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Lin L, He F, Jin X, Zhang X, Li Y, Wang D, Wang J, Zheng L, Song H, Zhu X, Cheng Q, Zhao Y, Liang J, Ma J, Gao J, Tong J, Shi L. Liquid-liquid phase separation in normal hematopoiesis and hematological diseases. Cell Tissue Res 2025:10.1007/s00441-025-03974-2. [PMID: 40381034 DOI: 10.1007/s00441-025-03974-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2025] [Accepted: 04/30/2025] [Indexed: 05/19/2025]
Abstract
Liquid-liquid phase separation (LLPS) is an emerging research field in cellular biology. LLPS-driven biomolecular condensates act as reaction chambers and regulatory hubs for critical processes, including chromatin architecture, gene expression, and metabolism. The dysregulation of these processes frequently impedes the proper execution of physiological functions. Current research indicates that abnormal phase separation plays a significant role in the pathogenesis of diseases and aging. This review briefly overviews the fundamental concepts and research methods related to phase separation. We also summarize studies concerning its physiological functions, particularly emphasizing its role in hematopoiesis. We further discuss how abnormal phase separation can lead to hematological disorders, specifically summarizing its involvement in the pathogenesis of leukemia. Despite recent advancements, elucidating LLPS mechanisms in hematopoiesis remains challenging due to the intricate interplay between biomolecular condensates and cellular function. Future research efforts aiming to reveal the role of LLPS in hematological diseases hold promise for novel therapeutic interventions and a deeper understanding of hematopoietic processes.
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Affiliation(s)
- Lexuan Lin
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Heping District, Tianjin, 300020, China
| | - Fang He
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Heping District, Tianjin, 300020, China
| | - Xu Jin
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Heping District, Tianjin, 300020, China
| | - Xiaoru Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Heping District, Tianjin, 300020, China
| | - Yue Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Heping District, Tianjin, 300020, China
| | - Di Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Heping District, Tianjin, 300020, China
| | - Jingwei Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Heping District, Tianjin, 300020, China
| | - Lingyue Zheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Heping District, Tianjin, 300020, China
| | - Haoze Song
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Heping District, Tianjin, 300020, China
| | - Xu Zhu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Heping District, Tianjin, 300020, China
| | - Qimei Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Heping District, Tianjin, 300020, China
| | - Yitong Zhao
- Haihe Laboratory of Cell Ecosystem, Tianjin Medical University, Tianjin, China
| | - Jing Liang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Heping District, Tianjin, 300020, China
| | - Jinfa Ma
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Heping District, Tianjin, 300020, China
| | - Jie Gao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Heping District, Tianjin, 300020, China
| | - Jingyuan Tong
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Heping District, Tianjin, 300020, China
| | - Lihong Shi
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Heping District, Tianjin, 300020, China.
- Tianjin Institutes of Health Science, Tianjin, 301600, China.
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Li J, Li Z, Yin J, Wang Y, Zheng D, Cai L, Wang GG. The sotos syndrome gene Nsd1 safeguards developmental gene enhancers poised for transcription by maintaining the precise deposition of histone methylation. J Biol Chem 2025; 301:108423. [PMID: 40118455 PMCID: PMC12033923 DOI: 10.1016/j.jbc.2025.108423] [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: 12/24/2024] [Revised: 02/27/2025] [Accepted: 03/13/2025] [Indexed: 03/23/2025] Open
Abstract
Germline haploinsufficiency of NSD1 is implicated as the etiology of Sotos syndrome; however, the underlying mechanism remains far from being clear. Here, we use mouse embryonic stem cell (mESC) differentiation as a model system to address this question. We found Nsd1 to be indispensable for the faithful differentiation of mESCs into three primary germ layers, particularly, meso-endodermal cell lineages related to the development of the heart and the skeletal system. Time-course transcriptomic profiling following the mESC differentiation revealed that Nsd1 not only facilitates the basal expression but also permits the differentiation-accompanied rapid induction of a suite of meso-endoderm lineage-specifying transcription factor genes such as T and Gata4. Mechanistically, Nsd1 directly occupies putative distal enhancers of the lineage transcription factor genes under the pluripotent cell state, where it deposits H3K36me2 to antagonize the excessive H3K27me3 and maintains the basal H3K27ac level, thereby safeguarding these gene enhancers at a primed state that responds readily to differentiation cues. In agreement, gene rescue assays using the Nsd1 KO mESCs showed that the H3K36me2 catalysis by Nsd1 requires several functional modules within Nsd1 (namely, PHD1-4, PWWP2, and SET) to a similar degree. Disruption of either one of these Nsd1 modules severely abrogated H3K36me2 in mESCs and significantly impaired appropriate induction of developmental genes upon mESC differentiation. Altogether, our study provides novel molecular insight into how the NSD1 perturbation derails normal development and causes the disease.
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Affiliation(s)
- Jie Li
- Division of Hematology and Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, New York, USA
| | - Zhucui Li
- Department of Biochemistry, Weill Cornell Medicine, Cornell University, New York, New York, USA
| | - Jiekai Yin
- Environmental Toxicology Graduate Program and Department of Chemistry, University of California Riverside, Riverside, California, USA
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program and Department of Chemistry, University of California Riverside, Riverside, California, USA
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA; Department of Neurology and Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Ling Cai
- Department of Pathology, Duke University School of Medicine, Durham, North Carolina, USA.
| | - Gang Greg Wang
- Department of Pathology, Duke University School of Medicine, Durham, North Carolina, USA; Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina, USA.
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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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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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