In PLOS Genetics, researchers from Vanderbilt University and the University of Wisconsin explore variations in the way synonymous DNA codons are used in hundreds of yeast species. The team delved into available genome sequence data for 327 budding yeast species from the Saccharomycotina sub-phylum, analyzing synonymous codon usage in these species through the lens of selection and within broader sequence, amino acid, location, and gene contexts. "[W]hereas codon usage bias for most codons appears to be strongly associated with mutational bias and largely driven by genetic drift across the entire subphylum, patterns of codon usage bias in a few codons, as well as in many genes in nearly all genomes of budding yeast, deviate from neutral expectations," the authors report, noting that selection pressure related to codon-transfer RNA interactions during translation seems to contribute to codon biases.
A team from Taiwan takes a look at lung cancer features that may be linked to driver mutations in the MET gene for a paper in PLOS One. Using quantitative PCR, targeted sequencing, and other approaches, the researchers assessed MET mutations in nearly 200 formalin-fixed, paraffin-embedded lung cancer samples collected at a hospital in Chiayi over more than a decade, from 2006 to 2917. In the process, they identified MET amplification, overexpression, or exon skipping (involving MET exon 14) in a small subset of the lung cancers, prompting analyses that took into account available clinicopathological features from those cases. "[O]ne of the MET exon 14 skipping mutation cases identified from a pulmonary carcinosarcoma … highlighted the necessity to broaden the screening scope for this mutation in other minority lung subtypes" the authors argue.
In another study appearing in PLOS One, Japanese researchers describe apparent interactions between germline mutations in the tumor suppressor gene TP53 and recurrent somatic mutations found in bladder cancer. That team relied on Taqman genotyping, targeted sequencing, and RNA sequencing to profile somatic mutations in 50 cancer related genes — and to search for a specific TP53 germline mutation involving codon 72 — in 44 individuals with muscle invasive bladder cancer and 59 individuals with non-muscle-invasive bladder cancer. With these approaches, the authors tracked down potential ties between TP53 codon 72 germline variants and somatic mutations affecting the FGFR3 and RAS genes in the non-muscle-invasive forms of bladder cancer.