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Huntington's disease (HD) is a fatal, dominantly inherited neurodegenerative disorder caused by CAG trinucleotide expansion in exon 1 of the huntingtin (HTT) gene. Since the reduction of pathogenic mutant HTT messenger RNA is therapeutic, we developed a mutant allele-sensitive CAGEX RNA-targeting CRISPR-Cas13d system (Cas13d-CAGEX) that eliminates toxic CAGEX RNA in fibroblasts derived from patients with HD and induced pluripotent stem cell-derived neurons. We show that intrastriatal delivery of Cas13d-CAGEX via an adeno-associated viral vector selectively reduces mutant HTT mRNA and protein levels in the striatum of heterozygous zQ175 mice, a model of HD. This also led to improved motor coordination, attenuated striatal atrophy and reduction of mutant HTT protein aggregates. These phenotypic improvements lasted for at least eight months without adverse effects and with minimal off-target transcriptomic effects. Taken together, we demonstrate proof of principle of an RNA-targeting CRISPR-Cas13d system as a therapeutic approach for HD, a strategy with implications for the treatment of other dominantly inherited disorders.

Single and metagenome de novo assembly of long reads is still one of the most difficult problems in bioinformatics. Often used paradigm, called Overlap-Layout-Consensus, aims at finding a Hamiltonian path through an assembly graph obtained from overlapping reads in a sample. However, these graphs can be extremely complex due to repetitive regions in genomes and sequencing artifacts such as chimeric reads, which lead to higher fragmentation of the assembly genomes. A popular approach for tackling this problem is based on dividing reads into three categories and processing them appropriately. These three categories of reads are regular, repetitive, and chimeric. A drawback of read classification with heuristic algorithms in existing assemblers is a manual selection of parameters based on just several genomes. In this work, we propose a deep learning approach for classification of reads based on their pile-o-grams, plots of coverage versus base index. The model was trained on a hand-labeled dataset consisting of pile-o-gram images from multiple bacteria, and tested on a different bacteria species not included in the training set. With such a setup, and with classes being balanced, an accuracy of 93% was achieved which opens the possibility of creating more accurate and less contiguous assemblies.

BackgroundOptimal management of patients with stable chest pain relies on the prognostic information provided by noninvasive cardiovascular testing, but there are limited data from randomized trials comparing anatomic with functional testing.MethodsIn the PROMISE trial (Prospective Multicenter Imaging Study for Evaluation of Chest Pain), patients with stable chest pain and intermediate pretest probability for obstructive coronary artery disease (CAD) were randomly assigned to functional testing (exercise electrocardiography, nuclear stress, or stress echocardiography) or coronary computed tomography angiography (CTA). Site-based diagnostic test reports were classified as normal or mildly, moderately, or severely abnormal. The primary end point was death, myocardial infarction, or unstable angina hospitalizations over a median follow-up of 26.1 months.ResultsBoth the prevalence of normal test results and incidence rate of events in these patients were significantly lower among 4500 patients randomly assigned to CTA in comparison with 4602 patients randomly assigned to functional testing (33.4% versus 78.0%, and 0.9% versus 2.1%, respectively; both P10%) who had a normal functional test were reclassified as being mildly abnormal, the discriminatory capacity improved to 0.69 (95% CI, 0.64-0.74).ConclusionsCoronary CTA, by identifying patients at risk because of nonobstructive CAD, provides better prognostic information than functional testing in contemporary patients who have stable chest pain with a low burden of obstructive CAD, myocardial ischemia, and events.Clinical trial registrationURL: http://www.clinicaltrials.gov. Unique identifier: NCT01174550.

Obesity has become increasingly prevalent worldwide. Studies characterize obesity as a low-grade chronic state of inflammation and identify macrophages as having a role in this response. Macrophage polarization may influence the pro- and anti-inflammatory responses associated with obese and lean phenotypes, respectively. This study exploited the differences in substrate utilization between M1 and M2 polarized macrophages to observe whether there was a change in the inflammatory phenotype with obesity. M1-polarized macrophages are pro-inflammatory and use glucose as fuel whereas M2-polarized macrophages are anti-inflammatory and preferentially use fatty acids as fuel. Specifically in this experiment, mice containing macrophages that were FATP1 knockout or wildtype were fed either a low fat diet (10% kcal from fat, LFD)or a high fat diet (45% kcal from fat, HFD) to test our hypothesis that FATP1 is important in macrophage M2 polarization. Four groups were used in this experiment: low fat-fedwildtype and knockout (LFD FATP1B+/+ and LFD FATP1B-/-), and high fat-fedwildtype and knockout (HFD FATP1B+/+ and HFD FATP1B-/-). HFD FATP1B-/- mice gained more weight and had heavier epididymal white adipose tissue (eWAT) than HFD FATP1B+/+ mice. HFD FATP1B-/- also had higher percentage body fat and higher plasma leptin levels when compared to HFD FATP1B+/+ mice. HFD FATP1B-/- had higher expression of inflammatory markers in eWATcompared to HFD FATP1B+/+ mice. The HFD FATP1B-/- group had significantly increased expression of macrophage markers F4/80, CD11C, and CD11B in eWAT. Inflammatory cytokine IL6 was also significantly elevated in eWAT in HFD-fedFATP1B-/- mice when compared to HFD-fed FATP1B+/+ mice. Glucose transporter GLUT1 and components of the Nlrp3 inflammasomeexpressionwere also increased in HFD-fed FATP1B-/- in eWAT. Taken together, these data indicate that deletion of FATP1 from macrophages is associated with increased susceptibility to high fat diet-induced weight gain, increased macrophage adipose tissue infiltration, and a shift towards M1-like pro-inflammatory macrophage polarization. ThusM2 macrophages’ inability to use fatty acids as fuel drove a more pro-inflammatory phenotype. This study reveals insight into a possible mechanism for the polarization of macrophages that may be relevant to the propagation of obesity.