The University of California San Francisco Shared Research and Teaching Laboratory: a Non-Federal Human Embryonic Stem Cell Resource for the Bay Area Community

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. This trend has continued in the field of stem cell biology, in part, with funding from CIRM. In this context, the goal of this CIRM-funded initiative is to establish and operate a Shared Research and Teaching Laboratory that gives scientists access to nonfederally funded research and tissue culture space, as well as equipment for experiments that utilize second generation human embryonic stem cells (hESCs). We are also providing training to UCSF scientists at all stages of their careers and to investigators at our Bay Area partnering institutions. As part of the CIRM Bridges Program, we are supporting the training and work of students who are enrolled at San Francisco State University and Humboldt State University. The operating budget for the UCSF Shared Laboratory began in June of 2009. Equipment installation was complete by the end of October. Thus, operations began in November of 2009 when the laboratory and specialized equipment became fully functional, which doubled the size of newly remodeled nonfederal research space that is available to our users. The operations of the facility were optimized by hiring a manager and supporting personnel with a great deal of experience in hESC biology and the primary analytical techniques that are used in this field. With regard to the shared laboratory component, the tissue culture facilities are used by investigators who are involved in diverse aspects of hESC research. For example, two laboratories are producing induced pluripotent stem cells and differentiating the lines along the major lineages including precursors of pancreatic beta cells. Scientists from another laboratory are banking newly derived hESC lines for distribution. Investigators from other groups are pursuing hESC projects in many other areas including neuronal, blood, and cancer applications. Light microscopy and videomicroscopy setups are being fully utilized in routine applications and novel configurations such as a high throughput screening workflow. The Becton Dickinson cell analyzer we purchased is used seven days a week for a minimum of 12 hours per day by approximately 40 stem cell researchers a month. Thus, the Shared Laboratory is now fully operational. With regard to the training component, the Shared Laboratory and Teaching Facility offers two types of learning experiences. One type is a formal one-week course with lecture and laboratory components that is taught by UCSF faculty members who are noted stem cell biologists and experienced laboratory personnel. The 5-day course, “The Basics of hESC Biology," was offered for the first time in November, 2009. Most of the enrollees were from the Humboldt State CIRM Bridges program and San Francisco City College, one of our partnering institutions. The lectures covered basic aspects of human embryonic development and the fundamentals of organogenesis. Additional topics included hESC derivation, propagation, and differentiation. In the laboratory portion, students learned how to culture hESCs. Analysis techniques included various forms of microscopy (light, video, and confocal), cell sorting, and chromosome enumeration. The second type of training experience is one-on-one instruction that is offered on an ongoing basis to researchers who want to incorporate hESC approaches into their programs. Most often, scientists want to learn basic methods for culturing the cells, but instruction in analysis techniques is also highly sought after. Since the facility opened, we have provided individualized training to more than 20 investigators. Finally, a great deal of effort has gone into the construction of a website that will support both the research and training portions of the laboratory’s operation. With regard to research, investigators will be able to schedule blocks of time for using the tissue culture hoods and incubators as well as the specialized equipment that the laboratory houses. This system capture details, which will allow us to tailor our operations to the needs of our users. Numerous protocols will also be made available through the site. With regard to teaching, the portal will be used by applicants to our formal course offering. Faculty will use an embedded system to review the qualifications of prospective students and to choose attendees. We will also use the website to distribute course materials and publish schedules. This site will have other features that will optimize our interactions with users. For example, there will be a chat section where researchers can ask questions that facility faculty and staff will answer in real time. We will also use this portal to post exciting research papers published by our users and stem cell scientists across the world. Lastly, we will highlight public policy issues.

The University of California San Francisco (UCSF) Shared Research and Teaching Laboratory is now in its 2nd year of operation. Our goal is to support stem cell research in Northern California. We are particularly focused on enabling scientists at our institution and our colleagues in the Bridges programs at Humboldt State University, San Francisco State University, Berkeley City College and City College of San Francisco. With regard to the Shared Research portion of the program, we offer our users 3 state-of-the-art tissue culture rooms that are fully equipped for growing and studying various types of human stem cells including those derived from embryos. Our major instrumentation includes highly power microscopes, of which some take movies, that allow us to do many types of imaging studies including applications that use live cells. We also provide access to equipment that researchers use to analyze and sort stem cells and their descendents based on their unique fingerprints. Currently our research laboratory has 37 users who work in all the major areas of stem cell research. These include studying the basic biology of human embryonic stem cells and what they can teach us about the initial steps of human development. Other well-represented research interests include regenerative therapies with neural, pancreatic, liver and cancer stem cell applications. Dr. Linda Guidice is the Director of the program. She is Chair of the Department of Obstetrics, Gynecology and Reproductive Sciences. She is a renowned reproductive biologist/endocrinologist and IVF practitioner whose expertise includes human embryonic stem cell biology. Dr. Susan Fisher, member of the same department, is the Associate Program Director. Her expertise and that of her group includes methods for deriving, growing, characterizing and differentiating human embryonic stem cells. Mr. Nick Larocque oversees the day-to-day operations of the facility. He has nearly 10 years of experience working with human embryonic stem cells and is an expert in the methods that are used in their growth and analysis. The leadership team is ably assisted by a group of scientists who are stem cell biologists with various individual strengths including many decades of experience with the specialized approaches that are used in the regenerative medicine field. Finally, an Oversight Committee helps evaluate priorities and establish new directions. With regard to the Teaching portion of the program, we offer several different kinds of learning experiences. Formal instruction consists of 5 full-day courses. Lectures, which are given by prominent members of the UCSF stem cell community, occupy the mornings. The topics that are covered include human embryonic development, stem cell derivation, and egg/sperm formation. A major focus is placed on translational aspects of regenerative therapies for numerous conditions including diabetes and Parkinson’s disease as well as applications in many types of cancer including those that involve the liver and blood cells. The laboratory portion of the course occupies the afternoons. This is an intensive hands-on experience in which the students learn by directly interacting with program personnel. They begin with the methods that are used to propagate human embryonic stem cells in a research laboratory. This includes recognizing the appearance of the cells as they self-renew or when they begin to differentiate. They are also taught the techniques that are used to store human embryonic stem cells in a frozen state for future use. Thereafter, the focus is on analytical techniques for determining their developmental potential. This year we gave four courses. Three were filled with UCSF trainees at all levels of the educational process and one was offered to students in the Humboldt State University Bridges program. These learning experiences were well received and the students gave them high marks. Therefore, we plan to include the same overall content in the courses that we teach next year, and we update as technology in this field advances. We also have made a major commitment to teaching stem cell techniques to our users on an informal ongoing basis. We strongly feel those scientists who need to learn a technique should not have to wait until a course covering that method is offered. Therefore, facility personnel spend a great deal of their time in one-on-one instruction. Typically, new users want to master the basic methods that are used to grow human embryonic and other types of stem cells. We also receive many requests from scientists who want to learn how to use the specialized instruments with which our lab is equipped. Our large number of users is a reflection of the success of our formal and informal teaching efforts. Finally, we matched interns from four Bridges programs with laboratories who are doing research in which they are interested. These research experiences have been rewarding for the hosts and the trainees.

The UCSF Shared Research and Teaching Laboratory has had a very successful third year of operation. With regard to the research component, the large scope of the projects we support reflects the breadth and depth of stem cell research at this institution. The users of our facility include faculty members and their laboratory personnel who focus on the inner workings of stem cells as well as neuronal, uterine, placental, pancreatic, blood cell and cancer biology. This year the number of scientists using our CIRM-sponsored laboratories increased by approximately 50%. Here they grow human embryonic stem cells and induced pluripotent stem cells, i.e., adult cells that have been reprogrammed back to a naïve state. Our investigators also make full use of our equipment, which includes state-of-the-art microscopes for examining the fine structure of cells and for taking movies that enable analysis of their behavior. We also use our CIRM Laboratory to demonstrate new equipment such as a machine that uses very gentle conditions to do live sorts of stem cell subpopulations. Thus, these cells can be studied in the laboratory or injected into animals to determine their regenerative capacity. This capability augments other sorting methods that are well established in our facility. Our management team and oversight committee have been stable since the Laboratory opened. Drs. Linda Giudice and Susan Fisher continue to establish overall directions. Dr. Fisher is responsible for day-to-day operations, which are overseen by Mr. Nick LaRoque. He works closely with the users to make sure that they comply with facility rules that ensure maximum use while maintaining the equipment in good working order. As facility usage dramatically increased this year, Mr. LaRoque’s high level of involvement was a major factor in making sure that our Shared Laboratory continued to function optimally. The remaining members of our team play crucial roles in teaching the lecture and laboratory portions of our course. Our oversight committee, which is headed by Dr. Arnold Kriegstein, the Director of the Eli & Edith Broad Center for Regeneration Medicine and Stem Cell Research at UCSF, is composed of our management team and leading UCSF stem cell researchers who represent the major disease pipelines at our institution and who are major users of our CIRM Laboratory. A major accomplishment during the current year was the establishment of a recharge system that enables us to provide our users with supplies and medium at substantially reduced costs, which are achieved by making bulk purchases. Mr. LaRoque, Mr. Jones and Dr. Fisher managed the process whereby we submitted a recharge proposal, which was approved by UCSF, and the roll out of this new, very popular service, which enables our users to purchase supplies at reduced rates, which are made possible by bulk purchases. With regard to our Teaching efforts, we offer a 5-day course. Dr. Fisher, Dr. McMaster and Mr. LaRoque direct the didactic portion, which occupies the mornings. They and the entire staff participate in the laboratories, which are held in the afternoons. Mr. Keith Jones provides a great deal of administrative support. Mr. LaRoque handles subsequent communications with our attendees, directing inquiries to the appropriate course instructor. This year we taught 4 one-week courses that were attended by 34 students at all levels including undergraduates from the City College and State University systems who are our partners in the Bridges Program. The lectures included a substantial amount of material on the early stages of human development, important information for stem cell scientists who are trying to recapitulate these processes for therapeutic purposes. Other topics are related to development/diseases of the pancreas, liver, blood cells, heart, brain and digestive system. We also cover current concepts with regard to the role of cancer stem cells in tumor formation, metastasis and recurrence. In the laboratory portion of the course, students learn how to grow and bank human embryonic stem cells. We also teach state-of-the-art methods for analyzing these cells. Finally, we offer one-on-one training sessions in stem cell culture and methods of analysis for scientists who need to jumpstart their projects and, therefore, cannot wait for our next course offering. For the first time this year we offered a specialized workshop on neural induction. The day started with an overview lecture. The group of 18 attendees was divided into 3 sections for the laboratory portion of the course in which they learned how to produce and passage these cell clusters. In summary, the users and the Oversight Committee are happy with the way our facility is working. Therefore, no major operational adjustments are anticipated. The courses and the workshops were also highly rated by the participants. Therefore, we do not plan any major changes to our curriculum during the coming year.

This CIRM Shared Laboratory Research and Teaching Facility continues to support a very large number of laboratories that are engaged in stem cell-related research at the University of California, San Francisco (UCSF). As to research, working with stem cells, particularly those derived from human sources, requires very rigorous laboratory conditions, essentially higher standards than are needed for work with less demanding models. The laboratory space in which our users work, which was remodeled with CIRM funds awarded via the Shared Laboratory mechanism, meets these standards. Additionally, work with stem cells often requires specialized pieces of equipment that enable us to test the effects of important variables such as the oxygen the cells “breathe.” We also have setups whereby stem cell scientists can carefully examine the cells with which they work, either by magnifying them using special optics or by molecular profiling. Finally, we stock laboratory supplies that are commonly used by most of the laboratories. By buying in bulk, we can offer our users substantial discounts over what they would pay as individual investigators. In addition, this mechanism provides substantial savings in time, as experiments need not be delayed waiting for reagents to arrive. The investigators who work in our facility and use its equipment are doing an exciting array of projects that are representative of all the major themes of contemporary stem cell biology. For example, some investigators are doing work that addresses fundamental questions about the inner workings of stem cells, trying to understand their special properties in terms of being able to make identical copies of themselves and differentiate into the myriad components of the human body. Other investigators are addressing important questions regarding the body’s surveillance systems, which are designed to guard against infection, that may identify stem cell transplants as foreign and destroy them as they would any invader that might cause harm. Many of the projects are directly related to formulating regenerative medicine therapies for the most common diseases that dramatically affect quality of life or are life-threatening. These include diabetes, skeletal abnormalities, neurological problems, liver pathologies and blood disorders. Finally, our users study cancer in the context of stem cell biology as the same properties that make the latter cells so flexible in terms of their fate could help tumor cells escape the therapies that are designed to eradicate them. The management team that directs this Facility has been in place from the beginning. Therefore, our methods of operation are very well established. The Faculty Directors are senior researchers with extensive experience in directing large-scale scientific efforts, including all the enabling technologies that this Facility offers. The director of operations is a very experienced stem cell biologist with outstanding technical, managerial and communication skills, which facilitates our interactions with the users, making sure that the laboratory and the equipment it contains are optimally used at all times. The day-to-day operations also involve a very strong team of individuals who as a group are experts in many areas of stem cell biology and the methods of analysis that are used in this field. Finally, the Facility greatly benefits from a strong oversight committee made up of leaders in the field of stem cell biology who also benefit from the resources we offer. Their guidance assures that we are responsive to our users' needs while adopting state-of-the-art approaches. In summary, our CIRM Shared Facility is running smoothly, providing important research infrastructure and services to the UCSF stem cell community. We do not expect any major changes in direction during the next year. As our previous history suggests, we think that our user base will grow. As to teaching, we have a very active program that serves numerous Bay Area institutions, including UCSF, University of California Berkeley, Stanford, City College of Berkeley, San Francisco State University, Humboldt State University, the Blood Systems Research Institute and the City College of San Francisco. We presented 5 one-week long courses to trainees with diverse backgrounds, ranging from undergraduates to faculty members. The mornings were occupied with lectures, which began by providing a foundation in terms of the first 8 weeks of human development, which enabled a better understanding of stem cell origins and functions, topics that are also covered. Facility faculty gave these lectures. Top stem cell scientists at UCSF gave the remaining lectures. The afternoons were devoted to learning laboratory techniques that are critical to stem cell biology. Trainees learned how to culture human embryonic stem cells and related methods of analysis. The consistently high evaluations that the courses received were evidence of its value.

The CIRM Shared Research and Teaching Laboratory at UCSF had a successful year of operation. As to the research component of our activities, there is an extensive and varied group of stem cell scientists, including faculty and members of their research groups, that use the Facility. The importance of this resource is reflected in the fact that the full range of stem cell research areas at UCSF is represented in our users. These include projects that focus on stem cell pluripotency and reprogramming, as well as early human development, hematopoiesis (blood cell development), pregnancy, uterine, neuronal, pancreatic, and liver biology. In addition, several of our user groups work on cancer stem cells and malignancy. The Facility is used by scientists to culture and study human embryonic stem cells and induced pluripotent stem cells (adult cells that have been reprogrammed back to a naïve state). Much of the work in the Facility is highly specialized since the requirements for stem cell culture are more stringent than for other types of cells. The equipment, including state-of-the-art incubators, hoods and microscopes is housed in a space that is maintained with near “clean room” standards since antibiotics use, common practice with other cell types, is often precluded for stem cells. In addition, we have the equipment to perform videomicroscopy. We can also separate live cells based on specific characteristics. Subsequently, they can be studied in isolation, or transplanted into animals to determine their potential for regenerative medicine applications. The Facility was run by the Operational Director, Mr. Nick Larocque, under the supervision of Dr. Susan Fisher. Mr. Larocque worked closely with users on a day-to-day basis providing informal training and answering questions. In addition, he made sure all the equipment was in working order and utilized efficiently. In March, Mr. Larocque’s duties were taken over by Dr. Tamara Marsh, an embryologist and stem cell biologist with extensive experience working in the Facility. Drs. Linda Giudice and Susan Fisher establish overall direction of the Facility as they have from its inception. The Oversight Committee was led by Dr. Arnold Kriegstein, the Director of the Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research at UCSF. He and the rest of the Committee provided valuable insight since they work in many of the key areas of stem cell research and are major users of the Facility. With regard to our teaching activities, as in past years we conducted week-long courses that consisted of lectures in the morning and a laboratory component in the afternoon. Drs. McMaster and Fisher design and oversee the lectures and Mr. Larocque (and starting with our most recent course in March, Dr. Marsh) direct the laboratory portion in which our students learn basic and advanced techniques for stem cell culture and research. Mr. Slomovits played a key role in advertising and communications for the courses. This year we offered the course 5 times, to a total of 46 participants. Students at all levels attended, with a significant number from undergraduate programs at the City and State Colleges who are our partners in the CIRM Bridges Program. We also had many participants from California Universities. The didactic components of the courses included presentations on human development, important foundations for scientists who will be applying these principles to application of regenerative medicine therapies in the future. We also discussed development and diseases of the brain and nervous system, pancreas, liver, digestive tract and blood. Depending on the group and their background and interests, we covered cancer biology, including cancer stem cells and concepts of malignancy and recurrence. With regard to the laboratory components of the courses, we taught the participants principles and specific methods for growing human embryonic stem cells and performing morphological assessments. We also taught methods (e.g., flow sorting) to analyze the cells for expression of key molecules, determine their state of pluripotency and/or assess their differentiation into the various kinds of cells in the body. The courses have been well attended and the students report that they are very useful and informative. Therefore we have no plan for altering our established curriculum in stem cell biology. In addition to the one-week courses, we performed one-on-one training sessions for scientists who wanted to learn how to do more elaborate types of experiments or more highly specialized methods. In summary, the Oversight Committee and user group have determined that the Facility is working efficiently and provides a vital resource. Aside from the change in the Operational Director from Mr. Larocque to Dr. Marsh in March, we anticipate no major turnovers in the coming year. The teaching activities are also highly rated so we plan no major changes to the curriculum.

The University of California San Francisco (UCSF) was funded to establish a CIRM Shared Laboratory and Teaching Facility. This effort was extremely successful. We supported the research efforts of more than 150 investigators and taught courses to over 300 students at all levels from undergraduates to postdoctoral and clinical fellows. We think that our efforts constituted a major contribution to achieving CIRM’s mission of delivering cures. The scope of work that took place in our Shared Laboratory Facility was broad and deep. Our investigators have made major contributions to key research areas. For example, some of the researchers worked on the most basic aspects of human embryonic stem cells and induced pluripotent stem cells, which have the potential to differentiate into all the cell types in the body. The questions they asked included how do they make perfect copies of themselves? What are their special properties as compared to mature cells? Other investigators worked on differentiating human embryonic and induced stem cells down specific pathways. They included cells of the pancreas that malfunction in diabetes and the cells of the brain that go awry in conditions such as Parkinson's or Alzheimer's disease. Another area that was well represented was liver biology, an important field of investigation since the only remedy for failure is transplantation of a donor organ. Bone biology was another major focus as was studying pluripotent stem cells in relationship to the normal development of blood cells and diseases of these cells that are caused by inherited defects in the DNA. Finally, several investigators studied the role of stem cells in various cancers. From its inception, two senior faculty members directed the Shared Laboratory. They were assisted by a scientist who is an expert in human embryonic stem cell biology. Together the leadership team established systems that helped our users work efficiently in the Shared Laboratory. For example, we set up a recharge system that enabled investigators to buy supplies that they routinely used at a reduced rate because we purchased the items in bulk quantities. We also purchased specialized equipment that our users found very valuable. These items included microscopes for observing cells as they grew in the lab. Of these the most sophisticated has the ability to make time-lapse videos so the cells could be monitored over extended periods of time. Another piece of equipment that is heavily used enabled analysis and separation of cells according to their molecular profiles. The Shared Laboratory also served as a central location for demonstrating new scientific equipment that is of potential use to stem cell biologists. Finally, we housed equipment that was purchased by other mechanisms, which enabled easy access for our users. One example was a workstation for high throughput assessment of the effects of a large number of compounds on cells. Our Shared Laboratory also had a teaching component that was very successful. During the final year of funding, we taught three courses. The students were from a variety of institutions including San Francisco State University, City College of San Francisco, Berkeley City College, Humboldt State University and UCSF. The mornings were devoted to lectures, which were given by experts in particular areas of stem cell biology and regenerative medicine. The goal of the initial lectures was to provide a foundation of knowledge in human embryology on which to build basic concepts in stem cell biology and regenerative medicine. When possible we tailored the rest of the topics to the specific interests of the students. The lecturers were UCSF professors who are experts in their fields. The topics that we covered were relevant to many disorders that are the target of stem cell therapies, including diabetes and other chronic diseases (e.g., Alzheimer's, Parkinson's, and cardiovascular) as well as several forms of cancer. The afternoons consisted of hands-on laboratories. We taught the students many useful methods. First and foremost they learned how to grow human embryonic stem cells in the laboratory. As part of this process they became familiar with how the cells look when they are healthy and growing well. They also learned methods that are typically used to study the cells. As part of this process they received training in the specialized equipment that our CIRM Shared Laboratory housed. In general, students rated our course more highly each year. An important part of our success was that we made every effort to stay in contact with our graduates. Throughout the course we emphasized the fact that we were here as a resource for them as they move forward in their scientific careers. In fact, many of them contacted us for technical advice and other sorts of information long after they had graduated. Although hard to quantify, we feel that this is another important measure of the effectiveness of our program.