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Zhai Z, Meng F, Kuang J, Pei D. Phase Separation in Chromatin Organization and Human Diseases. Int J Mol Sci 2025; 26:5156. [PMID: 40507965 PMCID: PMC12154030 DOI: 10.3390/ijms26115156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2025] [Revised: 05/25/2025] [Accepted: 05/26/2025] [Indexed: 06/16/2025] Open
Abstract
Understanding how the genome is organized into multi-level chromatin structures within cells and how these chromatin structures regulate gene transcription influencing animal development and human diseases has long been a major goal in genetics and cell biology. Recent evidence suggests that chromatin structure formation and remodeling is regulated not only by chromatin loop extrusion but also by phase-separated condensates. Here, we discuss recent findings on the mechanisms of chromatin organization mediated by phase separation, with a focus on the roles of phase-separated condensates in chromatin structural dysregulation in human diseases. Indeed, these mechanistic revelations herald promising therapeutic strategies targeting phase-separated condensates-leveraging their intrinsic biophysical susceptibilities to restore chromatin structure dysregulated by aberrant phase separation.
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Affiliation(s)
- Ziwei Zhai
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong SAR, China; (Z.Z.); (F.M.)
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou 310024, China
| | - Fei Meng
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong SAR, China; (Z.Z.); (F.M.)
| | - Junqi Kuang
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou 310024, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China
| | - Duanqing Pei
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou 310024, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China
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2
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Yu Y, Yu X, Pan B, Chan HM, Kaniskan HÜ, Jin J, Cai L, Wang GG. Pharmacologic degradation of WDR5 suppresses oncogenic activities of SS18::SSX and provides a therapeutic of synovial sarcoma. SCIENCE ADVANCES 2025; 11:eads7876. [PMID: 40267190 PMCID: PMC12017321 DOI: 10.1126/sciadv.ads7876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2024] [Accepted: 03/19/2025] [Indexed: 04/25/2025]
Abstract
Cancer-causing aberrations recurrently target the chromatic-regulatory factors, leading to epigenetic dysregulation. Almost all patients with synovial sarcoma (SS) carry a characteristic gene fusion, SS18::SSX, which produces a disease-specific oncoprotein that is incorporated into the switch/sucrose non-fermentable (SWI/SNF) chromatin-remodeling complexes and profoundly alters their functionalities. Targeting epigenetic dependency in cancers holds promise for improving current treatment. Leveraging on cancer cell dependency dataset, pharmacological tools, and genomic profiling, we find WDR5, a factor critical for depositing histone H3 lysine 4 (H3K4) methylation, to be an unexplored vulnerability in SS. Mechanistically, WDR5 and SS18::SSX interact and colocalize at oncogenes where WDR5 promotes H3K4 methylation and the chromatin association of SS18::SSX-containing chromatin-remodeling complexes. WDR5 degradation by proteolysis-targeting chimera (PROTAC) not only suppresses the SS18::SSX-related oncogenic programs but additionally causes the ribosomal protein deregulations leading to p53 activation. WDR5-targeted PROTAC suppresses SS growth in vitro and in vivo, providing a promising strategy for the SS treatment.
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Affiliation(s)
- Yao Yu
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Xufen Yu
- Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Bo Pan
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Ho Man Chan
- Research and Early Development, Oncology R&D, AstraZeneca, Waltham, MA 02451, USA
| | - H. Ümit Kaniskan
- Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jian Jin
- Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ling Cai
- Department of Pathology, Duke University School of Medicine, Durham, NC 27710, USA
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Gang Greg Wang
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Pathology, Duke University School of Medicine, Durham, NC 27710, USA
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC 27710, USA
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3
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Lyons H, Pradhan P, Prakasam G, Vashishtha S, Li X, Eppert M, Fornero C, Tcheuyap VT, McGlynn K, Yu Z, Raju DR, Koduru PR, Xing C, Kapur P, Brugarolas J, Sabari BR. RNA polymerase II partitioning is a shared feature of diverse oncofusion condensates. Cell 2025:S0092-8674(25)00404-0. [PMID: 40286793 DOI: 10.1016/j.cell.2025.04.002] [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: 05/17/2024] [Revised: 12/12/2024] [Accepted: 04/01/2025] [Indexed: 04/29/2025]
Abstract
Condensates regulate transcription by selectively compartmentalizing biomolecules, yet the rules of specificity and their relationship to function remain enigmatic. To identify rules linked to function, we leverage the genetic selection bias of condensate-promoting oncofusions. Focusing on the three most frequent oncofusions driving translocation renal cell carcinoma, we find that they promote the formation of condensates that activate transcription by gain-of-function RNA polymerase II partitioning through a shared signature of elevated π and π-interacting residues and depletion of aliphatic residues. This signature is shared among a broad set of DNA-binding oncofusions associated with diverse cancers. We find that this signature is necessary and sufficient for RNA polymerase II partitioning, gene activation, and cancer cell phenotypes. Our results reveal that dysregulated condensate specificity is a shared molecular mechanism of diverse oncofusions, highlighting the functional role of condensate composition and the power of disease genetics in investigating relationships between condensate specificity and function.
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Affiliation(s)
- Heankel Lyons
- Laboratory of Nuclear Organization, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Research, Department of Obstetrics and Gynecology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Prashant Pradhan
- Laboratory of Nuclear Organization, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Research, Department of Obstetrics and Gynecology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Gopinath Prakasam
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Hematology-Oncology Division, Department of Internal Medicine, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Shubham Vashishtha
- Laboratory of Nuclear Organization, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Research, Department of Obstetrics and Gynecology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xiang Li
- Laboratory of Nuclear Organization, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Research, Department of Obstetrics and Gynecology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Mikayla Eppert
- Laboratory of Nuclear Organization, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Research, Department of Obstetrics and Gynecology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Christy Fornero
- Laboratory of Nuclear Organization, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Research, Department of Obstetrics and Gynecology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Vanina T Tcheuyap
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Hematology-Oncology Division, Department of Internal Medicine, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kathleen McGlynn
- Laboratory of Nuclear Organization, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Research, Department of Obstetrics and Gynecology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ze Yu
- Eugene McDermott Center for Human Growth and Development, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Dinesh Ravindra Raju
- Eugene McDermott Center for Human Growth and Development, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Prasad R Koduru
- Department of Pathology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Chao Xing
- Eugene McDermott Center for Human Growth and Development, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Lyda Hill Department of Bioinformatics, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Peter O'Donnell School of Public Health, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Payal Kapur
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pathology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Urology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - James Brugarolas
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Hematology-Oncology Division, Department of Internal Medicine, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Benjamin R Sabari
- Laboratory of Nuclear Organization, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Research, Department of Obstetrics and Gynecology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Molecular Biology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Hamon Center for Regenerative Science and Medicine, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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4
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Seufert I, Vargas C, Wille SJ, Rippe K. Deregulated enhancer-promoter communication in cancer through altered nuclear architecture. Int J Cancer 2025. [PMID: 40219822 DOI: 10.1002/ijc.35424] [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: 11/24/2024] [Revised: 03/07/2025] [Accepted: 03/17/2025] [Indexed: 04/14/2025]
Abstract
Enhancers are critical regulators of gene expression. Structural variations in cancer genomes can lead to enhancer hijacking, where oncogenes are activated by mistargeted enhancer activity. Novel enhancer-promoter interactions may also arise through chromosomal rearrangements that create extrachromosomal DNA elements. Additionally, fusion proteins and other mutation-induced alterations in protein properties can lead to the aberrant assembly of proteins into large complexes on the size scale of 0.1-1 μm termed onco-condensates. Transcription factors and co-activators accumulate with cis-regulatory elements in these structures, driving oncogenic programs. Here, we review current evidence of how altered genome architecture and macromolecular assembly result in deregulated enhancer-promoter communication. We discuss emerging strategies to exploit these mechanisms for clinical applications.
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Affiliation(s)
- Isabelle Seufert
- German Cancer Research Center (DKFZ) Heidelberg, Division of Chromatin Networks, Heidelberg, Germany
- Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), Heidelberg University, Heidelberg, Germany
| | - Claire Vargas
- German Cancer Research Center (DKFZ) Heidelberg, Division of Chromatin Networks, Heidelberg, Germany
- Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), Heidelberg University, Heidelberg, Germany
| | - Sina Jasmin Wille
- German Cancer Research Center (DKFZ) Heidelberg, Division of Chromatin Networks, Heidelberg, Germany
- Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), Heidelberg University, Heidelberg, Germany
| | - Karsten Rippe
- German Cancer Research Center (DKFZ) Heidelberg, Division of Chromatin Networks, Heidelberg, Germany
- Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), Heidelberg University, Heidelberg, Germany
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5
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Ahn JH, Guo Y, Lyons H, Mackintosh SG, Lau BK, Edmondson RD, Byrum SD, Storey AJ, Tackett AJ, Cai L, Sabari BR, Wang GG. The phenylalanine-and-glycine repeats of NUP98 oncofusions form condensates that selectively partition transcriptional coactivators. Mol Cell 2025; 85:708-725.e9. [PMID: 39922194 DOI: 10.1016/j.molcel.2024.12.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 10/21/2024] [Accepted: 12/30/2024] [Indexed: 02/10/2025]
Abstract
Recurrent cancer-causing fusions of NUP98 produce higher-order assemblies known as condensates. How NUP98 oncofusion-driven condensates activate oncogenes remains poorly understood. Here, we investigate NUP98-PHF23, a leukemogenic chimera of the disordered phenylalanine-and-glycine (FG)-repeat-rich region of NUP98 and the H3K4me3/2-binding plant homeodomain (PHD) finger domain of PHF23. Our integrated analyses using mutagenesis, proteomics, genomics, and condensate reconstitution demonstrate that the PHD domain targets condensate to the H3K4me3/2-demarcated developmental genes, while FG repeats determine the condensate composition and gene activation. FG repeats are necessary to form condensates that partition a specific set of transcriptional regulators, notably the KMT2/MLL H3K4 methyltransferases, histone acetyltransferases, and BRD4. FG repeats are sufficient to partition transcriptional regulators and activate a reporter when tethered to a genomic locus. NUP98-PHF23 assembles the chromatin-bound condensates that partition multiple positive regulators, initiating a feedforward loop of reading-and-writing the active histone modifications. This network of interactions enforces an open chromatin landscape at proto-oncogenes, thereby driving cancerous transcriptional programs.
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Affiliation(s)
- Jeong Hyun Ahn
- Institute for Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
| | - Yiran Guo
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Heankel Lyons
- Laboratory of Nuclear Organization, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Research, Department of Obstetrics and Gynecology, Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Samuel G Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Benjamin K Lau
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Ricky D Edmondson
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Stephanie D Byrum
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Aaron J Storey
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Alan J Tackett
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Ling Cai
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Pathology, Duke University School of Medicine, Durham, NC 27710, USA.
| | - Benjamin R Sabari
- Laboratory of Nuclear Organization, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Research, Department of Obstetrics and Gynecology, Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Gang Greg Wang
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Pathology, Duke University School of Medicine, Durham, NC 27710, USA.
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6
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Li J, Liu S, Kim S, Goell J, Drum Z, Flores J, Ma A, Mahata B, Escobar M, Raterink A, Ahn JH, Terán E, Guerra-Resendez R, Zhou Y, Yu B, Diehl M, Wang GG, Gustavsson AK, Phanstiel D, Hilton I. Biomolecular condensation of human IDRs initiates endogenous transcription via intrachromosomal looping or high-density promoter localization. Nucleic Acids Res 2025; 53:gkaf056. [PMID: 39933697 PMCID: PMC11811730 DOI: 10.1093/nar/gkaf056] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2024] [Revised: 01/02/2025] [Accepted: 01/22/2025] [Indexed: 02/13/2025] Open
Abstract
Protein intrinsically disordered regions (IDRs) are critical gene-regulatory components and aberrant fusions between IDRs and DNA-binding/chromatin-associating domains cause diverse human cancers. Despite this importance, how IDRs influence gene expression, and how aberrant IDR fusion proteins provoke oncogenesis, remains incompletely understood. Here we develop a series of synthetic dCas9-IDR fusions to establish that locus-specific recruitment of IDRs can be sufficient to stimulate endogenous gene expression. Using dCas9 fused to the paradigmatic leukemogenic NUP98 IDR, we also demonstrate that IDRs can activate transcription via localized biomolecular condensation and in a manner that is dependent upon overall IDR concentration, local binding density, and amino acid composition. To better clarify the oncogenic role of IDRs, we construct clinically observed NUP98 IDR fusions and show that, while generally non-overlapping, oncogenic NUP98-IDR fusions convergently drive a core leukemogenic gene expression program in donor-derived human hematopoietic stem cells. Interestingly, we find that this leukemic program arises through differing mechanistic routes based upon IDR fusion partner; either distributed intragenic binding and intrachromosomal looping, or dense binding at promoters. Altogether, our studies clarify the gene-regulatory roles of IDRs and, for the NUP98 IDR, connect this capacity to pathological cellular programs, creating potential opportunities for generalized and mechanistically tailored therapies.
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Affiliation(s)
- Jing Li
- Department of Bioengineering, Rice University, Houston, TX, 77030, United States
| | - Shizhe Liu
- Department of BioSciences, Rice University, Houston, TX, 77030, United States
| | - Sunghwan Kim
- Department of Bioengineering, Rice University, Houston, TX, 77030, United States
| | - Jacob Goell
- Department of Bioengineering, Rice University, Houston, TX, 77030, United States
| | - Zachary Allen Drum
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, United States
| | - John Patrick Flores
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, United States
| | - Alex J Ma
- Department of Bioengineering, Rice University, Houston, TX, 77030, United States
| | - Barun Mahata
- Department of Bioengineering, Rice University, Houston, TX, 77030, United States
| | - Mario Escobar
- Department of Bioengineering, Rice University, Houston, TX, 77030, United States
| | - Alex Raterink
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, Houston, TX, 77030, United States
| | - Jeong Hyun Ahn
- Lineberger Comprehensive Cancer Center and Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, United States
| | - Erik R Terán
- Department of BioSciences, Rice University, Houston, TX, 77030, United States
| | | | - Yuhao Zhou
- Department of Bioengineering, Rice University, Houston, TX, 77030, United States
| | - Bo Yu
- Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Michael R Diehl
- Department of Bioengineering, Rice University, Houston, TX, 77030, United States
- Department of Chemistry, Rice University, Houston, TX, 77030, United States
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center and Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, United States
- Department of Pharmacology and Cancer Biology and Duke Cancer Institute, Duke University, Durham, NC, 27710, United States
| | - Anna-Karin Gustavsson
- Department of BioSciences, Rice University, Houston, TX, 77030, United States
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, Houston, TX, 77030, United States
- Department of Chemistry, Rice University, Houston, TX, 77030, United States
| | - Douglas H Phanstiel
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, United States
| | - Isaac B Hilton
- Department of Bioengineering, Rice University, Houston, TX, 77030, United States
- Department of BioSciences, Rice University, Houston, TX, 77030, United States
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, Houston, TX, 77030, United States
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7
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Kodali S, Sands CM, Guo L, Huang Y, Di Stefano B. Biomolecular condensates in immune cell fate. Nat Rev Immunol 2025:10.1038/s41577-025-01130-z. [PMID: 39875604 DOI: 10.1038/s41577-025-01130-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/02/2025] [Indexed: 01/30/2025]
Abstract
Fate decisions during immune cell development require temporally precise changes in gene expression. Evidence suggests that the dynamic modulation of these changes is associated with the formation of diverse, membrane-less nucleoprotein assemblies that are termed biomolecular condensates. These condensates are thought to orchestrate fate-determining transcriptional and post-transcriptional processes by locally and transiently concentrating DNA or RNA molecules alongside their regulatory proteins. Findings have established a link between condensate formation and the gene regulatory networks that ensure the proper development of immune cells. Conversely, condensate dysregulation has been linked to impaired immune cell fates, including ageing and malignant transformation. This Review explores the putative mechanistic links between condensate assembly and the gene regulatory frameworks that govern normal and pathological development in the immune system.
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Affiliation(s)
- Srikanth Kodali
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Caroline M Sands
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Lei Guo
- Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
- Department of Translational Medical Sciences, School of Medicine, Texas A&M University, Houston, TX, USA
| | - Yun Huang
- Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
- Department of Translational Medical Sciences, School of Medicine, Texas A&M University, Houston, TX, USA
| | - Bruno Di Stefano
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA.
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.
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8
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Li X, Liu C, Lei Z, Chen H, Wang L. Phase-separated chromatin compartments: Orchestrating gene expression through condensation. CELL INSIGHT 2024; 3:100213. [PMID: 39512706 PMCID: PMC11541479 DOI: 10.1016/j.cellin.2024.100213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2024] [Revised: 10/07/2024] [Accepted: 10/07/2024] [Indexed: 11/15/2024]
Abstract
Eukaryotic genomes are organized into distinct chromatin compartments, some of which exhibit properties of biomolecular condensates. These condensates primarily form due to chromatin-associated proteins/complexes (CAPs). CAPs play a crucial role in gene expression, functioning as either transcriptional repressors or activators. Phase separation, a well-established biophysical phenomenon, is a key driver of chromatin condensate formation by CAPs. Notably, multivalent CAPs with the ability to engage in diverse interactions promote chromatin compaction, leading to the formation of transcriptionally repressed compartments. Conversely, interactions between intrinsically disordered region (IDR)-containing transcriptional regulators, mediated by their multivalent IDRs, lead to the formation of protein-rich, transcriptionally active droplets on decondensed genomic regions. Interestingly, both repressive heterochromatin and activating euchromatin condensates exhibit spontaneous phase separation and selectively enrich components with concordant transcriptional functions. This review delves into the mechanisms by which transcriptionally repressive CAPs orchestrate the formation of repressed chromatin domains. We further explore how a diverse array of transcription-related CAPs or core histone variants, via phase separation, influence gene expression by inducing erroneous transcription events, regulating expression levels, and facilitating the interconversion of transcriptionally repressed and active regions.
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Affiliation(s)
- Xin Li
- Beijing Life Science Academy, Beijing, 102209, China
| | - Chengzhi Liu
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Zhichao Lei
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, 430079, Hubei, China
| | - Huan Chen
- Beijing Life Science Academy, Beijing, 102209, China
| | - Liang Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, Hubei, China
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9
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Li P, Zhai Z, Fan Y, Li W, Ke M, Li X, Gao H, Fu Y, Ma Z, Zhang W, Yi H, Ming J, Qin Y, Wang B, Kuang J, Pei D. Condensate remodeling reorganizes innate SS18 in synovial sarcomagenesis. Oncogenesis 2024; 13:38. [PMID: 39468035 PMCID: PMC11519567 DOI: 10.1038/s41389-024-00539-w] [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: 02/29/2024] [Revised: 09/26/2024] [Accepted: 10/10/2024] [Indexed: 10/30/2024] Open
Abstract
SS18-SSX onco-fusion protein formed through aberrant chromosomal translocation t (X, 18; p11, q11), is the hallmark and plays a critical role in synovial sarcomagenesis. The recent works indicated that both the pathological SS18-SSX tumorigenic fusion and the corresponding intrinsic physiological SS18 protein can form condensates but appear to have disparate properties. The underlying regulatory mechanism and the consequent biological significance remain largely unknown. We show that the physical properties of oncogenic fusion protein SS18-SSX condensates within cells undergo alterations compared to the proto-oncogene protein SS18. By small-molecule screening and mutant assay, we identified the recognition of H2AK119ub histone modification could account for the distinctive properties of SS18-SSX1 condensates. Notably, we show that SS18-SSX1 condensates have impact on SS18 condensates and hijack that in a phase separation manner, resulting in the relocation of protein SS18 to the H2AK119ub modification targeted by SS18-SSX1. Consequently, this leads to the downregulation of tumor suppressor genes occupied by SS18 physiologically, like CAV1 and DAB2. These results reveal the underlying mechanism of genomic disorder and tumorigenesis caused by the remodeling of oncoprotein SS18-SSX1 condensates at the macroscopic level.
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Affiliation(s)
- Pengli Li
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ziwei Zhai
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yixin Fan
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wei Li
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Minjing Ke
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoxi Li
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Huiru Gao
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yu Fu
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
| | - Zhaoyi Ma
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
| | - Wenhui Zhang
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
| | - Hongyan Yi
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
| | - Jin Ming
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
| | - Yue Qin
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
| | - Bo Wang
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
| | - Junqi Kuang
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China.
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China.
| | - Duanqing Pei
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China.
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China.
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10
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Godschalk R, Faulk C, LaRocca J, van Benthem J, Marchetti F. Epigenotoxicity: Decoding the epigenetic imprints of genotoxic agents and their implications for regulatory genetic toxicology. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2024. [PMID: 39262275 DOI: 10.1002/em.22626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 08/16/2024] [Accepted: 08/20/2024] [Indexed: 09/13/2024]
Abstract
Regulatory genetic toxicology focuses on DNA damage and subsequent gene mutations. However, genotoxic agents can also affect epigenetic marks, and incorporation of epigenetic data into the regulatory framework may thus enhance the accuracy of risk assessment. Additionally, epigenetic alterations may identify non-genotoxic carcinogens that are not captured with the current battery of tests. Epigenetic alterations could also explain long-term consequences and potential transgenerational effects in the absence of DNA mutations. Therefore, at the 2022 International Workshops on Genotoxicity Testing (IWGT) in Ottawa (Ontario, Canada), an expert workgroup explored whether including epigenetic endpoints would improve regulatory genetic toxicology. Here we summarize the presentations and the discussions on technical advancements in assessing epigenetics, how the assessment of epigenetics can enhance strategies for detecting genotoxic and non-genotoxic carcinogens and the correlation between epigenetic alterations with other relevant apical endpoints.
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Affiliation(s)
- Roger Godschalk
- Department of Pharmacology and Toxicology, School for Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands
| | | | | | - Jan van Benthem
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Francesco Marchetti
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, Canada
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11
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Le DJ, Hafner A, Gaddam S, Wang KC, Boettiger AN. Super-enhancer interactomes from single cells link clustering and transcription. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.08.593251. [PMID: 38766104 PMCID: PMC11100725 DOI: 10.1101/2024.05.08.593251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Regulation of gene expression hinges on the interplay between enhancers and promoters, traditionally explored through pairwise analyses. Recent advancements in mapping genome folding, like GAM, SPRITE, and multi-contact Hi-C, have uncovered multi-way interactions among super-enhancers (SEs), spanning megabases, yet have not measured their frequency in single cells or the relationship between clustering and transcription. To close this gap, here we used multiplexed imaging to map the 3D positions of 376 SEs across thousands of mammalian nuclei. Notably, our single-cell images reveal that while SE-SE contacts are rare, SEs often form looser associations we termed "communities". These communities, averaging 4-5 SEs, assemble cooperatively under the combined effects of genomic tethers, Pol2 clustering, and nuclear compartmentalization. Larger communities are associated with more frequent and larger transcriptional bursts. Our work provides insights about the SE interactome in single cells that challenge existing hypotheses on SE clustering in the context of transcriptional regulation.
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Affiliation(s)
- Derek J. Le
- Department of Developmental Biology, Stanford University, Stanford, CA, United States
- Cancer Biology Program, Stanford University, Stanford, CA, United States
- Department of Dermatology, Stanford University, Stanford, CA, United States
- These authors contributed equally
| | - Antonina Hafner
- Department of Developmental Biology, Stanford University, Stanford, CA, United States
- These authors contributed equally
| | - Sadhana Gaddam
- Department of Dermatology, Stanford University, Stanford, CA, United States
| | - Kevin C. Wang
- Department of Dermatology, Stanford University, Stanford, CA, United States
| | - Alistair N. Boettiger
- Department of Developmental Biology, Stanford University, Stanford, CA, United States
- Lead contact
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12
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Gan P, Eppert M, De La Cruz N, Lyons H, Shah AM, Veettil RT, Chen K, Pradhan P, Bezprozvannaya S, Xu L, Liu N, Olson EN, Sabari BR. Coactivator condensation drives cardiovascular cell lineage specification. SCIENCE ADVANCES 2024; 10:eadk7160. [PMID: 38489358 PMCID: PMC10942106 DOI: 10.1126/sciadv.adk7160] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 02/12/2024] [Indexed: 03/17/2024]
Abstract
During development, cells make switch-like decisions to activate new gene programs specifying cell lineage. The mechanisms underlying these decisive choices remain unclear. Here, we show that the cardiovascular transcriptional coactivator myocardin (MYOCD) activates cell identity genes by concentration-dependent and switch-like formation of transcriptional condensates. MYOCD forms such condensates and activates cell identity genes at critical concentration thresholds achieved during smooth muscle cell and cardiomyocyte differentiation. The carboxyl-terminal disordered region of MYOCD is necessary and sufficient for condensate formation. Disrupting this region's ability to form condensates disrupts gene activation and smooth muscle cell reprogramming. Rescuing condensate formation by replacing this region with disordered regions from functionally unrelated proteins rescues gene activation and smooth muscle cell reprogramming. Our findings demonstrate that MYOCD condensate formation is required for gene activation during cardiovascular differentiation. We propose that the formation of transcriptional condensates at critical concentrations of cell type-specific regulators provides a molecular switch underlying the activation of key cell identity genes during development.
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Affiliation(s)
- Peiheng Gan
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Mikayla Eppert
- Laboratory of Nuclear Organization, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Nancy De La Cruz
- Laboratory of Nuclear Organization, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Heankel Lyons
- Laboratory of Nuclear Organization, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Akansha M. Shah
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Reshma T. Veettil
- Laboratory of Nuclear Organization, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kenian Chen
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Prashant Pradhan
- Laboratory of Nuclear Organization, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Svetlana Bezprozvannaya
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lin Xu
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ning Liu
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Eric N. Olson
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Benjamin R. Sabari
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Laboratory of Nuclear Organization, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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13
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Shahrajabian MH, Sun W. Characterization of Intrinsically Disordered Proteins in Healthy and Diseased States by Nuclear Magnetic Resonance. Rev Recent Clin Trials 2024; 19:176-188. [PMID: 38409704 DOI: 10.2174/0115748871271420240213064251] [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: 09/13/2023] [Revised: 11/10/2023] [Accepted: 12/13/2023] [Indexed: 02/28/2024]
Abstract
INTRODUCTION Intrinsically Disordered Proteins (IDPs) are active in different cellular procedures like ordered assembly of chromatin and ribosomes, interaction with membrane, protein, and ligand binding, molecular recognition, binding, and transportation via nuclear pores, microfilaments and microtubules process and disassembly, protein functions, RNA chaperone, and nucleic acid binding, modulation of the central dogma, cell cycle, and other cellular activities, post-translational qualification and substitute splicing, and flexible entropic linker and management of signaling pathways. METHODS The intrinsic disorder is a precise structural characteristic that permits IDPs/IDPRs to be involved in both one-to-many and many-to-one signaling. IDPs/IDPRs also exert some dynamical and structural ordering, being much less constrained in their activities than folded proteins. Nuclear magnetic resonance (NMR) spectroscopy is a major technique for the characterization of IDPs, and it can be used for dynamic and structural studies of IDPs. RESULTS AND CONCLUSION This review was carried out to discuss intrinsically disordered proteins and their different goals, as well as the importance and effectiveness of NMR in characterizing intrinsically disordered proteins in healthy and diseased states.
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Affiliation(s)
- Mohamad Hesam Shahrajabian
- National Key Laboratory of Agricultural Microbiology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wenli Sun
- National Key Laboratory of Agricultural Microbiology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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14
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Laghmach R, Di Pierro M, Potoyan DA. Four-Dimensional Mesoscale Liquid Model of Nucleus Resolves Chromatin's Radial Organization. PRX LIFE 2024; 2:013006. [PMID: 38601142 PMCID: PMC11005002 DOI: 10.1103/prxlife.2.013006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
Recent advances chromatin capture, imaging techniques, and polymer modeling have dramatically enhanced quantitative understanding of chromosomal folding. However, the dynamism inherent in genome architectures due to physical and biochemical forces and their impact on nuclear architecture and cellular functions remains elusive. While imaging of chromatin in four dimensions is becoming more common, there is a conspicuous lack of physics-based computational tools appropriate for revealing the forces that shape nuclear architecture and dynamics. To this end, we have developed a multiphase liquid model of the nucleus, which can resolve chromosomal territories, compartments, and nuclear lamina using a physics-based and data-informed free-energy function. The model enables rapid hypothesis-driven prototyping of nuclear dynamics in four dimensions, thereby facilitating comparison with whole nucleus imaging experiments. As an application, we model the Drosophila nucleus and map phase diagram of various possible nuclear morphologies. We shed light on the interplay of adhesive and cohesive interactions which give rise to distinct radial organization seen in conventional, inverted, and senescent nuclear architectures. The results also show the highly dynamic nature of the radial organization, the disruption of which leads to significant variability in domain coarsening dynamics and consequently variability of chromatin architecture. The model also highlights the impact of oblate nuclear geometry and heterochromatin-subtype interactions on the global chromatin architecture and local asymmetry of chromatin compartments.
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Affiliation(s)
- Rabia Laghmach
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA
| | - Michele Di Pierro
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, USA
| | - Davit A. Potoyan
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA and Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA
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15
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Cai L, Wang GG. Through the lens of phase separation: intrinsically unstructured protein and chromatin looping. Nucleus 2023; 14:2179766. [PMID: 36821650 PMCID: PMC9980480 DOI: 10.1080/19491034.2023.2179766] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
The establishment, maintenance and dynamic regulation of three-dimensional (3D) chromatin structures provide an important means for partitioning of genome into functionally distinctive domains, which helps to define specialized gene expression programs associated with developmental stages and cell types. Increasing evidence supports critical roles for intrinsically disordered regions (IDRs) harbored within transcription factors (TFs) and chromatin-modulatory proteins in inducing phase separation, a phenomenon of forming membrane-less condensates through partitioning of biomolecules. Such a process is also critically involved in the establishment of high-order chromatin structures and looping. IDR- and phase separation-driven 3D genome (re)organization often goes wrong in disease such as cancer. This review discusses about recent advances in understanding how phase separation of intrinsically disordered proteins (IDPs) modulates chromatin looping and gene expression.
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Affiliation(s)
- Ling Cai
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA,Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA,Ling Cai Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC27599, USA
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA,Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA,CONTACT Gang Greg Wang Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC27599, USA
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16
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Tai J, Wang L, Yan Z, Liu J. Single-cell sequencing and transcriptome analyses in the construction of a liquid-liquid phase separation-associated gene model for rheumatoid arthritis. Front Genet 2023; 14:1210722. [PMID: 37953920 PMCID: PMC10634374 DOI: 10.3389/fgene.2023.1210722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 10/09/2023] [Indexed: 11/14/2023] Open
Abstract
Background: Rheumatoid arthritis (RA) is a disabling autoimmune disease that affects multiple joints. Accumulating evidence suggests that imbalances in liquid-liquid phase separation (LLPS) can lead to altered spatiotemporal coordination of biomolecular condensates, which play important roles in carcinogenesis and inflammatory diseases. However, the role of LLPS in the development and progression of RA remains unclear. Methods: We screened RA and normal samples from GSE12021, GSE55235, and GSE55457 transcriptome datasets and GSE129087 and GSE109449 single-cell sequencing datasets from Gene Expression Omnibus database to investigate the pathogenesis of LLPS-related hub genes at the transcriptome and single cell sequencing levels. Machine learning algorithms and weighted gene co-expression network analysis were applied to screen hub genes, and hub genes were validated using correlation studies. Results: Differential analysis showed that 36 LLPS-related genes were significantly differentially expressed in RA, further random forest and support vector machine identified four and six LLPS-related genes, respectively, and weighted gene co-expression network analysis identified 396 modular genes. Hybridization of the three sets revealed two hub genes, MYC and MAP1LC3B, with AUCs of 0.907 and 0.911, respectively. Further ROC analysis of the hub genes in the GSE55457 dataset showed that the AUCs of MYC and MAP1LC3B were 0.815 and 0.785, respectively. qRT-PCR showed that the expression of MYC and MAP1LC3B in RA synovial tissues was significantly lower than that in the normal control synovial tissues. Correlation analysis between hub genes and the immune microenvironment and single-cell sequencing analysis revealed that both MYC and MAP1LC3B were significantly correlated with the degree of infiltration of various innate and acquired immune cells. Conclusion: Our study reveals a possible mechanism for LLPS in RA pathogenesis and suggests that MYC and MAP1LC3B may be potential novel molecular markers for RA with immunological significance.
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Affiliation(s)
- Jiaojiao Tai
- Department of Orthopedics, Honghui Hospital, Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - Linbang Wang
- Department of Orthopedics, Peking University Third Hospital, Beijing, China
| | - Ziqiang Yan
- Department of Orthopedics, Honghui Hospital, Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - Jingkun Liu
- Department of Orthopedics, Honghui Hospital, Xi’an Jiaotong University, Xi’an, Shaanxi, China
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17
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Xu C, Kim A, Corbin JM, Wang GG. Onco-condensates: formation, multi-component organization, and biological functions. Trends Cancer 2023; 9:738-751. [PMID: 37349246 PMCID: PMC10524369 DOI: 10.1016/j.trecan.2023.05.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/16/2023] [Accepted: 05/23/2023] [Indexed: 06/24/2023]
Abstract
Numerous cellular processes occur in the context of condensates, a type of large, membrane-less biomolecular assembly generated through phase separation. These condensates function as a hub of diversified cellular events by concentrating the required components. Cancer frequently coopts biomolecular condensation mechanisms to promote survival and/or proliferation. Onco-condensates, which refer to those that have causal roles or are critically involved in tumorigenicity, operate to abnormally elevate biological output of a proliferative process, or to suppress a tumor-suppressive pathway, thereby promoting oncogenesis. Here, we summarize advances regarding how multi-component onco-condensates are established and organized to promote oncogenesis, with those related to chromatin and transcription deregulation used as showcases. A better understanding should enable development of new means of targeting onco-condensates as potential therapeutics.
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Affiliation(s)
- Chenxi Xu
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Arum Kim
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Joshua M Corbin
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA; Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
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18
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Jevtic Z, Allram M, Grebien F, Schwaller J. Biomolecular Condensates in Myeloid Leukemia: What Do They Tell Us? Hemasphere 2023; 7:e923. [PMID: 37388925 PMCID: PMC10306439 DOI: 10.1097/hs9.0000000000000923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/31/2023] [Indexed: 07/01/2023] Open
Abstract
Recent studies have suggested that several oncogenic and tumor-suppressive proteins carry out their functions in the context of specific membrane-less cellular compartments. As these compartments, generally referred to as onco-condensates, are specific to tumor cells and are tightly linked to disease development, the mechanisms of their formation and maintenance have been intensively studied. Here we review the proposed leukemogenic and tumor-suppressive activities of nuclear biomolecular condensates in acute myeloid leukemia (AML). We focus on condensates formed by oncogenic fusion proteins including nucleoporin 98 (NUP98), mixed-lineage leukemia 1 (MLL1, also known as KMT2A), mutated nucleophosmin (NPM1c) and others. We also discuss how altered condensate formation contributes to malignant transformation of hematopoietic cells, as described for promyelocytic leukemia protein (PML) in PML::RARA-driven acute promyelocytic leukemia (APL) and other myeloid malignancies. Finally, we discuss potential strategies for interfering with the molecular mechanisms related to AML-associated biomolecular condensates, as well as current limitations of the field.
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Affiliation(s)
- Zivojin Jevtic
- Department of Biomedicine (DBM), University Children’s Hospital Basel, University of Basel, Switzerland
| | - Melanie Allram
- Institute for Medical Biochemistry, University of Veterinary Medicine, Vienna, Austria
| | - Florian Grebien
- Institute for Medical Biochemistry, University of Veterinary Medicine, Vienna, Austria
- St. Anna Children’s Cancer Research Institute (CCRI), Vienna, Austria
| | - Juerg Schwaller
- Department of Biomedicine (DBM), University Children’s Hospital Basel, University of Basel, Switzerland
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19
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Eppert M, Sabari BR. Context is key: Modulated protein multivalency in disease. Mol Cell 2022; 82:3965-3967. [DOI: 10.1016/j.molcel.2022.10.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 10/07/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022]
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20
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Guo Y, Wang GG. Modulation of the high-order chromatin structure by Polycomb complexes. Front Cell Dev Biol 2022; 10:1021658. [PMID: 36274840 PMCID: PMC9579376 DOI: 10.3389/fcell.2022.1021658] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
The multi-subunit Polycomb Repressive Complex (PRC) 1 and 2 act, either independently or synergistically, to maintain and enforce a repressive state of the target chromatin, thereby regulating the processes of cell lineage specification and organismal development. In recent years, deep sequencing-based and imaging-based technologies, especially those tailored for mapping three-dimensional (3D) chromatin organization and structure, have allowed a better understanding of the PRC complex-mediated long-range chromatin contacts and DNA looping. In this review, we review current advances as for how Polycomb complexes function to modulate and help define the high-order chromatin structure and topology, highlighting the multi-faceted roles of Polycomb proteins in gene and genome regulation.
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Affiliation(s)
- Yiran Guo
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, United States
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, United States
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- *Correspondence: Yiran Guo, ; Gang Greg Wang,
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, United States
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, United States
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, United States
- *Correspondence: Yiran Guo, ; Gang Greg Wang,
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21
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Bellanger A, Madsen-Østerbye J, Galigniana NM, Collas P. Restructuring of Lamina-Associated Domains in Senescence and Cancer. Cells 2022; 11:1846. [PMID: 35681541 PMCID: PMC9180887 DOI: 10.3390/cells11111846] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/02/2022] [Accepted: 06/04/2022] [Indexed: 01/01/2023] Open
Abstract
Induction of cellular senescence or cancer is associated with a reshaping of the nuclear envelope and a broad reorganization of heterochromatin. At the periphery of mammalian nuclei, heterochromatin is stabilized at the nuclear lamina via lamina-associated domains (LADs). Alterations in the composition of the nuclear lamina during senescence lead to a loss of peripheral heterochromatin, repositioning of LADs, and changes in epigenetic states of LADs. Cancer initiation and progression are also accompanied by a massive reprogramming of the epigenome, particularly in domains coinciding with LADs. Here, we review recent knowledge on alterations in chromatin organization and in the epigenome that affect LADs and related genomic domains in senescence and cancer.
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Affiliation(s)
- Aurélie Bellanger
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0372 Oslo, Norway; (A.B.); (J.M.-Ø.); (N.M.G.)
| | - Julia Madsen-Østerbye
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0372 Oslo, Norway; (A.B.); (J.M.-Ø.); (N.M.G.)
| | - Natalia M. Galigniana
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0372 Oslo, Norway; (A.B.); (J.M.-Ø.); (N.M.G.)
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, 0372 Oslo, Norway
| | - Philippe Collas
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0372 Oslo, Norway; (A.B.); (J.M.-Ø.); (N.M.G.)
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, 0372 Oslo, Norway
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