The major goal set forth in R01 GM079359 called for the development of molecular tools to elucidate the underlying mechanisms of diseases. Such tools would be engineered using aptamers, which are oligonucleic acids that bind to a specific target molecule. Accordingly, during the previous funding period, we successfully developed and applied a cell-based aptamer selection technique called cell-based Systematic Evolution of Ligands by Exponential enrichment (cell-SELEX) to generate multiple aptamers for the specific recognition of various types of diseased cells. Some of these aptamers were tested with clinical samples, and they showed promising results in differentiating normal from diseased samples. We also explored the use of aptamers in other biomedical applications, including bio analysis, molecular imaging, targeted drug development and biomarker discovery. Based on this work, we have published a total of 86 papers and filed 6 patents. Great strides were made during the previous funding period in developing aptamer probes that can recognize various types of diseased cells. However, we need to further systematically investigate the clinical, bioanalytical and therapeutic potential of these aptamer probes. This renewal request responds to that need. To accomplish this, we will (1) improve aptamer selection strategies, including new aptamer selections against intra- and extracellular proteins, (2) develop and optimize DNA aptamer-based technologies for bioanalytical and clinical applications such as molecular imaging (MI) and circulating tumor cell (CTC) analysis, and (3) conduct experiments aimed at perfecting i) aptamer-assisted biomarker discovery and ii) aptamer-conjugated radio isomers for combined chemotherapy and radiation therapy using aptamer-based drug delivery techniques recently discovered by our group.
Our specific aims i n this new research program are as follows:
Aim 1. Develop and optimize DNA aptamers to recognize individual cells and proteins.
Aim 2. Test the biomedical and biotechnological utility of aptamers in biomarker development, using membrane-bound proteins.
Aim 3. Test and validate the clinical and bioanalytical utility of aptamers in circulating tumor cell detection and molecular imaging.
Aim 4. Test the therapeutic utility of aptamers in targeted drug delivery, using an aptamer-radioactive isomer bioconjugate combined with chemotherapy for small cell lung cancer. Overall, the principle guiding this renewal application holds that a single technology (cell-SELEX) and a single modality (nucleic acid molecules, i.e., aptamers) can, when properly optimized, produce a mutually inclusive convergence of biomedical applications leading to one single end: the early detection, diagnosis and treatment of life-threatening diseases, in particular lung cancer. To carry out the aims in thi research program, we have already established a set of existing aptamers poised for optimization (see Table 1);however, over the course of the tenure of this work, conditions will call for the development of new aptamers for equally new applications, especially those required for the early detection of lung cancer subpopulations, as described below, requiring the extra and innovative step of pyrosequencing or ion semiconductor sequencing. To successfully conduct the necessary experiments, we have assembled a group of accomplished scientists and clinicians who have previously collaborated on many similar studies. Our project is innovative and rationally designed, our research goal is significant and important, our research and development in the last funding cycle are successful, and our preliminary results for future studies in this renewal are strong.

Public Health Relevance

Modern molecular medicine has increasingly focused on developing novel target-specific molecular probes to improve the prognosis and diagnosis of diseases and to develop the best treatment regimens. Particularly, we established the technology enabling nucleic acid molecules, or aptamers, to specifically recognize diseased cells and identify biomarkers. Our research plan will optimize these molecular probes for clinical, bioanalytical, and therapeutic applications, including molecular imaging, biosensing, biomarker identification, and drug delivery.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM079359-06
Application #
8744278
Study Section
Enabling Bioanalytical and Imaging Technologies Study Section (EBIT)
Program Officer
Edmonds, Charles G
Project Start
2007-03-01
Project End
2017-06-30
Budget Start
2014-07-01
Budget End
2015-06-30
Support Year
6
Fiscal Year
2014
Total Cost
$320,143
Indirect Cost
$103,891
Name
University of Florida
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
969663814
City
Gainesville
State
FL
Country
United States
Zip Code
32611
Lyu, Yifan; Chen, Guang; Shangguan, Dihua et al. (2016) Generating Cell Targeting Aptamers for Nanotheranostics Using Cell-SELEX. Theranostics 6:1440-52
Zhang, Liqin; Yang, Zunyi; Le Trinh, Thu et al. (2016) Aptamers against Cells Overexpressing Glypican 3 from Expanded Genetic Systems Combined with Cell Engineering and Laboratory Evolution. Angew Chem Int Ed Engl 55:12372-5
Lv, Yifan; Peng, Ruizi; Zhou, Yu et al. (2016) Catalytic self-assembly of a DNA dendritic complex for efficient gene silencing. Chem Commun (Camb) 52:1413-5
Cai, Ren; Yang, Dan; Chen, Xigao et al. (2016) Three Dimensional Multipod Superstructure based on Cu(OH)2 as a Highly Efficient Nanozyme. J Mater Chem B Mater Biol Med 4:4657-4661
Long, Yuqian; Qin, Zhiqiang; Duan, Minlan et al. (2016) Screening and identification of DNA aptamers toward Schistosoma japonicum eggs via SELEX. Sci Rep 6:24986
Cui, Liang; Peng, Ruizi; Fu, Ting et al. (2016) Biostable L-DNAzyme for Sensing of Metal Ions in Biological Systems. Anal Chem 88:1850-5
Ocsoy, Ismail; Isiklan, Nuran; Cansiz, Sena et al. (2016) ICG-conjugated Magnetic Graphene Oxide for Dual Photothermal and Photodynamic Therapy. RSC Adv 6:30285-30292
Niu, Weijia; Chen, Xigao; Tan, Weihong et al. (2016) N-Heterocyclic Carbene-Gold(I) Complexes Conjugated to a Leukemia-Specific DNA Aptamer for Targeted Drug Delivery. Angew Chem Int Ed Engl 55:8889-93
Fan, Huanhuan; Yan, Guobei; Zhao, Zilong et al. (2016) A Smart Photosensitizer-Manganese Dioxide Nanosystem for Enhanced Photodynamic Therapy by Reducing Glutathione Levels in Cancer Cells. Angew Chem Int Ed Engl 55:5477-82
Li, Juan; Mo, Liuting; Lu, Chun-Hua et al. (2016) Functional nucleic acid-based hydrogels for bioanalytical and biomedical applications. Chem Soc Rev 45:1410-31

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