Martin M.T.,U.S. Environmental Protection Agency |
Dix D.J.,U.S. Environmental Protection Agency |
Judson R.S.,U.S. Environmental Protection Agency |
Kavlock R.J.,U.S. Environmental Protection Agency |
And 10 more authors.
Chemical Research in Toxicology | Year: 2010
Exposure to environmental chemicals adds to the burden of disease in humans and wildlife to a degree that is difficult to estimate and, thus, mitigate. The ability to assess the impact of existing chemicals for which little to no toxicity data are available or to foresee such effects during early stages of chemical development and use, and before potential exposure occurs, is a pressing need. However, the capacity of the current toxicity evaluation approaches to meet this demand is limited by low throughput and high costs. In the context of EPA's ToxCast project, we have evaluated a novel cellular biosensor system (Factorial1) that enables rapid, high-content assessment of a compound's impact on gene regulatory networks. The Factorial biosensors combined libraries of cis-and trans-regulated transcription factor reporter constructs with a highly homogeneous method of detection enabling simultaneous evaluation of multiplexed transcription factor activities. Here, we demonstrate the application of the technology toward determining bioactivity profiles by quantitatively evaluating the effects of 309 environmental chemicals on 25 nuclear receptors and 48 transcription factor response elements. We demonstrate coherent transcription factor activity across nuclear receptors and their response elements and that Nrf2 activity, a marker of oxidative stress, is highly correlated to the overall promiscuity of a chemical. Additionally, as part of the ToxCast program, we identify molecular targets that associate with in ViVo end points and represent modes of action that can serve as potential toxicity pathway biomarkers and inputs for predictive modeling of in ViVo toxicity. © 2010 American Chemical Society.
Burdick A.D.,Pfizer |
Sciabola S.,Pfizer |
Mantena S.R.,Pfizer |
Hollingshead B.D.,Pfizer |
And 9 more authors.
Nucleic Acids Research | Year: 2014
Fully phosphorothioate antisense oligonucleotides (ASOs) with locked nucleic acids (LNAs) improve target affinity, RNase H activation and stability. LNA modified ASOs can cause hepatotoxicity, and this risk is currently not fully understood. In vitro cytotoxicity screens have not been reliable predictors of hepatic toxicity in non-clinical testing; however, mice are considered to be a sensitive test species. To better understand the relationship between nucleotide sequence and hepatotoxicity, a structure-toxicity analysis was performed using results from 2 week repeated-dose-tolerability studies in mice administered LNA-modified ASOs. ASOs targeting human Apolipoprotien C3 (Apoc3), CREB (cAMP Response Element Binding Protein) Regulated Transcription Coactivator 2 (Crtc2) or Glucocorticoid Receptor (GR, NR3C1) were classified based upon the presence or absence of hepatotoxicity in mice. From these data, a random-decision forest-classification model generated from nucleotide sequence descriptors identified two trinucleotide motifs (TCC and TGC) that were present only in hepatotoxic sequences. We found that motif containing sequences were more likely to bind to hepatocellular proteins in vitro and increased P53 and NRF2 stress pathway activity in vivo. These results suggest in silico approaches can be utilized to establish structure-toxicity relationships of LNA-modified ASOs and decrease the likelihood of hepatotoxicity in preclinical testing. © 2014 © The Author(s) 2014. Published by Oxford University Press.
Slade G.D.,University of North Carolina at Chapel Hill |
Conrad M.S.,University of North Carolina at Chapel Hill |
Diatchenko L.,University of North Carolina at Chapel Hill |
Rashid N.U.,University of North Carolina at Chapel Hill |
And 7 more authors.
Pain | Year: 2011
For reasons unknown, temporomandibular disorder (TMD) can manifest as localized pain or in conjunction with widespread pain. We evaluated relationships between cytokines and TMD without or with widespread palpation tenderness (TMD-WPT or TMD+WPT, respectively) at protein, transcription factory activity, and gene levels. Additionally, we evaluated the relationship between cytokines and intermediate phenotypes characteristic of TMD and WPT. In a case-control study of 344 females, blood samples were analyzed for levels of 22 cytokines and activity of 48 transcription factors. Intermediate phenotypes were measured by quantitative sensory testing and questionnaires asking about pain, health, and psychological status. Single nucleotide polymorphisms (SNPs) coding cytokines and transcription factors were genotyped. TMD-WPT cases had elevated protein levels of proinflammatory cytokine monocyte chemotactic protein (MCP-1) and antiinflammatory cytokine interleukin (IL)-1ra, whereas TMD+WPT cases had elevated levels of proinflammatory cytokine IL-8. MCP-1, IL-1ra, and IL-8 were differentially associated with experimental pain, self-rated pain, self-rated health, and psychological phenotypes. TMD-WPT and TMD+WPT cases had inhibited transcription activity of the antiinflammatory cytokine transforming growth factor β1 (TGFβ1). Interactions were observed between TGFβ1 and IL-8 SNPs: an additional copy of the TGFβ1 rs2241719 minor T allele was associated with twice the odds of TMD+WPT among individuals homozygous for the IL-8 rs4073 major A allele, and half the odds of TMD+WPT among individuals heterozygous for rs4073. These results demonstrate how pro- and antiinflammatory cytokines contribute to the pathophysiology of TMD and WPT in genetically susceptible people. Furthermore, they identify MCP-1, IL-1ra, IL-8, and TGFβ1 as potential diagnostic markers and therapeutic targets for pain in patients with TMD. © 2011 International Association for the Study of Pain. Published by Elsevier B.V. All rights reserved.
Attagene Inc. | Date: 2012-09-08
A method of determining water quality of a water sample, comprising exposing the water sample to a test cell system; generating at least one profile of ensuing changes in activities of transcription factors in said test cell system in response to said exposing; and determining from the generated at least one profile the water quality of the water sample. Computer systems and kits for carrying out the water quality determination of water specimens are also described, in which water quality can be readily and accurately determined by transcription factor activity analysis.
Attagene Inc. | Date: 2012-09-08
A method of determining biosimilarity of a sample composition to a reference composition, including: exposing a test cell system to a sample composition so that the test cell system responds to the sample composition by change in transcription factor activity in the test cell system; generating from the test cell system response an output correlative to the change of transcription factor activity in the test cell system; and determining from comparison of said output with a transcription factor activity reference standard for the reference composition, the biosimilarity of the sample composition to the reference composition. Computer systems and kits for carrying out the determination of biosimilarity of compositions are also described, in which biosimilarity of compositions ranging from simple molecules to complex mixtures can be readily and accurately determined by transcription factor activity analysis.
Attagene Inc. | Date: 2015-01-09
A protein reporter system comprising at least one reporter including a response element responsive to the binding of a transcription factor, a secreted enzyme backbone and a recognition region for specific binding of an antibody. Multiplexed assays for binding, assaying and quantifying the activity of transcription factors are also described, in which the assays use protein reporters in sets, libraries or other groupings, as necessary to achieve desired quantification.