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Signaling pathways oversee highly efficient cellular mechanisms such as growth, division, and death. These processes are controlled by robust negative feedback loops that inhibit receptor-mediated growth factor pathways. Specifically, the ERK, the AKT, and the S6K feedback loops attenuate signaling via growth factor receptors and other kinase receptors to regulate cell growth. Irregularity in any of these supervised processes can lead to uncontrolled cell proliferation and possibly Cancer. These irregularities primarily occur as mutated genes, and an exhaustive search of the perfect drug combination by performing experiments can be both costly and complex. Hence, in this paper, we model the Lung Cancer pathway as a Modified Boolean Network that incorporates feedback. By simulating this network, we theoretically predict the drug combinations that achieve the desired goal for the majority of mutations. Our theoretical analysis identifies Cryptotanshinone, a traditional Chinese herb derivative, as a potent drug component in the fight against cancer. We validated these theoretical results using multiple wet lab experiments carried out on H2073 and SW900 lung cancer cell lines.

Background Several studies have highlighted both the extreme anticancer effects of Cryptotanshinone (CT), a Stat3 crippling component from Salvia miltiorrhiza, as well as other STAT3 inhibitors to fight cancer. Methods Data presented in this experiment incorporates 2 years of in vitro studies applying a comprehensive live-cell drug-screening analysis of human and canine cancer cells exposed to CT at 20 μM concentration, as well as to other drug combinations. As previously observed in other studies, dogs are natural cancer models, given to their similarity in cancer genetics, epidemiology and disease progression compared to humans. Results Results obtained from several types of human and canine cancer cells exposed to CT and varied drug combinations, verified CT efficacy at combating cancer by achieving an extremely high percentage of apoptosis within 24 hours of drug exposure. Conclusions CT anticancer efficacy in various human and canine cancer cell lines denotes its ability to interact across different biological processes and cancer regulatory cell networks, driving inhibition of cancer cell survival.

Colorectal cancer (CRC) is one of the most prevalent types of cancer in the world and ranks second in cancer deaths in the US. Despite the recent improvements in screening and treatment, the number of deaths associated with CRC is still very significant. The complexities involved in CRC therapy stem from multiple oncogenic mutations and crosstalk between abnormal pathways. This calls for using advanced molecular genetics to understand the underlying pathway interactions responsible for this cancer. In this paper, we construct the CRC pathway from the literature and using an existing public dataset on healthy vs tumor colon cells, we identify the genes and pathways that are mutated and are possibly responsible for the disease progression. We then introduce drugs in the CRC pathway, and using a boolean modeling technique, we deduce the drug combinations that produce maximum cell death. Our theoretical simulations demonstrate the effectiveness of Cryptotanshinone, a traditional Chinese herb derivative, achieved by targeting critical oncogenic mutations and enhancing cell death. Finally, we validate our theoretical results using wet lab experiments on HT29 and HCT116 human colorectal carcinoma cell lines.

Osteosarcoma (OS) is the most common primary malignant bone tumor of both children and pet canines. Its characteristic genomic instability and complexity coupled with the dearth of knowledge about its etiology has made improvement in the current treatment difficult. We use the existing literature about the biological pathways active in OS and combine it with the current research involving natural compounds to identify new targets and design more effective drug therapies. The key components of these pathways are modeled as a Boolean network with multiple inputs and multiple outputs. The combinatorial circuit is employed to theoretically predict the efficacies of various drugs in combination with Cryptotanshinone. We show that the action of the herbal drug, Cryptotanshinone on OS cell lines induces apoptosis by increasing sensitivity to TNF-related apoptosis-inducing ligand (TRAIL) through its multi-pronged action on STAT3, DRP1 and DR5. The Boolean framework is used to detect additional drug intervention points in the pathway that could amplify the action of Cryptotanshinone.

Colorectal cancer (CRC) is one of the most prevalent types of cancer in the world and ranks second in cancer deaths in the US. Despite the recent improvements in screening and treatment, the number of deaths associated with CRC is still very significant. The complexities involved in CRC therapy stem from multiple oncogenic mutations and crosstalk between abnormal pathways. This calls for using advanced molecular genetics to understand the underlying pathway interactions responsible for this cancer. In this paper, we construct the CRC pathway from the literature and using an existing public dataset on healthy vs tumor colon cells, we identify the genes/pathways that are mutated and are possibly responsible for the disease progression. We then introduce drugs in the CRC pathway, and using a boolean modeling technique, we deduce the drug combinations that produce maximum cell death. Our theoretical simulations demonstrate the effectiveness of Cryptotanshinone, a traditional Chinese herb derivative, achieved by targeting critical oncogenic mutations and enhancing cell death. Finally, we validate our theoretical results using wet lab experiments on HT29 and HCT116 human colorectal carcinoma cell lines.

Background: Osteosarcoma (OS) is the most common primary bone tumor in both humans and canines. This tumor has an aggressive course leading to the development of metastatic lesions in most patients diagnosed with this disease. Two new novel agents, MLN9708 and SH4-54, work as a proteasome inhibitor and a STAT3 inhibitor, respectively. Targets of these drugs have been shown to be overexpressed in OS in both species. Methods: Two human and two canine OS cell lines were exposed in vitro to both drugs alone and in combination. The number of cells undergoing apoptosis, as well as the number of cells capable of invasion through a matrigel basement membrane was evaluated after exposure to the drugs. Additionally, PCR and Western blots of downstream targets were evaluated. Finally, both drugs were tested against each cell line in an in vivo murine xenograft model. Results: All four cell lines were sensitive to MLN9708, one of the human cell lines and both canine cell lines were resistant to SH4-54. MLN9708 was also better at inhibiting invasion in three of the four cell lines. In the murine xenografts MLN9708 inhibited growth and metastasis in 143B (human OS) and the combination inhibited growth in the canine OS cell line (MCKOS). Conclusions: Though SH4-54 demonstrated robust cell killing in 143B in vitro, MLN9708 demonstrated broader activity across species for the treatment of OS. Further investigation into this drug is warranted as a treatment for OS. Combination of this drug with a STAT3 inhibitor may be worthwhile in canine OS.

BackgroundSeveral studies have highlighted both the extreme anticancer effects of Cryptotanshinone (CT), a Stat3 crippling component from Salvia miltiorrhiza, as well as other STAT3 inhibitors to fight cancer.MethodsData presented in this experiment incorporates 2 years of in vitro studies applying a comprehensive live-cell drug-screening analysis of human and canine cancer cells exposed to CT at 20 μM concentration, as well as to other drug combinations. As previously observed in other studies, dogs are natural cancer models, given to their similarity in cancer genetics, epidemiology and disease progression compared to humans.ResultsResults obtained from several types of human and canine cancer cells exposed to CT and varied drug combinations, verified CT efficacy at combating cancer by achieving an extremely high percentage of apoptosis within 24 hours of drug exposure.ConclusionsCT anticancer efficacy in various human and canine cancer cell lines denotes its ability to interact across different biological processes and cancer regulatory cell networks, driving inhibition of cancer cell survival.

Background Metastatic melanoma is an aggressive form of skin cancer that evades various anti-cancer treatments including surgery, radio-,immuno- and chemo-therapy. TRAIL-induced apoptosis is a desirable method to treat melanoma since, unlike other treatments, it does not harm non-cancerous cells. The pro-inflammatory response to melanoma by nF κB and STAT3 pathways makes the cancer cells resist TRAIL-induced apoptosis. We show that due to to its dual action on DR5, a death receptor for TRAIL and on STAT3, Cryptotanshinone can be used to increase sensitivity to TRAIL. Methods The development of chemoresistance and invasive properties in melanoma cells involves several biological pathways. The key components of these pathways are represented as a Boolean network with multiple inputs and multiple outputs. Results The possible mutations in genes that can lead to cancer are captured by faults in the combinatorial circuit and the model is used to theoretically predict the effectiveness of Cryptotanshinone for inducing apoptosis in melanoma cell lines. This prediction is experimentally validated by showing that Cryptotanshinone can cause enhanced cell death in A375 melanoma cells. Conclusion The results presented in this paper facilitate a better understanding of melanoma drug resistance. Furthermore, this framework can be used to detect additional drug intervention points in the pathway that could amplify the action of Cryptotanshinone. Electronic supplementary material The online version of this article (10.1186/s12885-018-4756-0) contains supplementary material, which is available to authorized users.

Metformin, a widely used anti-diabetic drug, has recently been associated with inhibition of cell proliferation in multiple cancers. However, it is not clear if the reduction in proliferation on treatment with metformin is a result of cell death or slowdown in the rate of growth of cancer cells, because cell viability assays measure only the number of cells at the beginning and end of the experiment. The aim of this study is to utilize a fluorescent imaging technique to directly follow cell death overtime in order to investigate the effect of metformin on colorectal cancer cells HCT116 and SW480. Epifluorescent imaging analysis carried out using ImageXpress Micro XLS High-Content Imaging System show that there is no significant change in cell death observed in the cancer cell lines, as compared to the control, over multiple closely spaced time points, suggesting that metformin in pharmacological doses may not be an effective inducer of cell death in these colon cancer cell lines.

Cell-based high-content screening (HCS) assays have become an increasingly attractive alternative to traditional in vitro and in vivo testing in pharmaceutical drug development and toxicological safety assessment. The time- and cost-effectiveness of HCS assays, combined with the organotypic nature of human induced pluripotent stem cell (iPSC)-derived cells, open new opportunities to employ physiologically relevant in vitro model systems to improve screening for potential chemical hazards. In this study, we used two human iPSC types, cardiomyocytes and hepatocytes, to test various high-content and molecular assay combinations for their applicability in a multiparametric screening format. Effects on cardiomyocyte beat frequency were characterized by calcium flux measurements for up to 90 min. Subsequent correlation with intracellular cAMP levels was used to determine if the effects on cardiac physiology were G-protein-coupled receptor dependent. In addition, we utilized high-content cell imaging to simultaneously determine cell viability, mitochondrial integrity, and reactive oxygen species (ROS) formation in both cell types. Kinetic analysis indicated that ROS formation is best detectable 30 min following initial treatment, whereas cytotoxic effects were most stable after 24 h. For hepatocytes, high-content imaging was also used to evaluate cytotoxicity and cytoskeletal integrity, as well as mitochondrial integrity and the potential for lipid accumulation. Lipid accumulation, a marker for hepatic steatosis, was most reliably detected 48 h following treatment with test compounds. Overall, our results demonstrate how a compendium of assays can be utilized for quantitative screening of chemical effects in iPSC cardiomyocytes and hepatocytes and enable rapid and cost-efficient multidimensional biological profiling of toxicity.

Background Cancer Tissue Heterogeneity is an important consideration in cancer research as it can give insights into the causes and progression of cancer. It is known to play a significant role in cancer cell survival, growth and metastasis. Determining the compositional breakup of a heterogeneous cancer tissue can also help address the therapeutic challenges posed by heterogeneity. This necessitates a low cost, scalable algorithm to address the challenge of accurate estimation of the composition of a heterogeneous cancer tissue. Methods In this paper, we propose an algorithm to tackle this problem by utilizing the data of accurate, but high cost, single cell line cell-by-cell observation methods in low cost aggregate observation method for heterogeneous cancer cell mixtures to obtain their composition in a Bayesian framework. Results The algorithm is analyzed and validated using synthetic data and experimental data. The experimental data is obtained from mixtures of three separate human cancer cell lines, HCT116 (Colorectal carcinoma), A2058 (Melanoma) and SW480 (Colorectal carcinoma). Conclusion The algorithm provides a low cost framework to determine the composition of heterogeneous cancer tissue which is a crucial aspect in cancer research.

Oxidative stress in spermatozoa has effects on subsequent embryo development. The aim of the present study was to elucidate whether sperm oxidative stress results in increased DNA damage in the embryo. To this end, bovine spermatozoa were incubated for 1 h at 37°C without or with 100 µM H2O2, resulting in non-oxidised (NOX-S) and oxidised (OX-S) spermatozoa respectively. Non-incubated spermatozoa served as the control group (CON-S). After IVF, developmental rates 30, 46 and 60 h and 7 days after IVF were assessed. DNA damage was analysed in embryos using the comet assay and a DNA damage marker (γH2AX immunostaining); the apoptotic index was determined in blastocysts. Exposure of spermatozoa to H2O2 induced a significant amount of sperm chromatin damage. The use of OX-S in IVF resulted in significantly reduced cleavage and blastocyst rates compared with the use of CON-S and NOX-S. Furthermore, in embryos resulting from the use of OX-S, a developmental delay was evident 30 and 46 h after IVF. γH2AX immunostaining was lower in blastocysts than in early embryos. In blastocysts, the comet and apoptotic indices were significantly higher in embryos resulting from the use of OX-S than CON-S and NOX-S. In conclusion, oxidative stress in spermatozoa induces developmental abnormalities and is a source of DNA damage in the resulting embryos.

Theoretical analyses suggest that the regularities indicative of holistic processing can be obtained by combinations of perceptual and decisional factors. Kuefner and colleagues used electrophysiological results to suggest that the composite face effect is driven solely by perceptual factors. Two limitations of their approach are (a) it did not involve behavioral measures of perceptual sensitivity or bias, and (b) it is unclear how the measures used in that study are consistent with other measures of perceptual and decisional processing. Eight observers completed three tasks involving the stimuli used by Kuefner et al.. The first was a direct replication. The second was a complete identification task, associated with the perceptual and decisional distinctions formalized in general recognition theory. The third was an implementation of the Eriksen fianker task, which allows for a pattern of results that have been interpreted in terms of perceptual and decisional influences. While the empirical distinctions used by Kuefner et al. were not consistent with either the EEG data from the other tasks or the established behavioral measures of perceptual sensitivity and decisional bias, the inferences drawn from the EEG and behavioral data from those tasks were consistent with one another, underscoring the importance of converging operations.

Insensitivity to standard clinical interventions, including chemotherapy, radiotherapy, and tyrosine kinase inhibitor (TKI) treatment, remains a substantial hindrance towards improving the prognosis of patients with non–small cell lung cancer (NSCLC). The molecular mechanism of therapeutic resistance remains poorly understood. The TNF-like weak inducer of apoptosis (TWEAK)–FGF-inducible 14 (TNFRSF12A/Fn14) signaling axis is known to promote cancer cell survival via NF-κB activation and the upregulation of prosurvival Bcl-2 family members. Here, a role was determined for TWEAK–Fn14 prosurvival signaling in NSCLC through the upregulation of myeloid cell leukemia sequence 1 (MCL1/Mcl-1). Mcl-1 expression significantly correlated with Fn14 expression, advanced NSCLC tumor stage, and poor patient prognosis in human primary NSCLC tumors. TWEAK stimulation of NSCLC cells induced NF-κB–dependent Mcl-1 protein expression and conferred Mcl-1–dependent chemo- and radioresistance. Depletion of Mcl-1 via siRNA or pharmacologic inhibition of Mcl-1, using EU-5148, sensitized TWEAK-treated NSCLC cells to cisplatin- or radiation-mediated inhibition of cell survival. Moreover, EU-5148 inhibited cell survival across a panel of NSCLC cell lines. In contrast, inhibition of Bcl-2/Bcl-xL function had minimal effect on suppressing TWEAK-induced cell survival. Collectively, these results position TWEAK–Fn14 signaling through Mcl-1 as a significant mechanism for NSCLC tumor cell survival and open new therapeutic avenues to abrogate the high mortality rate seen in NSCLC. Implications: The TWEAK–Fn14 signaling axis enhances lung cancer cell survival and therapeutic resistance through Mcl-1, positioning both TWEAK–Fn14 and Mcl-1 as therapeutic opportunities in lung cancer. Mol Cancer Res; 12(4); 550–9. ©2014 AACR.

Vulvovaginal candidiasis (VVC) affects a significant number of women, especially in working age. In an estimated 75% of women an episode of acute vulvovaginal candidiasis occurs during lifetime and another 5–10% of women develop recurrent vulvovaginal candidiasis (RVVC). This is mainly characterized by intense burning, itching, pain, abnormal discharge, dyspareunia. Immune response to candidiasis is both cellular (CMI) (natural protection mechanisms) and humoral (antibody production). Understanding the principles of immunity in candidiasis is also important for development of candida vaccines.CANDIVAC contains lyophilized Candida lysate (C. albicans, C. krusei, C. glabrata) together with immunostimulatory bacterial strain of Propionibacterium acnes. The product is taken orally in capsules for 10 days followed by a 20-day pause. It is administered for 3 to 6 months. The product has been tested in a total of 75 women at the age of 18–45 years. In these women at least 4 episodes of vulvovaginal candidiasis have been microscopically or laboratory diagnosed during the last 12 months. Following CANDIVAC administration, statistically significant changes occurred in the evaluation of subjective and some objective criteria. The most important marker of product efficiency is a significant reduction in recurrence compared to the recent state. This criterion has a fundamental importance in patient satisfaction. Before medication the patients suffered from at least 4 attacks, while after medication an attack occurred in only 31% of women and more than 2 attacks in only 3% of treated women.Compromised balance of immune system plays a major role in recurrent vulvovaginal candidiasis. Specific oral product CANDIVAC, prepared from the most common strains of yeast infections, supports immune mechanisms, ensuring resistance of the human organism against yeasts. Its administration significantly prolongs remission, leads to a reduction in application of antimycotics and also changes properties of cellular and humoral immunity in medicated patients.

Two issues are critical to the development of effective cancer-drug combinations. First, it is necessary to determine common combinations of alterations that exert strong control over proliferation and survival regulation for the general type of cancer being considered. Second, it is necessary to have a drug testing method that allows one to assess the variety of responses that can be provoked by drugs acting at key points in the cellular processes dictating proliferation and survival. Utilizing a previously reported GFP (green fluorescent protein) reporter-based technology that provides dynamic measurements of individual reporters in individual cells, the present paper proposes a dynamical systems approach to these issues. It involves a three-state experimental design: (1) formulate an oncologic pathway model of relevant processes; (2) perturb the pathways with the test drug and drugs with known effects on components of the pathways of interest; and (3) measure process activity indicators at various points on cell populations. This design addresses the fundamental problems in the design and analysis of combinatorial drug treatments. We apply the dynamical approach to three issues in the context of colon cancer cell lines: (1) identification of cell subpopulations possessing differing degrees of drug sensitivity; (2) the consequences of different drug dosing strategies on cellular processes; and (3) assessing the consequences of combinatorial versus monotherapy. Finally, we illustrate how the dynamical systems approach leads to a mechanistic hypothesis in the colon cancer HCT116 cell line.

Tumor heterogeneity has been increasingly recognized as one of the potentially contributing factors in explaining drug resistance. In order to gain better understanding of heterogeneous cancer cell populations and different cells' responses to various drugs, we use fluorescent proteins to mark the cells and a live-cell dynamic imaging platform to collect cell-by-cell measurements. After addressing the issue of fluorescent reporter variance in a Bayesian inference framework, we decompose the different cell types in the mixture and calculate their proportions and counts over time responding to different drug treatments. Additionally, the drug response as characterized by the cell death rate was also computed for these cells, and their different sensitivity was demonstrated. Overall, this work represents an important advancement toward evaluating cancer heterogeneity and drug responses in heterogeneous cancer cell populations.

Background Angular deformity is the most common complication of supracondylar humerus fracture. Baumann's angle (BA) is an established radiographic measure of coronal plane deformity after this injury. Numerous radiographic methods have been used to assess sagittal plane deformity, however, the mean, variability, and reliability of these measures has not been established. The purpose of this study was to determine the mean, SD, and intraobserver/interobserver reliability of the lateral capitellohumeral angle (LCHA) in children without evidence of fracture and compare them with those of BA. Methods Seventy-one sets of anteroposterior and lateral elbow radiographs were selected and stratified into 6-year age categories with equal number of males and females in each category. Five physicians performed 3 separate measurements of LCHA and BA on each film set. Statistical calculations were performed to determine mean, SD, measurement reliability, and differences between patients groups. Results The mean LCHA ±1 SD and BA ± 1 SD measurements were 50.8 ± 6 degrees and 71.5 ± 6.2 degrees, respectively, and did not vary significantly by age, side, or sex (P>0.05). The LCHA showed good intraobserver (correlation coefficient 0.67) and fair interobserver (0.37) reliability, whereas BA showed excellent intraobserver (0.86) and interobserver (0.80) reliability. The expected SD for repeated measurement of a radiograph by a single observer was 2.6 degrees for BA and 5.2 degrees for LCHA. Conclusions The LCHA is a simple measurement to perform using digital tools. In normal elbows, the mean angle is 51 ± 6 degrees and does not vary by age, side, or sex. LCHA variability in normal elbow radiographs is similar to BA. Its reliability is inferior to BA, but improves with age. Sagittal angulation abnormality of at least 12 degrees ( 63 degrees) is necessary to be confident that the change is not because of measurement error alone. Further research is needed to better define the relationship of sagittal plane angular deformity to clinical outcome. Level of evidence Diagnostic study with poor reference standard, Level IV.

This paper proposes a framework to study the drug effect at the molecular level in order to address the following question of current interest in the drug community: Given a fixed total delivered drug, which is better, frequent small or infrequent large drug dosages? A hybrid system model is proposed to link the drug's pharmacokinetic and pharmacodynamic information, and allows the drug effects for different dosages and treatment schedules to be compared. A hybrid model facilitates the modeling of continuous quantitative changes that leads to discrete transitions. An optimal dosage-frequency regimen and the necessary and sufficient conditions for the drug to be effective are obtained analytically when the drug is designed to control a target gene. Then, we extend the analysis to the case where the target gene is part of a genetic regulatory network. A crucial observation is that there exists a "sweet spot," defined as the "drug efficacy region (DER)" in this paper, for certain dosage and frequency arrangements given the total delivered drug. This paper quantifies the therapeutic benefits of dosage regimen lying within the DER. Simulations are performed using MATLAB/SIMULINK to validate the analytical results.

Summary. Background: Patients with cystic fibrosis (CF) frequently experience pulmonary exacerbations that may lead to a faster subsequent decline in pulmonary function; however, this relationship has not been clearly established. The purpose of this study was to determine the association between the frequency of pulmonary exacerbations and subsequent forced expiratory volume in 1 sec (FEV1) decline in adults and children with CF. Methods: Cohort study of subjects followed in the Cystic Fibrosis Foundation Patient Registry from 2003 through 2006. Mixed effects modeling was used to estimate differences in rates of decline in FEV1 in 2004‐2006 for patients with 0, 1, 2, or 3þ pulmonary exacerbation(s) in 2003. Results: Of 8,490 subjects who met inclusion criteria, 60% had 0 exacerbations, 23% had 1, 10% had 2, and 7% had 3þ exacerbations in 2003. Compared to children with no pulmonary exacerbations in 2003, children with one or more exacerbations experienced a significantly (P < 0.001) greater rate of FEV1 decline in 2004‐2006. In contrast, among adults, only those with 3þ exacerbations in 2003 had a significantly (P ¼ 0.01) greater rate of FEV1 decline in 2004‐2006 than those with no exacerbations in 2003. Conclusions: There is a strong association between the frequency of pulmonary exacerbations and subsequent decline in pulmonary function. In adults, having 3þ exacerbations, and among children, having any exacerbations is associated with a greater rate of decline in the ensuing 3 years. Improved prevention, identification, and treatment of pulmonary exacerbations are likely to have long-term benefits for patients with CF, especially children. Pediatr

Patients with cystic fibrosis periodically experience pulmonary exacerbations. Previous studies have noted that some patients' lung function (FEV(1)) does not improve with treatment.To determine the proportion of patients treated for a pulmonary exacerbation that does not recover to spirometric baseline, and to identify factors associated with the failure to recover to spirometric baseline.Cohort study using the Cystic Fibrosis Foundation Patient Registry from 2003-2006. We randomly selected one pulmonary exacerbation treated with intravenous antibiotics per patient and compared the best FEV(1) in the 3 months after treatment with the best FEV(1) in the 6 months before treatment. Recovery to baseline was defined as any FEV(1) in the 3 months after treatment that was greater than or equal to 90% of the baseline FEV(1). Multivariable logistic regression was used to estimate associations with the failure to recover to baseline FEV(1).Of 8,479 pulmonary exacerbations, 25% failed to recover to baseline FEV(1). A higher risk of failing to recover to baseline was associated with female sex; pancreatic insufficiency; being undernourished; Medicaid insurance; persistent infection with Pseudomonas aeruginosa, Burkholderia cepacia complex, or methicillin-resistant Staphylococcus aureus; allergic bronchopulmonary aspergillosis; a longer time since baseline spirometric assessment; and a larger drop in FEV(1) from baseline to treatment initiation.For a randomly selected pulmonary exacerbation, 25% of patients' pulmonary function did not recover to baseline after treatment with intravenous antibiotics. We identified factors associated with the failure to recover to baseline, allowing clinicians to identify patients who may benefit from closer monitoring and more aggressive treatment.

Objective To measure the abilities of the continuous measures of disease activity used in rheumatoid arthritis (RA) and the 3 versions of the Juvenile Arthritis Disease Activity Score (JADAS; based upon 10-, 27-, and 71-joint counts) to accurately classify the American College of Rheumatology (ACR) pediatric measures of response, flare, and inactive disease in polyarticular-course juvenile idiopathic arthritis (JIA). Methods We conducted a secondary analysis of a randomized trial of infliximab in polyarticular-course JIA. Disease activity was calculated at baseline and weeks 14, 28, and 52 using the Disease Activity Score (DAS), DAS in 28 joints, Simplified Disease Activity Index, Clinical Disease Activity Index, and JADAS. The ability of the RA measures and JADAS to classify each ACR pediatric measure, flare, and inactive disease was measured by areas under the receiver operating characteristic curve (AUCs). Positive predictive values (PPVs) for inactive disease were calculated. Results Data from 97 participants were available. The AUCs for the RA scores for each ACR pediatric measure were 0.73–0.89. The AUCs of the JADAS for the ACR pediatric measures were 0.75–0.92. The PPVs of the RA scores for inactive disease were 0.33–0.67. The PPVs of the JADAS for inactive disease were each 0.93. Based on the RA and JADAS scores, the percentage of visits misclassified as inactive disease ranged from 7–67%. Conclusion The RA measures and JADAS versions showed acceptable to excellent ability to classify participants for each pediatric outcome measure, but the clinical significance of differences between AUCs for these scores could not be assessed. Misclassification of active disease versus inactive disease by the RA and JADAS scores was not uncommon in this cohort.

Features for standard expression microarray and RNA-Seq classification are expression averages over collections of cells. Single cell provides expression measurements for individual cells in a collection of cells from a particular tissue sample. Hence, it can yield feature vectors consisting of higher order and mixed moments. This article demonstrates the advantage of using these expression moments in cancer-related classification. We use synthetic data generated from 2 real networks, the mammalian cell cycle network and a melanoma-related pathway network, and real single-cell data generated via fluorescent protein reporters from 2 cell lines, HT-29 and HCT-116. The networks consist of hidden binary regulatory networks with Gaussian observations. The steady-state distributions of both the original and mutated networks are found, and data are drawn from these for moment-based classification using the mean, variance, skewness, and mixed moments. For the real data, we only observe 1 gene at a time, so that only the mean, variance, and skewness are considered, the analysis being done for 2 genes, EGFR and ERRB2. For the synthetic data, classification improves as we move from just the mean to mean, variance, and skewness and then to these plus the mixed moments. Comparisons are done with 3, 4, or 5 features, using feature selection. Sample size effects are considered. For the real data, we only consider mean, variance, and skewness, with results improving when the higher order moments are used as features.

In this study, we generated three SAGE libraries from melanoma tissues. Using bioinformatics tools usually applied to microarray data, we identified several genes, including novel transcripts, which are preferentially expressed in melanoma. SAGE results converged with previous microarray analysis on the importance of intracellular calcium and G-protein signaling, and the Wnt/Frizzled family. We also examined the expression of CD74, which was specifically, albeit not abundantly, expressed in the melanoma libraries using a melanoma progression tissue microarray, and demonstrate that this protein is expressed by melanoma cells but not by benign melanocytes. Many genes involved in intracellular calcium and G-protein signaling were highly expressed in melanoma, results we had observed earlier from microarray studies (Bittner et al., 2000). One of the genes most highly expressed in our melanoma SAGE libraries was a calcium-regulated gene, calpain 3 (p94). Immunohistochemical analysis demonstrated that calpain 3 moves from the nuclei of non-neoplastic cells to the cytoplasm of malignant cells, suggesting activation of this intracellular proteinase. Our SAGE results and the clinical validation data demonstrate how SAGE profiles can highlight specific links between signaling pathways as well as associations with tumor progression. This may provide insights into new genes that may be useful for the diagnosis and therapy of melanoma.

Gene expression profiling identified human melanoma cells demonstrating increased cell motility and invasiveness. The gene WNT5A best determined in vitro invasive behavior. Melanoma cells were transfected with vectors constitutively overexpressing Wnt5a. Consistent changes included actin reorganization and increased cell adhesion. No increase in β-catenin expression or nuclear translocation was observed. There was, however, a dramatic increase in activated PKC. In direct correlation with Wnt5a expression and PKC activation, there was an increase in melanoma cell invasion. Blocking this pathway using antibodies to Frizzled-5, the receptor for Wnt5a, inhibited PKC activity and cellular invasion. Furthermore, Wnt5a expression in human melanoma biopsies directly correlated to increasing tumor grade. These observations support a role for Wnt5a in human melanoma progression.

Motivation: The simplest level of statistical analysis of cancer associated gene expression matrices is aimed at finding consistently up- or down-regulated genes within a given set of tumor samples. Considering the high level of gene expression diversity detected in cancer, one needs to assess the probability that the consistent mis-regulation of a given gene is due to chance. Furthermore, it is important to determine the required sample number that will ensure the meaningful statistical analysis of massively parallel gene expression measurements. Results: The probability of consistent mis-regulation is calculated in this paper for binarized gene expression data, using combinatorial considerations. For practical purposes, we also provide a set of accurate approximate formulas for determining the same probability in a computationally less intensive way. When the pool of mis-regulatable genes is restricted, the probability of consistent mis-regulation can be overestimated. We show, however, that this effect has little practical consequences for cancer associated gene expression measurements published in the literature. Finally, in order to aid experimental design, we have provided estimates on the required sample number that will ensure that the detected consistent mis-regulation is not due to chance. Our results suggest that less than 20 sufficiently diverse tumor samples may be enough to identify consistently mis-regulated genes in a statistically significant manner. Availability: An implementation using Mathematica tm of the main equation of the paper, (4), is available at www.me.chalmers.se/~mwahde/bioinfo.html. Contact: mwahde@me.chalmers.se, zszallasi@chip.org * To whom correspondence should be addressed.

The complex molecular responses to genotoxic stress are mediated by a variety of regulatory pathways. The transcription factor TP53 plays a central role in the cellular response to DNA-damaging agents such as ionizing radiation, but other pathways also play important roles. In addition, differences in radiation quality, such as the exposure to high-LET radiation that occurs during space travel, may influence the pattern of responses. The premise is developed that stress gene responses can be employed as molecular markers for radiation exposure using a combination of informatics and functional genomics approaches. Published studies from our laboratory have already demonstrated such transcriptional responses with doses of gamma rays as low as 2 cGy, and in peripheral blood lymphocytes (PBLs) irradiated ex vivo with doses as low as 20 cGy. We have also found several genes elevated in vivo 24 h after whole-body irradiation of mice with 20 cGy. Such studies should provide insight into the molecular responses to physiologically relevant doses, which cannot necessarily be extrapolated from high-dose studies. In addition, ongoing experiments are identifying large numbers of potential biomarkers using microarray hybridization and various irradiation protocols including expression at different times after exposure to low- and high-LET radiation. Computation-intensive informatics analysis methods are also being developed for management of the complex gene expression profiles resulting from these experiments. With further development of these approaches, it may be feasible to monitor changes in gene expression after low-dose radiation exposure and other physiological stresses that may be encountered during manned space flight, such as the planned mission to Mars.

Androgen deprivation therapy for advanced prostate cancer is often effective, but not curative. Molecular pathways mediating the therapeutic response and those contributing to the subsequent hormone-refractory cell growth remain poorly understood. Here, cDNA microarray analysis of human CWR22 prostate cancer xenografts during the course of androgen deprivation therapy revealed distinct global gene expression profiles in primary, regressing and recurrent tumors. Elucidation of the genes involved in the transition between these states implicated specific molecular mechanisms in therapy failure and tumor progression. First, we identified a set of androgen-responsive genes whose expression decreased during the therapy response, but was then systematically restored in the recurrent tumors. In addition, altered expression of genes that encode known targets of rapamycin or that converge on the PI3K/AKT/FRAP pathway was observed in the recurrent tumors. Further suggestion for the involvement of these genes in hormone-refractory prostate cancer came from the observation that cells established from the recurrent xenografts were strongly inhibited in vitro by rapamycin. The results of this functional genomic analysis suggest that the combined effect of re-expression of androgen-responsive genes as well as the activation of rapamycin-sensitive signaling may drive prostate cancer progression, and contribute to the failure of androgen-deprivation therapy.

Human herpesvirus 8 (HHV-8), a gammaherpesvirus implicated in Kaposi's sarcoma, primary effusion lymphoma, and Castleman's disease, encodes several pathogenically important cellular homologs. To define the HHV-8 transcription program, RNA obtained from latently infected body cavity-based lymphoma 1 cells induced to undergo lytic replication was used to query a custom HHV-8 DNA microarray containing nearly every known viral open reading frame. The patterns of viral gene expression offer insights into the replication and pathogenic strategies of HHV-8.

In this paper, a model that combining cell population and genetic regulation within a single cell by using stochastic hybrid systems is proposed. The objective is to study the response of a population of cancer cells to various drugs that targeting the proliferation and survival pathways. The proposed model captures both the dynamics of the cell population and the dynamics of gene regulations within each individual cell. We use drug Lapatinib applied to colon cancer cell line HCT-116 as an example to validate the proposed model. Simulation results demonstrate the phenomena that observed in TGen experiments.

The development and progression of cancer are believed to be due to multiple genetic alterations resulting in complex changes in expression of many genes. The parental malignant melanoma cell line UACC903 displays anchorage-independent growth, and the chromosome 6-suppressed subline UACC903(+6) displays anchorage-dependent growth. The anchorage-independent revertant cell line SRS3 derived from UACC903(+6) by retroviral transduction resembles the phenotype of UACC903. In this study, we first compared the expression profiles of 3317 genes between these three cell lines in pairs by cDNA microarrays, resulting in identification of genes with known suppressor activities. We then demonstrated connexin 43 (Cx43)-suppressing anchorage-independent growth of UACC903 on overexpression. Of 3317 genes with informative expression detected by cDNA microarray, 321 (9.68%) showed expression changes between at least one pair of the three cell lines. Notably, 12 genes displayed higher levels of expression in UACC903(+6) than in both UACC903 and SRS3, providing candidates for further identification of melanoma-suppressor genes. Genes encoding Cx43 (suppressor activity), monocyte chemotactic protein 1 (suppressor activity), and cysteine proteinase P32alpha (apoptotic activity) were all upregulated in UACC903(+6), in contrast to both UACC903 and SRS3. Transfection of Cx43, encoded on human chromosome 6q21-q23, a region frequently altered in malignant melanoma, resulted in its overexpression and the suppression of anchorage-independent growth of UACC903. Thus, our result proves the principle that the combination of the ability to alter cellular phenotype by successive genetic alterations and the ability to examine the global expression profiles facilitates the identification of tumor suppressor genes. Mol. Carcinog. 28:119-127, 2000.

Several systems for 24-color fluorescence in situ hybridization (FISH) have been developed and applied to karyotyping and detection of chromosomal abnormalities. We have developed a 42-color multicolor FISH (mFISH) technique (armFISH), which permits the detection of chromosomal aberrations at the resolution of chromosome arms. The armFISH uses a commercially available mFISH reagent kit (24XCyte, MetaSystems GmbH) supplemented with a set of differentially labeled chromosome arm-specific painting probes (arm-kit, comprising either p- or q-arms of all human chromosomes, except the p-arm of the acrocentric- and Y chromosomes). The mFISH-probe cocktail and the arm-kit are combined and hybridized together to metaphase chromosomes. The armFISH is analyzed in two steps; first, the conventional mFISH image analysis is performed, followed by the arm-kit analysis to reveal the chromosome arms involved. The examples demonstrate the utility of armFISH in defining chromosomal rearrangements of human cancers.

Fluorescence in situ hybridization (FISH) with microdissection probes from human chromosomes 3 and 6 was applied to visualize arm and subregional band domains in human amniotic fluid cell nuclei. Confocal laser scanning microscopy and quantitative three-dimensional image analysis showed a pronounced variability of p- and q-arm domain arrangements and shapes. Apparent intermingling of neighbouring arm domains was limited to the domain surface. Three-dimensional distance measurements with pter and qter probes supported a high variability of chromosome territory folding.

Multiple endocrine neoplasia type 1 (MEN1) is an autosomal dominant disorder that results in parathyroid, anterior pituitary, and pancreatic and duodenal endocrine tumors in affected individuals. The MEN1 locus is tightly linked to the marker PYGM on chromosome 11q13, and linkage analysis has placed the MEN1 gene within a 2-Mb interval flanked by D11S1883 and D11S449. As a step toward cloning the MEN1 gene, we have constructed a 2.8-Mb clone contig consisting of YAC and bacterial clones (PAC, BAC, and P1) for the D11S480 to D11S913 region. The bacterial clones alone represent nearly all of the 2.8-Mb contig. The contig was assembled based on a high-density STS-content analysis of 79 genomic clones (YAC, PAC, BAC, and P1) with 118 STSs. The STSs included 22 polymorphic markers and 20 transcripts, with the remainder primarily derived from the end sequences of the genomic clones. An independent cosmid contig for the 1-Mb PYGM-SEA region was also generated. Support for correctness of the 2.8-Mb contig map comes from an independent ordering of the clones by fiber-FISH. This sequence-ready contig will be a useful resource for positional cloning of MEN1 and other disease genes whose loci fall within this region.

Background Identifying similarities and differences in the molecular constitutions of various types of cancer is one of the key challenges in cancer research. The appearances of a cancer depend on complex molecular interactions, including gene regulatory networks and gene-environment interactions. This complexity makes it challenging to decipher the molecular origin of the cancer. In recent years, many studies reported methods to uncover heterogeneous depictions of complex cancers, which are often categorized into different subtypes. The challenge is to identify diverse molecular contexts within a cancer, to relate them to different subtypes, and to learn underlying molecular interactions specific to molecular contexts so that we can recommend context-specific treatment to patients. Results In this study, we describe a novel method to discern molecular interactions specific to certain molecular contexts. Unlike conventional approaches to build modular networks of individual genes, our focus is to identify cancer-generic and subtype-specific interactions between contextual gene sets, of which each gene set share coherent transcriptional patterns across a subset of samples, termed contextual gene set. We then apply a novel formulation for quantitating the effect of the samples from each subtype on the calculated strength of interactions observed. Two cancer data sets were analyzed to support the validity of condition-specificity of identified interactions. When compared to an existing approach, the proposed method was much more sensitive in identifying condition-specific interactions even in heterogeneous data set. The results also revealed that network components specific to different types of cancer are related to different biological functions than cancer-generic network components. We found not only the results that are consistent with previous studies, but also new hypotheses on the biological mechanisms specific to certain cancer types that warrant further investigations. Conclusions The analysis on the contextual gene sets and characterization of networks of interaction composed of these sets discovered distinct functional differences underlying various types of cancer. The results show that our method successfully reveals many subtype-specific regions in the identified maps of biological contexts, which well represent biological functions that can be connected to specific subtypes.

Amplification of sequences derived from 12q13-15 is frequent in human sarcomas and brain tumors. Detailed mapping studies of the amplified region are necessary for definition of the impact of these amplification events on the tumor cell phenotype. By using the genes in this region and genomic fragments isolated by chromosome microdissection, we have established a series of ordered probes from 12q13-15 for fluorescence in situ hybridization (FISH) and Southern blot analysis. These probes have been used for physical mapping of two portions of the interval from GLI to D12S8. The centromeric region extends 1.8 Mb from GLI to microclone M79 and contains at least five genes, including the cyclin-dependent kinase gene CDK4. The more telomeric region includes the p53 regulator MDM2 and covers 1.1 Mb. We used the same group of probes to determine the pattern of amplification in three cell lines and three tumor specimens carrying amplified sequences from 12q13-15. In addition, we used a yeast artificial chromosome (YAC) contig of several megabases covering the entire region from SAS to D12S8 for FISH to determine the pattern of amplification in the neuroblastoma cell line NGP-127. The results suggest that the MDM2 and CDK4 regions may be either coamplified or amplified independently, and they illustrate how the map positions of genes and their functions may interact to determine the pattern of DNA amplification in human malignancies. Genes Chromosom Cancer 17:205–214 (1996). © 1996 Wiley-Liss, Inc.1

Background Molecularly targeted agents (MTAs) are increasingly used for cancer treatment, the goal being to improve the efficacy and selectivity of cancer treatment by developing agents that block the growth of cancer cells by interfering with specific targeted molecules needed for carcinogenesis and tumor growth. This approach differs from traditional cytotoxic anticancer drugs. The lack of specificity of cytotoxic drugs allows a relatively straightforward approach in preclinical and clinical studies, where the optimal dose has usually been defined as the "maximum tolerated dose" (MTD). This toxicity-based dosing approach is founded on the assumption that the therapeutic anticancer effect and toxic effects of the drug increase in parallel as the dose is escalated. On the contrary, most MTAs are expected to be more selective and less toxic than cytotoxic drugs. Consequently, the maximum therapeutic effect may be achieved at a "biologically effective dose" (BED) well below the MTD. Hence, dosing study for MTAs should be different from cytotoxic drugs. Enhanced efforts to molecularly characterize the drug efficacy for MTAs in preclinical models will be valuable for successfully designing dosing regimens for clinical trials. Results A novel preclinical model combining experimental methods and theoretical analysis is proposed to investigate the mechanism of action and identify pharmacodynamic characteristics of the drug. Instead of fixed time point analysis of the drug exposure to drug effect, the time course of drug effect for different doses is quantitatively studied on cell line-based platforms using system identification, where tumor cells' responses to drugs through the use of fluorescent reporters are sampled over a time course. Results show that drug effect is time-varying and higher dosages induce faster and stronger responses as expected. However, the drug efficacy change along different dosages is not linear; on the contrary, there exist certain thresholds. This kind of preclinical study can provide valuable suggestions about dosing regimens for the in vivo experimental stage to increase productivity.

Cancer encompasses various diseases associated with loss of cell-cycle control, leading to uncontrolled cell proliferation and/or reduced apoptosis. Cancer is usually caused by malfunction(s) in the cellular signaling pathways. Malfunctions occur in different ways and at different locations in a pathway. Consequently, therapy design should first identify the location and type of malfunction and then arrive at a suitable drug combination. We consider the growth factor (GF) signaling pathways, widely studied in the context of cancer. Interactions between different pathway components are modeled using Boolean logic gates. All possible single malfunctions in the resulting circuit are enumerated and responses of the different malfunctioning circuits to a ‘test’ input are used to group the malfunctions into classes. Effects of different drugs, targeting different parts of the Boolean circuit, are taken into account in deciding drug efficacy, thereby mapping each malfunction to an appropriate set of drugs.

A novel preclinical model combining experimental methods and theoretical analysis is proposed to investigate the mechanism of action and identify pharmacodynamic characteristic of a drug. Instead of fixed time point analysis of the drug exposure to drug effect, the time course of drug effect for different doses are quantitatively studied on cell line-based platforms using Kalman filter, where tumor cells' responses to drugs through the use of fluorescent reporters are sampled frequently over a time-course. It is expected that such preclinical study will provide valuable suggestions about dosing regimens for in vivo experimental stage to increase productivity.

Motivation: Cancer encompasses various diseases associated with loss of cell cycle control, leading to uncontrolled cell proliferation and/or reduced apoptosis. Cancer is usually caused by malfunction(s) in the cellular signaling pathways. Malfunctions occur in different ways and at different locations in a pathway. Consequently, therapy design should first identify the location and type of malfunction to arrive at a suitable drug combination. Results: We consider the growth factor (GF) signaling pathways, widely studied in the context of cancer. Interactions between different pathway components are modeled using Boolean logic gates. All possible single malfunctions in the resulting circuit are enumerated and responses of the different malfunctioning circuits to a ‘test’ input are used to group the malfunctions into classes. Effects of different drugs, targeting different parts of the Boolean circuit, are taken into account in deciding drug efficacy, thereby mapping each malfunction to an appropriate set of drugs. Contact: edward@ece.tamu.edu

Objective Epidemiologic data addressing maternal risk factors for congenital urinary tract anomalies (CUTA) are limited, with conflicting results for preexisting diabetes mellitus, gestational diabetes, and tobacco and alcohol use. The purpose of this study was to examine the association between maternal risk factors and CUTA in a population-based case-control study. Methods A case-control analysis was performed using linked birth-hospital discharge records from Washington state for 1987–2007 to evaluate the association between maternal risk factors and CUTA. Cases were children with International Classification of Diseases, Ninth Revision, Clinical Modification codes for urinary anomalies. Controls without urinary tract anomalies were selected from Washington State birth records and matched by birth year in a ratio of 4:1. Logistic regression was performed to evaluate the association between maternal factors and CUTA. Results A total of 4673 cases and 18,692 controls were studied. In the multivariate analysis, gestational diabetes (OR 1.42, 95% CI 1.09–1.85), preexisting diabetes (OR 3.46, 95% CI 2.17–5.54), and maternal renal disease (OR 5.31, 95% CI 2.40–11.72) were all associated with an increased risk of kidney anomalies. Advanced maternal age (OR 1.20, 95% CI 1.06–1.35), gestational diabetes (OR 1.25, 95% CI 1.01–1.56), maternal renal disease (OR 4.06, 95% CI 1.95–8.46), and non-Caucasian race (OR 0.82, 95% CI .74–.91) were all associated with the risk of ureter, bladder, and urethra anomalies in multivariate analysis. Conclusion Several maternal factors are associated with the risk of CUTA, including diabetes mellitus and maternal renal disease. This information can be used for prenatal counseling and management of women with these risk factors.

Purpose To compare the progression-free survival (PFS) using a treatment regimen selected by molecular profiling (MP) of a patient's tumor with the PFS for the most recent regimen on which the patient had experienced progression (ie, patient as his own control). Patients and Methods Patients with refractory metastatic cancer had tissue samples submitted for MP in two formats including formalin-fixed tissue for immunohistochemistry and fluorescent in situ hybridization assays and immediately frozen tissue for oligonucleotide microarray (MA) gene expression assays (all performed in a Clinical Laboratory Improvement Amendments [ CLIA ] –certified laboratory). The MP approach was deemed of clinical benefit for the individual patient who had a PFS ratio (PFS on MP-selected therapy/PFS on prior therapy) of ≥ 1.3. Results In 86 patients who had MP attempted, there was a molecular target detected in 84 (98%). Sixty-six of the 84 patients were treated according to MP results. Eighteen (27%) of 66 patients had a PFS ratio of ≥ 1.3 (95% CI, 17% to 38%; one-sided, one-sample P = .007). Therefore, the null hypothesis (that ≤ 15% of this patient population would have a PFS ratio of ≥ 1.3) was rejected. Conclusion It is possible to identify molecular targets in patients' tumors from nine different centers across the United States. In 27% of patients, the MP approach resulted in a longer PFS on an MP-suggested regimen than on the regimen on which the patient had just experienced progression. Issues to be considered in interpretation of this study include limited prior experience with patients as their own controls as a study end point and overall patient attrition.

Background Organic foreign bodies swell when irrigated with water, potentially making extraction more difficult. As the degree and rate of swelling of different types of organic foreign bodies has not been established, we aimed to analyze the hydroscopic properties of different organic foreign bodies in body temperature water. Methods Dry kidney beans, brown beans, peas, popcorn kernels, and dried fruits were soaked in a body temperature (37oC) water bath. Volume of these organic materials was measured hourly to 8 hours, then at 12, 16, 24, 28, 36 and 48 hours. Results All dried fruits and beans increased in volume over time. The volume increase from baseline at 6 hours was between 43% (popcorn kernels) and 383% (kidney beans). Peas, popcorn, and raisins did not increase volume further after 6 hours. Kidney and brown beans had the greatest increase in volume overall (1268% and 482% respectively), and the greatest continued increase after 24 hours. Conclusions Many organic substances that frequently present as aural foreign bodies may swell enough in water to lodge tightly in the ear canal. Typical popcorn kernels and dried peas will not swell sufficiently to lodge tightly in the ear canal of a typical child one year or older. A retained organic foreign body in a moist ear canal may cause inflammation until the foreign body can be removed. These risks may be offset by the advantages of successful removal with irrigation. Keywords Foreign body; Irrigation; Organic; Ear; Hydroscopic; Procedure; Removal

The 60 cell lines of the National Cancer Institute Anticancer Drug Screen (NCI-60) constitute the most extensively characterized in vitro cancer cell model. They have been tested for sensitivity to more than 100,000 potential chemotherapy agents and have been profiled extensively at the DNA, RNA, protein, functional, and pharmacologic levels. We have used the NCI-60 cell lines and three additional lines to develop a database of responses of cancer cells to ionizing radiation. We compared clonogenic survival, apoptosis, and gene expression response by microarray. Although several studies have profiled relative basal gene expression in the NCI-60, this is the first comparison of large-scale gene expression changes in response to genotoxic stress. Twenty-two genes were differentially regulated in cells with low survival after 2-Gy γ-rays; 14 genes identified lines more sensitive to 8 Gy. Unlike reported basal gene expression patterns, changes in expression in response to radiation showed little tissue-of-origin effect, except for differentiating the lymphoblastoid cell lines from other cell types. Basal expression patterns, however, discriminated well between radiosensitive and more resistant lines, possibly being more informative than radiation response signatures. The most striking patterns in the radiation data were a set of genes up-regulated preferentially in the p53 wild-type lines and a set of cell cycle regulatory genes down-regulated across the entire NCI-60 panel. The response of those genes to γ-rays seems to be unaffected by the myriad of genetic differences across this diverse cell set; it represents the most penetrant gene expression response to ionizing radiation yet observed. [Cancer Res 2008;68(2):415–24]

Although AKT1 (v-akt murine thymoma viral oncogene homologue 1) kinase is a central member of possibly the most frequently activated proliferation and survival pathway in cancer, mutation of AKT1 has not been widely reported. Here we report the identification of a somatic mutation in human breast, colorectal and ovarian cancers that results in a glutamic acid to lysine substitution at amino acid 17 (E17K) in the lipid-binding pocket of AKT1. Lys 17 alters the electrostatic interactions of the pocket and forms new hydrogen bonds with a phosphoinositide ligand. This mutation activates AKT1 by means of pathological localization to the plasma membrane, stimulates downstream signalling, transforms cells and induces leukaemia in mice. This mechanism indicates a direct role of AKT1 in human cancer, and adds to the known genetic alterations that promote oncogenesis through the phosphatidylinositol-3-OH kinase/AKT pathway. Furthermore, the E17K substitution decreases the sensitivity to an allosteric kinase inhibitor, so this mutation may have important clinical utility for AKT drug development.