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Liu S, Wei W, Wang P, Liu C, Jiang X, Li T, Li F, Wu Y, Chen S, Sun K, Xu R. LOF variants identifying candidate genes of laterality defects patients with congenital heart disease. PLoS Genet 2022; 18:e1010530. [PMID: 36459505 DOI: 10.1371/journal.pgen.1010530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 12/14/2022] [Accepted: 11/15/2022] [Indexed: 12/03/2022] Open
Abstract
Defects in laterality pattern can result in abnormal positioning of the internal organs during the early stages of embryogenesis, as manifested in heterotaxy syndrome and situs inversus, while laterality defects account for 3~7% of all congenital heart defects (CHDs). However, the pathogenic mechanism underlying most laterality defects remains unknown. In this study, we recruited 70 laterality defect patients with CHDs to identify candidate disease genes by exome sequencing. We then evaluated rare, loss-of-function (LOF) variants, identifying candidates by referring to previous literature. We chose TRIP11, DNHD1, CFAP74, and EGR4 as candidates from 776 LOF variants that met the initial screening criteria. After the variants-to-gene mapping, we performed function research on these candidate genes. The expression patterns and functions of these four candidate genes were studied by whole-mount in situ hybridization, gene knockdown, and gene rescue methods in zebrafish models. Among the four genes, trip11, dnhd1, and cfap74 morphant zebrafish displayed abnormalities in both cardiac looping and expression patterns of early signaling molecules, suggesting that these genes play important roles in the establishment of laterality patterns. Furthermore, we performed immunostaining and high-speed cilia video microscopy to investigate Kupffer's vesicle organogenesis and ciliogenesis of morphant zebrafish. Impairments of Kupffer's vesicle organogenesis or ciliogenesis were found in trip11, dnhd1, and cfap74 morphant zebrafish, which revealed the possible pathogenic mechanism of their LOF variants in laterality defects. These results highlight the importance of rare, LOF variants in identifying disease-related genes and identifying new roles for TRIP11, DNHD1, and CFAP74 in left-right patterning. Additionally, these findings are consistent with the complex genetics of laterality defects.
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Affiliation(s)
- Sijie Liu
- Department of Pediatric Cardiology, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Wei Wei
- Department of Pediatric Cardiology, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Pengcheng Wang
- Department of Pediatric Cardiology, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Chunjie Liu
- Department of Pediatric Cardiology, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xuechao Jiang
- Scientific Research Center, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Tingting Li
- Department of Pediatric Cardiology, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Fen Li
- Department of Cardiology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yurong Wu
- Department of Pediatric Cardiology, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Sun Chen
- Department of Pediatric Cardiology, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Kun Sun
- Department of Pediatric Cardiology, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Rang Xu
- Scientific Research Center, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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2
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Al Asoom L, Khan J, Al Sunni A, Rafique N, Latif R, Alabdali M, AbdulAzeez S, Borgio JF. A Pilot Mitochondrial Genome-Wide Association on Migraine Among Saudi Arabians. Int J Gen Med 2022; 15:6249-6258. [PMID: 35903646 PMCID: PMC9316482 DOI: 10.2147/ijgm.s371707] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 07/06/2022] [Indexed: 12/12/2022] Open
Abstract
Background Mitochondrial DNA (mtDNA) mutations have been reported in multiple neurological diseases and helped to explain the pathophysiology of these diseases. Similarly, variations in mtDNA might exist in migraine and can explain the effect of low ATP production in the neurons on the initiation of migraine attack. Therefore, in the current study we aim to explore the association of mtDNA mutations on migraine in the Saudi population. Subjects and Methods Over 1950 young Saudi female students were screened for migraine, among that a total of 103 satisfied the ICHD-3 criteria. However, 20 migraine cases confirmed in the neurology clinic and gave consent to participate in the study. Another 20 age-matched healthy controls were also recruited. Mitochondrial sequence variations were filtered from exome sequencing using NCBI GenBank Reference Sequence: NC_012920.1 and analysed using MITOMAP. Genes with significant single nucleotide polymorphisms (SNPs) were investigated by the gene functional classification tool DAVID and functional enrichment analysis of protein-protein interaction networks through STRING 11.5 for the most significant associated genes. Results Genome wide analysis of the mitochondrial sequence variations between the patients with migraine and control revealed the association of 30 SNPs (p < 0.05) in the mitochondrial genome. The highest significance (p = 0.001033) was observed in a coding SNP (rs1603225278) in the CYTB gene and rs386829281 in the region of origin of replication. Twenty-four significant SNPs were in the coding region of nine (ND5, ND4, COX2, COX1, ND3, CYTB, COX3, ND2 and ND1) genes. Conclusion This is the first study to demonstrate the association of mtDNA variations with migraine in the Saudi population. The current findings will help to highlight the significance of mtDNA mutations to migraine pathophysiology and will serve as a reference data for larger national and international studies.
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Affiliation(s)
- Lubna Al Asoom
- Department of Physiology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, 31541, Saudi Arabia
| | - Johra Khan
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Majmaah, 11952, Saudi Arabia.,Health and Basic Sciences Research Center, Majmaah University, Majmaah, 11952, Saudi Arabia
| | - Ahmad Al Sunni
- Department of Physiology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, 31541, Saudi Arabia
| | - Nazish Rafique
- Department of Physiology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, 31541, Saudi Arabia
| | - Rabia Latif
- Department of Physiology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, 31541, Saudi Arabia
| | - Majed Alabdali
- Department of Neurology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, 31952, Saudi Arabia
| | - Sayed AbdulAzeez
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, 31441, Saudi Arabia
| | - J Francis Borgio
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, 31441, Saudi Arabia
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Gao L, Cao M, Du GH, Qin XM. Huangqin Decoction Exerts Beneficial Effects on Rotenone-Induced Rat Model of Parkinson's Disease by Improving Mitochondrial Dysfunction and Alleviating Metabolic Abnormality of Mitochondria. Front Aging Neurosci 2022; 14:911924. [PMID: 35912075 PMCID: PMC9334858 DOI: 10.3389/fnagi.2022.911924] [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: 04/03/2022] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
Parkinson's disease (PD) is a common neurodegenerative disease, and the pathogenesis of PD is closely related to mitochondrial dysfunction. Previous studies have indicated that traditional Chinese medicine composition of Huangqin Decoction (HQD), including Scutellariae Radix, licorice, and Paeoniae Radix Alba, has therapeutic effects on PD, but whether HQD has a therapeutic effect on PD has not been reported. In this study, the protective effects of HQD on rotenone-induced PD rats were evaluated by behavioral assays (open field, rotating rod, suspension, gait, inclined plate, and grid) and immunohistochemistry. The mechanisms of HQD on attenuation of mitochondrial dysfunction were detected by biochemical assays and mitochondrial metabolomics. The results showed that HQD (20 g/kg) can protect rats with PD by improving motor coordination and muscle strength, increasing the number of tyrosine hydroxylase (TH)-positive neurons in rats with PD. Besides, HQD can improve mitochondrial dysfunction by increasing the content of adenosine triphosphate (ATP) and mitochondrial complex I. Mitochondrial metabolomics analysis revealed that the ketone body of acetoacetic acid (AcAc) in the rotenone group was significantly higher than that of the control group. Ketone bodies have been known to be used as an alternative energy source to provide energy to the brain when glucose was deficient. Further studies demonstrated that HQD could increase the expression of glucose transporter GLUT1, the content of tricarboxylic acid cycle rate-limiting enzyme citrate synthase (CS), and the level of hexokinase (HK) in rats with PD but could decrease the content of ketone bodies [AcAc and β-hydroxybutyric acid (β-HB)] and the expression of their transporters (MCT1). Our study revealed that the decrease of glucose metabolism in the rotenone group was parallel to the increase of substitute substrates (ketone bodies) and related transporters, and HQD could improve PD symptoms by activating the aerobic glycolysis pathway.
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Affiliation(s)
- Li Gao
- Modern Research Center for Traditional Chinese Medicine, The Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, China
- Key Laboratory of Effective Substances Research and Utilization in TCM of Shanxi Province, Taiyuan, China
- *Correspondence: Li Gao
| | - Min Cao
- Modern Research Center for Traditional Chinese Medicine, The Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, China
- Key Laboratory of Effective Substances Research and Utilization in TCM of Shanxi Province, Taiyuan, China
| | - Guan-hua Du
- Peking Union Medical College, Institute of Materia Medica, Chinese Academy of Medical Sciences, Beijing, China
| | - Xue-mei Qin
- Modern Research Center for Traditional Chinese Medicine, The Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, China
- Key Laboratory of Effective Substances Research and Utilization in TCM of Shanxi Province, Taiyuan, China
- Xue-mei Qin
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4
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Doccini S, Marchese M, Morani F, Gammaldi N, Mero S, Pezzini F, Soliymani R, Santi M, Signore G, Ogi A, Rocchiccioli S, Kanninen KM, Simonati A, Lalowski MM, Santorelli FM. Lysosomal Proteomics Links Disturbances in Lipid Homeostasis and Sphingolipid Metabolism to CLN5 Disease. Cells 2022; 11:1840. [PMID: 35681535 PMCID: PMC9180748 DOI: 10.3390/cells11111840] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/29/2022] [Accepted: 06/01/2022] [Indexed: 12/01/2022] Open
Abstract
CLN5 disease (MIM: 256731) represents a rare late-infantile form of neuronal ceroid lipofuscinosis (NCL), caused by mutations in the CLN5 gene that encodes the CLN5 protein (CLN5p), whose physiological roles stay unanswered. No cure is currently available for CLN5 patients and the opportunities for therapies are lagging. The role of lysosomes in the neuro-pathophysiology of CLN5 disease represents an important topic since lysosomal proteins are directly involved in the primary mechanisms of neuronal injury occurring in various NCL forms. We developed and implemented a lysosome-focused, label-free quantitative proteomics approach, followed by functional validations in both CLN5-knockout neuronal-like cell lines and Cln5-/- mice, to unravel affected pathways and modifying factors involved in this disease scenario. Our results revealed a key role of CLN5p in lipid homeostasis and sphingolipid metabolism and highlighted mutual NCL biomarkers scored with high lysosomal confidence. A newly generated cln5 knockdown zebrafish model recapitulated most of the pathological features seen in NCL disease. To translate the findings from in-vitro and preclinical models to patients, we evaluated whether two FDA-approved drugs promoting autophagy via TFEB activation or inhibition of the glucosylceramide synthase could modulate in-vitro ROS and lipid overproduction, as well as alter the locomotor phenotype in zebrafish. In summary, our data advance the general understanding of disease mechanisms and modifying factors in CLN5 disease, which are recurring in other NCL forms, also stimulating new pharmacological treatments.
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Affiliation(s)
- Stefano Doccini
- Molecular Medicine–IRCCS Stella Maris, 56128 Pisa, Italy; (M.M.); (N.G.); (S.M.); (A.O.)
| | - Maria Marchese
- Molecular Medicine–IRCCS Stella Maris, 56128 Pisa, Italy; (M.M.); (N.G.); (S.M.); (A.O.)
| | - Federica Morani
- Department of Biology, University of Pisa, 56126 Pisa, Italy;
| | - Nicola Gammaldi
- Molecular Medicine–IRCCS Stella Maris, 56128 Pisa, Italy; (M.M.); (N.G.); (S.M.); (A.O.)
- Ph.D. Program in Neuroscience, University of Florence, 50121 Florence, Italy
| | - Serena Mero
- Molecular Medicine–IRCCS Stella Maris, 56128 Pisa, Italy; (M.M.); (N.G.); (S.M.); (A.O.)
| | - Francesco Pezzini
- Department of Surgery, Dentistry, Paediatrics and Gynaecology, University of Verona, 37129 Verona, Italy; (F.P.); (A.S.)
| | - Rabah Soliymani
- HiLIFE, Meilahti Clinical Proteomics Core Facility, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland;
| | - Melissa Santi
- NEST, Scuola Normale Superiore and Istituto Nanoscienze-CNR, 56127 Pisa, Italy;
| | | | - Asahi Ogi
- Molecular Medicine–IRCCS Stella Maris, 56128 Pisa, Italy; (M.M.); (N.G.); (S.M.); (A.O.)
| | | | - Katja M. Kanninen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70210 Kuopio, Finland;
| | - Alessandro Simonati
- Department of Surgery, Dentistry, Paediatrics and Gynaecology, University of Verona, 37129 Verona, Italy; (F.P.); (A.S.)
| | - Maciej M. Lalowski
- HiLIFE, Meilahti Clinical Proteomics Core Facility, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland;
- Institute of Bioorganic Chemistry, PAS, Department of Biomedical Proteomics, 61-704 Poznan, Poland
| | - Filippo M. Santorelli
- Molecular Medicine–IRCCS Stella Maris, 56128 Pisa, Italy; (M.M.); (N.G.); (S.M.); (A.O.)
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5
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Single-Cell RNA-Seq Analysis of Cells from Degenerating and Non-Degenerating Intervertebral Discs from the Same Individual Reveals New Biomarkers for Intervertebral Disc Degeneration. Int J Mol Sci 2022; 23:ijms23073993. [PMID: 35409356 PMCID: PMC8999935 DOI: 10.3390/ijms23073993] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 02/07/2023] Open
Abstract
In this study, we used single-cell transcriptomic analysis to identify new specific biomarkers for nucleus pulposus (NP) and inner annulus fibrosis (iAF) cells, and to define cell populations within non-degenerating (nD) and degenerating (D) human intervertebral discs (IVD) of the same individual. Cluster analysis based on differential gene expression delineated 14 cell clusters. Gene expression profiles at single-cell resolution revealed the potential functional differences linked to degeneration, and among NP and iAF subpopulations. GO and KEGG analyses discovered molecular functions, biological processes, and transcription factors linked to cell type and degeneration state. We propose two lists of biomarkers, one as specific cell type, including C2orf40, MGP, MSMP, CD44, EIF1, LGALS1, RGCC, EPYC, HILPDA, ACAN, MT1F, CHI3L1, ID1, ID3 and TMED2. The second list proposes predictive IVD degeneration genes, including MT1G, SPP1, HMGA1, FN1, FBXO2, SPARC, VIM, CTGF, MGST1, TAF1D, CAPS, SPTSSB, S100A1, CHI3L2, PLA2G2A, TNRSF11B, FGFBP2, MGP, SLPI, DCN, MT-ND2, MTCYB, ADIRF, FRZB, CLEC3A, UPP1, S100A2, PRG4, COL2A1, SOD2 and MT2A. Protein and mRNA expression of MGST1, vimentin, SOD2 and SYF2 (p29) genes validated our scRNA-seq findings. Our data provide new insights into disc cells phenotypes and biomarkers of IVD degeneration that could improve diagnostic and therapeutic options.
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Vecchia SD, Tessa A, Dosi C, Baldacci J, Pasquariello R, Antenora A, Astrea G, Bassi MT, Battini R, Casali C, Cioffi E, Conti G, De Michele G, Ferrari AR, Filla A, Fiorillo C, Fusco C, Gallone S, Germiniasi C, Guerrini R, Haggiag S, Lopergolo D, Martinuzzi A, Melani F, Mignarri A, Panzeri E, Pini A, Pinto AM, Pochiero F, Primiano G, Procopio E, Renieri A, Romaniello R, Sancricca C, Servidei S, Spagnoli C, Ticci C, Rubegni A, Santorelli FM. Monoallelic KIF1A-related disorders: a multicenter cross sectional study and systematic literature review. J Neurol 2022; 269:437-450. [PMID: 34487232 DOI: 10.1007/s00415-021-10792-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/01/2021] [Accepted: 09/01/2021] [Indexed: 01/24/2023]
Abstract
BACKGROUND Monoallelic variants in the KIF1A gene are associated with a large set of clinical phenotypes including neurodevelopmental and neurodegenerative disorders, underpinned by a broad spectrum of central and peripheral nervous system involvement. METHODS In a multicenter study conducted in patients presenting spastic gait or complex neurodevelopmental disorders, we analyzed the clinical, genetic and neuroradiological features of 28 index cases harboring heterozygous variants in KIF1A. We conducted a literature systematic review with the aim to comparing our findings with previously reported KIF1A-related phenotypes. RESULTS Among 28 patients, we identified nine novel monoallelic variants, and one a copy number variation encompassing KIF1A. Mutations arose de novo in most patients and were prevalently located in the motor domain. Most patients presented features of a continuum ataxia-spasticity spectrum with only five cases showing a prevalently pure spastic phenotype and six presenting congenital ataxias. Seventeen mutations occurred in the motor domain of the Kinesin-1A protein, but location of mutation did not correlate with neurological and imaging presentations. When tested in 15 patients, muscle biopsy showed oxidative metabolism alterations (6 cases), impaired respiratory chain complexes II + III activity (3/6) and low CoQ10 levels (6/9). Ubiquinol supplementation (1gr/die) was used in 6 patients with subjective benefit. CONCLUSIONS This study broadened our clinical, genetic, and neuroimaging knowledge of KIF1A-related disorders. Although highly heterogeneous, it seems that manifestations of ataxia-spasticity spectrum disorders seem to occur in most patients. Some patients also present secondary impairment of oxidative metabolism; in this subset, ubiquinol supplementation therapy might be appropriate.
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Affiliation(s)
| | - Alessandra Tessa
- IRCCS Stella Maris Foundation, Calambrone, via dei Giacinti 2, 56128, Pisa, Italy.
| | - Claudia Dosi
- Child Neurology, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133, Milan, Italy
| | - Jacopo Baldacci
- Kode Solutions, Lungarno Galileo Galilei 1, 56125, Pisa, Italy
| | - Rosa Pasquariello
- IRCCS Stella Maris Foundation, Calambrone, via dei Giacinti 2, 56128, Pisa, Italy
| | - Antonella Antenora
- Department of Neurosciences, Reproductive and Odontostomatological Sciences, Federico II University, 80131, Naples, Italy
| | - Guja Astrea
- IRCCS Stella Maris Foundation, Calambrone, via dei Giacinti 2, 56128, Pisa, Italy
| | - Maria Teresa Bassi
- Laboratory of Molecular Biology, Scientific Institute IRCCS Eugenio Medea, Bosisio Parini, 23842, Lecco, Italy
| | - Roberta Battini
- IRCCS Stella Maris Foundation, Calambrone, via dei Giacinti 2, 56128, Pisa, Italy.,Department of Clinical and Experimental Medicine, Neurological Institute, University of Pisa, 56125, Pisa, Italy
| | - Carlo Casali
- Department of Medical and Surgical Sciences and Biotechnologies, Sapienza University of Rome, 40100, Latina, Italy
| | - Ettore Cioffi
- Department of Medical and Surgical Sciences and Biotechnologies, Sapienza University of Rome, 40100, Latina, Italy
| | - Greta Conti
- Neurology Unit and Neurogenetics Laboratories, Meyer Children University Hospital, University of Florence, 50139, Florence, Italy
| | - Giovanna De Michele
- Department of Neurosciences, Reproductive and Odontostomatological Sciences, Federico II University, 80131, Naples, Italy
| | - Anna Rita Ferrari
- IRCCS Stella Maris Foundation, Calambrone, via dei Giacinti 2, 56128, Pisa, Italy
| | - Alessandro Filla
- Department of Neurosciences, Reproductive and Odontostomatological Sciences, Federico II University, 80131, Naples, Italy
| | - Chiara Fiorillo
- Neuromuscular Disorders Unit, IRCCS Istituto Giannina Gaslini, DINOGMI, University of Genoa, Genoa, Italy
| | - Carlo Fusco
- Child Neurology Unit, Pediatric Neurophysiology Laboratory, Department of Pediatrics, Azienda USL-IRCCS Di Reggio Emilia, 42122, Reggio Emilia, Italy
| | - Salvatore Gallone
- Clinical Neurogenetics, Department Neurosciences, Az. Osp. Città della Salute e della Scienza di Torino, 1026, Torino, Italy
| | - Chiara Germiniasi
- Neuromuscular Unit, Scientific Institute IRCCS E. Medea, Bosisio Parini, 23842, Lecco, Italy
| | - Renzo Guerrini
- Neurology Unit and Neurogenetics Laboratories, Meyer Children University Hospital, University of Florence, 50139, Florence, Italy
| | - Shalom Haggiag
- Department of Neurology, Azienda Ospedaliera San Camillo Forlanini, 00152, Rome, Italy
| | - Diego Lopergolo
- IRCCS Stella Maris Foundation, Calambrone, via dei Giacinti 2, 56128, Pisa, Italy.,Unit of Neurology and Neurometabolic Disorders, Department of Medicine, Surgery and Neurosciences, University of Siena, 53100, Siena, Italy
| | - Andrea Martinuzzi
- Scientific Institute IRCCS E. Medea, Unità Operativa Conegliano, 31015, Treviso, Italy
| | - Federico Melani
- Neurology Unit and Neurogenetics Laboratories, Meyer Children University Hospital, University of Florence, 50139, Florence, Italy
| | - Andrea Mignarri
- Unit of Neurology and Neurometabolic Disorders, Department of Medicine, Surgery and Neurosciences, University of Siena, 53100, Siena, Italy
| | - Elena Panzeri
- Laboratory of Molecular Biology, Scientific Institute IRCCS Eugenio Medea, Bosisio Parini, 23842, Lecco, Italy
| | - Antonella Pini
- Neuromuscular Pediatric Unit, IRRCS Istituto delle Scienze Neurologiche di Bologna, 40139, Bologna, Italy
| | - Anna Maria Pinto
- Medical Genetics Unit, University of Siena, Azienda Ospedaliera Universitaria Senese, 53100, Siena, Italy
| | - Francesca Pochiero
- Department of Metabolic and Muscular, Meyer Children's University Hospital, 50139, Florence, Italy
| | - Guido Primiano
- Neurofisiopathology Unit, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168, Rome, Italy
| | - Elena Procopio
- Department of Metabolic and Muscular, Meyer Children's University Hospital, 50139, Florence, Italy
| | - Alessandra Renieri
- Medical Genetics Unit, University of Siena, Azienda Ospedaliera Universitaria Senese, 53100, Siena, Italy
| | - Romina Romaniello
- Neuropsychiatry and Neurorehabilitation Unit, Scientific Institute, IRCCS Eugenio Medea, Bosisio Parini, 23842, Lecco, Italy
| | - Cristina Sancricca
- Neurofisiopathology Unit, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168, Rome, Italy
| | - Serenella Servidei
- Neurofisiopathology Unit, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168, Rome, Italy.,Dipartimento Universitario di Neuroscienze, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
| | - Carlotta Spagnoli
- Child Neurology Unit, Pediatric Neurophysiology Laboratory, Department of Pediatrics, Azienda USL-IRCCS Di Reggio Emilia, 42122, Reggio Emilia, Italy
| | - Chiara Ticci
- IRCCS Stella Maris Foundation, Calambrone, via dei Giacinti 2, 56128, Pisa, Italy.,Department of Metabolic and Muscular, Meyer Children's University Hospital, 50139, Florence, Italy
| | - Anna Rubegni
- IRCCS Stella Maris Foundation, Calambrone, via dei Giacinti 2, 56128, Pisa, Italy
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7
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Zanfardino P, Doccini S, Santorelli FM, Petruzzella V. Tackling Dysfunction of Mitochondrial Bioenergetics in the Brain. Int J Mol Sci 2021; 22:8325. [PMID: 34361091 PMCID: PMC8348117 DOI: 10.3390/ijms22158325] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 12/15/2022] Open
Abstract
Oxidative phosphorylation (OxPhos) is the basic function of mitochondria, although the landscape of mitochondrial functions is continuously growing to include more aspects of cellular homeostasis. Thanks to the application of -omics technologies to the study of the OxPhos system, novel features emerge from the cataloging of novel proteins as mitochondrial thus adding details to the mitochondrial proteome and defining novel metabolic cellular interrelations, especially in the human brain. We focussed on the diversity of bioenergetics demand and different aspects of mitochondrial structure, functions, and dysfunction in the brain. Definition such as 'mitoexome', 'mitoproteome' and 'mitointeractome' have entered the field of 'mitochondrial medicine'. In this context, we reviewed several genetic defects that hamper the last step of aerobic metabolism, mostly involving the nervous tissue as one of the most prominent energy-dependent tissues and, as consequence, as a primary target of mitochondrial dysfunction. The dual genetic origin of the OxPhos complexes is one of the reasons for the complexity of the genotype-phenotype correlation when facing human diseases associated with mitochondrial defects. Such complexity clinically manifests with extremely heterogeneous symptoms, ranging from organ-specific to multisystemic dysfunction with different clinical courses. Finally, we briefly discuss the future directions of the multi-omics study of human brain disorders.
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Affiliation(s)
- Paola Zanfardino
- Department of Medical Basic Sciences, Neurosciences and Sense Organs, University of Bari Aldo Moro, 70124 Bari, Italy;
| | - Stefano Doccini
- IRCCS Fondazione Stella Maris, Calambrone, 56128 Pisa, Italy;
| | | | - Vittoria Petruzzella
- Department of Medical Basic Sciences, Neurosciences and Sense Organs, University of Bari Aldo Moro, 70124 Bari, Italy;
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8
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Ceccatelli Berti C, di Punzio G, Dallabona C, Baruffini E, Goffrini P, Lodi T, Donnini C. The Power of Yeast in Modelling Human Nuclear Mutations Associated with Mitochondrial Diseases. Genes (Basel) 2021; 12:300. [PMID: 33672627 PMCID: PMC7924180 DOI: 10.3390/genes12020300] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 12/17/2022] Open
Abstract
The increasing application of next generation sequencing approaches to the analysis of human exome and whole genome data has enabled the identification of novel variants and new genes involved in mitochondrial diseases. The ability of surviving in the absence of oxidative phosphorylation (OXPHOS) and mitochondrial genome makes the yeast Saccharomyces cerevisiae an excellent model system for investigating the role of these new variants in mitochondrial-related conditions and dissecting the molecular mechanisms associated with these diseases. The aim of this review was to highlight the main advantages offered by this model for the study of mitochondrial diseases, from the validation and characterisation of novel mutations to the dissection of the role played by genes in mitochondrial functionality and the discovery of potential therapeutic molecules. The review also provides a summary of the main contributions to the understanding of mitochondrial diseases emerged from the study of this simple eukaryotic organism.
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Affiliation(s)
| | | | | | | | | | | | - Claudia Donnini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy; (C.C.B.); (G.d.P.); (C.D.); (E.B.); (P.G.); (T.L.)
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9
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Doccini S, Morani F, Nesti C, Pezzini F, Calza G, Soliymani R, Signore G, Rocchiccioli S, Kanninen KM, Huuskonen MT, Baumann MH, Simonati A, Lalowski MM, Santorelli FM. Proteomic and functional analyses in disease models reveal CLN5 protein involvement in mitochondrial dysfunction. Cell Death Discov 2020; 6:18. [PMID: 32257390 PMCID: PMC7105465 DOI: 10.1038/s41420-020-0250-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 02/27/2020] [Accepted: 03/04/2020] [Indexed: 12/20/2022] Open
Abstract
CLN5 disease is a rare form of late-infantile neuronal ceroid lipofuscinosis (NCL) caused by mutations in the CLN5 gene that encodes a protein whose primary function and physiological roles remains unresolved. Emerging lines of evidence point to mitochondrial dysfunction in the onset and progression of several forms of NCL, offering new insights into putative biomarkers and shared biological processes. In this work, we employed cellular and murine models of the disease, in an effort to clarify disease pathways associated with CLN5 depletion. A mitochondria-focused quantitative proteomics approach followed by functional validations using cell biology and immunofluorescence assays revealed an impairment of mitochondrial functions in different CLN5 KO cell models and in Cln5 - /- cerebral cortex, which well correlated with disease progression. A visible impairment of autophagy machinery coupled with alterations of key parameters of mitophagy activation process functionally linked CLN5 protein to the process of neuronal injury. The functional link between impaired cellular respiration and activation of mitophagy pathways in the human CLN5 disease condition was corroborated by translating organelle-specific proteome findings to CLN5 patients' fibroblasts. Our study highlights the involvement of CLN5 in activation of mitophagy and mitochondrial homeostasis offering new insights into alternative strategies towards the CLN5 disease treatment.
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Affiliation(s)
- Stefano Doccini
- Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, IRCCS Stella Maris Foundation, Pisa, Italy
| | - Federica Morani
- Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, IRCCS Stella Maris Foundation, Pisa, Italy
| | - Claudia Nesti
- Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, IRCCS Stella Maris Foundation, Pisa, Italy
| | - Francesco Pezzini
- Neurology (Child Neurology and Neuropathology), Department of Neuroscience, Biomedicine and Movement, University of Verona, Verona, Italy
| | - Giulio Calza
- Medicum, Biochemistry/Developmental Biology and HiLIFE, Meilahti Clinical Proteomics Core Facility, University of Helsinki, Helsinki, Finland
| | - Rabah Soliymani
- Medicum, Biochemistry/Developmental Biology and HiLIFE, Meilahti Clinical Proteomics Core Facility, University of Helsinki, Helsinki, Finland
| | - Giovanni Signore
- NEST, Scuola Normale Superiore, Pisa, Italy
- Fondazione Pisana per la Scienza, Pisa, Italy
| | | | - Katja M. Kanninen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Mikko T. Huuskonen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Marc H. Baumann
- Medicum, Biochemistry/Developmental Biology and HiLIFE, Meilahti Clinical Proteomics Core Facility, University of Helsinki, Helsinki, Finland
| | - Alessandro Simonati
- Neurology (Child Neurology and Neuropathology), Department of Neuroscience, Biomedicine and Movement, University of Verona, Verona, Italy
| | - Maciej M. Lalowski
- Medicum, Biochemistry/Developmental Biology and HiLIFE, Meilahti Clinical Proteomics Core Facility, University of Helsinki, Helsinki, Finland
| | - Filippo M. Santorelli
- Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, IRCCS Stella Maris Foundation, Pisa, Italy
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10
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Tolomeo D, Rubegni A, Severino M, Pochiero F, Bruno C, Cassandrini D, Madeo A, Doccini S, Pedemonte M, Rossi A, D'Amore F, Donati M, Di Rocco M, Santorelli F, Nesti C. Clinical and neuroimaging features of the m.10197G>A mtDNA mutation: New case reports and expansion of the phenotype variability. J Neurol Sci 2019; 399:69-75. [DOI: 10.1016/j.jns.2019.02.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Revised: 02/01/2019] [Accepted: 02/05/2019] [Indexed: 12/20/2022]
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11
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Integrative analysis of differentially expressed genes and miRNAs predicts complex T3-mediated protective circuits in a rat model of cardiac ischemia reperfusion. Sci Rep 2018; 8:13870. [PMID: 30218079 PMCID: PMC6138681 DOI: 10.1038/s41598-018-32237-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 07/12/2018] [Indexed: 12/22/2022] Open
Abstract
Thyroid hormone (T3) dyshomeostasis in the cardiac ischemia-reperfusion (IR) setting negatively impacts on mitochondria function and extracellular matrix remodeling. The modulation of cardiac miRNAs may represent the underlying molecular mechanisms, but a systems biology perspective investigating this critical issue in depth is still lacking. A rat model of myocardial IR, with or without an early short-term T3-replacement, was used to predict putative T3-dependent miRNA-gene interactions targeted to mitochondria quality control and wound healing repair. As evidenced by mRNA and miRNA expression profiling, the T3 supplementation reverted the expression of 87 genes and 11 miRNAs that were dysregulated in the untreated group. In silico crossing and functional analysis of the T3-associated differentially expressed transcripts, identified a signature of interconnected miRNA-gene regulatory circuits that confer resistance to noxious cascades of acute stress. In this network the T3-down-regulated Tp53, Jun and Sp1 transcription factors emerge as critical nodes linking intrinsic cell death and oxidative stress pathways to adverse remodeling cascades. The data presented here provide a novel insight into the molecular basis of T3 cardioprotection in the early post-IR phase and highlight the contribution of a previously unappreciated complex T3-regulatory network that may be helpful in translating T3 replacement into clinical practice.
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12
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De Michele G, Sorrentino P, Nesti C, Rubegni A, Ruggiero L, Peluso S, Antenora A, Quarantelli M, Filla A, De Michele G, Santorelli FM. Reversible Valproate-Induced Subacute Encephalopathy Associated With a MT-ATP8 Variant in the Mitochondrial Genome. Front Neurol 2018; 9:728. [PMID: 30214424 PMCID: PMC6125373 DOI: 10.3389/fneur.2018.00728] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 08/09/2018] [Indexed: 11/13/2022] Open
Abstract
Introduction: There are several reported cases of patients developing motor and cognitive neurological impairment under treatment with valproic acid (VPA). We describe a woman who developed a subacute encephalopathy after VPA intake, harboring a mitochondrial DNA variant, previously described as causing VPA sensitivity in one pediatric patient. Material and Methods: A 65-year old woman developed a progressive, severe neurological deterioration after a 3 month treatment with valproate sodium, 800 mg daily. Magnetic resonance spectroscopy (MRS), muscle histochemical analysis and assay of mitochondrial enzymatic activities, and mitochondrial DNA sequencing were performed. Results: Neurological examination showed drowsiness, vertical gaze palsy, inability to either stand or walk, diffuse weakness, increased tendon reflexes. Blood lactate was increased, EEG showed diffuse theta and delta activity, MRI subcortical atrophy and leukoencephalopathy, MRS marked reduction of the NAA spectrum, with a small signal compatible with presence of lactate. Muscle biopsy evidenced presence of ragged red fibers (20%) and reduced COX reactivity. Assay of the muscle enzymatic activities showed multiple deficiencies of the electron transport chain and reduced ATP production. The mt.8393C>T variant in the MT-ATP8 gene was found in homoplasmy. The patient considerably improved after valproate withdrawal. Conclusion: The variant we found has been reported both as a polymorphism and, in a single patient, as related to the valproate-induced encephalopathy. The present case is the first bearing this mutation in homoplasmy. In case of neurological symptoms after starting VPA therapy, once hyperammonemia and liver failure have been ruled out, mtDNA abnormalities should be considered.
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Affiliation(s)
- Giovanna De Michele
- Department of Neurosciences and Reproductive and Odontostomatological Sciences, Università degli Studi di Napoli Federico II, Napoli, Italy
| | - Pierpaolo Sorrentino
- Department of Neurosciences and Reproductive and Odontostomatological Sciences, Università degli Studi di Napoli Federico II, Napoli, Italy
| | - Claudia Nesti
- Molecular Medicine, IRCCS Fondazione Stella Maris, Pisa, Italy
| | - Anna Rubegni
- Molecular Medicine, IRCCS Fondazione Stella Maris, Pisa, Italy
| | - Lucia Ruggiero
- Department of Neurosciences and Reproductive and Odontostomatological Sciences, Università degli Studi di Napoli Federico II, Napoli, Italy
| | - Silvio Peluso
- Department of Neurosciences and Reproductive and Odontostomatological Sciences, Università degli Studi di Napoli Federico II, Napoli, Italy
| | - Antonella Antenora
- Department of Neurosciences and Reproductive and Odontostomatological Sciences, Università degli Studi di Napoli Federico II, Napoli, Italy
| | - Mario Quarantelli
- Institute of Biostructure and Bioimaging, National Research Council, Naples, Italy
| | - Alessandro Filla
- Department of Neurosciences and Reproductive and Odontostomatological Sciences, Università degli Studi di Napoli Federico II, Napoli, Italy
| | - Giuseppe De Michele
- Department of Neurosciences and Reproductive and Odontostomatological Sciences, Università degli Studi di Napoli Federico II, Napoli, Italy
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13
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Liu X, Xu G. Recent advances in using mass spectrometry for mitochondrial metabolomics and lipidomics - A review. Anal Chim Acta 2017; 1037:3-12. [PMID: 30292306 DOI: 10.1016/j.aca.2017.11.080] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 11/28/2017] [Accepted: 11/29/2017] [Indexed: 01/09/2023]
Abstract
Metabolomics and lipidomics generally targets a huge number of intermediate and end products of cellular metabolism in body fluids, tissues, and cells etc. At present, mass spectrometry (MS) based metabolic or lipid profiling of routine biological specimens including the whole cells, tissues, plasma, serum and urine etc., can cover hundreds of metabolites or lipid species in one analysis, which has qualified deep elucidation of global metabolic and lipid networks. Mitochondria are important intracellular organelles and many critical biochemical reactions occur here, they provide building block for new cells, control redox balance, participate in apoptosis and behave as a signalling platform. Evidence suggests high prevalence of mitochondrial dysfunction occurs in a variety of cancers and other diseases, thus there is an urgent demand for investigating and clarifying mitochondrial metabolic and lipid alterations induced by diseases. Nevertheless, mitochondria contribute a small fraction to cellular contents, profiling of whole cell is probably unsuitable for monitoring alterations in mitochondria. Therefore, metabolomics and lipidomics analyses specially for mitochondria are necessary to understand disturbed metabolic and lipid pathways induced by environment and diseases. However, methods for comprehensively profiling metabolites and lipids in mitochondria have been limited at present. This review summarizes the current states and progress of MS-based mitochondrial metabolomics and lipidomics study. Details of mitochondrial isolation procedure, analytical methods and their applications are described. The challenges and opportunities are also given.
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Affiliation(s)
- Xinyu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Guowang Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
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14
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Doccini S, Meschini MC, Mei D, Guerrini R, Sicca F, Santorelli FM. Mitochondrial respiratory chain defects in skin fibroblasts from patients with Dravet syndrome. Neurol Sci 2015; 36:2151-5. [PMID: 26169758 DOI: 10.1007/s10072-015-2324-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Accepted: 07/02/2015] [Indexed: 10/23/2022]
Affiliation(s)
- Stefano Doccini
- Molecular Medicine, IRCCS Stella Maris, via dei Giacinti 2, 56128, Calambrone-Pisa, Italy
| | - Maria Chiara Meschini
- Molecular Medicine, IRCCS Stella Maris, via dei Giacinti 2, 56128, Calambrone-Pisa, Italy
| | - Davide Mei
- Pediatric Neurology and Neurogenetics Unit and Laboratories, Department of Neuroscience, Pharmacology and Child Health, A. Meyer Children's Hospital, University of Florence, Florence, Italy
| | - Renzo Guerrini
- Pediatric Neurology and Neurogenetics Unit and Laboratories, Department of Neuroscience, Pharmacology and Child Health, A. Meyer Children's Hospital, University of Florence, Florence, Italy
| | - Federico Sicca
- Molecular Medicine, IRCCS Stella Maris, via dei Giacinti 2, 56128, Calambrone-Pisa, Italy. .,Clinical Neurophysiology Laboratory, IRCCS Fondazione Stella Maris, Calambrone-Pisa, Italy.
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