Funding opportunities

Safety Implications of Epigenetic and Genetic Adaptation of Human Embryonic Stem Cells to Culture In Vitro

Funding Type: 
Tools and Technologies I
Grant Number: 
Funds requested: 
$970 017
Funding Recommendations: 
Not recommended
Grant approved: 
Public Abstract: 
Ten years after the discovery of human embryonic stem (ES) cells, we are on the verge of the first clinical trials of products derived from this unique, remarkable and renewable source of healthy human tissue for transplantation therapies. However, safety concerns around the use of ES cell grafts are holding back clinical applications. A key issue is the known potential for formation of tumors or other inappropriate growths in ES cell derived grafts. This concern is amplified by the known propensity for ES cells to develop genetic alterations during their growth in the laboratory; these genetic changes resemble those associated with various forms of human cancers. Also, ES cells can undergo what are known as epigenetic alterations, or heritable changes in the way the cell reads out its genetic code. These epigenetic alterations may also predispose affected cells to form cancers. Although there is concern, in fact there have been few studies to assess how these epigenetic and genetic changes might arise, how best to detect them, and what their implication is for cell behavior in vivo. It is imperative for the future of regenerative medicine that we understand this area better: concern certainly is warranted, but an overly cautious approach will delay the implementation of therapies that have great potential to alleviate suffering. This study aims to provide a scientific basis for assessing and monitoring the process of how ES cells acquire cancer-like properties during propagation in the laboratory, and for understanding the implication of changes in the cell for the safe use of ES products in the clinic. We will examine carefully how the cells change in terms of their growth properties, and how this affects their ability to turn into specialised cells that would be used in treating patients. We will see what genetic and epigenetic changes in the cells occur, and we will monitor several key pathways in cancer development that might be expected to affect ES cells. Using this information, we will design sensitive tests that can detect small numbers of abnormal cells in a culture population. We will then see how the process of genetic and epigenetic change affects the behavior of cells in vivo, whether the changes cause tumor formation or disturbances in the formation of specialized tissues like nerve cells. We will also assess how sensitive current animal assays are for detection of abnormal cells. The results of this work will provide a strong basis for preclinical assessment of ES cell safety. This is an essential step on the road to therapy.
Statement of Benefit to California: 
Cell products derived from embryonic stem cells are rapidly moving towards clinical trials for several devastating medical conditions. However, there are safety concerns that surround the use of these products, in particular, the possibility that ES derived cells might form tumors or other inappropriate growths following transplantation. There is little scientific data in the public domain to guide regulatory decisions in this area, but much at stake: excessive haste could result in adverse outcomes that could hold back progress for years, whilst an overly conservative approach likewise could needlessly delay the implementation of new therapies of great potential. This study will provide a scientific basis for safety assessment of stem cell based therapeutics. By putting the process of safety assessment on a stronger scientific foundation, we will ensure that patients in California and elsewhere see the benefits of stem cell based therapies as soon as possible and with the minimum of risk. If the State is to take the lead in translating stem cell research into clinical benefit, we must address this critical area in a timely fashion.
Review Summary: 
The goal of this proposal is to elucidate the genomic and epigenetic changes that human embryonic stem cells (hESC) undergo when adapting to long term cell culture, and to use this knowledge to identify biomarkers for detecting abnormalities. To achieve these ends, the applicants first propose to assess growth and differentiation properties of 15-20 cell lines at different stages of adaptation. Genome wide SNP analysis will be utilized to assess changes in gene copy number, and DNA methylation studies will be used to assess epigenetic changes in selected genes. In addition, the applicants propose to examine how key cancer pathways are affected as cells adapt in culture. In the next phase, the applicants propose to evaluate the significance of their findings by investigating how the observed genomic and epigenetic changes affect neural differentiation and malignancy in vivo, and by assessing the sensitivity of the in vivo assays for detecting the presence of abnormal or undifferentiated cells in differentiated neural tissue. The impact of this proposal was considered to be fairly high by most of the reviewers, as the identification of genomic and epigenetic signatures that are indicative of tumorigenicity or other detrimental attributes could be used to replace the costly and time consuming functional assays that are currently in use. However, one reviewer was unconvinced that biomarkers are likely to be adopted as a surrogate for tumorigenicity of hESC and their derivatives, and felt that analyzing the sensitivity of the in vivo assays, as proposed, may yield more important information. One reviewer argued that the impact would have been higher if the applicants had proposed to use the acquired information to optimize culture conditions for maintaining genomic stability rather than merely describing them. Another criticized that the applicants did not discuss plans for immediate development of the technology in the event that useful assays are obtained. The feasibility of this proposal was judged to be somewhat uncertain. The reviewers agreed that the investigators are exceptionally qualified to conduct the described research, and the high quality preliminary data convinced them that this approach has merit. Some reviewers raised concerns about the scope of the proposal and thought that the numbers of cell lines to be evaluated, and the list of assays to be performed, were in excess of what could be realistically achieved in the limited time frame of this effort. In addition, one reviewer felt that many, if not most of the proposed in vitro assays were unlikely to provide definitive information indicative of malignancy. Instead, it was argued that expanding the differentiation analysis to include lineages other than the neural lineage would have provided a more meaningful analysis. The applicants were described as exceptionally well qualified to perform the described research. The principal investigator is an experienced stem cell investigator and a leader in the field. The assembled team has an excellent track record and has made important contributions to both the technical and conceptual aspects of stem cell biology. Overall, while the technology described in this proposal could be of great value, the reviewers were not sufficiently convinced of its feasibility and applicability.

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