Skip to main content
SpringerLink
Log in
Book cover

International Conference on Computational Systems-Biology and Bioinformatics

CSBio 2010: Computational Systems-Biology and Bioinformatics pp 193–207Cite as

A Vaccine Strategy for Plant Allergy by RNA Interference – An in Silico Approach

  • Conference paper

  • 829 Accesses

Part of the book series: Communications in Computer and Information Science ((CCIS,volume 115))

Abstract

Worldwide population affected by allergic rhinitis and asthma are estimated to 400 million and 300 million respectively, and the medical costs for treatment are estimated to exceed that of tuberculosis and AIDS allied. The main objective of this research is to propose a vaccine design strategy for the management of allergy through siRNA vaccination in silencing IgE VH region. The allergen Che a 3 was chosen to demonstrate our approach. Docking interactions between Che a 3 and modeled structures of heavy chain variable region of 31 Immunoglobulin E clones were analyzed in AutoDock. Concurrently, small interference RNA sequences targeting the Immunoglobulin E clone with least binding energy were designed in siDRM.

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

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   39.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   54.99
Price excludes VAT (USA)
  • Compact, lightweight 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

Learn about institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Zhang, G., Khan, A., Srinivasan, K., Heiny, A., Lee, K., Kwoh, C., et al.: Hotspot Hunter: a computational system for large-scale screening and selection of candidate immunological hotspots in pathogen proteomes. BMC Bioinformatics 9 (suppl. 1:S19) (2008)

    Google Scholar 

  2. Holgate, S.T., Polosa, R.: Treatment strategies for allergy and asthma. Nat. Rev. Immunol. 8(3), 218–230 (2008)

    Article  CAS  PubMed  Google Scholar 

  3. Bisgaard, H., Hermansen, M.N., Loland, L., Halkjaer, L.B., Buchvald, F.: Intermittent inhaled corticosteroids in infants with episodic wheezing. The New England Journal of Medicine 354, 1998–2005 (2006)

    Article  CAS  PubMed  Google Scholar 

  4. Guilbert, T., Morgan, W., Zeiger, R., Mauger, D., Boehmer, S., Szefler, S., et al.: Long-term inhaled corticosteroids in preschool children at high risk for asthma. The New England Journal of Medicine 354, 1985–1997 (2006)

    Article  CAS  PubMed  Google Scholar 

  5. Harrison, T.W., Oborne, J., Newton, S., Tattersfield, A.E.: Doubling the dose of inhaled corticosteroid to prevent asthma exacerbations: randomised controlled trial. Lancet. 363, 271–275 (2004)

    Article  CAS  PubMed  Google Scholar 

  6. MacLennan, S., Barbara, J.A.J.: Risks and side effects of therapy with plasma and plasma fractions. Best Practice and Research Clinical Haematology 19(1), 169–189 (2006)

    Article  CAS  PubMed  Google Scholar 

  7. Hindmarch, I., Parrott, A.: A repeated dose comparison of the side effects of five antihistamines on objective assessments of psychomotor performance, central nervous system arousal and subjective appraisals of sleep and early morning behaviour. Arzneimittelforschung 28(3), 483–486 (1978)

    CAS  PubMed  Google Scholar 

  8. Cuvillo, A., Mullol, J., Bartra, J., Dvila, I., Juregui, I., Montoro, J., et al.: Comparative pharmacology of the H1 antihistamines. Journal of Investigational Allergology and Clinical Immunology 16(1), 3–12 (2006)

    PubMed  Google Scholar 

  9. Kindt, T.J., Goldsby, R.A., Osborne, B.A., Kuby, J.: Kuby immunology, 6th edn. W.H. Freeman, New York (2006)

    Google Scholar 

  10. Gawchik, S., Saccar, C.: Pollinex Quattro Tree: allergy vaccine. Expert Opinion on Biological Therapy 9(3), 377–382 (2009)

    Article  CAS  PubMed  Google Scholar 

  11. Carns, J., Robinson, D.: New strategies for allergen immunotherapy. Recent Patents on Inflammation and Allergy Drug Discovery 2(2), 92–101 (2008)

    Article  Google Scholar 

  12. Popescu, F.-D.: Antisense- and RNA interference-based therapeutic strategies in allergy. Journal of Cellular and Molecular Medicine 9(4), 840–853 (2005)

    Article  CAS  PubMed  Google Scholar 

  13. Kurreck, J.: Antisense technologies. Improvement through novel chemical modifications. European Journal of Biochemistry 270(8), 1628–1644 (2003)

    Article  CAS  PubMed  Google Scholar 

  14. Wadhwa, R.K.S., Miyagishi, M., Taira, K.: Know-how of RNA interference and its applications in research and therapy. Mutatation Research 567(1), 71–84 (2004)

    Article  CAS  Google Scholar 

  15. Bagasra, O., Prilliman, K.R.: RNA interference: The molecular immune system. Journal of Molecular Histology 35(6), 545–553 (2004)

    CAS  PubMed  Google Scholar 

  16. Suzuki, M., Zheng, X., Zhang, X., Li, M., Vladau, C., Ichim, T.E., et al.: Novel Vaccination for Allergy through Gene Silencing of CD40 Using Small Interfering RNA. The Journal of Immunology 180, 8461–8469 (2008)

    Article  CAS  PubMed  Google Scholar 

  17. Taylor, P.A., Friedman, T.M., Korngold, R., Noelle, R.J., Blazar, B.R.: Tolerance induction of alloreactive T cells via ex vivo blockade of the CD40: CD40L costimulatory pathway results in the generation of a potent immune regulatory cell. Blood 99, 4601–4609 (2002)

    Article  CAS  PubMed  Google Scholar 

  18. Taylor, J.J., Mohrs, M., Pearce, E.J.: Regulatory T cell responses develop in parallel to Th responses and control the magnitude and phenotype of the Th effector population. Journal of Immunology 176, 5839–5847 (2006)

    Article  CAS  Google Scholar 

  19. Thornton, C., Holloway, J., Popplewell, E., Shute, J., Boughton, J., Warner, J.: Fetal exposure to intact immunoglobulin E occurs via the gastrointestinal tract. Clinical and Experimental Allergy 33, 306–311 (2003)

    Article  CAS  PubMed  Google Scholar 

  20. Poole, J.A., Meng, J., Reff, M., Spellman, M.C., Rosenwasser, L.J.: Anti-CD23 monoclonal antibody, lumiliximab, inhibited allergen-induced responses in antigen-presenting cells and T cells from atopic subjects. Journal of Allergy and Clinical Immunology 116, 780–788 (2005)

    Article  CAS  PubMed  Google Scholar 

  21. Holgate, S., Casale, T., Wenzel, S., Bousquet, J., Deniz, Y., Reisner, C.: The anti-inflammatory effects of omalizumab confirm the central role of IgE in allergic inflammation. Journal of Allergy and Clinical Immunology 115, 459–465 (2005)

    Article  CAS  PubMed  Google Scholar 

  22. Duarte, J., Deshpande, P., Guiyedi, V., Mcheri, S., Fesel, C., Cazenave, P.-A., et al.: Total and functional parasite specific IgE responses in Plasmodium falciparum-infected patients exhibiting different clinical status. Malaria Journal 6(1) (2007)

    Google Scholar 

  23. Erb, K.J.: Helminths, allergic disorders and IgE-mediated immune responses: Where do we stand? European Journal of Immunology 37, 1170–1173 (2007)

    Article  CAS  PubMed  Google Scholar 

  24. Naohiro Watanabe, F.B., Korenaga, M.: IgE: a question of protective immunity in Trichinella spiralis infection. Trends in Parasitology 21(4), 175–178 (2005)

    Article  PubMed  Google Scholar 

  25. Karagiannis, S.N., Wang, Q., East, N., Burke, F., Riffard, S., Bracher, M.G., et al.: Activity of human monocytes in IgE antibodydependent surveillance and killing of ovarian tumor cells. European Journal of Immunology 33, 1030–1040 (2003)

    Article  CAS  PubMed  Google Scholar 

  26. Alt, F.W., Yancopoulos, G.D., Blackwell, T.K.: Ordered rearrangement of immunoglobulin heavy chain variable region segments. EMBO Journal 3, 1209–1219 (1984)

    CAS  PubMed  PubMed Central  Google Scholar 

  27. Alt, F., Oltz, E., Young, F., Gorman, J., Taccioli, G., Chen, J.: VDJ recombination. Immunology Today 13, 306–314 (1992)

    Article  CAS  PubMed  Google Scholar 

  28. Stephanie Culler, T.R.H., Glassy, M., Chau, P.C.: Canonical Structure Repertoire of the Antigen-binding Site of Immunoglobulins Suggests Strong Geometrical Restrictions Associated to the Mechanism of Immune Recognition. Journal of Molecular Biology 254(3-1), 497–504 (1995)

    Google Scholar 

  29. Chothia, C., Lesk, A.M.: Canonical structures for the hypervariable regions of immunoglobulins. Journal of Molecular Biology 196, 901–917 (1987)

    Article  CAS  PubMed  Google Scholar 

  30. Gong, W., Ren, Y., Zhou, H., Wang, Y., Kang, S., Li, T.: siDRM: an effective and generally applicable online siRNA design tool. Bioinformatics 24(20), 2405–2406 (2008)

    Article  CAS  PubMed  Google Scholar 

  31. Goodsell, D., Olson, A.: Automated docking of substrates to proteins by simulated annealing. Proteins 8, 195–202 (1990)

    Article  CAS  PubMed  Google Scholar 

  32. Morris, G., Goodsell, D., Huey, R., Olson, A.: Distributed automated docking of flexible ligands to proteins: parallel applications of AutoDock 2.4. Journal of Computer-Aided Molecular Design 10, 293–304 (1996)

    Article  CAS  PubMed  Google Scholar 

  33. Morris, G., Goodsell, D., Halliday, R., Huey, R., Hart, W., Belew, R., et al.: Automated docking using a Lamarckian genetic algorithm and empirical binding free energy function. Journal of Computational Chemistry 19, 1639–1662 (1998)

    Article  CAS  Google Scholar 

  34. Alasdair, T.R.L., Richard, M.J.: Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites. Bioinformatics 29(9), 1908–1916 (2005)

    Google Scholar 

  35. Coker, H.A., Harries, H.E., Banfield, G.K., Carr, V.A., Durham, S.R., Chevretton, E., et al.: Biased use of VH5 IgE-positive B cells in the nasal mucosa in allergic rhinitis. Journal of Allergy and Clinical Immunology 116(2), 445–452 (2005)

    Article  CAS  PubMed  Google Scholar 

  36. Bordoli, L., Kiefer, F., Arnold, K., Benkert, P., Battey, J., Schwede, T.: Protein structure homology modeling using SWISS-MODEL workspace. Nature Protocols 4(1-3) (2009)

    Google Scholar 

  37. Hilemana, R.E., Silvanovicha, A., Goodmana, R.E., Ricea, E.A., Holleschaka, G., Astwooda, J.D., et al.: Bioinformatic Methods for Allergenicity Assessment Using a Comprehensive Allergen Database. International Archives of Allergy and Immunology 128(4) (2002)

    Google Scholar 

  38. Bairoch, A., Apweiler, R.: The SWISS-PROT protein sequence data bank and its supplement TrEMBL. Nucleic Acids Research 25(1), 31–36 (1997)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Kroemer, R.T., Hecht, P., Guessregen, S., Liedl, K.R.: Improving the Predictive Quality of CoMFA Models. In: 3D QSAR in Drug Design, pp. 41–56. Springer, Netherlands (2006)

    Google Scholar 

  40. Birmingham, A., Anderson, E., Sullivan, K., Reynolds, A., Boese, Q., Leake, D., et al.: A protocol for designing siRNAs with high functionality and specificity. Nature Protocols 2(9), 2068–2078 (2007)

    Article  CAS  PubMed  Google Scholar 

  41. Kosloff, M., Kolodny, R.: Sequence-similar, structure-dissimilar protein pairs in the PDB. Proteins 71(2), 891–902 (2008)

    Article  CAS  PubMed  Google Scholar 

  42. Arnold, K., Bordoli, L., Kopp, J., Schwede, T.: The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics 22, 195–201 (2006)

    Article  CAS  PubMed  Google Scholar 

  43. Wheeler, D.L., Barrett, T., Benson, D.A., Bryant, S.H., Canese, K., Chetvernin, V., et al.: Database resources of the National Center for Biotechnology Information. Nucleic Acids Research 35(D5-D12) (2007)

    Google Scholar 

  44. Schwede, T., Kopp, J., Guex, N., Peitsch, M.: SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Research 31, 3381–3385 (2003)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Guex, N., Peitsch, M.C.: SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modelling. Electrophoresis 18, 2714–2723 (1997)

    Article  CAS  PubMed  Google Scholar 

  46. Melo, F., Feytmans, E.: Assessing protein structures with a non-local atomic interaction energy. Journal of Molecular Biology 277, 1141–1152 (1998)

    Article  CAS  PubMed  Google Scholar 

  47. Xu, J., Davis, M.: Diversity in the CDR3 region of V(H) is sufficient for most antibody specificities. Immunity 13, 37–45 (2000)

    Article  CAS  PubMed  Google Scholar 

  48. Ichim, T., Popov, I., Riordan, N., Izadi, H., Zhong, Z., Yijian, L., et al.: A novel method of modifying immune responses by vaccination with lipiodol-siRNA mixtures. Journal of Translational Medicine 3(4) (2006)

    Google Scholar 

  49. Behnecke, A., Chen, L., Saxon, A., Zhang, K.: Development of an IgE-based Allergen Gene Vaccine for Severe Food Allergy. Journal of Allergy and Clinical Immunology 121(2), S212 (2008)

    Article  Google Scholar 

  50. Katia, S.G., Raja, J., Elena, Z., Teresa, M.P.: Predicting domain-domain interactions using a parsimony approach. Genome Biology 7, R104 (2006)

    Article  Google Scholar 

  51. Kaplan, W., Littlejohn, T.G.: Swiss-PDB Viewer (Deep View). Briefings in Bioinformatics 2(2), 195–197 (2001)

    Article  CAS  PubMed  Google Scholar 

  52. Huang, B., Schroeder, M.: Using protein binding site prediction to improve protein docking. Gene. 422(1-2), 14–21 (2008)

    Article  CAS  PubMed  Google Scholar 

  53. Ghersi, D., Sanchez, R.: Improving accuracy and efficiency of blind protein-ligand docking by focusing on predicted binding sites. Proteins: Structure, Function, and Bioinformatics 74(2), 417–424 (2009)

    Article  CAS  Google Scholar 

  54. Dunker, A.K., Obradovic, Z.: The protein trinitylinking function and disorder. Nature Biotechnology 19, 805–806 (2001)

    Article  CAS  PubMed  Google Scholar 

  55. Reichmann, D., Rahata, O., Cohena, M., Neuvirtha, H., Schreiber, G.: The molecular architecture of protein-protein binding sites. Current Opinion in Structural Biology 17(1), 67–76 (2007)

    Article  CAS  PubMed  Google Scholar 

  56. Horn, J.R., Kraybill, B., Petro, E.J., Coales, S.J., Morrow, J.A., Hamuro, Y., et al.: The Role of Protein Dynamics in Increasing Binding Affinity for an Engineered ProteinProtein Interaction Established by H/D Exchange Mass Spectrometry. Biochemistry 45(58), 8488–8498 (2006)

    Article  CAS  PubMed  Google Scholar 

  57. Verdino, P., Barderas, R., Villalba, M., Westritschnig, K., Valenta, R., Rodriguez, R., et al.: Three-Dimensional Structure of the Cross-Reactive Pollen Allergen Che a 3: Visualizing Cross-Reactivity on the molecular Surfaces of Weed, Grass, and Tree Pollen Alergens. The Journal of Immunology (2007)

    Google Scholar 

  58. Hornung, V., Guenthner-Biller, M., Bourquin, C., Ablasser, A., Schlee, M., Uematsu, S., et al.: Sequence-specific potent induction of IFN-alpha by short interfering RNA in plasmacytoid dendritic cells through TLR7. Nature Medicine 2005(3), 263–270 (2005)

    Article  Google Scholar 

  59. Lewis, B., Burge, C., Bartel, D.: Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120(1), 15–20 (2005)

    Article  CAS  PubMed  Google Scholar 

  60. Sinha, S., Tompa, M.: YMF: a Program for Discovery of Novel Transcription Factor Binding Sites by Statistical Overrepresentation. Nucleic Acids Research 31(13), 3586–3588 (2003)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Sinha, S., Tompa, M.: Discovery of Novel Transcription Factor Binding Sites by Statistical Overrepresentation. Nucleic Acids Research 30(24), 5549–5560 (2002)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Sinha, S., Tompa, M.: A Statistical Method for Finding Transcription Factor Binding Sites. In: Eighth International Conference on Intelligent Systems for Molecular Biology, San Diego, CA, pp. 344–354 (August 2000)

    Google Scholar 

  63. Blanchette, M., Sinha, S.: Separating real motifs from their artifacts. Bioinformatics 17, S30–S38 (2001)

    Article  Google Scholar 

  64. Andrasson, U., Flicker, S., Lindstedt, M., Valenta, R., Greiff, L., Korsgren, M., et al.: The human IgE-encoding transcriptome to assess antibody repertoires and repertoire evolution. Journal of Molecular Biology 362(2), 212–227 (2006)

    Article  Google Scholar 

  65. Dahlke, I., Nott, D., Ruhno, J., Sewell, W., Collins, A.: Antigen selection in the IgE response of allergic and nonallergic individuals. Journal of Allergy and Clinical Immunology 117(6), 1477–1483 (2006)

    Article  CAS  PubMed  Google Scholar 

  66. Galibert, L., van Dooren, J., Durand, I., Rousset, F., Jefferis, R., Banchereau, J., et al.: Anti-CD40 plus interleukin-4-activated human naive B cell lines express unmutated immunoglobulin genes with intraclonal heavy chain isotype variability. European Journal of Immunology 25(3), 733–777 (1995)

    Article  CAS  PubMed  Google Scholar 

  67. Davies, J.M., O’Hehir, R.E.: Immunogenetic characteristics of immunoglobulin E in allergic disease. Clinical & Experimental Allergy 38(4), 566–578 (2008)

    Article  CAS  Google Scholar 

  68. Snow, R., Djukanovic, R., Stevenson, F.: Analysis of immunoglobulin E VH transcripts in a bronchial biopsy of an asthmatic patient confirms bias towards VH5, and indicates local clonal expansion, somatic mutation and isotype switch events. Immunology 98(4), 646–651 (1999)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. van der Stoep, N., van der Linden, J., Logtenberg, T.: Molecular evolution of the human immunoglobulin E response: high incidence of shared mutations and clonal relatedness among epsilon VH5 transcripts from three unrelated patients with atopic dermatitis. Journal of Experimental Medicine 177(1), 99–107 (1993)

    Article  PubMed  Google Scholar 

  70. Pettifer, S.R., Sinnott, J.R., Attwood, T.K.: UTOPIAUser-Friendly Tools for Operating Informatics Applications. Comparative and Functional Genomics 5(1), 56–60 (2004)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. School of Computer Engineering, Nanyang Technological University, Nanyang Avenue, Singapore, 639798

    Ramya Ramadoss & Chee Keong Kwoh

Authors
  1. Ramya Ramadoss
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Chee Keong Kwoh
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. School of Information Technology, King Mongkut’s University of Technology Thonburi, 126 Pracha U-Thit Rd, Bangmod, Thungkru, 10140, Bangkok, Thailand

    Jonathan H. Chan

  2. School of Computer Engineering, Nanyang Technological University, Block N4, 2b-39,Nanyang Avenue, 639798, Singapore

    Yew-Soon Ong

  3. Dept. of Computer Science, Yonsei University, 134 Shinchon-dong, Sudaemoon-ku, 120-749, Seoul, South Korea

    Sung-Bae Cho

Rights and permissions

Reprints and permissions

Copyright information

© 2010 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Ramadoss, R., Kwoh, C.K. (2010). A Vaccine Strategy for Plant Allergy by RNA Interference – An in Silico Approach. In: Chan, J.H., Ong, YS., Cho, SB. (eds) Computational Systems-Biology and Bioinformatics. CSBio 2010. Communications in Computer and Information Science, vol 115. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-16750-8_17

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-16750-8_17

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-16749-2

  • Online ISBN: 978-3-642-16750-8

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation