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This Week in Cell: Aug 24, 2016

A team from the University of California, Los Angeles, Rutgers Cancer Institute, and elsewhere untangles patient-specific prostate cancer networks based on phosphoproteomic profiles in tumor tissue from lethal, metastatic, castration-resistant prostate cancer cases. The researchers considered phosphoproteomic patterns in the tumor samples, alongside autopsy profiles and clinical information. These data allowed them to track down transcriptional shifts, activated kinase enzymes, and mutated genes, which they used to establish so-called "phosphorylation-based cancer hallmarks using integrated personalized signatures," or pCHIPS.

Using the Saccharomyces cerevisiae yeast model, researchers from Israel took a look at ways gene expression influences fitness. The team used a combination of synthetic promoters to tweak the expression of around 100 genes to about 100 levels of expression in yeast growing in a pooled growth competition over several generations. By doing deep sequencing on the resulting population, the investigators were able to begin untangling the relative fitness effects associated with changes in expression of the genes of interest. The study's authors say the work "addresses a fundamental gap in understanding the functional significance of gene expression regulation and offers a framework for evaluating the phenotypic effects of expression variation."

Israeli and French researchers report on microbiome features that seem to impact innate lymphoid cell-based immune activity in the mouse intestine. Using RNA sequencing, single-cell RNA sequencing, ATAC-seq, indexing-first chromatin immunoprecipitation sequencing, and mass spectrometry, the team characterized chromatin and transcriptional profiles in ILCs in the small intestines of conventional mice, antibiotic-treated mice, and germ-free mice. The analysis uncovered known ILC subtypes, along with at least two sub-populations that did not fit into the current classification scheme for ILC.