Papers by Johnathan Cooper-Knock
Neuropathology, 2015
Amyotrophic lateral sclerosis (ALS) is characterised by motor neurone loss resulting in muscle we... more Amyotrophic lateral sclerosis (ALS) is characterised by motor neurone loss resulting in muscle weakness, spasticity and ultimately death. Whilst most cases are sporadic, 5-10% are caused by inherited mutations, most commonly C9ORF72, SOD1, TARDBP and FUS.
Neurobiology of Aging, 2015
Cohorts of amyotrophic lateral sclerosis (ALS) patients and control individuals of Caucasian orig... more Cohorts of amyotrophic lateral sclerosis (ALS) patients and control individuals of Caucasian origin from the Central European Russia (Moscow city and region) were analyzed for the presence of hexanucleotide repeat GGGGCC expansion within the first intron of the C9ORF72 gene. The presence of a large (>40) repeat expansion was found in 15% of familial ALS cases (3 of 20 unrelated familial cases) and 2.5% of sporadic ALS cases (6 of 238) but in none of control cases. These results suggest that the frequency of C9ORF72 hexanucleotide repeats expansions in the Central European Russian ALS patients is significantly lower than in Western European or Northern American ALS patients of Caucasian origin but higher than in Asian ALS patients.
Neuropathology and applied neurobiology, Jan 11, 2015
Intermediate-length cytosine-adenine-guanine repeat expansions in the ATXN2 gene (which encodes f... more Intermediate-length cytosine-adenine-guanine repeat expansions in the ATXN2 gene (which encodes for Ataxin-2 protein) have been linked to increased risk for motor neurone disease/amyotrophic lateral sclerosis (ALS). We screened DNA from cases for which we had post-mortem brain tissue to enable characterization of the neuropathology associated with this mutation. Polymerase chain reaction and sequencing of DNA from frozen brain tissue on a cohort of 178 amyotrophic lateral sclerosis (ALS) autopsy cases from the north of England and 159 controls was performed. This was followed by tinctorial staining and immunohistochemistry (including for Ataxin-2) on selected blocks from ALS cases with intermediate-length expansions (ATXN2-ALS), sporadic ALS cases and neurologically healthy controls. Four ALS cases with intermediate-length CAG repeat expansions within ATXN2 were identified. One such case also had a mutation of the C9ORF72 gene. All had lower motor neurone depletion, and three out of...
Molecular Neurodegeneration
Background Sizing of GGGGCC hexanucleotide repeat expansions within the C9ORF72 locus, which acco... more Background Sizing of GGGGCC hexanucleotide repeat expansions within the C9ORF72 locus, which account for approximately 10% of all amyotrophic lateral sclerosis (ALS) cases, is urgently required to answer fundamental questions about mechanisms of pathogenesis in this important genetic variant. Currently employed PCR protocols are limited to discrimination between the presence and absence of a modified allele with more than 30 copies of the repeat, while Southern hybridisation-based methods are confounded by the somatic heterogeneity commonly present in blood samples, which might cause false-negative or ambiguous results. Results We describe an optimised Southern hybridisation-based protocol that allows confident detection of the presence of a C9ORF72 repeat expansion alongside independent assessment of its heterogeneity and the number of repeat units. The protocol can be used with either a radiolabeled or non-radiolabeled probe. Using this method we have successfully sized the C9ORF7...
Neurobiology of aging
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease of motor neurons. Single-nucle... more Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease of motor neurons. Single-nucleotide polymorphism rs3849942 is associated with ALS, tagging a hexanucleotide repeat mutation in the C9orf72 gene. It is possible that there is more than 1 disease-causing genetic variation at this locus, in which case association might remain after removal of cases carrying the mutation. DNA from patients with ALS was therefore tested for the mutation. Genome-wide association testing was performed first using all samples, and then restricting the analysis to samples not carrying the mutation. rs3849942 and rs903603 were strongly associated with ALS when all samples were included (rs3849942, p = [3 × 2] × 10(-6), rank 7/442,057; rs903603, p = [7 × 6] × 10(-8), rank 2/442,057). Removal of the mutation-carrying cases resulted in loss of association for rs3849942 (p = [2 × 6] × 10(-3), rank 1225/442,068), but had little effect on rs903603 (p = [1 × 9] × 10(-5), rank 8/442,068). Those with a...
PloS one, 2015
An intronic GGGGCC-repeat expansion of C9ORF72 is the most common genetic variant of amyotrophic ... more An intronic GGGGCC-repeat expansion of C9ORF72 is the most common genetic variant of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia. The mechanism of neurodegeneration is unknown, but a direct effect on RNA processing mediated by RNA foci transcribed from the repeat sequence has been proposed. Gene expression profiling utilised total RNA extracted from motor neurons and lymphoblastoid cell lines derived from human ALS patients, including those with an expansion of C9ORF72, and controls. In lymphoblastoid cell lines, expansion length and the frequency of sense and antisense RNA foci was also examined. Gene level analysis revealed a number of differentially expressed networks and both cell types exhibited dysregulation of a network functionally enriched for genes encoding 'RNA splicing' proteins. There was a significant overlap of these genes with an independently generated list of GGGGCC-repeat protein binding partners. At the exon level, in lymphoblastoid ce...
Acta Neuropathologica, 2015
data suggest that, although sense and antisense RNA molecules might be expected to be equally tox... more data suggest that, although sense and antisense RNA molecules might be expected to be equally toxic via their shared protein binding partners, distinct patterns of expression in various CNS neuronal populations could lead to relative differences in their contribution to the pathogenesis of neuronal injury. Moreover in motor neurons, which are the primary target of pathology in ALS, the presence of antisense foci (χ 2 , p < 0.00001) but not sense foci (χ 2 , p = 0.75) correlated with mislocalisation of TDP-43, which is the hallmark of ALS neurodegeneration. This has implications for translational approaches to C9ORF72 disease, and furthermore interacting RNA-processing factors and transcriptional activators responsible for antisense versus sense transcription might represent novel therapeutic targets.
Decoding the pathophysiological mechanisms that underlie RNA dysregulation in neurodegenerative d... more Decoding the pathophysiological mechanisms that underlie RNA dysregulation in neurodegenerative disorders: a review of the current state of the art Altered RNA metabolism is a key pathophysiological component causing several neurodegenerative diseases. Genetic mutations causing neurodegeneration occur in coding and noncoding regions of seemingly unrelated genes whose products do not always contribute to the gene expression process. Several pathogenic mechanisms may coexist within a single neuronal cell, including RNA/ protein toxic gain-of-function and/or protein loss-offunction. Genetic mutations that cause neurodegenerative disorders disrupt healthy gene expression at diverse levels, from chromatin remodelling, transcription, splicing, through to axonal transport and repeat-associated non-ATG (RAN) translation. We address neurodegeneration in repeat expansion disorders [Huntington's disease, spinocerebellar ataxias, C9ORF72-related amyotrophic lateral sclerosis (ALS)] and in diseases caused by deletions or point mutations (spinal muscular atrophy, most subtypes of familial ALS). Some neurodegenerative disorders exhibit broad dysregulation of gene expression with the synthesis of hundreds to thousands of abnormal messenger RNA (mRNA) molecules. However, the number and identity of aberrant mRNAs that are translated into proteins -and how these lead to neurodegeneration -remain unknown. The field of RNA biology research faces the challenge of identifying pathophysiological events of dysregulated gene expression. In conclusion, we discuss current research limitations and future directions to improve our characterization of pathological mechanisms that trigger disease onset and progression.
Brain : a journal of neurology, 2014
GGGGCC repeat expansions of C9orf72 represent the most common genetic variant of amyotrophic late... more GGGGCC repeat expansions of C9orf72 represent the most common genetic variant of amyotrophic lateral sclerosis and frontotemporal degeneration, but the mechanism of pathogenesis is unclear. Recent reports have suggested that the transcribed repeat might form toxic RNA foci that sequester various RNA processing proteins. Consensus as to the identity of the binding partners is missing and whole neuronal proteome investigation is needed. Using RNA fluorescence in situ hybridization we first identified nuclear and cytoplasmic RNA foci in peripheral and central nervous system biosamples from patients with amyotrophic lateral sclerosis with a repeat expansion of C9orf72 (C9orf72+), but not from those patients without a repeat expansion of C9orf72 (C9orf72-) or control subjects. Moreover, in the cases examined, the distribution of foci-positive neurons correlated with the clinical phenotype (t-test P < 0.05). As expected, RNA foci are ablated by RNase treatment. Interestingly, we identi...
Colloquium Series on Genomic and Molecular Medicine, 2013
Neurotherapeutics : the journal of the American Society for Experimental NeuroTherapeutics, Jan 3, 2015
The discovery that a hexanucleotide repeat expansion in C9orf72 is the most numerous genetic vari... more The discovery that a hexanucleotide repeat expansion in C9orf72 is the most numerous genetic variant of both amyotrophic lateral sclerosis and frontotemporal dementia has opened a rapidly growing field, which may provide long hoped for advances in the understanding and treatment of these devastating diseases. In this review we describe the various phenotypes, clinical and pathological, associated with expansion of C9orf72, which go beyond amyotrophic lateral sclerosis and frontotemporal dementia to include neurodegeneration more broadly. Next we take a step back and summarize the current understanding of the C9orf72 expansion and its protein products at a molecular level. Three mechanisms are prominent: toxicity mediated directly by RNA transcribed from the repeat; toxicity mediated by dipeptide repeat proteins translated from the repeat sequence; and haploinsufficiency resulting from reduced transcription of the C9orf72 exonic sequence. A series of exciting advances have recently d...
... Emily F. Goodall, Joanna J. Bury, Johnathan Cooper-Knock, Pamela J. Shaw and Janine Kirby She... more ... Emily F. Goodall, Joanna J. Bury, Johnathan Cooper-Knock, Pamela J. Shaw and Janine Kirby Sheffield Institute for Translational Neuroscience ... have been identified with pathogenic mutations in the microtubule associated protein tau (MAPT) gene located on chr17 (Hutton et al ...
Amyotrophic lateral sclerosis & frontotemporal degeneration, Jan 20, 2016
Annals of Clinical and Translational Neurology, 2014
Objective: The prominent histopathological feature of the amyotrophic lateral sclerosis (ALS) is ... more Objective: The prominent histopathological feature of the amyotrophic lateral sclerosis (ALS) is the presence of intracellular inclusions in degenerating neurons and their axons. The appearance and localization of these pathological structures depend on an aggregated protein that forms their scaffold. We investigated if c-synuclein, an aggregation-prone protein highly expressed in healthy motor neurons, and predominantly localized in their axons and synaptic terminals is involved in ALS pathology. Methods: Immunostaining of histological sections and sequential protein extraction from postmortem neural samples followed by immunoblotting. Results: Immunohistochemical screening revealed a subset of sporadic (9 of 31) and familial (8 of 23) ALS cases with a novel type of pathology characterized by the accumulation of c-synuclein in distinct profiles within the dorsolateral column. Sequential fractionation of proteins from the spinal cord tissues revealed detergent-insoluble c-synuclein species specifically in the dorsolateral corticospinal tracts of a ALS patient with c-synuclein-positive profiles in this region. These profiles are negative for protein markers commonly found in pathological inclusions in the spinal cord of ALS patients and most probably represent degenerated axons of upper motor neurons that have lost their neurofilaments. A subset of these profiles was found in association with phagocytic cells positive for Mac-2/Galectin-3. A smaller subset of studied ALS cases (4 of 54) contained large cytoplasmic inclusions in the cell body of remaining spinal motor neurons. Interpretation: Our observations suggest that pathological aggregation of c-synuclein might contribute to the pathogenesis of ALS.
Amyotrophic Lateral Sclerosis and Frontotemporal Degeneration, 2013
Neuropathology and Applied Neurobiology, 2014
Altered RNA metabolism is a key pathophysiological component causing several neurodegenerative di... more Altered RNA metabolism is a key pathophysiological component causing several neurodegenerative diseases. Genetic mutations causing neurodegeneration occur in coding and non-coding regions of seemingly unrelated genes whose products do not always contribute to the gene expression process.
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Papers by Johnathan Cooper-Knock