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Ortiz ANR, Zhang L, Ash PE, Basu A, Puri S, van der Spek SJ, Wang Z, Dorrian L, Emili A, Wolozin B. Proximity labeling reveals dynamic changes in the SQSTM1 protein network. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.12.571324. [PMID: 38168279 PMCID: PMC10760047 DOI: 10.1101/2023.12.12.571324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Sequestosome1 (SQSTM1) is an autophagy receptor that mediates degradation of intracellular cargo, including protein aggregates, through multiple protein interactions. These interactions form the SQSTM1 protein network, and these interactions are mediated by SQSTM1 functional interaction domains, which include LIR, PB1, UBA and KIR. Technological advances in cell biology continue to expand our knowledge of the SQSTM1 protein network and of the relationship of the actions of the SQSTM1 protein network in cellular physiology and disease states. Here we apply proximity profile labeling to investigate the SQSTM1 protein interaction network by fusing TurboID with the human protein SQSTM1 (TurboID::SQSTM1). This chimeric protein displayed well-established SQSTM1 features including production of SQSTM1 intracellular bodies, binding to known SQSTM1 interacting partners, and capture of novel SQSTM1 protein interactors. Strikingly, aggregated tau protein altered the protein interaction network of SQSTM1 to include many stress-associated proteins. We demonstrate the importance of the PB1 and/or UBA domains for binding network members, including the K18 domain of tau. Overall, our work reveals the dynamic landscape of the SQSTM1 protein network and offers a resource to study SQSTM1 function in cellular physiology and disease state.
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Affiliation(s)
- Alejandro N. Rondón Ortiz
- Department of Biology, Boston University, Boston, MA 02215, USA
- Center for Network Systems Biology, Boston University, Boston, MA 02215, USA
- Departments of Anatomy & Neurobiology, Boston University, Boston, MA 02215, USA
| | - Lushuang Zhang
- Departments of Anatomy & Neurobiology, Boston University, Boston, MA 02215, USA
| | - Peter E.A. Ash
- Departments of Anatomy & Neurobiology, Boston University, Boston, MA 02215, USA
| | - Avik Basu
- Center for Network Systems Biology, Boston University, Boston, MA 02215, USA
- Department of Biochemistry, Boston University, Boston, MA 02115, USA
- Department of Chemical Physiology & Biochemistry, Oregon Health Sciences University, Portland, OR 97239, USA
| | - Sambhavi Puri
- Departments of Anatomy & Neurobiology, Boston University, Boston, MA 02215, USA
| | | | - Zihan Wang
- Departments of Anatomy & Neurobiology, Boston University, Boston, MA 02215, USA
| | - Luke Dorrian
- Departments of Anatomy & Neurobiology, Boston University, Boston, MA 02215, USA
| | - Andrew Emili
- Center for Network Systems Biology, Boston University, Boston, MA 02215, USA
- Department of Biochemistry, Boston University, Boston, MA 02115, USA
- Department of Chemical Physiology & Biochemistry, Oregon Health Sciences University, Portland, OR 97239, USA
| | - Benjamin Wolozin
- Departments of Anatomy & Neurobiology, Boston University, Boston, MA 02215, USA
- Center for Systems Neuroscience, Boston University, Boston, MA 02115, USA
- Center for Neurophotonics, Boston University, Boston, MA 02115, USA
- Department of Neurology, Boston University, Boston, MA 02115, USA
- Department of Pharmacology, Physiology and Biophysics
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2
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Brady ST, Mesnard-Hoaglin NA, Mays S, Priego M, Dziechciowska J, Morris S, Kang M, Tsai MY, Purks JL, Klein A, Gaona A, Melloni A, Connors T, Hyman B, Song Y, Morfini GA. Toxic effects of mutant huntingtin in axons are mediated by its proline-rich domain. Brain 2024; 147:2098-2113. [PMID: 37633260 PMCID: PMC11146425 DOI: 10.1093/brain/awad280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 05/13/2023] [Accepted: 07/17/2023] [Indexed: 08/28/2023] Open
Abstract
Huntington's disease results from expansion of a polyglutamine tract (polyQ) in mutant huntingtin (mHTT) protein, but mechanisms underlying polyQ expansion-mediated toxic gain-of-mHTT function remain elusive. Here, deletion and antibody-based experiments revealed that a proline-rich domain (PRD) adjacent to the polyQ tract is necessary for mHTT to inhibit fast axonal transport and promote axonal pathology in cultured mammalian neurons. Further, polypeptides corresponding to subregions of the PRD sufficed to elicit the toxic effect on fast axonal transport, which was mediated by c-Jun N-terminal kinases (JNKs) and involved PRD binding to one or more SH3-domain containing proteins. Collectively, these data suggested a mechanism whereby polyQ tract expansion in mHTT promotes aberrant PRD exposure and interactions of this domain with SH3 domain-containing proteins including some involved in activation of JNKs. In support, biochemical and immunohistochemical experiments linked aberrant PRD exposure to increased JNK activation in striatal tissues of the zQ175 mouse model and from post-mortem Huntington's disease patients. Together, these findings support a critical role of PRD on mHTT toxicity, suggesting a novel framework for the potential development of therapies aimed to halt or reduce axonal pathology in Huntington's disease.
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Affiliation(s)
- Scott T Brady
- Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, IL 60612, USA
- Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | | | - Sarah Mays
- Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, IL 60612, USA
- Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Mercedes Priego
- Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Joanna Dziechciowska
- Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Sarah Morris
- Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, IL 60612, USA
- Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Minsu Kang
- Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, IL 60612, USA
- Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Ming Ying Tsai
- Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, IL 60612, USA
| | | | - Alison Klein
- Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Angelica Gaona
- Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Alexandra Melloni
- Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Theresa Connors
- Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Bradley Hyman
- Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02129, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02129, USA
| | - Yuyu Song
- Marine Biological Laboratory, Woods Hole, MA 02543, USA
- Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02129, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02129, USA
| | - Gerardo A Morfini
- Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, IL 60612, USA
- Marine Biological Laboratory, Woods Hole, MA 02543, USA
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3
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Liu X, Abad L, Chatterjee L, Cristea IM, Varjosalo M. Mapping protein-protein interactions by mass spectrometry. MASS SPECTROMETRY REVIEWS 2024. [PMID: 38742660 DOI: 10.1002/mas.21887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 04/22/2024] [Indexed: 05/16/2024]
Abstract
Protein-protein interactions (PPIs) are essential for numerous biological activities, including signal transduction, transcription control, and metabolism. They play a pivotal role in the organization and function of the proteome, and their perturbation is associated with various diseases, such as cancer, neurodegeneration, and infectious diseases. Recent advances in mass spectrometry (MS)-based protein interactomics have significantly expanded our understanding of the PPIs in cells, with techniques that continue to improve in terms of sensitivity, and specificity providing new opportunities for the study of PPIs in diverse biological systems. These techniques differ depending on the type of interaction being studied, with each approach having its set of advantages, disadvantages, and applicability. This review highlights recent advances in enrichment methodologies for interactomes before MS analysis and compares their unique features and specifications. It emphasizes prospects for further improvement and their potential applications in advancing our knowledge of PPIs in various biological contexts.
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Affiliation(s)
- Xiaonan Liu
- Department of Physiology, Faculty of Medical Sciences in Katowice, Medical University of Silesia in Katowice, Katowice, Poland
- Institute of Biotechnology, HiLIFE Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Lawrence Abad
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Lopamudra Chatterjee
- Institute of Biotechnology, HiLIFE Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Markku Varjosalo
- Institute of Biotechnology, HiLIFE Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
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4
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Hwang I, Kim BS, Lee HY, Cho SW, Lee SE, Ahn JY. PA2G4/EBP1 ubiquitination by PRKN/PARKIN promotes mitophagy protecting neuron death in cerebral ischemia. Autophagy 2024; 20:365-379. [PMID: 37712850 PMCID: PMC10813645 DOI: 10.1080/15548627.2023.2259215] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 09/08/2023] [Accepted: 09/11/2023] [Indexed: 09/16/2023] Open
Abstract
Cerebral ischemia induces massive mitochondrial damage, leading to neuronal death. The elimination of damaged mitochondria via mitophagy is critical for neuroprotection. Here we show that the level of PA2G4/EBP1 (proliferation-associated 2G4) was notably increased early during transient middle cerebral artery occlusion and prevented neuronal death by eliciting cerebral ischemia-reperfusion (IR)-induced mitophagy. Neuron-specific knockout of Pa2g4 increased infarct volume and aggravated neuron loss with impaired mitophagy and was rescued by introduction of adeno-associated virus serotype 2 expressing PA2G4/EBP1. We determined that PA2G4/EBP1 is ubiquitinated on lysine 376 by PRKN/PARKIN on the damaged mitochondria and interacts with receptor protein SQSTM1/p62 for mitophagy induction. Thus, our study suggests that PA2G4/EBP1 ubiquitination following cerebral IR-injury promotes mitophagy induction, which may be implicated in neuroprotection.Abbreviations: AAV: adeno-associated virus; ACTB: actin beta; BNIP3L/NIX: BCL2 interacting protein 3 like; CA1: Cornu Ammonis 1; CASP3: caspase 3; CCCP: carbonyl cyanide m-chlorophenyl hydrazone; DMSO: dimethyl sulfoxide; PA2G4/EBP1: proliferation-associated 2G4; FUNDC1: FUN14 domain containing 1; IB: immunoblotting; ICC: immunocytochemistry; IHC: immunohistochemistry; IP: immunoprecipitation; MCAO: middle cerebral artery occlusion; MEF: mouse embryonic fibroblast; OGD: oxygen-glucose deprivation; PRKN/PARKIN: parkin RBR E3 ubiquitin protein ligase; PINK1: PTEN induced kinase 1; RBFOX3/NeuN: RNA binding fox-1 homolog 3; SQSTM1/p62: sequestosome 1; TIMM23: translocase of inner mitochondrial membrane 23; TOMM20: translocase of outer mitochondrial membrane 20; TUBB: tubulin beta class I; WT: wild-type.
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Affiliation(s)
- Inwoo Hwang
- Department of Molecular Cell Biology, Single Cell Network Research Center, Sungkyunkwan University School of Medicine, Suwon, Korea
- Single Cell Network Research Center, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Byeong-Seong Kim
- Department of Molecular Cell Biology, Single Cell Network Research Center, Sungkyunkwan University School of Medicine, Suwon, Korea
- Single Cell Network Research Center, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Ho Yun Lee
- Department of Radiology and Center for Imaging Science, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Sung-Woo Cho
- Department of Biochemistry and Molecular Biology, University of Ulsan, College of Medicine, Seoul, Korea
| | - Seung Eun Lee
- Research Animal Resources Center, Korea Institute of Science and Technology, Seongbuk-gu, Republic of Korea
| | - Jee-Yin Ahn
- Department of Molecular Cell Biology, Single Cell Network Research Center, Sungkyunkwan University School of Medicine, Suwon, Korea
- Single Cell Network Research Center, Sungkyunkwan University School of Medicine, Suwon, Korea
- Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Korea
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5
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Xiong J, Pang X, Song X, Yang L, Pang C. The coherence between PSMC6 and α-ring in the 26S proteasome is associated with Alzheimer's disease. Front Mol Neurosci 2024; 16:1330853. [PMID: 38357597 PMCID: PMC10864545 DOI: 10.3389/fnmol.2023.1330853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 12/22/2023] [Indexed: 02/16/2024] Open
Abstract
Alzheimer's disease (AD) is a heterogeneous age-dependent neurodegenerative disorder. Its hallmarks involve abnormal proteostasis, which triggers proteotoxicity and induces neuronal dysfunction. The 26S proteasome is an ATP-dependent proteolytic nanomachine of the ubiquitin-proteasome system (UPS) and contributes to eliminating these abnormal proteins. This study focused on the relationship between proteasome and AD, the hub genes of proteasome, PSMC6, and 7 genes of α-ring, are selected as targets to study. The following three characteristics were observed: 1. The total number of proteasomes decreased with AD progression because the proteotoxicity damaged the expression of proteasome proteins, as evidenced by the downregulation of hub genes. 2. The existing proteasomes exhibit increased activity and efficiency to counterbalance the decline in total proteasome numbers, as evidenced by enhanced global coordination and reduced systemic disorder of proteasomal subunits as AD advances. 3. The synergy of PSMC6 and α-ring subunits is associated with AD. Synergistic downregulation of PSMC6 and α-ring subunits reflects a high probability of AD risk. Regarding the above discovery, the following hypothesis is proposed: The aggregation of pathogenic proteins intensifies with AD progression, then proteasome becomes more active and facilitates the UPS selectively targets the degradation of abnormal proteins to maintain CNS proteostasis. In this paper, bioinformatics and support vector machine learning methods are applied and combined with multivariate statistical analysis of microarray data. Additionally, the concept of entropy was used to detect the disorder of proteasome system, it was discovered that entropy is down-regulated continually with AD progression against system chaos caused by AD. Another conception of the matrix determinant was used to detect the global coordination of proteasome, it was discovered that the coordination is enhanced to maintain the efficiency of degradation. The features of entropy and determinant suggest that active proteasomes resist the attack caused by AD like defenders, on the one hand, to protect themselves (entropy reduces), and on the other hand, to fight the enemy (determinant reduces). It is noted that these are results from biocomputing and need to be supported by further biological experiments.
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Affiliation(s)
- Jing Xiong
- College of Computer Science, Sichuan Normal University, Chengdu, China
| | - Xinping Pang
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Xianghu Song
- College of Computer Science, Sichuan Normal University, Chengdu, China
| | - Lin Yang
- College of Computer Science, Sichuan Normal University, Chengdu, China
| | - Chaoyang Pang
- College of Computer Science, Sichuan Normal University, Chengdu, China
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6
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McClatchy DB, Powell SB, Yates JR. In vivo mapping of protein-protein interactions of schizophrenia risk factors generates an interconnected disease network. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.12.571320. [PMID: 38168169 PMCID: PMC10759996 DOI: 10.1101/2023.12.12.571320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Genetic analyses of Schizophrenia (SCZ) patients have identified thousands of risk factors. In silico protein-protein interaction (PPI) network analysis has provided strong evidence that disrupted PPI networks underlie SCZ pathogenesis. In this study, we performed in vivo PPI analysis of several SCZ risk factors in the rodent brain. Using endogenous antibody immunoprecipitations coupled to mass spectrometry (MS) analysis, we constructed a SCZ network comprising 1612 unique PPI with a 5% FDR. Over 90% of the PPI were novel, reflecting the lack of previous PPI MS studies in brain tissue. Our SCZ PPI network was enriched with known SCZ risk factors, which supports the hypothesis that an accumulation of disturbances in selected PPI networks underlies SCZ. We used Stable Isotope Labeling in Mammals (SILAM) to quantitate phencyclidine (PCP) perturbations in the SCZ network and found that PCP weakened most PPI but also led to some enhanced or new PPI. These findings demonstrate that quantitating PPI in perturbed biological states can reveal alterations to network biology.
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7
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Cristi AC, Rapuri S, Coyne AN. Nuclear pore complex and nucleocytoplasmic transport disruption in neurodegeneration. FEBS Lett 2023; 597:2546-2566. [PMID: 37657945 PMCID: PMC10612469 DOI: 10.1002/1873-3468.14729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 07/29/2023] [Accepted: 08/24/2023] [Indexed: 09/03/2023]
Abstract
Nuclear pore complexes (NPCs) play a critical role in maintaining the equilibrium between the nucleus and cytoplasm, enabling bidirectional transport across the nuclear envelope, and are essential for proper nuclear organization and gene regulation. Perturbations in the regulatory mechanisms governing NPCs and nuclear envelope homeostasis have been implicated in the pathogenesis of several neurodegenerative diseases. The ESCRT-III pathway emerges as a critical player in the surveillance and preservation of well-assembled, functional NPCs, as well as nuclear envelope sealing. Recent studies have provided insights into the involvement of nuclear ESCRT-III in the selective reduction of specific nucleoporins associated with neurodegenerative pathologies. Thus, maintaining quality control of the nuclear envelope and NPCs represents a pivotal element in the pathological cascade leading to neurodegenerative diseases. This review describes the constituents of the nuclear-cytoplasmic transport machinery, encompassing the nuclear envelope, NPC, and ESCRT proteins, and how their structural and functional alterations contribute to the development of neurodegenerative diseases.
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Affiliation(s)
- América Chandía Cristi
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore MD 21205, USA
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore MD 21205, USA
| | - Sampath Rapuri
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore MD 21205, USA
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore MD 21205, USA
| | - Alyssa N Coyne
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore MD 21205, USA
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore MD 21205, USA
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8
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Boeddrich A, Haenig C, Neuendorf N, Blanc E, Ivanov A, Kirchner M, Schleumann P, Bayraktaroğlu I, Richter M, Molenda CM, Sporbert A, Zenkner M, Schnoegl S, Suenkel C, Schneider LS, Rybak-Wolf A, Kochnowsky B, Byrne LM, Wild EJ, Nielsen JE, Dittmar G, Peters O, Beule D, Wanker EE. A proteomics analysis of 5xFAD mouse brain regions reveals the lysosome-associated protein Arl8b as a candidate biomarker for Alzheimer's disease. Genome Med 2023; 15:50. [PMID: 37468900 PMCID: PMC10357615 DOI: 10.1186/s13073-023-01206-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 06/22/2023] [Indexed: 07/21/2023] Open
Abstract
BACKGROUND Alzheimer's disease (AD) is characterized by the intra- and extracellular accumulation of amyloid-β (Aβ) peptides. How Aβ aggregates perturb the proteome in brains of patients and AD transgenic mouse models, remains largely unclear. State-of-the-art mass spectrometry (MS) methods can comprehensively detect proteomic alterations, providing relevant insights unobtainable with transcriptomics investigations. Analyses of the relationship between progressive Aβ aggregation and protein abundance changes in brains of 5xFAD transgenic mice have not been reported previously. METHODS We quantified progressive Aβ aggregation in hippocampus and cortex of 5xFAD mice and controls with immunohistochemistry and membrane filter assays. Protein changes in different mouse tissues were analyzed by MS-based proteomics using label-free quantification; resulting MS data were processed using an established pipeline. Results were contrasted with existing proteomic data sets from postmortem AD patient brains. Finally, abundance changes in the candidate marker Arl8b were validated in cerebrospinal fluid (CSF) from AD patients and controls using ELISAs. RESULTS Experiments revealed faster accumulation of Aβ42 peptides in hippocampus than in cortex of 5xFAD mice, with more protein abundance changes in hippocampus, indicating that Aβ42 aggregate deposition is associated with brain region-specific proteome perturbations. Generating time-resolved data sets, we defined Aβ aggregate-correlated and anticorrelated proteome changes, a fraction of which was conserved in postmortem AD patient brain tissue, suggesting that proteome changes in 5xFAD mice mimic disease-relevant changes in human AD. We detected a positive correlation between Aβ42 aggregate deposition in the hippocampus of 5xFAD mice and the abundance of the lysosome-associated small GTPase Arl8b, which accumulated together with axonal lysosomal membranes in close proximity of extracellular Aβ plaques in 5xFAD brains. Abnormal aggregation of Arl8b was observed in human AD brain tissue. Arl8b protein levels were significantly increased in CSF of AD patients. CONCLUSIONS We report a comprehensive biochemical and proteomic investigation of hippocampal and cortical brain tissue derived from 5xFAD transgenic mice, providing a valuable resource to the neuroscientific community. We identified Arl8b, with significant abundance changes in 5xFAD and AD patient brains. Arl8b might enable the measurement of progressive lysosome accumulation in AD patients and have clinical utility as a candidate biomarker.
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Affiliation(s)
- Annett Boeddrich
- Neuroproteomics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Christian Haenig
- Neuroproteomics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Nancy Neuendorf
- Neuroproteomics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Eric Blanc
- Core Unit Bioinformatics, Berlin Institute of Health at Charité - University Medicine Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Andranik Ivanov
- Core Unit Bioinformatics, Berlin Institute of Health at Charité - University Medicine Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Marieluise Kirchner
- Core Unit Proteomics, Berlin Institute of Health at Charité - University Medicine Berlin, Lindenberger Weg 80, 13125, Berlin, Germany
| | - Philipp Schleumann
- Neuroproteomics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Irem Bayraktaroğlu
- Neuroproteomics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Matthias Richter
- Advanced Light Microscopy, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Christine Mirjam Molenda
- Advanced Light Microscopy, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Anje Sporbert
- Advanced Light Microscopy, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Martina Zenkner
- Neuroproteomics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Sigrid Schnoegl
- Neuroproteomics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Christin Suenkel
- Systems Biology of Gene Regulatory Elements, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Luisa-Sophie Schneider
- Department of Psychiatry, Charité - University Medicine Berlin, Hindenburgdamm 30, 12203, Berlin, Germany
| | - Agnieszka Rybak-Wolf
- Systems Biology of Gene Regulatory Elements, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Bianca Kochnowsky
- Department of Psychiatry, Charité - University Medicine Berlin, Hindenburgdamm 30, 12203, Berlin, Germany
| | - Lauren M Byrne
- UCL Huntington's Disease Centre, UCL Queen Square Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Edward J Wild
- UCL Huntington's Disease Centre, UCL Queen Square Institute of Neurology, Queen Square, London, WC1N 3BG, UK
- National Hospital for Neurology & Neurosurgery, Queen Square, London, WC1N 3BG, UK
| | - Jørgen E Nielsen
- Neurogenetics Clinic & Research Lab, Danish Dementia Research Centre, Rigshospitalet, University of Copenhagen, Section 8008, Inge Lehmanns Vej 8, 2100, Copenhagen, Denmark
| | - Gunnar Dittmar
- Core Unit Proteomics, Berlin Institute of Health at Charité - University Medicine Berlin, Lindenberger Weg 80, 13125, Berlin, Germany
- Proteomics of Cellular Signalling, Luxembourg Institute of Health, 1a Rue Thomas Edison, 1445, Strassen, Luxembourg
| | - Oliver Peters
- Department of Psychiatry, Charité - University Medicine Berlin, Hindenburgdamm 30, 12203, Berlin, Germany
- German Center for Neurodegenerative Diseases (DZNE), Charitéplatz 1, 10117, Berlin, Germany
| | - Dieter Beule
- Core Unit Bioinformatics, Berlin Institute of Health at Charité - University Medicine Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Erich E Wanker
- Neuroproteomics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125, Berlin, Germany.
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9
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Sousa e Silva R, Sousa AD, Vieira J, Vieira CP. The Josephin domain (JD) containing proteins are predicted to bind to the same interactors: Implications for spinocerebellar ataxia type 3 (SCA3) studies using Drosophila melanogaster mutants. Front Mol Neurosci 2023; 16:1140719. [PMID: 37008788 PMCID: PMC10050893 DOI: 10.3389/fnmol.2023.1140719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 02/21/2023] [Indexed: 03/17/2023] Open
Abstract
Spinocerebellar ataxia type 3, also known as Machado-Joseph disease (SCA3/ MJD), is the most frequent polyglutamine (polyQ) neurodegenerative disorder. It is caused by a pathogenic expansion of the polyQ tract, located at the C-terminal region of the protein encoded by the ATXN3 gene. This gene codes for a deubiquitinating enzyme (DUB) that belongs to a gene family, that in humans is composed by three more genes (ATXN3L, JOSD1, and JOSD2), that define two gene lineages (the ATXN3 and the Josephins). These proteins have in common the N-terminal catalytic domain (Josephin domain, JD), that in Josephins is the only domain present. In ATXN3 knock-out mouse and nematode models, the SCA3 neurodegeneration phenotype is not, however, reproduced, suggesting that in the genome of these species there are other genes that are able to compensate for the lack of ATXN3. Moreover, in mutant Drosophila melanogaster, where the only JD protein is coded by a Josephin-like gene, expression of the expanded human ATXN3 gene reproduces multiple aspects of the SCA3 phenotype, in contrast with the results of the expression of the wild type human form. In order to explain these findings, phylogenetic, as well as, protein–protein docking inferences are here performed. Here we show multiple losses of JD containing genes across the animal kingdom, suggesting partial functional redundancy of these genes. Accordingly, we predict that the JD is essential for binding with ataxin-3 and proteins of the Josephin lineages, and that D. melanogaster mutants are a good model of SCA3 despite the absence of a gene from the ATXN3 lineage. The molecular recognition regions of the ataxin-3 binding and those predicted for the Josephins are, however, different. We also report different binding regions between the two ataxin-3 forms (wild-type (wt) and expanded (exp)). The interactors that show an increase in the interaction strength with exp ataxin-3, are enriched in extrinsic components of mitochondrial outer membrane and endoplasmatic reticulum membrane. On the other hand, the group of interactors that show a decrease in the interaction strength with exp ataxin-3 is significantly enriched in extrinsic component of cytoplasm.
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10
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Contini C, Serrao S, Manconi B, Olianas A, Iavarone F, Guadalupi G, Messana I, Castagnola M, Masullo C, Bizzarro A, Turck CW, Maccarrone G, Cabras T. Characterization of Cystatin B Interactome in Saliva from Healthy Elderly and Alzheimer’s Disease Patients. Life (Basel) 2023; 13:life13030748. [PMID: 36983903 PMCID: PMC10054399 DOI: 10.3390/life13030748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/27/2023] [Accepted: 03/07/2023] [Indexed: 03/12/2023] Open
Abstract
Cystatin B is a small, multifunctional protein involved in the regulation of inflammation, innate immune response, and neuronal protection and found highly abundant in the brains of patients with Alzheimer’s disease (AD). Recently, our study demonstrated a significant association between the level of salivary cystatin B and AD. Since the protein is able to establish protein-protein interaction (PPI) in different contexts and aggregation-prone proteins and the PPI networks are relevant for AD pathogenesis, and due to the relevance of finding new AD markers in peripheral biofluids, we thought it was interesting to study the possible involvement of cystatin B in PPIs in saliva and to evaluate differences and similarities between AD and age-matched elderly healthy controls (HC). For this purpose, we applied a co-immunoprecipitation procedure and a bottom-up proteomics analysis to purify, identify, and quantify cystatin B interactors. Results demonstrated for the first time the existence of a salivary cystatin B-linked multi-protein complex composed by 82 interactors and largely expressed in the body. Interactors are involved in neutrophil activation, antimicrobial activity, modulation of the cytoskeleton and extra-cellular matrix (ECM), and glucose metabolism. Preliminary quantitative data showed significantly lower levels of triosophosphate isomerase 1 and higher levels of mucin 7, BPI, and matrix Gla protein in AD with respect to HC, suggesting implications associated with AD of altered glucose metabolism, antibacterial activities, and calcification-associated processes. Data are available via ProteomeXchange with identifiers PXD039286 and PXD030679.
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Affiliation(s)
- Cristina Contini
- Department of Life and Environmental Sciences, University of Cagliari, 09124 Cagliari, Italy
| | - Simone Serrao
- Department of Life and Environmental Sciences, University of Cagliari, 09124 Cagliari, Italy
| | - Barbara Manconi
- Department of Life and Environmental Sciences, University of Cagliari, 09124 Cagliari, Italy
- Correspondence:
| | - Alessandra Olianas
- Department of Life and Environmental Sciences, University of Cagliari, 09124 Cagliari, Italy
| | - Federica Iavarone
- Department of Basic Biotechnological Sciences, Intensive and Perioperative Clinics, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
- Policlinico Universitario “A. Gemelli” Foundation IRCCS, 00168 Rome, Italy
| | - Giulia Guadalupi
- Department of Life and Environmental Sciences, University of Cagliari, 09124 Cagliari, Italy
| | - Irene Messana
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta”, Consiglio Nazionale delle Ricerche, 00168 Rome, Italy
| | - Massimo Castagnola
- Proteomics Laboratory, European Center for Brain Research, (IRCCS) Santa Lucia Foundation, 00168 Rome, Italy
| | - Carlo Masullo
- Department of Neuroscience, Neurology Section, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | | | - Christoph W. Turck
- Proteomics and Biomarkers, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Giuseppina Maccarrone
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Tiziana Cabras
- Department of Life and Environmental Sciences, University of Cagliari, 09124 Cagliari, Italy
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11
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D’Egidio F, Castelli V, Cimini A, d’Angelo M. Cell Rearrangement and Oxidant/Antioxidant Imbalance in Huntington's Disease. Antioxidants (Basel) 2023; 12:571. [PMID: 36978821 PMCID: PMC10045781 DOI: 10.3390/antiox12030571] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/17/2023] [Accepted: 02/22/2023] [Indexed: 03/02/2023] Open
Abstract
Huntington's Disease (HD) is a hereditary neurodegenerative disorder caused by the expansion of a CAG triplet repeat in the HTT gene, resulting in the production of an aberrant huntingtin (Htt) protein. The mutant protein accumulation is responsible for neuronal dysfunction and cell death. This is due to the involvement of oxidative damage, excitotoxicity, inflammation, and mitochondrial impairment. Neurons naturally adapt to bioenergetic alteration and oxidative stress in physiological conditions. However, this dynamic system is compromised when a neurodegenerative disorder occurs, resulting in changes in metabolism, alteration in calcium signaling, and impaired substrates transport. Thus, the aim of this review is to provide an overview of the cell's answer to the stress induced by HD, focusing on the role of oxidative stress and its balance with the antioxidant system.
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Affiliation(s)
| | | | | | - Michele d’Angelo
- Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy
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12
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Xu H, Bensalel J, Raju S, Capobianco E, Lu ML, Wei J. Characterization of huntingtin interactomes and their dynamic responses in living cells by proximity proteomics. J Neurochem 2023; 164:512-528. [PMID: 36437609 DOI: 10.1111/jnc.15726] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 10/28/2022] [Accepted: 11/10/2022] [Indexed: 11/29/2022]
Abstract
Huntingtin (Htt) is a large protein without clearly defined molecular functions. Mutation in this protein causes Huntington's disease (HD), a fatal inherited neurodegenerative disorder. Identification of Htt-interacting proteins by the traditional approaches including yeast two-hybrid systems and affinity purifications has greatly facilitated the understanding of Htt function. However, these methods eliminated the intracellular spatial information of the Htt interactome during sample preparations. Moreover, the temporal changes of the Htt interactome in response to acute cellular stresses cannot be easily resolved with these approaches. Ascorbate peroxidase (APEX2)-based proximity labeling has been used to spatiotemporally investigate protein-protein interactions in living cells. In this study, we generated stable human SH-SY5Y cell lines expressing full-length Htt23Q and Htt145Q with N-terminus tagged Flag-APEX2 to quantitatively map the spatiotemporal changes of Htt interactome to a mild acute proteotoxic stress. Our data revealed that normal and mutant Htt (muHtt) are associated with distinct intracellular microenvironments. Specifically, mutant Htt is preferentially associated with intermediate filaments and myosin complexes. Furthermore, the dynamic changes of Htt interactomes in response to stress are different between normal and mutant Htt. Vimentin is identified as one of the most significant proteins that preferentially interacts with muHtt in situ. Further functional studies demonstrated that mutant Htt affects the vimentin's function of regulating proteostasis in healthy and HD human neural stem cells. Taken together, our data offer important insights into the molecular functions of normal and mutant Htt by providing a list of Htt-interacting proteins in their natural cellular context for further studies in different HD models.
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Affiliation(s)
- Hongyuan Xu
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, Florida, USA
| | - Johanna Bensalel
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, Florida, USA
| | - Sunil Raju
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, Florida, USA
| | | | - Michael L Lu
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, Florida, USA
| | - Jianning Wei
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, Florida, USA
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13
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Janacova L, Stenckova M, Lapcik P, Hrachovinova S, Bouchalova P, Potesil D, Hrstka R, Müller P, Bouchal P. Catechol-O-methyl transferase suppresses cell invasion and interplays with MET signaling in estrogen dependent breast cancer. Sci Rep 2023; 13:1285. [PMID: 36690660 PMCID: PMC9870911 DOI: 10.1038/s41598-023-28078-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 01/12/2023] [Indexed: 01/25/2023] Open
Abstract
Catechol-O-methyl transferase (COMT) is involved in detoxification of catechol estrogens, playing cancer-protective role in cells producing or utilizing estrogen. Moreover, COMT suppressed migration potential of breast cancer (BC) cells. To delineate COMT role in metastasis of estrogen receptor (ER) dependent BC, we investigated the effect of COMT overexpression on invasion, transcriptome, proteome and interactome of MCF7 cells, a luminal A BC model, stably transduced with lentiviral vector carrying COMT gene (MCF7-COMT). 2D and 3D assays revealed that COMT overexpression associates with decreased cell invasion (p < 0.0001 for Transwell assay, p < 0.05 for spheroid formation). RNA-Seq and LC-DIA-MS/MS proteomics identified genes associated with invasion (FTO, PIR, TACSTD2, ANXA3, KRT80, S100P, PREX1, CLEC3A, LCP1) being downregulated in MCF7-COMT cells, while genes associated with less aggressive phenotype (RBPMS, ROBO2, SELENBP, EPB41L2) were upregulated both at transcript (|log2FC|> 1, adj. p < 0.05) and protein (|log2FC|> 0.58, q < 0.05) levels. Importantly, proteins driving MET signaling were less abundant in COMT overexpressing cells, and pull-down confirmed interaction between COMT and Kunitz-type protease inhibitor 2 (SPINT2), a negative regulator of MET (log2FC = 5.10, q = 1.04-7). In conclusion, COMT may act as tumor suppressor in ER dependent BC not only by detoxification of catechol estrogens but also by suppressing cell invasion and interplay with MET pathway.
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Affiliation(s)
- Lucia Janacova
- Department of Biochemistry, Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Michaela Stenckova
- Research Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Petr Lapcik
- Department of Biochemistry, Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Sarka Hrachovinova
- Department of Biochemistry, Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Pavla Bouchalova
- Department of Biochemistry, Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - David Potesil
- Proteomics Core Facility, Central European Institute for Technology, Masaryk University, Brno, Czech Republic
| | - Roman Hrstka
- Research Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Petr Müller
- Research Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Pavel Bouchal
- Department of Biochemistry, Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic.
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14
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Jia K, Xia W, Su Q, Yang S, Zhang Y, Ni X, Su Z, Meng D. RNA methylation pattern and immune microenvironment characteristics mediated by m6A regulator in ischemic stroke. Front Genet 2023; 14:1148510. [PMID: 37139237 PMCID: PMC10150022 DOI: 10.3389/fgene.2023.1148510] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 04/05/2023] [Indexed: 05/05/2023] Open
Abstract
Background: Ischemic stroke (IS) is a highly heterogeneous disease. Recent studies have shown that epigenetic variables affect the immune response. However, only a few studies have examined the relationship between IS and m6A immunoregulation. Therefore, we aim to explore the methylation of RNA mediated by m6A regulatory factor and the immune microenvironment characteristics of IS. Methods: Differentially expressed m6A regulators were detected in IS microarray datasets GSE22255 and GSE58294. We used a series of machine learning algorithms to identify key IS-related m6A regulators and validated them on blood samples of IS patients, oxygen-glucose deprivation/reoxygenation (OGD/R) microglia and GSE198710 independent data sets. Different m6A modification modes were determined and the patients were classified. In addition, we systematically associate these modification patterns with the characteristics of immune microenvironment, including infiltrating immune cells, immune function genes and immune response genes. Then we developed a model of m6A score to quantify the m6A modification in IS samples. Results: Through the analysis of the differences between the control group and IS patients, METTL16, LRPPRC, and RBM15 showed strong diagnostic significance in three independent data sets. In addition, qRT-PCR and Western blotting also confirmed that the expression of METTL16 and LRPPRC was downregulated and the expression of RBM15 was upregulated after ischemia. Two m6A modification modes and two m6A gene modification modes were also identified. m6A gene cluster A (high m6A value group) was positively correlated with acquired immunity, while m6A gene cluster B (low m6A value group) was positively correlated with innate immunity. Similarly, five immune-related hub genes were significantly associated with m6Acore (CD28, IFNG, LTF, LCN2, and MMP9). Conclusion: The modification of m6A is closely related to the immune microenvironment. The evaluation of individual m6A modification pattern may be helpful for future immunomodulatory therapy of anti-ischemic response.
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Affiliation(s)
- Kejuan Jia
- The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
- The Key Laboratory of Myocardial Ischemia, Harbin Medical University, Ministry of Education, Harbin, Heilongjiang, China
| | - Wenbo Xia
- The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
- The Key Laboratory of Myocardial Ischemia, Harbin Medical University, Ministry of Education, Harbin, Heilongjiang, China
| | - Qian Su
- The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
- The Key Laboratory of Myocardial Ischemia, Harbin Medical University, Ministry of Education, Harbin, Heilongjiang, China
| | - Shiqi Yang
- The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Yanli Zhang
- The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Xunran Ni
- Heilongjiang Provincial Hospital, Harbin, Heilongjiang, China
| | - Zhiqiang Su
- The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
- *Correspondence: Delong Meng, ; Zhiqiang Su,
| | - Delong Meng
- The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
- *Correspondence: Delong Meng, ; Zhiqiang Su,
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15
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He Z, Liu L, Belloy ME, Le Guen Y, Sossin A, Liu X, Qi X, Ma S, Gyawali PK, Wyss-Coray T, Tang H, Sabatti C, Candès E, Greicius MD, Ionita-Laza I. GhostKnockoff inference empowers identification of putative causal variants in genome-wide association studies. Nat Commun 2022; 13:7209. [PMID: 36418338 PMCID: PMC9684164 DOI: 10.1038/s41467-022-34932-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 11/09/2022] [Indexed: 11/27/2022] Open
Abstract
Recent advances in genome sequencing and imputation technologies provide an exciting opportunity to comprehensively study the contribution of genetic variants to complex phenotypes. However, our ability to translate genetic discoveries into mechanistic insights remains limited at this point. In this paper, we propose an efficient knockoff-based method, GhostKnockoff, for genome-wide association studies (GWAS) that leads to improved power and ability to prioritize putative causal variants relative to conventional GWAS approaches. The method requires only Z-scores from conventional GWAS and hence can be easily applied to enhance existing and future studies. The method can also be applied to meta-analysis of multiple GWAS allowing for arbitrary sample overlap. We demonstrate its performance using empirical simulations and two applications: (1) a meta-analysis for Alzheimer's disease comprising nine overlapping large-scale GWAS, whole-exome and whole-genome sequencing studies and (2) analysis of 1403 binary phenotypes from the UK Biobank data in 408,961 samples of European ancestry. Our results demonstrate that GhostKnockoff can identify putatively functional variants with weaker statistical effects that are missed by conventional association tests.
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Affiliation(s)
- Zihuai He
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, 94305, USA. .,Quantitative Sciences Unit, Department of Medicine, Stanford University, Stanford, CA, 94305, USA.
| | - Linxi Liu
- Department of Statistics, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Michael E Belloy
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, 94305, USA
| | - Yann Le Guen
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, 94305, USA.,Institut du Cerveau - Paris Brain Institute - ICM, Paris, 75013, France
| | - Aaron Sossin
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA
| | - Xiaoxia Liu
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, 94305, USA
| | - Xinran Qi
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, 94305, USA
| | - Shiyang Ma
- Department of Biostatistics, Columbia University, New York, NY, 10032, USA
| | - Prashnna K Gyawali
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, 94305, USA
| | - Tony Wyss-Coray
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, 94305, USA
| | - Hua Tang
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Chiara Sabatti
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA
| | - Emmanuel Candès
- Department of Statistics, Stanford University, Stanford, CA, 94305, USA.,Department of Mathematics, Stanford University, Stanford, CA, 94305, USA
| | - Michael D Greicius
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, 94305, USA
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16
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Galyan SM, Ewald CY, Jalencas X, Masrani S, Meral S, Mestres J. Fragment-based virtual screening identifies a first-in-class preclinical drug candidate for Huntington's disease. Sci Rep 2022; 12:19642. [PMID: 36385140 PMCID: PMC9668931 DOI: 10.1038/s41598-022-21900-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 10/05/2022] [Indexed: 11/17/2022] Open
Abstract
Currently, there are no therapies available to modify the disease progression of Huntington's disease (HD). Recent clinical trial failures of antisense oligonucleotide candidates in HD have demonstrated the need for new therapeutic approaches. Here, we developed a novel in-silico fragment scanning approach across the surface of mutant huntingtin (mHTT) polyQ and predicted four hit compounds. Two rounds of compound analoging using a strategy of testing structurally similar compounds in an affinity assay rapidly identified GLYN122. In vitro, GLYN122 directly binds and reduces mHTT and induces autophagy in neurons. In vivo, our results confirm that GLYN122 can reduce mHTT in the cortex and striatum of the R/2 mouse model of Huntington's disease and subsequently improve motor symptoms. Thus, the in-vivo pharmacology profile of GLYN122 is a potential new preclinical candidate for the treatment of HD.
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Affiliation(s)
| | - Collin Y. Ewald
- grid.5801.c0000 0001 2156 2780Laboratory of Extracellular Matrix Regeneration, Department of Health Sciences and Technology, Institute of Translational Medicine, ETH Zürich, 8603 Schwerzenbach, Switzerland
| | - Xavier Jalencas
- grid.5841.80000 0004 1937 0247Chemotargets SL, Parc Científic de Barcelona, 08028 Barcelona, Catalonia Spain ,IMIM Hospital del Mar Medical Research Institute, Parc de Recerca Biomèdica de Barcelona (PRBB), 08003 Barcelona, Catalonia Spain
| | - Shyam Masrani
- Medicxi Ventures, 25 Great Pulteney St, London, W1F 9NH UK
| | - Selin Meral
- Biomedical Center Munich of the University of Munich, Großhaderner Str. 9, 82152 Planegg, Germany
| | - Jordi Mestres
- grid.5841.80000 0004 1937 0247Chemotargets SL, Parc Científic de Barcelona, 08028 Barcelona, Catalonia Spain ,IMIM Hospital del Mar Medical Research Institute, Parc de Recerca Biomèdica de Barcelona (PRBB), 08003 Barcelona, Catalonia Spain
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17
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Deolankar SC, Najar MA, Ramesh P, Kanichery A, Kudva AK, Raghu SV, Prasad TSK. Discovery of Molecular Networks of Neuroprotection Conferred by Brahmi Extract in Aβ 42-Induced Toxicity Model of Drosophila melanogaster Using a Quantitative Proteomic Approach. Mol Neurobiol 2022; 60:303-316. [PMID: 36261695 DOI: 10.1007/s12035-022-03066-0] [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: 06/06/2022] [Accepted: 10/03/2022] [Indexed: 11/30/2022]
Abstract
Accumulation of Aβ42 peptides forming plaque in various regions of the brain is a hallmark of Alzheimer's disease (AD) progression. However, to date, there is no effective management strategy reported for attenuation of Aβ42-induced toxicity in the early stages of the disease. Alternate medicinal systems such as Ayurveda in the past few decades show promising results in the management of neuronal complications. Medhya Rasayana such as Brahmi is known for its neuroprotective properties via resolving memory-related issues, while the underlying molecular mechanism of the same remains unclear. In the present study, we aimed to understand the neuroprotective effects of the aqueous extract of Bacopa monnieri and Centella asiatica (both commonly known as Brahmi) against the Aβ42 expressing model of the Drosophila melanogaster. By applying a quantitative proteomics approach, the study identified > 90% of differentially expressed proteins from Aβ42 expressing D. melanogaster were either restored to their original expression pattern or showed no change in expression pattern upon receiving either Brahmi extract treatment. The Brahmi restored proteins were part of neuronal pathways associated with cell cycle re-entry, apoptosis, and mitochondrial dynamics. The neuroprotective effect of Brahmi was also validated by negative geotaxis behavioral analysis suggesting its protective role against behavioral deficits exerted by Aβ42 toxicity. We believe that these discoveries will provide a platform for developing novel therapeutics for AD management by deciphering molecular targets of neuroprotection conferred by an aqueous extract of Bacopa monnieri or Centella asiatica.
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Affiliation(s)
- Sayali Chandrashekhar Deolankar
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, India
| | - Mohd Altaf Najar
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, India
| | - Poornima Ramesh
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, India
| | - Anagha Kanichery
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, India
| | - Avinash K Kudva
- Department of Biochemistry, Mangalore University, Mangalore, India
| | | | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, India.
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18
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Spead O, Zaepfel BL, Rothstein JD. Nuclear Pore Dysfunction in Neurodegeneration. Neurotherapeutics 2022; 19:1050-1060. [PMID: 36070178 PMCID: PMC9587172 DOI: 10.1007/s13311-022-01293-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2022] [Indexed: 10/14/2022] Open
Abstract
The nuclear pore complex (NPC) is a large multimeric structure that is interspersed throughout the membrane of the nucleus and consists of at least 33 protein components. Individual components cooperate within the nuclear pore to facilitate selective passage of materials between the nucleus and cytoplasm while simultaneously performing pore-independent roles throughout the cell. NPC dysfunction is a hallmark of neurodegenerative disorders including Alzheimer's disease, Huntington's disease, and amyotrophic lateral sclerosis (ALS). NPC components can become mislocalized or altered in expression in neurodegeneration. These alterations in NPC structure are often detrimental to the neuronal function and ultimately lead to neuronal loss. This review highlights the importance of nucleocytoplasmic transport and NPC integrity and how dysfunction of such may contribute to neurodegeneration.
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Affiliation(s)
- Olivia Spead
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Benjamin L Zaepfel
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Jeffrey D Rothstein
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
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19
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Coyne AN, Rothstein JD. Nuclear pore complexes - a doorway to neural injury in neurodegeneration. Nat Rev Neurol 2022; 18:348-362. [PMID: 35488039 PMCID: PMC10015220 DOI: 10.1038/s41582-022-00653-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2022] [Indexed: 12/13/2022]
Abstract
The genetic underpinnings and end-stage pathological hallmarks of neurodegenerative diseases are increasingly well defined, but the cellular pathophysiology of disease initiation and propagation remains poorly understood, especially in sporadic forms of these diseases. Altered nucleocytoplasmic transport is emerging as a prominent pathomechanism of multiple neurodegenerative diseases, including amyotrophic lateral sclerosis, Alzheimer disease, frontotemporal dementia and Huntington disease. The nuclear pore complex (NPC) and interactions between its individual nucleoporin components and nuclear transport receptors regulate nucleocytoplasmic transport, as well as genome organization and gene expression. Specific nucleoporin abnormalities have been identified in sporadic and familial forms of neurodegenerative disease, and these alterations are thought to contribute to disrupted nucleocytoplasmic transport. The specific nucleoporins and nucleocytoplasmic transport proteins that have been linked to different neurodegenerative diseases are partially distinct, suggesting that NPC injury contributes to the cellular specificity of neurodegenerative disease and could be an early initiator of the pathophysiological cascades that underlie neurodegenerative disease. This concept is consistent with the fact that rare genetic mutations in some nucleoporins cause cell-type-specific neurological disease. In this Review, we discuss nucleoporin and NPC disruptions and consider their impact on cellular function and the pathophysiology of neurodegenerative disease.
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Affiliation(s)
- Alyssa N Coyne
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. .,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Jeffrey D Rothstein
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. .,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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20
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Calabrese G, Molzahn C, Mayor T. Protein interaction networks in neurodegenerative diseases: from physiological function to aggregation. J Biol Chem 2022; 298:102062. [PMID: 35623389 PMCID: PMC9234719 DOI: 10.1016/j.jbc.2022.102062] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 04/26/2022] [Accepted: 05/18/2022] [Indexed: 11/25/2022] Open
Abstract
The accumulation of protein inclusions is linked to many neurodegenerative diseases that typically develop in older individuals, due to a combination of genetic and environmental factors. In rare familial neurodegenerative disorders, genes encoding for aggregation-prone proteins are often mutated. While the underlying mechanism leading to these diseases still remains to be fully elucidated, efforts in the past 20 years revealed a vast network of protein–protein interactions that play a major role in regulating the aggregation of key proteins associated with neurodegeneration. Misfolded proteins that can oligomerize and form insoluble aggregates associate with molecular chaperones and other elements of the proteolytic machineries that are the frontline workers attempting to protect the cells by promoting clearance and preventing aggregation. Proteins that are normally bound to aggregation-prone proteins can become sequestered and mislocalized in protein inclusions, leading to their loss of function. In contrast, mutations, posttranslational modifications, or misfolding of aggregation-prone proteins can lead to gain of function by inducing novel or altered protein interactions, which in turn can impact numerous essential cellular processes and organelles, such as vesicle trafficking and the mitochondria. This review examines our current knowledge of protein–protein interactions involving several key aggregation-prone proteins that are associated with Alzheimer’s disease, Parkinson’s disease, Huntington’s disease, or amyotrophic lateral sclerosis. We aim to provide an overview of the protein interaction networks that play a central role in driving or mitigating inclusion formation, while highlighting some of the key proteomic studies that helped to uncover the extent of these networks.
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Affiliation(s)
- Gaetano Calabrese
- Michael Smith Laboratories, University of British Columbia, V6T 1Z4 Vancouver BC, Canada.
| | - Cristen Molzahn
- Michael Smith Laboratories, University of British Columbia, V6T 1Z4 Vancouver BC, Canada
| | - Thibault Mayor
- Michael Smith Laboratories, University of British Columbia, V6T 1Z4 Vancouver BC, Canada.
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21
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Chen F, Ni C, Wang X, Cheng R, Pan C, Wang Y, Liang J, Zhang J, Cheng J, Chin YE, Zhou Y, Wang Z, Guo Y, Chen S, Htun S, Mathes EF, de Alba Campomanes AG, Slavotinek AM, Zhang S, Li M, Yao Z. S1P defects cause a new entity of cataract, alopecia, oral mucosal disorder, and psoriasis-like syndrome. EMBO Mol Med 2022; 14:e14904. [PMID: 35362222 PMCID: PMC9081911 DOI: 10.15252/emmm.202114904] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 02/28/2022] [Accepted: 03/08/2022] [Indexed: 11/17/2022] Open
Abstract
In this report, we discovered a new entity named cataract, alopecia, oral mucosal disorder, and psoriasis‐like (CAOP) syndrome in two unrelated and ethnically diverse patients. Furthermore, patient 1 failed to respond to regular treatment. We found that CAOP syndrome was caused by an autosomal recessive defect in the mitochondrial membrane‐bound transcription factor peptidase/site‐1 protease (MBTPS1, S1P). Mitochondrial abnormalities were observed in patient 1 with CAOP syndrome. Furthermore, we found that S1P is a novel mitochondrial protein that forms a trimeric complex with ETFA/ETFB. S1P enhances ETFA/ETFB flavination and maintains its stability. Patient S1P variants destabilize ETFA/ETFB, impair mitochondrial respiration, decrease fatty acid β‐oxidation activity, and shift mitochondrial oxidative phosphorylation (OXPHOS) to glycolysis. Mitochondrial dysfunction and inflammatory lesions in patient 1 were significantly ameliorated by riboflavin supplementation, which restored the stability of ETFA/ETFB. Our study discovered that mutations in MBTPS1 resulted in a new entity of CAOP syndrome and elucidated the mechanism of the mutations in the new disease.
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Affiliation(s)
- Fuying Chen
- Department of Dermatology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Institute of Dermatology, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Cheng Ni
- Department of Dermatology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Institute of Dermatology, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xiaoxiao Wang
- Department of Dermatology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Institute of Dermatology, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Ruhong Cheng
- Department of Dermatology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Institute of Dermatology, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Chaolan Pan
- Department of Dermatology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Institute of Dermatology, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yumeng Wang
- Department of Dermatology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Institute of Dermatology, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jianying Liang
- Department of Dermatology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jia Zhang
- Department of Dermatology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jinke Cheng
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Y Eugene Chin
- Instituteof Health Sciences, Chinese Academy of Sciences, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yi Zhou
- Department of gastroenterology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Zhen Wang
- Department of Dermatology, Children's Hospital of Shanghai Jiaotong University, Shanghai, China
| | - Yiran Guo
- Center for Data Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, PA, USA
| | - She Chen
- NHC Key Laboratory of Glycoconjugate Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Stephanie Htun
- Division of Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Erin F Mathes
- Departments of Dermatology and Pediatrics, University California, San Francisco, CA, USA
| | | | - Anne M Slavotinek
- Division of Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Si Zhang
- NHC Key Laboratory of Glycoconjugate Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Ming Li
- Department of Dermatology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Institute of Dermatology, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Zhirong Yao
- Department of Dermatology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Institute of Dermatology, Shanghai Jiaotong University School of Medicine, Shanghai, China
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22
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Karayel-Basar M, Uras I, Kiris I, Sahin B, Akgun E, Baykal AT. Spatial proteomic alterations detected via MALDI-MS imaging implicate neuronal loss in a Huntington's disease mouse (YAC128) brain. Mol Omics 2022; 18:336-347. [PMID: 35129568 DOI: 10.1039/d1mo00440a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Huntington's disease (HD) is an autosomal dominant neurodegenerative disorder that occurs with the increase of CAG trinucleotide repeats in the huntingtin gene. To understand the mechanisms of HD, powerful proteomics techniques, such as liquid chromatography-tandem mass spectrometry (LC-MS/MS) were employed. However, one major drawback of these methods is loss of the region-specific quantitative information of the proteins due to analysis of total tissue lysates. Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) is a MS-based label-free technique that works directly on tissue sections and gathers m/z values with their respective regional information. In this study, we established a data processing protocol that includes several software programs and methods to determine spatial protein alterations between the brain samples of a 12 month-old YAC128 HD mouse model and their non-transgenic littermates. 22 differentially expressed proteins were revealed with their respective regional information, and possible relationships of several proteins were discussed. As a validation of the MALDI-MSI analysis, a differentially expressed protein (GFAP) was verified using immunohistochemical staining. Furthermore, since several proteins detected in this study have previously been associated with neuronal loss, neuronal loss in the cortical region was demonstrated using an anti-NeuN immunohistochemical staining method. In conclusion, the findings of this research have provided insights into the spatial proteomic changes between HD transgenic and non-transgenic littermates and therefore, we suggest that MALDI-MSI is a powerful technique to determine spatial proteomic alterations between biological samples, and the data processing that we present here can be employed as a complementary tool for the data analysis.
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Affiliation(s)
- Merve Karayel-Basar
- Department of Medical Biochemistry and Molecular Biology, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Irep Uras
- Department of Medical Biochemistry and Molecular Biology, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Irem Kiris
- Department of Medical Biochemistry and Molecular Biology, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Betul Sahin
- Acibadem Labmed Clinical Laboratories, R&D Center, Istanbul, Turkey
| | - Emel Akgun
- Department of Medical Biochemistry and Molecular Biology, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Ahmet Tarik Baykal
- Department of Medical Biochemistry, Faculty of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
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23
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Lange J, Wood-Kaczmar A, Ali A, Farag S, Ghosh R, Parker J, Casey C, Uno Y, Kunugi A, Ferretti P, Andre R, Tabrizi SJ. Mislocalization of Nucleocytoplasmic Transport Proteins in Human Huntington's Disease PSC-Derived Striatal Neurons. Front Cell Neurosci 2021; 15:742763. [PMID: 34658796 PMCID: PMC8519404 DOI: 10.3389/fncel.2021.742763] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/09/2021] [Indexed: 11/17/2022] Open
Abstract
Huntington's disease (HD) is an inherited neurodegenerative disorder caused by a CAG repeat expansion in the huntingtin gene (HTT). Disease progression is characterized by the loss of vulnerable neuronal populations within the striatum. A consistent phenotype across HD models is disruption of nucleocytoplasmic transport and nuclear pore complex (NPC) function. Here we demonstrate that high content imaging is a suitable method for detecting mislocalization of lamin-B1, RAN and RANGAP1 in striatal neuronal cultures thus allowing a robust, unbiased, highly powered approach to assay nuclear pore deficits. Furthermore, nuclear pore deficits extended to the selectively vulnerable DARPP32 + subpopulation neurons, but not to astrocytes. Striatal neuron cultures are further affected by changes in gene and protein expression of RAN, RANGAP1 and lamin-B1. Lowering total HTT using HTT-targeted anti-sense oligonucleotides partially restored gene expression, as well as subtly reducing mislocalization of proteins involved in nucleocytoplasmic transport. This suggests that mislocalization of RAN, RANGAP1 and lamin-B1 cannot be normalized by simply reducing expression of CAG-expanded HTT in the absence of healthy HTT protein.
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Affiliation(s)
- Jenny Lange
- Huntington’s Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Alison Wood-Kaczmar
- Huntington’s Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Aneesa Ali
- Huntington’s Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Sahar Farag
- Huntington’s Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Rhia Ghosh
- Huntington’s Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Jennifer Parker
- Huntington’s Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Caroline Casey
- Huntington’s Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Yumiko Uno
- Neuroscience Drug Discovery Unit, Takeda Pharmaceutical Company Limited, Fujisawa, Japan
| | - Akiyoshi Kunugi
- Neuroscience Drug Discovery Unit, Takeda Pharmaceutical Company Limited, Fujisawa, Japan
| | - Patrizia Ferretti
- Stem Cell and Regenerative Medicine Section, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Ralph Andre
- Huntington’s Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Sarah J. Tabrizi
- Huntington’s Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
- UK Dementia Research Institute, University College London, London, United Kingdom
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24
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Rybak-Wolf A, Plass M. RNA Dynamics in Alzheimer's Disease. Molecules 2021; 26:5113. [PMID: 34500547 PMCID: PMC8433936 DOI: 10.3390/molecules26175113] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/09/2021] [Accepted: 08/17/2021] [Indexed: 02/06/2023] Open
Abstract
Alzheimer's disease (AD) is the most common age-related neurodegenerative disorder that heavily burdens healthcare systems worldwide. There is a significant requirement to understand the still unknown molecular mechanisms underlying AD. Current evidence shows that two of the major features of AD are transcriptome dysregulation and altered function of RNA binding proteins (RBPs), both of which lead to changes in the expression of different RNA species, including microRNAs (miRNAs), circular RNAs (circRNAs), long non-coding RNAs (lncRNAs), and messenger RNAs (mRNAs). In this review, we will conduct a comprehensive overview of how RNA dynamics are altered in AD and how this leads to the differential expression of both short and long RNA species. We will describe how RBP expression and function are altered in AD and how this impacts the expression of different RNA species. Furthermore, we will also show how changes in the abundance of specific RNA species are linked to the pathology of AD.
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Affiliation(s)
- Agnieszka Rybak-Wolf
- Max Delbrück Center for Molecular Medicine (MDC), Berlin Institute for Medical Systems Biology (BIMSB), 10115 Berlin, Germany
| | - Mireya Plass
- Gene Regulation of Cell Identity, Regenerative Medicine Program, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, 08908 Barcelona, Spain
- Program for Advancing Clinical Translation of Regenerative Medicine of Catalonia, P-CMR[C], L'Hospitalet del Llobregat, 08908 Barcelona, Spain
- Center for Networked Biomedical Research on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 28029 Madrid, Spain
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25
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Cendelin J, Cvetanovic M, Gandelman M, Hirai H, Orr HT, Pulst SM, Strupp M, Tichanek F, Tuma J, Manto M. Consensus Paper: Strengths and Weaknesses of Animal Models of Spinocerebellar Ataxias and Their Clinical Implications. THE CEREBELLUM 2021; 21:452-481. [PMID: 34378174 DOI: 10.1007/s12311-021-01311-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 07/21/2021] [Indexed: 01/02/2023]
Abstract
Spinocerebellar ataxias (SCAs) represent a large group of hereditary degenerative diseases of the nervous system, in particular the cerebellum, and other systems that manifest with a variety of progressive motor, cognitive, and behavioral deficits with the leading symptom of cerebellar ataxia. SCAs often lead to severe impairments of the patient's functioning, quality of life, and life expectancy. For SCAs, there are no proven effective pharmacotherapies that improve the symptoms or substantially delay disease progress, i.e., disease-modifying therapies. To study SCA pathogenesis and potential therapies, animal models have been widely used and are an essential part of pre-clinical research. They mainly include mice, but also other vertebrates and invertebrates. Each animal model has its strengths and weaknesses arising from model animal species, type of genetic manipulation, and similarity to human diseases. The types of murine and non-murine models of SCAs, their contribution to the investigation of SCA pathogenesis, pathological phenotype, and therapeutic approaches including their advantages and disadvantages are reviewed in this paper. There is a consensus among the panel of experts that (1) animal models represent valuable tools to improve our understanding of SCAs and discover and assess novel therapies for this group of neurological disorders characterized by diverse mechanisms and differential degenerative progressions, (2) thorough phenotypic assessment of individual animal models is required for studies addressing therapeutic approaches, (3) comparative studies are needed to bring pre-clinical research closer to clinical trials, and (4) mouse models complement cellular and invertebrate models which remain limited in terms of clinical translation for complex neurological disorders such as SCAs.
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Affiliation(s)
- Jan Cendelin
- Department of Pathophysiology, Faculty of Medicine in Pilsen, Charles University, alej Svobody 75, 323 00, Plzen, Czech Republic. .,Laboratory of Neurodegenerative Disorders, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, alej Svobody 75, 323 00, Plzen, Czech Republic.
| | - Marija Cvetanovic
- Department of Neuroscience, Institute for Translational Neuroscience, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Mandi Gandelman
- Department of Neurology, University of Utah, 175 North Medical Drive East, Salt Lake City, UT, 84132, USA
| | - Hirokazu Hirai
- Department of Neurophysiology and Neural Repair, Gunma University Graduate School of Medicine, 3-39-22, Gunma, 371-8511, Japan.,Viral Vector Core, Gunma University Initiative for Advanced Research (GIAR), Gunma, 371-8511, Japan
| | - Harry T Orr
- Department of Laboratory Medicine and Pathology, Institute for Translational Neuroscience, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Stefan M Pulst
- Department of Neurology, University of Utah, 175 North Medical Drive East, Salt Lake City, UT, 84132, USA
| | - Michael Strupp
- Department of Neurology and German Center for Vertigo and Balance Disorders, Hospital of the Ludwig-Maximilians University, Munich, Campus Grosshadern, Marchioninistr. 15, 81377, Munich, Germany
| | - Filip Tichanek
- Department of Pathophysiology, Faculty of Medicine in Pilsen, Charles University, alej Svobody 75, 323 00, Plzen, Czech Republic.,Laboratory of Neurodegenerative Disorders, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, alej Svobody 75, 323 00, Plzen, Czech Republic
| | - Jan Tuma
- Department of Pathophysiology, Faculty of Medicine in Pilsen, Charles University, alej Svobody 75, 323 00, Plzen, Czech Republic.,The Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, MC 7843, San Antonio, TX, 78229, USA
| | - Mario Manto
- Unité des Ataxies Cérébelleuses, Service de Neurologie, CHU-Charleroi, Charleroi, Belgium.,Service des Neurosciences, Université de Mons, UMons, Mons, Belgium
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26
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Sap KA, Guler AT, Bury A, Dekkers D, Demmers JAA, Reits EA. Identification of Full-Length Wild-Type and Mutant Huntingtin Interacting Proteins by Crosslinking Immunoprecipitation in Mice Brain Cortex. J Huntingtons Dis 2021; 10:335-347. [PMID: 34151850 PMCID: PMC8609692 DOI: 10.3233/jhd-210476] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Background: Huntington’s disease is a neurodegenerative disorder caused by a CAG expansion in the huntingtin gene, resulting in a polyglutamine expansion in the ubiquitously expressed mutant huntingtin protein. Objective: Here we set out to identify proteins interacting with the full-length wild-type and mutant huntingtin protein in the mice cortex brain region to understand affected biological processes in Huntington’s disease pathology. Methods: Full-length huntingtin with 20 and 140 polyQ repeats were formaldehyde-crosslinked and isolated via their N-terminal Flag-tag from 2-month-old mice brain cortex. Interacting proteins were identified and quantified by label-free liquid chromatography-mass spectrometry (LC-MS/MS). Results: We identified 30 interactors specific for wild-type huntingtin, 14 interactors specific for mutant huntingtin and 14 shared interactors that interacted with both wild-type and mutant huntingtin, including known interactors such as F8a1/Hap40. Syt1, Ykt6, and Snap47, involved in vesicle transport and exocytosis, were among the proteins that interacted specifically with wild-type huntingtin. Various other proteins involved in energy metabolism and mitochondria were also found to associate predominantly with wild-type huntingtin, whereas mutant huntingtin interacted with proteins involved in translation including Mapk3, Eif3h and Eef1a2. Conclusion: Here we identified both shared and specific interactors of wild-type and mutant huntingtin, which are involved in different biological processes including exocytosis, vesicle transport, translation and metabolism. These findings contribute to the understanding of the roles that wild-type and mutant huntingtin play in a variety of cellular processes both in healthy conditions and Huntington’s disease pathology.
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Affiliation(s)
- Karen A Sap
- Department of Medical Biology, Amsterdam UMC, location AMC, Amsterdam, The Netherlands
| | - Arzu Tugce Guler
- Department of Medical Biology, Amsterdam UMC, location AMC, Amsterdam, The Netherlands
| | - Aleksandra Bury
- Department of Medical Biology, Amsterdam UMC, location AMC, Amsterdam, The Netherlands
| | - Dick Dekkers
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jeroen A A Demmers
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Eric A Reits
- Department of Medical Biology, Amsterdam UMC, location AMC, Amsterdam, The Netherlands
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27
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Interactome Mapping Provides a Network of Neurodegenerative Disease Proteins and Uncovers Widespread Protein Aggregation in Affected Brains. Cell Rep 2021; 32:108050. [PMID: 32814053 DOI: 10.1016/j.celrep.2020.108050] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 02/15/2020] [Accepted: 07/28/2020] [Indexed: 12/12/2022] Open
Abstract
Interactome maps are valuable resources to elucidate protein function and disease mechanisms. Here, we report on an interactome map that focuses on neurodegenerative disease (ND), connects ∼5,000 human proteins via ∼30,000 candidate interactions and is generated by systematic yeast two-hybrid interaction screening of ∼500 ND-related proteins and integration of literature interactions. This network reveals interconnectivity across diseases and links many known ND-causing proteins, such as α-synuclein, TDP-43, and ATXN1, to a host of proteins previously unrelated to NDs. It facilitates the identification of interacting proteins that significantly influence mutant TDP-43 and HTT toxicity in transgenic flies, as well as of ARF-GEP100 that controls misfolding and aggregation of multiple ND-causing proteins in experimental model systems. Furthermore, it enables the prediction of ND-specific subnetworks and the identification of proteins, such as ATXN1 and MKL1, that are abnormally aggregated in postmortem brains of Alzheimer's disease patients, suggesting widespread protein aggregation in NDs.
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28
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Ding B, Sepehrimanesh M. Nucleocytoplasmic Transport: Regulatory Mechanisms and the Implications in Neurodegeneration. Int J Mol Sci 2021; 22:4165. [PMID: 33920577 PMCID: PMC8072611 DOI: 10.3390/ijms22084165] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 04/13/2021] [Accepted: 04/15/2021] [Indexed: 12/12/2022] Open
Abstract
Nucleocytoplasmic transport (NCT) across the nuclear envelope is precisely regulated in eukaryotic cells, and it plays critical roles in maintenance of cellular homeostasis. Accumulating evidence has demonstrated that dysregulations of NCT are implicated in aging and age-related neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), Alzheimer's disease (AD), and Huntington disease (HD). This is an emerging research field. The molecular mechanisms underlying impaired NCT and the pathogenesis leading to neurodegeneration are not clear. In this review, we comprehensively described the components of NCT machinery, including nuclear envelope (NE), nuclear pore complex (NPC), importins and exportins, RanGTPase and its regulators, and the regulatory mechanisms of nuclear transport of both protein and transcript cargos. Additionally, we discussed the possible molecular mechanisms of impaired NCT underlying aging and neurodegenerative diseases, such as ALS/FTD, HD, and AD.
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Affiliation(s)
- Baojin Ding
- Department of Biology, University of Louisiana at Lafayette, 410 East Saint Mary Boulevard, Lafayette, LA 70503, USA;
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29
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Battista T, Pascarella G, Staid DS, Colotti G, Rosati J, Fiorillo A, Casamassa A, Vescovi AL, Giabbai B, Semrau MS, Fanelli S, Storici P, Squitieri F, Morea V, Ilari A. Known Drugs Identified by Structure-Based Virtual Screening Are Able to Bind Sigma-1 Receptor and Increase Growth of Huntington Disease Patient-Derived Cells. Int J Mol Sci 2021; 22:1293. [PMID: 33525510 PMCID: PMC7865886 DOI: 10.3390/ijms22031293] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/15/2021] [Accepted: 01/22/2021] [Indexed: 02/07/2023] Open
Abstract
Huntington disease (HD) is a devastating and presently untreatable neurodegenerative disease characterized by progressively disabling motor and mental manifestations. The sigma-1 receptor (σ1R) is a protein expressed in the central nervous system, whose 3D structure has been recently determined by X-ray crystallography and whose agonists have been shown to have neuroprotective activity in neurodegenerative diseases. To identify therapeutic agents against HD, we have implemented a drug repositioning strategy consisting of: (i) Prediction of the ability of the FDA-approved drugs publicly available through the ZINC database to interact with σ1R by virtual screening, followed by computational docking and visual examination of the 20 highest scoring drugs; and (ii) Assessment of the ability of the six drugs selected by computational analyses to directly bind purified σ1R in vitro by Surface Plasmon Resonance and improve the growth of fibroblasts obtained from HD patients, which is significantly impaired with respect to control cells. All six of the selected drugs proved able to directly bind purified σ1R in vitro and improve the growth of HD cells from both or one HD patient. These results support the validity of the drug repositioning procedure implemented herein for the identification of new therapeutic tools against HD.
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Affiliation(s)
- Theo Battista
- Institute of Molecular Biology and Pathology, National Research Council of Italy, 00185 Rome, Italy; (T.B.); (G.P.); (D.S.S.); (G.C.)
- Department of Biochemical Sciences “A. Rossi Fanelli”, “Sapienza” University, 00185 Rome, Italy;
| | - Gianmarco Pascarella
- Institute of Molecular Biology and Pathology, National Research Council of Italy, 00185 Rome, Italy; (T.B.); (G.P.); (D.S.S.); (G.C.)
- Department of Biochemical Sciences “A. Rossi Fanelli”, “Sapienza” University, 00185 Rome, Italy;
| | - David Sasah Staid
- Institute of Molecular Biology and Pathology, National Research Council of Italy, 00185 Rome, Italy; (T.B.); (G.P.); (D.S.S.); (G.C.)
- Department of Biochemical Sciences “A. Rossi Fanelli”, “Sapienza” University, 00185 Rome, Italy;
| | - Gianni Colotti
- Institute of Molecular Biology and Pathology, National Research Council of Italy, 00185 Rome, Italy; (T.B.); (G.P.); (D.S.S.); (G.C.)
| | - Jessica Rosati
- Cellular Reprogramming Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy; (J.R.); (A.C.); (A.L.V.)
| | - Annarita Fiorillo
- Department of Biochemical Sciences “A. Rossi Fanelli”, “Sapienza” University, 00185 Rome, Italy;
| | - Alessia Casamassa
- Cellular Reprogramming Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy; (J.R.); (A.C.); (A.L.V.)
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania Luigi Vanvitelli, 81100 Caserta, Italy
| | - Angelo Luigi Vescovi
- Cellular Reprogramming Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy; (J.R.); (A.C.); (A.L.V.)
| | - Barbara Giabbai
- Protein Facility, Structural Biology Lab, Elettra Sincrotrone Trieste, 34149 Basovizza, Italy; (B.G.); (M.S.S.); (P.S.)
| | - Marta Stefania Semrau
- Protein Facility, Structural Biology Lab, Elettra Sincrotrone Trieste, 34149 Basovizza, Italy; (B.G.); (M.S.S.); (P.S.)
- Department of Cellular, Computational and Integrative Biology—CIBIO, University of Trento, 38123 Trento, Italy
| | - Sergio Fanelli
- Huntington and Rare Diseases Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy; (S.F.); (F.S.)
| | - Paola Storici
- Protein Facility, Structural Biology Lab, Elettra Sincrotrone Trieste, 34149 Basovizza, Italy; (B.G.); (M.S.S.); (P.S.)
| | - Ferdinando Squitieri
- Huntington and Rare Diseases Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy; (S.F.); (F.S.)
| | - Veronica Morea
- Institute of Molecular Biology and Pathology, National Research Council of Italy, 00185 Rome, Italy; (T.B.); (G.P.); (D.S.S.); (G.C.)
| | - Andrea Ilari
- Institute of Molecular Biology and Pathology, National Research Council of Italy, 00185 Rome, Italy; (T.B.); (G.P.); (D.S.S.); (G.C.)
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30
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Li F, Du Z, Huang X, Dong C, Ren J. Analyses of p73 Protein Oligomerization and p73-MDM2 Interaction in Single Living Cells Using In Situ Single Molecule Spectroscopy. Anal Chem 2021; 93:886-894. [PMID: 33393764 DOI: 10.1021/acs.analchem.0c03521] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein oligomerization and protein-protein interaction are crucial to regulate protein functions and biological processes. p73 protein is a very important transcriptional factor and can promote apoptosis and cell cycle arrest, and its transcriptional activity is regulated by p73 oligomerization and p73-MDM2 interaction. Although extracellular studies on p73 oligomerization and p73-MDM2 interaction have been carried out, it is unclear how p73 oligomerization and p73-MDM2 interaction occur in living cells. In our study, we described an in situ method for studying p73 oligomerization and p73-MDM2 interaction in living cells by combining fluorescence cross-correlation spectroscopy with a fluorescent protein labeling technique. Lentiviral transfection was used to transfect cells with a plasmid for either p73 or MDM2, each fused to a different fluorescent protein. p73 oligomerization was evaluated using brightness per particle, and the p73-MDM2 interaction was quantified using the cross-correlation value. We constructed a series of p73 mutants in three domains (transactivation domain, DNA binding domain, and oligomerization domain) and MDM2 mutants. We systematically studied p73 oligomerization and the effects of p73 oligomerization and the p73 and MDM2 structures on the p73-MDM2 interaction in single living cells. We have found that the p73 protein can form oligomers and that the p73 structure changes in the oligomerization domain significantly influence its oligomerization. p73 oligomerization and the structure changes significantly affect the p73-MDM2 interaction. Furthermore, the effects of inhibitors on p73 oligomerization and p73-MDM2 interaction were studied.
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Affiliation(s)
- Fucai Li
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Zhixue Du
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Xiangyi Huang
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Chaoqing Dong
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Jicun Ren
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
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31
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Pluciennik A, Liu Y, Molotsky E, Marsh GB, Ranxhi B, Arnold FJ, St.-Cyr S, Davidson B, Pourshafie N, Lieberman AP, Gu W, Todi SV, Merry DE. Deubiquitinase USP7 contributes to the pathogenicity of spinal and bulbar muscular atrophy. J Clin Invest 2021; 131:134565. [PMID: 33170804 PMCID: PMC7773404 DOI: 10.1172/jci134565] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 10/29/2020] [Indexed: 12/24/2022] Open
Abstract
Polyglutamine (polyQ) diseases are devastating, slowly progressing neurodegenerative conditions caused by expansion of polyQ-encoding CAG repeats within the coding regions of distinct, unrelated genes. In spinal and bulbar muscular atrophy (SBMA), polyQ expansion within the androgen receptor (AR) causes progressive neuromuscular toxicity, the molecular basis of which is unclear. Using quantitative proteomics, we identified changes in the AR interactome caused by polyQ expansion. We found that the deubiquitinase USP7 preferentially interacts with polyQ-expanded AR and that lowering USP7 levels reduced mutant AR aggregation and cytotoxicity in cell models of SBMA. Moreover, USP7 knockdown suppressed disease phenotypes in SBMA and spinocerebellar ataxia type 3 (SCA3) fly models, and monoallelic knockout of Usp7 ameliorated several motor deficiencies in transgenic SBMA mice. USP7 overexpression resulted in reduced AR ubiquitination, indicating the direct action of USP7 on AR. Using quantitative proteomics, we identified the ubiquitinated lysine residues on mutant AR that are regulated by USP7. Finally, we found that USP7 also differentially interacts with mutant Huntingtin (HTT) protein in striatum and frontal cortex of a knockin mouse model of Huntington's disease. Taken together, our findings reveal a critical role for USP7 in the pathophysiology of SBMA and suggest a similar role in SCA3 and Huntington's disease.
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Affiliation(s)
- Anna Pluciennik
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Yuhong Liu
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Elana Molotsky
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Gregory B. Marsh
- Department of Pharmacology and Neurology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Bedri Ranxhi
- Department of Pharmacology and Neurology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Frederick J. Arnold
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Sophie St.-Cyr
- Department of Pathology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Beverly Davidson
- Department of Pathology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Naemeh Pourshafie
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, Maryland, USA
- George Washington University, Institute of Biomedical Sciences, Washington, DC, USA
| | - Andrew P. Lieberman
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Wei Gu
- Department of Pathology and Cell Biology and Institute for Cancer Genetics, Columbia University, New York, New York, USA
| | - Sokol V. Todi
- Department of Pharmacology and Neurology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Diane E. Merry
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
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32
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Richards AL, Eckhardt M, Krogan NJ. Mass spectrometry-based protein-protein interaction networks for the study of human diseases. Mol Syst Biol 2021; 17:e8792. [PMID: 33434350 PMCID: PMC7803364 DOI: 10.15252/msb.20188792] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/23/2020] [Accepted: 11/03/2020] [Indexed: 12/13/2022] Open
Abstract
A better understanding of the molecular mechanisms underlying disease is key for expediting the development of novel therapeutic interventions. Disease mechanisms are often mediated by interactions between proteins. Insights into the physical rewiring of protein-protein interactions in response to mutations, pathological conditions, or pathogen infection can advance our understanding of disease etiology, progression, and pathogenesis and can lead to the identification of potential druggable targets. Advances in quantitative mass spectrometry (MS)-based approaches have allowed unbiased mapping of these disease-mediated changes in protein-protein interactions on a global scale. Here, we review MS techniques that have been instrumental for the identification of protein-protein interactions at a system-level, and we discuss the challenges associated with these methodologies as well as novel MS advancements that aim to address these challenges. An overview of examples from diverse disease contexts illustrates the potential of MS-based protein-protein interaction mapping approaches for revealing disease mechanisms, pinpointing new therapeutic targets, and eventually moving toward personalized applications.
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Affiliation(s)
- Alicia L Richards
- Quantitative Biosciences Institute (QBI)University of California San FranciscoSan FranciscoCAUSA
- J. David Gladstone InstitutesSan FranciscoCAUSA
- Department of Cellular and Molecular PharmacologyUniversity of California San FranciscoSan FranciscoCAUSA
| | - Manon Eckhardt
- Quantitative Biosciences Institute (QBI)University of California San FranciscoSan FranciscoCAUSA
- J. David Gladstone InstitutesSan FranciscoCAUSA
- Department of Cellular and Molecular PharmacologyUniversity of California San FranciscoSan FranciscoCAUSA
| | - Nevan J Krogan
- Quantitative Biosciences Institute (QBI)University of California San FranciscoSan FranciscoCAUSA
- J. David Gladstone InstitutesSan FranciscoCAUSA
- Department of Cellular and Molecular PharmacologyUniversity of California San FranciscoSan FranciscoCAUSA
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33
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Diez L, Wegmann S. Nuclear Transport Deficits in Tau-Related Neurodegenerative Diseases. Front Neurol 2020; 11:1056. [PMID: 33101165 PMCID: PMC7546323 DOI: 10.3389/fneur.2020.01056] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 08/11/2020] [Indexed: 12/14/2022] Open
Abstract
Tau is a cytosolic microtubule binding protein that is highly abundant in the axons of the central nervous system. However, alternative functions of tau also in other cellular compartments are suggested, for example, in the nucleus, where interactions of tau with specific nuclear entities such as DNA, the nucleolus, and the nuclear envelope have been reported. We would like to review the current knowledge about tau-nucleus interactions and lay out possible neurotoxic mechanisms that are based on the (pathological) interactions of tau with the nucleus.
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Affiliation(s)
- Lisa Diez
- German Center for Neurodegenerative Diseases, Berlin, Germany
| | - Susanne Wegmann
- German Center for Neurodegenerative Diseases, Berlin, Germany
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34
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Dynamics of a Protein Interaction Network Associated to the Aggregation of polyQ-Expanded Ataxin-1. Genes (Basel) 2020; 11:genes11101129. [PMID: 32992839 PMCID: PMC7600199 DOI: 10.3390/genes11101129] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/14/2020] [Accepted: 09/23/2020] [Indexed: 12/13/2022] Open
Abstract
Background: Several experimental models of polyglutamine (polyQ) diseases have been previously developed that are useful for studying disease progression in the primarily affected central nervous system. However, there is a missing link between cellular and animal models that would indicate the molecular defects occurring in neurons and are responsible for the disease phenotype in vivo. Methods: Here, we used a computational approach to identify dysregulated pathways shared by an in vitro and an in vivo model of ATXN1(Q82) protein aggregation, the mutant protein that causes the neurodegenerative polyQ disease spinocerebellar ataxia type-1 (SCA1). Results: A set of common dysregulated pathways were identified, which were utilized to construct cerebellum-specific protein-protein interaction (PPI) networks at various time-points of protein aggregation. Analysis of a SCA1 network indicated important nodes which regulate its function and might represent potential pharmacological targets. Furthermore, a set of drugs interacting with these nodes and predicted to enter the blood–brain barrier (BBB) was identified. Conclusions: Our study points to molecular mechanisms of SCA1 linked from both cellular and animal models and suggests drugs that could be tested to determine whether they affect the aggregation of pathogenic ATXN1 and SCA1 disease progression.
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35
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Tabrizi SJ, Flower MD, Ross CA, Wild EJ. Huntington disease: new insights into molecular pathogenesis and therapeutic opportunities. Nat Rev Neurol 2020; 16:529-546. [PMID: 32796930 DOI: 10.1038/s41582-020-0389-4] [Citation(s) in RCA: 216] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/29/2020] [Indexed: 12/11/2022]
Abstract
Huntington disease (HD) is a neurodegenerative disease caused by CAG repeat expansion in the huntingtin gene (HTT) and involves a complex web of pathogenic mechanisms. Mutant HTT (mHTT) disrupts transcription, interferes with immune and mitochondrial function, and is aberrantly modified post-translationally. Evidence suggests that the mHTT RNA is toxic, and at the DNA level, somatic CAG repeat expansion in vulnerable cells influences the disease course. Genome-wide association studies have identified DNA repair pathways as modifiers of somatic instability and disease course in HD and other repeat expansion diseases. In animal models of HD, nucleocytoplasmic transport is disrupted and its restoration is neuroprotective. Novel cerebrospinal fluid (CSF) and plasma biomarkers are among the earliest detectable changes in individuals with premanifest HD and have the sensitivity to detect therapeutic benefit. Therapeutically, the first human trial of an HTT-lowering antisense oligonucleotide successfully, and safely, reduced the CSF concentration of mHTT in individuals with HD. A larger trial, powered to detect clinical efficacy, is underway, along with trials of other HTT-lowering approaches. In this Review, we discuss new insights into the molecular pathogenesis of HD and future therapeutic strategies, including the modulation of DNA repair and targeting the DNA mutation itself.
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Affiliation(s)
- Sarah J Tabrizi
- Huntington's Disease Centre, University College London, London, UK. .,Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London, London, UK. .,UK Dementia Research Institute, University College London, London, UK.
| | - Michael D Flower
- Huntington's Disease Centre, University College London, London, UK.,Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London, London, UK.,UK Dementia Research Institute, University College London, London, UK
| | - Christopher A Ross
- Departments of Neurology, Neuroscience and Pharmacology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Edward J Wild
- Huntington's Disease Centre, University College London, London, UK.,Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London, London, UK
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36
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Karakostis K, Vadivel Gnanasundram S, López I, Thermou A, Wang L, Nylander K, Olivares-Illana V, Fåhraeus R. A single synonymous mutation determines the phosphorylation and stability of the nascent protein. J Mol Cell Biol 2020; 11:187-199. [PMID: 30252118 DOI: 10.1093/jmcb/mjy049] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 05/29/2018] [Accepted: 06/19/2018] [Indexed: 01/06/2023] Open
Abstract
p53 is an intrinsically disordered protein with a large number of post-translational modifications and interacting partners. The hierarchical order and subcellular location of these events are still poorly understood. The activation of p53 during the DNA damage response (DDR) requires a switch in the activity of the E3 ubiquitin ligase MDM2 from a negative to a positive regulator of p53. This is mediated by the ATM kinase that regulates the binding of MDM2 to the p53 mRNA facilitating an increase in p53 synthesis. Here we show that the binding of MDM2 to the p53 mRNA brings ATM to the p53 polysome where it phosphorylates the nascent p53 at serine 15 and prevents MDM2-mediated degradation of p53. A single synonymous mutation in p53 codon 22 (L22L) prevents the phosphorylation of the nascent p53 protein and the stabilization of p53 following genotoxic stress. The ATM trafficking from the nucleus to the p53 polysome is mediated by MDM2, which requires its interaction with the ribosomal proteins RPL5 and RPL11. These results show how the ATM kinase phosphorylates the p53 protein while it is being synthesized and offer a novel mechanism whereby a single synonymous mutation controls the stability and activity of the encoded protein.
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Affiliation(s)
- Konstantinos Karakostis
- Équipe Labellisée Ligue Contre le Cancer, Université Paris 7, INSERM UMR 1162, 27 Rue Juliette Dodu, Paris, France
| | | | - Ignacio López
- Équipe Labellisée Ligue Contre le Cancer, Université Paris 7, INSERM UMR 1162, 27 Rue Juliette Dodu, Paris, France
| | - Aikaterini Thermou
- Équipe Labellisée Ligue Contre le Cancer, Université Paris 7, INSERM UMR 1162, 27 Rue Juliette Dodu, Paris, France
| | - Lixiao Wang
- Department of Medical Biosciences, Umeå University, Umeå, Sweden
| | - Karin Nylander
- Department of Medical Biosciences, Umeå University, Umeå, Sweden
| | | | - Robin Fåhraeus
- Équipe Labellisée Ligue Contre le Cancer, Université Paris 7, INSERM UMR 1162, 27 Rue Juliette Dodu, Paris, France.,Department of Medical Biosciences, Umeå University, Umeå, Sweden.,RECAMO, Masaryk Memorial Cancer Institute, Zluty kopec 7, Brno, Czech Republic
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37
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Zhang S, Williamson NA, Duvick L, Lee A, Orr HT, Korlin-Downs A, Yang P, Mok YF, Jans DA, Bogoyevitch MA. The ataxin-1 interactome reveals direct connection with multiple disrupted nuclear transport pathways. Nat Commun 2020; 11:3343. [PMID: 32620905 PMCID: PMC7334205 DOI: 10.1038/s41467-020-17145-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 06/09/2020] [Indexed: 11/21/2022] Open
Abstract
The expanded polyglutamine (polyQ) tract form of ataxin-1 drives disease progression in spinocerebellar ataxia type 1 (SCA1). Although known to form distinctive intranuclear bodies, the cellular pathways and processes that polyQ-ataxin-1 influences remain poorly understood. Here we identify the direct and proximal partners constituting the interactome of ataxin-1[85Q] in Neuro-2a cells, pathways analyses indicating a significant enrichment of essential nuclear transporters, pointing to disruptions in nuclear transport processes in the presence of elevated levels of ataxin-1. Our direct assessments of nuclear transporters and their cargoes confirm these observations, revealing disrupted trafficking often with relocalisation of transporters and/or cargoes to ataxin-1[85Q] nuclear bodies. Analogous changes in importin-β1, nucleoporin 98 and nucleoporin 62 nuclear rim staining are observed in Purkinje cells of ATXN1[82Q] mice. The results highlight a disruption of multiple essential nuclear protein trafficking pathways by polyQ-ataxin-1, a key contribution to furthering understanding of pathogenic mechanisms initiated by polyQ tract proteins.
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Affiliation(s)
- Sunyuan Zhang
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Nicholas A Williamson
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Lisa Duvick
- Institute of Translational Neuroscience, and Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Alexander Lee
- Nuclear Signalling Lab., Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia
| | - Harry T Orr
- Institute of Translational Neuroscience, and Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Austin Korlin-Downs
- Institute of Translational Neuroscience, and Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Praseuth Yang
- Institute of Translational Neuroscience, and Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Yee-Foong Mok
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - David A Jans
- Nuclear Signalling Lab., Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia.
| | - Marie A Bogoyevitch
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC, 3010, Australia
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Abstract
Amyloids are protein polymers that were initially linked to human diseases. Across the whole Tree of Life, many disease-unrelated proteins are now emerging for which amyloids represent distinct functional states. Most bacterial amyloids described are extracellular, contributing to biofilm formation. However, only a few have been found in the bacterial cytosol. This paper reviews from the perspective of synthetic biology (SynBio) our understanding of the subtle line that separates functional from pathogenic and transmissible amyloids (prions). Amyloids are protein polymers that were initially linked to human diseases. Across the whole Tree of Life, many disease-unrelated proteins are now emerging for which amyloids represent distinct functional states. Most bacterial amyloids described are extracellular, contributing to biofilm formation. However, only a few have been found in the bacterial cytosol. This paper reviews from the perspective of synthetic biology (SynBio) our understanding of the subtle line that separates functional from pathogenic and transmissible amyloids (prions). In particular, it is focused on RepA-WH1, a functional albeit unconventional natural amyloidogenic protein domain that participates in controlling DNA replication of bacterial plasmids. SynBio approaches, including protein engineering and the design of allosteric effectors such as diverse ligands and an optogenetic module, have enabled the generation in RepA-WH1 of an intracellular cytotoxic prion-like agent in bacteria. The synthetic RepA-WH1 prion has the potential to develop into novel antimicrobials.
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39
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Intercellular Transmission of a Synthetic Bacterial Cytotoxic Prion-Like Protein in Mammalian Cells. mBio 2020; 11:mBio.02937-19. [PMID: 32291306 PMCID: PMC7157824 DOI: 10.1128/mbio.02937-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Proteotoxic amyloid seeds can be transmitted between mammalian cells, arguing that the intercellular exchange of prion-like protein aggregates can be a common phenomenon. RepA-WH1 is derived from a bacterial intracellular functional amyloid protein, engineered to become cytotoxic in Escherichia coli. Here, we have studied if such bacterial aggregates can also be transmitted to, and become cytotoxic to, mammalian cells. We demonstrate that RepA-WH1 is capable of entering naive cells, thereby inducing the cytotoxic aggregation of a soluble RepA-WH1 variant expressed in the cytosol, following the same trend that had been described in bacteria. These findings highlight the universality of one of the central principles underlying prion biology: No matter the biological origin of a given prion-like protein, it can be transmitted to a phylogenetically unrelated recipient cell, provided that the latter expresses a soluble protein onto which the incoming protein can readily template its amyloid conformation. RepA is a bacterial protein that builds intracellular amyloid oligomers acting as inhibitory complexes of plasmid DNA replication. When carrying a mutation enhancing its amyloidogenesis (A31V), the N-terminal domain (WH1) generates cytosolic amyloid particles that are inheritable within a bacterial lineage. Such amyloids trigger in bacteria a lethal cascade reminiscent of mitochondrial impairment in human cells affected by neurodegeneration. To fulfill all the criteria to qualify as a prion-like protein, horizontal (intercellular) transmissibility remains to be demonstrated for RepA-WH1. Since this is experimentally intractable in bacteria, here we transiently expressed in a murine neuroblastoma cell line the soluble, barely cytotoxic RepA-WH1 wild type [RepA-WH1(WT)] and assayed its response to exposure to in vitro-assembled RepA-WH1(A31V) amyloid fibers. In parallel, murine cells releasing RepA-WH1(A31V) aggregates were cocultured with human neuroblastoma cells expressing RepA-WH1(WT). Both the assembled fibers and donor-derived RepA-WH1(A31V) aggregates induced, in the cytosol of recipient cells, the formation of cytotoxic amyloid particles. Mass spectrometry analyses of the proteomes of both types of injured cells pointed to alterations in mitochondria, protein quality triage, signaling, and intracellular traffic. Thus, a synthetic prion-like protein can be propagated to, and become cytotoxic to, cells of organisms placed at such distant branches of the tree of life as bacteria and mammalia, suggesting that mechanisms of protein aggregate spreading and toxicity follow default pathways.
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40
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Laidou S, Alanis-Lobato G, Pribyl J, Raskó T, Tichy B, Mikulasek K, Tsagiopoulou M, Oppelt J, Kastrinaki G, Lefaki M, Singh M, Zink A, Chondrogianni N, Psomopoulos F, Prigione A, Ivics Z, Pospisilova S, Skladal P, Izsvák Z, Andrade-Navarro MA, Petrakis S. Nuclear inclusions of pathogenic ataxin-1 induce oxidative stress and perturb the protein synthesis machinery. Redox Biol 2020; 32:101458. [PMID: 32145456 PMCID: PMC7058924 DOI: 10.1016/j.redox.2020.101458] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 01/29/2020] [Accepted: 02/06/2020] [Indexed: 12/20/2022] Open
Abstract
Spinocerebellar ataxia type-1 (SCA1) is caused by an abnormally expanded polyglutamine (polyQ) tract in ataxin-1. These expansions are responsible for protein misfolding and self-assembly into intranuclear inclusion bodies (IIBs) that are somehow linked to neuronal death. However, owing to lack of a suitable cellular model, the downstream consequences of IIB formation are yet to be resolved. Here, we describe a nuclear protein aggregation model of pathogenic human ataxin-1 and characterize IIB effects. Using an inducible Sleeping Beauty transposon system, we overexpressed the ATXN1(Q82) gene in human mesenchymal stem cells that are resistant to the early cytotoxic effects caused by the expression of the mutant protein. We characterized the structure and the protein composition of insoluble polyQ IIBs which gradually occupy the nuclei and are responsible for the generation of reactive oxygen species. In response to their formation, our transcriptome analysis reveals a cerebellum-specific perturbed protein interaction network, primarily affecting protein synthesis. We propose that insoluble polyQ IIBs cause oxidative and nucleolar stress and affect the assembly of the ribosome by capturing or down-regulating essential components. The inducible cell system can be utilized to decipher the cellular consequences of polyQ protein aggregation. Our strategy provides a broadly applicable methodology for studying polyQ diseases.
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Affiliation(s)
- Stamatia Laidou
- Institute of Applied Biosciences/Centre for Research and Technology Hellas, 57001, Thessaloniki, Greece
| | - Gregorio Alanis-Lobato
- Faculty of Biology, Johannes Gutenberg University Mainz, 55122, Mainz, Germany; Human Embryo and Stem Cell Laboratory, The Francis Crick Institute, NW1 1AT, London, UK
| | - Jan Pribyl
- Central European Institute of Technology, Masaryk University, 62500, Brno, Czech Republic
| | - Tamás Raskó
- Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association, Berlin, 13125, Germany
| | - Boris Tichy
- Central European Institute of Technology, Masaryk University, 62500, Brno, Czech Republic
| | - Kamil Mikulasek
- Central European Institute of Technology, Masaryk University, 62500, Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500, Brno, Czech Republic
| | - Maria Tsagiopoulou
- Institute of Applied Biosciences/Centre for Research and Technology Hellas, 57001, Thessaloniki, Greece
| | - Jan Oppelt
- Central European Institute of Technology, Masaryk University, 62500, Brno, Czech Republic
| | - Georgia Kastrinaki
- Aerosol and Particle Technology Laboratory/Chemical Process & Energy Resources Institute/Centre for Research and Technology Hellas, 57001, Thessaloniki, Greece
| | - Maria Lefaki
- Institute of Biology, Medicinal Chemistry & Biotechnology/National Hellenic Research Foundation, 11365, Athens, Greece
| | - Manvendra Singh
- Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association, Berlin, 13125, Germany
| | - Annika Zink
- Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association, Berlin, 13125, Germany; Department of General Pediatrics, Neonatology and Pediatric Cardiology, University Children's Hospital, Heinrich Heine University, 40225, Düsseldorf, Germany
| | - Niki Chondrogianni
- Institute of Biology, Medicinal Chemistry & Biotechnology/National Hellenic Research Foundation, 11365, Athens, Greece
| | - Fotis Psomopoulos
- Institute of Applied Biosciences/Centre for Research and Technology Hellas, 57001, Thessaloniki, Greece; Department of Molecular Medicine and Surgery, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Alessandro Prigione
- Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association, Berlin, 13125, Germany; Department of General Pediatrics, Neonatology and Pediatric Cardiology, University Children's Hospital, Heinrich Heine University, 40225, Düsseldorf, Germany
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul-Ehrlich-Institute, 63225, Langen, Germany
| | - Sarka Pospisilova
- Central European Institute of Technology, Masaryk University, 62500, Brno, Czech Republic
| | - Petr Skladal
- Central European Institute of Technology, Masaryk University, 62500, Brno, Czech Republic
| | - Zsuzsanna Izsvák
- Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association, Berlin, 13125, Germany.
| | | | - Spyros Petrakis
- Institute of Applied Biosciences/Centre for Research and Technology Hellas, 57001, Thessaloniki, Greece.
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41
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Network Medicine Approach for Analysis of Alzheimer's Disease Gene Expression Data. Int J Mol Sci 2020; 21:ijms21010332. [PMID: 31947790 PMCID: PMC6981840 DOI: 10.3390/ijms21010332] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/21/2019] [Accepted: 12/30/2019] [Indexed: 12/18/2022] Open
Abstract
Alzheimer’s disease (AD) is the most widespread diagnosed cause of dementia in the elderly. It is a progressive neurodegenerative disease that causes memory loss as well as other detrimental symptoms that are ultimately fatal. Due to the urgent nature of this disease, and the current lack of success in treatment and prevention, it is vital that different methods and approaches are applied to its study in order to better understand its underlying mechanisms. To this end, we have conducted network-based gene co-expression analysis on data from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) database. By processing and filtering gene expression data taken from the blood samples of subjects with varying disease states and constructing networks based on that data to evaluate gene relationships, we have been able to learn about gene expression correlated with the disease, and we have identified several areas of potential research interest.
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Li X, Wang L, Cykowski M, He T, Liu T, Chakranarayan J, Rivera A, Zhao H, Powell S, Xia W, Wong STC. OCIAD1 contributes to neurodegeneration in Alzheimer's disease by inducing mitochondria dysfunction, neuronal vulnerability and synaptic damages. EBioMedicine 2020; 51:102569. [PMID: 31931285 PMCID: PMC6957876 DOI: 10.1016/j.ebiom.2019.11.030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 11/10/2019] [Accepted: 11/19/2019] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Hyperamyloidosis in the brain is known as the earliest neuropathological change and a unique etiological factor in Alzheimer's disease (AD), while progressive neurodegeneration in certain vulnerable brain regions forms the basis of clinical syndromes. It is not clear how early hyperamyloidosis is implicated in progressive neurodegeneration and what factors contribute to the selective brain vulnerability in AD. METHODS Bioinformatics and experimental neurobiology methods were integrated to identify novel factors involved in the hyperamyloidosis-induced brain vulnerability in AD. We first examined neurodegeneration-specific gene signatures from sporadic AD patients and synaptic protein changes in young transgenic AD mice. Then, we systematically assessed the association of a top candidate gene with AD and investigated its mechanistic role in neurodegeneration. FINDINGS We identified the ovary-orientated protein OCIAD1 (Ovarian-Carcinoma-Immunoreactive-Antigen-Domain-Containing-1) as a neurodegeneration-associated factor for AD. Higher levels of OCIAD1, found in vulnerable brain areas and dystrophic neurites, were correlated with disease severity. Multiple early AD pathological events, particularly Aβ/GSK-3β signaling, elevate OCIAD1, which in turn interacts with BCL-2 to impair mitochondrial function and facilitates mitochondria-associated neuronal injury. Notably, elevated OCIAD1 by Aβ increases cell susceptibility to other AD pathological challenges. INTERPRETATION Our findings suggest that OCIAD1 contributes to neurodegeneration in AD by impairing mitochondria function, and subsequently leading to neuronal vulnerability, and synaptic damages. FUNDING Ting Tsung & Wei Fong Chao Foundation, John S Dunn Research Foundation, Cure Alzheimer's Fund, and NIH R01AG057635 to STCW.
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Affiliation(s)
- Xuping Li
- Ting Tsung & Wei Fong Chao Center for BRAIN, Weill Cornell Medicine, Houston Methodist Research Institute, 6670 Bertner Ave, Houston, TX 77030, USA.
| | - Lin Wang
- Department of Informatics Development, Houston Methodist Hospital, Houston, TX 77030, USA
| | - Matthew Cykowski
- Departments of Pathology and Genome Medicine, Weill Cornell Medicine, Houston Methodist Hospital, Houston, TX 77030, USA
| | - Tiancheng He
- Department of Informatics Development, Houston Methodist Hospital, Houston, TX 77030, USA
| | - Timothy Liu
- Ting Tsung & Wei Fong Chao Center for BRAIN, Weill Cornell Medicine, Houston Methodist Research Institute, 6670 Bertner Ave, Houston, TX 77030, USA
| | - Joshua Chakranarayan
- Ting Tsung & Wei Fong Chao Center for BRAIN, Weill Cornell Medicine, Houston Methodist Research Institute, 6670 Bertner Ave, Houston, TX 77030, USA
| | - Andreana Rivera
- Departments of Pathology and Genome Medicine, Weill Cornell Medicine, Houston Methodist Hospital, Houston, TX 77030, USA
| | - Hong Zhao
- Ting Tsung & Wei Fong Chao Center for BRAIN, Weill Cornell Medicine, Houston Methodist Research Institute, 6670 Bertner Ave, Houston, TX 77030, USA
| | - Suzanne Powell
- Departments of Pathology and Genome Medicine, Weill Cornell Medicine, Houston Methodist Hospital, Houston, TX 77030, USA
| | - Weiming Xia
- Ting Tsung & Wei Fong Chao Center for BRAIN, Weill Cornell Medicine, Houston Methodist Research Institute, 6670 Bertner Ave, Houston, TX 77030, USA; Geriatric Research Education Clinical Center, Edith Nourse Rogers Memorial Veterans Hospital, Bedford, MA 01730, USA; Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA 02118, USA
| | - Stephen T C Wong
- Ting Tsung & Wei Fong Chao Center for BRAIN, Weill Cornell Medicine, Houston Methodist Research Institute, 6670 Bertner Ave, Houston, TX 77030, USA; Department of Informatics Development, Houston Methodist Hospital, Houston, TX 77030, USA; Departments of Pathology and Genome Medicine, Weill Cornell Medicine, Houston Methodist Hospital, Houston, TX 77030, USA; Departments of Radiology, Weill Cornell Medicine, Houston Methodist Hospital, Houston, TX 77030, USA.
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Ripolone M, Lucchini V, Ronchi D, Fagiolari G, Bordoni A, Fortunato F, Mondello S, Bonato S, Meregalli M, Torrente Y, Corti S, Comi GP, Moggio M, Sciacco M. Purkinje cell COX deficiency and mtDNA depletion in an animal model of spinocerebellar ataxia type 1. J Neurosci Res 2019; 96:1576-1585. [PMID: 30113722 DOI: 10.1002/jnr.24263] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 05/09/2018] [Accepted: 05/09/2018] [Indexed: 12/19/2022]
Abstract
Spinocerebellar ataxias (SCAs) are a genetically heterogeneous group of cerebellar degenerative disorders, characterized by progressive gait unsteadiness, hand incoordination, and dysarthria. Ataxia type 1 (SCA1) is caused by the expansion of a CAG trinucleotide repeat in the SCA1 gene resulting in the atypical extension of a polyglutamine (polyQ) tract within the ataxin-1 protein. Our main objective was to investigate the mitochondrial oxidative metabolism in the cerebellum of transgenic SCA1 mice. SCA1 transgenic mice develop clinical features in the early life stages (around 5 weeks of age) presenting pathological cerebellar signs with concomitant progressive Purkinje neuron atrophy and relatively little cell loss; this evidence suggests that the SCA1 phenotype is not the result of cell death per se, but a possible effect of cellular dysfunction that occurs before neuronal demise. We studied the mitochondrial oxidative metabolism in cerebellar cells from both homozygous and heterozygous transgenic SCA1 mice, aged 2 and 6 months. Histochemical examination showed a cytochrome-c-oxidase (COX) deficiency in the Purkinje cells (PCs) of both heterozygous and homozygous mice, the oxidative defect being more prominent in older mice, in which the percentage of COX-deficient PC was up to 30%. Using a laser-microdissector, we evaluated the mitochondrial DNA (mtDNA) content on selectively isolated COX-competent and COX-deficient PC by quantitative Polymerase Chain Reaction and we found mtDNA depletion in those with oxidative dysfunction. In conclusion, the selective oxidative metabolism defect observed in neuronal PC expressing mutant ataxin occurs as early as 8 weeks of age thus representing an early step in the PC degeneration process in SCA1 disease.
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Affiliation(s)
- Michela Ripolone
- Neuromuscular and Rare Diseases Unit, Department of Neuroscience, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Valeria Lucchini
- Neuromuscular and Rare Diseases Unit, Department of Neuroscience, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Dario Ronchi
- Neurology Unit, Neuroscience Section, Department of Pathophysiology and Transplantation, Dino Ferrari Centre, IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, University of Milan, Milan, Italy
| | - Gigliola Fagiolari
- Neuromuscular and Rare Diseases Unit, Department of Neuroscience, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Andreina Bordoni
- Neurology Unit, Neuroscience Section, Department of Pathophysiology and Transplantation, Dino Ferrari Centre, IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, University of Milan, Milan, Italy
| | - Francesco Fortunato
- Neurology Unit, Neuroscience Section, Department of Pathophysiology and Transplantation, Dino Ferrari Centre, IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, University of Milan, Milan, Italy
| | - Stefania Mondello
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy
| | - Sara Bonato
- Neurology Unit, Neuroscience Section, Department of Pathophysiology and Transplantation, Dino Ferrari Centre, IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, University of Milan, Milan, Italy
| | - Mirella Meregalli
- Department of Pathophysiology and Transplantation, Stem Cell Laboratory, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico di Milano, Centro Dino Ferrari, Milan, Italy
| | - Yvan Torrente
- Department of Pathophysiology and Transplantation, Stem Cell Laboratory, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico di Milano, Centro Dino Ferrari, Milan, Italy
| | - Stefania Corti
- Neurology Unit, Neuroscience Section, Department of Pathophysiology and Transplantation, Dino Ferrari Centre, IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, University of Milan, Milan, Italy
| | - Giacomo P Comi
- Neurology Unit, Neuroscience Section, Department of Pathophysiology and Transplantation, Dino Ferrari Centre, IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, University of Milan, Milan, Italy
| | - Maurizio Moggio
- Neuromuscular and Rare Diseases Unit, Department of Neuroscience, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Monica Sciacco
- Neuromuscular and Rare Diseases Unit, Department of Neuroscience, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
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Rocha S, Vieira J, Vázquez N, López-Fernández H, Fdez-Riverola F, Reboiro-Jato M, Sousa AD, Vieira CP. ATXN1 N-terminal region explains the binding differences of wild-type and expanded forms. BMC Med Genomics 2019; 12:145. [PMID: 31655597 PMCID: PMC6814966 DOI: 10.1186/s12920-019-0594-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 09/24/2019] [Indexed: 12/21/2022] Open
Abstract
Background Wild-type (wt) polyglutamine (polyQ) regions are implicated in stabilization of protein-protein interactions (PPI). Pathological polyQ expansion, such as that in human Ataxin-1 (ATXN1), that causes spinocerebellar ataxia type 1 (SCA1), results in abnormal PPI. For ATXN1 a larger number of interactors has been reported for the expanded (82Q) than the wt (29Q) protein. Methods To understand how the expanded polyQ affects PPI, protein structures were predicted for wt and expanded ATXN1, as well as, for 71 ATXN1 interactors. Then, the binding surfaces of wt and expanded ATXN1 with the reported interactors were inferred. Results Our data supports that the polyQ expansion alters the ATXN1 conformation and that it enhances the strength of interaction with ATXN1 partners. For both ATXN1 variants, the number of residues at the predicted binding interface are greater after the polyQ, mainly due to the AXH domain. Moreover, the difference in the interaction strength of the ATXN1 variants was due to an increase in the number of interactions at the N-terminal region, before the polyQ, for the expanded form. Conclusions There are three regions at the AXH domain that are essential for ATXN1 PPI. The N-terminal region is responsible for the strength of the PPI with the ATXN1 variants. How the predicted motifs in this region affect PPI is discussed, in the context of ATXN1 post-transcriptional modifications.
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Affiliation(s)
- Sara Rocha
- Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - Jorge Vieira
- Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - Noé Vázquez
- ESEI - Escuela Superior de Ingeniería Informática, Edificio Politécnico, Campus Universitario As Lagoas s/n, Universidad de Vigo, 32004, Ourense, Spain.,Centro de Investigaciones Biomédicas (Centro Singular de Investigación de Galicia), Vigo, Spain.,SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur). SERGAS-UVIGO, Vigo, Spain
| | - Hugo López-Fernández
- Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,ESEI - Escuela Superior de Ingeniería Informática, Edificio Politécnico, Campus Universitario As Lagoas s/n, Universidad de Vigo, 32004, Ourense, Spain.,Centro de Investigaciones Biomédicas (Centro Singular de Investigación de Galicia), Vigo, Spain.,SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur). SERGAS-UVIGO, Vigo, Spain
| | - Florentino Fdez-Riverola
- ESEI - Escuela Superior de Ingeniería Informática, Edificio Politécnico, Campus Universitario As Lagoas s/n, Universidad de Vigo, 32004, Ourense, Spain.,Centro de Investigaciones Biomédicas (Centro Singular de Investigación de Galicia), Vigo, Spain.,SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur). SERGAS-UVIGO, Vigo, Spain
| | - Miguel Reboiro-Jato
- ESEI - Escuela Superior de Ingeniería Informática, Edificio Politécnico, Campus Universitario As Lagoas s/n, Universidad de Vigo, 32004, Ourense, Spain.,Centro de Investigaciones Biomédicas (Centro Singular de Investigación de Galicia), Vigo, Spain.,SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur). SERGAS-UVIGO, Vigo, Spain
| | - André D Sousa
- Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - Cristina P Vieira
- Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen, 208, 4200-135, Porto, Portugal. .,Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.
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Abraham JR, Szoko N, Barnard J, Rubin RA, Schlatzer D, Lundberg K, Li X, Natowicz MR. Proteomic Investigations of Autism Brain Identify Known and Novel Pathogenetic Processes. Sci Rep 2019; 9:13118. [PMID: 31511657 PMCID: PMC6739414 DOI: 10.1038/s41598-019-49533-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Accepted: 08/23/2019] [Indexed: 12/27/2022] Open
Abstract
Autism Spectrum Disorder (ASD) is a set of heterogeneous neurodevelopmental conditions defined by impairments in social communication and restricted, repetitive behaviors, interests or activities. Only a minority of ASD cases are determined to have a definitive etiology and the pathogenesis of most ASD is poorly understood. We hypothesized that a global analysis of the proteomes of human ASD vs. control brain, heretofore not done, would provide important data with which to better understand the underlying neurobiology of autism. In this study, we characterized the proteomes of two brain regions, Brodmann area 19 (BA19) and posterior inferior cerebellum (CB), from carefully selected idiopathic ASD cases and matched controls using label-free HPLC-tandem mass spectrometry. The data revealed marked differences between ASD and control brain proteomes for both brain regions. Unlike earlier transcriptomic analyses using frontal and temporal cortex, however, our proteomic analysis did not support ASD attenuating regional gene expression differences. Bioinformatic analyses of the differentially expressed proteins between cases and controls highlighted canonical pathways involving glutamate receptor signaling and glutathione-mediated detoxification in both BA19 and CB; other pathways such as Sertoli cell signaling and fatty acid oxidation were specifically enriched in BA19 or CB, respectively. Network analysis of both regions of ASD brain showed up-regulation of multiple pre- and post-synaptic membrane or scaffolding proteins including glutamatergic ion channels and related proteins, up-regulation of proteins involved in intracellular calcium signaling, and down-regulation of neurofilament proteins, with DLG4 and MAPT as major hub proteins in BA19 and CB protein interaction networks, respectively. Upstream regulator analysis suggests neurodegeneration-associated proteins drive the differential protein expression for ASD in both BA19 and CB. Overall, the proteomic data provide support for shared dysregulated pathways and upstream regulators for two brain regions in human ASD brain, suggesting a common ASD pathophysiology that has distinctive regional expression.
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Affiliation(s)
- Joseph R Abraham
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH, 44195, USA
| | - Nicholas Szoko
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH, 44195, USA
| | - John Barnard
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Robert A Rubin
- Department of Mathematics, Whittier College, Whittier, CA, 90602, USA
| | - Daniela Schlatzer
- Center for Proteomics, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Kathleen Lundberg
- Center for Proteomics, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Xiaolin Li
- Center for Proteomics, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Marvin R Natowicz
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH, 44195, USA. .,Pathology and Laboratory Medicine, Genomic Medicine, Neurological and Pediatrics Institutes, Cleveland Clinic, Cleveland, OH, 44195, USA.
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46
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Moutaoufik MT, Malty R, Amin S, Zhang Q, Phanse S, Gagarinova A, Zilocchi M, Hoell L, Minic Z, Gagarinova M, Aoki H, Stockwell J, Jessulat M, Goebels F, Broderick K, Scott NE, Vlasblom J, Musso G, Prasad B, Lamantea E, Garavaglia B, Rajput A, Murayama K, Okazaki Y, Foster LJ, Bader GD, Cayabyab FS, Babu M. Rewiring of the Human Mitochondrial Interactome during Neuronal Reprogramming Reveals Regulators of the Respirasome and Neurogenesis. iScience 2019; 19:1114-1132. [PMID: 31536960 PMCID: PMC6831851 DOI: 10.1016/j.isci.2019.08.057] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 06/28/2019] [Accepted: 08/29/2019] [Indexed: 12/13/2022] Open
Abstract
Mitochondrial protein (MP) assemblies undergo alterations during neurogenesis, a complex process vital in brain homeostasis and disease. Yet which MP assemblies remodel during differentiation remains unclear. Here, using mass spectrometry-based co-fractionation profiles and phosphoproteomics, we generated mitochondrial interaction maps of human pluripotent embryonal carcinoma stem cells and differentiated neuronal-like cells, which presented as two discrete cell populations by single-cell RNA sequencing. The resulting networks, encompassing 6,442 high-quality associations among 600 MPs, revealed widespread changes in mitochondrial interactions and site-specific phosphorylation during neuronal differentiation. By leveraging the networks, we show the orphan C20orf24 as a respirasome assembly factor whose disruption markedly reduces respiratory chain activity in patients deficient in complex IV. We also find that a heme-containing neurotrophic factor, neuron-derived neurotrophic factor [NENF], couples with Parkinson disease-related proteins to promote neurotrophic activity. Our results provide insights into the dynamic reorganization of mitochondrial networks during neuronal differentiation and highlights mechanisms for MPs in respirasome, neuronal function, and mitochondrial diseases. Rewiring of mitochondrial (mt) protein interaction network in distinct cell states Dramatic changes in site-specific phosphorylation during neuronal differentiation C20orf24 is a respirasome assembly factor depleted in patients deficient in CIV NENF binding with DJ-1/PINK1 promotes neurotrophic activity and neuronal survival
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Affiliation(s)
| | - Ramy Malty
- Department of Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Shahreen Amin
- Department of Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Qingzhou Zhang
- Department of Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Sadhna Phanse
- Department of Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Alla Gagarinova
- Department of Biochemistry, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Mara Zilocchi
- Department of Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Larissa Hoell
- Department of Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Zoran Minic
- Department of Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Maria Gagarinova
- Department of Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Hiroyuki Aoki
- Department of Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Jocelyn Stockwell
- Department of Surgery, Neuroscience Research Group, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Matthew Jessulat
- Department of Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Florian Goebels
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Kirsten Broderick
- Department of Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Nichollas E Scott
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - James Vlasblom
- Department of Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Gabriel Musso
- Department of Medicine, Harvard Medical School and Cardiovascular Division, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Bhanu Prasad
- Department of Medicine, Regina Qu'Appelle Health Region, Regina, SK S4P 0W5, Canada
| | - Eleonora Lamantea
- Medical Genetics and Neurogenetics Unit, Fondazione IRCCS Instituto Neurologico Carlo Besta, via L. Temolo, 4, 20126 Milan, Italy
| | - Barbara Garavaglia
- Medical Genetics and Neurogenetics Unit, Fondazione IRCCS Instituto Neurologico Carlo Besta, via L. Temolo, 4, 20126 Milan, Italy
| | - Alex Rajput
- Department of Medicine, Division of Neurology, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Kei Murayama
- Department of Metabolism, Chiba Children's Hospital, 579-1 Heta-cho, Midori, Chiba 266-0007, Japan
| | - Yasushi Okazaki
- Graduate School of Medicine, Intractable Disease Research Center, Juntendo University, Hongo 2-1-1, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Leonard J Foster
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Gary D Bader
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Francisco S Cayabyab
- Department of Surgery, Neuroscience Research Group, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Mohan Babu
- Department of Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada.
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Carter FE, Moore ME, Pickrell AM. Methods to detect mitophagy in neurons during disease. J Neurosci Methods 2019; 325:108351. [PMID: 31299189 PMCID: PMC6688849 DOI: 10.1016/j.jneumeth.2019.108351] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 07/05/2019] [Accepted: 07/06/2019] [Indexed: 01/29/2023]
Abstract
Mitophagy is the selective degradation of mitochondria by autophagy. Methods to study mitophagy in neurons is of increasing importance as neurodegenerative diseases such as Parkinson's and Alzheimer's display disrupted mitophagy as part of their pathogenesis. Since the last decade, researchers have determined how selective mitophagy pathways such as PINK1/Parkin and Mul1 function at the cellular level. Thus, advances in techniques to study these pathways specifically in neurons and glia have arisen. This review will introduce mitophagy pathways studied in neurons and evaluate current techniques available to investigate mitophagy.
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Affiliation(s)
- Faith E. Carter
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA,Virginia Tech Post-Baccalaureate Program, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA,Present address: Graduate Program in Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - M. Elyse Moore
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Alicia M. Pickrell
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA,Correspondence should be addressed to: Alicia M. Pickrell, 970 Washington Street SW, Life Science I Room 217, Blacksburg, VA 24061, Tel: 540-232-8465; Fax: 540-231-1475;
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48
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Wan H, Wang Q, Chen X, Zeng Q, Shao Y, Fang H, Liao X, Li HS, Liu MG, Xu TL, Diao M, Li D, Meng B, Tang B, Zhang Z, Liao L. WDR45 contributes to neurodegeneration through regulation of ER homeostasis and neuronal death. Autophagy 2019; 16:531-547. [PMID: 31204559 DOI: 10.1080/15548627.2019.1630224] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Mutations in the macroautophagy/autophagy gene WDR45 cause β-propeller protein-associated neurodegeneration (BPAN); however the molecular and cellular mechanism of the disease process is largely unknown. Here we generated constitutive wdr45 knockout (KO) mice that displayed cognitive impairments, abnormal synaptic transmission and lesions in several brain regions. Immunohistochemistry analysis showed loss of neurons in prefrontal cortex and basal ganglion in aged mice, and increased apoptosis in prefrontal cortex, recapitulating a hallmark of neurodegeneration. Quantitative proteomic analysis showed accumulation of endoplasmic reticulum (ER) proteins in KO mouse. At the cellular level, accumulation of ER proteins due to WDR45 deficiency resulted in increased ER stress and impaired ER quality control. The unfolded protein response (UPR) was elevated through ERN1/IRE1 or EIF2AK3/PERK pathway, and eventually led to neuronal apoptosis. Suppression of ER stress or activation of autophagy through MTOR inhibition alleviated cell death. Thus, the loss of WDR45 cripples macroautophagy machinery in neurons and leads to impairment in organelle autophagy, which provides a mechanistic understanding of cause of BPAN and a potential therapeutic strategy to treat this genetic disorder.Abbreviations: 7-ADD: 7-aminoactinomycin D; ASD: autistic spectrum disorder; ATF6: activating transcription factor 6; ATG: autophagy-related; BafA1: bafilomycin A1; BCAP31: B cell receptor associated protein 31; BPAN: β-propeller protein-associated neurodegeneration; CCCP: carbonyl cyanide m-chlorophenylhydrazone; CDIPT: CDP-diacylglycerol-inositol 3-phosphatidyltransferase (phosphatidylinositol synthase); DDIT3/CHOP: DNA-damage inducible transcript 3; EIF2A: eukaryotic translation initiation factor 2A; EIF2AK3/PERK: eukaryotic translation initiation factor 2 alpha kinase 3; ER: endoplasmic reticulum; ERN1/IRE1: endoplasmic reticulum to nucleus signaling 1; GFP: green fluorescent protein; HIP: hippocampus; HSPA5/GRP78: heat shock protein family A (HSP70) member 5; KO: knockout; LAMP1: lysosomal-associated membrane 1; mEPSCs: miniature excitatory postsynaptic currents; MG132: N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal; MIB: mid-brain; MTOR: mechanistic target of rapamycin kinase; PCR: polymerase chain reaction; PFA: paraformaldehyde; PFC: prefrontal cortex; PRM: parallel reaction monitoring; RBFOX3/NEUN: RNA binding protein, fox-1 homolog [C. elegans] 3; RTN3: reticulon 3; SEC22B: SEC22 homolog B, vesicle trafficking protein; SEC61B: SEC61 translocon beta subunit; SEM: standard error of the mean; SNR: substantia nigra; SQSTM1/p62: sequestosome 1; TH: tyrosine hydroxylase; Tm: tunicamycin; TMT: tandem mass tag; TUDCA: tauroursodeoxycholic acid; TUNEL: terminal deoxynucleotidyl transferase dUTP nick-end labeling; UPR: unfolded protein response; WDR45: WD repeat domain 45; WT: wild type; XBP1: X-box binding protein 1.
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Affiliation(s)
- Huida Wan
- Shanghai Key Laboratory of Regulatory Biology, and Shanghai Key Laboratory of Brain Functional Genomics, School of Life Sciences, East China Normal University, Shanghai, China
| | - Qi Wang
- Shanghai Key Laboratory of Regulatory Biology, and Shanghai Key Laboratory of Brain Functional Genomics, School of Life Sciences, East China Normal University, Shanghai, China
| | - Xiuting Chen
- Shanghai Key Laboratory of Regulatory Biology, and Shanghai Key Laboratory of Brain Functional Genomics, School of Life Sciences, East China Normal University, Shanghai, China
| | - Qiufang Zeng
- Shanghai Key Laboratory of Regulatory Biology, and Shanghai Key Laboratory of Brain Functional Genomics, School of Life Sciences, East China Normal University, Shanghai, China
| | - Yanjiao Shao
- Shanghai Key Laboratory of Regulatory Biology, and Shanghai Key Laboratory of Brain Functional Genomics, School of Life Sciences, East China Normal University, Shanghai, China
| | - Houqin Fang
- Shanghai Key Laboratory of Regulatory Biology, and Shanghai Key Laboratory of Brain Functional Genomics, School of Life Sciences, East China Normal University, Shanghai, China
| | - Xun Liao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Hu-Song Li
- Collaborative Innovation Center for Brain Science, Department of Anatomy and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ming-Gang Liu
- Collaborative Innovation Center for Brain Science, Department of Anatomy and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tian-Le Xu
- Collaborative Innovation Center for Brain Science, Department of Anatomy and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Miaomiao Diao
- Shanghai Key Laboratory of Regulatory Biology, and Shanghai Key Laboratory of Brain Functional Genomics, School of Life Sciences, East China Normal University, Shanghai, China
| | - Dali Li
- Shanghai Key Laboratory of Regulatory Biology, and Shanghai Key Laboratory of Brain Functional Genomics, School of Life Sciences, East China Normal University, Shanghai, China
| | - Bo Meng
- Shanghai Key Laboratory of Regulatory Biology, and Shanghai Key Laboratory of Brain Functional Genomics, School of Life Sciences, East China Normal University, Shanghai, China
| | - Bin Tang
- Shanghai Key Laboratory of Regulatory Biology, and Shanghai Key Laboratory of Brain Functional Genomics, School of Life Sciences, East China Normal University, Shanghai, China
| | - Zhuohua Zhang
- Institute of Precision Medicine, the Xiangya Hospital, the Xiangya Medical School, Central South University, Changsha, Hunan, China
| | - Lujian Liao
- Shanghai Key Laboratory of Regulatory Biology, and Shanghai Key Laboratory of Brain Functional Genomics, School of Life Sciences, East China Normal University, Shanghai, China
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49
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Hawe JS, Theis FJ, Heinig M. Inferring Interaction Networks From Multi-Omics Data. Front Genet 2019; 10:535. [PMID: 31249591 PMCID: PMC6582773 DOI: 10.3389/fgene.2019.00535] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 05/16/2019] [Indexed: 01/24/2023] Open
Abstract
A major goal in systems biology is a comprehensive description of the entirety of all complex interactions between different types of biomolecules—also referred to as the interactome—and how these interactions give rise to higher, cellular and organism level functions or diseases. Numerous efforts have been undertaken to define such interactomes experimentally, for example yeast-two-hybrid based protein-protein interaction networks or ChIP-seq based protein-DNA interactions for individual proteins. To complement these direct measurements, genome-scale quantitative multi-omics data (transcriptomics, proteomics, metabolomics, etc.) enable researchers to predict novel functional interactions between molecular species. Moreover, these data allow to distinguish relevant functional from non-functional interactions in specific biological contexts. However, integration of multi-omics data is not straight forward due to their heterogeneity. Numerous methods for the inference of interaction networks from homogeneous functional data exist, but with the advent of large-scale paired multi-omics data a new class of methods for inferring comprehensive networks across different molecular species began to emerge. Here we review state-of-the-art techniques for inferring the topology of interaction networks from functional multi-omics data, encompassing graphical models with multiple node types and quantitative-trait-loci (QTL) based approaches. In addition, we will discuss Bayesian aspects of network inference, which allow for leveraging already established biological information such as known protein-protein or protein-DNA interactions, to guide the inference process.
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Affiliation(s)
- Johann S Hawe
- Institute of Computational Biology, HelmholtzZentrum München, Munich, Germany.,Department of Informatics, Technische Universität München, Munich, Germany
| | - Fabian J Theis
- Institute of Computational Biology, HelmholtzZentrum München, Munich, Germany.,Department of Mathematics, Technische Universität München, Munich, Germany
| | - Matthias Heinig
- Institute of Computational Biology, HelmholtzZentrum München, Munich, Germany.,Department of Informatics, Technische Universität München, Munich, Germany
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50
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Hedl TJ, San Gil R, Cheng F, Rayner SL, Davidson JM, De Luca A, Villalva MD, Ecroyd H, Walker AK, Lee A. Proteomics Approaches for Biomarker and Drug Target Discovery in ALS and FTD. Front Neurosci 2019; 13:548. [PMID: 31244593 PMCID: PMC6579929 DOI: 10.3389/fnins.2019.00548] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 05/13/2019] [Indexed: 12/11/2022] Open
Abstract
Neurodegenerative disorders such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are increasing in prevalence but lack targeted therapeutics. Although the pathological mechanisms behind these diseases remain unclear, both ALS and FTD are characterized pathologically by aberrant protein aggregation and inclusion formation within neurons, which correlates with neurodegeneration. Notably, aggregation of several key proteins, including TAR DNA binding protein of 43 kDa (TDP-43), superoxide dismutase 1 (SOD1), and tau, have been implicated in these diseases. Proteomics methods are being increasingly applied to better understand disease-related mechanisms and to identify biomarkers of disease, using model systems as well as human samples. Proteomics-based approaches offer unbiased, high-throughput, and quantitative results with numerous applications for investigating proteins of interest. Here, we review recent advances in the understanding of ALS and FTD pathophysiology obtained using proteomics approaches, and we assess technical and experimental limitations. We compare findings from various mass spectrometry (MS) approaches including quantitative proteomics methods such as stable isotope labeling by amino acids in cell culture (SILAC) and tandem mass tagging (TMT) to approaches such as label-free quantitation (LFQ) and sequential windowed acquisition of all theoretical fragment ion mass spectra (SWATH-MS) in studies of ALS and FTD. Similarly, we describe disease-related protein-protein interaction (PPI) studies using approaches including immunoprecipitation mass spectrometry (IP-MS) and proximity-dependent biotin identification (BioID) and discuss future application of new techniques including proximity-dependent ascorbic acid peroxidase labeling (APEX), and biotinylation by antibody recognition (BAR). Furthermore, we explore the use of MS to detect post-translational modifications (PTMs), such as ubiquitination and phosphorylation, of disease-relevant proteins in ALS and FTD. We also discuss upstream technologies that enable enrichment of proteins of interest, highlighting the contributions of new techniques to isolate disease-relevant protein inclusions including flow cytometric analysis of inclusions and trafficking (FloIT). These recently developed approaches, as well as related advances yet to be applied to studies of these neurodegenerative diseases, offer numerous opportunities for discovery of potential therapeutic targets and biomarkers for ALS and FTD.
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Affiliation(s)
- Thomas J Hedl
- Neurodegeneration Pathobiology Laboratory, Queensland Brain Institute, The University of Queensland, St Lucia, QLD, Australia
| | - Rebecca San Gil
- Neurodegeneration Pathobiology Laboratory, Queensland Brain Institute, The University of Queensland, St Lucia, QLD, Australia
| | - Flora Cheng
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Stephanie L Rayner
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Jennilee M Davidson
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Alana De Luca
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Maria D Villalva
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Heath Ecroyd
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
| | - Adam K Walker
- Neurodegeneration Pathobiology Laboratory, Queensland Brain Institute, The University of Queensland, St Lucia, QLD, Australia.,Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Albert Lee
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, North Ryde, NSW, Australia
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