1
|
Predicting Parkinson disease related genes based on PyFeat and gradient boosted decision tree. Sci Rep 2022; 12:10004. [PMID: 35705654 PMCID: PMC9200794 DOI: 10.1038/s41598-022-14127-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Accepted: 06/01/2022] [Indexed: 11/10/2022] Open
Abstract
Identifying genes related to Parkinson’s disease (PD) is an active research topic in biomedical analysis, which plays a critical role in diagnosis and treatment. Recently, many studies have proposed different techniques for predicting disease-related genes. However, a few of these techniques are designed or developed for PD gene prediction. Most of these PD techniques are developed to identify only protein genes and discard long noncoding (lncRNA) genes, which play an essential role in biological processes and the transformation and development of diseases. This paper proposes a novel prediction system to identify protein and lncRNA genes related to PD that can aid in an early diagnosis. First, we preprocessed the genes into DNA FASTA sequences from the University of California Santa Cruz (UCSC) genome browser and removed the redundancies. Second, we extracted some significant features of DNA FASTA sequences using the PyFeat method with the AdaBoost as feature selection. These selected features achieved promising results compared with extracted features from some state-of-the-art feature extraction techniques. Finally, the features were fed to the gradient-boosted decision tree (GBDT) to diagnose different tested cases. Seven performance metrics were used to evaluate the performance of the proposed system. The proposed system achieved an average accuracy of 78.6%, the area under the curve equals 84.5%, the area under precision-recall (AUPR) equals 85.3%, F1-score equals 78.3%, Matthews correlation coefficient (MCC) equals 0.575, sensitivity (SEN) equals 77.1%, and specificity (SPC) equals 80.2%. The experiments demonstrate promising results compared with other systems. The predicted top-rank protein and lncRNA genes are verified based on a literature review.
Collapse
|
2
|
Barbier M, Bahlo M, Pennisi A, Jacoupy M, Tankard RM, Ewenczyk C, Davies KC, Lino-Coulon P, Colace C, Rafehi H, Auger N, Ansell BRE, van der Stelt I, Howell KB, Coutelier M, Amor DJ, Mundwiller E, Guillot-Noël L, Storey E, Gardner RJM, Wallis MJ, Brusco A, Corti O, Rötig A, Leventer RJ, Brice A, Delatycki MB, Stevanin G, Lockhart PJ, Durr A. Heterozygous PNPT1 variants cause spinocerebellar ataxia type 25. Ann Neurol 2022; 92:122-137. [PMID: 35411967 DOI: 10.1002/ana.26366] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 04/04/2022] [Accepted: 04/08/2022] [Indexed: 11/08/2022]
Abstract
OBJECTIVE Dominant spinocerebellar ataxias (SCA) are characterized by genetic heterogeneity. Some mapped and named loci remain without a causal gene identified. Here we applied next generation sequencing (NGS) to uncover the genetic etiology of the SCA25 locus. METHODS Whole-exome and whole-genome sequencing were performed in families linked to SCA25, including the French family in which the SCA25 locus was originally mapped. Whole exome sequence data was interrogated in a cohort of 796 ataxia patients of unknown aetiology. RESULTS The SCA25 phenotype spans a slowly evolving sensory and cerebellar ataxia, in most cases attributed to ganglionopathy. A pathogenic variant causing exon skipping was identified in the gene encoding Polyribonucleotide Nucleotidyltransferase PNPase 1 (PNPT1) located in the SCA25 linkage interval. A second splice variant in PNPT1 was detected in a large Australian family with a dominant ataxia also mapping to SCA25. An additional nonsense variant was detected in an unrelated individual with ataxia. Both nonsense and splice heterozygous variants result in premature stop codons, all located in the S1-domain of PNPase. In addition, an elevated type I interferon response was observed in blood from all affected heterozygous carriers tested. PNPase notably prevents the abnormal accumulation of double-stranded mtRNAs in the mitochondria and leakage into the cytoplasm, associated with triggering a type I interferon response. INTERPRETATION This study identifies PNPT1 as a new SCA gene, responsible for SCA25, and highlights biological links between alterations of mtRNA trafficking, interferonopathies and ataxia. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Mathieu Barbier
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Alessandra Pennisi
- Necker Hospital, APHP, Reference Center for Mitochondrial Diseases, Genetics Department, Institut Imagine, University of Paris, Paris, France.,Inserm UMR_S1163, Institut Imagine, Paris, France
| | - Maxime Jacoupy
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Rick M Tankard
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Claire Ewenczyk
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Kayli C Davies
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Melbourne, Victoria, 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Patricia Lino-Coulon
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Claire Colace
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Haloom Rafehi
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Nicolas Auger
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France.,Paris Sciences Lettres Research University, EPHE, Paris, France
| | - Brendan R E Ansell
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Ivo van der Stelt
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Victoria, 3010, Australia.,Donders Centre for Neuroscience, Faculty of Science, Radboud University, The Netherlands
| | - Katherine B Howell
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, 3010, Australia.,Department of Neurology, Royal Children's Hospital, Melbourne, Victoria, 3052, Australia.,Murdoch Children's Research Institute, Melbourne, Victoria, 3052, Australia
| | - Marie Coutelier
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France.,Paris Sciences Lettres Research University, EPHE, Paris, France
| | - David J Amor
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, 3010, Australia.,Murdoch Children's Research Institute, Melbourne, Victoria, 3052, Australia
| | - Emeline Mundwiller
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Lena Guillot-Noël
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France.,Paris Sciences Lettres Research University, EPHE, Paris, France
| | - Elsdon Storey
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, 3004, Australia
| | | | - Mathew J Wallis
- Clinical Genetics Service, Austin Health, Melbourne, Australia; Department of Medicine, University of Melbourne, Austin Health, Melbourne, Australia.,School of Medicine and Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, Torino, Italy
| | - Olga Corti
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Agnès Rötig
- Necker Hospital, APHP, Reference Center for Mitochondrial Diseases, Genetics Department, Institut Imagine, University of Paris, Paris, France.,Inserm UMR_S1163, Institut Imagine, Paris, France
| | - Richard J Leventer
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, 3010, Australia.,Department of Neurology, Royal Children's Hospital, Melbourne, Victoria, 3052, Australia.,Murdoch Children's Research Institute, Melbourne, Victoria, 3052, Australia
| | - Alexis Brice
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Martin B Delatycki
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Melbourne, Victoria, 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, 3010, Australia.,Victorian Clinical Genetics Service, Melbourne, 3052, Australia
| | - Giovanni Stevanin
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France.,Paris Sciences Lettres Research University, EPHE, Paris, France
| | - Paul J Lockhart
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Melbourne, Victoria, 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Alexandra Durr
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
| |
Collapse
|
3
|
Panda SP, Soni U. A review of dementia, focusing on the distinct roles of viral protein corona and MMP9 in dementia: Potential pharmacotherapeutic priorities. Ageing Res Rev 2022; 75:101560. [PMID: 35031512 DOI: 10.1016/j.arr.2022.101560] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 12/27/2021] [Accepted: 01/07/2022] [Indexed: 02/08/2023]
Abstract
Dementia, in particular, is a defining feature of Alzheimer's and Parkinson's diseases. Because of the combination of motor and cognitive impairments, Parkinson's disease dementia (PDD) has a greater impact on affected people than Alzheimer's disease dementia (ADD) and others. If one family member develops dementia, the other members will suffer greatly in terms of social and occupational functioning. Currently, no relevant treatment is available based on an examination of the absolute pathophysiology of dementia. As a result, our objective of current review encouraged to look for dementia pharmacotherapy based on their pathogenesis. We systematically searched electronic databases such as PubMed, Scopus, and ESCI for information on the pathophysiology of demetia, as well as their treatment with allopathic and herbal medications. By modulating intermediate proteins, oxidative stress, viral protein corona, and MMP9 are etiological factors that cause dementia. The pathophysiology of ADD was described by two hypotheses: the amyloid cascade hypothesis and the tau and tangle hypothesis. ADD is caused by an increase in amyloid-beta (Aβ) and neurofibrillary tangles in the cerebrum. The viral protein corona (VPC) is more contagious and helps to form amyloid-beta (Aβ) plaques and neurofibrillary tangles in the cerebrum. Thioredoxin interacting protein (TXNIP) inside the BBB encourages Aβ to become more engaged. PDD is caused by decreased or absent dopamine secretion from nerve cells in the substantia nigra, as well as PRKN gene deletion/duplication mutations, and shift in the PRKN-PACRG organisation, all of which are linked to ageing. This article discussed the pathophysiology of dementia, as well as a list of herbal medications that can easily cross the BBB and have a therapeutic effect on dementia.
Collapse
|
4
|
Li W, Huang Q, Zhang L, Liu H, Zhang D, Yuan S, Yap Y, Qu W, Shiang R, Song S, Hess RA, Zhang Z. A single amino acid mutation in the mouse MEIG1 protein disrupts a cargo transport system necessary for sperm formation. J Biol Chem 2021; 297:101312. [PMID: 34673028 PMCID: PMC8592874 DOI: 10.1016/j.jbc.2021.101312] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/08/2021] [Accepted: 10/09/2021] [Indexed: 11/22/2022] Open
Abstract
Mammalian spermatogenesis is a highly coordinated process that requires cooperation between specific proteins to coordinate diverse biological functions. For example, mouse Parkin coregulated gene (PACRG) recruits meiosis-expressed gene 1 (MEIG1) to the manchette during normal spermiogenesis. Here we mutated Y68 of MEIG1 using the CRISPR/cas9 system and examined the biological and physiological consequences in mice. All homozygous mutant males examined were completely infertile, and sperm count was dramatically reduced. The few developed sperm were immotile and displayed multiple abnormalities. Histological staining showed impaired spermiogenesis in these mutant mice. Immunofluorescent staining further revealed that this mutant MEIG1 was still present in the cell body of spermatocytes, but also that more MEIG1 accumulated in the acrosome region of round spermatids. The mutant MEIG1 and a cargo protein of the MEIG1/PACRG complex, sperm-associated antigen 16L (SPAG16L), were no longer found to be present in the manchette; however, localization of the PACRG component was not changed in the mutants. These findings demonstrate that Y68 of MEIG1 is a key amino acid required for PACRG to recruit MEIG1 to the manchette to transport cargo proteins during sperm flagella formation. Given that MEIG1 and PACRG are conserved in humans, small molecules that block MEIG1/PACRG interaction are likely ideal targets for the development of male contraconception drugs.
Collapse
Affiliation(s)
- Wei Li
- Department of Physiology, Wayne State University, Detroit, Michigan, USA
| | - Qian Huang
- Department of Physiology, Wayne State University, Detroit, Michigan, USA; Department of Occupational and Environmental Health, School of Public Health, Wuhan University of Science and Technology, Wuhan, Hubei, China
| | - Ling Zhang
- Department of Occupational and Environmental Health, School of Public Health, Wuhan University of Science and Technology, Wuhan, Hubei, China
| | - Hong Liu
- Department of Physiology, Wayne State University, Detroit, Michigan, USA; Department of Occupational and Environmental Health, School of Public Health, Wuhan University of Science and Technology, Wuhan, Hubei, China
| | - David Zhang
- School of Arts and Sciences, College of William and Mary, Williamsburg, Virginia, USA
| | - Shuo Yuan
- Department of Physiology, Wayne State University, Detroit, Michigan, USA; Department of Occupational and Environmental Health, School of Public Health, Wuhan University of Science and Technology, Wuhan, Hubei, China
| | - Yitian Yap
- Department of Physiology, Wayne State University, Detroit, Michigan, USA
| | - Wei Qu
- Department of Physiology, Wayne State University, Detroit, Michigan, USA; Department of Occupational and Environmental Health, School of Public Health, Wuhan University of Science and Technology, Wuhan, Hubei, China
| | - Rita Shiang
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Shizheng Song
- Department of Occupational and Environmental Health, School of Public Health, Wuhan University of Science and Technology, Wuhan, Hubei, China
| | - Rex A Hess
- Department of Comparative Biosciences, College of Veterinary Medicine, University of Illinois, Urbana, Illinois, USA
| | - Zhibing Zhang
- Department of Physiology, Wayne State University, Detroit, Michigan, USA; Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan, USA.
| |
Collapse
|
5
|
Khan N, Pelletier D, McAlear TS, Croteau N, Veyron S, Bayne AN, Black C, Ichikawa M, Khalifa AAZ, Chaaban S, Kurinov I, Brouhard G, Bechstedt S, Bui KH, Trempe JF. Crystal structure of human PACRG in complex with MEIG1 reveals roles in axoneme formation and tubulin binding. Structure 2021; 29:572-586.e6. [PMID: 33529594 DOI: 10.1016/j.str.2021.01.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 12/16/2020] [Accepted: 01/08/2021] [Indexed: 02/07/2023]
Abstract
The Parkin co-regulated gene protein (PACRG) binds at the inner junction between doublet microtubules of the axoneme, a structure found in flagella and cilia. PACRG binds to the adaptor protein meiosis expressed gene 1 (MEIG1), but how they bind to microtubules is unknown. Here, we report the crystal structure of human PACRG in complex with MEIG1. PACRG adopts a helical repeat fold with a loop that interacts with MEIG1. Using the structure of the axonemal doublet microtubule from the protozoan Chlamydomonas reinhardtii and single-molecule fluorescence microscopy, we propose that PACRG binds to microtubules while simultaneously recruiting free tubulin to catalyze formation of the inner junction. We show that the homologous PACRG-like protein also mediates dual tubulin interactions but does not bind MEIG1. Our findings establish a framework to assess the function of the PACRG family of proteins and MEIG1 in regulating axoneme assembly.
Collapse
Affiliation(s)
- Nimra Khan
- Department of Pharmacology & Therapeutics, McGill University, Montreal, QC, Canada; Centre de Recherche en Biologie Structurale - FRQS, McGill University, Montreal, QC, Canada
| | - Dylan Pelletier
- Department of Pharmacology & Therapeutics, McGill University, Montreal, QC, Canada; Centre de Recherche en Biologie Structurale - FRQS, McGill University, Montreal, QC, Canada
| | - Thomas S McAlear
- Department of Anatomy & Cell Biology, McGill University, Montreal, QC, Canada; Centre de Recherche en Biologie Structurale - FRQS, McGill University, Montreal, QC, Canada
| | - Nathalie Croteau
- Department of Pharmacology & Therapeutics, McGill University, Montreal, QC, Canada; Centre de Recherche en Biologie Structurale - FRQS, McGill University, Montreal, QC, Canada
| | - Simon Veyron
- Department of Pharmacology & Therapeutics, McGill University, Montreal, QC, Canada; Centre de Recherche en Biologie Structurale - FRQS, McGill University, Montreal, QC, Canada
| | - Andrew N Bayne
- Department of Pharmacology & Therapeutics, McGill University, Montreal, QC, Canada; Centre de Recherche en Biologie Structurale - FRQS, McGill University, Montreal, QC, Canada
| | - Corbin Black
- Department of Anatomy & Cell Biology, McGill University, Montreal, QC, Canada; Centre de Recherche en Biologie Structurale - FRQS, McGill University, Montreal, QC, Canada
| | - Muneyoshi Ichikawa
- Department of Anatomy & Cell Biology, McGill University, Montreal, QC, Canada
| | - Ahmad Abdelzaher Zaki Khalifa
- Department of Anatomy & Cell Biology, McGill University, Montreal, QC, Canada; Centre de Recherche en Biologie Structurale - FRQS, McGill University, Montreal, QC, Canada
| | - Sami Chaaban
- Department of Biology, McGill University, Montreal, QC, Canada; Centre de Recherche en Biologie Structurale - FRQS, McGill University, Montreal, QC, Canada
| | - Igor Kurinov
- NECAT, Cornell University, Department of Chemistry and Chemical Biology, Argonne, IL, USA
| | - Gary Brouhard
- Department of Biology, McGill University, Montreal, QC, Canada; Centre de Recherche en Biologie Structurale - FRQS, McGill University, Montreal, QC, Canada
| | - Susanne Bechstedt
- Department of Anatomy & Cell Biology, McGill University, Montreal, QC, Canada; Centre de Recherche en Biologie Structurale - FRQS, McGill University, Montreal, QC, Canada
| | - Khanh Huy Bui
- Department of Anatomy & Cell Biology, McGill University, Montreal, QC, Canada; Centre de Recherche en Biologie Structurale - FRQS, McGill University, Montreal, QC, Canada
| | - Jean-François Trempe
- Department of Pharmacology & Therapeutics, McGill University, Montreal, QC, Canada; Centre de Recherche en Biologie Structurale - FRQS, McGill University, Montreal, QC, Canada.
| |
Collapse
|
6
|
Ludwig-Słomczyńska AH, Seweryn MT, Kapusta P, Pitera E, Mantaj U, Cyganek K, Gutaj P, Dobrucka Ł, Wender-Ożegowska E, Małecki MT, Wołkow PP. The transcriptome-wide association search for genes and genetic variants which associate with BMI and gestational weight gain in women with type 1 diabetes. Mol Med 2021; 27:6. [PMID: 33472578 PMCID: PMC7818927 DOI: 10.1186/s10020-020-00266-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 12/30/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Clinical data suggest that BMI and gestational weight gain (GWG) are strongly interconnected phenotypes; however, the genetic basis of the latter is rather unclear. Here we aim to find genes and genetic variants which influence BMI and/or GWG. METHODS We have genotyped 316 type 1 diabetics using Illumina Infinium Omni Express Exome-8 v1.4 arrays. The GIANT, ARIC and T2D-GENES summary statistics were used for TWAS (performed with PrediXcan) in adipose tissue. Next, the analysis of association of imputed expression with BMI in the general and diabetic cohorts (Analysis 1 and 2) or GWG (Analysis 3 and 4) was performed, followed by variant association analysis (1 Mb around identified loci) with the mentioned phenotypes. RESULTS In Analysis 1 we have found 175 BMI associated genes and 19 variants (p < 10-4) which influenced GWG, with the strongest association for rs11465293 in CCL24 (p = 3.18E-06). Analysis 2, with diabetes included in the model, led to discovery of 1812 BMI associated loci and 207 variants (p < 10-4) influencing GWG, with the strongest association for rs9690213 in PODXL (p = 9.86E-07). In Analysis 3, among 648 GWG associated loci, 2091 variants were associated with BMI (FDR < 0.05). In Analysis 4, 7 variants in GWG associated loci influenced BMI in the ARIC cohort. CONCLUSIONS Here, we have shown that loci influencing BMI might have an impact on GWG and GWG associated loci might influence BMI, both in the general and T1DM cohorts. The results suggest that both phenotypes are related to insulin signaling, glucose homeostasis, mitochondrial metabolism, ubiquitinoylation and inflammatory responses.
Collapse
Affiliation(s)
| | - Michał T Seweryn
- Center for Medical Genomics OMICRON, Jagiellonian University Medical College, Kraków, Poland
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Przemysław Kapusta
- Center for Medical Genomics OMICRON, Jagiellonian University Medical College, Kraków, Poland
| | - Ewelina Pitera
- Center for Medical Genomics OMICRON, Jagiellonian University Medical College, Kraków, Poland
| | - Urszula Mantaj
- Department of Reproduction, Poznan University of Medical Sciences, Poznan, Poland
| | - Katarzyna Cyganek
- Department of Metabolic Diseases, University Hospital Kraków, Kraków, Poland
- Department of Metabolic Diseases, Jagiellonian University Medical College, Kraków, Poland
| | - Paweł Gutaj
- Department of Reproduction, Poznan University of Medical Sciences, Poznan, Poland
| | - Łucja Dobrucka
- Department of Metabolic Diseases, University Hospital Kraków, Kraków, Poland
| | - Ewa Wender-Ożegowska
- Department of Reproduction, Poznan University of Medical Sciences, Poznan, Poland
| | - Maciej T Małecki
- Department of Metabolic Diseases, University Hospital Kraków, Kraków, Poland
- Department of Metabolic Diseases, Jagiellonian University Medical College, Kraków, Poland
| | - Paweł P Wołkow
- Center for Medical Genomics OMICRON, Jagiellonian University Medical College, Kraków, Poland.
| |
Collapse
|
7
|
Krishnan D, Menon RN, Gopala S. SHARPIN: Role in Finding NEMO and in Amyloid-Beta Clearance and Degradation (ABCD) Pathway in Alzheimer's Disease? Cell Mol Neurobiol 2021; 42:1267-1281. [PMID: 33400084 DOI: 10.1007/s10571-020-01023-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 11/28/2020] [Indexed: 12/11/2022]
Abstract
SHANK- associated RH domain-interacting protein (SHARPIN) is a multifunctional protein associated with numerous physiological functions and many diseases. The primary role of the protein as a LUBAC-dependent component in regulating the activation of the transcription factor NF-κB accounts to its role in inflammation and antiapoptosis. Hence, an alteration of SHARPIN expression or genetic mutations or polymorphisms leads to the alteration of the above-mentioned primary physiological functions contributing to inflammation-associated diseases and cancer, respectively. However, there are complications of targeting SHARPIN as a therapeutic approach, which arises from the wide-range of LUBAC-independent functions and yet unknown roles of SHARPIN including neuronal functions. The identification of SHARPIN as a postsynaptic protein and the emerging studies indicating its role in several neurodegenerative diseases including Alzheimer's disease suggests a strong role of SHARPIN in neuronal functioning. This review summarizes the functional roles of SHARPIN in normal physiology and disease pathogenesis and strongly suggests a need for concentrating more studies on identifying the unknown neuronal functions of SHARPIN and hence its role in neurodegenerative diseases.
Collapse
Affiliation(s)
- Dhanya Krishnan
- Department of Biochemistry, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, 695011, Kerala, India
| | - Ramsekhar N Menon
- Department of Neurology, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, 695011, Kerala, India
| | - Srinivas Gopala
- Department of Biochemistry, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, 695011, Kerala, India.
| |
Collapse
|
8
|
Quinn PMJ, Moreira PI, Ambrósio AF, Alves CH. PINK1/PARKIN signalling in neurodegeneration and neuroinflammation. Acta Neuropathol Commun 2020; 8:189. [PMID: 33168089 PMCID: PMC7654589 DOI: 10.1186/s40478-020-01062-w] [Citation(s) in RCA: 203] [Impact Index Per Article: 50.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 10/17/2020] [Indexed: 12/13/2022] Open
Abstract
Mutations in the PTEN-induced kinase 1 (PINK1) and Parkin RBR E3 ubiquitin-protein ligase (PARKIN) genes are associated with familial forms of Parkinson’s disease (PD). PINK1, a protein kinase, and PARKIN, an E3 ubiquitin ligase, control the specific elimination of dysfunctional or superfluous mitochondria, thus fine-tuning mitochondrial network and preserving energy metabolism. PINK1 regulates PARKIN translocation in impaired mitochondria and drives their removal via selective autophagy, a process known as mitophagy. As knowledge obtained using different PINK1 and PARKIN transgenic animal models is being gathered, growing evidence supports the contribution of mitophagy impairment to several human pathologies, including PD and Alzheimer’s diseases (AD). Therefore, therapeutic interventions aiming to modulate PINK1/PARKIN signalling might have the potential to treat these diseases. In this review, we will start by discussing how the interplay of PINK1 and PARKIN signalling helps mediate mitochondrial physiology. We will continue by debating the role of mitochondrial dysfunction in disorders such as amyotrophic lateral sclerosis, Alzheimer’s, Huntington’s and Parkinson’s diseases, as well as eye diseases such as age-related macular degeneration and glaucoma, and the causative factors leading to PINK1/PARKIN-mediated neurodegeneration and neuroinflammation. Finally, we will discuss PINK1/PARKIN gene augmentation possibilities with a particular focus on AD, PD and glaucoma.
Collapse
|
9
|
Gao Y, Wilson GR, Stephenson SEM, Oulad-Abdelghani M, Charlet-Berguerand N, Bozaoglu K, McLean CA, Thomas PQ, Finkelstein DI, Lockhart PJ. Distribution of Parkinson's disease associated RAB39B in mouse brain tissue. Mol Brain 2020; 13:52. [PMID: 32228644 PMCID: PMC7106796 DOI: 10.1186/s13041-020-00584-7] [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: 12/03/2019] [Accepted: 03/10/2020] [Indexed: 12/22/2022] Open
Abstract
Pathogenic variants in the gene encoding the small GTPase Ras analogue in Brain 39b (RAB39B) are associated with early-onset parkinsonism. In this study we investigated the expression and localization of RAB39B (RNA and protein) in mouse brain tissue to gain a better understanding of its normal physiological function(s) and role in disease. We developed novel resources, including monoclonal antibodies directed against RAB39B and mice with Rab39b knockout, and performed real-time PCR and western blot analysis on whole brain lysates. To determine the spatial localization of Rab39b RNA and protein, we performed in-situ hybridization and immunohistochemistry on fresh frozen and fixed brain tissue. Our results show that RAB39B is localized throughout the cortex, hippocampus and substantia nigra of mice throughout postnatal life. We found high levels of RAB39B within MAP2 positive cortical and hippocampal neurons, and TH positive dopaminergic neurons in the substantia nigra pars compacta. Our studies support and extend current knowledge of the localization of RAB39B. We validate RAB39B as a neuron-enriched protein and demonstrate that it is present throughout the mouse cortex and hippocampus. Further, we observe high levels in the substantia nigra pars compacta, the brain region most affected in Parkinson’s disease pathology. The distribution of Rab39b is consistent with human disease associations with parkinsonism and cognitive impairment. We also describe and validate novel resources, including monoclonal antibodies directed against RAB39B and mice with Rab39b knockout, both of which are valuable tools for future studies of the molecular function of RAB39B.
Collapse
Affiliation(s)
- Yujing Gao
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, 50 Flemington Road, Parkville, Victoria, 3052, Australia.,Department of Paediatrics, The University of Melbourne, 30 Royal Parade, Parkville, Victoria, 3052, Australia
| | - Gabrielle R Wilson
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, 50 Flemington Road, Parkville, Victoria, 3052, Australia.,Department of Paediatrics, The University of Melbourne, 30 Royal Parade, Parkville, Victoria, 3052, Australia
| | - Sarah E M Stephenson
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, 50 Flemington Road, Parkville, Victoria, 3052, Australia.,Department of Paediatrics, The University of Melbourne, 30 Royal Parade, Parkville, Victoria, 3052, Australia
| | - Mustapha Oulad-Abdelghani
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964, CNRS UMR7104, Strasbourg University, 67400, Illkirch, France
| | - Nicolas Charlet-Berguerand
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964, CNRS UMR7104, Strasbourg University, 67400, Illkirch, France
| | - Kiymet Bozaoglu
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, 50 Flemington Road, Parkville, Victoria, 3052, Australia.,Department of Paediatrics, The University of Melbourne, 30 Royal Parade, Parkville, Victoria, 3052, Australia
| | - Catriona A McLean
- Anatomical Pathology, Alfred Hospital, Melbourne, Victoria, 3004, Australia
| | - Paul Q Thomas
- Robinson Research Institute and School of Medicine, University of Adelaide, Adelaide, SA, 5005, Australia
| | - David I Finkelstein
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, 30 Royal Parade, Parkville, Victoria, 3052, Australia
| | - Paul J Lockhart
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, 50 Flemington Road, Parkville, Victoria, 3052, Australia. .,Department of Paediatrics, The University of Melbourne, 30 Royal Parade, Parkville, Victoria, 3052, Australia.
| |
Collapse
|
10
|
Meschede J, Šadić M, Furthmann N, Miedema T, Sehr DA, Müller-Rischart AK, Bader V, Berlemann LA, Pilsl A, Schlierf A, Barkovits K, Kachholz B, Rittinger K, Ikeda F, Marcus K, Schaefer L, Tatzelt J, Winklhofer KF. The parkin-coregulated gene product PACRG promotes TNF signaling by stabilizing LUBAC. Sci Signal 2020; 13:13/617/eaav1256. [PMID: 32019898 DOI: 10.1126/scisignal.aav1256] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The Parkin-coregulated gene (PACRG), which encodes a protein of unknown function, shares a bidirectional promoter with Parkin (PRKN), which encodes an E3 ubiquitin ligase. Because PRKN is important in mitochondrial quality control and protection against stress, we tested whether PACRG also affected these pathways in various cultured human cell lines and in mouse embryonic fibroblasts. PACRG did not play a role in mitophagy but did play a role in tumor necrosis factor (TNF) signaling. Similarly to Parkin, PACRG promoted nuclear factor κB (NF-κB) activation in response to TNF. TNF-induced nuclear translocation of the NF-κB subunit p65 and NF-κB-dependent transcription were decreased in PACRG-deficient cells. Defective canonical NF-κB activation in the absence of PACRG was accompanied by a decrease in linear ubiquitylation mediated by the linear ubiquitin chain assembly complex (LUBAC), which is composed of the two E3 ubiquitin ligases HOIP and HOIL-1L and the adaptor protein SHARPIN. Upon TNF stimulation, PACRG was recruited to the activated TNF receptor complex and interacted with LUBAC components. PACRG functionally replaced SHARPIN in this context. In SHARPIN-deficient cells, PACRG prevented LUBAC destabilization, restored HOIP-dependent linear ubiquitylation, and protected cells from TNF-induced apoptosis. This function of PACRG in positively regulating TNF signaling may help to explain the association of PACRG and PRKN polymorphisms with an increased susceptibility to intracellular pathogens.
Collapse
Affiliation(s)
- Jens Meschede
- Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Maria Šadić
- Neurobiochemistry, Adolf Butenandt Institute, Ludwig Maximilians University, 80336 Munich, Germany
| | - Nikolas Furthmann
- Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Tim Miedema
- Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Dominik A Sehr
- Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | | | - Verian Bader
- Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Lena A Berlemann
- Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Anna Pilsl
- Neurobiochemistry, Adolf Butenandt Institute, Ludwig Maximilians University, 80336 Munich, Germany
| | - Anita Schlierf
- Neurobiochemistry, Adolf Butenandt Institute, Ludwig Maximilians University, 80336 Munich, Germany
| | - Katalin Barkovits
- Medizinisches Proteom-Center, Ruhr University Bochum, 44801 Bochum, Germany
| | - Barbara Kachholz
- Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | | | - Fumiyo Ikeda
- Institute of Molecular Biotechnology (IMBA), 1030 Vienna, Austria
| | - Katrin Marcus
- Medizinisches Proteom-Center, Ruhr University Bochum, 44801 Bochum, Germany
| | - Liliana Schaefer
- Pharmacenter Frankfurt/ZAFES, Institute for General Pharmacology and Toxicology, Goethe University, 60590 Frankfurt am Main, Germany
| | - Jörg Tatzelt
- Neurobiochemistry, Adolf Butenandt Institute, Ludwig Maximilians University, 80336 Munich, Germany.,Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Konstanze F Winklhofer
- Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801 Bochum, Germany. .,Neurobiochemistry, Adolf Butenandt Institute, Ludwig Maximilians University, 80336 Munich, Germany
| |
Collapse
|
11
|
Ogier JM, Lockhart PJ, Burt RA. Intravenously delivered aminoglycoside antibiotics, tobramycin and amikacin, are not ototoxic in mice. Hear Res 2020; 386:107870. [PMID: 31864009 DOI: 10.1016/j.heares.2019.107870] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 11/24/2019] [Accepted: 12/09/2019] [Indexed: 12/20/2022]
Abstract
Many drugs on the World Health Organization's list of critical medicines are ototoxic, destroying sensory hair cells within the ear. These drugs preserve life, but patients can experience side effects including permanent hearing loss and vestibular dysfunction. Aminoglycoside ototoxicity was first recognised 80 years ago. However, no preventative treatments have been developed. In order to develop such treatments, we must identify the factors driving hair cell death. In vivo, studies of cell death are typically conducted using mouse models. However, a robust model of aminoglycoside ototoxicity does not exist. Previous studies testing aminoglycoside delivery via intraperitoneal or subcutaneous injection have produced variable ototoxic effects in the mouse. As a result, surgical drug delivery to the rodent ear is often used to achieve ototoxicity. However, this technique does not accurately model clinical practice. In the clinic, aminoglycosides are administered to humans intravenously (i.v.). However, repeated i.v. delivery has not been reported in the mouse. This study evaluated whether repeated i.v. administration of amikacin or tobramycin would induce hearing loss. Daily i.v. injections over a two-week period were well tolerated and transient low frequency hearing loss was observed in the aminoglycoside treatment groups. However, the hearing changes observed did not mimic the high frequency patterns of hearing loss observed in humans. Our results indicate that the i.v. delivery of tobramycin or amikacin is not an effective technique for inducing ototoxicity in mice. This result is consistent with previously published reports indicating that the mouse cochlea is resistant to systemically delivered aminoglycoside ototoxicity.
Collapse
Affiliation(s)
- Jacqueline M Ogier
- Bruce Lefroy Centre, Murdoch Children's Research Institute, 50 Flemington Road, Parkville, VIC, 3052, Australia; Department of Paediatrics, University of Melbourne, Parkville, VIC, 3010, Australia.
| | - Paul J Lockhart
- Bruce Lefroy Centre, Murdoch Children's Research Institute, 50 Flemington Road, Parkville, VIC, 3052, Australia; Department of Paediatrics, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Rachel A Burt
- Bruce Lefroy Centre, Murdoch Children's Research Institute, 50 Flemington Road, Parkville, VIC, 3052, Australia; School of Biosciences, University of Melbourne, Parkville, VIC, 3010, Australia
| |
Collapse
|
12
|
Gao Y, Martínez-Cerdeño V, Hogan KJ, McLean CA, Lockhart PJ. Clinical and Neuropathological Features Associated With Loss of RAB39B. Mov Disord 2020; 35:687-693. [PMID: 31951675 DOI: 10.1002/mds.27951] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 11/10/2019] [Accepted: 11/25/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Pathogenic variants in the small GTPase Ras Analogue in Brain 39b (RAB39B) have been linked to the development of early-onset parkinsonism. The study was aimed at delineating the clinical and neuropathological features associated with a previously reported pathogenic variant in RAB39B (c.503C>A p.T168K) and testing for dysregulation of RAB39B in idiopathic PD. METHODS Clinical details of a male individual hemizygous for the T168K variant were collected by systematic review of medical records. Neuropathological studies of fixed brain tissue were performed and steady-state RAB39B levels were determined by western blot analysis. RESULTS Neuropathological examination showed extensive dopaminergic neuron loss, widespread Lewy pathology, and iron accumulation in the substantia nigra. Additional pathology was observed in the hippocampus and thalamus. Western blot analysis demonstrated that the T168K variant results in loss of RAB39B. In individuals with idiopathic PD (n = 10, 6 male/4 female), steady-state RAB39B was significantly reduced in the prefrontal cortex and substantia nigra. CONCLUSIONS T168K RAB39B is unstable in vivo and associated with dopaminergic neuron loss and Lewy pathology. Dysregulation of RAB39B in the prefrontal cortex and substantia nigra of individuals with idiopathic PD potentially implicates the protein more broadly in the pathological mechanisms underlying PD and related Lewy body disorders. © 2020 International Parkinson and Movement Disorder Society.
Collapse
Affiliation(s)
- Yujing Gao
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Pediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Verónica Martínez-Cerdeño
- Department of Pathology and Laboratory Medicine, UC Davis School of Medicine; Institute for Pediatric Regenerative Medicine and Shriners Hospitals for Children of Northern California, Davis, California, USA
- MIND Institute, UC Davis Medical Center, Davis, California, USA
| | - Kirk J Hogan
- Department of Anesthesiology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
- Wisconsin Alzheimer's Institute, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Catriona A McLean
- Anatomical Pathology, Alfred Hospital, Melbourne, Victoria, Australia
| | - Paul J Lockhart
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Pediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| |
Collapse
|
13
|
Amor DJ, Stephenson SE, Mustapha M, Mensah MA, Ockeloen CW, Lee WS, Tankard RM, Phelan DG, Shinawi M, de Brouwer AP, Pfundt R, Dowling C, Toler TL, Sutton VR, Agolini E, Rinelli M, Capolino R, Martinelli D, Zampino G, Dumić M, Reardon W, Shaw-Smith C, Leventer RJ, Delatycki MB, Kleefstra T, Mundlos S, Mortier G, Bahlo M, Allen NJ, Lockhart PJ. Pathogenic Variants in GPC4 Cause Keipert Syndrome. Am J Hum Genet 2019; 104:914-924. [PMID: 30982611 DOI: 10.1016/j.ajhg.2019.02.026] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 02/25/2019] [Indexed: 12/22/2022] Open
Abstract
Glypicans are a family of cell-surface heparan sulfate proteoglycans that regulate growth-factor signaling during development and are thought to play a role in the regulation of morphogenesis. Whole-exome sequencing of the Australian family that defined Keipert syndrome (nasodigitoacoustic syndrome) identified a hemizygous truncating variant in the gene encoding glypican 4 (GPC4). This variant, located in the final exon of GPC4, results in premature termination of the protein 51 amino acid residues prior to the stop codon, and in concomitant loss of functionally important N-linked glycosylation (Asn514) and glycosylphosphatidylinositol (GPI) anchor (Ser529) sites. We subsequently identified seven affected males from five additional kindreds with novel and predicted pathogenic variants in GPC4. Segregation analysis and X-inactivation studies in carrier females provided supportive evidence that the GPC4 variants caused the condition. Furthermore, functional studies of recombinant protein suggested that the truncated proteins p.Gln506∗ and p.Glu496∗ were less stable than the wild type. Clinical features of Keipert syndrome included a prominent forehead, a flat midface, hypertelorism, a broad nose, downturned corners of mouth, and digital abnormalities, whereas cognitive impairment and deafness were variable features. Studies of Gpc4 knockout mice showed evidence of the two primary features of Keipert syndrome: craniofacial abnormalities and digital abnormalities. Phylogenetic analysis demonstrated that GPC4 is most closely related to GPC6, which is associated with a bone dysplasia that has a phenotypic overlap with Keipert syndrome. Overall, we have shown that pathogenic variants in GPC4 cause a loss of function that results in Keipert syndrome, making GPC4 the third human glypican to be linked to a genetic syndrome.
Collapse
|