1
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Lin Y, Zheng J, Mai Z, Lin P, Lu Y, Cui L, Zhao X. Unveiling the veil of RNA binding protein phase separation in cancer biology and therapy. Cancer Lett 2024; 601:217160. [PMID: 39111384 DOI: 10.1016/j.canlet.2024.217160] [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: 05/31/2024] [Revised: 07/27/2024] [Accepted: 08/02/2024] [Indexed: 08/13/2024]
Abstract
RNA-binding protein (RBP) phase separation in oncology reveals a complex interplay crucial for understanding tumor biology and developing novel therapeutic strategies. Aberrant phase separation of RBPs significantly influences gene regulation, signal transduction, and metabolic reprogramming, contributing to tumorigenesis and drug resistance. Our review highlights the integral roles of RBP phase separation in stress granule dynamics, mRNA stabilization, and the modulation of transcriptional and translational processes. Furthermore, interactions between RBPs and non-coding RNAs add a layer of complexity, providing new insights into their collaborative roles in cancer progression. The intricate relationship between RBPs and phase separation poses significant challenges but also opens up novel opportunities for targeted therapeutic interventions. Advancing our understanding of the molecular mechanisms and regulatory networks governing RBP phase separation could lead to breakthroughs in cancer treatment strategies.
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Affiliation(s)
- Yunfan Lin
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, 510280, Guangdong, China
| | - Jiarong Zheng
- Department of Dentistry, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Zizhao Mai
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, 510280, Guangdong, China
| | - Pei Lin
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, 510280, Guangdong, China
| | - Ye Lu
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, 510280, Guangdong, China
| | - Li Cui
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, 510280, Guangdong, China; School of Dentistry, University of California, Los Angeles, Los Angeles, 90095, CA, USA.
| | - Xinyuan Zhao
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, 510280, Guangdong, China.
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2
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Conn VM, Chinnaiyan AM, Conn SJ. Circular RNA in cancer. Nat Rev Cancer 2024; 24:597-613. [PMID: 39075222 DOI: 10.1038/s41568-024-00721-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/13/2024] [Indexed: 07/31/2024]
Abstract
Over the past decade, circular RNA (circRNA) research has evolved into a bona fide research field shedding light on the functional consequence of this unique family of RNA molecules in cancer. Although the method of formation and the abundance of circRNAs can differ from their cognate linear mRNA, the spectrum of interacting partners and their resultant cellular functions in oncogenesis are analogous. However, with 10 times more diversity in circRNA variants compared with linear RNA variants, combined with their hyperstability in the cell, circRNAs are equipped to influence every stage of oncogenesis. This is an opportune time to address the breadth of circRNA in cancer focused on their spatiotemporal expression, mutations in biogenesis factors and contemporary functions through each stage of cancer. In this Review, we highlight examples of functional circRNAs in specific cancers, which satisfy critical criteria, including their physical co-association with the target and circRNA abundance at stoichiometrically valid quantities. These considerations are essential to develop strategies for the therapeutic exploitation of circRNAs as biomarkers and targeted anticancer agents.
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Affiliation(s)
- Vanessa M Conn
- Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, South Australia, Australia
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Urology, University of Michigan, Ann Arbor, MI, USA
| | - Simon J Conn
- Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, South Australia, Australia.
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3
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Brumbaugh-Reed EH, Gao Y, Aoki K, Toettcher JE. Rapid and reversible dissolution of biomolecular condensates using light-controlled recruitment of a solubility tag. Nat Commun 2024; 15:6717. [PMID: 39112465 PMCID: PMC11306331 DOI: 10.1038/s41467-024-50858-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 07/23/2024] [Indexed: 08/10/2024] Open
Abstract
Biomolecular condensates are broadly implicated in both normal cellular regulation and disease. Consequently, several chemical biology and optogenetic approaches have been developed to induce phase separation of a protein of interest. However, few tools are available to perform the converse function - dissolving a condensate of interest on demand. Such a tool would aid in testing whether the condensate plays specific functional roles. Here we show that light-gated recruitment of a solubilizing domain, maltose-binding protein (MBP), results in rapid and controlled dissolution of condensates formed from proteins of interest. Our optogenetic MBP-based dissolution strategy (OptoMBP) is rapid, reversible, and can be spatially controlled with subcellular precision. We also provide a proof-of-principle application of OptoMBP by disrupting condensation of the oncogenic fusion protein FUS-CHOP and reverting FUS-CHOP driven transcriptional changes. We envision that the OptoMBP system could be broadly useful for disrupting constitutive protein condensates to probe their biological functions.
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Affiliation(s)
- Ellen H Brumbaugh-Reed
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
- Omenn-Darling Bioengineering Institute, Princeton University, Princeton, NJ, 08544, USA
- International Research Collaboration Center (IRCC), National Institutes of Natural Sciences, Tokyo, 105-0001, Japan
| | - Yang Gao
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Kazuhiro Aoki
- International Research Collaboration Center (IRCC), National Institutes of Natural Sciences, Tokyo, 105-0001, Japan
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi, 444-8787, Japan
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi, 444-8787, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, 444-8787, Japan
- Laboratory of Cell Cycle Regulation Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto, 606-8315, Japan
| | - Jared E Toettcher
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA.
- Omenn-Darling Bioengineering Institute, Princeton University, Princeton, NJ, 08544, USA.
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4
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Zhang X, Yuan L, Zhang W, Zhang Y, Wu Q, Li C, Wu M, Huang Y. Liquid-liquid phase separation in diseases. MedComm (Beijing) 2024; 5:e640. [PMID: 39006762 PMCID: PMC11245632 DOI: 10.1002/mco2.640] [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: 12/25/2023] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 07/16/2024] Open
Abstract
Liquid-liquid phase separation (LLPS), an emerging biophysical phenomenon, can sequester molecules to implement physiological and pathological functions. LLPS implements the assembly of numerous membraneless chambers, including stress granules and P-bodies, containing RNA and protein. RNA-RNA and RNA-protein interactions play a critical role in LLPS. Scaffolding proteins, through multivalent interactions and external factors, support protein-RNA interaction networks to form condensates involved in a variety of diseases, particularly neurodegenerative diseases and cancer. Modulating LLPS phenomenon in multiple pathogenic proteins for the treatment of neurodegenerative diseases and cancer could present a promising direction, though recent advances in this area are limited. Here, we summarize in detail the complexity of LLPS in constructing signaling pathways and highlight the role of LLPS in neurodegenerative diseases and cancers. We also explore RNA modifications on LLPS to alter diseases progression because these modifications can influence LLPS of certain proteins or the formation of stress granules, and discuss the possibility of proper manipulation of LLPS process to restore cellular homeostasis or develop therapeutic drugs for the eradication of diseases. This review attempts to discuss potential therapeutic opportunities by elaborating on the connection between LLPS, RNA modification, and their roles in diseases.
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Affiliation(s)
- Xinyue Zhang
- College of Life and Health Sciences Northeastern University Shenyang China
| | - Lin Yuan
- Laboratory of Research in Parkinson's Disease and Related Disorders Health Sciences Institute China Medical University Shenyang China
| | - Wanlu Zhang
- College of Life and Health Sciences Northeastern University Shenyang China
| | - Yi Zhang
- College of Life and Health Sciences Northeastern University Shenyang China
| | - Qun Wu
- Department of Pediatrics Ruijin Hospital Affiliated to Shanghai Jiaotong University School of Medicine Shanghai China
| | - Chunting Li
- College of Life and Health Sciences Northeastern University Shenyang China
| | - Min Wu
- Wenzhou Institute University of Chinese Academy of Sciences Wenzhou Zhejiang China
- The Joint Research Center Affiliated Xiangshan Hospital of Wenzhou Medical University Ningbo China
| | - Yongye Huang
- College of Life and Health Sciences Northeastern University Shenyang China
- Key Laboratory of Bioresource Research and Development of Liaoning Province College of Life and Health Sciences Northeastern University Shenyang China
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5
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Gu Y, Wei K, Wang J. Phase separation and transcriptional regulation in cancer development. J Biomed Res 2024; 38:307-321. [PMID: 39113127 PMCID: PMC11300516 DOI: 10.7555/jbr.37.20230214] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/29/2023] [Accepted: 01/02/2024] [Indexed: 08/10/2024] Open
Abstract
Liquid-liquid phase separation, a novel biochemical phenomenon, has been increasingly studied for its medical applications. It underlies the formation of membrane-less organelles and is involved in many cellular and biological processes. During transcriptional regulation, dynamic condensates are formed through interactions between transcriptional elements, such as transcription factors, coactivators, and mediators. Cancer is a disease characterized by uncontrolled cell proliferation, but the precise mechanisms underlying tumorigenesis often remain to be elucidated. Emerging evidence has linked abnormal transcriptional condensates to several diseases, especially cancer, implying that phase separation plays an important role in tumorigenesis. Condensates formed by phase separation may have an effect on gene transcription in tumors. In the present review, we focus on the correlation between phase separation and transcriptional regulation, as well as how this phenomenon contributes to cancer development.
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Affiliation(s)
- Yan Gu
- Department of Thoracic Surgery, Jiangsu Province Hospital, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Ke Wei
- Department of Thoracic Surgery, Jiangsu Province Hospital, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Jun Wang
- Department of Thoracic Surgery, Jiangsu Province Hospital, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
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6
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Eustermann S, Patel AB, Hopfner KP, He Y, Korber P. Energy-driven genome regulation by ATP-dependent chromatin remodellers. Nat Rev Mol Cell Biol 2024; 25:309-332. [PMID: 38081975 DOI: 10.1038/s41580-023-00683-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2023] [Indexed: 03/28/2024]
Abstract
The packaging of DNA into chromatin in eukaryotes regulates gene transcription, DNA replication and DNA repair. ATP-dependent chromatin remodelling enzymes (re)arrange nucleosomes at the first level of chromatin organization. Their Snf2-type motor ATPases alter histone-DNA interactions through a common DNA translocation mechanism. Whether remodeller activities mainly catalyse nucleosome dynamics or accurately co-determine nucleosome organization remained unclear. In this Review, we discuss the emerging mechanisms of chromatin remodelling: dynamic remodeller architectures and their interactions, the inner workings of the ATPase cycle, allosteric regulation and pathological dysregulation. Recent mechanistic insights argue for a decisive role of remodellers in the energy-driven self-organization of chromatin, which enables both stability and plasticity of genome regulation - for example, during development and stress. Different remodellers, such as members of the SWI/SNF, ISWI, CHD and INO80 families, process (epi)genetic information through specific mechanisms into distinct functional outputs. Combinatorial assembly of remodellers and their interplay with histone modifications, histone variants, DNA sequence or DNA-bound transcription factors regulate nucleosome mobilization or eviction or histone exchange. Such input-output relationships determine specific nucleosome positions and compositions with distinct DNA accessibilities and mediate differential genome regulation. Finally, remodeller genes are often mutated in diseases characterized by genome dysregulation, notably in cancer, and we discuss their physiological relevance.
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Affiliation(s)
- Sebastian Eustermann
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Avinash B Patel
- Department of Molecular Biosciences, Robert H. Lurie Comprehensive Cancer Center, Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
| | - Karl-Peter Hopfner
- Gene Center and Department of Biochemistry, Faculty of Chemistry and Pharmacy, LMU Munich, Munich, Germany
| | - Yuan He
- Department of Molecular Biosciences, Robert H. Lurie Comprehensive Cancer Center, Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA.
| | - Philipp Korber
- Biomedical Center (BMC), Molecular Biology, Faculty of Medicine, LMU Munich, Martinsried, Germany.
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7
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Davis RB, Supakar A, Ranganath AK, Moosa MM, Banerjee PR. Heterotypic interactions can drive selective co-condensation of prion-like low-complexity domains of FET proteins and mammalian SWI/SNF complex. Nat Commun 2024; 15:1168. [PMID: 38326345 PMCID: PMC10850361 DOI: 10.1038/s41467-024-44945-5] [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: 04/12/2023] [Accepted: 01/08/2024] [Indexed: 02/09/2024] Open
Abstract
Prion-like domains (PLDs) are low-complexity protein sequences enriched within nucleic acid-binding proteins including those involved in transcription and RNA processing. PLDs of FUS and EWSR1 play key roles in recruiting chromatin remodeler mammalian SWI/SNF (mSWI/SNF) complex to oncogenic FET fusion protein condensates. Here, we show that disordered low-complexity domains of multiple SWI/SNF subunits are prion-like with a strong propensity to undergo intracellular phase separation. These PLDs engage in sequence-specific heterotypic interactions with the PLD of FUS in the dilute phase at sub-saturation conditions, leading to the formation of PLD co-condensates. In the dense phase, homotypic and heterotypic PLD interactions are highly cooperative, resulting in the co-mixing of individual PLD phases and forming spatially homogeneous condensates. Heterotypic PLD-mediated positive cooperativity in protein-protein interaction networks is likely to play key roles in the co-phase separation of mSWI/SNF complex with transcription factors containing homologous low-complexity domains.
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Affiliation(s)
- Richoo B Davis
- Department of Physics, University at Buffalo, Buffalo, NY, 14260, USA
| | - Anushka Supakar
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA
| | | | | | - Priya R Banerjee
- Department of Physics, University at Buffalo, Buffalo, NY, 14260, USA.
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA.
- Department of Chemical and Biological Engineering, University at Buffalo, Buffalo, NY, 14260, USA.
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8
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Brumbaugh-Reed EH, Aoki K, Toettcher JE. Rapid and reversible dissolution of biomolecular condensates using light-controlled recruitment of a solubility tag. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.16.575860. [PMID: 38293146 PMCID: PMC10827175 DOI: 10.1101/2024.01.16.575860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Biomolecular condensates are broadly implicated in both normal cellular regulation and disease. Consequently, several chemical biology and optogenetic approaches have been developed to induce phase separation of a protein of interest. However, few tools are available to perform the converse function-dissolving a condensate of interest on demand. Such a tool would aid in testing whether the condensate plays specific functional roles, a major question in cell biology and drug development. Here we report an optogenetic approach to selectively dissolve a condensate of interest in a reversible and spatially controlled manner. We show that light-gated recruitment of maltose-binding protein (MBP), a commonly used solubilizing domain in protein purification, results in rapid and controlled dissolution of condensates formed from proteins of interest. Our optogenetic MBP-based dissolution strategy (OptoMBP) is rapid, reversible, and can be spatially controlled with subcellular precision. We also provide a proof-of-principle application of OptoMBP, showing that disrupting condensation of the oncogenic fusion protein FUS-CHOP results in reversion of FUS-CHOP driven transcriptional changes. We envision that the OptoMBP system could be broadly useful for disrupting constitutive protein condensates to probe their biological functions.
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Affiliation(s)
- Ellen H Brumbaugh-Reed
- Department of Molecular Biology, Princeton University, Princeton NJ 08544
- Omenn-Darling Bioengineering Institute, Princeton University, Princeton NJ 08544
- International Research Collaboration Center (IRCC), National Institutes of Natural Sciences, Tokyo 105-0001, Japan
| | - Kazuhiro Aoki
- International Research Collaboration Center (IRCC), National Institutes of Natural Sciences, Tokyo 105-0001, Japan
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8787, Japan
- Laboratory of Cell Cycle Regulation, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto 606-8315, Japan
| | - Jared E Toettcher
- Department of Molecular Biology, Princeton University, Princeton NJ 08544
- Omenn-Darling Bioengineering Institute, Princeton University, Princeton NJ 08544
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9
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Liu J, Chen Y, Nong B, Luo X, Cui K, Li Z, Zhang P, Tan W, Yang Y, Ma W, Liang P, Songyang Z. CRISPR-assisted transcription activation by phase-separation proteins. Protein Cell 2023; 14:874-887. [PMID: 36905356 PMCID: PMC10691850 DOI: 10.1093/procel/pwad013] [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: 11/25/2022] [Accepted: 01/11/2023] [Indexed: 03/12/2023] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 system has been widely used for genome engineering and transcriptional regulation in many different organisms. Current CRISPR-activation (CRISPRa) platforms often require multiple components because of inefficient transcriptional activation. Here, we fused different phase-separation proteins to dCas9-VPR (dCas9-VP64-P65-RTA) and observed robust increases in transcriptional activation efficiency. Notably, human NUP98 (nucleoporin 98) and FUS (fused in sarcoma) IDR domains were best at enhancing dCas9-VPR activity, with dCas9-VPR-FUS IDR (VPRF) outperforming the other CRISPRa systems tested in this study in both activation efficiency and system simplicity. dCas9-VPRF overcomes the target strand bias and widens gRNA designing windows without affecting the off-target effect of dCas9-VPR. These findings demonstrate the feasibility of using phase-separation proteins to assist in the regulation of gene expression and support the broad appeal of the dCas9-VPRF system in basic and clinical applications.
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Affiliation(s)
- Jiaqi Liu
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yuxi Chen
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Baoting Nong
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
- Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
| | - Xiao Luo
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Kaixin Cui
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Zhan Li
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Pengfei Zhang
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | | | - Yue Yang
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Wenbin Ma
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Puping Liang
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Zhou Songyang
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
- Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
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10
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Thompson VF, Wieland DR, Mendoza-Leon V, Janis HI, Lay MA, Harrell LM, Schwartz JC. Binding of the nuclear ribonucleoprotein family member FUS to RNA prevents R-loop RNA:DNA hybrid structures. J Biol Chem 2023; 299:105237. [PMID: 37690693 PMCID: PMC10556777 DOI: 10.1016/j.jbc.2023.105237] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 08/17/2023] [Accepted: 08/25/2023] [Indexed: 09/12/2023] Open
Abstract
The protein FUS (FUSed in sarcoma) is a metazoan RNA-binding protein that influences RNA production by all three nuclear polymerases. FUS also binds nascent transcripts, RNA processing factors, RNA polymerases, and transcription machinery. Here, we explored the role of FUS binding interactions for activity during transcription. In vitro run-off transcription assays revealed FUS-enhanced RNA produced by a non-eukaryote polymerase. The activity also reduced the formation of R-loops between RNA products and their DNA template. Analysis by domain mutation and deletion indicated RNA-binding was required for activity. We interpret that FUS binds and sequesters nascent transcripts to prevent R-loops from forming with nearby DNA. DRIP-seq analysis showed that a knockdown of FUS increased R-loop enrichment near expressed genes. Prevention of R-loops by FUS binding to nascent transcripts has the potential to affect transcription by any RNA polymerase, highlighting the broad impact FUS can have on RNA metabolism in cells and disease.
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Affiliation(s)
- Valery F Thompson
- Department of Pharmacology, University of Arizona, Tucson, Arizona, USA; University of Arizona Cancer Center, Tucson, Arizona, USA
| | - Daniel R Wieland
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, USA
| | - Vivian Mendoza-Leon
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, USA
| | - Helen I Janis
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, USA
| | - Michelle A Lay
- Department of Pharmacology, University of Arizona, Tucson, Arizona, USA; University of Arizona Cancer Center, Tucson, Arizona, USA; Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, USA
| | - Lucas M Harrell
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, USA
| | - Jacob C Schwartz
- Department of Pharmacology, University of Arizona, Tucson, Arizona, USA; University of Arizona Cancer Center, Tucson, Arizona, USA.
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11
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Tripathi S, Shirnekhi HK, Gorman SD, Chandra B, Baggett DW, Park CG, Somjee R, Lang B, Hosseini SMH, Pioso BJ, Li Y, Iacobucci I, Gao Q, Edmonson MN, Rice SV, Zhou X, Bollinger J, Mitrea DM, White MR, McGrail DJ, Jarosz DF, Yi SS, Babu MM, Mullighan CG, Zhang J, Sahni N, Kriwacki RW. Defining the condensate landscape of fusion oncoproteins. Nat Commun 2023; 14:6008. [PMID: 37770423 PMCID: PMC10539325 DOI: 10.1038/s41467-023-41655-2] [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: 11/10/2022] [Accepted: 09/13/2023] [Indexed: 09/30/2023] Open
Abstract
Fusion oncoproteins (FOs) arise from chromosomal translocations in ~17% of cancers and are often oncogenic drivers. Although some FOs can promote oncogenesis by undergoing liquid-liquid phase separation (LLPS) to form aberrant biomolecular condensates, the generality of this phenomenon is unknown. We explored this question by testing 166 FOs in HeLa cells and found that 58% formed condensates. The condensate-forming FOs displayed physicochemical features distinct from those of condensate-negative FOs and segregated into distinct feature-based groups that aligned with their sub-cellular localization and biological function. Using Machine Learning, we developed a predictor of FO condensation behavior, and discovered that 67% of ~3000 additional FOs likely form condensates, with 35% of those predicted to function by altering gene expression. 47% of the predicted condensate-negative FOs were associated with cell signaling functions, suggesting a functional dichotomy between condensate-positive and -negative FOs. Our Datasets and reagents are rich resources to interrogate FO condensation in the future.
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Affiliation(s)
- Swarnendu Tripathi
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Hazheen K Shirnekhi
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Scott D Gorman
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Arrakis Therapeutics, 830 Winter St, Waltham, MA, 02451, USA
| | - Bappaditya Chandra
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - David W Baggett
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Cheon-Gil Park
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ramiz Somjee
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Rhodes College, Memphis, TN, USA
- Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO, 63110, USA
| | - Benjamin Lang
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Center of Excellence for Data-Driven Discovery, Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Seyed Mohammad Hadi Hosseini
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Center of Excellence for Data-Driven Discovery, Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Brittany J Pioso
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yongsheng Li
- Livestrong Cancer Institutes, Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Ilaria Iacobucci
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Qingsong Gao
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Michael N Edmonson
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Stephen V Rice
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Xin Zhou
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - John Bollinger
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Diana M Mitrea
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Dewpoint Therapeutics, 451 D Street, Suite 104, Boston, MA, 02210, USA
| | - Michael R White
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- IDEXX Laboratories, Inc., One IDEXX Drive, Westbrook, ME, 04092, USA
| | - Daniel J McGrail
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, OH, USA
- Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Daniel F Jarosz
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - S Stephen Yi
- Livestrong Cancer Institutes, Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, 78712, USA
- Department of Biomedical Engineering, and Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, TX, USA
| | - M Madan Babu
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Center of Excellence for Data-Driven Discovery, Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Nidhi Sahni
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA
| | - Richard W Kriwacki
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Sciences Center, Memphis, TN, USA.
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12
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Tanaka M, Nakamura T. Targeting epigenetic aberrations of sarcoma in CRISPR era. Genes Chromosomes Cancer 2023; 62:510-525. [PMID: 36967299 DOI: 10.1002/gcc.23142] [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: 02/09/2023] [Revised: 03/21/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023] Open
Abstract
Sarcomas are rare malignancies that exhibit diverse biological, genetic, morphological, and clinical characteristics. Genetic alterations, such as gene fusions, mutations in transcriptional machinery components, histones, and DNA methylation regulatory molecules, play an essential role in sarcomagenesis. These mutations induce and/or cooperate with specific epigenetic aberrations required for the growth and maintenance of sarcomas. Appropriate mouse models have been developed to clarify the significance of genetic and epigenetic interactions in sarcomas. Studies using the mouse models for human sarcomas have demonstrated major advances in our understanding the developmental processes as well as tumor microenvironment of sarcomas. Recent technological progresses in epigenome editing will not only improve the studies using animal models but also provide a direct clue for epigenetic therapies. In this manuscript, we review important epigenetic aberrations in sarcomas and their representative mouse models, current methods of epigenetic editing using CRISPR/dCas9 systems, and potential applications in sarcoma studies and therapeutics.
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Affiliation(s)
- Miwa Tanaka
- Project for Cancer Epigenomics, The Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
- Department of Experimental Pathology, Institute of Medical Science, Tokyo Medical University, Tokyo, Japan
| | - Takuro Nakamura
- Department of Experimental Pathology, Institute of Medical Science, Tokyo Medical University, Tokyo, Japan
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13
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Sun Z, Fan J, Dang Y, Zhao Y. Enhancer in cancer pathogenesis and treatment. Genet Mol Biol 2023; 46:e20220313. [PMID: 37548349 PMCID: PMC10405138 DOI: 10.1590/1678-4685-gmb-2022-0313] [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: 10/31/2022] [Accepted: 06/19/2023] [Indexed: 08/08/2023] Open
Abstract
Enhancers are essential cis-acting regulatory elements that determine cell identity and tumor progression. Enhancer function is dependent on the physical interaction between the enhancer and its target promoter inside its local chromatin environment. Enhancer reprogramming is an important mechanism in cancer pathogenesis and can be driven by both cis and trans factors. Super enhancers are acquired at oncogenes in numerous cancer types and represent potential targets for cancer treatment. BET and CDK inhibitors act through mechanisms of enhancer function and have shown promising results in therapy for various types of cancer. Genome editing is another way to reprogram enhancers in cancer treatment. The relationship between enhancers and cancer has been revised by several authors in the past few years, which mainly focuses on the mechanisms by which enhancers can impact cancer. Here, we emphasize SE's role in cancer pathogenesis and the new therapies involving epigenetic regulators (BETi and CDKi). We suggest that understanding mechanisms of activity would aid clinical success for these anti-cancer agents.
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Affiliation(s)
- Zhuo Sun
- Xi’an Medical University, Xi’an Key Laboratory of Pathogenic Microorganism and Tumor Immunity, Weiyang District, Xi’an, Shaanxi, China
- Institute of Basic Medical Sciences, No.1 XinWang Rd, Weiyang District, Shaanxi, China
| | - Jinbo Fan
- Xi’an Medical University, Xi’an Key Laboratory of Pathogenic Microorganism and Tumor Immunity, Weiyang District, Xi’an, Shaanxi, China
| | - Yixiong Dang
- Xi’an Medical University, School of Public Health, Weiyang District, Xi’an, 710021 Shaanxi, China
| | - Yufeng Zhao
- Institute of Basic Medical Sciences, No.1 XinWang Rd, Weiyang District, Shaanxi, China
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14
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Guo G, Wang X, Zhang Y, Li T. Sequence variations of phase-separating proteins and resources for studying biomolecular condensates. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1119-1132. [PMID: 37464880 PMCID: PMC10423696 DOI: 10.3724/abbs.2023131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 06/06/2023] [Indexed: 07/20/2023] Open
Abstract
Phase separation (PS) is an important mechanism underlying the formation of biomolecular condensates. Physiological condensates are associated with numerous biological processes, such as transcription, immunity, signaling, and synaptic transmission. Changes in particular amino acids or segments can disturb the protein's phase behavior and interactions with other biomolecules in condensates. It is thus presumed that variations in the phase-separating-prone domains can significantly impact the properties and functions of condensates. The dysfunction of condensates contributes to a number of pathological processes. Pharmacological perturbation of these condensates is proposed as a promising way to restore physiological states. In this review, we characterize the variations observed in PS proteins that lead to aberrant biomolecular compartmentalization. We also showcase recent advancements in bioinformatics of membraneless organelles (MLOs), focusing on available databases useful for screening PS proteins and describing endogenous condensates, guiding researchers to seek the underlying pathogenic mechanisms of biomolecular condensates.
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Affiliation(s)
- Gaigai Guo
- Department of Biomedical InformaticsSchool of Basic Medical SciencesPeking University Health Science CenterBeijing100191China
| | - Xinxin Wang
- Department of Biomedical InformaticsSchool of Basic Medical SciencesPeking University Health Science CenterBeijing100191China
| | - Yi Zhang
- Department of Biomedical InformaticsSchool of Basic Medical SciencesPeking University Health Science CenterBeijing100191China
| | - Tingting Li
- Department of Biomedical InformaticsSchool of Basic Medical SciencesPeking University Health Science CenterBeijing100191China
- Key Laboratory for NeuroscienceMinistry of Education/National Health Commission of ChinaPeking UniversityBeijing100191China
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15
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Yoshida SR, Maity BK, Chong S. Visualizing Protein Localizations in Fixed Cells: Caveats and the Underlying Mechanisms. J Phys Chem B 2023; 127:4165-4173. [PMID: 37161904 DOI: 10.1021/acs.jpcb.3c01658] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Fluorescence microscopy techniques have been widely adopted in biology for their ability to visualize the structure and dynamics of a wide range of cellular and subcellular processes. The specificity and sensitivity that these techniques afford have made them primary tools in the characterization of protein localizations within cells. Many of the fluorescence microscopy techniques require cells to be fixed via chemical or alternative methods before being imaged. However, some fixation methods have been found to induce the redistribution of particular proteins in the cell, resulting in artifacts in the characterization of protein localizations and functions under physiological conditions. Here, we review the ability of commonly used cell fixation methods to faithfully preserve the localizations of proteins that bind to chromatin, undergo liquid-liquid phase separation (LLPS), and are involved in the formation of various membrane-bound organelles. We also review the mechanisms underlying various fixation artifacts and discuss potential alternative fixation methods to minimize the artifacts while investigating different proteins and cellular structures. Overall, fixed-cell fluorescence microscopy is a very powerful tool in biomedical research; however, each experiment demands the careful selection of an appropriate fixation method to avoid potential artifacts and may benefit from live-cell imaging validation.
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Affiliation(s)
- Shawn R Yoshida
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Barun K Maity
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Shasha Chong
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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16
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Di Giorgio E, Benetti R, Kerschbamer E, Xodo L, Brancolini C. Super-enhancer landscape rewiring in cancer: The epigenetic control at distal sites. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2023; 380:97-148. [PMID: 37657861 DOI: 10.1016/bs.ircmb.2023.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/03/2023]
Abstract
Super-enhancers evolve as elements at the top of the hierarchical control of gene expression. They are important end-gatherers of signaling pathways that control stemness, differentiation or adaptive responses. Many epigenetic regulations focus on these regions, and not surprisingly, during the process of tumorigenesis, various alterations can account for their dysfunction. Super-enhancers are emerging as key drivers of the aberrant gene expression landscape that sustain the aggressiveness of cancer cells. In this review, we will describe and discuss about the structure of super-enhancers, their epigenetic regulation, and the major changes affecting their functionality in cancer.
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Affiliation(s)
- Eros Di Giorgio
- Laboratory of Biochemistry, Department of Medicine, Università degli Studi di Udine, Udine, Italy
| | - Roberta Benetti
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, Udine, Italy
| | - Emanuela Kerschbamer
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, Udine, Italy
| | - Luigi Xodo
- Laboratory of Biochemistry, Department of Medicine, Università degli Studi di Udine, Udine, Italy
| | - Claudio Brancolini
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, Udine, Italy.
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17
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Niu X, Zhang L, Wu Y, Zong Z, Wang B, Liu J, Zhang L, Zhou F. Biomolecular condensates: Formation mechanisms, biological functions, and therapeutic targets. MedComm (Beijing) 2023; 4:e223. [PMID: 36875159 PMCID: PMC9974629 DOI: 10.1002/mco2.223] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 01/20/2023] [Accepted: 02/02/2023] [Indexed: 03/06/2023] Open
Abstract
Biomolecular condensates are cellular structures composed of membraneless assemblies comprising proteins or nucleic acids. The formation of these condensates requires components to change from a state of solubility separation from the surrounding environment by undergoing phase transition and condensation. Over the past decade, it has become widely appreciated that biomolecular condensates are ubiquitous in eukaryotic cells and play a vital role in physiological and pathological processes. These condensates may provide promising targets for the clinic research. Recently, a series of pathological and physiological processes have been found associated with the dysfunction of condensates, and a range of targets and methods have been demonstrated to modulate the formation of these condensates. A more extensive description of biomolecular condensates is urgently needed for the development of novel therapies. In this review, we summarized the current understanding of biomolecular condensates and the molecular mechanisms of their formation. Moreover, we reviewed the functions of condensates and therapeutic targets for diseases. We further highlighted the available regulatory targets and methods, discussed the significance and challenges of targeting these condensates. Reviewing the latest developments in biomolecular condensate research could be essential in translating our current knowledge on the use of condensates for clinical therapeutic strategies.
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Affiliation(s)
- Xin Niu
- Department of Otolaryngology Head and Neck Surgery The First Affiliated Hospital of Soochow University Suzhou China.,MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network Life Sciences Institute Zhejiang University Hangzhou China
| | - Lei Zhang
- Department of Orthopedics The First Affiliated Hospital of Wenzhou Medical University Wenzhou China
| | - Yuchen Wu
- Department of Clinical Medicine, The First School of Medicine Wenzhou Medical University Wenzhou China
| | - Zhi Zong
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network Life Sciences Institute Zhejiang University Hangzhou China
| | - Bin Wang
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network Life Sciences Institute Zhejiang University Hangzhou China
| | - Jisheng Liu
- Department of Otolaryngology Head and Neck Surgery The First Affiliated Hospital of Soochow University Suzhou China
| | - Long Zhang
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network Life Sciences Institute Zhejiang University Hangzhou China
| | - Fangfang Zhou
- Institutes of Biology and Medical Science Soochow University Suzhou China
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18
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Krainer G, Saar KL, Arter WE, Welsh TJ, Czekalska MA, Jacquat RPB, Peter Q, Traberg WC, Pujari A, Jayaram AK, Challa P, Taylor CG, van der Linden LM, Franzmann T, Owens RM, Alberti S, Klenerman D, Knowles TPJ. Direct digital sensing of protein biomarkers in solution. Nat Commun 2023; 14:653. [PMID: 36746944 PMCID: PMC9902533 DOI: 10.1038/s41467-023-35792-x] [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: 06/12/2020] [Accepted: 01/03/2023] [Indexed: 02/08/2023] Open
Abstract
The detection of proteins is of central importance to biomolecular analysis and diagnostics. Typical immunosensing assays rely on surface-capture of target molecules, but this constraint can limit specificity, sensitivity, and the ability to obtain information beyond simple concentration measurements. Here we present a surface-free, single-molecule microfluidic sensing platform for direct digital protein biomarker detection in solution, termed digital immunosensor assay (DigitISA). DigitISA is based on microchip electrophoretic separation combined with single-molecule detection and enables absolute number/concentration quantification of proteins in a single, solution-phase step. Applying DigitISA to a range of targets including amyloid aggregates, exosomes, and biomolecular condensates, we demonstrate that the assay provides information beyond stoichiometric interactions, and enables characterization of immunochemistry, binding affinity, and protein biomarker abundance. Taken together, our results suggest a experimental paradigm for the sensing of protein biomarkers, which enables analyses of targets that are challenging to address using conventional immunosensing approaches.
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Affiliation(s)
- Georg Krainer
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Kadi L Saar
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - William E Arter
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Timothy J Welsh
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Magdalena A Czekalska
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.,Fluidic Analytics Limited, Unit A The Paddocks Business Centre, Cherry Hinton Road, Cambridge, CB1 8DH, UK
| | - Raphaël P B Jacquat
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Quentin Peter
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Walther C Traberg
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
| | - Arvind Pujari
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.,Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
| | - Akhila K Jayaram
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Pavankumar Challa
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Christopher G Taylor
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Lize-Mari van der Linden
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Tatzberg 47/49, Dresden, Germany
| | - Titus Franzmann
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Tatzberg 47/49, Dresden, Germany
| | - Roisin M Owens
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
| | - Simon Alberti
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Tatzberg 47/49, Dresden, Germany
| | - David Klenerman
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Tuomas P J Knowles
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK. .,Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Ave, Cambridge, CB3 0HE, UK.
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19
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Li W, Jiang H. Analysis of Phase-Separated Biomolecular Condensates in Cancer. Methods Mol Biol 2023; 2660:345-356. [PMID: 37191808 DOI: 10.1007/978-1-0716-3163-8_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Phase-separated biomolecular condensates play important roles in virtually all cellular processes, and their dysregulation is associated with many pathological processes including cancer. Here we concisely review some basic methodologies and strategies to analyze the phase-separated biomolecular condensates in cancer, including physical characterization of phase separation for the protein of interest, functional demonstration of this property in cancer regulation, as well as mechanistic studies on how phase separation regulates the protein's function in cancer.
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Affiliation(s)
- Wei Li
- Hunan Provincial Key Laboratory of Medical Virology, College of Biology, Hunan University, Changsha, Hunan, China
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Hao Jiang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA.
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20
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Luo Y, Xiang S, Feng J. Protein Phase Separation: New Insights into Carcinogenesis. Cancers (Basel) 2022; 14:cancers14235971. [PMID: 36497453 PMCID: PMC9740862 DOI: 10.3390/cancers14235971] [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: 11/06/2022] [Revised: 11/29/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
Phase separation is now acknowledged as an essential biologic mechanism wherein distinct activated molecules assemble into a different phase from the surrounding constituents of a cell. Condensates formed by phase separation play an essential role in the life activities of various organisms under normal physiological conditions, including the advanced structure and regulation of chromatin, autophagic degradation of incorrectly folded or unneeded proteins, and regulation of the actin cytoskeleton. During malignant transformation, abnormally altered condensate assemblies are often associated with the abnormal activation of oncogenes or inactivation of tumor suppressors, resulting in the promotion of the carcinogenic process. Thus, understanding the role of phase separation in various biological evolutionary processes will provide new ideas for the development of drugs targeting specific condensates, which is expected to be an effective cancer therapy strategy. However, the relationship between phase separation and cancer has not been fully elucidated. In this review, we mainly summarize the main processes and characteristics of phase separation and the main methods for detecting phase separation. In addition, we summarize the cancer proteins and signaling pathways involved in phase separation and discuss their promising future applications in addressing the unmet clinical therapeutic needs of people with cancer. Finally, we explain the means of targeted phase separation and cancer treatment.
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21
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Ren J, Zhang Z, Zong Z, Zhang L, Zhou F. Emerging Implications of Phase Separation in Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2202855. [PMID: 36117111 PMCID: PMC9631093 DOI: 10.1002/advs.202202855] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 08/26/2022] [Indexed: 05/19/2023]
Abstract
In eukaryotic cells, biological activities are executed in distinct cellular compartments or organelles. Canonical organelles with membrane-bound structures are well understood. Cells also inherently contain versatile membrane-less organelles (MLOs) that feature liquid or gel-like bodies. A biophysical process termed liquid-liquid phase separation (LLPS) elucidates how MLOs form through dynamic biomolecule assembly. LLPS-related molecules often have multivalency, which is essential for low-affinity inter- or intra-molecule interactions to trigger phase separation. Accumulating evidence shows that LLPS concentrates and organizes desired molecules or segregates unneeded molecules in cells. Thus, MLOs have tunable functional specificity in response to environmental stimuli and metabolic processes. Aberrant LLPS is widely associated with several hallmarks of cancer, including sustained proliferative signaling, growth suppressor evasion, cell death resistance, telomere maintenance, DNA damage repair, etc. Insights into the molecular mechanisms of LLPS provide new insights into cancer therapeutics. Here, the current understanding of the emerging concepts of LLPS and its involvement in cancer are comprehensively reviewed.
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Affiliation(s)
- Jiang Ren
- School of MedicineZhejiang University City CollegeHangzhou215123China
- The Eighth Affiliated HospitalSun Yat‐sen UniversityShenzhen518033China
| | - Zhenyu Zhang
- Department of NeurosurgeryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouHenan450003China
| | - Zhi Zong
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling NetworkLife Sciences InstituteZhejiang UniversityHangzhou310058China
| | - Long Zhang
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling NetworkLife Sciences InstituteZhejiang UniversityHangzhou310058China
- International Biomed‐X Research Center, Second Affiliated Hospital of Zhejiang University School of MedicineZhejiang UniversityHangzhouChina
- Cancer CenterZhejiang UniversityHangzhou215123China
| | - Fangfang Zhou
- School of MedicineZhejiang University City CollegeHangzhou215123China
- Institutes of Biology and Medical SciencesSoochow UniversitySuzhou215123China
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22
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Conti BA, Oppikofer M. Biomolecular condensates: new opportunities for drug discovery and RNA therapeutics. Trends Pharmacol Sci 2022; 43:820-837. [PMID: 36028355 DOI: 10.1016/j.tips.2022.07.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 07/15/2022] [Accepted: 07/22/2022] [Indexed: 11/18/2022]
Abstract
Biomolecular condensates organize cellular functions in the absence of membranes. These membraneless organelles can form through liquid-liquid phase separation coalescing RNA and proteins into well-defined, yet dynamic, structures distinct from the surrounding cellular milieu. Numerous physiological and disease-causing processes link to biomolecular condensates, which could impact drug discovery in several ways. First, disruption of pathological condensates seeded by mutated proteins or RNAs may provide new opportunities to treat disease. Second, condensates may be leveraged to tackle difficult-to-drug targets lacking binding pockets whose function depends on phase separation. Third, condensate-resident small molecules and RNA therapeutics may display unexpected pharmacology. We discuss the potential impact of phase separation on drug discovery and RNA therapeutics, leveraging concrete examples, towards novel clinical opportunities.
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Affiliation(s)
- Brooke A Conti
- Pfizer Centers for Therapeutic Innovation, Pfizer Inc., New York, NY, USA
| | - Mariano Oppikofer
- Pfizer Centers for Therapeutic Innovation, Pfizer Inc., New York, NY, USA.
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23
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Davis RB, Moosa MM, Banerjee PR. Ectopic biomolecular phase transitions: fusion proteins in cancer pathologies. Trends Cell Biol 2022; 32:681-695. [PMID: 35484036 PMCID: PMC9288518 DOI: 10.1016/j.tcb.2022.03.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/13/2022] [Accepted: 03/18/2022] [Indexed: 12/22/2022]
Abstract
Biomolecular condensates are membraneless organelles (MLOs) that are enriched in specific proteins and nucleic acids, compartmentalized to perform biochemical functions. Such condensates are formed by phase separation (PS) enabled by protein domains that allow multivalent interactions. Chromosomal translocation-derived in-frame gene fusions often generate proteins with non-native domain combinations that rewire protein-protein interaction networks. Several recent studies have shown that, for a subset of these fusion proteins, pathogenesis can be driven by the ability of the fusion protein to undergo phase transitions at non-physiological cellular locations to form ectopic condensates. We highlight how such ectopic phase transitions can alter biological processes and posit that dysfunction via protein PS at non-physiological locations represents a generic route to oncogenic transformation.
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Affiliation(s)
- Richoo B Davis
- Department of Physics, State University of New York (SUNY) at Buffalo, Buffalo, NY 14260, USA
| | - Mahdi Muhammad Moosa
- Department of Physics, State University of New York (SUNY) at Buffalo, Buffalo, NY 14260, USA.
| | - Priya R Banerjee
- Department of Physics, State University of New York (SUNY) at Buffalo, Buffalo, NY 14260, USA.
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24
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Quiroga IY, Ahn JH, Wang GG, Phanstiel D. Oncogenic fusion proteins and their role in three-dimensional chromatin structure, phase separation, and cancer. Curr Opin Genet Dev 2022; 74:101901. [PMID: 35427897 PMCID: PMC9156545 DOI: 10.1016/j.gde.2022.101901] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/17/2022] [Accepted: 03/05/2022] [Indexed: 11/27/2022]
Abstract
Three-dimensional (3D) chromatin structure plays a critical role in development, gene regulation, and cellular identity. Alterations to this structure can have profound effects on cellular phenotypes and have been associated with a variety of diseases including multiple types of cancer. One of several forces that help shape 3D chromatin structure is liquid-liquid phase separation, a form of self-association between biomolecules that can sequester regions of chromatin into subnuclear droplets or even membraneless organelles like nucleoli. This review focuses on a class of oncogenic fusion proteins that appear to exert their oncogenic function via phase-separation-driven alterations to 3D chromatin structure. Here, we review what is known about the mechanisms by which these oncogenic fusion proteins phase separate in the nucleus and their role in shaping the 3D chromatin structure. We discuss the potential for this phenomenon to be a more widespread mechanism of oncogenesis.
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Affiliation(s)
- Ivana Y Quiroga
- Thurston Arthritis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jeong Hyun Ahn
- 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.
| | - Douglas Phanstiel
- Thurston Arthritis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA; Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
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25
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Lindén M, Vannas C, Österlund T, Andersson L, Osman A, Escobar M, Fagman H, Ståhlberg A, Åman P. FET fusion oncoproteins interact with BRD4 and SWI/SNF chromatin remodeling complex subtypes in sarcoma. Mol Oncol 2022; 16:2470-2495. [PMID: 35182012 PMCID: PMC9251840 DOI: 10.1002/1878-0261.13195] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 11/25/2021] [Accepted: 02/17/2022] [Indexed: 11/24/2022] Open
Abstract
FET fusion oncoproteins containing one of the FET (FUS, EWSR1, TAF15) family proteins juxtaposed to alternative transcription‐factor partners are characteristic of more than 20 types of sarcoma and leukaemia. FET oncoproteins bind to the SWI/SNF chromatin remodelling complex, which exists in three subtypes: cBAF, PBAF and GBAF/ncBAF. We used comprehensive biochemical analysis to characterize the interactions between FET oncoproteins, SWI/SNF complexes and the transcriptional coactivator BRD4. Here, we report that FET oncoproteins bind all three main SWI/SNF subtypes cBAF, PBAF and GBAF, and that FET oncoproteins interact indirectly with BRD4 via their shared interaction partner SWI/SNF. Furthermore, chromatin immunoprecipitation sequencing and proteomic analysis showed that FET oncoproteins, SWI/SNF components and BRD4 co‐localize on chromatin and interact with mediator and RNA Polymerase II. Our results provide a possible molecular mechanism for the FET‐fusion‐induced oncogenic transcriptional profiles and may lead to novel therapies targeting aberrant SWI/SNF complexes and/or BRD4 in FET‐fusion‐caused malignancies.
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Affiliation(s)
- Malin Lindén
- Sahlgrenska Center for Cancer Research, Institute of Biomedicine, Department of Laboratory Medicine, Sahlgrenska Academy, University of Gothenburg, Box 425, 40530, Gothenburg, Sweden
| | - Christoffer Vannas
- Sahlgrenska Center for Cancer Research, Institute of Biomedicine, Department of Laboratory Medicine, Sahlgrenska Academy, University of Gothenburg, Box 425, 40530, Gothenburg, Sweden
| | - Tobias Österlund
- Sahlgrenska Center for Cancer Research, Institute of Biomedicine, Department of Laboratory Medicine, Sahlgrenska Academy, University of Gothenburg, Box 425, 40530, Gothenburg, Sweden.,Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Sweden
| | - Lisa Andersson
- Sahlgrenska Center for Cancer Research, Institute of Biomedicine, Department of Laboratory Medicine, Sahlgrenska Academy, University of Gothenburg, Box 425, 40530, Gothenburg, Sweden
| | - Ayman Osman
- Sahlgrenska Center for Cancer Research, Institute of Biomedicine, Department of Laboratory Medicine, Sahlgrenska Academy, University of Gothenburg, Box 425, 40530, Gothenburg, Sweden
| | - Mandy Escobar
- Sahlgrenska Center for Cancer Research, Institute of Biomedicine, Department of Laboratory Medicine, Sahlgrenska Academy, University of Gothenburg, Box 425, 40530, Gothenburg, Sweden
| | - Henrik Fagman
- Sahlgrenska Center for Cancer Research, Institute of Biomedicine, Department of Laboratory Medicine, Sahlgrenska Academy, University of Gothenburg, Box 425, 40530, Gothenburg, Sweden
| | - Anders Ståhlberg
- Sahlgrenska Center for Cancer Research, Institute of Biomedicine, Department of Laboratory Medicine, Sahlgrenska Academy, University of Gothenburg, Box 425, 40530, Gothenburg, Sweden.,Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Sweden.,Region Västra Götaland, Sahlgrenska University Hospital, Department of Clinical Genetics and Genomics, Gothenburg, Sweden
| | - Pierre Åman
- Sahlgrenska Center for Cancer Research, Institute of Biomedicine, Department of Laboratory Medicine, Sahlgrenska Academy, University of Gothenburg, Box 425, 40530, Gothenburg, Sweden
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Irgen-Gioro S, Yoshida S, Walling V, Chong S. Fixation can change the appearance of phase separation in living cells. eLife 2022; 11:79903. [PMID: 36444977 PMCID: PMC9817179 DOI: 10.7554/elife.79903] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 11/28/2022] [Indexed: 11/30/2022] Open
Abstract
Fixing cells with paraformaldehyde (PFA) is an essential step in numerous biological techniques as it is thought to preserve a snapshot of biomolecular transactions in living cells. Fixed-cell imaging techniques such as immunofluorescence have been widely used to detect liquid-liquid phase separation (LLPS) in vivo. Here, we compared images, before and after fixation, of cells expressing intrinsically disordered proteins that are able to undergo LLPS. Surprisingly, we found that PFA fixation can both enhance and diminish putative LLPS behaviors. For specific proteins, fixation can even cause their droplet-like puncta to artificially appear in cells that do not have any detectable puncta in the live condition. Fixing cells in the presence of glycine, a molecule that modulates fixation rates, can reverse the fixation effect from enhancing to diminishing LLPS appearance. We further established a kinetic model of fixation in the context of dynamic protein-protein interactions. Simulations based on the model suggest that protein localization in fixed cells depends on an intricate balance of protein-protein interaction dynamics, the overall rate of fixation, and notably, the difference between fixation rates of different proteins. Consistent with simulations, live-cell single-molecule imaging experiments showed that a fast overall rate of fixation relative to protein-protein interaction dynamics can minimize fixation artifacts. Our work reveals that PFA fixation changes the appearance of LLPS from living cells, presents a caveat in studying LLPS using fixation-based methods, and suggests a mechanism underlying the fixation artifact.
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Affiliation(s)
- Shawn Irgen-Gioro
- Division of Chemistry and Chemical Engineering, California Institute of TechnologyPasadenaUnited States
| | - Shawn Yoshida
- Division of Chemistry and Chemical Engineering, California Institute of TechnologyPasadenaUnited States,Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Victoria Walling
- Division of Chemistry and Chemical Engineering, California Institute of TechnologyPasadenaUnited States
| | - Shasha Chong
- Division of Chemistry and Chemical Engineering, California Institute of TechnologyPasadenaUnited States
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First person – Izzy Owen. J Cell Sci 2021. [DOI: 10.1242/jcs.259298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
ABSTRACT
First Person is a series of interviews with the first authors of a selection of papers published in Journal of Cell Science, helping early-career researchers promote themselves alongside their papers. Izzy Owen is first author on ‘ The oncogenic transcription factor FUS-CHOP can undergo nuclear liquid–liquid phase separation’, published in JCS. Izzy is a PhD student in the lab of Frank Shewmaker at Uniformed Services University of the Health Sciences, Bethesda, USA, where her research interests involve understanding protein phase separation at the molecular and functional levels in disease.
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