1
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Huang Y, Xia P. Biomolecular condensates in plant cells: Mediating and integrating environmental signals and development. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 347:112178. [PMID: 38971467 DOI: 10.1016/j.plantsci.2024.112178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 06/23/2024] [Accepted: 06/30/2024] [Indexed: 07/08/2024]
Abstract
In response to the spatiotemporal coordination of various biochemical reactions and membrane-encapsulated organelles, plants appear to provide another effective mechanism for cellular organization by phase separation that allows the internal compartmentalization of cells to form a variety of membrane-less organelles. Most of the research on phase separation has centralized in various non-plant systems, such as yeast and animal systems. Recent studies have shown a remarkable correlation between the formation of condensates in plant systems and the formation of condensates in these systems. Moreover, the last decade has made new advances in phase separation research in the context of plant biology. Here, we provide an overview of the physicochemical forces and molecular factors that drive liquid-liquid phase separation in plant cells and the biochemical characterization of condensates. We then explore new developments in phase separation research specific to plants, discussing examples of condensates found in green plants and detailing their role in plant growth and development. We propose that phase separation may be a conserved organizational mechanism in plant evolution to help plants respond rapidly and effectively to various environmental stresses as sessile organisms.
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Affiliation(s)
- Yang Huang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Pengguo Xia
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China.
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2
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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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3
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Ziaunys M, Sulskis D, Veiveris D, Kopustas A, Snieckute R, Mikalauskaite K, Sakalauskas A, Tutkus M, Smirnovas V. Liquid-liquid phase separation of alpha-synuclein increases the structural variability of fibrils formed during amyloid aggregation. FEBS J 2024. [PMID: 39116032 DOI: 10.1111/febs.17244] [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: 02/02/2024] [Revised: 04/25/2024] [Accepted: 07/25/2024] [Indexed: 08/10/2024]
Abstract
Protein liquid-liquid phase separation (LLPS) is a rapidly emerging field of study on biomolecular condensate formation. In recent years, this phenomenon has been implicated in the process of amyloid fibril formation, serving as an intermediate step between the native protein transition into their aggregated state. The formation of fibrils via LLPS has been demonstrated for a number of proteins related to neurodegenerative disorders, as well as other amyloidoses. Despite the surge in amyloid-related LLPS studies, the influence of protein condensate formation on the end-point fibril characteristics is still far from fully understood. In this work, we compare alpha-synuclein aggregation under different conditions, which promote or negate its LLPS and examine the differences between the formed aggregates. We show that alpha-synuclein phase separation generates a wide variety of assemblies with distinct secondary structures and morphologies. The LLPS-induced structures also possess higher levels of toxicity to cells, indicating that biomolecular condensate formation may be a critical step in the appearance of disease-related fibril variants.
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Affiliation(s)
- Mantas Ziaunys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Lithuania
| | - Darius Sulskis
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Lithuania
| | - Dominykas Veiveris
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Lithuania
| | - Aurimas Kopustas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Lithuania
- Department of Molecular Compound Physics, Center for Physical Sciences and Technology, Vilnius, Lithuania
| | - Ruta Snieckute
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Lithuania
| | | | - Andrius Sakalauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Lithuania
| | - Marijonas Tutkus
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Lithuania
- Department of Molecular Compound Physics, Center for Physical Sciences and Technology, Vilnius, Lithuania
| | - Vytautas Smirnovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Lithuania
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4
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Kim YR, Joo J, Lee HJ, Kim C, Park JC, Yu YS, Kim CR, Lee DH, Cha J, Kwon H, Hanssen KM, Grünewald TGP, Choi M, Han I, Bae S, Jung I, Shin Y, Baek SH. Prion-like domain mediated phase separation of ARID1A promotes oncogenic potential of Ewing's sarcoma. Nat Commun 2024; 15:6569. [PMID: 39095374 PMCID: PMC11297139 DOI: 10.1038/s41467-024-51050-0] [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: 04/09/2024] [Accepted: 07/26/2024] [Indexed: 08/04/2024] Open
Abstract
Liquid-liquid phase separation (LLPS) facilitates the formation of membraneless organelles within cells, with implications in various biological processes and disease states. AT-rich interactive domain-containing protein 1A (ARID1A) is a chromatin remodeling factor frequently associated with cancer mutations, yet its functional mechanism remains largely unknown. Here, we find that ARID1A harbors a prion-like domain (PrLD), which facilitates the formation of liquid condensates through PrLD-mediated LLPS. The nuclear condensates formed by ARID1A LLPS are significantly elevated in Ewing's sarcoma patient specimen. Disruption of ARID1A LLPS results in diminished proliferative and invasive abilities in Ewing's sarcoma cells. Through genome-wide chromatin structure and transcription profiling, we identify that the ARID1A condensate localizes to EWS/FLI1 target enhancers and induces long-range chromatin architectural changes by forming functional chromatin remodeling hubs at oncogenic target genes. Collectively, our findings demonstrate that ARID1A promotes oncogenic potential through PrLD-mediated LLPS, offering a potential therapeutic approach for treating Ewing's sarcoma.
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Affiliation(s)
- Yong Ryoul Kim
- Creative Research Initiatives Center for Epigenetic Code and Diseases, School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Jaegeon Joo
- Department of Biological Sciences, Korea Advanced Institute of Science & Technology, Daejeon, South Korea
| | - Hee Jung Lee
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, South Korea
| | - Chaelim Kim
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, South Korea
| | - Ju-Chan Park
- Research Center of Genomic Medicine Institute, Seoul National University College of Medicine, Seoul, South Korea
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, South Korea
| | - Young Suk Yu
- Creative Research Initiatives Center for Epigenetic Code and Diseases, School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Chang Rok Kim
- Creative Research Initiatives Center for Epigenetic Code and Diseases, School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Do Hui Lee
- Creative Research Initiatives Center for Epigenetic Code and Diseases, School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Joowon Cha
- Creative Research Initiatives Center for Epigenetic Code and Diseases, School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Hyemin Kwon
- Creative Research Initiatives Center for Epigenetic Code and Diseases, School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Kimberley M Hanssen
- Hopp-Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, (A Partnership) Between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
| | - Thomas G P Grünewald
- Hopp-Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, (A Partnership) Between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Murim Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Ilkyu Han
- Department of Orthopaedic Surgery, Seoul National University College of Medicine, Seoul, South Korea
| | - Sangsu Bae
- Research Center of Genomic Medicine Institute, Seoul National University College of Medicine, Seoul, South Korea
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, South Korea
| | - Inkyung Jung
- Department of Biological Sciences, Korea Advanced Institute of Science & Technology, Daejeon, South Korea.
| | - Yongdae Shin
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, South Korea.
- Department of Mechanical Engineering, Seoul National University, Seoul, South Korea.
| | - Sung Hee Baek
- Creative Research Initiatives Center for Epigenetic Code and Diseases, School of Biological Sciences, Seoul National University, Seoul, South Korea.
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5
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Shan L, Wang W, Du L, Li D, Wang Y, Xie Y, Li H, Wang J, Shi Z, Zhou Y, Zhu D, Sui G, Liu F. SP1 undergoes phase separation and activates RGS20 expression through super-enhancers to promote lung adenocarcinoma progression. Proc Natl Acad Sci U S A 2024; 121:e2401834121. [PMID: 38976739 PMCID: PMC11260144 DOI: 10.1073/pnas.2401834121] [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: 01/28/2024] [Accepted: 05/28/2024] [Indexed: 07/10/2024] Open
Abstract
Lung adenocarcinoma (LUAD) is the leading cause of cancer-related death worldwide, but the underlying molecular mechanisms remain largely unclear. The transcription factor (TF) specificity protein 1 (SP1) plays a crucial role in the development of various cancers, including LUAD. Recent studies have indicated that master TFs may form phase-separated macromolecular condensates to promote super-enhancer (SE) assembly and oncogene expression. In this study, we demonstrated that SP1 undergoes phase separation and that its zinc finger 3 in the DNA-binding domain is essential for this process. Through Cleavage Under Targets & Release Using Nuclease (CUT&RUN) using antibodies against SP1 and H3K27ac, we found a significant correlation between SP1 enrichment and SE elements, identified the regulator of the G protein signaling 20 (RGS20) gene as the most likely target regulated by SP1 through SE mechanisms, and verified this finding using different approaches. The oncogenic activity of SP1 relies on its phase separation ability and RGS20 gene activation, which can be abolished by glycogen synthase kinase J4 (GSK-J4), a demethylase inhibitor. Together, our findings provide evidence that SP1 regulates its target oncogene expression through phase separation and SE mechanisms, thereby promoting LUAD cell progression. This study also revealed an innovative target for LUAD therapies through intervening in SP1-mediated SE formation.
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Affiliation(s)
- Liying Shan
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin150081, China
| | - Wenmeng Wang
- College of Life Science, Northeast Forestry University, Harbin150040, China
| | - Lijuan Du
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin150081, China
| | - Dangdang Li
- College of Life Science, Northeast Forestry University, Harbin150040, China
| | - Yunxuan Wang
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin150081, China
| | - Yuyan Xie
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin150081, China
| | - Hongyan Li
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin150081, China
| | - Jiale Wang
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin150081, China
| | - Zhihao Shi
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin150081, China
| | - Yang Zhou
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin150081, China
| | - Daling Zhu
- College of Pharmacy, Harbin Medical University (Daqing), Daqing163319, China
| | - Guangchao Sui
- College of Life Science, Northeast Forestry University, Harbin150040, China
| | - Fang Liu
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin150081, China
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6
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Kiang KM, Ahad L, Zhong X, Lu QR. Biomolecular condensates: hubs of Hippo-YAP/TAZ signaling in cancer. Trends Cell Biol 2024; 34:566-577. [PMID: 38806345 DOI: 10.1016/j.tcb.2024.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 04/14/2024] [Accepted: 04/30/2024] [Indexed: 05/30/2024]
Abstract
Biomolecular condensates, the membraneless cellular compartments formed by liquid-liquid phase separation (LLPS), represent an important mechanism for physiological and tumorigenic processes. Recent studies have advanced our understanding of how these condensates formed in the cytoplasm or nucleus regulate Hippo signaling, a central player in organogenesis and tumorigenesis. Here, we review recent findings on the dynamic formation and function of biomolecular condensates in regulating the Hippo-yes-associated protein (YAP)/transcription coactivator with PDZ-binding motif (TAZ) signaling pathway under physiological and pathological processes. We further discuss how the nuclear condensates of YAP- or TAZ-fusion oncoproteins compartmentalize crucial transcriptional co-activators and alter chromatin architecture to promote oncogenic programs. Finally, we highlight key questions regarding how these findings may pave the way for novel therapeutics to target cancer.
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Affiliation(s)
- Karrie M Kiang
- Department of Pediatrics, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Department of Surgery, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong
| | - Leena Ahad
- Department of Pediatrics, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Xiaowen Zhong
- Department of Pediatrics, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Q Richard Lu
- Department of Pediatrics, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
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7
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Hao S, Lee YJ, Benhamou Goldfajn N, Flores E, Liang J, Fuehrer H, Demmerle J, Lippincott-Schwartz J, Liu Z, Sukenik S, Cai D. YAP condensates are highly organized hubs. iScience 2024; 27:109927. [PMID: 38784009 PMCID: PMC11111833 DOI: 10.1016/j.isci.2024.109927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 10/24/2023] [Accepted: 05/03/2024] [Indexed: 05/25/2024] Open
Abstract
YAP/TEAD signaling is essential for organismal development, cell proliferation, and cancer progression. As a transcriptional coactivator, how YAP activates its downstream target genes is incompletely understood. YAP forms biomolecular condensates in response to hyperosmotic stress, concentrating transcription-related factors to activate downstream target genes. However, whether YAP forms condensates under other signals, how YAP condensates organize and function, and how YAP condensates activate transcription in general are unknown. Here, we report that endogenous YAP forms sub-micron scale condensates in response to Hippo pathway regulation and actin cytoskeletal tension. YAP condensates are stabilized by the transcription factor TEAD1, and recruit BRD4, a coactivator that is enriched at active enhancers. Using single-particle tracking, we found that YAP condensates slowed YAP diffusion within condensate boundaries, a possible mechanism for promoting YAP target search. These results reveal that YAP condensate formation is a highly regulated process that is critical for YAP/TEAD target gene expression.
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Affiliation(s)
- Siyuan Hao
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Ye Jin Lee
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Nadav Benhamou Goldfajn
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
- Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Eduardo Flores
- Department of Chemistry and Chemical Biology, University of California, Merced, Merced, CA 95343, USA
| | - Jindayi Liang
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Hannah Fuehrer
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Justin Demmerle
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | | | - Zhe Liu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Shahar Sukenik
- Department of Chemistry and Chemical Biology, University of California, Merced, Merced, CA 95343, USA
| | - Danfeng Cai
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
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8
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Vincoff S, Goel S, Kholina K, Pulugurta R, Vure P, Chatterjee P. FusOn-pLM: A Fusion Oncoprotein-Specific Language Model via Focused Probabilistic Masking. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.03.597245. [PMID: 38895377 PMCID: PMC11185609 DOI: 10.1101/2024.06.03.597245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Fusion oncoproteins, a class of chimeric proteins arising from chromosomal translocations, drive and sustain various cancers, particularly those impacting children. Unfortunately, due to their intrinsically disordered nature, large size, and lack of well-defined, druggable pockets, they have been historically challenging to target therapeutically: neither small molecule-based methods nor structure-based approaches for binder design are strong options for this class of molecules. Recently, protein language models (pLMs) have demonstrated success at representing protein sequences with information-rich embeddings, enabling downstream design applications from sequence alone. However, no current pLM has been trained on fusion oncoprotein sequences and thus may not produce optimal representations for these proteins. In this work, we introduce FusOn-pLM, a novel pLM that fine-tunes the state-of-the-art ESM-2 model on fusion oncoprotein sequences. We specifically introduce a novel masked language modeling (MLM) strategy, employing a binding-site probability predictor to focus masking on key amino acid residues, thereby generating more optimal fusion oncoprotein-aware embeddings. Our model improves performance on both fusion oncoprotein-specific benchmarks and disorder prediction tasks in comparison to baseline ESM-2 representations, as well as manually-constructed biophysical embeddings, motivating downstream usage of FusOn-pLM embeddings for therapeutic design tasks targeting these fusions. We have made our model publicly available to the community at https://huggingface.co/ChatterjeeLab/FusOn-pLM.
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Affiliation(s)
| | - Shrey Goel
- Department of Computer Science, Duke University
| | | | | | - Pranay Vure
- Department of Biomedical Engineering, Duke University
| | - Pranam Chatterjee
- Department of Biomedical Engineering, Duke University
- Department of Computer Science, Duke University
- Department of Biostatistics and Bioinformatics, Duke University
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9
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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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10
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Lin CC, Suen KM, Lidster J, Ladbury JE. The emerging role of receptor tyrosine kinase phase separation in cancer. Trends Cell Biol 2024; 34:371-379. [PMID: 37777392 DOI: 10.1016/j.tcb.2023.09.002] [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: 05/30/2023] [Revised: 08/17/2023] [Accepted: 09/06/2023] [Indexed: 10/02/2023]
Abstract
Receptor tyrosine kinase (RTK)-mediated signal transduction is fundamental to cell function and drives important cellular outcomes which, when dysregulated, can lead to malignant tumour growth and metastasis. The initiation of signals from plasma membrane-bound RTKs is subjected to multiple regulatory mechanisms that control downstream effector protein recruitment and function. The high propensity of RTKs to condense via liquid-liquid phase separation (LLPS) into membraneless organelles with downstream effector proteins provides a further fundamental mechanism for signal regulation. Herein we highlight how this phenomenon contributes to cancer signalling and consider the potential impact of LLPS on outcomes for cancer patients.
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Affiliation(s)
- Chi-Chuan Lin
- School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK.
| | - Kin Man Suen
- School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Jessica Lidster
- School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - John E Ladbury
- School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK.
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11
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Petrauskas A, Fortunati DL, Kandi AR, Pothapragada SS, Agrawal K, Singh A, Huelsmeier J, Hillebrand J, Brown G, Chaturvedi D, Lee J, Lim C, Auburger G, VijayRaghavan K, Ramaswami M, Bakthavachalu B. Structured and disordered regions of Ataxin-2 contribute differently to the specificity and efficiency of mRNP granule formation. PLoS Genet 2024; 20:e1011251. [PMID: 38768217 PMCID: PMC11166328 DOI: 10.1371/journal.pgen.1011251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 06/11/2024] [Accepted: 04/05/2024] [Indexed: 05/22/2024] Open
Abstract
Ataxin-2 (ATXN2) is a gene implicated in spinocerebellar ataxia type II (SCA2), amyotrophic lateral sclerosis (ALS) and Parkinsonism. The encoded protein is a therapeutic target for ALS and related conditions. ATXN2 (or Atx2 in insects) can function in translational activation, translational repression, mRNA stability and in the assembly of mRNP-granules, a process mediated by intrinsically disordered regions (IDRs). Previous work has shown that the LSm (Like-Sm) domain of Atx2, which can help stimulate mRNA translation, antagonizes mRNP-granule assembly. Here we advance these findings through a series of experiments on Drosophila and human Ataxin-2 proteins. Results of Targets of RNA Binding Proteins Identified by Editing (TRIBE), co-localization and immunoprecipitation experiments indicate that a polyA-binding protein (PABP) interacting, PAM2 motif of Ataxin-2 may be a major determinant of the mRNA and protein content of Ataxin-2 mRNP granules. Experiments with transgenic Drosophila indicate that while the Atx2-LSm domain may protect against neurodegeneration, structured PAM2- and unstructured IDR- interactions both support Atx2-induced cytotoxicity. Taken together, the data lead to a proposal for how Ataxin-2 interactions are remodelled during translational control and how structured and non-structured interactions contribute differently to the specificity and efficiency of RNP granule condensation as well as to neurodegeneration.
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Affiliation(s)
- Arnas Petrauskas
- Trinity College Institute of Neuroscience, School of Genetics and Microbiology, Smurfit Institute of Genetics and School of Natural Sciences, Trinity College Dublin, Dublin, Ireland
| | - Daniel L. Fortunati
- Trinity College Institute of Neuroscience, School of Genetics and Microbiology, Smurfit Institute of Genetics and School of Natural Sciences, Trinity College Dublin, Dublin, Ireland
| | - Arvind Reddy Kandi
- School of Biosciences and Bioengineering, Indian Institute of Technology, Mandi, India
| | | | - Khushboo Agrawal
- Tata Institute for Genetics and Society Centre at inStem, Bellary Road, Bangalore, India
- School of Biotechnology, Amrita Vishwa Vidyapeetham University, Kollam, Kerala, India
| | - Amanjot Singh
- National Centre for Biological Sciences, TIFR, Bangalore, India
- Manipal Institute of Regenerative Medicine, MAHE-Bengaluru, Govindapura, Bengaluru, India
| | - Joern Huelsmeier
- Trinity College Institute of Neuroscience, School of Genetics and Microbiology, Smurfit Institute of Genetics and School of Natural Sciences, Trinity College Dublin, Dublin, Ireland
| | - Jens Hillebrand
- Trinity College Institute of Neuroscience, School of Genetics and Microbiology, Smurfit Institute of Genetics and School of Natural Sciences, Trinity College Dublin, Dublin, Ireland
| | - Georgia Brown
- Trinity College Institute of Neuroscience, School of Genetics and Microbiology, Smurfit Institute of Genetics and School of Natural Sciences, Trinity College Dublin, Dublin, Ireland
| | | | - Jongbo Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan, Republic of Korea
| | - Chunghun Lim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan, Republic of Korea
| | - Georg Auburger
- Experimental Neurology, Medical School, Goethe University, Frankfurt, Germany
| | | | - Mani Ramaswami
- Trinity College Institute of Neuroscience, School of Genetics and Microbiology, Smurfit Institute of Genetics and School of Natural Sciences, Trinity College Dublin, Dublin, Ireland
- National Centre for Biological Sciences, TIFR, Bangalore, India
| | - Baskar Bakthavachalu
- School of Biosciences and Bioengineering, Indian Institute of Technology, Mandi, India
- Tata Institute for Genetics and Society Centre at inStem, Bellary Road, Bangalore, India
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12
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Khorsand FR, Uversky VN. Liquid-liquid phase separation as triggering factor of fibril formation. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 206:143-182. [PMID: 38811080 DOI: 10.1016/bs.pmbts.2024.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
Liquid-liquid phase separation (LLPS) refers to the phenomenon, where a homogeneous solution spontaneously undergoes a transition into two or more immiscible phases. Through transient weak multivalent macromolecular interactions, a homogeneous solution can spontaneously separate into two phases: one rich in biomolecules and the other poor in biomolecules. Phase separation is believed to serve as the physicochemical foundation for the formation of membrane-less organelles (MLOs) and bio-molecular condensates within cells. Moreover, numerous biological processes depend on LLPS, such as transcription, immunological response, chromatin architecture, DNA damage response, stress granule formation, viral infection, etc. Abnormalities in phase separation can lead to diseases, such as cancer, neurodegeneration, and metabolic disorders. LLPS is regulated by various factors, such as concentration of molecules undergoing LLPS, salt concentration, pH, temperature, post-translational modifications, and molecular chaperones. Recent research on LLPS of biomolecules has progressed rapidly and led to the development of databases containing information pertaining to various aspects of the biomolecule separation analysis. However, more comprehensive research is still required to fully comprehend the specific molecular mechanisms and biological effects of LLPS.
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Affiliation(s)
| | - Vladimir N Uversky
- Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Institute for Biological Instrumentation, Pushchino, Moscow, Russia; Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, United States.
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13
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Park J, Kim JJ, Ryu JK. Mechanism of phase condensation for chromosome architecture and function. Exp Mol Med 2024; 56:809-819. [PMID: 38658703 PMCID: PMC11059216 DOI: 10.1038/s12276-024-01226-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 02/23/2024] [Accepted: 02/28/2024] [Indexed: 04/26/2024] Open
Abstract
Chromosomal phase separation is involved in a broad spectrum of chromosome organization and functional processes. Nonetheless, the intricacy of this process has left its molecular mechanism unclear. Here, we introduce the principles governing phase separation and its connections to physiological roles in this context. Our primary focus is contrasting two phase separation mechanisms: self-association-induced phase separation (SIPS) and bridging-induced phase separation (BIPS). We provide a comprehensive discussion of the distinct features characterizing these mechanisms and offer illustrative examples that suggest their broad applicability. With a detailed understanding of these mechanisms, we explore their associations with nucleosomes and chromosomal biological functions. This comprehensive review contributes to the exploration of uncharted territory in the intricate interplay between chromosome architecture and function.
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Affiliation(s)
- Jeongveen Park
- Department of Physics and Astronomy, Seoul National University, Seoul, 08826, South Korea
| | - Jeong-Jun Kim
- Department of Physics and Astronomy, Seoul National University, Seoul, 08826, South Korea
| | - Je-Kyung Ryu
- Department of Physics and Astronomy, Seoul National University, Seoul, 08826, South Korea.
- Institute of Applied Physics of Seoul National University, Seoul, 08826, South Korea.
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, 08826, South Korea.
- Department of Biological Sciences, Seoul National University, Seoul, 08826, South Korea.
- Interdisciplinary Program in Neuroscience, Seoul National University, Seoul, 08826, South Korea.
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14
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Erazo-Oliveras A, Muñoz-Vega M, Salinas ML, Wang X, Chapkin RS. Dysregulation of cellular membrane homeostasis as a crucial modulator of cancer risk. FEBS J 2024; 291:1299-1352. [PMID: 36282100 PMCID: PMC10126207 DOI: 10.1111/febs.16665] [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: 06/18/2022] [Revised: 09/09/2022] [Accepted: 10/24/2022] [Indexed: 11/07/2022]
Abstract
Cellular membranes serve as an epicentre combining extracellular and cytosolic components with membranous effectors, which together support numerous fundamental cellular signalling pathways that mediate biological responses. To execute their functions, membrane proteins, lipids and carbohydrates arrange, in a highly coordinated manner, into well-defined assemblies displaying diverse biological and biophysical characteristics that modulate several signalling events. The loss of membrane homeostasis can trigger oncogenic signalling. More recently, it has been documented that select membrane active dietaries (MADs) can reshape biological membranes and subsequently decrease cancer risk. In this review, we emphasize the significance of membrane domain structure, organization and their signalling functionalities as well as how loss of membrane homeostasis can steer aberrant signalling. Moreover, we describe in detail the complexities associated with the examination of these membrane domains and their association with cancer. Finally, we summarize the current literature on MADs and their effects on cellular membranes, including various mechanisms of dietary chemoprevention/interception and the functional links between nutritional bioactives, membrane homeostasis and cancer biology.
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Affiliation(s)
- Alfredo Erazo-Oliveras
- Program in Integrative Nutrition and Complex Diseases; Texas A&M University; College Station, Texas, 77843; USA
- Department of Nutrition; Texas A&M University; College Station, Texas, 77843; USA
| | - Mónica Muñoz-Vega
- Program in Integrative Nutrition and Complex Diseases; Texas A&M University; College Station, Texas, 77843; USA
- Department of Nutrition; Texas A&M University; College Station, Texas, 77843; USA
| | - Michael L. Salinas
- Program in Integrative Nutrition and Complex Diseases; Texas A&M University; College Station, Texas, 77843; USA
- Department of Nutrition; Texas A&M University; College Station, Texas, 77843; USA
| | - Xiaoli Wang
- Program in Integrative Nutrition and Complex Diseases; Texas A&M University; College Station, Texas, 77843; USA
- Department of Nutrition; Texas A&M University; College Station, Texas, 77843; USA
| | - Robert S. Chapkin
- Program in Integrative Nutrition and Complex Diseases; Texas A&M University; College Station, Texas, 77843; USA
- Department of Nutrition; Texas A&M University; College Station, Texas, 77843; USA
- Center for Environmental Health Research; Texas A&M University; College Station, Texas, 77843; USA
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15
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Kan C, Tan Z, Liu L, Liu B, Zhan L, Zhu J, Li X, Lin K, Liu J, Liu Y, Yang F, Wong M, Wang S, Zheng H. Phase separation of SHP2E76K promotes malignant transformation of mesenchymal stem cells by activating mitochondrial complexes. JCI Insight 2024; 9:e170340. [PMID: 38451719 PMCID: PMC11141883 DOI: 10.1172/jci.insight.170340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 03/05/2024] [Indexed: 03/09/2024] Open
Abstract
Mesenchymal stem cells (MSCs), suffering from diverse gene hits, undergo malignant transformation and aberrant osteochondral differentiation. Src homology region 2-containing protein tyrosine phosphatase 2 (SHP2), a nonreceptor protein tyrosine phosphatase, regulates multicellular differentiation, proliferation, and transformation. However, the role of SHP2 in MSC fate determination remains unclear. Here, we showed that MSCs bearing the activating SHP2E76K mutation underwent malignant transformation into sarcoma stem-like cells. We revealed that the SHP2E76K mutation in mouse MSCs led to hyperactive mitochondrial metabolism by activating mitochondrial complexes I and III. Inhibition of complexes I and III prevented hyperactive mitochondrial metabolism and malignant transformation of SHP2E76K MSCs. Mechanistically, we verified that SHP2 underwent liquid-liquid phase separation (LLPS) in SHP2E76K MSCs. SHP2 LLPS led to its dissociation from complexes I and III, causing their hyperactivation. Blockade of SHP2 LLPS by LLPS-defective mutations or allosteric inhibitors suppressed complex I and III hyperactivation as well as malignant transformation of SHP2E76K MSCs. These findings reveal that complex I and III hyperactivation driven by SHP2 LLPS promotes malignant transformation of SHP2E76K MSCs and suggest that inhibition of SHP2 LLPS could be a potential therapeutic target for the treatment of activated SHP2-associated cancers.
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Affiliation(s)
- Chen Kan
- Department of Pathophysiology, School of Basic Medical Sciences, Stem Cell Regeneration Research Center, Anhui Medical University, Hefei, China
| | - Zhenya Tan
- Department of Pathophysiology, School of Basic Medical Sciences, Stem Cell Regeneration Research Center, Anhui Medical University, Hefei, China
| | - Liwei Liu
- Department of Pathogen Biology and Immunology, School of Medical Technology, Anhui Medical College, Hefei, China
| | - Bo Liu
- Department of Cell Center, 901st Hospital of PLA Joint Logistic Support Force, Anhui, Hefei, China
| | - Li Zhan
- Department of Pathophysiology, School of Basic Medical Sciences, Stem Cell Regeneration Research Center, Anhui Medical University, Hefei, China
| | - Jicheng Zhu
- Department of Pathophysiology, School of Basic Medical Sciences, Stem Cell Regeneration Research Center, Anhui Medical University, Hefei, China
| | - Xiaofei Li
- Department of Pathophysiology, School of Basic Medical Sciences, Stem Cell Regeneration Research Center, Anhui Medical University, Hefei, China
| | - Keqiong Lin
- Department of Pathophysiology, School of Basic Medical Sciences, Stem Cell Regeneration Research Center, Anhui Medical University, Hefei, China
| | - Jia Liu
- Department of Pathophysiology, School of Basic Medical Sciences, Stem Cell Regeneration Research Center, Anhui Medical University, Hefei, China
| | - Yakun Liu
- Department of Pathophysiology, School of Basic Medical Sciences, Stem Cell Regeneration Research Center, Anhui Medical University, Hefei, China
| | - Fan Yang
- Department of Pathophysiology, School of Basic Medical Sciences, Stem Cell Regeneration Research Center, Anhui Medical University, Hefei, China
| | - Mandy Wong
- Department of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Siying Wang
- Department of Pathophysiology, School of Basic Medical Sciences, Stem Cell Regeneration Research Center, Anhui Medical University, Hefei, China
| | - Hong Zheng
- Department of Pathophysiology, School of Basic Medical Sciences, Stem Cell Regeneration Research Center, Anhui Medical University, Hefei, China
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16
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Wang J, Chen Y, Xiao Z, Liu X, Liu C, Huang K, Chen H. Phase Separation of Chromatin Structure-related Biomolecules: A Driving Force for Epigenetic Regulations. Curr Protein Pept Sci 2024; 25:553-566. [PMID: 38551058 DOI: 10.2174/0113892037296216240301074253] [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: 01/03/2024] [Revised: 02/12/2024] [Accepted: 02/16/2024] [Indexed: 07/25/2024]
Abstract
Intracellularly, membrane-less organelles are formed by spontaneous fusion and fission of macro-molecules in a process called phase separation, which plays an essential role in cellular activities. In certain disease states, such as cancers and neurodegenerative diseases, aberrant phase separations take place and participate in disease progression. Chromatin structure-related proteins, based on their characteristics and upon external stimuli, phase separate to exert functions like genome assembly, transcription regulation, and signal transduction. Moreover, many chromatin structure-related proteins, such as histones, histone-modifying enzymes, DNA-modifying enzymes, and DNA methylation binding proteins, are involved in epigenetic regulations through phase separation. This review introduces phase separation and how phase separation affects epigenetics with a focus on chromatin structure-related molecules.
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Affiliation(s)
- Jiao Wang
- Wuhan No.1 Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
| | - Yuchen Chen
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Zixuan Xiao
- ISA Wenhua Wuhan High School, Fenglin Road, Junshan New Town, Wuhan Economics & Technological Development Zone, Wuhan, Hubei 430119, China
| | - Xikai Liu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Chengyu Liu
- Wuhan No.1 Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
| | - Kun Huang
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Hong Chen
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
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17
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Szoke T, Goldberger O, Albocher-Kedem N, Barsheshet M, Dezorella N, Nussbaum-Shochat A, Wiener R, Schuldiner M, Amster-Choder O. Regulation of major bacterial survival strategies by transcripts sequestration in a membraneless organelle. Cell Rep 2023; 42:113393. [PMID: 37934665 DOI: 10.1016/j.celrep.2023.113393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/10/2023] [Accepted: 10/20/2023] [Indexed: 11/09/2023] Open
Abstract
TmaR, the only known pole-localizer protein in Escherichia coli, was shown to cluster at the cell poles and control localization and activity of the major sugar regulator in a tyrosine phosphorylation-dependent manner. Here, we show that TmaR assembles by phase separation (PS) via heterotypic interactions with RNA in vivo and in vitro. An unbiased automated mutant screen combined with directed mutagenesis and genetic manipulations uncovered the importance of a predicted nucleic-acid-binding domain, a disordered region, and charged patches, one containing the phosphorylated tyrosine, for TmaR condensation. We demonstrate that, by protecting flagella-related transcripts, TmaR controls flagella production and, thus, cell motility and biofilm formation. These results connect PS in bacteria to survival and provide an explanation for the linkage between metabolism and motility. Intriguingly, a point mutation or increase in its cellular concentration induces irreversible liquid-to-solid transition of TmaR, similar to human disease-causing proteins, which affects cell morphology and division.
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Affiliation(s)
- Tamar Szoke
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, Jerusalem 91120, Israel
| | - Omer Goldberger
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, Jerusalem 91120, Israel
| | - Nitsan Albocher-Kedem
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, Jerusalem 91120, Israel
| | - Meshi Barsheshet
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, Jerusalem 91120, Israel
| | - Nili Dezorella
- Electron Microscopy Unit, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Anat Nussbaum-Shochat
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, Jerusalem 91120, Israel
| | - Reuven Wiener
- Department of Biochemistry and Molecular Biology, IMRIC, The Hebrew University Faculty of Medicine, Jerusalem 91120, Israel
| | - Maya Schuldiner
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Orna Amster-Choder
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, Jerusalem 91120, Israel.
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18
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Suganuma T, Workman JL. Chromatin balances cell redox and energy homeostasis. Epigenetics Chromatin 2023; 16:46. [PMID: 38017471 PMCID: PMC10683155 DOI: 10.1186/s13072-023-00520-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 10/30/2023] [Indexed: 11/30/2023] Open
Abstract
Chromatin plays a central role in the conversion of energy in cells: alteration of chromatin structure to make DNA accessible consumes energy, and compaction of chromatin preserves energy. Alteration of chromatin structure uses energy sources derived from carbon metabolism such as ATP and acetyl-CoA; conversely, chromatin compaction and epigenetic modification feedback to metabolism and energy homeostasis by controlling gene expression and storing metabolites. Coordination of these dual chromatin events must be flexibly modulated in response to environmental changes such as during development and exposure to stress. Aging also alters chromatin structure and the coordination of metabolism, chromatin dynamics, and other cell processes. Noncoding RNAs and other RNA species that associate directly with chromatin or with chromatin modifiers contribute to spatiotemporal control of transcription and energy conversion. The time required for generating the large amounts of RNAs and chromatin modifiers observed in super-enhancers may be critical for regulation of transcription and may be impacted by aging. Here, taking into account these factors, we review alterations of chromatin that are fundamental to cell responses to metabolic changes due to stress and aging to maintain redox and energy homeostasis. We discuss the relationship between spatiotemporal control of energy and chromatin function, as this emerging concept must be considered to understand how cell homeostasis is maintained.
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Affiliation(s)
- Tamaki Suganuma
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO, 64110, USA.
| | - Jerry L Workman
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO, 64110, USA
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19
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Chou MC, Wang YH, Chen FY, Kung CY, Wu KP, Kuo JC, Chan SJ, Cheng ML, Lin CY, Chou YC, Ho MC, Firestine S, Huang JR, Chen RH. PAICS ubiquitination recruits UBAP2 to trigger phase separation for purinosome assembly. Mol Cell 2023; 83:4123-4140.e12. [PMID: 37848033 DOI: 10.1016/j.molcel.2023.09.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 07/10/2023] [Accepted: 09/22/2023] [Indexed: 10/19/2023]
Abstract
Purinosomes serve as metabolons to enhance de novo purine synthesis (DNPS) efficiency through compartmentalizing DNPS enzymes during stressed conditions. However, the mechanism underpinning purinosome assembly and its pathophysiological functions remains elusive. Here, we show that K6-polyubiquitination of the DNPS enzyme phosphoribosylaminoimidazole carboxylase and phosphoribosylaminoimidazolesuccinocarboxamide synthetase (PAICS) by cullin-5/ankyrin repeat and SOCS box containing 11 (Cul5/ASB11)-based ubiquitin ligase plays a driving role in purinosome assembly. Upon several purinosome-inducing cues, ASB11 is upregulated by relieving the H3K9me3/HP1α-mediated transcriptional silencing, thus stimulating PAICS polyubiquitination. The polyubiquitinated PAICS recruits ubiquitin-associated protein 2 (UBAP2), a ubiquitin-binding protein with multiple stretches of intrinsically disordered regions, thereby inducing phase separation to trigger purinosome assembly for enhancing DNPS pathway flux. In human melanoma, ASB11 is highly expressed to facilitate a constitutive purinosome formation to which melanoma cells are addicted for supporting their proliferation, viability, and tumorigenesis in a xenograft model. Our study identifies a driving mechanism for purinosome assembly in response to cellular stresses and uncovers the impact of purinosome formation on human malignancies.
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Affiliation(s)
- Ming-Chieh Chou
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan; Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 106, Taiwan
| | - Yi-Hsuan Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan; Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 106, Taiwan
| | - Fei-Yun Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Chun-Ying Kung
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan; Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 106, Taiwan
| | - Kuen-Phon Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan; Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 106, Taiwan
| | - Jean-Cheng Kuo
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Shu-Jou Chan
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Mei-Ling Cheng
- Metabolomics Core Laboratory, Healthy Aging Research Center, Chang Gung University, Taoyuan 333, Taiwan; Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; Clinical Metabolomics Core Laboratory, Chang Gung Memorial Hospital at Linkou, Taoyuan 333, Taiwan
| | - Chih-Yu Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Chi Chou
- Biomedical Translation Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Meng-Chiao Ho
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan; Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 106, Taiwan
| | - Steven Firestine
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI 48201, USA
| | - Jie-Rong Huang
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Ruey-Hwa Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan; Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 106, Taiwan.
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20
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Kotekar A, Singh AK, Devaiah BN. BRD4 and MYC: power couple in transcription and disease. FEBS J 2023; 290:4820-4842. [PMID: 35866356 PMCID: PMC9867786 DOI: 10.1111/febs.16580] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/16/2022] [Accepted: 07/20/2022] [Indexed: 01/26/2023]
Abstract
The MYC proto-oncogene and BRD4, a BET family protein, are two cardinal proteins that have a broad influence in cell biology and disease. Both proteins are expressed ubiquitously in mammalian cells and play central roles in controlling growth, development, stress responses and metabolic function. As chromatin and transcriptional regulators, they play a critical role in regulating the expression of a burgeoning array of genes, maintaining chromatin architecture and genome stability. Consequently, impairment of their function or regulation leads to many diseases, with cancer being the most predominant. Interestingly, accumulating evidence indicates that regulation of the expression and functions of MYC are tightly intertwined with BRD4 at both transcriptional and post-transcriptional levels. Here, we review the mechanisms by which MYC and BRD4 are regulated, their functions in governing various molecular mechanisms and the consequences of their dysregulation that lead to disease. We present a perspective of how the regulatory mechanisms for the two proteins could be entwined at multiple points in a BRD4-MYC nexus that leads to the modulation of their functions and disease upon dysregulation.
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Affiliation(s)
- Aparna Kotekar
- Experimental Immunology Branch, NCI, NIH, Bethesda, MD 20892, USA
| | - Amit Kumar Singh
- Experimental Immunology Branch, NCI, NIH, Bethesda, MD 20892, USA
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21
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Zou Y, Zheng H, Ning Y, Yang Y, Wen Q, Fan S. New insights into the important roles of phase seperation in the targeted therapy of lung cancer. Cell Biosci 2023; 13:150. [PMID: 37580790 PMCID: PMC10426191 DOI: 10.1186/s13578-023-01101-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 08/04/2023] [Indexed: 08/16/2023] Open
Abstract
Lung cancer is a complex and heterogeneous disease characterized by abnormal growth and proliferation of lung cells. It is the leading cause of cancer-related deaths worldwide, accounting for approximately 18% of all cancer deaths. In recent years, targeted therapy has emerged as a promising approach to treat lung cancer, which involves the use of drugs that selectively target specific molecules or signaling pathways that are critical for the growth and survival of cancer cells. Liquid-liquid phase separation (LLPS) is a fundamental biological process that occurs when proteins and other biomolecules separate into distinct liquid phases in cells. LLPS is essential for various cellular functions, including the formation of membraneless organelles, the regulation of gene expression, and the response to stress and other stimuli. Recent studies have shown that LLPS plays a crucial role in targeted therapy of lung cancer, including the sequestration of oncogenic proteins and the development of LLPS-based drug delivery systems. Understanding the mechanisms of LLPS in these processes could provide insights into new therapeutic strategies to overcome drug resistance in lung cancer cells.
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Affiliation(s)
- Ying Zou
- Department of Pathology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Hongmei Zheng
- Department of Pathology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Yue Ning
- Department of Pathology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Yang Yang
- Department of Pathology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Qiuyuan Wen
- Department of Pathology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Songqing Fan
- Department of Pathology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China.
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22
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Li M, Zhang Y, Zhao J, Wang D. The global landscape and research trend of phase separation in cancer: a bibliometric analysis and visualization. Front Oncol 2023; 13:1170157. [PMID: 37333812 PMCID: PMC10272442 DOI: 10.3389/fonc.2023.1170157] [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: 02/20/2023] [Accepted: 05/09/2023] [Indexed: 06/20/2023] Open
Abstract
Background Cancer as a deathly disease with high prevalence has impelled researchers to investigate its causative mechanisms in the search for effective therapeutics. Recently, the concept of phase separation has been introduced to biological science and extended to cancer research, which helps reveal various pathogenic processes that have not been identified before. As a process of soluble biomolecules condensed into solid-like and membraneless structures, phase separation is associated with multiple oncogenic processes. However, there are no bibliometric characteristics for these results. To provide future trends and identify new frontiers in this field, a bibliometric analysis was conducted in this study. Methods The Web of Science Core Collection (WoSCC) was used to search for literature on phase separation in cancer from 1/1/2009 to 31/12/2022. After screening the literature, statistical analysis and visualization were carried out by the VOSviewer software (version 1.6.18) and Citespace software (Version 6.1.R6). Results A total of 264 publications, covering 413 organizations and 32 countries, were published in 137 journals, with an increasing trend in publication and citation numbers per year. The USA and China were the two countries with the largest number of publications, and the University of Chinese Academy of Sciences was the most active institution based on the number of articles and cooperations. Molecular Cell was the most frequent publisher with high citations and H-index. The most productive authors were Fox AH, De Oliveira GAP, and Tompa P. Overlay, whilst few authors had a strong collaboration with each other. The combined analysis of concurrent and burst keywords revealed that the future research hotspots of phase separation in cancer were related to tumor microenvironments, immunotherapy, prognosis, p53, and cell death. Conclusion Phase separation-related cancer research remained in the hot streak period and exhibited a promising outlook. Although inter-agency collaboration existed, cooperation among research groups was rare, and no author dominated this field at the current stage. Investigating the interfaced effects between phase separation and tumor microenvironments on carcinoma behaviors, and constructing relevant prognoses and therapeutics such as immune infiltration-based prognosis and immunotherapy might be the next research trend in the study of phase separation and cancer.
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Affiliation(s)
- Mengzhu Li
- Department of Endocrinology, Shandong Provincial Hospital, Shandong University, Jinan, China
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China
- Shandong Institute of Endocrine and Metabolic Diseases, Jinan, China
- Key Laboratory of Endocrine Glucose & Lipids Metabolism and Brain Aging (Shandong First Medical University), Ministry of Education, Jinan, China
| | - Yizhan Zhang
- Department of Endocrinology, Shandong Provincial Hospital, Shandong University, Jinan, China
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China
- Shandong Institute of Endocrine and Metabolic Diseases, Jinan, China
- Key Laboratory of Endocrine Glucose & Lipids Metabolism and Brain Aging (Shandong First Medical University), Ministry of Education, Jinan, China
| | - Jiajun Zhao
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China
- Shandong Institute of Endocrine and Metabolic Diseases, Jinan, China
- Key Laboratory of Endocrine Glucose & Lipids Metabolism and Brain Aging (Shandong First Medical University), Ministry of Education, Jinan, China
| | - Dawei Wang
- Department of Endocrinology, Shandong Provincial Hospital, Shandong University, Jinan, China
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China
- Shandong Institute of Endocrine and Metabolic Diseases, Jinan, China
- Key Laboratory of Endocrine Glucose & Lipids Metabolism and Brain Aging (Shandong First Medical University), Ministry of Education, Jinan, China
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23
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Dall'Agnese G, Dall'Agnese A, Banani SF, Codrich M, Malfatti MC, Antoniali G, Tell G. Role of condensates in modulating DNA repair pathways and its implication for chemoresistance. J Biol Chem 2023:104800. [PMID: 37164156 DOI: 10.1016/j.jbc.2023.104800] [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: 11/22/2022] [Revised: 05/03/2023] [Accepted: 05/04/2023] [Indexed: 05/12/2023] Open
Abstract
For cells, it is important to repair DNA damage, such as double strand and single strand DNA breaks, because unrepaired DNA can compromise genetic integrity, potentially leading to cell death or cancer. Cells have multiple DNA damage repair pathways that have been the subject of detailed genetic, biochemical, and structural studies. Recently, the scientific community has started to gain evidence that the repair of DNA double strand breaks may occur within biomolecular condensates and that condensates may also contribute to DNA damage through concentrating genotoxic agents used to treat various cancers. Here, we summarize key features of biomolecular condensates and note where they have been implicated in the repair of DNA double strand breaks. We also describe evidence suggesting that condensates may be involved in the repair of other types of DNA damage, including single strand DNA breaks, nucleotide modifications (e.g., mismatch and oxidized bases) and bulky lesions, among others. Finally, we discuss old and new mysteries that could now be addressed considering the properties of condensates, including chemoresistance mechanisms.
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Affiliation(s)
- Giuseppe Dall'Agnese
- Laboratory of Molecular Biology and DNA repair, Department of Medicine, University of Udine, 33100 Udine, Italy; Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | | | - Salman F Banani
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Marta Codrich
- Laboratory of Molecular Biology and DNA repair, Department of Medicine, University of Udine, 33100 Udine, Italy
| | - Matilde Clarissa Malfatti
- Laboratory of Molecular Biology and DNA repair, Department of Medicine, University of Udine, 33100 Udine, Italy
| | - Giulia Antoniali
- Laboratory of Molecular Biology and DNA repair, Department of Medicine, University of Udine, 33100 Udine, Italy
| | - Gianluca Tell
- Laboratory of Molecular Biology and DNA repair, Department of Medicine, University of Udine, 33100 Udine, Italy.
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24
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Hojo H. Emerging RUNX2-Mediated Gene Regulatory Mechanisms Consisting of Multi-Layered Regulatory Networks in Skeletal Development. Int J Mol Sci 2023; 24:ijms24032979. [PMID: 36769300 PMCID: PMC9917854 DOI: 10.3390/ijms24032979] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Skeletal development is tightly coordinated by chondrocytes and osteoblasts, which are derived from skeletal progenitors, and distinct cell-type gene regulatory programs underlie the specification and differentiation of cells. Runt-related transcription factor 2 (Runx2) is essential to chondrocyte hypertrophy and osteoblast differentiation. Genetic studies have revealed the biological functions of Runx2 and its involvement in skeletal genetic diseases. Meanwhile, molecular biology has provided a framework for our understanding of RUNX2-mediated transactivation at a limited number of cis-regulatory elements. Furthermore, studies using next-generation sequencing (NGS) have provided information on RUNX2-mediated gene regulation at the genome level and novel insights into the multiple layers of gene regulatory mechanisms, including the modes of action of RUNX2, chromatin accessibility, the concept of pioneer factors and phase separation, and three-dimensional chromatin organization. In this review, I summarize the emerging RUNX2-mediated regulatory mechanism from a multi-layer perspective and discuss future perspectives for applications in the treatment of skeletal diseases.
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Affiliation(s)
- Hironori Hojo
- Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
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25
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From the Catastrophic Objective Irreproducibility of Cancer Research and Unavoidable Failures of Molecular Targeted Therapies to the Sparkling Hope of Supramolecular Targeted Strategies. Int J Mol Sci 2023; 24:ijms24032796. [PMID: 36769134 PMCID: PMC9917659 DOI: 10.3390/ijms24032796] [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: 11/30/2022] [Revised: 01/22/2023] [Accepted: 01/23/2023] [Indexed: 02/05/2023] Open
Abstract
The unprecedented non-reproducibility of the results published in the field of cancer research has recently come under the spotlight. In this short review, we try to highlight some general principles in the organization and evolution of cancerous tumors, which objectively lead to their enormous variability and, consequently, the irreproducibility of the results of their investigation. This heterogeneity is also extremely unfavorable for the effective use of molecularly targeted medicine. Against the seemingly comprehensive background of this heterogeneity, we single out two supramolecular characteristics common to all tumors: the clustered nature of tumor interactions with their microenvironment and the formation of biomolecular condensates with tumor-specific distinctive features. We suggest that these features can form the basis of strategies for tumor-specific supramolecular targeted therapies.
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26
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Nuclear condensates of YAP fusion proteins alter transcription to drive ependymoma tumourigenesis. Nat Cell Biol 2023; 25:323-336. [PMID: 36732631 DOI: 10.1038/s41556-022-01069-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 12/01/2022] [Indexed: 02/04/2023]
Abstract
Nuclear localization of HIPPO-YAP fusion proteins has been implicated in supratentorial ependymoma development. Here, unexpectedly, we find that liquid-liquid phase separation, rather than nuclear localization, of recurrent patient-derived YAP fusions, YAP-MAMLD1 and C11ORF95-YAP, underlies ependymoma tumourigenesis from neural progenitor cells. Mutagenesis and chimaera assays demonstrate that an intrinsically disordered region promotes oligomerization of the YAP fusions into nuclear, puncta-like, membrane-less condensates. Oligomerization and nuclear condensates induced by YAP fusion with a coiled-coil domain of transcriptional activator GCN4 also promote ependymoma formation. YAP-MAMLD1 concentrates transcription factors and co-activators, including BRD4, MED1 and TEAD, in condensates while excluding transcriptional repressive PRC2, and induces long-range enhancer-promoter interactions that promote transcription and oncogenic programmes. Blocking condensate-mediated transcriptional co-activator activity inhibits tumourigenesis, indicating a critical role of liquid phase separation for YAP fusion oncogenic activity in ependymoma. YAP fusions containing the intrinsically disordered region features are common in human tumours, suggesting that nuclear condensates could be targeted to treat YAP-fusion-induced cancers.
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27
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Tani I, Oikawa Y, Doi S, Janairo JIB, Kamada R, Sakaguchi K. Ribosomal protein uL30 undergoes phase separation with nucleophosmin and regulates nucleolar formation in the absence of RNA. Biochem Biophys Res Commun 2023; 642:35-40. [PMID: 36543022 DOI: 10.1016/j.bbrc.2022.12.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
The nucleolus is a membrane-less structure that exists in the nucleus of cells and plays a crucial role in ribosome biogenesis. It is known to be formed through liquid-liquid phase separation (LLPS) caused by the interaction of various nucleolar proteins and nucleic acids. Recently, many studies on LLPS with nucleolar proteins in the presence of RNA showed the importance of electrostatic interactions and cation-pi interactions among RNA and intrinsically disordered regions of proteins. However, it is reported that the initiation of nucleolar formation is RNA polymerase I-independent. The mechanism of nucleolar formation in the early stage remains obscure. In this study, we showed for the first time that the ribosomal protein uL30 and a major nucleolar protein, nucleophosmin (NPM) formed liquid droplets in vitro in the absence of RNA. The liquid droplet formation with uL30 and NPM may be derived from the interaction between the basic regions of uL30 and acidic regions of the oligomeric NPM. The knockdown of uL30 in cells significantly reduced the number of nucleoli, while it did not alter the protein level of NPM. The results showed that LLPS and nucleolar formation were affected by changes in uL30 levels. Our results suggest that the protein-protein interaction between nucleolar proteins may play an important role in nucleolar formation in the early stages when the rRNA content is very low.
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Affiliation(s)
- Itsumi Tani
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Yui Oikawa
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Seiyo Doi
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Jose Isagani B Janairo
- Department of Biology, College of Science, De La Salle University, Manila, 0922, Philippines
| | - Rui Kamada
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Kazuyasu Sakaguchi
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan.
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28
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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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29
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Zhang F, Biswas M, Massah S, Lee J, Lingadahalli S, Wong S, Wells C, Foo J, Khan N, Morin H, Saxena N, Kung SY, Sun B, Parra Nuñez A, Sanchez C, Chan N, Ung L, Altıntaş U, Bui J, Wang Y, Fazli L, Oo H, Rennie P, Lack N, Cherkasov A, Gleave M, Gsponer J, Lallous N. Dynamic phase separation of the androgen receptor and its coactivators key to regulate gene expression. Nucleic Acids Res 2022; 51:99-116. [PMID: 36535377 PMCID: PMC9841400 DOI: 10.1093/nar/gkac1158] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 10/27/2022] [Accepted: 11/21/2022] [Indexed: 12/24/2022] Open
Abstract
Numerous cancers, including prostate cancer (PCa), are addicted to transcription programs driven by specific genomic regions known as super-enhancers (SEs). The robust transcription of genes at such SEs is enabled by the formation of phase-separated condensates by transcription factors and coactivators with intrinsically disordered regions. The androgen receptor (AR), the main oncogenic driver in PCa, contains large disordered regions and is co-recruited with the transcriptional coactivator mediator complex subunit 1 (MED1) to SEs in androgen-dependent PCa cells, thereby promoting oncogenic transcriptional programs. In this work, we reveal that full-length AR forms foci with liquid-like properties in different PCa models. We demonstrate that foci formation correlates with AR transcriptional activity, as this activity can be modulated by changing cellular foci content chemically or by silencing MED1. AR ability to phase separate was also validated in vitro by using recombinant full-length AR protein. We also demonstrate that AR antagonists, which suppress transcriptional activity by targeting key regions for homotypic or heterotypic interactions of this receptor, hinder foci formation in PCa cells and phase separation in vitro. Our results suggest that enhanced compartmentalization of AR and coactivators may play an important role in the activation of oncogenic transcription programs in androgen-dependent PCa.
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Affiliation(s)
- Fan Zhang
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak St., Vancouver, BC V6H 3Z6, Canada
| | | | | | - Joseph Lee
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak St., Vancouver, BC V6H 3Z6, Canada
| | - Shreyas Lingadahalli
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak St., Vancouver, BC V6H 3Z6, Canada
| | - Samantha Wong
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak St., Vancouver, BC V6H 3Z6, Canada
| | - Christopher Wells
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak St., Vancouver, BC V6H 3Z6, Canada
| | - Jane Foo
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak St., Vancouver, BC V6H 3Z6, Canada
| | - Nabeel Khan
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak St., Vancouver, BC V6H 3Z6, Canada
| | - Helene Morin
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak St., Vancouver, BC V6H 3Z6, Canada
| | - Neetu Saxena
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak St., Vancouver, BC V6H 3Z6, Canada
| | - Sonia H Y Kung
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak St., Vancouver, BC V6H 3Z6, Canada
| | - Bei Sun
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak St., Vancouver, BC V6H 3Z6, Canada
| | - Ana Karla Parra Nuñez
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak St., Vancouver, BC V6H 3Z6, Canada
| | - Christophe Sanchez
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak St., Vancouver, BC V6H 3Z6, Canada
| | - Novia Chan
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak St., Vancouver, BC V6H 3Z6, Canada
| | - Lauren Ung
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak St., Vancouver, BC V6H 3Z6, Canada
| | - Umut Berkay Altıntaş
- School of Medicine, Koç University, Rumelifeneri Yolu, Istanbul 34450, Turkey,Koç University Research Centre for Translational Medicine (KUTTAM), Koç University, Rumelifeneri Yolu, Istanbul 34450, Turkey
| | - Jennifer M Bui
- Michael Smith Laboratories, Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Yuzhuo Wang
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak St., Vancouver, BC V6H 3Z6, Canada
| | - Ladan Fazli
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak St., Vancouver, BC V6H 3Z6, Canada
| | - Htoo Zarni Oo
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak St., Vancouver, BC V6H 3Z6, Canada
| | - Paul S Rennie
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak St., Vancouver, BC V6H 3Z6, Canada
| | - Nathan A Lack
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak St., Vancouver, BC V6H 3Z6, Canada,School of Medicine, Koç University, Rumelifeneri Yolu, Istanbul 34450, Turkey,Koç University Research Centre for Translational Medicine (KUTTAM), Koç University, Rumelifeneri Yolu, Istanbul 34450, Turkey
| | - Artem Cherkasov
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak St., Vancouver, BC V6H 3Z6, Canada
| | - Martin E Gleave
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak St., Vancouver, BC V6H 3Z6, Canada
| | - Jörg Gsponer
- Correspondence may also be addressed to Jörg Gsponer.
| | - Nada Lallous
- To whom correspondence should be addressed. Tel: +1 604 875 4111; Fax: +1 604 875 5654;
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30
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Müller F, Christiansen H, Janke W. Phase-Separation Kinetics in the Two-Dimensional Long-Range Ising Model. PHYSICAL REVIEW LETTERS 2022; 129:240601. [PMID: 36563254 DOI: 10.1103/physrevlett.129.240601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 11/08/2022] [Indexed: 06/17/2023]
Abstract
Using Monte Carlo computer simulations, we investigate the kinetics of phase separation in the two-dimensional conserved Ising model with power-law decaying long-range interactions, the prototypical model for many long-range interacting systems. A long-standing analytical prediction for the characteristic length is shown to be applicable. In the simulation, we relied on our novel algorithm which provides a massive speedup for long-range interacting systems.
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Affiliation(s)
- Fabio Müller
- Institut für Theoretische Physik, Universität Leipzig, IPF 231101, 04081 Leipzig, Germany
| | - Henrik Christiansen
- Institut für Theoretische Physik, Universität Leipzig, IPF 231101, 04081 Leipzig, Germany
| | - Wolfhard Janke
- Institut für Theoretische Physik, Universität Leipzig, IPF 231101, 04081 Leipzig, Germany
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31
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Mitrea DM, Mittasch M, Gomes BF, Klein IA, Murcko MA. Modulating biomolecular condensates: a novel approach to drug discovery. Nat Rev Drug Discov 2022; 21:841-862. [PMID: 35974095 PMCID: PMC9380678 DOI: 10.1038/s41573-022-00505-4] [Citation(s) in RCA: 89] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/08/2022] [Indexed: 12/12/2022]
Abstract
In the past decade, membraneless assemblies known as biomolecular condensates have been reported to play key roles in many cellular functions by compartmentalizing specific proteins and nucleic acids in subcellular environments with distinct properties. Furthermore, growing evidence supports the view that biomolecular condensates often form by phase separation, in which a single-phase system demixes into a two-phase system consisting of a condensed phase and a dilute phase of particular biomolecules. Emerging understanding of condensate function in normal and aberrant cellular states, and of the mechanisms of condensate formation, is providing new insights into human disease and revealing novel therapeutic opportunities. In this Perspective, we propose that such insights could enable a previously unexplored drug discovery approach based on identifying condensate-modifying therapeutics (c-mods), and we discuss the strategies, techniques and challenges involved.
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32
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van Tartwijk FW, Kaminski CF. Protein Condensation, Cellular Organization, and Spatiotemporal Regulation of Cytoplasmic Properties. Adv Biol (Weinh) 2022; 6:e2101328. [PMID: 35796197 DOI: 10.1002/adbi.202101328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 05/15/2022] [Indexed: 01/28/2023]
Abstract
The cytoplasm is an aqueous, highly crowded solution of active macromolecules. Its properties influence the behavior of proteins, including their folding, motion, and interactions. In particular, proteins in the cytoplasm can interact to form phase-separated assemblies, so-called biomolecular condensates. The interplay between cytoplasmic properties and protein condensation is critical in a number of functional contexts and is the subject of this review. The authors first describe how cytoplasmic properties can affect protein behavior, in particular condensate formation, and then describe the functional implications of this interplay in three cellular contexts, which exemplify how protein self-organization can be adapted to support certain physiological phenotypes. The authors then describe the formation of RNA-protein condensates in highly polarized cells such as neurons, where condensates play a critical role in the regulation of local protein synthesis, and describe how different stressors trigger extensive reorganization of the cytoplasm, both through signaling pathways and through direct stress-induced changes in cytoplasmic properties. Finally, the authors describe changes in protein behavior and cytoplasmic properties that may occur in extremophiles, in particular organisms that have adapted to inhabit environments of extreme temperature, and discuss the implications and functional importance of these changes.
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Affiliation(s)
- Francesca W van Tartwijk
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
| | - Clemens F Kaminski
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
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33
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de Jesus Salazar-Estrada I, Kamath KS, Liu F. Precision Targeting of Endogenous Epidermal Growth Factor Receptor (EGFR) by Structurally Aligned Dual-Modifier Labeling. ACS Pharmacol Transl Sci 2022; 5:859-871. [PMID: 36268127 PMCID: PMC9578136 DOI: 10.1021/acsptsci.2c00155] [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: 07/31/2022] [Indexed: 11/28/2022]
Abstract
Covalent modification of endogenous proteins by chemical probes is used for proteome-wide profiling of cellular protein function and drug discovery. However, probe selectivity in the complex cellular environment is a challenge, and new probes with better target selectivity are continuously needed. On the basis of the success of monocovalent activity-based and reactivity-based probes, an approach of structurally aligned dual-modifier labeling (SADL) was investigated here on its potential in improving target precision. Two reactive groups, based on the acrylamide and NHS ester chemistry, were linked with structural alignment to be under the same anilinoquinazoline ligand-directive for targeting the epidermal growth factor receptor (EGFR) protein kinase as the model system for proteome-wide profiling. The SADL approach was compared with its monocovalent precursors in a label-free MaxLFQ workflow using MDA-MB-468 triple negative breast cancer cells. The dual-modifier probe consistently showed labeling of EGFR with improved precision over both monocovalent precursors under various controls. The workflow also labeled endogenous USP34 and PKMYT1 with high selectivity. Precision labeling with two covalent modifiers under a common ligand directive may broaden protein identification opportunities in the native environment to complement genetic and antibody-based approaches for elucidating biological or disease mechanisms, as well as accelerating drug target discovery.
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Affiliation(s)
| | | | - Fei Liu
- School
of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
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34
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Tension of plus-end tracking protein Clip170 confers directionality and aggressiveness during breast cancer migration. Cell Death Dis 2022; 13:856. [PMID: 36209218 PMCID: PMC9547975 DOI: 10.1038/s41419-022-05306-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 11/17/2022]
Abstract
The microtubule (MT) plus-end binding protein Clip170 is associated closely with breast cancer invasion and migration. In this study, Clip170 tension observed by a newly designed cpstFRET tension probe was suggested to be positive related to breast cancer aggressiveness, which could be regulated by α-tubulin detyrosination-induced MT disassembly. Clip170 phosphorylation induced by Ribosomal protein S6 kinase (RSK) could also increase its tension and promote the conversion of a discrete comet-like Clip-170 distribution into a spotty pattern during cancer metastasis. Heightened Clip170 tension was correlated with the formation of cortactin-associated filopodia and lamellipodia, and then promoted invasion and metastasis both in vitro and in vivo. Meanwhile, Clip170 tension enhanced at the leading edge in directional migration, accompanying with IQGAP1 subcellular distribution variation. Our work indicates that the malignancy and directionality during breast cancer migration depend on the magnitude and polarization of Clip170 tension, and we suggest Clip170 tension as a new potential drug target for breast cancer therapy.
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35
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Shillcock JC, Lagisquet C, Alexandre J, Vuillon L, Ipsen JH. Model biomolecular condensates have heterogeneous structure quantitatively dependent on the interaction profile of their constituent macromolecules. SOFT MATTER 2022; 18:6674-6693. [PMID: 36004748 DOI: 10.1039/d2sm00387b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Biomolecular condensates play numerous roles in cells by selectively concentrating client proteins while excluding others. These functions are likely to be sensitive to the spatial organization of the scaffold proteins forming the condensate. We use coarse-grained molecular simulations to show that model intrinsically-disordered proteins phase separate into a heterogeneous, structured fluid characterized by a well-defined length scale. The proteins are modelled as semi-flexible polymers with punctate, multifunctional binding sites in good solvent conditions. Their dense phase is highly solvated with a spatial structure that is more sensitive to the separation of the binding sites than their affinity. We introduce graph theoretic measures to quantify their heterogeneity, and find that it increases with increasing binding site number, and exhibits multi-timescale dynamics. The model proteins also swell on passing from the dilute solution to the dense phase. The simulations predict that the structure of the dense phase is modulated by the location and affinity of binding sites distant from the termini of the proteins, while sites near the termini more strongly affect its phase behaviour. The relations uncovered between the arrangement of weak interaction sites on disordered proteins and the material properties of their dense phase can be experimentally tested to give insight into the biophysical properties, pathological effects, and rational design of biomolecular condensates.
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Affiliation(s)
- Julian C Shillcock
- Blue Brain Project and Laboratory of Molecular and Chemical Biology of Neurodegeneration, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
| | - Clément Lagisquet
- LAMA, Univ. Savoie Mont Blanc, CNRS, LAMA, 73376 Le Bourget du Lac, France.
| | - Jérémy Alexandre
- Brain Mind Institute, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Laurent Vuillon
- LAMA, Univ. Savoie Mont Blanc, CNRS, LAMA, 73376 Le Bourget du Lac, France.
| | - John H Ipsen
- Dept. of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
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36
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Chakravarty AK, McGrail DJ, Lozanoski TM, Dunn BS, Shih DJ, Cirillo KM, Cetinkaya SH, Zheng WJ, Mills GB, Yi SS, Jarosz DF, Sahni N. Biomolecular Condensation: A New Phase in Cancer Research. Cancer Discov 2022; 12:2031-2043. [PMID: 35852417 PMCID: PMC9437557 DOI: 10.1158/2159-8290.cd-21-1605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 04/06/2022] [Accepted: 06/08/2022] [Indexed: 01/09/2023]
Abstract
Multicellularity was a watershed development in evolution. However, it also meant that individual cells could escape regulatory mechanisms that restrict proliferation at a severe cost to the organism: cancer. From the standpoint of cellular organization, evolutionary complexity scales to organize different molecules within the intracellular milieu. The recent realization that many biomolecules can "phase-separate" into membraneless organelles, reorganizing cellular biochemistry in space and time, has led to an explosion of research activity in this area. In this review, we explore mechanistic connections between phase separation and cancer-associated processes and emerging examples of how these become deranged in malignancy. SIGNIFICANCE One of the fundamental functions of phase separation is to rapidly and dynamically respond to environmental perturbations. Importantly, these changes often lead to alterations in cancer-relevant pathways and processes. This review covers recent advances in the field, including emerging principles and mechanisms of phase separation in cancer.
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Affiliation(s)
- Anupam K. Chakravarty
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan
| | - Daniel J. McGrail
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, Ohio
| | | | - Brandon S. Dunn
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - David J.H. Shih
- School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, Texas
| | - Kara M. Cirillo
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sueda H. Cetinkaya
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Wenjin Jim Zheng
- School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, Texas
| | - Gordon B. Mills
- Department of Cell, Developmental and Cancer Biology, Knight Cancer Institute, Oregon Health and Sciences University, Portland, Oregon
| | - S. Stephen Yi
- Department of Oncology, Livestrong Cancer Institutes, The University of Texas at Austin, Austin, Texas
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas
- Interdisciplinary Life Sciences Graduate Programs (ILSGP) and Oden Institute for Computational Engineering and Sciences (ICES), The University of Texas at Austin, Austin, Texas
| | - Daniel F. Jarosz
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California
| | - Nidhi Sahni
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Program in Quantitative and Computational Biosciences (QCB), Baylor College of Medicine, Houston, Texas
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
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Peng Q, Tan S, Xia L, Wu N, Oyang L, Tang Y, Su M, Luo X, Wang Y, Sheng X, Zhou Y, Liao Q. Phase separation in Cancer: From the Impacts and Mechanisms to Treatment potentials. Int J Biol Sci 2022; 18:5103-5122. [PMID: 35982902 PMCID: PMC9379413 DOI: 10.7150/ijbs.75410] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 07/16/2022] [Indexed: 12/14/2022] Open
Abstract
Cancer is a public health problem of great concern, and it is also one of the main causes of death in the world. Cancer is a disease characterized by dysregulation of diverse cellular processes, including avoiding growth inhibitory factors, avoiding immune damage and promoting metastasis, etc. However, the precise mechanism of tumorigenesis and tumor progression still needs to be further elucidated. Formations of liquid-liquid phase separation (LLPS) condensates are a common strategy for cells to achieve diverse functions, such as chromatin organization, signal transduction, DNA repair and transcriptional regulation, etc. The biomolecular aggregates formed by LLPS are mainly driven by multivalent weak interactions mediated by intrinsic disordered regions (IDRs) in proteins. In recent years, aberrant phase separations and transition have been reported to be related to the process of various diseases, such as neurodegenerative diseases and cancer. Herein, we discussed recent findings that phase separation regulates tumor-related signaling pathways and thus contributes to tumor progression. We also reviewed some tumor virus-associated proteins to regulate the development of virus-associated tumors via phase separation. Finally, we discussed some possible strategies for treating tumors by targeting phase separation.
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Affiliation(s)
- Qiu Peng
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Shiming Tan
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Longzheng Xia
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Nayiyuan Wu
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Linda Oyang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Yanyan Tang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Min Su
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Xia Luo
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Ying Wang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Xiaowu Sheng
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Yujuan Zhou
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China.,Hunan Key Laboratory of Translational Radiation Oncology, 283 Tongzipo Road, Changsha 410013, Hunan, China
| | - Qianjin Liao
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China.,Hunan Key Laboratory of Translational Radiation Oncology, 283 Tongzipo Road, Changsha 410013, Hunan, China
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Liquid-liquid phase separation in tumor biology. Signal Transduct Target Ther 2022; 7:221. [PMID: 35803926 PMCID: PMC9270353 DOI: 10.1038/s41392-022-01076-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/16/2022] [Accepted: 06/21/2022] [Indexed: 12/12/2022] Open
Abstract
Liquid–liquid phase separation (LLPS) is a novel principle for explaining the precise spatial and temporal regulation in living cells. LLPS compartmentalizes proteins and nucleic acids into micron-scale, liquid-like, membraneless bodies with specific functions, which were recently termed biomolecular condensates. Biomolecular condensates are executors underlying the intracellular spatiotemporal coordination of various biological activities, including chromatin organization, genomic stability, DNA damage response and repair, transcription, and signal transduction. Dysregulation of these cellular processes is a key event in the initiation and/or evolution of cancer, and emerging evidence has linked the formation and regulation of LLPS to malignant transformations in tumor biology. In this review, we comprehensively summarize the detailed mechanisms of biomolecular condensate formation and biophysical function and review the recent major advances toward elucidating the multiple mechanisms involved in cancer cell pathology driven by aberrant LLPS. In addition, we discuss the therapeutic perspectives of LLPS in cancer research and the most recently developed drug candidates targeting LLPS modulation that can be used to combat tumorigenesis.
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Lsm7 phase-separated condensates trigger stress granule formation. Nat Commun 2022; 13:3701. [PMID: 35764627 PMCID: PMC9240020 DOI: 10.1038/s41467-022-31282-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 06/02/2022] [Indexed: 11/09/2022] Open
Abstract
Stress granules (SGs) are non-membranous organelles facilitating stress responses and linking the pathology of age-related diseases. In a genome-wide imaging-based phenomic screen, we identify Pab1 co-localizing proteins under 2-deoxy-D-glucose (2-DG) induced stress in Saccharomyces cerevisiae. We find that deletion of one of the Pab1 co-localizing proteins, Lsm7, leads to a significant decrease in SG formation. Under 2-DG stress, Lsm7 rapidly forms foci that assist in SG formation. The Lsm7 foci form via liquid-liquid phase separation, and the intrinsically disordered region and the hydrophobic clusters within the Lsm7 sequence are the internal driving forces in promoting Lsm7 phase separation. The dynamic Lsm7 phase-separated condensates appear to work as seeding scaffolds, promoting Pab1 demixing and subsequent SG initiation, seemingly mediated by RNA interactions. The SG initiation mechanism, via Lsm7 phase separation, identified in this work provides valuable clues for understanding the mechanisms underlying SG formation and SG-associated human diseases.
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Li M, Park BM, Dai X, Xu Y, Huang J, Sun F. Controlling synthetic membraneless organelles by a red-light-dependent singlet oxygen-generating protein. Nat Commun 2022; 13:3197. [PMID: 35680863 PMCID: PMC9184582 DOI: 10.1038/s41467-022-30933-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 05/19/2022] [Indexed: 12/05/2022] Open
Abstract
Membraneless organelles (MLOs) formed via protein phase separation have great implications for both physiological and pathological processes. However, the inability to precisely control the bioactivities of MLOs has hindered our understanding of their roles in biology, not to mention their translational applications. Here, by combining intrinsically disordered domains such as RGG and mussel-foot proteins, we create an in cellulo protein phase separation system, of which various biological activities can be introduced via metal-mediated protein immobilization and further controlled by the water-soluble chlorophyll protein (WSCP)-a remarkably stable, red-light-responsive singlet oxygen generator. The WSCP-laden protein condensates undergo a liquid-to-solid phase transition on light exposure, due to oxidative crosslinking, providing a means to control catalysis within synthetic MLOs. Moreover, these photoresponsive condensates, which retain the light-induced phase-transition behavior in living cells, exhibit marked membrane localization, reminiscent of the semi-membrane-bound compartments like postsynaptic densities in nervous systems. Together, this engineered system provides an approach toward controllable synthetic MLOs and, alongside its light-induced phase transition, may well serve to emulate and explore the aging process at the subcellular or even molecular level.
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Affiliation(s)
- Manjia Li
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Byung Min Park
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Xin Dai
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Laboratory for Synthetic Chemistry and Chemical Biology, Health@InnoHK, Hong Kong Science Park, Hong Kong, China
| | - Yingjie Xu
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory, Shenzhen, 518036, China
| | - Jinqing Huang
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Fei Sun
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China.
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory, Shenzhen, 518036, China.
- Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, 518036, China.
- HKUST Shenzhen Research Institute, Shenzhen, 518057, China.
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41
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Lu X, Wang J, Wang W, Lu C, Qu T, He X, Liu X, Guo R, Zhang E. Copy number amplification and SP1-activated lncRNA MELTF-AS1 regulates tumorigenesis by driving phase separation of YBX1 to activate ANXA8 in non-small cell lung cancer. Oncogene 2022; 41:3222-3238. [PMID: 35508543 DOI: 10.1038/s41388-022-02292-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 03/17/2022] [Accepted: 03/22/2022] [Indexed: 02/07/2023]
Abstract
Long non-coding RNAs (lncRNAs) are reported to play key roles in tumorigenesis. However, the mechanisms underlying lncRNA-mediated regulation of RNA-binding protein phase separation in tumorigenesis have not been completely elucidated. In this study, an oncogenic lncRNA MELTF-AS1 was identified using systematic data analysis, screening, and verification. MELTF-AS1 was markedly upregulated in non-small cell lung cancer (NSCLC). High MELTF-AS1 levels were associated with advanced tumor-node-metastasis stage (TNM), high tumor size, and decreased survival time. Functionally, MELTF-AS1 regulated cell proliferation and metastasis in vitro and in vivo. RNA sequencing analysis revealed that MELTF-AS1 knockdown specifically modulated genes associated with cell proliferation, apoptosis, and migration. Mechanistically, at the genome level, copy number amplification promoted MELTF-AS1 expression. At the transcriptional level, the transcription factor SP1 directly activated MELTF-AS1 transcription by binding to its promoter. Furthermore, MELTF-AS1 could directly bind and drive the phase separation of YBX1, which was an RNA-binding protein and involved in tumorigenesis, thus activating ANXA8 transcription and promoting tumorigenesis of NSCLC. Aberrant activation of ANXA8 and promotion of tumorigenesis have been found in a variety of tumors. These novel findings demonstrated the critical role of MELTF-AS1-driven phase separation-mediated transcriptional regulation and provided a potential novel diagnostic and therapeutic target for NSCLC.
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Affiliation(s)
- Xiyi Lu
- Department of Oncology, The first Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Jing Wang
- Department of Anatomy, Histology and Embryology, State Key Laboratory of Reproductive Medicine, The Research Center for Bone and Stem Cells, Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Wei Wang
- Department of Thoracic surgery, The first Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Chenfei Lu
- Department of Clinical Medicine, Medical College of Yangzhou University, Yangzhou, Jiangsu, People's Republic of China
| | - Tianyu Qu
- Department of Oncology, The first Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Xuezhi He
- Department of Anatomy, Histology and Embryology, State Key Laboratory of Reproductive Medicine, The Research Center for Bone and Stem Cells, Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Xinyin Liu
- Department of Oncology, The first Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Renhua Guo
- Department of Oncology, The first Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China.
| | - Erbao Zhang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, China.
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42
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Deng S, Feng Y, Pauklin S. 3D chromatin architecture and transcription regulation in cancer. J Hematol Oncol 2022; 15:49. [PMID: 35509102 PMCID: PMC9069733 DOI: 10.1186/s13045-022-01271-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 04/21/2022] [Indexed: 12/18/2022] Open
Abstract
Chromatin has distinct three-dimensional (3D) architectures important in key biological processes, such as cell cycle, replication, differentiation, and transcription regulation. In turn, aberrant 3D structures play a vital role in developing abnormalities and diseases such as cancer. This review discusses key 3D chromatin structures (topologically associating domain, lamina-associated domain, and enhancer-promoter interactions) and corresponding structural protein elements mediating 3D chromatin interactions [CCCTC-binding factor, polycomb group protein, cohesin, and Brother of the Regulator of Imprinted Sites (BORIS) protein] with a highlight of their associations with cancer. We also summarise the recent development of technologies and bioinformatics approaches to study the 3D chromatin interactions in gene expression regulation, including crosslinking and proximity ligation methods in the bulk cell population (ChIA-PET and HiChIP) or single-molecule resolution (ChIA-drop), and methods other than proximity ligation, such as GAM, SPRITE, and super-resolution microscopy techniques.
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Affiliation(s)
- Siwei Deng
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, UK
| | - Yuliang Feng
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, UK
| | - Siim Pauklin
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, UK.
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43
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Nag N, Sasidharan S, Uversky VN, Saudagar P, Tripathi T. Phase separation of FG-nucleoporins in nuclear pore complexes. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2022; 1869:119205. [PMID: 34995711 DOI: 10.1016/j.bbamcr.2021.119205] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/14/2021] [Accepted: 12/23/2021] [Indexed: 12/11/2022]
Abstract
The nuclear envelope (NE) is a bilayer membrane that separates and physically isolates the genetic material from the cytoplasm. Nuclear pore complexes (NPCs) are cylindrical structures embedded in the NE and remain the sole channel of communication between the nucleus and the cytoplasm. The interior of NPCs contains densely packed intrinsically disordered FG-nucleoporins (FG-Nups), consequently forming a permeability barrier. This barrier facilitates the selection and specificity of the cargoes that are imported, exported, or shuttled through the NPCs. Recent studies have revealed that FG-Nups undergo the process of liquid-liquid phase separation into liquid droplets. Moreover, these liquid droplets mimic the permeability barrier observed in the interior of NPCs. This review highlights the phase separation of FG-Nups occurring inside the NPCs rooted in the NE. We discuss the phase separation of FG-Nups and compare the different aspects contributing to their phase separation. Furthermore, several diseases caused by the aberrant phase separation of the proteins are examined with respect to NEs. By understanding the fundamental process of phase separation at the nuclear membrane, the review seeks to explore the parameters influencing this phenomenon as well as its importance, ultimately paving the way for better research on the structure-function relationship of biomolecular condensates.
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Affiliation(s)
- Niharika Nag
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Santanu Sasidharan
- Department of Biotechnology, National Institute of Technology Warangal, Warangal 506004, India
| | - Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33620, United States; Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy pereulok, 9, Dolgoprudny, Moscow Region 141700, Russia
| | - Prakash Saudagar
- Department of Biotechnology, National Institute of Technology Warangal, Warangal 506004, India.
| | - Timir Tripathi
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India.
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Mehta S, Zhang J. Liquid-liquid phase separation drives cellular function and dysfunction in cancer. Nat Rev Cancer 2022; 22:239-252. [PMID: 35149762 PMCID: PMC10036213 DOI: 10.1038/s41568-022-00444-7] [Citation(s) in RCA: 119] [Impact Index Per Article: 59.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/12/2022] [Indexed: 12/11/2022]
Abstract
Cancer is a disease of uncontrollably reproducing cells. It is governed by biochemical pathways that have escaped the regulatory bounds of normal homeostatic balance. This balance is maintained through precise spatiotemporal regulation of these pathways. The formation of biomolecular condensates via liquid-liquid phase separation (LLPS) has recently emerged as a widespread mechanism underlying the spatiotemporal coordination of biological activities in cells. Biomolecular condensates are widely observed to directly regulate key cellular processes involved in cancer cell pathology, and the dysregulation of LLPS is increasingly implicated as a previously hidden driver of oncogenic activity. In this Perspective, we discuss how LLPS shapes the biochemical landscape of cancer cells.
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Affiliation(s)
- Sohum Mehta
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA.
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45
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Veling MT, Nguyen DT, Thadani NN, Oster ME, Rollins NJ, Brock KP, Bethel NP, Lim S, Baker D, Way JC, Marks DS, Chang RL, Silver PA. Natural and Designed Proteins Inspired by Extremotolerant Organisms Can Form Condensates and Attenuate Apoptosis in Human Cells. ACS Synth Biol 2022; 11:1292-1302. [PMID: 35176859 DOI: 10.1021/acssynbio.1c00572] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Many organisms can survive extreme conditions and successfully recover to normal life. This extremotolerant behavior has been attributed in part to repetitive, amphipathic, and intrinsically disordered proteins that are upregulated in the protected state. Here, we assemble a library of approximately 300 naturally occurring and designed extremotolerance-associated proteins to assess their ability to protect human cells from chemically induced apoptosis. We show that several proteins from tardigrades, nematodes, and the Chinese giant salamander are apoptosis-protective. Notably, we identify a region of the human ApoE protein with similarity to extremotolerance-associated proteins that also protects against apoptosis. This region mirrors the phase separation behavior seen with such proteins, like the tardigrade protein CAHS2. Moreover, we identify a synthetic protein, DHR81, that shares this combination of elevated phase separation propensity and apoptosis protection. Finally, we demonstrate that driving protective proteins into the condensate state increases apoptosis protection, and highlights the ability of DHR81 condensates to sequester caspase-7. Taken together, this work draws a link between extremotolerance-associated proteins, condensate formation, and designing human cellular protection.
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Affiliation(s)
- Mike T. Veling
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts 02115, United States
| | - Dan T. Nguyen
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts 02115, United States
| | - Nicole N. Thadani
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Michela E. Oster
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts 02115, United States
| | - Nathan J. Rollins
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts 02115, United States
| | - Kelly P. Brock
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Neville P. Bethel
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, United States
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Samuel Lim
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts 02115, United States
| | - David Baker
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, United States
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, United States
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, United States
| | - Jeffrey C. Way
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts 02115, United States
| | - Debora S. Marks
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
| | - Roger L. Chang
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts 02115, United States
- Department of Systems & Computational Biology, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Pamela A. Silver
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts 02115, United States
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Wilkinson E, Cui YH, He YY. Roles of RNA Modifications in Diverse Cellular Functions. Front Cell Dev Biol 2022; 10:828683. [PMID: 35350378 PMCID: PMC8957929 DOI: 10.3389/fcell.2022.828683] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 02/14/2022] [Indexed: 12/19/2022] Open
Abstract
Chemical modifications of RNA molecules regulate both RNA metabolism and fate. The deposition and function of these modifications are mediated by the actions of writer, reader, and eraser proteins. At the cellular level, RNA modifications regulate several cellular processes including cell death, proliferation, senescence, differentiation, migration, metabolism, autophagy, the DNA damage response, and liquid-liquid phase separation. Emerging evidence demonstrates that RNA modifications play active roles in the physiology and etiology of multiple diseases due to their pervasive roles in cellular functions. Here, we will summarize recent advances in the regulatory and functional role of RNA modifications in these cellular functions, emphasizing the context-specific roles of RNA modifications in mammalian systems. As m6A is the best studied RNA modification in biological processes, this review will summarize the emerging advances on the diverse roles of m6A in cellular functions. In addition, we will also provide an overview for the cellular functions of other RNA modifications, including m5C and m1A. Furthermore, we will also discuss the roles of RNA modifications within the context of disease etiologies and highlight recent advances in the development of therapeutics that target RNA modifications. Elucidating these context-specific functions will increase our understanding of how these modifications become dysregulated during disease pathogenesis and may provide new opportunities for improving disease prevention and therapy by targeting these pathways.
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Affiliation(s)
- Emma Wilkinson
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL, United States
- Committee on Cancer Biology, University of Chicago, Chicago, IL, United States
| | - Yan-Hong Cui
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL, United States
| | - Yu-Ying He
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL, United States
- Committee on Cancer Biology, University of Chicago, Chicago, IL, United States
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Yerramilli VS, Ross AH, Scarlata S, Gericke A. IQGAP1 scaffolding links phosphoinositide kinases to cytoskeletal reorganization. Biophys J 2022; 121:793-807. [PMID: 35077666 PMCID: PMC8943696 DOI: 10.1016/j.bpj.2022.01.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 09/24/2021] [Accepted: 01/21/2022] [Indexed: 11/02/2022] Open
Abstract
IQGAP1 is a multidomain scaffold protein that coordinates the direction and impact of multiple signaling pathways by scaffolding its various binding partners. However, the spatial and temporal resolution of IQGAP1 scaffolding remains unclear. Here, we use fluorescence imaging and correlation methods that allow for real-time live-cell changes in IQGAP1 localization and complex formation during signaling. We find that IQGAP1 and PIPKIγ interact on both the plasma membrane and in cytosol. Epidermal growth factor (EGF) stimulation, which can initiate cytoskeletal changes, drives the movement of the cytosolic pool toward the plasma membrane to promote cytoskeletal changes. We also observe that a significant population of cytosolic IQGAP1-PIPKIγ complexes localize to early endosomes, and in some instances form aggregated clusters which become highly mobile upon EGF stimulation. Our imaging studies show that PIPKIγ and PI3K bind simultaneously to IQGAP1, which may accelerate conversion of PI4P to PI(3,4,5)P3 that is required for cytoskeletal changes. Additionally, we find that IQGAP1 is responsible for PIPKIγ association with two proteins associated with cytoskeletal changes, talin and Cdc42, during EGF stimulation. These results directly show that IQGAP1 provides a physical link between phosphoinositides (through PIPKIγ), focal adhesion formation (through talin), and cytoskeletal reorganization (through Cdc42) upon EGF stimulation. Taken together, our results support the importance of IQGAP1 in regulating cell migration by linking phosphoinositide lipid signaling with cytoskeletal reorganization.
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Affiliation(s)
- V. Siddartha Yerramilli
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts
| | - Alonzo H. Ross
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts,Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Suzanne Scarlata
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts
| | - Arne Gericke
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts.
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Abstract
The 14-3-3 family proteins are vital scaffold proteins that ubiquitously expressed in various tissues. They interact with numerous protein targets and mediate many cellular signaling pathways. The 14-3-3 binding motifs are often embedded in intrinsically disordered regions which are closely associated with liquid-liquid phase separation (LLPS). In the past ten years, LLPS has been observed for a variety of proteins and biological processes, indicating that LLPS plays a fundamental role in the formation of membraneless organelles and cellular condensates. While extensive investigations have been performed on 14-3-3 proteins, its involvement in LLPS is overlooked. To date, 14-3-3 proteins have not been reported to undergo LLPS alone or regulate LLPS of their binding partners. To reveal the potential involvement of 14-3-3 proteins in LLPS, in this review, we summarized the LLPS propensity of 14-3-3 binding partners and found that about one half of them may undergo LLPS spontaneously. We further analyzed the phase separation behavior of representative 14-3-3 binders and discussed how 14-3-3 proteins may be involved. By modulating the conformation and valence of interactions and recruiting other molecules, we speculate that 14-3-3 proteins can efficiently regulate the functions of their targets in the context of LLPS. Considering the critical roles of 14-3-3 proteins, there is an urgent need for investigating the involvement of 14-3-3 proteins in the phase separation process of their targets and the underling mechanisms.
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Loh D, Reiter RJ. Melatonin: Regulation of Prion Protein Phase Separation in Cancer Multidrug Resistance. Molecules 2022; 27:705. [PMID: 35163973 PMCID: PMC8839844 DOI: 10.3390/molecules27030705] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/11/2022] [Accepted: 01/17/2022] [Indexed: 12/13/2022] Open
Abstract
The unique ability to adapt and thrive in inhospitable, stressful tumor microenvironments (TME) also renders cancer cells resistant to traditional chemotherapeutic treatments and/or novel pharmaceuticals. Cancer cells exhibit extensive metabolic alterations involving hypoxia, accelerated glycolysis, oxidative stress, and increased extracellular ATP that may activate ancient, conserved prion adaptive response strategies that exacerbate multidrug resistance (MDR) by exploiting cellular stress to increase cancer metastatic potential and stemness, balance proliferation and differentiation, and amplify resistance to apoptosis. The regulation of prions in MDR is further complicated by important, putative physiological functions of ligand-binding and signal transduction. Melatonin is capable of both enhancing physiological functions and inhibiting oncogenic properties of prion proteins. Through regulation of phase separation of the prion N-terminal domain which targets and interacts with lipid rafts, melatonin may prevent conformational changes that can result in aggregation and/or conversion to pathological, infectious isoforms. As a cancer therapy adjuvant, melatonin could modulate TME oxidative stress levels and hypoxia, reverse pH gradient changes, reduce lipid peroxidation, and protect lipid raft compositions to suppress prion-mediated, non-Mendelian, heritable, but often reversible epigenetic adaptations that facilitate cancer heterogeneity, stemness, metastasis, and drug resistance. This review examines some of the mechanisms that may balance physiological and pathological effects of prions and prion-like proteins achieved through the synergistic use of melatonin to ameliorate MDR, which remains a challenge in cancer treatment.
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Affiliation(s)
- Doris Loh
- Independent Researcher, Marble Falls, TX 78654, USA
| | - Russel J. Reiter
- Department of Cellular and Structural Biology, UT Health San Antonio, San Antonio, TX 78229, USA
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Gadhe L, Sakunthala A, Mukherjee S, Gahlot N, Bera R, Sawner AS, Kadu P, Maji SK. Intermediates of α-synuclein aggregation: Implications in Parkinson's disease pathogenesis. Biophys Chem 2021; 281:106736. [PMID: 34923391 DOI: 10.1016/j.bpc.2021.106736] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/27/2021] [Accepted: 11/27/2021] [Indexed: 12/11/2022]
Abstract
Cytoplasmic deposition of aberrantly misfolded α-synuclein (α-Syn) is a common feature of synucleinopathies, including Parkinson's disease (PD). However, the precise pathogenic mechanism of α-Syn in synucleinopathies remains elusive. Emerging evidence has suggested that α-Syn may contribute to PD pathogenesis in several ways; wherein the contribution of fibrillar species, for exerting toxicity and disease transmission, cannot be neglected. Further, the oligomeric species could be the most plausible neurotoxic species causing neuronal cell death. However, understanding the structural and molecular insights of these oligomers are very challenging due to the heterogeneity and transient nature of the species. In this review, we discuss the recent advancements in understanding the formation and role of α-Syn oligomers in PD pathogenesis. We also summarize the different types of α-Syn oligomeric species and potential mechanisms to exert neurotoxicity. Finally, we address the possible ways to target α-Syn as a promising approach against PD and the possible future directions.
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Affiliation(s)
- Laxmikant Gadhe
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India
| | - Arunima Sakunthala
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India
| | - Semanti Mukherjee
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India
| | - Nitisha Gahlot
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India
| | - Riya Bera
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India
| | - Ajay Singh Sawner
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India
| | - Pradeep Kadu
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India
| | - Samir K Maji
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India.
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