In PLOS Biology, researchers from Peking University and elsewhere describe epigenetic, expression, and gene regulatory differences between distinct heart chambers and between heart samples from different species. Using RNA sequencing and a nucleosome occupancy and methylome sequencing (NOMe-seq) method, the team assessed gene expression, DNA methylation, and chromatin accessibility patterns across all four chambers from 11 healthy adult human hearts, three fetal hearts, and more than a dozen mouse hearts, highlighting atrial and ventricle expression differences, human-specific long non-coding RNAs, and other chamber- and species-specific features. "Our results revealed chamber-specific and species-specific characteristics of gene expression, DNA methylation, and chromatin accessibility of human and mouse hearts," the authors write, adding that the "resulting multi-omics map of healthy human and mouse hearts can be used as a reference to identify novel biomarkers or drug targets when compared with malfunctioning hearts."
A team from Belgium, the US, and South Africa retraces SARS-CoV-2 circulation in New York City's boroughs during early stages of the COVID-19 pandemic for a paper in PLOS Pathogens. Based on their phylogenetic analyses of genome sequences for more than 800 SARS-CoV-2 isolates collected in the state, the researchers mapped viral relationships and spread between New York City's boroughs and beyond during the spring of 2020, describing more than 100 introduction events in the area. "Our analyses describe the dispersal dynamics of viral lineages at the state and city levels, illustrating that peripheral samples likely correspond to distinct dispersal events originating from the main metropolitan city areas," they write, noting that "our results highlight the relatively important role of the borough of Queens as a transmission hub associated with higher local circulation and dispersal of viral lineages toward the surrounding boroughs."
Investigators in China explore potential ties between COL6A4P2 gene variants and lung cancer risk in individuals from the Han Chinese population for a study in PLOS One, focusing on five candidate SNPs selected based on allele frequency data from the 1000 Genomes Project. Based on genotyping array profiles for 510 Southern Han Chinese individuals with lung cancer and 495 without, the team tracked down at least one COL6A4P2 variant that appeared to coincide with lung cancer risk, along with additional SNPs linked to lung cancer in specific analytical models or subset of individuals. "We identified that rs34445363 in COL6A4P2 was associated with an increased risk of [lung cancer]," the authors report, adding that "rs34445363 site mutations increase the risk of [lung adenocarcinoma (LUAD)], while the mutation of rs61733464 significantly decreased the LUAD risk."