Stem Cell Modeling Expertise
Stem Cell-Based Modeling Offered at the UCSB CIRM SRL
The UCSB CIRM SRL is happy to share unique stem cell-based models related to Neural Development and Disease. These models include:
A. Novel patient-derived hiPSC and CRSPR-engineered hPSC lines for modeling neural development and disease.
Researchers at UC Santa Barbara are actively investigating a variety of neural diseases using stem cell models. A number of diverse cell lines have been generated and characterized by making iPSC from patient samples, CRSPR engineering of hESC and iPSC lines, and differentiating specific cell types related to neural disease. 89 cell lines that are sharable (not proprietary) are listed here (insert link).
Neural Signaling Pathways in Neural Development; DNA Repair during Neural Differentiation and Disease. Investigators in the Wilson, Streichan and Dey labs are combining light-switchable (optogenetic) molecules to precisely tune inputs to molecular and cellular networks involved in neural development. This approach is coupled with the development of a variety of fluorescent output reporters. Lines developed include constructs to regulate WNT and ERK signaling, with corresponding output reporters (Table 1; 1-4). These are invaluable tools for studying neural cell signaling in stem cell-derived cells, as well as many other differentiation pathways. We believe these optogenetic lines will be of interest to many stem cell researchers in California. The Chris Richardson Lab is investigating regulation of repair in various (mostly neural) diseases using stem-cell based models. They have engineered lines with DOX-inducible CAS9 to give rise to mutations relevant to neural diseases.
Neurodegenerative Diseases /Alzheimer’s Disease / Frontotemporal Dementia. Ken Kosik and colleagues in the UC Santa Barbara Neuroscience Research Institute have been very active in modeling hiPSC harboring mutations that cause neurodegeneration / Alzheimer’s Disease. Dr. Kosik, who was instrumental in showing the presence of Tau in neurofibrillary tangles, has gone on to study tauopathies using stem cell models and brain organoids. He and colleagues at the Tau Consortium have generated a number of cell lines with tau mutations linked to disease. (Karch et al., 2019) These lines now make it possible to study the disease processes in human cells and human brain organoids (Glasauer et al., 2022). Another focus of Kosik’s work is TAR DNA-binding protein 43 (TDP-43) where mutations are associated with frontotemporal dementia, Alzheimer’s Disease, and amyotrophic lateral sclerosis. The availability of disease lines makes it possible to get at the molecular mechanisms of aggregation and inclusion body formation. We are happy to bank and share these lines. In addition, we will make available human iPSC APOE lines with different apolipoprotein E (APOE) isoforms known to influence Alzheimer’s risk. Finally, we will make available iPSC with CRSPR-engineered presenilin-1 (PSEN-1) mutations that cause early onset AD. Making these lines widely available will accelerate progress.
Cri du chat Syndrome, Williams Syndrome, Peroxisomal Import. Cri du chat is caused by deletions in chromosome 5 and we have generated multiple cri du chat iPSCs lines. Williams syndrome is caused by a large deletion of genes on chromosome 7. The development of iPSC with this deletion allows study of the disease in novel ways. (Lalli et al., 2016). A number of neural diseases result defects in peroxisomal function, yet these maladies are not well studied. Profs Chris Richardson and Brooke Gardner have generated multiple cell lines using CRSPR I to create new stem cell models for these neglected diseases, especially Zellweger’s Syndrome. The lines include mutations in PEX genes.
Age-Related Macular Degeneration / Retinitis Pigmentosa / Danon Disease. The Clegg and Coffey labs study retinal pigmented epithelial (RPE) cells in the eye. RPE are crucial support cells for the rod and cone photoreceptors, and loss of RPE cells gives rise to Age-Related Macular Degeneration. UC Santa Barbara investigators have been studying gene mutations that are associated pigmentation and these will be shared. In addition, high-quality hESC-RPE will be provided to interested researchers.
Allen Cell Lines. Using CRISPR/Cas9 technology, Allen Institute scientists have been growing the portfolio of 56 hIPScell lines harboring fluorescent protein fusion constructs that light up 43 individual organelles/structures. UCSB has partnered with the Allen Institute to make these cell lines available via our core facility.
B. Integrated Embryo Models for modeling early neural development.
Integrated Embryo Models are organized three-dimensional cell assemblages derived from pluripotent stem cells that recapitulate early human development. Exciting advances have been made via the combination of both embryonic and extra-embryonic cells, from hESC or hiPSC. This allows experimental modeling of the earliest stages of embryonic development, including gastrulation and neural tube formation. These studies have the potential to uncover the molecular mechanisms of human development, and help us understand early developmental origins of congenital defects, especially in the nervous system
ISSCR’s guidelines have been modified to allow ethical, compelling studies of human embryo models past day 14, opening up this exciting new area of inquiry. The Wilson, Dey and Streichan labs have pioneered new methods for generation of human 2D and 3D “gastruloids” to allow study of gastrulation and neural tube formation.
C. Brain and Retinal Organoid Models for modeling the development of neural connectivity, neural disease, and ocular maladies.
Researchers at UC Santa Santa Barbara study the biology of neuronal fate establishment and neuronal differentiation human PSCs into brain organoids. These processes are investigated in wildtype cells and in cells with mutations that cause neurodevelopmental disorders such as Williams Syndrome, or in the context of neurodegenerative diseases associated to Tau such as Frontotemporal dementia, in cells carrying Tau mutations. To promote discovery in this area we use state-of-the art techniques including 3D cell culturing and cerebral organoids production in suspension cultures, and viral-mediated direct reprogramming. High-throughput data of cellular identity is analyzed by an array of methods including fluorescent confocal microscopy, multi-electrode array electrophysiological analysis, and single-cell RNA sequencing.
Another area of interest is using retinal organoids to study retinal disease. Researchers have used these models to study retinitis pigmentosa, Danon Disease, age-related macular degeneration, and Zika and Herpes viral infections.
D. Access to advanced Imaging, and spatial and single cell transcriptomics, to analyzed cells and cell assemblies.
The Neuroscience Research Institute (NRI) and the Department of Molecular, Cellular and Developmental Biology (MCDB) jointly operate a shared core microscopy facility. Dr. Benjamin Lopez, a highly accomplished researcher with extensive expertise in microscopy, serves as the full-time Director of the Facility. The instrumentation includes four confocal instruments all with environmental chambers. Additionally, the core provides: a Zeiss Z.1 Lightsheet microscope with 6 laser lines and dual sCMOS camera system, a JEOL transmission electron microscope, and 5 research grade compound microscopes equipped with fluorescence, phase, DIC, darkfield, and bright field capabilities. A novel new instrument, the Nanolive 3D Cell Explorer, offers label-free low photodamage imaging for long-term timelapse imaging. We will share this expertise in advanced image analysis of neural cells and organoids.
E. Access to the UCSB BioFoundry for culture optimization, genetic and pharmacological screening.
UCSB was recently awarded a $9.8M grant from the Department of Defense to establish the UC Santa Barbara BioFoundry. A portion of this facility, designed to advance the discipline of synthetic biology, will be dedicated to studies of mammalian cells. We are happy to share access to this facility for stem cell researchers across the state. The workflow and stations proposed for this facility, which will be adjacent to the stem cell core, are shown in the figure. The Synthetic Biofoundry houses a state-of-the-art synthetic biology facility with capabilities that are particularly germane to cutting-edge research in stem cell engineering. The foundry boasts a high-throughput drug screening facility capable of screening over 400,000 compounds, representing one of the largest and most diverse compound libraries in the field. Furthermore, it is equipped with tools for genome-wide CRISPR interference (CRISPRi) and activation (CRISPRa) applications across a broad spectrum of cell types. The capacity for high-throughput generation of lentivirus complements this genome editing prowess. Additionally, the facility is adept at conducting high-throughput ELISAs, ensuring efficient quantitative measurement of proteins. At the imaging front, UCSB’s foundry excels with ultra-high-content imaging capabilities, enabling detailed visualization of cells, organoids, and both 2D and 3D tissue constructs using confocal fluorescence microscopy.
F. Access to the UCSB Materials Research Lab for investigation of novel materials for encapsulation and scaffolding to support cell therapies.
Stem cell research at the UC Santa Barbara core includes multiple efforts to develop materials for encapsulation and scaffolding for cells. These biotic-abiotic interactions can improve stem cell culture, influence cell differentiation, and sustain cell survival and function after transplantation. Micropatterned materials are used to stimulate the differentiation of 3D and 2D integrated embryo models in the Streichan, Dey and Wilson labs. (Karzburn et al., 2021). Efforts in the Pitenis and Wilson groups have given rise to promising encapsulation materials (Mansson et al., 2022). The Clegg and Coffey labs have developed scaffolds for hESC-RPE that are already in clinical trials (Kashani et al., 2021; da Cruz et al., 2018). The Stowers and Pruitt groups have studied how various substrate materials influence the mechanobiology of stem cell derivatives (Tayler and Stowers, 2021; Castillo et al., 2020). We are happy to share this expertise with stem cell researchers throughout the state. We can also provide access to the Materials Research Lab (MRL), an advanced materials core. (www.mrl.ucsb.edu).
