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PNAS Studies Look at Inca Resettlement, Spermatogonial Stem Cell Transcriptomes, More

Editor's Note: Some of the articles described below are not yet available at the PNAS site, but they are scheduled to be posted some time this week.

Researchers from the UK, US, and Peru present genetic evidence for Incan movements from the north to south coast of Peru in the 1400s and early 1500s, which appear to line up with findings from archeological, historical, and other analyses. After sequencing half a dozen individuals buried at cemeteries in southern Peru's Chincha Valley between 1400 and 1825, the team compared the sequences with those from ancient individuals genotyped in South and North America in the past, as well as available sequence data from hundreds of modern-day Native American individuals. The genomic clues lined up with other available data sources in Peru, consistent with resettlement stemming from an Incan state policy. "Genomic analyses indicate that these individuals are genetically most similar to ancient and present-day populations from the north Peruvian coast located several hundred kilometers away," the authors report, and "provide some of the strongest evidence yet of state-sponsored resettlement in the pre-Colonial Andes."

A team from the University of California, San Diego, and the University of Pittsburgh take a look at transcriptome patterns in spermatogonial stem cells that go on to develop into sperm. Using single-cell RNA sequencing, the researchers tracked gene expression over the course of differentiation in samples enriched for spermatogonial stem cells, identifying enhanced activity by AKT, JAK-STAT, and other signaling pathways along the way. When they interfered with these pathways in follow-up cell line experiments, the authors saw hints that undifferentiated spermatogonia cultures got a boost by dialing down AKT signaling — an approach that "raises the possibility that supplementation with an AKT inhibitor could be used to culture human [spermatogonial stem cells] in vitro for therapeutic applications."

For a study set to appear in PNAS this week, researchers in Israel, Belgium, and the US explore the energetics of genomic instability in cancer samples from efforts such as The Cancer Genome Atlas project. Based on copy number clues gleaned from exome sequencing and other data from samples from several cancer types, the team saw apparent ties between ploidy and free energy dynamics in the tumors. Along with distinct free energy features found in tumors with or without a history of whole-genome duplications, the authors noted that their findings "point to [copy number] changes that are more common in high-ploidy tumors and thus support altered selection pressures upon [whole-genome duplication]."