Combining a prioritization strategy and functional studies nominates 5’UTR variants underlying inherited retinal disease

BACKGROUND: 5’ untranslated regions (5’UTRs) are essential modulators of protein translation. Predicting the impact of 5’UTR variants is challenging and rarely performed in routine diagnostics. Here, we present a combined approach of a comprehensive prioritization strategy and functional assays to evaluate 5’UTR variation in two large cohorts of patients with inherited retinal diseases (IRDs). METHODS: We performed an isoform-level re-analysis of retinal RNA-seq data to identify the protein-coding transcripts of 378 IRD genes with highest expression in retina. We evaluated the coverage of their 5’UTRs by different whole exome sequencing (WES) kits. The selected 5’UTRs were analyzed in whole genome sequencing (WGS) and WES data from IRD sub-cohorts from the 100,000 Genomes Project (n = 2397 WGS) and an in-house database (n = 1682 WES), respectively. Identified variants were annotated for 5’UTR-relevant features and classified into seven categories based on their predicted functional consequence. We developed a variant prioritization strategy by integrating population frequency, specific criteria for each category, and family and phenotypic data. A selection of candidate variants underwent functional validation using diverse approaches. RESULTS: Isoform-level re-quantification of retinal gene expression revealed 76 IRD genes with a non-canonical retina-enriched isoform, of which 20 display a fully distinct 5’UTR compared to that of their canonical isoform. Depending on the probe design, 3–20% of IRD genes have 5’UTRs fully captured by WES. After analyzing these regions in both cohorts, we prioritized 11 (likely) pathogenic variants in 10 genes (ARL3, MERTK, NDP, NMNAT1, NPHP4, PAX6, PRPF31, PRPF4, RDH12, RD3), of which 7 were novel. Functional analyses further supported the pathogenicity of three variants. Mis-splicing was demonstrated for the PRPF31:c.-9+1G>T variant. The MERTK:c.-125G>A variant, overlapping a transcriptional start site, was shown to significantly reduce both luciferase mRNA levels and activity. The RDH12:c.-123C>T variant was found in cis with the hypomorphic RDH12:c.701G>A (p.Arg234His) variant in 11 patients. This 5’UTR variant, predicted to introduce an upstream open reading frame, was shown to result in reduced RDH12 protein but unaltered mRNA levels. CONCLUSIONS: This study demonstrates the importance of 5’UTR variants implicated in IRDs and provides a systematic approach for 5’UTR annotation and validation that is applicable to other inherited diseases

SPARC REport No. 7

peer reviewedThe Montreal Protocol (MP) controls the production and consumption of carbon tetrachloride (CCl4 or CTC) and other ozone-depleting substances (ODSs) for emissive uses. CCl4 is a major ODS, accounting for about 12% of the globally averaged inorganic chlorine and bromine in the stratosphere, compared to 14% for CFC-12 in 2012. In spite of the MP controls, there are large ongoing emissions of CCl4 into the atmosphere. Estimates of emissions from various techniques ought to yield similar numbers. However, the recent WMO/UNEP Scientific Assessment of Ozone Depletion [WMO, 2014] estimated a 2007-2012 CCl4 bottom-up emission of 1-4 Gg/year (1-4 kilotonnes/year), based on country-by-country reports to UNEP, and a global top-down emissions estimate of 57 Gg/ year, based on atmospheric measurements. This 54 Gg/year difference has not been explained. In order to assess the current knowledge on global CCl4 sources and sinks, stakeholders from industrial, governmental, and the scientific communities came together at the “Solving the Mystery of Carbon Tetrachloride” workshop, which was held from 4-6 October 2015 at Empa in Dübendorf, Switzerland. During this workshop, several new findings were brought forward by the participants on CCl4 emissions and related science. • Anthropogenic production and consumption for feedstock and process agent uses (e.g., as approved solvents) are reported to UNEP under the MP. Based on these numbers, global bottom-up emissions of 3 (0-8) Gg/year are estimated for 2007-2013 in this report. This number is also reasonably consistent with this report’s new industry-based bottom-up estimate for fugitive emissions of 2 Gg/year. • By-product emissions from chloromethanes and perchloroethylene plants are newly proposed in this report as significant CCl4 sources, with global emissions estimated from these plants to be 13 Gg/year in 2014. • This report updates the anthropogenic CCl4 emissions estimation as a maximum of ~25 Gg/year. This number is derived by combining the above fugitive and by-product emissions (2 Gg/year and 13 Gg/year, respectively) with 10 Gg/year from legacy emissions plus potential unreported inadvertent emissions from other sources. • Ongoing atmospheric CCl4 measurements within global networks have been exploited for assessing regional emissions. In addition to existing emissions estimates from China and Australia, the workshop prompted research on emissions in the U.S. and Europe. The sum of these four regional emissions is estimated as 21±7.5a Gg/year, but this is not a complete global accounting. These regional top-down emissions estimates also show that most of the CCl4 emissions originate from chemical industrial regions, and are not linked to major population centres. • The total CCl4 lifetime is critical for calculating top-down global emissions. CCl4 is destroyed in the stratosphere, oceans, and soils, complicating the total lifetime estimate. The atmospheric lifetime with respect to stratospheric loss was recently revised to 44 (36-58) years, and remains unchanged in this report. New findings from additional measurement campaigns and reanalysis of physical parameters lead to changes in the ocean lifetime from 94 years to 210 (157-313) years, and in the soil lifetime from 195 years to 375 (288-536) years. • These revised lifetimes lead to an increase of the total lifetime from 26 years in WMO [2014] to 33 (28-41) years. Consequently, CCl4 is lost at a slower rate from the atmosphere. With this new total lifetime, the global top-down emissions calculation decreases from 57 (40-74) Gg/year in WMO [2014] to 40 (25-55) Gg/year. This estimate is relatively consistent with the independent gradient top-down emissions of 30 (25-35) Gg/year, based upon differences between atmospheric measurements of CCl4 in the Northern and Southern Hemispheres. In addition, this new total lifetime implies an upper limit of 3-4 Gg/year of natural emissions, based upon newly reported observations of old air in firn snow. These new CCl4 emissions estimates from the workshop make considerable progress toward closing the emissions discrepancy. The new industrial bottom-up emissions estimate (15 Gg/year total) includes emissions from chloromethanes plants (13 Gg/year) and feedstock fugitive emissions (2 Gg/year). When combined with legacy emissions and unreported inadvertent emissions, this could be up to 25 Gg/year. Top-down emissions estimates are: global 40 (25-55) Gg/year, gradient 30 (25-35) Gg/year, and regional 21 (14-28) Gg/year. While the new bottom-up value is still less than the aggregated top-down values, these estimates reconcile the CCl4 budget discrepancy when considered at the edges of their uncertainties

An Implantable Vascularized Protein Gel Construct That Supports Human Fetal Hepatoblast Survival and Infection by Hepatitis C Virus in Mice

Widely accessible small animal models suitable for the study of hepatitis C virus (HCV) in vivo are lacking, primarily because rodent hepatocytes cannot be productively infected and because human hepatocytes are not easily engrafted in immunodeficient mice.We report here on a novel approach for human hepatocyte engraftment that involves subcutaneous implantation of primary human fetal hepatoblasts (HFH) within a vascularized rat collagen type I/human fibronectin (rCI/hFN) gel containing Bcl-2-transduced human umbilical vein endothelial cells (Bcl-2-HUVEC) in severe combined immunodeficient X beige (SCID/bg) mice. Maturing hepatic epithelial cells in HFH/Bcl-2-HUVEC co-implants displayed endocytotic activity at the basolateral surface, canalicular microvilli and apical tight junctions between adjacent cells assessed by transmission electron microscopy. Some primary HFH, but not Huh-7.5 hepatoma cells, appeared to differentiate towards a cholangiocyte lineage within the gels, based on histological appearance and cytokeratin 7 (CK7) mRNA and protein expression. Levels of human albumin and hepatic nuclear factor 4alpha (HNF4alpha) mRNA expression in gel implants and plasma human albumin levels in mice engrafted with HFH and Bcl-2-HUVEC were somewhat enhanced by including murine liver-like basement membrane (mLBM) components and/or hepatocyte growth factor (HGF)-HUVEC within the gel matrix. Following ex vivo viral adsorption, both HFH/Bcl-2-HUVEC and Huh-7.5/Bcl-2-HUVEC co-implants sustained HCV Jc1 infection for at least 2 weeks in vivo, based on qRT-PCR and immunoelectron microscopic (IEM) analyses of gel tissue.The system described here thus provides the basis for a simple and robust small animal model of HFH engraftment that is applicable to the study of HCV infections in vivo

Model Sensitivity Studies of the Decrease in Atmospheric Carbon Tetrachloride

Carbon tetrachloride is an ozone-depleting substance, which is controlled by the Montreal Protocol and for which the atmospheric abundance is decreasing. However, the current observed rate of this decrease is known to be slower than expected based on reported CCl₄ emissions and its estimated overall atmospheric lifetime. Here we use a three-dimensional (3- D) chemical transport model to investigate the impact on its predicted decay of uncertainties in the rates at which CCl₄ is removed from the atmosphere by photolysis, by ocean uptake and by degradation in soils. The largest sink is atmospheric photolysis (76% of total) but a reported 10% uncertainty in its combined photolysis cross-section and quantum yield has only a modest impact on the modelled rate of CCl₄ decay. This is partly due to the limiting effect of the rate of transport of CCl₄ from the main tropospheric reservoir to the stratosphere where photolytic loss occurs. The model suggests large interannual variability in the magnitude of this stratospheric photolysis sink caused by variations in transport. The impact of uncertainty in the minor soil sink (9% of total) is also relatively small. In contrast, the model shows that uncertainty in ocean loss (15% of total) has the largest impact on modelled CCl₄ decay due to its sizeable contribution to CCl₄ loss and large uncertainty range (157 to 313 years). With an assumed CCl₄ emission rate of 39 Gg/yr, the reference simulation with best estimate of loss processes still underestimates the observed CCl₄ (overestimates the decay) over the past two decades but to a smaller extent than previous studies. Changes to the rate of CCl₄ loss processes, in line with known uncertainties, could bring the model into agreement with in situ surface and remote-sensing measurements, as could an increase in emissions to around 45 Gg/yr. Further progress in constraining the CCl₄ budget is partly limited by systematic biases between observational datasets. For example, surface observations from the NOAA network are larger than from the AGAGE network but have shown a steeper decreasing trend over the past two decades. These differences imply a difference in emissions which is significant relative to uncertainties in the magnitudes of the CCl₄ sinks

Operating a full tungsten actively cooled tokamak: overview of WEST first phase of operation

WEST is an MA class superconducting, actively cooled, full tungsten (W) tokamak, designed to operate in long pulses up to 1000 s. In support of ITER operation and DEMO conceptual activities, key missions of WEST are: (i) qualification of high heat flux plasma-facing components in integrating both technological and physics aspects in relevant heat and particle exhaust conditions, particularly for the tungsten monoblocks foreseen in ITER divertor; (ii) integrated steady-state operation at high confinement, with a focus on power exhaust issues. During the phase 1 of operation (2017–2020), a set of actively cooled ITER-grade plasma facing unit prototypes was integrated into the inertially cooled W coated startup lower divertor. Up to 8.8 MW of RF power has been coupled to the plasma and divertor heat flux of up to 6 MW m−2 were reached. Long pulse operation was started, using the upper actively cooled divertor, with a discharge of about 1 min achieved. This paper gives an overview of the results achieved in phase 1. Perspectives for phase 2, operating with the full capability of the device with the complete ITER-grade actively cooled lower divertor, are also described

Observation of the Rare Decay of the η Meson to Four Muons

A search for the rare η→μ+μ−μ+μ− double-Dalitz decay is performed using a sample of proton-proton collisions, collected by the CMS experiment at the CERN LHC with high-rate muon triggers during 2017 and 2018 and corresponding to an integrated luminosity of 101  fb−1. A signal having a statistical significance well in excess of 5 standard deviations is observed. Using the η→μ+μ− decay as normalization, the branching fraction B(η→μ+μ−μ+μ−)=[5.0±0.8(stat)±0.7(syst)±0.7(B2μ)]×10−9 is measured, where the last term is the uncertainty in the normalization channel branching fraction. This work achieves an improved precision of over 5 orders of magnitude compared to previous results, leading to the first measurement of this branching fraction, which is found to agree with theoretical predictions