Neuropathologically informed imaging of cortical grey matter lesions in MS - A pilot study.

Multiple sclerosis (MS) is frequently misdiagnosed based on MRI abnormalities detected in the brain white matter. Cortical lesions have been well described neuropathologically, but remain challenging to detect in clinical practice. Therefore, the ability to detect cortical lesions offers real potential to reduce misdiagnosis. Cortical lesions have been shown to have a predilection for regions with CSF stasis - such as the insula and cingulate gyrus. This pathological observation forms the basis of our current pilot MR imaging study, which successfully uses high spatial resolution imaging of these two anatomical regions to clearly identify cortical lesions in MS.

Primary Lateral Sclerosis: Clinical, radiological and molecular features.

Primary Lateral Sclerosis (PLS) is an uncommon motor neuron disorder. Despite the well-recognisable constellation of clinical manifestations, the initial diagnosis can be challenging and therapeutic options are currently limited. There have been no recent clinical trials of disease-modifying therapies dedicated to this patient cohort and awareness of recent research developments is limited. The recent consensus diagnostic criteria introduced the category 'probable' PLS which is likely to curtail the diagnostic journey of patients. Extra-motor clinical manifestations are increasingly recognised, challenging the view of PLS as a 'pure' upper motor neuron condition. The post mortem literature of PLS has been expanded by seminal TDP-43 reports and recent PLS studies increasingly avail of meticulous genetic profiling. Research in PLS has gained unprecedented momentum in recent years generating novel academic insights, which may have important clinical ramifications.

High-throughput functional characterization of protein phosphorylation sites in yeast.

Phosphorylation is a critical post-translational modification involved in the regulation of almost all cellular processes. However, fewer than 5% of thousands of recently discovered phosphosites have been functionally annotated. In this study, we devised a chemical genetic approach to study the functional relevance of phosphosites in Saccharomyces cerevisiae. We generated 474 yeast strains with mutations in specific phosphosites that were screened for fitness in 102 conditions, along with a gene deletion library. Of these phosphosites, 42% exhibited growth phenotypes, suggesting that these are more likely functional. We inferred their function based on the similarity of their growth profiles with that of gene deletions and validated a subset by thermal proteome profiling and lipidomics. A high fraction exhibited phenotypes not seen in the corresponding gene deletion, suggestive of a gain-of-function effect. For phosphosites conserved in humans, the severity of the yeast phenotypes is indicative of their human functional relevance. This high-throughput approach allows for functionally characterizing individual phosphosites at scale.

Erratum: Publisher Correction: Genetic interaction networks mediate individual statin drug response in Saccharomyces cerevisiae.

[This corrects the article DOI: 10.1038/s41540-019-0112-5.].

Adaptive functional reorganization in amyotrophic lateral sclerosis: coexisting degenerative and compensatory changes.

BACKGROUND AND PURPOSE: Considerable functional reorganization takes place in amyotrophic lateral sclerosis (ALS) in face of relentless structural degeneration. This study evaluates functional adaptation in ALS patients with lower motor neuron predominant (LMNp) and upper motor neuron predominant (UMNp) dysfunction. METHODS: Seventeen LMNp ALS patients, 14 UMNp ALS patients and 14 controls participated in a functional magnetic resonance imaging study. Study-group-specific activation patterns were evaluated during preparation for a motor task. Connectivity analyses were carried out using the supplementary motor area (SMA), cerebellum and striatum as seed regions and correlations were explored with clinical measures. RESULTS: Increased cerebellar, decreased dorsolateral prefrontal cortex and decreased SMA activation were detected in UMNp patients compared to controls. Increased cerebellar activation was also detected in UMNp patients compared to LMNp patients. UMNp patients exhibit increased effective connectivity between the cerebellum and caudate, and decreased connectivity between the SMA and caudate and between the SMA and cerebellum when performing self-initiated movement. In UMNp patients, a positive correlation was detected between clinical variables and striato-cerebellar connectivity. CONCLUSIONS: Our findings indicate that, despite the dysfunction of SMA-striatal and SMA-cerebellar networks, cerebello-striatal connectivity increases in ALS indicative of compensatory processes. The coexistence of circuits with decreased and increased connectivity suggests concomitant neurodegenerative and adaptive changes in ALS.

The impact of the genetic background on gene deletion phenotypes in Saccharomyces cerevisiae.

Loss-of-function (LoF) mutations associated with disease do not manifest equally in different individuals. The impact of the genetic background on the consequences of LoF mutations remains poorly characterized. Here, we systematically assessed the changes in gene deletion phenotypes for 3,786 gene knockouts in four Saccharomyces cerevisiae strains and 38 conditions. We observed 18.5% of deletion phenotypes changing between pairs of strains on average with a small fraction conserved in all four strains. Conditions causing higher wild-type growth differences and the deletion of pleiotropic genes showed above-average changes in phenotypes. In addition, we performed a genome-wide association study (GWAS) for growth under the same conditions for a panel of 925 yeast isolates. Gene-condition associations derived from GWAS were not enriched for genes with deletion phenotypes under the same conditions. However, cases where the results were congruent indicate the most likely mechanism underlying the GWAS signal. Overall, these results show a high degree of genetic background dependencies for LoF phenotypes.

Genetic interaction networks mediate individual statin drug response in Saccharomyces cerevisiae.

Eukaryotic genetic interaction networks (GINs) are extensively described in the Saccharomyces cerevisiae S288C model using deletion libraries, yet being limited to this one genetic background, not informative to individual drug response. Here we created deletion libraries in three additional genetic backgrounds. Statin response was probed with five queries against four genetic backgrounds. The 20 resultant GINs representing drug-gene and gene-gene interactions were not conserved by functional enrichment, hierarchical clustering, and topology-based community partitioning. An unfolded protein response (UPR) community exhibited genetic background variation including different betweenness genes that were network bottlenecks, and we experimentally validated this UPR community via measurements of the UPR that were differentially activated and regulated in statin-resistant strains relative to the statin-sensitive S288C background. These network analyses by topology and function provide insight into the complexity of drug response influenced by genetic background.

Conserved phosphorylation hotspots in eukaryotic protein domain families.

Protein phosphorylation is the best characterized post-translational modification that regulates almost all cellular processes through diverse mechanisms such as changing protein conformations, interactions, and localization. While the inventory for phosphorylation sites across different species has rapidly expanded, their functional role remains poorly investigated. Here, we combine 537,321 phosphosites from 40 eukaryotic species to identify highly conserved phosphorylation hotspot regions within domain families. Mapping these regions onto structural data reveals that they are often found at interfaces, near catalytic residues and tend to harbor functionally important phosphosites. Notably, functional studies of a phospho-deficient mutant in the C-terminal hotspot region within the ribosomal S11 domain in the yeast ribosomal protein uS11 shows impaired growth and defective cytoplasmic 20S pre-rRNA processing at 16 °C and 20 °C. Altogether, our study identifies phosphorylation hotspots for 162 protein domains suggestive of an ancient role for the control of diverse eukaryotic domain families.

A resource of variant effect predictions of single nucleotide variants in model organisms.

The effect of single nucleotide variants (SNVs) in coding and noncoding regions is of great interest in genetics. Although many computational methods aim to elucidate the effects of SNVs on cellular mechanisms, it is not straightforward to comprehensively cover different molecular effects. To address this, we compiled and benchmarked sequence and structure-based variant effect predictors and we computed the impact of nearly all possible amino acid and nucleotide variants in the reference genomes of Homo sapiens, Saccharomyces cerevisiae and Escherichia coli Studied mechanisms include protein stability, interaction interfaces, post-translational modifications and transcription factor binding sites. We apply this resource to the study of natural and disease coding variants. We also show how variant effects can be aggregated to generate protein complex burden scores that uncover protein complex to phenotype associations based on a set of newly generated growth profiles of 93 sequenced S. cerevisiae strains in 43 conditions. This resource is available through mutfunc (www.mutfunc.com), a tool by which users can query precomputed predictions by providing amino acid or nucleotide-level variants.

'Khatatonia' - cathinone-induced hypertensive encephalopathy.

Khat consumption is an under-recognised cause of hypertensive encephalopathy and intraparenchymal brain haemorrhage. We report the radiological findings of extensive periventricular, subcortical and brain stem white matter pathology of a patient who had consumed excessive amounts of Khat. The Khat plant contains cathinone, an amphetamine-like alkaloid which has been associated with chronic hypertensive end-organ damage, but is seldom considered a cause of cerebrovascular events in northern Europe.

The segmental diffusivity profile of amyotrophic lateral sclerosis associated white matter degeneration.

BACKGROUND AND PURPOSE: Magnetic resonance diffusivity indices have been repeatedly proposed as biomarkers of neurodegeneration in amyotrophic lateral sclerosis (ALS), but no consensus exists as to which diffusivity parameter is the most sensitive to identify early degenerative changes. Despite numerous studies, surprisingly little is known of the segmental vulnerability of the corticospinal tracts and corpus callosum. Our objective was to characterize the core three-dimensional white matter signature of ALS, to describe phenotype-specific patterns of white matter degeneration and to evaluate the diffusivity profile of individual patients and controls in specific white matter segments. METHODS: A large neuroimaging study was undertaken with 62 patients and 55 age-matched healthy controls. White matter alterations were explored based on fractional anisotropy and radial, mean and axial diffusivity indices. Atlas-based region of interest analyses were carried out in the corona radiata, internal capsules, cerebral peduncles, and in the splenium, body and genu of the corpus callosum. Percentage change and receiver operating characteristic (ROC) curves were used to characterize disease-state discriminating diffusivity measures and white matter regions. RESULTS: Bulbar onset patients exhibit extensive corticobulbar tract involvement in the genu of the internal capsule and in the lateral fibres of the corona radiata subjacent to the bulbar representation of the motor homunculus. Spinal onset patients show predominantly posterior internal capsule involvement and medial corona radiata pathology. ROC curve analyses revealed that diffusivity measures of the cerebral crura best discriminate patients and controls (area under the curve 80.1%). CONCLUSIONS: Amyotrophic lateral sclerosis is associated with a core, disease-specific three-dimensional white matter signature which is best demonstrated by radial diffusivity measurements. The main ALS motor phenotypes are manifestations of the relatively selective involvement of corticospinal and corticobulbar fibres.

Revisiting the spectrum of lower motor neuron diseases with snake eyes appearance on magnetic resonance imaging.

BACKGROUND AND PURPOSE: The 'snake eyes' sign refers to bilateral hyperintensities of the anterior horns on axial spinal cord imaging. Based on sporadic reports, it has been associated with a range of lower motor neuron (LMN) syndromes, such as spondylotic amyotrophy and Hirayama disease, as well as spinal cord infarction. The objective of our study was to comprehensively characterize the full diagnostic spectrum of LMN syndromes with this radiological clue and discuss potential aetiological factors. METHODS: A large patient cohort with snake eyes sign and upper limb LMN degeneration was recruited from three French neuromuscular units. Patients underwent detailed electrophysiological, radiological, clinical and anamnestic profiling. RESULTS: Twenty-nine patients were ascertained and followed up for 9.5 ± 8.6 years. The majority of the patients were male (86.2%) with a mean age of 37.3 ± 14.4 years. Symptoms were bilateral in most cases (86.2%). Patients with predominantly proximal and distal deficits were equally represented (44.8% and 55.2%, respectively). A history of preceding trauma or intense physical activity was confirmed in 58.6% of the cases; 27.6% of the patients were given an initial clinical diagnosis of amyotrophic lateral sclerosis (ALS), and 51.7% were originally suspected to have multifocal motor neuropathy. None of the patients developed ALS on longitudinal follow-up. CONCLUSION: The snake eyes sign on magnetic resonance imaging is associated with a wide spectrum of neurological conditions and is more common in young men with a history of strenuous activity or antecedent trauma. The recognition of this syndrome is crucial as many of these patients are initially misdiagnosed with ALS.

Molecular basis for fungicidal action of neothyonidioside, a triterpene glycoside from the sea cucumber, Australostichopus mollis.

Neothyonidioside is a triterpene glycoside (TG) isolated from the sea cucumber, Australostichopus mollis, that is potently cytotoxic to S. cerevisiae, but does not permeabilize cellular membranes. We mutagenized S. cerevisiae and isolated a neothionidioside-resistant (neo(R)) strain. Using synthetic genetic array mapping and sequencing, we identified NCP1 as the resistance locus. Quantitative HPLC revealed that neo(R)/ncp1 mutants have reduced ergosterol content. Ergosterol added to growth media reversed toxicity, demonstrating that neothionidioside binds directly to ergosterol, similar to the polyene natamycin. Ergosterol synthesis inhibitors ketoconazole and atorvastatin conferred resistance to neothionidioside in a dose-dependent manner showing that a threshold ergosterol concentration is required for toxicity. A genome-wide screen of deletion mutants against neothionidioside revealed hypersensitivity of many of the component genes in the ESCRT complexes relating to multivesicular body formation. Confocal microscopy of cells stained with a vital dye showed blockage at this step. Thus, we propose neothionidioside may affect membrane curvature and fusion capability in the endosome-vacuole pathway.

On the development of markers for pathological TDP-43 in amyotrophic lateral sclerosis with and without dementia.

Pathological 43-kDa transactive response sequence DNA-binding protein (TDP-43) has been recognized as the major disease protein in amyotrophic lateral sclerosis (ALS), frontotemporal lobar degeneration with ubiquitin positive, tau and α-synuclein negative inclusions (FTLD-U) and the transitional forms between these multisystem conditions. In order to develop TDP-43 into a successful ALS biomarker, the natural history of TDP-43 pathology needs to be characterized and the underlying pathophysiology established. Here we propose a spatial and temporal "two-axes" model of central nervous system vulnerability for TDP-43 linked degeneration and review recent studies on potential biomarkers related to pathological TDP-43 in the cerebrospinal fluid (CSF), blood, and skeletal muscle. The model includes the following two arms: Firstly, a "motor neuron disease" or "spinal cord/brainstem to motor cortex" axis (with degeneration possibly ascending from the lower motor neurons to the upper motor neurons); and secondly, a "dementia" or "corticoid/allocortex to neocortex" axis (with a probable spread of TDP-43 linked degeneration from the mediotemporal lobe to wider mesocortical and neocortical brain areas). At the cellular level, there is a gradual disappearance of normal TDP-43 in the nucleus in combination with the formation of pathological aggregates in the cell body and cellular processes, which can also be used to identify the stage of the disease process. Moreover, TDP-43 lesions in subpial/subependymal or perivascular localizations have been noted, and this might account for increased CSF and blood TDP-43 levels through mechanisms that remain to be elucidated.

Executive dysfunction is a negative prognostic indicator in patients with ALS without dementia.

BACKGROUND: The prognostic implications of cognitive impairment in amyotrophic lateral sclerosis (ALS) are not established. OBJECTIVES: To investigate the survival effect of the comorbid frontotemporal dementia (FTD) and to determine whether, in the absence of dementia, impairment in different cognitive domains affects outcome. METHODS: A prospective population-based study of incident cases of ALS in the Republic of Ireland included home-based neuropsychological assessments using age-, sex-, and education-matched controls. Four cognitive domains were evaluated: executive function, memory, language, and visuospatial skills. RESULTS: Mean age of the participants (n = 139) was 63.3 years; 61.2% were male and 35.3% had bulbar-onset ALS. Factors associated with shorter survival included age more than 60, severe disability at baseline, shorter delay to diagnosis, and early respiratory involvement. Comorbid FTD was associated with significantly shorter survival time (hazard ratio [HR] 2.67, 95% confidence interval [CI] 1.04-6.85, p = 0.041). In patients with ALS without dementia, the presence of executive dysfunction was significantly associated with shorter survival. This was confirmed in a multivariate model that included age, delay to diagnosis, disease severity at baseline, education, and respiratory status (HR 3.44, 95% CI 1.45-8.18, p = 0.005). In the absence of executive dysfunction, single or multi-domain impairment in other cognitive domains had no significant effect on survival. CONCLUSION: Comorbid frontotemporal dementia is a negative prognostic indicator. In patients with ALS without dementia, executive dysfunction, but not impairment in other cognitive domains, is an important negative prognostic indicator.