Rescuing Nucleic Acids from Formalin Damage in Cancer Specimens

SUMMARY Our proposed research is aimed at developing catalytic molecules and methods that greatly improve the recovery of biomolecular information from formalin fixed tissue specimensFormalinformaldehydetreatment of tissue is universally used in preparation of hundreds of millions of biopsy and surgery specimens worldwideUnfortunatelythe formaldehyde forms many adducts and crosslinks with the biomolecules in the specimensstrongly inhibiting the ability to obtain sequences and quantification of RNAs and DNAs from such specimensinformation that is increasingly essential to diagnosis and treatment of cancerStandard heating based methods of RNA DNA extraction remove only a fraction of adductsand they are harshdamaging the nucleic acids in the processIn our phase I work we demonstrated that the use of catalytic methods could greatly enhance the removal of formaldehyde adducts from DNA and RNA basesImportantlywe were able to develop catalytic protocols that function successfully with actual formalin fixed specimensAmplifiable RNA was recovered in amounts as much asfold greater than a world leading commercial protocolan unprecedented magnitude of improvementThe 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 typesWe will further optimize our catalytic protocols for DNA recovery and minimization of damagefor application in nextgeneration sequencingNGSWe will test whether new catalyst structures can be yet more effective than early examplesand we will examine whether optimal RNA recovery results in improved representation of gene expression and microRNA expression by NGS and microarray analysisFinallywe will test application in lung tumor needle biopsieswhich can be difficult to analyze by current methods because of the small amount of material presentThis research program is innovative because it represents the first concept of using catalysts to reverse formaldehyde adducts of biomoleculesand because newnd generation catalysts and protocols are plannedThe work we propose is significant because FFPE methodology is the universal worldwide standard for storing tissue specimens during cancer diagnosisApproximatelymillion existing specimens could benefit from success of the workand millions of new patients could be positively affected annuallyWe expect that our catalytic methods will become part of the new standard of practice for molecular diagnosis and therapy