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This Week in PLOS: Mar 4, 2019

In PLOS Genetics, researchers from the Hospital for Sick Children, the University of Toronto, and elsewhere report on potential cystic fibrosis modifiers, focusing on an intestinal obstruction complication called meconium ileus. Using genotype data for 6,770 CF patients from the US, Canada, and France enrolled in the CF Gene Modifier Consortium, the team identified a previously unappreciated modifier at a chromosome 13 locus containing ATP12A and shored up prior associations involving the SLC6A14 and SLC26A9 genes — results that were interpreted further using transcriptomic profiles and expression quantitative trait locus data from nasal epithelia tissues for more than five dozen CF patients. "Aided by transcriptomics of nasal epithelia from CF patients we found that each locus impacts variation in gene expression of SLC6A14 with tissue specificity," the authors write. "Understanding the contributing tissue and responsible gene are necessary to prioritize modifiers as alternative therapeutic targets."

A Shandong University-led team describes a potential survival signature in the kidney cancer papillary renal cell carcinoma (pRCC) for a paper in PLOS One. The researchers narrowed in on the five-gene signature for pRCC survival with the help of almost 300 tumor and normal samples profiled for the Cancer Genome Atlas project. Based on differentially expressed gene in high-risk cases, the investigators found five survival-related genes — CCNB2, IGF2BP3, KIF18A, PTTG1, and BUB1 — that could distinguish 53 high-risk pRCC patients from 89 low-risk patients in a subsequent validation analysis. The authors suggest the signature has "potential prognostic and therapeutic implications for the pRCC patient management," though "further research is needed to validate our findings and establish molecular mechanisms for the [messenger RNA interactions] and papillary renal cell carcinoma progression."

Finally, researchers from Japan and Saudi Arabia share a multiplex PCR and next-generation amplicon sequencing-based test for detecting and gauging genetic diversity in trypanosomes for a paper in PLOS Neglected Tropical Diseases. The team applied its pipeline to hundreds of wild-caught tsetse flies collected in Zambia and Zimbabwe, uncovering several Trypanosoma species in infected tsetse flies from the Zambian and Zimbabwean sites sampled and relationships between the sub-species. Based on their results, the authors suggest that the strategy "is more accurate than traditional, gel-based analyses which are prone to misidentification of species."