SBIR-STTR Award

Current assays employed to assess the potential of drugs and environmental agents for their potential to cause birth defects involve the use of animal models. Not only are these models costly and time consuming, but they also have poor concordance to human data. SteminaTM Biomarker Discovery (Stemina) has developed a screening assay that utilizes human embryonic stem (hES) cells and metabolomics to study the secretome of hES cells exposed to test compounds in an all human model system to identify compounds with teratogenic potential. Integrated Laboratory Systems (ILS) and Stemina have formalized a partnership to advance devTOXTM, Stemina's stem cell-based toxicology testing platform. This SBIR will deepen and extend the unique devTOXTM platform by interrogating impact on the human genome and epigenome of hES cells from toxicant exposures. Toxicity testing screens focused on effects to the epigenome are aspect of toxicity based screening that with a few exceptions is virtually absent in high content cellular based toxicity assays. The focus of this SBIR is to: 1. conduct time course and dose-response studies directed at evaluating known and investigative epigenetic biomarkers indicative of aberrant hES cell function using the devTOXTM platform and 2. integrate toxicogenomics-based mRNA and miRNA biomarkers to the devTOXTM platform to assess the impact of toxicants on the genome and epigenome in three specific aims. Specific Aim 1 is to assess stability of biomarker genes and miRNAS associated with maintaining self- renewal and pluripotency of hES cells during cell culture expansion. Specific aim 2 Assess the impact of a reference set of test compounds on genomic and epigenomic response biomarkers in hES cells. Specific aim 3 will test 10 blinded chemicals provided by DOW Chemical Company in DevTOXTM integrated with genomic and epigenomic response biomarkers, then compare results to Dow "in-house" test results from other developmental toxicology screens. We anticipate that the integration of the gene expression and epigenomic profiling with the devTOXTM will increase the predictivity of the devTOXTM platform increasing its use as a weight- of-evidence tool in predicting potential development and reproductive toxicity.

Public Health Relevance:
Stem cells have the unique ability among all of the cells of the human body of self- renewal, that is, they can remain in a primitive unspecialized state. Under the right conditions, they can give rise to specialized cells of the body (differentiation) like th heart, liver, or pancreas. Human embryonic stem cells are being developed as a toxicity testing platform for the assessment of developmental toxicity. These cells present a unique model system to understand and assess the effects of environmental agents and new drug candidates to predict or anticipate toxicity in humans.

Public Health Relevance Statement:
Stem cells have the unique ability among all of the cells of the human body of self- renewal, that is, they can remain in a primitive unspecialized state. Under the right conditions, they can give rise to specialized cells of the body (differentiation) like th heart, liver, or pancreas. Human embryonic stem cells are being developed as a toxicity testing platform for the assessment of developmental toxicity. These cells present a unique model system to understand and assess the effects of environmental agents and new drug candidates to predict or anticipate toxicity in humans.

NIH Spending Category:
Biotechnology; Genetics; Human Genome; Regenerative Medicine; Stem Cell Research; Stem Cell Research - Embryonic - Human

Project Terms:
Animal Model; base; Biological Assay; Biological Markers; Biological Models; Blinded; cell body (neuron); Cell Culture Techniques; Cell physiology; Cells; Chemicals; Congenital Abnormality; Data; design; Development; developmental toxicology; DNA Methylation; Dose; drug candidate; Embryo; environmental agent; Epigenetic Process; epigenomics; Gene Expression; Gene Expression Profiling; Genes; Genome; Genome Stability; Genomics; Growth; Heart; high throughput screening; histone modification; Housing; Human; Human body; human data; human embryonic stem cell; Human Genome; human stem cells; In Vitro; Laboratories; Liver; Messenger RNA; metabolomics; MicroRNAs; Modeling; Pancreas; Pharmaceutical Preparations; Phase; Play; pluripotency; Reporting; reproductive development; response; Risk Assessment; Rodent; Role; Safety; Sampling; Screening procedure; self-renewal; Small Business Innovation Research Grant; stem; Stem cells; System; Technology Transfer; Test Result; Testing; Time; tool; Toxic effect; toxicant; Toxicant exposure; Toxicity Tests; Toxicogenomics; Toxicology; Training; Untranslated RNA; Weight; Zebrafish

In utero exposure to environmental chemicals or drugs accounts for approximately 5% of all birth defects and can have an impact in adult life by disrupting the epigenetic developmental programs that are activated later in life (e.g., puberty, aging). The currently accepted regulatory test for identifying potential teratogens involves the use of thousands of animals, is costly, takes two years to complete, and shows poor concordance (~60%) for human teratogens. The recent European Union ban on animal testing makes the reliance on non-animal test systems more urgent. Human embryonic stem (hES) cells reflect a unique biological system that cannot be represented by any other cell type used in toxicology. This proposal is focused on developing and validating a rapid toxicogenomics-based signature profiling assay for seamless integration into the Stemina Biomarker Discovery devTOX(tm) metabolomics-based platform. The combined expertise at ILS and Stemina will enable an innovative 'systems biology' approach to in vitro developmental toxicology screening in a human-relevant assay using the cell type at the origin of human development, the hES cell. We will identify a toxicogenomics-based signature profile built on the unique stem cell transcriptome response (protein coding mRNA and non-coding RNAs), and cellular response pathways to toxicant exposures, using bioinformatics-driven computational methods. Ultimately, this Phase II SBIR will result in the development, validation, and implementation of a medium throughput assay using transcriptome-based profiling with a high predictive value for potential developmental toxicants. This objective will be completed in three Specific Aims: Specific Aim 1: Conduct expression profiling of hES cells exposed to known/suspect teratogens and nonteratogens using a training set of 62 compounds to construct a predictive transcriptome-based signature of developmental toxicity; Specific Aim 2: Develop and implement bioassay standard operating procedures, quality control criteria, and validation of instrumentation and GLP-compliant protocols for the conduct of the devTOX(tm) assay integrated with transcriptomics; Specific Aim 3: Test the transcriptome-based signature derived from the training set with a blinded set of test articles using qRT-PCR assays for specific mRNAs, lncRNAs and miRNAs. This will allow development of a biologically relevant signature profile based on dysfunction of the highly regulated genome and epigenome circuitry that maintains stem cell functions.

Thesaurus Terms:
Accounting;Adult;Aging;Animal Testing;Animals;Base;Biochemical;Bioinformatics;Biological;Biological Assay;Biological Markers;Biological Systems;Blinded;Cell Physiology;Cell Type;Chemical Exposure;Chemicals;Code;Computing Methodologies;Congenital Abnormality;Daughter Cell;Development;Developmental Toxicology;Environmental Chemical;Epigenetic Process;Epigenome;European Union;Exposure To;Functional Disorder;Functional Rna;Gene Expression Profile;Genes;Genome;Genomics;Human;Human Development;Human Embryonic Stem Cell;In Vitro;In Vitro Testing;Innovation;Instrumentation;Late Effects;Lead;Life;Messenger Rna;Metabolomics;Methods;Micrornas;Modeling;Molecular Profiling;Nervous System Disorder;Organism;Pathway Interactions;Perinatal Exposure;Pharmaceutical Preparations;Pharmacologic Substance;Phase;Predictive Modeling;Predictive Value;Procedures;Programs;Property;Proteins;Protocols Documentation;Puberty;Public Health Relevance;Quality Control;Reliance;Response;Safety;Screening;Small Business Innovation Research Grant;Spontaneous Abortion;Stem Cells;Stimulus;System;Systems Biology;Teratogens;Testing;Toxic Effect;Toxicant;Toxicant Exposure;Toxicogenomics;Toxicology;Training;Transcriptomics;Validation;