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Wang J, Yan L, Wang X, Jia R, Guo J. Surface PD-1 expression in T cells is suppressed by HNRNPK through an exonic splicing silencer on exon 3. Inflamm Res 2024; 73:1123-1135. [PMID: 38698180 DOI: 10.1007/s00011-024-01887-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 04/12/2024] [Accepted: 04/16/2024] [Indexed: 05/05/2024] Open
Abstract
OBJECTIVE Immunotherapy targeting programmed cell death 1 (PDCD1 or PD-1) and its ligands has shown remarkable promise and the regulation mechanism of PD-1 expression has received arising attention in recent years. PDCD1 exon 3 encodes the transmembrane domain and the deletion of exon 3 produces a soluble protein isoform of PD-1 (sPD-1), which can enhance immune response by competing with full-length PD-1 protein (flPD-1 or surface PD-1) on T cell surface. However, the mechanism of PDCD1 exon 3 skipping is unclear. METHODS The online SpliceAid program and minigene expression system were used to analyze potential splicing factors involved in the splicing event of PDCD1 exon 3. The potential binding motifs of heterogeneous nuclear ribonucleoprotein K (HNRNPK) on exon 3 predicted by SpliceAid were mutated by site-directed mutagenesis technology, which were further verified by pulldown assay. Antisense oligonucleotides (ASOs) targeting the exonic splicing silencer (ESS) on PDCD1 exon 3 were synthesized and screened to suppress the skipping of exon 3. The alternative splicing of PDCD1 exon 3 was analyzed by semiquantitative reverse transcription PCR. Western blot and flow cytometry were performed to detect the surface PD-1 expression in T cells. RESULTS HNRNPK was screened as a key splicing factor that promoted PDCD1 exon 3 skipping, causing a decrease in flPD-1 expression on T cell membrane and an increase in sPD-1 expression. Mechanically, a key ESS has been identified on exon 3 and can be bound by HNRNPK protein to promote exon 3 skipping. Blocking the interaction between ESS and HNRNPK with an ASO significantly reduced exon 3 skipping. Importantly, HNRNPK can promote exon 3 skipping of mouse Pdcd1 gene as well. CONCLUSIONS Our study revealed a novel evolutionarily conserved regulatory mechanism of PD-1 expression. The splicing factor HNRNPK markedly promoted PDCD1 exon 3 skipping by binding to the ESS on PDCD1 exon 3, resulting in decreased expression of flPD-1 and increased expression of sPD-1 in T cells.
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Affiliation(s)
- Jiayun Wang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China
| | - Lingyan Yan
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China
| | - Xu Wang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China
| | - Rong Jia
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China
- RNA Institute, Wuhan University, Wuhan, 430072, China
| | - Jihua Guo
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China.
- Department of Endodontics, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China.
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2
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Brandão-Teles C, Antunes ASLM, de Moraes Vrechi TA, Martins-de-Souza D. The Roles of hnRNP Family in the Brain and Brain-Related Disorders. Mol Neurobiol 2024; 61:3578-3595. [PMID: 37999871 DOI: 10.1007/s12035-023-03747-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/25/2023] [Indexed: 11/25/2023]
Abstract
Heterogeneous nuclear ribonucleoproteins (hnRNPs) belong to a complex family of RNA-binding proteins that are essential to control alternative splicing, mRNA trafficking, synaptic plasticity, stress granule formation, cell cycle regulation, and axonal transport. Over the past decade, hnRNPs have been associated with different brain disorders such as Alzheimer's disease, multiple sclerosis, and schizophrenia. Given their essential role in maintaining cell function and integrity, it is not surprising that dysregulated hnRNP levels lead to neurological implications. This review aims to explore the primary functions of hnRNPs in neurons, oligodendrocytes, microglia, and astrocytes, and their roles in brain disorders. We also discuss proteomics and other technologies and their potential for studying and evaluating hnRNPs in brain disorders, including the discovery of new therapeutic targets and possible pharmacological interventions.
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Affiliation(s)
- Caroline Brandão-Teles
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, Brazil.
| | - André S L M Antunes
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Talita Aparecida de Moraes Vrechi
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Daniel Martins-de-Souza
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, Brazil.
- D'Or Institute for Research and Education (IDOR), São Paulo, Brazil.
- Experimental Medicine Research Cluster (EMRC), University of Campinas, Campinas, SP, 13083-862, Brazil.
- INCT in Modelling Human Complex Diseases with 3D Platforms (Model3D), São Paulo, Brazil.
- Conselho Nacional de Desenvolvimento Científico e Tecnológico, Instituto Nacional de Biomarcadores em Neuropsiquiatria, São Paulo, Brazil.
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3
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Koike Y. Molecular mechanisms linking loss of TDP-43 function to amyotrophic lateral sclerosis/frontotemporal dementia-related genes. Neurosci Res 2024:S0168-0102(24)00063-4. [PMID: 38723906 DOI: 10.1016/j.neures.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/18/2024] [Accepted: 05/01/2024] [Indexed: 05/13/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are characterized by nuclear depletion and cytoplasmic aggregation of TAR DNA-binding protein-43 (TDP-43). TDP-43 plays a key role in regulating the splicing of numerous genes, including TARDBP. This review aims to delineate two aspects of ALS/FTD pathogenesis associated with TDP-43 function. First, we provide novel mechanistic insights into the splicing of UNC13A, a TDP-43 target gene. Single nucleotide polymorphisms (SNPs) in UNC13A are the most common risk factors for ALS/FTD. We found that TDP-43 represses "cryptic exon" inclusion during UNC13A RNA splicing. A risk-associated SNP in this exon results in increased RNA levels of UNC13A retaining the cryptic exon. Second, we described the perturbation of the TDP-43 autoregulatory mechanism caused by age-related DNA demethylation. Aging is a major risk factor for sporadic ALS/FTD. Typically, TDP-43 levels are regulated via alternative splicing of TARDBP mRNA. We hypothesized that TARDBP methylation is altered by aging, thereby disrupting TDP-43 autoregulation. We found that demethylation reduces the efficiency of alternative splicing and increases TARDBP mRNA levels. Moreover, we demonstrated that, with aging, this region is demethylated in the human motor cortex and is associated with the early onset of ALS.
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Affiliation(s)
- Yuka Koike
- Department of Molecular Neuroscience, Brain Research Institute, Niigata University, Japan.
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4
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Udine E, DeJesus-Hernandez M, Tian S, das Neves SP, Crook R, Finch NA, Baker MC, Pottier C, Graff-Radford NR, Boeve BF, Petersen RC, Knopman DS, Josephs KA, Oskarsson B, Da Mesquita S, Petrucelli L, Gendron TF, Dickson DW, Rademakers R, van Blitterswijk M. Abundant transcriptomic alterations in the human cerebellum of patients with a C9orf72 repeat expansion. Acta Neuropathol 2024; 147:73. [PMID: 38641715 PMCID: PMC11031479 DOI: 10.1007/s00401-024-02720-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 02/28/2024] [Accepted: 03/18/2024] [Indexed: 04/21/2024]
Abstract
The most prominent genetic cause of both amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) is a repeat expansion in the gene C9orf72. Importantly, the transcriptomic consequences of the C9orf72 repeat expansion remain largely unclear. Here, we used short-read RNA sequencing (RNAseq) to profile the cerebellar transcriptome, detecting alterations in patients with a C9orf72 repeat expansion. We focused on the cerebellum, since key C9orf72-related pathologies are abundant in this neuroanatomical region, yet TDP-43 pathology and neuronal loss are minimal. Consistent with previous work, we showed a reduction in the expression of the C9orf72 gene and an elevation in homeobox genes, when comparing patients with the expansion to both patients without the C9orf72 repeat expansion and control subjects. Interestingly, we identified more than 1000 alternative splicing events, including 4 in genes previously associated with ALS and/or FTLD. We also found an increase of cryptic splicing in C9orf72 patients compared to patients without the expansion and controls. Furthermore, we demonstrated that the expression level of select RNA-binding proteins is associated with cryptic splice junction inclusion. Overall, this study explores the presence of widespread transcriptomic changes in the cerebellum, a region not confounded by severe neurodegeneration, in post-mortem tissue from C9orf72 patients.
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Affiliation(s)
- Evan Udine
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd S, Jacksonville, FL, 32224, USA
- Neuroscience Ph.D. Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL, 32224, USA
| | | | - Shulan Tian
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, 55905, USA
| | | | - Richard Crook
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd S, Jacksonville, FL, 32224, USA
| | - NiCole A Finch
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd S, Jacksonville, FL, 32224, USA
| | - Matthew C Baker
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd S, Jacksonville, FL, 32224, USA
| | - Cyril Pottier
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd S, Jacksonville, FL, 32224, USA
| | | | | | | | | | | | - Björn Oskarsson
- Department of Neurology, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Sandro Da Mesquita
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd S, Jacksonville, FL, 32224, USA
- Neuroscience Ph.D. Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Leonard Petrucelli
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd S, Jacksonville, FL, 32224, USA
- Neuroscience Ph.D. Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Tania F Gendron
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd S, Jacksonville, FL, 32224, USA
- Neuroscience Ph.D. Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Dennis W Dickson
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd S, Jacksonville, FL, 32224, USA
- Neuroscience Ph.D. Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Rosa Rademakers
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd S, Jacksonville, FL, 32224, USA
- VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Marka van Blitterswijk
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd S, Jacksonville, FL, 32224, USA.
- Neuroscience Ph.D. Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL, 32224, USA.
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5
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Salapa HE, Thibault PA, Libner CD, Ding Y, Clarke JPWE, Denomy C, Hutchinson C, Abidullah HM, Austin Hammond S, Pastushok L, Vizeacoumar FS, Levin MC. hnRNP A1 dysfunction alters RNA splicing and drives neurodegeneration in multiple sclerosis (MS). Nat Commun 2024; 15:356. [PMID: 38191621 PMCID: PMC10774274 DOI: 10.1038/s41467-023-44658-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 12/22/2023] [Indexed: 01/10/2024] Open
Abstract
Neurodegeneration is the primary driver of disease progression in multiple sclerosis (MS) resulting in permanent disability, creating an urgent need to discover its underlying mechanisms. Herein, we establish that dysfunction of the RNA binding protein heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) results in differential of binding to RNA targets causing alternative RNA splicing, which contributes to neurodegeneration in MS and its models. Using RNAseq of MS brains, we discovered differential expression and aberrant splicing of hnRNP A1 target RNAs involved in neuronal function and RNA homeostasis. We confirmed this in vivo in experimental autoimmune encephalomyelitis employing CLIPseq specific for hnRNP A1, where hnRNP A1 differentially binds and regulates RNA, including aberrantly spliced targets identified in human samples. Additionally, dysfunctional hnRNP A1 expression in neurons caused neurite loss and identical changes in splicing, corroborating hnRNP A1 dysfunction as a cause of neurodegeneration. Collectively, these data indicate hnRNP A1 dysfunction causes altered neuronal RNA splicing, resulting in neurodegeneration in MS.
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Affiliation(s)
- Hannah E Salapa
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Cameco MS Neuroscience Research Centre, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Neurology Division, Department of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 0X8, Canada
| | - Patricia A Thibault
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Cameco MS Neuroscience Research Centre, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Neurology Division, Department of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 0X8, Canada
| | - Cole D Libner
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Cameco MS Neuroscience Research Centre, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Department of Health Sciences, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Yulian Ding
- Division of Oncology, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
- Division of Biomedical Engineering, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5A9, Canada
| | - Joseph-Patrick W E Clarke
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Cameco MS Neuroscience Research Centre, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Neurology Division, Department of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 0X8, Canada
| | - Connor Denomy
- Division of Oncology, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Catherine Hutchinson
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Cameco MS Neuroscience Research Centre, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Neurology Division, Department of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 0X8, Canada
| | - Hashim M Abidullah
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Cameco MS Neuroscience Research Centre, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Department of Anatomy, Physiology and Pharmacology, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - S Austin Hammond
- Next-Generation Sequencing Facility, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Landon Pastushok
- Advanced Diagnostics Research Laboratory, Department of Pathology and Lab Medicine, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Frederick S Vizeacoumar
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Michael C Levin
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada.
- Cameco MS Neuroscience Research Centre, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada.
- Neurology Division, Department of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 0X8, Canada.
- Department of Anatomy, Physiology and Pharmacology, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada.
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6
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Bhat AA, Afzal O, Afzal M, Gupta G, Thapa R, Ali H, Hassan Almalki W, Kazmi I, Alzarea SI, Saleem S, Samuel VP, Gubbiyappa SK, Subramaniyan V. MALAT1: A key regulator in lung cancer pathogenesis and therapeutic targeting. Pathol Res Pract 2024; 253:154991. [PMID: 38070223 DOI: 10.1016/j.prp.2023.154991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 11/21/2023] [Accepted: 11/27/2023] [Indexed: 01/24/2024]
Abstract
Lung cancer remains a formidable global health burden, necessitating a comprehensive understanding of the underlying molecular mechanisms driving its progression. Recently, lncRNAs have become necessary controllers of various biological functions, including cancer development. MALAT1 has garnered significant attention due to its multifaceted role in lung cancer progression. Lung cancer, among other malignancies, upregulates MALAT1. Its overexpression has been associated with aggressive tumor behavior and poor patient prognosis. MALAT1 promotes cellular proliferation, epithelial-mesenchymal transition (EMT), and angiogenesis in lung cancer, collectively facilitating tumor growth and metastasis. Additionally, MALAT1 enhances cancer cell invasion by interacting with numerous signaling pathways. Furthermore, MALAT1 has been implicated in mediating drug resistance in lung cancer, contributing to the limited efficacy of conventional therapies. Recent advancements in molecular biology and high-throughput sequencing technologies have offered fresh perspectives into the regulatory networks of MALAT1 in lung cancer. It exerts its oncogenic effects by acting as a ceRNA to sponge microRNAs, thereby relieving their inhibitory effects on target genes. Moreover, MALAT1 also influences chromatin remodeling and post-translational modifications to modulate gene expression, further expanding its regulatory capabilities. This review sheds light on the multifaceted roles of MALAT1 in lung cancer progression, underscoring its potential as an innovative therapeutic target and diagnostic biomarker. Targeting MALAT1 alone or combined with existing therapies holds promise to mitigate lung cancer progression and improve patient outcomes.
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Affiliation(s)
- Asif Ahmad Bhat
- School of Pharmacy, Suresh Gyan Vihar University, Mahal Road, Jagatpura, Jaipur 302017, India
| | - Obaid Afzal
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al Kharj 11942, Saudi Arabia
| | - Muhammad Afzal
- Department of Pharmaceutical Sciences, Pharmacy Program, Batterjee Medical College, P.O. Box 6231, Jeddah 21442, Saudi Arabia
| | - Gaurav Gupta
- Centre for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, India; School of Pharmacy, Graphic Era Hill University, Dehradun 248007, India
| | - Riya Thapa
- School of Pharmacy, Suresh Gyan Vihar University, Mahal Road, Jagatpura, Jaipur 302017, India
| | - Haider Ali
- Department of Pharmacology, Kyrgyz State Medical College, Bishkek, Kyrgyzstan
| | - Waleed Hassan Almalki
- Department of Pharmacology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Imran Kazmi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Sami I Alzarea
- Department of Pharmacology, College of Pharmacy, Jouf University, Sakaka, Al-Jouf, Saudi Arabia
| | - Shakir Saleem
- Department of Public Health. College of Health Sciences, Saudi Electronic University, Riyadh, Saudi Arabia
| | - Vijaya Paul Samuel
- Department of Anatomy, RAK College of Medicine, RAK Medical and Health Sciences University, Ras Al Khaimah, UAE
| | | | - Vetriselvan Subramaniyan
- Pharmacology Unit, Jeffrey Cheah School of Medicine and Health Sciences, Monash University, Jalan Lagoon Selatan, Bandar Sunway, Selangor Darul Ehsan 47500, Malaysia
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7
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Humphrey J, Brophy E, Kosoy R, Zeng B, Coccia E, Mattei D, Ravi A, Efthymiou AG, Navarro E, Muller BZ, Snijders GJLJ, Allan A, Münch A, Kitata RB, Kleopoulos SP, Argyriou S, Shao Z, Francoeur N, Tsai CF, Gritsenko MA, Monroe ME, Paurus VL, Weitz KK, Shi T, Sebra R, Liu T, de Witte LD, Goate AM, Bennett DA, Haroutunian V, Hoffman GE, Fullard JF, Roussos P, Raj T. Long-read RNA-seq atlas of novel microglia isoforms elucidates disease-associated genetic regulation of splicing. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.01.23299073. [PMID: 38076956 PMCID: PMC10705658 DOI: 10.1101/2023.12.01.23299073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Microglia, the innate immune cells of the central nervous system, have been genetically implicated in multiple neurodegenerative diseases. We previously mapped the genetic regulation of gene expression and mRNA splicing in human microglia, identifying several loci where common genetic variants in microglia-specific regulatory elements explain disease risk loci identified by GWAS. However, identifying genetic effects on splicing has been challenging due to the use of short sequencing reads to identify causal isoforms. Here we present the isoform-centric microglia genomic atlas (isoMiGA) which leverages the power of long-read RNA-seq to identify 35,879 novel microglia isoforms. We show that the novel microglia isoforms are involved in stimulation response and brain region specificity. We then quantified the expression of both known and novel isoforms in a multi-ethnic meta-analysis of 555 human microglia short-read RNA-seq samples from 391 donors, the largest to date, and found associations with genetic risk loci in Alzheimer's disease and Parkinson's disease. We nominate several loci that may act through complex changes in isoform and splice site usage.
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Affiliation(s)
- Jack Humphrey
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Erica Brophy
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Roman Kosoy
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Biao Zeng
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Elena Coccia
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daniele Mattei
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ashvin Ravi
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Anastasia G. Efthymiou
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Elisa Navarro
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Biochemistry and Molecular Biology, Faculty of Medicine (Universidad Complutense de Madrid), Madrid, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
- Instituto Ramon y Cajal de Investigacion Sanitaria (IRYCIS), Madrid, Spain
| | - Benjamin Z. Muller
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gijsje JLJ Snijders
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Amanda Allan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexandra Münch
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Reta Birhanu Kitata
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Steven P Kleopoulos
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Stathis Argyriou
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Zhiping Shao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Nancy Francoeur
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Marina A Gritsenko
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Matthew E Monroe
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Vanessa L Paurus
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Karl K Weitz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Lot D. de Witte
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Alison M. Goate
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - David A. Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, Illinois, USA
| | - Vahram Haroutunian
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mental Illness Research Education, and Clinical Center (VISN 2 South), James J. Peters VA Medical Center, Bronx, NY, USA
| | - Gabriel E. Hoffman
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA
| | - John F. Fullard
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Panos Roussos
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA
- Mental Illness Research Education, and Clinical Center (VISN 2 South), James J. Peters VA Medical Center, Bronx, NY, USA
| | - Towfique Raj
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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8
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Ziff OJ, Harley J, Wang Y, Neeves J, Tyzack G, Ibrahim F, Skehel M, Chakrabarti AM, Kelly G, Patani R. Nucleocytoplasmic mRNA redistribution accompanies RNA binding protein mislocalization in ALS motor neurons and is restored by VCP ATPase inhibition. Neuron 2023; 111:3011-3027.e7. [PMID: 37480846 DOI: 10.1016/j.neuron.2023.06.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 05/09/2023] [Accepted: 06/22/2023] [Indexed: 07/24/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is characterized by nucleocytoplasmic mislocalization of the RNA-binding protein (RBP) TDP-43. However, emerging evidence suggests more widespread mRNA and protein mislocalization. Here, we employed nucleocytoplasmic fractionation, RNA sequencing, and mass spectrometry to investigate the localization of mRNA and protein in induced pluripotent stem cell-derived motor neurons (iPSMNs) from ALS patients with TARDBP and VCP mutations. ALS mutant iPSMNs exhibited extensive nucleocytoplasmic mRNA redistribution, RBP mislocalization, and splicing alterations. Mislocalized proteins exhibited a greater affinity for redistributed transcripts, suggesting a link between RBP mislocalization and mRNA redistribution. Notably, treatment with ML240, a VCP ATPase inhibitor, partially restored mRNA and protein localization in ALS mutant iPSMNs. ML240 induced changes in the VCP interactome and lysosomal localization and reduced oxidative stress and DNA damage. These findings emphasize the link between RBP mislocalization and mRNA redistribution in ALS motor neurons and highlight the therapeutic potential of VCP inhibition.
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Affiliation(s)
- Oliver J Ziff
- The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK; Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, WC1N 3BG London, UK; National Hospital for Neurology and Neurosurgery, University College London NHS Foundation Trust, WC1N 3BG London, UK.
| | - Jasmine Harley
- The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK; Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, WC1N 3BG London, UK; Institute of Molecular and Cell Biology, A(∗)STAR Research Entities, Singapore 138673, Singapore
| | - Yiran Wang
- The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK; Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, WC1N 3BG London, UK
| | - Jacob Neeves
- The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK; Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, WC1N 3BG London, UK
| | - Giulia Tyzack
- The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK; Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, WC1N 3BG London, UK
| | - Fairouz Ibrahim
- The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK
| | - Mark Skehel
- The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK
| | | | - Gavin Kelly
- The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK; Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, WC1N 3BG London, UK
| | - Rickie Patani
- The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK; Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, WC1N 3BG London, UK; National Hospital for Neurology and Neurosurgery, University College London NHS Foundation Trust, WC1N 3BG London, UK.
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9
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Rezvykh A, Ustyugov A, Chaprov K, Teterina E, Nebogatikov V, Spasskaya D, Evgen’ev M, Morozov A, Funikov S. Cytoplasmic aggregation of mutant FUS causes multistep RNA splicing perturbations in the course of motor neuron pathology. Nucleic Acids Res 2023; 51:5810-5830. [PMID: 37115004 PMCID: PMC10287951 DOI: 10.1093/nar/gkad319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 04/12/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023] Open
Abstract
Dysfunction of the RNA-binding protein (RBP) FUS implicated in RNA metabolism can cause amyotrophic lateral sclerosis (ALS) and other neurodegenerative diseases. Mutations affecting FUS nuclear localization can drive RNA splicing defects and stimulate the formation of non-amyloid inclusions in affected neurons. However, the mechanism by which FUS mutations contribute to the development of ALS remains uncertain. Here we describe a pattern of RNA splicing changes in the dynamics of the continuous proteinopathy induced by mislocalized FUS. We show that the decrease in intron retention of FUS-associated transcripts represents the hallmark of the pathogenesis of ALS and is the earliest molecular event in the course of progression of the disease. As FUS aggregation increases, the pattern of RNA splicing changes, becoming more complex, including a decrease in the inclusion of neuron-specific microexons and induction of cryptic exon splicing due to the sequestration of additional RBPs into FUS aggregates. Crucially, the identified features of the pathological splicing pattern are also observed in ALS patients in both sporadic and familial cases. Our data provide evidence that both a loss of nuclear FUS function due to mislocalization and the subsequent cytoplasmic aggregation of mutant protein lead to the disruption of RNA splicing in a multistep fashion during FUS aggregation.
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Affiliation(s)
- Alexander P Rezvykh
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Moscow, 119991, Russian Federation
| | - Aleksey A Ustyugov
- Institute of Physiologically Active Compounds at Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry of Russian Academy of Sciences, Chernogolovka, 142432, Russian Federation
| | - Kirill D Chaprov
- Institute of Physiologically Active Compounds at Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry of Russian Academy of Sciences, Chernogolovka, 142432, Russian Federation
| | - Ekaterina V Teterina
- Institute of Physiologically Active Compounds at Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry of Russian Academy of Sciences, Chernogolovka, 142432, Russian Federation
| | - Vladimir O Nebogatikov
- Institute of Physiologically Active Compounds at Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry of Russian Academy of Sciences, Chernogolovka, 142432, Russian Federation
| | - Daria S Spasskaya
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Moscow, 119991, Russian Federation
| | - Michael B Evgen’ev
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Moscow, 119991, Russian Federation
| | - Alexey V Morozov
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Moscow, 119991, Russian Federation
| | - Sergei Yu Funikov
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Moscow, 119991, Russian Federation
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10
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Jiang X, Gatt A, Lashley T. HnRNP Pathologies in Frontotemporal Lobar Degeneration. Cells 2023; 12:1633. [PMID: 37371103 DOI: 10.3390/cells12121633] [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: 05/04/2023] [Revised: 06/06/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
Frontotemporal dementia (FTD) is the second most common form of young-onset (<65 years) dementia. Clinically, it primarily manifests as a disorder of behavioural, executive, and/or language functions. Pathologically, frontotemporal lobar degeneration (FTLD) is the predominant cause of FTD. FTLD is a proteinopathy, and the main pathological proteins identified so far are tau, TAR DNA-binding protein 43 (TDP-43), and fused in sarcoma (FUS). As TDP-43 and FUS are members of the heterogeneous ribonucleic acid protein (hnRNP) family, many studies in recent years have expanded the research on the relationship between other hnRNPs and FTLD pathology. Indeed, these studies provide evidence for an association between hnRNP abnormalities and FTLD. In particular, several studies have shown that multiple hnRNPs may exhibit nuclear depletion and cytoplasmic mislocalisation within neurons in FTLD cases. However, due to the diversity and complex association of hnRNPs, most studies are still at the stage of histological discovery of different hnRNP abnormalities in FTLD. We herein review the latest studies relating hnRNPs to FTLD. Together, these studies outline an important role of multiple hnRNPs in the pathogenesis of FTLD and suggest that future research into FTLD should include the whole spectrum of this protein family.
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Affiliation(s)
- Xinwa Jiang
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London WC1N 1PJ, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Ariana Gatt
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London WC1N 1PJ, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Tammaryn Lashley
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London WC1N 1PJ, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
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11
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De Marchi F, Franjkic T, Schito P, Russo T, Nimac J, Chami AA, Mele A, Vidatic L, Kriz J, Julien JP, Apic G, Russell RB, Rogelj B, Cannon JR, Baralle M, Agosta F, Hecimovic S, Mazzini L, Buratti E, Munitic I. Emerging Trends in the Field of Inflammation and Proteinopathy in ALS/FTD Spectrum Disorder. Biomedicines 2023; 11:1599. [PMID: 37371694 PMCID: PMC10295684 DOI: 10.3390/biomedicines11061599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/27/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Proteinopathy and neuroinflammation are two main hallmarks of neurodegenerative diseases. They also represent rare common events in an exceptionally broad landscape of genetic, environmental, neuropathologic, and clinical heterogeneity present in patients. Here, we aim to recount the emerging trends in amyotrophic lateral sclerosis (ALS) and frontotemporal degeneration (FTD) spectrum disorder. Our review will predominantly focus on neuroinflammation and systemic immune imbalance in ALS and FTD, which have recently been highlighted as novel therapeutic targets. A common mechanism of most ALS and ~50% of FTD patients is dysregulation of TAR DNA-binding protein 43 (TDP-43), an RNA/DNA-binding protein, which becomes depleted from the nucleus and forms cytoplasmic aggregates in neurons and glia. This, in turn, via both gain and loss of function events, alters a variety of TDP-43-mediated cellular events. Experimental attempts to target TDP-43 aggregates or manipulate crosstalk in the context of inflammation will be discussed. Targeting inflammation, and the immune system in general, is of particular interest because of the high plasticity of immune cells compared to neurons.
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Affiliation(s)
- Fabiola De Marchi
- Department of Neurology and ALS Centre, University of Piemonte Orientale, Maggiore Della Carità Hospital, Corso Mazzini 18, 28100 Novara, Italy; (F.D.M.); (A.M.)
| | - Toni Franjkic
- Laboratory for Molecular Immunology, Department of Biotechnology, University of Rijeka, R. Matejcic 2, 51000 Rijeka, Croatia;
- Metisox, Cambridge CB24 9NL, UK;
| | - Paride Schito
- Department of Neurology & Neuropathology Unit, Institute of Experimental Neurology (INSPE), Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (P.S.); (T.R.)
| | - Tommaso Russo
- Department of Neurology & Neuropathology Unit, Institute of Experimental Neurology (INSPE), Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (P.S.); (T.R.)
| | - Jerneja Nimac
- Department of Biotechnology, Jozef Stefan Institute, SI-1000 Ljubljana, Slovenia; (J.N.); (B.R.)
- Graduate School of Biomedicine, Faculty of Medicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Anna A. Chami
- CERVO Research Centre, Laval University, Quebec City, QC G1J 2G3, Canada; (A.A.C.); (J.K.); (J.-P.J.)
| | - Angelica Mele
- Department of Neurology and ALS Centre, University of Piemonte Orientale, Maggiore Della Carità Hospital, Corso Mazzini 18, 28100 Novara, Italy; (F.D.M.); (A.M.)
| | - Lea Vidatic
- Laboratory for Neurodegenerative Disease Research, Division of Molecular Medicine, Ruder Boskovic Institute, 10000 Zagreb, Croatia; (L.V.); (S.H.)
| | - Jasna Kriz
- CERVO Research Centre, Laval University, Quebec City, QC G1J 2G3, Canada; (A.A.C.); (J.K.); (J.-P.J.)
| | - Jean-Pierre Julien
- CERVO Research Centre, Laval University, Quebec City, QC G1J 2G3, Canada; (A.A.C.); (J.K.); (J.-P.J.)
| | | | | | - Boris Rogelj
- Department of Biotechnology, Jozef Stefan Institute, SI-1000 Ljubljana, Slovenia; (J.N.); (B.R.)
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Jason R. Cannon
- School of Health Sciences, Purdue University, West Lafayette, IN 47907, USA;
- Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN 47907, USA
| | | | - Federica Agosta
- Neuroimaging Research Unit, Institute of Experimental Neurology, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy;
| | - Silva Hecimovic
- Laboratory for Neurodegenerative Disease Research, Division of Molecular Medicine, Ruder Boskovic Institute, 10000 Zagreb, Croatia; (L.V.); (S.H.)
| | - Letizia Mazzini
- Department of Neurology and ALS Centre, University of Piemonte Orientale, Maggiore Della Carità Hospital, Corso Mazzini 18, 28100 Novara, Italy; (F.D.M.); (A.M.)
| | - Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, 34149 Trieste, Italy
| | - Ivana Munitic
- Laboratory for Molecular Immunology, Department of Biotechnology, University of Rijeka, R. Matejcic 2, 51000 Rijeka, Croatia;
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12
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Lazo PA, Morejón-García P. VRK1 variants at the cross road of Cajal body neuropathogenic mechanisms in distal neuropathies and motor neuron diseases. Neurobiol Dis 2023; 183:106172. [PMID: 37257665 DOI: 10.1016/j.nbd.2023.106172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/09/2023] [Accepted: 05/24/2023] [Indexed: 06/02/2023] Open
Abstract
Distal hereditary neuropathies and neuro motor diseases are complex neurological phenotypes associated with pathogenic variants in a large number of genes, but in some the origin is unknown. Recently, rare pathogenic variants of the human VRK1 gene have been associated with these neurological phenotypes. All VRK1 pathogenic variants are recessive, and their clinical presentation occurs in either homozygous or compound heterozygous patients. The pathogenic VRK1 gene pathogenic variants are located in three clusters within the protein sequence. The main, and initial, shared clinical phenotype among VRK1 pathogenic variants is a distal progressive loss of motor and/or sensory function, which includes diseases such as spinal muscular atrophy, Charcot-Marie-Tooth, amyotrophic lateral sclerosis and hereditary spastic paraplegia. In most cases, symptoms start early in infancy, or in utero, and are slowly progressive. Additional neurological symptoms vary among non-related patients, probably because of their different VRK1 variants and their genetic background. The underlying common pathogenic mechanism, by its functional impairment, is a likely consequence of the roles that the VRK1 protein plays in the regulation on the stability and assembly of Cajal bodies, which affect RNA maturation and processing, neuronal migration of RNPs along axons, and DNA-damage responses. Alterations of these processes are associated with several neuro sensory or motor syndromes. The clinical heterogeneity of the neurological phenotypes associated with VRK1 is a likely consequence of the protein complexes in which VRK1 is integrated, which include several proteins known to be associated with Cajal bodies and DNA damage responses. Several hereditary distal neurological diseases are a consequence of pathogenic variants in genes that alter these cellular functions. We conclude that VRK1-related distal hereditary neuropathies and motor neuron diseases represent a novel subgroup of Cajal body related neurological syndromes.
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Affiliation(s)
- Pedro A Lazo
- Molecular Mechanisms of Cancer Program, Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC) - Universidad de Salamanca, Salamanca, Spain; Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, Salamanca, Spain.
| | - Patricia Morejón-García
- Molecular Mechanisms of Cancer Program, Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC) - Universidad de Salamanca, Salamanca, Spain; Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, Salamanca, Spain.
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13
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Koike Y, Pickles S, Estades Ayuso V, Jansen-West K, Qi YA, Li Z, Daughrity LM, Yue M, Zhang YJ, Cook CN, Dickson DW, Ward M, Petrucelli L, Prudencio M. TDP-43 and other hnRNPs regulate cryptic exon inclusion of a key ALS/FTD risk gene, UNC13A. PLoS Biol 2023; 21:e3002028. [PMID: 36930682 PMCID: PMC10057836 DOI: 10.1371/journal.pbio.3002028] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 03/29/2023] [Accepted: 02/08/2023] [Indexed: 03/18/2023] Open
Abstract
A major function of TAR DNA-binding protein-43 (TDP-43) is to repress the inclusion of cryptic exons during RNA splicing. One of these cryptic exons is in UNC13A, a genetic risk factor for amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). The accumulation of cryptic UNC13A in disease is heightened by the presence of a risk haplotype located within the cryptic exon itself. Here, we revealed that TDP-43 extreme N-terminus is important to repress UNC13A cryptic exon inclusion. Further, we found hnRNP L, hnRNP A1, and hnRNP A2B1 bind UNC13A RNA and repress cryptic exon inclusion, independently of TDP-43. Finally, higher levels of hnRNP L protein associate with lower burden of UNC13A cryptic RNA in ALS/FTD brains. Our findings suggest that while TDP-43 is the main repressor of UNC13A cryptic exon inclusion, other hnRNPs contribute to its regulation and may potentially function as disease modifiers.
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Affiliation(s)
- Yuka Koike
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, United States of America
- Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, Florida, United States of America
| | - Sarah Pickles
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, United States of America
- Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, Florida, United States of America
| | - Virginia Estades Ayuso
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, United States of America
| | - Karen Jansen-West
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, United States of America
| | - Yue A. Qi
- Center for Alzheimer’s and Related Dementias, National Institute on Aging, NIH, Bethesda, Maryland, United States of America
| | - Ziyi Li
- Center for Alzheimer’s and Related Dementias, National Institute on Aging, NIH, Bethesda, Maryland, United States of America
| | - Lillian M. Daughrity
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, United States of America
| | - Mei Yue
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, United States of America
| | - Yong-Jie Zhang
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, United States of America
- Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, Florida, United States of America
| | - Casey N. Cook
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, United States of America
- Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, Florida, United States of America
| | - Dennis W. Dickson
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, United States of America
- Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, Florida, United States of America
| | - Michael Ward
- Center for Alzheimer’s and Related Dementias, National Institute on Aging, NIH, Bethesda, Maryland, United States of America
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, Maryland, United States of America
| | - Leonard Petrucelli
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, United States of America
- Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, Florida, United States of America
| | - Mercedes Prudencio
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, United States of America
- Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, Florida, United States of America
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14
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Yagita K, Sasagasako N, Koyama S, Noguchi H, Honda H. Amyotrophic lateral sclerosis with TDP-43 abnormalities exhibiting globular glial tau inclusions in frontotemporal lobes and pallido-nigral system. Neuropathology 2023; 43:117-126. [PMID: 36003035 DOI: 10.1111/neup.12862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/28/2022] [Accepted: 08/03/2022] [Indexed: 02/04/2023]
Abstract
Here we present the autopsy case of an 80-year-old woman with a 9-year history of motor neuron disease and atypical Parkinsonism. Her initial symptom was gait disturbance, and she subsequently developed limb weakness and Parkinsonism without response to levodopa. Her motor symptoms progressed to bulbar palsy, and she died of respiratory failure. Postmortem examination revealed characteristic findings of amyotrophic lateral sclerosis (ALS), including motor neuronal loss with astrogliosis, corticospinal tract degeneration, and TAR DNA-binding protein of 43 kDa abnormalities, including nuclear loss and skein-like inclusions. In contrast, severe tau pathological changes were seen in the frontotemporal lobes and pallido-nigral system. Tau pathologies affected not only neuronal components, such as neurofibrillary tangles and neuropil threads, but also glial cells (astrocytes and oligodendrocytes). Some glial tau pathologies exhibited peculiar round accumulations, reminiscent of globular glial inclusions (GGIs) in globular glial tauopathy. This unique autopsy case demonstrates that ALS with TDP-43 could be comorbid with globular glial tau inclusions and indicates that common pathological mechanisms exist among ALS and GGI formation.
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Affiliation(s)
- Kaoru Yagita
- Department of Neuropathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Naokazu Sasagasako
- Department of Neurology, Neuro-Muscular Center, National Omuta Hospital, Omuta, Japan
| | - Sachiko Koyama
- Department of Neuropathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hideko Noguchi
- Department of Neuropathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hiroyuki Honda
- Department of Neuropathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
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15
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Mofrad RB, Del Campo M, Peeters CFW, Meeter LHH, Seelaar H, Koel-Simmelink M, Ramakers IHGB, Middelkoop HAM, De Deyn PP, Claassen JAHR, van Swieten JC, Bridel C, Hoozemans JJM, Scheltens P, van der Flier WM, Pijnenburg YAL, Teunissen CE. Plasma proteome profiling identifies changes associated to AD but not to FTD. Acta Neuropathol Commun 2022; 10:148. [PMID: 36273219 PMCID: PMC9587555 DOI: 10.1186/s40478-022-01458-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: 10/04/2022] [Accepted: 10/06/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Frontotemporal dementia (FTD) is caused by frontotemporal lobar degeneration (FTLD), characterized mainly by inclusions of Tau (FTLD-Tau) or TAR DNA binding43 (FTLD-TDP) proteins. Plasma biomarkers are strongly needed for specific diagnosis and potential treatment monitoring of FTD. We aimed to identify specific FTD plasma biomarker profiles discriminating FTD from AD and controls, and between FTD pathological subtypes. In addition, we compared plasma results with results in post-mortem frontal cortex of FTD cases to understand the underlying process. METHODS Plasma proteins (n = 1303) from pathologically and/or genetically confirmed FTD patients (n = 56; FTLD-Tau n = 16; age = 58.2 ± 6.2; 44% female, FTLD-TDP n = 40; age = 59.8 ± 7.9; 45% female), AD patients (n = 57; age = 65.5 ± 8.0; 39% female), and non-demented controls (n = 148; 61.3 ± 7.9; 41% female) were measured using an aptamer-based proteomic technology (SomaScan). In addition, exploratory analysis in post-mortem frontal brain cortex of FTD (n = 10; FTLD-Tau n = 5; age = 56.2 ± 6.9, 60% female, and FTLD-TDP n = 5; age = 64.0 ± 7.7, 60% female) and non-demented controls (n = 4; age = 61.3 ± 8.1; 75% female) were also performed. Differentially regulated plasma and tissue proteins were identified by global testing adjusting for demographic variables and multiple testing. Logistic lasso regression was used to identify plasma protein panels discriminating FTD from non-demented controls and AD, or FTLD-Tau from FTLD-TDP. Performance of the discriminatory plasma protein panels was based on predictions obtained from bootstrapping with 1000 resampled analysis. RESULTS Overall plasma protein expression profiles differed between FTD, AD and controls (6 proteins; p = 0.005), but none of the plasma proteins was specifically associated to FTD. The overall tissue protein expression profile differed between FTD and controls (7-proteins; p = 0.003). There was no difference in overall plasma or tissue expression profile between FTD subtypes. Regression analysis revealed a panel of 12-plasma proteins discriminating FTD from AD with high accuracy (AUC: 0.99). No plasma protein panels discriminating FTD from controls or FTD pathological subtypes were identified. CONCLUSIONS We identified a promising plasma protein panel as a minimally-invasive tool to aid in the differential diagnosis of FTD from AD, which was primarily associated to AD pathophysiology. The lack of plasma profiles specifically associated to FTD or its pathological subtypes might be explained by FTD heterogeneity, calling for FTD studies using large and well-characterize cohorts.
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Affiliation(s)
- R Babapour Mofrad
- Neurochemistry Laboratory and Biobank, Department of Clinical Chemistry, Amsterdam Neuroscience, VU University Medical Center, Amsterdam UMC, Vrije Universiteit Amsterdam, PO Box 7057, 1007 MB, Amsterdam, The Netherlands.,Alzheimer Center and Department of Neurology Amsterdam, Department of Neurology, Neuroscience Campus Amsterdam Neuroscience, VU University Medical Center, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - M Del Campo
- Neurochemistry Laboratory and Biobank, Department of Clinical Chemistry, Amsterdam Neuroscience, VU University Medical Center, Amsterdam UMC, Vrije Universiteit Amsterdam, PO Box 7057, 1007 MB, Amsterdam, The Netherlands.,Departamento de Ciencias Farmacéuticas y de la Salud, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Madrid, Spain.,Barcelonaβeta Brain Research Center (BBRC), Pasqual Maragall Foundation, Barcelona, Spain
| | - C F W Peeters
- Department of Epidemiology and Biostatistics, VU University Medical Center, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Mathematical and Statistical Methods Group (Biometris), Wageningen University and Research Wageningen, Wageningen, The Netherlands
| | - L H H Meeter
- Alzheimer Center Erasmus MC and Department of Neurology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - H Seelaar
- Alzheimer Center Rotterdam and Department of Neurology, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - M Koel-Simmelink
- Neurochemistry Laboratory and Biobank, Department of Clinical Chemistry, Amsterdam Neuroscience, VU University Medical Center, Amsterdam UMC, Vrije Universiteit Amsterdam, PO Box 7057, 1007 MB, Amsterdam, The Netherlands
| | - I H G B Ramakers
- Alzheimer Center Limburg, Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, The Netherlands
| | - H A M Middelkoop
- Institute of Psychology, Health, Medical and Neuropsychology Unit, Leiden University, Leiden, the Netherlands.,Department of Neurology, Leiden University Medical Centre, Leiden, The Netherlands
| | - P P De Deyn
- Laboratory of Neurochemistry and Behavior, Department of Biomedical Sciences, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium.,Department of Neurology and Alzheimer Center, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - J A H R Claassen
- Department of Geriatric Medicine, Radboud University Medical Center, Radboudumc Alzheimer Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - J C van Swieten
- Alzheimer Center Erasmus MC and Department of Neurology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - C Bridel
- Neurochemistry Laboratory and Biobank, Department of Clinical Chemistry, Amsterdam Neuroscience, VU University Medical Center, Amsterdam UMC, Vrije Universiteit Amsterdam, PO Box 7057, 1007 MB, Amsterdam, The Netherlands
| | - J J M Hoozemans
- Department of Pathology, Amsterdam University Medical Centers Location VUmc, Amsterdam, The Netherlands
| | - P Scheltens
- Alzheimer Center and Department of Neurology Amsterdam, Department of Neurology, Neuroscience Campus Amsterdam Neuroscience, VU University Medical Center, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - W M van der Flier
- Alzheimer Center and Department of Neurology Amsterdam, Department of Neurology, Neuroscience Campus Amsterdam Neuroscience, VU University Medical Center, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Department of Epidemiology and Biostatistics, VU University Medical Center, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Y A L Pijnenburg
- Alzheimer Center and Department of Neurology Amsterdam, Department of Neurology, Neuroscience Campus Amsterdam Neuroscience, VU University Medical Center, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Charlotte E Teunissen
- Neurochemistry Laboratory and Biobank, Department of Clinical Chemistry, Amsterdam Neuroscience, VU University Medical Center, Amsterdam UMC, Vrije Universiteit Amsterdam, PO Box 7057, 1007 MB, Amsterdam, The Netherlands.
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16
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Avar M, Heinzer D, Thackray AM, Liu Y, Hruska‐Plochan M, Sellitto S, Schaper E, Pease DP, Yin J, Lakkaraju AKK, Emmenegger M, Losa M, Chincisan A, Hornemann S, Polymenidou M, Bujdoso R, Aguzzi A. An arrayed genome-wide perturbation screen identifies the ribonucleoprotein Hnrnpk as rate-limiting for prion propagation. EMBO J 2022; 41:e112338. [PMID: 36254605 PMCID: PMC9713719 DOI: 10.15252/embj.2022112338] [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: 08/10/2022] [Revised: 09/17/2022] [Accepted: 09/22/2022] [Indexed: 01/15/2023] Open
Abstract
A defining characteristic of mammalian prions is their capacity for self-sustained propagation. Theoretical considerations and experimental evidence suggest that prion propagation is modulated by cell-autonomous and non-autonomous modifiers. Using a novel quantitative phospholipase protection assay (QUIPPER) for high-throughput prion measurements, we performed an arrayed genome-wide RNA interference (RNAi) screen aimed at detecting cellular host-factors that can modify prion propagation. We exposed prion-infected cells in high-density microplates to 35,364 ternary pools of 52,746 siRNAs targeting 17,582 genes representing the majority of the mouse protein-coding transcriptome. We identified 1,191 modulators of prion propagation. While 1,151 modified the expression of both the pathological prion protein, PrPSc , and its cellular counterpart, PrPC , 40 genes selectively affected PrPSc . Of the latter 40 genes, 20 augmented prion production when suppressed. A prominent limiter of prion propagation was the heterogeneous nuclear ribonucleoprotein Hnrnpk. Psammaplysene A (PSA), which binds Hnrnpk, reduced prion levels in cultured cells and protected them from cytotoxicity. PSA also reduced prion levels in infected cerebellar organotypic slices and alleviated locomotor deficits in prion-infected Drosophila melanogaster expressing ovine PrPC . Hence, genome-wide QUIPPER-based perturbations can discover actionable cellular pathways involved in prion propagation. Further, the unexpected identification of a prion-controlling ribonucleoprotein suggests a role for RNA in the generation of infectious prions.
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Affiliation(s)
- Merve Avar
- Institute of NeuropathologyUniversity of ZurichZurichSwitzerland
| | - Daniel Heinzer
- Institute of NeuropathologyUniversity of ZurichZurichSwitzerland
| | - Alana M Thackray
- Department of Veterinary MedicineUniversity of CambridgeCambridgeUK
| | - Yingjun Liu
- Institute of NeuropathologyUniversity of ZurichZurichSwitzerland
| | | | - Stefano Sellitto
- Institute of NeuropathologyUniversity of ZurichZurichSwitzerland
| | - Elke Schaper
- Institute of NeuropathologyUniversity of ZurichZurichSwitzerland
| | - Daniel P Pease
- Institute of NeuropathologyUniversity of ZurichZurichSwitzerland
| | - Jiang‐An Yin
- Institute of NeuropathologyUniversity of ZurichZurichSwitzerland
| | | | - Marc Emmenegger
- Institute of NeuropathologyUniversity of ZurichZurichSwitzerland
| | - Marco Losa
- Institute of NeuropathologyUniversity of ZurichZurichSwitzerland
| | - Andra Chincisan
- Institute of NeuropathologyUniversity of ZurichZurichSwitzerland
| | - Simone Hornemann
- Institute of NeuropathologyUniversity of ZurichZurichSwitzerland
| | | | - Raymond Bujdoso
- Department of Veterinary MedicineUniversity of CambridgeCambridgeUK
| | - Adriano Aguzzi
- Institute of NeuropathologyUniversity of ZurichZurichSwitzerland
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17
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Kavanagh T, Halder A, Drummond E. Tau interactome and RNA binding proteins in neurodegenerative diseases. Mol Neurodegener 2022; 17:66. [PMID: 36253823 PMCID: PMC9575286 DOI: 10.1186/s13024-022-00572-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 09/30/2022] [Indexed: 11/19/2022] Open
Abstract
Pathological tau aggregation is a primary neuropathological feature of many neurodegenerative diseases. Intriguingly, despite the common presence of tau aggregates in these diseases the affected brain regions, clinical symptoms, and morphology, conformation, and isoform ratio present in tau aggregates varies widely. The tau-mediated disease mechanisms that drive neurodegenerative disease are still unknown. Tau interactome studies are critically important for understanding tauopathy. They reveal the interacting partners that define disease pathways, and the tau interactions present in neuropathological aggregates provide potential insight into the cellular environment and protein interactions present during pathological tau aggregation. Here we provide a combined analysis of 12 tau interactome studies of human brain tissue, human cell culture models and rodent models of disease. Together, these studies identified 2084 proteins that interact with tau in human tissue and 1152 proteins that interact with tau in rodent models of disease. Our combined analysis of the tau interactome revealed consistent enrichment of interactions between tau and proteins involved in RNA binding, ribosome, and proteasome function. Comparison of human and rodent tau interactome studies revealed substantial differences between the two species. We also performed a second analysis to identify the tau interacting proteins that are enriched in neurons containing granulovacuolar degeneration or neurofibrillary tangle pathology. These results revealed a timed dysregulation of tau interactions as pathology develops. RNA binding proteins, particularly HNRNPs, emerged as early disease-associated tau interactors and therefore may have an important role in driving tau pathology.
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Affiliation(s)
- Tomas Kavanagh
- Brain and Mind Centre and School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, 94 Mallett Street, Sydney, NSW, Australia
| | - Aditi Halder
- Brain and Mind Centre and School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, 94 Mallett Street, Sydney, NSW, Australia
| | - Eleanor Drummond
- Brain and Mind Centre and School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, 94 Mallett Street, Sydney, NSW, Australia.
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18
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The Advance on Frontotemporal Dementia (FTD)’s Neuropathology and Molecular Genetics. Mediators Inflamm 2022; 2022:5003902. [PMID: 36274975 PMCID: PMC9584734 DOI: 10.1155/2022/5003902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/05/2022] [Accepted: 09/12/2022] [Indexed: 11/25/2022] Open
Abstract
The morbidity of frontotemporal dementia (FTD), one of the most prevalent dementias praccox, is second to Alzheimer disease (AD). It is different with AD that FTD has a rapider course and a higher mortality. FTD has not yet been fully understood in terms of etiology or pathogenesis, but genetic factors are believed to be involved. In this paper, we were committed to providing a comprehensive overview to FTD in aspects of the neuropathology features and the relevant molecular genetics advances, so that there would be insights to those researchers in search of novel approaches in FTD diagnosis and treatment.
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19
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Braems E, Bercier V, Van Schoor E, Heeren K, Beckers J, Fumagalli L, Dedeene L, Moisse M, Geudens I, Hersmus N, Mehta AR, Selvaraj BT, Chandran S, Ho R, Thal DR, Van Damme P, Swinnen B, Van Den Bosch L. HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS. Acta Neuropathol 2022; 144:465-488. [PMID: 35895140 PMCID: PMC9381635 DOI: 10.1007/s00401-022-02471-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/24/2022] [Accepted: 07/11/2022] [Indexed: 11/21/2022]
Abstract
A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). The exact mechanism resulting in these neurodegenerative diseases remains elusive, but C9 repeat RNA toxicity has been implicated as a gain-of-function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS-linked phenotype. We discovered that the RNA-binding protein heterogeneous nuclear ribonucleoprotein K (HNRNPK) reverses the toxicity of both sense and antisense repeat RNA, which is dependent on its subcellular localization and RNA recognition, and not on C9orf72 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts, induced pluripotent stem cell (iPSC)-derived motor neurons and post-mortem motor cortex and spinal cord, in line with a disrupted HNRNPK function in C9orf72 ALS. In C9orf72 ALS/FTD patient tissue, we discovered an increased nuclear translocation, but reduced expression of ribonucleotide reductase regulatory subunit M2 (RRM2), a downstream target of HNRNPK involved in the DNA damage response. Last but not least, we showed that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9orf72 RNA toxicity zebrafish model. Overall, our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9orf72 ALS and demonstrates its link with an aberrant DNA damage response, opening novel therapeutic avenues for C9orf72 ALS/FTD.
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Affiliation(s)
- Elke Braems
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, Leuven, Belgium
- Center for Brain & Disease Research, Laboratory of Neurobiology, VIB, Campus Gasthuisberg, O&N5, Herestraat 49, PB 602, 3000, Leuven, Belgium
| | - Valérie Bercier
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, Leuven, Belgium.
- Center for Brain & Disease Research, Laboratory of Neurobiology, VIB, Campus Gasthuisberg, O&N5, Herestraat 49, PB 602, 3000, Leuven, Belgium.
| | - Evelien Van Schoor
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, Leuven, Belgium
- Center for Brain & Disease Research, Laboratory of Neurobiology, VIB, Campus Gasthuisberg, O&N5, Herestraat 49, PB 602, 3000, Leuven, Belgium
- Department of Imaging and Pathology, Laboratory of Neuropathology and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, Leuven, Belgium
| | - Kara Heeren
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, Leuven, Belgium
- Center for Brain & Disease Research, Laboratory of Neurobiology, VIB, Campus Gasthuisberg, O&N5, Herestraat 49, PB 602, 3000, Leuven, Belgium
| | - Jimmy Beckers
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, Leuven, Belgium
- Center for Brain & Disease Research, Laboratory of Neurobiology, VIB, Campus Gasthuisberg, O&N5, Herestraat 49, PB 602, 3000, Leuven, Belgium
| | - Laura Fumagalli
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, Leuven, Belgium
- Center for Brain & Disease Research, Laboratory of Neurobiology, VIB, Campus Gasthuisberg, O&N5, Herestraat 49, PB 602, 3000, Leuven, Belgium
| | - Lieselot Dedeene
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, Leuven, Belgium
- Center for Brain & Disease Research, Laboratory of Neurobiology, VIB, Campus Gasthuisberg, O&N5, Herestraat 49, PB 602, 3000, Leuven, Belgium
- Department of Imaging and Pathology, Laboratory of Neuropathology and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, Leuven, Belgium
- Department of Neurosciences, Laboratory for Molecular Neurobiomarker Research and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, Leuven, Belgium
| | - Matthieu Moisse
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, Leuven, Belgium
- Center for Brain & Disease Research, Laboratory of Neurobiology, VIB, Campus Gasthuisberg, O&N5, Herestraat 49, PB 602, 3000, Leuven, Belgium
| | - Ilse Geudens
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, Leuven, Belgium
- Center for Brain & Disease Research, Laboratory of Neurobiology, VIB, Campus Gasthuisberg, O&N5, Herestraat 49, PB 602, 3000, Leuven, Belgium
| | - Nicole Hersmus
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, Leuven, Belgium
- Center for Brain & Disease Research, Laboratory of Neurobiology, VIB, Campus Gasthuisberg, O&N5, Herestraat 49, PB 602, 3000, Leuven, Belgium
| | - Arpan R Mehta
- UK Dementia Research Institute, University of Edinburgh, Edinburgh, UK
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Bhuvaneish T Selvaraj
- UK Dementia Research Institute, University of Edinburgh, Edinburgh, UK
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Siddharthan Chandran
- UK Dementia Research Institute, University of Edinburgh, Edinburgh, UK
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Ritchie Ho
- Cedars-Sinai Medical Center, Board of Governors Regenerative Medicine Institute, Los Angeles, CA, USA
| | - Dietmar R Thal
- Department of Imaging and Pathology, Laboratory of Neuropathology and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, Leuven, Belgium
- Department of Pathology, University Hospitals Leuven, Leuven, Belgium
| | - Philip Van Damme
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, Leuven, Belgium
- Center for Brain & Disease Research, Laboratory of Neurobiology, VIB, Campus Gasthuisberg, O&N5, Herestraat 49, PB 602, 3000, Leuven, Belgium
- Department of Neurology, University Hospitals Leuven, Leuven, Belgium
| | - Bart Swinnen
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, Leuven, Belgium
- Center for Brain & Disease Research, Laboratory of Neurobiology, VIB, Campus Gasthuisberg, O&N5, Herestraat 49, PB 602, 3000, Leuven, Belgium
| | - Ludo Van Den Bosch
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, Leuven, Belgium.
- Center for Brain & Disease Research, Laboratory of Neurobiology, VIB, Campus Gasthuisberg, O&N5, Herestraat 49, PB 602, 3000, Leuven, Belgium.
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20
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Paron F, Barattucci S, Cappelli S, Romano M, Berlingieri C, Stuani C, Laurents D, Mompeán M, Buratti E. Unravelling the toxic effects mediated by the neurodegenerative disease-associated S375G mutation of TDP-43 and its S375E phosphomimetic variant. J Biol Chem 2022; 298:102252. [PMID: 35835219 PMCID: PMC9364110 DOI: 10.1016/j.jbc.2022.102252] [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: 01/15/2022] [Revised: 06/23/2022] [Accepted: 06/25/2022] [Indexed: 12/05/2022] Open
Abstract
TAR DNA-binding protein 43 (TDP-43) is a nucleic acid–binding protein found in the nucleus that accumulates in the cytoplasm under pathological conditions, leading to proteinopathies, such as frontotemporal dementia and ALS. An emerging area of TDP-43 research is represented by the study of its post-translational modifications, the way they are connected to disease-associated mutations, and what this means for pathological processes. Recently, we described a novel mutation in TDP-43 in an early onset ALS case that was affecting a potential phosphorylation site in position 375 (S375G). A preliminary characterization showed that both the S375G mutation and its phosphomimetic variant, S375E, displayed altered nuclear–cytoplasmic distribution and cellular toxicity. To better investigate these effects, here we established cell lines expressing inducible WT, S375G, and S375E TDP-43 variants. Interestingly, we found that these mutants do not seem to affect well-studied aspects of TDP-43, such as RNA splicing or autoregulation, or protein conformation, dynamics, or aggregation, although they do display dysmorphic nuclear shape and cell cycle alterations. In addition, RNA-Seq analysis of these cell lines showed that although the disease-associated S375G mutation and its phosphomimetic S375E variant regulate distinct sets of genes, they have a common target in mitochondrial apoptotic genes. Taken together, our data strongly support the growing evidence that alterations in TDP-43 post-translational modifications can play a potentially important role in disease pathogenesis and provide a further link between TDP-43 pathology and mitochondrial health.
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Affiliation(s)
- Francesca Paron
- Molecular Pathology, International Centre for Genetic and Engineering Biotechnology (ICGEB), Trieste, Italy
| | - Simone Barattucci
- Molecular Pathology, International Centre for Genetic and Engineering Biotechnology (ICGEB), Trieste, Italy
| | - Sara Cappelli
- Molecular Pathology, International Centre for Genetic and Engineering Biotechnology (ICGEB), Trieste, Italy
| | - Maurizio Romano
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Christian Berlingieri
- Molecular Pathology, International Centre for Genetic and Engineering Biotechnology (ICGEB), Trieste, Italy
| | - Cristiana Stuani
- Molecular Pathology, International Centre for Genetic and Engineering Biotechnology (ICGEB), Trieste, Italy
| | - Douglas Laurents
- "Rocasolano" Institute for Physical Chemistry, Spanish National Research Council, Serrano 119, 28006, Madrid, Spain
| | - Miguel Mompeán
- "Rocasolano" Institute for Physical Chemistry, Spanish National Research Council, Serrano 119, 28006, Madrid, Spain
| | - Emanuele Buratti
- Molecular Pathology, International Centre for Genetic and Engineering Biotechnology (ICGEB), Trieste, Italy.
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21
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Esteban-García N, Fernández-Beltrán LC, Godoy-Corchuelo JM, Ayala JL, Matias-Guiu JA, Corrochano S. Body Complexion and Circulating Lipids in the Risk of TDP-43 Related Disorders. Front Aging Neurosci 2022; 14:838141. [PMID: 35401153 PMCID: PMC8990802 DOI: 10.3389/fnagi.2022.838141] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 02/04/2022] [Indexed: 12/13/2022] Open
Abstract
Objective Frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS) are two distinct degenerative disorders with overlapping genetics, clinical manifestations, and pathology, including the presence of TDP-43 aggregates in nearly 50% of patients with FTD and 98% of all patients with ALS. Here, we evaluate whether different genetically predicted body lipid metabolic traits are causally associated with the risk of FTD with TDP-43 aggregates, compare it to their causal role in the risk of ALS, and identify genetic variants shared between these two TDP43 related disorders in relation to lipid metabolic traits. Methods We conducted two-sample Mendelian randomization analyses (2SMR) to evaluate the causal association of 9 body complexion and 9 circulating lipids traits with the risk of FTD with TDP-43 aggregates and the risk of ALS. The inverse-variance weighted method was the primary analysis, followed by secondary sensitive analyses. We then looked for common genetic variants between FTD and ALS in relation to lipid metabolic traits. Results Genetically increased trunk-predicted mass, fat-free mass, and higher circulating triglycerides levels were suggestively associated with a higher risk of FTD with TDP-43 aggregates. Circulating lipids, mainly LDL cholesterol, were causally associated with a higher risk of ALS. We identified two genetic variants, EIF4ENIF1 and HNRNPK, in relation to body complexion and circulating lipids shared between FTD with TDP-43 aggregates and ALS. Conclusion This work provides evidence that body complexion and circulating lipids traits impact differentially on the risk of FTD and ALS, suggesting new and specific interventional approaches in the control of body lipid metabolism for FTD and ALS, and identified HNRNPK as a potential link between circulating lipids levels and these disorders.
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Affiliation(s)
- Noelia Esteban-García
- Neurological Disorders Group, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | - Luis C. Fernández-Beltrán
- Neurological Disorders Group, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | - Juan Miguel Godoy-Corchuelo
- Neurological Disorders Group, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | - Jose L. Ayala
- Department of Computer Architecture and Automation, Universidad Complutense de Madrid, Madrid, Spain
| | - Jordi A. Matias-Guiu
- Neurological Disorders Group, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | - Silvia Corrochano
- Neurological Disorders Group, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
- *Correspondence: Silvia Corrochano,
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22
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Hasan R, Humphrey J, Bettencourt C, Newcombe J, Lashley T, Fratta P, Raj T. Transcriptomic analysis of frontotemporal lobar degeneration with TDP-43 pathology reveals cellular alterations across multiple brain regions. Acta Neuropathol 2022; 143:383-401. [PMID: 34961893 DOI: 10.1007/s00401-021-02399-9/figures/4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 12/07/2021] [Accepted: 12/10/2021] [Indexed: 05/23/2023]
Abstract
Frontotemporal lobar degeneration (FTLD) is a group of heterogeneous neurodegenerative disorders affecting the frontal and temporal lobes of the brain. Nuclear loss and cytoplasmic aggregation of the RNA-binding protein TDP-43 represents the major FTLD pathology, known as FTLD-TDP. To date, there is no effective treatment for FTLD-TDP due to an incomplete understanding of the molecular mechanisms underlying disease development. Here we compared postmortem tissue RNA-seq transcriptomes from the frontal cortex, temporal cortex, and cerebellum between 28 controls and 30 FTLD-TDP patients to profile changes in cell-type composition, gene expression and transcript usage. We observed downregulation of neuronal markers in all three regions of the brain, accompanied by upregulation of microglia, astrocytes, and oligodendrocytes, as well as endothelial cells and pericytes, suggesting shifts in both immune activation and within the vasculature. We validate our estimates of neuronal loss using neuropathological atrophy scores and show that neuronal loss in the cortex can be mainly attributed to excitatory neurons, and that increases in microglial and endothelial cell expression are highly correlated with neuronal loss. All our analyses identified a strong involvement of the cerebellum in the neurodegenerative process of FTLD-TDP. Altogether, our data provides a detailed landscape of gene expression alterations to help unravel relevant disease mechanisms in FTLD.
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Affiliation(s)
- Rahat Hasan
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jack Humphrey
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Conceição Bettencourt
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK
| | - Jia Newcombe
- NeuroResource, Department of Neuroinflammation, UCL Queen Square Institute of Neurology, London, UK
| | - Tammaryn Lashley
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK
| | - Pietro Fratta
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Towfique Raj
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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23
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Hasan R, Humphrey J, Bettencourt C, Newcombe J, Lashley T, Fratta P, Raj T. Transcriptomic analysis of frontotemporal lobar degeneration with TDP-43 pathology reveals cellular alterations across multiple brain regions. Acta Neuropathol 2022; 143:383-401. [PMID: 34961893 PMCID: PMC10725322 DOI: 10.1007/s00401-021-02399-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 12/07/2021] [Accepted: 12/10/2021] [Indexed: 12/28/2022]
Abstract
Frontotemporal lobar degeneration (FTLD) is a group of heterogeneous neurodegenerative disorders affecting the frontal and temporal lobes of the brain. Nuclear loss and cytoplasmic aggregation of the RNA-binding protein TDP-43 represents the major FTLD pathology, known as FTLD-TDP. To date, there is no effective treatment for FTLD-TDP due to an incomplete understanding of the molecular mechanisms underlying disease development. Here we compared postmortem tissue RNA-seq transcriptomes from the frontal cortex, temporal cortex, and cerebellum between 28 controls and 30 FTLD-TDP patients to profile changes in cell-type composition, gene expression and transcript usage. We observed downregulation of neuronal markers in all three regions of the brain, accompanied by upregulation of microglia, astrocytes, and oligodendrocytes, as well as endothelial cells and pericytes, suggesting shifts in both immune activation and within the vasculature. We validate our estimates of neuronal loss using neuropathological atrophy scores and show that neuronal loss in the cortex can be mainly attributed to excitatory neurons, and that increases in microglial and endothelial cell expression are highly correlated with neuronal loss. All our analyses identified a strong involvement of the cerebellum in the neurodegenerative process of FTLD-TDP. Altogether, our data provides a detailed landscape of gene expression alterations to help unravel relevant disease mechanisms in FTLD.
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Affiliation(s)
- Rahat Hasan
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jack Humphrey
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Conceição Bettencourt
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK
| | - Jia Newcombe
- NeuroResource, Department of Neuroinflammation, UCL Queen Square Institute of Neurology, London, UK
| | - Tammaryn Lashley
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK
| | - Pietro Fratta
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Towfique Raj
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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24
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Keegan NP, Wilton SD, Fletcher S. Analysis of Pathogenic Pseudoexons Reveals Novel Mechanisms Driving Cryptic Splicing. Front Genet 2022; 12:806946. [PMID: 35140743 PMCID: PMC8819188 DOI: 10.3389/fgene.2021.806946] [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: 11/01/2021] [Accepted: 12/09/2021] [Indexed: 12/16/2022] Open
Abstract
Understanding pre-mRNA splicing is crucial to accurately diagnosing and treating genetic diseases. However, mutations that alter splicing can exert highly diverse effects. Of all the known types of splicing mutations, perhaps the rarest and most difficult to predict are those that activate pseudoexons, sometimes also called cryptic exons. Unlike other splicing mutations that either destroy or redirect existing splice events, pseudoexon mutations appear to create entirely new exons within introns. Since exon definition in vertebrates requires coordinated arrangements of numerous RNA motifs, one might expect that pseudoexons would only arise when rearrangements of intronic DNA create novel exons by chance. Surprisingly, although such mutations do occur, a far more common cause of pseudoexons is deep-intronic single nucleotide variants, raising the question of why these latent exon-like tracts near the mutation sites have not already been purged from the genome by the evolutionary advantage of more efficient splicing. Possible answers may lie in deep intronic splicing processes such as recursive splicing or poison exon splicing. Because these processes utilize intronic motifs that benignly engage with the spliceosome, the regions involved may be more susceptible to exonization than other intronic regions would be. We speculated that a comprehensive study of reported pseudoexons might detect alignments with known deep intronic splice sites and could also permit the characterisation of novel pseudoexon categories. In this report, we present and analyse a catalogue of over 400 published pseudoexon splice events. In addition to confirming prior observations of the most common pseudoexon mutation types, the size of this catalogue also enabled us to suggest new categories for some of the rarer types of pseudoexon mutation. By comparing our catalogue against published datasets of non-canonical splice events, we also found that 15.7% of pseudoexons exhibit some splicing activity at one or both of their splice sites in non-mutant cells. Importantly, this included seven examples of experimentally confirmed recursive splice sites, confirming for the first time a long-suspected link between these two splicing phenomena. These findings have the potential to improve the fidelity of genetic diagnostics and reveal new targets for splice-modulating therapies.
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Affiliation(s)
- Niall P. Keegan
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
- *Correspondence: Niall P. Keegan,
| | - Steve D. Wilton
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
| | - Sue Fletcher
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
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25
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Sidhu R, Gatt A, Fratta P, Lashley T, Bampton A. HnRNP K mislocalisation in neurons of the dentate nucleus is a novel neuropathological feature of neurodegenerative disease and ageing. Neuropathol Appl Neurobiol 2022; 48:e12793. [PMID: 35064577 PMCID: PMC9208575 DOI: 10.1111/nan.12793] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 12/10/2021] [Accepted: 12/12/2021] [Indexed: 11/28/2022]
Abstract
Nuclear depletion and cytoplasmic mislocalisation of the RNA‐binding protein heterogeneous ribonucleoprotein K (hnRNP K) within pyramidal neurons of the frontal cortex have been shown to be a common neuropathological feature in frontotemporal lobar degeneration (FTLD) and elderly control brain. Here, we describe a second neuronal subtype vulnerable to mislocalisation within the dentate nucleus of the cerebellum. In contrast to neurons within the cerebellar cortex that typically exhibited normal, nuclear staining, many neurons of the dentate nucleus exhibited striking mislocalisation of hnRNP K to the cytoplasm within neurodegenerative disease brain. Mislocalisation frequency in this region was found to be significantly higher in both FTLD‐TDP A and Alzheimer's disease (AD) brain than in age‐matched controls. However, within control (but not disease) subjects, mislocalisation frequency was significantly associated with age‐at‐death with more elderly controls typically exhibiting greater levels of the pathology. This study provides further evidence for hnRNP K mislocalisation being a more anatomically diverse pathology than previously thought and suggests that potential dysfunction of the protein may be more broadly relevant to the fields of neurodegeneration and ageing.
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Affiliation(s)
- Rahul Sidhu
- The Queen Square Brain Bank for Neurological Disorders, Department of Clinical and Movement Neuroscience, UCL Queen Square Institute of Neurology, London, UK.,Department of Neurodegenerative diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Ariana Gatt
- The Queen Square Brain Bank for Neurological Disorders, Department of Clinical and Movement Neuroscience, UCL Queen Square Institute of Neurology, London, UK.,Department of Neurodegenerative diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Pietro Fratta
- Department of Neuromuscular diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Tammaryn Lashley
- The Queen Square Brain Bank for Neurological Disorders, Department of Clinical and Movement Neuroscience, UCL Queen Square Institute of Neurology, London, UK.,Department of Neurodegenerative diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Alexander Bampton
- The Queen Square Brain Bank for Neurological Disorders, Department of Clinical and Movement Neuroscience, UCL Queen Square Institute of Neurology, London, UK.,Department of Neurodegenerative diseases, UCL Queen Square Institute of Neurology, London, UK
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26
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Petersen USS, Doktor TK, Andresen BS. Pseudoexon activation in disease by non-splice site deep intronic sequence variation - wild type pseudoexons constitute high-risk sites in the human genome. Hum Mutat 2021; 43:103-127. [PMID: 34837434 DOI: 10.1002/humu.24306] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 11/02/2021] [Accepted: 11/06/2021] [Indexed: 12/27/2022]
Abstract
Accuracy of pre-messenger RNA (pre-mRNA) splicing is crucial for normal gene expression. Complex regulation supports the spliceosomal distinction between authentic exons and the many seemingly functional splice sites delimiting pseudoexons. Pseudoexons are nonfunctional intronic sequences that can be activated for aberrant inclusion in mRNA, which may cause disease. Pseudoexon activation is very challenging to predict, in particular when activation occurs by sequence variants that alter the splicing regulatory environment without directly affecting splice sites. As pseudoexon inclusion often evades detection due to activation of nonsense-mediated mRNA decay, and because conventional diagnostic procedures miss deep intronic sequence variation, pseudoexon activation is a heavily underreported disease mechanism. Pseudoexon characteristics have mainly been studied based on in silico predicted sequences. Moreover, because recognition of sequence variants that create or strengthen splice sites is possible by comparison with well-established consensus sequences, this type of pseudoexon activation is by far the most frequently reported. Here we review all known human disease-associated pseudoexons that carry functional splice sites and are activated by deep intronic sequence variants located outside splice site sequences. We delineate common characteristics that make this type of wild type pseudoexons distinct high-risk sites in the human genome.
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Affiliation(s)
- Ulrika S S Petersen
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
| | - Thomas K Doktor
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
| | - Brage S Andresen
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
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