1
|
Zhao Y, Ai Y, Li L, Jane JL, Hendrich S, Birt DF. Inhibition of azoxymethane-induced preneoplastic lesions in the rat colon by a stearic acid complexed high-amylose cornstarch using different cooking methods and assessing potential gene targets. J Funct Foods 2014. [DOI: 10.1016/j.jff.2013.11.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
|
2
|
Cunningham AR, Carrasquer CA, Qamar S, Maguire JM, Cunningham SL, Trent JO. Global structure-activity relationship model for nonmutagenic carcinogens using virtual ligand-protein interactions as model descriptors. Carcinogenesis 2012; 33:1940-5. [PMID: 22678118 PMCID: PMC3463155 DOI: 10.1093/carcin/bgs197] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Revised: 05/16/2012] [Accepted: 05/26/2012] [Indexed: 11/13/2022] Open
Abstract
Structure-activity relationship (SAR) models are powerful tools to investigate the mechanisms of action of chemical carcinogens and to predict the potential carcinogenicity of untested compounds. We describe the use of a traditional fragment-based SAR approach along with a new virtual ligand-protein interaction-based approach for modeling of nonmutagenic carcinogens. The ligand-based SAR models used descriptors derived from computationally calculated ligand-binding affinities for learning set agents to 5495 proteins. Two learning sets were developed. One set was from the Carcinogenic Potency Database, where chemicals tested for rat carcinogenesis along with Salmonella mutagenicity data were provided. The second was from Malacarne et al. who developed a learning set of nonalerting compounds based on rodent cancer bioassay data and Ashby's structural alerts. When the rat cancer models were categorized based on mutagenicity, the traditional fragment model outperformed the ligand-based model. However, when the learning sets were composed solely of nonmutagenic or nonalerting carcinogens and noncarcinogens, the fragment model demonstrated a concordance of near 50%, whereas the ligand-based models demonstrated a concordance of 71% for nonmutagenic carcinogens and 74% for nonalerting carcinogens. Overall, these findings suggest that expert system analysis of virtual chemical protein interactions may be useful for developing predictive SAR models for nonmutagenic carcinogens. Moreover, a more practical approach for developing SAR models for carcinogenesis may include fragment-based models for chemicals testing positive for mutagenicity and ligand-based models for chemicals devoid of DNA reactivity.
Collapse
Affiliation(s)
- Albert R. Cunningham
- James Graham Brown Cancer Center, University of Louisville505 South Hancock Street,Louisville, KY 40202, USA,
- Department of Medicine, University of LouisvilleLouisville, KY 40292, USA,
- Department of Pharmacology and Toxicology, University of Louisville500 South Preston Street,Louisville, KY 40202, USA and
- Gnarus Systems, Inc.,201 E. Jefferson Street, Suite 125, Louisville, KY 40202, USA
| | - C. Alex Carrasquer
- James Graham Brown Cancer Center, University of Louisville505 South Hancock Street,Louisville, KY 40202, USA,
| | - Shahid Qamar
- James Graham Brown Cancer Center, University of Louisville505 South Hancock Street,Louisville, KY 40202, USA,
| | - Jon M. Maguire
- James Graham Brown Cancer Center, University of Louisville505 South Hancock Street,Louisville, KY 40202, USA,
| | | | - John O. Trent
- James Graham Brown Cancer Center, University of Louisville505 South Hancock Street,Louisville, KY 40202, USA,
- Department of Medicine, University of LouisvilleLouisville, KY 40292, USA,
| |
Collapse
|
3
|
Fielden MR, Adai A, Dunn RT, Olaharski A, Searfoss G, Sina J, Aubrecht J, Boitier E, Nioi P, Auerbach S, Jacobson-Kram D, Raghavan N, Yang Y, Kincaid A, Sherlock J, Chen SJ, Car B. Development and Evaluation of a Genomic Signature for the Prediction and Mechanistic Assessment of Nongenotoxic Hepatocarcinogens in the Rat. Toxicol Sci 2011; 124:54-74. [DOI: 10.1093/toxsci/kfr202] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
|
4
|
Stegmaier P, Voss N, Meier T, Kel A, Wingender E, Borlak J. Advanced computational biology methods identify molecular switches for malignancy in an EGF mouse model of liver cancer. PLoS One 2011; 6:e17738. [PMID: 21464922 PMCID: PMC3065454 DOI: 10.1371/journal.pone.0017738] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Accepted: 02/09/2011] [Indexed: 01/04/2023] Open
Abstract
The molecular causes by which the epidermal growth factor receptor tyrosine kinase induces malignant transformation are largely unknown. To better understand EGFs' transforming capacity whole genome scans were applied to a transgenic mouse model of liver cancer and subjected to advanced methods of computational analysis to construct de novo gene regulatory networks based on a combination of sequence analysis and entrained graph-topological algorithms. Here we identified transcription factors, processes, key nodes and molecules to connect as yet unknown interacting partners at the level of protein-DNA interaction. Many of those could be confirmed by electromobility band shift assay at recognition sites of gene specific promoters and by western blotting of nuclear proteins. A novel cellular regulatory circuitry could therefore be proposed that connects cell cycle regulated genes with components of the EGF signaling pathway. Promoter analysis of differentially expressed genes suggested the majority of regulated transcription factors to display specificity to either the pre-tumor or the tumor state. Subsequent search for signal transduction key nodes upstream of the identified transcription factors and their targets suggested the insulin-like growth factor pathway to render the tumor cells independent of EGF receptor activity. Notably, expression of IGF2 in addition to many components of this pathway was highly upregulated in tumors. Together, we propose a switch in autocrine signaling to foster tumor growth that was initially triggered by EGF and demonstrate the knowledge gain form promoter analysis combined with upstream key node identification.
Collapse
Affiliation(s)
| | - Nico Voss
- BIOBASE GmbH, Wolfenbuettel, Germany
| | - Tatiana Meier
- Department Molecular Medicine and Medical Biotechnology, Fraunhofer Institute of Toxicology and Experimental Medicine, Hannover, Germany
- Centre for Pharmacology and Toxicology, Hannover Medical School, Hannover, Germany
| | - Alexander Kel
- BIOBASE GmbH, Wolfenbuettel, Germany
- GeneXplain GmbH, Wolfenbuettel, Germany
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - Edgar Wingender
- BIOBASE GmbH, Wolfenbuettel, Germany
- GeneXplain GmbH, Wolfenbuettel, Germany
- Department of Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Juergen Borlak
- Department Molecular Medicine and Medical Biotechnology, Fraunhofer Institute of Toxicology and Experimental Medicine, Hannover, Germany
- Centre for Pharmacology and Toxicology, Hannover Medical School, Hannover, Germany
- * E-mail:
| |
Collapse
|