Skip to main content
NCBI home page
Springer Nature - PMC COVID-19 Collection logoLink to Springer Nature - PMC COVID-19 Collection
. 2009 Jan 19;52(1):43–49. doi: 10.1007/s11427-009-0006-7

Current research status of immunology in the genomic era

HaoWen Li 1, JinZhi Li 1, GuoPing Zhao 2, Ying Wang 1,2,✉
PMCID: PMC7089291  PMID: 19152083

Abstract

This review updates the current status of immunology research under the influence of genomics, both conceptually and technologically. It particularly highlights the advantages of employing the high-throughput and large-scale technology, the large genomic database, and bioinformatic power in the immunology research. The fast development in the fields of basic immunology, clinical immunology (tumor and infectious immunology) and vaccine designing is illustrated with respect to the successful usage of genomic strategy. We also speculate the future research directions of immunology in the era of genomics and post-genomics.

Keywords: genomics, immunology, clinical immunology, vaccine design

Footnotes

Supported by the National High-Tech Research and Development Program of China (Grant No.2006AA02A252), National Natural Science Foundation of China (Grant No.30771965) and Shanghai Pujiang Program (Grant No.07pj14066).

References

  • 1.Zhou G. Y. Immunology. Shanghai: Shanghai Science & Technology Press; 2007. [Google Scholar]
  • 2.Mak T. W. The T cell antigen receptor: “The Hunting of the Snark”. Eur J Immunol. 2007;37(Suppl1):S83–S93. doi: 10.1002/eji.200737443. [DOI] [PubMed] [Google Scholar]
  • 3.Nicholson L. B., Kuchroo V. K. T cell recognition of self and altered self antigens. Crit Rev Immunol. 1997;17(5–6):449–462. [PubMed] [Google Scholar]
  • 4.Takeda K., Akira S. Roles of Toll-like receptors in innate immune responses. Genes Cells. 2001;6(9):733–742. doi: 10.1046/j.1365-2443.2001.00458.x. [DOI] [PubMed] [Google Scholar]
  • 5.Klysik J. Concept of immunomics: a new frontier in the battle for gene function? Acta Biotheor. 2001;49(3):191–202. doi: 10.1023/A:1011901410166. [DOI] [PubMed] [Google Scholar]
  • 6.Santamaria P., Lindstrom A. L., Boyce-Jacino M. T., et al. HLA class I sequence-based typing. Hum Immunol. 1993;37(1):39–50. doi: 10.1016/0198-8859(93)90141-M. [DOI] [PubMed] [Google Scholar]
  • 7.Lemaitre B., Nicolas E., Michaut L., et al. The dorsoventral regulatory gene cassette spatzle/Toll/cactus controls the potent antifungal response in Drosophila adults. Cell. 1996;86(6):973–983. doi: 10.1016/S0092-8674(00)80172-5. [DOI] [PubMed] [Google Scholar]
  • 8.Rock F. L., Hardiman G., Timans J. C., et al. A family of human receptors structurally related to Drosophila Toll. Proc Natl Acad Sci USA. 1998;95(2):588–593. doi: 10.1073/pnas.95.2.588. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 9.Lu B., Zagouras P., Fischer J. E., et al. Kinetic analysis of genomewide gene expression reveals molecule circuitries that control T cell activation and Th1/2 differentiation. Proc Natl Acad Sci USA. 2004;101(9):3023–3028. doi: 10.1073/pnas.0307743100. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 10.Lund R. J., Löytömäki M., Naumanen T., et al. Genome-wide identification of novel genes involved in early Th1 and Th2 cell differentiation. J Immunol. 2007;178(6):3648–3660. doi: 10.4049/jimmunol.178.6.3648. [DOI] [PubMed] [Google Scholar]
  • 11.Santegoets S. J., Gibbs S., Kroeze K., et al. Transcriptional profiling of human skin-resident Langerhans cells and CD1a+ dermal dendritic cells: differential activation states suggest distinct functions. J Leukoc Biol. 2008;84(1):143–151. doi: 10.1189/jlb.1107750. [DOI] [PubMed] [Google Scholar]
  • 12.Harenberg A., Guillaume F., Ryan E. J., et al. Gene profiling analysis of ALVAC infected human monocyte derived dendritic cells. Vaccine. 2008;26(39):5004–5013. doi: 10.1016/j.vaccine.2008.07.050. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 13.Tarama R., Kato H., Ishikawa Y., et al. Gene expression changes induced by type IV allergy-inducible chemicals in dendritic cells. J Vet Med Sci. 2008;70(7):673–680. doi: 10.1292/jvms.70.673. [DOI] [PubMed] [Google Scholar]
  • 14.Miles A. K., Matharoo-Ball B., Li G., et al. The identification of human tumour antigens: Current status and future developments. Cancer Immunol Immunother. 2006;55(8):996–1003. doi: 10.1007/s00262-005-0115-5. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 15.Van der Bruggen P., Traversari C., Chomez P., et al. A gene encoding an antigen recognized by cytolytic T lymphocytes on a human melanoma. Science. 1991;254(5038):1643–1647. doi: 10.1126/science.1840703. [DOI] [PubMed] [Google Scholar]
  • 16.Sahin U., Türeci O., Schmitt H., et al. Human neoplasms elicit multiple specific immune responses in the autologous host. Proc Natl Acad Sci USA. 1995;92(25):11810–11813. doi: 10.1073/pnas.92.25.11810. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 17.Fortunato G., Calcagno G., Bresciamorra V., et al. Multiple sclerosis and hepatitis C virus infection are associated with single nucleotide polymorphisms in interferon pathway genes. J Interferon Cytokine Res. 2008;28(3):141–152. doi: 10.1089/jir.2007.0049. [DOI] [PubMed] [Google Scholar]
  • 18.Liou J. M., Lin J. T., Wang H. P., et al. IL-1B-511 C→T polymorphism is associated with increased host susceptibility to Helicobacter pylori infection in Chinese. Helicobacter. 2007;12(2):142–149. doi: 10.1111/j.1523-5378.2007.00484.x. [DOI] [PubMed] [Google Scholar]
  • 19.Wurfel M. M., Gordon A. C., Holden T. D., et al. Toll-like receptor 1 polymorphisms affect innate immune responses and outcomes in sepsis. Am J Respir Crit Care Med. 2008;178(7):710–720. doi: 10.1164/rccm.200803-462OC. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 20.Masignani V., Rappuoli R., Pizza M. Reverse vaccinology: a genome- based approach for vaccine development. Expert Opin Biol Ther. 2002;2(8):895–905. doi: 10.1517/14712598.2.8.895. [DOI] [PubMed] [Google Scholar]
  • 21.Pizza M., Scarlato V., Masignani V., et al. Identification of vaccine candidates against serogroup B meningococcus by whole-genome sequencing. Science. 2000;287(5459):1816–1820. doi: 10.1126/science.287.5459.1816. [DOI] [PubMed] [Google Scholar]
  • 22.Tettelin H., Saunders N. J., Heidelberg J., et al. Complete genome sequence of Neisseria meningitidis serogroup B strain MC58. Science. 2000;287(5459):1809–1815. doi: 10.1126/science.287.5459.1809. [DOI] [PubMed] [Google Scholar]
  • 23.Wizemann T. M., Heinrichs J. H., Adamou J. E., et al. Use of a whole genome approach to identify vaccine molecules affording protection against Streptococcus pneumoniae infection. Infect Immun. 2001;69(3):1593–1598. doi: 10.1128/IAI.69.3.1593-1598.2001. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 24.Maione D., Margarit I., Rinaudo C. D., et al. Identification of a universal group B streptococcus vaccine by multiple genome screen. Science. 2005;309(5731):148–150. doi: 10.1126/science.1109869. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 25.Bodilis J., Barray S. Molecular evolution of the major outer-membrane protein gene (oprF) of Pseudomonas. Microbiology. 2006;152(Pt4):1075–1088. doi: 10.1099/mic.0.28656-0. [DOI] [PubMed] [Google Scholar]
  • 26.Ren S. X., Fu G., Jiang X. G., et al. Unique physiological and pathogenic features of Leptospira interrogans revealed by whole-genome sequencing. Nature. 2003;422(6934):888–893. doi: 10.1038/nature01597. [DOI] [PubMed] [Google Scholar]
  • 27.Yang H. L., Zhu Y. Z., Qin J. H., et al. In silico and microarray-based genomic approaches to identifying potential vaccine candidates against Leptospira interrogans. BMC Genomics. 2006;7:293. doi: 10.1186/1471-2164-7-293. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 28.Hassainya Y., Garcia-Pons F., Kratzer R., et al. Identification of naturally processed HLA-A2-restricted proinsulin epitopes by reverse immunology. Diabetes. 2005;54(7):2053–2059. doi: 10.2337/diabetes.54.7.2053. [DOI] [PubMed] [Google Scholar]
  • 29.Singh H., Raghava G. P. ProPred: prediction of HLA-DR binding sites. Bioinformatics. 2001;17(12):1236–1237. doi: 10.1093/bioinformatics/17.12.1236. [DOI] [PubMed] [Google Scholar]
  • 30.Donnes P., Elofsson A. Prediction of MHC class I binding peptides, using SVMHC. BMC Bioinformatics. 2002;3:25. doi: 10.1186/1471-2105-3-25. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 31.Akiyama Y., Maruyama K., Nara N., et al. Cytotoxic T cell induction against human malignant melanoma cells using HLA-A24-restricted melanoma peptide cocktail. Anticancer Res. 2004;24(2B):571–577. [PubMed] [Google Scholar]
  • 32.Correa I., Plunkett T. Update on HER-2 as a target for cancer therapy: HER2/neu peptides as tumour vaccines for T cell recognition. Breast Cancer Res. 2001;3(6):399–403. doi: 10.1186/bcr330. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 33.Jin S., Wang Y., Zhang Y., et al. Humoral immune responses against tumor-associated antigen OVA66 originally defined by serological analysis of recombinant cDNA expression libraries and its potentiality in cellular immunity. Cancer Sci. 2008;99(8):1670–1678. doi: 10.1111/j.1349-7006.2008.00860.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 34.Doytchinova I. A., Guan P., Flower D. R. Quantitative structure-activity relationships and the prediction of MHC supermotifs. Methods. 2004;34(4):444–453. doi: 10.1016/j.ymeth.2004.06.007. [DOI] [PubMed] [Google Scholar]
  • 35.Haste Andersen P., Nielsen M., Lund O. Prediction of residues in discontinuous B-cell epitopes using protein 3D structures. Protein Sci. 2006;15(11):2558–2567. doi: 10.1110/ps.062405906. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 36.Saha S., Bhasin M., Raghava G. P. Bcipep: a database of B-cell epitopes. BMC Genomics. 2005;6(1):79. doi: 10.1186/1471-2164-6-79. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 37.Reiche N., Jung A., Brabletz T., et al. Generation and characterization of human monoclonal scFv antibodies against Helicobacter pylori antigens. Infect Immun. 2002;70(8):4158–4164. doi: 10.1128/IAI.70.8.4158-4164.2002. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 38.Duan J., Yan X., Guo X., et al. A human SARS-CoV neutralizing antibody against epitope on S2 protein. Biochem Biophys Res Commun. 2005;333(1):186–193. doi: 10.1016/j.bbrc.2005.05.089. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Science in China. Series C, Life Sciences are provided here courtesy of Nature Publishing Group

RESOURCES