Funding opportunities

Defining the function of RNA modification in human pluripotent stem cells

Funding Type: 
Basic Biology V
Grant Number: 
Funds requested: 
$708 000
Funding Recommendations: 
Not recommended
Grant approved: 
Public Abstract: 
Human embryonic stem cells (hESCs) and induced pluripotent stem cells (hiPSCs) have two unique properties that make them invaluable resources for regenerative medicine: they are able to renew themselves indefinitely and to develop into every type of cell in the body. These cells therefore have tremendous potential for the development of patient-specific cell therapies for a variety of diseases. To capitalize on this potential, we must develop methods to ensure that hESCs and hiPSCs can maintain their undifferentiated state when expanded in culture. This requires a deep understanding of gene regulation in stem cells and is the area of focus for this proposal. For a typical gene, DNA is the blueprint, RNA is the messenger, and protein is the final product. Although most studies of gene regulation in stem cells have focused on DNA and proteins, it is now clear that RNA is much more than the ‘middle-man’. We plan to determine whether a particular type of chemical change in RNA, termed methylation, is essential for maintaining hESC/hiPSCs in their undifferentiated state. We will examine how RNA methylation occurs and how it regulates genes that control stem cell differentiation. This is a novel, unexplored area of stem cell biology, and the results of the proposed work could lead to the development of methods to sustain hESC/hiPSCs in culture as an unlimited source for cell therapy.
Statement of Benefit to California: 
Our highly innovative and exploratory research will benefit the state of California in several ways. First, human pluripotent stem cells have tremendous potential for the development of patient-specific cell therapies for a variety of diseases, thereby contributing to the health of all Californians. Second, by investigating a novel and fundamental gene regulatory mechanism involving RNA modification in human pluripotent stem cells, the proposed study will further our understanding of pluripotency and cell commitment and advance stem cell biology into a previously unexplored area, thereby maintaining California at the forefront of biomedical research, both nationally and internationally. Third, the proposed work will have direct and tangible benefits to Californian scientific and business communities. The results could provide a foundation for the design of new diagnostics and treatments in regenerative medicine, which will create jobs for Californians with a range of skill levels. In addition, most of the proposed work will be performed at local scientific core facilities using reagents and equipment from local vendors. Finally, local students and postdoctoral fellows who will be trained with the support of CIRM will be the driving force for biomedical research in California in the future.
Review Summary: 
The ability of human pluripotent stem cells to self-renew themselves indefinitely and differentiate to every type of cell in the body make them invaluable resources for regenerative medicine. To capitalize on this potential, methods must be developed to insure that human embryonic stem cells (hESCs) and human induced pluripotent stem cells (hiPCSs) can maintain their undifferentiated state when expanded in culture. The goal of the proposal is to determine whether a particular type of chemical modification in cellular RNA, the methylation of adenosine residues, is essential for maintaining hESCs/hiPCSs in their undifferentiated state. In Aim 1, methylation targets in hESCs and hiESCs will be uncovered. These targets will be compared to what has previously been uncovered in a nonhuman vertebrate model. In Aim 2, targeted genes will be knocked down to determine if a particular type of methylation is required to maintain hESCs in a desired state. The results of the proposed study could provide strategies to manipulate the stability of specific RNAs to maintain hESCs/hiPCSs in culture as an unlimited cell source for cell therapy. Novelty and Transformative Potential - The methylation of adenosine in RNA as a means of regulating gene expression in ESCs is an innovative and potentially important idea. - The overall study has limited novelty as the proposed investigation essentially repeats with human stem cells experiments previously done with non-human stem cells. While interesting to confirm the presence and targets in human ESCs, the direct impact in the field is not clear. - Based on the project goals and quality of the preliminary data, reviewers seriously doubted that study results would be transformative. Feasibility and Experimental Design - The preliminary data presented in the application are of extremely poor quality. The evidence that the methyl transferases are responsible for down regulating mRNAs involved in differentiation rather than pluripotency is unconvincing. - Reviewers had serious concerns about interpretation of results of proposed gene knock-down studies, whether results would be specific to ESCs and if experiments are adequately focused on the switch between self-renewal and differentiation. - There was limited confidence that the research team could carry out the complicated studies that are proposed. - Appropriate facilities are available to conduct the proposed research. Principal Investigator (PI) and Research Team - The PI has relevant expertise but only a modest track record as an independent investigator. - The research team appears to have appropriate expertise to conduct the proposed experiments, but would have benefited from collaborating with an embryonic stem cell biologist. Responsiveness to the RFA - The proposal plans to utilize hESCs and hiPSCs in the experimental design and is responsive to the RFA. No other relevant concerns were highlighted under this review criterion.

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