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Xie B, Dean A. Noncoding function of super enhancer derived Cpox pre-mRNA in modulating neighbouring gene expression and chromatin interactions. RNA Biol 2025; 22:1-17. [PMID: 40051047 PMCID: PMC11913378 DOI: 10.1080/15476286.2025.2475421] [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: 09/24/2024] [Revised: 01/09/2025] [Accepted: 02/17/2025] [Indexed: 03/12/2025] Open
Abstract
Super enhancers are important regulators of gene expression that often overlap with protein-coding genes. However, it is unclear whether the overlapping protein-coding genes and the RNA derived from them contribute to enhancer activity. Using an erythroid-specific super enhancer that overlaps the Cpox gene as a model, Cpox pre-mRNA is found to have a non-coding function in regulating neighbouring protein-coding genes, eRNA expression and TAD interactions. Depletion of Cpox pre-mRNA leads to accumulation of H3K27me3 and release of p300 from the Cpox locus, activating an intra-TAD enhancer and gene expression. Additionally, a head-to-tail interaction between the TAD boundary genes Cpox and Dcbld2 is identified, facilitated by a novel type of repressive loop anchored by p300 and PRC2/H3K27me3. These results uncover a regulatory role for pre-mRNA transcribed within a super enhancer context and provide insight into head-to-tail inter-gene interaction in the regulation of gene expression and oncogene activation.
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Affiliation(s)
- Bingning Xie
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ann Dean
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
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2
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Ang DA, Harmston N, Li Y. ATF4:p52 complex activates oncogenic enhancers in multiple myeloma via p300/CBP recruitment to regulate BACH1. Cancer Lett 2025; 623:217727. [PMID: 40250789 DOI: 10.1016/j.canlet.2025.217727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2025] [Revised: 04/03/2025] [Accepted: 04/16/2025] [Indexed: 04/20/2025]
Abstract
Multiple myeloma (MM) is a B-cell malignancy accounting for 20 % of all blood-associated cancers. MM patients with a poorer prognosis and high-risk stratification were previously observed to be causally linked to the constitutive activation of non-canonical NF-κB (ncNF-κB) pathway. Consistent with this, the ncNF-κB p52 transcription factor was earlier found to regulate the enhancer landscape of MM to potentiate oncogenic transcription. However, the mechanism by which aberrant p52 expression is involved in coordinating enhancer activity has not been well explored. In this study, we analysed H3K27ac ChIP-seq and ATAC-seq data from MM cell lines and patient samples to screen for putative transcription factors that cooperate with p52 to regulate enhancers activated in MM. We report that ATF4 interacts with p52 and together, this complex mediates the activity of a subset of MM-associated enhancers through the recruitment of histone acetyltransferases (HATs), p300 and CBP (CREB-binding protein). We also identified a ATF4:p52 regulated target gene BACH1 under the regulation of a proximal super-enhancer, which was found to drive oncogenesis in MM by promoting cell cycle progression and proliferation. Together, our findings provide further mechanistic insights into how aberrant enhancer activation observed in MM tumours could lead to disease progression.
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Affiliation(s)
- Daniel Aron Ang
- School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Nathan Harmston
- Molecular Biosciences Division, Cardiff School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK
| | - Yinghui Li
- School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore, 637551, Singapore.
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3
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Jiang M, Zhang K, Wei G, Qi F, Yu D, Ma J, Zhang X, Chen L, Xie Y, Yu Z, Chen J, Chen D. HDAC4 super-enhancer drives CEBPB-mediated TWIST2 transcription to promote chemoresistance in LUAD. Cancer Lett 2025; 623:217716. [PMID: 40222483 DOI: 10.1016/j.canlet.2025.217716] [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: 12/16/2024] [Revised: 04/01/2025] [Accepted: 04/10/2025] [Indexed: 04/15/2025]
Abstract
Lung cancer remains one of the most prevalent malignancies worldwide. This study investigates the role of histone deacetylase 4 (HDAC4) in mediating chemoresistance in lung adenocarcinoma (LUAD). Super-enhancers (SEs), known to regulate aberrant gene expression, are critical drivers of tumor progression. We identified a specific super-enhancer region associated with HDAC4, referred to as HDAC4-SE. Among its nearby genes, TWIST2 emerged as a key player, strongly linked to chemoresistance and the epithelial-to-mesenchymal transition (EMT). We demonstrated that HDAC4-SE regulates TWIST2 expression, thereby contributing to chemoresistance in LUAD. Through bioinformatics analysis, we identified transcription factors binding to both the promoter of TWIST2 and the activation region of HDAC4-SE, with CCAAT/enhancer-binding protein beta (CEBPB) identified as a central regulator. Chromatin immunoprecipitation (ChIP) assays confirmed that CEBPB binds to both the HDAC4-SE and the TWIST2 promoter. Additionally, our investigation into the involvement of long non-coding RNAs (lncRNAs) revealed that LINC01940 might mediate the regulatory effects of HDAC4-SE on downstream genes. In conclusion, we uncovered a novel HDAC4-SE/LINC01940/CEBPB/TWIST2 signaling pathway that drives chemoresistance and tumor progression in LUAD. This pathway offers promising insights into potential therapeutic targets to overcome chemoresistance in lung cancer.
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Affiliation(s)
- Min Jiang
- Department of Medical Oncology, the First Affiliated Hospital of Soochow University, No.188 Shizi Street, Gusu District, Suzhou, 215006, Jiangsu, China
| | - Kai Zhang
- Department of Respiratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, 210006, Jiangsu, China
| | - Guohao Wei
- The Second Hospital of Nanjing, Affiliated Hospital to Nanjing University of Chinese Medicine, 210003, Nanjing, China
| | - Feng Qi
- Department of Pharmacy, the Yancheng Clinical College of Xuzhou Medical University, the First People's Hospital of Yancheng, No.166 West Yulong Road, Yancheng, 224006, Jiangsu, China
| | - Danlei Yu
- Department of Medical Oncology, the First Affiliated Hospital of Soochow University, No.188 Shizi Street, Gusu District, Suzhou, 215006, Jiangsu, China
| | - Jingjing Ma
- Department of Pharmacy, Dushu Lake Hospital, Soochow University, No.9 Chongwen Road, Suzhou, 215100, Jiangsu, China
| | - Xiaofei Zhang
- Department of Medical Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, No.160 Pujian Road, Pudong New District, Shanghai, 200127, China
| | - Longbang Chen
- Department of Medical Oncology, Nanjing Jinling Hospital, School of Medicine, Nanjing University, Nanjing, 210008, Jiangsu, China
| | - Yuhao Xie
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, New York, 11439, USA
| | - Zhengyuan Yu
- Department of Medical Oncology, the First Affiliated Hospital of Soochow University, No.188 Shizi Street, Gusu District, Suzhou, 215006, Jiangsu, China.
| | - Jing Chen
- Department of Biochemistry and Molecular Biology, School of Medicine, Nanjing University of Chinese Medicine, No.138 Xianlin Avenue, Nanjing, 210023, Jiangsu, China; Jiangsu Province Engineering Research Center of TCM Health Preservation, Nanjing, Jiangsu, China.
| | - Dongqin Chen
- Department of Medical Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, No.160 Pujian Road, Pudong New District, Shanghai, 200127, China; Department of Oncology, Nantong City No. 1 People's Hospital and Second Affiliated Hospital of Nantong University, No. 666 Shengli Road, Nantong, 226000, Jiangsu, China; Department of Medical Oncology, Baoshan Branch, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, No.1058 Huanzhen North Road, Baoshan District, Shanghai, 200444, China.
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4
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Zhou X, Zhou X, Li J, He Y, Qiu S, Xu Y, Liu Z, Yao Y, Liu J, Wen Y, Xie S, Chen J, Liu L, Ou Z, Cai C, Lin J, Lei B, Zou F. Bclaf1 mediates super-enhancer-driven activation of POLR2A to enhance chromatin accessibility in nitrosamine-induced esophageal carcinogenesis. JOURNAL OF HAZARDOUS MATERIALS 2025; 492:138218. [PMID: 40220379 DOI: 10.1016/j.jhazmat.2025.138218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2025] [Revised: 03/30/2025] [Accepted: 04/07/2025] [Indexed: 04/14/2025]
Abstract
Gene-environment interactions are pivotal contributors to nitrosamine-induced esophageal carcinogenesis. While genetic mechanisms in esophageal carcinoma (ESCA) are well-defined, epigenetic drivers remain elusive. This study identifies a novel mechanism of epigenetic regulation centered on B-cell lymphoma-2-associated transcription factor 1 (Bclaf1) in nitrosamine-induced (Methylnitronitrosoguanidine, MNNG) esophageal carcinogenesis. In nitrosamine-induced malignant transformation cells (MNNG-M), Bclaf1 expression is progressively increased with malignancy, and elevated Bclaf1 levels are correlated with poor prognosis in ESCA patients. Functionally, Bclaf1 significantly promotes the abnormal proliferation of MNNG-M and ESCA cells in vitro and in vivo. Mechanistically, transposase-accessible chromatin sequencing (ATAC-seq) results suggest that Bclaf1 silencing markedly reduces chromatin accessibility, thereby impairing the synthesis of newly transcribed RNA. Bclaf1 activates RNA polymerase II subunit POLR2A to promote chromatin accessibility through distinct transcriptional and splicing mechanisms. More specifically, cleavage under targets and tagmentation (CUT&Tag) assays revealed Bclaf1/P300/H3K27ac co-recruitment at the POLR2A promoter, driving transcription via the E2/E3 elements of the POLR2A super-enhancer. Additionally, RNA-binding protein immunoprecipitation (RIP) assays demonstrated that the Bclaf1 cofactor, small nuclear ribonucleoprotein polypeptide A (SNRPA), interacts with pre-POLR2A to regulate its splicing. Collectively, our study reveals that Bclaf1 facilitates nitrosamine-induced ESCA by controlling POLR2A transcriptional and splicing activities, providing novel insight for early detection and intervention.
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Affiliation(s)
- Xiangjun Zhou
- Department of Occupational Health and Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, 1838 Guangzhou Road North, Guangzhou 510515, China
| | - Xueqiong Zhou
- Department of Occupational Health and Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, 1838 Guangzhou Road North, Guangzhou 510515, China.
| | - Jun Li
- Department of thoracic surgery, The third affiliated hospital of Southern Medical University, Guangzhou, Guangdong 510630, China
| | - Yingzheng He
- Department of Occupational Health and Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, 1838 Guangzhou Road North, Guangzhou 510515, China
| | - Shizhen Qiu
- Department of Occupational Health and Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, 1838 Guangzhou Road North, Guangzhou 510515, China
| | - Ye Xu
- Department of Immunology and Microbiology, School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, China
| | - Zeyu Liu
- Department of Occupational Health and Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, 1838 Guangzhou Road North, Guangzhou 510515, China
| | - Yina Yao
- Department of Occupational Health and Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, 1838 Guangzhou Road North, Guangzhou 510515, China
| | - Jia Liu
- Department of Occupational Health and Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, 1838 Guangzhou Road North, Guangzhou 510515, China
| | - Ying Wen
- Guangzhou Women and Children's Medical Centre, Guangzhou Medical University Institute of Pediatrics, 9 Jinsui Road, Guangzhou 510623, China
| | - Sitong Xie
- Department of Occupational Health and Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, 1838 Guangzhou Road North, Guangzhou 510515, China
| | - Jialong Chen
- Department of Preventive Medicine, School of Public Health, Guangdong Medical University, Dongguan, 523808, China
| | - Linhua Liu
- Department of Preventive Medicine, School of Public Health, Guangdong Medical University, Dongguan, 523808, China
| | - Zejin Ou
- Key Laboratory of Occupational Environment and Health, Guangzhou Twelfth People's Hospital, Guangzhou, 510620, China
| | - Chunqing Cai
- Department of Occupational Health and Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, 1838 Guangzhou Road North, Guangzhou 510515, China
| | - Junyuan Lin
- Department of Occupational Health and Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, 1838 Guangzhou Road North, Guangzhou 510515, China
| | - Bingxi Lei
- Department of Neurosurgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.
| | - Fei Zou
- Department of Occupational Health and Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, 1838 Guangzhou Road North, Guangzhou 510515, China.
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5
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Crump NT, Milne TA. Is Enhancer Function Driven by Protein-Protein Interactions? From Bacteria to Leukemia. Bioessays 2025; 47:e70006. [PMID: 40195782 PMCID: PMC12101050 DOI: 10.1002/bies.70006] [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: 07/07/2024] [Revised: 03/23/2025] [Accepted: 03/25/2025] [Indexed: 04/09/2025]
Abstract
The precise regulation of the transcription of genes is essential for normal development and for the maintenance of life. Aberrant gene expression changes drive many human diseases. Despite this, we still do not completely understand how precise gene regulation is controlled in living systems. Enhancers are key regulatory elements that enable cells to specifically activate genes in response to environmental cues, or in a stage or tissue-specific manner. Any model of enhancer activity needs to answer two main questions: (1) how enhancers are able to identify and act on specific genes and (2) how enhancers influence transcription. To address these points, we first outline some of the basic principles that can be established from simpler prokaryotic systems, then discuss recent work on aberrant enhancer activity in leukemia. We argue that highly specific protein-protein interactions are a key driver of enhancer-promoter proximity, allowing enhancer-bound factors to directly act on RNA polymerase and activate transcription.
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Affiliation(s)
- Nicholas T. Crump
- Hugh and Josseline Langmuir Centre for Myeloma ResearchCentre for HaematologyDepartment of Immunology and InflammationImperial College LondonLondonUK
| | - Thomas A. Milne
- MRC Molecular Haematology UnitMRC Weatherall Institute of Molecular MedicineRadcliffe Department of MedicineUniversity of OxfordOxfordUK
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6
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Sur I, Zhao W, Zhang J, Kling Pilström M, Webb AT, Cheng H, Ristimäki A, Katajisto P, Enge M, Rannikmae H, de la Roche M, Taipale J. Shared requirement for MYC upstream super-enhancer region in tissue regeneration and cancer. Life Sci Alliance 2025; 8:e202403090. [PMID: 40180576 PMCID: PMC11969384 DOI: 10.26508/lsa.202403090] [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: 10/14/2024] [Revised: 03/14/2025] [Accepted: 03/14/2025] [Indexed: 04/05/2025] Open
Abstract
Cancer has been characterized as a wound that does not heal. Malignant cells are morphologically distinct from normal proliferating cells but have extensive similarities to tissues undergoing wound healing and/or regeneration. The mechanistic basis of this similarity has, however, remained enigmatic. Here, we show that the genomic region upstream of Myc, which carries more cancer susceptibility in humans than any other genomic region, is required for intestinal regeneration after radiation damage. Failure to regenerate is associated with inefficient Ly6a/Sca1+ stem/progenitor cell mobilization, and almost complete failure to re-establish Lgr5+ cell compartment in the intestinal crypts. The Myc upstream region is also critical for growth of adult intestinal cells in 3D organoid culture. We show that culture conditions recapitulating most aspects of adult normal tissue architecture still reprogram normal cells to proliferate using a mechanism similar to that employed by cancer cells. Our results establish a function for the Myc 2-540 super-enhancer region as the genetic link between tissue regeneration and tumorigenesis, and demonstrates that normal tissue renewal and regeneration of tissues after severe damage are mechanistically distinct.
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Affiliation(s)
- Inderpreet Sur
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Wenshuo Zhao
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Jilin Zhang
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | | | - Anna T Webb
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Huaitao Cheng
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Ari Ristimäki
- Applied Tumor Genomics Program, Biomedicum, University of Helsinki, Helsinki, Finland
- Department of Pathology, HUSLAB, HUS Diagnostic Center, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Pekka Katajisto
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
- Molecular and Integrative Bioscience Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Martin Enge
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Helena Rannikmae
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Marc de la Roche
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Jussi Taipale
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Applied Tumor Genomics Program, Biomedicum, University of Helsinki, Helsinki, Finland
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7
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Chen Q, Wang S, Zhang J, Xie M, Lu B, He J, Zhen Z, Li J, Zhu J, Li R, Li P, Wang H, Vakoc CR, Roeder RG, Chen M. JMJD1C forms condensate to facilitate a RUNX1-dependent gene expression program shared by multiple types of AML cells. Protein Cell 2025; 16:338-364. [PMID: 39450904 DOI: 10.1093/procel/pwae059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 09/26/2024] [Indexed: 10/26/2024] Open
Abstract
JMJD1C (Jumonji Domain Containing 1C), a member of the lysine demethylase 3 (KDM3) family, is universally required for the survival of several types of acute myeloid leukemia (AML) cells with different genetic mutations, representing a therapeutic opportunity with broad application. Yet how JMJD1C regulates the leukemic programs of various AML cells is largely unexplored. Here we show that JMJD1C interacts with the master hematopoietic transcription factor RUNX1, which thereby recruits JMJD1C to the genome to facilitate a RUNX1-driven transcriptional program that supports leukemic cell survival. The underlying mechanism hinges on the long N-terminal disordered region of JMJD1C, which harbors two inseparable abilities: condensate formation and direct interaction with RUNX1. This dual capability of JMJD1C may influence enhancer-promoter contacts crucial for the expression of key leukemic genes regulated by RUNX1. Our findings demonstrate a previously unappreciated role for the non-catalytic function of JMJD1C in transcriptional regulation, underlying a mechanism shared by different types of leukemias.
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MESH Headings
- Core Binding Factor Alpha 2 Subunit/metabolism
- Core Binding Factor Alpha 2 Subunit/genetics
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Jumonji Domain-Containing Histone Demethylases/metabolism
- Jumonji Domain-Containing Histone Demethylases/genetics
- Jumonji Domain-Containing Histone Demethylases/chemistry
- Gene Expression Regulation, Leukemic
- Oxidoreductases, N-Demethylating/metabolism
- Oxidoreductases, N-Demethylating/genetics
- Cell Line, Tumor
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Affiliation(s)
- Qian Chen
- State Key Laboratory of Molecular Oncology, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Saisai Wang
- State Key Laboratory of Molecular Oncology, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Juqing Zhang
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Min Xie
- School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Bin Lu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, United States
| | - Jie He
- Nuclear Radiation Injury Protection and Treatment Department, Navy Medical Center of People Liberation Army (PLA), Second Military Medical University (Naval Medical University), Shanghai 200052, China
| | - Zhuoran Zhen
- State Key Laboratory of Molecular Oncology, Tsinghua-Peking Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Jing Li
- Department of Precision Medicine, Changhai Hospital, Second Military Medical University (Naval Medical University), Shanghai 200433, China
| | - Jiajun Zhu
- State Key Laboratory of Molecular Oncology, Tsinghua-Peking Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Rong Li
- Nuclear Radiation Injury Protection and Treatment Department, Navy Medical Center of People Liberation Army (PLA), Second Military Medical University (Naval Medical University), Shanghai 200052, China
| | - Pilong Li
- State Key Laboratory of Membrane Biology, Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University-Peking University Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Haifeng Wang
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | | | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, United States
| | - Mo Chen
- State Key Laboratory of Molecular Oncology, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
- SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, Shanxi Medical University, Taiyuan 030607, China
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8
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Mei J, Huang W, Meng Z, Wen S, Ou L, Bai J, Wang X, Yuan H, Li Y, Zhang L, You Y, Chen Y, Zheng X, Li F, Wang S, Zhu X, Wang Z, Zhu D, Nie X, Ma C. Super-Enhancer-Driven HCG20 Promotes Pulmonary Hypertension Through U2AF2 Splicing. Circ Res 2025. [PMID: 40433695 DOI: 10.1161/circresaha.125.326133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2025] [Revised: 05/09/2025] [Accepted: 05/19/2025] [Indexed: 05/29/2025]
Abstract
BACKGROUND Pulmonary artery endothelial cell (PAEC) dysfunction is a pathological hallmark of pulmonary hypertension (PH). Yet, the roles of long noncoding RNAs (lncRNAs) driven by super-enhancers (SEs) in PAECs are not well understood. In this study, we focused on the PAEC-specific SE-associated lncRNA HCG20 (HLA complex group 20) and to elucidate its role and underlying mechanisms in the progression of PH. METHODS ChIP-qPCR, chromosome conformation capture followed by PCR, CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/clustered regularly interspaced short palindromic repeat-associated 9), and dual-luciferase reporter assays were used to identify dysregulated SE-associated lncRNAs in PAECs and to investigate the pathological role of HCG20. The role of HCG20 in pathological processes was validated in rodent models of PH induced by SU5416/hypoxia, monocrotaline, or hypoxia alone, through adeno-associated virus-mediated endothelial-specific HCG20 overexpression or knockdown of HCG20. RNA pull-down, mass spectrometry, RNA immunoprecipitation, and RNA sequencing were used to elucidate the underlying mechanisms of HCG20-mediated PAEC dysfunction. RESULTS We identified the SE-associated lncRNA HCG20 from histone H3 lysine-27 acetylation (H3K27ac) and histone H3 lysine-4 monomethylation (H3K4me1) ChIP-seq data derived from PAECs of patients with PH. A significant upregulation of HCG20 was found in hypoxia-induced human PAECs, lung tissues, and the plasma of patients with PH. Antisense oligonucleotide and CRISPR/Cas9, which, respectively, target HCG20 and its SE, alleviate hypoxia-induced pyroptosis and subsequent endothelial-to-mesenchymal transition. Human pulmonary artery smooth muscle cells internalize human PAEC-derived exosomes containing HCG20, inducing their excessive proliferation. Targeted delivery of HCG20 into the pulmonary vascular endothelium induced pulmonary vasculature remodeling and increased pulmonary artery systolic blood pressure in rodents. Mechanistically, HCG20 directly bound and stabilized the U2AF2 (U2 small nuclear RNA auxiliary factor 2) protein, thereby facilitating its impact on the alternative splicing of EIF2AK2 (eukaryotic translation initiation factor 2 alpha kinase 2). Furthermore, we identified a novel mouse ortholog gene, 4833427F10Rik (named Hcg20), of HCG20 for the first time. Our study demonstrated that specific interference with Hcg20 in the pulmonary vascular intima has been shown to ameliorate hypoxia-induced PH. CONCLUSIONS Collectively, our data suggest that HCG20, driven by SE, contributes to PAEC dysfunction through U2AF2-mediated alternative splicing of EIF2AK2. Our work underscores the potential of using HCG20 as a novel biomarker and a promising target for the treatment of PH.
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Affiliation(s)
- Jian Mei
- College of Medical Laboratory Science and Technology, Harbin Medical University, Daqing, PR China. (J.M., Z.M., S. Wen, L.O., L.Z., Y.C., X. Zheng, X. Zhu, Z.W., D.Z., C.M.)
| | - Wei Huang
- Department of Cardiology, the First Affiliated Hospital of Chongqing Medical University, PR China (W.H., Y.Y.)
| | - Zitong Meng
- College of Medical Laboratory Science and Technology, Harbin Medical University, Daqing, PR China. (J.M., Z.M., S. Wen, L.O., L.Z., Y.C., X. Zheng, X. Zhu, Z.W., D.Z., C.M.)
| | - Shiqing Wen
- College of Medical Laboratory Science and Technology, Harbin Medical University, Daqing, PR China. (J.M., Z.M., S. Wen, L.O., L.Z., Y.C., X. Zheng, X. Zhu, Z.W., D.Z., C.M.)
| | - Langlin Ou
- College of Medical Laboratory Science and Technology, Harbin Medical University, Daqing, PR China. (J.M., Z.M., S. Wen, L.O., L.Z., Y.C., X. Zheng, X. Zhu, Z.W., D.Z., C.M.)
| | - June Bai
- College of Pharmacy, Harbin Medical University, PR China (J.B., H.Y.)
| | - Xiaoying Wang
- College of Pharmacy, Harbin Medical University, Daqing, PR China. (X.W.)
| | - Hao Yuan
- College of Pharmacy, Harbin Medical University, PR China (J.B., H.Y.)
| | - Yanyu Li
- Department of Medical Informatics, Harbin Medical University, Daqing, PR China. (Y.L.)
| | - Lixin Zhang
- College of Medical Laboratory Science and Technology, Harbin Medical University, Daqing, PR China. (J.M., Z.M., S. Wen, L.O., L.Z., Y.C., X. Zheng, X. Zhu, Z.W., D.Z., C.M.)
| | - Yuwei You
- Department of Cardiology, the First Affiliated Hospital of Chongqing Medical University, PR China (W.H., Y.Y.)
| | - Yingli Chen
- College of Medical Laboratory Science and Technology, Harbin Medical University, Daqing, PR China. (J.M., Z.M., S. Wen, L.O., L.Z., Y.C., X. Zheng, X. Zhu, Z.W., D.Z., C.M.)
| | - Xiaodong Zheng
- College of Medical Laboratory Science and Technology, Harbin Medical University, Daqing, PR China. (J.M., Z.M., S. Wen, L.O., L.Z., Y.C., X. Zheng, X. Zhu, Z.W., D.Z., C.M.)
| | - Fei Li
- College of Basic Medical Sciences, Harbin Medical University, Daqing, PR China. (F.L., S. Wang)
| | - Song Wang
- College of Basic Medical Sciences, Harbin Medical University, Daqing, PR China. (F.L., S. Wang)
| | - Xiangrui Zhu
- College of Medical Laboratory Science and Technology, Harbin Medical University, Daqing, PR China. (J.M., Z.M., S. Wen, L.O., L.Z., Y.C., X. Zheng, X. Zhu, Z.W., D.Z., C.M.)
| | - Zhaosi Wang
- College of Medical Laboratory Science and Technology, Harbin Medical University, Daqing, PR China. (J.M., Z.M., S. Wen, L.O., L.Z., Y.C., X. Zheng, X. Zhu, Z.W., D.Z., C.M.)
| | - Daling Zhu
- College of Medical Laboratory Science and Technology, Harbin Medical University, Daqing, PR China. (J.M., Z.M., S. Wen, L.O., L.Z., Y.C., X. Zheng, X. Zhu, Z.W., D.Z., C.M.)
| | - Xiaowei Nie
- Department of Human Cell Biology and Genetics, School of Medicine, Southern University of Science and Technology, Shenzhen, PR China (X.N.)
| | - Cui Ma
- College of Medical Laboratory Science and Technology, Harbin Medical University, Daqing, PR China. (J.M., Z.M., S. Wen, L.O., L.Z., Y.C., X. Zheng, X. Zhu, Z.W., D.Z., C.M.)
- Institute of Cardiovascular Diseases, Xiamen Cardiovascular Hospital, School of Medicine, Xiamen University, Fujian Branch of National Clinical Research Center for Cardiovascular Diseases, PR China (C.M.)
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9
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Arulsamy K, Xia B, Yu Y, Chen H, Pu WT, Zhang L, Chen K. SCIG: Machine learning uncovers cell identity genes in single cells by genetic sequence codes. Nucleic Acids Res 2025; 53:gkaf431. [PMID: 40433981 DOI: 10.1093/nar/gkaf431] [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: 08/21/2024] [Revised: 04/09/2025] [Accepted: 05/09/2025] [Indexed: 05/29/2025] Open
Abstract
Deciphering cell identity genes is pivotal to understanding cell differentiation, development, and cell identity dysregulation involving diseases. Here, we introduce SCIG, a machine-learning method to uncover cell identity genes in single cells. In alignment with recent reports that cell identity genes (CIGs) are regulated with unique epigenetic signatures, we found CIGs exhibit distinctive genetic sequence signatures, e.g. unique enrichment patterns of cis-regulatory elements. Using these genetic sequence signatures, along with gene expression information from single-cell RNA-seq data, SCIG uncovers the identity genes of a cell without a need for comparison to other cells. CIG score defined by SCIG surpassed expression value in network analysis to reveal the master transcription factors (TFs) regulating cell identity. Applying SCIG to the human endothelial cell atlas revealed that the tissue microenvironment is a critical supplement to master TFs for cell identity refinement. SCIG is publicly available at https://doi.org/10.5281/zenodo.14726426 , offering a valuable tool for advancing cell differentiation, development, and regenerative medicine research.
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Affiliation(s)
- Kulandaisamy Arulsamy
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, United States
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, United States
| | - Bo Xia
- Independent Researcher, Clemson, United States
| | - Yang Yu
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, United States
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, United States
| | - Hong Chen
- Vascular Biology Program, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, United States
| | - William T Pu
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, United States
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, United States
| | - Lili Zhang
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, United States
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, United States
| | - Kaifu Chen
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, United States
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, United States
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10
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Chen L, Li W, Zai W, Zheng X, Meng X, Yao Q, Li W, Liang Y, Ye M, Zhou K, Liu M, Yang Z, Mao Z, Wei H, Yang S, Shi G, Yuan Z, Yu W. HBV sequence integrated to enhancer acting as oncogenic driver epigenetically promotes hepatocellular carcinoma development. J Exp Clin Cancer Res 2025; 44:155. [PMID: 40405227 PMCID: PMC12096768 DOI: 10.1186/s13046-025-03413-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2025] [Accepted: 05/09/2025] [Indexed: 05/24/2025] Open
Abstract
BACKGROUND HBV integration is considered as the main contributor to hepatocellular carcinoma (HCC). However, whether HBV integrated sequences determine genotype pathogenicity and how to block their function during HCC progression remains unclear. METHODS An in vitro HBV-infected PHH model and liver cancer cell lines were established to confirm the pathogenic potential of HBV-SITEs. The roles of HBV-SITE-1 in HCC development were analyzed using cellular phenotypic assays and molecular biology techniques, including the combined analysis of RNA-seq and ChIP-seq. Animal models were also used to evaluate the therapeutic effect of HBV-miR-2 inhibitors. RESULTS We identified nine fragments of HBV Sequences Integrated To Enhancer, termed as "HBV-SITEs". Particularly, a single nucleotide variation (T > G) was embedded at seed sequence of HBV-miR-2 in the highest integrated HBV-SITE-1 between genotypes B and H. Unexpectedly, B-HBV-SITE-1, not H-HBV-SITE-1, could abnormally activate oncogenic genes including TERT and accelerate HCC cell proliferation and migration. Meanwhile, HBV-miR-2 was gradually increased in HBV-infected cells and patient plasma with different HCC stages. Importantly, 227 genes upregulated by HBV, were also activated by HBV-miR-2 through triggering HBV-SITE-1 enhancer. Conversely, enhancer activities were particularly decreased by HBV-miR-2 inhibitors, and further downregulated activated oncogenic genes. Finally, HCC growth was dramatically restrained and HBV-induced transcripts were systematically reduced via injection of HBV-miR-2 inhibitors in animal models. CONCLUSION HBV-SITEs were identified as novel oncogenic elements for HCC, which provides an insightful perspective for the other cancers caused by oncogenic DNA viruses. We demonstrated that the integrated HBV sequence itself acted as oncogenic enhancers and nucleotide variations of HBV genotypes account for particular pathogenic progression, supporting that the viral nucleotide sequences are vital pathogenic substances beyond viral proteins. And modulation of their enhancer activities could be clinically achievable strategy for blocking DNA viruses-related cancer progression in the future.
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Affiliation(s)
- Lu Chen
- Shanghai Public Health Clinical Center & Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences & Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wenxuan Li
- Shanghai Public Health Clinical Center & Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences & Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wenjing Zai
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Research Unit of Cure of Chronic Hepatitis B Virus Infection (CAMS), Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
- Liver Cancer Institute, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xiangyi Zheng
- Shanghai Public Health Clinical Center & Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences & Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xianlong Meng
- Department of Liver Surgery and Transplantation, Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Qunyan Yao
- Department of Liver Surgery and Transplantation, Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Wei Li
- Shanghai Public Health Clinical Center & Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences & Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ying Liang
- Precision Pharmacy and Drug Development Center, Department of Pharmacy, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Mu Ye
- Department of Liver Surgery and Transplantation, Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Kaicheng Zhou
- Shanghai Public Health Clinical Center & Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences & Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute, Shanghai Medical College, Fudan University, Shanghai, China
| | - Mengxing Liu
- Shanghai Public Health Clinical Center & Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences & Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhicong Yang
- Shanghai Public Health Clinical Center & Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences & Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhanrui Mao
- Shanghai Public Health Clinical Center & Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences & Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hongyan Wei
- Shanghai Public Health Clinical Center & Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences & Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shuai Yang
- Shanghai Public Health Clinical Center & Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences & Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute, Shanghai Medical College, Fudan University, Shanghai, China.
- Research and Development Department, Shanghai Epicurer Biotechnology Co., Ltd., Shanghai, China.
| | - Guoming Shi
- Department of Liver Surgery and Transplantation, Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Zhenghong Yuan
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Research Unit of Cure of Chronic Hepatitis B Virus Infection (CAMS), Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Wenqiang Yu
- Shanghai Public Health Clinical Center & Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences & Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute, Shanghai Medical College, Fudan University, Shanghai, China.
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11
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Marsh GP, Cooper MS, Goggins S, Reynolds SJ, Wheeler DF, Cresser-Brown JO, Arnold RE, Babcock EG, Hughes G, Bosnakovski D, Kyba M, Ojeda S, Harrison DA, Ott CJ, Maple HJ. Development of p300-targeting degraders with enhanced selectivity and onset of degradation. RSC Med Chem 2025; 16:2049-2060. [PMID: 40093518 PMCID: PMC11905989 DOI: 10.1039/d4md00969j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2024] [Accepted: 02/17/2025] [Indexed: 03/19/2025] Open
Abstract
p300 and CBP are paralogous epigenetic regulators that are considered promising therapeutic targets for cancer treatment. Small molecule p300/CBP inhibitors have so far been unable to differentiate between these closely related proteins, yet selectivity is desirable in order to probe their distinct cellular functions. Additionally, in multiple cancers, loss-of-function CREBBP mutations set up a paralog dependent synthetic lethality with p300, that could be exploited with a selective therapeutic agent. To address this, we developed p300-targeting heterobifunctional degraders that recruit p300 through its HAT domain using the potent spiro-hydantoin-based inhibitor, iP300w. Lead degrader, BT-O2C, demonstrates improved selectivity and a faster onset of action compared to a recently disclosed A 485-based degrader in HAP1 cells and is cytotoxic in CIC::DUX4 sarcoma (CDS) cell lines (IC50 = 152-221 nM), significantly reducing expression of CDS target genes (ETV1, ETV4, ETV5). Taken together, our results demonstrate that BT-O2C represents a useful tool degrader for further exploration of p300 degradation as a therapeutic strategy.
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Affiliation(s)
- Graham P Marsh
- Bio-Techne (Tocris) The Watkins Building, Atlantic Road, Avonmouth Bristol BS11 9QD UK
| | - Mark S Cooper
- Bio-Techne (Tocris) The Watkins Building, Atlantic Road, Avonmouth Bristol BS11 9QD UK
| | - Sean Goggins
- Bio-Techne (Tocris) The Watkins Building, Atlantic Road, Avonmouth Bristol BS11 9QD UK
| | - Stephen J Reynolds
- Bio-Techne (Tocris) The Watkins Building, Atlantic Road, Avonmouth Bristol BS11 9QD UK
| | - Dean F Wheeler
- Bio-Techne (Tocris) The Watkins Building, Atlantic Road, Avonmouth Bristol BS11 9QD UK
| | - Joel O Cresser-Brown
- Bio-Techne (Tocris) The Watkins Building, Atlantic Road, Avonmouth Bristol BS11 9QD UK
| | - Robert E Arnold
- Bio-Techne (Tocris) The Watkins Building, Atlantic Road, Avonmouth Bristol BS11 9QD UK
| | - Emily G Babcock
- Bio-Techne (Tocris) The Watkins Building, Atlantic Road, Avonmouth Bristol BS11 9QD UK
| | - Gareth Hughes
- Bio-Techne (Tocris) The Watkins Building, Atlantic Road, Avonmouth Bristol BS11 9QD UK
| | - Darko Bosnakovski
- Lillehei Heart Institute Minneapolis USA
- Department of Pediatrics, University of Minnesota Minneapolis MN 55455 USA
| | - Michael Kyba
- Lillehei Heart Institute Minneapolis USA
- Department of Pediatrics, University of Minnesota Minneapolis MN 55455 USA
| | - Samuel Ojeda
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Charlestown MA 02129 USA
| | - Drew A Harrison
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Charlestown MA 02129 USA
| | - Christopher J Ott
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Charlestown MA 02129 USA
- Department of Medicine, Harvard Medical School Boston MA 02115 USA
| | - Hannah J Maple
- Bio-Techne (Tocris) The Watkins Building, Atlantic Road, Avonmouth Bristol BS11 9QD UK
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12
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Ye Z, Hu QX, Wei ML, Chen JD, Shi J, Yang NR, Jiang L, Chen J, Chen ZY, Yu WM, Xiao Y, Qian KY, Xu Z, Wang Z, Qi WL, Xiao XY, Duan YY, Xiao Y, Li LY, Ju LG, Chen MK, Wu M. A Feedback Loop Between Fatty Acid Metabolism and Epigenetics in Clear Cell Renal Carcinoma. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2025:e04532. [PMID: 40391655 DOI: 10.1002/advs.202504532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2025] [Revised: 04/15/2025] [Indexed: 05/22/2025]
Abstract
Lipid storage and epigenetic dysregulation are key features for clear cell renal carcinoma (ccRCC). However, the interplay between fatty acid metabolism and epigenetics in ccRCC remains to be further demonstrated. Here, the landscape of active enhancers is profiled in paired ccRCC samples and identifies 10171 gain variant enhancer loci (VELs) in the tumor tissues. Experimental validation reveals the enhancers targeting FABP5, FABP6, LPCAT1, MET, SEMA5B, SH3GL1, SNX33, and RHBDF2 are oncogenic. Further studies in organoids and animal models prove FABP5 as an oncogene. HIF-2α and ZNF692 transcription factors regulate FABP5 expression through directly binding to its promoter and enhancer. FABP5 is essential for the lipid droplet formation driven by HIFs and critical for H3K27ac and enhancer activity in ccRCC cells. Thus, the study has identified potential targets for drug design and diagnosis and discovered the function of a feedback loop between epigenetics and lipid metabolism regulated by FABP5 in ccRCC.
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Affiliation(s)
- Zhou Ye
- State Key Laboratory of Metabolism and Regulation in Complex Organisms, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, College of Life Sciences, Taikang Center for Life and Medical Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, 430072, China
| | - Qi-Xin Hu
- State Key Laboratory of Metabolism and Regulation in Complex Organisms, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, College of Life Sciences, Taikang Center for Life and Medical Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, 430072, China
| | - Ming-Liang Wei
- State Key Laboratory of Metabolism and Regulation in Complex Organisms, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, College of Life Sciences, Taikang Center for Life and Medical Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, 430072, China
| | - Ji-Dong Chen
- State Key Laboratory of Metabolism and Regulation in Complex Organisms, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, College of Life Sciences, Taikang Center for Life and Medical Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, 430072, China
| | - Jia Shi
- State Key Laboratory of Metabolism and Regulation in Complex Organisms, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, College of Life Sciences, Taikang Center for Life and Medical Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, 430072, China
| | - Ning-Rong Yang
- State Key Laboratory of Metabolism and Regulation in Complex Organisms, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, College of Life Sciences, Taikang Center for Life and Medical Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, 430072, China
| | - Lu Jiang
- State Key Laboratory of Metabolism and Regulation in Complex Organisms, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, College of Life Sciences, Taikang Center for Life and Medical Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, 430072, China
| | - Jian Chen
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, 430072, China
| | - Zhi-Yuan Chen
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Wei-Min Yu
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Yu Xiao
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Human Genetic Resources Preservation Center of Hubei Province, Wuhan, 430071, China
| | - Kai-Yu Qian
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Human Genetic Resources Preservation Center of Hubei Province, Wuhan, 430071, China
| | - Zilin Xu
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Human Genetic Resources Preservation Center of Hubei Province, Wuhan, 430071, China
| | - Zhong Wang
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, 430072, China
| | - Wen-Lu Qi
- State Key Laboratory of Metabolism and Regulation in Complex Organisms, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, College of Life Sciences, Taikang Center for Life and Medical Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, 430072, China
| | - Xin-Yi Xiao
- State Key Laboratory of Metabolism and Regulation in Complex Organisms, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, College of Life Sciences, Taikang Center for Life and Medical Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, 430072, China
| | - Yu-Yu Duan
- Hubei University of Chinese Medicine, Wuhan, Hubei, 430065, China
| | - Yong Xiao
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, 430072, China
| | - Lian-Yun Li
- State Key Laboratory of Metabolism and Regulation in Complex Organisms, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, College of Life Sciences, Taikang Center for Life and Medical Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, 430072, China
| | - Lin-Gao Ju
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Human Genetic Resources Preservation Center of Hubei Province, Wuhan, 430071, China
| | - Ming-Kai Chen
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, 430072, China
| | - Min Wu
- State Key Laboratory of Metabolism and Regulation in Complex Organisms, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, College of Life Sciences, Taikang Center for Life and Medical Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, 430072, China
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13
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Mizutani A, Tan C, Sugita Y, Takada S. Heterogeneous condensates of transcription factors in embryonic stem cells: Molecular simulations. Biophys J 2025; 124:1587-1598. [PMID: 40195119 DOI: 10.1016/j.bpj.2025.04.001] [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: 10/21/2024] [Revised: 02/18/2025] [Accepted: 04/02/2025] [Indexed: 04/09/2025] Open
Abstract
Biomolecular condensates formed via liquid-liquid phase separation are ubiquitous in cells, especially in the nucleus. While condensates containing one or two kinds of biomolecules have been relatively well characterized, those with more heterogeneous biomolecular components and interactions between biomolecules inside are largely unknown. This study used residue-resolution molecular dynamics simulations to investigate heterogeneous protein assemblies that include four master transcription factors in mammalian embryonic stem cells: Oct4, Sox2, Klf4, and Nanog. Molecular dynamics simulations of the mixture systems showed highly heterogeneous and dynamic behaviors; protein condensates mainly contain Sox2, Klf4, and Nanog, while most Oct4 are dissolved into the dilute phase. The condensate forms loosely interacting clusters where Klf4 is the most abundant, suggesting that Klf4 serves as a scaffold of the condensate, and Sox2 and Nanog are bound to Klf4 for stabilizing the condensate. Oct4 is moderately recruited to the condensate, serving as a client mainly via its interaction with Sox2. This study highlights the importance of intermolecular interaction between different transcription factors on the condensate formations with heterogeneous biomolecular components.
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Affiliation(s)
- Azuki Mizutani
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Cheng Tan
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Hyogo, Japan
| | - Yuji Sugita
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Hyogo, Japan; Theoretical Molecular Science Laboratory, RIKEN Pioneering Research Institute, 2-1 Hirosawa, Wako, Saitama, Japan
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan.
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14
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Shinkai N, Asada K, Machino H, Takasawa K, Takahashi S, Kouno N, Komatsu M, Hamamoto R, Kaneko S. SEgene identifies links between super enhancers and gene expression across cell types. NPJ Syst Biol Appl 2025; 11:49. [PMID: 40389443 PMCID: PMC12089303 DOI: 10.1038/s41540-025-00533-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: 01/15/2025] [Accepted: 05/11/2025] [Indexed: 05/21/2025] Open
Abstract
Enhancers are non-coding DNA regions that facilitate gene transcription, with a specialized subset, super-enhancers, known to exert exceptionally strong transcriptional activation effects. Super-enhancers have been implicated in oncogenesis, and their identification is achievable through histone mark chromatin immunoprecipitation followed by sequencing data using existing analytical tools. However, conventional super-enhancer detection methodologies often do not accurately reflect actual gene expression levels, and the large volume of identified super-enhancers complicates comprehensive analysis. To address these limitations, we developed the super-enhancer to gene links (SE-to-gene Links) analysis, a platform named "SEgene" which incorporates the peak-to-gene links approach-a statistical method designed to reveal correlations between genes and peak regions ( https://github.com/hamamoto-lab/SEgene ). This platform enables a targeted evaluation of super-enhancer regions in relation to gene expression, facilitating the identification of super-enhancers that are functionally linked to transcriptional activity. Here, we demonstrate the application of SE-to-gene Links analysis to public datasets, confirming its efficacy in accurately detecting super-enhancers and identifying functionally associated genes. Additionally, SE-to-gene Links analysis identified ERBB2 as a significant gene of interest in the lung adenocarcinoma dataset from the National Cancer Center Japan cohort, suggesting a potential impact across multiple patient samples. Thus, the SE-to-gene Links analysis provides an analytical tool for evaluating super-enhancers as potential therapeutic targets, supporting the identification of clinically significant super-enhancer regions and their functionally associated genes.
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Affiliation(s)
- Norio Shinkai
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo, Japan
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
- Department of NCC Cancer Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Ken Asada
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo, Japan
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
| | - Hidenori Machino
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo, Japan
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
| | - Ken Takasawa
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo, Japan
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
| | - Satoshi Takahashi
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo, Japan
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
| | - Nobuji Kouno
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo, Japan
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
| | - Masaaki Komatsu
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo, Japan
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
| | - Ryuji Hamamoto
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo, Japan.
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo, Japan.
- Department of NCC Cancer Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.
| | - Syuzo Kaneko
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo, Japan.
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo, Japan.
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15
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Huang H, Baxter AE, Zhang Z, Good CR, Alexander KA, Chen Z, Garcia PAA, Samareh P, Collins SM, Glastad KM, Wang L, Donahue G, Manne S, Giles JR, Shi J, Berger SL, Wherry EJ. Deciphering the role of histone modifications in memory and exhausted CD8 T cells. Sci Rep 2025; 15:17359. [PMID: 40389726 PMCID: PMC12089470 DOI: 10.1038/s41598-025-99804-0] [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: 12/20/2024] [Accepted: 04/23/2025] [Indexed: 05/21/2025] Open
Abstract
Exhausted CD8 T cells (TEX) arising during chronic infections and cancer have reduced functional capacity and limited fate flexibility that prevents optimal disease control and response to immunotherapies. Compared to memory (TMEM) cells, TEX have a unique open chromatin landscape underlying a distinct gene expression program. How TEX transcriptional and epigenetic landscapes are regulated through histone post-translational modifications (hPTMs) remains unclear. Here, we profiled key activating (H3K27ac and H3K4me3) and repressive (H3K27me3 and H3K9me3) histone modifications in naive CD8 T cells (TN), TMEM and TEX. We identified H3K27ac-associated super-enhancers that distinguish TN, TMEM and TEX, along with key transcription factor networks predicted to regulate these different transcriptional landscapes. Promoters of some key genes were poised in TN, but activated in TMEM or TEX whereas other genes poised in TN were repressed in TMEM or TEX, indicating that both repression and activation of poised genes may enforce these distinct cell states. Moreover, narrow peaks of repressive H3K9me3 were associated with increased gene expression in TEX, suggesting an atypical role for this modification. These data indicate that beyond chromatin accessibility, hPTMs differentially regulate specific gene expression programs of TEX compared to TMEM through both activating and repressive pathways.
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Affiliation(s)
- Hua Huang
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Amy E Baxter
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Zhen Zhang
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, Hefei, 230601, Anhui, China
| | - Charly R Good
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Katherine A Alexander
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Cold Spring Harbor Laboratories, Cold Spring Harbor, NY, 11724, USA
| | - Zeyu Chen
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Cell Biology and Pathology, Harvard Medical School, Boston, MA, 02115, USA
| | - Paula A Agudelo Garcia
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Department of Biomedical Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Parisa Samareh
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Sierra M Collins
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Karl M Glastad
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Department of Biology, University of Rochester, Rochester, NY, 14620, USA
| | - Lu Wang
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Sam and Ann Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
- Department of Biochemistry and Structural Biology, University of Texas Health Sciences Center at San Antonio, San Antonio, TX, 78229, USA
| | - Gregory Donahue
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Sasikanth Manne
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Josephine R Giles
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Parker Institute for Cancer Immunotherapy, University of Pennsylvania, Philadelphia, PA, USA
| | - Junwei Shi
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Shelley L Berger
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - E John Wherry
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.
- Parker Institute for Cancer Immunotherapy, University of Pennsylvania, Philadelphia, PA, USA.
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16
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Sun Y, Li M, Ning C, Gao L, Liu Z, Zhong S, Lv J, Ke Y, Wang X, Ma Q, Liu Z, Wu S, Yu H, Zhao F, Zhang J, Gong Q, Liu J, Wu Q, Wang X, Chen X. Spatiotemporal 3D chromatin organization across multiple brain regions during human fetal development. Cell Discov 2025; 11:50. [PMID: 40374600 DOI: 10.1038/s41421-025-00798-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Accepted: 02/21/2025] [Indexed: 05/17/2025] Open
Abstract
Elucidating the regulatory mechanisms underlying the development of different brain regions in humans is essential for understanding advanced cognition and neuropsychiatric disorders. However, the spatiotemporal organization of three-dimensional (3D) chromatin structure and its regulatory functions across different brain regions remain poorly understood. Here, we generated an atlas of high-resolution 3D chromatin structure across six developing human brain regions, including the prefrontal cortex (PFC), primary visual cortex (V1), cerebellum (CB), subcortical corpus striatum (CS), thalamus (TL), and hippocampus (HP), spanning gestational weeks 11-26. We found that the spatial and temporal dynamics of 3D chromatin organization play a key role in regulating brain region development. We also identified H3K27ac-marked super-enhancers as key contributors to shaping brain region-specific 3D chromatin structures and gene expression patterns. Finally, we uncovered hundreds of neuropsychiatric GWAS SNP-linked genes, shedding light on critical molecules in various neuropsychiatric disorders. In summary, our findings provide important insights into the 3D chromatin regulatory mechanisms governing brain region-specific development and can serve as a valuable resource for advancing our understanding of neuropsychiatric disorders.
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Affiliation(s)
- Yaoyu Sun
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangdong, China
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Min Li
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Science, Beijing, China
| | - Chao Ning
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing, China
| | - Lei Gao
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing, China
| | - Zhenbo Liu
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing, China
| | - Suijuan Zhong
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China
- IDG/McGovern Institute for Brain Research, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, China
| | - Junjie Lv
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangdong, China
- College of Biological Science, China Agricultural University, Beijing, China
| | - Yuwen Ke
- College of Biological Science, China Agricultural University, Beijing, China
| | - Xinxin Wang
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangdong, China
| | - Qiang Ma
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Science, Beijing, China
| | | | - Shuaishuai Wu
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing, China
| | - Hao Yu
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing, China
| | - Fangqi Zhao
- Obstetrics and Gynecology Medical Center of Severe Cardiovascular of Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - Jun Zhang
- Obstetrics and Gynecology Medical Center of Severe Cardiovascular of Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - Qian Gong
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangdong, China
| | - Jiang Liu
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing, China
| | - Qian Wu
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China
- IDG/McGovern Institute for Brain Research, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, China
| | - Xiaoqun Wang
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Science, Beijing, China.
- IDG/McGovern Institute for Brain Research, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, China.
- Changping Laboratory, Beijing, China.
| | - Xuepeng Chen
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangdong, China.
- The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangdong, China.
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17
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Ojo OA, Shen H, Ingram JT, Bonner JA, Welner RS, Lacaud G, Zajac AJ, Shi LZ. Gfi1 controls the formation of effector-like CD8 + T cells during chronic infection and cancer. Nat Commun 2025; 16:4542. [PMID: 40374625 PMCID: PMC12081725 DOI: 10.1038/s41467-025-59784-1] [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: 05/16/2024] [Accepted: 05/02/2025] [Indexed: 05/17/2025] Open
Abstract
During chronic infection and tumor progression, CD8+ T cells lose their effector functions and become exhausted. These exhausted CD8+ T cells are heterogeneous and comprised of progenitors that give rise to effector-like or terminally-exhausted cells. The precise cues and mechanisms directing subset formation are incompletely understood. Here, we show that growth factor independent-1 (Gfi1) is dynamically regulated in exhausted CD8+ T cells. During chronic LCMV Clone 13 infection, a previously under-described Ly108+CX3CR1+ subset expresses low levels of Gfi1 while other established subsets have high expression. Ly108+CX3CR1+ cells possess distinct chromatin profiles and represent a transitory subset that develops to effector-like and terminally-exhausted cells, a process dependent on Gfi1. Similarly, Gfi1 in tumor-infiltrating CD8+ T cells is required for the formation of terminally differentiated cells and endogenous as well as anti-CTLA-induced anti-tumor responses. Taken together, Gfi1 is a key regulator of the subset formation of exhausted CD8+ T cells.
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Affiliation(s)
- Oluwagbemiga A Ojo
- Department of Radiation Oncology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Hongxing Shen
- Department of Radiation Oncology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jennifer T Ingram
- Department of Microbiology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - James A Bonner
- Department of Radiation Oncology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Robert S Welner
- Department of Hematology & Oncology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
- O'Neal Comprehensive Cancer Center, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
- Immunology Institute, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Georges Lacaud
- Cancer Research UK Manchester Institute, The University of Manchester, Manchester, UK
| | - Allan J Zajac
- Department of Microbiology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
- O'Neal Comprehensive Cancer Center, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
- Immunology Institute, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Lewis Z Shi
- Department of Radiation Oncology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA.
- Department of Microbiology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA.
- O'Neal Comprehensive Cancer Center, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA.
- Immunology Institute, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA.
- Department of Pharmacology and Toxicology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA.
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18
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Nagel M, Taatjes DJ. Regulation of RNA polymerase II transcription through re-initiation and bursting. Mol Cell 2025; 85:1907-1919. [PMID: 40378829 DOI: 10.1016/j.molcel.2025.04.011] [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: 12/20/2024] [Revised: 03/13/2025] [Accepted: 04/07/2025] [Indexed: 05/19/2025]
Abstract
The regulation of RNA polymerase II (RNAPII) activity requires orchestrated responses among genomic regulatory sequences and an expansive set of proteins and protein complexes. Despite intense study over five decades, mechanistic insights continue to emerge. Within the past 10 years, live-cell imaging and single-cell transcriptomics experiments have yielded new information about enhancer-promoter communication, transcription factor dynamics, and the kinetics of RNAPII transcription activation. These insights have established RNAPII re-initiation and bursting as a common regulatory phenomenon with widespread implications for gene regulation in health and disease. Here, we summarize regulatory strategies that help control RNAPII bursting in eukaryotic cells, which is defined as short periods of active transcription followed by longer periods of inactivity. We focus on RNAPII re-initiation (i.e., a "burst" of two or more polymerases that initiate from the same promoter), with an emphasis on molecular mechanisms, open questions, and controversies surrounding this distinct regulatory stage.
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Affiliation(s)
- Michael Nagel
- Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA
| | - Dylan J Taatjes
- Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA.
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19
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Ogikubo K, Nishida J, Takahashi-Yamashiro K, Morikawa M, Ehata S, Watabe T, Miyazono K, Koinuma D. OCT-2 Is Associated With Pro-Metastatic Epigenomic Properties of Triple-Negative Breast Cancer Cells. Cancer Sci 2025. [PMID: 40364745 DOI: 10.1111/cas.70093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2025] [Revised: 04/18/2025] [Accepted: 04/26/2025] [Indexed: 05/15/2025] Open
Abstract
Triple-negative breast cancer (TNBC) is a malignant type of breast cancer. Owing to the lack of expression of receptors that serve as molecular targets for standard therapy for breast cancer, conventional cytotoxic chemotherapy is the primary treatment option for TNBC. However, TNBC exhibits a high degree of genomic heterogeneity, rendering it resistant to chemotherapy. Therefore, there is an urgent need to identify novel therapeutic targets for the treatment of TNBC. Advances in massively parallel sequencing technology have enabled the identification of cancer cell-specific gene expression patterns and epigenetic alterations that regulate their expression. Cancer cell-specific super-enhancers (SEs) have been identified as effective therapeutic targets for cancer. In this study, we identified the functional roles of epigenetic changes and their regulatory mechanisms in TNBC cells. TNBC cell-specific SEs were formed near several genes that contribute to malignant cancer cell acquisition. We found that the transcription factor OCT-2 (encoded by POU2F2) was responsible for the formation of SEs and the expression of genes encoded in the vicinity of the SE regions. Overexpression of POU2F2 enhances the metastasis of TNBC cells in mice, and its expression is highly correlated to poor prognosis of TNBC patients. Our findings provide a new insight into cancer cell-specific epigenetic changes induced by OCT-2, which trigger the progression of TNBC, and suggest possible candidates that could be targeted for the treatment of TNBC.
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Affiliation(s)
- Kazuki Ogikubo
- Department of Applied Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Molecular Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Jun Nishida
- Department of Molecular Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA
- Department of Medicine, Harvard Medical School, Boston, USA
| | - Kei Takahashi-Yamashiro
- Department of Molecular Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Chemistry, Faculty of Science, University of Alberta, Alberta, Canada
- Laboratory for Cancer Invasion and Metastasis, Institute for Medical Sciences, Yokohama, Japan
| | - Masato Morikawa
- Department of Molecular Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Advanced Comprehensive Research Organization, Teikyo University, Tokyo, Japan
| | - Shogo Ehata
- Department of Molecular Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Pathology, Wakayama Medical University, Wakayama, Japan
| | - Tetsuro Watabe
- Department of Biochemistry, Graduate School of Medical and Dental Sciences, Institute of Science Tokyo, Tokyo, Japan
| | - Kohei Miyazono
- Department of Applied Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Molecular Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Laboratory for Cancer Invasion and Metastasis, Institute for Medical Sciences, Yokohama, Japan
| | - Daizo Koinuma
- Department of Molecular Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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20
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Fu H, Itoh Y, Sawaguchi T, Otake S, Omata C, Saitoh M, Miyazawa K. Identification of a Distal Enhancer That Regulates TGF-β-Induced SNAI1 Expression. Cancer Sci 2025. [PMID: 40364580 DOI: 10.1111/cas.70091] [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: 11/15/2024] [Revised: 04/14/2025] [Accepted: 04/23/2025] [Indexed: 05/15/2025] Open
Abstract
Snail is a zinc finger transcription factor encoded by the SNAI1 gene and triggers a cellular process termed epithelial-mesenchymal transition (EMT) upon its increased expression and/or functional activation. Snail expression and activity are regulated by various extracellular stimuli, including cytokines and environmental factors. Transforming growth factor-β (TGF-β) is a Snail inducer that functions via Smad3-mediated transcriptional activation. In the present study, we identified a distal enhancer that modulates TGF-β-induced SNAI1 expression. ChIP-seq and Hi-C analyses showed that the enhancer is located 46 kb downstream of the SNAI1 gene; in TGF-β-stimulated cells, it associates with Smad3 and interacts with the SNAI1 proximal promoter. Inhibiting the activity of the enhancer using CRISPRi attenuated TGF-β-induced SNAI1 expression, stress fiber formation, and cell motility enhancement, suggesting that the enhancer mediates TGF-β-induced EMT. The enhancer contains a Smad-binding CAGA motif and an activator protein-1 (AP-1) binding motif that function in transcriptional activation. Ras-responsive element binding protein 1 (RREB1), a transcription factor required for TGF-β-induced Snail expression, regulated the basal activity of the enhancer but not its inducibility by TGF-β. In contrast to the enhancer, the association of Smad3 with the proximal promoter was not evident. These findings suggest that the proximal promoter and the distal enhancer respond to distinct signaling cues, integrate them, and cooperatively function to drive SNAI1 expression.
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Affiliation(s)
- Hao Fu
- Department of Biochemistry, Graduate School of Medicine, University of Yamanashi, Chuo, Japan
| | - Yuka Itoh
- Department of Biochemistry, Graduate School of Medicine, University of Yamanashi, Chuo, Japan
| | - Tomoe Sawaguchi
- Department of Biochemistry, Graduate School of Medicine, University of Yamanashi, Chuo, Japan
- Research Training Program for Undergraduates, Graduate School of Medicine, University of Yamanashi, Chuo, Japan
| | - Shigeo Otake
- Department of Biochemistry, Graduate School of Medicine, University of Yamanashi, Chuo, Japan
| | - Chiho Omata
- Department of Biochemistry, Graduate School of Medicine, University of Yamanashi, Chuo, Japan
| | - Masao Saitoh
- Department of Biochemistry, Graduate School of Medicine, University of Yamanashi, Chuo, Japan
- Center for Medical Education and Sciences, Graduate School of Medicine, University of Yamanashi, Chuo, Japan
| | - Keiji Miyazawa
- Department of Biochemistry, Graduate School of Medicine, University of Yamanashi, Chuo, Japan
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21
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Chen QS, Cai RZ, Wang Y, Liang GH, Zhang KM, Yang XY, Yang D, Zhao DC, Zhu XF, Deng R, Tang J. Profiling triple-negative breast cancer-specific super-enhancers identifies high-risk mesenchymal development subtype and BETi-Targetable vulnerabilities. Mol Cancer 2025; 24:141. [PMID: 40361105 PMCID: PMC12070678 DOI: 10.1186/s12943-025-02342-6] [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: 11/10/2024] [Accepted: 04/23/2025] [Indexed: 05/15/2025] Open
Abstract
BACKGROUND Super-enhancers (SEs) are critical regulators of tumorigenesis and represent promising targets for bromodomain and extra-terminal domain inhibitors (BETi). However, clinical studies across various solid tumors, including triple-negative breast cancer (TNBC), have demonstrated limited BETi efficacy. This study aims to investigate SE heterogeneity in TNBC and its influence on BETi effectiveness, with the goal of advancing BETi precision treatment strategies and enhancing therapeutic efficacy. METHODS We conducted a comprehensive analysis of H3K27ac ChIP-Seq data from TNBC cell lines and clinical samples, integrating multiple bulk RNA-Seq, scRNA-Seq, and stRNA-Seq datasets to characterize the SE landscape and heterogeneity in TNBC. Utilizing various bioinformatics algorithms, CERES scoring, and clinical prognostic data on transcription factors (TFs), we identified core transcriptional regulatory circuits (CRCs) composed of TNBC-specific SEs and master regulators, characterizing different TNBC subtypes. The biological significance of CRCs in these different TNBC subtypes and their influence on BETi sensitivity were evaluated using in vitro and in vivo models. RESULTS Our findings revealed a distinct SE landscape in TNBC compared to non-TNBC and normal breast epithelium, allowing TNBC to be classified into distinct subtypes based on TNBC-specific SEs. Importantly, we identified a high-risk mesenchymal development subtype, validated across cell lines and transcriptomic analyses, primarily driven by a CRC consisting of the master regulator VAX2 and a TNBC-specific SE. This SE-VAX2 CRC is essential for sustaining the malignant traits of this subtype and increasing its sensitivity to BETi. CONCLUSIONS Our research clarifies the heterogeneity of SEs in TNBC and identifies a high-risk mesenchymal development subtype driven by the SE-VAX2 CRC. The subtype shows more sensitivity to BETi, supporting its precision application in TNBC.
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Affiliation(s)
- Qing-Shan Chen
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
- Department of Breast Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Rui-Zhao Cai
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
- Department of Breast Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yan Wang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
- Department of Breast Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ge-Hao Liang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
- Department of Breast Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Kai-Ming Zhang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
- Department of Breast Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xiao-Yu Yang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
| | - Dong Yang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
| | - De-Chang Zhao
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
- Department of Breast Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xiao-Feng Zhu
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China.
| | - Rong Deng
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China.
| | - Jun Tang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China.
- Department of Breast Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China.
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22
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Wang W, Han F, Qi Z, Yan C, Su B, Wang J. Phase Separation: Orchestrating Biological Adaptations to Environmental Fluctuations. Int J Mol Sci 2025; 26:4614. [PMID: 40429758 DOI: 10.3390/ijms26104614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2025] [Revised: 04/23/2025] [Accepted: 05/08/2025] [Indexed: 05/29/2025] Open
Abstract
Organisms have evolved various protective mechanisms to survive in complex and dynamic environments. Phase separation is a ubiquitous mechanism in plants, animals, and microorganisms. It facilitates the aggregation of biomolecules through weak interactions, forming membrane-less organelles that help organisms respond effectively to stress signals. These biomolecular condensates include DNA, RNA, and proteins. Proteins are categorized into scaffold and client proteins, whose coordinated actions ensure the compartmentalization of cellular signals, thereby regulating various biological processes. Studies indicate that, in response to stress, phase separation modulates gene expression, signal transduction, cytoskeleton dynamics, and protein homeostasis, ensuring the precise spatiotemporal control of cellular functions. These insights underscore the crucial role of phase separation in maintaining cellular integrity and adaptability.
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Affiliation(s)
- Wenxiu Wang
- National Key Laboratory of Agricultural Microbiology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Science, Inner Mongolia University, Hohhot 010021, China
| | - Fangbing Han
- College of Agriculture, Henan University, Kaifeng 475004, China
| | - Zhi Qi
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Science, Inner Mongolia University, Hohhot 010021, China
| | - Chunxia Yan
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Science, Inner Mongolia University, Hohhot 010021, China
| | - Bodan Su
- National Key Laboratory of Agricultural Microbiology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jin Wang
- National Key Laboratory of Agricultural Microbiology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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23
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Verhagen PGA, Hansen MMK. Exploring the central dogma through the lens of gene expression noise. J Mol Biol 2025:169202. [PMID: 40354878 DOI: 10.1016/j.jmb.2025.169202] [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: 03/06/2025] [Revised: 04/30/2025] [Accepted: 05/07/2025] [Indexed: 05/14/2025]
Abstract
Over the past two decades, cell-to-cell heterogeneity has garnered increasing attention due to its critical role in both developmental and pathological processes. This growing interest has been driven, in part, by the advancements in live-cell and single-molecule imaging techniques. These techniques have provided mechanistic insights into how processes, transcription in particular, contribute to gene expression noise and, ultimately, cell-to-cell heterogeneity. More recently, however, research has expanded to explore how downstream steps in the central dogma influence gene expression noise. In this review, we mostly examine the impact of transcriptional processes on the generation of gene expression noise but also discuss how post-transcriptional mechanisms modulate noise and its propagation to the protein level. This evaluation emphasizes the need for further investigation into how processes beyond transcription shape gene expression noise, highlighting unanswered questions that remain in the field.
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Affiliation(s)
- Pieter G A Verhagen
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands; Oncode Institute, Nijmegen, The Netherlands
| | - Maike M K Hansen
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands; Oncode Institute, Nijmegen, The Netherlands.
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24
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Umphred-Wilson K, Ratnayake S, Tang Q, Wang R, Chaudhary SG, Ballachanda DN, Trichka J, Wisniewski J, Zhou L, Chen Q, Meerzaman D, Singer DS, Adoro S. The ESCRT protein CHMP5 promotes T cell leukemia by enabling BRD4-p300-dependent transcription. Nat Commun 2025; 16:4133. [PMID: 40319015 PMCID: PMC12049546 DOI: 10.1038/s41467-025-59504-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 04/24/2025] [Indexed: 05/07/2025] Open
Abstract
Addiction to oncogene-rewired transcriptional networks is a therapeutic vulnerability in cancer cells, underscoring a need to better understand mechanisms that relay oncogene signals to the transcriptional machinery. Here, using human and mouse T cell acute lymphoblastic leukemia (T-ALL) models, we identify an essential requirement for the endosomal sorting complex required for transport protein CHMP5 in T-ALL epigenetic and transcriptional programming. CHMP5 is highly expressed in T-ALL cells where it mediates recruitment of the coactivator BRD4 and the histone acetyl transferase p300 to enhancers and super-enhancers that enable transcription of T-ALL genes. Consequently, CHMP5 depletion causes severe downregulation of critical T-ALL genes, mitigates chemoresistance and impairs T-ALL initiation by oncogenic NOTCH1 in vivo. Altogether, our findings uncover a non-oncogene dependency on CHMP5 that enables T-ALL initiation and maintenance.
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Affiliation(s)
- Katharine Umphred-Wilson
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
- Immunology Training Program, Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Shashikala Ratnayake
- Computational Genomics and Bioinformatics Branch, Center for Biomedical Informatics & Information Technology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20850, USA
| | - Qianzi Tang
- College of Animal Science and Technology, Sichuan Agricultural University, 611130, Chengdu, China
| | - Rui Wang
- College of Animal Science and Technology, Sichuan Agricultural University, 611130, Chengdu, China
| | - Sneha Ghosh Chaudhary
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Devaiah N Ballachanda
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Josephine Trichka
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
- Immunology Training Program, Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Jan Wisniewski
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Lan Zhou
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, 77030, USA
| | - Qingrong Chen
- Computational Genomics and Bioinformatics Branch, Center for Biomedical Informatics & Information Technology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20850, USA
| | - Daoud Meerzaman
- Computational Genomics and Bioinformatics Branch, Center for Biomedical Informatics & Information Technology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20850, USA
| | - Dinah S Singer
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Stanley Adoro
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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25
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Alrouji M, Alshammari MS, Anwar S, Venkatesan K, Shamsi A. Mechanistic Roles of Transcriptional Cyclin-Dependent Kinases in Oncogenesis: Implications for Cancer Therapy. Cancers (Basel) 2025; 17:1554. [PMID: 40361480 PMCID: PMC12071579 DOI: 10.3390/cancers17091554] [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: 03/07/2025] [Revised: 04/27/2025] [Accepted: 04/30/2025] [Indexed: 05/15/2025] Open
Abstract
Cyclin-dependent kinases (CDKs) are pivotal in regulating cell cycle progression and transcription, making them crucial targets in cancer research. The two types of CDKs that regulate different biological activities are transcription-associated CDKs (e.g., CDK7, 8, 9, 12, and 13) and cell cycle-associated CDKs (e.g., CDK1, 2, 4, and 6). One characteristic of cancer is the dysregulation of CDK activity, which results in unchecked cell division and tumor expansion. Targeting transcriptional CDKs, which control RNA polymerase II activity and gene expression essential for cancer cell survival, has shown promise as a therapeutic approach in recent research. While research into selective inhibitors for transcriptional CDKs is ongoing, inhibitors that target CDK4/6, such as palbociclib and ribociclib, have demonstrated encouraging outcomes in treating breast cancer. CDK7, CDK8, and CDK9 are desirable targets for therapy since they have shown oncogenic roles in a variety of cancer types, such as colorectal, ovarian, and breast malignancies. Even with significant advancements, creating selective inhibitors with negligible off-target effects is still difficult. This review highlights the need for more research to optimize therapeutic strategies and improve patient outcomes by giving a thorough overview of the non-transcriptional roles of CDKs in cancer biology, their therapeutic potential, and the difficulties in targeting these kinases for cancer treatment.
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Affiliation(s)
- Mohammed Alrouji
- Department of Medical Laboratories, College of Applied Medical Sciences, Shaqra University, Shaqra 11961, Saudi Arabia;
| | - Mohammed S. Alshammari
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Shaqra University, Shaqra 11961, Saudi Arabia;
| | - Saleha Anwar
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India;
| | - Kumar Venkatesan
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Khalid University, Abha 62529, Saudi Arabia;
| | - Anas Shamsi
- Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman P.O. Box 346, Saudi Arabia
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26
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Gao J, Zhao D, Nouri HR, Chu HW, Huang H. Transcriptional Regulation of Mouse Mast Cell Differentiation and the Role of Human Lung Mast Cells in Airway Inflammation. Immunol Rev 2025; 331:e70026. [PMID: 40211768 PMCID: PMC12017346 DOI: 10.1111/imr.70026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2024] [Revised: 03/12/2025] [Accepted: 03/21/2025] [Indexed: 04/25/2025]
Abstract
Mast cells (MCs) play a critical role in allergic inflammation, anaphylaxis, and chronic inflammatory diseases such as asthma, COPD, and osteoarthritis. Dysregulated MC activation can lead to MC activation syndrome (MACS), which is observed in patients with long COVID. MCs express the high-affinity receptor for IgE and, upon activation, release mediators and cytokines that trigger anaphylactic shock and promote allergic inflammation. They also interact with epithelial and nerve cells, which are crucial in forming a complex network of cell-cell and gene-gene interactions driving chronic inflammation that can confer resistance to treatment. In this review, in the context of the literature, we focus on experiments conducted in our laboratory investigating how transcription factors and enhancers regulate genes critical in mouse MC differentiation and function related to human lung inflammation.
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Affiliation(s)
- Junfeng Gao
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO 80206, USA
| | - Dianzheng Zhao
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO 80206, USA
| | - Hamid Reza Nouri
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA
| | - Hong Wei Chu
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA
| | - Hua Huang
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO 80206, USA
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
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27
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Yamamoto T, Yamazaki T, Ninomiya K, Nakagawa S, Hirose T. Biophysical Aspect of Assembly and Regulation of Nuclear Bodies Scaffolded by Architectural RNA. J Mol Biol 2025; 437:169016. [PMID: 39978724 DOI: 10.1016/j.jmb.2025.169016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2024] [Revised: 02/03/2025] [Accepted: 02/14/2025] [Indexed: 02/22/2025]
Abstract
A growing body of evidence suggests that nuclear bodies, condensates of RNAs and proteins within the nucleus, are assembled through liquid-liquid phase separation. Some nuclear bodies, such as paraspeckles, are scaffolded by a class of RNAs known as architectural RNAs. From a materials science perspective, RNAs are categorized as polymers, which have been extensively studied in soft matter physics. While soft matter physics has the potential to provide significant insights, it is not directly applicable because transcription and other biochemical processes differentiate RNAs from other polymers studied in this field. Therefore, an interdisciplinary research fusing molecular biology and soft matter physics offers a powerful approach to studying nuclear bodies. This review introduces the biophysical insights provided by such interdisciplinary research in the assembly and regulation of nuclear bodies.
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Affiliation(s)
- Tetsuya Yamamoto
- Institute for Chemical Reaction Design and Discovery, Hokkaido University, Kita 21, Nishi 10, Kita-ku, Sapporo 001-0021, Japan.
| | - Tomohiro Yamazaki
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita 565-0871, Japan
| | - Kensuke Ninomiya
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita 565-0871, Japan
| | - Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo 060-0812, Japan
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita 565-0871, Japan; Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 1-3 Yamadaoka, Suita 565-0871, Japan
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28
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Guo S, Zhang L, Ren J, Lu Z, Ma X, Liu X, Jin H, Li J. The roles of enhancer, especially super-enhancer-driven genes in tumor metabolism and immunity. Int J Biol Macromol 2025; 308:142414. [PMID: 40132720 DOI: 10.1016/j.ijbiomac.2025.142414] [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: 10/16/2024] [Revised: 03/19/2025] [Accepted: 03/20/2025] [Indexed: 03/27/2025]
Abstract
Abnormal metabolism is a characteristic of malignant tumors. Numerous factors play roles in the regulation of tumor metabolism. As epigenetic regulators, enhancers, especially the super-enhancers (SEs), serve as platforms for transcription factors that regulate the expression of metabolism-related enzymes or transporters at the gene level. In this study, we review the effects of enhancer/ SE-driven genes on tumor metabolism and immunity. Enhancers/SEs play regulatory roles in glucose metabolism (glycolysis, gluconeogenesis, tricarboxylic acid (TCA) cycle, pyruvate, and pentose phosphate pathway, lipid metabolism (cholesterol, fatty acid, phosphatide, and sphingolipid), and amino acid metabolism (glutamine, tryptophan, arginine, and cystine). By regulating tumor metabolism, enhancers and SEs can reprogram tumor microenvironment, especially the status of various immune cells. Therefore, interfering enhancers/SEs that regulate the tumor metabolism is likely to enhance the effectiveness of immunotherapy.
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Affiliation(s)
- Songyue Guo
- Department of Oncology, Affiliated Hospital of Shandong Second Medical University, School of Clinical Medicine, Shandong Second Medical University, Weifang 261053, Shandong, China; Clinical Research Center, Affiliated Hospital of Shandong Second Medical University, Shandong Second Medical University, Weifang 261053, Shandong, China
| | - Lu Zhang
- Department of Oncology, Affiliated Hospital of Shandong Second Medical University, School of Clinical Medicine, Shandong Second Medical University, Weifang 261053, Shandong, China; Clinical Research Center, Affiliated Hospital of Shandong Second Medical University, Shandong Second Medical University, Weifang 261053, Shandong, China
| | - Jiao Ren
- Department of Oncology, Affiliated Hospital of Shandong Second Medical University, School of Clinical Medicine, Shandong Second Medical University, Weifang 261053, Shandong, China; Clinical Research Center, Affiliated Hospital of Shandong Second Medical University, Shandong Second Medical University, Weifang 261053, Shandong, China
| | - Zhong Lu
- Department of Oncology, Affiliated Hospital of Shandong Second Medical University, School of Clinical Medicine, Shandong Second Medical University, Weifang 261053, Shandong, China
| | - Xiaolin Ma
- Department of Oncology, Affiliated Hospital of Shandong Second Medical University, School of Clinical Medicine, Shandong Second Medical University, Weifang 261053, Shandong, China
| | - Xinling Liu
- Clinical Research Center, Affiliated Hospital of Shandong Second Medical University, Shandong Second Medical University, Weifang 261053, Shandong, China.
| | - Hongchuan Jin
- Department of Medical Oncology, Cancer Center of Zhejiang University, Sir Run Run Shaw hospital, School of Medicine, Zhejiang University, Hangzhou 310016, Zhejiang, China.
| | - Jiaqiu Li
- Department of Oncology, Affiliated Hospital of Shandong Second Medical University, School of Clinical Medicine, Shandong Second Medical University, Weifang 261053, Shandong, China; Clinical Research Center, Affiliated Hospital of Shandong Second Medical University, Shandong Second Medical University, Weifang 261053, Shandong, China.
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29
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Xu M, Jiang SY, Tang S, Zhu M, Hu Y, Li J, Yan J, Qin C, Tan D, An Y, Qu Y, Song BL, Ma H, Qi W. Nuclear SREBP2 condensates regulate the transcriptional activation of lipogenic genes and cholesterol homeostasis. Nat Metab 2025; 7:1034-1051. [PMID: 40394324 DOI: 10.1038/s42255-025-01291-0] [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: 06/04/2024] [Accepted: 03/25/2025] [Indexed: 05/22/2025]
Abstract
The precursor of sterol regulatory element-binding protein-2 (SREBP2) is a membrane-bound transcription factor regulating cholesterol biosynthesis. Under cholesterol-deficient conditions, mature SREBP2 is released from membrane-bound precursors through proteolytic cleavage and enters the nucleus. However, regulation of the transcriptional activity of nuclear SREBP2 (nSREBP2) is poorly understood. In the present study, we reported that nSREBP2 forms nuclear condensates through its amino-terminal, intrinsically disordered region (IDR) and works together with transcription coactivators, partly on superenhancers, for the transcriptional activation of SREBP2 target genes. Substitution of a conserved phenylalanine by alanine within the IDR abolishes the formation of nSREBP2 condensates and reduces its transcriptional activity. This can be effectively rescued by fusion with a phase separation driving FUS-IDR. Knock-in of the phenylalanine-to-alanine substitution in male mice compromises feeding-induced nSREBP2 activity and lowers hepatic and circulating cholesterol levels, underscoring the functional significance of nSREBP2 condensates. Together, the present study reveals that nuclear condensates driven by nSREBP2 N-terminal IDR facilitate the efficient activation of lipogenic genes and play an important role in cholesterol homeostasis.
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Affiliation(s)
- Mengqiang Xu
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Shi-You Jiang
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- State Key Laboratory of Phytochemistry and Natural Medicines, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Shuocheng Tang
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Meimei Zhu
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yueer Hu
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Juewan Li
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Jizhi Yan
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Chenyang Qin
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Lingang Laboratory, Shanghai, China
| | - Dongxia Tan
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yang An
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yuxiu Qu
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Bao-Liang Song
- College of Life Sciences, Taikang Center for Life and Medical Sciences, Taikang Medical School, Wuhan University, Wuhan, China
| | - Hanhui Ma
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Wei Qi
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- Lingang Laboratory, Shanghai, China.
- Shanghai Clinical Research and Trial Center, Shanghai, China.
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30
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Chen YJ, Zhao Y, Yao MY, Wang YF, Ma M, Yu CC, Jiang HL, Wei W, Shen J, Xu XW, Xie CY. Concurrent inhibition of p300/CBP and FLT3 enhances cytotoxicity and overcomes resistance in acute myeloid leukemia. Acta Pharmacol Sin 2025; 46:1390-1403. [PMID: 39885312 PMCID: PMC12032420 DOI: 10.1038/s41401-025-01479-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2024] [Accepted: 12/22/2024] [Indexed: 02/01/2025]
Abstract
FMS-like tyrosine kinase-3 (FLT3), a class 3 receptor tyrosine kinase, can be activated by mutations of internal tandem duplication (FLT3-ITD) or point mutations in the tyrosine kinase domain (FLT3-TKD), leading to constitutive activation of downstream signaling cascades, including the JAK/STAT5, PI3K/AKT/mTOR and RAS/MAPK pathways, which promote the progression of leukemic cells. Despite the initial promise of FLT3 inhibitors, the discouraging outcomes in the treatment of FLT3-ITD-positive acute myeloid leukemia (AML) promote the pursuit of more potent and enduring therapeutic approaches. The histone acetyltransferase complex comprising the E1A binding protein P300 and its paralog CREB-binding protein (p300/CBP) is a promising therapeutic target, but the development of effective p300/CBP inhibitors faces challenges due to inherent resistance and low efficacy, often exacerbated by the absence of reliable clinical biomarkers for patient stratification. In this study we investigated the role of p300/CBP in FLT3-ITD AML and evaluated the therapeutic potential of targeting p300/CBP alone or in combination with FLT3 inhibitors. We showed that high expression of p300 was significantly associated with poor prognosis in AML patients and positively correlated with FLT3 expression. We unveiled that the p300/CBP inhibitors A485 or CCS1477 dose-dependently downregulated FLT3 transcription via abrogation of histone acetylation in FLT3-ITD AML cells; in contrast, the FLT3 inhibitor quizartinib reduced the level of H3K27Ac. Concurrent inhibition of p300/CBP and FLT3 enhanced the suppression of FLT3 signaling and H3K27 acetylation, concomitantly reducing the phosphorylation of STAT5, AKT, ERK and the expression of c-Myc, thereby leading to synergistic antileukemic effects both in vitro and in vivo. Moreover, we found that p300/CBP-associated transcripts were highly expressed in quizartinib-resistant AML cells with FLT3-TKD mutation. Targeting p300/CBP with A485 or CCS1477 retained the efficacy of quizartinib, suggesting marked synergy when combined with p300/CBP inhibitors in quizartinib-resistant AML models, as well as primary FLT3-ITD+ AML samples. These results demonstrate a potential therapeutic strategy of combining p300/CBP and FLT3 inhibitors to treat FLT3-ITD and FLT3-TKD AML.
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Affiliation(s)
- Yu-Jun Chen
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
| | - Yu Zhao
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
| | | | - Ya-Fang Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
| | - Ming Ma
- Lingang Laboratory, Shanghai, 200031, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | | | - Hua-Liang Jiang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
- Drug Discovery and Development Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Wu Wei
- Lingang Laboratory, Shanghai, 200031, China
| | - Jie Shen
- Department of Pharmacy, The SATCM Third Grade Laboratory of Traditional Chinese Medicine Preparations, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
| | - Xiao-Wei Xu
- Department of Hematology, Shanghai Jiao Tong University School of Medicine Affiliated Shanghai General Hospital, Shanghai, 200080, China.
| | - Cheng-Ying Xie
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China.
- Lingang Laboratory, Shanghai, 200031, China.
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31
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Mondal S, Liu PY, Seneviratne J, De Weck A, Venkat P, Mayoh C, Wu J, Maag J, Chen J, Wong M, Bartonicek N, Khoo P, Jin L, Ludlow LE, Ziegler DS, Trahair T, Mestdagh P, Cheung BB, Li J, Dinger ME, Street I, Zhang XD, Marshall GM, Liu T. The Super Enhancer-Driven Long Noncoding RNA PRKCQ-AS1 Promotes Neuroblastoma Tumorigenesis by Interacting With MSI2 Protein and Is Targetable by Small Molecule Compounds. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2025; 12:e2412520. [PMID: 40103284 PMCID: PMC12079515 DOI: 10.1002/advs.202412520] [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] [Subscribe] [Scholar Register] [Received: 10/08/2024] [Revised: 01/24/2025] [Indexed: 03/20/2025]
Abstract
Tumorigenic drivers of MYCN gene nonamplified neuroblastoma remain largely uncharacterized. Long noncoding RNAs (lncRNAs) regulate tumorigenesis, however, there is little literature on therapeutic targeting of lncRNAs with small molecule compounds. Here PRKCQ-AS1 is identified as the lncRNA most overexpressed in MYCN nonamplified, compared with MYCN-amplified, neuroblastoma cell lines. PRKCQ-AS1 expression is controlled by super-enhancers, and PRKCQ-AS1 RNA bound to MSI2 protein. RNA immunoprecipitation and sequencing identified BMX mRNA as the transcript most significantly disrupted from binding to MSI2 protein, after PRKCQ-AS1 knockdown. PRKCQ-AS1 or MSI2 knockdown reduces, while its overexpression enhances, BMX mRNA stability and expression, ERK protein phosphorylation and MYCN nonamplified neuroblastoma cell proliferation. PRKCQ-AS1 knockdown significantly suppresses neuroblastoma progression in mice. In human neuroblastoma tissues, high levels of PRKCQ-AS1 and MSI2 expression correlate with poor patient outcomes, independent of current prognostic markers. AlphaScreen of a compound library identifies NSC617570 as an efficient inhibitor of PRKCQ-AS1 RNA and MSI2 protein interaction, and NSC617570 reduces BMX expression, ERK protein phosphorylation, neuroblastoma cell proliferation in vitro and tumor progression in mice. The study demonstrates that PRKCQ-AS1 RNA interacts with MSI2 protein to induce neuroblastoma tumorigenesis, and that targeting PRKCQ-AS1 and MSI2 interaction with small molecule compounds is an effective anticancer strategy.
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Affiliation(s)
- Sujanna Mondal
- Children's Cancer Institute Australia and UNSW Centre for Childhood Cancer ResearchUniversity of New South WalesSydneyNSW2052Australia
| | - Pei Y. Liu
- Children's Cancer Institute Australia and UNSW Centre for Childhood Cancer ResearchUniversity of New South WalesSydneyNSW2052Australia
| | - Janith Seneviratne
- Children's Cancer Institute Australia and UNSW Centre for Childhood Cancer ResearchUniversity of New South WalesSydneyNSW2052Australia
| | - Antoine De Weck
- Children's Cancer Institute Australia and UNSW Centre for Childhood Cancer ResearchUniversity of New South WalesSydneyNSW2052Australia
| | - Pooja Venkat
- Children's Cancer Institute Australia and UNSW Centre for Childhood Cancer ResearchUniversity of New South WalesSydneyNSW2052Australia
| | - Chelsea Mayoh
- Children's Cancer Institute Australia and UNSW Centre for Childhood Cancer ResearchUniversity of New South WalesSydneyNSW2052Australia
| | - Jing Wu
- Children's Cancer Institute Australia and UNSW Centre for Childhood Cancer ResearchUniversity of New South WalesSydneyNSW2052Australia
| | - Jesper Maag
- Garvan Institute of Medical ResearchGenome InformaticsGenomics & Epigenetics Division, 384 Victoria St.DarlinghurstNSW2010Australia
| | - Jingwei Chen
- Children's Cancer Institute Australia and UNSW Centre for Childhood Cancer ResearchUniversity of New South WalesSydneyNSW2052Australia
| | - Matthew Wong
- Children's Cancer Institute Australia and UNSW Centre for Childhood Cancer ResearchUniversity of New South WalesSydneyNSW2052Australia
| | - Nenad Bartonicek
- Garvan Institute of Medical ResearchGenome InformaticsGenomics & Epigenetics Division, 384 Victoria St.DarlinghurstNSW2010Australia
| | - Poh Khoo
- Children's Cancer Institute Australia and UNSW Centre for Childhood Cancer ResearchUniversity of New South WalesSydneyNSW2052Australia
| | - Lei Jin
- School of Medicine and Public HealthUniversity of NewcastleCallaghanNSW2308Australia
- Translational Research InstituteHenan Provincial People's HospitalTianjian Laboratory of Advanced Biomedical ScienceAcademy of Medical SciencesZhengzhou UniversityZhengzhouChina
| | - Louise E. Ludlow
- Murdoch Children's Research InstituteThe Royal Children's Hospital & Department of PaediatricsUniversity of MelbourneMelbourneAustralia
| | - David S. Ziegler
- Children's Cancer Institute Australia and UNSW Centre for Childhood Cancer ResearchUniversity of New South WalesSydneyNSW2052Australia
- Kids Cancer CentreSydney Children's HospitalHigh StreetRandwickNSW2031Australia
| | - Toby Trahair
- Children's Cancer Institute Australia and UNSW Centre for Childhood Cancer ResearchUniversity of New South WalesSydneyNSW2052Australia
- Kids Cancer CentreSydney Children's HospitalHigh StreetRandwickNSW2031Australia
| | - Pieter Mestdagh
- Center for Medical Genetics GhentGhent UniversityGhentBelgium
| | - Belamy B. Cheung
- Children's Cancer Institute Australia and UNSW Centre for Childhood Cancer ResearchUniversity of New South WalesSydneyNSW2052Australia
| | - Jinyan Li
- Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhenChina
| | - Marcel E. Dinger
- School of Life and Environmental SciencesFaculty of ScienceThe University of SydneySydneyNSWAustralia
| | - Ian Street
- Children's Cancer Institute Australia and UNSW Centre for Childhood Cancer ResearchUniversity of New South WalesSydneyNSW2052Australia
- School of Clinical MedicineUNSW Medicine & HealthUNSW SydneyKensingtonNSWAustralia
| | - Xu D. Zhang
- Translational Research InstituteHenan Provincial People's HospitalTianjian Laboratory of Advanced Biomedical ScienceAcademy of Medical SciencesZhengzhou UniversityZhengzhouChina
- School of Medicine and Public HealthPriority Research Centre for Cancer ResearchUniversity of NewcastleCallaghanNSW2308Australia
| | - Glenn M. Marshall
- Children's Cancer Institute Australia and UNSW Centre for Childhood Cancer ResearchUniversity of New South WalesSydneyNSW2052Australia
- Kids Cancer CentreSydney Children's HospitalHigh StreetRandwickNSW2031Australia
| | - Tao Liu
- Children's Cancer Institute Australia and UNSW Centre for Childhood Cancer ResearchUniversity of New South WalesSydneyNSW2052Australia
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Lai PH, Tyrer JP, Pharoah P, Gayther SA, Jones MR, Peng PC. Characterizing somatic mutations in ovarian cancer germline risk regions. Commun Biol 2025; 8:676. [PMID: 40301634 PMCID: PMC12041368 DOI: 10.1038/s42003-025-08072-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2024] [Accepted: 04/10/2025] [Indexed: 05/01/2025] Open
Abstract
Epithelial ovarian cancer (EOC) genetics research has been focused on germline or somatic mutations independently. Emerging evidence suggests that the somatic mutational landscape can be shaped by the germline genetic background. In this study, we aim to unravel the role of somatic alterations within EOC germline susceptibility regions by incorporating functional annotations. We investigate somatic events, including mutational signatures, point mutations, copy number alterations, and transcription factor binding disruptions, within 33 EOC germline susceptibility regions. Our analysis identifies significant associations between candidate germline susceptibility genes and somatic mutational signatures known to be key risk factors for EOC, such as mismatch repair deficiency, age-related mutagenesis, and homologous recombination deficiency. In addition, we find somatic point mutations and copy number alterations are significantly enriched in histotype-specific active enhancers and promoters within EOC risk loci. Furthermore, we examine the impact of germline variants and somatic mutations on transcription factor binding sites, identifying cancer developmental transcription factor motifs frequently affected by both types of mutations. Overall, our study highlights the importance of integrating germline and somatic mutations with regulatory and epigenomic data to gain insights into the genetic basis of EOC.
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Affiliation(s)
- Ping-Hung Lai
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, West Hollywood, CA, USA
| | - Jonathan P Tyrer
- CR-UK Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Paul Pharoah
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, West Hollywood, CA, USA
| | - Simon A Gayther
- Center for Inherited Oncogenesis, Department of Medicine, UT Health San Antonio, San Antonio, TX, USA
| | - Michelle R Jones
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Pei-Chen Peng
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, West Hollywood, CA, USA.
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Higuchi Y, Teo JL, Yi D, Kahn M. Safely Targeting Cancer, the Wound That Never Heals, Utilizing CBP/Beta-Catenin Antagonists. Cancers (Basel) 2025; 17:1503. [PMID: 40361430 PMCID: PMC12071182 DOI: 10.3390/cancers17091503] [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: 03/25/2025] [Revised: 04/25/2025] [Accepted: 04/25/2025] [Indexed: 05/15/2025] Open
Abstract
Stem cells, both normal somatic (SSC) and cancer stem cells (CSC) exist in minimally two states, i.e., quiescent and activated. Regulation of these two states, including their reliance on different metabolic processes, i.e., FAO and glycolysis in quiescent versus activated stem cells respectively, involves the analysis of a complex array of factors (nutrient and oxygen levels, adhesion molecules, cytokines, etc.) to initiate the epigenetic changes to either depart or enter quiescence. Quiescence is a critical feature of SSC that is required to maintain the genomic integrity of the stem cell pool, particularly in long lived complex organisms. Quiescence in CSC, whether they are derived from mutations arising in SSC, aberrant microenvironmental regulation, or via dedifferentiation of more committed progenitors, is a critical component of therapy resistance and disease latency and relapse. At the beginning of vertebrate evolution, approximately 450 million years ago, a gene duplication generated the two members of the Kat3 family, CREBBP (CBP) and EP300 (p300). Despite their very high degree of homology, these two Kat3 coactivators play critical and non-redundant roles at enhancers and super-enhancers via acetylation of H3K27, thereby controlling stem cell quiescence versus activation and the cells metabolic requirements. In this review/perspective, we discuss the unique regulatory roles of CBP and p300 and how specifically targeting the CBP/β-catenin interaction utilizing small molecule antagonists, can correct lineage infidelity and safely eliminate quiescent CSC.
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Affiliation(s)
- Yusuke Higuchi
- Beckman Research Institute, City of Hope, Duarte, CA 91010, USA;
| | - Jia-Ling Teo
- Department of Cancer Biology and Molecular Medicine, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA; (J.-L.T.); (D.Y.)
| | - Daniel Yi
- Department of Cancer Biology and Molecular Medicine, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA; (J.-L.T.); (D.Y.)
| | - Michael Kahn
- Department of Cancer Biology and Molecular Medicine, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA; (J.-L.T.); (D.Y.)
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34
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Cheng Z, Wang H, Zhang Y, Ren B, Fu Z, Li Z, Tu C. Deciphering the role of liquid-liquid phase separation in sarcoma: Implications for pathogenesis and treatment. Cancer Lett 2025; 616:217585. [PMID: 39999920 DOI: 10.1016/j.canlet.2025.217585] [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: 12/10/2024] [Revised: 02/04/2025] [Accepted: 02/21/2025] [Indexed: 02/27/2025]
Abstract
Liquid-liquid phase separation (LLPS) is a significant reversible and dynamic process in organisms. Cells form droplets that are distinct from membrane-bound cell organelles by phase separation to keep biochemical processes in order. Nevertheless, the pathological state of LLPS contributes to the progression of a variety of tumor-related pathogenic issues. Sarcoma is one kind of highly malignant tumor characterized by aggressive metastatic potential and resistance to conventional therapeutic agents. Despite the significant clinical relevance, research on phase separation in sarcomas currently faces several major challenges. These include the limited availability of sarcoma samples, insufficient attention from the research community, and the complex genetic heterogeneity of sarcomas. Recently, emerging evidence have elaborated the specific effects and pathways of phase separation on different sarcoma subtypes, including the effect of sarcoma fusion proteins and other physicochemical factors on phase separation. This review aims to summarize the multiple roles of phase separation in sarcoma and novel molecular inhibitors that target phase separation. These insights will broaden the understanding of the mechanisms concerning sarcoma and offer new perspectives for future therapeutic strategies.
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Affiliation(s)
- Zehao Cheng
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China; Hunan Key Laboratory of Tumor Models and Individualized Medicine, Hunan Engineering Research Center of AI Medical Equipment, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China; Xiangya School of Medicine, Central South University, Changsha, Hunan, 410011, China
| | - Hua Wang
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China; Hunan Key Laboratory of Tumor Models and Individualized Medicine, Hunan Engineering Research Center of AI Medical Equipment, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Yibo Zhang
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China; Hunan Key Laboratory of Tumor Models and Individualized Medicine, Hunan Engineering Research Center of AI Medical Equipment, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China; Xiangya School of Medicine, Central South University, Changsha, Hunan, 410011, China
| | - Bolin Ren
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Zheng Fu
- Shanghai Xinyi Biomedical Technology Co., Ltd, Shanghai, 201306, China
| | - Zhihong Li
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China; Hunan Key Laboratory of Tumor Models and Individualized Medicine, Hunan Engineering Research Center of AI Medical Equipment, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Chao Tu
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China; Hunan Key Laboratory of Tumor Models and Individualized Medicine, Hunan Engineering Research Center of AI Medical Equipment, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China; Changsha Medical University, Changsha, Hunan, 410219, China.
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35
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Morrison TA, Vigee J, Tovar KA, Talley TA, Mujal AM, Kono M, Philips R, Nagashima H, Brooks SR, Dada H, Rozich I, Hudspeth K, Lau CM, Yao C, Sciumè G, Sun HW, Bonifacino JS, Kanno Y, Dustin ML, Randazzo D, Proia RL, Sun JC, Shih HY, O'Shea JJ. Selective requirement of glycosphingolipid synthesis for natural killer and cytotoxic T cells. Cell 2025:S0092-8674(25)00409-X. [PMID: 40306279 DOI: 10.1016/j.cell.2025.04.007] [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: 12/22/2024] [Revised: 03/11/2025] [Accepted: 04/03/2025] [Indexed: 05/02/2025]
Abstract
Cell identity genes that exhibit complex regulation are marked by super-enhancer (SE) architecture. Assessment of SEs in natural killer (NK) cells identified Ugcg, encoding the enzyme responsible for glycosphingolipid (GSL) synthesis. Conditional deletion of Ugcg in early hematopoiesis abrogated NK cell generation while sparing other lineages. Pharmacological inhibition of UGCG disrupted cytotoxic granules and cytotoxicity, reduced expansion after viral infection, and promoted apoptosis. B4galt5 transcribes an enzyme downstream of UGCG and possesses SE structure. Addition of its product, lactosylceramide (LacCer), reversed apoptosis due to UGCG inhibition. By contrast, complex GSLs, such as asialo-GM1, were not required for NK cell viability and granule integrity. Ugcg and B4galt5 were upregulated in CD8+ T cells during viral infection, correlating with the acquisition of cytotoxic machinery. Antigen-specific CD8+ T cells lacking Ugcg failed to expand during infection. Our study reveals a selective and essential role of GSL metabolism in NK and CD8+ T cell biology.
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Affiliation(s)
- Tasha A Morrison
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, MD, USA; Lymphocyte Signaling Unit, Molecular Immunology and Inflammation Branch, NIAMS, NIH, Bethesda, MD, USA.
| | - Jaelyn Vigee
- Lymphocyte Signaling Unit, Molecular Immunology and Inflammation Branch, NIAMS, NIH, Bethesda, MD, USA
| | - Kevin A Tovar
- Lymphocyte Signaling Unit, Molecular Immunology and Inflammation Branch, NIAMS, NIH, Bethesda, MD, USA
| | - Taylor A Talley
- Lymphocyte Signaling Unit, Molecular Immunology and Inflammation Branch, NIAMS, NIH, Bethesda, MD, USA
| | - Adriana M Mujal
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mari Kono
- Genetics of Development and Disease Section, Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD, USA
| | - Rachael Philips
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Hiroyuki Nagashima
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Stephen R Brooks
- Biodata Mining and Discovery Section, NIAMS, NIH, Bethesda, MD, USA
| | - Hannah Dada
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Isaiah Rozich
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Kelly Hudspeth
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Colleen M Lau
- Department of Microbiology and Immunology, Cornell University College of Veterinary Medicine, Ithaca, NY, USA
| | - Chen Yao
- Department of Immunology, University of Texas Southwestern Medical School, Dallas, TX, USA
| | - Giuseppe Sciumè
- Department of Molecular Medicine, Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, "Sapienza" University of Rome, Rome, Italy
| | - Hong-Wei Sun
- Biodata Mining and Discovery Section, NIAMS, NIH, Bethesda, MD, USA
| | - Juan S Bonifacino
- Division of Neurosciences and Cellular Structure, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Yuka Kanno
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Michael L Dustin
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | | | - Richard L Proia
- Genetics of Development and Disease Section, Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD, USA
| | - Joseph C Sun
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Han-Yu Shih
- Neuro-immune Regulome Unit, National Eye Institute, NIH, Bethesda, MD, USA
| | - John J O'Shea
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, MD, USA.
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36
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Dhar SS, Brown C, Rizvi A, Reed L, Kotla S, Zod C, Abraham J, Abe JI, Rajaram V, Chen K, Lee MG. Heterozygous Kmt2d loss diminishes enhancers to render medulloblastoma cells vulnerable to combinatory inhibition of LSD1 and OXPHOS. Cell Rep 2025; 44:115619. [PMID: 40286267 DOI: 10.1016/j.celrep.2025.115619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Revised: 02/17/2025] [Accepted: 04/04/2025] [Indexed: 04/29/2025] Open
Abstract
The histone H3 lysine 4 (H3K4) methyltransferase KMT2D (also called MLL4) is one of the most frequently mutated epigenetic modifiers in many cancers, including medulloblastoma (MB). Notably, heterozygous KMT2D loss frequently occurs in MB and other cancers. However, its oncogenic role remains largely uncharacterized. Here, we show that heterozygous Kmt2d loss in murine cerebellar regions promotes MB genesis driven by heterozygous loss of the MB-suppressor gene Ptch via the upregulation of tumor-promoting programs (e.g., oxidative phosphorylation [OXPHOS]). Downregulation of the transcription-repressive tumor suppressor NCOR2 by heterozygous Kmt2d loss, along with Ptch+/--increased MYCN, upregulated tumor-promoting genes. Heterozygous Kmt2d loss substantially diminished enhancer marks (H3K4me1 and H3K27ac) and the H3K4me3 signature, including those for Ncor2. Combinatory pharmacological inhibition of the enhancer-decommissioning H3K4 demethylase LSD1 and OXPHOS significantly reduced the tumorigenicity of MB cells bearing heterozygous Kmt2d loss. Our findings suggest the molecular and epigenetic pathogenesis underlying the MB-promoting effect of heterozygous KMT2D loss.
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Affiliation(s)
- Shilpa S Dhar
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA.
| | - Calena Brown
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Ali Rizvi
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Lauren Reed
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Sivareddy Kotla
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Constantin Zod
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Janak Abraham
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Jun-Ichi Abe
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Veena Rajaram
- Department of Pathology, The University of Texas Southwestern Medical Center, Dallas, TX 75235, USA
| | - Kaifu Chen
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Min Gyu Lee
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA.
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Xiao L, Jin H, Dang Y, Zhao P, Li S, Shi Y, Wang S, Zhang K. DUX-mediated configuration of p300/CBP drives minor zygotic genome activation independent of its catalytic activity. Cell Rep 2025; 44:115544. [PMID: 40202846 DOI: 10.1016/j.celrep.2025.115544] [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: 12/03/2024] [Revised: 02/18/2025] [Accepted: 03/19/2025] [Indexed: 04/11/2025] Open
Abstract
Maternal-deposited factors initiate zygotic genome activation (ZGA), driving the maternal-to-zygotic transition; however, the coordination between maternal coactivators and transcription factors (TFs) in this process remains unclear. In this study, by profiling the dynamic landscape of p300 during mouse ZGA, we reveal its role in promoting RNA polymerase II (Pol II) pre-configuration at ZGA gene regions and sequentially establishing enhancer activity and regulatory networks. Moreover, p300/CBP-catalyzed acetylation drives Pol II elongation and minor ZGA gene expression by inducing pivotal TFs such as Dux. Remarkably, the supplementation of exogenous Dux rescues ZGA failure and developmental defects caused by the loss of p300/CBP acetylation. DUX functions as a pioneer factor, guiding p300 and Pol II to minor ZGA gene regions and activating them in a manner dependent on the non-catalytic functions of p300/CBP. Together, our findings reveal a mutual dependency between p300/CBP and DUX, highlighting their coordinated role in regulating minor ZGA activation.
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Affiliation(s)
- Lieying Xiao
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Hao Jin
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yanna Dang
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Panpan Zhao
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Shuang Li
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yan Shi
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Shaohua Wang
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Kun Zhang
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
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38
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Gao C, Gao A, Jiang Y, Gao R, Guo Y, Peng Z, Jiang W, Zhang M, Zhou Z, Yan C, Fang W, Hu H, Zhu G, Zhang J. Hypoxia-induced phase separation of ZHX2 alters chromatin looping to drive cancer metastasis. Mol Cell 2025; 85:1525-1542.e10. [PMID: 40185097 DOI: 10.1016/j.molcel.2025.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 01/12/2025] [Accepted: 03/07/2025] [Indexed: 04/07/2025]
Abstract
Hypoxia and dysregulated phase separation can both activate oncogenic transcriptomic profiles. However, whether hypoxia regulates transcription-associated phase separation remains unknown. Here, we find that zinc fingers and homeoboxes 2 (ZHX2) undergoes phase separation in response to hypoxia, promoting their occupancy on chromatin and activating a cluster of oncogene transcription that is enriched by metastatic genes distinct from the targets of hypoxia-inducible factor (HIF) and pathologically relevant to breast cancer. Hypoxia induces ZHX2 phase separation via a proline-rich intrinsically disordered region (IDR), enhancing phosphorylation of ZHX2 at S625 and S628 that incorporates CCCTC-binding factor (CTCF) in condensates to alter chromatin looping, consequently driving metastatic gene transcription and cancer metastasis. Our findings provide significant insight into oncogene activation and suggest a phase-separation-based therapeutic strategy for cancer.
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Affiliation(s)
- Chuan Gao
- Department of Urology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Ang Gao
- Department of Urology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Yulong Jiang
- Department of Urology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Ronghui Gao
- Department of Urology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Yan Guo
- Lingang Laboratory, Shanghai 201210, China
| | - Zirou Peng
- Department of Urology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Weiwei Jiang
- Department of Urology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Mengyao Zhang
- Department of Urology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Zirui Zhou
- Department of Urology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Chaojun Yan
- Department of Urology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Wentong Fang
- Department of Pharmacy, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Hankun Hu
- Department of Pharmacy, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | | | - Jing Zhang
- Department of Urology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China; Hubei Key Laboratory of Tumor Biological Behavior, Wuhan 430071, China.
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39
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Li F, Wang S, Chen L, Jiang N, Chen X, Li J. Systemic genome-epigenome analysis captures a lineage-specific super-enhancer for MYB in gastrointestinal adenocarcinoma. Mol Syst Biol 2025:10.1038/s44320-025-00098-1. [PMID: 40234694 DOI: 10.1038/s44320-025-00098-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2024] [Revised: 03/26/2025] [Accepted: 03/31/2025] [Indexed: 04/17/2025] Open
Abstract
Gastrointestinal adenocarcinoma is a major cancer type for the digestive system, ranking as the top cause of cancer-related deaths worldwide. While there has been extensive research on mutations in protein-coding regions, the knowledge of the landscape of its non-coding regulatory elements is still insufficient. Combining the analysis of active enhancer profiles and genomic structural variation, we discovered and validated a lineage-specific super-enhancer for MYB in gastrointestinal adenocarcinoma. This super-enhancer is composed of a predominant enhancer e4 and several additional enhancers, whose transcriptional activity is regulated by the direct binding of HNF4A and MYB itself. Suppression of the super-enhancer downregulated the expression of MYB, inhibited downstream Notch signaling and prevented the development of gastrointestinal adenocarcinoma both in vitro and in vivo. Our study uncovers a mechanism driven by non-coding variations that regulate MYB expression in a lineage-specific manner, offering new insights into the carcinogenic mechanism and potential therapeutic strategies for gastrointestinal adenocarcinoma.
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Affiliation(s)
- Fuyuan Li
- State Key Laboratory of Genetics and Development of Complex Phenotype, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, 200438, China
| | - Shangzi Wang
- State Key Laboratory of Genetics and Development of Complex Phenotype, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, 200438, China
| | - Lian Chen
- State Key Laboratory of Genetics and Development of Complex Phenotype, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, 200438, China
| | - Ning Jiang
- State Key Laboratory of Genetics and Development of Complex Phenotype, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, 200438, China
| | - Xingdong Chen
- State Key Laboratory of Genetics and Development of Complex Phenotype, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, 200438, China.
- Fudan University Taizhou Institute of Health Sciences, Taizhou, China.
- Yiwu Research Institute of Fudan University, Yiwu, Zhejiang, China.
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China.
| | - Jin Li
- State Key Laboratory of Genetics and Development of Complex Phenotype, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, 200438, China.
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40
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Liu SQ, Cheng XX, He S, Xia T, Li YQ, Peng W, Zhou YQ, Xu ZH, He MS, Liu Y, Wei PP, Yuan SH, Liu C, Sun SL, Zou DL, Zheng M, Lan CY, Luo CL, Bei JX. Super-enhancer-driven EFNA1 fuels tumor progression in cervical cancer via the FOSL2-Src/AKT/STAT3 axis. J Clin Invest 2025; 135:e177599. [PMID: 39964764 PMCID: PMC11996870 DOI: 10.1172/jci177599] [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: 11/17/2023] [Accepted: 02/13/2025] [Indexed: 02/20/2025] Open
Abstract
Super-enhancers (SEs) are expansive cis-regulatory elements known for amplifying oncogene expression across various cancers. However, their role in cervical cancer (CC), a remarkable global malignancy affecting women, remains underexplored. Here we applied integrated epigenomic and transcriptomic profiling to delineate the distinct SE landscape in CC by analyzing paired tumor and normal tissues. Our study identifies a tumor-specific SE at the EFNA1 locus that drives EFNA1 expression in CC. Mechanically, the EFNA1-SE region contains consensus sequences for the transcription factor FOSL2, whose knockdown markedly suppressed luciferase activity and diminished H3K27ac enrichment within the SE region. Functional analyses further underlined EFNA1's oncogenic role in CC, linking its overexpression to poor patient outcomes. EFNA1 knockdown strikingly reduced CC cell proliferation, migration, and tumor growth. Moreover, EFNA1 cis-interacted with its receptor EphA2, leading to decreased EphA2 tyrosine phosphorylation and subsequent activation of the Src/AKT/STAT3 forward signaling pathway. Inhibition of this pathway with specific inhibitors substantially attenuated the tumorigenic capacity of EFNA1-overexpressing CC cells in both in vitro and in vivo models. Collectively, our study unveils the critical role of SEs in promoting tumor progression through the FOSL2-EFNA1-EphA2-Src/AKT/STAT3 axis, providing new prognostic and therapeutic avenues for CC patients.
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Affiliation(s)
- Shu-Qiang Liu
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, China
- Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xi-Xi Cheng
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Shuai He
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Tao Xia
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yi-Qi Li
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Wan Peng
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ya-Qing Zhou
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Zi-Hao Xu
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Mi-Si He
- Department of Gynecologic Oncology, Chongqing University Cancer Hospital & Chongqing Cancer Institute & Chongqing Cancer Hospital, Chongqing, China
| | - Yang Liu
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Pan-Pan Wei
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Song-Hua Yuan
- Department of Gynecology, The First People’s Hospital of Foshan, Foshan, China
| | - Chang Liu
- Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, China
| | - Shu-Lan Sun
- Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, China
| | - Dong-Ling Zou
- Department of Gynecologic Oncology, Chongqing University Cancer Hospital & Chongqing Cancer Institute & Chongqing Cancer Hospital, Chongqing, China
| | - Min Zheng
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Chun-Yan Lan
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Chun-Ling Luo
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jin-Xin Bei
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, China
- Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Medical Oncology, National Cancer Centre Singapore, Singapore
- Sun Yat-sen University Institute of Advanced Studies Hong Kong, Science Park, Hong Kong, China
- Department of Clinical Oncology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China
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41
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Renatino Canevarolo R, Sudalagunta PR, Meads MB, Silva M, Zhao X, Magaletti D, Alugubelli RR, DeAvila G, Persi E, Maura F, Bell ET, Bishop RT, Cubitt CL, Sansil SS, Zhang W, Teer JK, Teng M, Yoder SJ, Siegel EM, Shah BD, Nishihori T, Hazlehurst LA, Lynch CC, Landgren O, Hampton O, Gatenby RA, Sullivan DM, Brayer JB, Dalton WS, Cleveland JL, Alsina M, Baz R, Shain KH, Silva AS. Epigenetic Plasticity Drives Carcinogenesis and Multi-Therapy Resistance in Multiple Myeloma. RESEARCH SQUARE 2025:rs.3.rs-6306816. [PMID: 40321765 PMCID: PMC12048002 DOI: 10.21203/rs.3.rs-6306816/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/09/2025]
Abstract
We demonstrate that carcinogenesis and multi-therapy resistance in multiple myeloma (MM)-a treatable yet incurable plasma cell malignancy-are driven by epigenetic dysregulation. In this new paradigm, genomic and cytogenetic events unlock epigenetic plasticity, reshaping MM cell biology to evade tumor microenvironment constraints and therapeutic pressure. These conclusions are derived from a newly assembled cohort of nearly 1,000 patients, spanning premalignant to late-stage refractory MM, comprehensively characterized at molecular and clinical levels. Our findings provide a unifying framework to explain inter-patient genomic heterogeneity and the emergence of therapy resistance in sequential samples without new genomic alterations. In conclusion, we propose targeting epigenetic plasticity-mediated plasma cell evasion as a promising therapeutic strategy in MM.
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Affiliation(s)
- Rafael Renatino Canevarolo
- Department of Metabolism and Physiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Praneeth Reddy Sudalagunta
- Department of Metabolism and Physiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Mark B. Meads
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Maria Silva
- Department of Metabolism and Physiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Xiaohong Zhao
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Dario Magaletti
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | | | - Gabriel DeAvila
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Erez Persi
- Computational Biology Branch, Division of Intramural Research, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Francesco Maura
- Division of Myeloma, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Elissa T. Bell
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Ryan T. Bishop
- Department of Tumor Microenvironment and Metastasis, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Christopher L. Cubitt
- Immune Monitoring Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Samer S. Sansil
- Cancer Pharmacokinetics and Pharmacodynamics Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Wei Zhang
- Department of Computer Science, University of Central Florida, Orlando, Florida, USA
| | - Jamie K. Teer
- Department of Biostatistics & Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Mingxiang Teng
- Department of Biostatistics & Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Sean J. Yoder
- Molecular Genomics Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Erin M. Siegel
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Bijal D. Shah
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Taiga Nishihori
- Department of Blood & Marrow Transplant and Cellular Therapies, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Lori A. Hazlehurst
- Department of Pharmaceutical Sciences, West Virginia University, Morgantown, WV, USA
| | - Conor C. Lynch
- Department of Tumor Microenvironment and Metastasis, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Ola Landgren
- Division of Myeloma, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | | | - Robert A. Gatenby
- Departments of Radiology and Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Daniel M. Sullivan
- Department of Blood & Marrow Transplant and Cellular Therapies, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Jason B. Brayer
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - William S. Dalton
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - John L. Cleveland
- Department of Tumor Microenvironment and Metastasis, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Melissa Alsina
- Department of Blood & Marrow Transplant and Cellular Therapies, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Rachid Baz
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Kenneth H. Shain
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
- Department of Tumor Microenvironment and Metastasis, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Ariosto Siqueira Silva
- Department of Metabolism and Physiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
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42
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Rosario GX, Brown S, Karmakar S, Rumi MAK, Nayak NR. Super-Enhancers in Placental Development and Diseases. J Dev Biol 2025; 13:11. [PMID: 40265369 PMCID: PMC12015882 DOI: 10.3390/jdb13020011] [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: 02/09/2025] [Revised: 03/24/2025] [Accepted: 04/03/2025] [Indexed: 04/24/2025] Open
Abstract
The proliferation of trophoblast stem (TS) cells and their differentiation into multiple lineages are pivotal for placental development and functions. Various transcription factors (TFs), such as CDX2, EOMES, GATA3, TFAP2C, and TEAD4, along with their binding sites and cis-regulatory elements, have been studied for their roles in trophoblast cells. While previous studies have primarily focused on individual enhancer regions in trophoblast development and differentiation, recent attention has shifted towards investigating the role of super-enhancers (SEs) in different trophoblast cell lineages. SEs are clusters of regulatory elements enriched with transcriptional regulators, forming complex gene regulatory networks via differential binding patterns and the synchronized stimulation of multiple target genes. Although the exact role of SEs remains unclear, they are commonly found near master regulator genes for specific cell types and are implicated in the transcriptional regulation of tissue-specific stem cells and lineage determination. Additionally, super-enhancers play a crucial role in regulating cellular growth and differentiation in both normal development and disease pathologies. This review summarizes recent advances on SEs' role in placental development and the pathophysiology of placental diseases, emphasizing the potential for identifying SE-driven networks in the placenta to provide valuable insights for developing therapeutic strategies to address placental dysfunctions.
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Affiliation(s)
- Gracy X. Rosario
- Department of Obstetrics and Gynecology, University of Missouri-Kansas City, Kansas City, MO 64108, USA; (S.B.); (N.R.N.)
| | - Samuel Brown
- Department of Obstetrics and Gynecology, University of Missouri-Kansas City, Kansas City, MO 64108, USA; (S.B.); (N.R.N.)
| | - Subhradip Karmakar
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi 110029, India;
| | - Mohammad A. Karim Rumi
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA;
| | - Nihar R. Nayak
- Department of Obstetrics and Gynecology, University of Missouri-Kansas City, Kansas City, MO 64108, USA; (S.B.); (N.R.N.)
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43
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Liu J, Huang H, An F, Wu S, Guo H, Wang B, Han Z, Tan J, Lin Z, Fang Y, Liu J, Ye H, Du Y, Mo K, Huang Y, Li M, Wang L, Mao Z, Ouyang H. FOXO4-SP6 axis controls surface epithelium commitment by mediating epigenomic remodeling. Stem Cell Reports 2025; 20:102445. [PMID: 40086444 PMCID: PMC12069900 DOI: 10.1016/j.stemcr.2025.102445] [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: 11/01/2024] [Revised: 02/10/2025] [Accepted: 02/11/2025] [Indexed: 03/16/2025] Open
Abstract
Proper development of surface epithelium (SE) is a requisite for the normal development and function of ectodermal appendages; however, the molecular mechanisms underlying SE commitment remain largely unexplored. Here, we developed a KRT8 reporter system and utilized it to identify FOXO4 and SP6 as novel, essential regulators governing SE commitment. We found that the FOXO4-SP6 axis governs SE fate and its abrogation markedly impedes SE fate determination. Mechanistically, FOXO4 regulates SE initiation by shaping the SE chromatin accessibility landscape and regulating the deposition of H3K4me3. SP6, as a novel effector of FOXO4, activates SE-specific genes through modulating the H3K27ac deposition across their super-enhancers. Our work highlights the regulatory function of the FOXO4-SP6 axis in SE development, contributing to an improved understanding of SE fate decisions and providing a research foundation for the therapeutic application of ectodermal dysplasia.
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Affiliation(s)
- Jiafeng Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Huaxing Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Fengjiao An
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Siqi Wu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Huizhen Guo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Bofeng Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Zhuo Han
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Jieying Tan
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Zesong Lin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Yihang Fang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Jinpeng Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Hanning Ye
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510060, China
| | - Yuru Du
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510060, China
| | - Kunlun Mo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Ying Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Mingsen Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Li Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Zhen Mao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Hong Ouyang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China; Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510060, China.
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44
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Betti MJ, Lin P, Aldrich MC, Gamazon ER. Genetically regulated eRNA expression predicts chromatin contact frequency and reveals genetic mechanisms at GWAS loci. Nat Commun 2025; 16:3193. [PMID: 40180945 PMCID: PMC11968980 DOI: 10.1038/s41467-025-58023-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: 06/07/2024] [Accepted: 02/18/2025] [Indexed: 04/05/2025] Open
Abstract
The biological functions of extragenic enhancer RNAs and their impact on disease risk remain relatively underexplored. In this work, we develop in silico models of genetically regulated expression of enhancer RNAs across 49 cell and tissue types, characterizing their degree of genetic control. Leveraging the estimated genetically regulated expression for enhancer RNAs and canonical genes in a large-scale DNA biobank (N > 70,000) and high-resolution Hi-C contact data, we train a deep learning-based model of pairwise three-dimensional chromatin contact frequency for enhancer-enhancer and enhancer-gene pairs in cerebellum and whole blood. Notably, the use of genetically regulated expression of enhancer RNAs provides substantial tissue-specific predictive power, supporting a role for these transcripts in modulating spatial chromatin organization. We identify schizophrenia-associated enhancer RNAs independent of GWAS loci using enhancer RNA-based TWAS and determine the causal effects of these enhancer RNAs using Mendelian randomization. Using enhancer RNA-based TWAS, we generate a comprehensive resource of tissue-specific enhancer associations with complex traits in the UK Biobank. Finally, we show that a substantially greater proportion (63%) of GWAS associations colocalize with causal regulatory variation when enhancer RNAs are included.
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Affiliation(s)
- Michael J Betti
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, 2525 West End Avenue, Suite 700, Nashville, TN, 37203, USA.
| | - Phillip Lin
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, 2525 West End Avenue, Suite 700, Nashville, TN, 37203, USA
| | - Melinda C Aldrich
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, 2525 West End Avenue, Suite 700, Nashville, TN, 37203, USA
| | - Eric R Gamazon
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, 2525 West End Avenue, Suite 700, Nashville, TN, 37203, USA.
- Clare Hall, University of Cambridge, Herschel Rd, Cambridge, CB3 9AL, UK.
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45
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Altendorfer E, Mundlos S, Mayer A. A transcription coupling model for how enhancers communicate with their target genes. Nat Struct Mol Biol 2025; 32:598-606. [PMID: 40217119 DOI: 10.1038/s41594-025-01523-7] [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: 07/18/2024] [Accepted: 02/27/2025] [Indexed: 04/16/2025]
Abstract
How enhancers communicate with their target genes to influence transcription is an unresolved question of fundamental importance. Current models of the mechanism of enhancer-target gene or enhancer-promoter (E-P) communication are transcription-factor-centric and underappreciate major findings, including that enhancers are themselves transcribed by RNA polymerase II, which correlates with enhancer activity. In this Perspective, we posit that enhancer transcription and its products, enhancer RNAs, are elementary components of enhancer-gene communication. Specifically, we discuss the possibility that transcription at enhancers and at their cognate genes are linked and that this coupling is at the basis of how enhancers communicate with their targets. This model of transcriptional coupling between enhancers and their target genes is supported by growing experimental evidence and represents a synthesis of recent key discoveries.
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Affiliation(s)
- Elisabeth Altendorfer
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Stefan Mundlos
- Development and Disease group, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Andreas Mayer
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany.
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46
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Tanwar VS, Reddy MA, Dey S, Malek V, Lanting L, Chen Z, Ganguly R, Natarajan R. Palmitic acid alters enhancers/super-enhancers near inflammatory and efferocytosis-associated genes in human monocytes. J Lipid Res 2025; 66:100774. [PMID: 40068774 PMCID: PMC12002881 DOI: 10.1016/j.jlr.2025.100774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2024] [Revised: 02/20/2025] [Accepted: 03/07/2025] [Indexed: 04/07/2025] Open
Abstract
Free fatty acids like palmitic acid (PA) are elevated in obesity and diabetes and dysregulate monocyte and macrophage functions, contributing to enhanced inflammation in these cardiometabolic diseases. Epigenetic mechanisms regulating enhancer functions play key roles in inflammatory gene expression, but their role in PA-induced monocyte/macrophage dysfunction is unknown. We found that PA treatment altered the epigenetic landscape of enhancers and super-enhancers (SEs) in human monocytes. Integration with RNA-seq data revealed that PA-induced enhancers/SEs correlated with PA-increased expression of inflammatory and immune response genes, while PA-inhibited enhancers correlated with downregulation of phagocytosis and efferocytosis genes. These genes were similarly regulated in macrophages from mouse models of diabetes and accelerated atherosclerosis, human atherosclerosis, and infectious agents. PA-regulated enhancers/SEs harbored SNPs associated with diabetes, obesity, and body mass index indicating disease relevance. We verified increased chromatin interactions between PA-regulated enhancers/SEs and inflammatory gene promoters and reduced interactions at efferocytosis genes. PA-induced gene expression was reduced by inhibitors of BRD4, and NF-κB. PA treatment inhibited phagocytosis and efferocytosis in human macrophages. Together, our findings demonstrate that PA-induced enhancer dynamics at key monocyte/macrophage enhancers/SEs regulate inflammatory and immune genes and responses. Targeting these PA-regulated epigenetic changes could provide novel therapeutic opportunities for cardiometabolic disorders.
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Affiliation(s)
- Vinay Singh Tanwar
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Marpadga A Reddy
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Suchismita Dey
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Vajir Malek
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Linda Lanting
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Zhuo Chen
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Rituparna Ganguly
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Rama Natarajan
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, USA; Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA.
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Tan X, Li Y, Song M, Yuan L, Zhao Z, Liu Y, Meng Q, Huang X, Ma Y, Xu Z. The Molecular Mechanism of Interaction Between SEPALLATA3 and APETALA1 in Arabidopsis thaliana. PLANT DIRECT 2025; 9:e70052. [PMID: 40166359 PMCID: PMC11955279 DOI: 10.1002/pld3.70052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2024] [Revised: 10/31/2024] [Accepted: 02/06/2025] [Indexed: 04/02/2025]
Abstract
Flower formation has been a primary focus in botanical research, leading to the identification of multiple factors regulating flowering over the past 30 years. The MADS transcription factors SEPALLATA3 (SEP3) and APETALA1 (AP1) are essential for floral meristem development and organ identity. In Arabidopsis, SEP3 functions as a central integrator, combining MADS proteins into a tetrameric complex, with its interaction with AP1 playing a key role in sepal and petal formation. This research explores AtSEP3 and AtAP1, with particular emphasis on the Leu residue in the K1 subfunctional domain of AtSEP3, which is necessary for their interaction. A predicted structural model of AP1 was used, followed by protein docking with SEP3, which indicated that Leu residues at positions 115 and 116 are critical binding sites. Mutations at these position were examined through yeast two-hybrid assays and other techniques, identifying Leu 116 as a significant site. Subsequent purification and EMSA analysis revealed that mutations in the leucine zipper of SEP3 decreased its DNA binding ability. Observations of transgenic plants showed that disruption of AtSEP3 and AtAP1 interaction resulted in extended vegetative growth, increased size and number of rosette leaves, and modifications in floral structures. This study offers new insights into the interaction mechanism between AP1 and SEP3 during flowering.
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Affiliation(s)
- Xiao‐Min Tan
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), Shaanxi Provincial Key Laboratory of BiotechnologyCollege of Life Sciences, Northwest UniversityXi'anShaanxiPeople's Republic of China
| | - Ya‐Ru Li
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), Shaanxi Provincial Key Laboratory of BiotechnologyCollege of Life Sciences, Northwest UniversityXi'anShaanxiPeople's Republic of China
| | - Man‐Ru Song
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), Shaanxi Provincial Key Laboratory of BiotechnologyCollege of Life Sciences, Northwest UniversityXi'anShaanxiPeople's Republic of China
| | - Ling‐Na Yuan
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), Shaanxi Provincial Key Laboratory of BiotechnologyCollege of Life Sciences, Northwest UniversityXi'anShaanxiPeople's Republic of China
| | - Zi‐Xin Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), Shaanxi Provincial Key Laboratory of BiotechnologyCollege of Life Sciences, Northwest UniversityXi'anShaanxiPeople's Republic of China
| | - Ye Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), Shaanxi Provincial Key Laboratory of BiotechnologyCollege of Life Sciences, Northwest UniversityXi'anShaanxiPeople's Republic of China
| | - Qi Meng
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), Shaanxi Provincial Key Laboratory of BiotechnologyCollege of Life Sciences, Northwest UniversityXi'anShaanxiPeople's Republic of China
| | - Xuan Huang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), Shaanxi Provincial Key Laboratory of BiotechnologyCollege of Life Sciences, Northwest UniversityXi'anShaanxiPeople's Republic of China
| | - Ye‐Ye Ma
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), Shaanxi Provincial Key Laboratory of BiotechnologyCollege of Life Sciences, Northwest UniversityXi'anShaanxiPeople's Republic of China
| | - Zi‐Qin Xu
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), Shaanxi Provincial Key Laboratory of BiotechnologyCollege of Life Sciences, Northwest UniversityXi'anShaanxiPeople's Republic of China
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48
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Sasse SK, Dahlin A, Sanford L, Gruca MA, Gupta A, Gally F, Wu AC, Iribarren C, Dowell RD, Weiss ST, Gerber AN. Enhancer RNA transcription pinpoints functional genetic variants linked to asthma. Nat Commun 2025; 16:2750. [PMID: 40164603 PMCID: PMC11958640 DOI: 10.1038/s41467-025-57693-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: 11/08/2022] [Accepted: 02/28/2025] [Indexed: 04/02/2025] Open
Abstract
Bidirectional enhancer RNA (eRNA) transcription is a widespread response to environmental signals and glucocorticoids. We investigated whether single nucleotide polymorphisms (SNPs) within dynamically regulated eRNA-transcribing regions contribute to genetic variation in asthma. Through applying multivariate regression modeling with permutation-based significance thresholding to a large clinical cohort, we identified novel associations between asthma and 35 SNPs located in eRNA-transcribing regions implicated in regulating cellular processes relevant to asthma, including rs258760 (mean allele frequency = 0.34, asthma odds ratio = 0.95; P = 5.04E-03). We show that rs258760 disrupts an active aryl hydrocarbon receptor (AHR) response element linked to transcriptional regulation of the glucocorticoid receptor gene by AHR ligands, which are commonly found in combusted air pollution. The role of rs258760 as a protective variant for asthma was independently validated using UK Biobank data. Our findings establish eRNA signatures as a tool for discovery of functional genetic variants and define a novel association between air pollution, glucocorticoid signaling and asthma.
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Affiliation(s)
- Sarah K Sasse
- Department of Medicine, National Jewish Health, Denver, CO, USA
| | - Amber Dahlin
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Lynn Sanford
- BioFrontiers Institute, University of Colorado, Boulder, CO, USA
| | - Margaret A Gruca
- BioFrontiers Institute, University of Colorado, Boulder, CO, USA
| | - Arnav Gupta
- Department of Medicine, National Jewish Health, Denver, CO, USA
- Department of Medicine, University of Colorado, Aurora, CO, USA
| | - Fabienne Gally
- Department of Medicine, University of Colorado, Aurora, CO, USA
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO, USA
| | - Ann Chen Wu
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Carlos Iribarren
- Kaiser Permanente Division of Research, Kaiser Permanente, Oakland, CA, USA
| | - Robin D Dowell
- BioFrontiers Institute, University of Colorado, Boulder, CO, USA
- Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA
- Computer Science, University of Colorado, Boulder, CO, USA
| | - Scott T Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Anthony N Gerber
- Department of Medicine, National Jewish Health, Denver, CO, USA.
- Department of Medicine, University of Colorado, Aurora, CO, USA.
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO, USA.
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49
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Benhassoun R, Morel AP, Jacquot V, Puisieux A, Ouzounova M. The epipliancy journey: Tumor initiation at the mercy of identity crisis and epigenetic drift. Biochim Biophys Acta Rev Cancer 2025; 1880:189307. [PMID: 40174706 DOI: 10.1016/j.bbcan.2025.189307] [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: 10/25/2024] [Revised: 03/05/2025] [Accepted: 03/27/2025] [Indexed: 04/04/2025]
Abstract
Cellular pliancy refers to the unique disposition of different stages of cellular differentiation to transform when exposed to specific oncogenic insults. This concept highlights a strong interconnection between cellular identity and tumorigenesis, and implies overcoming of epigenetic barriers defining cellular states. Emerging evidence suggests that the cell-type-specific response to intrinsic and extrinsic stresses is modulated by accessibility to certain areas of the genome. Understanding the interplay between epigenetic mechanisms, cellular differentiation, and oncogenic insults is crucial for deciphering the complex nature of tumorigenesis and developing targeted therapies. Hence, cellular pliancy relies on a dynamic cooperation between the cellular identity and the cellular context through epigenetic control, including the reactivation of cellular mechanisms, such as epithelial-to-mesenchymal transition (EMT). Such mechanisms and pathways confer plasticity to the cell allowing it to adapt to a hostile environment in a context of tumor initiation, thus changing its cellular identity. Indeed, growing evidence suggests that cancer is a disease of cell identity crisis, whereby differentiated cells lose their defined identity and gain progenitor characteristics. The loss of cell fate commitment is a central feature of tumorigenesis and appears to be a prerequisite for neoplastic transformation. In this context, EMT-inducing transcription factors (EMT-TFs) cooperate with mitogenic oncoproteins to foster malignant transformation. The aberrant activation of EMT-TFs plays an active role in tumor initiation by alleviating key oncosuppressive mechanisms and by endowing cancer cells with stem cell-like properties, including the ability to self-renew, thus changing the course of tumorigenesis. This highly dynamic phenotypic change occurs concomitantly to major epigenome reorganization, a key component of cell differentiation and cancer cell plasticity regulation. The concept of pliancy was initially proposed to address a fundamental question in cancer biology: why are some cells more likely to become cancerous in response to specific oncogenic events at particular developmental stages? We propose the concept of epipliancy, whereby a difference in epigenetic configuration leads to malignant transformation following an oncogenic insult. Here, we present recent studies furthering our understanding of how the epigenetic landscape may impact the modulation of cellular pliancy during early stages of cancer initiation.
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Affiliation(s)
- Rahma Benhassoun
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, France; LabEx DEVweCAN, Université de Lyon, France
| | - Anne-Pierre Morel
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, France; LabEx DEVweCAN, Université de Lyon, France
| | - Victoria Jacquot
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, France
| | - Alain Puisieux
- Equipe labellisée Ligue contre le cancer, U1339 Inserm - UMR3666 CNRS, Paris, France; Institut Curie, PSL Research University, Paris, France
| | - Maria Ouzounova
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, France; LabEx DEVweCAN, Université de Lyon, France.
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50
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Inagaki T, Kumar A, Wang KH, Komaki S, Espera JM, Bautista CSA, Nakajima KI, Izumiya C, Izumiya Y. Studies on Gene Enhancer with KSHV mini-chromatin. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.24.644916. [PMID: 40196677 PMCID: PMC11974746 DOI: 10.1101/2025.03.24.644916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2025]
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) genome contains a terminal repeats (TR) sequence. Previous studies demonstrated that KSHV TR functions as a gene enhancer for inducible lytic gene promoters. Gene enhancers anchor bromodomain-containing protein 4 (BRD4) at specific genomic region, where BRD4 interacts flexibly with transcription-related proteins through its intrinsically disordered domain and exerts transcription regulatory function. Here, we generated recombinant KSHV with reduced TR copy numbers and studied BRD4 recruitment and its contributions to the inducible promoter activation. Reducing the TR copy numbers from 21 (TR21) to 5 (TR5) strongly attenuated viral gene expression during de novo infection and impaired reactivation. The EF1α promoter encoded in the KSHV BAC backbone also showed reduced promoter activity, suggesting a global attenuation of transcription activity within TR5 latent episomes. Isolation of reactivating cells confirmed that the reduced inducible gene transcription from TR-shortened DNA template and is mediated by decreased efficacies of BRD4 recruitment to viral gene promoters. Separating the reactivating iSLK cell population from non-responders showed that reactivatable iSLK cells harbored larger LANA nuclear bodies (NBs) compared to non-responders. The cells with larger LANA NBs, either due to prior transcription activation or TR copy number, supported KSHV reactivation more efficiently than those with smaller LANA NBs. With auxin-inducible LANA degradation, we confirmed that LANA is responsible for BRD4 occupancies on latent chromatin. Finally, with purified fluorescence-tagged proteins, we demonstrated that BRD4 is required for LANA to form liquid-liquid phase-separated dots. The inclusion of TR DNA fragments further facilitated the formation of larger BRD4-containing LLPS in the presence of LANA, similar to the "cellular enhancer dot" formed by transcription factor-DNA bindings. These results suggest that LANA binding to TR establishes an enhancer domain for infected KSHV episomes. The strength of this enhancer, regulated by TR length or transcription memory, determines the outcome of KSHV replication.
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Affiliation(s)
- Tomoki Inagaki
- Department of Dermatology, School of Medicine, the University of California Davis (UC Davis), Sacramento, California, USA
| | - Ashish Kumar
- Department of Dermatology, School of Medicine, the University of California Davis (UC Davis), Sacramento, California, USA
| | - Kang-Hsin Wang
- Department of Dermatology, School of Medicine, the University of California Davis (UC Davis), Sacramento, California, USA
| | - Somayeh Komaki
- Department of Dermatology, School of Medicine, the University of California Davis (UC Davis), Sacramento, California, USA
| | - Jonna M. Espera
- Department of Dermatology, School of Medicine, the University of California Davis (UC Davis), Sacramento, California, USA
| | - Christopher S. A. Bautista
- Department of Dermatology, School of Medicine, the University of California Davis (UC Davis), Sacramento, California, USA
| | - Ken-ichi Nakajima
- Department of Dermatology, School of Medicine, the University of California Davis (UC Davis), Sacramento, California, USA
| | - Chie Izumiya
- Department of Dermatology, School of Medicine, the University of California Davis (UC Davis), Sacramento, California, USA
| | - Yoshihiro Izumiya
- Department of Dermatology, School of Medicine, the University of California Davis (UC Davis), Sacramento, California, USA
- Department of Biochemistry and Molecular Medicine, School of Medicine, UC Davis, Sacramento, California, USA
- UC Davis Comprehensive Cancer Center, Sacramento, California, USA
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