Novel robust biomarkers for human bladder cancer based on activation of intracellular signaling pathways

Sherpa Romeo blue journal. Open access article. Creative Commons Attribution 3.0 License (CC BY 3.0) applies.We recently proposed a new bioinformatic algorithm called OncoFinder for quantifying the activation of intracellular signaling pathways. It was proved advantageous for minimizing errors of high-throughput gene expression analyses and showed strong potential for identifying new biomarkers. Here, for the first time, we applied OncoFinder for normal and cancerous tissues of the human bladder to identify biomarkers of bladder cancer. Using Illumina HT12v4 microarrays, we profiled gene expression in 17 cancer and seven non-cancerous bladder tissue samples. These experiments were done in two independent laboratories located in Russia and Canada. We calculated pathway activation strength values for the investigated transcriptomes and identified signaling pathways that were regulated differently in bladder cancer (BC) tissues compared with normal controls. We found, for both experimental datasets, 44 signaling pathways that serve as excellent new biomarkers of BC, supported by high area under the curve (AUC) values. We conclude that the OncoFinder approach is highly efficient in finding new biomarkers for cancer. These markers are mathematical functions involving multiple gene products, which distinguishes them from “traditional” expression biomarkers that only assess concentrations of single genes.Ye

New function of the myostatin/activin type I receptor (ALK4) as a mediator of muscle atrophy and muscle regeneration

Skeletal muscle fibrosis and impaired muscle regeneration are major contributors to muscle wasting in Duchenne muscular dystrophy (DMD). Muscle growth is negatively regulated by myostatin (MSTN) and activins. Blockage of these pathways may improve muscle quality and function in DMD. Antisense oligonucleotides (AONs) were designed specifically to block the function of ALK4, a key receptor for the MSTN/activin pathway in skeletal muscle. AON-induced exon skipping resulted in specific Alk4 down-regulation, inhibition of MSTN activity, and increased myoblast differentiation in vitro Unexpectedly, a marked decrease in muscle mass (10%) was found after Alk4 AON treatment in mdx mice. In line with in vitro results, muscle regeneration was stimulated, and muscle fiber size decreased markedly. Notably, when Alk4 was down-regulated in adult wild-type mice, muscle mass decreased even more. RNAseq analysis revealed dysregulated metabolic functions and signs of muscle atrophy. We conclude that ALK4 inhibition increases myogenesis but also regulates the tight balance of protein synthesis and degradation. Therefore, caution must be used when developing therapies that interfere with MSTN/activin pathways

Intrasubtype Reassortments Cause Adaptive Amino Acid Replacements in H3N2 Influenza Genes

<div><p>Reassortments and point mutations are two major contributors to diversity of Influenza A virus; however, the link between these two processes is unclear. It has been suggested that reassortments provoke a temporary increase in the rate of amino acid changes as the viral proteins adapt to new genetic environment, but this phenomenon has not been studied systematically. Here, we use a phylogenetic approach to infer the reassortment events between the 8 segments of influenza A H3N2 virus since its emergence in humans in 1968. We then study the amino acid replacements that occurred in genes encoded in each segment subsequent to reassortments. In five out of eight genes (NA, M1, HA, PB1 and NS1), the reassortment events led to a transient increase in the rate of amino acid replacements on the descendant phylogenetic branches. In NA and HA, the replacements following reassortments were enriched with parallel and/or reversing replacements; in contrast, the replacements at sites responsible for differences between antigenic clusters (in HA) and at sites under positive selection (in NA) were underrepresented among them. Post-reassortment adaptive walks contribute to adaptive evolution in Influenza A: in NA, an average reassortment event causes at least 2.1 amino acid replacements in a reassorted gene, with, on average, 0.43 amino acid replacements per evolving post-reassortment lineage; and at least ∼9% of all amino acid replacements are provoked by reassortments.</p></div

Phylogenetic distances from reassortments for different classes of amino acid replacements.

<p>The phylogenetic distances to the most recent ancestral RCB are compared between a given class of amino acid replacements and all remaining replacements. Classes that are significantly (p<0.05) closer to the most recent RCB are in boldface, and classes that are farther from RCB, in italic.</p

Reassortments involving NA.

<p>The 14 non-terminal, non-pre-terminal RCBs are shown. The table shows the observed and expected distances between the amino acid replacements and the preceding reassortment, and the Wilcoxon p-value for the difference between the observed and expected values. The RCBs are ordered by the Wilcoxon p-value.</p><p>^a Substitutions at phylogenetic distances up to 0.003 ds units after the reassortment.</p><p>^b Phylogenetically independent substitutions are such that none of them are descendant to any of the remaining ones.</p><p>^c Number of substitutions accumulated per lineage.</p><p>^d RCBs also described in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004037#pgen.1004037-Holmes1" target="_blank">[7]</a>.</p><p>^e RCBs confirmed by sampling times.</p

Characteristics of RCBs and amino acid replacements.

<p>The mean distances between the amino acid replacements and most recent RCBs that were significantly (p<0.05) lower than expected are in boldface.</p><p>Pre-terminal branches are those immediately ancestral to the terminal branches.</p