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PLOS Studies Explore Alternatively Spliced Gene in COPD, Avian Flu Evolution, and More

In PLOS Genetics, members of two large consortia describe an alternatively spliced form of the FBXO38 gene that appears to contribute to chronic obstructive pulmonary disease (COPD). Using a combination of RNA sequencing and COPD risk SNP results from prior genome-wide association studies, the researchers searched for COPD associations involving alternative splicing quantitative trait loci (sQTL). Starting with blood transcriptome data for 376 participants in the COPDGene Investigators project, the team tracked down sQTL influencing splice sites in more than 6,400 genes, including 156 SNPs implicated in COPD in prior GWAS. The top associations involved SNPs in FBXO38 that were verified with qPCR profiling on blood and lung samples, authors report, noting that results so far "indicate that analysis of alternative splicing may provide novel insights into disease mechanisms."

Researchers in Japan and Egypt take a look at the evolution of avian influenza virus H9N2 in the Middle East for a paper appearing in PLOS Pathogens. The team used phylogenetics, cell-based assays, and other approaches to identify and characterize suspicious PB2 gene mutations in a clade of so-called "G1-like" H9N2 viruses circulating in birds in Egypt and other parts of the Middle East that have jumped to humans on occasion. The analyses highlighted PB2 mutations that appeared to bump up replication and virulence of H9N2 in human cells and mouse models of disease. "Our data showed that, during about two decades of evolution in nature, G1-like subclade strains evolved to produce strains with appreciably higher replication phenotypes in Central Asia and the Middle East," the investigators write, "which led to their expanded host range."

A Swiss team takes a look at microRNA profiles in blood samples from individuals with chronic pain for a PLOS One study. After a pilot analysis involving a smaller group of participants, the researchers assessed the expression of 184 miRNAs in blood samples from 73 individuals with chronic musculoskeletal pain following traumatic skeletal muscle injury, comparing these miRNA profiles with one another and with those in 21 healthy controls. From the miRNA expression patterns there, they took 10 miRNAs forward for further validation testing in 100 individuals, narrowing in on two circulating miRNAs that appeared to coincide with individuals with neuropathic or nociceptive pain sources — pain originating in the somatosensory nervous system or non-neural tissue respectively. 

The Scan

Germline-Targeting HIV Vaccine Shows Promise in Phase I Trial

A National Institutes of Health-led team reports in Science that a broadly neutralizing antibody HIV vaccine induced bnAb precursors in 97 percent of those given the vaccine.

Study Uncovers Genetic Mutation in Childhood Glaucoma

A study in the Journal of Clinical Investigation ties a heterozygous missense variant in thrombospondin 1 to childhood glaucoma.

Gene Co-Expression Database for Humans, Model Organisms Gets Update

GeneFriends has been updated to include gene and transcript co-expression networks based on additional RNA-seq data from human and mouse samples, a new paper in Nucleic Acids Research says.

New Study Investigates Genomics of Fanconi Anemia Repair Pathway in Cancer

A Rockefeller University team reports in Nature that FA repair deficiency leads to structural variants that can contribute to genomic instability.