Trans-eQTLs Reveal That Independent Genetic Variants Associated with a Complex Phenotype Converge on Intermediate Genes, with a Major Role for the HLA

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Transient foaming behavior of aqueous alcohol solutions as related to their dilational surface properties

The foamability of aqueous alcohol solutions can be measured by continuously sparging air in a closed loop through the solution under standard conditions. The amount of foam produced in the steady state is taken as a measure for the foamability. Aqueous alcohol solutions show transient foaming behavior. This can be explained by assuming that, due to lack of disjoining pressure, thin aqueous alcohol films collapse when due to drainage a critical film thickness has been reached. This means that the drainage rate of these films determines to a large extent the lifetime of these films. Film drainage can be slowed down by surface tension gradients opposing the liquid flow in the film. The ability of aqueous alcohol solutions to generate a surface tension gradient can be measured by means of the overflowing cylinder technique. By changing the alcohol concentration for ethanol, 1-butanol, 1-hexanol, and 1-octanol it is found that both the foamability and the ability to generate a surface tension gradient pass over a maximum value at an alcohol concentration which is characteristic for the alcohol considered. This alcohol concentration coincides with the alcohol content at which a maximum in the ability to generate a surface tension gradient is found. It is concluded that the transient foaming behavior of these aqueous alcohol solutions is mainly determined by their ability to generate a surface tension gradient

Mapping of Gene Expression Reveals CYP27A1 as a Susceptibility Gene for Sporadic ALS

Amyotrophic lateral sclerosis (ALS) is a progressive, neurodegenerative disease characterized by loss of upper and lower motor neurons. ALS is considered to be a complex trait and genome-wide association studies (GWAS) have implicated a few susceptibility loci. However, many more causal loci remain to be discovered. Since it has been shown that genetic variants associated with complex traits are more likely to be eQTLs than frequency-matched variants from GWAS platforms, we conducted a two-stage genome-wide screening for eQTLs associated with ALS. In addition, we applied an eQTL analysis to finemap association loci. Expression profiles using peripheral blood of 323 sporadic ALS patients and 413 controls were mapped to genome-wide genotyping data. Subsequently, data from a two-stage GWAS (3,568 patients and 10,163 controls) were used to prioritize eQTLs identified in the first stage (162 ALS, 207 controls). These prioritized eQTLs were carried forward to the second sample with both gene-expression and genotyping data (161 ALS, 206 controls). Replicated eQTL SNPs were then tested for association in the second-stage GWAS data to find SNPs associated with disease, that survived correction for multiple testing. We thus identified twelve cis eQTLs with nominally significant associations in the second-stage GWAS data. Eight SNP-transcript pairs of highest significance (lowest p = 1.27 x 10(-51)) withstood multiple-testing correction in the second stage and modulated CYP27A1 gene expression. Additionally, we show that C9orf72 appears to be the only gene in the 9p21.2 locus that is regulated in cis, showing the potential of this approach in identifying causative genes in association loci in ALS. This study has identified candidate genes for sporadic ALS, most notably CYP27A1. Mutations in CYP27A1 are causal to cerebrotendinous xanthomatosis which can present as a clinical mimic of ALS with progressive upper motor neuron loss, making it a plausible susceptibility gene for ALS

Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma

Liver cancer has the second highest worldwide cancer mortality rate and has limited therapeutic options. We analyzed 363 hepatocellular carcinoma (HCC) cases by whole-exome sequencing and DNA copy number analyses, and we analyzed 196 HCC cases by DNA methylation, RNA, miRNA, and proteomic expression also. DNA sequencing and mutation analysis identified significantly mutated genes, including LZTR1, EEF1A1, SF3B1, and SMARCA4. Significant alterations by mutation or downregulation by hypermethylation in genes likely to result in HCC metabolic reprogramming (ALB, APOB, and CPS1) were observed. Integrative molecular HCC subtyping incorporating unsupervised clustering of five data platforms identified three subtypes, one of which was associated with poorer prognosis in three HCC cohorts. Integrated analyses enabled development of a p53 target gene expression signature correlating with poor survival. Potential therapeutic targets for which inhibitors exist include WNT signaling, MDM4, MET, VEGFA, MCL1, IDH1, TERT, and immune checkpoint proteins CTLA-4, PD-1, and PD-L1