Funding opportunities

Funding Type: 
Shared Labs
Grant Number: 
Principle Investigator: 
Funds requested: 
$4 093 557
Funding Recommendations: 
Grant approved: 
Public Abstract: 

The University of California, San Francisco (UCSF) has a long history of making innovative discoveries that change the way scientists and clinicians think about disease processes and their approaches to finding cures. Accordingly, researchers at this institution were quick to appreciate the enormous promise of human embryonic stem cells (hESCs) as research tools for understanding how the body normally works, thus laying the groundwork to identify disease-related aberrations. Therefore, in 2001, when the federal government decided to limit government funding to work with existing hESCs, which they banked, U.S. scientists were faced with a dilemma. Would we abide by these unprecedented restrictions, which meant that research would be limited to first-generation cells, or could we find ways to develop second-generation, higher-quality hESCs? Investigators on our applicant team took both approaches. Since UCSF contributed two hESC lines to the federal registry, our team members participated in the government’s program to distribute these cells, which entailed teaching scientists how to use them. We also sought nonfederal funding sources to derive new hESC lines. Thus, we have a great deal of experience that is directly relevant to achieving the California Institute for Regenerative Medicine’s (CIRM’s) goal of establishing Shared Research Laboratories that also offer hands-on courses. We give the highest priority to teaching hESC techniques in the context of the ethical issues surrounding this work. Here, we propose to expand the nonfederal laboratory space that already exists at UCSF. Renovating and equipping an adjacent lab will significantly increase our capacity for growing and analyzing second and subsequent generations of hESCs. Our goal is to make the existing space, renovated with UCSF funds, and the new lab to be created with this CIRM award, available to our colleagues. We also want to jump-start their work by teaching them how to grow and analyze hESCs. Thus far, 16 graduate- and postgraduate trainees are funded by our CIRM training grant; 32 UCSF scientists have applied for CIRM SEED and Comprehensive grants, and we expect many more will follow. We also want to support the work of our colleagues at 10 neighboring institutions. At the same time, we will use this lab to derive new and higher-quality hESC lines. We will also teach these techniques to highly motivated California scientists. Our work is important because the researchers who use our laboratory are studying the causes of major human diseases that occur as the result of trauma (e.g., paralysis), cell death (e.g., Parkinson’s and Alzheimer’s diseases, diabetes, cardiac failure), or cell malfunction (e.g., cancer). Thus, by sharing our laboratory space, scientific equipment and technical expertise with colleagues at UCSF and other institutions, we will play an important role in helping scientists accomplish CIRM’s ultimate goal of finding cures for human diseases.

Statement of Benefit to California: 

By voting in favor of Proposition 71, which funds research involving human embryonic stem cells (hESCs) that is not supported by the federal government, the citizens of California sent a clear message that they want scientists in our state to play an important role in research that could revolutionize medical treatments and render significant economic benefits. Currently, these treatments largely consist of surgical or pharmacological interventions, and transplantation approaches that involve significant hurdles. For example, human cells carry unique identifiers—molecular “bar codes”—that must be closely matched or the transplant will be rejected. And, unless the bar codes match perfectly, the recipient has to take powerful drugs to suppress rejection. Finally, there are major shortages of cells and organs for use in transplantation procedures. With the advent of hESCs, researchers are envisioning new therapeutic approaches. In theory, these cells, the building blocks of the entire body, can become any cell type. Thus, there is a great deal of excitement about using hESC-based transplantation techniques to cure human diseases. Why haven’t these approaches moved forward full throttle? In 2001 the federal government limited hESC research to existing cell lines. This unprecedented move created additional barriers. If scientists want to make new hESC lines or work with higher-quality cells that were established after 2001, they have to use labs that are completely devoid of government funding—that means building materials, equipment and supplies. Therefore, these labs must be created with funds from nonfederal sources, one of the reasons that the California Institute for Regenerative Medicine was created. We envision that our proposed Shared Research Laboratory and Teaching Facility will help us create a major center for conducting the most exciting aspects of hESC research that will ultimately lead to cures for many of the most devastating human diseases.

Review Summary: 


SYNOPSIS OF PROPOSAL: This is a proposal for funds for a Shared Research Laboratory (SRL) and Stem Cell Techniques Course to expand existing non-federal laboratory resources and to institute a stem cell training course. The proposal would nearly double the size of a newly remodeled non-federal research laboratory by remodeling an additional approximately 1000 square feet of adjacent space, and would redirect the use of this space to create a shared facility in order to develop and distribute hESC lines, and to support junior and established investigators in their non-federal hESC work. The proposal involves 28 UCSF faculty, 2 SFSU faculty, plus other potential users listed in the application that includes alliances with 10 other Bay Area institutions. The community of UCSF investigators includes 16 CIRM trainees and 8 investigators who have been approved for funding for Leon J. Thal SEED grants at the time of application. The investigators work in areas of great biomedical importance, including human development, neurologic disorders, diabetes, heart disease and cancer.

The course plan is to offer three modes of instruction to meet the needs of a diverse group of investigators. The course offerings include: 1) a formal core course of one week duration offered quarterly that will include lectures, seminars, and hands-on laboratory experience and cover growth, propagation and analysis of nonfederal hESCs; 2) a course on hESC derivation and 3) a less formal course of instruction for CIRM SRL users will be provided on a rolling basis as needed.

QUALITY AND IMPACT OF THE SCIENCE: Dr. Linda Giudice and colleagues seek to double the size of a newly remodeled non-federal research laboratory by developing adjacent space to create a shared facility for hESC growth and propagation. All program leaders, including Drs. Giudice and Fisher, are well-established in relevant fields of investigation. Specific projects are only briefly described in the application, but the success of UCSF investigators in obtaining peer-reviewed support from CIRM is testimony to the quality and originality of the ongoing work. The eight SEED grants, awarded to Guidice (trophoblast cells), Guo and Ramalho-Santos (transcriptional regulation), Tlsty (cell cycle regulation), Blelloch (microRNAs), Willenbring (cell fusion), Weaver (niches), and Daldrup-Link (imaging) address an impressive array of important stem cell research areas. In addition to the already approved SEED grants, the narrative describes seven comprehensive grants designed to address a broad range of stem cell issues from a human embryonic fate map to the development of therapeutic approaches to Parkinsons, heart disease and blood disorders. Collaborations with SFSU, Blood Centers of the Pacific and the Gladstone Institutes provide additional opportunities, including development of Good Manufacturing Practices.

The plan is to “create a bank of nonfederal hESC lines” to supply participating investigators with characterized cells of uniform quality. UCSF has a long history of supporting hESC work. In fact, they were one of two US medical institutions to contribute hESCs to the NIH registry. They have been very good in maintaining and distributing cells to colleagues. After the NIH registry was closed in 2001, this team did not stop their derivation efforts, and set up a small private space where they could continue derivation, and have derived new lines since then. Thirteen hESC lines were created by investigators listed in this application, including some that are part of the NIH registry. In addition, they will create a bank of feeder layers: human fibroblasts and placental cell lines. The quality of the investigators and the research proposed is excellent, and the need for additional non-federal stem cell resources for the expansion of the existing facility to construct a CIRM research and teaching laboratory that will serve as a cell culture resource for UCSF investigators and their colleagues in California is well-justified and compelling.

APPROPRIATENESS OF SPACE AND EQUIPMENT TO SCOPE OF PLAN: UCSF funds were used for a recently completed remodeling project resulting in a 1,147 square feet nonfederal micromanipulation lab, two imaging rooms comprising 124 square feet and a small tissue culture area. The proposed renovation of 1,054 sq ft of laboratory space would be adjacent to this newly remodeled space, linked to it by a heavy equipment room, thus avoiding unnecessary duplication of large equipment items and optimizing efficiency. This renovation would approximately double the space available for non-federal hESC research. The stated vision is of a CIRM SRL to be the hub, with the spokes being nonfederal areas in the laboratories of individual PIs. This grant proposal is requesting funds to build and equip a suite of three tissue culture rooms. New construction will also include a “pass-through window” to the UCSF Human Gamete and Embryo Bank (also already part of existing research area). Existing equipment includes three -80 freezers, a -20 freezer, a bench top centrifuge, a Nulceovisio gel documentation system, a Speed-Vac, two Bio Rad MyQ real-time PCR machines, an Eppendorf micromanipulation system, liquid nitrogen tanks, a cryostat, and a Zeiss fluorescent confocal microsope. Funds are requested for a FACSAria cell sorter, a requirement of many projects of PIs involved. The list of equipment is detailed, well justified and appropriate for the goals. There may be some space constraints for the teaching plans, but those are addressed in the application.

The proposal also describes the accounting and administrative mechanisms at UCSF to facilitate the creation of nonfederal research areas, as well as transitioning projects from the core research area to individual PIs’ laboratories. The space and equipment is perfectly appropriate and in line with the mission as defined by the abstract.

QUALITY OF MANAGEMENT PLAN: This application brings together many experienced investigators in both basic and clinical studies, as well as good experience in the management of core facilities. These investigators are drawn from the UCSF community and the Bay Area. The quality of the director and key personnel is very high, and many of those involved have been recommended for Leon J. Thal SEED funding from CIRM. The overall program will be led by Dr. Giudice (Program Director) and Dr. Fisher (Associate Program Director). Each is experienced and highly qualified to lead this effort, and they effectively collaborate in other areas. Dr. Fisher’s experience as leader of a proteomic core facility is relevant to utilization of this shared resource. Drs. Guidice and Fisher will participate in the direction of both the SRL and SCTC, devoting 5% of their time, and requesting 5% of their salary, for each. Dr. Olga Genbacev will devote 25% of her time to each activity, the remaining 50% is spent as “the lead scientist in the Fisher lab on all projects involving hESCs.” She will direct the day to day operations of the SRL. Juanito Meneses will devote 12% of his effort to each activity, the other 76% is devoted to research. Dr. Alicia Barcena will also devote 12% of her effort to each activity, the remaining 76% will be spent heading up FACS analysis in the Fisher lab, in consultation with Dr. Genbacev. Sarah VonBrandt, a newly hired research embryologist in the UCSF In Vitro Fertilization Clinic, will devote 25% of her effort to each activity, the remaining to clinical embryology duties. Tara Calcagni, a FACS technician in the UCSF Comprehensive Cancer Center (NCI-funded) will devote 12% of her effort to each activity, the remaining effort to FACS analysis in the Cancer Center. Tamara Zdravkovic, a research technician in the Fisher lab, will devote 5% of her effort to each activity, focusing especially on confocal microscopy, the remaining 90% will be spent in the Fisher lab. Meagan Cron will devote 5% effort to each project and will control access into the SRL, her time is not being charged. A total of 2.9 FTE is being requested as personnel for the SRL and the SCTC, divided among 13 individuals. No one will work full time for either activity. Dr. Genbacev and Sarah VonBrandt, the new hire in the IVF clinic will be the largest contributors to both the SRL and SCTC, 50% of their efforts. A to be named web developer will also devote half-time to both activities. It isn’t clear who will do all the stem cell culture, characterization, and banking. Juanito Meneses “will play an important role in the day-to-day operations of the facility” but is only listed as devoting 12% effort to the SRL. Everyone else is listed as devoting lesser effort, generally on a specific task, such as FACS analysis or confocal microscopy. One reviewer thought that the application did not draw a clear distinction between the efforts of several participants in the Shared Research Laboratory and their role in the Fisher laboratory. Another reviewer considered the personnel budget to be essentially additional funding for Fisher lab technical people. This reviewer believed that this could become administratively problematic since Dr. Guidice is listed as the director of the SLR, but it is unclear whether any technical staff report directly to her and the SLR manager, Dr. Genbacev, is actually the lead hESC scientist in the Fisher lab. This is viewed by the reviewer as a major problem with this application.

A four-step process is proposed to prioritize use and allocate time of the shared facility, modeled on Dr. Fisher’s process implemented in UCSF’s proteomics mass spectrometry core facility. First, an oversight committee will set priorities, giving additional weight to CIRM-funded investigators and trainees and other non-federally funded investigators. The Oversight Committee includes, in addition to the Program Director and additional key SRL management, appropriate representation among physicians, scientists, administrators, and members from outside UCSF. Second, the associate program director and / or the director of operations (Drs. Fisher and Genbacev) will meet regularly with every trainee and PI together with their group to establish appropriate needs and equipment. Thirdly, the shared facility will help investigators on a rolling basis to initiate their projects, including training in culture and proper consent preparation. The fourth step will include a webpage to act as a discussion forum, notice board, and scheduling system. It is unclear from the application how many groups will be able to simultaneously use the suite of three newly-renovated tissue culture rooms, what is the anticipated rate of turnover, and how space will be prioritized for research versus teaching.

The institution has made a substantial commitment to the Shared Research Laboratory. A letter from Dean David Kessler describes a previous commitment of more than one half million dollars for renovation of adjacent space, and support for architectural plans and a willingness to absorb cost overruns for the planned space. UCSF’s commitment to supporting hESC research with a shared research lab is evident from the last five years, during which they have created the existing shared space and formed the institutional oversight necessary for these projects.

DISCUSSION: This is a beautifully written, wonderfully detailed application from a very well established investigator who has assembled a world class team of investigators and excellent collaborations for this SRL. UCSF is arguably one of the leading institutions in the world in the derivation and propagation of human embryonic stem cell lines, with a strong history of supporting and utilizing core research facilities. There is already recently renovated space at the institution for non-federal research and some of the administrative infrastructure. The proposal is to renovate an additional approximately 1000 sq. ft. to enable a core shared lab as well as shared core equipment. UCSF currently has a CIRM training grant and has been approved (at the time of application) for the award of 8 SEED grants and has Comprehensive applications pending (at the time of application), thus there is a lot of scientific depth. The research interests of the participating faculty include such areas as stem cell niche and transcription regulation. The applicants propose to create a bank of hESC lines with a goal of ensuring uniform quality and there is a track record at UCSF of successful line derivation. The reviewers were disappointed that the proposal did not include line derivation from PGD disease embryos – at least one reviewer considered this a flaw – and that SCNT research was not included, despite resident expertise which is very difficult to find. One reviewer noted that doing SCNT research generally brings more punishment than rewards; also for line derivation from PGD embryos, this reviewer noted that it can be very difficult to get consent from the patient. Therefore this reviewer believed that the applicants should not be penalized for not proposing line derivation from PGD embryos nor for not including SCNT in the proposal. Similarly, a reviewer was disappointed at the absence of GMP as part of the Shared Research laboratory and considered that ommission a real hole in the proposal.

It was unclear to some of the reviewers whether this shared lab would in fact be available to investigators not already on the payroll and that a more ecumenical use would be better. A discussant noted that there was a large base of investigators who were proposed as users of the lab. This raised the question of whether there was a management plan to determine access. A reviewer believed that access was to be decided by Dr. Guidice and ratified by the oversight committee. There was concern among some of the reviewers on the way the management of the shared lab management was structured and a belief among the reviewers that the management plan mainly allowed additional funding for the Fisher lab given that many of the shared lab personnel were drawn from her staff and that there was no plan to hire anyone from outside her (S. Fisher’s) team to manage and run the SRL. There was the concern that 13 persons were contributing between 5 and 25% of their time to each of the SRL and SCTC which was thought to be insufficient in that the SRL was no one person’s full time job.

Overall, this application received high marks for the science and the investigators listed are excellent, but the way the proposal is written, the personnel design and usage of the SRL is problematic. As described, the SRL is essentially an extension of the Fisher laboratory with no single individual devoted exclusively to the success of the SRL.

PROGRAMMATIC REVIEW: A motion was made to recommend this Shared Research Laboratory application for funding. The course was uniformly regarded as excellent but the course can not be funded without the lab. There were some concerns among the reviewers’ with regard to the management plan of the SRL and whether this was really a shared resource. Specifically the concerns were the following. There was no one identified person responsible for the core – rather the involvement of 13 persons at an average percent effort of 5%. This led to a discussion of a proposal for a more dedicated person to staff the core. There was also the expectation that the lab manager should report to the program director. Finally, the panel wanted to address the concern regarding access to ensure that the prioritization plan enabled broad use. A discussant noted that there are plenty of prospective users. The proposal was made to recommend for funding with conditions to address the these concerns. The conditions proposed are the following: 1) the management plan for the SRL will ensure that the program director has adequate authority to direct the management of the shared lab including staff independent of Dr. Fisher’s lab; 2) there will be a prioritization plan for access to the SRL and oversight to ensure access is available to the many PI’s listed as interested in hESC culture and 3) continued compliance with prioritization and access plan. The annual progress report should demonstrate that these conditions are being met. The motion to recommend this Shared Research Laboratory application for funding with the aforementioned conditions passed.


QUALITY OF THE PROPOSED TECHNIQUES COURSE: This is one of the highest levels of teaching and course offerings, not only in California but perhaps the entire country. This is a well described, excellent teaching resource; Dr. Fisher has lots of teaching and course management experience; this is the stronger part of the application. The plan to offer three modes of instruction to meet the needs of a diverse group of investigators is an excellent one, and one that the team can carry out. The planned courses are well described, and a sample curriculum is provided including a detailed program for every day of the week. The course offerings include the following. There will be a formal core course of one week duration offered quarterly that will include lectures, seminars, and hands-on laboratory experience and cover growth, propagation and analysis of nonfederal hESCs. A smaller, methods-based course will teach hESC derivation. Finally. a less formal course of instruction for CIRM Shared Laboratory users will be provided on a rolling basis as needed. The Course faculty includes 15 outstanding stem cell investigators with the breadth of experience necessary and appropriate for quality instruction. A detailed plan for follow up and evaluation of the effectiveness of the course is included. An attempt to train a variety of investigators from a variety of institutions is an integral part of the description of course "advertising." As presented, given the experience of the instructors and the resources of the UCSF, this course could become a very valuable bay area resource for investigators.

QUALIFICATIONS OF THE INSTITUTION: No details of other laboratory-based instruction are provided nor are details regarding assessment of its effectiveness available. However, UCSF has a very good track record in training researchers in the derivation and culture of hESCs, perhaps the best in the country. Several of the investigators involved in this proposal have successfully distributed the HSF1 and 6 lines as part of an NIH R24 grant. The applicants have drawn on this success, and expanded their curriculum from the NIH-funded R24 course. Given the institution’s academic and research mission, it’s resources, the quality of the instructors, and the detailed curriculum that is included in the application; there is no doubt about the ability of the institution to support this well described and important teaching activity.

DISCUSSION: The course proposal was outstanding, the quality of the instructors and persons involved was outstanding. Dr. Fisher has been teaching for some time and has assembled an outstanding group of investigators who have shown an impressive commitment to teaching to participate in teaching the course. The 1 week formal introductory course to hESC lab techniques would be offered several times a year and would include derivation of trophoblastic feeder cell lines – this is a unique feature. There would be rolling course offerings customized for users. The course description was detailed and overall excellent. This would be the best place to learn hESC techniques as generally no one has enough embryos to teach line derivation – this is a unique and incredible offering.

PROGRAMMATIC REVIEW: A motion was made to recommend this Techniques Course application for funding and the motion passed.