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This Week in PLOS: Apr 29, 2019

An international team led by investigators in the US and Korea reports on SNP and amino acid changes in the human leukocyte antigen (HLA) region that apparent to contribute to systemic lupus erythematosus (SLE) risk in individuals from East Asia for a paper in PLOS Genetics. Using array-based genotyping data for 4,915 individuals with SLE and more than 13,500 without, the researchers imputed additional variants across eight HLA genes, which they used to search for new associations, do conditional analyses, and profile potential autoantibody effects. The authors identified an SLE risk allele at HLA-DRB1 that was subsequently used to find half a dozen other HLA associations through conditional analyses. "Together," they write, "these seven residues increased the proportion of explained heritability due to HLA to 2.6 [percent]." 

Researchers from Emory University and the Icahn School of Medicine at Mount Sinai present findings from an epigenome-wide association study on placental tissue from night shift workers for a paper on maternal circadian disruption in PLOS One. The team did array-based methylation profiling on placenta samples from 237 participants in the Rhode Island Child Health Study — including 53 night shift workers and 184 non-night shift workers — to enhanced or diminished cytosine methylation levels in or around several genes in available placenta samples. A subsequent functional analysis hinted that the genes involved included representatives from cell adhesion pathways and loci previously implicated in psoriasis. "Circadian disruption may contribute to immune-mediated and inflammatory disease," the authors write, "but it is still unclear how this exposure may affect fetal development and infant health." 

In PLOS One, researchers from the US and Ireland describe a deconvolution method for identifying cellular subtypes from available gene expression and/or methylation data. After demonstrating the potential insights that could be gained by re-analyzing array-based gene expression or cytosine methylation data from embryonic mouse kidney samples and peripheral blood samples from humans with asthma or systemic lupus erythematosus, the team used a similar cell type prediction approach to uncover 16 cell subtypes from single-cell RNA sequence data on mouse kidney samples and to analyze data from mouse knockout models. From these and other findings, the authors suggest that "cell subtype proportions themselves should be estimated as a specific goal of functional genomic studies, rather than discarded as a confounding influence."