Development of the Stem Cell Matrix, a Shared Database of Stem Cell Information
All stem cells have similar features, like the ability to differentiate into multiple types of tissues. But not all stem cells are alike. Not only are human embryonic stem cells (hESCs) and somatic (adult) stem cells very different from each other, but different preparations of the same kind of stem cell can have vastly diverse characteristics. This means that some stem cell lines may be preferable to others for particular research projects or clinical therapies. But how can scientists decide which lines to use? The answer is for scientists to share with other scientists the information they gather from their experiments with individual cell lines or types. We pioneered this effort by creating a website called the Stem Cell Community, but while the website is useful for creating a sense of community, scientists need a means to share the immense amounts of data that are generated by modern molecular methods. In particular, we have been using the power of the human genome project to examine the qualities of different types of stem cells. Using a high-throughput gene expression microarray method, we are identifying a distinctive "molecular signature" for each stem cell line. We are also using molecular analysis to study how particular genes are turned on and off during stem cell differentiation, and we are using the tools of personalized medicine to look for genetic changes in the cells. Each of our experiments generates several million data points, and our challenge is to find a way to make these data useful for other scientists.
Our solution is to develop a sort of "Google" for stem cells, a web-based database that will allow scientists to browse through molecular profiles; this database will also link this information with a variety of other kinds of information such as results of other scientists' experiments and preclinical and clinical data on stem cell therapies. It is our hope that the Stem Cell Matrix will not only aid in design of experiments for fundamental and preclinical research, but will also enable clinical insights, the "eureka" moments that will lead to bold new approaches to diagnostic tests and cures.
“California has the fastest growing population in the U.S., and the fastest growing segment of California’s population is persons age 85 and over. The number of people over 60 years of age will grow from 4.9 million in 2000 to 9.0 million in 2020.”
Governors Budget Summary, 2001-01, Aging with Dignity
Californians are a large and diverse population that poses unique challenges for the future of medical care. To its benefit, California has a tradition of taking the lead in technology and medical breakthroughs, not only by invention and innovation, but also by following through with research, development, and commercialization of ideas. Californians have a tradition of encouraging an entrepreneurial spirit, making the state an attractive site to launch new and risky ventures.
Our proposal takes advantage of California's greatest strengths: innovative scientific research and high tech expertise. We propose a collaborative effort that integrates cutting edge laboratory research with the imaginative computer technology that launched many successful high tech ventures in California. We will generate and analyze a large amount of information about stem cells and use high-level software analysis to put the molecular signatures of these cells in perspective with scientific data and tests of efficacy in preclinical development and clinical trials. The database that we are building, which we call the "Stem Cell Matrix" will have the unique feature of being accessible to scientists who have little or no experience in molecular biology or bioinformatics. In order to achieve this goal, we are drawing on the talents of two groups of California researchers: one is actively developing high-throughput molecular analysis methods, and the other is designing accessible web-based knowledge databases Our goal is to make stem cell data accessible to scientists so that they can make intelligent choices about which of the hundreds of embryonic and somatic stem cell lines will be best for their needs. This will eliminate wasted resources by creating a shared information database, encourage collaboration among a diverse group of scientists, and immediately enable scientists to plan and carry out their experiments in a sound scientific context. This database has the potential to make California a significant stem cell and life science content provider. This project will create a magnet for other researchers, inside and outside California, to contribute their own information and expertise, which will leverage the power of the California stem cell community to explore novel approaches. The proposed project will be a springboard to new commercial ventures, and attract investment in research and development. Ultimately, by encouraging sharing of information, the project will help maintain high standards of scientific research, and speed the development of clinical applications for stem cells that will benefit all Californians.