1
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Zeng Y, Sun ML, Liu D, Huang Y, Xie S, Zhao YX, Wu ZX, Liu Y, Ma G, Xie L, Dang YT, Hao LY, Wang QH, Wang HJ, Yang L, Xue ZY, Pan ZQ. Kv3.1 Interaction with UBR5 Is Required for Chronic Inflammatory Pain. Mol Neurobiol 2024:10.1007/s12035-024-04259-5. [PMID: 38865078 DOI: 10.1007/s12035-024-04259-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 05/22/2024] [Indexed: 06/13/2024]
Abstract
Chronic inflammatory pain caused by neuronal hyperactivity is a common and refractory disease. Kv3.1, a member of the Kv3 family of voltage-dependent K+ channels, is a major determinant of the ability of neurons to generate high-frequency action potentials. However, little is known about its role in chronic inflammatory pain. Here, we show that although Kv3.1 mRNA expression was unchanged, Kv3.1 protein expression was decreased in the dorsal spinal horn of mice after plantar injection of complete Freund's adjuvant (CFA), a mouse model of inflammatory pain. Upregulating Kv3.1 expression alleviated CFA-induced mechanical allodynia and heat hyperalgesia, whereas downregulating Kv3.1 induced nociception-like behaviors. Additionally, we found that ubiquitin protein ligase E3 component n-recognin 5 (UBR5), a key factor in the initiation of chronic pain, binds directly to Kv3.1 to drive its ubiquitin degradation. Intrathecal injection of the peptide TP-CH-401, a Kv3.1 ubiquitination motif sequence, rescued the decrease in Kv3.1 expression and Kv currents through competitive binding to UBR5, and consequently attenuated mechanical and thermal hypersensitivity. These findings demonstrate a previously unrecognized pathway of Kv3.1 abrogation by UBR5 and indicate that Kv3.1 is critically involved in the regulation of nociceptive behavior. Kv3.1 is thus a promising new target for treating inflammatory pain.
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Affiliation(s)
- Ying Zeng
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Tong Shan Road no. 209, Xuzhou, 221004, Jiangsu Province, China
| | - Meng-Lan Sun
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Tong Shan Road no. 209, Xuzhou, 221004, Jiangsu Province, China
| | - Di Liu
- Department of Anesthesiology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yue Huang
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Tong Shan Road no. 209, Xuzhou, 221004, Jiangsu Province, China
| | - Shan Xie
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Tong Shan Road no. 209, Xuzhou, 221004, Jiangsu Province, China
| | - Ya-Xuan Zhao
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Tong Shan Road no. 209, Xuzhou, 221004, Jiangsu Province, China
| | - Zi-Xuan Wu
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Tong Shan Road no. 209, Xuzhou, 221004, Jiangsu Province, China
| | - Ya Liu
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Tong Shan Road no. 209, Xuzhou, 221004, Jiangsu Province, China
| | - Gan Ma
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Tong Shan Road no. 209, Xuzhou, 221004, Jiangsu Province, China
| | - Ling Xie
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Tong Shan Road no. 209, Xuzhou, 221004, Jiangsu Province, China
| | - Yu-Tao Dang
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Tong Shan Road no. 209, Xuzhou, 221004, Jiangsu Province, China
| | - Ling-Yun Hao
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Tong Shan Road no. 209, Xuzhou, 221004, Jiangsu Province, China
| | - Qi-Hui Wang
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Tong Shan Road no. 209, Xuzhou, 221004, Jiangsu Province, China
| | - Hong-Jun Wang
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Tong Shan Road no. 209, Xuzhou, 221004, Jiangsu Province, China
| | - Li Yang
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Tong Shan Road no. 209, Xuzhou, 221004, Jiangsu Province, China
| | - Zhou-Ya Xue
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Tong Shan Road no. 209, Xuzhou, 221004, Jiangsu Province, China.
- Department of Anesthesiology, The Yancheng Clinical College of Xuzhou Medical University, The First People's Hospital of Yancheng, Yancheng, 224008, China.
| | - Zhi-Qiang Pan
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Tong Shan Road no. 209, Xuzhou, 221004, Jiangsu Province, China.
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2
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Clausen L, Okarmus J, Voutsinos V, Meyer M, Lindorff-Larsen K, Hartmann-Petersen R. PRKN-linked familial Parkinson's disease: cellular and molecular mechanisms of disease-linked variants. Cell Mol Life Sci 2024; 81:223. [PMID: 38767677 PMCID: PMC11106057 DOI: 10.1007/s00018-024-05262-8] [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: 02/27/2024] [Revised: 04/25/2024] [Accepted: 05/02/2024] [Indexed: 05/22/2024]
Abstract
Parkinson's disease (PD) is a common and incurable neurodegenerative disorder that arises from the loss of dopaminergic neurons in the substantia nigra and is mainly characterized by progressive loss of motor function. Monogenic familial PD is associated with highly penetrant variants in specific genes, notably the PRKN gene, where homozygous or compound heterozygous loss-of-function variants predominate. PRKN encodes Parkin, an E3 ubiquitin-protein ligase important for protein ubiquitination and mitophagy of damaged mitochondria. Accordingly, Parkin plays a central role in mitochondrial quality control but is itself also subject to a strict protein quality control system that rapidly eliminates certain disease-linked Parkin variants. Here, we summarize the cellular and molecular functions of Parkin, highlighting the various mechanisms by which PRKN gene variants result in loss-of-function. We emphasize the importance of high-throughput assays and computational tools for the clinical classification of PRKN gene variants and how detailed insights into the pathogenic mechanisms of PRKN gene variants may impact the development of personalized therapeutics.
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Affiliation(s)
- Lene Clausen
- Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Justyna Okarmus
- Department of Neurobiology Research, Institute of Molecular Medicine, University of Southern Denmark, 5230, Odense, Denmark
| | - Vasileios Voutsinos
- Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Morten Meyer
- Department of Neurobiology Research, Institute of Molecular Medicine, University of Southern Denmark, 5230, Odense, Denmark
- Department of Neurology, Odense University Hospital, 5000, Odense, Denmark
- Department of Clinical Research, BRIDGE, Brain Research Inter Disciplinary Guided Excellence, University of Southern Denmark, 5230, Odense, Denmark
| | - Kresten Lindorff-Larsen
- Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Rasmus Hartmann-Petersen
- Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, 2200, Copenhagen, Denmark.
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3
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Sharma K, Chib S, Gupta A, Singh R, Chalotra R. Interplay between α-synuclein and parkin genes: Insights of Parkinson's disease. Mol Biol Rep 2024; 51:586. [PMID: 38683365 DOI: 10.1007/s11033-024-09520-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 04/03/2024] [Indexed: 05/01/2024]
Abstract
Parkinson's disease (PD) is a complex and debilitating neurodegenerative disorder characterized by the progressive loss of dopaminergic neurons in the substantia nigra. The pathogenesis of PD is intimately linked to the roles of two key molecular players, α-synuclein (α-syn) and Parkin. Understanding the intricate interplay between α-syn and Parkin is essential for unravelling the molecular underpinnings of PD. Their roles in synaptic function and protein quality control underscore their significance in neuronal health. Dysregulation of these processes, as seen in PD, highlights the potential for targeted therapeutic strategies aimed at restoring normal protein homeostasis and mitigating neurodegeneration. Investigating the connections between α-syn, Parkin, and various pathological mechanisms provides insights into the complex web of factors contributing to PD pathogenesis and offers hope for the development of more effective treatments for this devastating neurological disorder. The present compilation provides an overview of their structures, regional and cellular locations, associations, physiological functions, and pathological roles in the context of PD.
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Affiliation(s)
- Kajal Sharma
- Department of Pharmacology, Central University of Punjab, Bathinda, 151401, India
| | - Shivani Chib
- Department of Pharmacology, Central University of Punjab, Bathinda, 151401, India
| | - Aniket Gupta
- Department of Pharmacology, Central University of Punjab, Bathinda, 151401, India
| | - Randhir Singh
- Department of Pharmacology, Central University of Punjab, Bathinda, 151401, India.
| | - Rishabh Chalotra
- Department of Pharmacology, Central University of Punjab, Bathinda, 151401, India
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4
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Markham BN, Ramnarine C, Kim S, Grever WE, Soto-Beasley AI, Heckman M, Ren Y, Osborne AC, Bhagwate AV, Liu Y, Wang C, Kim J, Wszolek ZK, Ross OA, Springer W, Fiesel FC. miRNA family miR-29 inhibits PINK1-PRKN dependent mitophagy via ATG9A. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.17.576122. [PMID: 38293184 PMCID: PMC10827147 DOI: 10.1101/2024.01.17.576122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Loss-of-function mutations in the genes encoding PINK1 and PRKN result in early-onset Parkinson disease (EOPD). Together the encoded enzymes direct a neuroprotective pathway that ensures the elimination of damaged mitochondria via autophagy. We performed a genome-wide high content imaging miRNA screen for inhibitors of the PINK1-PRKN pathway and identified all three members of the miRNA family 29 (miR-29). Using RNAseq we identified target genes and found that siRNA against ATG9A phenocopied the effects of miR-29 and inhibited the initiation of PINK1-PRKN mitophagy. Furthermore, we discovered two rare, potentially deleterious, missense variants (p.R631W and p.S828L) in our EOPD cohort and tested them experimentally in cells. While expression of wild-type ATG9A was able to rescue the effects of miR-29a, the EOPD-associated variants behaved like loss-of-function mutations. Together, our study validates miR-29 and its target gene ATG9A as novel regulators of mitophagy initiation. It further serves as proof-of-concept of finding novel, potentially disease-causing EOPD-linked variants specifically in mitophagy regulating genes. The nomination of genetic variants and biological pathways is important for the stratification and treatment of patients that suffer from devastating diseases, such as EOPD.
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Affiliation(s)
- Briana N Markham
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Chloe Ramnarine
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Songeun Kim
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | | | | | - Michael Heckman
- Division of Clinical Trials and Biostatistics, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Yingxue Ren
- Department of Quantitative Health Science, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Andrew C Osborne
- Department of Quantitative Health Science, Mayo Clinic, Rochester, MN 55905, USA
| | - Aditya V Bhagwate
- Department of Quantitative Health Science, Mayo Clinic, Rochester, MN 55905, USA
| | - Yuanhang Liu
- Department of Quantitative Health Science, Mayo Clinic, Rochester, MN 55905, USA
| | - Chen Wang
- Department of Quantitative Health Science, Mayo Clinic, Rochester, MN 55905, USA
| | - Jungsu Kim
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | | | - Owen A Ross
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
- Neuroscience PhD Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL 32224, USA
| | - Wolfdieter Springer
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
- Neuroscience PhD Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL 32224, USA
| | - Fabienne C Fiesel
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
- Neuroscience PhD Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL 32224, USA
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5
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Zanon A, Guida M, Lavdas AA, Corti C, Castelo Rueda MP, Negro A, Pramstaller PP, Domingues FS, Hicks AA, Pichler I. Intracellular delivery of Parkin-RING0-based fragments corrects Parkin-induced mitochondrial dysfunction through interaction with SLP-2. J Transl Med 2024; 22:59. [PMID: 38229174 DOI: 10.1186/s12967-024-04850-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 01/02/2024] [Indexed: 01/18/2024] Open
Abstract
BACKGROUND Loss-of-function mutations in the PRKN gene, encoding Parkin, are the most common cause of autosomal recessive Parkinson's disease (PD). We have previously identified mitoch ondrial Stomatin-like protein 2 (SLP-2), which functions in the assembly of respiratory chain proteins, as a Parkin-binding protein. Selective knockdown of either Parkin or SLP-2 led to reduced mitochondrial and neuronal function in neuronal cells and Drosophila, where a double knockdown led to a further worsening of Parkin-deficiency phenotypes. Here, we investigated the minimal Parkin region involved in the Parkin-SLP-2 interaction and explored the ability of Parkin-fragments and peptides from this minimal region to restore mitochondrial function. METHODS In fibroblasts, human induced pluripotent stem cell (hiPSC)-derived neurons, and neuroblastoma cells the interaction between Parkin and SLP-2 was investigated, and the Parkin domain responsible for the binding to SLP-2 was mapped. High resolution respirometry, immunofluorescence analysis and live imaging were used to analyze mitochondrial function. RESULTS Using a proximity ligation assay, we quantitatively assessed the Parkin-SLP-2 interaction in skin fibroblasts and hiPSC-derived neurons. When PD-associated PRKN mutations were present, we detected a significantly reduced interaction between the two proteins. We found a preferential binding of SLP-2 to the N-terminal part of Parkin, with a highest affinity for the RING0 domain. Computational modeling based on the crystal structure of Parkin protein predicted several potential binding sites for SLP-2 within the Parkin RING0 domain. Amongst these, three binding sites were observed to overlap with natural PD-causing missense mutations, which we demonstrated interfere substantially with the binding of Parkin to SLP-2. Finally, delivery of the isolated Parkin RING0 domain and a Parkin mini-peptide, conjugated to cell-permeant and mitochondrial transporters, rescued compromised mitochondrial function in Parkin-deficient neuroblastoma cells and hiPSC-derived neurons with endogenous, disease causing PRKN mutations. CONCLUSIONS These findings place further emphasis on the importance of the protein-protein interaction between Parkin and SLP-2 for the maintenance of optimal mitochondrial function. The possibility of restoring an abolished binding to SLP-2 by delivering the Parkin RING0 domain or the Parkin mini-peptide involved in this specific protein-protein interaction into cells might represent a novel organelle-specific therapeutic approach for correcting mitochondrial dysfunction in Parkin-linked PD.
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Affiliation(s)
- Alessandra Zanon
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Marianna Guida
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Alexandros A Lavdas
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Corrado Corti
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | | | - Alessandro Negro
- Department of Biomedical Sciences, University of Padova, Padua, Italy
| | - Peter P Pramstaller
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
- Department of Neurology, University Medical Center Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Francisco S Domingues
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Andrew A Hicks
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Irene Pichler
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy.
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6
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Zheng C, Nguyen KK, Vishnivetskiy SA, Gurevich VV, Gurevich EV. Arrestin-3 binds parkin and enhances parkin-dependent mitophagy. J Neurochem 2024. [PMID: 38196269 DOI: 10.1111/jnc.16043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 12/12/2023] [Accepted: 12/14/2023] [Indexed: 01/11/2024]
Abstract
Arrestins were discovered for their role in homologous desensitization of G-protein-coupled receptors (GPCRs). Later non-visual arrestins were shown to regulate several signaling pathways. Some of these pathways require arrestin binding to GPCRs, the regulation of others is receptor independent. Here, we demonstrate that arrestin-3 binds the E3 ubiquitin ligase parkin via multiple sites, preferentially interacting with its RING0 domain. Identification of the parkin domains involved suggests that arrestin-3 likely relieves parkin autoinhibition and/or stabilizes the enzymatically active "open" conformation of parkin. Arrestin-3 binding enhances ubiquitination by parkin of the mitochondrial protein mitofusin-1 and facilitates parkin-mediated mitophagy in HeLa cells. Furthermore, arrestin-3 and its mutant with enhanced parkin binding rescue mitofusin-1 ubiquitination and mitophagy in the presence of the Parkinson's disease-associated R275W parkin mutant, which is defective in both functions. Thus, modulation of parkin activity via arrestin-3 might be a novel strategy of anti-parkinsonian therapy.
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Affiliation(s)
- Chen Zheng
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee, USA
| | - Kevin K Nguyen
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee, USA
| | | | - Vsevolod V Gurevich
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee, USA
| | - Eugenia V Gurevich
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee, USA
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7
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Connelly EM, Frankel KS, Shaw GS. Parkin and mitochondrial signalling. Cell Signal 2023; 106:110631. [PMID: 36803775 DOI: 10.1016/j.cellsig.2023.110631] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 02/19/2023]
Abstract
Aging, toxic chemicals and changes to the cellular environment are sources of oxidative damage to mitochondria which contribute to neurodegenerative conditions including Parkinson's disease. To counteract this, cells have developed signalling mechanisms to identify and remove select proteins and unhealthy mitochondria to maintain homeostasis. Two important proteins that work in concert to control mitochondrial damage are the protein kinase PINK1 and the E3 ligase parkin. In response to oxidative stress, PINK1 phosphorylates ubiquitin present on proteins at the mitochondrial surface. This signals the translocation of parkin, accelerates further phosphorylation, and stimulates ubiquitination of outer mitochondrial membrane proteins such as Miro1/2 and Mfn1/2. The ubiquitination of these proteins is the key step needed to target them for degradation via the 26S proteasomal machinery or eliminate the entire organelle through mitophagy. This review highlights the signalling mechanisms used by PINK1 and parkin and presents several outstanding questions yet to be resolved.
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Affiliation(s)
- Elizabeth M Connelly
- Department of Biochemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Karling S Frankel
- Department of Biochemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Gary S Shaw
- Department of Biochemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada.
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8
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Fiesel FC, Fričová D, Hayes CS, Coban MA, Hudec R, Bredenberg JM, Broadway BJ, Markham BN, Yan T, Boneski PK, Fiorino G, Watzlawik JO, Hou X, McCarty AM, Lewis-Tuffin LJ, Zhong J, Madden BJ, Ordureau A, An H, Puschmann A, Wszolek ZK, Ross OA, Harper JW, Caulfield TR, Springer W. Substitution of PINK1 Gly411 modulates substrate receptivity and turnover. Autophagy 2022:1-22. [PMID: 36469690 DOI: 10.1080/15548627.2022.2151294] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The ubiquitin (Ub) kinase-ligase pair PINK1-PRKN mediates the degradation of damaged mitochondria by macroautophagy/autophagy (mitophagy). PINK1 surveils mitochondria and upon stress accumulates on the mitochondrial surface where it phosphorylates serine 65 of Ub to activate PRKN and to drive mitochondrial turnover. While loss of either PINK1 or PRKN is genetically linked to Parkinson disease (PD) and activating the pathway seems to have great therapeutic potential, there is no formal proof that stimulation of mitophagy is always beneficial. Here we used biochemical and cell biological methods to study single nucleotide variants in the activation loop of PINK1 to modulate the enzymatic function of this kinase. Structural modeling and in vitro kinase assays were used to investigate the molecular mechanism of the PINK1 variants. In contrast to the PD-linked PINK1G411S mutation that diminishes Ub kinase activity, we found that the PINK1G411A variant significantly boosted Ub phosphorylation beyond levels of PINK1 wild type. This resulted in augmented PRKN activation, mitophagy rates and increased viability after mitochondrial stress in midbrain-derived, gene-edited neurons. Mechanistically, the G411A variant stabilizes the kinase fold of PINK1 and transforms Ub to adopt the preferred, C-terminally retracted conformation for improved substrate turnover. In summary, we identify a critical role of residue 411 for substrate receptivity that may now be exploited for drug discovery to increase the enzymatic function of PINK1. The genetic substitution of Gly411 to Ala increases mitophagy and may be useful to confirm neuroprotection in vivo and might serve as a critical positive control during therapeutic development.Abbreviations: ATP: adenosine triphosphate; CCCP: carbonyl cyanide m-chlorophenyl hydrazone; Ub-CR: ubiquitin with C-terminally retracted tail; CTD: C-terminal domain (of PINK1); ELISA: enzyme-linked immunosorbent assay; HCI: high-content imaging; IB: immunoblot; IF: immunofluorescence; NPC: neuronal precursor cells; MDS: molecular dynamics simulation; PD: Parkinson disease; p-S65-Ub: ubiquitin phosphorylated at Ser65; RMSF: root mean scare fluctuation; TOMM: translocase of outer mitochondrial membrane; TVLN: ubiquitin with T66V and L67N mutation, mimics Ub-CR; Ub: ubiquitin; WT: wild-type.
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Affiliation(s)
- Fabienne C Fiesel
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.,Neuroscience PhD Program, Mayo Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL, USA
| | | | - Caleb S Hayes
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Mathew A Coban
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, USA
| | - Roman Hudec
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | | | | | - Tingxiang Yan
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Paige K Boneski
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Gabriella Fiorino
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.,Neuroscience PhD Program, Mayo Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL, USA
| | | | - Xu Hou
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | - Laura J Lewis-Tuffin
- Cytometry and Imaging Laboratory, Department of Research, Mayo Clinic, Jacksonville, FL, USA
| | - Jun Zhong
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Benjamin J Madden
- Proteomics Core, Medical Genome Facility, Mayo Clinic, Rochester, MN, USA
| | - Alban Ordureau
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Heeseon An
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Andreas Puschmann
- Department of Neurology, Lund University, Skane University Hospital, Sweden
| | | | - Owen A Ross
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.,Neuroscience PhD Program, Mayo Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL, USA
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Thomas R Caulfield
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.,Neuroscience PhD Program, Mayo Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL, USA.,Department of Neurosurgery, Mayo Clinic, Jacksonville, FL, USA
| | - Wolfdieter Springer
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.,Neuroscience PhD Program, Mayo Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL, USA
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9
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Systematic Functional Analysis of PINK1 and PRKN Coding Variants. Cells 2022; 11:cells11152426. [PMID: 35954270 PMCID: PMC9367835 DOI: 10.3390/cells11152426] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/22/2022] [Accepted: 07/27/2022] [Indexed: 11/17/2022] Open
Abstract
Loss of either PINK1 or PRKN causes an early onset Parkinson’s disease (PD) phenotype. Functionally, PINK1 and PRKN work together to mediate stress-activated mitochondrial quality control. Upon mitochondrial damage, PINK1, a ubiquitin kinase and PRKN, a ubiquitin ligase, decorate damaged organelles with phosphorylated ubiquitin for sequestration and degradation in lysosomes, a process known as mitophagy. While several genetic mutations are established to result in loss of mitophagy function, many others have not been extensively characterized and are of unknown significance. Here, we analyzed a set of twenty variants, ten in each gene, focusing on understudied variants mostly from the Parkinson’s progressive marker initiative, with sensitive assays to define potential functional deficits. Our results nominate specific rare genetic PINK1 and PRKN variants that cause loss of enzymatic function in line with a potential causative role for PD. Additionally, we identify several variants with intermediate phenotypes and follow up on two of them by gene editing midbrain-derived neuronal precursor cells. Thereof derived isogenic neurons show a stability defect of the rare PINK1 D525N mutation, while the common PINK1 Q115L substitution results in reduced kinase activity. Our strategy to analyze variants with sensitive functional readouts will help aid diagnostics and disease treatment in line with current genomic and therapeutic advances.
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10
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Selvam P, Jain A, Abbott J, Ahuja AS, Cheema A, Bruno KA, Atwal H, Forghani I, Caulfield T, Atwal PS. Molecular Modeling and Phenotypic Description of a Patient with a Novel Exonic Deletion of GALNS with Resultant Morquio Syndrome with Two Successful Pregnancies. Mol Syndromol 2022; 13:282-289. [PMID: 36158053 PMCID: PMC9421684 DOI: 10.1159/000519326] [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: 06/07/2020] [Accepted: 08/30/2021] [Indexed: 01/03/2023] Open
Abstract
In this report, we describe phenotypic features of a patient with mucopolysaccharidosis type IVA (Morquio syndrome) harboring a novel exon 1 deletion in GALNS with enzymatic confirmation consistent with Morquio syndrome. To our knowledge, this is the first reported case of this variant. Additionally, we protein modelled wild-type GALNS and the pathogenic variant with an exon 1 deletion for comparative analysis using statistical mechanics methods described herein. We demonstrate that, even when the protein is translated, the mutation would affect protein stability and function via homodimer interaction modifications. Lastly, given the patient's 2 successful pregnancies, data about the management of pregnancies in mucopolysaccharidoses are reviewed, and we discuss the management of pregnancy in patients with Morquio syndrome.
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Affiliation(s)
| | | | | | - Abhimanyu S. Ahuja
- Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, Florida, USA
| | | | | | | | - Irman Forghani
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida, USA
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11
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Angelopoulou E, Bougea A, Papageorgiou SG, Villa C. Psychosis in Parkinson's Disease: A Lesson from Genetics. Genes (Basel) 2022; 13:genes13061099. [PMID: 35741861 PMCID: PMC9222985 DOI: 10.3390/genes13061099] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/17/2022] [Accepted: 06/18/2022] [Indexed: 02/06/2023] Open
Abstract
Psychosis in Parkinson's disease (PDP) represents a common and debilitating condition that complicates Parkinson's disease (PD), mainly in the later stages. The spectrum of psychotic symptoms are heterogeneous, ranging from minor phenomena of mild illusions, passage hallucinations and sense of presence to severe psychosis consisting of visual hallucinations (and rarely, auditory and tactile or gustatory) and paranoid delusions. PDP is associated with increased caregiver stress, poorer quality of life for patients and carers, reduced survival and risk of institutionalization with a significant burden on the healthcare system. Although several risk factors for PDP development have been identified, such as aging, sleep disturbances, long history of PD, cognitive impairment, depression and visual disorders, the pathophysiology of psychosis in PD is complex and still insufficiently clarified. Additionally, several drugs used to treat PD can aggravate or even precipitate PDP. Herein, we reviewed and critically analyzed recent studies exploring the genetic architecture of psychosis in PD in order to further understand the pathophysiology of PDP, the risk factors as well as the most suitable therapeutic strategies.
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Affiliation(s)
- Efthalia Angelopoulou
- Department of Neurology, Eginition University Hospital, National and Kapodistrian University of Athens, 11528 Athens, Greece; (E.A.); (A.B.); (S.G.P.)
| | - Anastasia Bougea
- Department of Neurology, Eginition University Hospital, National and Kapodistrian University of Athens, 11528 Athens, Greece; (E.A.); (A.B.); (S.G.P.)
| | - Sokratis G. Papageorgiou
- Department of Neurology, Eginition University Hospital, National and Kapodistrian University of Athens, 11528 Athens, Greece; (E.A.); (A.B.); (S.G.P.)
| | - Chiara Villa
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
- Correspondence: ; Tel.: +39-02-6448-8138
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12
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Haslem L, Hays JM, Hays FA. p66Shc in Cardiovascular Pathology. Cells 2022; 11:cells11111855. [PMID: 35681549 PMCID: PMC9180016 DOI: 10.3390/cells11111855] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/30/2022] [Accepted: 06/01/2022] [Indexed: 02/06/2023] Open
Abstract
p66Shc is a widely expressed protein that governs a variety of cardiovascular pathologies by generating, and exacerbating, pro-apoptotic ROS signals. Here, we review p66Shc’s connections to reactive oxygen species, expression, localization, and discuss p66Shc signaling and mitochondrial functions. Emphasis is placed on recent p66Shc mitochondrial function discoveries including structure/function relationships, ROS identity and regulation, mechanistic insights, and how p66Shc-cyt c interactions can influence p66Shc mitochondrial function. Based on recent findings, a new p66Shc mitochondrial function model is also put forth wherein p66Shc acts as a rheostat that can promote or antagonize apoptosis. A discussion of how the revised p66Shc model fits previous findings in p66Shc-mediated cardiovascular pathology follows.
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Affiliation(s)
- Landon Haslem
- Biochemistry and Molecular Biology Department, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (L.H.); (J.M.H.)
| | - Jennifer M. Hays
- Biochemistry and Molecular Biology Department, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (L.H.); (J.M.H.)
| | - Franklin A. Hays
- Biochemistry and Molecular Biology Department, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (L.H.); (J.M.H.)
- Stephenson Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Harold Hamm Diabetes Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Correspondence:
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13
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Distinct phosphorylation signals drive acceptor versus free ubiquitin chain targeting by Parkin. Biochem J 2022; 479:751-766. [PMID: 35262643 PMCID: PMC9022993 DOI: 10.1042/bcj20210741] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 03/07/2022] [Accepted: 03/09/2022] [Indexed: 11/24/2022]
Abstract
The RBR E3 ligase parkin is recruited to the outer mitochondrial membrane (OMM) during oxidative stress where it becomes activated and ubiquitinates numerous proteins. Parkin activation involves binding of a phosphorylated ubiquitin (pUb), followed by phosphorylation of the Ubl domain in parkin, both mediated by the OMM kinase, PINK1. How an OMM protein is selected for ubiquitination is unclear. Parkin targeted OMM proteins have little structural or sequence similarity, with the commonality between substrates being proximity to the OMM. Here, we used chimeric proteins, tagged with ubiquitin (Ub), to evaluate parkin ubiquitination of mitochondrial acceptor proteins pre-ligated to Ub. We find that pUb tethered to the mitochondrial target proteins, Miro1 or CISD1, is necessary for parkin recruitment and essential for target protein ubiquitination. Surprisingly, phosphorylation of parkin is not necessary for the ubiquitination of either Miro1 or CISD1. Thus, parkin lacking its Ubl domain efficiently ubiquitinates a substrate tethered to pUb. Instead, phosphorylated parkin appears to stimulate free Ub chain formation. We also demonstrate that parkin ubiquitination of pUb-tethered substrates occurs on the substrate, rather than the pUb modification. We propose divergent parkin mechanisms whereby parkin-mediated ubiquitination of acceptor proteins is driven by binding to pre-existing pUb on the OMM protein and subsequent parkin phosphorylation triggers free Ub chain formation. This finding accounts for the broad spectrum of OMM proteins ubiquitinated by parkin and has implications on target design for therapeutics.
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14
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Guadagnolo D, Piane M, Torrisi MR, Pizzuti A, Petrucci S. Genotype-Phenotype Correlations in Monogenic Parkinson Disease: A Review on Clinical and Molecular Findings. Front Neurol 2021; 12:648588. [PMID: 34630269 PMCID: PMC8494251 DOI: 10.3389/fneur.2021.648588] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 03/08/2021] [Indexed: 12/30/2022] Open
Abstract
Parkinson disease (PD) is a complex neurodegenerative disorder, usually with multifactorial etiology. It is characterized by prominent movement disorders and non-motor symptoms. Movement disorders commonly include bradykinesia, rigidity, and resting tremor. Non-motor symptoms can include behavior disorders, sleep disturbances, hyposmia, cognitive impairment, and depression. A fraction of PD cases instead is due to Parkinsonian conditions with Mendelian inheritance. The study of the genetic causes of these phenotypes has shed light onto common pathogenetic mechanisms underlying Parkinsonian conditions. Monogenic Parkinsonisms can present autosomal dominant, autosomal recessive, or even X-linked inheritance patterns. Clinical presentations vary from forms indistinguishable from idiopathic PD to severe childhood-onset conditions with other neurological signs. We provided a comprehensive description of each condition, discussing current knowledge on genotype-phenotype correlations. Despite the broad clinical spectrum and the many genes involved, the phenotype appears to be related to the disrupted cell function and inheritance pattern, and several assumptions about genotype-phenotype correlations can be made. The interest in these assumptions is not merely speculative, in the light of novel promising targeted therapies currently under development.
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Affiliation(s)
- Daniele Guadagnolo
- Department of Experimental Medicine, Policlinico Umberto i Hospital, Sapienza University of Rome, Rome, Italy
| | - Maria Piane
- Department of Clinical and Molecular Medicine, Sapienza University of Rome, Rome, Italy.,Medical Genetics and Advanced Cell Diagnostics Unit, S. Andrea University Hospital, Rome, Italy
| | - Maria Rosaria Torrisi
- Department of Clinical and Molecular Medicine, Sapienza University of Rome, Rome, Italy.,Medical Genetics and Advanced Cell Diagnostics Unit, S. Andrea University Hospital, Rome, Italy
| | - Antonio Pizzuti
- Department of Experimental Medicine, Policlinico Umberto i Hospital, Sapienza University of Rome, Rome, Italy
| | - Simona Petrucci
- Department of Clinical and Molecular Medicine, Sapienza University of Rome, Rome, Italy.,Medical Genetics and Advanced Cell Diagnostics Unit, S. Andrea University Hospital, Rome, Italy
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15
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Bastien J, Menon S, Messa M, Nyfeler B. Molecular targets and approaches to restore autophagy and lysosomal capacity in neurodegenerative disorders. Mol Aspects Med 2021; 82:101018. [PMID: 34489092 DOI: 10.1016/j.mam.2021.101018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/18/2021] [Accepted: 08/25/2021] [Indexed: 01/18/2023]
Abstract
Autophagy is a catabolic process that promotes cellular fitness by clearing aggregated protein species, pathogens and damaged organelles through lysosomal degradation. The autophagic process is particularly important in the nervous system where post-mitotic neurons rely heavily on protein and organelle quality control in order to maintain cellular health throughout the lifetime of the organism. Alterations of autophagy and lysosomal function are hallmarks of various neurodegenerative disorders. In this review, we conceptualize some of the mechanistic and genetic evidence pointing towards autophagy and lysosomal dysfunction as a causal driver of neurodegeneration. Furthermore, we discuss rate-limiting pathway nodes and potential approaches to restore pathway activity, from autophagy initiation, cargo sequestration to lysosomal capacity.
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Affiliation(s)
- Julie Bastien
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Suchithra Menon
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Mirko Messa
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Beat Nyfeler
- Novartis Institutes for BioMedical Research, Basel, Switzerland.
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16
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Coban MA, Morrison J, Maharjan S, Hernandez Medina DH, Li W, Zhang YS, Freeman WD, Radisky ES, Le Roch KG, Weisend CM, Ebihara H, Caulfield TR. Attacking COVID-19 Progression Using Multi-Drug Therapy for Synergetic Target Engagement. Biomolecules 2021; 11:biom11060787. [PMID: 34071060 PMCID: PMC8224684 DOI: 10.3390/biom11060787] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/19/2021] [Accepted: 05/20/2021] [Indexed: 12/23/2022] Open
Abstract
COVID-19 is a devastating respiratory and inflammatory illness caused by a new coronavirus that is rapidly spreading throughout the human population. Over the past 12 months, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for COVID-19, has already infected over 160 million (>20% located in United States) and killed more than 3.3 million people around the world (>20% deaths in USA). As we face one of the most challenging times in our recent history, there is an urgent need to identify drug candidates that can attack SARS-CoV-2 on multiple fronts. We have therefore initiated a computational dynamics drug pipeline using molecular modeling, structure simulation, docking and machine learning models to predict the inhibitory activity of several million compounds against two essential SARS-CoV-2 viral proteins and their host protein interactors-S/Ace2, Tmprss2, Cathepsins L and K, and Mpro-to prevent binding, membrane fusion and replication of the virus, respectively. All together, we generated an ensemble of structural conformations that increase high-quality docking outcomes to screen over >6 million compounds including all FDA-approved drugs, drugs under clinical trial (>3000) and an additional >30 million selected chemotypes from fragment libraries. Our results yielded an initial set of 350 high-value compounds from both new and FDA-approved compounds that can now be tested experimentally in appropriate biological model systems. We anticipate that our results will initiate screening campaigns and accelerate the discovery of COVID-19 treatments.
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Affiliation(s)
- Mathew A. Coban
- Department of Cancer Biology, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL 32224, USA; (M.A.C.); (E.S.R.)
| | - Juliet Morrison
- Department of Microbiology and Plant Pathology, University of California, 900 University, Riverside, CA 92521, USA;
| | - Sushila Maharjan
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 65 Landsdowne St, Cambridge, MA 02139, USA; (S.M.); (D.H.H.M.); (W.L.); (Y.S.Z.)
| | - David Hyram Hernandez Medina
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 65 Landsdowne St, Cambridge, MA 02139, USA; (S.M.); (D.H.H.M.); (W.L.); (Y.S.Z.)
| | - Wanlu Li
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 65 Landsdowne St, Cambridge, MA 02139, USA; (S.M.); (D.H.H.M.); (W.L.); (Y.S.Z.)
| | - Yu Shrike Zhang
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 65 Landsdowne St, Cambridge, MA 02139, USA; (S.M.); (D.H.H.M.); (W.L.); (Y.S.Z.)
| | - William D. Freeman
- Department of Neurology, Mayo Clinic, 4500 San Pablo South, Jacksonville, FL 32224, USA;
| | - Evette S. Radisky
- Department of Cancer Biology, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL 32224, USA; (M.A.C.); (E.S.R.)
| | - Karine G. Le Roch
- Department of Molecular, Cell and Systems Biology, University of California, 900 University, Riverside, CA 92521, USA;
| | - Carla M. Weisend
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN 55905, USA; (C.M.W.); (H.E.)
| | - Hideki Ebihara
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN 55905, USA; (C.M.W.); (H.E.)
| | - Thomas R. Caulfield
- Department of Cancer Biology, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL 32224, USA; (M.A.C.); (E.S.R.)
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
- Department of Quantitative Health Science, Division of Computational Biology, Mayo Clinic, Jacksonville, FL 32224, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN 55905, USA
- Department of Biochemistry & Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
- Correspondence: ; Tel.: +1-904-953-6072
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17
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Pitt AS, Buchanan SK. A Biochemical and Structural Understanding of TOM Complex Interactions and Implications for Human Health and Disease. Cells 2021; 10:cells10051164. [PMID: 34064787 PMCID: PMC8150904 DOI: 10.3390/cells10051164] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/01/2021] [Accepted: 05/07/2021] [Indexed: 12/15/2022] Open
Abstract
The central role mitochondria play in cellular homeostasis has made its study critical to our understanding of various aspects of human health and disease. Mitochondria rely on the translocase of the outer membrane (TOM) complex for the bulk of mitochondrial protein import. In addition to its role as the major entry point for mitochondrial proteins, the TOM complex serves as an entry pathway for viral proteins. TOM complex subunits also participate in a host of interactions that have been studied extensively for their function in neurodegenerative diseases, cardiovascular diseases, innate immunity, cancer, metabolism, mitophagy and autophagy. Recent advances in our structural understanding of the TOM complex and the protein import machinery of the outer mitochondrial membrane have made structure-based therapeutics targeting outer mitochondrial membrane proteins during mitochondrial dysfunction an exciting prospect. Here, we describe advances in understanding the TOM complex, the interactome of the TOM complex subunits, the implications for the development of therapeutics, and our understanding of the structure/function relationship between components of the TOM complex and mitochondrial homeostasis.
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18
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PGC-1s in the Spotlight with Parkinson's Disease. Int J Mol Sci 2021; 22:ijms22073487. [PMID: 33800548 PMCID: PMC8036867 DOI: 10.3390/ijms22073487] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 12/12/2022] Open
Abstract
Parkinson's disease is one of the most common neurodegenerative disorders worldwide, characterized by a progressive loss of dopaminergic neurons mainly localized in the substantia nigra pars compacta. In recent years, the detailed analyses of both genetic and idiopathic forms of the disease have led to a better understanding of the molecular and cellular pathways involved in PD, pointing to the centrality of mitochondrial dysfunctions in the pathogenic process. Failure of mitochondrial quality control is now considered a hallmark of the disease. The peroxisome proliferator-activated receptor gamma coactivator 1 (PGC-1) family acts as a master regulator of mitochondrial biogenesis. Therefore, keeping PGC-1 level in a proper range is fundamental to guarantee functional neurons. Here we review the major findings that tightly bond PD and PGC-1s, raising important points that might lead to future investigations.
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19
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Kamienieva I, Duszyński J, Szczepanowska J. Multitasking guardian of mitochondrial quality: Parkin function and Parkinson's disease. Transl Neurodegener 2021; 10:5. [PMID: 33468256 PMCID: PMC7816312 DOI: 10.1186/s40035-020-00229-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 12/30/2020] [Indexed: 12/27/2022] Open
Abstract
The familial form of Parkinson’s disease (PD) is linked to mutations in specific genes. The mutations in parkin are one of the most common causes of early-onset PD. Mitochondrial dysfunction is an emerging active player in the pathology of neurodegenerative diseases, because mitochondria are highly dynamic structures integrated with many cellular functions. Herein, we overview and discuss the role of the parkin protein product, Parkin E3 ubiquitin ligase, in the cellular processes related to mitochondrial function, and how parkin mutations can result in pathology in vitro and in vivo.
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Affiliation(s)
- Iryna Kamienieva
- Nencki Institute of Experimental Biology, Polish Academy of Science, 02-093, Warsaw, Poland
| | - Jerzy Duszyński
- Nencki Institute of Experimental Biology, Polish Academy of Science, 02-093, Warsaw, Poland
| | - Joanna Szczepanowska
- Nencki Institute of Experimental Biology, Polish Academy of Science, 02-093, Warsaw, Poland.
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20
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Norris GA, Tsai ACH, Schneider KW, Wu YH, Caulfield T, Green AL. A novel, germline, deactivating CBL variant p.L493F alters domain orientation and is associated with multiple childhood cancers. Cancer Genet 2021; 254-255:18-24. [PMID: 33550024 DOI: 10.1016/j.cancergen.2021.01.008] [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: 06/15/2020] [Revised: 11/26/2020] [Accepted: 01/18/2021] [Indexed: 10/22/2022]
Abstract
CBL is a mammalian gene encoding the protein CBL, which is an E3 ubiquitin-protein ligase involved in cell signaling and protein ubiquitination. Pathogenic variants in this gene have been implicated in a number of human cancers, particularly acute myeloid leukemia (AML). Here, we present a 5-year-old male patient with a history of AML, diffuse midline glioma, and left brain lesion with histiocytic features. A variant of uncertain significance (VUS): p.L493F was detected in his CBL gene via clinical evaluation. Protein modeling predicts this variant to be pathogenic. Details of the clinical evaluation and modeling assay are discussed.
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Affiliation(s)
- Gregory A Norris
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Children's Hospital Colorado, Aurora, CO USA
| | - Anne Chun-Hui Tsai
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Children's Hospital Colorado, Aurora, CO USA
| | - Kami Wolfe Schneider
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Children's Hospital Colorado, Aurora, CO USA
| | - Yuan-Haw Wu
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Children's Hospital Colorado, Aurora, CO USA
| | - Thomas Caulfield
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA; Mayo Graduate School, Neurobiology of Disease, Mayo Clinic, Jacksonville, FL USA
| | - Adam L Green
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Children's Hospital Colorado, Aurora, CO USA; Morgan Adams Foundation Pediatric Brain Tumor Research Program, Aurora, CO USA.
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21
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Richter JE, Hines S, Selvam P, Atwal H, Farres H, Caulfield TR, Atwal PS. Clinical description & molecular modeling of novel MAX pathogenic variant causing pheochromocytoma in family, supports paternal parent-of-origin effect. Cancer Genet 2021; 252-253:107-110. [PMID: 33493868 DOI: 10.1016/j.cancergen.2021.01.004] [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: 06/22/2020] [Revised: 12/01/2020] [Accepted: 01/15/2021] [Indexed: 10/22/2022]
Abstract
The titular member of the MAX network of proteins, MYC-associated factor X (MAX), serves an important regulatory function in transcription of E-box genes associated with cell proliferation, differentiation, and apoptosis. Wild type MAX dimerizes with both MYC and MAD, both of which are members of the MAX network, and can promote or repress cell functions as needed. However, pathogenic variants in MAX are known to upset this balance, leading to uncontrolled oncogenic activity and disease phenotypes such as paragangliomas and pheochromocytomas. We report a 58-year-old male and his 32-year-old daughter, both of which have a history of pheochromocytoma and the unique nonsense MAX variant c.271C>T (p.Q91X). These individuals were diagnosed with pheochromocytomas in their early twenties that were later removed through corrective surgery. The father now presents with recurrent symptoms of hypertension, hyperhidrosis, and headaches, which accompany new pheochromocytomas of his remaining adrenal gland. Pathogenicity of this MAX variant is proven through molecular modeling. The case of this father-daughter pair supports both heritability of pheochromocytoma and the paternal parent-of-origin effect for MAX pathogenic variants.
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Affiliation(s)
- John E Richter
- Department of Clinical Genomics, Mayo Clinic, Jacksonville, FL 32224, USA
| | - S Hines
- Department of Medicine, Mayo Clinic, Jacksonville, FL, USA
| | - Pavalan Selvam
- Atwal Clinic: Genomic & Personalized Medicine, Palm Beach, FL 33480, USA
| | - Herjot Atwal
- Atwal Clinic: Genomic & Personalized Medicine, Palm Beach, FL 33480, USA
| | - Houssam Farres
- Department of Surgery, Mayo Clinic, Jacksonville, FL, USA
| | - Thomas R Caulfield
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA; Mayo Graduate School, Neurobiology of Disease, Mayo Clinic, Jacksonville, FL, USA
| | - Paldeep S Atwal
- Atwal Clinic: Genomic & Personalized Medicine, Palm Beach, FL 33480, USA.
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22
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Milanowski LM, Oshinaike O, Broadway BJ, Lindemann JA, Soto-Beasley AI, Walton RL, Hanna Al-Shaikh R, Strongosky AJ, Fiesel FC, Ross OA, Springer W, Ogun SA, Wszolek ZK. Early-Onset Parkinson Disease Screening in Patients From Nigeria. Front Neurol 2021; 11:594927. [PMID: 33519679 PMCID: PMC7841006 DOI: 10.3389/fneur.2020.594927] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 11/25/2020] [Indexed: 01/18/2023] Open
Abstract
Introduction: Nigeria is one of the most populated countries in the world; however, there is a scarcity of studies in patients with age-related neurodegenerative diseases, such as Parkinson disease (PD). The aim of this study was to screen patients with PD including a small cohort of early-onset PD (EOPD) cases from Nigeria for PRKN, PINK1, DJ1, SNCA multiplication, and LRRK2 p.G2019S. Methods: We assembled a cohort of 109 Nigerian patients with PD from the four main Nigerian tribes: Yoruba, Igbo, Edo, and Hausa. Fifteen cases [14 from the Yoruba tribe (93.3%)] had EOPD (defined as age-at-onset <50 years). All patients with EOPD were sequenced for the coding regions of PRKN, PINK1, and DJ1. Exon dosage analysis was performed with a multiplex ligation-dependent probe amplification assay, which also included a SNCA probe and LRRK2 p.G2019S. We screened for LRRK2 p.G2019S in the entire PD cohort using a genotyping assay. The PINK1 p.R501Q functional analysis was conducted. Results: In 15 patients with EOPD, 22 variants were observed [PRKN, 9 (40.9%); PINK1, 10 (45.5%); and DJ1, 3 (13.6%)]. Three (13.6%) rare, nonsynonymous variants were identified, but no homozygous or compound heterozygous carriers were found. No exonic rearrangements were present in the three genes, and no carriers of SNCA genomic multiplications or LRRK2 p.G2019S were identified. The PINK1 p.R501Q functional analysis revealed pathogenic loss of function. Conclusion: More studies on age-related neurodegenerative diseases are needed in sub-Saharan African countries, including Nigeria. Population-specific variation may provide insight into the genes involved in PD in the local population but may also contribute to larger studiesperformed in White and Asian populations.
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Affiliation(s)
- Lukasz M Milanowski
- Department of Neurology, Mayo Clinic Florida, Jacksonville, FL, United States.,Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, United States
| | - Olajumoke Oshinaike
- Department of Neurology, Lagos State University Teaching Hospital, Lagos, Nigeria
| | - Benjamin J Broadway
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, United States
| | - Jennifer A Lindemann
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, United States
| | | | - Ronald L Walton
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, United States
| | | | - Audrey J Strongosky
- Department of Neurology, Mayo Clinic Florida, Jacksonville, FL, United States
| | - Fabienne C Fiesel
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, United States.,Neuroscience PhD Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, United States
| | - Owen A Ross
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, United States.,Neuroscience PhD Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, United States.,Department of Clinical Genomics, Mayo Clinic Florida, Jacksonville, FL, United States
| | - Wolfdieter Springer
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, United States.,Neuroscience PhD Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, United States
| | | | - Zbigniew K Wszolek
- Department of Neurology, Mayo Clinic Florida, Jacksonville, FL, United States
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23
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Caulfield TR, Hayes KE, Qiu Y, Coban M, Seok Oh J, Lane AL, Yoshimitsu T, Hazlehurst L, Copland JA, Tun HW. A Virtual Screening Platform Identifies Chloroethylagelastatin A as a Potential Ribosomal Inhibitor. Biomolecules 2020; 10:E1407. [PMID: 33027969 PMCID: PMC7599554 DOI: 10.3390/biom10101407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 09/11/2020] [Accepted: 09/29/2020] [Indexed: 12/03/2022] Open
Abstract
Chloroethylagelastatin A (CEAA) is an analogue of agelastatin A (AA), a natural alkaloid derived from a marine sponge. It is under development for therapeutic use against brain tumors as it has excellent central nervous system (CNS) penetration and pre-clinical therapeutic activity against brain tumors. Recently, AA was shown to inhibit protein synthesis by binding to the ribosomal A-site. In this study, we developed a novel virtual screening platform to perform a comprehensive screening of various AA analogues showing that AA analogues with proven therapeutic activity including CEAA have significant ribosomal binding capacity whereas therapeutically inactive analogues show poor ribosomal binding and revealing structural fingerprint features essential for drug-ribosome interactions. In particular, CEAA was found to have greater ribosomal binding capacity than AA. Biological tests showed that CEAA binds the ribosome and contributes to protein synthesis inhibition. Our findings suggest that CEAA may possess ribosomal inhibitor activity and that our virtual screening platform may be a useful tool in discovery and development of novel ribosomal inhibitors.
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Affiliation(s)
- Thomas R. Caulfield
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL 32224, USA; (Y.Q.); (M.C.); (A.L.L.); (J.A.C.)
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
- Department of Neurosurgery, Mayo Clinic, Jacksonville, FL 32224, USA
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Karen E. Hayes
- Modulation Therapeutics, Inc., Morgantown, WV 26506, USA;
| | - Yushi Qiu
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL 32224, USA; (Y.Q.); (M.C.); (A.L.L.); (J.A.C.)
| | - Mathew Coban
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL 32224, USA; (Y.Q.); (M.C.); (A.L.L.); (J.A.C.)
| | - Joon Seok Oh
- Department of Chemistry, University of North Florida, Jacksonville, FL 32224, USA;
| | - Amy L. Lane
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL 32224, USA; (Y.Q.); (M.C.); (A.L.L.); (J.A.C.)
- Department of Chemistry, University of North Florida, Jacksonville, FL 32224, USA;
| | - Takehiko Yoshimitsu
- Division of Pharmaceutical Sciences, Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan;
| | - Lori Hazlehurst
- Department of Pharmaceutical Sciences, West Virginia University, Morgantown, WV 26506, USA;
| | - John A. Copland
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL 32224, USA; (Y.Q.); (M.C.); (A.L.L.); (J.A.C.)
| | - Han W. Tun
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL 32224, USA; (Y.Q.); (M.C.); (A.L.L.); (J.A.C.)
- Department of Hematology/Oncology, Mayo Clinic, Jacksonville, FL 32224, USA
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24
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Ahuja AS, Selvam P, Vadlamudi C, Chopra H, Richter JE, Macklin SK, Samreen A, Helmi H, Mohammaad AN, Hines S, Davila MC, Atwal PS, Caulfield TR. Genomics combined with a protein informatics platform to assess a novel pathogenic variant c.1024 A>G (p.K342E) in OPA1 in a patient with autosomal dominant optic atrophy. Ophthalmic Genet 2020; 41:563-569. [PMID: 32940104 DOI: 10.1080/13816810.2020.1814344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
BACKGROUND Autosomal Dominant Optic Atrophy (ADOA) is caused by mutations in the Optic Atrophy 1 Gene which disrupts the OPA1 protein. This disruption affects the normal function of the protein; impairs fusion of the mitochondrial inner membrane; and prevents normal OPA1 protein degradation. These events cause damage in retinal ganglion cells that could affect the patients with symptoms ranging from none to legally blind. MATERIALS AND METHODS Our study identifies a missense variant mutation, c.1024 A > G (p.K342E), in OPA1 gene causing ADOA. Diagnosed clinically in three family members and the presence of this mutation was confirmed in two members by genetic testing. Pathogenic variants in OPA1 impact the secondary protein structure and function by causing non-conservative amino acid substitutions. We also modeled this mutation and compared it to the wild type using statistical mechanics. RESULTS AND CONCLUSIONS The proband's pathogenic variant, c.1024 A > G (p.K342E), is located in the GTPase domain of OPA1 and causes changes in the protein structure by affecting the oligomerization pattern thus resulting in ADOA. Identifying the pathogenic potential of the missense mutations in the OPA1 gene using neoteric protein modeling techniques would help in the early detection of ADOA in patients who have family history of blindness. This action would help in providing early follow up, possible treatment in the future, and genetic counseling. Abbreviations: ADOA: Autosomal Dominant Optic Atrophy; CYCS: Caspase Activator Cytochrome C; OPA1: Optic Atrophy Gene 1; RGC: Retinal Ganglion Cells; VUS: Variant of Uncertain Significance.
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Affiliation(s)
- Abhimanyu S Ahuja
- Charles E. Schmidt College of Medicine, Florida Atlantic University , Boca Raton, Florida, USA
| | - Pavalan Selvam
- Department of Clinical Genomics, Atwal Clinic , Jacksonville, Florida, USA
| | - Charitha Vadlamudi
- Department of Clinical Genomics, Atwal Clinic , Jacksonville, Florida, USA
| | - Hayley Chopra
- Department of Molecular and Human Genetics, Baylor College of Medicine , Houston, Texas, USA
| | | | | | - Ayesha Samreen
- Department of Molecular and Human Genetics, Baylor College of Medicine , Houston, Texas, USA
| | - Haytham Helmi
- Department of Endocrinology, Mayo Clinic , Jacksonville, Florida, USA
| | - Ahmed N Mohammaad
- Department of Endocrinology, Mayo Clinic , Jacksonville, Florida, USA
| | - Stephanie Hines
- Department of Medicine, Division of Diagnostic & Consultative Medicine, Mayo Clinic , Jacksonville, Florida, USA
| | | | - Paldeep S Atwal
- Department of Clinical Genomics, Atwal Clinic , Jacksonville, Florida, USA
| | - Thomas R Caulfield
- Department of Neuroscience, Mayo Clinic , Jacksonville, Florida, USA.,Department of Neurosurgery, Mayo Clinic , Jacksonville, Florida, USA.,Department of Cancer Biology, Mayo Clinic , Jacksonville, Florida, USA.,Department of Health Sciences Research, Mayo Clinic , Jacksonville, Florida, USA
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25
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González-Casacuberta I, Juárez-Flores DL, Ezquerra M, Fucho R, Catalán-García M, Guitart-Mampel M, Tobías E, García-Ruiz C, Fernández-Checa JC, Tolosa E, Martí MJ, Grau JM, Fernández-Santiago R, Cardellach F, Morén C, Garrabou G. Mitochondrial and autophagic alterations in skin fibroblasts from Parkinson disease patients with Parkin mutations. Aging (Albany NY) 2020; 11:3750-3767. [PMID: 31180333 PMCID: PMC6594812 DOI: 10.18632/aging.102014] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 06/01/2019] [Indexed: 12/28/2022]
Abstract
PRKN encodes an E3-ubiquitin-ligase involved in multiple cell processes including mitochondrial homeostasis and autophagy. Previous studies reported alterations of mitochondrial function in fibroblasts from patients with PRKN mutation-associated Parkinson’s disease (PRKN-PD) but have been only conducted in glycolytic conditions, potentially masking mitochondrial alterations. Additionally, autophagy flux studies in this cell model are missing. We analyzed mitochondrial function and autophagy in PRKN-PD skin-fibroblasts (n=7) and controls (n=13) in standard (glucose) and mitochondrial-challenging (galactose) conditions. In glucose, PRKN-PD fibroblasts showed preserved mitochondrial bioenergetics with trends to abnormally enhanced mitochondrial respiration that, accompanied by decreased CI, may account for the increased oxidative stress. In galactose, PRKN-PD fibroblasts exhibited decreased basal/maximal respiration vs. controls and reduced mitochondrial CIV and oxidative stress compared to glucose, suggesting an inefficient mitochondrial oxidative capacity to meet an extra metabolic requirement. PRKN-PD fibroblasts presented decreased autophagic flux with reduction of autophagy substrate and autophagosome synthesis in both conditions. The alterations exhibited under neuron-like oxidative environment (galactose), may be relevant to the disease pathogenesis potentially explaining the increased susceptibility of dopaminergic neurons to undergo degeneration. Abnormal PRKN-PD phenotype supports the usefulness of fibroblasts to model disease and the view of PD as a systemic disease where molecular alterations are present in peripheral tissues.
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Affiliation(s)
- Ingrid González-Casacuberta
- Laboratory of Muscle Research and Mitochondrial Function, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona (UB), Department of Internal Medicine, Hospital Clínic of Barcelona (HCB), Barcelona 08036, Spain.,Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Raras (CIBERER), Madrid 28029, Spain
| | - Diana-Luz Juárez-Flores
- Laboratory of Muscle Research and Mitochondrial Function, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona (UB), Department of Internal Medicine, Hospital Clínic of Barcelona (HCB), Barcelona 08036, Spain.,Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Raras (CIBERER), Madrid 28029, Spain
| | - Mario Ezquerra
- Laboratory of Neurodegenerative Disorders, IDIBAPS, UB, Department of Neurology, HCB, Barcelona 08036, Spain.,CIBER de Enfermedades Neurodegenerativas (CIBERNED), Madrid 28031, Spain
| | - Raquel Fucho
- Cell Death and Proliferation, IDIBAPS, Consejo Superior Investigaciones Científicas (CSIC), Barcelona, Spain.,Liver Unit, HCB, IDIBAPS and CIBER de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Marc Catalán-García
- Laboratory of Muscle Research and Mitochondrial Function, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona (UB), Department of Internal Medicine, Hospital Clínic of Barcelona (HCB), Barcelona 08036, Spain.,Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Raras (CIBERER), Madrid 28029, Spain
| | - Mariona Guitart-Mampel
- Laboratory of Muscle Research and Mitochondrial Function, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona (UB), Department of Internal Medicine, Hospital Clínic of Barcelona (HCB), Barcelona 08036, Spain.,Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Raras (CIBERER), Madrid 28029, Spain
| | - Ester Tobías
- Laboratory of Muscle Research and Mitochondrial Function, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona (UB), Department of Internal Medicine, Hospital Clínic of Barcelona (HCB), Barcelona 08036, Spain.,Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Raras (CIBERER), Madrid 28029, Spain
| | - Carmen García-Ruiz
- Cell Death and Proliferation, IDIBAPS, Consejo Superior Investigaciones Científicas (CSIC), Barcelona, Spain.,Liver Unit, HCB, IDIBAPS and CIBER de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain.,USC Research Center for ALPD, Keck School of Medicine, Los Angeles, CA 90033, USA
| | - José Carlos Fernández-Checa
- Cell Death and Proliferation, IDIBAPS, Consejo Superior Investigaciones Científicas (CSIC), Barcelona, Spain.,Liver Unit, HCB, IDIBAPS and CIBER de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain.,USC Research Center for ALPD, Keck School of Medicine, Los Angeles, CA 90033, USA
| | - Eduard Tolosa
- Laboratory of Neurodegenerative Disorders, IDIBAPS, UB, Department of Neurology, HCB, Barcelona 08036, Spain.,CIBER de Enfermedades Neurodegenerativas (CIBERNED), Madrid 28031, Spain
| | - María-José Martí
- Laboratory of Neurodegenerative Disorders, IDIBAPS, UB, Department of Neurology, HCB, Barcelona 08036, Spain.,CIBER de Enfermedades Neurodegenerativas (CIBERNED), Madrid 28031, Spain
| | - Josep Maria Grau
- Laboratory of Muscle Research and Mitochondrial Function, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona (UB), Department of Internal Medicine, Hospital Clínic of Barcelona (HCB), Barcelona 08036, Spain.,Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Raras (CIBERER), Madrid 28029, Spain
| | - Rubén Fernández-Santiago
- Laboratory of Neurodegenerative Disorders, IDIBAPS, UB, Department of Neurology, HCB, Barcelona 08036, Spain.,CIBER de Enfermedades Neurodegenerativas (CIBERNED), Madrid 28031, Spain
| | - Francesc Cardellach
- Laboratory of Muscle Research and Mitochondrial Function, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona (UB), Department of Internal Medicine, Hospital Clínic of Barcelona (HCB), Barcelona 08036, Spain.,Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Raras (CIBERER), Madrid 28029, Spain
| | - Constanza Morén
- Laboratory of Muscle Research and Mitochondrial Function, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona (UB), Department of Internal Medicine, Hospital Clínic of Barcelona (HCB), Barcelona 08036, Spain.,Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Raras (CIBERER), Madrid 28029, Spain
| | - Glòria Garrabou
- Laboratory of Muscle Research and Mitochondrial Function, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona (UB), Department of Internal Medicine, Hospital Clínic of Barcelona (HCB), Barcelona 08036, Spain.,Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Raras (CIBERER), Madrid 28029, Spain
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26
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Examination of Molecular Effects of MYLK Deletion in a Patient with Extensive Aortic, Carotid, and Abdominal Dissections That Underlie the Genetic Dysfunction. Case Rep Med 2020; 2020:5108052. [PMID: 32655646 PMCID: PMC7327611 DOI: 10.1155/2020/5108052] [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: 11/02/2019] [Revised: 04/12/2020] [Accepted: 05/27/2020] [Indexed: 11/17/2022] Open
Abstract
We describe the phenotype of a patient with extensive aortic, carotid, and abdominal dissections. The proband was found to have a heterozygous deletion of exons 21-34 in MYLK, which is a rare finding, as deletions in this gene have been infrequently reported. We describe this finding following detection in a proband with an extensive history of aortic, carotid, and abdominal dissections. Neoteric molecular modeling techniques to help determine the impact of this deletion on protein function indicated loss of function due to lack of any kinase domain. We also provide the electrostatics calculations from the wild type and mutant variant. Through a combined multiomic approach of clinical, functional, and protein informatics, we arrive at a data fusion for determination of pathogenicity embedded within the genetic code for this particular genetic variant, which, as a platform, continues to broaden its scope across the field of variants of uncertain significance classification.
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27
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Hou X, Watzlawik JO, Fiesel FC, Springer W. Autophagy in Parkinson's Disease. J Mol Biol 2020; 432:2651-2672. [PMID: 32061929 PMCID: PMC7211126 DOI: 10.1016/j.jmb.2020.01.037] [Citation(s) in RCA: 185] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 01/24/2020] [Accepted: 01/30/2020] [Indexed: 02/07/2023]
Abstract
Impaired protein homeostasis and accumulation of damaged or abnormally modified protein are common disease mechanisms in many neurodegenerative disorders, including Parkinson's disease (PD). As one of the major degradation pathways, autophagy plays a pivotal role in maintaining effective turnover of proteins and damaged organelles in cells. Several decades of research efforts led to insights into the potential contribution of impaired autophagy machinery to α-synuclein accumulation and the degeneration of dopaminergic neurons, two major features of PD pathology. In this review, we summarize recent pathological, genetic, and mechanistic findings that link defective autophagy with PD pathogenesis in human patients, animals, and cellular models and discuss current challenges in the field.
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Affiliation(s)
- Xu Hou
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | | | - Wolfdieter Springer
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA; Neuroscience PhD Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA.
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28
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Yi W, MacDougall EJ, Tang MY, Krahn AI, Gan-Or Z, Trempe JF, Fon EA. The landscape of Parkin variants reveals pathogenic mechanisms and therapeutic targets in Parkinson's disease. Hum Mol Genet 2020; 28:2811-2825. [PMID: 30994895 DOI: 10.1093/hmg/ddz080] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 04/02/2019] [Accepted: 04/15/2019] [Indexed: 11/14/2022] Open
Abstract
Mutations in Parkin (PARK2), which encodes an E3 ubiquitin ligase implicated in mitophagy, are the most common cause of early-onset Parkinson's disease (EOPD). Hundreds of naturally occurring Parkin variants have been reported, both in Parkinson's disease (PD) patient and population databases. However, the effects of the majority of these variants on the function of Parkin and in PD pathogenesis remain unknown. Here we develop a framework for classification of the pathogenicity of Parkin variants based on the integration of clinical and functional evidence-including measures of mitophagy and protein stability and predictive structural modeling-and assess 51 naturally occurring Parkin variants accordingly. Surprisingly, only a minority of Parkin variants, even among those previously associated with PD, disrupted Parkin function. Moreover, a few of these naturally occurring Parkin variants actually enhanced mitophagy. Interestingly, impaired mitophagy in several of the most common pathogenic Parkin variants could be rescued both by naturally occurring (p.V224A) and structure-guided designer (p.W403A; p.F146A) hyperactive Parkin variants. Together, the findings provide a coherent framework to classify Parkin variants based on pathogenicity and suggest that several pathogenic Parkin variants represent promising targets to stratify patients for genotype-specific drug design.
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Affiliation(s)
- Wei Yi
- McGill Parkinson Program, Neurodegenerative Diseases Group, Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - Emma J MacDougall
- McGill Parkinson Program, Neurodegenerative Diseases Group, Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - Matthew Y Tang
- McGill Parkinson Program, Neurodegenerative Diseases Group, Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - Andrea I Krahn
- McGill Parkinson Program, Neurodegenerative Diseases Group, Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - Ziv Gan-Or
- Montreal Neurological Institute and Hospital, Department of Neurology and Neurosurgery, Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Jean-François Trempe
- Groupe de Recherche Axé sur la Structure des Protéines, Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada
| | - Edward A Fon
- McGill Parkinson Program, Neurodegenerative Diseases Group, Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
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29
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Characterization of a Pathogenic Variant in the ABCD1 Gene Through Protein Molecular Modeling. Case Rep Genet 2020; 2020:3256539. [PMID: 32047678 PMCID: PMC7003284 DOI: 10.1155/2020/3256539] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 11/19/2019] [Indexed: 11/18/2022] Open
Abstract
Background The ATP-binding cassette, subfamily D, member 1 (ABCD1) protein is a peroxisomal half-transporter that allows for very long chain fatty acid (VLCFA) degradation. Pathogenic variants of ABCD1 cause VLCFAs to build up in various tissues and bodily fluids, resulting in a disorder called X-linked adrenoleukodystrophy (X-ALD). This disorder is most commonly marked by adrenocortical insufficiency and high VLCFA concentration, and has varying levels of neurological involvement depending on phenotype. For example, the Addison-only form of X-ALD has no neurological impact, while the cerebral form of X-ALD often causes severe sensory loss, motor function impairment, cognitive decline, and death. Methods A newly characterized and suspected pathogenic variant in ABCD1 cause VLCFAs to build up in various tissues and bodily fluids, resulting in a disorder called X-linked adrenoleukodystrophy (X-ALD). This disorder is most commonly marked by adrenocortical insufficiency and high VLCFA concentration, and has varying levels of neurological involvement depending on phenotype. For example, the Addison-only form of X-ALD has no neurological impact, while the cerebral form of X-ALD often causes severe sensory loss, motor function impairment, cognitive decline, and death. Results A case of adult onset adrenomyeloneuropathy (AMN) and a novel ABCD1 cause VLCFAs to build up in various tissues and bodily fluids, resulting in a disorder called X-linked adrenoleukodystrophy (X-ALD). This disorder is most commonly marked by adrenocortical insufficiency and high VLCFA concentration, and has varying levels of neurological involvement depending on phenotype. For example, the Addison-only form of X-ALD has no neurological impact, while the cerebral form of X-ALD often causes severe sensory loss, motor function impairment, cognitive decline, and death. Conclusions Data fusion from multiple sources was combined in a comprehensive approach yielding an enriched assessment of the patient's disease and prognosis. Molecular modeling was performed on the variant to better characterize its clinical significance and confirm pathogenicity.
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30
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Siciliano RA, Mazzeo MF, Ferretta A, Pacelli C, Rosato A, Papa F, Scacco S, Papa S, Cocco T, Lippolis R. Decreased amount of vimentin N-terminal truncated proteolytic products in parkin-mutant skin fibroblasts. Biochem Biophys Res Commun 2020; 521:693-698. [PMID: 31699368 DOI: 10.1016/j.bbrc.2019.10.154] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 10/22/2019] [Indexed: 10/25/2022]
Abstract
Vimentin, a member of cytoskeleton intermediate filaments proteins, plays a critical role in cell structure and dynamics. The present proteomic study reveals reduced amount of six different lengths, N-terminal truncated proteolytic products of vimentin, in the primary skin fibroblasts from two unrelated PD patients, as compared to control fibroblasts. The decreased amount of N-terminal truncated forms of vimentin in parkin-mutant fibroblasts, could contribute to impairment of cellular function, potentially contributing to the pathogenesis of Parkinson disease.
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Affiliation(s)
| | | | - Anna Ferretta
- Department of Basic Medical Sciences, Neurosciences and Sense Organs University of Bari "Aldo Moro" Bari, Italy
| | - Consiglia Pacelli
- Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Antonio Rosato
- Department of Chemistry, University of Bari "Aldo Moro", Bari, Italy
| | - Francesco Papa
- Department of Basic Medical Sciences, Neurosciences and Sense Organs University of Bari "Aldo Moro" Bari, Italy
| | - Salvatore Scacco
- Department of Basic Medical Sciences, Neurosciences and Sense Organs University of Bari "Aldo Moro" Bari, Italy
| | - Sergio Papa
- Department of Basic Medical Sciences, Neurosciences and Sense Organs University of Bari "Aldo Moro" Bari, Italy; Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Tiziana Cocco
- Department of Basic Medical Sciences, Neurosciences and Sense Organs University of Bari "Aldo Moro" Bari, Italy.
| | - Rosa Lippolis
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council (CNR), Bari, Italy.
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31
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Parkin truncating variants result in a loss-of-function phenotype. Sci Rep 2019; 9:16150. [PMID: 31695088 PMCID: PMC6834586 DOI: 10.1038/s41598-019-52534-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 10/16/2019] [Indexed: 11/08/2022] Open
Abstract
Parkinson disease (PD) is the second most common neurodegenerative disorder. Most cases of PD are sporadic, while 5-10% have a known genetic basis. Variants in the PARK2 gene are the most frequent cause of autosomal recessive juvenile-onset PD. PARK2 encodes parkin, a multi-domain protein that functions as an ubiquitin E3 ligase. Numerous variants spanning all parkin domains have been identified, although the pathogenic relevance for several of those remains unclear. In this study, we aimed to functionally characterize two truncating parkin variants: N52Mfs*29, which is highly prevalent in the Portuguese and Spanish populations, and L358Rfs*77, recently identified in the Portuguese population. Our results indicate that both variants are prematurely degraded by the proteasome, even though proteins levels are still moderate. We also showed that they are aggregation-prone and lead to mislocalized parkin. Interestingly, the L358Rfs*77 variant is mislocalized to the nucleus, which was never reported for parkin variants. While N52Mfs*29 impaired self-ubiquitination activity, the L358Rfs*77 variant seemed to retain it. Both variants, however, fail to ubiquitinate p62 substrate and did not relocalize to depolarized mitochondria. Therefore, we conclude that parkin truncating variants cause loss of parkin function, thus showing their causative role in PD pathogenesis.
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Huang T, Gao CY, Wu L, Gong PY, Wang JZ, Tian YY, Zhang YD. Han Chinese family with early-onset Parkinson's disease carries novel compound heterozygous mutations in the PARK2 gene. Brain Behav 2019; 9:e01372. [PMID: 31386307 PMCID: PMC6749482 DOI: 10.1002/brb3.1372] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 05/19/2019] [Accepted: 07/01/2019] [Indexed: 01/12/2023] Open
Abstract
PURPOSE To identify deletions, duplications, and point mutations in 55 previously reported genes associated with Parkinson's disease (PD) and certain genes associated with tremor, spinocerebellar ataxia, and dystonia in a Han Chinese pedigree with early-onset Parkinson's disease (EOPD). PATIENTS AND METHODS Clinical examinations and genomic analyses were performed on six subjects belonging to three generations of a Han Chinese family. Target region capture and high-throughput sequencing were used to screen these genes associated with PD, tremor, spinocerebellar ataxia, and dystonia. The multiplex ligation-dependent probe amplification (MLPA) method was applied to detect rearrangements in PARK2 exons. Direct Sanger sequencing of samples from all subjects further verified the detected abnormal PRKRA, SPTBN2, and ATXN2 gene fragments. RESULTS Two family members were diagnosed with PD based on the clinical manifestations, imaging analyses. PARK2 gene heterozygous deletion of exon 3 and heterozygous duplication of exon 6 were identified in them (II-3 and 4). A single heterozygous deletion of exon 3 in PARK2 was detected in II-5 and III-10. A single duplication of exon 6 in PARK2 was detected in I1. Both the heterozygous mutation c.2834G>A (p. R945H) in exon 16 and the heterozygous mutation c.1924 C>T (p. R642W) in exon 14 of the SPTBN2 gene were identified in II-3, II-4, and III-10. The heterozygous mutation c.2989 C>T (p. R997X) in exon 24 of the ATXN2 gene was detected in II-4 and II-5, and the heterozygous mutation c.170 C>A (p. S57Y) in exon 2 of the PRKRA gene was detected in II-3, II-4, and III-10. Other mutations in some genes associated with PD, tremor, spinocerebellar ataxia, and dystonia were not detected. CONCLUSIONS Novel compound heterozygous mutations were identified in a Han Chinese pedigree and might represent a cause of EOPD.
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Affiliation(s)
- Ting Huang
- Department of Neurology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Chen-Yu Gao
- Department of Neurology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Liang Wu
- Department of Neurology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Peng-Yu Gong
- Department of Neurology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Ji-Zheng Wang
- Department of Endocrine and Metabolic Diseases, The First People's Hospital of Hefei, Anhui Medical University, Hefei, China
| | - You-Yong Tian
- Department of Neurology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Ying-Dong Zhang
- Department of Neurology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
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Hines SL, Mohammad AN, Jackson J, Macklin S, Caulfield TR. Integrative data fusion for comprehensive assessment of a novel CHEK2 variant using combined genomics, imaging, and functional-structural assessments via protein informatics. Mol Omics 2019; 15:59-66. [PMID: 30633282 DOI: 10.1039/c8mo00137e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The CHEK2 gene and its encoded protein Chk2 have a well-known role in cancers, especially those related to breast cancer mediated through the BRCA1 gene. Additionally Chk2 has a crucial role in DNA repair, apoptosis and the cell cycle, which is why classification of variants of uncertain significance (VUS) is an area highly sought for a better elucidation of the "genomic effect" that results. Because it can often take years before enough clinical data is accumulated, and the costly and expensive functional analysis for individual variants presents a significant hurdle, it is important to identify other tools to help aid in clarifying the impact of specific variants on a protein's function and eventually the patient's health outcome. Here we describe a newly identified CHEK2 variant and analyze with an integrated approach combining genomics (whole exome analysis), clinical study, radiographic imaging, and protein informatics to identify and predict the functional impact of the VUS on the protein's behavior and predicted impact on the related pathways. The observed and analyzed defects in the protein were consistent with the expected clinical effect. Here, we support the use of personalized protein modeling and informatics and further our goal of developing a large-scale protein deposition archive for all protein-level VUS.
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Affiliation(s)
- Stephanie L Hines
- Department of Clinical Genomics, Mayo Clinic, Jacksonville, FL 32224, USA
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Puschmann A, Fiesel FC, Caulfield TR, Hudec R, Ando M, Truban D, Hou X, Ogaki K, Heckman MG, James ED, Swanberg M, Jimenez-Ferrer I, Hansson O, Opala G, Siuda J, Boczarska-Jedynak M, Friedman A, Koziorowski D, Rudzinska-Bar M, Aasly JO, Lynch T, Mellick GD, Mohan M, Silburn PA, Sanotsky Y, Vilariño-Güell C, Farrer MJ, Chen L, Dawson VL, Dawson TM, Wszolek ZK, Ross OA, Springer W. Reply: Heterozygous PINK1 p.G411S in rapid eye movement sleep behaviour disorder. Brain 2019; 140:e33. [PMID: 28379295 DOI: 10.1093/brain/awx077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Andreas Puschmann
- Lund University, Department of Clinical Sciences Lund, Neurology, Sweden.,Department of Neurology, Skåne University Hospital, Sweden
| | - Fabienne C Fiesel
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | | | - Roman Hudec
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Maya Ando
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Dominika Truban
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Xu Hou
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Kotaro Ogaki
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Michael G Heckman
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Elle D James
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Maria Swanberg
- Lund University, Department of Experimental Medical Science, Lund, Sweden
| | | | - Oskar Hansson
- Clinical Memory Research Unit, Department of Clinical Sciences Malmö, Lund University, Sweden.,Memory Clinic, Skåne University Hospital, Malmö, Sweden
| | - Grzegorz Opala
- Department of Neurology, School of Medicine in Katowice, Medical University of Silesia, Katowice, Poland
| | - Joanna Siuda
- Department of Neurology, School of Medicine in Katowice, Medical University of Silesia, Katowice, Poland
| | | | | | | | - Monika Rudzinska-Bar
- Department of Neurology, School of Medicine in Katowice, Medical University of Silesia, Katowice, Poland
| | - Jan O Aasly
- Department of Neurology, St. Olav's Hospital, and Department of Neuroscience, Norwegian University of Science and Technology, Trondheim, Norway
| | - Timothy Lynch
- Dublin Neurological Institute at the Mater Misericordiae University Hospital, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - George D Mellick
- Eskitis Institute for Drug Discovery, Griffith University, Nathan, Queensland, Australia
| | - Megha Mohan
- Eskitis Institute for Drug Discovery, Griffith University, Nathan, Queensland, Australia
| | - Peter A Silburn
- Eskitis Institute for Drug Discovery, Griffith University, Nathan, Queensland, Australia.,University of Queensland, Asia-Pacific Centre for Neuromodulation, Centre for Clinical Research, Brisbane, Queensland, Australia
| | | | - Carles Vilariño-Güell
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Matthew J Farrer
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Li Chen
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Solomon H Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA 70130-2685, USA
| | - Valina L Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Solomon H Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA 70130-2685, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ted M Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Solomon H Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA 70130-2685, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | - Owen A Ross
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA.,School of Medicine and Medical Science, University College Dublin, Dublin, Ireland.,Mayo Graduate School, Neurobiology of Disease, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Wolfdieter Springer
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA.,Mayo Graduate School, Neurobiology of Disease, Mayo Clinic, Jacksonville, FL 32224, USA
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Genomic Observations of a Rare/Pathogenic SMAD3 Variant in Loeys⁻Dietz Syndrome 3 Confirmed by Protein Informatics and Structural Investigations. ACTA ACUST UNITED AC 2019; 55:medicina55050137. [PMID: 31096651 PMCID: PMC6571799 DOI: 10.3390/medicina55050137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 03/29/2019] [Accepted: 05/10/2019] [Indexed: 12/12/2022]
Abstract
Background and objectives: Loeys–Dietz syndrome 3, also known as aneurysms-–osteoarthritis syndrome, is an autosomal dominant genetic connective tissue disease caused by pathogenic variants in SMAD3, a transcription factor involved in TGF-β signaling. This disorder is characterized by early-onset osteoarthritis and arterial aneurysms. Common features include scoliosis, uvula abnormalities, striae, and velvety skin. Materials and Methods: The pathogenicity of a variant of uncertain significance in the SMAD3 gene was evaluated (variant c.220C > T) through personalized protein informatics and molecular studies. Results: The case of a 44-year-old male, who was originally presumed to have Marfan syndrome, is presented. An expanded gene panel determined the probable cause to be a variant in SMAD3, c.220C > T (p.R74W). His case was complicated by a history of stroke, but his phenotype was otherwise characteristic for Loeys–Dietz syndrome 3. Conclusion: This case emphasizes the importance of comprehensive genetic testing to evaluate patients for connective tissue disorders, as well as the potential benefit of utilizing a protein informatics platform for the assessment of variant pathogenicity.
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Hines SL, Richter JE, Mohammad AN, Mahim J, Atwal PS, Caulfield TR. Protein informatics combined with multiple data sources enriches the clinical characterization of novel TRPV4 variant causing an intermediate skeletal dysplasia. Mol Genet Genomic Med 2019; 7:e566. [PMID: 30693671 PMCID: PMC6418443 DOI: 10.1002/mgg3.566] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 11/02/2018] [Accepted: 12/02/2018] [Indexed: 01/19/2023] Open
Abstract
Background Transient receptor potential cation channel subfamily V member 4 (TRPV4) is an ion channel permeable to Ca2+ that is sensitive to physical, hormonal, and chemical stimuli. This protein is expressed in many cell types, including osteoclasts, chondrocytes, and sensory neurons. As such, pathogenic variants of this gene are associated with skeletal dysplasias and neuromuscular disorders. Pathogenesis of these phenotypes is not yet completely understood, but it is known that genotype–phenotype correlations for TRPV4 pathogenic variants often are not present. Methods Newly characterized, suspected pathogenic variant in TRPV4 was analyzed using protein informatics and personalized protein‐level molecular studies, genomic exome analysis, and clinical study. Results This statement is demonstrated in the family of our proband, a 47‐year‐old female having the novel c.2401A>G (p.K801E) variant of TRPV4. We discuss the common symptoms between the proband, her father, and her daughter, and compare her phenotype to known TRPV4‐associated skeletal dysplasias. Conclusions Protein informatics and molecular modeling are used to confirm the pathogenicity of the unique TRPV4 variant found in this family. Multiple data were combined in a comprehensive manner to give complete overall perspective on the patient disease and prognosis.
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Affiliation(s)
- Stephanie L Hines
- Department of Clinical Genomics, Mayo Clinic, Jacksonville, Florida.,Department of General Internal Medicine, Mayo Clinic, Jacksonville, Florida.,Center for Individualized Medicine, Mayo Clinic, Jacksonville, Florida
| | - John E Richter
- Department of Clinical Genomics, Mayo Clinic, Jacksonville, Florida
| | - Ahmed N Mohammad
- Department of Clinical Genomics, Mayo Clinic, Jacksonville, Florida
| | - Jain Mahim
- Department of Pediatrics, Johns Hopkins School of Medicine, Baltimore, Maryland
| | | | - Thomas R Caulfield
- Center for Individualized Medicine, Mayo Clinic, Jacksonville, Florida.,Department of Neuroscience, Mayo Clinic, Jacksonville, Florida.,Mayo Graduate School, Neurobiology of Disease, Mayo Clinic, Jacksonville, Florida
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Hanna Al Shaikh R, Caulfield T, Strongosky AJ, Matthew M, Jansen-West KR, Prudencio M, Fryer JD, Petrucelli L, Uitti RJ, Wszolek ZK. TRIO gene segregation in a family with cerebellar ataxia. Neurol Neurochir Pol 2018; 52:743-749. [DOI: 10.1016/j.pjnns.2018.09.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 08/28/2018] [Accepted: 09/12/2018] [Indexed: 11/25/2022]
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Zhu M, Cortese GP, Waites CL. Parkinson's disease-linked Parkin mutations impair glutamatergic signaling in hippocampal neurons. BMC Biol 2018; 16:100. [PMID: 30200940 PMCID: PMC6130078 DOI: 10.1186/s12915-018-0567-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 08/24/2018] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Parkinson's disease (PD)-associated E3 ubiquitin ligase Parkin is enriched at glutamatergic synapses, where it ubiquitinates multiple substrates, suggesting that its mutation/loss-of-function could contribute to the etiology of PD by disrupting excitatory neurotransmission. Here, we evaluate the impact of four common PD-associated Parkin point mutations (T240M, R275W, R334C, G430D) on glutamatergic synaptic function in hippocampal neurons. RESULTS We find that expression of these point mutants in cultured hippocampal neurons from Parkin-deficient and Parkin-null backgrounds alters NMDA and AMPA receptor-mediated currents and cell-surface levels and prevents the induction of long-term depression. Mechanistically, we demonstrate that Parkin regulates NMDA receptor trafficking through its ubiquitination of GluN1, and that all four mutants are impaired in this ubiquitinating activity. Furthermore, Parkin regulates synaptic AMPA receptor trafficking via its binding and retention of the postsynaptic scaffold Homer1, and all mutants are similarly impaired in this capacity. CONCLUSION Our findings demonstrate that pathogenic Parkin mutations disrupt glutamatergic synaptic transmission in hippocampal neurons by impeding NMDA and AMPA receptor trafficking. Such effects may contribute to the pathophysiology of PD in PARK2 patients.
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Affiliation(s)
- Mei Zhu
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032 USA
| | - Giuseppe P. Cortese
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032 USA
- Department of Psychiatry, Columbia University Medical Center, New York, NY USA
| | - Clarissa L. Waites
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032 USA
- Department of Neuroscience, Columbia University, New York, NY USA
- Waites Lab, 650 W. 168th St. Black Building 1210B, New York, NY 10032 USA
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Richter JE, Zimmermann MT, Blackburn PR, Mohammad AN, Klee EW, Pollard LM, Macmurdo CF, Atwal PS, Caulfield TR. Protein modeling and clinical description of a novel in-frame GLB1 deletion causing GM1 gangliosidosis type II. Mol Genet Genomic Med 2018; 6:1229-1235. [PMID: 30187681 PMCID: PMC6305665 DOI: 10.1002/mgg3.454] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 03/14/2018] [Accepted: 06/12/2018] [Indexed: 12/04/2022] Open
Abstract
Background Beta‐galactosidase‐1 (GLB1) is a lysosomal hydrolase that is responsible for breaking down specific glycoconjugates, particularly GM1 (monosialotetrahexosylganglioside). Pathogenic variants in GLB1 cause two different lysosomal storage disorders: GM1 gangliosidosis and mucopolysaccharidosis type IVB. In GM1 gangliosidosis, decreased β‐galactosidase‐1 enzymatic activity leads to the accumulation of GM1 gangliosides, predominantly within the CNS. We present a 22‐month‐old proband with GM1 gangliosidosis type II (late‐infantile form) in whom a novel homozygous in‐frame deletion (c.1468_1470delAAC, p.Asn490del) in GLB1 was detected. Methods We used an experimental protein structure of β‐galactosidase‐1 to generate a model of the p.Asn490del mutant and performed molecular dynamic simulations to determine whether this mutation leads to altered ligand positioning compared to the wild‐type protein. In addition, residual mutant enzyme activity in patient leukocytes was evaluated using a fluorometric assay. Results Molecular dynamics simulations showed the deletion to alter the catalytic site leading to misalignment of the catalytic residues and loss of collective motion within the model. We predict this misalignment will lead to impaired catalysis of β‐galactosidase‐1 substrates. Enzyme assays confirmed diminished GLB1 enzymatic activity (~3% of normal activity) in the proband. Conclusions We have described a novel, pathogenic in‐frame deletion of GLB1 in a patient with GM1 gangliosidosis type II.
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Affiliation(s)
- John E. Richter
- Department of Clinical GenomicsMayo ClinicJacksonvilleFlorida
- Center for Individualized MedicineMayo ClinicJacksonvilleFlorida
| | - Michael T. Zimmermann
- Division of Biomedical Statistics and InformaticsDepartment of Health Sciences ResearchMayo ClinicRochesterMinnesota
| | - Patrick R. Blackburn
- Division of Biomedical Statistics and InformaticsDepartment of Health Sciences ResearchMayo ClinicRochesterMinnesota
- Center for Individualized MedicineMayo ClinicRochesterMinnesota
- Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesota
| | | | - Eric W. Klee
- Department of Clinical GenomicsMayo ClinicJacksonvilleFlorida
- Division of Biomedical Statistics and InformaticsDepartment of Health Sciences ResearchMayo ClinicRochesterMinnesota
- Center for Individualized MedicineMayo ClinicRochesterMinnesota
- Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesota
| | - Laura M. Pollard
- Biochemical Genetics LaboratoryGreenwood Genetic CenterGreenwoodSouth Carolina
| | | | - Paldeep S. Atwal
- Department of Clinical GenomicsMayo ClinicJacksonvilleFlorida
- Center for Individualized MedicineMayo ClinicJacksonvilleFlorida
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Foote PK, Statsyuk AV. Monitoring PARKIN RBR Ubiquitin Ligase Activation States with UbFluor. ACTA ACUST UNITED AC 2018; 10:e45. [PMID: 30063295 DOI: 10.1002/cpch.45] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
PARKIN is a RING-Between-RING (RBR) E3 ligase, which ubiquitinates mitochondrial proteins in response to mitochondrial damage. Ser65 of PARKIN is phosphorylated by kinase PINK1 (pPARKIN), which causes partial PARKIN activation. PINK1 also phosphorylates Ser65 of ubiquitin (pUb), which further activates pPARKIN. Due to the lack of precise and quantitative assays to quantify the activity of PARKIN, there were many conflicting reports on the role of pUb as a PARKIN activator, whether S65E PARKIN is a true phosphomimetic of pPARKIN, and the effect of substrate of PARKIN turnover was also not known. This protocol provides a step-by-step guide on the use of the UbFluor probe to precisely quantitate changes in the activity of PARKIN in response to phosphorylation, allosteric activation by pUb, protein substrates, and activating structural mutations. These results pave the way to discover PARKIN activators and to precisely quantify the activity of other RBR E3s. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Peter K Foote
- Department of Chemistry, Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois
| | - Alexander V Statsyuk
- Department of Chemistry, Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois.,The Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, Texas
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Caulfield TR, Richter JE, Brown EE, Mohammad AN, Judge DP, Atwal PS. Protein molecular modeling techniques investigating novel TAB2 variant R347X causing cardiomyopathy and congenital heart defects in multigenerational family. Mol Genet Genomic Med 2018; 6:666-672. [PMID: 29700987 PMCID: PMC6081229 DOI: 10.1002/mgg3.401] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 03/07/2018] [Accepted: 03/09/2018] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Haploinsufficiency of TAB2 is known to cause congenital heart defects and cardiomyopathy due to its important roles in cardiovascular tissue, both during development and through adult life. We report a sibling pair displaying adult-onset cardiomyopathy, hypermobility, and mild myopia. Our proband, a 39-year-old male, presents only with the above symptoms, while his 36-year-old sister was also notable for a ventricular septal defect in her infancy. METHODS Whole-exome sequencing was utilized to identify the molecular basis of the phenotype found in two siblings. A molecular modeling technique that takes advantage of conformational sampling advances (Maxwell's demon molecular dynamics and Monte Carlo) were used to make a model of the mutant variant for comparative analytics to the wild-type. RESULTS Exome sequencing revealed a novel, heterogeneous pathogenic variant in TAB2, c.1039 C>T (p.R347X), that was present in both individuals. This pathogenic variant removes just over half the residues from the TAB2 protein and severely impacts its functional ability, which we describe in detail. CONCLUSIONS Analysis of the proband's family showed a history of cardiomyopathy, but no congenital heart defects or connective tissue disease. We highlight the heterogeneity in phenotype of TAB2 pathogenic variants and confirm the pathogenicity of this new variant through neoteric protein modeling techniques.
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Affiliation(s)
- Thomas R. Caulfield
- Department of NeuroscienceMayo ClinicJacksonvilleFLUSA
- Mayo Graduate SchoolNeurobiology of DiseaseMayo ClinicJacksonvilleFLUSA
| | | | - Emily E. Brown
- Center for Inherited Heart DiseaseJohns Hopkins UniversityBaltimoreMDUSA
| | | | - Daniel P. Judge
- Center for Inherited Heart DiseaseJohns Hopkins UniversityBaltimoreMDUSA
- Division of CardiologyMedical University of South CarolinaCharlestonSCUSA
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Ordureau A, Paulo JA, Zhang W, Ahfeldt T, Zhang J, Cohn EF, Hou Z, Heo JM, Rubin LL, Sidhu SS, Gygi SP, Harper JW. Dynamics of PARKIN-Dependent Mitochondrial Ubiquitylation in Induced Neurons and Model Systems Revealed by Digital Snapshot Proteomics. Mol Cell 2018; 70:211-227.e8. [PMID: 29656925 DOI: 10.1016/j.molcel.2018.03.012] [Citation(s) in RCA: 127] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 02/21/2018] [Accepted: 03/08/2018] [Indexed: 11/24/2022]
Abstract
Flux through kinase and ubiquitin-driven signaling systems depends on the modification kinetics, stoichiometry, primary site specificity, and target abundance within the pathway, yet we rarely understand these parameters and their spatial organization within cells. Here we develop temporal digital snapshots of ubiquitin signaling on the mitochondrial outer membrane in embryonic stem cell-derived neurons, and we model HeLa cell systems upon activation of the PINK1 kinase and PARKIN ubiquitin ligase by proteomic counting of ubiquitylation and phosphorylation events. We define the kinetics and site specificity of PARKIN-dependent target ubiquitylation, and we demonstrate the power of this approach to quantify pathway modulators and to mechanistically define the role of PARKIN UBL phosphorylation in pathway activation in induced neurons. Finally, through modulation of pS65-Ub on mitochondria, we demonstrate that Ub hyper-phosphorylation is inhibitory to mitophagy receptor recruitment, indicating that pS65-Ub stoichiometry in vivo is optimized to coordinate PARKIN recruitment via pS65-Ub and mitophagy receptors via unphosphorylated chains.
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Affiliation(s)
- Alban Ordureau
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Wei Zhang
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, and Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, ON M5S3E1, Canada
| | - Tim Ahfeldt
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02132, USA
| | - Jiuchun Zhang
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Erin F Cohn
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Zhonggang Hou
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Jin-Mi Heo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Lee L Rubin
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02132, USA
| | - Sachdev S Sidhu
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, and Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, ON M5S3E1, Canada
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
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Aguirre JD, Dunkerley KM, Lam R, Rusal M, Shaw GS. Impact of altered phosphorylation on loss of function of juvenile Parkinsonism-associated genetic variants of the E3 ligase parkin. J Biol Chem 2018. [PMID: 29530980 PMCID: PMC5925814 DOI: 10.1074/jbc.ra117.000605] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Autosomal recessive juvenile Parkinsonism (ARJP) is an inherited neurodegenerative disease in which 50% of affected individuals harbor mutations in the gene encoding the E3 ligase parkin. Parkin regulates the mitochondrial recycling pathway, which is induced by oxidative stress. In its native state, parkin is auto-inhibited by its N-terminal ubiquitin-like (Ubl) domain, which blocks the binding site for an incoming E2∼ubiquitin conjugate, needed for parkin's ubiquitination activity. Parkin is activated via phosphorylation of Ser-65 in its Ubl domain by PTEN-induced putative kinase 1 (PINK1) and a ubiquitin molecule phosphorylated at a position equivalent to Ser-65 in parkin. Here we have examined the underlying molecular mechanism of phosphorylation of parkin's Ubl domain carrying ARJP-associated substitutions and how altered phosphorylation modulates parkin activation and ubiquitination. We found that three substitutions in the Ubl domain (G12R, R33Q, and R42P) significantly decrease PINK1's ability to phosphorylate the Ubl domain. We noted that two basic loss-of-function substitutions (R33Q and R42P) are close to acidic patches in the proposed PINK1–parkin interface, indicating that ionic interactions at this site may be important for efficient parkin phosphorylation. Increased auto-ubiquitination with unique ubiquitin chain patterns was observed for two other Ubl domain substitutions (G12R and T55I), suggesting that these substitutions, along with phosphorylation, increase parkin degradation. Moreover, Ubl domain phosphorylation decreased its affinity for the potential effector protein ataxin-3, which edits ubiquitin chain building by parkin. Overall, our work provides a framework for the mechanisms of parkin's loss-of-function, indicating an interplay between ARJP-associated substitutions and phosphorylation of its Ubl domain.
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Affiliation(s)
- Jacob D Aguirre
- From the Department of Biochemistry, University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Karen M Dunkerley
- From the Department of Biochemistry, University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Rica Lam
- From the Department of Biochemistry, University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Michele Rusal
- From the Department of Biochemistry, University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Gary S Shaw
- From the Department of Biochemistry, University of Western Ontario, London, Ontario N6A 5C1, Canada
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Whole Exome Sequencing and Molecular Modeling of a Missense Variant in TNFAIP3 That Segregates with Disease in a Family with Chronic Urticaria and Angioedema. Case Rep Genet 2018; 2018:6968395. [PMID: 29682366 PMCID: PMC5842716 DOI: 10.1155/2018/6968395] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 01/18/2018] [Indexed: 11/17/2022] Open
Abstract
Chronic urticaria is a common condition characterized by recurrent hives lasting several weeks or months and is usually idiopathic. Approximately half of the individuals with chronic urticaria will present with episodes of angioedema that can be severe and debilitating. In this report, we describe a 47-year-old Hispanic male who presented initially for an evaluation of chronic hives following hospitalization due to hive-induced anaphylaxis. The individual had a history significant for urticaria and angioedema beginning in his early 30s. Interestingly, both the individual's 41-year-old sister and 12-year-old daughter were also affected with chronic urticaria and severe angioedema. Whole exome sequencing of the proband and several family members revealed a heterozygous variant of uncertain significance in exon 2 of TNFAIP3, denoted as c.65G>A (p.R22Q), in all affected members. Variants in TNFAIP3 have been associated with multiple autoimmune diseases, susceptibility to allergy and asthma, and periodic fever syndromes, suggesting that this variant could potentially play a role in disease.
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González-Casacuberta I, Morén C, Juárez-Flores DL, Esteve-Codina A, Sierra C, Catalán-García M, Guitart-Mampel M, Tobías E, Milisenda JC, Pont-Sunyer C, Martí MJ, Cardellach F, Tolosa E, Artuch R, Ezquerra M, Fernández-Santiago R, Garrabou G. Transcriptional alterations in skin fibroblasts from Parkinson's disease patients with parkin mutations. Neurobiol Aging 2018; 65:206-216. [PMID: 29501959 DOI: 10.1016/j.neurobiolaging.2018.01.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 01/23/2018] [Accepted: 01/26/2018] [Indexed: 11/29/2022]
Abstract
Mutations in the parkin gene (PRKN) are the most common cause of autosomal-recessive juvenile Parkinson's disease (PD). PRKN encodes an E3 ubiquitin ligase that is involved in multiple regulatory functions including proteasomal-mediated protein turnover, mitochondrial function, mitophagy, and cell survival. However, the precise molecular events mediated by PRKN mutations in PRKN-associated PD (PRKN-PD) remain unknown. To elucidate the cellular impact of parkin mutations, we performed an RNA sequencing study in skin fibroblasts from PRKN-PD patients carrying different PRKN mutations (n = 4) and genetically unrelated healthy subjects (n = 4). We identified 343 differentially expressed genes in PRKN-PD fibroblasts. Gene ontology and canonical pathway analysis revealed enrichment of differentially expressed genes in processes such as cell adhesion, cell growth, and amino acid and folate metabolism among others. Our findings indicate that PRKN mutations are associated with large global gene expression changes as observed in fibroblasts from PRKN-PD patients and support the view of PD as a systemic disease affecting also non-neural peripheral tissues such as the skin.
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Affiliation(s)
- Ingrid González-Casacuberta
- Laboratory of Muscle Research and Mitochondrial Function-CELLEX, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Faculty of Medicine and Health Sciences, University of Barcelona (UB), Department of Internal Medicine-Hospital Clínic of Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Constanza Morén
- Laboratory of Muscle Research and Mitochondrial Function-CELLEX, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Faculty of Medicine and Health Sciences, University of Barcelona (UB), Department of Internal Medicine-Hospital Clínic of Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Diana-Luz Juárez-Flores
- Laboratory of Muscle Research and Mitochondrial Function-CELLEX, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Faculty of Medicine and Health Sciences, University of Barcelona (UB), Department of Internal Medicine-Hospital Clínic of Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Anna Esteve-Codina
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Cristina Sierra
- Department of Clinical Biochemistry, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Marc Catalán-García
- Laboratory of Muscle Research and Mitochondrial Function-CELLEX, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Faculty of Medicine and Health Sciences, University of Barcelona (UB), Department of Internal Medicine-Hospital Clínic of Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Mariona Guitart-Mampel
- Laboratory of Muscle Research and Mitochondrial Function-CELLEX, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Faculty of Medicine and Health Sciences, University of Barcelona (UB), Department of Internal Medicine-Hospital Clínic of Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Ester Tobías
- Laboratory of Muscle Research and Mitochondrial Function-CELLEX, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Faculty of Medicine and Health Sciences, University of Barcelona (UB), Department of Internal Medicine-Hospital Clínic of Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - José César Milisenda
- Laboratory of Muscle Research and Mitochondrial Function-CELLEX, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Faculty of Medicine and Health Sciences, University of Barcelona (UB), Department of Internal Medicine-Hospital Clínic of Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Claustre Pont-Sunyer
- Laboratory of Parkison Disease and Other Neurodegenerative Movement Disorders: Clinical and Experimental Research-CELLEX, IDIBAPS, Faculty of Medicine and Health Sciences, UB, Department of Neurology-Hospital Clínic of Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - María José Martí
- Laboratory of Parkison Disease and Other Neurodegenerative Movement Disorders: Clinical and Experimental Research-CELLEX, IDIBAPS, Faculty of Medicine and Health Sciences, UB, Department of Neurology-Hospital Clínic of Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Francesc Cardellach
- Laboratory of Muscle Research and Mitochondrial Function-CELLEX, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Faculty of Medicine and Health Sciences, University of Barcelona (UB), Department of Internal Medicine-Hospital Clínic of Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Eduard Tolosa
- Laboratory of Parkison Disease and Other Neurodegenerative Movement Disorders: Clinical and Experimental Research-CELLEX, IDIBAPS, Faculty of Medicine and Health Sciences, UB, Department of Neurology-Hospital Clínic of Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Rafael Artuch
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain; Department of Clinical Biochemistry, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Mario Ezquerra
- Laboratory of Parkison Disease and Other Neurodegenerative Movement Disorders: Clinical and Experimental Research-CELLEX, IDIBAPS, Faculty of Medicine and Health Sciences, UB, Department of Neurology-Hospital Clínic of Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain.
| | - Rubén Fernández-Santiago
- Laboratory of Parkison Disease and Other Neurodegenerative Movement Disorders: Clinical and Experimental Research-CELLEX, IDIBAPS, Faculty of Medicine and Health Sciences, UB, Department of Neurology-Hospital Clínic of Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain.
| | - Glòria Garrabou
- Laboratory of Muscle Research and Mitochondrial Function-CELLEX, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Faculty of Medicine and Health Sciences, University of Barcelona (UB), Department of Internal Medicine-Hospital Clínic of Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.
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Harper JW, Ordureau A, Heo JM. Building and decoding ubiquitin chains for mitophagy. Nat Rev Mol Cell Biol 2018; 19:93-108. [DOI: 10.1038/nrm.2017.129] [Citation(s) in RCA: 323] [Impact Index Per Article: 53.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Marote A, Pomeshchik Y, Goldwurm S, Collin A, Lamas NJ, Pinto L, Salgado AJ, Roybon L. Generation of an induced pluripotent stem cell line (CSC-44) from a Parkinson's disease patient carrying a compound heterozygous mutation (c.823C>T and EX6 del) in the PARK2 gene. Stem Cell Res 2018; 27:90-94. [PMID: 29353703 DOI: 10.1016/j.scr.2018.01.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 12/13/2017] [Accepted: 01/03/2018] [Indexed: 11/17/2022] Open
Abstract
Mutations in the PARK2 gene, which encodes PARKIN, are the most frequent cause of autosomal recessive Parkinson's disease (PD). We report the generation of an induced pluripotent stem cell (iPSC) line from a 78-year-old patient carrying a compound heterozygous mutation (c.823C>T and EX6del) in the PARK2 gene. Skin fibroblasts were reprogrammed using the non-integrating Sendai virus technology to deliver OCT3/4, SOX2, c-MYC and KLF4 factors. The generated cell line CSC-44 exhibits expression of common pluripotency markers, in vitro differentiation into the three germ layers and normal karyotype. This iPSC line can be used to explore the association between PARK2 mutations and PD.
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Affiliation(s)
- Ana Marote
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal; ICVS/3B's, PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Yuriy Pomeshchik
- Stem Cell Laboratory for CNS Disease Modeling, Wallenberg Neuroscience Center, Department of Experimental Medical Science, BMC A10, Lund University, Lund, Sweden; Strategic Research Area MultiPark, Lund University, Lund, Sweden; Lund Stem Cell Center, Lund University, Lund, Sweden
| | | | - Anna Collin
- Department of Clinical Genetics and Pathology, Office for Medical Services, Division of Laboratory Medicine, Lund, Sweden
| | - Nuno J Lamas
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal; ICVS/3B's, PT Government Associate Laboratory, Braga/Guimarães, Portugal; Anatomic Pathology Department, Braga Hospital, Braga, Portugal
| | - Luísa Pinto
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal; ICVS/3B's, PT Government Associate Laboratory, Braga/Guimarães, Portugal; BnML, Behavioral and Molecular Lab, Braga, Portugal
| | - António J Salgado
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal; ICVS/3B's, PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Laurent Roybon
- Stem Cell Laboratory for CNS Disease Modeling, Wallenberg Neuroscience Center, Department of Experimental Medical Science, BMC A10, Lund University, Lund, Sweden; Strategic Research Area MultiPark, Lund University, Lund, Sweden; Lund Stem Cell Center, Lund University, Lund, Sweden.
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48
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Fiesel FC, James ED, Hudec R, Springer W. Mitochondrial targeted HSP90 inhibitor Gamitrinib-TPP (G-TPP) induces PINK1/Parkin-dependent mitophagy. Oncotarget 2017; 8:106233-106248. [PMID: 29290944 PMCID: PMC5739729 DOI: 10.18632/oncotarget.22287] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 10/13/2017] [Indexed: 12/31/2022] Open
Abstract
Loss-of-function mutations in PINK1 or PARKIN are associated with early-onset Parkinson's disease. Upon mitochondrial stress, PINK1 and Parkin together mediate a response that protects cells from the accumulation of harmful, damaged mitochondria. PINK1, the upstream kinase accumulates on the mitochondrial surface and recruits the E3 ubiquitin ligase Parkin on site to ubiquitylate substrate proteins. The joint activity of both to generate phosphorylated poly-ubiquitin chains on the mitochondrial surface induces the recruitment of autophagy receptors and eventually whole organelles are cleared by autophagy. While this pathway is generally accepted to occur upon chemical uncoupling of mitochondria, the (patho-) physiologic relevance has been questioned. However, few studies have indicated that PINK1 and Parkin are also activated upon accumulation of misfolded proteins in the mitochondrial lumen upon overexpression of ΔOTC (Ornithine transcarbamylase). Here, we used the mitochondrial targeted HSP90 inhibitor Gamitrinib-triphenylphosphonium (G-TPP), an anti-cancer agent, to chemically interfere with mitochondrial protein folding. G-TPP treatment induced PINK1 accumulation, ubiquitin phosphorylation at Ser65, Parkin activation and its recruitment to mitochondria was specific for mitochondrial HSP90 inhibition and largely independent of mitochondrial membrane depolarization. Mitophagy induction was observed by monitoring autophagy receptor recruitment and the mitoKeima reporter. Importantly, mitophagy was not only induced in cancer cells but also in primary human fibroblasts and thereof converted neurons. G-TPP treatment might represent a novel strategy to study PINK1 and Parkin-mediated mitochondrial quality control using a more physiologically relevant stress.
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Affiliation(s)
- Fabienne C. Fiesel
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
- Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL 32224, USA
| | - Elle D. James
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Roman Hudec
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Wolfdieter Springer
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
- Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL 32224, USA
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Yu L, Wang X, Chen H, Yan Z, Wang M, Li Y. Neurochemical and Behavior Deficits in Rats with Iron and Rotenone Co-treatment: Role of Redox Imbalance and Neuroprotection by Biochanin A. Front Neurosci 2017; 11:657. [PMID: 29217997 PMCID: PMC5703859 DOI: 10.3389/fnins.2017.00657] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 11/10/2017] [Indexed: 12/21/2022] Open
Abstract
Increasing evidences show that the etiology of Parkinson's disease (PD) is multifactorial. Studying the combined effect of several factors is becoming a hot topic in PD research. On one hand, iron is one of the essential trace metals for human body; on the other hand, iron may be involved in the etiopathogenesis of PD. In our present study, the rats with increased neonatal iron (120 μg/g bodyweight) supplementation were treated with rotenone (0.5 mg/kg) when they were aged to 14 weeks. We observed that iron and rotenone co-treatment induced significant behavior deficits (time-dependent) and striatal dopamine depletion in the male and female rats, while they did not do so when they were used alone. No significant change in striatal 5-hydroxytryptamine content was observed in the male and female rats with iron and rotenone co-treatment. Also, iron and rotenone co-treatment significantly decreased substantia nigra TH expression in the male rats. Furthermore, co-treatment with iron and rotenone significantly induced malondialdehyde increase and glutathione decrease in the substantia nigra of male and female rats. There was no significant change in cerebellar malondialdehyde and glutathione content of the rats co-treated with iron and rotenone. Interestingly, biochanin A significantly attenuated striatal dopamine depletion and improved behavior deficits (dose-dependently) in the male and female rats with iron and rotenone co-treatment. Biochanin A treatment also significantly alleviated substantia nigra TH expression reduction in the male rats co-treated with iron and rotenone. Finally, biochanin A significantly decreased malondialdehyde content and increased glutathione content in the substantia nigra of male and female rats with iron and rotenone co-treatment. Our results indicate that iron and rotenone co-treatment may result in aggravated neurochemical and behavior deficits through inducing redox imbalance and increased neonatal iron supplementation may participate in the etiopathogenesis of PD. Moreover, biochanin A may exert dopaminergic neuroprotection by maintaining redox balance.
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Affiliation(s)
- Lijia Yu
- Department of Neurology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xijin Wang
- Department of Neurology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hanqing Chen
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, China
| | - Zhiqiang Yan
- Shanghai Laboratory Animal Center, Chinese Academy of Sciences, Shanghai, China
| | - Meihua Wang
- Department of Neurology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yunhong Li
- Department of Neurology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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50
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Park S, Foote PK, Krist DT, Rice SE, Statsyuk AV. UbMES and UbFluor: Novel probes for ring-between-ring (RBR) E3 ubiquitin ligase PARKIN. J Biol Chem 2017; 292:16539-16553. [PMID: 28710279 DOI: 10.1074/jbc.m116.773200] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Revised: 07/03/2017] [Indexed: 12/30/2022] Open
Abstract
Ring-between-ring (RBR) E3 ligases have been implicated in autoimmune disorders and neurodegenerative diseases. The functions of many RBR E3s are poorly defined, and their regulation is complex, involving post-translational modifications and allosteric regulation with other protein partners. The functional complexity of RBRs, coupled with the complexity of the native ubiquitination reaction that requires ATP and E1 and E2 enzymes, makes it difficult to study these ligases for basic research and therapeutic purposes. To address this challenge, we developed novel chemical probes, ubiquitin C-terminal fluorescein thioesters UbMES and UbFluor, to qualitatively and quantitatively assess the activity of the RBR E3 ligase PARKIN in a simple experimental setup and in real time using fluorescence polarization. First, we confirmed that PARKIN does not require an E2 enzyme for substrate ubiquitination, lysine selection, and polyubiquitin chain formation. Second, we confirmed that UbFluor quantitatively detects naturally occurring activation states of PARKIN caused by Ser65 phosphorylation (pPARKIN) and phosphorylated ubiquitin (pUb). Third, we showed that both pUb and the ubiquitin-accepting substrate contribute to maximal pPARKIN ubiquitin conjugation turnover. pUb enhances the transthiolation step, whereas the substrate clears the pPARKIN∼Ub thioester intermediate. Finally, we established that UbFluor can quantify activation or inhibition of PARKIN by structural mutations. These results demonstrate the feasibility of using UbFluor for quantitative studies of the biochemistry of RBR E3s and for high-throughput screening of small-molecule activators or inhibitors of PARKIN and other RBR E3 ligases.
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Affiliation(s)
- Sungjin Park
- From the Department of Cell and Molecular Biology, Northwestern University, Chicago, Illinois 60611
| | - Peter K Foote
- the Chemistry of Life Processes Institute, Department of Chemistry, Northwestern University, Evanston, Illinois 60208, and
| | - David T Krist
- the Chemistry of Life Processes Institute, Department of Chemistry, Northwestern University, Evanston, Illinois 60208, and
| | - Sarah E Rice
- From the Department of Cell and Molecular Biology, Northwestern University, Chicago, Illinois 60611
| | - Alexander V Statsyuk
- the Chemistry of Life Processes Institute, Department of Chemistry, Northwestern University, Evanston, Illinois 60208, and .,the Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, Texas 77204-5037
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