Implementation of a Multiplex and Quantitative Proteomics Platform for Assessing Protein Lysates Using DNA-Barcoded Antibodies

Jinho Lee, Gary K. Geiss, Gokhan Demirkan, Christopher P. Vellano, Brian Filanoski, Yiling Lu, Zhenlin Ju, Shuangxing Yu, Huifang Guo, Lisa Y. Bogatzki, Warren Carter, Rhonda K. Meredith, Savitri Krishnamurthy, Zhiyong Ding, Joseph M. Beechem, Gordon Mills

Research output: Contribution to journalArticle

10 Scopus citations

Abstract

Molecular analysis of tumors forms the basis for personalized cancer medicine and increasingly guides patient selection for targeted therapy. Future opportunities for personalized medicine are highlighted by the measurement of protein expression levels via immunohistochemistry, protein arrays, and other approaches; however, sample type, sample quantity, batch effects, and “time to result” are limiting factors for clinical application. Here, we present a development pipeline for a novel multiplexed DNA-labeled antibody platform which digitally quantifies protein expression from lysate samples. We implemented a rigorous validation process for each antibody and show that the platform is amenable to multiple protocols covering nitrocellulose and plate-based methods. Results are highly reproducible across technical and biological replicates, and there are no observed “batch effects” which are common for most multiplex molecular assays. Tests from basal and perturbed cancer cell lines indicate that this platform is comparable to orthogonal proteomic assays such as Reverse-Phase Protein Array, and applicable to measuring the pharmacodynamic effects of clinically-relevant cancer therapeutics. Furthermore, we demonstrate the potential clinical utility of the platform with protein profiling from breast cancer patient samples to identify molecular subtypes. Together, these findings highlight the potential of this platform for enhancing our understanding of cancer biology in a clinical translation setting.

Original languageEnglish (US)
Pages (from-to)1245-1258
Number of pages14
JournalMolecular and Cellular Proteomics
Volume17
Issue number6
DOIs
StatePublished - Jun 1 2018
Externally publishedYes

ASJC Scopus subject areas

  • Analytical Chemistry
  • Biochemistry
  • Molecular Biology

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    Lee, J., Geiss, G. K., Demirkan, G., Vellano, C. P., Filanoski, B., Lu, Y., Ju, Z., Yu, S., Guo, H., Bogatzki, L. Y., Carter, W., Meredith, R. K., Krishnamurthy, S., Ding, Z., Beechem, J. M., & Mills, G. (2018). Implementation of a Multiplex and Quantitative Proteomics Platform for Assessing Protein Lysates Using DNA-Barcoded Antibodies. Molecular and Cellular Proteomics, 17(6), 1245-1258. https://doi.org/10.1074/mcp.RA117.000291