Systems biology approaches to new vaccine development

Current Opinion in Immunology

Volumn 23, Issue 3, 2011, Pages 436-443

  Oberg, Ann L ^a   Kennedy, Richard B ^a   Li, Peter ^a   Ovsyannikova, Inna G ^a   Poland, Gregory A ^a  

^a MAYO CLINIC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

VACCINE;

BIOINFORMATICS; DRUG EFFICACY; DRUG RESEARCH; DRUG SAFETY; EXPERIMENTAL MODEL; FLOW CYTOMETRY; HIGH THROUGHPUT SCREENING; HOST RESISTANCE; HUMAN; IMMUNE RESPONSE; INFORMATION PROCESSING; KNOWLEDGE BASE; LIPIDOMICS; METABOLOMICS; PROTEOMICS; REVIEW; SYSTEMS BIOLOGY;

ANIMALS; DRUG DESIGN; HUMANS; MODELS, BIOLOGICAL; PROTEOMICS; SYSTEMS BIOLOGY; VACCINES;

EID: 79957777939     PISSN: 09527915     EISSN: 18790372     Source Type: Journal    
DOI: 10.1016/j.coi.2011.04.005     Document Type: Review

References (63)

1. Poland G.A. Pharmacology, vaccinomics, and the second golden age of vaccinology. Clin Pharmacol Ther 2007, 82:623-626.
2. Poland G.A., Ovsyannikova I.G., Jacobson R.M., Smith D.I. Heterogeneity in vaccine immune response: the role of immunogenetics and the emerging field of vaccinomics. Clin Pharmacol Ther 2007, 82:653-664.
3. Centers for Disease Control and Prevention Reported vaccine-preventable diseases - United States, 1993, and the childhood immunization initiative. MMWR 1994, 43:57-60.
4. Pulendran B., Li S., Nakaya H.I. Systems vaccinology. Immunity 2010, 33:516-529.
5. Kitano H. Computational systems biology. Nature 2002, 420:206-210.
6. Joyce A.R., Palsson B.O. The model organism as a system: integrating 'omics' data sets. Nat Rev Mol Cell Biol 2006, 7:198-210.
7. Ng A., Bursteinas B., Gao Q., Mollison E., Zvelebil M. Resources for integrative systems biology: from data through databases to networks and dynamic system models. Brief Bioinform 2006, 7:318-330.
8. Luber C.A., Cox J., Lauterbach H., Fancke B., Selbach M., Tschopp J., Akira S., Wiegand M., Hochrein H., O'Keeffe M., Mann M. Quantitative proteomics reveals subset-specific viral recognition in dendritic cells. Immunity 2010, 32:279-289.
9. Nita-Lazar A. Quantitative analysis of phosphorylation-based protein signaling networks in the immune system by mass spectrometry. Wiley Interdiscip Rev Syst Biol Med 2011, 3:368-376.
10. Bakal C., Perrimon N. Realizing the promise of RNAi high throughput screening. Dev Cell 2010, 18:506-507.
11. Aleksic J., Russell S. ChIPing away at the genome: the new frontier travel guide. Mol Biosyst 2009, 5:1421-1428.
12. Poland G.A., Ovsyannikova I.G., Jacobson R.M. Application of pharmacogenomics to vaccines. Pharmacogenomics 2009, 10:837-852.
13. Oberg A.L., Vitek O. Statistical design of quantitative mass spectrometry-based proteomic experiments. J Proteome Res 2009, 8:2144-2156.
14. Auer P.L., Doerge R.W. Statistical design and analysis of RNA sequencing data. Genetics 2010, 185:405-416.
15. Leek J.T., Scharpf R.B., Bravo H.C., Simcha D., Langmead B., Johnson W.E., Geman D., Baggerly K., Irizarry R.A. Tackling the widespread and critical impact of batch effects in high-throughput data. Nat Rev Genet 2010, 11:733-739.
16. Simon R.M., Paik S., Hayes D.F. Use of archived specimens in evaluation of prognostic and predictive biomarkers. J Natl Cancer Inst 2009, 101:1446-1452.
17. Ransohoff D.F., Gourlay M.L. Sources of bias in specimens for research about molecular markers for cancer. J Clin Oncol 2010, 28:698-704.
18. Subramanian J., Simon R. Gene expression-based prognostic signatures in lung cancer: ready for clinical use?. J Natl Cancer Inst 2010, 102:464-474.
19. Thomas G., Jacobs K.B., Kraft P., Yeager M., Wacholder S., Cox D.G., Hankinson S.E., Hutchinson A., Wang Z., Yu K., et al. A multistage genome-wide association study in breast cancer identifies two new risk alleles at 1p11.2 and 14q24.1 (RAD51L1). Nat Genet 2009, 41:579-584.
20. Witten D.M., Tibshirani R. Covariance-regularized regression and classification for high-dimensional problems. J R Stat Soc Series B Stat Methodol 2009, 71:615-636.
21. Davis N.A., Crowe J.E., Pajewski N.M., McKinney B.A. Surfing a genetic association interaction network to identify modulators of antibody response to smallpox vaccine. Genes Immun 2010, 11:630-636.
22. McKinney B.A., Crowe J.E., Guo J., Tian D. Capturing the spectrum of interaction effects in genetic association studies by simulated evaporative cooling network analysis. PLoS Genet 2009, 5:e1000432.
23. Zhao Y., Simon R. Development and validation of predictive indices for a continuous outcome using gene expression profiles. Cancer Inform 2010, 9:105-114.
24. Shi L., Campbell G., Jones W.D., Campagne F., Wen Z., Walker S.J., Su Z., Chu T.M., Goodsaid F.M., Pusztai L., et al. The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nat Biotechnol 2010, 28:827-838.
25. Subramanian J., Simon R. What should physicians look for in evaluating prognostic gene-expression signatures?. Nat Rev Clin Oncol 2010, 7:327-334.
26. Steyerberg E: Clinical Prediction Models: A Practical Approach to Development, Validation, and Updating. Statistics for Biology and Health. Springer; 2009.
27. Altman D.G., Vergouwe Y., Royston P., Moons K.G. Prognosis and prognostic research: validating a prognostic model. Br Med J 2009, 338:b605.
28. Frelinger J., Ottinger J., Gouttefangeas C., Chan C. Modeling flow cytometry data for cancer vaccine immune monitoring. Cancer Immunol Immunother 2010, 59:1435-1441.
29. Myers C.L., Chiriac C., Troyanskaya O.G. Discovering biological networks from diverse functional genomic data. Methods Mol Biol 2009, 563:157-175.
30. Reif D.M., Motsinger-Reif A.A., McKinney B.A., Rock M.T., Crowe J.E., Moore J.H. Integrated analysis of genetic and proteomic data identifies biomarkers associated with adverse events following smallpox vaccination. Genes Immun 2009, 10:112-119.
31. He Y., Xiang Z. Bioinformatics analysis of Brucella vaccines and vaccine targets using VIOLIN. Immunome Res 2010, 6 Suppl 1:S5.
32. Koraka P., Martina B.E., Osterhaus A.D. Bioinformatics in new generation flavivirus vaccines. J Biomed Biotechnol 2010, 2010:864029.
33. Heinz E., Tischler P., Rattei T., Myers G., Wagner M., Horn M. Comprehensive in silico prediction and analysis of chlamydial outer membrane proteins reflects evolution and life style of the Chlamydiae. BMC Genomics 2009, 10:634.
34. Khan J.M., Ranganathan S. pDOCK: a new technique for rapid and accurate docking of peptide ligands to Major Histocompatibility Complexes. Immunome Res 2010, 6 Suppl 1:S2.
35. Sanchez-Burgos G., Ramos-Castaneda J., Cedillo-Rivera R., Dumonteil E. Immunogenicity of novel Dengue virus epitopes identified by bioinformatic analysis. Virus Res 2010, 153:113-120.
36. Larsen M.V., Lelic A., Parsons R., Nielsen M., Hoof I., Lamberth K., Loeb M.B., Buus S., Bramson J., Lund O. Identification of CD8+ T cell epitopes in the West Nile virus polyprotein by reverse-immunology using NetCTL. PLoS ONE 2010, 5:e12697.
37. Steinbruck L., McHardy A.C. Allele dynamics plots for the study of evolutionary dynamics in viral populations. Nucleic Acids Res 2010.
38. Chong Y.L., Padhi A., Hudson P.J., Poss M. The effect of vaccination on the evolution and population dynamics of avian paramyxovirus-1. PLoS Pathog 2010, 6:e1000872.
39. Wang A., Johnston S.C., Chou J., Dean D. A systemic network for Chlamydia pneumoniae entry into human cells. J Bacteriol 2010, 192:2809-2815.
40. Guo X., Xu Y., Bian G., Pike A.D., Xie Y., Xi Z. Response of the mosquito protein interaction network to dengue infection. BMC Genomics 2010, 11:380.
41. Querec T.D., Akondy R.S., Lee E.K., Cao W., Nakaya H.I., Teuwen D., Pirani A., Gernert K., Deng J., Marzolf B., et al. Systems biology approach predicts immunogenicity of the yellow fever vaccine in humans. Nat Immunol 2009, 10:116-125.
42. Kumagai Y., Akira S. Identification and functions of pattern-recognition receptors. J Allergy Clin Immunol 2010, 125:985-992.
43. Jan M., Meng S., Chen N.C., Mai J., Wang H., Yang X.F. Inflammatory and autoimmune reactions in atherosclerosis and vaccine design informatics. J Biomed Biotechnol 2010, 2010:459798.
44. Ahlers J.D., Belyakov I.M. New paradigms for generating effective CD8+ T cell responses against HIV-1/AIDS. Discov Med 2010, 9:528-537.
45. Love T.M., Thurston S.W., Keefer M.C., Dewhurst S., Lee H.Y. Mathematical modeling of ultradeep sequencing data reveals that acute CD8+ T-lymphocyte responses exert strong selective pressure in simian immunodeficiency virus-infected macaques but still fail to clear founder epitope sequences. J Virol 2010, 84:5802-5814.
46. Kaewpongsri S., Sukasem C., Srichunrusami C., Pasomsub E., Zwang J., Pairoj W., Chantratita W. An integrated bioinformatics approach to the characterization of influenza A/H5N1 viral sequences by microarray data: implication for monitoring H5N1 emerging strains and designing appropriate influenza vaccines. Mol Cell Probes 2010, 24:387-395.
47. Romano C.M., de Carvalho-Mello I.M., Jamal L.F., de Melo F.L., Iamarino A., Motoki M., Pinho J.R., Holmes E.C., de Andrade Zanotto P.M. Social networks shape the transmission dynamics of hepatitis C virus. PLoS ONE 2010, 5:e11170.
48. Salathe M., Jones J.H. Dynamics and control of diseases in networks with community structure. PLoS Comput Biol 2010, 6:e1000736.
49. Pappalrado F., Zhang P., Halling-Brown M., Basford K., Scalia A., Shepherd A., Moss D., Motta S., Brusic V. Computational simulations of the immune systems for personalized medicine: state of the art and challenges. Curr Pharmacogenomics Person Med 2008, 6:260-271.
50. Yan Q. Immunoinformatics and systems biology methods for personalized medicine. Methods Mol Biol 2010, 662:203-220.
51. Poland G.A., Ovsyannikova I.G., Jacobson R.M., Vierkant R.A., Jacobsen S.J., Pankratz V.S., Schaid D.J. Identification of an association between HLA class II alleles and low antibody levels after measles immunization. Vaccine 2001, 20:430-438.
52. Ovsyannikova I.G., Jacobson R.M., Dhiman N., Vierkant R.A., Pankratz V.S., Poland G.A. Human leukocyte antigen and cytokine receptor gene polymorphisms associated with heterogeneous immune responses to mumps viral vaccine. Pediatrics 2008, 121:e1091-e1099.
53. McKinney B.A., Reif D.M., Rock M.T., Edwards K.M., Kingsmore S.F., Moore J.H., Crowe J.E. Cytokine expression patterns associated with systemic adverse events following smallpox immunization. J Infect Dis 2006, 194:444-453.
54. Pulendran B. Learning immunology from the yellow fever vaccine: innate immunity to systems vaccinology. Nat Rev Immunol 2009, 9:741-747.
55. Gaucher D., Therrien R., Kettaf N., Angermann B.R., Boucher G., Filali-Mouhim A., Moser J.M., Mehta R.S., Drake D.R., Castro E., et al. Yellow fever vaccine induces integrated multilineage and polyfunctional immune responses. J Exp Med 2008, 205:3119-3131.
56. Zahradnik J.M., Couch R.B., Gerin J.L. Safety and immunogenicity of a purified hepatitis B virus vaccine prepared by using recombinant DNA technology. J Infect Dis 1987, 155:903-908.
57. Lowy D.R., Schiller J.T. Prophylactic human papillomavirus vaccines. J Clin Invest 2006, 116:1167-1173.
58. Ovsyannikova I.G., johnson K.L., Bergen H.R., Poland G.A. Mass spectrometry and peptide-based vaccine development. Clin Pharmacol Ther 2007, 82:644-652.
59. Ovsyannikova I.G., Pankratz S.V., Vierkant R., Jacobson R.M., Poland G.A. Human leukocyte antigen haplotypes in the genetic control of immune response to measles-mumps-rubella vaccine. J Infect Dis 2006, 193:655-663.
60. Ovsyannikova I.G., Jacobson R.M., Vierkant R.A., Pankratz V.S., Poland G.A. HLA supertypes and immune responses to measles-mumps-rubella viral vaccine: findings and implications for vaccine design. Vaccine 2007, 25:3090-3100.
61. Baechler E.C., Batliwalla F.M., Karypis G., Gaffney P.M., Ortmann W.A., Espe K.J., Shark K.B., Grande W.J., Hughes K.M., Kapur V., et al. Interferon-inducible gene expression signature in peripheral blood cells of patients with severe lupus. Proc Natl Acad Sci USA 2003, 100:2610-2615.
62. Bennett L., Palucka A.K., Arce E., Cantrell V., Borvak J., Banchereau J., Pascual V. Interferon and granulopoiesis signatures in systemic lupus erythematosus blood. J Exp Med 2003, 197:711-723.
63. Bauer J.W., Baechler E.C., Petri M., Batliwalla F.M., Crawford D., Ortmann W.A., Espe K.J., Li W., Patel D.D., Gregersen P.K., Behrens T.W. Elevated serum levels of interferon-regulated chemokines are biomarkers for active human systemic lupus erythematosus. PLoS Med 2006, 3:e491.