] State the application's broad, long-term objectives and specific aims, making reference to the health relatedness of the project. Describe concisely the research design and methods for achieving these goals. Avoid summaries of past accomplishments and the use of the first person. This abstract is meant to serve as a succinct and accurate description of the proposed work when separated from the application. If the application is funded, this description, as is, will become public information. Therefore, do not include proprietary/confidential information. DO NOT EXCEED THE SPACE PROVIDED. High-throughput molecular biologic and proteomic methods provide several promising approaches for relating genetic changes, such as mutation or altered gene expression, to metastasis, to treatment outcomes, and to survival. In cancers where the interval between initial diagnosis and treatment and the appearance of metastases is long, clinical correlations would be more readily obtained if formalin-fixed paraffin-embedded (FFPE) tissues could be used instead of fresh or frozen specimens. Large-scale multiplex techniques, such as serial analysis of gene expression (SAGE), and gene chip methods yield experimental results that are somewhat different for FFPE tissue and unfixed tissue. The long-term goal of our research program is to use high-throughput molecular biologic screening methods to identify the molecular and genetic basis of cancer origins and behavior. The objective of this proposal is to identify the formaldehyde-induced chemical modifications that occur to nucleic acids during histologic tissue processing and to develop methods to reverse these modifications. Our centralhypothesis is that formaldehyde adducts and cross-links formed during tissue processing can be sequentially reversed by a series of heating and dialysis steps, carried out under appropriate solvation conditions. We formulated this hypothesis on the basis of preliminary data which show that the reversal of formaldehyde-induced chemical changes in proteins and nucleic acids is relatively facile in aqueous solutions, but less so following dehydration in the presence of organic solvents. The rationale for these studies is that their successful completion will provide a foundation for applying high-throughput screening methods to FFPE tissues. This will lead to improved practical interventions for the diagnosis, evaluation, treatment, and prevention of cancer and facilitate the development of therapeutic agents. Our studies are innovative in that we have pioneered a novel model system (tissue surrogates) ideally suited to identify the formaldehyde-induced modifications to proteins and nucleic acids that occur during tissue processing. At the completion of this project it is our expectation to have established a comprehensive understanding of the formaldehyde-induced chemical modifications to mRNA that occur during tissue histology, and methods for optimally reversing these modifications. This knowledge should result in an ability to carry out genomic analysis on FFPE tissue, significantly expanding our capability to conduct genomic research and opening important new areas to practical investigation. PERFORMANCE SITE(S) (organization, city, state) American Registry of Pathology University of Maryland, Baltimore County (UMBC) 1413 Research Boulevard, Building #102 Department of Chemistry and Biochemistry Rockville, MD 20850 1000 Hilltop Circle (application organization site) Baltimore, MD 21250 (contractual arrangement site) KEY PERSONNEL. See instructions. Use continuation pages as neededio provide the required information in the format shown below. Start with Principal Investigator. List all other key personnel in alphabetical order, last name first. Name Organization Role on Project O'Leary, Timothy J. Armed Forces Institute of Pathology Principal Investigator Cunningham, Robert E. Armed Forces Institute of Pathology Research Associate Fabris, Daniele University of Maryland, Bait. County Co-Investigator Mason, Jeffrey T. Armed Forces Institute of Pathology Co-Investigator Rait, Vladimir K. American Registry of Pathology Research Associate Sheng, Zongmei American Registry of Pathology Research Associate Disclosure Permission Statement. Applicable to SBIR/STTR Only. See instructions.' l~l Yes I | No PHS 398 (Rev. 05/01) Page 2 Form Page 2 Principal Investigator/Program Director (Last, first, middle): O'Leary, Timothy Joseph [The name of the principal investigator/program director must be provided at the top of each printed page and each continuation page.] RESEARCH GRANT
| Evers, David L; He, Junkun; Kim, Yeon Ho et al. (2011) Paraffin embedding contributes to RNA aggregation, reduced RNA yield, and low RNA quality. J Mol Diagn 13:687-94 |
| Evers, David L; Fowler, Carol B; Cunningham, Brady R et al. (2011) The effect of formaldehyde fixation on RNA: optimization of formaldehyde adduct removal. J Mol Diagn 13:282-8 |
| O'Leary, Tj; Fowler, Cb; Evers, Dl et al. (2009) Protein fixation and antigen retrieval: chemical studies. Biotech Histochem :1-5 |
| Evers, David L; Fowler, Carol B; Cunningham, Robert E et al. (2007) A novel HPLC method reveals that precipitation of 2'-deoxyadenosine 5'-monophosphate with lithium perchlorate/acetone leads to base depurination. Anal Biochem 370:255-7 |
