Funding opportunities

Development of Diagnostics to Assess Potential Teratoma Tumorigenicity in Human Stem Cell Derived Therapeutics

Funding Type: 
Tools and Technologies I
Grant Number: 
RT1-01069
Funds requested: 
$599 636
Funding Recommendations: 
Not recommended
Grant approved: 
No
Public Abstract: 
The primary goal of this application is to utilize [REDACTED] ultra-sensitive genetic and epigenetic fingerprinting technologies to identify unique biomarkers that distinguish between teratoma and hES cells, which can be used to develop diagnostic tests that evaluate ES cells to ensure that they are teratoma-free and suitable for clinical applications. Biologic therapies derived from human stem cells through tissue regeneration and the targeted delivery of genetic material are expected to provide effectiv treatments for a wide range of medical conditions. However, the potential for in vivo stem cell tumorigenicity due to teratoma development represents one of the primary safety concerns noted in the recent FDA Guidance on Stem Cells and a key issue confronting the development of cellular therapies derived from human embryonic stem cells. The specific aims of proposed research addresses these tumorigenicity concerns by using [REDACTED] ‘s established collection of ultra-sensitive profiling technologies t develop fingerprints for identifying teratoma-specific biomarkers suitable for screening hES cell preparations to assess their safety prior to their use in clinical applications. To accomplish these goals, comprehensive fingerprints of promoter/ enhancer interactions, methylation, multiple histone modifications, mRNA profiling, and protein expression will be compiled in hES and teratoma cells using [REDACTED] ‘s proprietary ChIP-on-Chip, and Next Generation Sequencing based ChIP-Seq and mRNA profiling technologies in conjunction with [REDACTED] ‘s collection of antibodies to the entire family of mouse and human transcription factors (TF). This will include genome-wide profilin of factor interactions identified with promoter (H3K4me3, TAF250, and Pol II) and enhancer (H3K4me1) activation, in conjunction with promoter DNA Methylation mapping, as well as studies involving germ-line specific antibody profiling. The utility of these identified targets that distinguish between teratoma and hES cells will subsequently be validated by tracing the teratoma status in a pancreatic beta cell differentiation lineage. These studies will facilitate the identification of unique teratoma-speciic biomarkers that will enable development of diagnostic tests that allow for rapid determination of the presence of contaminating teratoma cells in potential clinical ES cell samples by integrating multi-level profiling data to provide a comprehensive view of the transcriptional and translational networks that are active in ES and teratoma cells.
Statement of Benefit to California: 
The proposed research will be of great value to the people of California in potentiating the safe use of hES cell therapies currently being developed as therapeutic treatments for a wide range of medical conditions. The FDA has recently identified potential stem cell tumorigenicity due to teratoma development as a major safety concern and a key issue confronting the development of cellular therapies derived from human embryonic stem cells. The research in this proposal will address these concerns by identifying teratoma and hES cell specific biomarkers which will be incorporated into diagnostic tests that can quickly assess the tumorigenicity potential of hES cell derived therapeutics, and consequently expedite the safe use of stem cell therapeutics within the California population.
Review Summary: 
The goal of this proposal is to identify novel biomarkers that will distinguish between human embryonic stem cells (hESC) and teratoma cells. This identification will involve a comprehensive fingerprint analysis of promoter/enhancer interactions, epigenetic markers, mRNA profiles, and protein expression to be compiled for both hESC and teratoma cells. These analyses should yield markers for the screening of stem cell preparations for an assessment of tumor potential. The proposed work has a high potential impact. The identified biomarkers could be used to analyze hESC-derived preparations and ensure that they are free from teratoma-forming cells. The ability to rapidly and accurately perform this analysis could facilitate the identification of cell populations that are safe for clinical use and substantially reduce tumor risk in patients who are transplant recipients. The approach proposed for cellular analysis employs highly sensitive and powerful analytical tools that could allow the identification of markers that distinguish teratomas from hESC. However, reviewers had strong concerns about the implied premise underlying the proposal - that teratoma cells present throughout the differentiation process of hESC are passed along and are responsible for tumors in transplant recipients. This is contrary to the prevailing view that teratomas can arise after transplantation from either undifferentiated or incompletely differentiated embryonic stem cells. The applicant did not address this significant issue. Reviewer enthusiasm was further diminished by a lack of clarity in the research plan. Inadequate details were provided to understand how experiments will be conducted and analyses performed. Reviewers were also concerned that cell lines chosen for analysis were inappropriate and that significant differences in the analytical fingerprints of ESC and teratoma cell lines may be independent of the potential to generate teratomas. The Principal Investigator has much experience the high throughput analysis of transcription networks. The research team is well qualified to develop the proposed diagnostic tests and bioinformatic analysis. Reviewers expressed concerns that evidence of recent research productivity by key personnel was not apparent.
Conflicts: 

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