2D versus 3D human induced pluripotent stem cell-derived cultures for neurodegenerative disease modelling

Neurodegenerative diseases, such as Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD) and amyotrophic lateral sclerosis (ALS), affect millions of people every year and so far, there are no therapeutic cures available. Even though animal and histological models have been of great aid in understanding disease mechanisms and identifying possible therapeutic strategies, in order to find disease-modifying solutions there is still a critical need for systems that can provide more predictive and physiologically relevant results. One possible avenue is the development of patient-derived models, e.g. by reprogramming patient somatic cells into human induced pluripotent stem cells (hiPSCs), which can then be differentiated into any cell type for modelling. These systems contain key genetic information from the donors, and therefore have enormous potential as tools in the investigation of pathological mechanisms underlying disease phenotype, and progression, as well as in drug testing platforms. hiPSCs have been widely cultured in 2D systems, but in order to mimic human brain complexity, 3D models have been proposed as a more advanced alternative. This review will focus on the use of patient-derived hiPSCs to model AD, PD, HD and ALS. In brief, we will cover the available stem cells, types of 2D and 3D culture systems, existing models for neurodegenerative diseases, obstacles to model these diseases in vitro, and current perspectives in the field

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity.

Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability of a large dataset, well represented by both spike 614 variants, not all approaches showed a conclusive signal of positive selection. Population genetic analysis indicates that 614G increases in frequency relative to 614D in a manner consistent with a selective advantage. We do not find any indication that patients infected with the spike 614G variant have higher COVID-19 mortality or clinical severity, but 614G is associated with higher viral load and younger age of patients. Significant differences in growth and size of 614G phylogenetic clusters indicate a need for continued study of this variant

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity

Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability of a large dataset, well represented by both spike 614 variants, not all approaches showed a conclusive signal of positive selection. Population genetic analysis indicates that 614G increases in frequency relative to 614D in a manner consistent with a selective advantage. We do not find any indication that patients infected with the spike 614G variant have higher COVID-19 mortality or clinical severity, but 614G is associated with higher viral load and younger age of patients. Significant differences in growth and size of 614G phylogenetic clusters indicate a need for continued study of this variant

Increasing frailty is associated with higher prevalence and reduced recognition of delirium in older hospitalised inpatients: results of a multi-centre study

Purpose: Delirium is a neuropsychiatric disorder delineated by an acute change in cognition, attention, and consciousness. It is common, particularly in older adults, but poorly recognised. Frailty is the accumulation of deficits conferring an increased risk of adverse outcomes. We set out to determine how severity of frailty, as measured using the CFS, affected delirium rates, and recognition in hospitalised older people in the United Kingdom. Methods: Adults over 65 years were included in an observational multi-centre audit across UK hospitals, two prospective rounds, and one retrospective note review. Clinical Frailty Scale (CFS), delirium status, and 30-day outcomes were recorded. Results: The overall prevalence of delirium was 16.3% (483). Patients with delirium were more frail than patients without delirium (median CFS 6 vs 4). The risk of delirium was greater with increasing frailty [OR 2.9 (1.8–4.6) in CFS 4 vs 1–3; OR 12.4 (6.2–24.5) in CFS 8 vs 1–3]. Higher CFS was associated with reduced recognition of delirium (OR of 0.7 (0.3–1.9) in CFS 4 compared to 0.2 (0.1–0.7) in CFS 8). These risks were both independent of age and dementia. Conclusion: We have demonstrated an incremental increase in risk of delirium with increasing frailty. This has important clinical implications, suggesting that frailty may provide a more nuanced measure of vulnerability to delirium and poor outcomes. However, the most frail patients are least likely to have their delirium diagnosed and there is a significant lack of research into the underlying pathophysiology of both of these common geriatric syndromes

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Hippocampal lesions impair performance on a conditional delayed matching and non-matching to position task in the rat

The hippocampus is thought to be involved in a range of cognitive processes, from the ability to acquire new memories, to the ability to learn about spatial relationships. Humans and monkeys with damage to the hippocampus are typically impaired on delayed matching to sample tasks, of which the operant delayed matching to position task (DMTP) is a rat analogue. The reported effects of hippocampal damage on DMTP vary, ranging from delay-dependent deficits to no deficit whatsoever. The present study investigates a novel memory task; the conditional delayed matching/non-matching to position task (CDM/NMTP) in the Skinner box. CDM/NMTP uses the presence of specific stimulus cues to signify whether a particular trial is matching or non-matching in nature. Thus, it incorporates both the task contingencies within one session, and supplements the requirement for remembering the side of the lever in the sample phase with attending to the stimulus and remembering the conditional discrimination for the rule. Rats were trained preoperatively and the effects of bilateral excitotoxic lesions of the hippocampus were examined on postoperative retention of the task. Rats with lesions of the hippocampus incurred a significant impairment on the task that was manifest at all delays intervals. Despite a bias towards matching during training, trials of either type were performed with equivalent accuracy and neither rule was affected differentially by the lesion. This task may prove useful in determining the cognitive roles of a range of brain areas

Double dissociation between hippocampal and prefrontal lesions on an operant delayed matching task and a water maze reference memory task

The hippocampus and prefrontal cortex have both been implicated in various aspects of the acquisition, retention and performance of delayed matching to position (DMTP) tasks in the rat, although their precise respective contributions remain unclear. In the present study, rats were trained preoperatively on DMTP before receiving excitotoxic bilateral lesions of either the entire hippocampus or the medial prefrontal cortex. Rats with lesions of the prefrontal cortex exhibited a significant delay-dependent impairment on retention of the DMTP task, whereas hippocampal lesions were without effect. Rats were also exposed to a switch in the contingencies to a ‘non-matching’ rule, as an analogue of switching between decision rules in the human Wisconsin Card Sorting Test, in which human patients with prefrontal damage are impaired. Both lesion groups acquired the new contingency at control levels, providing no evidence towards a role for either of these areas in this type of rule-switching. The same rats were also assessed in a spatial reference memory task in the water maze, which revealed an impairment in escape latencies and path length that was specific to the hippocampal lesions. The results corroborate previous evidence that the hippocampus is not necessary for at least some aspects of working memory performance in the DMTP task, whereas the delay-dependent deficit in the prefrontal lesion group support this task as a potentially powerful tool for assessing the cognitive changes associated with frontal damage and repair

Meeting the UK driving vision standards with reduced contrast sensitivity

Purpose: The visual standard to hold a UK driver's license since 2012 includes visual acuity (VA) measured indoors and the ability to read a car numberplate outdoors. Individuals with reduced contrast sensitivity may have greater visual difficulties outdoors. The agreement between the two tests in the presence of combined reduction in contrast sensitivity and VA was investigated. Methods: Simulation glasses (‘sim-specs’) were used to reduce both high-contrast VA and contrast sensitivity (CS). Following evaluation of the influence of sim-specs on VA and CS, levels 2 to 4 were chosen to give a range of VAs on either side of the driving standard of 6/12. Sixty-two participants wearing sim-specs then had VA tested with Snellen and ETDRS charts indoors, and ability to read a numberplate assessed outdoors as per DVLA regulations. Results: Sim-specs reduced VA and CS by ~0.10 logMAR VA per 0.10 logCS. The sensitivity of test chart VA <6/12 to correctly predict failure on the numberplate was 61% for Snellen and 56% for ETDRS. Conclusion: False-negative and -positive rates were higher than in a previous study with uncorrected refractive error only. Reduced CS increased the lack of agreement between the two driving vision standards, which likely occurs as the VA test is performed indoors and the numberplate test outdoors. The increased likelihood of failing the numberplate test even though VA is 6/12 or better needs to be considered when advising patients on fitness to drive who have ocular disease such as cataract

Thresholds for sampled Sloan letters are smaller than sample spacing

Purpose: Although the effect of spatial sampling on the visibility of grating stimuli is well described and well understood, little research has been conducted into the effects of spatial sampling on the visibility of letter optotypes. The purpose of this study was to investigate whether thresholds for spatially sampled Sloan letters were equal to or significantly smaller than the spacing between spatial samples.----- Methods: For four visually normal subjects, we measured Sloan letter acuity thresholds, presented on a computer monitor, after the letters had been sampled by sampling arrays with 6.285 elements per square degree, (23.9 min of arc between samples for a square packed array). We used four different sampling arrays: square packed; hexagonally packed; a cone-like array with positive contrast; and a cone-like array with negative contrast. Thresholds were assessed using letter-counting rules and also Probit analysis.----- Results: Although results depended on array type, and the definition of sample spacing, letter acuity thresholds were substantially less than estimates of sample spacing by between 0.290 log units (49% less) (hexagonally sampled Probit thresholds compared with spacing between hexagonal samples) to 0.136 log units (27% less) (positive contrast cone-like sampled letter-counting thresholds compared with spacing between rows of hexagonal samples).----- Conclusions: Sample spacing is not an absolute limit for Sloan letter thresholds. By comparison with previous measurements of human foveal cone sampling of space, our findings suggest that cone sampling limits for Sloan letters could be as small as 20/4