Enabling RNA Analyses from Formaldehyde-fixed Tissues

Award Information
Agency:
Department of Health and Human Services
Branch
n/a
Amount:
$242,086.00
Award Year:
2004
Program:
SBIR
Phase:
Phase I
Contract:
1R43NS046958-01A1
Award Id:
71759
Agency Tracking Number:
NS046958
Solicitation Year:
n/a
Solicitation Topic Code:
n/a
Solicitation Number:
n/a
Small Business Information
2130 WOODWARD STREET, AUSTIN, TX, 78744
Hubzone Owned:
N
Minority Owned:
N
Woman Owned:
N
Duns:
n/a
Principal Investigator:
RICHARD CONRAD
(512) 651-0200
RCONRAD@AMBION.COM
Business Contact:
RIGO VALLEJO
(512) 651-0200
RVALLEJO@AMBION.COM
Research Institution:
n/a
Abstract
DESCRIPTION (provided by applicant): The overall goal is to develop a robust procedure for extracting RNA from tissues that have been fixed in formaldehyde, either neutral buffered formalin or buffered paraformaldehyde. Clinically interesting tissue from biopsies and necropsies is routinely archived after formaldehyde fixation by medical institutions. The primary use for these tissues is histological, as the RNA and other macromolecular components are so heavily crosslinked that they cannot be retrieved intact. The ability to use these samples in mRNA expression studies presents a huge opportunity. Procedures currently employed are inefficient and often are difficult to reproduce, so improvements are desired. A procedure is sought that provides RNA that is fully functional as a template for reverse transcription and can function in more classical analyses like Northern blots and ribonuclease protection assays (RPA's). Enhancement of the current extraction procedures by utilizing a mixture of hydrolytic enzymes and denaturants, to obtain RNA that has a normal appearance on electrophoresis will be pursued, as well as investigating methodologies for reversing the formaldehyde reaction. In the latter endeavor, methylene-N6-bis-adenosine, a common formaldehyde-generated crosslink, will be synthesized to be used as a test compound under controlled chemical tests to determine conditions for specifically removing the crosslink. This procedure can then be applied to RNA, either in situ (posthomogenization) or after extraction from tissue. Downstream procedures to analyze the RNA obtained will be extensively investigated, concentrating on reverse transcription (cDNA)-based methods. Much of this work will involve comparing the relative levels of different mRNA species inferred by these methods, especially between tissues split before fixing or freezing, to ensure the procedure does not bias the populational representation.

* information listed above is at the time of submission.

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