Citation:

Hester, S. AND D. Dalmas. PRESENTATION TYPE: Round Table Discussion (80 minutes) TITLE: Unlocking the ‘Omics Archive: Enabling Toxicogenomic/Proteomic Investigation from Archival Samples. 2018 SOT Annual Meeting, San Antonio, Texas, March 10 - 15, 2018.

Impact/Purpose:

Archival formalin-fixed paraffin-embedded (FFPE) tissue samples offer a vast but largely untapped resource for genomic research. The primary technical issues limiting use of FFPE samples are RNA yield and quality due to formalin fixation. In this rountable, we evaluated the state of the art of methods to enable the use of FFPE samples for toxicogenomic and proteomic profiling, Formalin fixation degrades RNA and results in cross-linking and fragmentation, which is thought to significantly impair transcriptomic/proteomic analyses. Because of the roadblocks, there is a need to develop novel methods that can reliably access gene and protein information from FFPE tissue enabling retrospective investigations from pathologically-anchored samples that would otherwise be very costly and require additional patient or animal samples to repeat to obtain this information from prospectively collected frozen tissue. The purpose of this roundtable is to highlight recently developed novel approaches to reliably access quantitative gene and protein information from FFPE tissue and how these approaches can be used to interrogate mechanisms of toxicity and aid in biomarker development/analysis from both nonclinical and clinical samples.These findings should also inform new ways to access different biorepository samples, which could provide a rich bioinformatics pipeline for environmental science and chemical safety.

Description:

Formalin fixation and paraffin embedding (FFPE) is a cross-industry gold standard for preparing nonclinical and clinical samples for histopathological assessment which preserves tissue architecture and enables storage of tissue in archival banks. These archival banks are an untapped resource and vast repository of tissue from regulatory toxicology studies, novel animal bioassays, clinical trials, or epidemiologic studies with corresponding detailed pathological assessments. Although these FFPE archives hold keys to various unknown mechanisms and or disease processes, direct use of archival samples for transcriptomic or proteomic profiling has been relatively limited. Formalin fixation degrades RNA and results in cross-linking and fragmentation, which is thought to significantly impair transcriptomic/proteomic analyses. Because of the roadblocks, there is a need to develop novel methods that can reliably access gene and protein information from FFPE tissue enabling retrospective investigations from pathologically-anchored samples that would otherwise be very costly and require additional patient or animal samples to repeat to obtain this information from prospectively collected frozen tissue. The goal of this symposium is to highlight recently developed novel approaches to reliably access quantitative gene and protein information from FFPE tissue and how these approaches can be used to interrogate mechanisms of toxicity and aid in biomarker development/analysis from both nonclinical and clinical samples. The symposium will first showcase novel methods to overcome limitations of using FFPE tissue archived for 4.5 years enabling access to robust transcriptomic and proteomic information from nonclinical regulatory toxicology studies and how these approaches have been utilized to support regulatory filings. The symposium will then highlight and compare gene expression profiles derived from archived FFPE tissue preserved in formalin for 8-, 19-, 26-years using novel methods developed for DNA microarray analysis as well as exosome enrichment approaches utilizing nucleic acid samples and whole-transcriptome sequencing (RNA-seq) library preparation methodologies. Despite individual efforts across industry, methods to enable RNA-Seq evaluation from limiting quantities and quality RNA, was until recently, still not possible. Because the issue is too complex to be solved by individual organizations working in isolation and with limited resources, the Health Environmental and Sciences Institute (HESI) Genomics Committee FFPE Working Group has been developing methods to “demodify” FFPE RNA enabling subsequent more robust RNA-Seq analysis. Novel methods developed to improve RNA yield and sequencing results from limiting quantities and quality RNA FFPE samples will be highlighted, followed by a comparison across frozen and FFPE samples fixed under varying alcohol and/or formalin conditions. Lastly, development and utilization of novel methods to enable global proteomic and phosphoproteomic analysis of case matched frozen and FFPE clinically derived samples using mass spec based technologies will be emphasized. Utilization of the novel methods described, now enable retrospective generation of quantitative gene and protein information from phenotypically-anchored archival nonclinical and clinical FFPE tissue to interrogate mechanisms of toxicity, aid in biomarker development, enable creation of a critical translational bridge between emerging in vitro and in vivo data, and evaluation of chemically induced adverse health effects established in prior toxicologic and epidemiologic studies as well as enabling data gaps to be closed in Adverse Outcome Pathways (AOPs).

Record Details: