Antigen arrays for antibody profiling

https://doi.org/10.1016/j.cbpa.2005.12.028Get rights and content

Antigen array technologies enable large-scale profiling of the specificity of antibody responses against autoantigens, tumor antigens and microbial antigens. Antibody profiling will provide insights into pathogenesis, and will enable development of novel tests for diagnosis and guiding therapy in the clinic. Recent advances in the field include development of antigen array-based approaches to examine immune responses against antigens encoded in genetic libraries, post-translationally modified proteins, and other biomolecules such as lipids. A promising application is the use of antibody profiling to guide development and selection of antigen-specific therapies to treat autoimmune disease. This review discusses these advances and the challenges ahead for development and refinement of antibody profiling technologies for use in the research laboratory and the clinic.

Introduction

Production of high-affinity, high-avidity antibodies is a hallmark of many autoimmune and infectious diseases. Further, detection of antibodies represents a mainstay in laboratory diagnostics for multiple autoimmune and infectious diseases. For example, detection of blood autoantibodies targeting immunoglobulin (rheumatoid factor) and/or citrullinated peptides contributes to the diagnosis of rheumatoid arthritis (RA) [1], whereas detection of autoantibodies targeting nuclear antigens (anti-nuclear antibodies [ANAs]) suggests the diagnosis of systemic lupus erythematosus (SLE) [2]. Microbial infections, including infections with Epstein Barr virus (EBV), hepatitis B virus (HBV) and human immunodeficiency virus (HIV), can be diagnosed by detection of host antibody responses against the microbe.

Antigen arrays represent a powerful approach for large-scale characterization of antibody responses against candidate antigens. Antigen arrays provide the ability to identify and characterize antibodies targeting known and novel antigens, and to identify antibody profiles that provide insights into the pathogenesis of disease and provide diagnostic and prognostic utility. This review provides an overview of antigen arrays and highlights several recent applications of antigen array technologies in autoimmune disease, cancer and infectious disease.

Section snippets

Antigen array technologies

A variety of antigen array technologies for antibody profiling have been developed. Proteins and peptides representing candidate autoantigens can be attached to planar surfaces in ordered arrays to survey autoantibody binding [3, 4, 5]. Antibody characterization can also be performed using arrays of in situ synthesized peptides generated by photolithography [6] or synthesized on pins [7, 8]. Arrays of mammalian cells [9] or yeast [10] expressing defined cDNAs, and arrays produced using in situ

Autoimmune disease

Autoimmune diseases affect an estimated 3% of the world population, and arise from aberrant activation of immune responses to target tissues or cells within the body. Examples of autoimmune diseases include RA, in which the synovial joints are targeted; autoimmune type I diabetes, in which β cells in the pancreatic islets of Langerhans are targeted; and SLE, in which a variety of nuclear components are targeted.

Despite knowledge of the specific tissues and cells targeted and the involvement of

Strategies for antigen discovery

A major limitation for most antigen array analyses is that the utilized antigens are limited to proteins and other biomolecules that are known to represent candidate targets, and for which synthetic or purified preparations are available. Further, for many autoimmune, malignant and infectious diseases the antigens remain poorly characterized. It is estimated that an individual cell expresses approximately 10 000 proteins [33]. The ability to produce or purify the constellation of polypeptide

Antibody and cytokine profiling identify molecular subsets of RA

We developed ‘arthritis arrays’ containing the putative autoantigens in RA. Arthritis microarrays revealed targeting of citrullinated proteins in a subpopulation of RA patients possessing clinical and laboratory features predictive of more severe arthritis [37] (Figure 1). We also performed multiplex analysis of blood cytokines in RA using a bead array. Integration of blood autoantibody and cytokine profiles revealed distinct subtypes of RA (W Hueber and W Robinson, unpublished data). We

Conclusions

Major progress is being made towards developing and refining antigen array technologies for profiling antibody responses in autoimmune, malignant and infectious diseases. Profiles of antibody reactivities are anticipated to provide superior diagnostic and predictive value as compared to individual specificities. Significant work remains to elucidate and define the antigen targets in a variety of autoimmune, infectious and malignant diseases. Major challenges also remain in the refinement,

References and recommended reading

Papers of particular interest, published within the annual period of review, have been highlighted as:

  • • of special interest

  • •• of outstanding interest

Acknowledgements

The author thanks Drs L Steinman and PJ Utz, as well as Drs W Hueber, J Kanter and other members of the Robinson, Steinman and Utz laboratories. This work was supported by NIH K08 AR02133, NIH NHLBI contract N01 HV 28183, and a Department of Veterans Affairs Merit Award to WHR and NIH P30 DK56339 to the Stanford Digestive Disease Center

References (44)

  • H.M. Geysen et al.

    Use of peptide synthesis to probe viral antigens for epitopes to a resolution of a single amino acid

    Proc Natl Acad Sci USA

    (1984)
  • J. James et al.

    Sequential autoantigenic determinants of the small nuclear ribonucleoprotein Sm D shared by human lupus autoantibodies and MRL lpr/lpr antibodies

    Clin Exp Immunol

    (1994)
  • J. Ziauddin et al.

    Microarrays of cells expressing defined cDNAs

    Nature

    (2001)
  • H. Zhu et al.

    Global analysis of protein activities using proteome chips

    Science

    (2001)
  • M. He et al.

    Single step generation of protein arrays from DNA by cell-free expression and in situ immobilisation (PISA method)

    Nucleic Acids Res

    (2001)
  • R.J. Fulton et al.

    Advanced multiplexed analysis with the FlowMetrix system

    Clin Chem

    (1997)
  • S.R. Nicewarner-Pena et al.

    Submicrometer metallic barcodes

    Science

    (2001)
  • P.J. Utz

    Protein arrays for studying blood cells and their secreted products

    Immunol Rev

    (2005)
  • H. Zhu et al.

    Proteomics

    Annu Rev Biochem

    (2003)
  • V.K. Kuchroo et al.

    T cell response in experimental autoimmune encephalomyelitis (EAE): role of self and cross-reactive antigens in shaping, tuning, and regulating the autopathogenic T cell repertoire

    Annu Rev Immunol

    (2002)
  • A. Vincent

    Unravelling the pathogenesis of myasthenia gravis

    Nat Rev Immunol

    (2002)
  • K.B. Yancey

    The pathophysiology of autoimmune blistering diseases

    J Clin Invest

    (2005)
  • Cited by (0)

    View full text