Embryonic stem (ES) cells have the unique ability to self-renew while maintaining a pluripotent state. They can readily be differentiated into all cell types upon exposure to the appropriate stimuli. The differentiation of ES cells into specialist cell types involves the activation of lineage-specific programs of gene expression and the silencing of genes that promote pluripotency. These changes are now well known to include epigenetic modifications such as DNA methylation and deposition of distinct histone marks across the genome. However, much remains to be learned as to how ES cells differ from differentiated progeny. In particular, it has remained unclear as to how the 3D-structures of the ES cell genome change upon developmental progression into a fully committed cell type and during reprogramming. Thus, we are now faced with the fundamental question as to how the 3D-structures of human ES cell genomes differ from that of differentiated progeny and how such differences relate to the establishment and maintenance of pluripotency versus differentiation. This is the focus of the studies proposed in this application.
Our studies would provide insights into the mechanisms that underpin the abilities of human embryonic stem cells to self renew and to differentiate into specific cell lineages. This research will serve as a foundation for understanding the basic properties of human embryonic stem cells and differentiated progeny. Understanding and modifying the properties of stem cells would directly impact novel approaches that are being developed to study stem cell models of many types of diseases and regenerative medicine. It would also permit the development of new avenues for the diagnosis and treatment of human disease and help to maintain the position of California as a leader in basic and applied biomedical research.
This Fundamental Mechanisms Track application elucidates the 3D topology of the genome in embryonic stem cell (ESCs), induced pluripotent stem cells (iPSCs), and their progeny and studies how the topology will affect the establishment and maintenance of pluripotency versus differentiation. To achieve this goal, the applicant proposes two aims. The first aim elucidates the 3D-genomes of human ESCs and differentiated lineage progeny. Then, Aim 2 focuses on the 3D-genomes of iPSCs derived from human peripheral blood.
Significance and Innovation
- The Principal Investigator (PI) proposes to study a highly significant, unsolved problem.
- Reviewers agreed that how the 3D topology of the genome affects gene expression is a timely and important question that is poorly understood.
- Reviewers were enthusiastic about the PI’s proposed experiments on how the epigenetic memory distinguishes iPSCs from ESCs and considered this to be significant as well.
- The methodological approaches proposed to study the two aims are state-of-the-art but not innovative. Overall, the project was assessed as moderately innovative.
Feasibility and Experimental Design
- The proposed research activities are logical and closely follow the strategy employed in an earlier publication by the PI.
- With the previous experience of the laboratory and the tools they have developed the milestones are achievable within the award timeframe.
- Reviewers cited some minor weaknesses in the experimental details that could compromise the completion of the research in a timely manner. For example, some of the reviewers questioned whether the applicants will be able to complete the 3D genome comparison in the time frame they have estimated.
- The reviewers commented that the work is largely descriptive. However, it was agreed that this was a limitation of the available technology, not necessarily a deficiency of the experimental design.
Principal Investigator (PI) and Research Team
- The PI has an excellent track record of publications in related research and is a leader in the field. The level of commitment is appropriate for the proposed study.
- The research team has the appropriate expertise and techniques available to conduct the proposed research.
Responsiveness to the RFA
- The study is designed to observe and understand the changes in the 3D topology of human stem cells, which is a fundamental element of basic stem cell biology and responsive to this RFA.