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Randomized Controlled Trial
. 2019 Apr 1;79(7):1549-1557.
doi: 10.1158/0008-5472.CAN-18-1536. Epub 2019 Feb 5.

Whole Genome-Derived Tiled Peptide Arrays Detect Prediagnostic Autoantibody Signatures in Non-Small-Cell Lung Cancer

Yuanqing Yan  1 , Nan Sun  2 , Hong Wang  2 , Makoto Kobayashi  2 , Jon J Ladd  3 , James P Long  1 , Ken C Lo  4 , Jigar Patel  4 , Eric Sullivan  4 , Thomas Albert  4 , Gary E Goodman  3 , Kim-Anh Do  1 , Samir M Hanash  5
Affiliations
Randomized Controlled Trial

Whole Genome-Derived Tiled Peptide Arrays Detect Prediagnostic Autoantibody Signatures in Non-Small-Cell Lung Cancer

Yuanqing Yan et al. Cancer Res. .

Abstract

The majority of non-small-cell lung cancer (NSCLC) cases are diagnosed at advanced stages, primarily because earlier stages of the disease are either asymptomatic or may be attributed to other causes such as infection or long-term effects from smoking. Therefore, early detection of NSCLC would likely increase response and survival rates due to timely intervention. Here, we utilize a novel approach based on whole genome-derived tiled peptide arrays to identify epitopes associated with autoantibody reactivity in NSCLC as a potential means for early detection. Arrays consisted of 2,781,902 tiled peptides representing 20,193 proteins encoded in the human genome. Analysis of 86 prediagnostic samples and 86 matched normal controls from a high-risk cohort revealed 48 proteins with three or more reactive epitopes in NSCLC samples relative to controls. Independent mass spectrometry analysis identified 40 of the 48 proteins in prediagnostic sera from NSCLC samples, of which, 21 occurred in the immunoglobulin-bound fraction. In addition, 63 and 34 proteins encompassed three or more epitopes that were distinct for squamous cell lung cancer and lung adenocarcinoma, respectively. Collectively, these data show that tiled peptide arrays provide a means to delineate epitopes encoded across the genome that trigger an autoantibody response associated with tumor development. SIGNIFICANCE: This study provides a modality for early diagnosis of NSCLC for precision oncology that can be applied to other cancer types.

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Conflict of interest statement

Conflict of interest: None.

Figures

Figure 1:
Figure 1:
Workflow for processing and analysis of peptide arrays
Figure 2:
Figure 2:
Combined performance of top nine proteins with AUCs >0.7 in the entire dataset
Figure 3.
Figure 3.
Hot spots representing repeat sequences in HRNR.
Figure 4.
Figure 4.
RNA based expression levels of HRNR in the TCGA lung (A) squamous cell carcinoma and (B) adenocarcinoma dataset
Figure 5.
Figure 5.
A. Annexin A1 peptide performance in lung adenocarcinomas vs controls B. Annexin A2 peptide performance in lung adenocarcinomas vs controls
See this image and copyright information in PMC

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