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PLOS Papers on Cerebellum Epigenetics, Copy Number Signature Tool, Acute Lung Injury Networks

In PLOS Genetics, a Duke University- and George Washington University-led team explores epigenetic features in the lateral cerebellum and dorsolateral prefrontal cortex (DLPFC), comparing DNA methylation profiles in samples from the brain regions in seven humans, eight chimpanzees, and seven rhesus macaques. Based on array-based DNA methylation profiles in these samples, the researchers focused on differentially methylated regions falling in parts of the genome marked by regulatory elements, before considering expression consequences of these epigenetic marks. Their findings pointed to an uptick in differentially methylated regions in human cerebellum samples, particularly at sites related to the regulation of synaptic plasticity, lipid metabolism, and other neurobiology-related genes. "Humans … specifically show methylation differences at genes involved in neurodevelopment, neuroinflammation, synaptic plasticity, and lipid metabolism," the authors write, noting that the such epigenetic distinctions "are relevant for understanding processes specific to humans, such as extensive plasticity, as well as pronounced and prevalent neurodegenerative conditions associated with aging."

For another paper in PLOS Genetics, investigators in China present an open-source bioinformatics tool designed for finding copy number signatures in cancer samples using copy number data from exome sequence- or SNP-based copy number data without relying on in-depth whole-genome sequence data. When the team applied Sigminer to exome sequence data for more than 1,000 primary or metastatic prostate cancers and matched normal samples, for example, it uncovered five characteristic copy number signatures, including copy number signatures that appeared to correspond more closely with patient outcomes than the three single-base substitution mutation signatures found using the same data. "This is different from the recently described rearrangement signatures, which require high coverage WGS data for analysis," the authors note, concluding that copy number signature analyses "can ultimately improve cancer patients' stratification, clinical prognosis, and therapeutic outcome prediction."

Small RNA and messenger RNA profiles can provide insights into the pathways involved in an inflammatory disease known as acute lung injury (ALI), according to a PLOS One paper by researchers at the University of Electronic Science and Technology in China and elsewhere. The team did RNA sequencing on samples from a mouse model of ALI induced with a lipopolysaccharide, identifying differentially expressed long non-coding RNA, circular RNA, microRNA, and mRNA transcripts in API, along with related lncRNA-miRNA-mRNA and circRNA-miRNA-mRNA regulatory networks. The results highlighted potential ALI biomarkers, as well as related signaling pathways that may contribute to ALI mechanisms, the authors note, though they added that further experiments are needed to validate the current findings.