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Davis RB, Supakar A, Ranganath AK, Moosa MM, Banerjee PR. Heterotypic interactions can drive selective co-condensation of prion-like low-complexity domains of FET proteins and mammalian SWI/SNF complex. Nat Commun 2024; 15:1168. [PMID: 38326345 PMCID: PMC10850361 DOI: 10.1038/s41467-024-44945-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 01/08/2024] [Indexed: 02/09/2024] Open
Abstract
Prion-like domains (PLDs) are low-complexity protein sequences enriched within nucleic acid-binding proteins including those involved in transcription and RNA processing. PLDs of FUS and EWSR1 play key roles in recruiting chromatin remodeler mammalian SWI/SNF (mSWI/SNF) complex to oncogenic FET fusion protein condensates. Here, we show that disordered low-complexity domains of multiple SWI/SNF subunits are prion-like with a strong propensity to undergo intracellular phase separation. These PLDs engage in sequence-specific heterotypic interactions with the PLD of FUS in the dilute phase at sub-saturation conditions, leading to the formation of PLD co-condensates. In the dense phase, homotypic and heterotypic PLD interactions are highly cooperative, resulting in the co-mixing of individual PLD phases and forming spatially homogeneous condensates. Heterotypic PLD-mediated positive cooperativity in protein-protein interaction networks is likely to play key roles in the co-phase separation of mSWI/SNF complex with transcription factors containing homologous low-complexity domains.
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Affiliation(s)
- Richoo B Davis
- Department of Physics, University at Buffalo, Buffalo, NY, 14260, USA
| | - Anushka Supakar
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA
| | | | | | - Priya R Banerjee
- Department of Physics, University at Buffalo, Buffalo, NY, 14260, USA.
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA.
- Department of Chemical and Biological Engineering, University at Buffalo, Buffalo, NY, 14260, USA.
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2
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Umeda M, Ma J, Westover T, Ni Y, Song G, Maciaszek JL, Rusch M, Rahbarinia D, Foy S, Huang BJ, Walsh MP, Kumar P, Liu Y, Yang W, Fan Y, Wu G, Baker SD, Ma X, Wang L, Alonzo TA, Rubnitz JE, Pounds S, Klco JM. A new genomic framework to categorize pediatric acute myeloid leukemia. Nat Genet 2024; 56:281-293. [PMID: 38212634 PMCID: PMC10864188 DOI: 10.1038/s41588-023-01640-3] [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: 05/11/2023] [Accepted: 12/05/2023] [Indexed: 01/13/2024]
Abstract
Recent studies on pediatric acute myeloid leukemia (pAML) have revealed pediatric-specific driver alterations, many of which are underrepresented in the current classification schemas. To comprehensively define the genomic landscape of pAML, we systematically categorized 887 pAML into 23 mutually distinct molecular categories, including new major entities such as UBTF or BCL11B, covering 91.4% of the cohort. These molecular categories were associated with unique expression profiles and mutational patterns. For instance, molecular categories characterized by specific HOXA or HOXB expression signatures showed distinct mutation patterns of RAS pathway genes, FLT3 or WT1, suggesting shared biological mechanisms. We show that molecular categories were strongly associated with clinical outcomes using two independent cohorts, leading to the establishment of a new prognostic framework for pAML based on these updated molecular categories and minimal residual disease. Together, this comprehensive diagnostic and prognostic framework forms the basis for future classification of pAML and treatment strategies.
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Affiliation(s)
- Masayuki Umeda
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jing Ma
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Tamara Westover
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yonghui Ni
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Guangchun Song
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jamie L Maciaszek
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Michael Rusch
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Delaram Rahbarinia
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Scott Foy
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Benjamin J Huang
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Michael P Walsh
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Priyadarshini Kumar
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yanling Liu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Wenjian Yang
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yiping Fan
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Gang Wu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Sharyn D Baker
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Xiaotu Ma
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Lu Wang
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Todd A Alonzo
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jeffrey E Rubnitz
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Stanley Pounds
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jeffery M Klco
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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3
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Schöpf J, Uhrig S, Heilig CE, Lee KS, Walther T, Carazzato A, Dobberkau AM, Weichenhan D, Plass C, Hartmann M, Diwan GD, Carrero ZI, Ball CR, Hohl T, Kindler T, Rudolph-Hähnel P, Helm D, Schneider M, Nilsson A, Øra I, Imle R, Banito A, Russell RB, Jones BC, Lipka DB, Glimm H, Hübschmann D, Hartmann W, Fröhling S, Scholl C. Multi-omic and functional analysis for classification and treatment of sarcomas with FUS-TFCP2 or EWSR1-TFCP2 fusions. Nat Commun 2024; 15:51. [PMID: 38168093 PMCID: PMC10761971 DOI: 10.1038/s41467-023-44360-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024] Open
Abstract
Linking clinical multi-omics with mechanistic studies may improve the understanding of rare cancers. We leverage two precision oncology programs to investigate rhabdomyosarcoma with FUS/EWSR1-TFCP2 fusions, an orphan malignancy without effective therapies. All tumors exhibit outlier ALK expression, partly accompanied by intragenic deletions and aberrant splicing resulting in ALK variants that are oncogenic and sensitive to ALK inhibitors. Additionally, recurrent CKDN2A/MTAP co-deletions provide a rationale for PRMT5-targeted therapies. Functional studies show that FUS-TFCP2 blocks myogenic differentiation, induces transcription of ALK and truncated TERT, and inhibits DNA repair. Unlike other fusion-driven sarcomas, TFCP2-rearranged tumors exhibit genomic instability and signs of defective homologous recombination. DNA methylation profiling demonstrates a close relationship with undifferentiated sarcomas. In two patients, sarcoma was preceded by benign lesions carrying FUS-TFCP2, indicating stepwise sarcomagenesis. This study illustrates the potential of linking precision oncology with preclinical research to gain insight into the classification, pathogenesis, and therapeutic vulnerabilities of rare cancers.
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Affiliation(s)
- Julia Schöpf
- Division of Applied Functional Genomics, German Cancer Research Center (DKFZ), and National Center for Tumor Diseases (NCT), NCT Heidelberg, a Partnership Between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
- Division of Translational Medical Oncology, DKFZ, and NCT Heidelberg, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Sebastian Uhrig
- Computational Oncology Group, Molecular Precision Oncology Program, NCT Heidelberg, and DKFZ, Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Christoph E Heilig
- Division of Translational Medical Oncology, DKFZ, and NCT Heidelberg, Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Kwang-Seok Lee
- Division of Translational Medical Oncology, DKFZ, and NCT Heidelberg, Heidelberg, Germany
| | - Tatjana Walther
- Division of Translational Medical Oncology, DKFZ, and NCT Heidelberg, Heidelberg, Germany
| | - Alexander Carazzato
- Division of Translational Medical Oncology, DKFZ, and NCT Heidelberg, Heidelberg, Germany
| | - Anna Maria Dobberkau
- Section of Translational Cancer Epigenomics, Division of Translational Medical Oncology, DKFZ, and NCT Heidelberg, Heidelberg, Germany
| | | | | | - Mark Hartmann
- Section of Translational Cancer Epigenomics, Division of Translational Medical Oncology, DKFZ, and NCT Heidelberg, Heidelberg, Germany
| | - Gaurav D Diwan
- Bioquant, Heidelberg University, Heidelberg, Germany
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Zunamys I Carrero
- Department for Translational Medical Oncology, NCT, NCT/UCC Dresden, a Partnership Between DKFZ, Heidelberg Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
| | - Claudia R Ball
- Department for Translational Medical Oncology, NCT, NCT/UCC Dresden, a Partnership Between DKFZ, Heidelberg Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD, Dresden, Germany
- Faculty of Biology, TUD Dresden University of Technology, Dresden, Germany
| | - Tobias Hohl
- Division of Applied Functional Genomics, German Cancer Research Center (DKFZ), and National Center for Tumor Diseases (NCT), NCT Heidelberg, a Partnership Between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Thomas Kindler
- University Cancer Center Mainz, Johannes Gutenberg University Mainz, Mainz, Germany
- Department of Hematology, Medical Oncology and Pneumology, University Medical Center, Mainz, Germany
- German Cancer Consortium (DKTK), Mainz, Germany
| | - Patricia Rudolph-Hähnel
- University Cancer Center Mainz, Johannes Gutenberg University Mainz, Mainz, Germany
- Department of Hematology, Medical Oncology and Pneumology, University Medical Center, Mainz, Germany
- German Cancer Consortium (DKTK), Mainz, Germany
| | - Dominic Helm
- Proteomics Core Facility, DKFZ, Heidelberg, Germany
| | | | - Anna Nilsson
- Pediatric Oncology and Coagulation, Karolinska University Hospital, Stockholm, Sweden
| | - Ingrid Øra
- Pediatric Oncology and Hematology, Skåne University Hospital, Lund University, Lund, Sweden
| | - Roland Imle
- Soft-Tissue Sarcoma Junior Research Group, DKFZ, Heidelberg, Germany
- Hopp Children's Cancer Center (KiTZ) and NCT Heidelberg, Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Ana Banito
- Soft-Tissue Sarcoma Junior Research Group, DKFZ, Heidelberg, Germany
- Hopp Children's Cancer Center (KiTZ) and NCT Heidelberg, Heidelberg, Germany
| | - Robert B Russell
- Bioquant, Heidelberg University, Heidelberg, Germany
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Barbara C Jones
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Hopp Children's Cancer Center (KiTZ) and NCT Heidelberg, Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Daniel B Lipka
- Section of Translational Cancer Epigenomics, Division of Translational Medical Oncology, DKFZ, and NCT Heidelberg, Heidelberg, Germany
| | - Hanno Glimm
- Department for Translational Medical Oncology, NCT, NCT/UCC Dresden, a Partnership Between DKFZ, Heidelberg Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD, Dresden, Germany
- Translational Functional Cancer Genomics, DKFZ, Heidelberg, Germany
| | - Daniel Hübschmann
- Computational Oncology Group, Molecular Precision Oncology Program, NCT Heidelberg, and DKFZ, Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Pattern Recognition and Digital Medicine Group, Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM), Heidelberg, Germany
| | - Wolfgang Hartmann
- Gerhard Domagk Institute of Pathology, University Hospital Münster, Münster, Germany
| | - Stefan Fröhling
- Division of Translational Medical Oncology, DKFZ, and NCT Heidelberg, Heidelberg, Germany.
- German Cancer Consortium (DKTK), Heidelberg, Germany.
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany.
| | - Claudia Scholl
- Division of Applied Functional Genomics, German Cancer Research Center (DKFZ), and National Center for Tumor Diseases (NCT), NCT Heidelberg, a Partnership Between DKFZ and Heidelberg University Hospital, Heidelberg, Germany.
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4
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Wang Y, Yu C, Pei G, Jia W, Li T, Li P. Dissolution of oncofusion transcription factor condensates for cancer therapy. Nat Chem Biol 2023; 19:1223-1234. [PMID: 37400539 DOI: 10.1038/s41589-023-01376-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 06/01/2023] [Indexed: 07/05/2023]
Abstract
Cancer-associated chromosomal rearrangements can result in the expression of numerous pathogenic fusion proteins. The mechanisms by which fusion proteins contribute to oncogenesis are largely unknown, and effective therapies for fusion-associated cancers are lacking. Here we comprehensively scrutinized fusion proteins found in various cancers. We found that many fusion proteins are composed of phase separation-prone domains (PSs) and DNA-binding domains (DBDs), and these fusions have strong correlations with aberrant gene expression patterns. Furthermore, we established a high-throughput screening method, named DropScan, to screen drugs capable of modulating aberrant condensates. One of the drugs identified via DropScan, LY2835219, effectively dissolved condensates in reporter cell lines expressing Ewing sarcoma fusions and partially rescued the abnormal expression of target genes. Our results indicate that aberrant phase separation is likely a common mechanism for these PS-DBD fusion-related cancers and suggest that modulating aberrant phase separation is a potential route to treat these diseases.
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Affiliation(s)
- Yuan Wang
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua University-Peking University Joint Centre for Life Sciences, Beijing, China
| | - Chunyu Yu
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China
| | - Gaofeng Pei
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua University-Peking University Joint Centre for Life Sciences, Beijing, China
| | - Wen Jia
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua University-Peking University Joint Centre for Life Sciences, Beijing, China
| | - Tingting Li
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.
- Key Laboratory for Neuroscience, Ministry of Education/National Health Commission of China, Peking University, Beijing, China.
| | - Pilong Li
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China.
- Tsinghua University-Peking University Joint Centre for Life Sciences, Beijing, China.
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5
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Ma S, Liao K, Li M, Wang X, Lv J, Zhang X, Huang H, Li L, Huang T, Guo X, Lin Y, Rong Z. Phase-separated DropCRISPRa platform for efficient gene activation in mammalian cells and mice. Nucleic Acids Res 2023; 51:5271-5284. [PMID: 37094074 PMCID: PMC10250237 DOI: 10.1093/nar/gkad301] [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: 06/27/2022] [Revised: 04/05/2023] [Accepted: 04/21/2023] [Indexed: 04/26/2023] Open
Abstract
Liquid-liquid phase separation (LLPS) plays a critical role in regulating gene transcription via the formation of transcriptional condensates. However, LLPS has not been reported to be engineered as a tool to activate endogenous gene expression in mammalian cells or in vivo. Here, we developed a droplet-forming CRISPR (clustered regularly interspaced short palindromic repeats) gene activation system (DropCRISPRa) to activate transcription with high efficiency via combining the CRISPR-SunTag system with FETIDR-AD fusion proteins, which contain an N-terminal intrinsically disordered region (IDR) of a FET protein (FUS or TAF15) and a transcription activation domain (AD, VP64/P65/VPR). In this system, the FETIDR-AD fusion protein formed phase separation condensates at the target sites, which could recruit endogenous BRD4 and RNA polymerase II with an S2 phosphorylated C-terminal domain (CTD) to enhance transcription elongation. IDR-FUS9Y>S and IDR-FUSG156E, two mutants with deficient and aberrant phase separation respectively, confirmed that appropriate phase separation was required for efficient gene activation. Further, the DropCRISPRa system was compatible with a broad set of CRISPR-associated (Cas) proteins and ADs, including dLbCas12a, dAsCas12a, dSpCas9 and the miniature dUnCas12f1, and VP64, P65 and VPR. Finally, the DropCRISPRa system could activate target genes in mice. Therefore, this study provides a robust tool to activate gene expression for foundational research and potential therapeutics.
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Affiliation(s)
- Shufeng Ma
- Department of Nephrology, Shenzhen Hospital, Southern Medical University, Shenzhen 518110, China
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou 510515, China
| | - Kaitong Liao
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou 510515, China
| | - Mengrao Li
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou 510515, China
| | - Xinlong Wang
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou 510515, China
| | - Jie Lv
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou 510515, China
| | - Xin Zhang
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou 510515, China
- Affiliated Dongguan Hospital, Southern Medical University, (Dongguan People's Hospital), Dongguan 523058, China
| | - Hongxin Huang
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| | - Lian Li
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou 510515, China
| | - Tao Huang
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou 510515, China
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| | - Xiaohua Guo
- Department of Nephrology, Shenzhen Hospital, Southern Medical University, Shenzhen 518110, China
| | - Ying Lin
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou 510515, China
- Experimental Education/Administration Center, School of Basic Medical Science, Southern Medical University, Guangzhou 510515, China
| | - Zhili Rong
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou 510515, China
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
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6
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Light, Water, and Melatonin: The Synergistic Regulation of Phase Separation in Dementia. Int J Mol Sci 2023; 24:ijms24065835. [PMID: 36982909 PMCID: PMC10054283 DOI: 10.3390/ijms24065835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 03/17/2023] [Indexed: 03/22/2023] Open
Abstract
The swift rise in acceptance of molecular principles defining phase separation by a broad array of scientific disciplines is shadowed by increasing discoveries linking phase separation to pathological aggregations associated with numerous neurodegenerative disorders, including Alzheimer’s disease, that contribute to dementia. Phase separation is powered by multivalent macromolecular interactions. Importantly, the release of water molecules from protein hydration shells into bulk creates entropic gains that promote phase separation and the subsequent generation of insoluble cytotoxic aggregates that drive healthy brain cells into diseased states. Higher viscosity in interfacial waters and limited hydration in interiors of biomolecular condensates facilitate phase separation. Light, water, and melatonin constitute an ancient synergy that ensures adequate protein hydration to prevent aberrant phase separation. The 670 nm visible red wavelength found in sunlight and employed in photobiomodulation reduces interfacial and mitochondrial matrix viscosity to enhance ATP production via increasing ATP synthase motor efficiency. Melatonin is a potent antioxidant that lowers viscosity to increase ATP by scavenging excess reactive oxygen species and free radicals. Reduced viscosity by light and melatonin elevates the availability of free water molecules that allow melatonin to adopt favorable conformations that enhance intrinsic features, including binding interactions with adenosine that reinforces the adenosine moiety effect of ATP responsible for preventing water removal that causes hydrophobic collapse and aggregation in phase separation. Precise recalibration of interspecies melatonin dosages that account for differences in metabolic rates and bioavailability will ensure the efficacious reinstatement of the once-powerful ancient synergy between light, water, and melatonin in a modern world.
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7
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MANF/EWSR1/ANXA6 pathway might as the bridge between hypolipidemia and major depressive disorder. Transl Psychiatry 2022; 12:527. [PMID: 36585419 PMCID: PMC9803680 DOI: 10.1038/s41398-022-02287-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 12/08/2022] [Accepted: 12/13/2022] [Indexed: 12/31/2022] Open
Abstract
Major depressive disorder (MDD) involves changes in lipid metabolism, but previous findings are contradictory. Mesencephalic astrocyte-derived neurotrophic factor (MANF) is considered to be a regulator of lipid metabolism. To date, the function of MANF has been studied in many brain disorders, but not in MDD. Therefore, to better understand the role of lipids in MDD, this study was conducted to examine lipid levels in the serum of MDD patients and to investigate the potential function of MANF in MDD. First, the data on total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), and triglyceride (TG) in serum from 354 MDD patients and 360 healthy controls (HCs) were collected and analyzed. The results showed that there were significantly lower concentrations of TC and LDL-C in MDD patients compared with HCs, and TC levels were positively correlated with LDL-C levels. Bioinformatics analysis indicated that MANF/EWSR1/ANXA6 pathway might serve as the connecting bridge through which hypolipidemia played a functional role in MDD. Second, to verify this hypothesis, serum samples were collected from 143 MDD patients, and 67 HCs to measure the levels of MANF, EWSR1, and ANXA6 using ELISA kits. The results showed that compared to HCs, MDD patients had a significantly lower level of MANF and higher levels of ANXA6 and EWSR1, and these molecules were significantly correlated with both TC level and Hamilton Depression Rating Scales (HDRS) score. In addition, a discriminative model consisting of MANF, EWSR1, and ANXA6 was identified. This model was capable of distinguishing MDD subjects from HCs, yielded an area under curve of 0.9994 in the training set and 0.9569 in the testing set. Taken together, our results suggested that MANF/EWSR1/ANXA6 pathway might act as the bridge between hypolipidemia and MDD, and these molecules held promise as potential biomarkers for MDD.
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8
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Ectopic biomolecular phase transitions: fusion proteins in cancer pathologies. Trends Cell Biol 2022; 32:681-695. [PMID: 35484036 PMCID: PMC9288518 DOI: 10.1016/j.tcb.2022.03.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/13/2022] [Accepted: 03/18/2022] [Indexed: 12/22/2022]
Abstract
Biomolecular condensates are membraneless organelles (MLOs) that are enriched in specific proteins and nucleic acids, compartmentalized to perform biochemical functions. Such condensates are formed by phase separation (PS) enabled by protein domains that allow multivalent interactions. Chromosomal translocation-derived in-frame gene fusions often generate proteins with non-native domain combinations that rewire protein-protein interaction networks. Several recent studies have shown that, for a subset of these fusion proteins, pathogenesis can be driven by the ability of the fusion protein to undergo phase transitions at non-physiological cellular locations to form ectopic condensates. We highlight how such ectopic phase transitions can alter biological processes and posit that dysfunction via protein PS at non-physiological locations represents a generic route to oncogenic transformation.
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9
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Loci-specific phase separation of FET fusion oncoproteins promotes gene transcription. Nat Commun 2021; 12:1491. [PMID: 33674598 PMCID: PMC7935978 DOI: 10.1038/s41467-021-21690-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 02/08/2021] [Indexed: 12/17/2022] Open
Abstract
Abnormally formed FUS/EWS/TAF15 (FET) fusion oncoproteins are essential oncogenic drivers in many human cancers. Interestingly, at the molecular level, they also form biomolecular condensates at specific loci. However, how these condensates lead to gene transcription and how features encoded in the DNA element regulate condensate formation remain unclear. Here, we develop an in vitro single-molecule assay to visualize phase separation on DNA. Using this technique, we observe that FET fusion proteins undergo phase separation at target binding loci and the phase separated condensates recruit RNA polymerase II and enhance gene transcription. Furthermore, we determine a threshold number of fusion-binding DNA elements that can enhance the formation of FET fusion protein condensates. These findings suggest that FET fusion oncoprotein promotes aberrant gene transcription through loci-specific phase separation, which may contribute to their oncogenic transformation ability in relevant cancers, such as sarcomas and leukemia.
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10
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Yu JSE, Colborne S, Hughes CS, Morin GB, Nielsen TO. The FUS-DDIT3 Interactome in Myxoid Liposarcoma. Neoplasia 2019; 21:740-751. [PMID: 31220736 PMCID: PMC6584455 DOI: 10.1016/j.neo.2019.05.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 05/10/2019] [Accepted: 05/13/2019] [Indexed: 12/13/2022] Open
Abstract
Myxoid liposarcoma is a malignant lipogenic tumor that develops in deep soft tissues. While local control rates are good, current chemotherapy options remain ineffective against metastatic disease. Myxoid liposarcoma is characterized by the FUS-DDIT3 fusion oncoprotein that is proposed to function as an aberrant transcription factor, but its exact mechanism of action has remained unclear. To identify the key functional interacting partners of FUS-DDIT3, this study utilized immunoprecipitation-mass spectrometry (IP-MS) to identify the FUS-DDIT3 interactome in whole cell lysates of myxoid liposarcoma cells, and results showed an enrichment of RNA processing proteins. Further quantitative MS analyses of FUS-DDIT3 complexes isolated from nuclear lysates showed that members of several chromatin regulatory complexes were present in the FUS-DDIT3 interactome, including NuRD, SWI/SNF, PRC1, PRC2, and MLL1 COMPASS-like complexes. Co-immunoprecipitation validated the associations of FUS-DDIT3 with BRG1/SMARCA4, BAF155/SMARCC1, BAF57/SMARCE1, and KDM1A. Data from this study provides candidates for functional validation as potential therapeutic targets, particularly for emerging epigenetic drugs.
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Affiliation(s)
- Jamie S E Yu
- Department of Pathology, University of British Columbia, Vancouver, BC V5Z 1M9, Canada.
| | - Shane Colborne
- British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada.
| | | | - Gregg B Morin
- British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada.
| | - Torsten O Nielsen
- Department of Pathology, University of British Columbia, Vancouver, BC V5Z 1M9, Canada.
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11
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Ouyang H, Zhang K, Fox-Walsh K, Yang Y, Zhang C, Huang J, Li H, Zhou Y, Fu XD. The RNA binding protein EWS is broadly involved in the regulation of pri-miRNA processing in mammalian cells. Nucleic Acids Res 2019; 45:12481-12495. [PMID: 30053258 PMCID: PMC5716145 DOI: 10.1093/nar/gkx912] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 09/27/2017] [Indexed: 12/13/2022] Open
Abstract
The Ewing Sarcoma protein (EWS) is a multifaceted RNA binding protein (RBP) with established roles in transcription, pre-mRNA processing and DNA damage response. By generating high quality EWS-RNA interactome, we uncovered its specific and prevalent interaction with a large subset of primary microRNAs (pri-miRNAs) in mammalian cells. Knockdown of EWS reduced, whereas overexpression enhanced, the expression of its target miRNAs. Biochemical analysis revealed that multiple elements in target pri-miRNAs, including the sequences flanking the stem-loop region, contributed to high affinity EWS binding and sequence swap experiments between target and non-target demonstrated that the flanking sequences provided the specificity for enhanced pri-miRNA processing by the Microprocessor Drosha/DGCR8. Interestingly, while repressing Drosha expression, as reported earlier, we found that EWS was able to enhance the recruitment of Drosha to chromatin. Together, these findings suggest that EWS may positively and negatively regulate miRNA biogenesis via distinct mechanisms, thus providing a new foundation to understand the function of EWS in development and disease.
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Affiliation(s)
- Huiwu Ouyang
- State Key Laboratory of Virology and Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Kai Zhang
- State Key Laboratory of Virology and Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Kristi Fox-Walsh
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA
| | - Yang Yang
- State Key Laboratory of Virology and Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Chen Zhang
- State Key Laboratory of Virology and Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jie Huang
- State Key Laboratory of Virology and Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Hairi Li
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA
| | - Yu Zhou
- State Key Laboratory of Virology and Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China.,Institue of Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Xiang-Dong Fu
- State Key Laboratory of Virology and Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China.,Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA
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12
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Lindén M, Thomsen C, Grundevik P, Jonasson E, Andersson D, Runnberg R, Dolatabadi S, Vannas C, Luna Santamarίa M, Fagman H, Ståhlberg A, Åman P. FET family fusion oncoproteins target the SWI/SNF chromatin remodeling complex. EMBO Rep 2019; 20:embr.201845766. [PMID: 30962207 PMCID: PMC6500973 DOI: 10.15252/embr.201845766] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Revised: 03/06/2019] [Accepted: 03/11/2019] [Indexed: 12/15/2022] Open
Abstract
Members of the human FET family of RNA‐binding proteins, comprising FUS, EWSR1, and TAF15, are ubiquitously expressed and engage at several levels of gene regulation. Many sarcomas and leukemias are characterized by the expression of fusion oncogenes with FET genes as 5′ partners and alternative transcription factor‐coding genes as 3′ partners. Here, we report that the N terminus of normal FET proteins and their oncogenic fusion counterparts interact with the SWI/SNF chromatin remodeling complex. In contrast to normal FET proteins, increased fractions of FET oncoproteins bind SWI/SNF, indicating a deregulated and enhanced interaction in cancer. Forced expression of FET oncogenes caused changes of global H3K27 trimethylation levels, accompanied by altered gene expression patterns suggesting a shift in the antagonistic balance between SWI/SNF and repressive polycomb group complexes. Thus, deregulation of SWI/SNF activity could provide a unifying pathogenic mechanism for the large group of tumors caused by FET fusion oncoproteins. These results may help to develop common strategies for therapy.
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Affiliation(s)
- Malin Lindén
- Department of Pathology and Genetics, Sahlgrenska Cancer Center, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Christer Thomsen
- Department of Pathology and Genetics, Sahlgrenska Cancer Center, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Pathology and Genetics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Pernilla Grundevik
- Department of Pathology and Genetics, Sahlgrenska Cancer Center, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Emma Jonasson
- Department of Pathology and Genetics, Sahlgrenska Cancer Center, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Daniel Andersson
- Department of Pathology and Genetics, Sahlgrenska Cancer Center, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Rikard Runnberg
- Department of Pathology and Genetics, Sahlgrenska Cancer Center, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Soheila Dolatabadi
- Department of Pathology and Genetics, Sahlgrenska Cancer Center, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Christoffer Vannas
- Department of Pathology and Genetics, Sahlgrenska Cancer Center, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Oncology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Manuel Luna Santamarίa
- Department of Pathology and Genetics, Sahlgrenska Cancer Center, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Henrik Fagman
- Department of Pathology and Genetics, Sahlgrenska Cancer Center, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Pathology and Genetics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Anders Ståhlberg
- Department of Pathology and Genetics, Sahlgrenska Cancer Center, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden .,Department of Clinical Pathology and Genetics, Sahlgrenska University Hospital, Gothenburg, Sweden.,Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Pierre Åman
- Department of Pathology and Genetics, Sahlgrenska Cancer Center, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden .,Department of Clinical Pathology and Genetics, Sahlgrenska University Hospital, Gothenburg, Sweden
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13
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Alonso R, Pisa D, Carrasco L. Searching for Bacteria in Neural Tissue From Amyotrophic Lateral Sclerosis. Front Neurosci 2019; 13:171. [PMID: 30863279 PMCID: PMC6399391 DOI: 10.3389/fnins.2019.00171] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 02/13/2019] [Indexed: 12/28/2022] Open
Abstract
Despite great efforts in the investigation, the exact etiology of amyotrophic lateral sclerosis (ALS) is a matter of intensive research. We recently advanced the idea that ALS might be caused by fungal infection. Indeed, fungal yeast and hyphal structures can be directly visualized in neural tissue of ALS patients, and a number of fungal species have been identified in the central nervous system (CNS). In the present work, we tested the possibility that bacterial infections can accompany these mycoses. Our findings establish the presence of bacterial DNA in different regions of the CNS from all ALS patients examined. Specifically, we used PCR and next generation sequencing (NGS) to precisely determine the bacterial species present in ALS tissue. Consistent with these findings, immunohistochemistry analysis of CNS sections using specific anti-bacterial antibodies identified prokaryotic cells in neural tissue. Finally, we assayed for the repeat expansion of the hexanucleotide repeat GGGGCC in C9orf72, which is considered the most common genetic cause of ALS in patients, using DNA extracted from ALS CNS tissue. We failed to find this repeated sequence in any of the eleven patients analyzed. Our results indicate that bacterial DNA and prokaryotic cells are present in CNS tissue, leading to the concept that both fungal and bacterial infections coexist in patients with ALS. These observations lay the groundwork for the use of appropriate therapies to eradicate the polymicrobial infections in ALS.
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Affiliation(s)
- Ruth Alonso
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | - Diana Pisa
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | - Luis Carrasco
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
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14
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Alonso R, Pisa D, Fernández-Fernández AM, Rábano A, Carrasco L. Fungal infection in neural tissue of patients with amyotrophic lateral sclerosis. Neurobiol Dis 2017; 108:249-260. [DOI: 10.1016/j.nbd.2017.09.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 08/24/2017] [Accepted: 09/03/2017] [Indexed: 12/11/2022] Open
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15
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Mackenzie IRA, Neumann M. Fused in Sarcoma Neuropathology in Neurodegenerative Disease. Cold Spring Harb Perspect Med 2017; 7:cshperspect.a024299. [PMID: 28096243 DOI: 10.1101/cshperspect.a024299] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Abnormal intracellular accumulation of the fused in sarcoma (FUS) protein is the characteristic pathological feature of cases of familial amyotrophic lateral sclerosis (ALS) caused by FUS mutations (ALS-FUS) and several uncommon disorders that may present with sporadic frontotemporal dementia (FTLD-FUS). Although these findings provide further support for the concept that ALS and FTD are closely related clinical syndromes with an overlapping molecular basis, important differences in the pathological features and results from experimental models indicate that ALS-FUS and FTLD-FUS have distinct pathogenic mechanisms.
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Affiliation(s)
- Ian R A Mackenzie
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada
| | - Manuela Neumann
- Department of Neuropathology, University of Tübingen and German Center for Neurodegenerative Diseases (DZNE), Tübingen 72076, Germany
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16
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Boulay G, Sandoval GJ, Riggi N, Iyer S, Buisson R, Naigles B, Awad ME, Rengarajan S, Volorio A, McBride MJ, Broye LC, Zou L, Stamenkovic I, Kadoch C, Rivera MN. Cancer-Specific Retargeting of BAF Complexes by a Prion-like Domain. Cell 2017; 171:163-178.e19. [PMID: 28844694 DOI: 10.1016/j.cell.2017.07.036] [Citation(s) in RCA: 295] [Impact Index Per Article: 42.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 06/14/2017] [Accepted: 07/21/2017] [Indexed: 12/21/2022]
Abstract
Alterations in transcriptional regulators can orchestrate oncogenic gene expression programs in cancer. Here, we show that the BRG1/BRM-associated factor (BAF) chromatin remodeling complex, which is mutated in over 20% of human tumors, interacts with EWSR1, a member of a family of proteins with prion-like domains (PrLD) that are frequent partners in oncogenic fusions with transcription factors. In Ewing sarcoma, we find that the BAF complex is recruited by the EWS-FLI1 fusion protein to tumor-specific enhancers and contributes to target gene activation. This process is a neomorphic property of EWS-FLI1 compared to wild-type FLI1 and depends on tyrosine residues that are necessary for phase transitions of the EWSR1 prion-like domain. Furthermore, fusion of short fragments of EWSR1 to FLI1 is sufficient to recapitulate BAF complex retargeting and EWS-FLI1 activities. Our studies thus demonstrate that the physical properties of prion-like domains can retarget critical chromatin regulatory complexes to establish and maintain oncogenic gene expression programs.
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Affiliation(s)
- Gaylor Boulay
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
| | - Gabriel J Sandoval
- Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Nicolo Riggi
- Institute of Pathology, Centre Hospitalier Universitaire Vaudois, Faculty of Biology and Medicine, University of Lausanne, 1011 Lausanne, Switzerland
| | - Sowmya Iyer
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Rémi Buisson
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
| | - Beverly Naigles
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
| | - Mary E Awad
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
| | - Shruthi Rengarajan
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
| | - Angela Volorio
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Institute of Pathology, Centre Hospitalier Universitaire Vaudois, Faculty of Biology and Medicine, University of Lausanne, 1011 Lausanne, Switzerland; Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
| | - Matthew J McBride
- Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Liliane C Broye
- Institute of Pathology, Centre Hospitalier Universitaire Vaudois, Faculty of Biology and Medicine, University of Lausanne, 1011 Lausanne, Switzerland
| | - Lee Zou
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
| | - Ivan Stamenkovic
- Institute of Pathology, Centre Hospitalier Universitaire Vaudois, Faculty of Biology and Medicine, University of Lausanne, 1011 Lausanne, Switzerland
| | - Cigall Kadoch
- Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
| | - Miguel N Rivera
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA.
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17
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Kapeli K, Martinez FJ, Yeo GW. Genetic mutations in RNA-binding proteins and their roles in ALS. Hum Genet 2017; 136:1193-1214. [PMID: 28762175 PMCID: PMC5602095 DOI: 10.1007/s00439-017-1830-7] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Accepted: 07/17/2017] [Indexed: 12/11/2022]
Abstract
Mutations in genes that encode RNA-binding proteins (RBPs) have emerged as critical determinants of neurological diseases, especially motor neuron disorders such as amyotrophic lateral sclerosis (ALS). RBPs are involved in all aspects of RNA processing, controlling the life cycle of RNAs from synthesis to degradation. Hallmark features of RBPs in neuron dysfunction include misregulation of RNA processing, mislocalization of RBPs to the cytoplasm, and abnormal aggregation of RBPs. Much progress has been made in understanding how ALS-associated mutations in RBPs drive pathogenesis. Here, we focus on several key RBPs involved in ALS—TDP-43, HNRNP A2/B1, HNRNP A1, FUS, EWSR1, and TAF15—and review our current understanding of how mutations in these proteins cause disease.
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Affiliation(s)
- Katannya Kapeli
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117593, Singapore
| | - Fernando J Martinez
- Department of Cellular and Molecular Medicine, Stem Cell Program and Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Gene W Yeo
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117593, Singapore.
- Department of Cellular and Molecular Medicine, Stem Cell Program and Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, 92093, USA.
- Molecular Engineering Laboratory, A*STAR, Singapore, 138673, Singapore.
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18
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Åman P, Dolatabadi S, Svec D, Jonasson E, Safavi S, Andersson D, Grundevik P, Thomsen C, Ståhlberg A. Regulatory mechanisms, expression levels and proliferation effects of the FUS-DDIT3 fusion oncogene in liposarcoma. J Pathol 2016; 238:689-99. [PMID: 26865464 DOI: 10.1002/path.4700] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 01/06/2016] [Accepted: 02/01/2016] [Indexed: 12/28/2022]
Abstract
Fusion oncogenes are among the most common types of oncogene in human cancers. The gene rearrangements result in new combinations of regulatory elements and functional protein domains. Here we studied a subgroup of sarcomas and leukaemias characterized by the FET (FUS, EWSR1, TAF15) family of fusion oncogenes, including FUS-DDIT3 in myxoid liposarcoma (MLS). We investigated the regulatory mechanisms, expression levels and effects of FUS-DDIT3 in detail. FUS-DDIT3 showed a lower expression than normal FUS at both the mRNA and protein levels, and single-cell analysis revealed a lack of correlation between FUS-DDIT3 and FUS expression. FUS-DDIT3 transcription was regulated by the FUS promotor, while its mRNA stability depended on the DDIT3 sequence. FUS-DDIT3 protein stability was regulated by protein interactions through the FUS part, rather than the leucine zipper containing DDIT3 part. In addition, in vitro as well as in vivo FUS-DDIT3 protein expression data displayed highly variable expression levels between individual MLS cells. Combined mRNA and protein analyses at the single-cell level showed that FUS-DDIT3 protein expression was inversely correlated to the expression of cell proliferation-associated genes. We concluded that FUS-DDIT3 is uniquely regulated at the transcriptional as well as the post-translational level and that its expression level is important for MLS tumour development. The FET fusion oncogenes are potentially powerful drug targets and detailed knowledge about their regulation and functions may help in the development of novel treatments.
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MESH Headings
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Cell Line, Tumor
- Cell Proliferation
- Gene Expression Regulation, Neoplastic
- Half-Life
- Humans
- Liposarcoma, Myxoid/genetics
- Liposarcoma, Myxoid/metabolism
- Liposarcoma, Myxoid/pathology
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Promoter Regions, Genetic
- Protein Binding
- Protein Processing, Post-Translational
- Protein Stability
- RNA Stability
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Signal Transduction
- Time Factors
- Transcription, Genetic
- Transfection
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Affiliation(s)
- Pierre Åman
- Sahlgrenska Cancer Centre, Department of Pathology, Institute of Biomedicine, University of Gothenburg, Sweden
| | - Soheila Dolatabadi
- Sahlgrenska Cancer Centre, Department of Pathology, Institute of Biomedicine, University of Gothenburg, Sweden
| | - David Svec
- Sahlgrenska Cancer Centre, Department of Pathology, Institute of Biomedicine, University of Gothenburg, Sweden
- Institute of Biotechnology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Emma Jonasson
- Sahlgrenska Cancer Centre, Department of Pathology, Institute of Biomedicine, University of Gothenburg, Sweden
| | - Setareh Safavi
- Sahlgrenska Cancer Centre, Department of Pathology, Institute of Biomedicine, University of Gothenburg, Sweden
| | - Daniel Andersson
- Sahlgrenska Cancer Centre, Department of Pathology, Institute of Biomedicine, University of Gothenburg, Sweden
| | - Pernilla Grundevik
- Sahlgrenska Cancer Centre, Department of Pathology, Institute of Biomedicine, University of Gothenburg, Sweden
| | - Christer Thomsen
- Sahlgrenska Cancer Centre, Department of Pathology, Institute of Biomedicine, University of Gothenburg, Sweden
| | - Anders Ståhlberg
- Sahlgrenska Cancer Centre, Department of Pathology, Institute of Biomedicine, University of Gothenburg, Sweden
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19
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Kapeli K, Pratt GA, Vu AQ, Hutt KR, Martinez FJ, Sundararaman B, Batra R, Freese P, Lambert NJ, Huelga SC, Chun SJ, Liang TY, Chang J, Donohue JP, Shiue L, Zhang J, Zhu H, Cambi F, Kasarskis E, Hoon S, Ares M, Burge CB, Ravits J, Rigo F, Yeo GW. Distinct and shared functions of ALS-associated proteins TDP-43, FUS and TAF15 revealed by multisystem analyses. Nat Commun 2016; 7:12143. [PMID: 27378374 PMCID: PMC4935974 DOI: 10.1038/ncomms12143] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 06/03/2016] [Indexed: 12/12/2022] Open
Abstract
The RNA-binding protein (RBP) TAF15 is implicated in amyotrophic lateral sclerosis (ALS). To compare TAF15 function to that of two ALS-associated RBPs, FUS and TDP-43, we integrate CLIP-seq and RNA Bind-N-Seq technologies, and show that TAF15 binds to ∼4,900 RNAs enriched for GGUA motifs in adult mouse brains. TAF15 and FUS exhibit similar binding patterns in introns, are enriched in 3' untranslated regions and alter genes distinct from TDP-43. However, unlike FUS and TDP-43, TAF15 has a minimal role in alternative splicing. In human neural progenitors, TAF15 and FUS affect turnover of their RNA targets. In human stem cell-derived motor neurons, the RNA profile associated with concomitant loss of both TAF15 and FUS resembles that observed in the presence of the ALS-associated mutation FUS R521G, but contrasts with late-stage sporadic ALS patients. Taken together, our findings reveal convergent and divergent roles for FUS, TAF15 and TDP-43 in RNA metabolism.
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Affiliation(s)
- Katannya Kapeli
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA.,Stem Cell Program and Institute for Genomic Medicine, University of California at San Diego, La Jolla, California 92093, USA.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117549, Singapore
| | - Gabriel A Pratt
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA.,Stem Cell Program and Institute for Genomic Medicine, University of California at San Diego, La Jolla, California 92093, USA.,Department of Bioinformatics and Systems Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - Anthony Q Vu
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA.,Stem Cell Program and Institute for Genomic Medicine, University of California at San Diego, La Jolla, California 92093, USA
| | - Kasey R Hutt
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA.,Stem Cell Program and Institute for Genomic Medicine, University of California at San Diego, La Jolla, California 92093, USA
| | - Fernando J Martinez
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA.,Stem Cell Program and Institute for Genomic Medicine, University of California at San Diego, La Jolla, California 92093, USA
| | - Balaji Sundararaman
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA.,Stem Cell Program and Institute for Genomic Medicine, University of California at San Diego, La Jolla, California 92093, USA
| | - Ranjan Batra
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA.,Stem Cell Program and Institute for Genomic Medicine, University of California at San Diego, La Jolla, California 92093, USA.,Department of Neurosciences, University of California at San Diego, La Jolla, California 92093, USA
| | - Peter Freese
- Department of Biology, MIT, Cambridge, Massachusetts 02142, USA
| | | | - Stephanie C Huelga
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA.,Stem Cell Program and Institute for Genomic Medicine, University of California at San Diego, La Jolla, California 92093, USA.,Department of Bioinformatics and Systems Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - Seung J Chun
- Ionis Pharmaceuticals, Carlsbad, California 92010, USA
| | - Tiffany Y Liang
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA.,Stem Cell Program and Institute for Genomic Medicine, University of California at San Diego, La Jolla, California 92093, USA
| | - Jeremy Chang
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA.,Stem Cell Program and Institute for Genomic Medicine, University of California at San Diego, La Jolla, California 92093, USA
| | - John P Donohue
- Department of Molecular, Cell and Developmental Biology, Sinsheimer Labs, University of California, Santa Cruz, California 95064, USA
| | - Lily Shiue
- Department of Molecular, Cell and Developmental Biology, Sinsheimer Labs, University of California, Santa Cruz, California 95064, USA
| | - Jiayu Zhang
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Haining Zhu
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Franca Cambi
- Department of Neurology, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Edward Kasarskis
- Department of Neurology, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Shawn Hoon
- Molecular Engineering Laboratory, A*STAR, Singapore 138673, Singapore
| | - Manuel Ares
- Department of Molecular, Cell and Developmental Biology, Sinsheimer Labs, University of California, Santa Cruz, California 95064, USA
| | | | - John Ravits
- Department of Neurosciences, University of California at San Diego, La Jolla, California 92093, USA
| | - Frank Rigo
- Ionis Pharmaceuticals, Carlsbad, California 92010, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA.,Stem Cell Program and Institute for Genomic Medicine, University of California at San Diego, La Jolla, California 92093, USA.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117549, Singapore.,Department of Bioinformatics and Systems Biology, University of California at San Diego, La Jolla, California 92093, USA.,Molecular Engineering Laboratory, A*STAR, Singapore 138673, Singapore
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20
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Reber S, Stettler J, Filosa G, Colombo M, Jutzi D, Lenzken SC, Schweingruber C, Bruggmann R, Bachi A, Barabino SM, Mühlemann O, Ruepp MD. Minor intron splicing is regulated by FUS and affected by ALS-associated FUS mutants. EMBO J 2016; 35:1504-21. [PMID: 27252488 DOI: 10.15252/embj.201593791] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 04/29/2016] [Indexed: 12/11/2022] Open
Abstract
Fused in sarcoma (FUS) is a ubiquitously expressed RNA-binding protein proposed to function in various RNA metabolic pathways, including transcription regulation, pre-mRNA splicing, RNA transport and microRNA processing. Mutations in the FUS gene were identified in patients with amyotrophic lateral sclerosis (ALS), but the pathomechanisms by which these mutations cause ALS are not known. Here, we show that FUS interacts with the minor spliceosome constituent U11 snRNP, binds preferentially to minor introns and directly regulates their removal. Furthermore, a FUS knockout in neuroblastoma cells strongly disturbs the splicing of minor intron-containing mRNAs, among them mRNAs required for action potential transmission and for functional spinal motor units. Moreover, an ALS-associated FUS mutant that forms cytoplasmic aggregates inhibits splicing of minor introns by trapping U11 and U12 snRNAs in these aggregates. Collectively, our findings suggest a possible pathomechanism for ALS in which mutated FUS inhibits correct splicing of minor introns in mRNAs encoding proteins required for motor neuron survival.
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Affiliation(s)
- Stefan Reber
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Jolanda Stettler
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Giuseppe Filosa
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy IFOM-FIRC Institute of Molecular Oncology, Milan, Italy
| | - Martino Colombo
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Daniel Jutzi
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Silvia C Lenzken
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Christoph Schweingruber
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Angela Bachi
- IFOM-FIRC Institute of Molecular Oncology, Milan, Italy
| | - Silvia Ml Barabino
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Oliver Mühlemann
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Marc-David Ruepp
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
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21
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Luo Y, Blechingberg J, Fernandes AM, Li S, Fryland T, Børglum AD, Bolund L, Nielsen AL. EWS and FUS bind a subset of transcribed genes encoding proteins enriched in RNA regulatory functions. BMC Genomics 2015; 16:929. [PMID: 26573619 PMCID: PMC4647676 DOI: 10.1186/s12864-015-2125-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 10/22/2015] [Indexed: 12/13/2022] Open
Abstract
Background FUS (TLS) and EWS (EWSR1) belong to the FET-protein family of RNA and DNA binding proteins. FUS and EWS are structurally and functionally related and participate in transcriptional regulation and RNA processing. FUS and EWS are identified in translocation generated cancer fusion proteins and involved in the human neurological diseases amyotrophic lateral sclerosis and fronto-temporal lobar degeneration. Results To determine the gene regulatory functions of FUS and EWS at the level of chromatin, we have performed chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq). Our results show that FUS and EWS bind to a subset of actively transcribed genes, that binding often is downstream the poly(A)-signal, and that binding overlaps with RNA polymerase II. Functional examinations of selected target genes identified that FUS and EWS can regulate gene expression at different levels. Gene Ontology analyses showed that FUS and EWS target genes preferentially encode proteins involved in regulatory processes at the RNA level. Conclusions The presented results yield new insights into gene interactions of EWS and FUS and have identified a set of FUS and EWS target genes involved in pathways at the RNA regulatory level with potential to mediate normal and disease-associated functions of the FUS and EWS proteins. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2125-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yonglun Luo
- Department of Biomedicine, Aarhus University, The Bartholin Building, Aarhus, DK-8000, Denmark.
| | - Jenny Blechingberg
- Department of Biomedicine, Aarhus University, The Bartholin Building, Aarhus, DK-8000, Denmark. .,Present address: Clinical Microbiological Section, Lillebælt Hospital, Vejle, Denmark.
| | - Ana Miguel Fernandes
- Department of Biomedicine, Aarhus University, The Bartholin Building, Aarhus, DK-8000, Denmark. .,Present address: Epigenetic Regulation and Chromatin Architecture group, Berlin Institute for Medical Systems Biology, Max-Delbrück Centre for Molecular Medicine, Berlin, Germany.
| | - Shengting Li
- Department of Biomedicine, Aarhus University, The Bartholin Building, Aarhus, DK-8000, Denmark. .,Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark. .,Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus University, Aarhus, Denmark.
| | - Tue Fryland
- Department of Biomedicine, Aarhus University, The Bartholin Building, Aarhus, DK-8000, Denmark. .,Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark. .,Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus University, Aarhus, Denmark.
| | - Anders D Børglum
- Department of Biomedicine, Aarhus University, The Bartholin Building, Aarhus, DK-8000, Denmark. .,Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark. .,Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus University, Aarhus, Denmark. .,Psychiatric Department P, Aarhus University Hospital, Aarhus, Denmark.
| | - Lars Bolund
- Department of Biomedicine, Aarhus University, The Bartholin Building, Aarhus, DK-8000, Denmark. .,Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark. .,BGI-Shenzhen, Shenzhen, China.
| | - Anders Lade Nielsen
- Department of Biomedicine, Aarhus University, The Bartholin Building, Aarhus, DK-8000, Denmark. .,Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark. .,Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus University, Aarhus, Denmark.
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22
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Alonso R, Pisa D, Marina AI, Morato E, Rábano A, Rodal I, Carrasco L. Evidence for fungal infection in cerebrospinal fluid and brain tissue from patients with amyotrophic lateral sclerosis. Int J Biol Sci 2015; 11:546-58. [PMID: 25892962 PMCID: PMC4400386 DOI: 10.7150/ijbs.11084] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 02/10/2015] [Indexed: 12/14/2022] Open
Abstract
Among neurogenerative diseases, amyotrophic lateral sclerosis (ALS) is a fatal illness characterized by a progressive motor neuron dysfunction in the motor cortex, brainstem and spinal cord. ALS is the most common form of motor neuron disease; yet, to date, the exact etiology of ALS remains unknown. In the present work, we have explored the possibility of fungal infection in cerebrospinal fluid (CSF) and in brain tissue from ALS patients. Fungal antigens, as well as DNA from several fungi, were detected in CSF from ALS patients. Additionally, examination of brain sections from the frontal cortex of ALS patients revealed the existence of immunopositive fungal antigens comprising punctate bodies in the cytoplasm of some neurons. Fungal DNA was also detected in brain tissue using PCR analysis, uncovering the presence of several fungal species. Finally, proteomic analyses of brain tissue demonstrated the occurrence of several fungal peptides. Collectively, our observations provide compelling evidence of fungal infection in the ALS patients analyzed, suggesting that this infection may play a part in the etiology of the disease or may constitute a risk factor for these patients.
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Affiliation(s)
- Ruth Alonso
- 1. Centro de Biología Molecular "Severo Ochoa". c/Nicolás Cabrera, 1. Universidad Autónoma de Madrid. Cantoblanco. 28049 Madrid. Spain
| | - Diana Pisa
- 1. Centro de Biología Molecular "Severo Ochoa". c/Nicolás Cabrera, 1. Universidad Autónoma de Madrid. Cantoblanco. 28049 Madrid. Spain
| | - Ana Isabel Marina
- 1. Centro de Biología Molecular "Severo Ochoa". c/Nicolás Cabrera, 1. Universidad Autónoma de Madrid. Cantoblanco. 28049 Madrid. Spain
| | - Esperanza Morato
- 1. Centro de Biología Molecular "Severo Ochoa". c/Nicolás Cabrera, 1. Universidad Autónoma de Madrid. Cantoblanco. 28049 Madrid. Spain
| | - Alberto Rábano
- 2. Department of Neuropathology and Tissue Bank, Unidad de Investigación Proyecto Alzheimer, Fundación CIEN, Instituto de Salud Carlos III, Madrid. Spain
| | - Izaskun Rodal
- 2. Department of Neuropathology and Tissue Bank, Unidad de Investigación Proyecto Alzheimer, Fundación CIEN, Instituto de Salud Carlos III, Madrid. Spain
| | - Luis Carrasco
- 1. Centro de Biología Molecular "Severo Ochoa". c/Nicolás Cabrera, 1. Universidad Autónoma de Madrid. Cantoblanco. 28049 Madrid. Spain
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23
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Grad LI, Fernando SM, Cashman NR. From molecule to molecule and cell to cell: prion-like mechanisms in amyotrophic lateral sclerosis. Neurobiol Dis 2015; 77:257-65. [PMID: 25701498 DOI: 10.1016/j.nbd.2015.02.009] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Revised: 08/13/2014] [Accepted: 02/09/2015] [Indexed: 12/12/2022] Open
Abstract
Prions, self-proliferating infectious agents consisting of misfolded protein, are most often associated with aggressive neurodegenerative diseases in animals and humans. Akin to the contiguous spread of a living pathogen, the prion paradigm provides a mechanism by which a mutant or wild-type misfolded protein can dominate pathogenesis through self-propagating protein misfolding, and subsequently spread from region to region through the central nervous system. The prion diseases, along with more common neurodegenerative disorders such as Alzheimer's disease, Parkinson's disease and the tauopathies belong to a larger group of protein misfolding disorders termed proteinopathies that feature aberrant misfolding and aggregation of specific proteins. Amyotrophic lateral sclerosis (ALS), a lethal disease characterized by progressive degeneration of motor neurons is currently understood as a classical proteinopathy; the disease is typified by the formation of inclusions consisting of aggregated protein within motor neurons that contribute to neurotoxicity. It is well established that misfolded/aggregated proteins such as SOD1 and TDP-43 contribute to the toxicity of motor neurons and play a prominent role in the pathology of ALS. Recent work has identified propagated protein misfolding properties in both mutant and wild-type SOD1, and to a lesser extent TDP-43, which may provide the molecular basis for the clinically observed contiguous spread of the disease through the neuroaxis. In this review we examine the current state of knowledge regarding the prion-like properties of proteins associated with ALS pathology as well as their possible mechanisms of transmission.
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Affiliation(s)
- Leslie I Grad
- Department of Medicine (Neurology), Brain Research Centre, University of British Columbia, 2211 Wesbrook Mall, Vancouver BC, Canada, V6T 2B5
| | - Sarah M Fernando
- Department of Medicine (Neurology), Brain Research Centre, University of British Columbia, 2211 Wesbrook Mall, Vancouver BC, Canada, V6T 2B5
| | - Neil R Cashman
- Department of Medicine (Neurology), Brain Research Centre, University of British Columbia, 2211 Wesbrook Mall, Vancouver BC, Canada, V6T 2B5.
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24
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Abstract
Members of the FET protein family, consisting of FUS, EWSR1, and TAF15, bind to RNA and contribute to the control of transcription, RNA processing, and the cytoplasmic fates of messenger RNAs in metazoa. FET proteins can also bind DNA, which may be important in transcription and DNA damage responses. FET proteins are of medical interest because chromosomal rearrangements of their genes promote various sarcomas and because point mutations in FUS or TAF15 can cause neurodegenerative diseases such as amyotrophic lateral sclerosis and frontotemporal lobar dementia. Recent results suggest that both the normal and pathological effects of FET proteins are modulated by low-complexity or prion-like domains, which can form higher-order assemblies with novel interaction properties. Herein, we review FET proteins with an emphasis on how the biochemical properties of FET proteins may relate to their biological functions and to pathogenesis.
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Affiliation(s)
- Jacob C Schwartz
- Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, and BioFrontiers Institute, University of Colorado, Boulder, Colorado 80309; , ,
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25
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Ståhlberg A, Kåbjörn Gustafsson C, Engtröm K, Thomsen C, Dolatabadi S, Jonasson E, Li CY, Ruff D, Chen SM, Åman P. Normal and functional TP53 in genetically stable myxoid/round cell liposarcoma. PLoS One 2014; 9:e113110. [PMID: 25393000 PMCID: PMC4231113 DOI: 10.1371/journal.pone.0113110] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 10/20/2014] [Indexed: 12/30/2022] Open
Abstract
Myxoid/round-cell liposarcoma (MLS/RCLS) is characterized by either the fusion gene FUS-DDIT3 or the less commonly occurring EWSR1-DDIT3 and most cases carry few or no additional cytogenetic changes. There are conflicting reports concerning the status and role of TP53 in MLS/RCLS. Here we analysed four MLS/RCLS derived cell lines for TP53 mutations, expression and function. Three SV40 transformed cell lines expressed normal TP53 proteins. Irradiation caused normal posttranslational modifications of TP53 and induced P21 expression in two of these cell lines. Transfection experiments showed that the FUS-DDIT3 fusion protein had no effects on irradiation induced TP53 responses. Ion Torrent AmpliSeq screening, using the Cancer Hotspot panel, showed no dysfunctional or disease associated alleles/mutations. In conclusion, our results suggest that most MLS/RCLS cases carry functional TP53 genes and this is consistent with the low numbers of secondary mutations observed in this tumor entity.
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Affiliation(s)
- Anders Ståhlberg
- Sahlgrenska Cancer Center, Department of Pathology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Christina Kåbjörn Gustafsson
- Sahlgrenska Cancer Center, Department of Pathology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Katarina Engtröm
- Department of Oncology, Institute of Medical Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Christer Thomsen
- Sahlgrenska Cancer Center, Department of Pathology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Soheila Dolatabadi
- Sahlgrenska Cancer Center, Department of Pathology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Emma Jonasson
- Sahlgrenska Cancer Center, Department of Pathology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Chieh-Yuan Li
- Genetic, Medical and Applied Sciences division, Life Science Group, Thermo Fisher Scientific, South San Francisco, CA, United States of America
| | - David Ruff
- Genetic, Medical and Applied Sciences division, Life Science Group, Thermo Fisher Scientific, South San Francisco, CA, United States of America
| | - Shiaw-Min Chen
- Genetic, Medical and Applied Sciences division, Life Science Group, Thermo Fisher Scientific, South San Francisco, CA, United States of America
| | - Pierre Åman
- Sahlgrenska Cancer Center, Department of Pathology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
- * E-mail:
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26
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Campos-Melo D, Droppelmann CA, Volkening K, Strong MJ. RNA-binding proteins as molecular links between cancer and neurodegeneration. Biogerontology 2014; 15:587-610. [PMID: 25231915 DOI: 10.1007/s10522-014-9531-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 09/11/2014] [Indexed: 12/12/2022]
Abstract
For many years, epidemiological studies have suggested an association between cancer and neurodegenerative disorders-two disease processes that seemingly have little in common. Although these two disease processes share disruptions in a wide range of cellular pathways, including cell survival, cell death and the cell cycle, the end result is very divergent: uncontrolled cell survival and proliferation in cancer and progressive neuronal cell death in neurodegeneration. Despite the clinical data connecting these two disease processes, little is known about the molecular links between them. Among the mechanisms affected in cancer and neurodegenerative diseases, alterations in RNA metabolism are obtaining significant attention given the critical role for RNA transcription, maturation, transport, stability, degradation and translation in normal cellular function. RNA-binding proteins (RBPs) are integral to each stage of RNA metabolism through their participation in the formation of ribonucleoprotein complexes (RNPs). RBPs have a broad range of functions including posttranscriptional regulation of mRNA stability, splicing, editing and translation, mRNA export and localization, mRNA polyadenylation and miRNA biogenesis, ultimately impacting the expression of every single gene in the cell. In this review, we examine the evidence for RBPs as being key a molecular linkages between cancer and neurodegeneration.
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Affiliation(s)
- Danae Campos-Melo
- Molecular Medicine Group, Robarts Research Institute, Western University, London, ON, Canada
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27
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Deng H, Gao K, Jankovic J. The role of FUS gene variants in neurodegenerative diseases. Nat Rev Neurol 2014; 10:337-48. [DOI: 10.1038/nrneurol.2014.78] [Citation(s) in RCA: 197] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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