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This Week in PNAS: Dec 5, 2017

In the Proceedings of the National Academy of Sciences online, Johns Hopkins University researchers present a genome-editing approach that combines CRISPR-Cas9-based engineering with linear synthetic donor DNA capable of high efficiency homology-directed repair. After using fluorescence tags and imaging to target PCR fragments with relatively short homology arms to a specific genomic locus in developing mice, the team demonstrated that the single- or double-stranded linear sequences spanning up to 1,000 bases could act as edit donors with homology arms that were just 35 base pairs long. Based on their analysis of sequences involved in linear DNA donor repair, meanwhile, the authors speculate that repair "is local, polarity sensitive, and prone to template switching, characteristics that are consistent with gene conversion by synthesis-dependent strand annealing." 

A team from the US, Canada, and Germany describes an in vitro, transcriptomics-informed strategy to help verify results from standard genotoxicity assays such as mammalian cell assays. For their proof-of-principle study, the researchers used a transcriptomic biomarker dubbed TGx-DDI — a multigene biomarker previously found to discern between compounds that did or did not induce DNA damage — in a high-throughput, cell-based assay with NanoString Technologies' nCounter technology to characterize DNA damaging toxicity by 45 compounds. The authors report that the assay "correctly identifies the vast majority of irrelevant genotoxicity results from in vitro chromosome damage assays."

Finally, a Genentech research team reports on results from a large-scale analysis of KRAS-mutant lung or pancreatic cancers, modeled in genetically engineered mice. The researchers used RNA sequencing and exome sequencing to track transcriptome patterns, single nucleotide changes, small insertions and deletions, copy number changes, and other alterations in 221 KRAS mutation-containing tumors from a genetically engineered mouse models (GEMM) of non-small cell lung cancer and two GEMMs of spontaneous pancreatic ductal adenocarcinoma. Though the mouse tumors tended to contain more copy number changes than previously profiled in KRAS-mutant human cancer, their results suggest many of the same genes are altered in both species. The authors also saw pronounced genetic diversity in the KRAS-mutated tumors that, they say, "represents an unrecognized opportunity to identify therapeutically susceptible genomic subsets preclinically."