Skip to main content
SpringerLink
Log in

TNFα Promoter Polymorphisms

  • Protocol
Tumor Necrosis Factor

Part of the book series: Methods in Molecular Medicine™ ((MIMM,volume 98))

  • 820 Accesses

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.

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 139.00
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

Notes

  1. 1.

    *

    For a Taq concentration of 5 U/μL.

  2. 2.

    *

    For a Taq concentration of 5 U/μL.

  3. 3.

    *

    For a Taq concentration of 5 U/μL.

References

  1. Hajeer, A. H. and Hutchinson, I. V. (2001) Influence of TNFalpha gene polymorphisms on TNFalpha production and disease. Hum. Immunol. 62, 1191–1199.

    Article  PubMed  CAS  Google Scholar 

  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.

    Article  PubMed  CAS  Google Scholar 

  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.

    Article  Google Scholar 

  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.

    Article  PubMed  CAS  Google Scholar 

  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.

    PubMed  Google Scholar 

  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.

    Article  PubMed  CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  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.

    PubMed  CAS  Google Scholar 

  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. 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.

    Article  CAS  Google Scholar 

  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.

    Article  PubMed  CAS  Google Scholar 

  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.

    Article  Google Scholar 

  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.

    PubMed  CAS  Google Scholar 

  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.

    Article  PubMed  CAS  Google Scholar 

  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.

    Article  PubMed  CAS  Google Scholar 

  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.

    Article  PubMed  Google Scholar 

  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.

    Article  PubMed  CAS  Google Scholar 

  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.

    Article  PubMed  CAS  Google Scholar 

  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.

    PubMed  CAS  Google Scholar 

  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.

    Article  PubMed  CAS  Google Scholar 

  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.

    Article  PubMed  CAS  Google Scholar 

  22. Field, M. (2001) Tumour necrosis factor polymorphisms in rheumatic diseases. Q.J.M. 94, 237–246.

    CAS  Google Scholar 

  23. Donaldson, P. T. (1999) TNF gene polymorphisms in primary biliary cirrhosis: a critical appraisal. J. Hepatol. 31, 366–368.

    Article  PubMed  CAS  Google Scholar 

  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.

    Article  PubMed  Google Scholar 

  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, 436–439

    Article  PubMed  CAS  Google Scholar 

  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.

    Article  PubMed  CAS  Google Scholar 

  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. 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.

    Article  PubMed  CAS  Google Scholar 

  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. 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.

    Article  PubMed  Google Scholar 

  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.

    Article  PubMed  CAS  Google Scholar 

  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 

Download references

Author information

Authors and Affiliations

  1. Department of Internal Medicine, Ospedale Maggiore Policlinico IRCCS, Università degli Studi, Padiglione Granelli, Milan, Italy

    Silvia Fargion, Luca Valenti, Paola Dongiovanni & Anna Ludovica Fracanzani

Authors
  1. Silvia Fargion
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Luca Valenti
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Paola Dongiovanni
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Anna Ludovica Fracanzani
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Department of Biological and Technological Research, Cancer Immunotherapy and Gene Therapy Program, San Raffaele H Scientific Institute, Milan, Italy

    Angelo Corti

  2. Mario Negri Institute for Pharmacological Research, Milan, Italy

    Pietro Ghezzi

Rights and permissions

Reprints and permissions

Copyright information

© 2004 Humana Press Inc.

About this protocol

Cite this protocol

Fargion, S., Valenti, L., Dongiovanni, P., Fracanzani, A.L. (2004). TNFα Promoter Polymorphisms. In: Corti, A., Ghezzi, P. (eds) Tumor Necrosis Factor. Methods in Molecular Medicine™, vol 98. Humana Press. https://doi.org/10.1385/1-59259-771-8:047

Download citation

  • DOI: https://doi.org/10.1385/1-59259-771-8:047

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-223-0

  • Online ISBN: 978-1-59259-771-0

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation