Impact of functional studies on exome sequence variant interpretation in early-onset cardiac conduction system diseases

Aims The genetic cause of cardiac conduction system disease (CCSD) has not been fully elucidated. Whole-exome sequencing (WES) can detect various genetic variants; however, the identification of pathogenic variants remains a challenge. We aimed to identify pathogenic or likely pathogenic variants in CCSD patients by using WES and 2015 American College of Medical Genetics and Genomics (ACMG) standards and guidelines as well as evaluating the usefulness of functional studies for determining them. Methods and Results We performed WES of 23 probands diagnosed with early-onset (<65 years) CCSD and analyzed 117 genes linked to arrhythmogenic diseases or cardiomyopathies. We focused on rare variants (minor allele frequency < 0.1%) that were absent from population databases. Five probands had protein truncating variants in EMD and LMNA which were classified as “pathogenic” by 2015 ACMG standards and guidelines. To evaluate the functional changes brought about by these variants, we generated a knock-out zebrafish with CRISPR-mediated insertions or deletions of the EMD or LMNA homologs in zebrafish. The mean heart rate and conduction velocities in the CRISPR/Cas9-injected embryos and F2 generation embryos with homozygous deletions were significantly decreased. Twenty-one variants of uncertain significance were identified in 11 probands. Cellular electrophysiological study and in vivo zebrafish cardiac assay showed that 2 variants in KCNH2 and SCN5A, 4 variants in SCN10A, and 1 variant in MYH6 damaged each gene, which resulted in the change of the clinical significance of them from “Uncertain significance” to “Likely pathogenic” in 6 probands. Conclusions Of 23 CCSD probands, we successfully identified pathogenic or likely pathogenic variants in 11 probands (48%). Functional analyses of a cellular electrophysiological study and in vivo zebrafish cardiac assay might be useful for determining the pathogenicity of rare variants in patients with CCSD. SCN10A may be one of the major genes responsible for CCSD. Translational Perspective Whole-exome sequencing (WES) may be helpful in determining the causes of cardiac conduction system disease (CCSD), however, the identification of pathogenic variants remains a challenge. We performed WES of 23 probands diagnosed with early-onset CCSD, and identified 12 pathogenic or likely pathogenic variants in 11 of these probands (48%) according to the 2015 ACMG standards and guidelines. In this context, functional analyses of a cellular electrophysiological study and in vivo zebrafish cardiac assay might be useful for determining the pathogenicity of rare variants, and SCN10A may be one of the major development factors in CCSD

Serum galectin-9 levels are elevated in the patients with type 2 diabetes and chronic kidney disease

Background: Galectin-9 (Gal-9) induces apoptosis in activated T helper 1 (T(H)1) cells as a ligand for T cell immunoglobulin mucin-3 (Tim-3). Gal-9 also inhibits the G1 phase cell cycle arrest and hypertrophy in db/db mice, the hallmark of early diabetic nephropathy, by reversing the high glucose-induced up-regulation of cyclin dependent kinase inhibitors such as p27(Kip1) and p21(Cip1). Methods: We investigated the serum levels of Gal-9 in the patients with type 2 diabetes and various stages of chronic kidney disease (CKD) (n = 182). Results: Serum Gal-9 levels in the patients with type 2 diabetes were 131.9 +/- 105.4 pg/ml and Log(10)Gal-9 levels significantly and positively correlated with age (r = 0.227, p = 0.002), creatinine (r = 0.175, p = 0.018), urea nitrogen (r = 0.162, p = 0.028) and osmotic pressure (r = 0.187, p = 0.014) and negatively correlated with estimated glomerular filtration rate (eGFR) (r = -0.188, p = 0.011). Log(10)Gal-9 levels increased along with the progression of GFR categories of G1 to G4, and they were statistically significant by Jonckheere-Terpstra test (p = 0.012). Log(10)Gal-9 levels remained similar levels in albuminuria stages of A1 to A3. Conclusion: The elevation of serum Gal-9 in the patients with type 2 diabetes is closely linked to GFR and they may be related to the alteration of the immune response and inflammation of the patients with type 2 diabetes and CKD

The Aqua-Planet Experiment (APE): CONTROL SST Simulation

Climate simulations by 16 atmospheric general circulation models (AGCMs) are compared on an aqua-planet, a water-covered Earth with prescribed sea surface temperature varying only in latitude. The idealised configuration is designed to expose differences in the circulation simulated by different models. Basic features of the aqua-planet climate are characterised by comparison with Earth. The models display a wide range of behaviour. The balanced component of the tropospheric mean flow, and mid-latitude eddy covariances subject to budget constraints, vary relatively little among the models. In contrast, differences in damping in the dynamical core strongly influence transient eddy amplitudes. Historical uncertainty in modelled lower stratospheric temperatures persists in APE.Aspects of the circulation generated more directly by interactions between the resolved fluid dynamics and parameterized moist processes vary greatly. The tropical Hadley circulation forms either a single or double inter-tropical convergence zone (ITCZ) at the equator, with large variations in mean precipitation. The equatorial wave spectrum shows a wide range of precipitation intensity and propagation characteristics. Kelvin mode-like eastward propagation with remarkably constant phase speed dominates in most models. Westward propagation, less dispersive than the equatorial Rossby modes, dominates in a few models or occurs within an eastward propagating envelope in others. The mean structure of the ITCZ is related to precipitation variability, consistent with previous studies.The aqua-planet global energy balance is unknown but the models produce a surprisingly large range of top of atmosphere global net flux, dominated by differences in shortwave reflection by clouds. A number of newly developed models, not optimised for Earth climate, contribute to this. Possible reasons for differences in the optimised models are discussed.The aqua-planet configuration is intended as one component of an experimental hierarchy used to evaluate AGCMs. This comparison does suggest that the range of model behaviour could be better understood and reduced in conjunction with Earth climate simulations. Controlled experimentation is required to explore individual model behavior and investigate convergence of the aqua-planet climate with increasing resolution

A decade of GOSAT Proxy satellite CH4_{4} observations

This work presents the latest release (v9.0) of the University of Leicester GOSAT Proxy XCH4 dataset. Since the launch of the GOSAT satellite in 2009, these data have been produced by the UK National Centre for Earth Observation (NCEO) as part of the ESA Greenhouse Gas Climate Change Initiative (GHG-CCI) and Copernicus Climate Change Services (C3S) projects. With now over a decade of observations, we outline the many scientific studies achieved using past versions of these data in order to highlight how this latest version may be used in the future. We describe in detail how the data are generated, providing information and statistics for the entire processing chain from the L1B spectral data through to the final quality-filtered column-averaged dry-air mole fraction (XCH4) data. We show that out of the 19.5 million observations made between April 2009 and December 2019, we determine that 7.3 million of these are sufficiently cloud-free (37.6 %) to process further and ultimately obtain 4.6 million (23.5 %) high-quality XCH4 observations. We separate these totals by observation mode (land and ocean sun glint) and by month, to provide data users with the expected data coverage, including highlighting periods with reduced observations due to instrumental issues. We perform extensive validation of the data against the Total Carbon Column Observing Network (TCCON), comparing to ground-based observations at 22 locations worldwide. We find excellent agreement with TCCON, with an overall correlation coefficient of 0.92 for the 88 345 co-located measurements. The single-measurement precision is found to be 13.72 ppb, and an overall global bias of 9.06 ppb is determined and removed from the Proxy XCH4 data. Additionally, we validate the separate components of the Proxy (namely the modelled XCO2 and the XCH4/XCO2 ratio) and find these to be in excellent agreement with TCCON. In order to show the utility of the data for future studies, we compare against simulated XCH4 from the TM5 model. We find a high degree of consistency between the model and observations throughout both space and time. When focusing on specific regions, we find average differences ranging from just 3.9 to 15.4 ppb. We find the phase and magnitude of the seasonal cycle to be in excellent agreement, with an average correlation coefficient of 0.93 and a mean seasonal cycle amplitude difference across all regions of -0.84 ppb

Inverse Correlation between Serum Levels of Selenoprotein P and Adiponectin in Patients with Type 2 Diabetes

Background: We recently identified selenoprotein P (SeP) as a liver-derived secretory protein that causes insulin resistance in the liver and skeletal muscle; however, it is unknown whether and, if so, how SeP acts on adipose tissue. The present study tested the hypothesis that SeP is related to hypoadiponectinemia in patients with type 2 diabetes. Methodology/Principal Findings: We compared serum levels of SeP with those of adiponectin and other clinical parameters in 36 patients with type 2 diabetes. We also measured levels of blood adiponectin in SeP knockout mice. Circulating SeP levels were positively correlated with fasting plasma glucose (r = 0.35, P = 0.037) and negatively associated with both total and high-molecular adiponectin in patients with type 2 diabetes (r = 20.355, P = 0.034; r = 20.367, P = 0.028). SeP was a predictor of both total and high-molecular adiponectin, independently of age, body weight, and quantitative insulin sensitivity index (b = 20.343, P = 0.022; b = 20.357, P = 0.017). SeP knockout mice exhibited an increase in blood adiponectin levels when fed regular chow or a high sucrose, high fat diet. Conclusions/Significance: These results suggest that overproduction of liver-derived secretory protein SeP is connected with hypoadiponectinemia in patients with type 2 diabetes

DNA demethylation-dependent enhancement of toll-like receptor-2 gene expression in cystic fibrosis epithelial cells involves SP1-activated transcription

<p>Abstract</p> <p>Background</p> <p>The clinical course of cystic fibrosis (CF) is characterized by recurrent pulmonary infections and chronic inflammation. We have recently shown that decreased methylation of the toll-like receptor-2 (TLR2) promoter leads to an apparent CF-related up-regulation of TLR2. This up-regulation could be responsible, in part, for the CF-associated enhanced proinflammatory responses to various bacterial products in epithelial cells. However, the molecular mechanisms underlying DNA hypomethylation-dependent enhancement of TLR2 expression in CF cells remain unknown.</p> <p>Results</p> <p>The present study indicates that there is a specific CpG region (CpG#18-20), adjacent to the SP1 binding site that is significantly hypomethylated in several CF epithelial cell lines. These CpGs encompass a minimal promoter region required for basal TLR2 expression, and suggests that CpG#18-20 methylation regulates TLR2 expression in epithelial cells. Furthermore, reporter gene analysis indicated that the SP1 binding site is involved in the methylation-dependent regulation of the TLR2 promoter. Inhibition of SP1 with mithramycin A decreased TLR2 expression in both CF and 5-azacytidine-treated non-CF epithelial cells. Moreover, even though SP1 binding was not affected by CpG methylation, SP1-dependent transcription was abolished by CpG methylation.</p> <p>Conclusion</p> <p>This report implicates SP1 as a critical component of DNA demethylation-dependent up-regulation of TLR2 expression in CF epithelial cells.</p