In PLOS Genetics, researchers from the University of British Columbia and elsewhere outline a multi-omic approach for focusing in on genetic risk variants with gene regulatory and phenotypic effects — an approach they applied to more than a dozen genome-wide association studies centered on brain-related traits. "The cascading epigenomic analysis for GWAS, which we refer to as CEWAS, comprises two types of models: one for linking cis genetic effects to epigenomic variation and another for linking cis epigenomic variation to gene expression," the team says. "Applying these models in cascade to GWAS summary statistics generates gene level statistics that reflect genetically-driven epigenomic effects."
For a paper in PLOS Pathogens, a team from the Netherlands, the US, and Germany presents findings from a transcriptomic analysis of the simian varicella virus (SVV) in Old World monkey cells and in infected animal models in an effort to understand the chickenpox- and shingles-causing human pathogen varicella-zoster virus. Using long-read RNA sequencing, the investigators assessed kidney epithelial cells from African green monkeys or rhesus macaques, uncovering expression, splicing, non-coding RNA and gene fusion patterns that were subsequently verified in infected cynomolgus macaques. "Together, this has led to the identification of numerous alternative RNA isoforms, mostly unique to SVV, and some of which may have functional implications for the virus," the authors write, noting that "we defined the SVV latency-associated transcript, which is highly similar to its [varicella-zoster virus] counterpart."
In a paper appearing in PLOS One, investigators at Hainan Medical University propose potential biomarkers for dermatomyositis, a rare inflammatory myopathy condition. With the help of a web-based tool called GEO2R, the team assessed available array-based gene expression data on skeletal muscle samples from 10 individuals with dermatomyositis and nine healthy unaffected control individuals, uncovering more than five dozen differentially expressed genes from pathways involved in viral response, immunity, and other processes. From there, the authors put together a protein interaction network involving three gene clusters and 10 hub genes with apparent ties to the autoimmune disease. "The identified hub genes all have good diagnostic performance, which may serve as new biomarkers for [dermatomyositis]," they write, adding that "[d]rugs targeting these hub genes would become new treatment options for this high-mortality disease."