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Lee J, Geiss GK, Demirkan G, Vellano CP, Filanoski B, Lu Y, Ju Z, Yu S, Guo H, Bogatzki LY, Carter W, Meredith RK, Krishnamurthy S, Ding Z, Beechem JM, Mills GB. Implementation of a Multiplex and Quantitative Proteomics Platform for Assessing Protein Lysates Using DNA-Barcoded Antibodies. Mol Cell Proteomics 2018; 17:1245-1258. [PMID: 29531020 PMCID: PMC5986246 DOI: 10.1074/mcp.ra117.000291] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 02/17/2018] [Indexed: 11/06/2022] Open
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.
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Affiliation(s)
- Jinho Lee
- From the ‡The University of Texas M.D. Anderson Cancer Center, Department of Systems Biology, 1300 Moursund St., Houston, Texas 77030;
| | - Gary K Geiss
- §NanoString Technologies, Inc., 530 Fairview Ave N., Seattle, Washington 98109;
| | - Gokhan Demirkan
- §NanoString Technologies, Inc., 530 Fairview Ave N., Seattle, Washington 98109
| | - Christopher P Vellano
- From the ‡The University of Texas M.D. Anderson Cancer Center, Department of Systems Biology, 1300 Moursund St., Houston, Texas 77030
| | - Brian Filanoski
- §NanoString Technologies, Inc., 530 Fairview Ave N., Seattle, Washington 98109
| | - Yiling Lu
- From the ‡The University of Texas M.D. Anderson Cancer Center, Department of Systems Biology, 1300 Moursund St., Houston, Texas 77030
| | - Zhenlin Ju
- ¶The University of Texas M.D. Anderson Cancer Center, Department of Pathology, 1515 Holcombe Blvd, Houston, Texas 77030
| | - Shuangxing Yu
- From the ‡The University of Texas M.D. Anderson Cancer Center, Department of Systems Biology, 1300 Moursund St., Houston, Texas 77030
| | - Huifang Guo
- From the ‡The University of Texas M.D. Anderson Cancer Center, Department of Systems Biology, 1300 Moursund St., Houston, Texas 77030
| | - Lisa Y Bogatzki
- §NanoString Technologies, Inc., 530 Fairview Ave N., Seattle, Washington 98109
| | - Warren Carter
- §NanoString Technologies, Inc., 530 Fairview Ave N., Seattle, Washington 98109
| | - Rhonda K Meredith
- §NanoString Technologies, Inc., 530 Fairview Ave N., Seattle, Washington 98109
| | - Savitri Krishnamurthy
- ¶The University of Texas M.D. Anderson Cancer Center, Department of Pathology, 1515 Holcombe Blvd, Houston, Texas 77030
| | - Zhiyong Ding
- From the ‡The University of Texas M.D. Anderson Cancer Center, Department of Systems Biology, 1300 Moursund St., Houston, Texas 77030
| | - Joseph M Beechem
- §NanoString Technologies, Inc., 530 Fairview Ave N., Seattle, Washington 98109
| | - Gordon B Mills
- From the ‡The University of Texas M.D. Anderson Cancer Center, Department of Systems Biology, 1300 Moursund St., Houston, Texas 77030;
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