Cancer is recognized as a highly complex disease involving myriad molecular processes and arises as the result of gradual accumulation of multiple genetic and proteomic alterations, which also serve as cancer biomarkers. A major focus of current cancer research is how to correlate these underlying molecular events with cancer development and progression. Recent advances in cancer molecular analysis and bioanalytical sciences have led to the development of DNA chips, ELISA, miniaturized biosensors, microfluidic devices (e.g., bioMEMS or microelectromechanical systems, and mass spectrometry. These enabling technologies have substantially influenced the way that we detect and analyze cancer, such as gene expression profiling, drug discovery, and clinical diagnostics. However, none of these technical platforms are sufficiently flexible to allow detection of both genetic alterations and protein profiles with sensitivity down to single molecule level. As current research in genomics and proteomics produces more sequence data, there is a strong need for new technologies that can rapidly screen a large number of nucleic acids and proteins. In this context, the primary goal of this proposal is to develop a versatile and sensitive technology that can quickly analyze cancer molecular profiles (such as DNAs, RNAs and proteins) in a highly multiplexed manner for accurate diagnostics, prognostics and effective therapeutics. The innovation and basic rationale of this technology lies in the novel optical properties of semiconductor quantum dots or QDs (e.g., tunable light emission, improved signal brightness, resistance against photobleaching, and simultaneous excitation of multiple colors) and our ability to make optical barcodes using these nanoparticles. Different from single QD based imaging;we propose to prepare QD encoded optical barcodes of both micrometer sizes and nanometer sizes. The micro-barcodes will be used to tag biomolecular probes, whereas the nanospheres will be used as reporters to enhance the current detection sensitivity by 2-3 orders of magnitude. We will also explore new surface encapsulation and pore sealing approaches to stabilize the optical barcodes, and chemical conjugation approaches to optimize biomolecular probe immobilization. We will further carry out experiments to detect mutations on both DNA and RNA level as well as the profiles of protein cancer biomarkers, which can be isolated from serum or homogenized cell and tissue specimens. We describe a new generation of QD-based optical barcoding technology for molecular analysis of cancer. The innovation arises from three levels: (1) the concept of using QDs for intensity-color based multiplexing, which has significantly higher multiplexing capability than traditional technology and simplified detection instrumentation;(2) the technique of using mesoporous material for micro barcodes and block-copolymer self assembly for nanobeads;and (3) the selection of clinically important biomarkers for cancer molecular analysis. It is built on our considerable expertise and strength in QD probe chemistry, optical imaging and cancer research. The major advantage of this versatile platform is that it allows simultaneous analysis of DNA, RNA as well as protein cancer markers with unprecedented sensitivity, which is not possible with other approaches.

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Research Project (R01)
Project #
5R01CA131797-04
Application #
7996033
Study Section
Special Emphasis Panel (ZRG1-BST-M (50))
Program Officer
Patriotis, Christos F
Project Start
2007-12-14
Project End
2012-11-30
Budget Start
2010-12-01
Budget End
2011-11-30
Support Year
4
Fiscal Year
2011
Total Cost
$308,845
Indirect Cost
Name
University of Washington
Department
Biomedical Engineering
Type
Schools of Engineering
DUNS #
605799469
City
Seattle
State
WA
Country
United States
Zip Code
98195
Li, Junwei; Zrazhevskiy, Pavel; Gao, Xiaohu (2016) Eliminating Size-Associated Diffusion Constraints for Rapid On-Surface Bioassays with Nanoparticle Probes. Small 12:1035-43
Zrazhevskiy, Pavel; Akilesh, Shreeram; Tai, Wanyi et al. (2016) Cross-Platform DNA Encoding for Single-Cell Imaging of Gene Expression. Angew Chem Int Ed Engl 55:8975-8
Shang, Jing; Zrazhevskiy, Pavel; Postupna, Nadia et al. (2015) Multiplexed In-cell Immunoassay for Same-sample Protein Expression Profiling. Sci Rep 5:13651
Wei, Chen-Wei; Nguyen, Thu-Mai; Xia, Jinjun et al. (2015) Real-time integrated photoacoustic and ultrasound (PAUS) imaging system to guide interventional procedures: ex vivo study. IEEE Trans Ultrason Ferroelectr Freq Control 62:319-28
Zrazhevskiy, Pavel; Dave, Shivang R; Gao, Xiaohu (2014) Addressing Key Technical Aspects of Quantum Dot Probe Preparation for Bioassays. Part Part Syst Charact 31:1291-1299
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Hu, Xiaoge; Wei, Chen-Wei; Xia, Jinjun et al. (2013) Trapping and photoacoustic detection of CTCs at the single cell per milliliter level with magneto-optical coupled nanoparticles. Small 9:2046-52, 2045
Probst, Christine E; Zrazhevskiy, Pavel; Bagalkot, Vaishali et al. (2013) Quantum dots as a platform for nanoparticle drug delivery vehicle design. Adv Drug Deliv Rev 65:703-18
Zrazhevskiy, Pavel; Gao, Xiaohu (2013) Quantum dot imaging platform for single-cell molecular profiling. Nat Commun 4:1619
O'Donnell, Matthew; Wei, Chen-Wei; Xia, Jinjun et al. (2013) Can molecular imaging enable personalized diagnostics? An example using magnetomotive photoacoustic imaging. Ann Biomed Eng 41:2237-47

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