Serum Profiling Using Protein Microarrays to Identify Disease Related Antigens

Abstract

Disease related antigens are of great importance in the clinic. They are used as markers to screen patients for various forms of cancer, to monitor response to therapy, or to serve as therapeutic targets (Chapman et al., Ann Oncol 18(5):868–873, 2007; Soussi et al., Cancer Res 60:1777–1788, 2000; Anderson and LaBaer, J Proteome Res 4:1123–1133, 2005; Levenson, Biochim Biophy Acta 1770:847–856, 2007). In cancer endogenous levels of protein expression may be disrupted or proteins may be expressed in an aberrant fashion resulting in an immune response that bypasses self tolerance (Soussi et al., Cancer Res 60:1777–1788, 2000; Disis et al., J Clin Oncol 15(11):3363–3367, 1997; Molina et al., Breast Cancer Res Treat 51:109–119, 1998). Protein microarrays, which represent a large fraction of the human proteome, have been used to identify antigens in multiple diseases including cancer (Anderson and LaBaer, J Proteome Res 4:1123–1133, 2005; Disis et al., J Clin Oncol 15(11):3363–3367, 1997; Hudson et al., Proc Natl Acad Sci U S A 104(44):17494–17499, 2007; Beyer et al., J Neuroimmunol 242:26–32, 2012). Typically, arrays are probed with immunoglobulin (Ig) samples from patients as well as healthy controls, then compared to determine which antigens (Ag's) are more reactive within the patient group (Hudson et al., Proc Natl Acad Sci U S A 104(44):17494–17499).

Autoantibody discovery across monogenic, acquired, and COVID-19-associated autoimmunity with scalable PhIP-seq

“…Two complementary approaches for proteome-wide autoantibody discovery include printed protein arrays and phage-immunoprecipitation sequencing (PhIP-seq) ( Jeong et al, 2012 ; Larman et al, 2011 ; Sharon and Snyder, 2014 ; Zhu et al, 2001 ). While powerful, printed protein arrays can be cost- and volume-prohibitive and are not flexible to adapting or generating new antigen libraries.…”

Proteome-wide survey of the autoimmune target repertoire in autoimmune polyendocrine syndrome type 1

“…Autoantibody markers in current clinical use have been identified over decades, often through hypothesis driven efforts. Now developments in protein array technology have opened a novel avenue for explorative biomarker studies in autoimmune diseases and for capturing a higher degree of complexity in autoimmune responses 5 6 7 . Current-day protein arrays contain many thousands of full-length human proteins and enable autoantibody screens at the proteome-scale.…”

PAWER: protein array web exploreR

“…Raw GPR files are uploaded to PAWER (1), then the system proceeds to identifying foreground and background intensities and a panel of control proteins that can be used for normalisation (2). Robust linear model is then used to estimate and remove the technical artifacts associated with each array and array block (3). Normalised data is then combined with sample metadata (4) to produce a list of differentially expressed proteins (5).…”

“…In functional protein microarrays, full-length functional protein targets or protein domains are attached to the surface of the slide and then incubated with a biological sample that contains interacting molecules (e.g. autoantibodies) [ 3 ]. After molecules bind to their targets, labelling is done via secondary antibody with a fluorescent marker attached.…”