Autoantigen discovery with a synthetic human peptidome

• Published in: Nature biotechnology 2011-06, Vol.29 (6), p.535-541
• Main Authors: Solimini, Nicole L, Elledge, Stephen J, Larman, H Benjamin, Zhao, Zhenming, Laserson, Uri, Li, Mamie Z, Ciccia, Alberto, Gakidis, M Angelica Martinez, Church, George M, Kesari, Santosh, LeProust, Emily M
• Format: Article
• Language: English
• Subjects: 631/45/475/2290; 631/61/24; 692/699/249/1313; Agriculture; Amino Acid Sequence; Analysis; Antigens; Antigens, Neoplasm - immunology; Autoantibodies - immunology; Autoantibodies - metabolism; Autoantigens; Autoantigens - genetics; Autoantigens - immunology; Autoantigens - isolation & purification; Autoimmune diseases; Autoimmune Diseases - genetics; Autoimmune Diseases - immunology; Bacteriophage T7 - metabolism; Bioinformatics; Biological and medical sciences; Biomedical and Life Sciences; Biomedical Engineering/Biotechnology; Biomedicine; Biotechnology; Carcinoma, Non-Small-Cell Lung - immunology; Cloning, Molecular; Deoxyribonucleic acid; Diverse techniques; DNA; Female; Fundamental and applied biological sciences. Psychology; Gene Library; Genome, Human; Health aspects; Health. Pharmaceutical industry; High-Throughput Nucleotide Sequencing; Humans; Immunology; Immunoprecipitation; Industrial applications and implications. Economical aspects; Life Sciences; Middle Aged; Miscellaneous; Molecular and cellular biology; Molecular Sequence Data; Nerve Tissue Proteins - immunology; Neuro-Oncological Ventral Antigen; Oligonucleotide Array Sequence Analysis; Open Reading Frames - immunology; Paraneoplastic Syndromes, Nervous System - immunology; Peptide Library; Peptides; Physiological aspects; Proteins; Proteome - genetics; Proteomics; Proteomics - methods; RNA-Binding Proteins - immunology; Sequence Analysis, RNA
• ISSN: 1087-0156; 1546-1696
• DOI: 10.1038/nbt.1856

Larman et al . create a phage library containing >400,000 sequences encoding peptides that cover all open reading frames in the human genome. They then use this synthetic peptidome to discover novel autoantigens targeted by antibodies in the cerebrospinal fluid of individuals with a neurological autoimmune disease. Immune responses targeting self-proteins (autoantigens) can lead to a variety of autoimmune diseases. Identification of these antigens is important for both diagnostic and therapeutic reasons. However, current approaches to characterize autoantigens have, in most cases, met only with limited success. Here we present a synthetic representation of the complete human proteome, the T7 peptidome phage display library (T7-Pep), and demonstrate its application to autoantigen discovery. T7-Pep is composed of >413,000 36-residue, overlapping peptides that cover all open reading frames in the human genome, and can be analyzed using high-throughput DNA sequencing. We developed a phage immunoprecipitation sequencing (PhIP-Seq) methodology to identify known and previously unreported autoantibodies contained in the spinal fluid of three individuals with paraneoplastic neurological syndromes. We also show how T7-Pep can be used more generally to identify peptide-protein interactions, suggesting the broader utility of our approach for proteomic research.