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PLOS Papers on Indonesian Archipelago Populations, Hookworm Secretome, Carotid Plaque GWAS

In PLOS Genetics, an international team documents gene expression and epigenetic similarities and differences between three populations living in distinct parts of the Indonesian archipelago. Using array-based DNA methylation profiling and RNA sequencing, the researchers gauged epigenetic profiles and gene expression of whole blood samples from 116 men from Mentawai, Sumba, and Korowai hunter-gatherer populations from Sumatra's west coast, central Indonesia, and West Papua, New Guinea, respectively. The results pointed to differential expression and related methylation shifts within or between islands that involved up to 10 percent of genes, they report, particularly involving genes from immune-related pathways. "These findings emphasize the need to consider a broad range of genetic and environmental backgrounds when examining how molecular patterns and processes are shared across human populations."

Researchers from Australia, Spain, and elsewhere take a look at the proteins secreted by Necator americanus hookworm parasites during the adult, small intestine stage of infection in humans for a paper in PLOS Neglected Tropical Diseases. "[W]e describe the [excretory/secretory] proteome of N. americanus and utilize this information along with RNA-seq data to conduct the first proteogenomic analysis of a parasitic helminth, significantly improving the available genome and thereby generating a robust description of the parasite secretome," they write. On the genome annotation side, for example, the team estimated that the N. americanus genome contained 15,728 predicted protein-coding genes — thousands fewer genes than previously estimated. The analysis also highlighted 198 proteins that appeared to be part of the adult hookworm secretome.

A German team presents findings from a sex-specific genome-wide association study focused on half a dozen carotid artery plaque burden-related traits that are expected to inform atherosclerosis risk for a paper in PLOS One. The GWAS, which included 727 men and 550 women participating in the LIFE-Adult population study, led to seven loci with possible ties to carotid artery plaque burden features overall. In the sex-specific analysis, meanwhile, the researchers saw a chromosome 5 locus with genome-wide significant ties to carotid plaque burden in men alone — an association that they pinned on the IL5 candidate gene using additional gene expression data.