In PLOS Genetics this week, Hebrew University researchers report on epigenetic shifts detected in human pluripotent stem cells through growth in cell culture. The team used methylation arrays and RNA sequencing to assess DNA methylation and expression, respectively, in low- and high-passage human pluripotent stem cell lines. By comparing patterns in these cell lines to one another — and to methylation and expression profiles previously reported for human pluripotent stem cells at multiple passage stages — the authors narrowed in on sites that were recurrently hyper-methylated and silenced after ongoing passage, including a testis-specific gene called TSPYL5 that's known to be dialed down in some cancer types.
A team from the UK and Israel describe herpesvirus microRNAs that contribute to the microenvironment surrounding related tumors. For a study published in PLOS Pathogens, the researchers began by looking at tumor microenvironment features mediated by Kaposi's sarcoma-associated herpesvirus miRNAs in lymphatic endothelial cells that precede full-blown Kaposi sarcoma. With these and other experiments, they saw signs that miRNAs from the herpesviruses make their way to the microenvironment using cellular exosomes, altering metabolic features in the neighborhood around infected cells. "This exosome-based crosstalk provides viruses with a mechanism for non-infectious transfer of genetic material without production of new viral particles," they write, arguing that "viruses and cancer cells use this mechanism to shape a specific metabolic niche that will contribute to their fitness."
Finally, investigators from China take a look at genetic variation patterns in relation to metabolic and physical features in two indigenous Chinese cattle breeds for a PLOS One paper. The team did whole-genome sequencing on four representatives apiece from the Nanyang (Bos indicus) and Qinchuan (B. taurus) cattle breeds, uncovering hundreds of thousands of small insertions and deletions, and more than 2,900 copy number variants. The analysis also unearthed more than 9 million Nanyang breed-specific SNPs and nearly 7 million SNPs that were new to the Qinchuan breed, providing a variant set that was subsequently used to explore breed-specific phenotypic features.