Abstract
The immune system plays an important role in the development of personalized medicine for a variety of diseases including cancer, autoimmune diseases, and infectious diseases. Immunoinformatics, or computational immunology, is an emerging area that provides fundamental methodologies in the study of immunomics, that is, immune-related genomics and proteomics. The integration of immunoinformatics with systems biology approaches may lead to a better understanding of immune-related diseases at various systems levels. Such methods can contribute to translational studies that bring scientific discoveries of the immune system into better clinical practice. One of the most intensely studied areas of the immune system is immune epitopes. Epitopes are important for disease understanding, host–pathogen interaction analyses, antimicrobial target discovery, and vaccine design. The information about genetic diversity of the immune system may help define patient subgroups for individualized vaccine or drug development. Cellular pathways and host immune-pathogen interactions have a crucial impact on disease pathogenesis and immunogen design. Epigenetic studies may help understand how environmental changes influence complex immune diseases such as allergy. High-throughput technologies enable the measurements and catalogs of genes, proteins, interactions, and behavior. Such perception may contribute to the understanding of the interaction network among humans, vaccines, and drugs, to enable new insights of diseases and therapeutic responses. The integration of immunomics information may ultimately lead to the development of optimized vaccines and drugs tailored to personalized prevention and treatment. An immunoinformatics portal containing relevant resources is available at http://immune.pharmtao.com.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Rapin N, Kesmir C, Frankild S et al (2006) Modelling the human immune system by combining bioinformatics and systems biology approaches. J Biol Phys 32:335–353
Brusic V, Petrovsky N (2003) Immuno-informatics – the new kid in town. Novartis Found Symp 254:3–13, discussion 13–22, 98–101, 250–252
Yan Q (2005) Pharmacogenomics and systems biology of membrane transporters. Mol Biotechnol 29:75–88
Yan Q (2008) Bioinformatics databases and tools in virology research: an overview. In Silico Biol 8:71–85
Ebert LM, Liu YC, Clements CS et al (2009) A long, naturally presented immunodominant epitope from NY-ESO-1 tumor antigen: implications for cancer vaccine design. Cancer Res 69:1046–1054
Evans MC (2008) Recent advances in immunoinformatics: application of in silico tools to drug development. Curr Opin Drug Discov Devel 11:233–241
Peters B, Sidney J, Bourne P et al (2005) The design and implementation of the immune epitope database and analysis resource. Immunogenetics 57:326–336
NIAID Category A, B, and C Priority Pathogens. Available at http://www3.niaid.nih.gov/topics/BiodefenseRelated/Biodefense/research/CatA.html. Accessed June 2009
Doytchinova IA, Guan P, Flower DR (2006) EpiJen: a server for multistep T cell epitope prediction. BMC Bioinform 7:131
Bhasin M, Raghava GP (2004) Prediction of CTL epitopes using QM, SVM and ANN techniques. Vaccine 22:3195–3204
Toseland CP, Clayton DJ, McSparron H et al (2005) AntiJen: a quantitative immunology database integrating functional, thermodynamic, kinetic, biophysical, and cellular data. Immunome Res 1:4
Yan Q (2003) Pharmacogenomics of membrane transporters: an overview. Methods Mol Biol 227:1–20
Lefranc MP, Giudicelli V, Ginestoux C et al (2009) IMGT, the international ImMunoGeneTics information system. Nucleic Acids Res 37:D1006–D1012
Altschul SF, Gish W, Miller W et al (1990) Basic local alignment search tool. J Mol Biol 215:403–410
Larkin MA, Blackshields G, Brown NP et al (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948
Pagni M, Ioannidis V, Cerutti L et al (2007) MyHits: improvements to an interactive resource for analyzing protein sequences. Nucleic Acids Res 35:W433–W437
Dutta S, Burkhardt K, Swaminathan GJ et al (2008) Data deposition and annotation at the worldwide protein data bank. Methods Mol Biol 426:81–101
Yan Q (2008) The integration of personalized and systems medicine: bioinformatics support for pharmacogenomics and drug discovery. Methods Mol Biol 448:1–19
Wang SS, Bratti MC, Rodriguez AC et al (2009) Common variants in immune and DNA repair genes and risk for human papillomavirus persistence and progression to cervical cancer. J Infect Dis 199:20–30
Onay VU, Briollais L, Knight JA et al (2006) SNP-SNP interactions in breast cancer susceptibility. BMC Cancer 6:114
Robinson J, Marsh SG (2007) IPD: the Immuno Polymorphism Database. Methods Mol Biol 409:61–74
Horton R, Gibson R, Coggill P et al (2008) Variation analysis and gene annotation of eight MHC haplotypes: the MHC Haplotype Project. Immunogenetics 60:1–18
Schuler MM, Donnes P, Nastke MD et al (2005) SNEP: SNP-derived epitope prediction program for minor H antigens. Immunogenetics 57:816–820
Halling-Brown M, Quartey-Papafio R, Travers PJ et al (2006) SiPep: a system for the prediction of tissue-specific minor histocompatibility antigens. Int J Immunogenet 33:289–295
Gardy JL, Lynn DJ, Brinkman FS et al (2009) Enabling a systems biology approach to immunology: focus on innate immunity. Trends Immunol 30:249–262
Lynn DJ, Winsor GL, Chan C et al (2008) InnateDB: facilitating systems-level analyses of the mammalian innate immune response. Mol Syst Biol 4:218
Driscoll T, Dyer MD, Murali TM et al (2009) PIG – the pathogen interaction gateway. Nucleic Acids Res 37:D647–D650
McSparron H, Blythe MJ, Zygouri C et al (2003) JenPep: a novel computational information resource for immunobiology and vaccinology. J Chem Inf Comput Sci 43:1276–1287
Chatr-aryamontri A, Ceol A, Peluso D et al (2009) VirusMINT: a viral protein interaction database. Nucleic Acids Res 37:D669–D673
Okuda S, Yamada T, Hamajima M et al (2008) KEGG Atlas mapping for global analysis of metabolic pathways. Nucleic Acids Res 36:W423–W426
Matthews L, Gopinath G, Gillespie M et al (2009) Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res 37:D619–D622
Xenarios I, Salwinski L, Duan XJ et al (2002) DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res 30:303–305
Cline MS, Smoot M, Cerami E et al (2007) Integration of biological networks and gene expression data using Cytoscape. Nat Protoc 2:2366–2382
Horton P, Park KJ, Obayashi T et al (2007) WoLF PSORT: protein localization predictor. Nucleic Acids Res 35:W585–W587
Hamosh A, Scott AF, Amberger JS et al (2005) Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res 33:D514–D517
Griffiths-Jones S, Saini HK, van Dongen S et al (2008) miRBase: tools for microRNA genomics. Nucleic Acids Res 36:D154–D158
Martino DJ, Prescott SL (2009) Silent mysteries: epigenetic paradigms could hold the key to conquering the epidemic of allergy and immune disease. Allergy 65:7–15
Tomasi TB, Magner WJ, Khan AN (2006) Epigenetic regulation of immune escape genes in cancer. Cancer Immunol Immunother 55:1159–1184
Setiadi AF, David MD, Seipp RP et al (2007) Epigenetic control of the immune escape mechanisms in malignant carcinomas. Mol Cell Biol 27:7886–7894
Amoreira C, Hindermann W, Grunau C (2003) An improved version of the DNA Methylation database (MethDB). Nucleic Acids Res 31:75–77
Nam MJ, Madoz-Gurpide J, Wang H et al (2003) Molecular profiling of the immune response in colon cancer using protein microarrays: occurrence of autoantibodies to ubiquitin C-terminal hydrolase L3. Proteomics 3:2108–2115
Wolter TR, Wong R, Sarkar SA et al (2009) DNA microarray analysis for the identification of innate immune pathways implicated in virus-induced autoimmune diabetes. Clin Immunol 132:103–115
Soreq L, Israel Z, Bergman H et al (2008) Advanced microarray analysis highlights modified neuro-immune signaling in nucleated blood cells from Parkinson’s disease patients. J Neuroimmunol 201–202:227–236
Korb M, Rust AG, Thorsson V et al (2008) The Innate Immune Database (IIDB). BMC Immunol 9:7
Hijikata A, Kitamura H, Kimura Y et al (2007) Construction of an open-access database that integrates cross-reference information from the transcriptome and proteome of immune cells. Bioinformatics 23:2934–2941
Barrett T, Edgar R (2006) Gene expression omnibus: microarray data storage, submission, retrieval, and analysis. Methods Enzymol 411:352–369
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2010 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Yan, Q. (2010). Immunoinformatics and Systems Biology Methods for Personalized Medicine. In: Yan, Q. (eds) Systems Biology in Drug Discovery and Development. Methods in Molecular Biology, vol 662. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-60761-800-3_10
Download citation
DOI: https://doi.org/10.1007/978-1-60761-800-3_10
Published:
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-60761-799-0
Online ISBN: 978-1-60761-800-3
eBook Packages: Springer Protocols