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This Week in PNAS: Nov 27, 2018

A Genentech team takes a look at the relationship between germline variants, tumor gene expression, and immune cell infiltration in two dozen human cancer types. For their analyses, the researchers considered tumor RNA sequence data and matched normal whole-genome genotypes from 4,840 cases profiled for the Cancer Genome Atlas project, narrowing in on nearly 64,100 expression quantitative trait loci influencing the expression of 18,210 genes. Immune-related genes appear to be over-represented in that group, they note, while at least 103 gene signature quantitative trait loci coincided with immune cell abundance in the tumor microenvironment. Based on the findings, the authors conclude that "expression of more than half of the genes in tumor tissues was associated with germline genetics, highlighting an underappreciated determinant of variable tumor gene expression and immune cell infiltration." 

For another PNAS paper, researchers from the US, Japan, and elsewhere explore relationships between so-called hemipteroid insects such as true bugs, lice, and thrips. Using transcriptome sequence data for almost 2,400 single-copy genes in 193 insects, the team saw distinct monophyletic lineages leading to the three hemipteroid insect orders. In particular, the results suggest the Hemiptera order of "true bugs" are most closely related to thrips in the Thysanoptera order, while bark lice and parasitic lice in the Psocodea are more distantly related to the other two orders. "[A]lthough the exact phylogenetic position of Psocodea remains to be resolved convincingly," the authors conclude, "our results based on transcriptomes for hemipteroid insects provide a strong phylogenetic framework for future studies of genomic, morphological, ecological, and behavioral characteristics of this important group of insects." 

A team from the University of California, Merced, and University of Hawaii describes interactions between the aster leafhopper and two nutritional symbionts — bacteria from the Nasuia and Sulcia genera — with small, streamlined genomes missing multiple metabolic and cellular pathways. Based on symbiont and host tissue transcriptomes, along with a new draft genome for the aster leafhopper, the researchers identified genes that are differentially expressed in the bacteriocyte cells that harbor the Nasuia or Sulcia symbionts. The authors found that the aster leafhopper "differentially expresses thousands of genes between the bacteriocyte types to meet the functional needs of each symbiont, including the provisioning of metabolites and support of cellular processes."