Epigenomic profiling of the infrapatellar fat pad in osteoarthritis.

Osteoarthritis is a prevalent, complex disease of the joints, and affects multiple intra-articular tissues. Here, we have examined genome-wide DNA methylation profiles of primary infrapatellar fat pad and matched blood samples from 70 osteoarthritis patients undergoing total knee replacement surgery. Comparing the DNA methylation profiles between these tissues reveal widespread epigenetic differences. We produce the first genome-wide methylation quantitative trait locus (mQTL) map of fat pad, and make the resource available to the wider community. Using two-sample Mendelian randomization and colocalization analyses, we resolve osteoarthritis GWAS signals and provide insights into the molecular mechanisms underpinning disease aetiopathology. Our findings provide the first view of the epigenetic landscape of infrapatellar fat pad primary tissue in osteoarthritis.

Genome-wide meta-analysis of 92 cardiometabolic protein serum levels.

OBJECTIVES: Global cardiometabolic disease prevalence has grown rapidly over the years, making it the leading cause of death worldwide. Proteins are crucial components in biological pathways dysregulated in disease states. Identifying genetic components that influence circulating protein levels may lead to the discovery of biomarkers for early stages of disease or offer opportunities as therapeutic targets. METHODS: Here, we carry out a genome-wide association study (GWAS) utilising whole genome sequencing data in 3,005 individuals from the HELIC founder populations cohort, across 92 proteins of cardiometabolic relevance. RESULTS: We report 322 protein quantitative trait loci (pQTL) signals across 92 proteins, of which 76 are located in or near the coding gene (cis-pQTL). We link those association signals with changes in protein expression and cardiometabolic disease risk using colocalisation and Mendelian randomisation (MR) analyses. CONCLUSIONS: The majority of previously unknown signals we describe point to proteins or protein interactions involved in inflammation and immune response, providing genetic evidence for the contributing role of inflammation in cardiometabolic disease processes.

Bridging the diversity gap: Analytical and study design considerations for improving the accuracy of trans-ancestry genetic prediction.

Genetic prediction of common complex disease risk is an essential component of precision medicine. Currently, genome-wide association studies (GWASs) are mostly composed of European-ancestry samples and resulting polygenic scores (PGSs) have been shown to poorly transfer to other ancestries partly due to heterogeneity of allelic effects between populations. Fixed-effects (FETA) and random-effects (RETA) trans-ancestry meta-analyses do not model such ancestry-related heterogeneity, while ancestry-specific (AS) scores may suffer from low power due to low sample sizes. In contrast, trans-ancestry meta-regression (TAMR) builds ancestry-aware PGS that account for more complex trans-ancestry architectures. Here, we examine the predictive performance of these four PGSs under multiple genetic architectures and ancestry configurations. We show that the predictive performance of FETA and RETA is strongly affected by cross-ancestry genetic heterogeneity, while AS PGS performance decreases in under-represented target populations. TAMR PGS is also impacted by heterogeneity but maintains good prediction performance in most situations, especially in ancestry-diverse scenarios. In simulations of human complex traits, TAMR scores currently explain 25% more phenotypic variance than AS in triglyceride levels and 33% more phenotypic variance than FETA in type 2 diabetes in most non-European populations. Importantly, a high proportion of non-European-ancestry individuals is needed to reach prediction levels that are comparable in those populations to the one observed in European-ancestry studies. Our results highlight the need to rebalance the ancestral composition of GWAS to enable accurate prediction in non-European-ancestry groups, and demonstrate the relevance of meta-regression approaches for compensating some of the current population biases in GWAS.

Exome sequencing identified five novel USH2A variants in Korean patients with retinitis pigmentosa.

BACKGROUND: Retinitis pigmentosa (RP) is an inherited disorder that causes progressive loss of vision. This study aimed to describe the possible causative variants of the USH2A gene in Korean RP families and their associated phenotypes. MATERIALS AND METHODS: We recruited 94 RP families (220 subjects, including 94 probands and 126 family members) in a Korean cohort, and analyzed USH2A gene variants through whole-exome sequencing. The pathogenicity of the variants was classified according to American College of Medical Genetics and Genomics and Association for Molecular Pathology guidelines. RESULTS: We found 14 USH2A disease-causing variants, including 5 novel variants. Disease causing variants were identified in 10 probands with RP, accounting for 10.6% (10/94) of the Korean RPs in the cohort. To visually represent the structural changes induced by novel variants, we modeled the three-dimensional structures of the wild-type and mutant proteins. CONCLUSIONS: This study expands the spectrum of USH2A variants and provides information for future therapeutic strategies for RP.

Gene-based whole genome sequencing meta-analysis of 250 circulating proteins in three isolated European populations.

OBJECTIVE: Deep sequencing offers unparalleled access to rare variants in human populations. Understanding their role in disease is a priority, yet prohibitive sequencing costs mean that many cohorts lack the sample size to discover these effects on their own. Meta-analysis of individual variant scores allows the combination of rare variants across cohorts and study of their aggregated effect at the gene level, boosting discovery power. However, the methods involved have largely not been field-tested. In this study, we aim to perform the first meta-analysis of gene-based rare variant aggregation optimal tests, applied to the human cardiometabolic proteome. METHODS: Here, we carry out this analysis across MANOLIS, Pomak and ORCADES, three isolated European cohorts with whole-genome sequencing (total N = 4,422). We examine the genetic architecture of 250 proteomic traits of cardiometabolic relevance. We use a containerised pipeline to harmonise variant lists across cohorts and define four sets of qualifying variants. For every gene, we interrogate protein-damaging variants, exonic variants, exonic and regulatory variants, and regulatory only variants, using the CADD and Eigen scores to weigh variants according to their predicted functional consequence. We perform single-cohort rare variant analysis and meta-analyse variant scores using the SMMAT package. RESULTS: We describe 5 rare variant pQTLs (RV-pQTL) which pass our stringent significance threshold (7.45 × 10-11) and quality control procedure. These were split between four cis signals for MARCO, TEK, MMP2 and MPO, and one trans association for GDF2 in the SERPINA11 gene. We show that the cis-MPO association, which was not detectable using the single-point data alone, is driven by 5 missense and frameshift variants. These include rs140636390 and rs119468010, which are specific to MANOLIS and ORCADES, respectively. We show how this kind of signal could improve the predictive accuracy of genetic factors in common complex disease such as stroke and cardiovascular disease. CONCLUSIONS: Our proof-of-concept study demonstrates the power of gene-based meta-analyses for discovering disease-relevant associations complementing common-variant signals by incorporating population-specific rare variation.

Evaluation of the antigenic stability of influenza virus like particles after exposure to acidic or basic pH.

PURPOSE: Virus-like particles (VLPs) are being developed as a promising vaccine platform and therapeutic delivery. Various strategies for effectively constructing VLPs have been studied, but relatively few studies have been done on various factors affecting storage. In this study, we investigated the antigenic changes of VLPs in an acidic or basic pH environment using influenza VLPs as an experimental model. MATERIALS AND METHODS: Influenza VLPs containing hemagglutination and M1 proteins were generated and their antigenicity and protective immunity in vitro and in vivo were evaluated after exposure to acidic (pH 4 and 5) or basic (pH 9 and 10) pH buffers. RESULTS: VLP exposed to basic pH showed similar levels of antigenicity to those stored in neutral pH, while antigenicity of VLP exposed to acidic pH was found to be significantly reduced compared to those expose neutral or basic pH. All groups of mice responded effectively to low concentrations of virus infections; however, VLP vaccine groups exposed to acid pH were found not to induce sufficient protective immune responses when a high concentration of influenza virus infection. CONCLUSION: In order for VLP to be used as a more powerful vaccine platform, it should be developed in a strategic way to respond well to external changes such as acidic pH conditions.

Whole-genome sequencing analysis of the cardiometabolic proteome.

The human proteome is a crucial intermediate between complex diseases and their genetic and environmental components, and an important source of drug development targets and biomarkers. Here, we comprehensively assess the genetic architecture of 257 circulating protein biomarkers of cardiometabolic relevance through high-depth (22.5×) whole-genome sequencing (WGS) in 1328 individuals. We discover 131 independent sequence variant associations (P < 7.45 × 10-11) across the allele frequency spectrum, all of which replicate in an independent cohort (n = 1605, 18.4x WGS). We identify for the first time replicating evidence for rare-variant cis-acting protein quantitative trait loci for five genes, involving both coding and noncoding variation. We construct and validate polygenic scores that explain up to 45% of protein level variation. We find causal links between protein levels and disease risk, identifying high-value biomarkers and drug development targets.

Influence of temperature on the antigenic changes of virus-like particles.

PURPOSE: In this study, we investigated whether the antigenic changes of the virus-like particles (VLPs) are affected by the temperature during storage. MATERIALS AND METHODS: After exposing the recombinant influenza VLPs to various temperatures for a period, antigenic changes were examined through in vitro hemagglutination receptor binding assay and in vivo mouse experiments. RESULTS: Influenza VLPs were exposed at three different temperatures of low, middle, and high on a thermo-hygrostat. High temperature exposed influenza VLPs were showed significantly reduced HA activity and immunogenicity after mouse single immunization over time compared low and middle. When the VLPs exposed to the high temperature were inoculated once in the mice, it was found that the immunogenicity was significantly reduced compared to the VLPs exposed to the low temperature. However, these differences were almost neglected when mice were inoculated twice even with VLPs exposed to high temperatures. CONCLUSION: This study suggests that similar protective effects can be expected by controlling the number of vaccination and storage conditions, although the antigenic change in the VLP vaccines occurred when exposed to high temperature.

Population-wide copy number variation calling using variant call format files from 6,898 individuals.

Copy number variants (CNVs) play an important role in a number of human diseases, but the accurate calling of CNVs remains challenging. Most current approaches to CNV detection use raw read alignments, which are computationally intensive to process. We use a regression tree-based approach to call germline CNVs from whole-genome sequencing (WGS, >18x) variant call sets in 6,898 samples across four European cohorts, and describe a rich large variation landscape comprising 1,320 CNVs. Eighty-one percent of detected events have been previously reported in the Database of Genomic Variants. Twenty-three percent of high-quality deletions affect entire genes, and we recapitulate known events such as the GSTM1 and RHD gene deletions. We test for association between the detected deletions and 275 protein levels in 1,457 individuals to assess the potential clinical impact of the detected CNVs. We describe complex CNV patterns underlying an association with levels of the CCL3 protein (MAF = 0.15, p = 3.6x10-12 ) at the CCL3L3 locus, and a novel cis-association between a low-frequency NOMO1 deletion and NOMO1 protein levels (MAF = 0.02, p = 2.2x10-7 ). This study demonstrates that existing population-wide WGS call sets can be mined for germline CNVs with minimal computational overhead, delivering insight into a less well-studied, yet potentially impactful class of genetic variant.

Mendelian Randomization Analysis Reveals a Causal Influence of Circulating Sclerostin Levels on Bone Mineral Density and Fractures.

In bone, sclerostin is mainly osteocyte-derived and plays an important local role in adaptive responses to mechanical loading. Whether circulating levels of sclerostin also play a functional role is currently unclear, which we aimed to examine by two-sample Mendelian randomization (MR). A genetic instrument for circulating sclerostin, derived from a genomewide association study (GWAS) meta-analysis of serum sclerostin in 10,584 European-descent individuals, was examined in relation to femoral neck bone mineral density (BMD; n = 32,744) in GEFOS and estimated bone mineral density (eBMD) by heel ultrasound (n = 426,824) and fracture risk (n = 426,795) in UK Biobank. Our GWAS identified two novel serum sclerostin loci, B4GALNT3 (standard deviation [SD]) change in sclerostin per A allele (ß = 0.20, p = 4.6 × 10-49 ) and GALNT1 (ß = 0.11 per G allele, p = 4.4 × 10-11 ). B4GALNT3 is an N-acetyl-galactosaminyltransferase, adding a terminal LacdiNAc disaccharide to target glycocoproteins, found to be predominantly expressed in kidney, whereas GALNT1 is an enzyme causing mucin-type O-linked glycosylation. Using these two single-nucleotide polymorphisms (SNPs) as genetic instruments, MR revealed an inverse causal relationship between serum sclerostin and femoral neck BMD (ß = -0.12, 95% confidence interval [CI] -0.20 to -0.05) and eBMD (ß = -0.12, 95% CI -0.14 to -0.10), and a positive relationship with fracture risk (ß = 0.11, 95% CI 0.01 to 0.21). Colocalization analysis demonstrated common genetic signals within the B4GALNT3 locus for higher sclerostin, lower eBMD, and greater B4GALNT3 expression in arterial tissue (probability >99%). Our findings suggest that higher sclerostin levels are causally related to lower BMD and greater fracture risk. Hence, strategies for reducing circulating sclerostin, for example by targeting glycosylation enzymes as suggested by our GWAS results, may prove valuable in treating osteoporosis. © 2019 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals, Inc.

Preparation and immunogenicity of influenza virus-like particles using nitrocellulose membrane filtration.

PURPOSE: Nitrocellulose membrane-based filtration system (NCFS) is widely used for protein concentration. In this study, we applied NCFS for production of virus-like particle (VLP) as a vaccine candidate and evaluated yield property and immunogenicity. MATERIALS AND METHODS: Influenza VLPs were generated by baculovirus-insect cell protein expression system. NCFS and sucrose gradient ultracentrifugation were used for purification of VLP. Immunogenicity of VLP was evaluated by animal experiment. RESULTS: Influenza VLPs expressing hemagglutinin (HA) and neuraminidase proteins derived from highly pathogenic influenza virus (H5N8) were effectively produced and purified by NCFS. HA activity of VLP which correlated with antigenicity was well conserved during multiple purification steps. This NCFS based purified VLPs induced influenza virus-specific antibody responses. CONCLUSION: Our results indicate that the influenza VLP vaccine could be prepared by NCFS without loss of immunogenicity and elicit antigen-specific immune responses.

Making soy sauce using direct fermentation of defatted soybean meal without the meju (soybean Koji) preparation process.

Soy sauce prepared via direct fermentation of defatted soybean meal (DFSM) using halophiles without addition of dried, fermented soybeans or meju was evaluated. DFSM was fermented using single and mixed cultures of Oceanobacillus kimchii and Bacillus pumilus under 18% salinity conditions. Amounts of total organic nitrogen, free amino acids, and organic acids in soy sauce prepared with the mixed culture were slightly higher than sauces prepared with single culture. The ingredient content was higher in soy sauce prepared via direct fermentation of DFSM than soy sauce prepared with meju. Microorganisms detected in DFSM fermentation were not detected in the meju culture, except for the 2 halophiles, based on metagenomic analysis. Direct fermentation of DFSM is better than using meju for preparation of soy sauce.

Suppression of tumor growth in lung cancer xenograft model mice by poly(sorbitol-co-PEI)-mediated delivery of osteopontin siRNA.

Small interfering RNA (siRNA)-mediated gene silencing represents a promising strategy for treating diseases such as cancer; however, specific gene silencing requires an effective delivery system to overcome the instability and low transfection efficiency of siRNAs. To address this issue, a polysorbitol-based transporter (PSOT) was prepared by low molecular weight branched polyethylenimine (bPEI) crosslinked with sorbitol diacrylate (SDA). Osteopontin (OPN) gene, which is highly associated with non-small cell lung cancer (NSCLC) was targeted by siRNA therapy using siRNA targeting OPN (siOPN). Characterization study confirmed that PSOT formed compact complexes with siOPN and protected siOPN against degradation by RNase. PSOT/siOPN complexes demonstrated low cytotoxicity and enhanced transfection efficiency in vitro, suggesting that this carrier may be suitable for gene silencing. In the A549 and H460 lung cancer cell lines, PSOT/siOPN complexes demonstrated significant silencing efficiency at both RNA and protein levels. To study in vivo tumor growth suppression, two lung cancer cell-xenograft mouse models were prepared and PSOT/siOPN complexes were delivered into the mice through intravenous injection. The siOPN-treated groups demonstrated significantly reduced OPN expression at both the RNA and protein levels as well as suppression of tumor volume and weight. Taken together, siOPN delivery using PSOT may present an effective and novel therapeutic system for lung cancer treatment.

Aerosol delivery of kinase-deficient Akt1 attenuates Clara cell injury induced by naphthalene in the lungs of dual luciferase mice.

Conventional lung cancer therapies are associated with poor survival rates; therefore, new approaches such as gene therapy are required for treating cancer. Gene therapies for treating lung cancer patients can involve several approaches. Among these, aerosol gene delivery is a potentially more effective approach. In this study, Akt1 kinase-deficient (KD) and wild-type (WT) Akt1 were delivered to the lungs of CMV-LucR-cMyc-IRES-LucF dual reporter mice through a nose only inhalation system using glucosylated polyethylenimine and naphthalene was administrated to the mice via intraperitoneal injection. Aerosol delivery of Akt1 WT and naphthalene treatment increased protein levels of downstream substrates of Akt signaling pathway while aerosol delivery of Akt1 KD did not. Our results showed that naphthalene affected extracellular signal-regulated kinase (ERK) protein levels, ERK-related signaling, and induced Clara cell injury. However, Clara cell injury induced by naphthalene was considerably attenuated in mice exposed to Akt1 KD. Furthermore, a dual luciferase activity assay showed that aerosol delivery of Akt1 WT and naphthalene treatment enhanced cap-dependent protein translation, while reduced cap-dependent protein translation was observed after delivering Akt1 KD. These studies demonstrated that our aerosol delivery is compatible for in vivo gene delivery.

Comparing the toxic mechanism of synthesized zinc oxide nanomaterials by physicochemical characterization and reactive oxygen species properties.

We studied the toxicity of ZnO nanomaterials in terms of physicochemical characteristics and reactive oxygen species (ROS) properties. ZnO nanorods [synthesized at room temperature (ZnO-RT, length; 18.0±4.2 nm) and at 60 °C (ZnO-60, length; 80.5±6.8 nm)] were used to evaluate the potential toxicity upon growth velocity-related particle size. The cytotoxicity of ZnO-60 was higher than that of ZnO-RT. We observed that the toxicity of ZnO-RT and ZnO-60 was related with ROS formation by using antioxidant N-acetylcysteine and electron spin resonance. Also, we found that the source of toxicity was not related to Zn(2+) ions released from ZnO in 24h treatment. Our results indicate that toxicity of ZnO nanorods is caused by the amounts of ROS. Our study strongly suggests that size of nanomaterial is not the sole factor to be considered, thus, the development of appropriate criteria based on morphological/physicochemical characteristics as well as synthesis procedures is needed to evaluate the precise toxicity.

[A case of hypervascular hyperplastic nodules mimicking hepatocellular carcinoma in alcoholic liver cirrhosis].

Benign hypervascular hyperplastic nodules (HHN) in liver cirrhosis are very rare. It is important to distinguish between regenerative nodules (hyperplastic nodules) and tumorous nodules (dysplastic or neoplastic nodules) in hepatocellular nodular lesions. The differential diagnosis between HHN and hepatocellular carcinoma on the basis of radiologic imaging is often difficult, and is clinically important when determining the therapeutic plan. Therefore, histological confirmation by needle biopsy sampling of the liver is necessary for a correct diagnosis of HHN. We report herein a case of benign HHN mimicking hepatocellular carcinoma in a 32-year-old male alcoholic liver cirrhosis patient without viral hepatitis infection.