Autoantigen discovery with a synthetic human peptidome

The founding PhIP-Seq paper: 413,611 phage-displayed peptides turn one-target-at-a-time autoantigen hunting into proteome-scale serology.

Larman HB, Zhao Z, Laserson U, Li MZ, Ciccia A, Martinez Gakidis MA, Church GM, Kesari S, LeProust EM, Solimini NL, Elledge SJ.

Nature Biotechnology · May 22, 2011 · DOI: 10.1038/nbt.1856

How to cite

AMA

Larman HB, Zhao Z, Laserson U, et al. Autoantigen discovery with a synthetic human peptidome. Nat Biotechnol. 2011;29(6):535-541. doi:10.1038/nbt.1856

APA

Larman, H. B., Zhao, Z., Laserson, U., Li, M. Z., Ciccia, A., Martinez Gakidis, M. A., Church, G. M., Kesari, S., LeProust, E. M., Solimini, N. L., & Elledge, S. J. (2011). Autoantigen discovery with a synthetic human peptidome. Nature Biotechnology, 29(6), 535–541. https://doi.org/10.1038/nbt.1856

BibTeX

@article{Larman2011PhIPSeq,
  author  = {Larman, H. Benjamin and Zhao, Zhenming and Laserson, Uri and Li, Mamie Z. and Ciccia, Alberto and Martinez Gakidis, M. Angelica and Church, George M. and Kesari, Santosh and LeProust, Emily M. and Solimini, Nicole L. and Elledge, Stephen J.},
  title   = {Autoantigen discovery with a synthetic human peptidome},
  journal = {Nature Biotechnology},
  year    = {2011},
  volume  = {29},
  number  = {6},
  pages   = {535--541},
  doi     = {10.1038/nbt.1856}
}

This is the founding paper of phage immunoprecipitation sequencing (PhIP-Seq). Larman and colleagues built a synthetic representation of the entire human proteome — 413,611 overlapping 36-mer peptides displayed on T7 bacteriophage — and used it to read out the autoantibody repertoire of patient cerebrospinal fluid in a single multiplexed serological assay. Applied to three patients with paraneoplastic neurological syndromes, the method recovered known autoantigens such as NOVA1 and GAD65 and discovered new ones including TGIF2LX and CTAG2. The work established the methodological template the field has built on ever since.

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In this publication:

The T7-Pep library tiles the human coding genome as 413,611 overlapping 36-mer peptides with 7-residue overlap; 83% of inserts are in-frame — versus <6% for prior cDNA expression libraries.
Illumina sequencing at 45-fold median depth detected 91.2% of designed clones; 78% fell within a 10-fold abundance window.
In Patient B (a panel-negative paraneoplastic case), PhIP-Seq enriched two non-overlapping GAD65 peptides from the Stiff Person Syndrome epitope domain; commercial radioimmunoassay confirmed anti-GAD65 at 5.12 nmol/L — more than 250-fold above the reference range.
Across three paraneoplastic patients, the assay simultaneously recovered known autoantigens (NOVA1, GAD65) and uncovered novel ones (TGIF2LX, CTAG2) in a single multiplexed CSF screen.

Before PhIP-Seq, autoantigen identification ran one candidate at a time on cDNA expression libraries where less than 6% of clones expressed in-frame. This paper introduced a synthetic library where 83% of inserts were in-frame and 91.2% of designed clones were sequenced at 45-fold median depth, turning a slow candidate-by-candidate search into a single high-throughput readout.

Applied to three patients with paraneoplastic neurological syndromes, the method recovered known autoantigens (NOVA1, GAD65) and discovered new ones (TGIF2LX, CTAG2). In Patient B, a panel-negative paraneoplastic case, PhIP-Seq enriched two non-overlapping GAD65 peptides from the Stiff Person Syndrome epitope domain, and anti-GAD65 was confirmed by commercial radioimmunoassay at 5.12 nmol/L — more than 250-fold above the reference range.

The combination of a designed peptidome plus deep sequencing established a methodological template that has since been adapted across human, viral, allergen, and microbiome serological screens. The entire generation of large-scale autoantibody-discovery work descends from this approach — including MIPSA (Molecular Indexing of Proteins by Self-Assembly) and Infinity Bio's HuSIGHT human-proteome antibody-reactome library.

Autoantigen discovery with a synthetic human peptidome

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