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Wang J, Liu J, Huang R, Chu T, Tang Q, Chen X. Proteomic Profiling of Messenger Ribonucleoproteins in Mouse Tissues Based on Formaldehyde Cross-Linking. J Proteome Res 2024; 23:1370-1378. [PMID: 38472149 DOI: 10.1021/acs.jproteome.3c00856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
Messenger ribonucleoprotein particles (mRNPs) are vital for tissue-specific gene expression via mediating posttranscriptional regulations. However, proteomic profiling of proteins in mRNPs, i.e., mRNA-associated proteins (mRAPs), has been challenging at the tissue level. Herein, we report the development of formaldehyde cross-linking-based mRNA-associated protein profiling (FAXRAP), a chemical strategy that enables the identification of mRAPs in both cultured cells and intact mouse organs. Applying FAXRAP, tissue-specific mRAPs were systematically profiled in the mouse liver, kidney, heart, and brain. Furthermore, brain mRAPs in Parkinson's disease (PD) mouse model were investigated, which revealed a global decrease of mRNP assembly in the brain of mice with PD. We envision that FAXRAP will facilitate uncovering the posttranscriptional regulation networks in various biological systems.
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Affiliation(s)
- Jiankun Wang
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China
| | - Jialin Liu
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China
| | - Rongbing Huang
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China
| | - Tianyu Chu
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China
| | - Qi Tang
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China
| | - Xing Chen
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China
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2
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Rathore D, Marino MJ, Issara-Amphorn J, Hwan Yoon S, Manes NP, Nita-Lazar A. Lipopolysaccharide Regulates the Macrophage RNA-Binding Proteome. J Proteome Res 2024. [PMID: 38527097 DOI: 10.1021/acs.jproteome.3c00838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
RNA-protein interactions within cellular signaling pathways have significant modulatory effects on RNA binding proteins' (RBPs') effector functions. During the innate immune response, specific RNA-protein interactions have been reported as a regulatory layer of post-transcriptional control. We investigated changes in the RNA-bound proteome of immortalized mouse macrophages (IMM) following treatment with lipopolysaccharide (LPS). Stable isotope labeling by amino acids in cell culture (SILAC) of cells followed by unbiased purification of RNP complexes at two time points after LPS stimulation and bottom-up proteomic analysis by LC-MS/MS resulted in a set of significantly affected RBPs. Global RNA sequencing and LFQ proteomics were used to characterize the correlation of transcript and protein abundance changes in response to LPS at different time points with changes in protein-RNA binding. Il1α, MARCKS, and ACOD1 were noted as RBP candidates involved in innate immune signaling. The binding sites of the RBP and RNA conjugates at amino acid resolution were investigated by digesting the cross-linked oligonucleotide from peptides remaining after elution using Nuclease P1. The combined data sets provide directions for further studies of innate immune signaling regulation by RBP interactions with different classes of RNA.
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Affiliation(s)
- Deepali Rathore
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Matthew J Marino
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Jiraphorn Issara-Amphorn
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Sung Hwan Yoon
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Nathan P Manes
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Aleksandra Nita-Lazar
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
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3
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Necarsulmer JC, Simon JM, Evangelista BA, Chen Y, Tian X, Nafees S, Marquez AB, Jiang H, Wang P, Ajit D, Nikolova VD, Harper KM, Ezzell JA, Lin FC, Beltran AS, Moy SS, Cohen TJ. RNA-binding deficient TDP-43 drives cognitive decline in a mouse model of TDP-43 proteinopathy. eLife 2023; 12:RP85921. [PMID: 37819053 PMCID: PMC10567115 DOI: 10.7554/elife.85921] [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] [Indexed: 10/13/2023] Open
Abstract
TDP-43 proteinopathies including frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS) are neurodegenerative disorders characterized by aggregation and mislocalization of the nucleic acid-binding protein TDP-43 and subsequent neuronal dysfunction. Here, we developed endogenous models of sporadic TDP-43 proteinopathy based on the principle that disease-associated TDP-43 acetylation at lysine 145 (K145) alters TDP-43 conformation, impairs RNA-binding capacity, and induces downstream mis-regulation of target genes. Expression of acetylation-mimic TDP-43K145Q resulted in stress-induced nuclear TDP-43 foci and loss of TDP-43 function in primary mouse and human-induced pluripotent stem cell (hiPSC)-derived cortical neurons. Mice harboring the TDP-43K145Q mutation recapitulated key hallmarks of FTLD, including progressive TDP-43 phosphorylation and insolubility, TDP-43 mis-localization, transcriptomic and splicing alterations, and cognitive dysfunction. Our study supports a model in which TDP-43 acetylation drives neuronal dysfunction and cognitive decline through aberrant splicing and transcription of critical genes that regulate synaptic plasticity and stress response signaling. The neurodegenerative cascade initiated by TDP-43 acetylation recapitulates many aspects of human FTLD and provides a new paradigm to further interrogate TDP-43 proteinopathies.
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Affiliation(s)
- Julie C Necarsulmer
- Department of Cell Biology and Physiology, University of North CarolinaChapel HillUnited States
- Department of Neurology, University of North CarolinaChapel HillUnited States
| | - Jeremy M Simon
- UNC Neuroscience Center, University of North CarolinaChapel HillUnited States
- Carolina Institute for Developmental Disabilities, University of North CarolinaChapel HillUnited States
- Department of Genetics, University of North CarolinaChapel HillUnited States
| | - Baggio A Evangelista
- Department of Cell Biology and Physiology, University of North CarolinaChapel HillUnited States
- Department of Neurology, University of North CarolinaChapel HillUnited States
| | - Youjun Chen
- Department of Neurology, University of North CarolinaChapel HillUnited States
| | - Xu Tian
- Department of Neurology, University of North CarolinaChapel HillUnited States
| | - Sara Nafees
- Department of Neurology, University of North CarolinaChapel HillUnited States
| | - Ariana B Marquez
- Human Pluripotent Stem Cell Core, University of North CarolinaChapel HillUnited States
| | - Huijun Jiang
- Department of Biostatistics, University of North CarolinaChapel HillUnited States
| | - Ping Wang
- Department of Neurology, University of North CarolinaChapel HillUnited States
| | - Deepa Ajit
- Department of Neurology, University of North CarolinaChapel HillUnited States
| | - Viktoriya D Nikolova
- Carolina Institute for Developmental Disabilities, University of North CarolinaChapel HillUnited States
- Department of Psychiatry, The University of North CarolinaChapel HillUnited States
| | - Kathryn M Harper
- Carolina Institute for Developmental Disabilities, University of North CarolinaChapel HillUnited States
- Department of Psychiatry, The University of North CarolinaChapel HillUnited States
| | - J Ashley Ezzell
- Department of Cell Biology & Physiology, Histology Research Core Facility, University of North CarolinaChapel HillUnited States
| | - Feng-Chang Lin
- Department of Biostatistics, University of North CarolinaChapel HillUnited States
| | - Adriana S Beltran
- Department of Genetics, University of North CarolinaChapel HillUnited States
- Human Pluripotent Stem Cell Core, University of North CarolinaChapel HillUnited States
- Department of Pharmacology, University of North CarolinaChapel HillUnited States
| | - Sheryl S Moy
- Carolina Institute for Developmental Disabilities, University of North CarolinaChapel HillUnited States
- Department of Psychiatry, The University of North CarolinaChapel HillUnited States
| | - Todd J Cohen
- Department of Cell Biology and Physiology, University of North CarolinaChapel HillUnited States
- Department of Neurology, University of North CarolinaChapel HillUnited States
- UNC Neuroscience Center, University of North CarolinaChapel HillUnited States
- Department of Biochemistry and Biophysics, University of North CarolinaChapel HillUnited States
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4
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Ratovitski T, Kamath SV, O'Meally RN, Gosala K, Holland CD, Jiang M, Cole RN, Ross CA. Arginine methylation of RNA-binding proteins is impaired in Huntington's disease. Hum Mol Genet 2023; 32:3006-3025. [PMID: 37535888 PMCID: PMC10549789 DOI: 10.1093/hmg/ddad125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 07/29/2023] [Accepted: 07/31/2023] [Indexed: 08/05/2023] Open
Abstract
Huntington's disease (HD) is a progressive neurodegenerative disorder caused by a CAG repeat expansion in the HD gene, coding for huntingtin protein (HTT). Mechanisms of HD cellular pathogenesis remain undefined and likely involve disruptions in many cellular processes and functions presumably mediated by abnormal protein interactions of mutant HTT. We previously found HTT interaction with several protein arginine methyl-transferase (PRMT) enzymes. Protein arginine methylation mediated by PRMT enzymes is an important post-translational modification with an emerging role in neurodegeneration. We found that normal (but not mutant) HTT can facilitate the activity of PRMTs in vitro and the formation of arginine methylation complexes. These interactions appear to be disrupted in HD neurons. This suggests an additional functional role for HTT/PRMT interactions, not limited to substrate/enzyme relationship, which may result in global changes in arginine protein methylation in HD. Our quantitative analysis of striatal precursor neuron proteome indicated that arginine protein methylation is significantly altered in HD. We identified a cluster highly enriched in RNA-binding proteins with reduced arginine methylation, which is essential to their function in RNA processing and splicing. We found that several of these proteins interact with HTT, and their RNA-binding and localization are affected in HD cells likely due to a compromised arginine methylation and/or abnormal interactions with mutant HTT. These studies reveal a potential new mechanism for disruption of RNA processing in HD, involving a direct interaction of HTT with methyl-transferase enzymes and modulation of their activity and highlighting methylation of arginine as potential new therapeutic target for HD.
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Affiliation(s)
- Tamara Ratovitski
- Department of Psychiatry and Behavioral Sciences, Division of Neurobiology, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Siddhi V Kamath
- Department of Psychiatry and Behavioral Sciences, Division of Neurobiology, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Robert N O'Meally
- Department of Biological Chemistry, Mass Spectrometry and Proteomics Facility, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Keerthana Gosala
- Department of Psychiatry and Behavioral Sciences, Division of Neurobiology, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Chloe D Holland
- Department of Psychiatry and Behavioral Sciences, Division of Neurobiology, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Mali Jiang
- Department of Psychiatry and Behavioral Sciences, Division of Neurobiology, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Robert N Cole
- Department of Biological Chemistry, Mass Spectrometry and Proteomics Facility, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Christopher A Ross
- Department of Psychiatry and Behavioral Sciences, Division of Neurobiology, Johns Hopkins University, Baltimore, MD 21287, USA
- Departments of Neurology, Neuroscience and Pharmacology, Johns Hopkins University, Baltimore, MD 21287, USA
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5
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McGoldrick P, Robertson J. Unraveling the impact of disrupted nucleocytoplasmic transport systems in C9orf72-associated ALS. Front Cell Neurosci 2023; 17:1247297. [PMID: 37720544 PMCID: PMC10501458 DOI: 10.3389/fncel.2023.1247297] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 08/08/2023] [Indexed: 09/19/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are two adult-onset neurodegenerative diseases that are part of a common disease spectrum due to clinical, genetic, and pathological overlap. A prominent genetic factor contributing to both diseases is a hexanucleotide repeat expansion in a non-coding region of the C9orf72 gene. This mutation in C9orf72 leads to nuclear depletion and cytoplasmic aggregation of Tar DNA-RNA binding protein 43 (TDP-43). TDP-43 pathology is characteristic of the majority of ALS cases, irrespective of disease causation, and is present in ~50% of FTD cases. Defects in nucleocytoplasmic transport involving the nuclear pore complex, the Ran-GTPase cycle, and nuclear transport factors have been linked with the mislocalization of TDP-43. Here, we will explore and discuss the implications of these system abnormalities of nucleocytoplasmic transport in C9orf72-ALS/FTD, as well as in other forms of familial and sporadic ALS.
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Affiliation(s)
- Philip McGoldrick
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON, Canada
| | - Janice Robertson
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
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6
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Hurtle BT, Xie L, Donnelly CJ. Disrupting pathologic phase transitions in neurodegeneration. J Clin Invest 2023; 133:e168549. [PMID: 37395272 DOI: 10.1172/jci168549] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2023] Open
Abstract
Solid-like protein deposits found in aged and diseased human brains have revealed a relationship between insoluble protein accumulations and the resulting deficits in neurologic function. Clinically diverse neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, frontotemporal lobar degeneration, and amyotrophic lateral sclerosis, exhibit unique and disease-specific biochemical protein signatures and abnormal protein depositions that often correlate with disease pathogenesis. Recent evidence indicates that many pathologic proteins assemble into liquid-like protein phases through the highly coordinated process of liquid-liquid phase separation. Over the last decade, biomolecular phase transitions have emerged as a fundamental mechanism of cellular organization. Liquid-like condensates organize functionally related biomolecules within the cell, and many neuropathology-associated proteins reside within these dynamic structures. Thus, examining biomolecular phase transitions enhances our understanding of the molecular mechanisms mediating toxicity across diverse neurodegenerative diseases. This Review explores the known mechanisms contributing to aberrant protein phase transitions in neurodegenerative diseases, focusing on tau and TDP-43 proteinopathies and outlining potential therapeutic strategies to regulate these pathologic events.
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Affiliation(s)
- Bryan T Hurtle
- Center for Neuroscience at the University of Pittsburgh Graduate Program
- Medical Scientist Training Program, University of Pittsburgh; and
- LiveLikeLou Center for ALS Research at the University of Pittsburgh Brain Institute; Pittsburgh, Pennsylvania, USA
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Longxin Xie
- LiveLikeLou Center for ALS Research at the University of Pittsburgh Brain Institute; Pittsburgh, Pennsylvania, USA
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- School of Medicine, Tsinghua University, Beijing, China
| | - Christopher J Donnelly
- Center for Neuroscience at the University of Pittsburgh Graduate Program
- Medical Scientist Training Program, University of Pittsburgh; and
- LiveLikeLou Center for ALS Research at the University of Pittsburgh Brain Institute; Pittsburgh, Pennsylvania, USA
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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7
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Varesi A, Campagnoli LIM, Barbieri A, Rossi L, Ricevuti G, Esposito C, Chirumbolo S, Marchesi N, Pascale A. RNA binding proteins in senescence: A potential common linker for age-related diseases? Ageing Res Rev 2023; 88:101958. [PMID: 37211318 DOI: 10.1016/j.arr.2023.101958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/09/2023] [Accepted: 05/18/2023] [Indexed: 05/23/2023]
Abstract
Aging represents the major risk factor for the onset and/or progression of various disorders including neurodegenerative diseases, metabolic disorders, and bone-related defects. As the average age of the population is predicted to exponentially increase in the coming years, understanding the molecular mechanisms underlying the development of aging-related diseases and the discovery of new therapeutic approaches remain pivotal. Well-reported hallmarks of aging are cellular senescence, genome instability, autophagy impairment, mitochondria dysfunction, dysbiosis, telomere attrition, metabolic dysregulation, epigenetic alterations, low-grade chronic inflammation, stem cell exhaustion, altered cell-to-cell communication and impaired proteostasis. With few exceptions, however, many of the molecular players implicated within these processes as well as their role in disease development remain largely unknown. RNA binding proteins (RBPs) are known to regulate gene expression by dictating at post-transcriptional level the fate of nascent transcripts. Their activity ranges from directing primary mRNA maturation and trafficking to modulation of transcript stability and/or translation. Accumulating evidence has shown that RBPs are emerging as key regulators of aging and aging-related diseases, with the potential to become new diagnostic and therapeutic tools to prevent or delay aging processes. In this review, we summarize the role of RBPs in promoting cellular senescence and we highlight their dysregulation in the pathogenesis and progression of the main aging-related diseases, with the aim of encouraging further investigations that will help to better disclose this novel and captivating molecular scenario.
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Affiliation(s)
- Angelica Varesi
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy.
| | | | - Annalisa Barbieri
- Department of Drug Sciences, Section of Pharmacology, University of Pavia, Pavia, Italy
| | - Lorenzo Rossi
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | | | - Ciro Esposito
- Department of Internal Medicine and Therapeutics, University of Pavia, Italy; Nephrology and dialysis unit, ICS S. Maugeri SPA SB Hospital, Pavia, Italy; High School in Geriatrics, University of Pavia, Italy
| | | | - Nicoletta Marchesi
- Department of Drug Sciences, Section of Pharmacology, University of Pavia, Pavia, Italy
| | - Alessia Pascale
- Department of Drug Sciences, Section of Pharmacology, University of Pavia, Pavia, Italy.
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8
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Ionescu A, Altman T, Perlson E. Looking for answers far away from the soma-the (un)known axonal functions of TDP-43, and their contribution to early NMJ disruption in ALS. Mol Neurodegener 2023; 18:35. [PMID: 37259156 DOI: 10.1186/s13024-023-00623-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 05/01/2023] [Indexed: 06/02/2023] Open
Abstract
Axon degeneration and Neuromuscular Junction (NMJ) disruption are key pathologies in the fatal neurodegenerative disease Amyotrophic Lateral Sclerosis (ALS). Despite accumulating evidence that axons and NMJs are impacted at a very early stage of the disease, current knowledge about the mechanisms leading to their degeneration remains elusive. Cytoplasmic mislocalization and accumulation of the protein TDP-43 are considered key pathological hallmarks of ALS, as they occur in ~ 97% of ALS patients, both sporadic and familial. Recent studies have identified pathological accumulation of TDP-43 in intramuscular nerves of muscle biopsies collected from pre-diagnosed, early symptomatic ALS patients. These findings suggest a gain of function for TDP-43 in axons, which might facilitate early NMJ disruption. In this review, we dissect the process leading to axonal TDP-43 accumulation and phosphorylation, discuss the known and hypothesized roles TDP-43 plays in healthy axons, and review possible mechanisms that connect TDP-43 pathology to the axon and NMJ degeneration in ALS.
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Affiliation(s)
- Ariel Ionescu
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Room 605, Ramat Aviv, 69978, Tel Aviv, Israel
| | - Topaz Altman
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Room 605, Ramat Aviv, 69978, Tel Aviv, Israel
| | - Eran Perlson
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Room 605, Ramat Aviv, 69978, Tel Aviv, Israel.
- Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv, Israel.
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9
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Ma Y, Mu X, Gao R, Zhang Y, Geng Y, Chen X, Yin X, Li F, He J. Maternal exposure to dibutyl phthalate regulates MSH6 crotonylation to impair homologous recombination in fetal oocytes. JOURNAL OF HAZARDOUS MATERIALS 2023; 455:131540. [PMID: 37167869 DOI: 10.1016/j.jhazmat.2023.131540] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 04/12/2023] [Accepted: 04/27/2023] [Indexed: 05/13/2023]
Abstract
Homologous recombination (HR) during early oogenesis repairs programmed double-strand breaks (DSBs) to ensure female fertility and offspring health. The exposure of fetal ovaries to endocrine disrupting chemicals (EDCs) can cause reproductive disorders in the adulthood. The EDC dibutyl phthalate (DBP) is widely distributed in flexible plastic products, leading to ubiquitous human exposure. Here, we report that maternal exposure to DBP caused gross aberrations in meiotic prophase I of fetal oocytes, including delayed progression, impaired DNA damage response, uncoupled localization of DMC1 and RAD51, and decreased HR. However, programmed DSBs were efficiently repaired. DBP exposure negatively regulated lysine crotonylation (Kcr) of MSH6. Similar meiotic defects were observed in fetal ovaries with targeted disruption of Msh6, and mutation of K544cr of MSH6 impaired its association with Ku70, thereby promoting non-homologous end joining (NHEJ) and inhibiting HR. Unlike mature F1 females, F2 female mice exhibited premature follicular activation, precocious puberty, and anxiety-like behaviors. Therefore, DBP can influence early meiotic events, and Kcr of MSH6 may regulate preferential induction of HR or NHEJ for DNA repair during meiosis.
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Affiliation(s)
- Yidan Ma
- Department of Health Toxicology, School of Public Health, Chongqing Medical University, Chongqing 400016, PR China; Joint International Research Laboratory of Reproduction & Development, Chongqing Medical University, Chongqing 400016, PR China
| | - Xinyi Mu
- Joint International Research Laboratory of Reproduction & Development, Chongqing Medical University, Chongqing 400016, PR China; College of Basic Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Rufei Gao
- Department of Health Toxicology, School of Public Health, Chongqing Medical University, Chongqing 400016, PR China; Joint International Research Laboratory of Reproduction & Development, Chongqing Medical University, Chongqing 400016, PR China
| | - Yan Zhang
- Department of Health Toxicology, School of Public Health, Chongqing Medical University, Chongqing 400016, PR China; Joint International Research Laboratory of Reproduction & Development, Chongqing Medical University, Chongqing 400016, PR China
| | - Yanqing Geng
- Joint International Research Laboratory of Reproduction & Development, Chongqing Medical University, Chongqing 400016, PR China; College of Basic Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Xuemei Chen
- Department of Health Toxicology, School of Public Health, Chongqing Medical University, Chongqing 400016, PR China; Joint International Research Laboratory of Reproduction & Development, Chongqing Medical University, Chongqing 400016, PR China
| | - Xin Yin
- Department of Health Toxicology, School of Public Health, Chongqing Medical University, Chongqing 400016, PR China; Joint International Research Laboratory of Reproduction & Development, Chongqing Medical University, Chongqing 400016, PR China
| | - Fangfang Li
- Department of Health Toxicology, School of Public Health, Chongqing Medical University, Chongqing 400016, PR China; Joint International Research Laboratory of Reproduction & Development, Chongqing Medical University, Chongqing 400016, PR China
| | - Junlin He
- Department of Health Toxicology, School of Public Health, Chongqing Medical University, Chongqing 400016, PR China; Joint International Research Laboratory of Reproduction & Development, Chongqing Medical University, Chongqing 400016, PR China.
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10
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O'Brien N, Mizielinska S. A cryptic clue to neurodegeneration? Science 2023; 379:1090-1091. [PMID: 36927030 DOI: 10.1126/science.adg8501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Antisense oligonucleotides rescue cryptic RNA splicing and neuron regeneration.
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Affiliation(s)
- Niamh O'Brien
- UK Dementia Research Institute at King's College London, London, UK
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, Camberwell, London, UK
| | - Sarah Mizielinska
- UK Dementia Research Institute at King's College London, London, UK
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, Camberwell, London, UK
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11
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Kakuo M, Horii T, Tonomura N, Sato R, Ogawa M, Okajima T, Kamemura K. Evidence that only EWS among the FET proteins acquires a low partitioning property for the hyperosmotic stress response by O-GlcNAc glycosylation on its low-complexity domain. Exp Cell Res 2023; 424:113504. [PMID: 36736606 DOI: 10.1016/j.yexcr.2023.113504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/28/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023]
Abstract
FET proteins (FUS, EWS, and TAF15) share a common domain organization, bind RNA/DNA, and perform similarly multifunctional roles in the regulation of gene expression. Of the FET proteins, however, only EWS appears to have a distinct property in the cellular stress response. Therefore, we focused on the relationship between hyperosmotic stress response and post-translational modifications of the FET proteins. We confirmed that the hyperosmotic stress-dependent translocation from the nucleus to the cytoplasm and the cellular granule formation of FET proteins, and that EWS is less likely to partition into cellular granules in the cytoplasm than FUS or TAF15. The domain involved in the less partitioning property of EWS was found to be its low-complexity domain (LCD). Chemoenzymatic labeling analysis of O-linked β-N-acetylglucosamine (O-GlcNAc) residues revealed that O-GlcNAc glycosylation occurs frequently in the LCD of EWS. A correlation was observed between the glycosylation of EWS and the less partitioning property under the hyperosmotic stress. These results suggest that among the FET proteins, only EWS has acquired the unique property through O-GlcNAc glycosylation. The glycosylation may play an essential role in regulating physiological functions of EWS, such as transcriptional activity, in addition to the property in cellular stress response.
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Affiliation(s)
- Manami Kakuo
- Department of Medical Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, 526-0829, Japan
| | - Takeshi Horii
- Department of Medical Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, 526-0829, Japan
| | - Naoto Tonomura
- Department of Medical Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, 526-0829, Japan
| | - Runa Sato
- Department of Medical Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, 526-0829, Japan
| | - Mitsutaka Ogawa
- Department of Molecular Biochemistry, Nagoya University Graduate School of Medicine, Nagoya, Aichi, 466-8550, Japan
| | - Tetsuya Okajima
- Department of Molecular Biochemistry, Nagoya University Graduate School of Medicine, Nagoya, Aichi, 466-8550, Japan
| | - Kazuo Kamemura
- Department of Medical Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, 526-0829, Japan.
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12
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TDP-43 Proteinopathy Specific Biomarker Development. Cells 2023; 12:cells12040597. [PMID: 36831264 PMCID: PMC9954136 DOI: 10.3390/cells12040597] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/31/2023] [Accepted: 02/07/2023] [Indexed: 02/16/2023] Open
Abstract
TDP-43 is the primary or secondary pathological hallmark of neurodegenerative diseases, such as amyotrophic lateral sclerosis, half of frontotemporal dementia cases, and limbic age-related TDP-43 encephalopathy, which clinically resembles Alzheimer's dementia. In such diseases, a biomarker that can detect TDP-43 proteinopathy in life would help to stratify patients according to their definite diagnosis of pathology, rather than in clinical subgroups of uncertain pathology. For therapies developed to target pathological proteins that cause the disease a biomarker to detect and track the underlying pathology would greatly enhance such undertakings. This article reviews the latest developments and outlooks of deriving TDP-43-specific biomarkers from the pathophysiological processes involved in the development of TDP-43 proteinopathy and studies using biosamples from clinical entities associated with TDP-43 pathology to investigate biomarker candidates.
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13
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Creating overview and summary figures. Trends Biochem Sci 2023; 48:97-99. [PMID: 36669467 DOI: 10.1016/j.tibs.2022.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 09/28/2022] [Indexed: 01/20/2023]
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14
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Huai Y, Mao W, Wang X, Lin X, Li Y, Chen Z, Qian A. How do RNA binding proteins trigger liquid-liquid phase separation in human health and diseases? Biosci Trends 2022; 16:389-404. [PMID: 36464283 DOI: 10.5582/bst.2022.01449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
RNA-binding proteins (RBPs) lie at the center of post-transcriptional regulation and protein synthesis, adding complexity to RNA life cycle. RBPs also participate in the formation of membrane-less organelles (MLOs) via undergoing liquid-liquid phase separation (LLPS), which underlies the formation of MLOs in eukaryotic cells. RBPs-triggered LLPS mainly relies on the interaction between their RNA recognition motifs (RRMs) and capped mRNA transcripts and the heterotypic multivalent interactions between their intrinsically disordered regions (IDRs) or prion-like domains (PLDs). In turn, the aggregations of RBPs are also dependent on the process of LLPS. RBPs-driven LLPS is involved in many intracellular processes (regulation of translation, mRNA storage and stabilization and cell signaling) and serves as the heart of cellular physiology and pathology. Thus, it is essential to comprehend the potential roles and investigate the internal mechanism of RPBs-triggered LLPS. In this review, we primarily expound on our current understanding of RBPs and they-triggered LLPS and summarize their physiological and pathological functions. Furthermore, we also summarize the potential roles of RBPs-triggered LLPS as novel therapeutic mechanism for human diseases. This review will help understand the mechanisms underlying LLPS and downstream regulation of RBPs and provide insights into the pathogenesis and therapy of complex diseases.
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Affiliation(s)
- Ying Huai
- Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,Key Lab for Space Biosciences and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,Research Center for Special Medicine and Health Systems Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Wenjing Mao
- Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,Key Lab for Space Biosciences and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,Research Center for Special Medicine and Health Systems Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Xuehao Wang
- Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,Key Lab for Space Biosciences and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,Research Center for Special Medicine and Health Systems Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Xiao Lin
- Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,Key Lab for Space Biosciences and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,Research Center for Special Medicine and Health Systems Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Yu Li
- Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,Key Lab for Space Biosciences and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,Research Center for Special Medicine and Health Systems Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Zhihao Chen
- Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,Key Lab for Space Biosciences and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,Research Center for Special Medicine and Health Systems Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,Department of Obstetrics and Gynecology, Xijing Hospital, The Fourth Military Medical University, Xi'an, China
| | - Airong Qian
- Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,Key Lab for Space Biosciences and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,Research Center for Special Medicine and Health Systems Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China
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15
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Xie C, Li Z, Hua Y, Sun S, Zhong L, Chen Q, Feng H, Ji N, Li T, Zhou X, Zeng X, Tang Z, Sun C, Li J, Chen Q. Identification of a BRAF/PA28γ/MEK1 signaling axis and its role in epithelial-mesenchymal transition in oral submucous fibrosis. Cell Death Dis 2022; 13:701. [PMID: 35961969 PMCID: PMC9374740 DOI: 10.1038/s41419-022-05152-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 07/26/2022] [Accepted: 07/29/2022] [Indexed: 01/21/2023]
Abstract
Oral submucous fibrosis (OSF) is a chronic and insidious oral potentially malignant disorder associated with a 4-17% risk of oral squamous cell carcinoma (OSCC). Our previous study found that proteasomal activator 28 gamma (PA28γ) is frequently overexpressed in oral squamous cell carcinoma and negatively correlated with poor patient prognosis. However, the role of PA28γ in the occurrence and development of OSF remains unclear. Here, we screened PA28γ-related genes and investigated their function in OSF. We demonstrated that the expression of PA28γ was positively associated with MEK1 and gradually elevated from normal to progressive stages of OSF tissue. Arecoline, a pathogenic component of OSF, could upregulate the protein levels of PA28γ and phosphorylated MEK1 and contribute to epithelial to mesenchymal transition (EMT) in epithelial cells. Notably, PA28γ could interact with MEK1 and upregulate its phosphorylation level. Furthermore, arecoline upregulated BRAF, which can interact with PA28γ and upregulate its protein level. Additionally, BRAF, PA28γ, and MEK1 could form protein complexes and then enhance the MEK1/ERK signaling pathways. The concrete mechanism of the protein stability of PA28γ is that BRAF mediates its degradation by inhibiting its ubiquitination. These findings underscore the instrumental role of PA28γ in the BRAF/MEK1 pathway and enhanced EMT through MEK1/ERK activation in OSF.
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Affiliation(s)
- Changqing Xie
- grid.13291.380000 0001 0807 1581State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stom atology, Sichuan University, Chengdu, Sichuan 610041 People’s Republic of China ,grid.216417.70000 0001 0379 7164Department of Oral and Maxillofacial Surgery, Xiangya Stomatological Hospital & School of Stomatology, Postdoctoral Research Workstation, Cancer Research Institute and School of Basic Medicine, Central South University, Changsha, Hunan 410078 People’s Republic of China
| | - Zaiye Li
- grid.13291.380000 0001 0807 1581State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stom atology, Sichuan University, Chengdu, Sichuan 610041 People’s Republic of China
| | - Yufei Hua
- grid.13291.380000 0001 0807 1581State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stom atology, Sichuan University, Chengdu, Sichuan 610041 People’s Republic of China
| | - Silu Sun
- grid.13291.380000 0001 0807 1581State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stom atology, Sichuan University, Chengdu, Sichuan 610041 People’s Republic of China
| | - Liang Zhong
- grid.13291.380000 0001 0807 1581State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stom atology, Sichuan University, Chengdu, Sichuan 610041 People’s Republic of China
| | - Qian Chen
- grid.13291.380000 0001 0807 1581State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stom atology, Sichuan University, Chengdu, Sichuan 610041 People’s Republic of China
| | - Hui Feng
- grid.13291.380000 0001 0807 1581State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stom atology, Sichuan University, Chengdu, Sichuan 610041 People’s Republic of China ,grid.216417.70000 0001 0379 7164Department of Oral and Maxillofacial Surgery, Xiangya Stomatological Hospital & School of Stomatology, Postdoctoral Research Workstation, Cancer Research Institute and School of Basic Medicine, Central South University, Changsha, Hunan 410078 People’s Republic of China
| | - Ning Ji
- grid.13291.380000 0001 0807 1581State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stom atology, Sichuan University, Chengdu, Sichuan 610041 People’s Republic of China
| | - Taiwen Li
- grid.13291.380000 0001 0807 1581State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stom atology, Sichuan University, Chengdu, Sichuan 610041 People’s Republic of China
| | - Xikun Zhou
- grid.13291.380000 0001 0807 1581State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041 People’s Republic of China
| | - Xin Zeng
- grid.13291.380000 0001 0807 1581State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stom atology, Sichuan University, Chengdu, Sichuan 610041 People’s Republic of China
| | - Zhangui Tang
- grid.216417.70000 0001 0379 7164Department of Oral and Maxillofacial Surgery, Xiangya Stomatological Hospital & School of Stomatology, Postdoctoral Research Workstation, Cancer Research Institute and School of Basic Medicine, Central South University, Changsha, Hunan 410078 People’s Republic of China
| | - Chongkui Sun
- grid.13291.380000 0001 0807 1581State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stom atology, Sichuan University, Chengdu, Sichuan 610041 People’s Republic of China
| | - Jing Li
- grid.13291.380000 0001 0807 1581State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stom atology, Sichuan University, Chengdu, Sichuan 610041 People’s Republic of China
| | - Qianming Chen
- grid.13291.380000 0001 0807 1581State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stom atology, Sichuan University, Chengdu, Sichuan 610041 People’s Republic of China
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16
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Chen J, Sun M, Huang L, Fang Y. The Long noncoding RNA LINC00200 Promotes the Malignant Progression of MYCN-Amplified Neuroblastoma via Binding to Insulin like growth factor 2 mRNA binding protein 3 (IGF2BP3) to Enhance the Stability of of Zic family member 2 (ZIC2) mRNA. Pathol Res Pract 2022; 237:154059. [DOI: 10.1016/j.prp.2022.154059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 07/24/2022] [Accepted: 08/03/2022] [Indexed: 12/09/2022]
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17
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Cracco L, Doud EH, Hallinan GI, Garringer HJ, Jacobsen MH, Richardson R, Buratti E, Vidal R, Ghetti B, Newell KL. Distinguishing post-translational modifications in dominantly inherited FTD: FTLD-TDP Type A (GRN) versus Type B (C9orf72). Neuropathol Appl Neurobiol 2022; 48:e12836. [PMID: 35836354 PMCID: PMC9452479 DOI: 10.1111/nan.12836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 07/07/2022] [Accepted: 07/09/2022] [Indexed: 11/29/2022]
Abstract
AIMS Frontotemporal dementias are neuropathologically characterized by frontotemporal lobar degeneration (FTLD). Intraneuronal inclusions of transactive response DNA-binding protein 43 kDa (TDP-43) are the defining pathologic hallmark of approximately half of the FTLD cases, being referred to as FTLD-TDP. The classification of FTLD-TDP into five subtypes (Type A to Type E) is based on pathologic phenotypes; however, the molecular determinants underpinning the phenotypic heterogeneity of FTLD-TDP are not well known. It is currently undetermined whether TDP-43 post-translational modifications (PTMs) may be related to the phenotypic diversity of the FTLDs. Thus, the investigation of FTLD-TDP Type A and Type B, associated with GRN and C9orf72 mutations, becomes an essential step. METHODS Immunohistochemistry was used to identify and map the intraneuronal inclusions. Sarkosyl-insoluble TDP-43 was extracted from brains of GRN and C9orf72 carriers post-mortem and studied by western blot analysis, immunoelectron microscopy and mass spectrometry. RESULTS Filaments of TDP-43 were present in all FTLD-TDP preparations. PTM profiling identified multiple phosphorylated, N-terminal acetylated, or otherwise modified residues, several of which have been identified for the first time as related to sarkosyl-insoluble TDP-43. Several PTMs were specific for either Type A or Type B, while others were identified in both types. CONCLUSIONS The current results provide evidence that the intraneuronal inclusions in the two genetic diseases contain TDP-43 filaments. The discovery of novel, potentially Type-specific TDP-43 PTMs emphasizes the need to determine the mechanisms leading to filament formation and PTMs, and the necessity of exploring the validity and occupancy of PTMs in a prognostic/diagnostic setting.
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Affiliation(s)
- Laura Cracco
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Emma H Doud
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Grace I Hallinan
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Holly J Garringer
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Max H Jacobsen
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Rose Richardson
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Emanuele Buratti
- Molecular Pathology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Ruben Vidal
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Bernardino Ghetti
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kathy L Newell
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
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18
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Paron F, Barattucci S, Cappelli S, Romano M, Berlingieri C, Stuani C, Laurents D, Mompeán M, Buratti E. Unravelling the toxic effects mediated by the neurodegenerative disease-associated S375G mutation of TDP-43 and its S375E phosphomimetic variant. J Biol Chem 2022; 298:102252. [PMID: 35835219 PMCID: PMC9364110 DOI: 10.1016/j.jbc.2022.102252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 06/23/2022] [Accepted: 06/25/2022] [Indexed: 12/05/2022] Open
Abstract
TAR DNA-binding protein 43 (TDP-43) is a nucleic acid–binding protein found in the nucleus that accumulates in the cytoplasm under pathological conditions, leading to proteinopathies, such as frontotemporal dementia and ALS. An emerging area of TDP-43 research is represented by the study of its post-translational modifications, the way they are connected to disease-associated mutations, and what this means for pathological processes. Recently, we described a novel mutation in TDP-43 in an early onset ALS case that was affecting a potential phosphorylation site in position 375 (S375G). A preliminary characterization showed that both the S375G mutation and its phosphomimetic variant, S375E, displayed altered nuclear–cytoplasmic distribution and cellular toxicity. To better investigate these effects, here we established cell lines expressing inducible WT, S375G, and S375E TDP-43 variants. Interestingly, we found that these mutants do not seem to affect well-studied aspects of TDP-43, such as RNA splicing or autoregulation, or protein conformation, dynamics, or aggregation, although they do display dysmorphic nuclear shape and cell cycle alterations. In addition, RNA-Seq analysis of these cell lines showed that although the disease-associated S375G mutation and its phosphomimetic S375E variant regulate distinct sets of genes, they have a common target in mitochondrial apoptotic genes. Taken together, our data strongly support the growing evidence that alterations in TDP-43 post-translational modifications can play a potentially important role in disease pathogenesis and provide a further link between TDP-43 pathology and mitochondrial health.
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Affiliation(s)
- Francesca Paron
- Molecular Pathology, International Centre for Genetic and Engineering Biotechnology (ICGEB), Trieste, Italy
| | - Simone Barattucci
- Molecular Pathology, International Centre for Genetic and Engineering Biotechnology (ICGEB), Trieste, Italy
| | - Sara Cappelli
- Molecular Pathology, International Centre for Genetic and Engineering Biotechnology (ICGEB), Trieste, Italy
| | - Maurizio Romano
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Christian Berlingieri
- Molecular Pathology, International Centre for Genetic and Engineering Biotechnology (ICGEB), Trieste, Italy
| | - Cristiana Stuani
- Molecular Pathology, International Centre for Genetic and Engineering Biotechnology (ICGEB), Trieste, Italy
| | - Douglas Laurents
- "Rocasolano" Institute for Physical Chemistry, Spanish National Research Council, Serrano 119, 28006, Madrid, Spain
| | - Miguel Mompeán
- "Rocasolano" Institute for Physical Chemistry, Spanish National Research Council, Serrano 119, 28006, Madrid, Spain
| | - Emanuele Buratti
- Molecular Pathology, International Centre for Genetic and Engineering Biotechnology (ICGEB), Trieste, Italy.
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19
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Jeon P, Ham HJ, Park S, Lee JA. Regulation of Cellular Ribonucleoprotein Granules: From Assembly to Degradation via Post-translational Modification. Cells 2022; 11:cells11132063. [PMID: 35805146 PMCID: PMC9265587 DOI: 10.3390/cells11132063] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/09/2022] [Accepted: 06/24/2022] [Indexed: 02/04/2023] Open
Abstract
Cells possess membraneless ribonucleoprotein (RNP) granules, including stress granules, processing bodies, Cajal bodies, or paraspeckles, that play physiological or pathological roles. RNP granules contain RNA and numerous RNA-binding proteins, transiently formed through the liquid–liquid phase separation. The assembly or disassembly of numerous RNP granules is strongly controlled to maintain their homeostasis and perform their cellular functions properly. Normal RNA granules are reversibly assembled, whereas abnormal RNP granules accumulate and associate with various neurodegenerative diseases. This review summarizes current studies on the physiological or pathological roles of post-translational modifications of various cellular RNP granules and discusses the therapeutic methods in curing diseases related to abnormal RNP granules by autophagy.
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20
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Ganne A, Balasubramaniam M, Griffin WST, Shmookler Reis RJ, Ayyadevara S. Glial Fibrillary Acidic Protein: A Biomarker and Drug Target for Alzheimer’s Disease. Pharmaceutics 2022; 14:pharmaceutics14071354. [PMID: 35890250 PMCID: PMC9322874 DOI: 10.3390/pharmaceutics14071354] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 06/21/2022] [Accepted: 06/22/2022] [Indexed: 02/05/2023] Open
Abstract
Glial fibrillary acidic protein (GFAP) is an intermediate filament structural protein involved in cytoskeleton assembly and integrity, expressed in high abundance in activated glial cells. GFAP is neuroprotective, as knockout mice are hypersensitive to traumatic brain injury. GFAP in cerebrospinal fluid is a biomarker of Alzheimer’s disease (AD), dementia with Lewy bodies, and frontotemporal dementia (FTD). Here, we present novel evidence that GFAP is markedly overexpressed and differentially phosphorylated in AD hippocampus, especially in AD with the apolipoprotein E [ε4, ε4] genotype, relative to age-matched controls (AMCs). Kinases that phosphorylate GFAP are upregulated in AD relative to AMC. A knockdown of these kinases in SH-SY5Y-APPSw human neuroblastoma cells reduced amyloid accrual and lowered protein aggregation and associated behavioral traits in C. elegans models of polyglutamine aggregation (as observed in Huntington’s disease) and of Alzheimer’s-like amyloid formation. In silico screening of the ChemBridge structural library identified a small molecule, MSR1, with stable and specific binding to GFAP. Both MSR1 exposure and GF AP-specific RNAi knockdown reduce aggregation with remarkably high concordance of aggregate proteins depleted. These data imply that GFAP and its phosphorylation play key roles in neuropathic aggregate accrual and provide valuable new biomarkers, as well as novel therapeutic targets to alleviate, delay, or prevent AD.
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Affiliation(s)
- Akshatha Ganne
- Central Arkansas Veterans Healthcare Service, Little Rock, AR 72205, USA; (A.G.); (M.B.); (W.S.T.G.)
- Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | | | - W. Sue T. Griffin
- Central Arkansas Veterans Healthcare Service, Little Rock, AR 72205, USA; (A.G.); (M.B.); (W.S.T.G.)
- BioInformatics Program, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Robert J. Shmookler Reis
- Central Arkansas Veterans Healthcare Service, Little Rock, AR 72205, USA; (A.G.); (M.B.); (W.S.T.G.)
- Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- BioInformatics Program, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- Department of Biochemistry & Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- Correspondence: (R.J.S.R.); (S.A.); Tel.: +1-501-526-5820 (R.J.S.R.); +1-501-526-7282 (S.A.)
| | - Srinivas Ayyadevara
- Central Arkansas Veterans Healthcare Service, Little Rock, AR 72205, USA; (A.G.); (M.B.); (W.S.T.G.)
- Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- BioInformatics Program, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- Correspondence: (R.J.S.R.); (S.A.); Tel.: +1-501-526-5820 (R.J.S.R.); +1-501-526-7282 (S.A.)
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21
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Lao Z, Dong X, Liu X, Li F, Chen Y, Tang Y, Wei G. Insights into the Atomistic Mechanisms of Phosphorylation in Disrupting Liquid-Liquid Phase Separation and Aggregation of the FUS Low-Complexity Domain. J Chem Inf Model 2022; 62:3227-3238. [PMID: 35709363 DOI: 10.1021/acs.jcim.2c00414] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fused in sarcoma (FUS), a nuclear RNA binding protein, can not only undergo liquid-liquid phase separation (LLPS) to form dynamic biomolecular condensates but also aggregate into solid amyloid fibrils which are associated with the pathology of amyotrophic lateral sclerosis and frontotemporal lobar degeneration diseases. Phosphorylation in the FUS low-complexity domain (FUS-LC) inhibits FUS LLPS and aggregation. However, it remains largely elusive what are the underlying atomistic mechanisms of this inhibitory effect and whether phosphorylation can disrupt preformed FUS fibrils, reversing the FUS gel/solid phase toward the liquid phase. Herein, we systematically investigate the impacts of phosphorylation on the conformational ensemble of the FUS37-97 monomer and dimer and the structure of the FUS37-97 fibril by performing extensive all-atom molecular dynamics simulations. Our simulations reveal three key findings: (1) phosphorylation shifts the conformations of FUS37-97 from the β-rich, fibril-competent state toward a helix-rich, fibril-incompetent state; (2) phosphorylation significantly weakens protein-protein interactions and enhances protein-water interactions, which disfavor FUS-LC LLPS as well as aggregation and facilitate the dissolution of the preformed FUS-LC fibril; and (3) the FUS37-97 peptide displays a high β-strand probability in the region spanning residues 52-67, and phosphorylation at S54 and S61 residues located in this region is crucial for the disruption of LLPS and aggregation of FUS-LC. This study may pave the way for ameliorating phase-separation-related pathologies via site-specific phosphorylation.
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Affiliation(s)
- Zenghui Lao
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200433, People's Republic of China
| | - Xuewei Dong
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200433, People's Republic of China
| | - Xianshi Liu
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200433, People's Republic of China
| | - Fangying Li
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200433, People's Republic of China
| | - Yujie Chen
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200433, People's Republic of China
| | - Yiming Tang
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200433, People's Republic of China
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200433, People's Republic of China
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22
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Gogia N, Ni L, Olmos V, Haidery F, Luttik K, Lim J. Exploring the Role of Posttranslational Modifications in Spinal and Bulbar Muscular Atrophy. Front Mol Neurosci 2022; 15:931301. [PMID: 35726299 PMCID: PMC9206542 DOI: 10.3389/fnmol.2022.931301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
Spinal and Bulbar Muscular Atrophy (SBMA) is an X-linked adult-onset progressive neuromuscular disease that affects the spinal and bulbar motor neurons and skeletal muscles. SBMA is caused by expansion of polymorphic CAG trinucleotide repeats in the Androgen Receptor (AR) gene, resulting in expanded glutamine tract in the AR protein. Polyglutamine (polyQ) expansion renders the mutant AR protein toxic, resulting in the formation of mutant protein aggregates and cell death. This classifies SBMA as one of the nine known polyQ diseases. Like other polyQ disorders, the expansion of the polyQ tract in the AR protein is the main genetic cause of the disease; however, multiple other mechanisms besides the polyQ tract expansion also contribute to the SBMA disease pathophysiology. Posttranslational modifications (PTMs), including phosphorylation, acetylation, methylation, ubiquitination, and SUMOylation are a category of mechanisms by which the functionality of AR has been found to be significantly modulated and can alter the neurotoxicity of SBMA. This review summarizes the different PTMs and their effects in regulating the AR function and discusses their pathogenic or protective roles in context of SBMA. This review also includes the therapeutic approaches that target the PTMs of AR in an effort to reduce the mutant AR-mediated toxicity in SBMA.
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Affiliation(s)
- Neha Gogia
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT, United States
| | - Luhan Ni
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT, United States
| | - Victor Olmos
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT, United States
| | - Fatema Haidery
- Yale College, Yale University, New Haven, CT, United States
| | - Kimberly Luttik
- Department of Neuroscience, Yale School of Medicine, Yale University, New Haven, CT, United States,Interdepartmental Neuroscience Program, Yale University, New Haven, CT, United States
| | - Janghoo Lim
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT, United States,Department of Neuroscience, Yale School of Medicine, Yale University, New Haven, CT, United States,Interdepartmental Neuroscience Program, Yale University, New Haven, CT, United States,Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale School of Medicine, Yale University, New Haven, CT, United States
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23
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Tabassum Z, Tseng JH, Isemann C, Tian X, Chen Y, Herring LE, Cohen TJ. Identification of a reciprocal negative feedback loop between tau-modifying proteins MARK2 kinase and CBP acetyltransferase. J Biol Chem 2022; 298:101977. [PMID: 35469920 PMCID: PMC9136110 DOI: 10.1016/j.jbc.2022.101977] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 04/14/2022] [Accepted: 04/16/2022] [Indexed: 11/30/2022] Open
Abstract
The posttranslational regulation of the neuronal proteome is critical for brain homeostasis but becomes dysregulated in the aged or diseased brain, in which abnormal posttranslational modifications (PTMs) are frequently observed. While the full extent of modified substrates that comprise the "PTM-ome" are slowly emerging, how the upstream enzymes catalyzing these processes are regulated themselves is not well understood, particularly in the context of neurodegeneration. Here, we describe the reciprocal regulation of a kinase, the microtubule affinity-regulating kinase 2 (MARK2), and an acetyltransferase, CREB-binding protein (CBP), two enzymes known to extensively modify tau proteins in the progression of Alzheimer's disease. We found that MARK2 negatively regulates CBP and, conversely, CBP directly acetylates and inhibits MARK2 kinase activity. These findings highlight a reciprocal negative feedback loop between a kinase and an acetyltransferase, which has implications for how PTM interplay is coordinated on substrates including tau. Our study suggests that PTM profiles occur through the posttranslational control of the master PTM remodeling enzymes themselves.
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Affiliation(s)
- Zarin Tabassum
- Department of Neurology, UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jui-Heng Tseng
- Department of Neurology, UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Camryn Isemann
- Department of Neurology, UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Xu Tian
- Department of Neurology, UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Youjun Chen
- Department of Neurology, UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Laura E Herring
- UNC Proteomics Core Facility, Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Todd J Cohen
- Department of Neurology, UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina, USA.
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24
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Krause LJ, Herrera MG, Winklhofer KF. The Role of Ubiquitin in Regulating Stress Granule Dynamics. Front Physiol 2022; 13:910759. [PMID: 35694405 PMCID: PMC9174786 DOI: 10.3389/fphys.2022.910759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/09/2022] [Indexed: 11/30/2022] Open
Abstract
Stress granules (SGs) are dynamic, reversible biomolecular condensates, which assemble in the cytoplasm of eukaryotic cells under various stress conditions. Formation of SGs typically occurs upon stress-induced translational arrest and polysome disassembly. The increase in cytoplasmic mRNAs triggers the formation of a protein-RNA network that undergoes liquid-liquid phase separation when a critical interaction threshold has been reached. This adaptive stress response allows a transient shutdown of several cellular processes until the stress is removed. During the recovery from stress, SGs disassemble to re-establish cellular activities. Persistent stress and disease-related mutations in SG components favor the formation of aberrant SGs that are impaired in disassembly and prone to aggregation. Recently, posttranslational modifications of SG components have been identified as major regulators of SG dynamics. Here, we summarize new insights into the role of ubiquitination in affecting SG dynamics and clearance and discuss implications for neurodegenerative diseases linked to aberrant SG formation.
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Affiliation(s)
- Laura J. Krause
- Department of Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
- RESOLV Cluster of Excellence, Ruhr University Bochum, Bochum, Germany
| | - Maria G. Herrera
- Department of Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Konstanze F. Winklhofer
- Department of Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
- RESOLV Cluster of Excellence, Ruhr University Bochum, Bochum, Germany
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25
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Milicevic K, Rankovic B, Andjus PR, Bataveljic D, Milovanovic D. Emerging Roles for Phase Separation of RNA-Binding Proteins in Cellular Pathology of ALS. Front Cell Dev Biol 2022; 10:840256. [PMID: 35372329 PMCID: PMC8965147 DOI: 10.3389/fcell.2022.840256] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 01/24/2022] [Indexed: 12/11/2022] Open
Abstract
Liquid-liquid phase separation (LLPS) is emerging as a major principle for the mesoscale organization of proteins, RNAs, and membrane-bound organelles into biomolecular condensates. These condensates allow for rapid cellular responses to changes in metabolic activities and signaling. Nowhere is this regulation more important than in neurons and glia, where cellular physiology occurs simultaneously on a range of time- and length-scales. In a number of neurodegenerative diseases, such as Amyotrophic Lateral Sclerosis (ALS), misregulation of biomolecular condensates leads to the formation of insoluble aggregates—a pathological hallmark of both sporadic and familial ALS. Here, we summarize how the emerging knowledge about the LLPS of ALS-related proteins corroborates with their aggregation. Understanding the mechanisms that lead to protein aggregation in ALS and how cells respond to these aggregates promises to open new directions for drug development.
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Affiliation(s)
- Katarina Milicevic
- Center for Laser Microscopy, Faculty of Biology, Institute of Physiology and Biochemistry “Ivan Djaja”, University of Belgrade, Belgrade, Serbia
| | - Branislava Rankovic
- Laboratory of Molecular Neuroscience, German Center for Neurodegenerative Diseases (DZNE), Berlin, Germany
| | - Pavle R. Andjus
- Center for Laser Microscopy, Faculty of Biology, Institute of Physiology and Biochemistry “Ivan Djaja”, University of Belgrade, Belgrade, Serbia
| | - Danijela Bataveljic
- Center for Laser Microscopy, Faculty of Biology, Institute of Physiology and Biochemistry “Ivan Djaja”, University of Belgrade, Belgrade, Serbia
- *Correspondence: Danijela Bataveljic, ; Dragomir Milovanovic,
| | - Dragomir Milovanovic
- Laboratory of Molecular Neuroscience, German Center for Neurodegenerative Diseases (DZNE), Berlin, Germany
- *Correspondence: Danijela Bataveljic, ; Dragomir Milovanovic,
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26
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Giambruno R, Grzybowska EA, Fawzi NL, Dormann D. Editorial: The Role of Protein Post-Translational Modifications in Protein-RNA Interactions and RNP Assemblies. Front Mol Biosci 2022; 8:831810. [PMID: 35059438 PMCID: PMC8764229 DOI: 10.3389/fmolb.2021.831810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 12/14/2021] [Indexed: 11/24/2022] Open
Affiliation(s)
- Roberto Giambruno
- Center for Genomic Science, Italian Institute of Technology (IIT), Milano, Italy
| | - Ewa A Grzybowska
- Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | | | - Dorothee Dormann
- Biocenter, Johannes Gutenberg University Mainz, Mainz, Germany.,Institute of Molecular Biology (IMB), Mainz, Germany
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27
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Dong W, Zhou R, Chen J, Shu Z, Duan M. Phosphorylation Regulation on the Homo-Dimeric Binding of Transactive Response DNA-Binding Protein. J Chem Inf Model 2022; 62:5267-5275. [PMID: 35040651 DOI: 10.1021/acs.jcim.1c01224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The dimerization of transactive response DNA-binding protein of 43 kDa (TDP-43) is crucial for the RNA metabolism, and the higher-order aggregation of TDP-43 would induce several neurodegenerative diseases. The dimerization and aggregation of TDP-43 are regulated by the phosphorylation on its N-terminal domain (NTD). Understanding the regulation mechanism of TDP-43 NTD dimerization is crucial for the preventing of harmful aggregation and the associated diseases. In this study, the dimerization processes of wild-type (WT), phosphorylated S48 (pS48), and phosphomimic S48E mutation (S48E) of TDP-43 NTD are characterized by the enhanced sampling technology. Our results show that the phosphorylation not only shift the conformation population of bound and unbound state of TDP-43 NTD, but also would regulate the dimerization processes, including increase the binding free-energy barrier. The phosphomimic mutation would also shift the conformational space of TDP-43 NTD dimer to the unbound structures; however, the thermodynamic and kinetic properties of the dimerization processes between the phosphorylated and phosphomimic mutant systems are distinct, which reminds us to carefully study the phosphorylation regulation by using the phosphomimic mutations.
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Affiliation(s)
- Wanqian Dong
- National & Local United Engineering Research Center of Industrial Microbiology and Fermentation Technoloy, College of Life Sciences, Fujian Normal University (Qishan Campus), Fuzhou 350117, Fujian, China.,National Centre for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, Hubei, China
| | - Rui Zhou
- National Centre for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, Hubei, China
| | - Jiawen Chen
- National Centre for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, Hubei, China
| | - Zhengyu Shu
- National & Local United Engineering Research Center of Industrial Microbiology and Fermentation Technoloy, College of Life Sciences, Fujian Normal University (Qishan Campus), Fuzhou 350117, Fujian, China
| | - Mojie Duan
- National Centre for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, Hubei, China
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28
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Pisano C, Benedetto U, Ruvolo G, Balistreri CR. Oxidative Stress in the Pathogenesis of Aorta Diseases as a Source of Potential Biomarkers and Therapeutic Targets, with a Particular Focus on Ascending Aorta Aneurysms. Antioxidants (Basel) 2022; 11:antiox11020182. [PMID: 35204065 PMCID: PMC8868543 DOI: 10.3390/antiox11020182] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/06/2022] [Accepted: 01/12/2022] [Indexed: 12/14/2022] Open
Abstract
Aorta diseases, such as ascending aorta aneurysm (AsAA), are complex pathologies, currently defined as inflammatory diseases with a strong genetic susceptibility. They are difficult to manage, being insidious and silent pathologies whose diagnosis is based only on imaging data. No diagnostic and prognostic biomarkers or markers of outcome have been known until now. Thus, their identification is imperative. Certainly, a deep understanding of the mechanisms and pathways involved in their pathogenesis might help in such research. Recently, the key role of oxidative stress (OS) on the pathophysiology of aorta disease has emerged. Here, we describe and discuss these aspects by revealing some OS pathways as potential biomarkers, their underlying limitations, and potential solutions and approaches, as well as some potential treatments.
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Affiliation(s)
- Calogera Pisano
- Department of Cardiac Surgery, Tor Vergata University Hospital, 00133 Rome, Italy; (C.P.); (G.R.)
| | - Umberto Benedetto
- Bristol Heart Institute, University of Bristol, Bristol BS2 8HW, UK;
| | - Giovanni Ruvolo
- Department of Cardiac Surgery, Tor Vergata University Hospital, 00133 Rome, Italy; (C.P.); (G.R.)
| | - Carmela Rita Balistreri
- Department of Biomedicine, Neuroscience and Advanced Diagnostics (Bi.N.D.), University of Palermo, 90134 Palermo, Italy
- Correspondence:
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