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Grochowski CM, Bengtsson JD, Du H, Gandhi M, Lun MY, Mehaffey MG, Park K, Höps W, Benito E, Hasenfeld P, Korbel JO, Mahmoud M, Paulin LF, Jhangiani SN, Hwang JP, Bhamidipati SV, Muzny DM, Fatih JM, Gibbs RA, Pendleton M, Harrington E, Juul S, Lindstrand A, Sedlazeck FJ, Pehlivan D, Lupski JR, Carvalho CMB. Inverted triplications formed by iterative template switches generate structural variant diversity at genomic disorder loci. CELL GENOMICS 2024; 4:100590. [PMID: 38908378 PMCID: PMC11293582 DOI: 10.1016/j.xgen.2024.100590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/27/2023] [Accepted: 05/31/2024] [Indexed: 06/24/2024]
Abstract
The duplication-triplication/inverted-duplication (DUP-TRP/INV-DUP) structure is a complex genomic rearrangement (CGR). Although it has been identified as an important pathogenic DNA mutation signature in genomic disorders and cancer genomes, its architecture remains unresolved. Here, we studied the genomic architecture of DUP-TRP/INV-DUP by investigating the DNA of 24 patients identified by array comparative genomic hybridization (aCGH) on whom we found evidence for the existence of 4 out of 4 predicted structural variant (SV) haplotypes. Using a combination of short-read genome sequencing (GS), long-read GS, optical genome mapping, and single-cell DNA template strand sequencing (strand-seq), the haplotype structure was resolved in 18 samples. The point of template switching in 4 samples was shown to be a segment of ∼2.2-5.5 kb of 100% nucleotide similarity within inverted repeat pairs. These data provide experimental evidence that inverted low-copy repeats act as recombinant substrates. This type of CGR can result in multiple conformers generating diverse SV haplotypes in susceptible dosage-sensitive loci.
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Affiliation(s)
| | | | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mira Gandhi
- Pacific Northwest Research Institute, Seattle, WA 98122, USA
| | - Ming Yin Lun
- Pacific Northwest Research Institute, Seattle, WA 98122, USA
| | | | - KyungHee Park
- Pacific Northwest Research Institute, Seattle, WA 98122, USA
| | - Wolfram Höps
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Eva Benito
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Patrick Hasenfeld
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Jan O Korbel
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Medhat Mahmoud
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Luis F Paulin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - James Paul Hwang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sravya V Bhamidipati
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jawid M Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | | | | | - Sissel Juul
- Oxford Nanopore Technologies, New York, NY 10013, USA
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden; Department of Clinical Genetics and Genomics, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Fritz J Sedlazeck
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Computer Science, Rice University, Houston TX 77030, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Section of Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA
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Bernal-Conde LD, Peña-Martínez V, Morato-Torres CA, Ramos-Acevedo R, Arias-Carrión Ó, Padilla-Godínez FJ, Delgado-González A, Palomero-Rivero M, Collazo-Navarrete O, Soto-Rojas LO, Gómez-Chavarín M, Schüle B, Guerra-Crespo M. Alpha-Synuclein Gene Alterations Modulate Tyrosine Hydroxylase in Human iPSC-Derived Neurons in a Parkinson's Disease Animal Model. Life (Basel) 2024; 14:728. [PMID: 38929711 PMCID: PMC11204703 DOI: 10.3390/life14060728] [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: 05/05/2024] [Revised: 05/27/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
Parkinson's disease (PD) caused by SNCA gene triplication (3XSNCA) leads to early onset, rapid progression, and often dementia. Understanding the impact of 3XSNCA and its absence is crucial. This study investigates the differentiation of human induced pluripotent stem cell (hiPSC)-derived floor-plate progenitors into dopaminergic neurons. Three different genotypes were evaluated in this study: patient-derived hiPSCs with 3XSNCA, a gene-edited isogenic line with a frame-shift mutation on all SNCA alleles (SNCA 4KO), and a normal wild-type control. Our aim was to assess how the substantia nigra pars compacta (SNpc) microenvironment, damaged by 6-hydroxydopamine (6-OHDA), influences tyrosine hydroxylase-positive (Th+) neuron differentiation in these genetic variations. This study confirms successful in vitro differentiation into neuronal lineage in all cell lines. However, the SNCA 4KO line showed unusual LIM homeobox transcription factor 1 alpha (Lmx1a) extranuclear distribution. Crucially, both 3XSNCA and SNCA 4KO lines had reduced Th+ neuron expression, despite initial successful neuronal differentiation after two months post-transplantation. This indicates that while the SNpc environment supports early neuronal survival, SNCA gene alterations-either amplification or knock-out-negatively impact Th+ dopaminergic neuron maturation. These findings highlight SNCA's critical role in PD and underscore the value of hiPSC models in studying neurodegenerative diseases.
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Affiliation(s)
- Luis Daniel Bernal-Conde
- Laboratory of Regenerative Medicine, Physiology Department, Faculty of Medicine, National Autonomous University of Mexico, Mexico City 04510, Mexico; (L.D.B.-C.); (V.P.-M.); (C.A.M.-T.); (R.R.-A.); (F.J.P.-G.); (A.D.-G.); (M.G.-C.)
- Molecular Neuropathology Department, Neuroscience Division, Institute of Cell Physiology, National Autonomous University of Mexico, Mexico City 04510, Mexico
| | - Verónica Peña-Martínez
- Laboratory of Regenerative Medicine, Physiology Department, Faculty of Medicine, National Autonomous University of Mexico, Mexico City 04510, Mexico; (L.D.B.-C.); (V.P.-M.); (C.A.M.-T.); (R.R.-A.); (F.J.P.-G.); (A.D.-G.); (M.G.-C.)
- Molecular Neuropathology Department, Neuroscience Division, Institute of Cell Physiology, National Autonomous University of Mexico, Mexico City 04510, Mexico
| | - C. Alejandra Morato-Torres
- Laboratory of Regenerative Medicine, Physiology Department, Faculty of Medicine, National Autonomous University of Mexico, Mexico City 04510, Mexico; (L.D.B.-C.); (V.P.-M.); (C.A.M.-T.); (R.R.-A.); (F.J.P.-G.); (A.D.-G.); (M.G.-C.)
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94304, USA;
| | - Rodrigo Ramos-Acevedo
- Laboratory of Regenerative Medicine, Physiology Department, Faculty of Medicine, National Autonomous University of Mexico, Mexico City 04510, Mexico; (L.D.B.-C.); (V.P.-M.); (C.A.M.-T.); (R.R.-A.); (F.J.P.-G.); (A.D.-G.); (M.G.-C.)
- Molecular Neuropathology Department, Neuroscience Division, Institute of Cell Physiology, National Autonomous University of Mexico, Mexico City 04510, Mexico
| | - Óscar Arias-Carrión
- Movement and Sleep Disorders Unit, Dr. Manuel Gea González General Hospital, Mexico City 14080, Mexico;
| | - Francisco J. Padilla-Godínez
- Laboratory of Regenerative Medicine, Physiology Department, Faculty of Medicine, National Autonomous University of Mexico, Mexico City 04510, Mexico; (L.D.B.-C.); (V.P.-M.); (C.A.M.-T.); (R.R.-A.); (F.J.P.-G.); (A.D.-G.); (M.G.-C.)
- Molecular Neuropathology Department, Neuroscience Division, Institute of Cell Physiology, National Autonomous University of Mexico, Mexico City 04510, Mexico
| | - Alexa Delgado-González
- Laboratory of Regenerative Medicine, Physiology Department, Faculty of Medicine, National Autonomous University of Mexico, Mexico City 04510, Mexico; (L.D.B.-C.); (V.P.-M.); (C.A.M.-T.); (R.R.-A.); (F.J.P.-G.); (A.D.-G.); (M.G.-C.)
- Molecular Neuropathology Department, Neuroscience Division, Institute of Cell Physiology, National Autonomous University of Mexico, Mexico City 04510, Mexico
| | - Marcela Palomero-Rivero
- Neurodevelopment and Physiology Department, Neuroscience Division, Institute of Cell Physiology, National Autonomous University of Mexico, Mexico City 04510, Mexico;
| | - Omar Collazo-Navarrete
- National Laboratory of Genomic Resources, Institute of Biomedical Research, National Autonomous University of Mexico, Mexico City 04510, Mexico;
| | - Luis O. Soto-Rojas
- Laboratory of Molecular Pathogenesis, Laboratory 4, Building A4, Medical Surgeon Career, Faculty of Higher Studies Iztacala, National Autonomous University of Mexico, Mexico City 54090, Mexico;
| | - Margarita Gómez-Chavarín
- Laboratory of Regenerative Medicine, Physiology Department, Faculty of Medicine, National Autonomous University of Mexico, Mexico City 04510, Mexico; (L.D.B.-C.); (V.P.-M.); (C.A.M.-T.); (R.R.-A.); (F.J.P.-G.); (A.D.-G.); (M.G.-C.)
| | - Birgitt Schüle
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94304, USA;
| | - Magdalena Guerra-Crespo
- Laboratory of Regenerative Medicine, Physiology Department, Faculty of Medicine, National Autonomous University of Mexico, Mexico City 04510, Mexico; (L.D.B.-C.); (V.P.-M.); (C.A.M.-T.); (R.R.-A.); (F.J.P.-G.); (A.D.-G.); (M.G.-C.)
- Molecular Neuropathology Department, Neuroscience Division, Institute of Cell Physiology, National Autonomous University of Mexico, Mexico City 04510, Mexico
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Sastre D, Zafar F, Torres CAM, Piper D, Kirik D, Sanders LH, Qi LS, Schüle B. Inactive S. aureus Cas9 downregulates alpha-synuclein and reduces mtDNA damage and oxidative stress levels in human stem cell model of Parkinson's disease. Sci Rep 2023; 13:17796. [PMID: 37853101 PMCID: PMC10584834 DOI: 10.1038/s41598-023-45078-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 10/16/2023] [Indexed: 10/20/2023] Open
Abstract
Parkinson's disease (PD) is one of the most common neurodegenerative diseases, but no disease modifying therapies have been successful in clinical translation presenting a major unmet medical need. A promising target is alpha-synuclein or its aggregated form, which accumulates in the brain of PD patients as Lewy bodies. While it is not entirely clear which alpha-synuclein protein species is disease relevant, mere overexpression of alpha-synuclein in hereditary forms leads to neurodegeneration. To specifically address gene regulation of alpha-synuclein, we developed a CRISPR interference (CRISPRi) system based on the nuclease dead S. aureus Cas9 (SadCas9) fused with the transcriptional repressor domain Krueppel-associated box to controllably repress alpha-synuclein expression at the transcriptional level. We screened single guide (sg)RNAs across the SNCA promoter and identified several sgRNAs that mediate downregulation of alpha-synuclein at varying levels. CRISPRi downregulation of alpha-synuclein in iPSC-derived neuronal cultures from a patient with an SNCA genomic triplication showed functional recovery by reduction of oxidative stress and mitochondrial DNA damage. Our results are proof-of-concept in vitro for precision medicine by targeting the SNCA gene promoter. The SNCA CRISPRi approach presents a new model to understand safe levels of alpha-synuclein downregulation and a novel therapeutic strategy for PD and related alpha-synucleinopathies.
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Affiliation(s)
- Danuta Sastre
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Dr., R271/217, Stanford, CA, 94305, USA
| | - Faria Zafar
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Dr., R271/217, Stanford, CA, 94305, USA
| | - C Alejandra Morato Torres
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Dr., R271/217, Stanford, CA, 94305, USA
| | - Desiree Piper
- Department of Biological Sciences, San Jose State University, San Jose, CA, 95192, USA
| | - Deniz Kirik
- Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Laurie H Sanders
- Departments of Neurology and Pathology, Duke Center for Neurodegeneration and Neurotherapeutics, Duke University Medical Center, Durham, NC, 27710, USA
| | - L Stanley Qi
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Birgitt Schüle
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Dr., R271/217, Stanford, CA, 94305, USA.
- Biosciences Division, SRI International, Menlo Park, CA, 94025, USA.
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Grochowski CM, Bengtsson JD, Du H, Gandhi M, Lun MY, Mehaffey MG, Park K, Höps W, Benito-Garagorri E, Hasenfeld P, Korbel JO, Mahmoud M, Paulin LF, Jhangiani SN, Muzny DM, Fatih JM, Gibbs RA, Pendleton M, Harrington E, Juul S, Lindstrand A, Sedlazeck FJ, Pehlivan D, Lupski JR, Carvalho CMB. Break-induced replication underlies formation of inverted triplications and generates unexpected diversity in haplotype structures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.02.560172. [PMID: 37873367 PMCID: PMC10592851 DOI: 10.1101/2023.10.02.560172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Background The duplication-triplication/inverted-duplication (DUP-TRP/INV-DUP) structure is a type of complex genomic rearrangement (CGR) hypothesized to result from replicative repair of DNA due to replication fork collapse. It is often mediated by a pair of inverted low-copy repeats (LCR) followed by iterative template switches resulting in at least two breakpoint junctions in cis . Although it has been identified as an important mutation signature of pathogenicity for genomic disorders and cancer genomes, its architecture remains unresolved and is predicted to display at least four structural variation (SV) haplotypes. Results Here we studied the genomic architecture of DUP-TRP/INV-DUP by investigating the genomic DNA of 24 patients with neurodevelopmental disorders identified by array comparative genomic hybridization (aCGH) on whom we found evidence for the existence of 4 out of 4 predicted SV haplotypes. Using a combination of short-read genome sequencing (GS), long- read GS, optical genome mapping and StrandSeq the haplotype structure was resolved in 18 samples. This approach refined the point of template switching between inverted LCRs in 4 samples revealing a DNA segment of ∼2.2-5.5 kb of 100% nucleotide similarity. A prediction model was developed to infer the LCR used to mediate the non-allelic homology repair. Conclusions These data provide experimental evidence supporting the hypothesis that inverted LCRs act as a recombinant substrate in replication-based repair mechanisms. Such inverted repeats are particularly relevant for formation of copy-number associated inversions, including the DUP-TRP/INV-DUP structures. Moreover, this type of CGR can result in multiple conformers which contributes to generate diverse SV haplotypes in susceptible loci .
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Duan R, Liu G, Han Y, Li P, Zhang B, Liu Y. Characterization of SNCA Multiplication in Parkinson's Disease: 2 New Cases and Evaluation of the Literature. Mov Disord Clin Pract 2023; 10:1536-1541. [PMID: 37868923 PMCID: PMC10585967 DOI: 10.1002/mdc3.13852] [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: 12/08/2022] [Revised: 07/07/2023] [Accepted: 07/16/2023] [Indexed: 10/24/2023] Open
Abstract
Background Alpha-synuclein (SNCA) copy number variations (CNV) have been certified as a causative mutation in patients with familial and sporadic Parkinson's disease (PD). Case We report three SNCA duplication cases diagnosed as PD. Through whole-exome sequencing, we identified a de novo 4.56 Mb repeated region in one patient and a 2.50 Mb repeated region in familial PD with two patients. Literature review In review of previous cases, we suggest that aggressive behavior is more remarkable in CNV4 patients. Meanwhile, frequency of cognition decline and dementia were slightly increased in CNV4 patients. We also illustrate a younger onset age in offspring than parent in familial SNCA multiplication PD cases. No difference was observed in disease duration between parent and offspring generation. Conclusions Our findings demonstrated the clinical and genetic characteristics in PD with SNCA multiplication and provided strong evidence for genetic anticipation. These results may be instructive for future disease diagnosis and genetic counseling.
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Affiliation(s)
- Ruo‐Nan Duan
- Department of Neurology, Qilu HospitalCheeloo College of Medicine, Shandong UniversityJinanChina
| | - Gui‐Yu Liu
- Cheeloo College of Medicine, Shandong UniversityJinanChina
| | - Yin‐Lian Han
- Department of Neurology, Qilu HospitalCheeloo College of Medicine, Shandong UniversityJinanChina
| | - Pei‐Zheng Li
- Department of Neurology, Qilu HospitalCheeloo College of Medicine, Shandong UniversityJinanChina
| | - Bo‐Han Zhang
- Department of Neurology, Qilu HospitalCheeloo College of Medicine, Shandong UniversityJinanChina
| | - Yi‐Ming Liu
- Department of Neurology, Qilu HospitalCheeloo College of Medicine, Shandong UniversityJinanChina
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Sastre D, Zafar F, Torres CAM, Piper D, Kirik D, Sanders LH, Qi S, Schüle B. Nuclease-dead S. aureus Cas9 downregulates alpha-synuclein and reduces mtDNA damage and oxidative stress levels in patient-derived stem cell model of Parkinson's disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.24.525105. [PMID: 36747875 PMCID: PMC9900844 DOI: 10.1101/2023.01.24.525105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Parkinson's disease (PD) is one of the most common neurodegenerative diseases, but no disease modifying therapies have been successful in clinical translation presenting a major unmet medical need. A promising target is alpha-synuclein or its aggregated form, which accumulates in the brain of PD patients as Lewy bodies. While it is not entirely clear which alpha-synuclein protein species is disease relevant, mere overexpression of alpha-synuclein in hereditary forms leads to neurodegeneration. To specifically address gene regulation of alpha-synuclein, we developed a CRISPR interference (CRISPRi) system based on the nuclease dead S. aureus Cas9 (SadCas9) fused with the transcriptional repressor domain Krueppel-associated box to controllably repress alpha-synuclein expression at the transcriptional level. We screened single guide (sg)RNAs across the SNCA promoter and identified several sgRNAs that mediate downregulation of alpha-synuclein at varying levels. CRISPRi downregulation of alpha-synuclein in iPSC-derived neuronal cultures from a patient with an SNCA genomic triplication showed functional recovery by reduction of oxidative stress and mitochondrial DNA damage. Our results are proof-of-concept in vitro for precision medicine by targeting the SNCA gene promoter. The SNCA CRISPRi approach presents a new model to understand safe levels of alpha-synuclein downregulation and a novel therapeutic strategy for PD and related alpha-synucleinopathies.
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Affiliation(s)
- Danuta Sastre
- Stanford University School of Medicine, Department of Pathology, Stanford, CA 94305, U.S.A
| | - Faria Zafar
- Stanford University School of Medicine, Department of Pathology, Stanford, CA 94305, U.S.A
| | | | - Desiree Piper
- San Jose State University, Department of Biological Sciences, San Jose, 95192 CA, U.S.A
| | - Deniz Kirik
- Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Laurie H. Sanders
- Departments of Neurology and Pathology, Duke Center for Neurodegeneration and Neurotherapeutics, Duke University Medical Center, Durham, NC 27710, U.S.A
| | - Stanley Qi
- Stanford University, Department of Bioengineering, Stanford, CA 94305, U.S.A
| | - Birgitt Schüle
- Stanford University School of Medicine, Department of Pathology, Stanford, CA 94305, U.S.A
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Wurster I, Quadalti C, Rossi M, Hauser AK, Deuschle C, Schulte C, Waniek K, Lachmann I, la Fougere C, Doppler K, Gasser T, Bender B, Parchi P, Brockmann K. Linking the phenotype of SNCA Triplication with PET-MRI imaging pattern and alpha-synuclein CSF seeding. NPJ Parkinsons Dis 2022; 8:117. [PMID: 36109514 PMCID: PMC9476413 DOI: 10.1038/s41531-022-00379-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 08/23/2022] [Indexed: 11/29/2022] Open
Abstract
Lewy-body pathology with aggregation of abnormal conformations of the protein alpha-synuclein (α-Syn) represent the histopathological hallmarks of Parkinson’s disease (PD). Genetic prototypes such as PD due to mutations in the alpha-synuclein gene (SNCA) offer the opportunity to evaluate α-Syn-related profiles in patient-derived biomaterial. We identified a family with a SNCA triplication and assessed the index patient for CSF α-Syn seeding capacity and levels of total α-Syn along with other neurodegenerative CSF markers (Aβ1-42, total-Tau, phospho-Tau, NFL). As no published CSF data in patients with SNCA triplication are available, we descriptively compared his CSF profiles to those of sporadic PD patients and PD patients with GBA mutations as these are also specifically associated with prominent α-Syn pathology. Additionally, skin biopsies with staining for phospho-α-Syn were done. To assess cerebral glucose metabolism and brain atrophy combined positron emission tomography and magnetic resonance imaging ([18F]FDG-PET/MRI) was performed. Age at onset was 24 years and motor impairment was accompanied by prominent non-motor symptoms with early development of dementia, depression, REM sleep behavior disorder, hyposmia, and dysautonomia. Correspondingly, PET-MRI showed hypometabolism and atrophy in frontal, temporoparietal and occipital regions. CSF levels of total α-Syn were threefold higher and RT-QuIC showed remarkable α-Syn seeding activity in all kinetic categories in the SNCATriplication patient compared to patients with GBA mutations. Our results are consistent with findings that not only mutant forms but also overexpression of the wild-type α-Syn protein lead to PD and PD dementia and show a striking CSF α-Syn seeding profile, thus substantiating the role of RT-QuIC as a specific in vivo biomarker of α-Syn brain pathology.
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Bukowska-Olech E, Sowińska-Seidler A, Wierzba J, Jamsheer A. SHFLD3 phenotypes caused by 17p13.3 triplication/ duplication encompassing Fingerin (BHLHA9) invariably. Orphanet J Rare Dis 2022; 17:325. [PMID: 36028842 PMCID: PMC9419377 DOI: 10.1186/s13023-022-02480-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 08/13/2022] [Indexed: 11/21/2022] Open
Abstract
Background Split-hand/ foot malformation with long bone deficiency 3 (SHFLD3) is an extremely rare condition associated with duplications located on 17p13.3, which invariably encompasses the BHLHA9 gene. The disease inherits with variable expressivity and significant incomplete penetrance as high as 50%. Results We have detected 17p13.3 locus one-allele triplication in a male proband from family 1 (F1.1), and duplication in a male proband from family 2 (F2.1) applying array comparative genomic hybridization (array CGH). The rearrangements mapped to the following chromosomal regions–arr[GRCh38] 17p13.3(960254–1291856)×4 in F1.1 and arr[GRCh38] 17p13.3(1227482–1302716)×3 in F2.1. The targeted quantitative PCR revealed that the 17p13.3 locus was also duplicated in the second affected member from family 2 (F2.2; brother of F2.1). In the next step, we performed segregation studies using quantitative PCR and revealed that F1.1 inherited the triplication from his healthy father—F1.2, whereas the locus was unremarkable in the mother of F2.1 & F2.2 and the healthy son of F2.1. However, the duplication was present in a healthy daughter of F2.2, an asymptomatic carrier. The breakpoint analysis allowed to define the exact size and span of the duplicated region in Family 2, i.e., 78,948 bp chr17:1225063–1304010 (HG38). Interestingly, all symptomatic carriers from both families presented with variable SHFLD3 phenotype. The involvement of secondary modifying locus could not be excluded, however, the Sanger sequencing screening of BHLHA9 entire coding sequence was unremarkable for both families. Conclusions We have shed light on the one-allele CNV triplication occurrence that should be considered when a higher probe (over duplication range) signal is noted. Second, all SHFLD3 patients were accurately described regarding infrequent limb phenotypes, which were highly variable even when familial. Of note, all symptomatic individuals were males. SHFLD3 still remains a mysterious ultra-rare disease and our findings do not answer crucial questions regarding the disease low penetrance, variable expression and heterogeneity. However, we have presented some clinical and molecular aspects that may be helpful in daily diagnostic routine, both dysmorphological and molecular assessment, of patients affected with SHFLD3. Supplementary Information The online version contains supplementary material available at 10.1186/s13023-022-02480-w.
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Affiliation(s)
| | - Anna Sowińska-Seidler
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznan, Poland
| | - Jolanta Wierzba
- Department of Pediatrics and Internal Medicine Nursing, Department of Rare Disorders, Medical University of Gdansk, Gdansk, Poland
| | - Aleksander Jamsheer
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznan, Poland. .,Centers for Medical Genetics GENESIS, Poznan, Poland.
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Prahl J, Coetzee GA. Genetic Elements at the Alpha-Synuclein Locus. Front Neurosci 2022; 16:889802. [PMID: 35898413 PMCID: PMC9309432 DOI: 10.3389/fnins.2022.889802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 06/24/2022] [Indexed: 11/30/2022] Open
Abstract
Genome-wide association studies have consistently shown that the alpha-synuclein locus is significantly associated with Parkinson's disease. The mechanism by which this locus modulates the disease pathology and etiology remains largely under-investigated. This is due to the assumption that SNCA is the only driver of the functional aspects of several single nucleotide polymorphism (SNP) risk-signals at this locus. Recent evidence has shown that the risk associated with the top GWAS-identified variant within this locus is independent of SNCA expression, calling into question the validity of assigning function to the nearest gene, SNCA. In this review, we examine additional genes and risk variants present at the SNCA locus and how they may contribute to Parkinson's disease. Using the SNCA locus as an example, we hope to demonstrate that deeper and detailed functional validations are required for high impact disease-linked variants.
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Affiliation(s)
- Jordan Prahl
- Department of Neurodegenerative Disease, Van Andel Institute, Grand Rapids, MI, United States
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10
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Fanning S, Cirka H, Thies JL, Jeong J, Niemi SM, Yoon J, Ho GPH, Pacheco JA, Dettmer U, Liu L, Clish CB, Hodgetts KJ, Hutchinson JN, Muratore CR, Caldwell GA, Caldwell KA, Selkoe D. Lipase regulation of cellular fatty acid homeostasis as a Parkinson's disease therapeutic strategy. NPJ Parkinsons Dis 2022; 8:74. [PMID: 35680956 PMCID: PMC9184586 DOI: 10.1038/s41531-022-00335-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 05/11/2022] [Indexed: 02/01/2023] Open
Abstract
Synucleinopathy (Parkinson's disease (PD); Lewy body dementia) disease-modifying treatments represent a huge unmet medical need. Although the PD-causing protein α-synuclein (αS) interacts with lipids and fatty acids (FA) physiologically and pathologically, targeting FA homeostasis for therapeutics is in its infancy. We identified the PD-relevant target stearoyl-coA desaturase: inhibiting monounsaturated FA synthesis reversed PD phenotypes. However, lipid degradation also generates FA pools. Here, we identify the rate-limiting lipase enzyme, LIPE, as a candidate target. Decreasing LIPE in human neural cells reduced αS inclusions. Patient αS triplication vs. corrected neurons had increased pSer129 and insoluble αS and decreased αS tetramer:monomer ratios. LIPE inhibition rescued all these and the abnormal unfolded protein response. LIPE inhibitors decreased pSer129 and restored tetramer:monomer equilibrium in αS E46K-expressing human neurons. LIPE reduction in vivo alleviated αS-induced dopaminergic neurodegeneration in Caenorhabditis elegans. Co-regulating FA synthesis and degradation proved additive in rescuing PD phenotypes, signifying co-targeting as a therapeutic strategy.
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Affiliation(s)
- Saranna Fanning
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
| | - Haley Cirka
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Jennifer L Thies
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, 35487, USA
| | - Jooyoung Jeong
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Sarah M Niemi
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Joon Yoon
- Department of Biostatistics, The Harvard Chan School of Public Health, Boston, MA, 02115, USA
| | - Gary P H Ho
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | | | - Ulf Dettmer
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Lei Liu
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Clary B Clish
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Kevin J Hodgetts
- Laboratory for Drug Discovery in Neuroscience, Department of Neurology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - John N Hutchinson
- Department of Biostatistics, The Harvard Chan School of Public Health, Boston, MA, 02115, USA
| | - Christina R Muratore
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Guy A Caldwell
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, 35487, USA
| | - Kim A Caldwell
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, 35487, USA
| | - Dennis Selkoe
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
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11
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Lupski JR. Biology in balance: human diploid genome integrity, gene dosage, and genomic medicine. Trends Genet 2022; 38:554-571. [PMID: 35450748 PMCID: PMC9222541 DOI: 10.1016/j.tig.2022.03.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/28/2022] [Accepted: 03/01/2022] [Indexed: 01/01/2023]
Abstract
The path to completion of the functional annotation of the haploid human genome reference build, exploration of the clan genomics hypothesis, understanding human gene and genome functional biology, and gene genome and organismal evolution, is in reach.
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Affiliation(s)
- James R Lupski
- Genetics & Genomics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX 77030, USA.
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12
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Miller SJ, Campbell CE, Jimenez-Corea HA, Wu GH, Logan R. Neuroglial Senescence, α-Synucleinopathy, and the Therapeutic Potential of Senolytics in Parkinson’s Disease. Front Neurosci 2022; 16:824191. [PMID: 35516803 PMCID: PMC9063319 DOI: 10.3389/fnins.2022.824191] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 03/22/2022] [Indexed: 12/02/2022] Open
Abstract
Parkinson’s disease (PD) is the most common movement disorder and the second most prevalent neurodegenerative disease after Alzheimer’s disease. Despite decades of research, there is still no cure for PD and the complicated intricacies of the pathology are still being worked out. Much of the research on PD has focused on neurons, since the disease is characterized by neurodegeneration. However, neuroglia has become recognized as key players in the health and disease of the central nervous system. This review provides a current perspective on the interactive roles that α-synuclein and neuroglial senescence have in PD. The self-amplifying and cyclical nature of oxidative stress, neuroinflammation, α-synucleinopathy, neuroglial senescence, neuroglial chronic activation and neurodegeneration will be discussed. Finally, the compelling role that senolytics could play as a therapeutic avenue for PD is explored and encouraged.
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Affiliation(s)
- Sean J. Miller
- Pluripotent Diagnostics Corp. (PDx), Molecular Medicine Research Institute, Sunnyvale, CA, United States
| | | | | | - Guan-Hui Wu
- Department of Neurology, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Robert Logan
- Pluripotent Diagnostics Corp. (PDx), Molecular Medicine Research Institute, Sunnyvale, CA, United States
- Department of Biology, Eastern Nazarene College, Quincy, MA, United States
- *Correspondence: Robert Logan,
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13
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Huang J, Cheng Y, Li C, Shang H. Genetic heterogeneity on sleep disorders in Parkinson's disease: a systematic review and meta-analysis. Transl Neurodegener 2022; 11:21. [PMID: 35395825 PMCID: PMC8991652 DOI: 10.1186/s40035-022-00294-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 03/09/2022] [Indexed: 02/08/2023] Open
Abstract
A growing amount of evidence has indicated contributions of variants in causative genes of Parkinson’s disease (PD) to the development of sleep disturbance in PD and prodromal PD stages. In this article, we aimed to investigate the role of genetics in sleep disorders in PD patients and asymptomatic carriers at prodromal stage of PD. A systematic review and meta-analysis of observational studies was conducted based on the MEDLINE, EMBASE and PsychINFO databases. A pooled effect size was calculated by odds ratio (OR) and standard mean difference (SMD). Forty studies were selected for quantitative analysis, including 17 studies on glucocerebrosidase (GBA), 25 studies on Leucine-rich repeat kinase 2 (LRRK2) and 7 on parkin (PRKN) genes, and 3 studies on alpha-synuclein gene (SNCA) were used for qualitative analysis. Patients with PD carrying GBA variants had a significantly higher risk for rapid-eye-movement behavior disorders (RBD) (OR, 1.82) and higher RBD Screening Questionnaire scores (SMD, 0.33). Asymptomatic carriers of GBA variants had higher severity of RBD during follow-up. Patients with PD carrying the LRRK2 G2019S variant had lower risk and severity of RBD compared with those without LRRK2 G2019S. Variants of GBA, LRRK2 and PRKN did not increase or decrease the risk and severity of excessive daytime sleepiness and restless legs syndrome in PD. Our findings suggest that the genetic heterogeneity plays a role in the development of sleep disorders, mainly RBD, in PD and the prodromal stage of PD.
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Affiliation(s)
- Jingxuan Huang
- Laboratory of Neurodegenerative Disorders, Department of Neurology, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yangfan Cheng
- Laboratory of Neurodegenerative Disorders, Department of Neurology, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Chunyu Li
- Laboratory of Neurodegenerative Disorders, Department of Neurology, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Huifang Shang
- Laboratory of Neurodegenerative Disorders, Department of Neurology, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China.
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14
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Isogenic human SNCA gene dosage induced pluripotent stem cells to model Parkinson’s disease. Stem Cell Res 2022; 60:102733. [DOI: 10.1016/j.scr.2022.102733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 01/18/2022] [Accepted: 02/25/2022] [Indexed: 10/19/2022] Open
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15
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Kakouri AC, Votsi C, Oulas A, Nicolaou P, Aureli M, Lunghi G, Samarani M, Compagnoni GM, Salani S, Di Fonzo A, Christophides T, Tanteles GA, Zamba-Papanicolaou E, Pantzaris M, Spyrou GM, Christodoulou K. Transcriptomic characterization of tissues from patients and subsequent pathway analyses reveal biological pathways that are implicated in spastic ataxia. Cell Biosci 2022; 12:29. [PMID: 35277195 PMCID: PMC8917697 DOI: 10.1186/s13578-022-00754-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 02/04/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Spastic ataxias (SAs) encompass a group of rare and severe neurodegenerative diseases, characterized by an overlap between ataxia and spastic paraplegia clinical features. They have been associated with pathogenic variants in a number of genes, including GBA2. This gene codes for the non-lysososomal β-glucosylceramidase, which is involved in sphingolipid metabolism through its catalytic role in the degradation of glucosylceramide. However, the mechanism by which GBA2 variants lead to the development of SA is still unclear. METHODS In this work, we perform next-generation RNA-sequencing (RNA-seq), in an attempt to discover differentially expressed genes (DEGs) in lymphoblastoid, fibroblast cell lines and induced pluripotent stem cell-derived neurons derived from patients with SA, homozygous for the GBA2 c.1780G > C missense variant. We further exploit DEGs in pathway analyses in order to elucidate candidate molecular mechanisms that are implicated in the development of the GBA2 gene-associated SA. RESULTS Our data reveal a total of 5217 genes with significantly altered expression between patient and control tested tissues. Furthermore, the most significant extracted pathways are presented and discussed for their possible role in the pathogenesis of the disease. Among them are the oxidative stress, neuroinflammation, sphingolipid signaling and metabolism, PI3K-Akt and MAPK signaling pathways. CONCLUSIONS Overall, our work examines for the first time the transcriptome profiles of GBA2-associated SA patients and suggests pathways and pathway synergies that could possibly have a role in SA pathogenesis. Lastly, it provides a list of DEGs and pathways that could be further validated towards the discovery of disease biomarkers.
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Affiliation(s)
- Andrea C. Kakouri
- Department of Neurogenetics, The Cyprus Institute of Neurology and Genetics, 2370 Nicosia, Cyprus
- Department of Bioinformatics, The Cyprus Institute of Neurology and Genetics, 2370 Nicosia, Cyprus
- The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, 2370 Nicosia, Cyprus
| | - Christina Votsi
- Department of Neurogenetics, The Cyprus Institute of Neurology and Genetics, 2370 Nicosia, Cyprus
- The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, 2370 Nicosia, Cyprus
| | - Anastasis Oulas
- Department of Bioinformatics, The Cyprus Institute of Neurology and Genetics, 2370 Nicosia, Cyprus
- The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, 2370 Nicosia, Cyprus
| | - Paschalis Nicolaou
- Department of Neurogenetics, The Cyprus Institute of Neurology and Genetics, 2370 Nicosia, Cyprus
- The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, 2370 Nicosia, Cyprus
| | - Massimo Aureli
- Department of Medical Biotechnology and Translational Medicine, University of Milan, 20090 Milano, Italy
| | - Giulia Lunghi
- Department of Medical Biotechnology and Translational Medicine, University of Milan, 20090 Milano, Italy
| | - Maura Samarani
- Unité de Trafic Membranaire ét PathogénèseDépartement de Biologie Cellulaire et Infection, Institut Pasteur, 75015 Paris, France
| | - Giacomo M. Compagnoni
- Neurology Unit, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
- School of Medicine and Surgery, University of Milano-Bicocca, 20126 Monza, Milan Italy
| | - Sabrina Salani
- Neurology Unit, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Alessio Di Fonzo
- Neurology Unit, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | | | - George A. Tanteles
- The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, 2370 Nicosia, Cyprus
- Department of Clinical Genetics and Genomics, The Cyprus Institute of Neurology and Genetics, 2370 Nicosia, Cyprus
| | - Eleni Zamba-Papanicolaou
- The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, 2370 Nicosia, Cyprus
- Neurology Clinic D, The Cyprus Institute of Neurology and Genetics, 2370 Nicosia, Cyprus
| | - Marios Pantzaris
- The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, 2370 Nicosia, Cyprus
- Neurology Clinic C, The Cyprus Institute of Neurology and Genetics, 2370 Nicosia, Cyprus
| | - George M. Spyrou
- Department of Bioinformatics, The Cyprus Institute of Neurology and Genetics, 2370 Nicosia, Cyprus
- The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, 2370 Nicosia, Cyprus
| | - Kyproula Christodoulou
- Department of Neurogenetics, The Cyprus Institute of Neurology and Genetics, 2370 Nicosia, Cyprus
- The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, 2370 Nicosia, Cyprus
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16
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Lupski JR. Clan genomics: From OMIM phenotypic traits to genes and biology. Am J Med Genet A 2021; 185:3294-3313. [PMID: 34405553 PMCID: PMC8530976 DOI: 10.1002/ajmg.a.62434] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/29/2021] [Accepted: 07/04/2021] [Indexed: 12/20/2022]
Abstract
Clinical characterization of a patient phenotype has been the quintessential approach for elucidating a differential diagnosis and a hypothesis to explore a potential clinical diagnosis. This has resulted in a language of medicine and a semantic ontology, with both specialty- and subspecialty-specific lexicons, that can be challenging to translate and interpret. There is no 'Rosetta Stone' of clinical medicine such as the genetic code that can assist translation and interpretation of the language of genetics. Nevertheless, the information content embodied within a clinical diagnosis can guide management, therapeutic intervention, and potentially prognostic outlook of disease enabling anticipatory guidance for patients and families. Clinical genomics is now established firmly in medical practice. The granularity and informative content of a personal genome is immense. Yet, we are limited in our utility of much of that personal genome information by the lack of functional characterization of the overwhelming majority of computationally annotated genes in the haploid human reference genome sequence. Whereas DNA and the genetic code have provided a 'Rosetta Stone' to translate genetic variant information, clinical medicine, and clinical genomics provide the context to understand human biology and disease. A path forward will integrate deep phenotyping, such as available in a clinical synopsis in the Online Mendelian Inheritance in Man (OMIM) entries, with personal genome analyses.
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Affiliation(s)
- James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Texas Children's Hospital, Houston, Texas, USA
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17
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Grangeon L, Cassinari K, Rousseau S, Croisile B, Formaglio M, Moreaud O, Boutonnat J, Le Meur N, Miné M, Coste T, Pipiras E, Tournier-Lasserve E, Rovelet-Lecrux A, Campion D, Wallon D, Nicolas G. Early-Onset Cerebral Amyloid Angiopathy and Alzheimer Disease Related to an APP Locus Triplication. Neurol Genet 2021; 7:e609. [PMID: 34532568 PMCID: PMC8439959 DOI: 10.1212/nxg.0000000000000609] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 06/08/2021] [Indexed: 11/30/2022]
Abstract
Background and Objective To report a triplication of the amyloid-β precursor protein (APP) locus along with relative messenger RNA (mRNA) expression in a family with autosomal dominant early-onset cerebral amyloid angiopathy (CAA) and Alzheimer disease (AD). Methods Four copies of the APP gene were identified by quantitative multiplex PCR of short fluorescent fragments, fluorescent in situ hybridization (FISH), and array comparative genomic hybridization. APP mRNA levels were assessed using reverse-transcription–digital droplet PCR in the proband's whole blood and compared with 10 controls and 9 APP duplication carriers. Results Beginning at age 39 years, the proband developed severe episodic memory deficits with a CSF biomarker profile typical of AD and multiple lobar microbleeds in the posterior regions on brain MRI. His father had seizures and recurrent cerebral hemorrhage since the age of 37 years. His cerebral biopsy showed abundant perivascular amyloid deposits, leading to a diagnosis of CAA. In the proband, we identified 4 copies of a 506-kb region located on chromosome 21q21.3 and encompassing the whole APP gene without any other gene. FISH suggested that the genotype of the proband was 3 copies/1 copy corresponding to an APP locus triplication, which was consistent with the presence of 2 APP copies in the healthy mother and with the paternal medical history. Analysis of the APP mRNA level showed a 2-fold increase in the proband and a 1.8 fold increase in APP duplication carriers compared with controls. Discussion Increased copy number of APP is sufficient to cause AD and CAA, with likely earlier onset in case of triplication compared with duplication.
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Affiliation(s)
- Lou Grangeon
- Department of Neurology and CNR-MAJ (L.G., D.W.), Normandie University, UNIROUEN, Inserm U1245, CHU Rouen, CIC-CRB1404, F 76000; Department of Genetics and CNR-MAJ (K.C., S.R., N.L.M., A.R.-L., D.C., G.N.), Normandie University, UNIROUEN, Inserm U1245 and CHU Rouen, F 76000; Department of Neurology (B.C., M.F.), Lyon University Hospital; Department of Neurology (O.M.), Grenoble University Hospital; Department of Histology (J.B.), Grenoble University Hospital; AP-HP (M.M., T.C., E.T.-L.), Groupe Hospitalier Saint-Louis Lariboisière-Fernand-Widal, Service de Génétique Moléculaire Neurovasculaire, INSERM UMR 1141, NeuroDiderot,Université de Paris; Department of Histology Embryology and Cytogenetics (E.P.), Jean Verdier Hospital; Paris 13 University (E.P.), Sorbonne Paris Cité, UFR SMBH Bobigny; and PROTECT (E.P.), INSERM, Paris Diderot University, Bondy, France
| | - Kévin Cassinari
- Department of Neurology and CNR-MAJ (L.G., D.W.), Normandie University, UNIROUEN, Inserm U1245, CHU Rouen, CIC-CRB1404, F 76000; Department of Genetics and CNR-MAJ (K.C., S.R., N.L.M., A.R.-L., D.C., G.N.), Normandie University, UNIROUEN, Inserm U1245 and CHU Rouen, F 76000; Department of Neurology (B.C., M.F.), Lyon University Hospital; Department of Neurology (O.M.), Grenoble University Hospital; Department of Histology (J.B.), Grenoble University Hospital; AP-HP (M.M., T.C., E.T.-L.), Groupe Hospitalier Saint-Louis Lariboisière-Fernand-Widal, Service de Génétique Moléculaire Neurovasculaire, INSERM UMR 1141, NeuroDiderot,Université de Paris; Department of Histology Embryology and Cytogenetics (E.P.), Jean Verdier Hospital; Paris 13 University (E.P.), Sorbonne Paris Cité, UFR SMBH Bobigny; and PROTECT (E.P.), INSERM, Paris Diderot University, Bondy, France
| | - Stéphane Rousseau
- Department of Neurology and CNR-MAJ (L.G., D.W.), Normandie University, UNIROUEN, Inserm U1245, CHU Rouen, CIC-CRB1404, F 76000; Department of Genetics and CNR-MAJ (K.C., S.R., N.L.M., A.R.-L., D.C., G.N.), Normandie University, UNIROUEN, Inserm U1245 and CHU Rouen, F 76000; Department of Neurology (B.C., M.F.), Lyon University Hospital; Department of Neurology (O.M.), Grenoble University Hospital; Department of Histology (J.B.), Grenoble University Hospital; AP-HP (M.M., T.C., E.T.-L.), Groupe Hospitalier Saint-Louis Lariboisière-Fernand-Widal, Service de Génétique Moléculaire Neurovasculaire, INSERM UMR 1141, NeuroDiderot,Université de Paris; Department of Histology Embryology and Cytogenetics (E.P.), Jean Verdier Hospital; Paris 13 University (E.P.), Sorbonne Paris Cité, UFR SMBH Bobigny; and PROTECT (E.P.), INSERM, Paris Diderot University, Bondy, France
| | - Bernard Croisile
- Department of Neurology and CNR-MAJ (L.G., D.W.), Normandie University, UNIROUEN, Inserm U1245, CHU Rouen, CIC-CRB1404, F 76000; Department of Genetics and CNR-MAJ (K.C., S.R., N.L.M., A.R.-L., D.C., G.N.), Normandie University, UNIROUEN, Inserm U1245 and CHU Rouen, F 76000; Department of Neurology (B.C., M.F.), Lyon University Hospital; Department of Neurology (O.M.), Grenoble University Hospital; Department of Histology (J.B.), Grenoble University Hospital; AP-HP (M.M., T.C., E.T.-L.), Groupe Hospitalier Saint-Louis Lariboisière-Fernand-Widal, Service de Génétique Moléculaire Neurovasculaire, INSERM UMR 1141, NeuroDiderot,Université de Paris; Department of Histology Embryology and Cytogenetics (E.P.), Jean Verdier Hospital; Paris 13 University (E.P.), Sorbonne Paris Cité, UFR SMBH Bobigny; and PROTECT (E.P.), INSERM, Paris Diderot University, Bondy, France
| | - Maïté Formaglio
- Department of Neurology and CNR-MAJ (L.G., D.W.), Normandie University, UNIROUEN, Inserm U1245, CHU Rouen, CIC-CRB1404, F 76000; Department of Genetics and CNR-MAJ (K.C., S.R., N.L.M., A.R.-L., D.C., G.N.), Normandie University, UNIROUEN, Inserm U1245 and CHU Rouen, F 76000; Department of Neurology (B.C., M.F.), Lyon University Hospital; Department of Neurology (O.M.), Grenoble University Hospital; Department of Histology (J.B.), Grenoble University Hospital; AP-HP (M.M., T.C., E.T.-L.), Groupe Hospitalier Saint-Louis Lariboisière-Fernand-Widal, Service de Génétique Moléculaire Neurovasculaire, INSERM UMR 1141, NeuroDiderot,Université de Paris; Department of Histology Embryology and Cytogenetics (E.P.), Jean Verdier Hospital; Paris 13 University (E.P.), Sorbonne Paris Cité, UFR SMBH Bobigny; and PROTECT (E.P.), INSERM, Paris Diderot University, Bondy, France
| | - Olivier Moreaud
- Department of Neurology and CNR-MAJ (L.G., D.W.), Normandie University, UNIROUEN, Inserm U1245, CHU Rouen, CIC-CRB1404, F 76000; Department of Genetics and CNR-MAJ (K.C., S.R., N.L.M., A.R.-L., D.C., G.N.), Normandie University, UNIROUEN, Inserm U1245 and CHU Rouen, F 76000; Department of Neurology (B.C., M.F.), Lyon University Hospital; Department of Neurology (O.M.), Grenoble University Hospital; Department of Histology (J.B.), Grenoble University Hospital; AP-HP (M.M., T.C., E.T.-L.), Groupe Hospitalier Saint-Louis Lariboisière-Fernand-Widal, Service de Génétique Moléculaire Neurovasculaire, INSERM UMR 1141, NeuroDiderot,Université de Paris; Department of Histology Embryology and Cytogenetics (E.P.), Jean Verdier Hospital; Paris 13 University (E.P.), Sorbonne Paris Cité, UFR SMBH Bobigny; and PROTECT (E.P.), INSERM, Paris Diderot University, Bondy, France
| | - Jean Boutonnat
- Department of Neurology and CNR-MAJ (L.G., D.W.), Normandie University, UNIROUEN, Inserm U1245, CHU Rouen, CIC-CRB1404, F 76000; Department of Genetics and CNR-MAJ (K.C., S.R., N.L.M., A.R.-L., D.C., G.N.), Normandie University, UNIROUEN, Inserm U1245 and CHU Rouen, F 76000; Department of Neurology (B.C., M.F.), Lyon University Hospital; Department of Neurology (O.M.), Grenoble University Hospital; Department of Histology (J.B.), Grenoble University Hospital; AP-HP (M.M., T.C., E.T.-L.), Groupe Hospitalier Saint-Louis Lariboisière-Fernand-Widal, Service de Génétique Moléculaire Neurovasculaire, INSERM UMR 1141, NeuroDiderot,Université de Paris; Department of Histology Embryology and Cytogenetics (E.P.), Jean Verdier Hospital; Paris 13 University (E.P.), Sorbonne Paris Cité, UFR SMBH Bobigny; and PROTECT (E.P.), INSERM, Paris Diderot University, Bondy, France
| | - Nathalie Le Meur
- Department of Neurology and CNR-MAJ (L.G., D.W.), Normandie University, UNIROUEN, Inserm U1245, CHU Rouen, CIC-CRB1404, F 76000; Department of Genetics and CNR-MAJ (K.C., S.R., N.L.M., A.R.-L., D.C., G.N.), Normandie University, UNIROUEN, Inserm U1245 and CHU Rouen, F 76000; Department of Neurology (B.C., M.F.), Lyon University Hospital; Department of Neurology (O.M.), Grenoble University Hospital; Department of Histology (J.B.), Grenoble University Hospital; AP-HP (M.M., T.C., E.T.-L.), Groupe Hospitalier Saint-Louis Lariboisière-Fernand-Widal, Service de Génétique Moléculaire Neurovasculaire, INSERM UMR 1141, NeuroDiderot,Université de Paris; Department of Histology Embryology and Cytogenetics (E.P.), Jean Verdier Hospital; Paris 13 University (E.P.), Sorbonne Paris Cité, UFR SMBH Bobigny; and PROTECT (E.P.), INSERM, Paris Diderot University, Bondy, France
| | - Manuele Miné
- Department of Neurology and CNR-MAJ (L.G., D.W.), Normandie University, UNIROUEN, Inserm U1245, CHU Rouen, CIC-CRB1404, F 76000; Department of Genetics and CNR-MAJ (K.C., S.R., N.L.M., A.R.-L., D.C., G.N.), Normandie University, UNIROUEN, Inserm U1245 and CHU Rouen, F 76000; Department of Neurology (B.C., M.F.), Lyon University Hospital; Department of Neurology (O.M.), Grenoble University Hospital; Department of Histology (J.B.), Grenoble University Hospital; AP-HP (M.M., T.C., E.T.-L.), Groupe Hospitalier Saint-Louis Lariboisière-Fernand-Widal, Service de Génétique Moléculaire Neurovasculaire, INSERM UMR 1141, NeuroDiderot,Université de Paris; Department of Histology Embryology and Cytogenetics (E.P.), Jean Verdier Hospital; Paris 13 University (E.P.), Sorbonne Paris Cité, UFR SMBH Bobigny; and PROTECT (E.P.), INSERM, Paris Diderot University, Bondy, France
| | - Thibault Coste
- Department of Neurology and CNR-MAJ (L.G., D.W.), Normandie University, UNIROUEN, Inserm U1245, CHU Rouen, CIC-CRB1404, F 76000; Department of Genetics and CNR-MAJ (K.C., S.R., N.L.M., A.R.-L., D.C., G.N.), Normandie University, UNIROUEN, Inserm U1245 and CHU Rouen, F 76000; Department of Neurology (B.C., M.F.), Lyon University Hospital; Department of Neurology (O.M.), Grenoble University Hospital; Department of Histology (J.B.), Grenoble University Hospital; AP-HP (M.M., T.C., E.T.-L.), Groupe Hospitalier Saint-Louis Lariboisière-Fernand-Widal, Service de Génétique Moléculaire Neurovasculaire, INSERM UMR 1141, NeuroDiderot,Université de Paris; Department of Histology Embryology and Cytogenetics (E.P.), Jean Verdier Hospital; Paris 13 University (E.P.), Sorbonne Paris Cité, UFR SMBH Bobigny; and PROTECT (E.P.), INSERM, Paris Diderot University, Bondy, France
| | - Eva Pipiras
- Department of Neurology and CNR-MAJ (L.G., D.W.), Normandie University, UNIROUEN, Inserm U1245, CHU Rouen, CIC-CRB1404, F 76000; Department of Genetics and CNR-MAJ (K.C., S.R., N.L.M., A.R.-L., D.C., G.N.), Normandie University, UNIROUEN, Inserm U1245 and CHU Rouen, F 76000; Department of Neurology (B.C., M.F.), Lyon University Hospital; Department of Neurology (O.M.), Grenoble University Hospital; Department of Histology (J.B.), Grenoble University Hospital; AP-HP (M.M., T.C., E.T.-L.), Groupe Hospitalier Saint-Louis Lariboisière-Fernand-Widal, Service de Génétique Moléculaire Neurovasculaire, INSERM UMR 1141, NeuroDiderot,Université de Paris; Department of Histology Embryology and Cytogenetics (E.P.), Jean Verdier Hospital; Paris 13 University (E.P.), Sorbonne Paris Cité, UFR SMBH Bobigny; and PROTECT (E.P.), INSERM, Paris Diderot University, Bondy, France
| | - Elisabeth Tournier-Lasserve
- Department of Neurology and CNR-MAJ (L.G., D.W.), Normandie University, UNIROUEN, Inserm U1245, CHU Rouen, CIC-CRB1404, F 76000; Department of Genetics and CNR-MAJ (K.C., S.R., N.L.M., A.R.-L., D.C., G.N.), Normandie University, UNIROUEN, Inserm U1245 and CHU Rouen, F 76000; Department of Neurology (B.C., M.F.), Lyon University Hospital; Department of Neurology (O.M.), Grenoble University Hospital; Department of Histology (J.B.), Grenoble University Hospital; AP-HP (M.M., T.C., E.T.-L.), Groupe Hospitalier Saint-Louis Lariboisière-Fernand-Widal, Service de Génétique Moléculaire Neurovasculaire, INSERM UMR 1141, NeuroDiderot,Université de Paris; Department of Histology Embryology and Cytogenetics (E.P.), Jean Verdier Hospital; Paris 13 University (E.P.), Sorbonne Paris Cité, UFR SMBH Bobigny; and PROTECT (E.P.), INSERM, Paris Diderot University, Bondy, France
| | - Anne Rovelet-Lecrux
- Department of Neurology and CNR-MAJ (L.G., D.W.), Normandie University, UNIROUEN, Inserm U1245, CHU Rouen, CIC-CRB1404, F 76000; Department of Genetics and CNR-MAJ (K.C., S.R., N.L.M., A.R.-L., D.C., G.N.), Normandie University, UNIROUEN, Inserm U1245 and CHU Rouen, F 76000; Department of Neurology (B.C., M.F.), Lyon University Hospital; Department of Neurology (O.M.), Grenoble University Hospital; Department of Histology (J.B.), Grenoble University Hospital; AP-HP (M.M., T.C., E.T.-L.), Groupe Hospitalier Saint-Louis Lariboisière-Fernand-Widal, Service de Génétique Moléculaire Neurovasculaire, INSERM UMR 1141, NeuroDiderot,Université de Paris; Department of Histology Embryology and Cytogenetics (E.P.), Jean Verdier Hospital; Paris 13 University (E.P.), Sorbonne Paris Cité, UFR SMBH Bobigny; and PROTECT (E.P.), INSERM, Paris Diderot University, Bondy, France
| | - Dominique Campion
- Department of Neurology and CNR-MAJ (L.G., D.W.), Normandie University, UNIROUEN, Inserm U1245, CHU Rouen, CIC-CRB1404, F 76000; Department of Genetics and CNR-MAJ (K.C., S.R., N.L.M., A.R.-L., D.C., G.N.), Normandie University, UNIROUEN, Inserm U1245 and CHU Rouen, F 76000; Department of Neurology (B.C., M.F.), Lyon University Hospital; Department of Neurology (O.M.), Grenoble University Hospital; Department of Histology (J.B.), Grenoble University Hospital; AP-HP (M.M., T.C., E.T.-L.), Groupe Hospitalier Saint-Louis Lariboisière-Fernand-Widal, Service de Génétique Moléculaire Neurovasculaire, INSERM UMR 1141, NeuroDiderot,Université de Paris; Department of Histology Embryology and Cytogenetics (E.P.), Jean Verdier Hospital; Paris 13 University (E.P.), Sorbonne Paris Cité, UFR SMBH Bobigny; and PROTECT (E.P.), INSERM, Paris Diderot University, Bondy, France
| | - David Wallon
- Department of Neurology and CNR-MAJ (L.G., D.W.), Normandie University, UNIROUEN, Inserm U1245, CHU Rouen, CIC-CRB1404, F 76000; Department of Genetics and CNR-MAJ (K.C., S.R., N.L.M., A.R.-L., D.C., G.N.), Normandie University, UNIROUEN, Inserm U1245 and CHU Rouen, F 76000; Department of Neurology (B.C., M.F.), Lyon University Hospital; Department of Neurology (O.M.), Grenoble University Hospital; Department of Histology (J.B.), Grenoble University Hospital; AP-HP (M.M., T.C., E.T.-L.), Groupe Hospitalier Saint-Louis Lariboisière-Fernand-Widal, Service de Génétique Moléculaire Neurovasculaire, INSERM UMR 1141, NeuroDiderot,Université de Paris; Department of Histology Embryology and Cytogenetics (E.P.), Jean Verdier Hospital; Paris 13 University (E.P.), Sorbonne Paris Cité, UFR SMBH Bobigny; and PROTECT (E.P.), INSERM, Paris Diderot University, Bondy, France
| | - Gael Nicolas
- Department of Neurology and CNR-MAJ (L.G., D.W.), Normandie University, UNIROUEN, Inserm U1245, CHU Rouen, CIC-CRB1404, F 76000; Department of Genetics and CNR-MAJ (K.C., S.R., N.L.M., A.R.-L., D.C., G.N.), Normandie University, UNIROUEN, Inserm U1245 and CHU Rouen, F 76000; Department of Neurology (B.C., M.F.), Lyon University Hospital; Department of Neurology (O.M.), Grenoble University Hospital; Department of Histology (J.B.), Grenoble University Hospital; AP-HP (M.M., T.C., E.T.-L.), Groupe Hospitalier Saint-Louis Lariboisière-Fernand-Widal, Service de Génétique Moléculaire Neurovasculaire, INSERM UMR 1141, NeuroDiderot,Université de Paris; Department of Histology Embryology and Cytogenetics (E.P.), Jean Verdier Hospital; Paris 13 University (E.P.), Sorbonne Paris Cité, UFR SMBH Bobigny; and PROTECT (E.P.), INSERM, Paris Diderot University, Bondy, France
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Heras-Garvin A, Stefanova N. From Synaptic Protein to Prion: The Long and Controversial Journey of α-Synuclein. Front Synaptic Neurosci 2020; 12:584536. [PMID: 33071772 PMCID: PMC7536368 DOI: 10.3389/fnsyn.2020.584536] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 08/26/2020] [Indexed: 12/12/2022] Open
Abstract
Since its discovery 30 years ago, α-synuclein (α-syn) has been one of the most studied proteins in the field of neuroscience. Dozens of groups worldwide have tried to reveal not only its role in the CNS but also in other organs. α-syn has been linked to several processes essential in brain homeostasis such as neurotransmitter release, synaptic function, and plasticity. However, despite the efforts made in this direction, the main function of α-syn is still unknown. Moreover, α-syn became a protein of interest for neurologists and neuroscientists when mutations in its gene were found associated with Parkinson's disease (PD) and even more when α-syn protein deposits were observed in the brain of PD, dementia with Lewy bodies (DLB), and multiple system atrophy (MSA) patients. At present, the abnormal accumulation of α-syn constitutes one of the pathological hallmarks of these disorders, also referred to as α-synucleinopathies, and it is used for post-mortem diagnostic criteria. Whether α-syn aggregation is cause or consequence of the pathogenic events underlying α-synucleinopathies remains unclear and under discussion. Recently, different in vitro and in vivo studies have shown the ability of pathogenic α-syn to spread between cells, not only within the CNS but also from peripheral locations such as the gut, salivary glands, and through the olfactory network into the CNS, inducing abnormal misfolding of endogenous α-syn and leading to neurodegeneration and motor and cognitive impairment in animal models. Thus, it has been suggested that α-syn should be considered a prion protein. Here we present an update of what we know about α-syn function, aggregation and spreading, and its role in neurodegeneration. We also discuss the rationale and findings supporting the hypothetical prion nature of α-syn, its weaknesses, and future perspectives for research and the development of disease-modifying therapies.
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Affiliation(s)
- Antonio Heras-Garvin
- Division of Neurobiology, Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Nadia Stefanova
- Division of Neurobiology, Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
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The Role of Alpha-Synuclein and Other Parkinson's Genes in Neurodevelopmental and Neurodegenerative Disorders. Int J Mol Sci 2020; 21:ijms21165724. [PMID: 32785033 PMCID: PMC7460874 DOI: 10.3390/ijms21165724] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 07/29/2020] [Accepted: 08/08/2020] [Indexed: 12/13/2022] Open
Abstract
Neurodevelopmental and late-onset neurodegenerative disorders present as separate entities that are clinically and neuropathologically quite distinct. However, recent evidence has highlighted surprising commonalities and converging features at the clinical, genomic, and molecular level between these two disease spectra. This is particularly striking in the context of autism spectrum disorder (ASD) and Parkinson's disease (PD). Genetic causes and risk factors play a central role in disease pathophysiology and enable the identification of overlapping mechanisms and pathways. Here, we focus on clinico-genetic studies of causal variants and overlapping clinical and cellular features of ASD and PD. Several genes and genomic regions were selected for our review, including SNCA (alpha-synuclein), PARK2 (parkin RBR E3 ubiquitin protein ligase), chromosome 22q11 deletion/DiGeorge region, and FMR1 (fragile X mental retardation 1) repeat expansion, which influence the development of both ASD and PD, with converging features related to synaptic function and neurogenesis. Both PD and ASD display alterations and impairments at the synaptic level, representing early and key disease phenotypes, which support the hypothesis of converging mechanisms between the two types of diseases. Therefore, understanding the underlying molecular mechanisms might inform on common targets and therapeutic approaches. We propose to re-conceptualize how we understand these disorders and provide a new angle into disease targets and mechanisms linking neurodevelopmental disorders and neurodegeneration.
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Robak LA, Du R, Yuan B, Gu S, Alfradique-Dunham I, Kondapalli V, Hinojosa E, Stillwell A, Young E, Zhang C, Song X, Du H, Gambin T, Jhangiani SN, Coban Akdemir Z, Muzny DM, Tejomurtula A, Ross OA, Shaw C, Jankovic J, Bi W, Posey JE, Lupski JR, Shulman JM. Integrated sequencing and array comparative genomic hybridization in familial Parkinson disease. NEUROLOGY-GENETICS 2020; 6:e498. [PMID: 32802956 PMCID: PMC7413630 DOI: 10.1212/nxg.0000000000000498] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 06/15/2020] [Indexed: 12/16/2022]
Abstract
Objective To determine how single nucleotide variants (SNVs) and copy number variants (CNVs) contribute to molecular diagnosis in familial Parkinson disease (PD), we integrated exome sequencing (ES) and genome-wide array-based comparative genomic hybridization (aCGH) and further probed CNV structure to reveal mutational mechanisms. Methods We performed ES on 110 subjects with PD and a positive family history; 99 subjects were also evaluated using genome-wide aCGH. We interrogated ES and aCGH data for pathogenic SNVs and CNVs at Mendelian PD gene loci. We confirmed SNVs via Sanger sequencing and further characterized CNVs with custom-designed high-density aCGH, droplet digital PCR, and breakpoint sequencing. Results Using ES, we discovered individuals with known pathogenic SNVs in GBA (p.Glu365Lys, p.Thr408Met, p.Asn409Ser, and p.Leu483Pro) and LRRK2 (p.Arg1441Gly and p.Gly2019Ser). Two subjects were each double heterozygotes for variants in GBA and LRRK2. Based on aCGH, we additionally discovered cases with an SNCA duplication and heterozygous intragenic GBA deletion. Five additional subjects harbored both SNVs (p.Asn52Metfs*29, p.Thr240Met, p.Pro437Leu, and p.Trp453*) and likely disrupting CNVs at the PRKN locus, consistent with compound heterozygosity. In nearly all cases, breakpoint sequencing revealed microhomology, a mutational signature consistent with CNV formation due to DNA replication errors. Conclusions Integrated ES and aCGH yielded a genetic diagnosis in 19.3% of our familial PD cohort. Our analyses highlight potential mechanisms for SNCA and PRKN CNV formation, uncover multilocus pathogenic variation, and identify novel SNVs and CNVs for further investigation as potential PD risk alleles.
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Affiliation(s)
- Laurie A Robak
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Renqian Du
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Bo Yuan
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Shen Gu
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Isabel Alfradique-Dunham
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Vismaya Kondapalli
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Evelyn Hinojosa
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Amanda Stillwell
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Emily Young
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Chaofan Zhang
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Xiaofei Song
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Haowei Du
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Tomasz Gambin
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Shalini N Jhangiani
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Zeynep Coban Akdemir
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Donna M Muzny
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Anusha Tejomurtula
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Owen A Ross
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Chad Shaw
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Joseph Jankovic
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Weimin Bi
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Jennifer E Posey
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - James R Lupski
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Joshua M Shulman
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
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Mariño L, Ramis R, Casasnovas R, Ortega-Castro J, Vilanova B, Frau J, Adrover M. Unravelling the effect of N(ε)-(carboxyethyl)lysine on the conformation, dynamics and aggregation propensity of α-synuclein. Chem Sci 2020; 11:3332-3344. [PMID: 34122841 PMCID: PMC8157327 DOI: 10.1039/d0sc00906g] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
α-Synuclein (αS) aggregation is a hallmark in several neurodegenerative diseases. Among them, Parkinson's disease is highlighted, characterized by the intraneuronal deposition of Lewy bodies (LBs) which causes the loss of dopaminergic neurons. αS is the main component of LBs and in them, it usually contains post-translational modifications. One of them is the formation of advanced glycation end-products (mainly CEL and MOLD) arising from its reaction with methylglyoxal. Despite its biological relevance, there are no data available proving the effect of glycation on the conformation of αS, nor on its aggregation mechanism. This has been hampered by the formation of a heterogeneous set of compounds that precluded conformational studies. To overcome this issue, we have here produced αS homogeneously glycated with CEL. Its use, together with different biophysical techniques and molecular dynamics simulations, allowed us to study for the first time the effect of glycation on the conformation of a protein. CEL extended the conformation of the N-terminal domain as a result of the loss of transient N-/C-terminal long-range contacts while increasing the heterogeneity of the conformational population. CEL also inhibited the αS aggregation, but it was not able to disassemble preexisting amyloid fibrils, thus proving that CEL found on LBs must be formed in a later event after aggregation. We study the effect of an advanced glycation end product (N(ε)-(carboxyethyl)lysine), found on the Lewy bodies of people suffering from Parkinson’s disease, on the conformational and aggregation features of alpha-synuclein.![]()
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Affiliation(s)
- Laura Mariño
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Institut d'Investigació Sanitària Illes Balears (IdISBa), Departament de Química, Universitat de les Illes Balears Ctra. Valldemossa km 7.5 E-07122 Palma de Mallorca Spain +34 971 173426 +34 971 173491
| | - Rafael Ramis
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Institut d'Investigació Sanitària Illes Balears (IdISBa), Departament de Química, Universitat de les Illes Balears Ctra. Valldemossa km 7.5 E-07122 Palma de Mallorca Spain +34 971 173426 +34 971 173491
| | - Rodrigo Casasnovas
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Institut d'Investigació Sanitària Illes Balears (IdISBa), Departament de Química, Universitat de les Illes Balears Ctra. Valldemossa km 7.5 E-07122 Palma de Mallorca Spain +34 971 173426 +34 971 173491
| | - Joaquín Ortega-Castro
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Institut d'Investigació Sanitària Illes Balears (IdISBa), Departament de Química, Universitat de les Illes Balears Ctra. Valldemossa km 7.5 E-07122 Palma de Mallorca Spain +34 971 173426 +34 971 173491
| | - Bartolomé Vilanova
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Institut d'Investigació Sanitària Illes Balears (IdISBa), Departament de Química, Universitat de les Illes Balears Ctra. Valldemossa km 7.5 E-07122 Palma de Mallorca Spain +34 971 173426 +34 971 173491
| | - Juan Frau
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Institut d'Investigació Sanitària Illes Balears (IdISBa), Departament de Química, Universitat de les Illes Balears Ctra. Valldemossa km 7.5 E-07122 Palma de Mallorca Spain +34 971 173426 +34 971 173491
| | - Miquel Adrover
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Institut d'Investigació Sanitària Illes Balears (IdISBa), Departament de Química, Universitat de les Illes Balears Ctra. Valldemossa km 7.5 E-07122 Palma de Mallorca Spain +34 971 173426 +34 971 173491
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22
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Seo SH, Bacolla A, Yoo D, Koo YJ, Cho SI, Kim MJ, Seong MW, Kim HJ, Kim JM, Tainer JA, Park SS, Kim JY, Jeon B. Replication-Based Rearrangements Are a Common Mechanism for SNCA Duplication in Parkinson's Disease. Mov Disord 2020; 35:868-876. [PMID: 32039503 DOI: 10.1002/mds.27998] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/10/2020] [Accepted: 01/27/2020] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND SNCA multiplication is a genomic cause of familial PD, showing dosage-dependent toxicity. Until now, nonallelic homologous recombination was suggested as the mechanism of SNCA duplication, based on various types of repetitive elements found in the spanning region of the breakpoints. However, the sequence at the breakpoint was analyzed only for 1 case. OBJECTIVES We have analyzed the breakpoint sequences of 6 patients with PD who had duplicated SNCA using whole-genome sequencing data to elucidate the mechanism of SNCA duplication. METHODS Six patient samples with SNCA duplication underwent whole-genome sequencing. The duplicated regions were defined with nucleotide-resolution breakpoints, which were confirmed by junction polymerase chain reaction and Sanger sequencing. The search for potential non-B DNA-forming sequences and stem-loop structure predictions was conducted. RESULTS Duplicated regions ranged from the smallest region of 718.3 kb to the largest one of 4,162 kb. Repetitive elements were found at 8 of the 12 breakpoint sequences on each side of the junction, but none of the pairs shared overt homologies. Five of these six junctions had microhomologies (2-4 bp) at the breakpoint, and a short stretch of sequences was inserted in 3 cases. All except one junction were located within or next to stem-loop structures. CONCLUSION Our study has determined that homologous recombination mechanisms involving repetitive elements are not the main cause of the duplication of SNCA. The presence of microhomology at the junctions and their position within stem-loop structures suggest that replication-based rearrangements may be a common mechanism for SNCA amplification. © 2020 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Soo Hyun Seo
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam, Korea.,Seoul National University College of Medicine, Seoul, Korea
| | - Albino Bacolla
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Dallah Yoo
- Department of Neurology, Kyung Hee University Hospital, Seoul, Korea
| | - Yoon Jung Koo
- Seoul National University College of Medicine, Seoul, Korea.,Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Sung Im Cho
- Seoul National University College of Medicine, Seoul, Korea.,Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Man Jin Kim
- Seoul National University College of Medicine, Seoul, Korea.,Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Moon-Woo Seong
- Seoul National University College of Medicine, Seoul, Korea.,Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Han-Joon Kim
- Seoul National University College of Medicine, Seoul, Korea.,Department of Neurology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Jong-Min Kim
- Seoul National University College of Medicine, Seoul, Korea.,Department of Neurology, Seoul National University Bundang Hospital, Seongnam, Korea
| | - John A Tainer
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sung Sup Park
- Seoul National University College of Medicine, Seoul, Korea.,Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea.,Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
| | - Ji Yeon Kim
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
| | - Beomseok Jeon
- Seoul National University College of Medicine, Seoul, Korea.,Department of Neurology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
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23
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Bernal-Conde LD, Ramos-Acevedo R, Reyes-Hernández MA, Balbuena-Olvera AJ, Morales-Moreno ID, Argüero-Sánchez R, Schüle B, Guerra-Crespo M. Alpha-Synuclein Physiology and Pathology: A Perspective on Cellular Structures and Organelles. Front Neurosci 2020; 13:1399. [PMID: 32038126 PMCID: PMC6989544 DOI: 10.3389/fnins.2019.01399] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 12/12/2019] [Indexed: 12/21/2022] Open
Abstract
Alpha-synuclein (α-syn) is localized in cellular organelles of most neurons, but many of its physiological functions are only partially understood. α-syn accumulation is associated with Parkinson's disease, dementia with Lewy bodies, and multiple system atrophy as well as other synucleinopathies; however, the exact pathomechanisms that underlie these neurodegenerative diseases remain elusive. In this review, we describe what is known about α-syn function and pathophysiological changes in different cellular structures and organelles, including what is known about its behavior as a prion-like protein. We summarize current knowledge of α-syn and its pathological forms, covering its effect on each organelle, including aggregation and toxicity in different model systems, with special interest on the mitochondria due to its relevance during the apoptotic process of dopaminergic neurons. Moreover, we explore the effect that α-syn exerts by interacting with chromatin remodeling proteins that add or remove histone marks, up-regulate its own expression, and resume the impairment that α-syn induces in vesicular traffic by interacting with the endoplasmic reticulum. We then recapitulate the events that lead to Golgi apparatus fragmentation, caused by the presence of α-syn. Finally, we report the recent findings about the accumulation of α-syn, indirectly produced by the endolysosomal system. In conclusion, many important steps into the understanding of α-syn have been made using in vivo and in vitro models; however, the time is right to start integrating observational studies with mechanistic models of α-syn interactions, in order to look at a more complete picture of the pathophysiological processes underlying α-synucleinopathies.
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Affiliation(s)
- Luis D. Bernal-Conde
- División de Neurociencias, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Laboratorio de Medicina Regenerativa, Departamento de Cirugía, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Rodrigo Ramos-Acevedo
- División de Neurociencias, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Laboratorio de Medicina Regenerativa, Departamento de Cirugía, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Mario A. Reyes-Hernández
- División de Neurociencias, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Laboratorio de Medicina Regenerativa, Departamento de Cirugía, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Andrea J. Balbuena-Olvera
- División de Neurociencias, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Laboratorio de Medicina Regenerativa, Departamento de Cirugía, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Ishbelt D. Morales-Moreno
- División de Neurociencias, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Laboratorio de Medicina Regenerativa, Departamento de Cirugía, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Rubén Argüero-Sánchez
- Laboratorio de Medicina Regenerativa, Departamento de Cirugía, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Birgitt Schüle
- Department of Pathology, Stanford School of Medicine, Stanford University, Stanford, CA, United States
| | - Magdalena Guerra-Crespo
- División de Neurociencias, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Laboratorio de Medicina Regenerativa, Departamento de Cirugía, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
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Perez-Rodriguez D, Kalyva M, Leija-Salazar M, Lashley T, Tarabichi M, Chelban V, Gentleman S, Schottlaender L, Franklin H, Vasmatzis G, Houlden H, Schapira AHV, Warner TT, Holton JL, Jaunmuktane Z, Proukakis C. Investigation of somatic CNVs in brains of synucleinopathy cases using targeted SNCA analysis and single cell sequencing. Acta Neuropathol Commun 2019; 7:219. [PMID: 31870437 PMCID: PMC6929293 DOI: 10.1186/s40478-019-0873-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 12/17/2019] [Indexed: 12/17/2022] Open
Abstract
Synucleinopathies are mostly sporadic neurodegenerative disorders of partly unexplained aetiology, and include Parkinson's disease (PD) and multiple system atrophy (MSA). We have further investigated our recent finding of somatic SNCA (α-synuclein) copy number variants (CNVs, specifically gains) in synucleinopathies, using Fluorescent in-situ Hybridisation for SNCA, and single-cell whole genome sequencing for the first time in a synucleinopathy. In the cingulate cortex, mosaicism levels for SNCA gains were higher in MSA and PD than controls in neurons (> 2% in both diseases), and for MSA also in non-neurons. In MSA substantia nigra (SN), we noted SNCA gains in > 3% of dopaminergic (DA) neurons (identified by neuromelanin) and neuromelanin-negative cells, including olig2-positive oligodendroglia. Cells with CNVs were more likely to have α-synuclein inclusions, in a pattern corresponding to cell categories mostly relevant to the disease: DA neurons in Lewy-body cases, and other cells in the striatonigral degeneration-dominant MSA variant (MSA-SND). Higher mosaicism levels in SN neuromelanin-negative cells may correlate with younger onset in typical MSA-SND, and in cingulate neurons with younger death in PD. Larger sample sizes will, however, be required to confirm these putative findings. We obtained genome-wide somatic CNV profiles from 169 cells from the substantia nigra of two MSA cases, and pons and putamen of one. These showed somatic CNVs in ~ 30% of cells, with clonality and origins in segmental duplications for some. CNVs had distinct profiles based on cell type, with neurons having a mix of gains and losses, and other cells having almost exclusively gains, although control data sets will be required to determine possible disease relevance. We propose that somatic SNCA CNVs may contribute to the aetiology and pathogenesis of synucleinopathies, and that genome-wide somatic CNVs in MSA brain merit further study.
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Affiliation(s)
- Diego Perez-Rodriguez
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Maria Kalyva
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Melissa Leija-Salazar
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Tammaryn Lashley
- Queen Square Brain Bank for Neurological disorders, UCL Queen Square Institute of Neurology, 1 Wakefield street, London, WC1N 1PJ, UK
| | - Maxime Tarabichi
- The Francis Crick Institute, Midland Road 1, London, NW1 1AT, UK
| | - Viorica Chelban
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- National Hospital for Neurology and Neurosurgery, Queen Square, London, WC1N 3BG, UK
| | | | - Lucia Schottlaender
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- National Hospital for Neurology and Neurosurgery, Queen Square, London, WC1N 3BG, UK
| | - Hannah Franklin
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - George Vasmatzis
- Center for Individualized Medicine, Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- National Hospital for Neurology and Neurosurgery, Queen Square, London, WC1N 3BG, UK
| | - Anthony H V Schapira
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Thomas T Warner
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- Queen Square Brain Bank for Neurological disorders, UCL Queen Square Institute of Neurology, 1 Wakefield street, London, WC1N 1PJ, UK
- National Hospital for Neurology and Neurosurgery, Queen Square, London, WC1N 3BG, UK
| | - Janice L Holton
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- Queen Square Brain Bank for Neurological disorders, UCL Queen Square Institute of Neurology, 1 Wakefield street, London, WC1N 1PJ, UK
| | - Zane Jaunmuktane
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- Queen Square Brain Bank for Neurological disorders, UCL Queen Square Institute of Neurology, 1 Wakefield street, London, WC1N 1PJ, UK
- National Hospital for Neurology and Neurosurgery, Queen Square, London, WC1N 3BG, UK
| | - Christos Proukakis
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK.
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Cota-Coronado A, Díaz-Martínez NF, Padilla-Camberos E, Díaz-Martínez NE. Editing the Central Nervous System Through CRISPR/Cas9 Systems. Front Mol Neurosci 2019; 12:110. [PMID: 31191241 PMCID: PMC6546027 DOI: 10.3389/fnmol.2019.00110] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 04/15/2019] [Indexed: 12/26/2022] Open
Abstract
The translational gap to treatments based on gene therapy has been reduced in recent years because of improvements in gene editing tools, such as the CRISPR/Cas9 system and its variations. This has allowed the development of more precise therapies for neurodegenerative diseases, where access is privileged. As a result, engineering of complexes that can access the central nervous system (CNS) with the least potential inconvenience is fundamental. In this review article, we describe current alternatives to generate systems based on CRISPR/Cas9 that can cross the blood-brain barrier (BBB) and may be used further clinically to improve treatment for neurodegeneration in Parkinson's and Alzheimer's disease (AD).
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Affiliation(s)
- Agustin Cota-Coronado
- Biotecnología Médica y Farmacéutica CONACYT, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco (CIATEJ), Guadalajara, Mexico
| | | | - Eduardo Padilla-Camberos
- Biotecnología Médica y Farmacéutica CONACYT, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco (CIATEJ), Guadalajara, Mexico
| | - N Emmanuel Díaz-Martínez
- Biotecnología Médica y Farmacéutica CONACYT, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco (CIATEJ), Guadalajara, Mexico
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26
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Nicolas G, Veltman JA. The role of de novo mutations in adult-onset neurodegenerative disorders. Acta Neuropathol 2019; 137:183-207. [PMID: 30478624 PMCID: PMC6513904 DOI: 10.1007/s00401-018-1939-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 11/14/2018] [Accepted: 11/14/2018] [Indexed: 12/13/2022]
Abstract
The genetic underpinnings of the most common adult-onset neurodegenerative disorders (AOND) are complex in majority of the cases. In some families, however, the disease can be inherited in a Mendelian fashion as an autosomal-dominant trait. Next to that, patients carrying mutations in the same disease genes have been reported despite a negative family history. Although challenging to demonstrate due to the late onset of the disease in most cases, the occurrence of de novo mutations can explain this sporadic presentation, as demonstrated for severe neurodevelopmental disorders. Exome or genome sequencing of patient-parent trios allows a hypothesis-free study of the role of de novo mutations in AOND and the discovery of novel disease genes. Another hypothesis that may explain a proportion of sporadic AOND cases is the occurrence of a de novo mutation after the fertilization of the oocyte (post-zygotic mutation) or even as a late-somatic mutation, restricted to the brain. Such somatic mutation hypothesis, that can be tested with the use of novel sequencing technologies, is fully compatible with the seeding and spreading mechanisms of the pathological proteins identified in most of these disorders. We review here the current knowledge and future perspectives on de novo mutations in known and novel candidate genes identified in the most common AONDs such as Alzheimer's disease, Parkinson's disease, the frontotemporal lobar degeneration spectrum and Prion disorders. Also, we review the first lessons learned from recent genomic studies of control and diseased brains and the challenges which remain to be addressed.
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Affiliation(s)
- Gaël Nicolas
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics and CNR-MAJ, Normandy Center for Genomic and Personalized Medicine, 22, Boulevard Gambetta, 76000, 76031, Rouen Cedex, France.
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
| | - Joris A Veltman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
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Piper DA, Sastre D, Schüle B. Advancing Stem Cell Models of Alpha-Synuclein Gene Regulation in Neurodegenerative Disease. Front Neurosci 2018; 12:199. [PMID: 29686602 PMCID: PMC5900030 DOI: 10.3389/fnins.2018.00199] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Accepted: 03/13/2018] [Indexed: 12/15/2022] Open
Abstract
Alpha-synuclein (non A4 component of amyloid precursor, SNCA, NM_000345.3) plays a central role in the pathogenesis of Parkinson's disease (PD) and related Lewy body disorders such as Parkinson's disease dementia, Lewy body dementia, and multiple system atrophy. Since its discovery as a disease-causing gene in 1997, alpha-synuclein has been a central point of scientific interest both at the protein and gene level. Mutations, including copy number variants, missense mutations, short structural variants, and single nucleotide polymorphisms, can be causative for PD and affect conformational changes of the protein, can contribute to changes in expression of alpha-synuclein and its isoforms, and can influence regulation of temporal as well as spatial levels of alpha-synuclein in different tissues and cell types. A lot of progress has been made to understand both the physiological transcriptional and epigenetic regulation of the alpha-synuclein gene and whether changes in transcriptional regulation could lead to disease and neurodegeneration in PD and related alpha-synucleinopathies. Although the histopathological changes in these neurodegenerative disorders are similar, the temporal and spatial presentation and progression distinguishes them which could be in part due to changes or disruption of transcriptional regulation of alpha-synuclein. In this review, we describe different genetic alterations that contribute to PD and neurodegenerative conditions and review aspects of transcriptional regulation of the alpha-synuclein gene in the context of the development of PD. New technologies, advanced gene engineering and stem cell modeling, are on the horizon to shed further light on a better understanding of gene regulatory processes and exploit them for therapeutic developments.
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Affiliation(s)
- Desiree A Piper
- Parkinson's Institute and Clinical Center, Sunnyvale, CA, United States
| | - Danuta Sastre
- Parkinson's Institute and Clinical Center, Sunnyvale, CA, United States
| | - Birgitt Schüle
- Parkinson's Institute and Clinical Center, Sunnyvale, CA, United States
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