Skip to main content
SpringerLink
Log in

Use of Traditional End Points and Gene Dysregulation to Understand Mechanisms of Toxicity: Toxicogenomics in Mechanistic Toxicology

  • Protocol
Essential Concepts in Toxicogenomics

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 460))

Summary

Microarray technologies can be used to generate massive amounts of gene expression information as an initial step to decipher the molecular mechanisms of toxicologic changes. Identifying genes whose expression is associated with specific toxic end points is an initial step in predicting, characterizing, and understanding toxicity. Analysis of gene function and the chronology of gene expression changes represent additional methods to generate hypotheses of the mechanisms of toxicity. Follow-up experiments are typically required to confirm or refute hypotheses derived from toxicogenomic data. Understanding the mechanism of toxicity for a compound is a critical step in forming a rational plan for developing counterscreens for toxicity and for increasing productivity of research and development while decreasing the risk of late-stage failure in pharmaceutical development.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Barefoot, J. C., Gronbaek, M., Feaganes, J. R., McPherson, R. S., Williams, R. B., and Siegler, I. C. (2002) Alcoholic beverage preference, diet, and health habits in the UNC Alumni Heart Study. Am. J. Clin. Nutr. 76, 466–472.

    CAS  PubMed  Google Scholar 

  2. Bono, H., and Okazaki, Y. (2002) Functional transcriptomes: comparative analysis of biological pathways and processes in eukaryotes to infer genetic networks among transcripts. Curr. Opin. Struct. Biol. 12, 355–361.

    Article  CAS  PubMed  Google Scholar 

  3. Larrey, D., Tinel, M., and Pessayre, D. (1983) Formation of inactive cytochrome P-450 Fe(II)-metabolite complexes with several erythromycin derivatives but not with josamycin and midecamycin in rats. Biochem. Pharmacol. 32, 1487–1493.

    Article  CAS  PubMed  Google Scholar 

  4. Amacher, D. E., Schomaker, S. J., Boldt, S. E., and Mirsky, M. (2006) The relationship among microsomal enzyme induction, liver weight, and histological change in cynomolgus monkey toxicology studies. Food Chem. Toxicol. 44, 528–537.

    Article  CAS  PubMed  Google Scholar 

  5. Lai, D. Y. (2004) Rodent carcinogenicity of peroxisome proliferators and issues on human relevance. J. Environ. Sci. Health C Environ. Carcinog. Ecotoxicol. Rev. 22, 37–55.

    PubMed  Google Scholar 

  6. Waring, J. F., Gum, R., Morfitt, D., Jolly, R. A., Ciurlionis, R., Heindel, M., et al. (2002) Identifying toxic mechanisms using DNA microarrays: evidence that an experimental inhibitor of cell adhesion molecule expression signals through the aryl hydrocarbon nuclear receptor. Toxicology 181–182, 537–550.

    Article  PubMed  Google Scholar 

  7. Wolfgang, G. H., Robertson, D. G., Welty, D. F., and Metz, A. L. (1995) Hepatic and adrenal toxicity of a novel lipid regulator in beagle dogs. Fundam. Appl. Toxicol. 26, 272–281.

    Article  CAS  PubMed  Google Scholar 

  8. Grasso, P., and Hinton, R. H. (1991) Evidence for and possible mechanisms of non-genotoxic carcinogenesis in rodent liver. Mutat. Res. 248, 271–290.

    CAS  PubMed  Google Scholar 

  9. Hamadeh, H. K., Bushel, P. R., Jayadev, S., Martin, K., DiSorbo, O., Sieber, S., et al. (2002) Gene expression analysis reveals chemical-specific profiles. Toxicol. Sci. 67, 219–231.

    Article  CAS  PubMed  Google Scholar 

  10. Kemper, B. (1998) Regulation of cytochrome P450 gene transcription by phenobarbital. Prog. Nucleic Acid Res. Mol. Biol. 61, 23–64.

    CAS  PubMed  Google Scholar 

  11. Voss, K. A., Liu, J., Anderson, S. P., Dunn, C., Miller, J. D., Owen, J. R., et al. (2006) Toxic effects of fumonisin in mouse liver are independent of the peroxisome proliferator-activated receptor alpha. Toxicol. Sci. 89, 108–119.

    Article  CAS  PubMed  Google Scholar 

  12. Fielden, M. R., Brennan, R., and Gollub, J. (2007) A gene expression biomarker provides early prediction and mechanistic assessment of hepatic tumor induction by non-genotoxic chemicals. Toxicol. Sci. 99, 90–100.

    Article  CAS  PubMed  Google Scholar 

  13. Nie, A. Y., McMillian, M., Parker, J. B., Leone, A., Bryant, S., Yieh, L., et al. (2006) Predictive toxicogenomics approaches reveal underlying molecular mechanisms of nongenotoxic carcinogenicity. Mol. Carcinog. 45, 914–933.

    Article  CAS  PubMed  Google Scholar 

  14. Wallace, K. B., Hausner, E., Herman, E., Holt, G. D., MacGregor, J. T., Metz, A. L., et al. (2004) Serum troponins as biomarkers of drug-induced cardiac toxicity. Toxicol. Pathol. 32, 106–121.

    Article  CAS  PubMed  Google Scholar 

  15. Singal, P. K., and Iliskovic, N. (1998) Doxorubicin-induced cardiomyopathy. N. Engl. J. Med. 339, 900–905.

    Article  CAS  PubMed  Google Scholar 

  16. Kalivendi, S. V., Konorev, E. A., Cunningham, S., Vanamala, S. K., Kaji, E. H., Joseph, J., and Kalyanaraman, B. (2005) Doxorubicin activates nuclear factor of activated T-lymphocytes and Fas ligand transcription: role of mitochondrial reactive oxygen species and calcium. Biochem. J. 389, 527–539.

    Article  CAS  PubMed  Google Scholar 

  17. Minotti, G., Menna, P., Salvatorelli, E., Cairo, G., and Gianni, L. (2004) Anthracyclines: molecular advances and pharmacologic developments in antitumor activity and cardiotoxicity. Pharmacol. Rev. 56, 185–229.

    Article  CAS  PubMed  Google Scholar 

  18. Robert, J. (2007) Preclinical assessment of anthracycline cardiotoxicity in laboratory animals: Predictiveness and pitfalls. Cell. Biol. Toxicol. 23, 27–37.

    Article  CAS  PubMed  Google Scholar 

  19. Chaiswing, L., Cole, M. P., St Clair, D. K., Ittarat, W., Szweda, L. I., and Oberley, T. D. (2004) Oxidative damage precedes nitrative damage in adriamycin-induced cardiac mitochondrial injury. Toxicol. Pathol. 32, 536–547.

    Article  CAS  PubMed  Google Scholar 

  20. Jang, Y. M., Kendaiah, S., Drew, B., Phillips, T., Selman, C., Julian, D., and Leeuwenburgh, C. (2004) Doxorubicin treatment in vivo activates caspase-12 mediated cardiac apoptosis in both male and female rats. FEBS Lett. 577, 483–490.

    Article  CAS  PubMed  Google Scholar 

  21. Gu, Y. G., Weitzberg, M., Clark, R. F., Xu, X., Li, Q., Lubbers, N. L., et al. (2007) N-{3-[2-(4-alkoxyphenoxy)thiazol-5-yl]-1-methylprop-2-ynyl}carboxy derivatives as acetyl-coA carboxylase inhibitors—improvement of cardiovascular and neurological liabilities via structural modifications. J. Med. Chem. 50, 1078–1082.

    Article  CAS  PubMed  Google Scholar 

  22. Ganter, B., Tugendreich, S., Pearson, C. I., Ayanoglu, E., Baumhueter, S., Bostian, K. A., et al. (2005) Development of a large-scale chemogenomics database to improve drug candidate selection and to understand mechanisms of chemical toxicity and action. J. Biotechnol. 119, 219–244.

    Article  CAS  PubMed  Google Scholar 

  23. Diel, P., Smolnikar, K., Schulz, T., Laudenbach-Leschowski, U., Michna, H., and Vollmer, G. (2001) Phytoestrogens and carcinogenesis-differential effects of genistein in experimental models of normal and malignant rat endometrium. Hum. Reprod. 16, 997–1006.

    Article  CAS  PubMed  Google Scholar 

  24. Kuiper, G. G., Enmark, E., Pelto-Huikko, M., Nilsson, S., and Gustafsson, J. A. (1996) Cloning of a novel receptor expressed in rat prostate and ovary. Proc. Natl. Acad. Sci. U. S. A. 93, 5925–5930.

    Article  CAS  PubMed  Google Scholar 

  25. Okada, A., Ohta, Y., Buchanan, D. L., Sato, T., Inoue, S., Hiroi, H., et al. (2002) Changes in ontogenetic expression of estrogen receptor alpha and not of estrogen receptor beta in the female rat reproductive tract. J. Mol. Endocrinol. 28, 87–97.

    Article  CAS  PubMed  Google Scholar 

  26. Matthews, J., and Gustafsson, J. A. (2003) Estrogen signaling: a subtle balance between ER alpha and ER beta. Mol. Interv. 3, 281–292.

    Article  CAS  PubMed  Google Scholar 

  27. Moriarty, K., Kim, K. H., and Bender, J. R. (2006) Minireview: estrogen receptor-mediated rapid signaling. Endocrinology 147, 5557–5563.

    Article  CAS  PubMed  Google Scholar 

  28. Hall, J. M., and McDonnell, D. P. (2005) Coregulators in nuclear estrogen receptor action: from concept to therapeutic targeting. Mol. Interv. 5, 343–357.

    Article  PubMed  Google Scholar 

  29. Filardo, E. J., and Thomas, P. (2005) GPR30: a seven-transmembrane-spanning estrogen receptor that triggers EGF release. Trends Endocrinol. Metab. 16, 362–367.

    Article  CAS  PubMed  Google Scholar 

  30. Bjornstrom, L., and Sjoberg, M. (2005) Mechanisms of estrogen receptor signaling: convergence of genomic and nongenomic actions on target genes. Mol. Endocrinol. 19, 833–842.

    Article  PubMed  Google Scholar 

  31. Levin, E. R. (2005) Integration of the extranuclear and nuclear actions of estrogen. Mol. Endocrinol. 19, 1951–1959.

    Article  CAS  PubMed  Google Scholar 

  32. Houston, K. D., Copland, J. A., Broaddus, R. R., Gottardis, M. M., Fischer, S. M., and Walker, C. L. (2003) Inhibition of proliferation and estrogen receptor signaling by peroxisome proliferator-activated receptor gamma ligands in uterine leiomyoma. Cancer Res. 63, 1221–1227.

    CAS  PubMed  Google Scholar 

  33. Rhen, T., Grissom, S., Afshari, C., and Cidlowski, J. A. (2003) Dexamethasone blocks the rapid biological effects of 17beta-estradiol in the rat uterus without antagonizing its global genomic actions. FASEB J. 17, 1849–1870.

    Article  CAS  PubMed  Google Scholar 

  34. Kazi, A. A., Jones, J. M., and Koos, R. D. (2005) Chromatin immunoprecipitation analysis of gene expression in the rat uterus in vivo: estrogen-induced recruitment of both estrogen receptor alpha and hypoxia-inducible factor 1 to the vascular endothelial growth factor promoter. Mol. Endocrinol. 19, 2006–2019.

    Article  CAS  PubMed  Google Scholar 

  35. Li, X. H., and Ong, D. E. (2003) Cellular retinoic acid-binding protein II gene expression is directly induced by estrogen, but not retinoic acid, in rat uterus. J. Biol. Chem. 278, 35819–35825.

    Article  CAS  PubMed  Google Scholar 

  36. Wu, X., Pang, S. T., Sahlin, L., Blanck, A., Norstedt, G., and Flores-Morales, A. (2003) Gene expression profiling of the effects of castration and estrogen treatment in the rat uterus. Biol. Reprod. 69, 1308–1317.

    Article  CAS  PubMed  Google Scholar 

  37. Moggs, J. G., Tinwell, H., Spurway, T., Chang, H. S., Pate, I., Lim, F. L., et al. (2004) Phenotypic anchoring of gene expression changes during estrogen-induced uterine growth. Environ. Health Perspect. 112, 1589–1606.

    Article  CAS  PubMed  Google Scholar 

  38. Naciff, J. M., Overmann, G. J., Torontali, S. M., Carr, G. J., Khambatta, Z. S., Tiesman, J. P., et al. (2007) Uterine temporal response to acute exposure to 17{alpha}-ethinyl estradiol in the immature rat. Toxicol. Sci. 97, 467–490.

    Article  CAS  PubMed  Google Scholar 

  39. Heryanto, B., Lipson, K. E., and Rogers, P. A. (2003) Effect of angiogenesis inhibitors on oestrogen-mediated endometrial endothelial cell proliferation in the ovariectomized mouse. Reproduction 125, 337–346.

    Article  CAS  PubMed  Google Scholar 

  40. Naciff, J. M., Overmann, G. J., Torontali, S. M., Carr, G. J., Tiesman, J. P., Richardson, B. D., and Daston, G. P. (2003) Gene expression profile induced by 17 alpha-ethynyl estradiol in the prepubertal female reproductive system of the rat. Toxicol. Sci. 72, 314–330.

    Article  CAS  PubMed  Google Scholar 

  41. Naciff, J. M., Overmann, G. J., Torontali, S. M., Carr, G. J., Tiesman, J. P., and Daston, G. P. (2004) Impact of the phytoestrogen content of laboratory animal feed on the gene expression profile of the reproductive system in the immature female rat. Environ. Health Perspect. 112, 1519–1526.

    Article  CAS  PubMed  Google Scholar 

  42. Helvering, L. M., Adrian, M. D., Geiser, A. G., Estrem, S. T., Wei, T., Huang, S., et al. U. (2005) Differential effects of estrogen and raloxifene on messenger RNA and matrix metalloproteinase 2 activity in the rat uterus. Biol. Reprod. 72, 830–841.

    Article  CAS  PubMed  Google Scholar 

  43. Creasy, D. M. (1997) Evaluation of testicular toxicity in safety evaluation studies: the appropriate use of spermatogenic staging. Toxicol. Pathol. 25, 119–131.

    Article  CAS  PubMed  Google Scholar 

  44. Stewart, J., and Turner, K. J. (2005) Inhibin B as a potential biomarker of testicular toxicity. Cancer Biomarkers 1, 75–91.

    CAS  PubMed  Google Scholar 

  45. Murugesan, P., Balaganesh, M., Balasubramanian, K., and Arunakaran, J. (2007) Effects of polychlorinated biphenyl (Aroclor 1254) on steroidogenesis and antioxidant system in cultured adult rat Leydig cells. J. Endocrinol. 192, 325–338.

    Article  CAS  PubMed  Google Scholar 

  46. Adachi, T., Koh, K. B., Tainaka, H., Matsuno, Y., Ono, Y., Sakurai, K., Fet al. (2004) Toxicogenomic difference between diethylstilbestrol and 17beta-estradiol in mouse testicular gene expression by neonatal exposure. Mol. Reprod. Dev. 67, 19–25.

    Article  CAS  PubMed  Google Scholar 

  47. Adachi, T., Ono, Y., Koh, K. B., Takashima, K., Tainaka, H., Matsuno, Y., et al. (2004) Long-term alteration of gene expression without morphological change in testis after neonatal exposure to genistein in mice: toxicogenomic analysis using cDNA microarray. Food Chem. Toxicol. 42, 445–452.

    Article  CAS  PubMed  Google Scholar 

  48. Moustafa, G. G., Ibrahim, Z. S., Hashimoto, Y., Alkelch, A. M., Sakamoto, K. Q., Ishizuka, M., and Fujita, S. (2007) Testicular toxicity of profenofos in matured male rats. Arch Toxicol. 81, 875–881.

    Article  CAS  PubMed  Google Scholar 

  49. Richburg, J. H., Johnson, K. J., Schoenfeld, H. A., Meistrich, M. L., and Dix, D. J. (2002) Defining the cellular and molecular mechanisms of toxicant action in the testis. Toxicol. Lett. 135, 167–183.

    Article  CAS  PubMed  Google Scholar 

  50. Shultz, V. D., Phillips, S., Sar, M., Foster, P. M., and Gaido, K. W. (2001) Altered gene profiles in fetal rat testes after in utero exposure to di(n-butyl) phthalate. Toxicol. Sci. 64, 233–242.

    Article  CAS  PubMed  Google Scholar 

  51. Tully, D. B., Bao, W., Goetz, A. K., Blystone, C. R., Ren, H., Schmid, J. E., et al. (2006) Gene expression profiling in liver and testis of rats to characterize the toxicity of triazole fungicides. Toxicol. Appl. Pharmacol. 215, 260–273.

    Article  CAS  PubMed  Google Scholar 

  52. Rockett, J. C., Christopher Luft, J., Brian Garges, J., Krawetz, S. A., Hughes, M. R., Hee Kirn, K., et al. (2001) Development of a 950-gene DNA array for examining gene expression patterns in mouse testis. Genome Biol. 2, 1–10.

    Google Scholar 

  53. Ryu, J. Y., Lee, B. M., Kacew, S., and Kim, H. S. (2007) Identification of differentially expressed genes in the testis of Sprague-Dawley rats treated with di(n-butyl) phthalate. Toxicology 234, 103–112.

    Article  CAS  PubMed  Google Scholar 

  54. Page, B. D., and Lacroix, G. M. (1995) The occurrence of phthalate ester and di-2-ethylhexyl adipate plasticizers in Canadian packaging and food sampled in 1985–1989: a survey. Food Addit. Contam. 12, 129–151.

    CAS  PubMed  Google Scholar 

  55. Saillenfait, A. M., Payan, J. P., Fabry, J. P., Beydon, D., Langonne, I., Gallissot, F., and Sabate, J. P. (1998) Assessment of the developmental toxicity, metabolism, and placental transfer of di-n-butyl phthalate administered to pregnant rats. Toxicol. Sci. 45, 212–224.

    CAS  PubMed  Google Scholar 

  56. Mylchreest, E., Cattley, R. C., and Foster, P. M. (1998) Male reproductive tract malformations in rats following gestational and lactational exposure to Di(n-butyl) phthalate: an antiandrogenic mechanism? Toxicol. Sci. 43, 47–60.

    CAS  PubMed  Google Scholar 

  57. Thompson, C. J., Ross, S. M., and Gaido, K. W. (2004) Di(n-butyl) phthalate impairs cholesterol transport and steroidogenesis in the fetal rat testis through a rapid and reversible mechanism. Endocrinology 145, 1227–1237.

    Article  CAS  PubMed  Google Scholar 

  58. Fukushima, T., Yamamoto, T., Kikkawa, R., Hamada, Y., Komiyama, M., Mori, C., and Horii, I. (2005) Effects of male reproductive toxicants on gene expression in rat testes. J. Toxicol. Sci. 30, 195–206.

    Article  CAS  PubMed  Google Scholar 

  59. Pelletier, G., Li, S., Luu-The, V., Tremblay, Y., Belanger, A., and Labrie, F. (2001) Immunoelectron microscopic localization of three key steroidogenic enzymes (cytochrome P450(scc), 3 beta-hydroxysteroid dehydrogenase and cytochrome P450(c17)) in rat adrenal cortex and gonads. J. Endocrinol. 171, 373–383.

    Article  CAS  PubMed  Google Scholar 

  60. Dalla Valle, L., Vianello, S., Belvedere, P., and Colombo, L. (2002) Rat cytochrome P450c17 gene transcription is initiated at different start sites in extraglandular and glandular tissues. J. Steroid Biochem. Mol. Biol. 82, 377–384.

    Article  CAS  PubMed  Google Scholar 

  61. Kaplowitz, N. (2005) Idiosyncratic drug hepatotoxicity. Nat. Rev. Drug Discov. 4, 489–499.

    Article  CAS  PubMed  Google Scholar 

  62. Liguori, M. J., and Waring, J. F. (2006) Investigations toward enhanced understanding of hepatic idiosyncratic drug reactions. Expert Opin. Drug Metab. Toxicol. 2, 835–846.

    Article  CAS  PubMed  Google Scholar 

  63. Uetrecht, J. (2007) Idiosyncratic drug reactions: current understanding. Annu. Rev. Pharmacol. Toxicol. 47, 513–539.

    Article  CAS  PubMed  Google Scholar 

  64. Waring, J. F., and Anderson, M. G. (2005) Idiosyncratic toxicity: mechanistic insights gained from analysis of prior compounds. Curr. Opin. Drug Discov. Dev. 8, 59–65.

    CAS  Google Scholar 

  65. Fielden, M. R., and Halbert, D. N. (2007) Iconix Biosciences, Inc. Pharmacogenomics 8, 401–405.

    Article  PubMed  Google Scholar 

  66. Leone, A. M., Kao, L. M., McMillian, M. K., Nie, A. Y., Parker, J. B., Kelley, M. F., et al. (2007) Evaluation of felbamate and other antiepileptic drug toxicity potential based on hepatic protein covalent binding and gene expression. Chem. Res. Toxicol. 20, 600–608.

    Article  CAS  PubMed  Google Scholar 

  67. Dieckhaus, C. M., Thompson, C. D., Roller, S. G., and Macdonald, T. L. (2002) Mechanisms of idiosyncratic drug reactions: the case of felbamate. Chem. Biol. Interact. 142, 99–117.

    Article  CAS  PubMed  Google Scholar 

  68. Naito, Y., Kuroda, M., Uchiyama, K., Mizushima, K., Akagiri, S., Takagi, T., et al. (2006) Inflammatory response of esophageal epithelium in combined-type esophagitis in rats: a transcriptome analysis. Int. J. Mol. Med. 18, 821–828.

    CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Cellular and Molecular Toxicology, Abbott Laboratories, Abbott Park, Illinois

    Wayne R. Buck, Jeffrey F. Waring & Eric A. Blomme

Authors
  1. Wayne R. Buck
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jeffrey F. Waring
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Eric A. Blomme
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Gene Logic Inc, Gaithersburg, MD, USA

    Donna L. Mendrick

  2. The Critical Path Institute, Rockville, MD, USA

    William B. Mattes

Rights and permissions

Reprints and permissions

Copyright information

© 2008 Humana Press, a part of Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Buck, W.R., Waring, J.F., Blomme, E.A. (2008). Use of Traditional End Points and Gene Dysregulation to Understand Mechanisms of Toxicity: Toxicogenomics in Mechanistic Toxicology. In: Mendrick, D.L., Mattes, W.B. (eds) Essential Concepts in Toxicogenomics. Methods in Molecular Biology™, vol 460. Humana Press. https://doi.org/10.1007/978-1-60327-048-9_2

Download citation

  • DOI: https://doi.org/10.1007/978-1-60327-048-9_2

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-638-2

  • Online ISBN: 978-1-60327-048-9

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation