We propose a CIRM Training Program in Systems Biology of Stem Cells featuring formal and supplemental education in a collaborative, interdisciplinary biomedical research environment. As part of the Institute for Biology of Stem Cells, this program brings together the unique strengths of faculty with expertise in key areas for advancing basic stem cell research. Our labs are developing computer and mathematical programs to analyze large volumes of stem cell data and to understand stem cell behavior. We have experts on DNA and RNA structure who are learning how those biomolecules instruct stem cells to self-renew or develop into specialized cell types. Other faculty are using animal models and advanced techniques to investigate important questions in stem cell biology, and our engineers are working on improving the technology for studying and utilizing stem cells. This program will provide an in-depth understanding of the biology of stem cells, the skills to use stem cells in one’s own research, and the ability to create computer programs and use the results of computer analyses in one’s own research. It will also provide the tools to make well-informed decisions regarding the ethical and social issues surrounding stem cell research. This Type II program will comprise six postdoctoral and four predoctoral positions lasting up to three years. Formal training includes three required courses (Introduction to Stem Cell Biology; Stem Cell Research: Scientific, Ethical, Social, and Legal Issues; and Current Protocols in Stem Cell Biology) plus 14 optional electives chosen to support trainee research goals and provide breadth. Supplemental training includes participation in a stem cell journal club, stem cell group meetings, the [REDACTED], seminars and other events. Trainees can also take the [REDACTED] Human Embryonic Stem Cell Lab course and will be encouraged to present at a national conference. These activities provide opportunities for trainees to expand their knowledge, present their work, and form a network of colleagues and potential collaborators. Our recently completed and operational Shared Stem Cell Facility and numerous other shared labs – including facilities for animal research, chemical screening, genome sequencing, microarray, proteomics, and bioinformatics – provide excellent resources to this program. We have a strong track record in graduate and postdoctoral training in biomedical research anchored in our Molecular, Cell and Development Biology and Bioinformatics programs. We are committed to offering more opportunities through the [REDACTED] CIRM Bridges program and our new interdisciplinary graduate Program in Biomedical Science and Engineering. We are also committed to increasing the numbers of underrepresented minorities in biomedical research and will continue our tradition of outreach and support to those populations.
The State of California has made a commitment to support stem cell research and to advance work that will lead to diagnostics, therapies, and cures for human injury and disease. The proposed training program will assist the State in reaching this goal by training graduate students and postdoctoral researchers in areas of basic stem cell research. Basic (or discovery) research uncovers the molecular and cellular details that instruct stem cells to remain as stem cells or to differentiate into the myriad types of cells of the human body. Knowledge of how stem cells function at this level is critical to utilizing them for devising medical breakthroughs. While in this program, trainees will not only be gaining an education, they will be making important contributions to the research project they have mapped out with their mentor, which should lead to publication and furthering the knowledge needed for stem cell medicine to succeed. Furthermore, many of these newly trained stem cell scientists will stay in California to build their own careers in academia or industry.
This application proposes the continuation of a Type II training program with a training cohort of 6 postdoctoral and 4 predoctoral positions. The application has a particular and strong focus on systems approaches to stem cell biology. The program benefits from the leadership of a prominent biomedical engineering professor, and several associate directors from biomedical engineering and molecular, cell and developmental biology. Overall, the program impressed reviewers as one which could not be replicated at any other institution, affording trainees wonderful opportunities.
The training environment and program design, given the chosen systems biology approaches, are excellent. Coursework for the trainees includes introduction to stem cell biology, ethics, and a techniques course with optional courses in cell biology and computational biology with 14 optional courses. The laboratory course curriculum suggests that the students will receive excellent practical training in basic methodology. The teamwork format of this course was considered a real plus. The director of the ethics course comes from the philosophy department and reviewers appreciated this contribution, and overall the curriculum was considered diverse, interesting, and well crafted. Because of the institution’s enormous strengths in computational biology and genomics, trainees have the option of gaining in-depth training in these areas. One reviewer felt that these opportunities, so important to the program, could be leveraged better by designing a curriculum that more firmly intertwined computational biology and laboratory stem cell biology, to cross-train more of the students. Students will be introduced to stem cell techniques at an intensive training program conducted by one of California’s premiere stem cell research institutions.
The institution recently reorganized its graduate training program into an integrated Biomedical Science and Engineering program, which will help to bring students with diverse scientific interests into the training program. The interaction between engineering, bioinformatics, and biology students was felt to be a refreshing feature of the program. Though the facilitation of recruitment of students into the predoctoral program was clear in the application, the mechanisms for recruiting the best postdoctoral trainees to the program seemed not well developed. Further, little information was given on performance and success of postdoctoral trainees currently in the program, leading to more concern on the part of one reviewer that the postdoctoral program structure needs some attention. Similarly, in contrast to the careful construction of the training program, metrics for assessing the program’s success were felt to be less sophisticated and deserve attention, including external advisory feedback.
The program has resulted in formation of an apparently active regional stem cell club. Further opportunities for trainees are organized journal clubs, quarterly institution-wide stem cell group meetings, and other retreats and conferences.
Though the institution’s stem cell institute is relatively new, the core faculty is highly experienced, and the executive committee is strong. Diverse work in model developmental organism systems adds to the strong computational/mathematical background of many of the faculty.
Leadership of the program was universally applauded, and reviewers felt that the director is exceptionally qualified. Associate directors include experienced professors and one assistant professor. Although faculty members largely entered stem cell biology from other fields, the students have large numbers of highly qualified mentors from which to choose. Recognized experts in genomics, chromatin regulation, RNA regulation, bioinformatics, computer science, and bioengineering all bring enormous strengths to the program. External advisors or business expertise were thought to be lacking on advisory committees. Though the recent history of the institution points to a major new commitment to stem cell biology in the context of its traditional strengths, reviewers were concerned about the lack of written institutional support letters.
Overall, the proposed training program takes advantage of the institutional strengths, giving students the unique opportunity to learn stem cell biology with a systems framework, and potential for cross training in computational biology and other mathematically intensive areas. Some reservations about the program included the reliance on junior faculty mentors, and the lack of a sophisticated internal review process. Reviewers were enthusiastic about the details of the curriculum, the systems focus, leadership of the program, and growing institutional strengths in stem cell biology.