Article | Published:

Autoantigen discovery with a synthetic human peptidome

Nature Biotechnology volume 29, pages 535541 (2011) | Download Citation

Abstract

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.

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Acknowledgements

This work was supported in part by grants from the Department of Defense (W81XWH-10-1-0994 and W81XWH-04-1-0197) to S.J.E., and in part by the US National Institutes of Health (K08CA124804), The American Recovery and Reinvestment Act (3P30CA023100-25S8), Sontag Foundation Distinguished Scientist Award and a James S. McDonnell Foundation award to S.K. N.L.S. is a fellow of the Susan G. Komen for the Cure Foundation. S.J.E. is an investigator with the Howard Hughes Medical Institute. We would like to thank S. Gowrisankar, O. Iartchouk and L. Merrill for assistance with Illumina sequencing, and D. Šćepanović for statistical support.

Author information

Author notes

    • Zhenming Zhao

    Present address: Biogen Idec, Cambridge, Massachusetts, USA.

Affiliations

  1. Harvard-MIT Division of Health Sciences and Technology, Cambridge, Massachusetts, USA.

    • H Benjamin Larman
    •  & Uri Laserson
  2. Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.

    • H Benjamin Larman
  3. Department of Genetics, Harvard University Medical School, and Division of Genetics, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, Massachusetts, USA.

    • H Benjamin Larman
    • , Zhenming Zhao
    • , Mamie Z Li
    • , Alberto Ciccia
    • , M Angelica Martinez Gakidis
    • , Nicole L Solimini
    •  & Stephen J Elledge
  4. Department of Mathematics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.

    • Uri Laserson
  5. Department of Genetics, Harvard University Medical School, Boston, Massachusetts, USA.

    • Uri Laserson
    •  & George M Church
  6. Division of Neuro-Oncology, Department of Neurosciences, University of California, San Diego, Moores Cancer Center, La Jolla, California, USA.

    • Santosh Kesari
  7. Agilent Technologies, Genomics, Santa Clara, California, USA.

    • Emily M LeProust

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Contributions

S.J.E. conceived the project, which was supervised by N.L.S. and S.J.E. Z.Z. designed the DNA sequences for synthesis. Oligo libraries were constructed by E.M.L. Cloning was performed by M.Z.L., M.A.M.G. and N.L.S. The T7-Pep, T7-NPep, and T7-CPep phage libraries were constructed by N.L.S. and characterized by N.L.S. and H.B.L. The PhIP-Seq protocol was developed and implemented by H.B.L. Clinical evaluations and patient sample acquisitions were performed by S.K. Statistical analysis of PhIP-Seq data was conceived by U.L. under the supervision of G.M.C. and implemented by H.B.L. PhIP-Seq candidates were confirmed by H.B.L. The RPA2 experiment was performed by A.C. The manuscript was prepared by H.B.L. and edited by N.L.S. and S.J.E.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Nicole L Solimini or Stephen J Elledge.

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DOI

https://doi.org/10.1038/nbt.1856