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      Mitochondrial bioenergetic deficits in C9orf72 amyotrophic lateral sclerosis motor neurons cause dysfunctional axonal homeostasis

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          Abstract

          Axonal dysfunction is a common phenotype in neurodegenerative disorders, including in amyotrophic lateral sclerosis (ALS), where the key pathological cell-type, the motor neuron (MN), has an axon extending up to a metre long. The maintenance of axonal function is a highly energy-demanding process, raising the question of whether MN cellular energetics is perturbed in ALS, and whether its recovery promotes axonal rescue. To address this, we undertook cellular and molecular interrogation of multiple patient-derived induced pluripotent stem cell lines and patient autopsy samples harbouring the most common ALS causing mutation, C9orf72. Using paired mutant and isogenic expansion-corrected controls, we show that C9orf72 MNs have shorter axons, impaired fast axonal transport of mitochondrial cargo, and altered mitochondrial bioenergetic function. RNAseq revealed reduced gene expression of mitochondrially encoded electron transport chain transcripts, with neuropathological analysis of C9orf72-ALS post-mortem tissue importantly confirming selective dysregulation of the mitochondrially encoded transcripts in ventral horn spinal MNs, but not in corresponding dorsal horn sensory neurons, with findings reflected at the protein level. Mitochondrial DNA copy number was unaltered, both in vitro and in human post-mortem tissue. Genetic manipulation of mitochondrial biogenesis in C9orf72 MNs corrected the bioenergetic deficit and also rescued the axonal length and transport phenotypes. Collectively, our data show that loss of mitochondrial function is a key mediator of axonal dysfunction in C9orf72-ALS, and that boosting MN bioenergetics is sufficient to restore axonal homeostasis, opening new potential therapeutic strategies for ALS that target mitochondrial function.

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          The online version of this article (10.1007/s00401-020-02252-5) contains supplementary material, which is available to authorized users.

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          Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.
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            Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biology research communities.
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              STAR: ultrafast universal RNA-seq aligner.

              Accurate alignment of high-throughput RNA-seq data is a challenging and yet unsolved problem because of the non-contiguous transcript structure, relatively short read lengths and constantly increasing throughput of the sequencing technologies. Currently available RNA-seq aligners suffer from high mapping error rates, low mapping speed, read length limitation and mapping biases. To align our large (>80 billon reads) ENCODE Transcriptome RNA-seq dataset, we developed the Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR outperforms other aligners by a factor of >50 in mapping speed, aligning to the human genome 550 million 2 × 76 bp paired-end reads per hour on a modest 12-core server, while at the same time improving alignment sensitivity and precision. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences. Using Roche 454 sequencing of reverse transcription polymerase chain reaction amplicons, we experimentally validated 1960 novel intergenic splice junctions with an 80-90% success rate, corroborating the high precision of the STAR mapping strategy. STAR is implemented as a standalone C++ code. STAR is free open source software distributed under GPLv3 license and can be downloaded from http://code.google.com/p/rna-star/.
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                Author and article information

                Contributors
                siddharthan.chandran@ed.ac.uk
                bthangar@ed.ac.uk
                Journal
                Acta Neuropathol
                Acta Neuropathol
                Acta Neuropathologica
                Springer Berlin Heidelberg (Berlin/Heidelberg )
                0001-6322
                1432-0533
                4 January 2021
                4 January 2021
                2021
                : 141
                : 2
                : 257-279
                Affiliations
                [1 ]GRID grid.4305.2, ISNI 0000 0004 1936 7988, UK Dementia Research Institute at University of Edinburgh, University of Edinburgh, ; Edinburgh bioQuarter, Chancellor’s Building, 49 Little France Crescent, Edinburgh, EH16 4SB UK
                [2 ]GRID grid.4305.2, ISNI 0000 0004 1936 7988, Centre for Clinical Brain Sciences, , University of Edinburgh, ; Edinburgh, UK
                [3 ]GRID grid.4305.2, ISNI 0000 0004 1936 7988, Anne Rowling Regenerative Neurology Clinic, , University of Edinburgh, ; Edinburgh, UK
                [4 ]GRID grid.4305.2, ISNI 0000 0004 1936 7988, Euan MacDonald Centre for MND Research, , University of Edinburgh, ; Edinburgh, UK
                [5 ]GRID grid.4991.5, ISNI 0000 0004 1936 8948, Nuffield Department of Clinical Neurosciences, , University of Oxford, ; Oxford, UK
                [6 ]GRID grid.4305.2, ISNI 0000 0004 1936 7988, MRC Edinburgh Brain Bank, Academic Department of Neuropathology, , University of Edinburgh, ; Edinburgh, UK
                [7 ]GRID grid.4305.2, ISNI 0000 0004 1936 7988, Edinburgh Pathology, , University of Edinburgh, ; Edinburgh, UK
                [8 ]GRID grid.4305.2, ISNI 0000 0004 1936 7988, Centre for Discovery Brain Sciences, , University of Edinburgh, ; Edinburgh, UK
                [9 ]GRID grid.4305.2, ISNI 0000 0004 1936 7988, University/British Heart Foundation Centre for Cardiovascular Science, , University of Edinburgh, ; Edinburgh, UK
                [10 ]GRID grid.475408.a, ISNI 0000 0004 4905 7710, Centre for Brain Development and Repair, , inStem, ; Bangalore, India
                Author information
                http://orcid.org/0000-0002-5715-5025
                http://orcid.org/0000-0001-7299-0910
                Article
                2252
                10.1007/s00401-020-02252-5
                7847443
                33398403
                4cb72fdf-b0e1-4cec-86c2-a07c4b748258
                © The Author(s) 2021

                Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 23 July 2020
                : 30 November 2020
                : 9 December 2020
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/501100000265, Medical Research Council;
                Award ID: MR/R001162/1
                Award ID: MR/L016400/1
                Award ID: MR/N013255/1
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100000406, Motor Neurone Disease Association;
                Award ID: MR/R001162/1
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100004440, Wellcome Trust;
                Award ID: 100981/Z/13/Z
                Award Recipient :
                Categories
                Original Paper
                Custom metadata
                © Springer-Verlag GmbH Germany, part of Springer Nature 2021

                Neurology
                amyotrophic lateral sclerosis,axon,energy metabolism,frontotemporal dementia,mitochondria,motor neuron,neurodegeneration

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