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This Week in PNAS: Jan 2, 2018

In the Proceedings of the National Academy of Sciences this week, researchers from the University of California, Los Angeles explore transcriptomic patterns in central nervous system samples in a mouse model of multiple sclerosis called experimental autoimmune encephalomyelitis (EAE). Using RiboTag mice and related cell type-specific ribosomal analyses — coupled with quantitative RT-PCR, sequencing, and other approaches — the team tracked expression in astrocyte cells spanning several neuroanatomical regions. Along with waning cholesterol synthesis gene expression in spinal cord and optic nerve astrocytes, the authors described rising immune gene representation during EAE.

A Shanghai Institute of Hematology-led team considers transcriptomic patterns and gene fusions in dozens of adult and pediatric cases of T-cell acute lymphoblastic leukemia (T-ALL). Using a combination of RNA sequencing, exome sequencing, and array-based rearrangement analyses, the researchers profiled samples from 61 adults with T-ALL and 69 pediatric T-ALL cases. Their search unearthed three-dozen gene fusions, including 18 new fusions that appeared to be recurrent, along with new and known genes marked by recurrent mutations in general. "Distinct T-ALL subgroups were defined according to the interplay among different genetic abnormalities and gene transcription patterns," the authors write, noting that SET-NUP214 fusions or enhanced expression of certain genes were over-represented in the adult T-ALL cases considered.

Members of an international team search for rare genetic contributors to type 2 diabetes through genomic analyses on more than 1,000 individuals from 20 type 2 diabetes-prone families of Mexican-American ancestry in the San Antonio region. Based on whole-genome sequencing, SNP genotyping, and/or array-based gene expression profiling on 1,034 family members, including 305 individuals with type 2 diabetes, the team saw rare variants influencing expression in the family members. Even so, the authors say, the available data did not unearth any rare variants with clear ties to type 2 diabetes or related traits, "suggesting that large-effect rare variants account for only a modest fraction of the genetic risk of these traits in this sample of families."

The Scan

Foxtail Millet Pangenome, Graph-Based Reference Genome

Researchers in Nature Genetics described their generation of a foxtail millet pangenome, which they say can help in crop trait improvement.

Protein Length Distribution Consistent Across Species

An analysis in Genome Biology compares the lengths of proteins across more than 2,300 species, finding similar length distributions.

Novel Genetic Loci Linked to Insulin Resistance in New Study

A team reports in Nature Genetics that it used glucose challenge test data to home in on candidate genes involved in GLUT4 expression or trafficking.

RNA Editing in Octopuses Seems to Help Acclimation to Shifts in Water Temperature

A paper in Cell reports that octopuses use RNA editing to help them adjust to different water temperatures.