An integrated genomic analysis of lung cancer reveals loss of DUSP4 in EGFR-mutant tumors.

To address the biological heterogeneity of lung cancer, we studied 199 lung adenocarcinomas by integrating genome-wide data on copy number alterations and gene expression with full annotation for major known somatic mutations in this cancer. This showed non-random patterns of copy number alterations significantly linked to EGFR and KRAS mutation status and to distinct clinical outcomes, and led to the discovery of a striking association of EGFR mutations with underexpression of DUSP4, a gene within a broad region of frequent single-copy loss on 8p. DUSP4 is involved in negative feedback control of EGFR signaling, and we provide functional validation for its role as a growth suppressor in EGFR-mutant lung adenocarcinoma. DUSP4 loss also associates with p16/CDKN2A deletion and defines a distinct clinical subset of lung cancer patients. Another novel observation is that of a reciprocal relationship between EGFR and LKB1 mutations. These results highlight the power of integrated genomics to identify candidate driver genes within recurrent broad regions of copy number alteration and to delineate distinct oncogenetic pathways in genetically complex common epithelial cancers

Protein interaction mapping with ribosome-displayed using PLATO ORF libraries

Identifying physical interactions between proteins and other molecules is a critical aspect of biological analysis. Here we describe PLATO, an in vitro method for mapping such interactions by affinity enrichment of a library of full-length open reading frames displayed on ribosomes, followed by massively parallel analysis using DNA sequencing. We demonstrate the broad utility of the method by identifying known and new interacting partners of LYN kinase, patient autoantibodies and the small molecules gefitinib and dasatinib

Lean and obese Zucker rats exhibit different patterns of p70s6 kinase regulation in the tibialis anterior muscle in response to high-force muscle contraction

Increased phosphorylation of the 70-kDa ribosomal S6 kinase (p70S6k) signaling is strongly correlated with the degree of muscle adaptation following exercise. Herein we compare the phosphorylation of p70S6k, Akt, and mammalian target of rapamycin (mTOR) in the tibialis anterior (TA) muscles of lean and obese Zucker rats following a bout of eccentric exercise. Exercise increased p70S6k (Thr389) phosphorylation immediately after (33.3 ± 7.2%) and during [1 h (24.0 ± 14.9%) and 3 h (24.6 ± 11.3%)] recovery in the lean TA and at 3 h (33.5 ± 8.0%) in the obese TA Zucker rats. mTOR (Ser2448) phosphorylation was elevated in the lean TA immediately after exercise (96.5 ± 40.3%) but remained unaltered in the obese TA. Exercise increased Akt (Thr308) and Akt (Ser473) phosphorylation in the lean but not the obese TA. These results suggest that insulin resistance is associated with alterations in the ability of muscle to activate p70S6k signaling following an acute bout of exercise. Muscle Nerve 39: 503–511 2009. Type 2 (non–insulin-dependent) diabetes mellitus (DM) is an emerging epidemic in Western cultures, and it is believed to afflict 150 million people worldwide.11 Insulin resistance is frequently accompanied by a variety of metabolic and cardiovascular abnormalities, including hypertension, glucose intolerance, type 2 diabetes, dyslipidemia, atherosclerosis, and central obesity. A number of studies that employ strength training regimens have been shown to improve glycemic control, increase skeletal muscle size and strength, and positively change body composition. The data suggest that anaerobic exercise may be an effective strategy for the treatment of insulin resistance and type 2 diabetes.6, 7, 49, 53 Recent reports have suggested that differences exist between normal and insulin-resistant muscle in their adaptation to an exercise regimen.5, 8, 20, 24, 48, 50 However, the direct effects of exercise on the phenotype of insulin-resistant muscle have not been widely studied. It is thought that the beneficial effects of exercise on muscle are mediated through activation of the various signaling cascades involved in regulating changes in gene expression, glucose uptake, and protein synthesis.2Whether insulin resistance alters exercise-induced signal transduction processes in muscle is unknown, but the differences, if present, may help to explain why exercise-induced skeletal muscle adaptations can differ between normal and insulin-resistant populations. It is well established that increased muscle loading increases the rates of muscle protein synthesis.27 This increase in protein synthesis, at least in part, is thought to be regulated by the phosphorylation of the p70 ribosomal protein S6 kinase (p70S6k),26 whose activation has been proposed to promote increased translation of messages that have a polypyrimide motif just downstream of the 5′ cap.45 It is believed that p70S6k activity is regulated by the mammalian target of rapamycin (mTOR), which functions as a growth factor and nutrient-sensing signaling molecule in mammalian cells.40 How mTOR activity is modulated is not clear; however, recent evidence suggests that mTOR is controlled by Akt or protein kinase B (PKB), which is activated in response to phospholipid products of the phosphatidylinositol 3-kinase (PI3K) reaction. It is well documented that binding of insulin to the membrane receptor stimulates a cascade of phosphorylation events resulting in activation of PI3K. It is likely that PKB/Akt directly increases mTOR activity by phosphorylating mTOR at Ser2448, and it has been hypothesized that this event is a critical point of control in the regulation of protein synthesis.4 It has been postulated that p70S6k signaling may be particularly important in mediating muscle adaptation given that the phosphorylation of this molecule following an exercise bout has been found to be strongly associated with the increase in muscle weight after 6 weeks of chronic stimulation. The purpose of the present study was to determine whether insulin resistance alters p70S6k signaling after an acute episode of contractile activity. To investigate this possibility, muscle signaling was examined in 12-week-old lean and obese Zucker rats, as it is widely accepted that the insulin resistance exhibited by these animals closely models the development of type 2 diabetes seen in humans.3, 18, 25, 39 We hypothesized that insulin resistance would be associated with differences in how muscle contraction regulates the phosphorylation of the Akt/TOR/p70S6k signaling cascade. To test this hypothesis, the contraction-mediated activation of Akt, mTOR, and p70S6k was assessed either immediately after or 1 or 3 h after a single bout of sciatic nerve stimulation. Taken together, our data suggest that insulin resistance alters contraction-induced p70S6k phosphorylation in skeletal muscle. These findings are consistent with the possibility that insulin resistance alters the way skeletal muscle “senses and responds” to contractile stimuli

Induction of BIM Is Essential for Apoptosis Triggered by EGFR Kinase Inhibitors in Mutant EGFR-Dependent Lung Adenocarcinomas

Using a panel of human drug-sensitive EGFR mutant lung cancer cells, William Pao and colleagues show that induction of BIM, a member of the BCL2 family, is essential for apoptosis triggered by EGFR kinase inhibitors

gRASping the redox lever to modulate cancer cell fate signaling

RAS proteins are critical regulators of signaling networks controlling diverse cellular functions such as cell proliferation and survival and its mutation are among the most powerful oncogenic drivers in human cancers. Despite intense efforts, direct RAS-targeting strategies remain elusive due to its “undruggable” nature. To that end, bulk of the research efforts has been directed towards targeting upstream and/or downstream of RAS signaling. However, the therapeutic efficacies of these treatments are limited in the long run due to the acquired drug resistance in RAS-driven cancers. Interestingly, recent studies have uncovered a potential role of RAS in redox-regulation as well as the interplay between ROS and RAS-associated signaling networks during process of cancer initiation and progression. More specifically, these studies provide ample evidence to implicate RAS as a redox-rheostat, manipulating ROS levels to provide a redox-milieu conducive for carcinogenesis. Importantly, the understanding of RAS-ROS interplay could provide us with novel targetable vulnerabilities for designing therapeutic strategies. In this review, we provide a brief summary of the advances in the field to illustrate the dual role of RAS in redox-regulation and its implications in RAS signaling outcomes and also emerging redox-based strategies to target RAS-driven cancers

Function-Based Discovery of Significant Transcriptional Temporal Patterns in Insulin Stimulated Muscle Cells

Background: Insulin action on protein synthesis (translation of transcripts) and post-translational modifications, especially of those involving the reversible modifications such as phosphorylation of various signaling proteins, are extensively studied but insulin effect on transcription of genes, especially of transcriptional temporal patterns remains to be fully defined. Methodology/Principal Findings: To identify significant transcriptional temporal patterns we utilized primary differentiated rat skeletal muscle myotubes which were treated with insulin and samples were collected every 20 min for 8 hours. Pooled samples at every hour were analyzed by gene array approach to measure transcript levels. The patterns of transcript levels were analyzed based on a novel method that integrates selection, clustering, and functional annotation to find the main temporal patterns associated to functional groups of differentially expressed genes. 326 genes were found to be differentially expressed in response to in vitro insulin administration in skeletal muscle myotubes. Approximately 20 % of the genes that were differentially expressed were identified as belonging to the insulin signaling pathway. Characteristic transcriptional temporal patterns include: (a) a slow and gradual decrease in gene expression, (b) a gradual increase in gene expression reaching a peak at about 5 hours and then reaching a plateau or an initial decrease and other different variable pattern of increase in gene expression over time. Conclusion/Significance: The new method allows identifying characteristic dynamic responses to insulin stimulus, commo

An overview of technical considerations for Western blotting applications to physiological research

The applications of Western/immuno-blotting (WB) techniques have reached multiple layers of the scientific community and are now considered routine procedures in the field of physiology. This is none more so than in relation to skeletal muscle physiology (i.e. resolving the mechanisms underpinning adaptations to exercise). Indeed, the inclusion of WB data is now considered an essential aspect of many such physiological publications to provide mechanistic insight into regulatory processes. Despite this popularity, and due to the ubiquitous and relatively inexpensive availability of WB equipment, the quality of WB in publications and subsequent analysis and interpretation of the data can be variable, perhaps resulting in spurious conclusions. This may be due to poor laboratory technique and/or lack of comprehension of the critical steps involved in WB and what quality control procedures should be in place to ensure robust data generation. The present review aims to provide a detailed description and critique of WB procedures and technicalities, from sample collection through preparation, blotting and detection to analysis of the data collected. We aim to provide the reader with improved expertise to critically conduct, evaluate and troubleshoot the WB process, to produce reproducible and reliable blots

A Serum Factor Induces Insulin-Independent Translocation of GLUT4 to the Cell Surface which Is Maintained in Insulin Resistance

In response to insulin, glucose transporter GLUT4 translocates from intracellular compartments towards the plasma membrane where it enhances cellular glucose uptake. Here, we show that sera from various species contain a factor that dose-dependently induces GLUT4 translocation and glucose uptake in 3T3-L1 adipocytes, human adipocytes, myoblasts and myotubes. Notably, the effect of this factor on GLUT4 is fully maintained in insulin-resistant cells. Our studies demonstrate that the serum-induced increase in cell surface GLUT4 levels is not due to inhibition of its internalization and is not mediated by insulin, PDGF, IGF-1, or HGF. Similarly to insulin, serum also augments cell surface levels of GLUT1 and TfR. Remarkably, the acute effect of serum on GLUT4 is largely additive to that of insulin, while it also sensitizes the cells to insulin. In accordance with these findings, serum does not appear to activate the same repertoire of downstream signaling molecules that are implicated in insulin-induced GLUT4 translocation. We conclude that in addition to insulin, at least one other biological proteinaceous factor exists that contributes to GLUT4 regulation and still functions in insulin resistance. The challenge now is to identify this factor