo A, Friedrich UA, Dahl A, Prexler C, Pandyra AA, Stepensky P, Takagi M, Borkhardt A, Heinäniemi M, Hauer J. Trajectories from single-cells to PAX5-driven leukemia reveal PAX5-MYC interplay in vivo. Leukemia 2025:10.1038/s41375-025-02626-2. [PMID: 40394211 DOI: 10.1038/s41375-025-02626-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Revised: 03/31/2025] [Accepted: 04/22/2025] [Indexed: 05/22/2025]
Abstract
PAX5 acts as a master regulator of B-cell proliferation and differentiation. Its germline and somatic deregulation have both been implicated in the development of B-cell precursor acute lymphoblastic leukemia (BCP-ALL). However, the process how reduced PAX5 transcriptional activity mediates progression to BCP-ALL, is still poorly understood. Here, we characterized the longitudinal effects of PAX5 reduction on healthy, pre-leukemic and BCP-ALL cells at the single-cell level. Cell-surface marker analysis revealed a genotype-driven enrichment of the pre-BII population in healthy Pax5± mice. This population showed downregulated B-cell receptor signaling, while DNA replication/repair and cell-cycle signaling pathways were upregulated. Moreover, we observed a shift in the kappa/lambda light chain ratio toward lambda rearranged B-cells. Transplantation experiments further validated a delay of Pax5± pre-BII cells in maturation and transition to IgM-positivity. Additionally, single-cell RNA-Sequencing and bulk ATAC-Sequencing of different stages of BCP-ALL evolution showed that Pax5± pre-leukemic cells lose their B-cell identity and display Myc activation. Subsequently, BCP-ALLs acquired additional RAG-mediated aberrations and driver mutations in JAK-STAT and RAS-signaling pathways. Together, this study elucidates molecular and functional checkpoints in PAX5-mediated pre-leukemic cell progression exploitable for therapeutic intervention and demonstrates that PAX5 reduction is sufficient to initiate clonal evolution to BCP-ALL through activation of MYC.
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Affiliation(s)
- Franziska Auer
- Technical University of Munich, Germany; School of Medicine and Health; Department of Pediatrics, Munich, Germany
| | - Mina N F Morcos
- Technical University of Munich, Germany; School of Medicine and Health; Department of Pediatrics, Munich, Germany
| | - Mikko Sipola
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Yliopistonranta 8, FI-70211, Kuopio, Finland
| | - Irfan Akhtar
- Technical University of Munich, Germany; School of Medicine and Health; Department of Pediatrics, Munich, Germany
| | - Sanni Moisio
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Yliopistonranta 8, FI-70211, Kuopio, Finland
| | - Julia Vogt
- Technical University of Munich, Germany; School of Medicine and Health; Department of Pediatrics, Munich, Germany
| | - Rebecca Haag
- Technical University of Munich, Germany; School of Medicine and Health; Department of Pediatrics, Munich, Germany
| | - Mari Lahnalampi
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Yliopistonranta 8, FI-70211, Kuopio, Finland
| | - Tiina J Tuononen
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Yliopistonranta 8, FI-70211, Kuopio, Finland
| | - Andrea Hanel
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Yliopistonranta 8, FI-70211, Kuopio, Finland
| | - Anna Viitasalo
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Yliopistonranta 8, FI-70211, Kuopio, Finland
| | - Ulrike A Friedrich
- DRESDEN-concept Genome Center, Technology Platform at the Center for Molecular and Cellular Bioengineering (CMCB), Dresden University of Technology (TUD), Dresden, Germany
- German Center for Diabetes Research (DZD e.V.), 85764, Neuherberg, Germany
- Paul Langerhans Institute Dresden of the Helmholtz Center Munich, University Hospital and Faculty of Medicine Carl Gustav Carus, Dresden University of Technology (TUD), Dresden, Germany
| | - Andreas Dahl
- DRESDEN-concept Genome Center, Technology Platform at the Center for Molecular and Cellular Bioengineering (CMCB), Dresden University of Technology (TUD), Dresden, Germany
| | - Carolin Prexler
- Technical University of Munich, Germany; School of Medicine and Health; Department of Pediatrics, Munich, Germany
| | - Aleksandra A Pandyra
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Bonn, Germany
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine University Duesseldorf, Medical Faculty, Duesseldorf, Germany
| | - Polina Stepensky
- Department of Bone Marrow Transplantation and Cancer Immunotherapy, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Masatoshi Takagi
- Department of Pediatrics and Developmental Biology, Institute of Science Tokyo, Tokyo, Japan
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine University Duesseldorf, Medical Faculty, Duesseldorf, Germany
| | - Merja Heinäniemi
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Yliopistonranta 8, FI-70211, Kuopio, Finland.
| | - Julia Hauer
- Technical University of Munich, Germany; School of Medicine and Health; Department of Pediatrics, Munich, Germany.
- German Cancer Consortium (DKTK), München, Germany.
- Pediatric Hematology and Oncology, Department of Pediatrics, University Hospital Carl Gustav Carus, Technical University of Dresden, Dresden, Germany.
- German Center for Child and Adolescent Health (DZKJ), partner site Munich, Munich, Germany.
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18
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Cheng P, Zhao H, Zhang S, Zong Z, Li C, Ming L, Xie W, Yu H. Feedback regulation of m 6A modification creates local auxin maxima essential for rice microsporogenesis. Dev Cell 2025; 60:1454-1466.e4. [PMID: 39809283 DOI: 10.1016/j.devcel.2024.12.034] [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: 06/25/2024] [Revised: 11/10/2024] [Accepted: 12/17/2024] [Indexed: 01/16/2025]
Abstract
N6-methyladenosine (m6A) RNA modification and its effectors control various plant developmental processes, yet whether and how these effectors are transcriptionally controlled to confer functional specificity so far remain elusive. Herein, we show that a rice C2H2 zinc-finger protein, OsZAF, specifically activates the expression of OsFIP37 encoding a core component of the m6A methyltransferase complex during microsporogenesis in rice anthers. OsFIP37, in turn, facilitates m6A modification and stabilization of an auxin biosynthesis gene OsYUCCA3 to promote auxin biosynthesis in anthers. This elevates auxin levels coinciding with upregulation of an auxin response factor OsARF12 that positively controls OsZAF, thus creating a positive feedback circuit whereby OsFIP37 is continuously activated for local auxin production. Our findings suggest that OsZAF-dependent feedback regulation of m6A modification is integral to local auxin biosynthesis and signaling in anthers, which facilitates the timely generation of auxin maxima required for male meiosis in rice.
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Affiliation(s)
- Peng Cheng
- Department of Biological Sciences and Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117543, Singapore
| | - Hu Zhao
- Department of Biological Sciences and Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117543, Singapore; National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China.
| | - Songyao Zhang
- Department of Biological Sciences and Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117543, Singapore
| | - Zhanxiang Zong
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Chengxiang Li
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Luchang Ming
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Weibo Xie
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Hao Yu
- Department of Biological Sciences and Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117543, Singapore.
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19
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Cui X, Yin Q, Gao Z, Li Z, Chen X, Lv H, Chen S, Liu Q, Zeng W, Jiang R. CREATE: cell-type-specific cis-regulatory element identification via discrete embedding. Nat Commun 2025; 16:4607. [PMID: 40382355 PMCID: PMC12085597 DOI: 10.1038/s41467-025-59780-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2024] [Accepted: 05/02/2025] [Indexed: 05/20/2025] Open
Abstract
Cis-regulatory elements (CREs), including enhancers, silencers, promoters and insulators, play pivotal roles in orchestrating gene regulatory mechanisms that drive complex biological traits. However, current approaches for CRE identification are predominantly sequence-based and typically focus on individual CRE types, limiting insights into their cell-type-specific functions and regulatory dynamics. Here, we present CREATE, a multimodal deep learning framework based on Vector Quantized Variational AutoEncoder, tailored for comprehensive CRE identification and characterization. CREATE integrates genomic sequences, chromatin accessibility, and chromatin interaction data to generate discrete CRE embeddings, enabling accurate multi-class classification and robust characterization of CREs. CREATE excels in identifying cell-type-specific CREs, and provides quantitative and interpretable insights into CRE-specific features, uncovering the underlying regulatory codes. By facilitating large-scale prediction of CREs in specific cell types, CREATE enhances the recognition of disease- or phenotype-associated biological variabilities of CREs, thus advancing our understanding of gene regulatory landscapes and their roles in health and disease.
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Affiliation(s)
- Xuejian Cui
- Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing, China
| | - Qijin Yin
- Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing, China
| | - Zijing Gao
- Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing, China
| | - Zhen Li
- Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing, China
| | - Xiaoyang Chen
- Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing, China
| | - Hairong Lv
- Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing, China
| | - Shengquan Chen
- School of Mathematical Sciences and LPMC, Nankai University, Tianjin, China
| | - Qiao Liu
- Department of Statistics, Stanford University, Stanford, CA, USA
| | - Wanwen Zeng
- Department of Statistics, Stanford University, Stanford, CA, USA.
| | - Rui Jiang
- Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing, China.
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20
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Yu Y, Cen C, Shao Z, Wang C, Wang Y, Miao Z, Sun M, Wang C, Xu Q, Liang K, Zhou J, Zhou D, Ji H, Xu G, Du Y. APE1 promotes lung adenocarcinoma through G4-mediated transcriptional reprogramming of urea cycle metabolism. iScience 2025; 28:112275. [PMID: 40276763 PMCID: PMC12019196 DOI: 10.1016/j.isci.2025.112275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 07/17/2024] [Accepted: 03/19/2025] [Indexed: 04/26/2025] Open
Abstract
Lung adenocarcinoma (LUAD) remains the leading cause of cancer deaths worldwide. Apurinic/apyrimidinic endonuclease 1 (APE1), an enzyme integral to DNA repair and redox signaling, is notably upregulated in LUAD. Here we reveal that APE1 amplification, primarily via allele duplication, strongly correlates with poor prognosis in LUAD patients. Using human LUAD cell lines and a KRAS-driven mouse model, we showed that APE1 deletion hampered cell proliferation and tumor growth, highlighting its role in tumorigenesis. Mechanistically, APE1 promoted the transcription of urea cycle genes CPS1 and ARG2 by modulating the presence of G-quadruplex (G4) structures in their promoter regions. APE1 loss disrupted the urea cycle and pyrimidine metabolism, inducing metabolic reprogramming and growth arrest, which could be rescued by CPS1 or pyrimidine restoration. These findings uncover APE1's role in transcriptional regulation of urea cycle metabolic reprogramming via G4 structure, providing a potential therapeutic target LUAD patients with elevated APE1 expression.
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Affiliation(s)
- Yanhao Yu
- CAS Key Laboratory of Epigenetic Regulation and Intervention, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Chaochao Cen
- CAS Key Laboratory of Epigenetic Regulation and Intervention, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhenyu Shao
- CAS Key Laboratory of Epigenetic Regulation and Intervention, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Chaohan Wang
- CAS Key Laboratory of Epigenetic Regulation and Intervention, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yiqin Wang
- CAS Key Laboratory of Epigenetic Regulation and Intervention, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zongjie Miao
- CAS Key Laboratory of Epigenetic Regulation and Intervention, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Meiling Sun
- CAS Key Laboratory of Epigenetic Regulation and Intervention, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Chao Wang
- CAS Key Laboratory of Epigenetic Regulation and Intervention, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Qing Xu
- CAS Key Laboratory of Epigenetic Regulation and Intervention, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Kaiwei Liang
- School of Basic Medical Sciences, Wuhan University, Wuhan 430072, China
| | - Jiaxin Zhou
- CAS Key Laboratory of Epigenetic Regulation and Intervention, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Dan Zhou
- Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Chinese Academy of Medical Sciences (RU069) & Zhongshan-Xuhui Hospital, Medical College of Fudan University, Shanghai 200032, China
| | - Hongbin Ji
- CAS Key Laboratory of Epigenetic Regulation and Intervention, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Guoliang Xu
- CAS Key Laboratory of Epigenetic Regulation and Intervention, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Chinese Academy of Medical Sciences (RU069) & Zhongshan-Xuhui Hospital, Medical College of Fudan University, Shanghai 200032, China
| | - Yarui Du
- CAS Key Laboratory of Epigenetic Regulation and Intervention, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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21
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Gill ME, Fischer M, De Geyter C, Peters AHFM. Normozoospermic infertile men possess subpopulations of sperm varying in DNA accessibility, relating to differing reproductive outcomes. Hum Reprod 2025:deaf081. [PMID: 40375809 DOI: 10.1093/humrep/deaf081] [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: 09/24/2024] [Revised: 02/19/2025] [Indexed: 05/18/2025] Open
Abstract
STUDY QUESTION Can a reliable assay be developed to quantify DNA accessibility in human sperm to help with the assessment of pre-implantation development affected by dense packaging of mammalian sperm's genetic material? SUMMARY ANSWER We adapted NicE-view, an assay that directly labels accessible DNA, for use in human sperm and applied it to examine spermatozoa from infertile individuals with distinct reproductive outcomes. WHAT IS KNOWN ALREADY Existing data suggest a connection between sperm chromatin compaction and reproductive outcomes. The assays used to generate this data, however, measure chromatin compaction indirectly and thus understanding their meaning is challenging. STUDY DESIGN, SIZE, DURATION Between April 2020 to December 2023, 60 normozoospermic infertile men were invited to participate in an experimental study and asked to provide a semen sample. PARTICIPANTS/MATERIALS, SETTING, METHODS Among the 60 individuals forty had undergone at least one treatment with ART. Among these ART-treated participants, 20 were included in the study because after fertilization only one or no embryos developed during embryo culture (low blastocyst growth rate, LBGR). The other 20 men were included as at least 50% of cultured embryos developed to the blastocyst stage (high blastocyst growth rate). Additionally, 20 previously infertile individuals obtained a pregnancy naturally (NATP) and were included as well. Washed spermatozoa obtained from seminal plasma or prepared by swim-up procedure were processed for NicE-view to determine DNA accessibility as a marker of chromatin condensation using confocal microscopy. Images of more than 3 million spermatozoa were acquired. Computer-assisted image segmentation was used to identify individual sperm heads and DNA accessibility levels were then quantified in each. We also compared NicE-view to chromomycin A3 (CMA3), a conventional marker of chromatin de-condensation, and ATAC-see, an alternative assay for measuring DNA accessibility. MAIN RESULTS AND THE ROLE OF CHANCE Both semen and swim-up samples of participants contained two well-delineated subpopulations of spermatozoa with distinct DNA accessibility levels, the frequencies of which varied among individuals. Interestingly, individuals with high frequencies of highly accessible sperm DNA, as measured in semen, possessed decreased sperm concentrations. Moreover, participants with high frequency of highly accessible sperm DNA were more common in the LBGR sub-group. Surprisingly, selection of motile sperm by swim-up enriched for sperm with high DNA accessibility in participants from all three sub-groups. Chromatin accessibility measurements by Nice-view were distinct from DNA staining with the fluorescent CMA3 dye, and NicE-view allowed much clearer separation of sperm subpopulations than ATAC-see. LIMITATIONS, REASONS FOR CAUTION This was a single-centre study with a cohort of 60 individuals. Sperm samples containing very high frequencies of sperm with increased DNA accessibility were more common in the LBGR sub-group. The number of individuals with this pattern was, however, limited, even within this category. WIDER IMPLICATIONS OF THE FINDINGS High DNA accessibility is associated with poor pre-implantation embryonic development in vitro and NicE-view may be used for the prediction of abnormal embryonic development in ART. Further studies examining samples from larger cohorts of participants and the localization of accessible regions within the sperm genome are needed to fully evaluate the utility of this method. STUDY FUNDING/COMPETING INTEREST(S) Swiss National Science Foundation (Grant No. 189264), Swiss Center for Applied Human Toxicology (SCAHT) research (Grant No. 1 'male reproductive toxicity') (both to C.D.G.), and the Novartis Research Foundation (to A.H.F.M.P.). M.E.G., C.D.G., and A.H.F.M.P. are authors on a patent application (EP23210754.0) on the use of NicE-view for the assessment of sperm. TRIAL REGISTRATION NUMBER ClinicalTrials.gov ID NCT04256668.
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Affiliation(s)
- Mark E Gill
- Reproductive Medicine and Gynecological Endocrinology (RME), Universitätsspital Basel, University of Basel, Basel, Switzerland
- Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland
| | - Manuel Fischer
- Reproductive Medicine and Gynecological Endocrinology (RME), Universitätsspital Basel, University of Basel, Basel, Switzerland
| | - Christian De Geyter
- Reproductive Medicine and Gynecological Endocrinology (RME), Universitätsspital Basel, University of Basel, Basel, Switzerland
- Department of Biomedicine (DBM), University of Basel, Basel, Switzerland
| | - Antoine H F M Peters
- Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland
- Faculty of Science, University of Basel, Basel, Switzerland
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22
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Alfano V, Pascucci GR, Corleone G, Cocca M, De Nicola F, Floriot O, Paturel A, Di Tocco FC, de Fromentel CC, Merle P, Rivoire M, Levrero M, Guerrieri F. HBV-driven host chromatin accessibility changes affect liver metabolic pathways, iron homeostasis and promote a preneoplastic phenotype. J Exp Clin Cancer Res 2025; 44:146. [PMID: 40380227 DOI: 10.1186/s13046-025-03414-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2025] [Accepted: 05/09/2025] [Indexed: 05/19/2025] Open
Abstract
BACKROUND AND AIMS Complex host-virus interactions account for adaptive and innate immunity dysfunctions and viral cccDNA mini-chromosome persistence, key features of HBV chronicity and challenges for HBV cure. The extent of HBV direct impact on liver transcriptome remains controversial. Transcriptional activation in eukaryotic cells is tightly linked with disruption of nucleosome organization at accessible genomic sites of remodeled chromatin. We sought to investigate the impact of HBV on chromatin accessibility and transcription. METHODS We used ATAC-seq (Assay for Transposase Accessible Chromatin followed by high throughput sequencing) to detect early changes in chromatin accessibility coupled with RNA-seq in HBV-infected Primary Human Hepatocytes (PHHs). RESULTS An increasing number of genomic sites change their nucleosome organization over time after HBV infection, with a prevalent, but not exclusive, reduction of chromatin accessibility at specific sites that is partially prevented by inhibiting HBV transcription and replication. ATAC-seq and RNA-seq integration showed that HBV infection impacts on liver fatty acids, bile acids, iron metabolism and liver cancer pathways. The upregulation of iron uptake genes leads to a significant increase of iron content in HBV-infected PHHs whereas iron chelation inhibits cccDNA transcription and viral replication. The chromatin accessibility and transcriptional changes imposed by HBV early after infection persist, as an epigenetic scar, in chronic HBV (CHB) patients and in HBV-related HCCs. These changes are to a large extent independent from viral replication levels and disease activity. CONCLUSIONS Altogether our results show that HBV infection impacts on host cell chromatin landscape and specific transcriptional programs including liver metabolism and liver cancer pathways. Re-wiring of iron metabolism boosts viral replication early after infection. The modulation of genes involved in cancer-related pathways may favor the development or the selection of a pro-neoplastic phenotype and persists in HBV-related HCCs.
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Affiliation(s)
- Vincenzo Alfano
- IHU EVEREST - Institut of Hepatology Lyon, UMR UCLB1 INSERM U1350 PaThLiv, 69004, Lyon, France
- INSERM U1052, Cancer Research Center of Lyon (CRCL), Lyon, France
| | - Giuseppe Rubens Pascucci
- Research Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children's Hospital, 00165, Rome, Italy
- Center for Life Nano Science (CNLS), Istituto Italiano Di Tecnologia (IIT), 00161, Rome, Italy
| | - Giacomo Corleone
- SAFU Laboratory, Department of Research, Advanced Diagnostics, and Technological Innovation, IRCCS Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Massimiliano Cocca
- IHU EVEREST - Institut of Hepatology Lyon, UMR UCLB1 INSERM U1350 PaThLiv, 69004, Lyon, France
| | - Francesca De Nicola
- SAFU Laboratory, Department of Research, Advanced Diagnostics, and Technological Innovation, IRCCS Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Océane Floriot
- INSERM U1052, Cancer Research Center of Lyon (CRCL), Lyon, France
| | - Alexia Paturel
- IHU EVEREST - Institut of Hepatology Lyon, UMR UCLB1 INSERM U1350 PaThLiv, 69004, Lyon, France
- Université Catholique de Lyon (UCLy), 69002, Lyon, France
| | | | | | - Philippe Merle
- IHU EVEREST - Institut of Hepatology Lyon, UMR UCLB1 INSERM U1350 PaThLiv, 69004, Lyon, France
- Department of Hepatology, Croix Rousse Hospital, Hospices Civils de Lyon, 69004, Lyon, France
| | - Michel Rivoire
- INSERM U1052, Centre de Lutte Contre Le Cancer Léon Bérard (CLB), 69003, Lyon, France
| | - Massimo Levrero
- IHU EVEREST - Institut of Hepatology Lyon, UMR UCLB1 INSERM U1350 PaThLiv, 69004, Lyon, France.
- Department of Hepatology, Croix Rousse Hospital, Hospices Civils de Lyon, 69004, Lyon, France.
| | - Francesca Guerrieri
- IHU EVEREST - Institut of Hepatology Lyon, UMR UCLB1 INSERM U1350 PaThLiv, 69004, Lyon, France.
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23
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Fu Y, Land M, Kavlashvili T, Cui R, Kim M, DeBitetto E, Lieber T, Ryu KW, Choi E, Masilionis I, Saha R, Takizawa M, Baker D, Tigano M, Lareau CA, Reznik E, Sharma R, Chaligne R, Thompson CB, Pe'er D, Sfeir A. Engineering mtDNA deletions by reconstituting end joining in human mitochondria. Cell 2025; 188:2778-2793.e21. [PMID: 40068680 DOI: 10.1016/j.cell.2025.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2024] [Revised: 01/22/2025] [Accepted: 02/13/2025] [Indexed: 03/19/2025]
Abstract
Recent breakthroughs in the genetic manipulation of mitochondrial DNA (mtDNA) have enabled precise base substitutions and the efficient elimination of genomes carrying pathogenic mutations. However, reconstituting mtDNA deletions linked to mitochondrial myopathies remains challenging. Here, we engineered mtDNA deletions in human cells by co-expressing end-joining (EJ) machinery and targeted endonucleases. Using mitochondrial EJ (mito-EJ) and mito-ScaI, we generated a panel of clonal cell lines harboring a ∼3.5 kb mtDNA deletion across the full spectrum of heteroplasmy. Investigating these cells revealed a critical threshold of ∼75% deleted genomes, beyond which oxidative phosphorylation (OXPHOS) protein depletion, metabolic disruption, and impaired growth in galactose-containing media were observed. Single-cell multiomic profiling identified two distinct nuclear gene deregulation responses: one triggered at the deletion threshold and another progressively responding to heteroplasmy. Ultimately, we show that our method enables the modeling of disease-associated mtDNA deletions across cell types and could inform the development of targeted therapies.
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Affiliation(s)
- Yi Fu
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Max Land
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tamar Kavlashvili
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ruobing Cui
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Minsoo Kim
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Emily DeBitetto
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Toby Lieber
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Keun Woo Ryu
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elim Choi
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ignas Masilionis
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rahul Saha
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Meril Takizawa
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daphne Baker
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marco Tigano
- Department of Pathology and Genomic Medicine, Thomas Jefferson University, Philadelphia, PA, USA
| | - Caleb A Lareau
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ed Reznik
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Roshan Sharma
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ronan Chaligne
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Craig B Thompson
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dana Pe'er
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Howard Hughes Medical Institute, New York, NY, USA
| | - Agnel Sfeir
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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24
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Ahmad K, Henikoff S. Profiling regulatory elements in vivo by genome-wide methods. Curr Opin Struct Biol 2025; 92:103064. [PMID: 40378608 DOI: 10.1016/j.sbi.2025.103064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2025] [Revised: 04/21/2025] [Accepted: 04/22/2025] [Indexed: 05/19/2025]
Abstract
The biology of gene regulation in eukaryotic genomes is a mature field. The biochemical principles of factor binding to DNA are well-known from in vitro studies, as are the structural interactions in which specific domains of these proteins interface across a short stretch of DNA to confer sequence-specific recognition. Whereas the basic principles of binding and dissociation defined in vitro apply in vivo, the living nucleus is a dynamic compartment crowded with molecules, including motors that drive chromatin movements critical for the regulation of gene expression. Understanding these dynamics in vivo has spurred the development of cutting-edge technologies to observe factor-DNA interactions. The biological significance of chromatin dynamics is now revealed by a wide variety of high-resolution chromatin profiling methods.
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Affiliation(s)
- Kami Ahmad
- Basic Science Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
| | - Steven Henikoff
- Basic Science Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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25
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Bubb KL, Hamm MO, Tullius TW, Min JK, Ramirez-Corona B, Mueth NA, Ranchalis J, Mao Y, Bergstrom EJ, Vollger MR, Trapnell C, Cuperus JT, Stergachis AB, Queitsch C. The regulatory potential of transposable elements in maize. NATURE PLANTS 2025:10.1038/s41477-025-02002-z. [PMID: 40360747 DOI: 10.1038/s41477-025-02002-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2024] [Accepted: 04/11/2025] [Indexed: 05/15/2025]
Abstract
The genomes of flowering plants consist largely of transposable elements (TEs), some of which modulate gene regulation and function. However, the repetitive nature of TEs and difficulty of mapping individual TEs by short-read sequencing have hindered our understanding of their regulatory potential. Here we show that long-read chromatin fibre sequencing (Fiber-seq) comprehensively identifies accessible chromatin regions (ACRs) and CpG methylation across the maize genome. We uncover stereotypical ACR patterns at young TEs that degenerate with evolutionary age, resulting in TE enhancers preferentially marked by a novel plant-specific epigenetic feature: simultaneous hyper-CpG methylation and chromatin accessibility. We show that TE ACRs are co-opted as gene promoters and that ACR-containing TEs can facilitate gene amplification. Lastly, we uncover a pervasive epigenetic signature-hypo-5mCpG methylation and diffuse chromatin accessibility-directing TEs to specific loci, including the loci that sparked McClintock's discovery of TEs.
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Affiliation(s)
- Kerry L Bubb
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Morgan O Hamm
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Thomas W Tullius
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Joseph K Min
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Nicholas A Mueth
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Jane Ranchalis
- Division of Medical Genetics, Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Yizi Mao
- Division of Medical Genetics, Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Erik J Bergstrom
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Mitchell R Vollger
- Division of Medical Genetics, Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA
| | - Josh T Cuperus
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA
| | - Andrew B Stergachis
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Division of Medical Genetics, Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA.
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA.
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA.
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26
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Barbadilla-Martínez L, Klaassen N, van Steensel B, de Ridder J. Predicting gene expression from DNA sequence using deep learning models. Nat Rev Genet 2025:10.1038/s41576-025-00841-2. [PMID: 40360798 DOI: 10.1038/s41576-025-00841-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/01/2025] [Indexed: 05/15/2025]
Abstract
Transcription of genes is regulated by DNA elements such as promoters and enhancers, the activity of which are in turn controlled by many transcription factors. Owing to the highly complex combinatorial logic involved, it has been difficult to construct computational models that predict gene activity from DNA sequence. Recent advances in deep learning techniques applied to data from epigenome mapping and high-throughput reporter assays have made substantial progress towards addressing this complexity. Such models can capture the regulatory grammar with remarkable accuracy and show great promise in predicting the effects of non-coding variants, uncovering detailed molecular mechanisms of gene regulation and designing synthetic regulatory elements for biotechnology. Here, we discuss the principles of these approaches, the types of training data sets that are available and the strengths and limitations of different approaches.
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Affiliation(s)
- Lucía Barbadilla-Martínez
- Oncode Institute, Utrecht, The Netherlands
- Center for Molecular Medicine, UMC Utrecht, Utrecht, The Netherlands
| | - Noud Klaassen
- Oncode Institute, Utrecht, The Netherlands
- Division of Molecular Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Bas van Steensel
- Oncode Institute, Utrecht, The Netherlands.
- Division of Molecular Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - Jeroen de Ridder
- Oncode Institute, Utrecht, The Netherlands.
- Center for Molecular Medicine, UMC Utrecht, Utrecht, The Netherlands.
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Zhang J, Ma L, Deng H, Yi W, Tohtihan A, Tang X, Wu X, Feng X. Multi-omics integration identifies NK cell-mediated cytotoxicity as a therapeutic target in systemic lupus erythematosus. Front Immunol 2025; 16:1580540. [PMID: 40433370 PMCID: PMC12106370 DOI: 10.3389/fimmu.2025.1580540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2025] [Accepted: 04/18/2025] [Indexed: 05/29/2025] Open
Abstract
Background Systemic lupus erythematosus (SLE) is an autoimmune condition that impacts various organs. Given the intricate clinical progression of SLE, it is imperative to explore novel avenues for precise diagnosis and treatment. Methods Peripheral blood mononuclear cells (PBMC) were isolated from 6 SLE patients before and after treatment, 7 healthy controls and 7 disease controls. Assay for Transposase Accessible Chromatin with high throughput Sequencing (ATAC-seq) was used to analyze the chromatin accessibility signatures and RNA-seq was used to identify the differentially expressed genes, mRNA, lncRNA, circRNA, miRNA. Then ATAC-seq and RNA-seq were integrated to further analyze hub genes and pathways. Finally, we validated gene expression levels and examined changes in key genes after treatment through in vitro experiments. Results Our analysis reveals dynamic changes in chromatin accessibility during the course of disease progression in SLE. Significantly higher numbers of differentially accessible regions, transcripts, genes, mRNA, lncRNA, circRNA, and miRNA were observed in SLE patients compared to other cohorts, with these variances markedly reduced post-treatment. Two gene clusters associated with SLE disease improvement were identified, with a total of 140 genes intersecting with ATAC results. Pathway analysis revealed that NK cell mediated cytotoxicity was the most differentiated and therapeutically altered pathway in SLE patients. Independent sample validation confirmed that the gene expression of this pathway was reduced in SLE patients and associated with disease activity, whereas hydroxychloroquine (HCQ) effectively elevated their expression in vitro. Conclusion Our findings suggest that these NK cell signature genes may be associated with the complex pathogenesis of SLE. The restoration of NK cell-mediated cytotoxicity may serve as a useful marker of improvement following SLE treatment.
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Affiliation(s)
- Jingjing Zhang
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Ling Ma
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Hanyin Deng
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Wenqian Yi
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Alim Tohtihan
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Xiaojun Tang
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Xiudi Wu
- Department of Rheumatology, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - Xuebing Feng
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
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Guichard V, Leão FB, Zhao J, Zhang Y, Ito T, Shirley S, Postler TS, Tian R, Huang Y, Ghosh S. Pre-existing epigenetic state and differential NF-κB activation shape type 2 immune cell responses. Immunity 2025:S1074-7613(25)00179-7. [PMID: 40367949 DOI: 10.1016/j.immuni.2025.04.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 12/20/2024] [Accepted: 04/15/2025] [Indexed: 05/16/2025]
Abstract
CD4+ T helper 2 (Th2) cells and group 2 innate lymphoid cells (ILC2s) drive type 2 immune responses via similar effector molecules that are primarily induced by different signals-interleukin (IL)-33 in ILC2s and TCR engagement in Th2 cells. Here, we examined the transcriptional regulation of type 2 immunity, focusing on the NF-κB pathway, which is differentially activated by TCR engagement or cytokine signaling. Conditional deletion of the NF-κB subunits c-Rel and p65 limited the expression of key type 2 genes, including Il13 and Il5, in ILC2s but not in Th2 cells. Genome-wide analysis revealed that the regulatory regions of such genes exist in an open chromatin state in ILC2s, allowing NF-κB binding upon IL-33 stimulation. These regions are less accessible in unstimulated Th2 cells, where NFAT plays a dominant role. Accordingly, p65 deletion impaired ILC2 activation and function during airway inflammation and helminth infection. Thus, innate and adaptive lymphocytes leverage distinct epigenetic landscapes and transcriptional regulators to control shared effector genes.
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Affiliation(s)
- Vincent Guichard
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Felipe Batista Leão
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Jingyao Zhao
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Yingyu Zhang
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Takamasa Ito
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Simon Shirley
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Thomas S Postler
- Vaccine Design and Development Laboratory, IAVI, New York, NY 10004, USA
| | - Ruxiao Tian
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Yuefeng Huang
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.
| | - Sankar Ghosh
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.
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29
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Tasan I, Eres I, Wei C, Bryant EE, Brisan E, Hubert R. Identification of Loci with High Transgene Expression in CHO Cells. ACS Synth Biol 2025. [PMID: 40357755 DOI: 10.1021/acssynbio.4c00678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2025]
Abstract
Chinese Hamster Ovary (CHO) cells are commonly used for producing therapeutic proteins in the biopharmaceutical industry. Targeted integration (TI) of therapeutic protein-encoding transgenes into predetermined high and stably expressing genomic loci can simplify the cell line development processes for biologics production. Establishing a successful TI system requires identifying genomic loci that allow a high expression of the integrated transgenes. In this work, we demonstrated that the Thousands of Reporters Integrated in Parallel (TRIP) technology can identify such transcriptional hotspots in CHO cells. TRIP simplifies screening for transcriptional hotspots since it utilizes randomly integrated barcoded reporters and uses each barcode as a unique identifier to track the genomic location and activity of the corresponding reporter by next-generation sequencing. Transcriptional hotspots identified by TRIP resulted in up to a 9.4-fold increase in mRNA levels and a 5.6-fold increase in fed-batch titers of a test molecule compared with a medium-expressing control locus. Moreover, single copy expression from one of the identified transcriptional hotspots resulted in up to a 1.6-fold higher titer in comparison to the piggyBac-mediated stable expression of the same molecule. Reporter expression levels from TRIP loci showed positive correlations with active chromatin marks; however, the proximity to active marks was not consistently deterministic. These results suggest that TRIP is a powerful functional screening method for identifying transcriptional hotspots in CHO cells without the need for more complex epigenomic analyses.
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Affiliation(s)
- Ipek Tasan
- Amgen Research, Amgen, Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Ittai Eres
- Amgen Research, Amgen, Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Christopher Wei
- Amgen Research, Amgen, Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Eric Edward Bryant
- Amgen Research, Amgen, Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Emil Brisan
- Amgen Research, Amgen, Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Rene Hubert
- Amgen Research, Amgen, Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
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30
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Sugata K, Rahman A, Niimura K, Monde K, Ueno T, Rajib SA, Takatori M, Sakhor W, Hossain MB, Sithi SN, Jahan MI, Matsuda K, Ueda M, Yamano Y, Ikeda T, Ueno T, Tsuchiya K, Tanaka Y, Tokunaga M, Maeda K, Utsunomiya A, Okuma K, Ono M, Satou Y. Intragenic viral silencer element regulates HTLV-1 latency via RUNX complex recruitment. Nat Microbiol 2025:10.1038/s41564-025-02006-7. [PMID: 40360701 DOI: 10.1038/s41564-025-02006-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Accepted: 04/07/2025] [Indexed: 05/15/2025]
Abstract
Retroviruses integrate their genetic material into the host genome, enabling persistent infection. Human T cell leukaemia virus type 1 (HTLV-1) and human immunodeficiency virus type 1 (HIV-1) share similarities in genome structure and target cells, yet their infection dynamics differ drastically. While HIV-1 leads to high viral replication and immune system collapse, HTLV-1 establishes latency, promoting the survival of infected cells and, in some cases, leading to leukaemia. The mechanisms underlying this latency preference remain unclear. Here we analyse blood samples from people with HTLV-1 and identify an open chromatin region within the HTLV-1 provirus that functions as a transcriptional silencer and regulates transcriptional burst. The host transcription factor RUNX1 binds to this open chromatin region, repressing viral expression. Mutation of this silencer enhances HTLV-1 replication and immunogenicity, while its insertion into HIV-1 suppresses viral production. These findings reveal a strategy by which HTLV-1 ensures long-term persistence, offering potential insights into retroviral evolution and therapeutic targets.
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Affiliation(s)
- Kenji Sugata
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Akhinur Rahman
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Koki Niimura
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
- School of Medicine, Kumamoto University, Kumamoto, Japan
| | - Kazuaki Monde
- Department of Microbiology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Takaharu Ueno
- Department of Microbiology, Kansai Medical University, Hirakata, Japan
| | - Samiul Alam Rajib
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Mitsuyoshi Takatori
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Wajihah Sakhor
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Md Belal Hossain
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Sharmin Nahar Sithi
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - M Ishrat Jahan
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Kouki Matsuda
- Division of Antiviral Therapy, Joint Research Center for Human Retrovirus Infection, Kagoshima University, Kagoshima, Japan
| | - Mitsuharu Ueda
- Department of Neurology, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Yoshihisa Yamano
- Department of Neurology, St. Marianna University School of Medicine, Kawasaki, Japan
- Department of Rare Diseases Research, Institute of Medical Science, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Terumasa Ikeda
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Takamasa Ueno
- Division of Infection and Immunity, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Kiyoto Tsuchiya
- AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Yuetsu Tanaka
- School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Masahito Tokunaga
- Department of Hematology, Imamura General Hospital, Kagoshima, Japan
| | - Kenji Maeda
- Division of Antiviral Therapy, Joint Research Center for Human Retrovirus Infection, Kagoshima University, Kagoshima, Japan
| | - Atae Utsunomiya
- Department of Hematology, Imamura General Hospital, Kagoshima, Japan
| | - Kazu Okuma
- Department of Microbiology, Kansai Medical University, Hirakata, Japan
| | - Masahiro Ono
- Department of Life Sciences, Imperial College London, London, UK
| | - Yorifumi Satou
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan.
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31
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Hyle J, Qi W, Djekidel MN, Rosikiewicz W, Xu B, Li C. Deciphering the role of RNA in regulating CTCF's DNA binding affinity in leukemia cells. Genome Biol 2025; 26:126. [PMID: 40355969 PMCID: PMC12067947 DOI: 10.1186/s13059-025-03582-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Accepted: 04/20/2025] [Indexed: 05/15/2025] Open
Abstract
BACKGROUND CTCF, a highly studied transcription factor, is essential for chromatin interaction maintenance. Several independent studies report that CTCF interacts with RNAs in vitro and in cells. Yet continuous debates about the authenticity of the RNA-binding affinity of CTCF and its biological role remain in large part due to limited research techniques available, such as CLIP-seq. RESULT Here, we investigate RNA's role in CTCF's transcription factor function through its chromatin occupancy. To systematically explore whether RNAs affect CTCF's ability to bind DNA, we perturb CTCF-RNA interactions by three independent approaches and examine CTCF genome occupancy by ChIP-seq. Although RNase A and triptolide treatment each affect a certain number of CTCF-binding peaks, few peaks overlap between treatment groups indicating the effect of RNA in regulating CTCF's DNA binding affinity is variable between loci. In addition, limited transcriptional or chromatin accessibility changes occur between cells expressing wild-type CTCF or CTCF lacking the RNA binding region. CONCLUSION Our data provide a complementary approach and in silico evidence to consider the significance of RNA affecting CTCF's DNA binding affinity globally.
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Affiliation(s)
- Judith Hyle
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Wenjie Qi
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Mohamed Nadhir Djekidel
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Wojciech Rosikiewicz
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Beisi Xu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
| | - Chunliang Li
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
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32
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Zahavi EE, Koppel I, Kawaguchi R, Oses-Prieto JA, Briner A, Monavarfeshani A, Dalla Costa I, van Niekerk E, Lee J, Matoo S, Hegarty S, Donahue RJ, Sahoo PK, Ben-Dor S, Feldmesser E, Ryvkin J, Leshkowitz D, Perry RBT, Cheng Y, Farber E, Abraham O, Samra N, Okladnikov N, Alber S, Albus CA, Rishal I, Ulitsky I, Tuszynski MH, Twiss JL, He Z, Burlingame AL, Fainzilber M. Repeat-element RNAs integrate a neuronal growth circuit. Cell 2025:S0092-8674(25)00498-2. [PMID: 40381624 DOI: 10.1016/j.cell.2025.04.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 11/12/2024] [Accepted: 04/23/2025] [Indexed: 05/20/2025]
Abstract
Neuronal growth and regeneration are regulated by local translation of mRNAs in axons. We examined RNA polyadenylation changes upon sensory neuron injury and found upregulation of a subset of polyadenylated B2-SINE repeat elements, hereby termed GI-SINEs (growth-inducing B2-SINEs). GI-SINEs are induced from ATF3 and other AP-1 promoter-associated extragenic loci in injured sensory neurons but are not upregulated in lesioned retinal ganglion neurons. Exogenous GI-SINE expression elicited axonal growth in injured sensory, retinal, and corticospinal tract neurons. GI-SINEs interact with ribosomal proteins and nucleolin, an axon-growth-regulating RNA-binding protein, to regulate translation in neuronal cytoplasm. Finally, antisense oligos against GI-SINEs perturb sensory neuron outgrowth and nucleolin-ribosome interactions. Thus, a specific subfamily of transposable elements is integral to a physiological circuit linking AP-1 transcription with localized RNA translation.
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Affiliation(s)
- Eitan Erez Zahavi
- Departments of Biomolecular Sciences and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Indrek Koppel
- Departments of Biomolecular Sciences and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel; Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia.
| | - Riki Kawaguchi
- Departments of Psychiatry and Neurology, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA 90024, USA
| | - Juan A Oses-Prieto
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Adam Briner
- Departments of Biomolecular Sciences and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Aboozar Monavarfeshani
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - Irene Dalla Costa
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Erna van Niekerk
- Department of Neurosciences, University of California, San Diego, and Veterans Administration Medical Center, San Diego, CA 92093, USA
| | - Jinyoung Lee
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Samaneh Matoo
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Shane Hegarty
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - Ryan J Donahue
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - Pabitra K Sahoo
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA; Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA
| | - Shifra Ben-Dor
- Bioinformatics Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Ester Feldmesser
- Bioinformatics Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Julia Ryvkin
- Bioinformatics Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Dena Leshkowitz
- Bioinformatics Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Rotem Ben-Tov Perry
- Departments of Immunology and Regenerative Biology and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Yuyan Cheng
- Department of Ophthalmology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Eli Farber
- Departments of Biomolecular Sciences and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Ofri Abraham
- Departments of Biomolecular Sciences and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Nitzan Samra
- Departments of Biomolecular Sciences and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Nataliya Okladnikov
- Departments of Biomolecular Sciences and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Stefanie Alber
- Departments of Biomolecular Sciences and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Christin A Albus
- Departments of Biomolecular Sciences and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel; Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle upon Tyne, UK
| | - Ida Rishal
- Departments of Biomolecular Sciences and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Igor Ulitsky
- Departments of Immunology and Regenerative Biology and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Mark H Tuszynski
- Department of Neurosciences, University of California, San Diego, and Veterans Administration Medical Center, San Diego, CA 92093, USA
| | - Jeffery L Twiss
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Zhigang He
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - Alma L Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Mike Fainzilber
- Departments of Biomolecular Sciences and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel.
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33
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Williams RM. Leveraging chicken embryos for studying human enhancers. Dev Biol 2025; 524:123-131. [PMID: 40368318 DOI: 10.1016/j.ydbio.2025.05.009] [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: 10/29/2024] [Revised: 04/30/2025] [Accepted: 05/12/2025] [Indexed: 05/16/2025]
Abstract
The dynamic activity of complex gene regulatory networks stands at the core of all cellular functions that define cell identity and behaviour. Gene regulatory networks comprise transcriptional enhancers, acted upon by cell-specific transcription factors to control gene expression in a spatial and temporal specific manner. Enhancers are found in the non-coding genome; pathogenic variants can disrupt enhancer activity and lead to disease. Correlating non-coding variants with aberrant enhancer activity remains a significant challenge. Due to their clinical significance, there is a longstanding interest in understanding enhancer function during early embryogenesis. With the onset of the omics era, it is now feasible to identify putative tissue-specific enhancers from epigenome data. However, such predictions in vivo require validation. The early stages of chick embryogenesis closely parallel those of human, offering an accessible in vivo model in which to assess the activity of putative human enhancer sequences. This review explores the unique advantages and recent advancements in employing chicken embryos to elucidate the activity of human transcriptional enhancers and the potential implications of these findings in human disease.
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Affiliation(s)
- Ruth M Williams
- University of Manchester, Faculty of Biology, Medicine and Health, Michael Smith Building, Oxford Road, Manchester, United Kingdom.
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34
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Shinozaki T, Togasaki K, Hamamoto J, Mitsuishi A, Fukushima T, Sugihara K, Ebisudani T, Okada M, Saito A, Shigematsu L, Takaoka H, Ito F, Ohgino K, Ishioka K, Watanabe K, Hishima T, Kurebayashi Y, Emoto K, Terai H, Ikemura S, Kawada I, Asakura K, Hishida T, Asamura H, Ohta Y, Takahashi S, Oda M, Saito M, Matano M, Soejima K, Fujii M, Fukunaga K, Yasuda H, Sato T. Basal-shift transformation leads to EGFR therapy-resistance in human lung adenocarcinoma. Nat Commun 2025; 16:4369. [PMID: 40350470 PMCID: PMC12066730 DOI: 10.1038/s41467-025-59623-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2024] [Accepted: 04/30/2025] [Indexed: 05/14/2025] Open
Abstract
Although EGFR tyrosine kinase inhibitors (EGFR-TKIs) are effective for EGFR-mutant lung adenocarcinoma (LUAD), resistance inevitably develops through diverse mechanisms, including secondary genetic mutations, amplifications and as-yet undefined processes. To comprehensively unravel the mechanisms of EGFR-TKI resistance, we establish a biobank of patient-derived EGFR-mutant lung cancer organoids, encompassing cases previously treated with EGFR-TKIs. Through comprehensive molecular profiling including single-cell analysis, here we identify a subgroup of EGFR-TKI-resistant LUAD organoids that lacks known resistance-related genetic lesions and instead exhibits a basal-shift phenotype characterized by the hybrid expression of LUAD- and squamous cell carcinoma-related genes. Prospective gene engineering demonstrates that NKX2-1 knockout induces the basal-shift transformation along with EGFR-target therapy resistance. Basal-shift LUADs frequently harbor CDKN2A/B loss and are sensitive to CDK4/6 inhibitors. Our EGFR-mutant lung cancer organoid library not only offers a valuable resource for lung cancer research but also provides insights into molecular underpinnings of EGFR-TKI resistance, facilitating the development of therapeutic strategies.
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Affiliation(s)
- Taro Shinozaki
- Division of Pulmonary Medicine, Department of Medicine, Keio University, School of Medicine, Tokyo, Japan
| | - Kazuhiro Togasaki
- Department of Integrative Medicine and Biochemistry, Keio University School of Medicine, Tokyo, Japan
- Department of Organoid Medicine, Keio University School of Medicine, Tokyo, Japan
- Department of Gastroenterology, Keio University, School of Medicine, Tokyo, Japan
| | - Junko Hamamoto
- Division of Pulmonary Medicine, Department of Medicine, Keio University, School of Medicine, Tokyo, Japan
| | - Akifumi Mitsuishi
- Division of Pulmonary Medicine, Department of Medicine, Keio University, School of Medicine, Tokyo, Japan
| | - Takahiro Fukushima
- Division of Pulmonary Medicine, Department of Medicine, Keio University, School of Medicine, Tokyo, Japan
| | - Kai Sugihara
- Division of Pulmonary Medicine, Department of Medicine, Keio University, School of Medicine, Tokyo, Japan
| | - Toshiki Ebisudani
- Division of Pulmonary Medicine, Department of Medicine, Keio University, School of Medicine, Tokyo, Japan
- Department of Organoid Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Masahiko Okada
- Division of Pulmonary Medicine, Department of Medicine, Keio University, School of Medicine, Tokyo, Japan
| | - Ayaka Saito
- Division of Pulmonary Medicine, Department of Medicine, Keio University, School of Medicine, Tokyo, Japan
| | - Lisa Shigematsu
- Division of Pulmonary Medicine, Department of Medicine, Keio University, School of Medicine, Tokyo, Japan
| | - Hatsuyo Takaoka
- Division of Pulmonary Medicine, Department of Medicine, Keio University, School of Medicine, Tokyo, Japan
| | - Fumimaro Ito
- Division of Pulmonary Medicine, Department of Medicine, Keio University, School of Medicine, Tokyo, Japan
| | - Keiko Ohgino
- Division of Pulmonary Medicine, Department of Medicine, Keio University, School of Medicine, Tokyo, Japan
| | - Kota Ishioka
- Division of Pulmonary Medicine, Department of Medicine, Keio University, School of Medicine, Tokyo, Japan
| | - Kageaki Watanabe
- Department of Thoracic Oncology and Respiratory Medicine, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, Tokyo, Japan
| | - Tsunekazu Hishima
- Department of Pathology, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, Tokyo, Japan
| | - Yutaka Kurebayashi
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Katsura Emoto
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Hideki Terai
- Division of Pulmonary Medicine, Department of Medicine, Keio University, School of Medicine, Tokyo, Japan
| | - Shinnosuke Ikemura
- Division of Pulmonary Medicine, Department of Medicine, Keio University, School of Medicine, Tokyo, Japan
| | - Ichiro Kawada
- Division of Pulmonary Medicine, Department of Medicine, Keio University, School of Medicine, Tokyo, Japan
| | - Keisuke Asakura
- Division of Thoracic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Tomoyuki Hishida
- Division of Thoracic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Hisao Asamura
- Division of Thoracic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Yuki Ohta
- Department of Integrative Medicine and Biochemistry, Keio University School of Medicine, Tokyo, Japan
- Department of Organoid Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Sirirat Takahashi
- Department of Integrative Medicine and Biochemistry, Keio University School of Medicine, Tokyo, Japan
- Department of Organoid Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Mayumi Oda
- Department of Integrative Medicine and Biochemistry, Keio University School of Medicine, Tokyo, Japan
- Department of Organoid Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Megumu Saito
- Department of Organoid Medicine, Keio University School of Medicine, Tokyo, Japan
- Otsuka Pharmaceutical Company Limited, Department of Drug Modality Development, Osaka Research Center for Drug Discovery, Osaka, Japan
| | - Mami Matano
- Department of Integrative Medicine and Biochemistry, Keio University School of Medicine, Tokyo, Japan
- Department of Organoid Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Kenzo Soejima
- Division of Pulmonary Medicine, Department of Medicine, Keio University, School of Medicine, Tokyo, Japan
| | - Masayuki Fujii
- Department of Integrative Medicine and Biochemistry, Keio University School of Medicine, Tokyo, Japan
- Department of Organoid Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Koichi Fukunaga
- Division of Pulmonary Medicine, Department of Medicine, Keio University, School of Medicine, Tokyo, Japan
| | - Hiroyuki Yasuda
- Division of Pulmonary Medicine, Department of Medicine, Keio University, School of Medicine, Tokyo, Japan.
| | - Toshiro Sato
- Department of Integrative Medicine and Biochemistry, Keio University School of Medicine, Tokyo, Japan.
- Department of Organoid Medicine, Keio University School of Medicine, Tokyo, Japan.
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35
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Liu X, Wang D, Zhang Z, Lin X, Xiao J. Epigenetic perspectives on wheat speciation, adaptation, and development. Trends Genet 2025:S0168-9525(25)00083-6. [PMID: 40348655 DOI: 10.1016/j.tig.2025.04.008] [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: 02/14/2025] [Revised: 04/16/2025] [Accepted: 04/18/2025] [Indexed: 05/14/2025]
Abstract
Bread wheat (Triticum aestivum) has undergone a complex evolutionary history shaped by polyploidization, domestication, and adaptation. Recent advances in multiomics approaches have shed light on the role of epigenetic mechanisms, including DNA methylation, histone modification, chromatin accessibility, and noncoding RNAs, in regulating gene expression throughout these processes. Epigenomic reprogramming contributes to genome stability and subgenome differentiation and modulates key agronomic traits by influencing flowering time, environmental responses, and developmental programs. This review synthesizes current insights into epigenetic regulation of wheat speciation, adaptation, and development, highlighting their potential applications in crop improvement. A deeper understanding of these mechanisms will facilitate targeted breeding strategies leveraging epigenetic variations to enhance wheat resilience and productivity in the face of changing environments.
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Affiliation(s)
- Xuemei Liu
- Laboratory of Advanced Breeding Technologies, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dongzhi Wang
- Laboratory of Advanced Breeding Technologies, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhaoheng Zhang
- Laboratory of Advanced Breeding Technologies, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuelei Lin
- Laboratory of Advanced Breeding Technologies, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jun Xiao
- Laboratory of Advanced Breeding Technologies, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, CAS, Beijing, 100101, China.
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36
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Dincer TU, Ernst J. ChromActivity: integrative epigenomic and functional characterization assay based annotation of regulatory activity across diverse human cell types. Genome Biol 2025; 26:123. [PMID: 40346707 PMCID: PMC12063466 DOI: 10.1186/s13059-025-03579-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 04/15/2025] [Indexed: 05/11/2025] Open
Abstract
We introduce ChromActivity, a computational framework for predicting and annotating regulatory activity across the genome through integration of multiple epigenomic maps and various functional characterization datasets. ChromActivity generates genomewide predictions of regulatory activity associated with each functional characterization dataset across many cell types based on available epigenomic data. It then for each cell type produces ChromScoreHMM genome annotations based on the combinatorial and spatial patterns within these predictions and ChromScore tracks of overall predicted regulatory activity. ChromActivity provides a resource for analyzing and interpreting the human regulatory genome across diverse cell types.
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Affiliation(s)
- Tevfik Umut Dincer
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Jason Ernst
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research at University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Computer Science Department, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
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37
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Guo S, Hu X, Cotton JL, Ma L, Li Q, Cui J, Wang Y, Thakare RP, Tao Z, Ip YT, Wu X, Wang J, Mao J. VGLL2 and TEAD1 fusion proteins identified in human sarcoma drive YAP/TAZ-independent tumorigenesis by engaging EP300. eLife 2025; 13:RP98386. [PMID: 40338073 PMCID: PMC12061476 DOI: 10.7554/elife.98386] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2025] Open
Abstract
Studies on Hippo pathway regulation of tumorigenesis largely center on YAP and TAZ, the transcriptional co-regulators of TEADs. Here, we present an oncogenic mechanism involving VGLL and TEAD fusions that is Hippo pathway-related but YAP/TAZ-independent. We characterize two recurrent fusions, VGLL2-NCOA2 and TEAD1-NCOA2, recently identified in human spindle cell rhabdomyosarcoma. We demonstrate that in contrast to VGLL2 and TEAD1 the fusion proteins are potent activators of TEAD-dependent transcription, and the function of these fusion proteins does not require YAP/TAZ. Furthermore, we identify that VGLL2 and TEAD1 fusions engage specific epigenetic regulation by recruiting histone acetyltransferase EP300 to control TEAD-mediated transcriptional and epigenetic landscapes. We show that small-molecule EP300 inhibition can suppress fusion protein-induced oncogenic transformation both in vitro and in vivo in mouse models. Overall, our study reveals a molecular basis for VGLL involvement in cancer and provides a framework for targeting tumors carrying VGLL, TEAD, or NCOA translocations.
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Affiliation(s)
- Susu Guo
- Department of Clinical Laboratory, Shanghai Chest Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Xiaodi Hu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - Jennifer L Cotton
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - Lifang Ma
- Department of Clinical Laboratory, Shanghai Chest Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Qi Li
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
- Program in Molecular Medicine, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - Jiangtao Cui
- Department of Clinical Laboratory, Shanghai Chest Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Yongjie Wang
- Department of Clinical Laboratory, Shanghai Chest Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Ritesh P Thakare
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - Zhipeng Tao
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical SchoolCharlestownUnited States
| | - Y Tony Ip
- Program in Molecular Medicine, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - Xu Wu
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical SchoolCharlestownUnited States
| | - Jiayi Wang
- Department of Clinical Laboratory, Shanghai Chest Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Junhao Mao
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
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38
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Jo Y, Greene TT, Chiale C, Zhang K, Fang Z, Dallari S, Marooki N, Wang W, Zuniga EI. Genomic analysis of progenitors in viral infection implicates glucocorticoids as suppressors of plasmacytoid dendritic cell generation. Proc Natl Acad Sci U S A 2025; 122:e2410092122. [PMID: 40294270 PMCID: PMC12067256 DOI: 10.1073/pnas.2410092122] [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: 05/20/2024] [Accepted: 02/19/2025] [Indexed: 04/30/2025] Open
Abstract
Plasmacytoid Dendritic cells (pDCs) are the most potent producers of interferons, which are critical antiviral cytokines. pDC development is, however, compromised following a viral infection, and this phenomenon, as well as its relationship to conventional (c)DC development is still incompletely understood. By using lymphocytic choriomeningitis virus (LCMV) infection in mice as a model system, we observed that DC progenitors skewed away from pDC and toward cDC development during in vivo viral infection. Subsequent characterization of the transcriptional and epigenetic landscape of fms-like tyrosine kinase 3+ (Flt3+) DC progenitors and follow-up studies revealed increased apoptosis and reduced proliferation in different individual DC-progenitors as well as a profound type I interferon (IFN-I)-dependent ablation of pre-pDCs, but not pre-DC precursors, after both acute and chronic LCMV infections. In addition, integrated genomic analysis identified altered activity of 34 transcription factors in Flt3+ DC progenitors from infected mice, including two regulators of Glucocorticoid (GC) responses. Subsequent studies demonstrated that addition of GCs to DC progenitors led to downregulated pDC-primed-genes while upregulating cDC-primed-genes, and that endogenous GCs selectively decreased pDC, but not cDC, numbers upon in vivo LCMV infection. These findings demonstrate a significant ablation of pre-pDCs in infected mice and identify GCs as suppressors of pDC generation from early progenitors. This provides a potential explanation for the impaired pDC development following viral infection and links pDC numbers to the hypothalamic-pituitary-adrenal axis.
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Affiliation(s)
- Yeara Jo
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA92093
| | - Trever T. Greene
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA92093
| | - Carolina Chiale
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA92093
| | - Kai Zhang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA92093
| | - Ziyan Fang
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA92093
| | - Simone Dallari
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA92093
| | - Nuha Marooki
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA92093
| | - Wei Wang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA92093
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA92093
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA92093
| | - Elina I. Zuniga
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA92093
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39
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Fang J, Singh S, Wells B, Wu Q, Jin H, Janke LJ, Wan S, Steele JA, Connelly JP, Murphy AJ, Wang R, Davidoff A, Ashcroft M, Pruett-Miller SM, Yang J. The context-dependent epigenetic and organogenesis programs determine 3D vs. 2D cellular fitness of MYC-driven murine liver cancer cells. eLife 2025; 14:RP101299. [PMID: 40326560 PMCID: PMC12055005 DOI: 10.7554/elife.101299] [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: 05/07/2025] Open
Abstract
3D cellular-specific epigenetic and transcriptomic reprogramming is critical to organogenesis and tumorigenesis. Here, we dissect the distinct cell fitness in 2D (normoxia vs. chronic hypoxia) vs 3D (normoxia) culture conditions for an MYC-driven murine liver cancer model. We identify over 600 shared essential genes and additional context-specific fitness genes and pathways. Knockout of the VHL-HIF1 pathway results in incompatible fitness defects under normoxia vs. 1% oxygen or 3D culture conditions. Moreover, deletion of each of the mitochondrial respiratory electron transport chain complex has distinct fitness outcomes. Notably, multicellular organogenesis signaling pathways including TGFβ-SMAD, which is upregulated in 3D culture, specifically constrict the uncontrolled cell proliferation in 3D while inactivation of epigenetic modifiers (Bcor, Kmt2d, Mettl3, and Mettl14) has opposite outcomes in 2D vs. 3D. We further identify a 3D-dependent synthetic lethality with partial loss of Prmt5 due to a reduction of Mtap expression resulting from 3D-specific epigenetic reprogramming. Our study highlights unique epigenetic, metabolic, and organogenesis signaling dependencies under different cellular settings.
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Affiliation(s)
- Jie Fang
- Department of Surgery, St Jude Children’s Research HospitalMemphisUnited States
| | - Shivendra Singh
- Department of Surgery, St Jude Children’s Research HospitalMemphisUnited States
| | - Brennan Wells
- Department of Surgery, St Jude Children’s Research HospitalMemphisUnited States
| | - Qiong Wu
- Department of Surgery, St Jude Children’s Research HospitalMemphisUnited States
| | - Hongjian Jin
- Center for Applied Bioinformatics, St Jude Children’s Research HospitalMemphisUnited States
| | - Laura J Janke
- Department of Pathology and Division of Comparative Pathology, St. Jude Children’s Research HospitalMemphisUnited States
| | - Shibiao Wan
- Bioinformatics and Systems Biology Core and Department of Genetics, Cell Biology and Anatomy University of Nebraska Medical CenterOmahaUnited States
| | - Jacob A Steele
- Department of Cell and Molecular Biology, Center for Advanced Genome Engineering, St. Jude Children's Research HospitalMemphisUnited States
| | - Jon P Connelly
- Department of Cell and Molecular Biology, Center for Advanced Genome Engineering, St. Jude Children's Research HospitalMemphisUnited States
| | - Andrew J Murphy
- Department of Surgery, St Jude Children’s Research HospitalMemphisUnited States
| | - Ruoning Wang
- Center for Childhood Cancer Research, Hematology/Oncology & BMT, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Department of Pediatrics at The Ohio State UniversityColumbusUnited States
| | - Andrew Davidoff
- Department of Surgery, St Jude Children’s Research HospitalMemphisUnited States
- St Jude Graduate School of Biomedical Sciences, St Jude Children’s Research HospitalMemphisUnited States
- Department of Pathology and Laboratory Medicine, College of Medicine, The University of Tennessee Health Science CenterMemphisUnited States
| | - Margaret Ashcroft
- Department of Medicine, University of CambridgeCambridgeUnited Kingdom
| | - Shondra M Pruett-Miller
- Department of Cell and Molecular Biology, Center for Advanced Genome Engineering, St. Jude Children's Research HospitalMemphisUnited States
| | - Jun Yang
- Department of Surgery, St Jude Children’s Research HospitalMemphisUnited States
- St Jude Graduate School of Biomedical Sciences, St Jude Children’s Research HospitalMemphisUnited States
- Department of Pathology and Laboratory Medicine, College of Medicine, The University of Tennessee Health Science CenterMemphisUnited States
- College of Graduate Health Sciences, University of Tennessee Health Science CenterMemphisUnited States
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40
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Marinov GK, Greenleaf WJ. Mapping the Simultaneously Accessible and ssDNA-Containing Genome With KAS-ATAC Sequencing. Bio Protoc 2025; 15:e5306. [PMID: 40364983 PMCID: PMC12067302 DOI: 10.21769/bioprotoc.5306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2025] [Revised: 04/09/2025] [Accepted: 04/11/2025] [Indexed: 05/15/2025] Open
Abstract
The KAS-ATAC assay provides a method to capture genomic DNA fragments that are simultaneously physically accessible and contain single-stranded DNA (ssDNA) bubbles. These are characteristic features of two of the key processes involved in regulating and expressing genes-on one hand, the activity of cis-regulatory elements (cREs), which are typically devoid of nucleosomes when active and occupied by transcription factors, and on the other, the association of RNA polymerases with DNA, which results in the presence of ssDNA structures. Here, we present a detailed protocol for carrying out KAS-ATAC as well as basic processing of KAS-ATAC datasets and discuss the key considerations for its successful application. Key features • Allows mapping of simultaneously accessible and ssDNA-containing DNA fragments. • Describes the execution of N3-kethoxal labeling and transposition of native chromatin. • Describes the pulldown of biotin-labeled DNA fragments and library generation. • Describes basic KAS-ATAC data processing steps.
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Affiliation(s)
- Georgi K. Marinov
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA
| | - William J. Greenleaf
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA
- Department of Applied Physics, Stanford University, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Stanford University, Arc Institute, Stanford, CA, USA
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41
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Cheng B, Peng SI, Jia YY, Tong E, Atwood SX, Sun BK. Comprehensive secretome profiling and CRISPR screen identifies SFRP1 as a key inhibitor of epidermal progenitor proliferation. Cell Death Dis 2025; 16:360. [PMID: 40319033 PMCID: PMC12049499 DOI: 10.1038/s41419-025-07691-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2024] [Revised: 04/11/2025] [Accepted: 04/23/2025] [Indexed: 05/07/2025]
Abstract
Secreted proteins are crucial for the structure and functions of the human epidermis, but the full repertoire of the keratinocyte secretome has not been experimentally defined. In this study, we performed mass spectrometry on conditioned media from primary human keratinocytes, identifying 406 proteins with diverse roles in adhesion, migration, proliferation, proteolysis, signal transduction, and innate immunity. To leverage this new dataset, we developed a novel colony formation assay-based CRISPR screen to investigate the functions of uncharacterized secreted proteins on epidermal stem cells. The screen identified six candidate proteins that promoted proliferation of epidermal progenitors and two proteins that inhibited it. Secreted frizzled-related protein-1 (SFRP1) was the most potent inhibitor. We discovered that SFRP1 restrained clonogenic keratinocyte proliferation by inhibiting Wnt signaling as well as blocking ectopic expression of leukemia inhibitory factor (LIF). Collectively, our study expands our knowledge of the keratinocyte secretome, establishes a novel CRISPR screen to assess the function of non-cell autonomous factors, and highlights SFRP1's role in regulating epidermal balance.
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Affiliation(s)
- Binbin Cheng
- Department of Dermatology, University of California Irvine, Irvine, CA, USA
| | | | - Yunlong Y Jia
- Department of Dermatology, University of California Irvine, Irvine, CA, USA
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA, USA
| | - Elton Tong
- Department of Dermatology, University of California Irvine, Irvine, CA, USA
| | - Scott X Atwood
- Department of Dermatology, University of California Irvine, Irvine, CA, USA
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA, USA
| | - Bryan K Sun
- Department of Dermatology, University of California Irvine, Irvine, CA, USA.
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42
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Sereti K, Russo AE, Raisner R, Ma TP, Gascoigne KE. PAX8 Interacts with the SWI/SNF Complex at Enhancers to Drive Proliferation in Ovarian Cancer. Mol Cancer Res 2025; 23:416-425. [PMID: 39918415 DOI: 10.1158/1541-7786.mcr-24-0710] [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: 08/01/2024] [Revised: 12/23/2024] [Accepted: 02/05/2025] [Indexed: 05/03/2025]
Abstract
Activation of lineage-specific gene expression programs is mediated by the recruitment of lineage-specific transcription factors and their coactivators to chromatin. The lineage factor PAX8 drives essential gene expression in ovarian cancer cells and is required for tumor proliferation. However, the molecular details surrounding cofactor recruitment and specific activation of transcription by PAX8 remain unknown. Here, we identify an important functional interaction between PAX8 and the switch/sucrose nonfermentable (SWI/SNF) chromatin remodeling complex. We show that PAX8 can recruit SWI/SNF complexes to DNA, in which they function to open chromatin and facilitate the expression of PAX8 target genes. Genetic deletion of PAX8 results in loss of SWI/SNF from PAX8-bound enhancers, loss of expression of associated target genes, and reduced proliferation. These results can be phenocopied by pharmacological inhibition of SWI/SNF ATPase activity. These data indicate that PAX8 mediates the expression of an essential ovarian cancer proliferative program in part by the recruitment of the SWI/SNF complex, highlighting a novel vulnerability in PAX8-dependent ovarian cancer. Implications: PAX8 recruits SWI/SNF complexes to enhancers to mediate the expression of genes essential for ovarian cancer proliferation.
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Affiliation(s)
- Kostianna Sereti
- Department of Discovery Oncology, Genentech Inc., South San Francisco, California
| | - Anna E Russo
- Department of Discovery Oncology, Genentech Inc., South San Francisco, California
| | - Ryan Raisner
- Department of Discovery Oncology, Genentech Inc., South San Francisco, California
| | - Taylur P Ma
- Department of Microchemistry, Proteomics and Lipidomics, Genentech Inc., South San Francisco, California
| | - Karen E Gascoigne
- Department of Discovery Oncology, Genentech Inc., South San Francisco, California
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43
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Abe K. Dynamic activity changes in transcription factors: Unlocking the mechanisms regulating physiological changes in the brain. Neurosci Res 2025; 214:16-22. [PMID: 39134224 DOI: 10.1016/j.neures.2024.08.001] [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: 08/03/2024] [Revised: 07/30/2024] [Accepted: 08/04/2024] [Indexed: 08/18/2024]
Abstract
Transcription factors (TFs) regulate the establishment and modulation of the transcriptome within cells, thereby playing a crucial role in various aspects of cellular physiology throughout the body. Quantitative measurement of TF activity during the development, function, and dysfunction of the brain is essential for gaining a deeper understanding of the regulatory mechanisms governing gene expression during these processes. Due to their role as regulators of gene expression, assessing and modulating detailed TF activity contributes to the development of practical methods to intervene in these processes, potentially offering more efficient treatments for diseases. Recent methodologies have revealed that TF activity is dynamically regulated within cells and organisms, including the adult brain. This review summarizes the regulatory mechanisms of TF activities and the methodologies used to assess them, emphasizing their importance in both fundamental research and clinical applications.
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Affiliation(s)
- Kentaro Abe
- Lab of Brain Development, Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, Miyagi 980-8577, Japan; Division for the Establishment of Frontier Sciences of the Organization for Advanced Studies, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, Miyagi 980-8577, Japan.
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44
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Loft A, Emont MP, Weinstock A, Divoux A, Ghosh A, Wagner A, Hertzel AV, Maniyadath B, Deplancke B, Liu B, Scheele C, Lumeng C, Ding C, Ma C, Wolfrum C, Strieder-Barboza C, Li C, Truong DD, Bernlohr DA, Stener-Victorin E, Kershaw EE, Yeger-Lotem E, Shamsi F, Hui HX, Camara H, Zhong J, Kalucka J, Ludwig JA, Semon JA, Jalkanen J, Whytock KL, Dumont KD, Sparks LM, Muir LA, Fang L, Massier L, Saraiva LR, Beyer MD, Jeschke MG, Mori MA, Boroni M, Walsh MJ, Patti ME, Lynes MD, Blüher M, Rydén M, Hamda N, Solimini NL, Mejhert N, Gao P, Gupta RK, Murphy R, Pirouzpanah S, Corvera S, Tang S, Das SK, Schmidt SF, Zhang T, Nelson TM, O'Sullivan TE, Efthymiou V, Wang W, Tong Y, Tseng YH, Mandrup S, Rosen ED. Towards a consensus atlas of human and mouse adipose tissue at single-cell resolution. Nat Metab 2025; 7:875-894. [PMID: 40360756 DOI: 10.1038/s42255-025-01296-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2024] [Accepted: 03/28/2025] [Indexed: 05/15/2025]
Abstract
Adipose tissue (AT) is a complex connective tissue with a high relative proportion of adipocytes, which are specialized cells with the ability to store lipids in large droplets. AT is found in multiple discrete depots throughout the body, where it serves as the primary repository for excess calories. In addition, AT has an important role in functions as diverse as insulation, immunity and regulation of metabolic homeostasis. The Human Cell Atlas Adipose Bionetwork was established to support the generation of single-cell atlases of human AT as well as the development of unified approaches and consensus for cell annotation. Here, we provide a first roadmap from this bionetwork, including our suggested cell annotations for humans and mice, with the aim of describing the state of the field and providing guidelines for the production, analysis, interpretation and presentation of AT single-cell data.
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Affiliation(s)
- Anne Loft
- Center for Functional Genomics and Tissue Plasticity (ATLAS), Department of Biochemistry and Molecular Biology, University of Southern Denmark (SDU), Odense, Denmark.
| | - Margo P Emont
- Section of Endocrinology, Diabetes and Metabolism, University of Chicago, Chicago, IL, USA.
| | - Ada Weinstock
- Department of Medicine, Section of Genetic Medicine, University of Chicago, Chicago, IL, USA
| | - Adeline Divoux
- Translational Research Institute, AdventHealth, Orlando, FL, USA
| | - Adhideb Ghosh
- Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zurich, Schwerzenbach, Switzerland
| | - Allon Wagner
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Ann V Hertzel
- Department of Biochemistry, Molecular Biology and Biophysics, Institute on the Biology of Aging and Metabolism, The University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Babukrishna Maniyadath
- Center for Functional Genomics and Tissue Plasticity (ATLAS), Department of Biochemistry and Molecular Biology, University of Southern Denmark (SDU), Odense, Denmark
| | - Bart Deplancke
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Boxiang Liu
- Department of Pharmacy and Pharmaceutical Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
- Department of Biomedical Informatics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Precision Medicine Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Cardiovascular-Metabolic Disease Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Camilla Scheele
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Carey Lumeng
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Changhai Ding
- Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Chenkai Ma
- Human Health, Health and Biosecurity, CSIRO, Canberra, Australian Capital Territory, Australia
| | - Christian Wolfrum
- Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zurich, Schwerzenbach, Switzerland
| | - Clarissa Strieder-Barboza
- Department of Veterinary Sciences, Texas Tech University, Lubbock, TX, USA
- School of Veterinary Medicine, Texas Tech University, Amarillo, TX, USA
| | - Congru Li
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Danh D Truong
- Department of Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - David A Bernlohr
- Department of Biochemistry, Molecular Biology and Biophysics, Institute on the Biology of Aging and Metabolism, The University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | | | - Erin E Kershaw
- Department of Medicine, Division of Endocrinology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Esti Yeger-Lotem
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Farnaz Shamsi
- Department of Molecular Pathobiology, New York University, New York, NY, USA
- Departments of Cell Biology and Medicine, Grossman School of Medicine, New York University, New York, NY, USA
| | - Hannah X Hui
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Henrique Camara
- Section on Integrative Physiology and Metabolism, Research Division, Joslin Diabetes Center, Harvard Medical School, Boston, MA, USA
| | - Jiawei Zhong
- Department of Medicine Huddinge (H7), Karolinska Institutet, Karolinska University Hospital Huddinge, Huddinge, Sweden
| | - Joanna Kalucka
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark
| | - Joseph A Ludwig
- Department of Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Julie A Semon
- Department of Biological Sciences, Missouri University of Science and Technology, Rolla, MO, USA
| | - Jutta Jalkanen
- Department of Medicine Huddinge (H7), Karolinska Institutet, Karolinska University Hospital Huddinge, Huddinge, Sweden
| | - Katie L Whytock
- Translational Research Institute, AdventHealth, Orlando, FL, USA
| | - Kyle D Dumont
- Molecular and Cellular Exercise Physiology, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Lauren M Sparks
- Translational Research Institute, AdventHealth, Orlando, FL, USA
| | - Lindsey A Muir
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Lingzhao Fang
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark
| | - Lucas Massier
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Leipzig, Germany
| | - Luis R Saraiva
- Sidra Medicine, Doha, Qatar
- Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT, USA
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Marc D Beyer
- Immunogenomics and Neurodegeneration, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Platform for Single Cell Genomics and Epigenomics (PRECISE), German Center for Neurodegenerative Diseases (DZNE) and University of Bonn and West German Genome Center (WGGC), Bonn, Germany
| | - Marc G Jeschke
- Centre for Burn Research, Hamilton Health Sciences Centre, Department of Surgery and Department of Biochemistry, McMaster University, Hamilton, Ontario, Canada
| | - Marcelo A Mori
- Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
- Obesity and Comorbidities Research Center (OCRC), Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - Mariana Boroni
- Laboratory of Bioinformatics and Computational Biology, Division of Experimental and Translational Research, Brazilian National Cancer Institute (INCA), Rio de Janeiro, Brazil
| | - Martin J Walsh
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mary-Elizabeth Patti
- Section on Integrative Physiology and Metabolism, Research Division, Joslin Diabetes Center, Harvard Medical School, Boston, MA, USA
| | | | - Matthias Blüher
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Leipzig, Germany
- Department of Medicine - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Mikael Rydén
- Department of Medicine (H7), Karolinska Institutet, C2-94, Karolinska University Hospital, Stockholm, Sweden
- Steno Diabetes Center Copenhagen, Herlev, Denmark
| | | | - Nicole L Solimini
- Department of Medical Oncology, Sarcoma Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Niklas Mejhert
- Department of Medicine (H7), Karolinska Institutet, C2-94, Karolinska University Hospital, Stockholm, Sweden
- Steno Diabetes Center Copenhagen, Herlev, Denmark
| | - Peng Gao
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Rana K Gupta
- Department of Medicine, Division of Endocrinology, and Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
| | - Rinki Murphy
- Department of Medicine, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Saeed Pirouzpanah
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Silvia Corvera
- University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Su'an Tang
- Department of Spinal Surgery, Orthopedic Medical Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Swapan K Das
- Department of Internal Medicine, Section on Endocrinology and Metabolism, Medical Center Boulevard, Wake Forest University Health Sciences, Winston-Salem, NC, USA
| | - Søren F Schmidt
- Center for Functional Genomics and Tissue Plasticity (ATLAS), Department of Biochemistry and Molecular Biology, University of Southern Denmark (SDU), Odense, Denmark
| | - Tao Zhang
- Substrate Metabolism Laboratory, School of Kinesiology, University of Michigan, Ann Arbor, MI, USA
| | - Theodore M Nelson
- Department of Physiology and Biophysics, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Timothy E O'Sullivan
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Vissarion Efthymiou
- Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zurich, Schwerzenbach, Switzerland
- Section on Integrative Physiology and Metabolism, Research Division, Joslin Diabetes Center, Harvard Medical School, Boston, MA, USA
| | - Wenjing Wang
- Department of Pharmacy and Pharmaceutical Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Yihan Tong
- Department of Pharmacy and Pharmaceutical Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Yu-Hua Tseng
- Section on Integrative Physiology and Metabolism, Research Division, Joslin Diabetes Center, Harvard Medical School, Boston, MA, USA
| | - Susanne Mandrup
- Center for Functional Genomics and Tissue Plasticity (ATLAS), Department of Biochemistry and Molecular Biology, University of Southern Denmark (SDU), Odense, Denmark.
| | - Evan D Rosen
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Harvard Medical School, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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45
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Xie L, Jakutis G, Dooley CM, Guenther S, Kontarakis Z, Howard SP, Juan T, Stainier DYR. Induction of a transcriptional adaptation response by RNA destabilization events. EMBO Rep 2025; 26:2262-2279. [PMID: 40128410 PMCID: PMC12069562 DOI: 10.1038/s44319-025-00427-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2024] [Revised: 03/03/2025] [Accepted: 03/10/2025] [Indexed: 03/26/2025] Open
Abstract
Transcriptional adaptation (TA) is a cellular process whereby mRNA-destabilizing mutations are associated with the transcriptional upregulation of so-called adapting genes. The nature of the TA-triggering factor(s) remains unclear, namely whether an mRNA-borne premature termination codon or the subsequent mRNA decay process, and/or its products, elicits TA. Here, working with mouse Actg1, we first establish two types of perturbations that lead to mRNA destabilization: Cas9-induced mutations predicted to lead to mutant mRNA decay, and Cas13d-mediated mRNA cleavage. We find that both types of perturbations are effective in degrading Actg1 mRNA, and that they both upregulate Actg2. Notably, increased chromatin accessibility at the Actg2 locus was observed only in the Cas9-induced mutant cells but not in the Cas13d-targeted cells, suggesting that chromatin remodeling is not required for Actg2 upregulation. We further show that ribozyme-mediated Actg1 pre-mRNA cleavage also leads to a robust upregulation of Actg2, and that this upregulation is again independent of chromatin remodeling. Together, these data highlight the critical role of RNA destabilization events as a trigger for TA, or at least a TA-like response.
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Affiliation(s)
- Lihan Xie
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Hessen, 61231, Germany
| | - Gabrielius Jakutis
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Hessen, 61231, Germany
| | - Christopher M Dooley
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Hessen, 61231, Germany
| | - Stefan Guenther
- ECCPS Bioinformatics and Deep Sequencing Platform, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Hessen, 61231, Germany
| | - Zacharias Kontarakis
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Hessen, 61231, Germany
- Genome Engineering and Measurement Laboratory (GEML), Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
- Functional Genomics Center Zürich, ETH Zürich/University of Zürich, Zürich, 8057, Switzerland
| | - Sarah P Howard
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Hessen, 61231, Germany
| | - Thomas Juan
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Hessen, 61231, Germany.
- German Centre for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Bad Nauheim, Hessen, 61231, Germany.
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Bad Nauheim, Giessen, Frankfurt, Germany.
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, 75 185, Sweden.
| | - Didier Y R Stainier
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Hessen, 61231, Germany.
- German Centre for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Bad Nauheim, Hessen, 61231, Germany.
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Bad Nauheim, Giessen, Frankfurt, Germany.
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46
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Miyashita Y, Tajima K, Izumi K, Matsumoto N, Hayakawa D, Nakamura IT, Katayama I, Wibowo A, Matsuda H, Winardi W, Amien BR, Mitsuishi Y, Takahashi F, Nakamura K, Uchibori K, Yanagitani N, Hayashi T, Takamochi K, Suzuki K, Katayama R, Takahashi K. Novel Approach to Overcome Osimertinib Resistance Using Bromodomain and Extra-Terminal Domain Inhibitors. Cancer Sci 2025; 116:1392-1404. [PMID: 40036147 PMCID: PMC12044652 DOI: 10.1111/cas.70032] [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: 11/29/2024] [Revised: 02/09/2025] [Accepted: 02/18/2025] [Indexed: 03/06/2025] Open
Abstract
Osimertinib, a third-generation EGFR-tyrosine kinase inhibitor, is the first-line therapy for lung cancer harboring EGFR mutations. The mechanisms underlying osimertinib resistance are diverse, with approximately half remaining unknown. Epigenetic dysregulation is implicated in drug resistance; however, the mechanisms remain unclear. Therefore, we investigated epigenetic involvement in osimertinib resistance and its therapeutic potential. We established osimertinib-resistant cells and used an assay for transposase-accessible chromatin using sequencing to evaluate chromatin accessibility, finding significant changes post-resistance. Combining the assay for transposase-accessible chromatin and RNA sequencing data, we identified FGF1 as a resistance-related gene regulated by histone modifications. FGF1 induced osimertinib resistance, and its suppression attenuated resistance. Bromodomain and extra-terminal domain inhibitors combined with osimertinib overcame osimertinib resistance by reducing FGF1 expression. Increased FGF1 expression was observed in osimertinib-resistant clinical samples. This combination therapy was effective in cell lines and mouse xenograft models. These results suggest targeting histone modifications using bromodomain and extra-terminal domain inhibitors as a novel approach to overcoming osimertinib resistance.
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Affiliation(s)
- Yosuke Miyashita
- Department of Respiratory MedicineJuntendo University Graduate School of MedicineTokyoJapan
- Research Institute for Diseases of Old AgeJuntendo University Graduate School of MedicineTokyoJapan
| | - Ken Tajima
- Department of Respiratory MedicineJuntendo University Graduate School of MedicineTokyoJapan
- Research Institute for Diseases of Old AgeJuntendo University Graduate School of MedicineTokyoJapan
| | - Kenta Izumi
- Department of Respiratory MedicineJuntendo University Graduate School of MedicineTokyoJapan
- Research Institute for Diseases of Old AgeJuntendo University Graduate School of MedicineTokyoJapan
| | - Naohisa Matsumoto
- Department of Respiratory MedicineJuntendo University Graduate School of MedicineTokyoJapan
- Research Institute for Diseases of Old AgeJuntendo University Graduate School of MedicineTokyoJapan
| | - Daisuke Hayakawa
- Department of Respiratory MedicineJuntendo University Graduate School of MedicineTokyoJapan
- Research Institute for Diseases of Old AgeJuntendo University Graduate School of MedicineTokyoJapan
| | - Ikuko Takeda Nakamura
- Department of Respiratory MedicineJuntendo University Graduate School of MedicineTokyoJapan
- Research Institute for Diseases of Old AgeJuntendo University Graduate School of MedicineTokyoJapan
| | - Isana Katayama
- Department of Respiratory MedicineJuntendo University Graduate School of MedicineTokyoJapan
- Research Institute for Diseases of Old AgeJuntendo University Graduate School of MedicineTokyoJapan
| | - Adityo Wibowo
- Department of Respiratory MedicineJuntendo University Graduate School of MedicineTokyoJapan
- Research Institute for Diseases of Old AgeJuntendo University Graduate School of MedicineTokyoJapan
| | - Hironari Matsuda
- Department of Respiratory MedicineJuntendo University Graduate School of MedicineTokyoJapan
- Research Institute for Diseases of Old AgeJuntendo University Graduate School of MedicineTokyoJapan
| | - Wira Winardi
- Department of Respiratory MedicineJuntendo University Graduate School of MedicineTokyoJapan
- Research Institute for Diseases of Old AgeJuntendo University Graduate School of MedicineTokyoJapan
| | - Bagus Radityo Amien
- Department of Respiratory MedicineJuntendo University Graduate School of MedicineTokyoJapan
- Research Institute for Diseases of Old AgeJuntendo University Graduate School of MedicineTokyoJapan
| | - Yoichiro Mitsuishi
- Department of Respiratory MedicineJuntendo University Graduate School of MedicineTokyoJapan
- Research Institute for Diseases of Old AgeJuntendo University Graduate School of MedicineTokyoJapan
| | - Fumiyuki Takahashi
- Department of Respiratory MedicineJuntendo University Graduate School of MedicineTokyoJapan
- Research Institute for Diseases of Old AgeJuntendo University Graduate School of MedicineTokyoJapan
| | - Kohta Nakamura
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research CenterJuntendo University Graduate School of MedicineTokyoJapan
| | - Ken Uchibori
- Department of Thoracic Medical Oncology, The Cancer Institute HospitalJapanese Foundation for Cancer ResearchTokyoJapan
| | - Noriko Yanagitani
- Department of Thoracic Medical Oncology, The Cancer Institute HospitalJapanese Foundation for Cancer ResearchTokyoJapan
| | - Takuo Hayashi
- Department of Human PathologyJuntendo University Graduate School of MedicineTokyoJapan
| | - Kazuya Takamochi
- Department of General Thoracic SurgeryJuntendo University Graduate School of MedicineTokyoJapan
| | - Kenji Suzuki
- Department of General Thoracic SurgeryJuntendo University Graduate School of MedicineTokyoJapan
| | - Ryohei Katayama
- Division of Experimental Chemotherapy, Cancer Chemotherapy CenterJapanese Foundation for Cancer ResearchTokyoJapan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier SciencesThe University of TokyoChibaJapan
| | - Kazuhisa Takahashi
- Department of Respiratory MedicineJuntendo University Graduate School of MedicineTokyoJapan
- Research Institute for Diseases of Old AgeJuntendo University Graduate School of MedicineTokyoJapan
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Vicanolo T, Özcan A, Li JL, Huerta-López C, Ballesteros I, Rubio-Ponce A, Dumitru AC, Nicolás-Ávila JÁ, Molina-Moreno M, Reyes-Gutierrez P, Johnston AD, Martone C, Greto E, Quílez-Alvarez A, Calvo E, Bonzon-Kulichenko E, Álvarez-Velez R, Chooi MY, Kwok I, González-Bermúdez B, Malleret B, Espinosa FM, Zhang M, Wang YL, Sun D, Zhen Chong S, El-Armouche A, Kim KK, Udalova IA, Greco V, Garcia R, Vázquez J, Dopazo A, Plaza GR, Alegre-Cebollada J, Uderhardt S, Ng LG, Hidalgo A. Matrix-producing neutrophils populate and shield the skin. Nature 2025; 641:740-748. [PMID: 40108463 PMCID: PMC12074881 DOI: 10.1038/s41586-025-08741-5] [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: 08/31/2023] [Accepted: 02/04/2025] [Indexed: 03/22/2025]
Abstract
Defence from environmental threats is provided by physical barriers that confer mechanical protection and prevent the entry of microorganisms1. If microorganisms overcome those barriers, however, innate immune cells use toxic chemicals to kill the invading cells2,3. Here we examine immune diversity across tissues and identify a population of neutrophils in the skin that expresses a broad repertoire of proteins and enzymes needed to build the extracellular matrix. In the naive skin, these matrix-producing neutrophils contribute to the composition and structure of the extracellular matrix, reinforce its mechanical properties and promote barrier function. After injury, these neutrophils build 'rings' of matrix around wounds, which shield against foreign molecules and bacteria. This structural program relies on TGFβ signalling; disabling the TGFβ receptor in neutrophils impaired ring formation around wounds and facilitated bacterial invasion. We infer that the innate immune system has evolved diverse strategies for defence, including one that physically shields the host from the outside world.
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Affiliation(s)
- Tommaso Vicanolo
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
| | - Alaz Özcan
- Vascular Biology and Therapeutics Program and Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Jackson LiangYao Li
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Carla Huerta-López
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
| | - Iván Ballesteros
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
- Department of Neuroscience and Biomedical Sciences, Universidad Carlos III de Madrid, Madrid, Spain
| | - Andrea Rubio-Ponce
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
| | - Andra C Dumitru
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
| | | | - Miguel Molina-Moreno
- Vascular Biology and Therapeutics Program and Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Pablo Reyes-Gutierrez
- Vascular Biology and Therapeutics Program and Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Andrew D Johnston
- Department of Dermatology, Yale School of Medicine, New Haven, CT, USA
| | - Catherine Martone
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Eric Greto
- Department of Internal Medicine 3-Rheumatology and Immunology, Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander University Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany
| | | | - Enrique Calvo
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
| | - Elena Bonzon-Kulichenko
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
- Biochemistry Area, Faculty of Environmental Sciences and Biochemistry, University of Castilla-La Mancha, Toledo, Spain
| | | | - Ming Yao Chooi
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
- Department of Microbiology and Immunology, Immunology Translational Research Programme, NUS Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Immanuel Kwok
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Blanca González-Bermúdez
- Center for Biomedical Technology, Universidad Politécnica de Madrid, Madrid, Spain
- Departamento de Ciencia de Materiales, ETSI de Caminos, Canales y Puertos, Universidad Politécnica de Madrid, Madrid, Spain
| | - Benoit Malleret
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
- Department of Microbiology and Immunology, Immunology Translational Research Programme, NUS Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | | | - Ming Zhang
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yu-Long Wang
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Dasheng Sun
- OPO and Organ Transplantation Leading Group, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shu Zhen Chong
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
- Department of Microbiology and Immunology, Immunology Translational Research Programme, NUS Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Ali El-Armouche
- Institute of Pharmacology and Toxicology, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Kevin K Kim
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Irina A Udalova
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Valentina Greco
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Ricardo Garcia
- Instituto de Ciencia de Materiales de Madrid, CSIC, Madrid, Spain
| | - Jesús Vázquez
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
- Centro de Investigación Biomédica en Red Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Ana Dopazo
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
- Centro de Investigación Biomédica en Red Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Gustavo R Plaza
- Instituto de Ciencia de Materiales de Madrid, CSIC, Madrid, Spain
| | | | - Stefan Uderhardt
- Department of Internal Medicine 3-Rheumatology and Immunology, Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander University Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany.
| | - Lai Guan Ng
- Shanghai Immune Therapy Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Andrés Hidalgo
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain.
- Vascular Biology and Therapeutics Program and Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.
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48
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Fan S, Li X, Xu X, Yin Y, Wang G, Shao A, Wang W, Fu J. Chromatin Accessibility and Translational Landscapes of Bermudagrass (Cynodon dactylon) Under Chilling Stress. PHYSIOLOGIA PLANTARUM 2025; 177:e70279. [PMID: 40432571 DOI: 10.1111/ppl.70279] [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: 09/04/2024] [Revised: 02/25/2025] [Accepted: 03/05/2025] [Indexed: 05/29/2025]
Abstract
Cold tolerance in plants is a complex trait regulated by a network of transcription factors (TFs) and their downstream genes. While C-repeat binding factors (CBFs) are well-known for their role in cold tolerance, other regulatory networks remain largely unexplored. This study utilizes a combined approach of Assay for Transposase-Accessible Chromatin with Sequencing (ATAC-seq) and RNA-seq to identify cold-responsive TFs in Cynodon dactylon (Bermudagrass), a species widely grown in southern China but limited by cold stress. Early-stage cold stress was found to induce dynamic changes in 331 differentially accessible regions (DARs), with over 45% located in gene promoter regions. Key TFs, including CAMTA1, CAMTA2, WRKY43, WRKY48, WRKY21, and DREB1G, were associated with gained DARs, highlighting their roles in cold response regulation. In contrast, several Heat Shock Factor (HSF) family members, such as HSFA6B, HSFB2A, HSFC1, and HSFB2B, were linked to lost DARs, underscoring their involvement in cold stress regulation. The correlation between chromatin accessibility and gene expression emphasizes the critical role of TFs in plant cold stress adaptation. This study highlights the potential of ATAC-seq and RNA-seq as powerful tools for uncovering novel TFs essential for cold tolerance in plants, offering insights for future research and breeding efforts.
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Affiliation(s)
- Shugao Fan
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, Shandong Province, China
- School of Hydraulic and Civil Engineering, Ludong University, Yantai, Shandong Province, China
| | - Xiaoning Li
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, Shandong Province, China
| | - Xiao Xu
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, Shandong Province, China
| | - Yanling Yin
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, Shandong Province, China
| | - Guangyang Wang
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, Shandong Province, China
| | - An Shao
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, Shandong Province, China
| | - Wei Wang
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, Shandong Province, China
| | - Jinmin Fu
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, Shandong Province, China
- College of Grassland Science, Qingdao Agricultural University, Qingdao, Shandong Province, China
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49
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Chai H, Huang X, Xiong G, Huang J, Pels KK, Meng L, Han J, Tang D, Pan G, Deng L, Xiao Q, Wang X, Zhang M, Banecki K, Plewczynski D, Wei CL, Ruan Y. Tri-omic single-cell mapping of the 3D epigenome and transcriptome in whole mouse brains throughout the lifespan. Nat Methods 2025; 22:994-1007. [PMID: 40301621 DOI: 10.1038/s41592-025-02658-7] [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: 11/14/2024] [Accepted: 03/13/2025] [Indexed: 05/01/2025]
Abstract
Exploring the genomic basis of transcriptional programs has been a long-standing research focus. Here we report a single-cell method, ChAIR, to map chromatin accessibility, chromatin interactions and RNA expression simultaneously. After validating in cultured cells, we applied ChAIR to whole mouse brains and delineated the concerted dynamics of epigenome, three-dimensional (3D) genome and transcriptome during maturation and aging. In particular, gene-centric chromatin interactions and open chromatin states provided 3D epigenomic mechanism underlying cell-type-specific transcription and revealed spatially resolved specificity. Importantly, the composition of short-range and ultralong chromatin contacts in individual cells is remarkably correlated with transcriptional activity, open chromatin state and genome folding density. This genomic property, along with associated cellular properties, differs in neurons and non-neuronal cells across different anatomic regions throughout the lifespan, implying divergent nuclear mechano-genomic mechanisms at play in brain cells. Our results demonstrate ChAIR's robustness in revealing single-cell 3D epigenomic states of cell-type-specific transcription in complex tissues.
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Affiliation(s)
- Haoxi Chai
- Life Sciences Institute and The Second Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Xingyu Huang
- Life Sciences Institute and The Second Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Guangzhou Xiong
- Life Sciences Institute and The Second Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Jiaxiang Huang
- Life Sciences Institute and The Second Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Katarzyna Karolina Pels
- Life Sciences Institute and The Second Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Lingyun Meng
- Life Sciences Institute and The Second Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Jin Han
- Life Sciences Institute and The Second Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Dongmei Tang
- Life Sciences Institute and The Second Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Guanjing Pan
- Life Sciences Institute and The Second Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Liang Deng
- Life Sciences Institute and The Second Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Qin Xiao
- Life Sciences Institute and The Second Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Xiaotao Wang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Shanghai Key Laboratory of Reproduction and Development, Fudan University, Shanghai, China
| | - Meng Zhang
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Krzysztof Banecki
- Laboratory of Bioinformatics and Computational Genomics, Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | - Dariusz Plewczynski
- Laboratory of Bioinformatics and Computational Genomics, Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | - Chia-Lin Wei
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Yijun Ruan
- Life Sciences Institute and The Second Affiliated Hospital, Zhejiang University, Hangzhou, China.
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Hui T, Zhou J, Yao M, Xie Y, Zeng H. Advances in Spatial Omics Technologies. SMALL METHODS 2025; 9:e2401171. [PMID: 40099571 DOI: 10.1002/smtd.202401171] [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: 07/29/2024] [Revised: 03/03/2025] [Indexed: 03/20/2025]
Abstract
Rapidly developing spatial omics technologies provide us with new approaches to deeply understanding the diversity and functions of cell types within organisms. Unlike traditional approaches, spatial omics technologies enable researchers to dissect the complex relationships between tissue structure and function at the cellular or even subcellular level. The application of spatial omics technologies provides new perspectives on key biological processes such as nervous system development, organ development, and tumor microenvironment. This review focuses on the advancements and strategies of spatial omics technologies, summarizes their applications in biomedical research, and highlights the power of spatial omics technologies in advancing the understanding of life sciences related to development and disease.
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Affiliation(s)
- Tianxiao Hui
- State Key Laboratory of Gene Function and Modulation Research, College of Future Technology, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Jian Zhou
- Peking-Tsinghua Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Muchen Yao
- College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yige Xie
- School of Nursing, Peking University, Beijing, 100871, China
| | - Hu Zeng
- State Key Laboratory of Gene Function and Modulation Research, College of Future Technology, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
- Beijing Advanced Center of RNA Biology (BEACON), Peking University, Beijing, 100871, China
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