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CL1-00506-1: Shared Stem Cell Facility

Laboratory Recommendation: Not recommended for funding

Public Abstract (provided by applicant)

We have assembled a team of researchers with the aim of elucidating the molecular and cellular mechanisms that regulate stem cell self renewal and differentiation. Drawing on their broad range of expertise in development, genetics, genomics, molecular, cell and computational biology, these researchers will use interdisciplinary approaches to tackle problems concerning how genes are regulated in human embryonic stem cells (hESCs), and how this regulation influences their ability to both self-renew and differentiate into specific cellular subtypes. Defining and ultimately controlling this process is an essential step in designing stem cell-based therapies. These projects are aimed at providing insights and tools for neurological and genetic conditions such as Parkinson’s Disease, ALS, CHARGE Syndrome, and Down Syndrome, and in aiding the development of gene therapy strategies. The work is funded in part from CIRM SEED grants to our faculty. In addition, we are committed to campus growth in this area, with faculty hires slated for expertise in various aspects of stem cell biology. Supported by a CIRM Training Grant, we are also committed to training a new generation of stem cell researchers – graduate students and postdoctoral fellows who will gain the knowledge and skills to embark on their own careers in this field.

To achieve these goals, we propose to build a Shared Stem Cell Facility (SSCF) by renovating 2000 square feet of space in the building where hESC research currently occurs. Our institution currently has no stem cell facility – hESC research is currently limited to NIH-approved lines because of the lack of separate, appropriately funded space. In addition, this facility will significantly expand and enhance the research space available for experimentation with hESC, in general, at our institution. The creation of a central facility dedicated to hESCs is essential for both on-going and new research, as well as for training. The resources and expertise provided by the SSCF will encourage additional faculty to use hESCs in their research and create new opportunities for faculty already committed to hESC research. For example, our faculty are eager to initiate projects that involve the use of non-approved cell lines that are free of the biological limitations of the approved lines, such as new hESC lines in which the mechanisms of self renewal and differentiation are altered, and in lines bearing disease causing mutations. This work will not be possible without a facility dedicated to hESC research that is free of federally-imposed restrictions.

Statement of Benefit to California (provided by applicant)

The California Institute for Regenerative Medicine came about because of a mandate from the citizens of California who voted to invest state money into human embryonic stem cell research. Supporters of Proposition 71 waved signs reading “Save Lives with Stem Cells” and news reports predicted that the measure’s passage would “put California at the forefront of the field.” While individual projects such as the shared stem cell facility in this proposal will not directly save lives or put California at the forefront, the work that will take place promises to move the field towards successful stem cell-based therapies, and to help give rise to technologies and intellectual property that can serve as the basis for new companies in California. The research to take place in the proposed facility will contribute to the characterization of stem cell lines that will populate an envisioned stem cell bank in California. By allowing advanced hESC research, this facility will strengthen pre-existing international collaborations and stimulate more, thus bringing together worldwide efforts in a common cause. Finally, the ability to perform hESC research at this and other CA institutions that is not restricted to the federally approved lines will attract highly talented researchers from around the country. The research to be carried out in these facilities will greatly accelerate the rate at which we acquire new knowledge about the properties and uses of stem cells. Californians will be proud of this investment in infrastructure to facilitate new discoveries and the training of new researchers, positioning California to lead the way to improving and saving lives through regenerative medicine.

Scientific Review Summary of Part One Application

SHARED LABORATORY

SYNOPSIS OF PROPOSAL: This application is for 3 years of funding to establish a Shared Research Laboratory (SRL) at the applicant institution. A 2000 sf (3200 gross) shared stem cell facility is proposed that will be used by multiple investigators. The laboratory will consist of 2 cell culture labs (1 core lab and 1 for teaching or for general use) plus cores for FACS, live cell imaginq, and cryopreservation. This facility will be located in an area that houses the departments of developmental biology and biomedical engineering. An appropriate oversight committee is in place. It is predicted that the SRL will provide services for 17 investigators, 9 from the applicant institution and 8 from a nearby institution. This includes 2 applicant institution faculty members who are approved to receive CIRM SEED grants. A broad range of scientific questions are being addressed by the 17 investigators.

QUALITY AND IMPACT OF THE SCIENCE: There is a comprehensive description of faculty stem cell research goals, many of which are hampered by the lack of resources, especially non-federally funded resources. According to one reviewer, the narrative provides a convincing argument for the value of this integrated team of stem cell investigators and indicated that the work proposed with hESCs is appropriate for the designed facilities.

The primary investigators (PIs) at the applicant institution are focusing on gene regulation, epigenetics and neurobiology in the context of human embryonic stem cells (hESCs). Academic strength lies primarily in bioinformatics and molecular biology. The bioinformatics component is led by an outstanding computational biologist who is analyzing regulatory elements in the human genome and rapidly evolving sequences. This individual also is director of the institution’s CIRM training program. One reviewer felt that all of these studies from the most basic to the most clinical in nature have the potential to reveal important findings that would be of relevance to human health and disease. The reviewer noted that there is a need for such facilities at the applicant institution, where none currently exist.

The reviewers agreed, however, that coalescence of stem cell biology on campus is still in its early stages. Presently, a critical mass is lacking and more expertise and faculty are needed to generate a robust center. Key faculty from a prominent nearby institution with experience in hESC will be playing important advisory roles. However, it is unclear how some of the other listed faculty from that institution will effectively interface with the applicant group.

A reviewer commented that the applicant institution has a strong and growing track-record in interdisciplinary biomedical research, as evidenced by the commitment to maintaining and expanding a worldwide genomics database tool. Much of the growth in this area has been due to the ability of key core faculty to attract funding to the institution, including two newly approved SEED grants. It was also noted that, although they are not applying for support for a stem cell techniques course, provisions for teaching stem cell culture to students and other faculty are described throughout the application.

APPROPRIATENESS OF SPACE AND EQUIPMENT TO SCOPE OF PLAN: In general, need for dedicated space is justified and the proposed lab is adequately configured, according to one reviewer. The detailed equipment list is also appropriate. The current stem cell space can only be used for NIH-approved stem cell lines and no shared facility is available at the applicant institution. The 2,000 square feet will add 30% more space – and more importantly non federally-funded, stem cell culture space. The facility has been designed for up to 5 researchers to be able to work simultaneously. There will be 1 cell culture room with 5 BSC and another core lab with 1 BSC. In addition, funds are being requested for a Zeiss Axiovert 200 motorized live cell imaging microscope, which could provide a unique resource for investigators working in the facility. A reviewer noted that the applicant did not make it clear who will be using this equipment, and for what purpose it will be used. This reviewer also thought that the space will be adequate for the number of investigators who propose to use it, but felt that this is an assumption, and the PD did not make an effort to justify the size based on the number of proposed users and the types of hESC research that they will be performing. Another reviewer felt that this is a good application for a shared facility but was disappointed by the lack of a plan to incorporate GMP guidelines into stem cell line expansion plans.

QUALITY OF MANAGEMENT PLAN: One reviewer indicated that the oversight committee, which includes key applicant faculty and faculty from a collaborating institution, is appropriate. It is not clear, however, how often the oversight committee will meet particularly given the involvement of the collaborating institution. The reviewer also felt that the description of general operations of the SRL is comprehensive and appropriate and additionally, that the plans for assisting and overseeing faculty activities are well thought out and will ensure excellent use of the resource. Another reviewer felt that although the PD presented a plan for administration of the lab with some oversight, the management plan is not as well worked-out or as sophisticated as those in other proposals, particularly with respect to the rules/regulations of growing hESCs. This could reflect inexperience by the applicant investigators with the requirements for creating and maintaining a hESC core lab.

The PD has put together a well-trained and experienced staff including 30% effort of a lab manager, who has a decade of experience in designing and managing mouse stem cell and transgenic cores. The proposed lab manager, however, is the current manager of the transgenic core. Because of the double role, one reviewer felt that the workload may become too much to handle as the facility begins to be heavily used. Another reviewer indicated that the 30% effort listed for the lab manager is very limiting. In addition, funds are requested for two laboratory technicians. One will handle hESCs and manage the FACS core. This is not optimal, according to one reviewer, as a dedicated technician will be needed to operate the high speed sorter that is being requested. The second technician will oversee the microscopy core.

A reviewer noted that the quality assurance plan for the hESC lab could have more detail regarding protocols for validation and auditing of the hESC lines including in vitro and in vivo differentiation assays, in addition to the proposed assessment for sterility and karyotype analyses. The PD has no hESC experience, but is an established associate professor with murine ESC experience, and has organized user groups for other shared resources.

The PD proposes to devote only 5% time to direct the stem cell facility, and the associate director will devote only 3% effort to the microscopy core, along with “scientific advisement” by another individual at 5% effort; this seems marginal and may be due to budget constraints since no salary appears to be requested for these positions.

DISCUSSION: This application has promise with research excellence in a number of areas, but the critical mass is not quite there yet. Thus, this application is not in the top quartile, according to one reviewer. The proposed users have three areas of academic focus: gene regulation, epigenetic modification and neurobiology. The stem cell program is admittedly a nascent program but there is an institutional commitment to build in this area. The applicant institution has a real strength in bioinformatics led by a world leader in this field. Many agreed that bioinformatics will be important for stem cell biology and this institution can provide complex genomics bioinformatics resources.

Overall, the constellation of faculty is good but not yet outstanding; they have 2 investigators approved for CIRM funding. The PD is a good choice given the noted experience with mouse ESCs, but the PD does not have experience with hESCs. This group is very new and starting from scratch. Six workstations are planned yet without an hESC expert to help set up.

They propose to interface with a nearby institution with expertise in hESCs for the oversight committee and for other advice, but it is unclear how effective that interaction is or will be. A single technician is proposed for maintaining hESC lines and to run the flow cytometer – this was perceived as insufficient personnel. Having the same person running the FACS and cell culture suggests inexperience since each of these tasks really need dedicated personnel. The person who will run the shared lab on a day-to-day basis currently runs the mouse transgenic core; in the long run this is not a good idea. Also the salary proposed is too low to recruit a manager with the right skill set. These and other issues reflect the inexperience of the applicants.

A second reviewer is torn because the applicant institution needs this facility – they have CIRM funding but no labs to do the work. The management plan is weak; quality control/access/SCRO are not mentioned and gives the impression that the group does not know quite what to do. The panel felt that “need” should not be considered a criterion for scientific scoring and is more relevant to a programmatic discussion. A third reviewer is enthusiastic because the applicant institution could become an outreach center for the more established collaborating institution, again pointing out that without this funding their research is stymied.

PROGRAMMATIC REVIEW: A motion was made to recommend that this Shared Research Laboratory application not be funded. Several points were discussed extensively during programmatic review. Overall, the science proposed is good, but management is lacking, and experience in hESCs is lacking. The main problem with the application is in not knowing how to run a hESC lab. One question was raised about the importance of funding bioinformatics. Bioinformatics was highlighted as a particular strength of this group, and there was some discussion about the relevance of this approach to stem cell research. One discussant pointed out that when done well, bioinformatics provides a tremendous tool. This group has the benefit that they have shown their ability to do it at the genomic level (their bioinformatics tool is used worldwide). The bioinformatics effort will continue without the SRL funding and likely wouldn’t be impacted adversely, but having the experimentalists would be helpful.

A proposal was put forth to recommend funding with conditions including requiring someone experienced in running an hESC lab to help set up this shared facility, and that there be a stated collaboration with the more experienced collaborating institution for a year to help in the initial set up and running of the facility. However, some committee members believed that establishing conditional funding is unworkable. Others believed the plan for management was so deeply flawed that administrative oversight would not work. These members of the panel considered this as essentially rewriting the application and rejected the proposal.

The motion to recommend that this Shared Research Laboratory application not be funded passed; however, there were sufficient votes against the motion that a minority report to the ICOC was issued.

The Minority Report states: “The strong science and opportunity to recruit unique bioinformatics expertise into stem cell research, and support funded CIRM investigators, overrides the weakness that the SRL Director has limited human embryonic stem cell culture experience. [The director] is an experienced cell culture investigator whose deficit could be alleviated either by training at [collaborating institution] or recruitment of an on-sight individual experienced in hESC culture.”

The following Grants Working Group members had a conflict of interest with this application and were therefore recused from participating in review of, discussion of, and voting on the application:

• Lansing, Sherry
• MacDonald, Raymond
• Studer, Lorenz