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Badve SS, Gökmen-Polar Y. Protein Profiling of Breast Cancer for Treatment Decision-Making. Am Soc Clin Oncol Educ Book 2022; 42:1-9. [PMID: 35580295 DOI: 10.1200/edbk_351207] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The increasing use of neoadjuvant therapy has resulted in therapeutic decisions being made on the basis of diagnostic needle core biopsy. For many patients, this method might yield the only fragment of tumor available for biomarker analysis, necessitating judicious use. Many multiplex protein analytic methods have been developed that employ fluorescence or other tags to overcome the limitations of immunohistochemistry while still retaining the spatial annotation. Interpretation of the data can be difficult because of the limitations of the human eye. Computational deconvolution of the signals may be necessary for some of these methods to enable identification of cell-specific localization and coexpression of biomarkers. Herein, we present the different methods that are coming of age and their application in cancer research, with a focus on breast cancer. We also discuss the limitations, which include high costs and long turnaround times. The methods are also based on the premise that preanalytical factors will have identical impact on all proteins analyzed. There is a need to establish standards to normalize the data and enable cross-sample comparisons. In spite of these limitations, the multiplex technologies are extremely valuable discovery tools and can provide novel insights into the biology of cancer and mechanisms of drug resistance.
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Affiliation(s)
- Sunil S Badve
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA
| | - Yesim Gökmen-Polar
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA
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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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Manna S, Senapati S, Lindsay S, Zhang P. A three-arm scaffold carrying affinity molecules for multiplex recognition imaging by atomic force microscopy: the synthesis, attachment to silicon tips, and detection of proteins. J Am Chem Soc 2015; 137:7415-23. [PMID: 25996033 DOI: 10.1021/jacs.5b03079] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We have developed a multiplex imaging method for detection of proteins using atomic force microscopy (AFM), which we call multiplex recognition imaging (mRI). AFM has been harnessed to identify protein using a tip functionalized with an affinity molecule at a single molecule level. However, many events in biochemistry require identification of colocated factors simultaneously, and this is not possible with only one type of affinity molecule on an AFM tip. To enable AFM detection of multiple analytes, we designed a recognition head made from conjugating two different affinity molecules to a three-arm linker. When it is attached to an AFM tip, the recognition head would allow the affinity molecules to function in concert. In the present study, we synthesized two recognition heads: one was composed of two nucleic acid aptamers, and the other one composed of an aptamer and a cyclic peptide. They were attached to AFM tips through a catalyst-free click reaction. Our imaging results show that each affinity unit in the recognition head can recognize its respective cognate in an AFM scanning process independently and specifically. The AFM method was sensitive, only requiring 2 to 3 μL of protein solution with a concentration of ∼2 ng/mL for the detection with our current setup. When a mixed sample was deposited on a surface, the ratio of proteins could be determined by counting numbers of the analytes. Thus, this mRI approach has the potential to be used as a label-free system for detection of low-abundance protein biomarkers.
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Affiliation(s)
- Saikat Manna
- †Biodesign Institute, ‡Department of Chemistry and Biochemistry, and §Department of Physics, Arizona State University, Tempe, Arizona 85287, United States
| | - Subhadip Senapati
- †Biodesign Institute, ‡Department of Chemistry and Biochemistry, and §Department of Physics, Arizona State University, Tempe, Arizona 85287, United States
| | - Stuart Lindsay
- †Biodesign Institute, ‡Department of Chemistry and Biochemistry, and §Department of Physics, Arizona State University, Tempe, Arizona 85287, United States
| | - Peiming Zhang
- †Biodesign Institute, ‡Department of Chemistry and Biochemistry, and §Department of Physics, Arizona State University, Tempe, Arizona 85287, United States
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