TNFα Promoter Polymorphisms

  • Silvia Fargion
  • Luca Valenti
  • Paola Dongiovanni
  • Anna Ludovica Fracanzani
Part of the Methods in Molecular Medicine™ book series (MIMM, volume 98)

Abstract

Polymorphisms in the promoter of the tumor necrosis factor alpha (TNFα) gene have been reported to affect the transcription rate and the release of this cytokine. Among the best studied, the −238 and −308 polymorphisms have been associated with an increased transcriptional activity and TNFα release, whereas the −863 polymorphism have been associated with a reduced transcriptional activity. A growing body of evidence indicates that these polymorphisms may affect susceptibility to different diseases.

Here we describe a method to detect the −238, −308, and −863 TNFα polymorphisms by the polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) analysis. Briefly, DNA is amplified by PCR using mutagenic primers containing a single base-pair mismatch adjacent to the polymorphic site to introduce a restriction site into the wild-type nucleotide sequences after amplification. The PCR products are then digested with specific restriction enzymes and analyzed by agarose gel electrophoresis.

Key Words

TNFα promoter polymorphism restriction analysis PCR TNFα −308 polymorphism TNFα −238 polymorphism TNFα −863 polymorphism genetic susceptibility 

References

  1. 1.
    Hajeer, A. H. and Hutchinson, I. V. (2001) Influence of TNFalpha gene polymorphisms on TNFalpha production and disease. Hum. Immunol. 62, 1191–1199.PubMedCrossRefGoogle Scholar
  2. 2.
    Daly, A. K. and Day, C. P. (2001) Candidate gene case-control association studies: advantages and potential pitfalls. Br. J. Clin. Pharmacol. 52, 489–499.PubMedCrossRefGoogle Scholar
  3. 3.
    Wilson, A. G., de Vries, N., Pociot, F., di Giovine, F. S., van de Putte, L. B. A., and Duff, G. W. (1993) An allelic polymorphism within the human tumour necrosis factor alpha promoter region is strongly associated with the HLA A1, B8 and DR3 alleles. J. Exp. Med. 177, 577–560.CrossRefGoogle Scholar
  4. 4.
    Wilson, A. G., di Giovine, F. S., Blakemore, A. I. F., and Duff G. W. (1992) Single base polymorphism in the human tumour necrosis factor alpha (TNFα) gene detectable by NcoI restriction of PCR product. Hum. Mol. Genet. 1, 353.PubMedCrossRefGoogle Scholar
  5. 5.
    D’Alfonso, S. and Richiardi, P. M. (1994) A polymorphic variation in a putative regulation box of the TNFα alpha promoter region. Immunogenetics 39, 150–154.PubMedGoogle Scholar
  6. 6.
    Wilson, A. G., Symon, J. A., McDowell, T. L., McDevitt, H. O., and Duff, G. W. (1997) Effects of a polymorphism in the human tumor necrosis factor alpha promoter on transcriptional activation. Proc. Natl. Acad. Sci. USA 94, 3195–3199.PubMedCrossRefGoogle Scholar
  7. 7.
    Abraham, L. J. and Koeger, K. M. (1999) Impact of the −308 TNF promoter polymorphism on the transcriptional regulation of the TNF gene: relevance to the disease. J. Leuk. Biol. 66, 562–566.Google Scholar
  8. 8.
    Drouet, C., Shakov, A. N., and Jongeneel, C. V. (1991) Enhancers and transcription factors controlling the inducibility of the tumor necrosis factor-α in primary macrophages. J. Immunol. 147, 1694–1700.PubMedGoogle Scholar
  9. 9.
    Ruwende, C., McGuire, W., Coleman, E., Kwiatkowski, D., Corrah, T., Whittle, H., et al. (1996) Association of a tumor necrosis factor promoter polymorphism with susceptibility to pulmonary tubercolosis. (Abstract) Clin. Sci. 90, 3P.Google Scholar
  10. 10.
    Kroeger, K. M., Carville, K. S., and Abraham, I. J. (1997) The −308 tumor necrosis factor-α promoter polymorphism affects transcription. Mol. Immmunol. 34, 391–399.CrossRefGoogle Scholar
  11. 11.
    Skoog, T., van’t Hooft, F. M., Kallin, B., Jovinge, S., Boquist, S., Nilsson, J., et al. (1999) A common functional polymorphism (C>A substitution at position −863) in the promoter region of the tumour necrosis factor-α(TNF-α) gene associated with reduced circulating levels of TNF-α. Hum. Mol. Genet. 8, 1443–1449.PubMedCrossRefGoogle Scholar
  12. 12.
    Kroeger, K. M., Steer, J. H., Joyce, D. A., and Abraham, L. J. (2000) Effects of stimulus and cell type on the expression of the −308 tumour necrosis factor promoter polymorphism. Cytokine 2, 110–119.CrossRefGoogle Scholar
  13. 13.
    Grimble, R. F., Howell, W. M., O’Reilly, G., Turner, S. J., Markovic, O., Hirrell, S., et al. (2002) The ability of fish oil to suppress tumor necrosis factor α production by peripheral blood mononuclear cells in healthy men is associated with polymorphisms in genes that influence tumor necrosis factor α production. Am. J. Clin. Nutr. 76, 454–459.PubMedGoogle Scholar
  14. 14.
    Pociot, F., D’Alfonso, S., Compasso, S., Scorza, R., and Richiardi, P. M. (1995) Functional analysis of a new polymorphism in the human TNF α gene promoter. Scand. J. Immunol. 42, 501–504.PubMedCrossRefGoogle Scholar
  15. 15.
    Kaijzel, E. L., Bayley, J.-P., van Krugten, M. V., Smith, L., van de Linde, P., Bakker, A. M., et al. (2001) Allele-specific quantification of tumor necrosis factor alpha (TNF) transcription and the role of promoter polymorphisms in rheumatoid arthritis patients and healthy individuals. Genes Immun. 2, 135–144.PubMedCrossRefGoogle Scholar
  16. 16.
    De Jong, B. A., Westendorp, R. G. J., Bakker, A. M., and Huizinga, T. W. J. (2002) Polymorphisms in or near tumour necrosis factor (TNF)-gene do not determine levels of endotoxin-induced TNF production. Genes Immun. 3, 25–29.PubMedCrossRefGoogle Scholar
  17. 17.
    Hohjoh, H. and Tokunaga, K. (2001) Allele specific binding of the ubiquitous transcription factor OCT-1 to the functional single nucleotide polymorphism (SNP) sites in the tumor necrosis factor-alpha gene (TNFα) promoter. Genes Immun. 2, 105–109.PubMedCrossRefGoogle Scholar
  18. 18.
    Wilson, A. G. (1999) Genetics of tumour necrosis factor (TNFα) in autoimmune liver diseases: red hot or red herring? J. Hepatol. 30, 331–333.PubMedCrossRefGoogle Scholar
  19. 19.
    Wilson, A. G., di Giovine, F. S., and Duff G. W. (1995) Genetics of tumour necrosis factor-α in autoimmune, infectious and neoplastic illnesses. J. Inflamm. 45, 1–42.PubMedGoogle Scholar
  20. 20.
    McGuire, W., Hill, A. V. S., Allsopp, C. E. F., Greenwood, B. M., and Kwiatkowski, D. (1994) Cerebral malaria is associated with a polymorphism in the promoter region of the human TNF-α gene. Nature 371, 508–511.PubMedCrossRefGoogle Scholar
  21. 21.
    Jacob, C. O., Fronek, Z., Lewis, G. D., Koo, M., Hansen, J. A., and McDevitt, H. O. (1990) Hereditable major histocompatibility complex class II-associated differences in production of tumour necrosis factor α: relevance to genetic predisposition to systemic lupus erythematosus. Proc. Natl. Acad. Sci. USA 87, 1233–1237.PubMedCrossRefGoogle Scholar
  22. 22.
    Field, M. (2001) Tumour necrosis factor polymorphisms in rheumatic diseases. Q.J.M. 94, 237–246.Google Scholar
  23. 23.
    Donaldson, P. T. (1999) TNF gene polymorphisms in primary biliary cirrhosis: a critical appraisal. J. Hepatol. 31, 366–368.PubMedCrossRefGoogle Scholar
  24. 24.
    Juszczynski, J., Kalinka, E., Bienvenu, J., Woszczech, G., Borowiec, M., Robak, T., et al. (2002) Human leukocyte antigens class II and tumor necrosis factor genetic polymorphisms are independent predictors of non-Hodgkin lymphoma outcome. Blood 100, 3037–3040.PubMedCrossRefGoogle Scholar
  25. 25.
    McCusker, S. M., Curran, M. D., Dynan, K. B., McCullagh, C. D., Urquhart, D. D., Middleton, D., et al. (2001) Association between polymorphism in the regulatory gene encoding tumour necrosis factor alpha and the risk of Alzheimer’s disease and vascular dementia: a case-control study. Lancet 357, 436–439PubMedCrossRefGoogle Scholar
  26. 26.
    Fargion, S., Valenti, L., Dongiovanni, P., Scaccabarozzi, A., Fracanzani, A. L., Taioli, E., et al. (2001) Tumor necrosis factor α promoter polymorphisms influence the phenotypic expression of hereditary hemochromatosis. Blood 97, 3707–3712.PubMedCrossRefGoogle Scholar
  27. 27.
    Hohler, T., Kruger, A., Gerken, G., Schneider, P. M., Meyer zum Buschenfelde, K. H., and Rittner, C. (1998) Tumor necrosis factor promoter polymorphism at position −238 is associated with chronic active hepatitis C infection. J. Med. Virol. 54, 173–177.Google Scholar
  28. 28.
    Valenti, L., Fracanzani, A. L., Dongiovanni, P., Santorelli, G., Branchi, A., Taioli, E., et al. (2002) Tumor necrosis factor α promoter polymorphisms and insulin resistance in nonalcoholic fatty liver disease. Gastroenterology 122, 274–280.PubMedCrossRefGoogle Scholar
  29. 29.
    Jang, W. H., Yang, Y. I., Yea, S. S., Lee, Y. J., Chun, J. H., Kim, H. I., et al. The −238 tumor necrosis factor-alpha promoter polymorphism is associated with decreased susceptibility to cancers. Cancer Lett. 166, 41–46.Google Scholar
  30. 30.
    Van Heel, D. A., Udalova, I. A., De Silva, A. P., McGovern, D. P., Kinouchi, Y., Hull, J., et al. (2002) Inflammatory bowel disease is associated with a TNF polymorphism that affects the interaction between the OCT1 and NF-κB transcription factors. Hum. Mol. Genet. 11, 1281–1289.PubMedCrossRefGoogle Scholar
  31. 31.
    Grove, J., Daly, A. K., Bassendine, M. F., and Day, C. P. (1997) Association of a tumor necrosis factor promoter polymorphism with susceptibility to alcoholic steatohepatitis. Hepatology 26, 143–146.PubMedCrossRefGoogle Scholar
  32. 32.
    Sambrook, J. and Russel, D. W., eds. Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 2001.Google Scholar

Copyright information

© Humana Press Inc. 2004

Authors and Affiliations

  • Silvia Fargion
    • 1
  • Luca Valenti
    • 1
  • Paola Dongiovanni
    • 1
  • Anna Ludovica Fracanzani
    • 1
  1. 1.Department of Internal MedicineOspedale Maggiore Policlinico IRCCS, Università degli Studi, Padiglione GranelliMilanItaly

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