1
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Du D, Qin M, Shi L, Liu C, Jiang J, Liao Z, Wang H, Zhang Z, Sun L, Fan H, Liu Z, Yu H, Li H, Peng J, Yuan S, Yang M, Xiong J. RNA binding motif protein 45-mediated phosphorylation enhances protein stability of ASCT2 to promote hepatocellular carcinoma progression. Oncogene 2023; 42:3127-3141. [PMID: 37658192 DOI: 10.1038/s41388-023-02795-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 07/17/2023] [Accepted: 07/24/2023] [Indexed: 09/03/2023]
Abstract
Targeting metabolic remodeling represents a potentially promising strategy for hepatocellular carcinoma (HCC) therapy. In-depth understanding on the regulation of the glutamine transporter alanine-serine-cysteine transporter 2 (ASCT2) contributes to the development of novel promising therapeutics. As a developmentally regulated RNA binding protein, RBM45 is capable to shuttle between nucleus and cytoplasm, and directly interacts with proteins. By bioinformatics analysis, we screened out that RBM45 was elevated in the HCC patient specimens and positively correlated with poor prognosis. RBM45 promoted cell proliferation, boosted xenograft tumorigenicity and accelerated HCC progression. Using untargeted metabolomics, it was found that RBM45 interfered with glutamine metabolism. Further results demonstrated that RBM45 positively associated with ASCT2 in human and mouse specimens. Moreover, RBM45 enhanced ASCT2 protein stability by counteracting autophagy-independent lysosomal degradation. Significantly, wild-type ASCT2, instead of phospho-defective mutants, rescued siRBM45-suppressed HCC cell proliferation. Using molecular docking approaches, we found AG-221, a mutant isocitrate dehydrogenase 2 (mIDH2) inhibitor for acute myeloid leukemia therapy, pharmacologically perturbed RBM45-ASCT2 interaction, decreased ASCT2 stability and suppressed HCC progression. These findings provide evidence that RBM45 plays a crucial role in HCC progression via interacting with and counteracting the degradation of ASCT2. Our findings suggest a novel alternative structural sites for the design of ASCT2 inhibitors and the agents interfering with RBM45-ASCT2 interaction may be a potential direction for HCC drug development.
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Affiliation(s)
- Danyu Du
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
- Institute of Pharmaceutical Sciences, China Pharmaceutical University, Nanjing, 210009, China
| | - Mengyao Qin
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
- Institute of Pharmaceutical Sciences, China Pharmaceutical University, Nanjing, 210009, China
| | - Li Shi
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Chan Liu
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
- Institute of Pharmaceutical Sciences, China Pharmaceutical University, Nanjing, 210009, China
| | - Jingwei Jiang
- Shuangyun BioMed Sci & Tech Co., Ltd., Suzhou, 215000, China
| | - Zhengguang Liao
- Institute of Pharmaceutical Sciences, China Pharmaceutical University, Nanjing, 210009, China
| | - Hongxv Wang
- Institute of Pharmaceutical Sciences, China Pharmaceutical University, Nanjing, 210009, China
| | - Zhibo Zhang
- Institute of Pharmaceutical Sciences, China Pharmaceutical University, Nanjing, 210009, China
| | - Li Sun
- Institute of Pharmaceutical Sciences, China Pharmaceutical University, Nanjing, 210009, China
| | - Hui Fan
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Zhengrui Liu
- Institute of Pharmaceutical Sciences, China Pharmaceutical University, Nanjing, 210009, China
| | - Hong Yu
- Department of Pathology, Taizhou People's Hospital Affiliated to Dalian Medical University, Taizhou, 225300, Jiangsu, China
| | - Hongyang Li
- Institute of Dermatology, Chinese Academy of Medical Science & Peking Union Medical College, Nanjing, 210042, China
| | - Jun Peng
- Institute of Pharmaceutical Sciences, China Pharmaceutical University, Nanjing, 210009, China
| | - Shengtao Yuan
- Institute of Pharmaceutical Sciences, China Pharmaceutical University, Nanjing, 210009, China.
| | - Mei Yang
- Institute of Pharmaceutical Sciences, China Pharmaceutical University, Nanjing, 210009, China.
| | - Jing Xiong
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
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2
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Choi SH, Flamand MN, Liu B, Zhu H, Hu M, Wang M, Sewell J, Holley CL, Al-Hashimi HM, Meyer KD. RBM45 is an m 6A-binding protein that affects neuronal differentiation and the splicing of a subset of mRNAs. Cell Rep 2022; 40:111293. [PMID: 36044854 PMCID: PMC9472474 DOI: 10.1016/j.celrep.2022.111293] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 07/14/2022] [Accepted: 08/10/2022] [Indexed: 11/16/2022] Open
Abstract
N6-methyladenosine (m6A) is deposited co-transcriptionally on thousands of cellular mRNAs and plays important roles in mRNA processing and cellular function. m6A is particularly abundant within the brain and is critical for neurodevelopment. However, the mechanisms through which m6A contributes to brain development are incompletely understood. RBM45 acts as an m6A-binding protein that is highly expressed during neurodevelopment. We find that RBM45 binds to thousands of cellular RNAs, predominantly within intronic regions. Rbm45 depletion disrupts the constitutive splicing of a subset of target pre-mRNAs, leading to altered mRNA and protein levels through both m6A-dependent and m6A-independent mechanisms. Finally, we find that RBM45 is necessary for neuroblastoma cell differentiation and that its depletion impacts the expression of genes involved in several neurodevelopmental signaling pathways. Altogether, our findings show a role for RBM45 in controlling mRNA processing and neuronal differentiation, mediated in part by the recognition of methylated RNA. Choi et al. identify RBM45 as an m6A-binding protein enriched in the developing brain. RBM45 binds to thousands of cellular RNAs, primarily within introns, and regulates constitutive splicing of target transcripts. Loss of RBM45 causes altered expression of neurodevelopmental genes and defects in the proliferation and differentiation of neuroblastoma cells.
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Affiliation(s)
- Seung H Choi
- Department of Biochemistry, Duke University School of Medicine, Durham NC 27710, USA
| | - Mathieu N Flamand
- Department of Biochemistry, Duke University School of Medicine, Durham NC 27710, USA
| | - Bei Liu
- Department of Biochemistry, Duke University School of Medicine, Durham NC 27710, USA
| | - Huanyu Zhu
- Department of Biochemistry, Duke University School of Medicine, Durham NC 27710, USA
| | - Meghan Hu
- Trinity College of Arts and Sciences, Duke University, Durham, NC 27710, USA
| | - Melanie Wang
- Trinity College of Arts and Sciences, Duke University, Durham, NC 27710, USA
| | - Jonathon Sewell
- Department of Biochemistry, Duke University School of Medicine, Durham NC 27710, USA
| | - Christopher L Holley
- Department of Medicine (Cardiology Division), Duke University School of Medicine, Durham, NC 27710, USA; Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Hashim M Al-Hashimi
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Kate D Meyer
- Department of Biochemistry, Duke University School of Medicine, Durham NC 27710, USA; Department of Neurobiology, Duke University School of Medicine, Durham, NC 27710, USA.
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3
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Yao Y, Yang B, Chen Y, Huang D, Liu C, Sun H, Hu X, Zhou Y, Wang Y, Chen J, Pei R, Wen Z, Chen X. RNA-Binding motif protein 38 (RBM38) mediates HBV pgRNA packaging into the nucleocapsid. Antiviral Res 2022; 198:105249. [PMID: 35041910 DOI: 10.1016/j.antiviral.2022.105249] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 12/10/2021] [Accepted: 01/12/2022] [Indexed: 12/12/2022]
Abstract
The binding of HBV polymerase (Pol) and the epsilon stem loop (ε) on the 5' terminal region of pgRNA is required for pgRNA packaging and HBV replication. Previous research has demonstrated that RNA binding motif protein 24 (RBM24) is involved in pgRNA packaging by mediating the interaction between HBV polymerase (Pol) and the ε element. Here, we demonstrate that RBM38 interacts with ε, pol, RBM24 and HBV core which mediate pgRNA packaging. RBM38 directly binds to the lower bulge of ε via RNA recognition submotifs (RNPs) and interacts with HBV Pol in an RNA-independent manner. RBM38 interacts with RBM24 and forms heterogeneous oligomers, which mediate Pol-ε binding and the formation of the Pol-RBM38/RBM24-ε complex. More important, RBM38 also binds to the HBV core via the C-terminal region (ARD domain), which facilitates the combination of Pol-ε with the HBV core protein. In conclusion, RBM38 facilitates the Pol-ε interaction and mediates Pol-ε in combining with the HBV core, triggering pgRNA packaging for reverse transcription and DNA synthesis. This study provides new insights into pgRNA encapsidation.
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Affiliation(s)
- Yongxuan Yao
- Joint Center of Translational Precision Medicine, Guangzhou Institute of Pediatrics, Guangzhou Women and Children Medical Center, Guangzhou, 510623, China; State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Bo Yang
- Joint Center of Translational Precision Medicine, Guangzhou Institute of Pediatrics, Guangzhou Women and Children Medical Center, Guangzhou, 510623, China; State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Yingshan Chen
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dan Huang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Canyu Liu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hao Sun
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xue Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Yuan Zhou
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Yun Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Jizheng Chen
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Rongjuan Pei
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China.
| | - Zhe Wen
- Joint Center of Translational Precision Medicine, Guangzhou Institute of Pediatrics, Guangzhou Women and Children Medical Center, Guangzhou, 510623, China.
| | - Xinwen Chen
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; Guangzhou Institutes of Biomedicine and Health, Guangzhou, 510530, China.
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4
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Yu R, Jin SB, Ankarcrona M, Lendahl U, Nistér M, Zhao J. The Molecular Assembly State of Drp1 Controls its Association With the Mitochondrial Recruitment Receptors Mff and MIEF1/2. Front Cell Dev Biol 2021; 9:706687. [PMID: 34805137 PMCID: PMC8602864 DOI: 10.3389/fcell.2021.706687] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 10/18/2021] [Indexed: 11/13/2022] Open
Abstract
Drp1 is a central player in mitochondrial fission and is recruited to mitochondria by Mff and MIEFs (MIEF1 and MIEF2), but little is known about how its assembly state affects Drp1 mitochondrial recruitment and fission. Here, we used in vivo chemical crosslinking to explore the self-assembly state of Drp1 and how it regulates the association of Drp1 with MIEFs and Mff. We show that in intact mammalian cells Drp1 exists as a mixture of multiple self-assembly forms ranging from the minimal, probably tetrameric, self-assembly subunit to several higher order oligomers. Precluding mitochondria-bound Drp1 in Mff/MIEF1/2-deficient cells does not affect the oligomerization state of Drp1, while conversely forced recruitment of Drp1 to mitochondria by MIEFs or Mff facilitates Drp1 oligomerization. Mff preferentially binds to higher order oligomers of Drp1, whereas MIEFs bind to a wider-range of Drp1 assembly subunits, including both lower and higher oligomeric states. Mff only recruits active forms of Drp1, while MIEFs are less selective and recruit both active and inactive Drp1 as well as oligomerization- or GTPase-deficient Drp1 mutants to mitochondria. Moreover, all the fission-incompetent Drp1 mutants tested (except the monomeric mutant K668E) affect Drp1-driven mitochondrial dynamics via incorporation of the mutants into the native oligomers to form function-deficient Drp1 assemblies. We here confirm that MIEFs also serve as a platform facilitating the binding of Drp1 to Mff and loss of MIEFs severely impairs the interaction between Drp1 and Mff. Collectively, our findings suggest that Mff and MIEFs respond differently to the molecular assembly state of Drp1 and that the extent of Drp1 oligomerization regulates mitochondrial dynamics.
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Affiliation(s)
- Rong Yu
- Department of Oncology-Pathology, Karolinska Institutet, BioClinicum, Karolinska University Hospital Solna, Solna, Sweden
| | - Shao-Bo Jin
- Department of Cell and Molecular Biology, Karolinska Institutet, Biomedicum, Stockholm, Sweden
| | - Maria Ankarcrona
- Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, Karolinska Institutet, BioClinicum, Solna, Sweden
| | - Urban Lendahl
- Department of Cell and Molecular Biology, Karolinska Institutet, Biomedicum, Stockholm, Sweden.,Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, Karolinska Institutet, BioClinicum, Solna, Sweden
| | - Monica Nistér
- Department of Oncology-Pathology, Karolinska Institutet, BioClinicum, Karolinska University Hospital Solna, Solna, Sweden
| | - Jian Zhao
- Department of Oncology-Pathology, Karolinska Institutet, BioClinicum, Karolinska University Hospital Solna, Solna, Sweden
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5
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Malik I, Tseng Y, Wright SE, Zheng K, Ramaiyer P, Green KM, Todd PK. SRSF protein kinase 1 modulates RAN translation and suppresses CGG repeat toxicity. EMBO Mol Med 2021; 13:e14163. [PMID: 34542927 PMCID: PMC8573603 DOI: 10.15252/emmm.202114163] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 08/28/2021] [Accepted: 08/30/2021] [Indexed: 11/20/2022] Open
Abstract
Transcribed CGG repeat expansions cause neurodegeneration in Fragile X-associated tremor/ataxia syndrome (FXTAS). CGG repeat RNAs sequester RNA-binding proteins (RBPs) into nuclear foci and undergo repeat-associated non-AUG (RAN) translation into toxic peptides. To identify proteins involved in these processes, we employed a CGG repeat RNA-tagging system to capture repeat-associated RBPs by mass spectrometry in mammalian cells. We identified several SR (serine/arginine-rich) proteins that interact selectively with CGG repeats basally and under cellular stress. These proteins modify toxicity in a Drosophila model of FXTAS. Pharmacologic inhibition of serine/arginine protein kinases (SRPKs), which alter SRSF protein phosphorylation, localization, and activity, directly inhibits RAN translation of CGG and GGGGCC repeats (associated with C9orf72 ALS/FTD) and triggers repeat RNA retention in the nucleus. Lowering SRPK expression suppressed toxicity in both FXTAS and C9orf72 ALS/FTD model flies, and SRPK inhibitors suppressed CGG repeat toxicity in rodent neurons. Together, these findings demonstrate roles for CGG repeat RNA binding proteins in RAN translation and repeat toxicity and support further evaluation of SRPK inhibitors in modulating RAN translation associated with repeat expansion disorders.
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Affiliation(s)
- Indranil Malik
- Department of NeurologyUniversity of MichiganAnn ArborMIUSA
| | - Yi‐Ju Tseng
- Department of NeurologyUniversity of MichiganAnn ArborMIUSA
- Cellular and Molecular Biology Graduate ProgramUniversity of MichiganAnn ArborMIUSA
| | - Shannon E Wright
- Department of NeurologyUniversity of MichiganAnn ArborMIUSA
- Neuroscience Graduate ProgramUniversity of MichiganAnn ArborMIUSA
| | - Kristina Zheng
- Department of NeurologyUniversity of MichiganAnn ArborMIUSA
| | | | - Katelyn M Green
- Department of NeurologyUniversity of MichiganAnn ArborMIUSA
- Cellular and Molecular Biology Graduate ProgramUniversity of MichiganAnn ArborMIUSA
| | - Peter K Todd
- Department of NeurologyUniversity of MichiganAnn ArborMIUSA
- Ann Arbor Veterans Administration HealthcareAnn ArborMIUSA
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6
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van der Zee J, Dillen L, Baradaran-Heravi Y, Gossye H, Koçoğlu C, Cuyt I, Dermaut B, Sieben A, Baets J, De Jonghe P, Vandenberghe R, De Deyn P, Cras P, Engelborghs S, Van Broeckhoven C. Family-based exome sequencing identifies RBM45 as a possible candidate gene for frontotemporal dementia and amyotrophic lateral sclerosis. Neurobiol Dis 2021; 156:105421. [PMID: 34118419 DOI: 10.1016/j.nbd.2021.105421] [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: 01/27/2021] [Revised: 04/30/2021] [Accepted: 06/04/2021] [Indexed: 12/01/2022] Open
Abstract
Neurodegenerative disorders like frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS) are pathologically characterized by toxic protein deposition in the cytoplasm or nucleus of affected neurons and glial cells. Many of these aggregated proteins belong to the class of RNA binding proteins (RBP), and, when mutated, account for a significant subset of familial ALS and FTD cases. Here, we present first genetic evidence for the RBP gene RBM45 in the FTD-ALS spectrum. RBM45 shows many parallels with other FTD-ALS associated genes and proteins. Multiple lines of evidence have demonstrated that RBM45 is an RBP that, upon mutation, redistributes to the cytoplasm where it co-aggregates with other RBPs into cytoplasmic stress granules (SG), evolving to persistent toxic TDP-43 immunoreactive inclusions. Exome sequencing in two affected first cousins of a heavily affected early-onset dementia family listed a number of candidate genes. The gene with the highest pathogenicity score was the RBP gene RBM45. In the family, the RBM45 Arg183* nonsense mutation co-segregated in both affected cousins. Validation in an unrelated patient (n = 548) / control (n = 734) cohort identified an additional RBM45 Arg183* carrier with bvFTD on a shared 4 Mb haplotype. Transcript and protein expression analysis demonstrated loss of nuclear RBM45, suggestive of a loss-of-function disease mechanism. Further, two more ultra-rare VUS, one in the nuclear localization signal (NLS, p.Lys456Arg) in an ALS patient and one in the intrinsically disordered homo-oligomer assembly (HOA) domain (p.Arg314Gln) in a patient with nfvPPA were detected. Our findings suggest that the pathomechanisms linking RBM45 with FTD and ALS may be related to its loss of nuclear function as a mediator of mRNA splicing, cytoplasmic retention or its inability to form homo-oligomers, leading to aggregate formation with trapping of other RBPs including TDP-43, which may accumulate into persisted TDP-43 inclusions.
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Affiliation(s)
- Julie van der Zee
- Neurodegenerative Brain Diseases, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium; Institute Born-Bunge, Antwerp, Belgium.
| | - Lubina Dillen
- Neurodegenerative Brain Diseases, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium; Institute Born-Bunge, Antwerp, Belgium
| | - Yalda Baradaran-Heravi
- Neurodegenerative Brain Diseases, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium; Institute Born-Bunge, Antwerp, Belgium
| | - Helena Gossye
- Neurodegenerative Brain Diseases, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium; Institute Born-Bunge, Antwerp, Belgium; Department of Neurology, Antwerp University Hospital, Antwerp, Belgium; Department of Neurology and Memory Clinic, Hospital Network Antwerp (ZNA), Middelheim and Hoge Beuken, Antwerp, Belgium
| | - Cemile Koçoğlu
- Neurodegenerative Brain Diseases, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium; Institute Born-Bunge, Antwerp, Belgium
| | - Ivy Cuyt
- Neurodegenerative Brain Diseases, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium; Institute Born-Bunge, Antwerp, Belgium
| | - Bart Dermaut
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Anne Sieben
- Institute Born-Bunge, Antwerp, Belgium; Department of Neurology, Ghent University Hospital, Ghent, Belgium
| | - Jonathan Baets
- Institute Born-Bunge, Antwerp, Belgium; Department of Neurology, Antwerp University Hospital, Antwerp, Belgium; Translational Neurosciences, Faculty of Medicine and Health Sciences, UAntwerpen, Antwerp, Belgium
| | - Peter De Jonghe
- Institute Born-Bunge, Antwerp, Belgium; Department of Neurology, Antwerp University Hospital, Antwerp, Belgium
| | - Rik Vandenberghe
- Department of Neurology University Hospitals and Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Peter De Deyn
- Institute Born-Bunge, Antwerp, Belgium; Department of Neurology and Memory Clinic, Hospital Network Antwerp (ZNA), Middelheim and Hoge Beuken, Antwerp, Belgium; Department of Neurology and Alzheimer Center Groningen, University Medical Center Groningen (UMCG), Groningen, The Netherlands
| | - Patrick Cras
- Institute Born-Bunge, Antwerp, Belgium; Department of Neurology, Antwerp University Hospital, Antwerp, Belgium
| | - Sebastiaan Engelborghs
- Institute Born-Bunge, Antwerp, Belgium; Department of Neurology and Center for Neurosciences, UZ Brussel and Vrije Universiteit Brussel, Brussels, Belgium
| | - Christine Van Broeckhoven
- Neurodegenerative Brain Diseases, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium; Institute Born-Bunge, Antwerp, Belgium.
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7
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Cui YH, Yang S, Wei J, Shea CR, Zhong W, Wang F, Shah P, Kibriya MG, Cui X, Ahsan H, He C, He YY. Autophagy of the m 6A mRNA demethylase FTO is impaired by low-level arsenic exposure to promote tumorigenesis. Nat Commun 2021; 12:2183. [PMID: 33846348 PMCID: PMC8041927 DOI: 10.1038/s41467-021-22469-6] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 03/16/2021] [Indexed: 12/14/2022] Open
Abstract
Here we show that FTO as an N6-methyladenosine (m6A) RNA demethylase is degraded by selective autophagy, which is impaired by low-level arsenic exposure to promote tumorigenesis. We found that in arsenic-associated human skin lesions, FTO is upregulated, while m6A RNA methylation is downregulated. In keratinocytes, chronic relevant low-level arsenic exposure upregulated FTO, downregulated m6A RNA methylation, and induced malignant transformation and tumorigenesis. FTO deletion inhibited arsenic-induced tumorigenesis. Moreover, in mice, epidermis-specific FTO deletion prevented skin tumorigenesis induced by arsenic and UVB irradiation. Targeting FTO genetically or pharmacologically inhibits the tumorigenicity of arsenic-transformed tumor cells. We identified NEDD4L as the m6A-modified gene target of FTO. Finally, arsenic stabilizes FTO protein through inhibiting p62-mediated selective autophagy. FTO upregulation can in turn inhibit autophagy, leading to a positive feedback loop to maintain FTO accumulation. Our study reveals FTO-mediated dysregulation of mRNA m6A methylation as an epitranscriptomic mechanism to promote arsenic tumorigenicity.
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Affiliation(s)
- Yan-Hong Cui
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL, USA
| | - Seungwon Yang
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL, USA
| | - Jiangbo Wei
- Departments of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
| | - Christopher R Shea
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL, USA
| | - Wen Zhong
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL, USA
- Department of Radiation Oncology, 4th Affiliated Hospital, China Medical University, Shenyang, China
| | - Fang Wang
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL, USA
- Department of Environmental Health, School of Public Health, China Medical University, Shenyang, China
| | - Palak Shah
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Muhammad G Kibriya
- Institute for Population and Precision Health, Department of Public Health Sciences, The University of Chicago, Chicago, IL, USA
| | - Xiaolong Cui
- Departments of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
| | - Habibul Ahsan
- Institute for Population and Precision Health, Department of Public Health Sciences, The University of Chicago, Chicago, IL, USA
| | - Chuan He
- Departments of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, University of Chicago, Chicago, IL, USA
| | - Yu-Ying He
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL, USA.
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8
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Chen X, Yang Z, Wang W, Qian K, Liu M, Wang J, Wang M. Structural basis for RNA recognition by the N-terminal tandem RRM domains of human RBM45. Nucleic Acids Res 2021; 49:2946-2958. [PMID: 33577684 PMCID: PMC7968997 DOI: 10.1093/nar/gkab075] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 01/16/2021] [Accepted: 01/28/2021] [Indexed: 12/20/2022] Open
Abstract
RBM45 is an RNA-binding protein involved in neural development, whose aggregation is associated with neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS) and frontotemporal lobar dementia (FTLD). However, the mechanisms of RNA-binding and aggregation of RBM45 remain unelucidated. Here, we report the crystal structure of the N-terminal tandem RRM domains of human RBM45 in complex with single-stranded DNA (ssDNA). Our structural and biochemical results revealed that both the RRM1 and RRM2 of RBM45 recognized the GAC sequence of RNA/ssDNA. Two aromatic residues and an arginine residue in each RRM were critical for RNA-binding, and the interdomain linker was also involved in RNA-binding. Two RRMs formed a pair of antiparallel RNA-binding sites, indicating that the N-terminal tandem RRM domains of RBM45 bound separate GAC motifs in one RNA strand or GAC motifs in different RNA strands. Our findings will be helpful in the identification of physiologic targets of RBM45 and provide evidence for understanding the physiologic and pathologic functions of RBM45.
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Affiliation(s)
- Xiaolei Chen
- Institutes of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Hefei 230601, Anhui, China.,School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei 230601, Anhui, China
| | - Zhongmei Yang
- Institutes of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Hefei 230601, Anhui, China.,School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei 230601, Anhui, China
| | - Wenfeng Wang
- Institutes of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Hefei 230601, Anhui, China.,School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei 230601, Anhui, China
| | - Kaiyue Qian
- Institutes of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Hefei 230601, Anhui, China.,School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei 230601, Anhui, China.,Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, 111 Jiulong Road, Hefei 230601, Anhui, China
| | - Mingjie Liu
- Institutes of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Hefei 230601, Anhui, China.,School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei 230601, Anhui, China.,Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, 111 Jiulong Road, Hefei 230601, Anhui, China
| | - Junchao Wang
- Institutes of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Hefei 230601, Anhui, China.,School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei 230601, Anhui, China.,Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, 111 Jiulong Road, Hefei 230601, Anhui, China
| | - Mingzhu Wang
- Institutes of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Hefei 230601, Anhui, China.,School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei 230601, Anhui, China.,Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, 111 Jiulong Road, Hefei 230601, Anhui, China
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9
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Collins M, Li Y, Bowser R. RBM45 associates with nuclear stress bodies and forms nuclear inclusions during chronic cellular stress and in neurodegenerative diseases. Acta Neuropathol Commun 2020; 8:91. [PMID: 32586379 PMCID: PMC7318465 DOI: 10.1186/s40478-020-00965-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 06/11/2020] [Indexed: 12/12/2022] Open
Abstract
The RNA binding protein (RBP) RBM45 forms nuclear and cytoplasmic inclusions in neurons and glia in amyotrophic lateral sclerosis (ALS), frontotemporal lobar degeneration with TDP-43 proteinopathy (FTLD-TDP), and Alzheimer's disease (AD). The normal functions of RBM45 are poorly understood, as are the mechanisms by which it forms inclusions in disease. To better understand the normal and pathological functions of RBM45, we evaluated whether the protein functions via association with several membraneless organelles and whether such an association could promote the formation of nuclear RBM45 inclusions. Under basal conditions, RBM45 is diffusely distributed throughout the nucleus and does not localize to membraneless organelles, including nuclear speckles, Cajal bodies, or nuclear gems. During cellular stress, however, nuclear RBM45 undergoes a reversible, RNA-binding dependent incorporation into nuclear stress bodies (NSBs). Chronic stress leads to the persistent association of RBM45 with NSBs and the irreversible accumulation of nuclear RBM45 inclusions. We also quantified the cell type- and disease-specific patterns of RBM45 pathology in ALS, FTLD-TDP, and AD. RBM45 nuclear and cytoplasmic inclusions are found in both neurons and glia in ALS, FTLD-TDP, and AD but are absent in non-neurologic disease controls. Across neurodegenerative diseases, RBM45 nuclear inclusion pathology occurs more frequently than cytoplasmic RBM45 inclusion pathology and exhibits cell type-specific variation. Collectively, our results define new stress-associated functions of RBM45, a mechanism for nuclear RBM45 inclusion formation, a role for NSBs in the pathogenesis of ALS, FTLD-TDP, and AD, and further underscore the importance of protein self-association to both the normal and pathological functions of RBPs in these diseases.
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10
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RNA Binding Motif Protein RBM45 Regulates Expression of the 11-Kilodalton Protein of Parvovirus B19 through Binding to Novel Intron Splicing Enhancers. mBio 2020; 11:mBio.00192-20. [PMID: 32156816 PMCID: PMC7064759 DOI: 10.1128/mbio.00192-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Human parvovirus B19 (B19V) is a human pathogen that causes severe hematological disorders in immunocompromised individuals. B19V infection has a remarkable tropism with respect to human erythroid progenitor cells (EPCs) in human bone marrow and fetal liver. During B19V infection, only one viral precursor mRNA (pre-mRNA) is transcribed by a single promoter of the viral genome and is alternatively spliced and alternatively polyadenylated, a process which plays a key role in expression of viral proteins. Our studies revealed that a cellular RNA binding protein, RBM45, binds to two intron splicing enhancers and is essential for the maturation of the small nonstructural protein 11-kDa-encoding mRNA. The 11-kDa protein plays an important role not only in B19V infection-induced apoptosis but also in viral DNA replication. Thus, the identification of the RBM45 protein and its cognate binding site in B19V pre-mRNA provides a novel target for antiviral development to combat B19V infection-caused severe hematological disorders. During infection of human parvovirus B19 (B19V), one viral precursor mRNA (pre-mRNA) is transcribed by a single promoter and is alternatively spliced and alternatively polyadenylated. Here, we identified a novel cis-acting sequence (5′-GUA AAG CUA CGG GAC GGU-3′), intronic splicing enhancer 3 (ISE3), which lies 72 nucleotides upstream of the second splice acceptor (A2-2) site of the second intron that defines the exon of the mRNA encoding the 11-kDa viral nonstructural protein. RNA binding motif protein 45 (RBM45) specifically binds to ISE3 with high affinity (equilibrium dissociation constant [KD] = 33 nM) mediated by its RNA recognition domain and 2-homo-oligomer assembly domain (RRM2-HOA). Knockdown of RBM45 expression or ectopic overexpression of RRM2-HOA in human erythroid progenitor cells (EPCs) expanded ex vivo significantly decreased the level of viral mRNA spliced at the A2-2 acceptor but not that of the mRNA spliced at A2-1 that encodes VP2. Moreover, silent mutations of ISE3 in an infectious DNA of B19V significantly reduced 11-kDa expression. Notably, RBM45 also specifically interacts in vitro with ISE2, which shares the octanucleotide (GGGACGGU) with ISE3. Taken together, our results suggest that RBM45, through binding to both ISE2 and ISE3, is an essential host factor for maturation of 11-kDa-encoding mRNA.
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11
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RNA recognition motifs of disease-linked RNA-binding proteins contribute to amyloid formation. Sci Rep 2019; 9:6171. [PMID: 30992467 PMCID: PMC6467989 DOI: 10.1038/s41598-019-42367-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 03/26/2019] [Indexed: 12/12/2022] Open
Abstract
Aberrant expression, dysfunction and particularly aggregation of a group of RNA-binding proteins, including TDP-43, FUS and RBM45, are associated with neurological disorders. These three disease-linked RNA-binding proteins all contain at least one RNA recognition motif (RRM). However, it is not clear if these RRMs contribute to their aggregation-prone character. Here, we compare the biophysical and fibril formation properties of five RRMs from disease-linked RNA-binding proteins and five RRMs from non-disease-associated proteins to determine if disease-linked RRMs share specific features making them prone to self-assembly. We found that most of the disease-linked RRMs exhibit reversible thermal unfolding and refolding, and have a slightly lower average thermal melting point compared to that of normal RRMs. The full domain of TDP-43 RRM1 and FUS RRM, as well as the β-peptides from these two RRMs, could self-assemble into fibril-like aggregates which are amyloids of parallel β-sheets as verified by X-ray diffraction and FT-IR spectroscopy. Our results suggest that some disease-linked RRMs indeed play important roles in amyloid formation and shed light on why RNA-binding proteins with RRMs are frequently identified in the cellular inclusions of neurodegenerative diseases.
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12
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Prasad A, Bharathi V, Sivalingam V, Girdhar A, Patel BK. Molecular Mechanisms of TDP-43 Misfolding and Pathology in Amyotrophic Lateral Sclerosis. Front Mol Neurosci 2019; 12:25. [PMID: 30837838 PMCID: PMC6382748 DOI: 10.3389/fnmol.2019.00025] [Citation(s) in RCA: 417] [Impact Index Per Article: 83.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 01/21/2019] [Indexed: 12/11/2022] Open
Abstract
TAR DNA binding protein 43 (TDP-43) is a versatile RNA/DNA binding protein involved in RNA-related metabolism. Hyper-phosphorylated and ubiquitinated TDP-43 deposits act as inclusion bodies in the brain and spinal cord of patients with the motor neuron diseases: amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). While the majority of ALS cases (90-95%) are sporadic (sALS), among familial ALS cases 5-10% involve the inheritance of mutations in the TARDBP gene and the remaining (90-95%) are due to mutations in other genes such as: C9ORF72, SOD1, FUS, and NEK1 etc. Strikingly however, the majority of sporadic ALS patients (up to 97%) also contain the TDP-43 protein deposited in the neuronal inclusions, which suggests of its pivotal role in the ALS pathology. Thus, unraveling the molecular mechanisms of the TDP-43 pathology seems central to the ALS therapeutics, hence, we comprehensively review the current understanding of the TDP-43's pathology in ALS. We discuss the roles of TDP-43's mutations, its cytoplasmic mis-localization and aberrant post-translational modifications in ALS. Also, we evaluate TDP-43's amyloid-like in vitro aggregation, its physiological vs. pathological oligomerization in vivo, liquid-liquid phase separation (LLPS), and potential prion-like propagation propensity of the TDP-43 inclusions. Finally, we describe the various evolving TDP-43-induced toxicity mechanisms, such as the impairment of endocytosis and mitotoxicity etc. and also discuss the emerging strategies toward TDP-43 disaggregation and ALS therapeutics.
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Affiliation(s)
| | | | | | | | - Basant K. Patel
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Sangareddy, India
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13
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Borroni B, Alberici A, Buratti E. Review: Molecular pathology of frontotemporal lobar degenerations. Neuropathol Appl Neurobiol 2019; 45:41-57. [DOI: 10.1111/nan.12534] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 12/04/2018] [Indexed: 02/07/2023]
Affiliation(s)
- B. Borroni
- Neurology Clinic; Department of Clinical and Experimental Sciences; University of Brescia; Brescia Italy
| | - A. Alberici
- Neurology Clinic; Department of Clinical and Experimental Sciences; University of Brescia; Brescia Italy
| | - E. Buratti
- International Centre for Genetic Engineering and Biotechnology (ICGEB); Trieste Italy
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14
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Devecchi A, De Cecco L, Dugo M, Penso D, Dagrada G, Brich S, Stacchiotti S, Sensi M, Canevari S, Pilotti S. The genomics of desmoplastic small round cell tumor reveals the deregulation of genes related to DNA damage response, epithelial-mesenchymal transition, and immune response. Cancer Commun (Lond) 2018; 38:70. [PMID: 30486883 PMCID: PMC6260689 DOI: 10.1186/s40880-018-0339-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 11/16/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Desmoplastic small round cell tumor (DSRCT) is a rare, aggressive, and poorly investigated simple sarcoma with a low frequency of genetic deregulation other than an Ewing sarcoma RNA binding protein 1 (EWSR1)-Wilm's tumor suppressor (WT1) translocation. We used whole-exome sequencing to interrogate six consecutive pre-treated DSRCTs whose gene expression was previously investigated. METHODS DNA libraries were prepared from formalin-fixed, paraffin-embedded archival tissue specimens following the Agilent SureSelectXT2 target enrichment protocol and sequenced on Illumina NextSeq 500. Raw sequence data were aligned to the reference genome with Burrows-Wheeler Aligner algorithm. Somatic mutations and copy number alterations (CNAs) were identified using MuTect2 and EXCAVATOR2, respectively. Biological functions associated with altered genes were investigated through Ingenuity Pathway Analysis (IPA) software. RESULTS A total of 137 unique somatic mutations were identified: 133 mutated genes were case-specific, and 2 were mutated in two cases but in different positions. Among the 135 mutated genes, 27% were related to two biological categories: DNA damage-response (DDR) network that was also identified through IPA and mesenchymal-epithelial reverse transition (MErT)/epithelial-mesenchymal transition (EMT) already demonstrated to be relevant in DSRCT. The mutated genes in the DDR network were involved in various steps of transcription and particularly affected pre-mRNA. Half of these genes encoded RNA-binding proteins or DNA/RNA-binding proteins, which were recently recognized as a new class of DDR players. CNAs in genes/gene families, involved in MErT/EMT and DDR, were recurrent across patients and mostly segregated in the MErT/EMT category. In addition, recurrent gains of regions in chromosome 1 involving many MErT/EMT gene families and loss of one arm or the entire chromosome 6 affecting relevant immune-regulatory genes were recorded. CONCLUSIONS The emerging picture is an extreme inter-tumor heterogeneity, characterized by the concurrent deregulation of the DDR and MErT/EMT dynamic and plastic programs that could favour genomic instability and explain the refractory DSRCT profile.
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Affiliation(s)
- Andrea Devecchi
- Platform of Integrated Biology, Department of Applied Research and Technology Development, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, 2133, Milan, Italy
| | - Loris De Cecco
- Platform of Integrated Biology, Department of Applied Research and Technology Development, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, 2133, Milan, Italy
| | - Matteo Dugo
- Platform of Integrated Biology, Department of Applied Research and Technology Development, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, 2133, Milan, Italy
| | - Donata Penso
- Platform of Integrated Biology, Department of Applied Research and Technology Development, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, 2133, Milan, Italy
| | - Gianpaolo Dagrada
- Department of Diagnostic Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, 20133, Milan, Italy
| | - Silvia Brich
- Department of Diagnostic Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, 20133, Milan, Italy
| | - Silvia Stacchiotti
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, 20133, Milan, Italy
| | - Marialuisa Sensi
- Platform of Integrated Biology, Department of Applied Research and Technology Development, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, 2133, Milan, Italy
| | - Silvana Canevari
- Platform of Integrated Biology, Department of Applied Research and Technology Development, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, 2133, Milan, Italy.
| | - Silvana Pilotti
- Department of Diagnostic Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, 20133, Milan, Italy.
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15
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Gong J, Huang M, Wang F, Ma X, Liu H, Tu Y, Xing L, Zhu X, Zheng H, Fang J, Li X, Wang Q, Wang J, Sun Z, Wang X, Wang Y, Guo C, Tang TS. RBM45 competes with HDAC1 for binding to FUS in response to DNA damage. Nucleic Acids Res 2018; 45:12862-12876. [PMID: 29140459 PMCID: PMC5728411 DOI: 10.1093/nar/gkx1102] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 10/24/2017] [Indexed: 12/12/2022] Open
Abstract
DNA damage response (DDR) is essential for genome stability and human health. Recently, several RNA binding proteins (RBPs), including fused-in-sarcoma (FUS), have been found unexpectedly to modulate this process. The role of FUS in DDR is closely linked to the pathogenesis of amyotrophic lateral sclerosis (ALS), a progressive neurodegenerative disease that affects nerve cells in the brain and the spinal cord. Given that RBM45 is also an ALS-associated RBP, we wondered whether RBM45 plays any function during this process. Here, we report that RBM45 can be recruited to laser microirradiation-induced DNA damage sites in a PAR- and FUS-dependent manner, but in a RNA-independent fashion. Depletion of RBM45 leads to abnormal DDR signaling and decreased efficiency in DNA double-stranded break repair. Interestingly, RBM45 is found to compete with histone deacetylase 1 (HDAC1) for binding to FUS, thereby regulating the recruitment of HDAC1 to DNA damage sites. A common familial ALS-associated FUS mutation (FUS-R521C) is revealed to prefer to cooperate with RBM45 than HDAC1. Our findings suggest that RBM45 is a key regulator in FUS-related DDR signaling whose dysfunction may contribute to the pathogenesis of ALS.
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Affiliation(s)
- Juanjuan Gong
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Min Huang
- CAS Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Fengli Wang
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaolu Ma
- CAS Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Hongmei Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Yingfeng Tu
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Lingyu Xing
- CAS Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Xuefei Zhu
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Hui Zheng
- CAS Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Junjie Fang
- CAS Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaoling Li
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Qiaochu Wang
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Jiuqiang Wang
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhongshuai Sun
- CAS Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Xi Wang
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Yun Wang
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Caixia Guo
- CAS Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Tie-Shan Tang
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
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16
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Uversky VN. The roles of intrinsic disorder-based liquid-liquid phase transitions in the "Dr. Jekyll-Mr. Hyde" behavior of proteins involved in amyotrophic lateral sclerosis and frontotemporal lobar degeneration. Autophagy 2017; 13:2115-2162. [PMID: 28980860 DOI: 10.1080/15548627.2017.1384889] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Pathological developments leading to amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are associated with misbehavior of several key proteins, such as SOD1 (superoxide dismutase 1), TARDBP/TDP-43, FUS, C9orf72, and dipeptide repeat proteins generated as a result of the translation of the intronic hexanucleotide expansions in the C9orf72 gene, PFN1 (profilin 1), GLE1 (GLE1, RNA export mediator), PURA (purine rich element binding protein A), FLCN (folliculin), RBM45 (RNA binding motif protein 45), SS18L1/CREST, HNRNPA1 (heterogeneous nuclear ribonucleoprotein A1), HNRNPA2B1 (heterogeneous nuclear ribonucleoprotein A2/B1), ATXN2 (ataxin 2), MAPT (microtubule associated protein tau), and TIA1 (TIA1 cytotoxic granule associated RNA binding protein). Although these proteins are structurally and functionally different and have rather different pathological functions, they all possess some levels of intrinsic disorder and are either directly engaged in or are at least related to the physiological liquid-liquid phase transitions (LLPTs) leading to the formation of various proteinaceous membrane-less organelles (PMLOs), both normal and pathological. This review describes the normal and pathological functions of these ALS- and FTLD-related proteins, describes their major structural properties, glances at their intrinsic disorder status, and analyzes the involvement of these proteins in the formation of normal and pathological PMLOs, with the ultimate goal of better understanding the roles of LLPTs and intrinsic disorder in the "Dr. Jekyll-Mr. Hyde" behavior of those proteins.
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Affiliation(s)
- Vladimir N Uversky
- a Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute , Morsani College of Medicine , University of South Florida , Tampa , FL , USA.,b Institute for Biological Instrumentation of the Russian Academy of Sciences , Pushchino, Moscow region , Russia
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17
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Goode A, Rea S, Sultana M, Shaw B, Searle MS, Layfield R. ALS-FTLD associated mutations of SQSTM1 impact on Keap1-Nrf2 signalling. Mol Cell Neurosci 2016; 76:52-58. [PMID: 27554286 PMCID: PMC5062946 DOI: 10.1016/j.mcn.2016.08.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 08/03/2016] [Accepted: 08/18/2016] [Indexed: 12/13/2022] Open
Abstract
The transcription factor Nrf2 and its repressor protein Keap1 play key roles in the regulation of antioxidant stress responses and both Keap1-Nrf2 signalling and oxidative stress have been implicated in the pathogenesis of the ALS-FTLD spectrum of neurodegenerative disorders. The Keap1-binding partner and autophagy receptor SQSTM1/p62 has also recently been linked genetically to ALS-FTLD, with some missense mutations identified in patients mapping within or close to its Keap1-interacting region (KIR, residues 347–352). Here we report the effects on protein function of four different disease associated mutations of SQSTM1/p62 which affect the KIR region. Only mutations mapping precisely to the KIR (P348L and G351A) were associated with a loss of Keap1 binding in co-immunoprecipitations comparable to wild-type SQSTM1/p62. These selective effects on Keap1 recognition were entirely rational based on protein structural models. Consistent with impaired Keap1 binding, the P348L and G351A KIR mutants showed reduced ability to activate Nrf2 signalling compared to wild-type SQSTM1/p62 in antioxidant response element (ARE)-luciferase reporter assays. The results suggest that SQSTM1 mutations within the KIR of SQSTM1/p62 contribute to aetiology of some cases of ALS-FTLD through a mechanism involving aberrant expression or regulation of oxidative response genes. ALS-FTLD associated KIR mutations of SQSTM1/p62 disrupt Keap1 binding. KIR mutants of SQSTM1/p62 are unable to activate Nrf2 signalling in reporter assays. Some SQSTM1 mutations may contribute to ALS-FTLD through an aberrant antioxidant stress response.
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Affiliation(s)
- Alice Goode
- School of Life Sciences, University of Nottingham, UK.
| | - Sarah Rea
- Harry Perkins Institute of Medical Research, University of Western Australia, Australia; Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
| | - Melanie Sultana
- Harry Perkins Institute of Medical Research, University of Western Australia, Australia; Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
| | - Barry Shaw
- School of Life Sciences, University of Nottingham, UK
| | - Mark S Searle
- Centre for Biomolecular Sciences, School of Chemistry, University of Nottingham, Nottingham, UK
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18
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Ratti A, Buratti E. Physiological functions and pathobiology of TDP-43 and FUS/TLS proteins. J Neurochem 2016; 138 Suppl 1:95-111. [PMID: 27015757 DOI: 10.1111/jnc.13625] [Citation(s) in RCA: 252] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 03/19/2016] [Accepted: 03/22/2016] [Indexed: 12/12/2022]
Abstract
The multiple roles played by RNA binding proteins in neurodegeneration have become apparent following the discovery of TAR DNA binding protein 43 kDa (TDP-43) and fused in sarcoma/translocated in liposarcoma (FUS/TLS) involvement in amyotrophic lateral sclerosis and frontotemporal lobar dementia. In these two diseases, the majority of patients display the presence of aggregated forms of one of these proteins in their brains. The study of their functional properties currently represents a very promising target for developing the effective therapeutic options that are still lacking. This aim, however, must be preceded by an accurate evaluation of TDP-43 and FUS/TLS biological functions, both in physiological and disease conditions. Recent findings have uncovered several aspects of RNA metabolism that can be affected by misregulation of these two proteins. Progress has also been made in starting to understand how the aggregation of these proteins occurs and spreads from cell to cell. The aim of this review will be to provide a general overview of TDP-43 and FUS/TLS proteins and to highlight their physiological functions. At present, the emerging picture is that TDP-43 and FUS/TLS control several aspects of an mRNA's life, but they can also participate in DNA repair processes and in non-coding RNA metabolism. Although their regulatory activities are similar, they regulate mainly distinct RNA targets and show different pathogenetic mechanisms in amyotrophic lateral sclerosis/frontotemporal lobar dementia diseases. The identification of key events in these processes represents today the best chance of finding targetable options for therapeutic approaches that might actually make a difference at the clinical level. The two major RNA Binding Proteins involved in Amyotrophic Lateral Sclerosisi and Frontotemporal Dementia are TDP-43 and FUST/TLS. Both proteins are involved in regulating all aspects of RNA and RNA life cycle within neurons, from transcription, processing, and transport/stability to the formation of cytoplasmic and nuclear stress granules. For this reason, the aberrant aggregation of these factors during disease can impair multiple RNA metabolic pathways and eventually lead to neuronal death/inactivation. The purpose of this review is to provide an up-to-date perspective on what we know about this issue at the molecular level. This article is part of the Frontotemporal Dementia special issue.
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Affiliation(s)
- Antonia Ratti
- Department of Pathophysiology and Transplantation, 'Dino Ferrari' Center - Università degli Studi di Milano, Milan, Italy.,Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
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19
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Mashiko T, Sakashita E, Kasashima K, Tominaga K, Kuroiwa K, Nozaki Y, Matsuura T, Hamamoto T, Endo H. Developmentally Regulated RNA-binding Protein 1 (Drb1)/RNA-binding Motif Protein 45 (RBM45), a Nuclear-Cytoplasmic Trafficking Protein, Forms TAR DNA-binding Protein 43 (TDP-43)-mediated Cytoplasmic Aggregates. J Biol Chem 2016; 291:14996-5007. [PMID: 27226551 DOI: 10.1074/jbc.m115.712232] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Indexed: 12/12/2022] Open
Abstract
Cytoplasmic protein aggregates are one of the pathological hallmarks of neurodegenerative disorders, including amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). Several RNA-binding proteins have been identified as components of inclusion bodies. Developmentally regulated RNA-binding protein 1 (Drb1)/RNA-binding motif protein 45 is an RNA-binding protein that was recently described as a component in ALS- and FTLD-related inclusion bodies. However, the molecular mechanism underlying cytoplasmic Drb1 aggregation remains unclear. Here, using an in vitro cellular model, we demonstrated that Drb1 co-localizes with cytoplasmic aggregates mediated by TAR DNA-binding protein 43, a major component of ALS and FTLD-related inclusion bodies. We also defined the domains involved in the subcellular localization of Drb1 to clarify the role of Drb1 in the formation of cytoplasmic aggregates in ALS and FTLD. Drb1 predominantly localized in the nucleus via a classical nuclear localization signal in its carboxyl terminus and is a shuttling protein between the nucleus and cytoplasm. Furthermore, we identify a double leucine motif serving as a nuclear export signal. The Drb1 mutant, presenting mutations in both nuclear localization signal and nuclear export signal, is prone to aggregate in the cytoplasm. The mutant Drb1-induced cytoplasmic aggregates not only recruit TAR DNA-binding protein 43 but also decrease the mitochondrial membrane potential. Taken together, these results indicate that perturbation of Drb1 nuclear-cytoplasmic trafficking induces toxic cytoplasmic aggregates, suggesting that mislocalization of Drb1 is involved in the cause of cytotoxicity in neuronal cells.
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Affiliation(s)
- Takafumi Mashiko
- From the Departments of Biochemistry and Division of Neurology, Department of Internal Medicine, Jichi Medical University School of Medicine, 3311-1 Yakushiji, Shimotsuke-shi, Tochigi 329-0498, Japan
| | | | | | | | | | | | - Tohru Matsuura
- Division of Neurology, Department of Internal Medicine, Jichi Medical University School of Medicine, 3311-1 Yakushiji, Shimotsuke-shi, Tochigi 329-0498, Japan
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Immunoprecipitation and mass spectrometry defines an extensive RBM45 protein-protein interaction network. Brain Res 2016; 1647:79-93. [PMID: 26979993 DOI: 10.1016/j.brainres.2016.02.047] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 02/25/2016] [Accepted: 02/28/2016] [Indexed: 12/12/2022]
Abstract
The pathological accumulation of RNA-binding proteins (RBPs) within inclusion bodies is a hallmark of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). RBP aggregation results in both toxic gain and loss of normal function. Determining the protein binding partners and normal functions of disease-associated RBPs is necessary to fully understand molecular mechanisms of RBPs in disease. Herein, we characterized the protein-protein interactions (PPIs) of RBM45, a RBP that localizes to inclusions in ALS/FTLD. Using immunoprecipitation coupled to mass spectrometry (IP-MS), we identified 132 proteins that specifically interact with RBM45 within HEK293 cells. Select PPIs were validated by immunoblot and immunocytochemistry, demonstrating that RBM45 associates with a number of other RBPs primarily via RNA-dependent interactions in the nucleus. Analysis of the biological processes and pathways associated with RBM45-interacting proteins indicates enrichment for nuclear RNA processing/splicing via association with hnRNP proteins and cytoplasmic RNA translation via eiF2 and eiF4 pathways. Moreover, several other ALS-linked RBPs, including TDP-43, FUS, Matrin-3, and hnRNP-A1, interact with RBM45, consistent with prior observations of these proteins within intracellular inclusions in ALS/FTLD. Taken together, our results define a PPI network for RBM45, suggest novel functions for this protein, and provide new insights into the contributions of RBM45 to neurodegeneration in ALS/FTLD. This article is part of a Special Issue entitled SI:RNA Metabolism in Disease.
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