This project will develop and characterize the application of RASL-Seq, a multiplexed targeted expression profiling technology that uses q sequencing read-out, to analysis of banked tissues. The technology detects hundreds of RNA targets at once in cell lysates, using oligo ligation, amplification, and next-generation sequencing for quantitation. This highly multiplexed assay will allow a simple, fixed tissue assay protocol that can be applied to different rodent tissues, while delivering a simple expression profiling report. The technology will promote toxicology research by enabling direct comparisons between expression profiles derived from compound screening in vitro to those observed in animals dosed with the same compounds. It will do so at a low cost/sample by multiplexing 20 to 100 or more samples/sequencing run, thus reducing the sequencing cost/sample to $6 from $600. We will optimize the lysis buffer/protocol for formalin-fixed paraffin-embedded (FFPE) tissues, design and test probes for degraded RNAs, build an assay panel for ~100 rodent genes of interest for animal testing in toxicology studies, and assess the performance of the assay on archived tissues from animals dosed with compounds with known impacts on gene expression. Performance measures will include reproducibility, dynamic range, fold difference detection, and correlation with organ-specific and compound-specific expression changes. If successful, the project will deliver a technology that will allow integration of in vitro and in vivo profiling, whch may provide enhanced compound response prediction, increasing the efficiency of animal testing, and also enable the development of reliable in vitro models which will lead to the use of fewer animals. Finally, the sensitivity of the RASL-Seq assay and gene expression read-out may permit sub-toxic adverse effects of compounds to be detected, permitting potential toxicity to be identified that is not observable by micro-histology.

Public Health Relevance

This project will develop and validate the application of the lysis-only RASL-Seq, a gene expression profiling technology that uses detection by sequencing, to analysis of banked fixed animal tissues from toxicology studies. This highly multiplexed assay, which does not require the extraction or reverse transcription of RNA, will measure 10 to 1,000 or more genes from each sample of banked FFPE tissue, sequencing 20 to 100 samples/run to reduce sequencing cost/sample and provide a cost effective assay that delivers the same sensitivity and accuracy from banked FFPE as from frozen tissue. By profiling toxicity through measurement of gene expression changes from archived tissues of animals previously dosed with compounds, RASL-Seq will advance toxicology research by enabling the correlation of gene expression changes seen in cell culture with those observed in animals, enabling reliable surrogate models that will reduce the use of animals, and provide an assay that can be routinely used by the pharmaceutical and cosmetics industries.

National Institute of Health (NIH)
National Institute of Environmental Health Sciences (NIEHS)
Small Business Innovation Research Grants (SBIR) - Phase I (R43)
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Special Emphasis Panel (ZES1)
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Shaughnessy, Daniel
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Biospyder Technologies, Inc.
Rancho Santa Fe
United States
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