A new microarray tool for discovering DNA methylation stem cell biomarkers
A significant barrier to progress in development of safe and effective stem cell therapies is the lack of reliable inexpensive tools that can be used for quality control and characterization of transplantable cells. This is particularly challenging for analysis of the epigenetic state of cells, which is critical to their normal function. We propose to develop a high-resolution tool that can be used routinely to monitor cells to be used for therapy, and to ensure that they have normal epigenetic profiles.
DNA methylation is an important epigenetic mechanism that helps to control the orderly expression of genes. Inappropriate methylation patterns are linked to genetic disease and to the uncontrolled growth characteristics of cancer cells. Given the consequences of abnormal DNA methylation it is critical that cells used for clinical therapy maintain a stable and normal DNA methylation pattern.
Existing DNA methylation detection methods are either limited in scope or extremely expensive and technically challenging. These factors limit the feasibility of using these methods for routine, large-scale profiling of DNA methylation status.
We propose to develop a high-density DNA methylation microarray, which will test 100,000 individual sites in promoter regions of all known coding genes and known microRNAs, as well as a sampling of CpG sites located in intergenic regions. The platform will be a cost-effective and accessible tool for routine analysis of cell cultures prior to their qualification for cell therapy.
The heath care system of California will greatly benefit from the taxpayer’s investment in stem cell research. But a significant barrier to progress in development of safe effective stem cell therapies is the lack of reliable inexpensive tools that can be used for quality control and to assure the safely of transplantable cells. This is particularly challenging for analysis of the epigenetic state of cells. The exquisite control of gene activity in normal cells is regulated through regulatory molecules collectively known as “epigenetic” factors because they determine what genes are active in the DNA sequence without altering the sequence itself. Changes in the epigenetic state of cells can lead to uncontrolled growth, as in cancer cells, or to abnormal differentiation of stem cells.
Our research has indicated that human embryonic stem cells have a very precise epigenetic profile that distinguishes them from all other cells, and that this profile changes in very predicable ways as the cells differentiate. Our current technology, however, lacks the resolution to monitor the epigenetic state of all the genes in human DNA. We propose to develop a greatly improved high-resolution tool that can be used routinely to monitor stem cells that will be used for therapy, to ensure that they have normal epigenetic profiles.This technology will be developed specifically for human embryonic stem cells and induced pluripotent stem cells in the proposed research project, but it will have wide applicability to cancer research and studies of other human disease.