New sequencing technologies allow genomic variation to be surveyed in much greater detail than previously possible. While detailed analysis of a single individual typically requires deep sequencing, ...when many individuals are sequenced it is possible to combine shallow sequence data across individuals to generate accurate calls in shared stretches of chromosome. Here, we show that, as progressively larger numbers of individuals are sequenced, increasingly accurate genotype calls can be generated for a given sequence depth. We evaluate the implications of low-coverage sequencing for complex trait association studies. We systematically compare study designs based on genotyping of tagSNPs, sequencing of many individuals at depths ranging between 2× and 30×, and imputation of variants discovered by sequencing a subset of individuals into the remainder of the sample. We show that sequencing many individuals at low depth is an attractive strategy for studies of complex trait genetics. For example, for disease-associated variants with frequency >0.2%, sequencing 3000 individuals at 4× depth provides similar power to deep sequencing of >2000 individuals at 30× depth but requires only ~20% of the sequencing effort. We also show low-coverage sequencing can be used to build a reference panel that can drive imputation into additional samples to increase power further. We provide guidance for investigators wishing to combine results from sequenced, genotyped, and imputed samples.
As a first step toward understanding how rare variants contribute to risk for complex diseases, we sequenced 15,585 human protein-coding genes to an average median depth of 111 x in 2440 individuals ...of European (n = 1351) and African (n = 1088) ancestry. We identified over 500,000 single-nucleotide variants (SNVs), the majority of which were rare (86% with a minor allele frequency less than 0.5%), previously unknown (82%), and population-specific (82%). On average, 2.3% of the 13,595 SNVs each person carried were predicted to affect protein function of -313 genes per genome, and -95.7% of SNVs predicted to be functionally important were rare. This excess of rare functional variants is due to the combined effects of explosive, recent accelerated population growth and weak purifying selection. Furthermore, we show that large sample sizes will be required to associate rare variants with complex traits.
Mesenchymal stem cells derived from Wharton's jelly of the umbilical cord (UC-MSCs) have immunomodulatory properties. The aim of this study was to explore whether extracts of MSCs (MSC-Ex) could ...augment the low therapeutic efficacy of the whole cells in an Aspergillus fumigatus (Af)-induced atopic dermatitis (AD) model. LPS- or TNF-α/IFN-γ-stimulated keratinocytes (HaCaT cells) were treated with MSC-Ex, and the Af-induced AD model was established in BALB/c mice. In HaCaT cells, MSC-Ex treatment significantly reduced the inflammatory cytokine (IL-6, IL-1β, IL-4, IL-5 and TNF-α), iNOS and NF-κB levels, and upregulated the anti-inflammatory cytokines (IL-10 and TGF-β1). In the AD mice, the MSC-Ex group showed greatly reduced dermatitis, and lower clinical symptom scores and IgE levels. The histological dermatitis scores were also markedly lower in the MSC-Ex-treated animals compared with the MSC-treated group. Decreased levels of IFN-γ (Th1) and IL-17 (Th17), IL-4 and IL-13 (Th2) were detected in T cells and the skin tissue from the MSC-Ex treated AD mice. The therapeutic capacity of MSC-Ex was preserved after lyophilization and reconstitution. MSC-Ex treatment reproducibly suppresses dermatitis and inhibits the induction of inflammatory cytokines in the skin of AD mice. MSC-Ex is therefore a potential new treatment agent for AD.
The demethylation of histone lysine residues, one of the most important modifications in transcriptional regulation, is associated with various physiological states. KDM2B is a demethylase of ...histones H3K4, H3K36, and H3K79 and is associated with the repression of transcription. Here, we present a novel mechanism by which KDM2B demethylates serum response factor (SRF) K165 to negatively regulate muscle differentiation, which is counteracted by the histone methyltransferase SET7. We show that KDM2B inhibited skeletal muscle differentiation by inhibiting the transcription of SRF-dependent genes. Both KDM2B and SET7 regulated the balance of SRF K165 methylation. SRF K165 methylation was required for the transcriptional activation of SRF and for the promoter occupancy of SRF-dependent genes. SET7 inhibitors blocked muscle cell differentiation. Taken together, these data indicate that SRF is a nonhistone target of KDM2B and that the methylation balance of SRF as maintained by KDM2B and SET7 plays an important role in muscle cell differentiation.
Lidocaine, a commonly used local anesthetic, has recently been developed into a number of ointment products to treat hemorrhoids. This study examined its efficient delivery to the dermis through the ...pharmaceutical improvement of hemorrhoid treatment ointments. We attempted to increase the amount of skin deposition of lidocaine by forming a nanoemulsion through the self-nanoemulsifying effect that occurs when glycerol monostearate (GMS) is saturated with water. Using Raman mapping, the depth of penetration of lidocaine was visualized and confirmed, and the local anesthetic effect was evaluated via an in vivo tail-flick test. Evaluation of the physicochemical properties confirmed that lidocaine was amorphous and evenly dispersed in the ointment. The in vitro dissolution test confirmed that the nanoemulsifying effect of GMS accelerated the release of the drug from the ointment. At a specific concentration of GMS, lidocaine penetrated deeper into the dermis; the in vitro permeation test showed similar results. When compared with reference product A in the tail-flick test, the L5 and L6 compounds containing GMS had a significantly higher anesthetic effect. Altogether, the self-nanoemulsifying effect of GMS accelerated the release of lidocaine from the ointment. The compound with 5% GMS, the lowest concentration that saturated the dermis, was deemed most appropriate.
Although plaque characterization by intravascular ultrasound (IVUS) is important for risk stratification, frame-by-frame analysis of a whole vascular segment is time-consuming. The aim was to develop ...IVUS-based algorithms for classifying attenuation and calcified plaques.
IVUS image sets of 598 coronary arteries from 598 patients were randomized into training and test sets with 5:1 ratio. Each IVUS frame at a 0.4-mm interval was circumferentially labeled as one of three classes: attenuated plaque, calcified plaque, or plaque without attenuation or calcification. The model was trained on multi-class classification with 5-fold cross validation. By converting from Cartesian to polar coordinate images, the class corresponding to each array from 0 to 360° was plotted.
At the angle-level, Dice similarity coefficients for identifying calcification vs. attenuation vs. none by using ensemble model were 0.79, 0.74 and 0.99, respectively. Also, the maximal accuracy was 98% to classify those groups in the test set. At the frame-level, the model identified the presence of attenuation with 80% sensitivity, 96% specificity, and 93% overall accuracy, and the presence of calcium with 86% sensitivity, 97% specificity, and 96% overall accuracy. In the per-vessel analysis, the attenuation and calcification burden index closely correlated with human measurements (r = 0.89 and r = 0.95, respectively), as did the maximal attenuation and calcification burden index over 4 mm (r = 0.82 and r = 0.91, respectively). The inference times were 0.05 s per frame and 7.8 s per vessel.
Our deep learning algorithms for plaque characterization may assist clinicians in recognizing high-risk coronary lesions.
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•Deep learning algorithms allow automatic learning without explicit programming, potentially improving diagnostic accuracy.•The IVUS-based model demonstrated good performance in classifying and quantifying tissue attenuation and calcification.•It supports clinicians in identifying high-risk lesions that potentially lead to stent under expansion and adverse events.
The genotype-phenotype correlation of the X-linked Alport syndrome (XLAS) has been well elucidated in males, whereas it remains unclear in females. In this multicenter retrospective study, we ...analyzed the genotype-phenotype correlation in 216 Korean patients (male:female = 130:86) with XLAS between 2000 and 2021. The patients were divided into three groups according to their genotypes: the non-truncating group, the abnormal splicing group, and the truncating group. In male patients, approximately 60% developed kidney failure at the median age of 25.0 years, and kidney survival showed significant differences between the non-truncating and truncating groups (P < 0.001, hazard ratio (HR) 2.8) and splicing and truncating groups (P = 0.002, HR 3.1). Sensorineural hearing loss was detected in 65.1% of male patients, while hearing survival periods showed a highly significant difference between the non-truncating and truncating groups (P < 0.001, HR 5.1). In female patients, approximately 20% developed kidney failure at the median age of 50.2 years. The kidney survival was significantly different between the non-truncating and truncating groups (P = 0.006, HR 5.7). Our findings support the presence of genotype-phenotype correlation not only in male patients but also in female patients with XLAS.
The aim of this study was to analyze the available knowledge about the potential association between dyslipidemia and the severity of coronavirus disease 2019 (COVID-19) as reported in previous ...published systematic reviews.
In this umbrella review (an overview of systematic reviews), we investigated the association between dyslipidemia and COVID-19 severity. A systematic search was performed of 4 main electronic databases (MEDLINE, Embase, Scopus, and the Cochrane Library databases) from inception until August 2020. We evaluated the methodological quality of the included studies using the A MeaSurement Tool to Assess systematic Reviews (AMSTAR) 2 tool and used the Grading of Recommendations, Assessment, Development, and Evaluation (GRADE) system to assess the quality of evidence for the outcome. In addition, we evaluated the strengths and limitations of the evidence and the methodological quality of the available studies.
Out of 35 articles identified, 2 systematic reviews were included in the umbrella review. A total of 7,951 COVID-19-positive patients were included. According to the AMSTAR 2 criteria and GRADE system, the quality of the included studies was not high. A history of dyslipidemia is likely to be associated with the severity of COVID-19 infection, but the contrary is the case for cholesterol levels at hospitalization.
Although existing research on dyslipidemia and COVID-19 is limited, our findings suggest that dyslipidemia may play a role in the severity of COVID-19 infection. More adequately powered studies are needed.
PROSPERO Identifier: CRD42020205979.
Genomewide association mapping in model organisms such as inbred mouse strains is a promising approach for the identification of risk factors related to human diseases. However, genetic association ...studies in inbred model organisms are confronted by the problem of complex population structure among strains. This induces inflated false positive rates, which cannot be corrected using standard approaches applied in human association studies such as genomic control or structured association. Recent studies demonstrated that mixed models successfully correct for the genetic relatedness in association mapping in maize and Arabidopsis panel data sets. However, the currently available mixed-model methods suffer from computational inefficiency. In this article, we propose a new method, efficient mixed-model association (EMMA), which corrects for population structure and genetic relatedness in model organism association mapping. Our method takes advantage of the specific nature of the optimization problem in applying mixed models for association mapping, which allows us to substantially increase the computational speed and reliability of the results. We applied EMMA to in silico whole-genome association mapping of inbred mouse strains involving hundreds of thousands of SNPs, in addition to Arabidopsis and maize data sets. We also performed extensive simulation studies to estimate the statistical power of EMMA under various SNP effects, varying degrees of population structure, and differing numbers of multiple measurements per strain. Despite the limited power of inbred mouse association mapping due to the limited number of available inbred strains, we are able to identify significantly associated SNPs, which fall into known QTL or genes identified through previous studies while avoiding an inflation of false positives. An R package implementation and webserver of our EMMA method are publicly available.
This study aimed to demonstrate the anti-obesity effect of Plocamium telfairiae (PT), a red seaweed. Different percentages of ethanol (0%, 20%, 40%, 60%, 80%, and 100%) were used for the preparation ...of PT extract. Furthermore, 3T3-L1 cells were used to determine the percentage of ethanol for optimal anti-adipogenesis of PT, and the anti-obesity properties of the optimized extract of PT (PTE) (40%) was assessed in obese mice. The results indicate that 40% ethanol extract (40 PTE) significantly decreased fat accumulation and suppressed the expression of major adipogenesis factors such as peroxisome proliferator-activated receptor-γ (PPAR-γ), sterol regulatory element-binding protein 1 (SREBP-1), CCAAT/enhancer-binding protein (C/EBP)-α, and phosphorylated ACC (pACC) in 3T3-L1 cells. Furthermore, in the high-fat diet-induced obese mice, 40 PTE significantly reduced the weights of white adipose tissue, as well as the levels of triglyceride, total cholesterol, adiponectin, and insulin in the serum. Liver histopathology showed that steatosis decreased in all the PTE treatment groups. The adipogenesis-related proteins, PPAR-γ and SREBP-1, were also significantly decreased in PTE treatment groups. Additionally, 40 PTE increased mRNA expression of mitochondrial uncoupling proteins (UCP)-1 and UCP-3 in brown adipose tissue. These findings provide evidence that 40 PTE can alleviate lipid droplet accumulation in 3T3-L1 adipocytes and obese C57BL/6 mice, indicating that PTE has strong anti-obesity effects and could be used as a therapeutic agent or a component of pharmaceutical drugs and functional foods.
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