In PLOS Genetics, researchers from the University of Pennsylvania, the Dana-Farber Cancer Institute, and elsewhere present findings from a transcriptomic and genomic analysis of prostate cancer cases occurring in men with mainly European or mainly African American ancestry. The team compared genetic ancestry features, somatic mutation profiles, differential gene expression patterns, regulatory features, and more in 498 prostate cancer assessed for the Cancer Genome Atlas project, reasoning that there may be genomic features contributing to the enhanced prostate cancer rates and reduced survival outcomes reported in African Americans. "We found that there is substantial heterogeneity in the genomic alterations and transcriptomic dysregulation occurring in men of African and European ancestry in the TCGA cancer cohort," they write, noting that "SPOP mutations, TMPRSS2-ERG fusions, PTEN deletions/losses, immune signaling, and expression of non-coding RNAs were identified as potential contributors to prostate cancer racial disparities."
For a PLOS One paper, a Korean team describes a handful of genes with potential ties to liver function in the Korean population, found through a genome-wide association study that included almost 6,500 participants. For the discovery stage of the analysis, the researchers searched for loci linked to levels of liver enzymes such as total bilirubin, alkaline phosphatase (ALP), alanine transaminase (ALT), and gamma-glutamyl transferase (GGT) in nearly 4,500 Korean participants, uncovering suspicious SNPs that were subsequently assessed in more than 2,000 additional individuals. Along with 13 SNPs that appeared to coincide with total bilirubin levels, they saw associations between ALP enzyme levels and variants in and around the ABO blood type gene as well as an apparent link between GGT levels and GGT1 variants. "These findings differ from reported results in GWAS in European populations in terms of associated genes and locations," they note, "suggesting different genetic mechanisms of liver enzyme regulation according to ethnicity."
Researchers in China and the UK explore genomic features in more than 100 Vibrio cholerae isolates from infected patients, non-symptomatic carriers, or environmental sources in Hangzhou, China over more than a decade, in an effort to find features involved in diarrhea disease risk involving non-toxigenic isolates. As the team reports in PLOS Neglected Tropical Diseases, genome sequence data for 119 Hangzhou isolates of V. cholerae and comparisons with publicly available sequences for another 850 isolates collected around the world highlighted two main lineages of non-toxigenic, risky V. cholerae classified as "CNTP" isolates based known virulence factor features. "Both lineages are not only circulating in local regions causing endemic disease, but have been spreading worldwide over the past 100 years," the authors note.