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This Week in Cell: Aug 28, 2014

A team from New York University, the IBM Thomas J. Watson Research Center, and Columbia University used a combination of deep RNA sequencing and chromatin immunoprecipitation sequencing to look at whether the Notch pathway signaling pathway glitches that have been associated with T cell lymphoblastic leukemia, or T-ALL, impact downstream long non-coding RNA targets. Indeed, the search uncovered lncRNA isoforms stemming from almost 2,000 gene loci, including a lncRNA called LUNAR that not only appeared to be regulated by Notch, but also contributed to T-ALL tumor growth and maintenance.

The expression levels of two sets of metabolic genes seem to be controlled by sirtuin proteins with slightly different modes of action in the mouse liver circadian cycle, according to a study by investigators at the University of California at Irvine and elsewhere. The team did array-based gene expression profiling on mouse liver samples to track the consequences of individually knocking out the sirtuin genes SIRT6 and SIRT1. In the process, the study authors saw partitioning between the metabolic genes influenced by each sirtuin, with SIRT6 exerting its influence over genes involved in fatty acid and cholesterol metabolism via interactions with chromatin.

Members of the Cancer Genome Atlas present 11 main cancer subtypes identified through integrated genomic profiling on samples from more than 3,500 individuals. Using a combination of array- and sequencing-based approaches, the team produced copy number, gene expression, microRNA expression, proteomic, methylation, and point mutation profiles for tumors from a dozen cancer types. Using these data, the researchers clustered the samples into several sub-types that coincided existing site of origin-based classification schemes. But still other tumor groups contained samples from more than one conventional cancer type, including a sub-type comprised of lung squamous tumors, head and neck cancers, and some of the bladder cancers.