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This Week in PNAS: Feb 11, 2014

A team from Australia and the US used a combination of arrays and RNA sequencing to look at gene splicing in a zebrafish line known to contain a recessive lethal point mutation in a gene called clbn that encodes part of the so-called U12-type spliceosome — a complex of small ribonucleoproteins tasked with splicing minor class pre-messenger RNAs. As they report online in Proceedings of the National Academy of Sciences, the researchers found ties between altered U12-type splicing in the zebrafish and expression shifts involving genes from a range of pathways, from transcription and nuclear export to mRNA processing and splicing. Together, study authors note, such disruptions appear to contribute to the arrested digestive organ development described in the mutant zebrafish.

High-grade bladder cancers can be sub-divided into at least two types that share molecular features with basal or luminal breast cancers, according to a study by researchers at the University of North Carolina at Chapel Hill and the Memorial Sloan-Kettering Cancer Center. The team started by assessing available data for 262 high-grade, muscle-invasive bladder cancers from public datasets. In the process, the researchers defined two gene expression-based sub-types — which they verified in additional bladder cancer samples — and designated a 47-gene signature for distinguishing between them.

Researchers from Canada and the US describe the genomic alterations they detected in human glioma cells expressing a cancer-associated coagulation and signaling related protein called tissue factor. In the absence of tissue factor, glioma cells remained relatively dormant over time when injected in mice. On the other hand, when the team tracked the effects of dialing up tissue factor expression using arrays, bisulfite sequencing, and other approaches, it saw cancer cells being kicked into action — a process that involved not only recruiting blood and inflammation-related cells, but also through the advent of new mutations and gene silencing.