Shared Services in the Lokey Stem Cell Building

In the Lorry I. Lokey Stem Cell Research Building, we will establish the following shared services:

Human embryo, oocyte, human embryonic stem cell and somatic cell bank

At present, Stanford has limited tissue and hESC banking capabilities. The infrastructure and initial facilities to maintain a cell bank and database have been established with support from the CIRM small facility grant. However, demands on this off-site resource have already reached capacity and the local community at Stanford and collaborating institutions would benefit greatly from a more centralized and expanded resource. Furthermore, the current locations limit utility to investigators on the main campus and do not provide an opportunity to coordinate banking efforts with GMP production. We will house a central repository in the building to provide key capabilities in derivation, embryology, somatic cell reprogramming and human developmental genetics studies. This core facility will be further expanded and maintained under the directorship of Dr. Barry Behr. Note: A human embryo, oocyte, human embryonic stem cell and somatic cell bank is an absolute requirement for advanced human embryonic stem cell research and education. Notably, Stanford has one of the largest and most successful Reproductive Clinic (IVF) in the state of California, a requirement to obtain embryos for hESC line derivation, eggs for reprogramming studies, and somatic cells from diverse patients for generation of disease-specific pluripotent stem cell lines.

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Human embryology, hESCs and nuclear reprogramming education core

This initiative, directed by Dr. Renee Reijo Pera, is a cornerstone of our mission to increase the number of researchers who benefit from the technologies and opportunities provided by embryo and hESC research methods. A formal curriculum has been established and classes will be hosted within the building to provide hands-on laboratory experience. Students and faculty will learn about hESC growth, derivation, differentiation and analysis, and stem cell reprogramming. Note: A dedicated center for instruction and sharing of reagents and resources is required for transmission of knowledge to the next generation and for maximizing of collaborative efforts. This core is based on a solid foundation of experience with a depth of knowledge lacking at many other institutions.

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Microfluidics core facility

Microfluidics is one of the most exciting technological developments for stem cell biology in the last decade. Stem cells are rare cells; thus, they are impossible to analyze with conventional assays that require large pools of cells. Dr. Stephen Quake is a world leader in single cell manipulation and analysis using microfluidics. Dr. Quake will provide these technologies by establishing a core facility within the building to enable genetic, epigenetic, and proteomic analyses on stem cells at the single cell levels. This capability is of central importance to stem cell science, the SISCB/RM community and the Stanford campus at large. Notably, the facility will be equipped with the most powerful commercially available analytical tools. It will also include space for Stanford researchers to develop new instruments which provide unique capabilities for stem cell analysis that are not available commercially. This will facilitate collaboration between stem cell researchers and the engineering community at Stanford. Note: This core is unique worldwide. For stem cell biology, we need nonstandard devices for performing molecular analyses of rare cells that are obtained in the tens to thousands of cells, not billions as is typical for most science. This special microfluidics facility offers novel machines, invented at Stanford University by Dr. Quake.

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Fluorescence activated cell sorting (FACS)

FACS is a fundamental technology required in all aspects of stem cell research. FACS allows rapid and accurate characterization of stem cell populations as well as isolation of rare stem cells or differentiated cells from contaminating cell populations. Many of the projects in the Stem Cell Institute center around the isolation of cancer stem cells from human samples. Success in such work is dependent upon the speed in which a tumor or blood sample is processed and sorted. Thus, one must be able to access a flow cytometer quickly for studies involving human tumor cells. With quick access to sorters available, each tumor sample can be analyzed in a timely and efficient manner, and data from each precious sample is not compromised by delays in processing because of lack of access to a flow cytometer. To ensure access to cell sorters for all types of stem cell research, Stanford University Stem Cell Institute has established a flow cytometry core for the use of investigators in the Institute. This stand-alone core is designed to house eight state-of-the-art multi-color cell sorters and/or analyzers in the building to augment the services currently provided by the Stanford Shared FACS Facility. This core will have a model of operation that differs from the Stanford Shared FACS Facility. Instead of providing technician-based services, a manager will provide oversight and training on user-friendly instrumentation so that each investigator is able to perform sorts and analysis on their own. This approach will allow for the instruments to be used to the highest capacity, as well as at the convenience of each investigator and their time-dependent samples. The manager will also provide technical help with the more complex sorts, ensure that the instruments are maintained properly, and will perform troubleshooting as necessary. This novel design will allow for critical stem cell sorts to be done efficiently and economically.

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Cancer tissue bank and rapid autopsy/tissue core

The progression of steps that lead a normal cell or stem cell to form large numbers of clonal progeny that exhibit poorly regulated or unregulated cell growth and survival leads to cancer. In many cancers tested the subset of cells that are poorly regulated are called cancer initiating or cancer stem cells. Studies in cancer stem cells are a central element of the SISCB/RM. The Cancer Tissue Bank provides comprehensive banking for surgical samples in a HIPAA (privacy)-compliant manner. Both decoded data and samples from numerous participating programs are maintained and distributed throughout the Stanford community. The database and distribution serve as a repository and also as a model for further expansion of the human oocyte, embryo and somatic cell initiative. This facility, directed by Drs. Matt van de Rijn and Jonathan Pollack, will expand our existing Cancer Tissue Bank. The Cancer Tissue Bank will support in its repository a new Rapid Autopsy Program that provides an unprecedented and important source of large samples of primary cancer sites, spread (metastatic) cancer sites, and normal tissues. Aliquots of tissue and viable cell suspensions will be cryopreserved and annotated for cancer stem cell isolations. Note: The operation of this tissue bank and rapid autopsy service is described in more detail in Section 3G under “Innovations.” This is truly innovative making transformative research possible through provision of a ready source of live cells for adult tissue stem cell and cancer stem cell research. We believe that this rapid autopsy service center with associated cell storage and annotation facility is unique in the State of California.

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Advanced in vivo imaging core

Dedicated imaging facilities are a top priority for any modern stem cell facility. The Lokey Stem Cell Imaging Core will focus on emerging technologies that are not yet represented on campus. Array tomography allows unprecedented 3D reconstruction of tissue and stem cell niche architecture at near-ultrastructural resolution. In vivo confocal microscopy allows live imaging of stem cell activity. Micro-PET and small animal ultrasound imaging allow physiological and anatomical monitoring of small numbers of normal or abnormal stem cells at levels of detail previously only imagined. A goal of the core is to provide imaging resolution of living cells in situ down to single cell and subcellular resolution in tissues and living animals. This will enable critical tracking of individual stem cells post-transplantation and monitoring of native stem cell niche and intracellular interactions in real time. Capabilities will include a full range of imaging technologies and modalities. No commercial alternative exists for these activities. The facility will be directed jointly by Drs. Sam Gambhir and Andrew Olson. Note: This core provides the specialized imaging facilities needed to track very rare injected stem cells (in the body), even a single cell. This facility is invaluable to those in each of our four major areas of stem cell inquiry (hESCs, reprogramming, adult [tissue specific] stem cells, and cancer stem cells). This facility is a must for preclinical tests for efficacy of stem cell derived tissue regeneration after proper homing and for preclinical tests for the location or single cancer stem cells that could be eliminated by surgery or radiotherapy if their location is known. This facility is based on pioneering studies at Stanford University in Bioengineering, Radiology and Photonics and is of the highest caliber possible.

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Behavioral and Functional Neuroscience Laboratory (BFNL)

Translation of stem cell research into real-world applications requires state-of-the-art functional testing in animals. The BFNL facility will provide physiological, toxicological and behavioral testing capabilities within the SPF barrier facility. The Barrier BFNL testing facility will extend the non-SPF testing capabilities currently maintained and directed by Dr. Mehrdad Shamloo. Capabilities provided to the stem cell research community will include state-of-the-art behavioral and functional testing in cognitive, psychiatric, sensory/motor function, physiology, and toxicology in rodents. The service will include experimental rodent models of neurodegenerative, neurological, and psychiatric disorders, available for preclinical assessment of stem cell therapies or therapies derived from knowledge of disease derived from these cells. Additionally, the SISCB/RM will host a central electrophysiology core with plans for up to 20 independent electrophysiological analysis stations enabling both in vivo and in vitro recording. Many stations also will be equipped with 2-photon confocal imaging capability. Note: Neurological disorders plague a significant portion of the men and women of California as they age while others are present at birth or during childhood. This facility allows the building of model systems to probe the molecular basis of neurological disorders and their treatment through stem cell based therapies. It will be heavily used by the Lokey Stem Cell community and researchers across Stanford and the State of California.

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GMP facility

Ultimately, therapy in humans requires that preclinical studies be performed using clinical grade GMP (Good Manufacturing Practices) cell lines and practices. Stanford currently maintains a GMP facility of limited capacity on the main campus that is devoted to bone marrow transplant. However, hESC and organ-specific stem cell production requires intensive culture and characterization capabilities; thus, to support translation of stem cell technologies to clinical arenas, we include a stem cell-dedicated GMP facility of approximately 1200 sq ft. Here, we will derive culture and differentiate stem cells under Standard Operating Procedures for application of technology for FDA pre-clinical data filing and FDA-approved clinical trials. This facility will also allow for the production of antibody and protein reagents for isolation of normal stem cells, for the removal of residual tumor-causing teratogenic hESCs from cultures of cells differentiating to the equivalent of tissue stem cells (also to be isolated using GMP-grade antibodies), and for treatment of abnormal and cancer stem cells in an FDA-compliant process. Design and fit out of the GMP facility will be delayed until after the opening of the building to ensure that the requirements are informed by the Stanford investigators who receive the future New Cell Line and Disease grants. The director of this facility is to be named. Note: The reviewers of our Part 1 application uniformly recommended that we provide GMP capabilities in the Lokey Stem Cell building; we have been responsive to this suggestion and incorporated a GMP facility to enable the establishment of master cell banks of stem cells, of crucial and new monoclonal antibodies, and of feeder cells and somatic cells for reprogramming strategies in anticipation of clinical translation.

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Computational Research Core

Computational research is essential for clinical research applications. Lab space for computational research will be programmed using the same 1,260 nasf lab module building block mentioned above. This space could be located in one of the 33 lab modules identified in the building, or in the support spaces. Computational researchers are also interspersed with their collaborators in wet labs, enabling deeper integration. The director of the Computational Research Core is to be named. Note: This facility may be located in dispersed areas within the building  but must be located in close proximity to the Clinical Trials Unit at the Stanford Freidenrich Center, which is devoted to translating basic science to the clinic. This core supports our Element Z and is built on our clinical practice and the substantial strength of Stanford’s programs in computer science, mathematics, and statistics.

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