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This Week in PNAS: Feb 9, 2016

In a study slated to appear online this week in the Proceedings of the National Academy of Sciences, researchers from Yale University and elsewhere describe findings from an effort to identify characteristic genomic features of clear cell renal cell carcinoma (ccRCC), a kidney cancer that may have sarcoma-like histological features. The team did exome sequencing on carcinomatous tumor, sarcomatoid tumor, and matched normal samples from 21 individuals who had ccRCC showing signs of sarcomatoid transformation. They identified recurrently mutated tumor genes such as VHL, PBRM1, SETD2, and PTEN. The analysis also uncovered differences between the carcinomatous and sarcomatoid tumor portions, including a jump in somatic variants and mutations in TP53 and other genes that appeared specific to the sarcomatoid elements.

Also in PNAS this week, a University of Louisville and University of Tennessee team describes differences in malaria severity that they detected in genetically similar mice harboring distinct gut microbial communities. After identifying malaria susceptibility differences in mice infected with multiple Plasmodium species, the researchers used 16S ribosomal RNA sequencing to characterize gut microbiome components in resistant or susceptible mice, which showed differences in Lactobacillus, Bifidobacterium, and other microbe levels. When they transplanted gut contents from resistant or susceptible mice into germ-free mice, meanwhile, the study's authors saw lower-than-usual parasite burdens in the animals that received microbes from the more resistant animals.

Finally this week, Yale University researchers report on findings from a phylogenetic analysis of metastatic cancer lineage evolution. Starting with normal tissue samples, primary tumor samples, and multiple metastatic tumor samples from 40 individuals with lung cancer, pancreatic cancer, or other cancer types, the team used exome sequencing to uncover somatic mutations that were subsequently used to assess tumor lineage phylogenies in each individual. The results were consistent with a branched model of metastatic evolution, sometimes involving more than one lineage and/or lineages that arose early on in tumor development. Our sister publication GenomeWeb Daily News has more on the study, here.