In PLOS Genetics, researchers in Norway describe differential transcript usage and transcript splicing in prefrontal cortex brain samples from dozens of individuals with Parkinson's disease. Starting with RNA sequencing profiles from prefrontal cortex samples for 17 individuals with Parkinson's disease and 11 individuals without, the team did a transcriptome-wide association study aimed at uncovering transcript usage patterns associated with the neurodegenerative disease, identifying almost two dozen Parkinson's-associated differential transcripts affecting 19 genes that were subsequently validated in 21 more Parkinson's disease cases or controls. "Our findings provide the first insight into the [differential transcript usage] landscape of [Parkinson's disease] and identify novel disease-associated genes," the authors report, suggesting differential transcript usage may become "an essential complement to differential gene expression studies."
For another PLOS Genetics paper, an international team led by investigators in Germany presents findings from an exome sequencing and transcriptome sequencing analysis of enteric nervous system development in mouse tissue models and in humans — work aimed at identifying genes involved in a rare congenital condition called Hirschsprung disease, which is marked by missing enteric nerve cells in the gut and related large intestine obstructions. The team considered exome sequence data for two individuals with Hirschsprung disease and their unaffected parents, along with exome sequence, transcriptome sequence, network, and other clues from mouse embryonic enteric nervous system samples, focusing in on four genes with apparent ties to Hirschsprung disease. "Transcriptomics revealed that these genes are expressed in embryonic and fetal gastrointestinal tissues," they report, noting that neuronal cells lacking these genes "demonstrated impaired cell differentiation, proliferation, and/or survival."
Buffalo-based investigators reporting in PLOS One outline their search for blood-based transcript markers for unruptured intracranial aneurysms. The team reasoned that RNA sequencing on peripheral blood samples from individuals with or without the risky cerebrovasculature bulges might lead to a set of blood expression features for finding the yet-to-rupture aneurysms, since past research hinted at an apparent circulating neutrophil immune signature in those with intracranial aneurysms. For the new study, researchers came up with an 18-gene blood predictor based on RNA sequence data from 47 intracranial aneurysm cases or controls, subsequently demonstrating that that machine learning classifier picked up intracranial aneurysm with 85 percent accuracy in 20 more cases or controls. "Bioinformatics analyses indicate that critical inflammatory pathways are captured by the model genes," the authors note, "which is consistent with our previous findings using neutrophils."