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This Week in Clinical Cancer Research: Apr 13, 2012

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In Clinical Cancer Research this week, researchers in Canada report on the L1 cell adhesion molecule in non-small cell lung cancer. The team analyzed four independent, published mRNA expression datasets of primary non-small-cell lung cancers, and found that the molecule is an independent prognostic marker in resected cancer patients, with over-expression indicating a poor prognosis. "L1CAM downregulation significantly decreased cell motility and invasiveness in lung cancer cells and reduced tumor formation and growth in mice," the authors write. "Cells with L1CAM downregulation were deficient in constitutive extracellular signal–regulated kinase activation. Orthotopic studies showed that L1CAM suppression in highly metastatic lung cancer cells significantly decreases spread to distant organs, including bone and kidney."

Also in Clinical Cancer Research this week, researchers in the US and China explore the frequency of driver mutations in lung adenocarcinomas from female never smokers. The team genotyped 349 resected lung tumors from female never smokers and found that 266 harbored EGFR mutations, 16 had HER2 mutations, 15 had EML4-ALK fusions, seven had KRAS mutations, and two had BRAF mutations. "In univariate analysis, patients harboring EGFR mutations were significantly older, whereas patients harboring HER2 mutations were significantly younger," the authors write. "Higher prevalence of KRAS and HER2 mutations was found in invasive mucinous adenocarcinoma. The frequency of EGFR mutations was positively correlated with acinar predominant tumors."

Finally in Clinical Cancer Research this week, researchers in the US and Canada have identified RFC3 as an amplified candidate oncogene in esophageal cancer. "Whole genome tiling-path array comparative genomic hybridization was used to identify significant regions of copy number alteration in 20 [esophageal adenocarcinomas] and 10 matching [Barrett's esophagus] tissues," the authors write. "We identified RFC3 as a novel, candidate oncogene activated by amplification in approximately 25 percent of EAC samples."

The Scan

Study Points to Tuberculosis Protection by Gaucher Disease Mutation

A mutation linked to Gaucher disease in the Ashkenazi Jewish population appears to boost Mycobacterium tuberculosis resistance in a zebrafish model of the lysosomal storage condition, a new PNAS study finds.

SpliceVault Portal Provides Look at RNA Splicing Changes Linked to Genetic Variants

The portal, described in Nature Genetics, houses variant-related messenger RNA splicing insights drawn from RNA sequencing data in nearly 335,700 samples — a set known as the 300K-RNA resource.

Automated Sequencing Pipeline Appears to Allow Rapid SARS-CoV-2 Lineage Detection in Nevada Study

Researchers in the Journal of Molecular Diagnostics describe and assess a Clear Labs Dx automated workflow, sequencing, and bioinformatic analysis method for quickly identifying SARS-CoV-2 lineages.

UK Team Presents Genetic, Epigenetic Sequencing Method

Using enzymatic DNA preparation steps, researchers in Nature Biotechnology develop a strategy for sequencing DNA, along with 5-methylcytosine and 5-hydroxymethylcytosine, on existing sequencers.