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Genomics in the Journals: Mar 14, 2013

NEW YORK (GenomeWeb News) – In the journal Cancer Epidemiology, Biomarkers, and Prevention, Korean researchers reported on a trio of protein biomarkers that seem to show promise for detecting early-stage renal cell carcinoma, a form of kidney cancer. Together with collaborators from the Korean firm Genomine, the team developed an immunoassay for determining the blood plasma levels of the three proteins — nicotinamide N-methyltransferase, L-plastin, and non-metastatic cells 1 protein — that were previously implicated in renal cell carcinoma studies.

After working out the scoring criteria for the assay using blood samples from 87 individuals with kidney cancer and 102 unaffected controls, the researchers went on to show that the three-marker approach could detect nearly 96 percent of kidney cancer cases (assuming 90 percent specificity) in a set of almost 200 blinded samples.

"Renal cell carcinoma, a malignant tumor arising from the kidney, is one of the most difficult forms of cancer to detect and treat properly because it remains silent until disseminating to other organs," Yonsei University Health System's Nam Hoon Cho, who is corresponding author on the study, said in a statement.

"[B]ecause imaging, which is high-cost, is seldom performed without any specific reasons, developing a blood-tumor biomarker is a great chance to detect the silent killer," he said, adding, "If this biomarker is truly valid and accurate to detect renal cell carcinoma, a number of patients with renal cell carcinoma could potentially be saved through early diagnosis."

The European Molecular Biology Laboratory's Wolfgang Huber and Lars Steinmetz and their colleagues in Germany described findings from genomic and transcriptomic sequencing analyses of HeLa cells in the journal G3: Genes, Genomes, Genetics. With the newly generated DNA and RNA sequence data, the team cataloged mutations, aneuplodies, and structural variations that exist in the model human cell line, which is derived from a cervical cancer tumor and has been grown in research labs since the 1950s.

In addition, through expression profiles provided by the RNA sequence data, the investigators pinpointed pathways in HeLa cells that show pronounced expression changes relative to cells in typical human tissues. In particular, they noted, HeLa cells seem to show higher-than-usual expression of DNA damage response-related genes and genes from other pathways contributing to cell cycle control, transcription, and translation.

"Our results provide the first detailed account of genomic variants in the HeLa genome, yielding insight into their impact on gene expression and cellular function as well as their origins," Huber, Steinmetz, and co-authors noted.

The group cautioned that the analysis "underscores the importance of accounting for the strikingly aberrant characteristics of HeLa cells when designing and interpreting experiments, and has implications for the use of HeLa as a model of human biology."

Contact sports such as roller derby can alter players' skin microbial communities, according to a study appearing in the journal PeerJ. Researchers based in Oregon, Arizona, and New Mexico used 16S ribosomal RNA gene sequencing to catalog microbiome community members present in skin swabs from players' upper arms before and after flat-track roller derby bouts.

Based on data on more than 80 samples collected from players on three teams over two roller derby bouts, the researchers found that individuals on the same teams — originating from Oregon, California, and Washington, DC — tended to have skin microbial communities that clustered more closely with one another than with the microbiomes of players on the other teams. But investigators also saw shifts in skin microbiomes following each roller derby bout, with upper arm skin microbial communities from players on each team becoming a bit more like those found on the opposing team.

"Our results are consistent with the hypothesis that the human skin microbiome shifts in composition during activities involving human to human contact," corresponding author James Meadow, with the University of Oregon's Institute of Ecology, and Evolution, and colleagues wrote, "and that contact sports provide an ideal setting in which to evaluate dispersal of microorganisms between people."

A Science study looked at how mutations within a lone locus in the genome can impact local adaptation and variation in animal traits. Researchers from the US and Switzerland turned to targeted enrichment and next-generation sequencing to assess variant profiles across the coat color-related Agouti locus in deer mice from a population in the Nebraska Sand Hills, exploring relationships between mouse color phenotypes and variants patterns in and around the locus. They also folded in findings from a field study that used clay mouse models to determine which coat colors are advantageous or detrimental in the Sand Hills environment.

The group's data indicates that haplotypes with ties to light color traits have been under selection in the Sand Hills mice — a notion that's consistent with field study results, which suggest light coloring provides protection from predators that rely on vision to hunt the mice. But the fair phenotype also appeared to be a consequence of multiple pigmentation traits stemming from a range of variants at the Agouti locus.

"[F]or each candidate SNP," authors of the study noted, "the stronger its effect on color phenotype, the stronger the estimate of selection strength, suggesting that these mutations likely have minimal pleiotropic consequences."

"These results, when combined with results from the clay model experiment, the extensive recombination across this region, and the association mapping, all support a scenario in which multiple independent Agouti mutations — each contributing to a distinct trait associated with the light phenotype — have been selected for cryptic coloration on the Sand Hills," they argued.

Genomics In The Journals is a weekly feature pointing readers to select, recently published articles involving genomics and related research.