Rescuing Nucleic Acids from Formalin Damage in Cancer Specimens

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SUMMARY Our proposed research is aimed at developing catalytic molecules and methods that greatly improve the recovery of biomolecular information from formalin-fixed tissue specimens. Formalin (formaldehyde) treatment of tissue is universally used in preparation of hundreds of millions of biopsy and surgery specimens worldwide. Unfortunately, the formaldehyde forms many adducts and crosslinks with the biomolecules in the specimens, strongly inhibiting the ability to obtain sequences and quantification of RNAs and DNAs from such specimens, information that is increasingly essential to diagnosis and treatment of cancer. Standard heating-based methods of RNA/DNA extraction remove only a fraction of adducts, and they are harsh, damaging the nucleic acids in the process. In our phase I work we demonstrated that the use of catalytic methods could greatly enhance the removal of formaldehyde adducts from DNA and RNA bases. Importantly, we were able to develop catalytic protocols that function successfully with actual formalin-fixed specimens. Amplifiable RNA was recovered in amounts as much as 25-fold greater than a world-leading commercial protocol, an unprecedented magnitude of improvement. The goals of this collaborative phase II research are to move to practical development of this technology for application in clinically important applications with multiple tissue types. We will further optimize our catalytic protocols for DNA recovery and minimization of damage, for application in next- generation sequencing (NGS). We will test whether new catalyst structures can be yet more effective than early examples, and we will examine whether optimal RNA recovery results in improved representation of gene expression and microRNA expression by NGS and microarray analysis. Finally, we will test application in lung tumor needle biopsies, which can be difficult to analyze by current methods because of the small amount of material present. This research program is innovative because it represents the first concept of using catalysts to reverse formaldehyde adducts of biomolecules, and because new, 2nd-generation catalysts and protocols are planned. The work we propose is significant because FFPE methodology is the universal worldwide standard for storing tissue specimens during cancer diagnosis. Approximately 400 million existing specimens could benefit from success of the work, and millions of new patients could be positively affected annually. We expect that our catalytic methods will become part of the new standard of practice for molecular diagnosis and therapy.