Skip to main content
Premium Trial:

Request an Annual Quote

This Week in Genome Biology: Jun 15, 2016

A German team explores relationships between ovarian cancer outcomes and the signaling pathway activity in the tumor microenvironment. The researchers did RNA sequencing on tumor cells and tumor-associated macrophages in abdominal fluid from more than two-dozen women with serous ovarian carcinoma, using the resulting transcripts to put together common and ovarian cancer-related autocrine and paracrine signaling networks. From the patient-specific signaling activity uncovered in those samples, together with available array-based expression patterns from more than 1,000 other ovarian cancer samples, they search for signaling components coincided with outcomes such as early relapse or better-than-usual survival patterns.

Based on results from their single-cell genome sequencing study of neurons from individuals with or without Alzheimer's disease, researchers from the Netherlands, Germany, and Canada argue against the notion that neuronal aneuploidy plays a role in the disease. Using fresh-frozen postmortem frontal cortex samples from 10 individuals with Alzheimer's disease, half a dozen unaffected controls, and one control individual with Down syndrome, the team sequenced more than 1,500 individual neurons. Their results revealed low rates of aneuploidy in Alzheimer's cases and unaffected controls, affecting only a few individuals and no more than 4 percent of cells tested. "[A]lthough more [Alzheimer's disease]-affected brains should be assessed to exclude rare cases, our results do not support an important role for neuronal aneuploidy in the pathogenesis of [Alzheimer's disease]," they write.

Finally, an international team led by investigators in the UK presents findings from a genome sequencing study of the yellow potato cyst nematode, Globodera rostochiensis. With the new genome assembly, which spans nearly 96 million bases, they uncovered almost 14,400 genes, including hundreds of genes suspected of being acquired by horizontal gene transfer. To explore genetic features behind the parasite's ability to infect host plants — such as the secretion of effector proteins altering certain plant processes — the team not only compared the G. rostochiensis genome to sequences from related species, but also resequenced representatives from eight G. rostochiensis populations and did transcriptome sequencing on tissue from four of the pathogen's life cycle stages.