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Frisch C, Kostes WW, Galyon B, Whitman B, Tekel SJ, Standage-Beier K, Srinivasan G, Wang X, Brafman DA. PINE-TREE enables highly efficient genetic modification of human cell lines. Mol Ther Nucleic Acids 2023; 33:483-492. [PMID: 37588683 PMCID: PMC10425837 DOI: 10.1016/j.omtn.2023.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 07/11/2023] [Indexed: 08/18/2023]
Abstract
Prime editing technologies enable precise genome editing without the caveats of CRISPR nuclease-based methods. Nonetheless, current approaches to identify and isolate prime-edited cell populations are inefficient. Here, we established a fluorescence-based system, prime-induced nucleotide engineering using a transient reporter for editing enrichment (PINE-TREE), for real-time enrichment of prime-edited cell populations. We demonstrated the broad utility of PINE-TREE for highly efficient introduction of substitutions, insertions, and deletions at various genomic loci. Finally, we employ PINE-TREE to rapidly and efficiently generate clonal isogenic human pluripotent stem cell lines, a cell type recalcitrant to genome editing.
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Affiliation(s)
- Carlye Frisch
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
| | - William W. Kostes
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
| | - Brooke Galyon
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
| | - Brycelyn Whitman
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
| | - Stefan J. Tekel
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
| | - Kylie Standage-Beier
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
- Molecular and Cellular Biology Graduate Program, Arizona State University, Tempe, AZ 85287, USA
| | - Gayathri Srinivasan
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
| | - Xiao Wang
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
| | - David A. Brafman
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
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2
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Kostes WW, Brafman DA. The Multifaceted Role of WNT Signaling in Alzheimer's Disease Onset and Age-Related Progression. Cells 2023; 12:cells12081204. [PMID: 37190113 DOI: 10.3390/cells12081204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 04/12/2023] [Accepted: 04/17/2023] [Indexed: 05/17/2023] Open
Abstract
The evolutionary conserved WNT signaling pathway orchestrates numerous complex biological processes during development and is critical to the maintenance of tissue integrity and homeostasis in the adult. As it relates to the central nervous system, WNT signaling plays several roles as it relates to neurogenesis, synaptic formation, memory, and learning. Thus, dysfunction of this pathway is associated with multiple diseases and disorders, including several neurodegenerative disorders. Alzheimer's disease (AD) is characterized by several pathologies, synaptic dysfunction, and cognitive decline. In this review, we will discuss the various epidemiological, clinical, and animal studies that demonstrate a precise link between aberrant WNT signaling and AD-associated pathologies. In turn, we will discuss the manner in which WNT signaling influences multiple molecular, biochemical, and cellular pathways upstream of these end-point pathologies. Finally, we will discuss how merging tools and technologies can be used to generate next generation cellular models to dissect the relationship between WNT signaling and AD.
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Affiliation(s)
- William W Kostes
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
| | - David A Brafman
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
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3
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Knittel J, Srinivasan G, Frisch C, Brookhouser N, Raman S, Essuman A, Brafman DA. A microcarrier-based protocol for scalable generation and purification of human induced pluripotent stem cell-derived neurons and astrocytes. STAR Protoc 2022; 3:101632. [PMID: 36035791 PMCID: PMC9405537 DOI: 10.1016/j.xpro.2022.101632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Here, we describe a protocol for a microcarrier (MC)-based, large-scale generation and cryopreservation of human-induced pluripotent stem cell (hiPSC)-derived neurons and astrocytes. We also detail steps to isolate these populations with a high degree of purity. Finally, we describe how to cryopreserve these cell types while maintaining high levels of viability and preserving cellular function post-thaw. For complete details on the use and execution of this protocol, please refer to Brookhouser et al. (2021).
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Affiliation(s)
- Jacob Knittel
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
| | - Gayathri Srinivasan
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
| | - Carlye Frisch
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
| | - Nicholas Brookhouser
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA; Graduate Program in Clinical Translational Sciences, University of Arizona College of Medicine-Phoenix, Phoenix, AZ 85004, USA
| | - Sreedevi Raman
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
| | - Albert Essuman
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
| | - David A Brafman
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA.
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4
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Srinivasan G, Brafman DA. The Emergence of Model Systems to Investigate the Link Between Traumatic Brain Injury and Alzheimer’s Disease. Front Aging Neurosci 2022; 13:813544. [PMID: 35211003 PMCID: PMC8862182 DOI: 10.3389/fnagi.2021.813544] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 12/20/2021] [Indexed: 12/12/2022] Open
Abstract
Numerous epidemiological studies have demonstrated that individuals who have sustained a traumatic brain injury (TBI) have an elevated risk for developing Alzheimer’s disease and Alzheimer’s-related dementias (AD/ADRD). Despite these connections, the underlying mechanisms by which TBI induces AD-related pathology, neuronal dysfunction, and cognitive decline have yet to be elucidated. In this review, we will discuss the various in vivo and in vitro models that are being employed to provide more definite mechanistic relationships between TBI-induced mechanical injury and AD-related phenotypes. In particular, we will highlight the strengths and weaknesses of each of these model systems as it relates to advancing the understanding of the mechanisms that lead to TBI-induced AD onset and progression as well as providing platforms to evaluate potential therapies. Finally, we will discuss how emerging methods including the use of human induced pluripotent stem cell (hiPSC)-derived cultures and genome engineering technologies can be employed to generate better models of TBI-induced AD.
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5
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Zhao J, Lu W, Ren Y, Fu Y, Martens YA, Shue F, Davis MD, Wang X, Chen K, Li F, Liu CC, Graff-Radford NR, Wszolek ZK, Younkin SG, Brafman DA, Ertekin-Taner N, Asmann YW, Dickson DW, Xu Z, Pan M, Han X, Kanekiyo T, Bu G. Correction to: Apolipoprotein E regulates lipid metabolism and α‑synuclein pathology in human iPSC‑derived cerebral organoids. Acta Neuropathol 2022; 143:119-121. [PMID: 34724591 DOI: 10.1007/s00401-021-02380-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
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6
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Cutts J, Kostes W, Brafman DA. Generation of 3X FLAG-tagged human embryonic stem cell (hESC) line to study WNT-induced β-catenin DNA interactions (HVRDe009-A-2). Stem Cell Res 2021; 57:102586. [PMID: 34736039 DOI: 10.1016/j.scr.2021.102586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 10/18/2021] [Accepted: 10/24/2021] [Indexed: 10/20/2022] Open
Abstract
In the canonical WNT signaling pathway, active WNT signaling results in the nuclear translocation of β-catenin where it regulates target gene expression. As a tool to understand these β-catenin DNA interactions, we used a CRISPR/Cas9 based approach to engineer a human embryonic stem cell line (hESC) harboring a 3X FLAG sequence fused to the C-terminus of β-catenin. Engineered cells displayed a characteristic hESC morphology, expressed pluripotency-associated markers, retained tri-lineage differentiation potential, and had a normal euploid karyotype. This cell line represents a valuable tool to dissect the transcriptional mechanisms by which WNT signalling regulates pluripotent cell fate.
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Affiliation(s)
- Joshua Cutts
- School of Biological and Health Systems Engineering, Arizona State University, United States
| | - Warner Kostes
- School of Biological and Health Systems Engineering, Arizona State University, United States
| | - David A Brafman
- School of Biological and Health Systems Engineering, Arizona State University, United States
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7
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Cook M, Richey A, Brafman DA, Frow EK. Weighing up the evidence used by direct-to-consumer stem cell businesses. Stem Cell Reports 2021; 16:2852-2860. [PMID: 34767748 PMCID: PMC8693621 DOI: 10.1016/j.stemcr.2021.10.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 10/12/2021] [Accepted: 10/13/2021] [Indexed: 12/04/2022] Open
Abstract
Hundreds of businesses across the United States offer direct-to-consumer stem-cell-based interventions that have not been approved by the Food and Drug Administration. Here, we characterize the types of evidence used on the websites of 59 stem cell businesses in the Southwest United States to market their services. We identify over a dozen forms of evidence, noting that businesses are less likely to rely on “gold-standard” scientific evidence, like randomized clinical trials, and instead draw substantially on forms of evidence that we identify as being “ambiguous.” Ambiguous evidence has some scientific or medical basis, but its interpretation is highly context-dependent. These findings highlight the interpretive responsibility placed on prospective patients. We identify actions for regulators and professional societies to assist with evaluating evidence, but caution that focusing on the (in)validity of particular evidence types is unlikely to eliminate demand for stem-cell-based treatments in this complex marketplace. We characterize the evidence used by 59 stem cell businesses in the Southwest United States We identify that clinics rely on scientifically and medically “ambiguous” evidence Ambiguous evidence places interpretive responsibility on prospective patients We offer suggestions to help prospective patients navigate this complex landscape
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Affiliation(s)
- Margaret Cook
- School of Biological & Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
| | - Alexandra Richey
- School of Biological & Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
| | - David A Brafman
- School of Biological & Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
| | - Emma K Frow
- School of Biological & Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA; School for the Future of Innovation in Society, Arizona State University, Tempe, AZ 85287, USA.
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8
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Zhao J, Lu W, Ren Y, Fu Y, Martens YA, Shue F, Davis MD, Wang X, Chen K, Li F, Liu CC, Graff-Radford NR, Wszolek ZK, Younkin SG, Brafman DA, Ertekin-Taner N, Asmann YW, Dickson DW, Xu Z, Pan M, Han X, Kanekiyo T, Bu G. Apolipoprotein E regulates lipid metabolism and α-synuclein pathology in human iPSC-derived cerebral organoids. Acta Neuropathol 2021; 142:807-825. [PMID: 34453582 PMCID: PMC8500881 DOI: 10.1007/s00401-021-02361-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 07/31/2021] [Accepted: 08/17/2021] [Indexed: 12/25/2022]
Abstract
APOE4 is a strong genetic risk factor for Alzheimer’s disease and Dementia with Lewy bodies; however, how its expression impacts pathogenic pathways in a human-relevant system is not clear. Here using human iPSC-derived cerebral organoid models, we find that APOE deletion increases α-synuclein (αSyn) accumulation accompanied with synaptic loss, reduction of GBA levels, lipid droplet accumulation and dysregulation of intracellular organelles. These phenotypes are partially rescued by exogenous apoE2 and apoE3, but not apoE4. Lipidomics analysis detects the increased fatty acid utilization and cholesterol ester accumulation in apoE-deficient cerebral organoids. Furthermore, APOE4 cerebral organoids have increased αSyn accumulation compared to those with APOE3. Carrying APOE4 also increases apoE association with Lewy bodies in postmortem brains from patients with Lewy body disease. Our findings reveal the predominant role of apoE in lipid metabolism and αSyn pathology in iPSC-derived cerebral organoids, providing mechanistic insights into how APOE4 drives the risk for synucleinopathies.
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Affiliation(s)
- Jing Zhao
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
- Center for Regenerative Medicine, Neuroregeneration Laboratory, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Wenyan Lu
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
- Center for Regenerative Medicine, Neuroregeneration Laboratory, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Yingxue Ren
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Yuan Fu
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Yuka A Martens
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
- Center for Regenerative Medicine, Neuroregeneration Laboratory, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Francis Shue
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Mary D Davis
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
- Center for Regenerative Medicine, Neuroregeneration Laboratory, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Xue Wang
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Kai Chen
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Fuyao Li
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Chia-Chen Liu
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
| | | | | | - Steven G Younkin
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - David A Brafman
- School of Biological & Health Systems Engineering, Arizona State University, Tempe, AZ, 85287, USA
| | - Nilüfer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
- Department of Neurology, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Yan W Asmann
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Dennis W Dickson
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Ziying Xu
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center At San Antonio, San Antonio, TX, 78229, USA
| | - Meixia Pan
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center At San Antonio, San Antonio, TX, 78229, USA
| | - Xianlin Han
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center At San Antonio, San Antonio, TX, 78229, USA
- Department of Medicine, University of Texas Health Science Center At San Antonio, San Antonio, TX, 78229, USA
| | - Takahisa Kanekiyo
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
- Center for Regenerative Medicine, Neuroregeneration Laboratory, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Guojun Bu
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA.
- Center for Regenerative Medicine, Neuroregeneration Laboratory, Mayo Clinic, Jacksonville, FL, 32224, USA.
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9
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Brookhouser N, Raman S, Frisch C, Srinivasan G, Brafman DA. APOE2 mitigates disease-related phenotypes in an isogenic hiPSC-based model of Alzheimer's disease. Mol Psychiatry 2021; 26:5715-5732. [PMID: 33837271 PMCID: PMC8501163 DOI: 10.1038/s41380-021-01076-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 02/26/2021] [Accepted: 03/23/2021] [Indexed: 02/02/2023]
Abstract
Genome-wide association studies (GWAS) have identified polymorphism in the Apolipoprotein E gene (APOE) to be the most prominent risk factor for Alzheimer's disease (AD). Compared to individuals homozygous for the APOE3 variant, individuals with the APOE4 variant have a significantly elevated risk of AD. On the other hand, longitudinal studies have shown that the presence of the APOE2 variant reduces the lifetime risk of developing AD by 40 percent. While there has been significant research that has identified the risk-inducing effects of APOE4, the underlying mechanisms by which APOE2 influences AD onset and progression have not been extensively explored. In this study, we utilize an isogenic human induced pluripotent stem cell (hiPSC)-based system to demonstrate that conversion of APOE3 to APOE2 greatly reduced the production of amyloid-beta (Aβ) peptides in hiPSC-derived neural cultures. Mechanistically, analysis of pure populations of neurons and astrocytes derived from these neural cultures revealed that mitigating effects of APOE2 are mediated by cell autonomous and non-autonomous effects. In particular, we demonstrated the reduction in Aβ is potentially driven by a mechanism related to non-amyloidogenic processing of amyloid precursor protein (APP), suggesting a gain of the protective function of the APOE2 variant. Together, this study provides insights into the risk-modifying effects associated with the APOE2 allele and establishes a platform to probe the mechanisms by which APOE2 enhances neuroprotection against AD.
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Affiliation(s)
- Nicholas Brookhouser
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA
- Graduate Program in Clinical Translational Sciences, University of Arizona College of Medicine-Phoenix, Phoenix, AZ, USA
| | - Sreedevi Raman
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA
| | - Carlye Frisch
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA
| | - Gayathri Srinivasan
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA
| | - David A Brafman
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA.
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10
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Tekel SJ, Brookhouser N, Standage-Beier K, Wang X, Brafman DA. Cytosine and adenosine base editing in human pluripotent stem cells using transient reporters for editing enrichment. Nat Protoc 2021; 16:3596-3624. [PMID: 34172975 DOI: 10.1038/s41596-021-00552-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 04/06/2021] [Indexed: 02/06/2023]
Abstract
Deaminase fused-Cas9 base editing technologies have enabled precise single-nucleotide genomic editing without the need for the introduction of damaging double-stranded breaks and inefficient homology-directed repair. However, current methods to isolate base-edited cell populations are ineffective, especially when utilized with human pluripotent stem cells, a cell type resistant to genome modification. Here, we outline a series of methods that employ transient reporters of editing enrichment (TREE) to facilitate the highly efficient single-base editing of human cells at precise genomic loci. Briefly, these transient reporters of editing enrichment based methods employ a transient episomal fluorescent reporter that allows for the real-time, flow-cytometry-based enrichment of cells that have had single nucleotide changes at precise genomic locations. This protocol details how these approaches can enable the rapid (~3-4 weeks) and efficient (clonal editing efficiencies >80%) generation of biallelic or multiplexed edited isogenic hPSC lines using adenosine and cytosine base editors.
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Affiliation(s)
- Stefan J Tekel
- School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, AZ, USA
| | - Nicholas Brookhouser
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA
| | - Kylie Standage-Beier
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA
- Molecular and Cellular Biology Graduate Program, Arizona State University, Tempe, AZ, USA
| | - Xiao Wang
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA.
| | - David A Brafman
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA.
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11
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Zhao J, Fu Y, Yamazaki Y, Ren Y, Davis MD, Liu CC, Lu W, Wang X, Chen K, Cherukuri Y, Jia L, Martens YA, Job L, Shue F, Nguyen TT, Younkin SG, Graff-Radford NR, Wszolek ZK, Brafman DA, Asmann YW, Ertekin-Taner N, Kanekiyo T, Bu G. Author Correction: APOE4 exacerbates synapse loss and neurodegeneration in Alzheimer's disease patient iPSC-derived cerebral organoids. Nat Commun 2021; 12:2707. [PMID: 33953196 PMCID: PMC8100123 DOI: 10.1038/s41467-021-23081-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Affiliation(s)
- Jing Zhao
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.,Center for Regenerative Medicine, Neuroregeneration Lab, Mayo Clinic, Jacksonville, FL, USA
| | - Yuan Fu
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Yu Yamazaki
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Yingxue Ren
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, USA
| | - Mary D Davis
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.,Center for Regenerative Medicine, Neuroregeneration Lab, Mayo Clinic, Jacksonville, FL, USA
| | - Chia-Chen Liu
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Wenyan Lu
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.,Center for Regenerative Medicine, Neuroregeneration Lab, Mayo Clinic, Jacksonville, FL, USA
| | - Xue Wang
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, USA
| | - Kai Chen
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Yesesri Cherukuri
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, USA
| | - Lin Jia
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Yuka A Martens
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Lucy Job
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.,Center for Regenerative Medicine, Neuroregeneration Lab, Mayo Clinic, Jacksonville, FL, USA
| | - Francis Shue
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | | | | | | | - David A Brafman
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA
| | - Yan W Asmann
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, USA
| | - Nilüfer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.,Department of Neurology, Mayo Clinic, Jacksonville, FL, USA
| | - Takahisa Kanekiyo
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.,Center for Regenerative Medicine, Neuroregeneration Lab, Mayo Clinic, Jacksonville, FL, USA
| | - Guojun Bu
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA. .,Center for Regenerative Medicine, Neuroregeneration Lab, Mayo Clinic, Jacksonville, FL, USA.
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12
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Abstract
CRISPR-based technologies are paramount in genome engineering and synthetic biology. Prime editing (PE) is a technology capable of installing genomic edits without double-stranded DNA breaks (DSBs) or donor DNA. Prime editing guide RNAs (pegRNAs) simultaneously encode both guide and edit template sequences. They are more design intensive than CRISPR single guide RNAs (sgRNAs). As such, application of PE technology is hindered by the limited throughput of manual pegRNA design. To that end, we designed a software tool, Prime Induced Nucleotide Engineering Creator of New Edits (PINE-CONE), that enables high-throughput automated design of pegRNAs and prime editing strategies. PINE-CONE translates edit coordinates and sequences into pegRNA designs, accessory guides, and oligonucleotides for facile cloning workflows. To demonstrate PINE-CONE's utility in studying disease-relevant genotypes, we rapidly design a library of pegRNAs targeting Alzheimer's Disease single nucleotide polymorphisms (SNPs). Overall, PINE-CONE will accelerate the application of PEs in synthetic biology and biomedical research.
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Affiliation(s)
- Kylie Standage-Beier
- School
of Biological and Health Systems Engineering, Molecular and Cellular Biology
Graduate Program, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, Arizona 85287, United States
| | - Stefan J. Tekel
- School
of Biological and Health Systems Engineering, Molecular and Cellular Biology
Graduate Program, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, Arizona 85287, United States
| | - David A. Brafman
- School
of Biological and Health Systems Engineering, Molecular and Cellular Biology
Graduate Program, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, Arizona 85287, United States
| | - Xiao Wang
- School
of Biological and Health Systems Engineering, Molecular and Cellular Biology
Graduate Program, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, Arizona 85287, United States
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13
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Brookhouser N, Nguyen T, Tekel SJ, Standage-Beier K, Wang X, Brafman DA. A Cas9-mediated adenosine transient reporter enables enrichment of ABE-targeted cells. BMC Biol 2020. [PMID: 33317513 DOI: 10.1186/s12915-020-00929-7.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Adenine base editors (ABE) enable single nucleotide modifications without the need for double-stranded DNA breaks (DSBs) induced by conventional CRIPSR/Cas9-based approaches. However, most approaches that employ ABEs require inefficient downstream technologies to identify desired targeted mutations within large populations of manipulated cells. In this study, we developed a fluorescence-based method, named "Cas9-mediated adenosine transient reporter for editing enrichment" (CasMAs-TREE; herein abbreviated XMAS-TREE), to facilitate the real-time identification of base-edited cell populations. RESULTS To establish a fluorescent-based assay able to detect ABE activity within a cell in real time, we designed a construct encoding a mCherry fluorescent protein followed by a stop codon (TGA) preceding the coding sequence for a green fluorescent protein (GFP), allowing translational readthrough and expression of GFP after A-to-G conversion of the codon to "TGG." At several independent loci, we demonstrate that XMAS-TREE can be used for the highly efficient purification of targeted cells. Moreover, we demonstrate that XMAS-TREE can be employed in the context of multiplexed editing strategies to simultaneous modify several genomic loci. In addition, we employ XMAS-TREE to efficiently edit human pluripotent stem cells (hPSCs), a cell type traditionally resistant to genetic modification. Furthermore, we utilize XMAS-TREE to generate clonal isogenic hPSCs at target sites not editable using well-established reporter of transfection (RoT)-based strategies. CONCLUSION We established a method to detect adenosine base-editing activity within a cell, which increases the efficiency of editing at multiple genomic locations through an enrichment of edited cells. In the future, XMAS-TREE will greatly accelerate the application of ABEs in biomedical research.
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Affiliation(s)
- Nicholas Brookhouser
- School of Biological and Health Systems Engineering, Arizona State University, 501 E. Tyler Mall, ECG 334A, Tempe, AZ, 85287, USA.,Graduate Program in Clinical Translational Sciences, University of Arizona College of Medicine-Phoenix, Phoenix, AZ, 85004, USA
| | - Toan Nguyen
- School of Biological and Health Systems Engineering, Arizona State University, 501 E. Tyler Mall, ECG 334A, Tempe, AZ, 85287, USA
| | - Stefan J Tekel
- School of Biological and Health Systems Engineering, Arizona State University, 501 E. Tyler Mall, ECG 334A, Tempe, AZ, 85287, USA
| | - Kylie Standage-Beier
- School of Biological and Health Systems Engineering, Arizona State University, 501 E. Tyler Mall, ECG 334A, Tempe, AZ, 85287, USA.,Molecular and Cellular Biology Graduate Program, Arizona State University, Tempe, AZ, 85287, USA
| | - Xiao Wang
- School of Biological and Health Systems Engineering, Arizona State University, 501 E. Tyler Mall, ECG 334A, Tempe, AZ, 85287, USA.
| | - David A Brafman
- School of Biological and Health Systems Engineering, Arizona State University, 501 E. Tyler Mall, ECG 334A, Tempe, AZ, 85287, USA.
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14
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Brookhouser N, Nguyen T, Tekel SJ, Standage-Beier K, Wang X, Brafman DA. A Cas9-mediated adenosine transient reporter enables enrichment of ABE-targeted cells. BMC Biol 2020; 18:193. [PMID: 33317513 PMCID: PMC7737295 DOI: 10.1186/s12915-020-00929-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 11/18/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Adenine base editors (ABE) enable single nucleotide modifications without the need for double-stranded DNA breaks (DSBs) induced by conventional CRIPSR/Cas9-based approaches. However, most approaches that employ ABEs require inefficient downstream technologies to identify desired targeted mutations within large populations of manipulated cells. In this study, we developed a fluorescence-based method, named "Cas9-mediated adenosine transient reporter for editing enrichment" (CasMAs-TREE; herein abbreviated XMAS-TREE), to facilitate the real-time identification of base-edited cell populations. RESULTS To establish a fluorescent-based assay able to detect ABE activity within a cell in real time, we designed a construct encoding a mCherry fluorescent protein followed by a stop codon (TGA) preceding the coding sequence for a green fluorescent protein (GFP), allowing translational readthrough and expression of GFP after A-to-G conversion of the codon to "TGG." At several independent loci, we demonstrate that XMAS-TREE can be used for the highly efficient purification of targeted cells. Moreover, we demonstrate that XMAS-TREE can be employed in the context of multiplexed editing strategies to simultaneous modify several genomic loci. In addition, we employ XMAS-TREE to efficiently edit human pluripotent stem cells (hPSCs), a cell type traditionally resistant to genetic modification. Furthermore, we utilize XMAS-TREE to generate clonal isogenic hPSCs at target sites not editable using well-established reporter of transfection (RoT)-based strategies. CONCLUSION We established a method to detect adenosine base-editing activity within a cell, which increases the efficiency of editing at multiple genomic locations through an enrichment of edited cells. In the future, XMAS-TREE will greatly accelerate the application of ABEs in biomedical research.
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Affiliation(s)
- Nicholas Brookhouser
- School of Biological and Health Systems Engineering, Arizona State University, 501 E. Tyler Mall, ECG 334A, Tempe, AZ, 85287, USA
- Graduate Program in Clinical Translational Sciences, University of Arizona College of Medicine-Phoenix, Phoenix, AZ, 85004, USA
| | - Toan Nguyen
- School of Biological and Health Systems Engineering, Arizona State University, 501 E. Tyler Mall, ECG 334A, Tempe, AZ, 85287, USA
| | - Stefan J Tekel
- School of Biological and Health Systems Engineering, Arizona State University, 501 E. Tyler Mall, ECG 334A, Tempe, AZ, 85287, USA
| | - Kylie Standage-Beier
- School of Biological and Health Systems Engineering, Arizona State University, 501 E. Tyler Mall, ECG 334A, Tempe, AZ, 85287, USA
- Molecular and Cellular Biology Graduate Program, Arizona State University, Tempe, AZ, 85287, USA
| | - Xiao Wang
- School of Biological and Health Systems Engineering, Arizona State University, 501 E. Tyler Mall, ECG 334A, Tempe, AZ, 85287, USA.
| | - David A Brafman
- School of Biological and Health Systems Engineering, Arizona State University, 501 E. Tyler Mall, ECG 334A, Tempe, AZ, 85287, USA.
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15
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Sanicola HW, Stewart CE, Mueller M, Ahmadi F, Wang D, Powell SK, Sarkar K, Cutbush K, Woodruff MA, Brafman DA. Guidelines for establishing a 3-D printing biofabrication laboratory. Biotechnol Adv 2020; 45:107652. [PMID: 33122013 DOI: 10.1016/j.biotechadv.2020.107652] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 10/21/2020] [Accepted: 10/23/2020] [Indexed: 12/23/2022]
Abstract
Advanced manufacturing and 3D printing are transformative technologies currently undergoing rapid adoption in healthcare, a traditionally non-manufacturing sector. Recent development in this field, largely enabled by merging different disciplines, has led to important clinical applications from anatomical models to regenerative bioscaffolding and devices. Although much research to-date has focussed on materials, designs, processes, and products, little attention has been given to the design and requirements of facilities for enabling clinically relevant biofabrication solutions. These facilities are critical to overcoming the major hurdles to clinical translation, including solving important issues such as reproducibility, quality control, regulations, and commercialization. To improve process uniformity and ensure consistent development and production, large-scale manufacturing of engineered tissues and organs will require standardized facilities, equipment, qualification processes, automation, and information systems. This review presents current and forward-thinking guidelines to help design biofabrication laboratories engaged in engineering model and tissue constructs for therapeutic and non-therapeutic applications.
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Affiliation(s)
- Henry W Sanicola
- Faculty of Medicine, The University of Queensland, Brisbane 4006, Australia
| | - Caleb E Stewart
- Department of Neurosurgery, Louisiana State Health Sciences Center, Shreveport, LA 71103, USA.
| | | | - Farzad Ahmadi
- Department of Electrical and Computer Engineering, Youngstown State University, Youngstown, OH 44555, USA
| | - Dadong Wang
- Quantitative Imaging Research Team, Data61, Commonwealth Scientific and Industrial Research Organization, Marsfield, NSW 2122, Australia
| | - Sean K Powell
- Science and Engineering Faculty, Queensland University of Technology, Brisbane 4029, Australia
| | - Korak Sarkar
- M3D Laboratory, Ochsner Health System, New Orleans, LA 70121, USA
| | - Kenneth Cutbush
- Faculty of Medicine, The University of Queensland, Brisbane 4006, Australia
| | - Maria A Woodruff
- Science and Engineering Faculty, Queensland University of Technology, Brisbane 4029, Australia.
| | - David A Brafman
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA.
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16
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Veldhuizen J, Cutts J, Brafman DA, Migrino RQ, Nikkhah M. Engineering anisotropic human stem cell-derived three-dimensional cardiac tissue on-a-chip. Biomaterials 2020; 256:120195. [DOI: 10.1016/j.biomaterials.2020.120195] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 05/15/2020] [Accepted: 06/09/2020] [Indexed: 01/02/2023]
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17
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Raman S, Srinivasan G, Brookhouser N, Nguyen T, Henson T, Morgan D, Cutts J, Brafman DA. A Defined and Scalable Peptide-Based Platform for the Generation of Human Pluripotent Stem Cell-Derived Astrocytes. ACS Biomater Sci Eng 2020; 6:3477-3490. [PMID: 32550261 PMCID: PMC7284803 DOI: 10.1021/acsbiomaterials.0c00067] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 05/06/2020] [Indexed: 01/07/2023]
Abstract
![]()
Astrocytes
comprise the most abundant cell type in the central
nervous system (CNS) and play critical roles in maintaining neural
tissue homeostasis. In addition, astrocyte dysfunction and death has
been implicated in numerous neurological disorders such as multiple
sclerosis, Alzheimer’s disease, amyotrophic lateral sclerosis
(ALS), and Parkinson’s disease (PD). As such, there is much
interest in using human pluripotent stem cell (hPSC)-derived astrocytes
for drug screening, disease modeling, and regenerative medicine applications.
However, current protocols for generation of astrocytes from hPSCs
are limited by the use of undefined xenogeneic components and two-dimensional
(2D) culture surfaces, which limits their downstream applications
where large-quantities of cells generated under defined conditions
are required. Here, we report the use of a completely synthetic, peptide-based
substrate that allows for the differentiation of highly pure populations
of astrocytes from several independent hPSC lines, including those
derived from patients with neurodegenerative disease. This substrate,
which we demonstrate is compatible with both conventional 2D culture
formats and scalable microcarrier (MC)-based technologies, leads to
the generation of cells that express high levels of canonical astrocytic
markers as well as display properties characteristic of functionally
mature cells including production of apolipoprotein E (ApoE), responsiveness
to inflammatory stimuli, ability to take up amyloid-β (Aβ),
and appearance of robust calcium transients. Finally, we show that
these astrocytes can be cryopreserved without any loss of functionality.
In the future, we anticipate that these methods will enable the development
of bioprocesses for the production of hPSC-derived astrocytes needed
for biomedical research and clinical applications.
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Affiliation(s)
- Sreedevi Raman
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287, United States
| | - Gayathri Srinivasan
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287, United States
| | - Nicholas Brookhouser
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287, United States.,Graduate Program in Clinical Translational Sciences, University of Arizona College of Medicine-Phoenix, Phoenix, Arizona 85004, United States
| | - Toan Nguyen
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287, United States
| | - Tanner Henson
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287, United States
| | - Daylin Morgan
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287, United States
| | - Joshua Cutts
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287, United States
| | - David A Brafman
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287, United States
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18
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Standage-Beier K, Brookhouser N, Balachandran P, Zhang Q, Brafman DA, Wang X. RNA-Guided Recombinase-Cas9 Fusion Targets Genomic DNA Deletion and Integration. CRISPR J 2020; 2:209-222. [PMID: 31436506 DOI: 10.1089/crispr.2019.0013] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
CRISPR-based technologies have become central to genome engineering. However, CRISPR-based editing strategies are dependent on the repair of DNA breaks via endogenous DNA repair mechanisms, which increases susceptibility to unwanted mutations. Here we complement Cas9 with a recombinase's functionality by fusing a hyperactive mutant resolvase from transposon Tn3, a member of serine recombinases, to a catalytically inactive Cas9, which we term integrase Cas9 (iCas9). We demonstrate iCas9 targets DNA deletion and integration. First, we validate iCas9's function in Saccharomyces cerevisiae using a genome-integrated reporter. Cooperative targeting by CRISPR RNAs at spacings of 22 or 40 bp enables iCas9-mediated recombination. Next, iCas9's ability to target DNA deletion and integration in human HEK293 cells is demonstrated using dual GFP-mCherry fluorescent reporter plasmid systems. Finally, we show that iCas9 is capable of targeting integration into a genomic reporter locus. We envision targeting and design concepts of iCas9 will contribute to genome engineering and synthetic biology.
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Affiliation(s)
- Kylie Standage-Beier
- School of Biological and Health Systems Engineering and University of Arizona College of Medicine-Phoenix, Phoenix, Arizona.,Molecular and Cellular Biology Graduate Program, Arizona State University, Tempe, Arizona; University of Arizona College of Medicine-Phoenix, Phoenix, Arizona
| | - Nicholas Brookhouser
- School of Biological and Health Systems Engineering and University of Arizona College of Medicine-Phoenix, Phoenix, Arizona.,Graduate Program in Clinical Translational Sciences, University of Arizona College of Medicine-Phoenix, Phoenix, Arizona
| | - Parithi Balachandran
- School of Biological and Health Systems Engineering and University of Arizona College of Medicine-Phoenix, Phoenix, Arizona
| | - Qi Zhang
- School of Biological and Health Systems Engineering and University of Arizona College of Medicine-Phoenix, Phoenix, Arizona
| | - David A Brafman
- School of Biological and Health Systems Engineering and University of Arizona College of Medicine-Phoenix, Phoenix, Arizona
| | - Xiao Wang
- School of Biological and Health Systems Engineering and University of Arizona College of Medicine-Phoenix, Phoenix, Arizona
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19
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Raman S, Brookhouser N, Brafman DA. Using human induced pluripotent stem cells (hiPSCs) to investigate the mechanisms by which Apolipoprotein E (APOE) contributes to Alzheimer's disease (AD) risk. Neurobiol Dis 2020; 138:104788. [PMID: 32032733 PMCID: PMC7098264 DOI: 10.1016/j.nbd.2020.104788] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 01/14/2020] [Accepted: 01/31/2020] [Indexed: 01/02/2023] Open
Abstract
Although the biochemical and pathological hallmarks of Alzheimer's disease (AD), such as axonal transport defects, synaptic loss, and selective neuronal death, are well characterized, the underlying mechanisms that cause AD are largely unknown, thereby making it difficult to design effective therapeutic interventions. Genome-wide association studies (GWAS) studies have identified several factors associated with increased AD risk. Of these genetic factors, polymorphisms in the Apolipoprotein E (APOE) gene are the strongest and most prevalent. While it has been established that the ApoE protein modulates the formation of amyloid plaques and neurofibrillary tangles, the precise molecular mechanisms by which various ApoE isoforms enhance or mitigate AD onset and progression in aging adults are yet to be elucidated. Advances in cellular reprogramming to generate disease-in-a-dish models now provide a simplified and accessible system that complements animal and primary cell models to study ApoE in the context of AD. In this review, we will describe the use and manipulation of human induced pluripotent stem cells (hiPSCs) in dissecting the interaction between ApoE and AD. First, we will provide an overview of the proposed roles that ApoE plays in modulating pathophysiology of AD. Next, we will summarize the recent studies that have employed hiPSCs to model familial and sporadic AD. Lastly, we will speculate on how current advances in genome editing technologies and organoid culture systems can be used to improve hiPSC-based tools to investigate ApoE-dependent modulation of AD onset and progression.
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Affiliation(s)
- Sreedevi Raman
- School of Biological and Health Systems Engineering, Arizona State University, United States of America
| | - Nicholas Brookhouser
- School of Biological and Health Systems Engineering, Arizona State University, United States of America; Graduate Program in Clinical Translational Sciences, University of Arizona College of Medicine-Phoenix, United States of America
| | - David A Brafman
- School of Biological and Health Systems Engineering, Arizona State University, United States of America.
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20
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Brookhouser N, Tekel SJ, Standage-Beier K, Nguyen T, Schwarz G, Wang X, Brafman DA. BIG-TREE: Base-Edited Isogenic hPSC Line Generation Using a Transient Reporter for Editing Enrichment. Stem Cell Reports 2020. [PMID: 32004495 DOI: 10.1016/j.stemcr.2019.12.013.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Current CRISPR-targeted single-nucleotide modifications and subsequent isogenic cell line generation in human pluripotent stem cells (hPSCs) require the introduction of deleterious double-stranded DNA breaks followed by inefficient homology-directed repair (HDR). Here, we utilize Cas9 deaminase base-editing technologies to co-target genomic loci and an episomal reporter to enable single-nucleotide genomic changes in hPSCs without HDR. Together, this method entitled base-edited isogenic hPSC line generation using a transient reporter for editing enrichment (BIG-TREE) allows for single-nucleotide editing efficiencies of >80% across multiple hPSC lines. In addition, we show that BIG-TREE allows for efficient generation of loss-of-function hPSC lines via introduction of premature stop codons. Finally, we use BIG-TREE to achieve efficient multiplex editing of hPSCs at several independent loci. This easily adoptable method will allow for the precise and efficient base editing of hPSCs for use in developmental biology, disease modeling, drug screening, and cell-based therapies.
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Affiliation(s)
- Nicholas Brookhouser
- School of Biological and Health Systems Engineering, Arizona State University, 501 E. Tyler Mall, ECG 334A, Tempe, AZ 85287, USA; Graduate Program in Clinical Translational Sciences, University of Arizona College of Medicine-Phoenix, Phoenix, AZ 85004, USA
| | - Stefan J Tekel
- School of Biological and Health Systems Engineering, Arizona State University, 501 E. Tyler Mall, ECG 334A, Tempe, AZ 85287, USA
| | - Kylie Standage-Beier
- School of Biological and Health Systems Engineering, Arizona State University, 501 E. Tyler Mall, ECG 334A, Tempe, AZ 85287, USA; Molecular and Cellular Biology Graduate Program, Arizona State University, Tempe, AZ 85287, USA
| | - Toan Nguyen
- School of Biological and Health Systems Engineering, Arizona State University, 501 E. Tyler Mall, ECG 334A, Tempe, AZ 85287, USA
| | - Grace Schwarz
- School of Biological and Health Systems Engineering, Arizona State University, 501 E. Tyler Mall, ECG 334A, Tempe, AZ 85287, USA
| | - Xiao Wang
- School of Biological and Health Systems Engineering, Arizona State University, 501 E. Tyler Mall, ECG 334A, Tempe, AZ 85287, USA.
| | - David A Brafman
- School of Biological and Health Systems Engineering, Arizona State University, 501 E. Tyler Mall, ECG 334A, Tempe, AZ 85287, USA.
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21
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Brookhouser N, Tekel SJ, Standage-Beier K, Nguyen T, Schwarz G, Wang X, Brafman DA. BIG-TREE: Base-Edited Isogenic hPSC Line Generation Using a Transient Reporter for Editing Enrichment. Stem Cell Reports 2020; 14:184-191. [PMID: 32004495 PMCID: PMC7013208 DOI: 10.1016/j.stemcr.2019.12.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 12/22/2019] [Accepted: 12/28/2019] [Indexed: 01/09/2023] Open
Abstract
Current CRISPR-targeted single-nucleotide modifications and subsequent isogenic cell line generation in human pluripotent stem cells (hPSCs) require the introduction of deleterious double-stranded DNA breaks followed by inefficient homology-directed repair (HDR). Here, we utilize Cas9 deaminase base-editing technologies to co-target genomic loci and an episomal reporter to enable single-nucleotide genomic changes in hPSCs without HDR. Together, this method entitled base-edited isogenic hPSC line generation using a transient reporter for editing enrichment (BIG-TREE) allows for single-nucleotide editing efficiencies of >80% across multiple hPSC lines. In addition, we show that BIG-TREE allows for efficient generation of loss-of-function hPSC lines via introduction of premature stop codons. Finally, we use BIG-TREE to achieve efficient multiplex editing of hPSCs at several independent loci. This easily adoptable method will allow for the precise and efficient base editing of hPSCs for use in developmental biology, disease modeling, drug screening, and cell-based therapies. Generation of hPSC-MSCs by stepwise and chemically defined protocol Ascorbate promotes the specification and chondrogenesis of hPSC-MSCs Ascorbate promotes the specification of hPS-MSCs and promotes osteochondrogenesis hPSC-MSCs are able to fully repair the cartilage defects
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Affiliation(s)
- Nicholas Brookhouser
- School of Biological and Health Systems Engineering, Arizona State University, 501 E. Tyler Mall, ECG 334A, Tempe, AZ 85287, USA; Graduate Program in Clinical Translational Sciences, University of Arizona College of Medicine-Phoenix, Phoenix, AZ 85004, USA
| | - Stefan J Tekel
- School of Biological and Health Systems Engineering, Arizona State University, 501 E. Tyler Mall, ECG 334A, Tempe, AZ 85287, USA
| | - Kylie Standage-Beier
- School of Biological and Health Systems Engineering, Arizona State University, 501 E. Tyler Mall, ECG 334A, Tempe, AZ 85287, USA; Molecular and Cellular Biology Graduate Program, Arizona State University, Tempe, AZ 85287, USA
| | - Toan Nguyen
- School of Biological and Health Systems Engineering, Arizona State University, 501 E. Tyler Mall, ECG 334A, Tempe, AZ 85287, USA
| | - Grace Schwarz
- School of Biological and Health Systems Engineering, Arizona State University, 501 E. Tyler Mall, ECG 334A, Tempe, AZ 85287, USA
| | - Xiao Wang
- School of Biological and Health Systems Engineering, Arizona State University, 501 E. Tyler Mall, ECG 334A, Tempe, AZ 85287, USA.
| | - David A Brafman
- School of Biological and Health Systems Engineering, Arizona State University, 501 E. Tyler Mall, ECG 334A, Tempe, AZ 85287, USA.
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22
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Standage-Beier K, Tekel SJ, Brookhouser N, Schwarz G, Nguyen T, Wang X, Brafman DA. A transient reporter for editing enrichment (TREE) in human cells. Nucleic Acids Res 2020; 48:1602. [PMID: 31943066 PMCID: PMC7026629 DOI: 10.1093/nar/gkaa027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Kylie Standage-Beier
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA.,Molecular and Cellular Biology graduate program, Arizona State University, Tempe, AZ 85287, USA
| | - Stefan J Tekel
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
| | - Nicholas Brookhouser
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA.,Graduate Program in Clinical Translational Sciences, University of Arizona College of Medicine-Phoenix, Phoenix, AZ 85004, USA
| | - Grace Schwarz
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
| | - Toan Nguyen
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
| | - Xiao Wang
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
| | - David A Brafman
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
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23
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Standage-Beier K, Tekel SJ, Brookhouser N, Schwarz G, Nguyen T, Wang X, Brafman DA. A transient reporter for editing enrichment (TREE) in human cells. Nucleic Acids Res 2019; 47:e120. [PMID: 31428784 PMCID: PMC6821290 DOI: 10.1093/nar/gkz713] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 08/01/2019] [Accepted: 08/05/2019] [Indexed: 12/21/2022] Open
Abstract
Current approaches to identify cell populations that have been modified with deaminase base editing technologies are inefficient and rely on downstream sequencing techniques. In this study, we utilized a blue fluorescent protein (BFP) that converts to green fluorescent protein (GFP) upon a C-to-T substitution as an assay to report directly on base editing activity within a cell. Using this assay, we optimize various base editing transfection parameters and delivery strategies. Moreover, we utilize this assay in conjunction with flow cytometry to develop a transient reporter for editing enrichment (TREE) to efficiently purify base-edited cell populations. Compared to conventional cell enrichment strategies that employ reporters of transfection (RoT), TREE significantly improved the editing efficiency at multiple independent loci, with efficiencies approaching 80%. We also employed the BFP-to-GFP conversion assay to optimize base editor vector design in human pluripotent stem cells (hPSCs), a cell type that is resistant to genome editing and in which modification via base editors has not been previously reported. At last, using these optimized vectors in the context of TREE allowed for the highly efficient editing of hPSCs. We envision TREE as a readily adoptable method to facilitate base editing applications in synthetic biology, disease modeling, and regenerative medicine.
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Affiliation(s)
- Kylie Standage-Beier
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
- Molecular and Cellular Biology graduate program, Arizona State University, Tempe, AZ 85287, USA
| | - Stefan J Tekel
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
| | - Nicholas Brookhouser
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
- Graduate Program in Clinical Translational Sciences, University of Arizona College of Medicine-Phoenix, Phoenix, AZ 85004, USA
| | - Grace Schwarz
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
| | - Toan Nguyen
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
| | - Xiao Wang
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
| | - David A Brafman
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
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24
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Frow EK, Brafman DA, Muldoon A, Krum L, Williams P, Becker B, Nelson JP, Pritchett A. Characterizing Direct-to-Consumer Stem Cell Businesses in the Southwest United States. Stem Cell Reports 2019; 13:247-253. [PMID: 31378670 PMCID: PMC6700498 DOI: 10.1016/j.stemcr.2019.07.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 06/28/2019] [Accepted: 07/01/2019] [Indexed: 11/10/2022] Open
Abstract
There are currently hundreds of businesses across the United States offering direct-to-consumer stem cell treatments that have not been through regulatory approval by the Food and Drug Administration (FDA). Here, we provide a detailed characterization of nearly 170 stem cell businesses operating in the Southwest United States. We draw specific attention to two as-yet understudied facets of these businesses. First, we identify differences in the degree to which a given business focuses their practice on stem cell treatments. Second, we compare the stated expertise of the care providers in stem cell businesses with the range of conditions they purport to treat. These findings deepen our knowledge of the growing industry around unapproved stem cell treatments, and are used here to offer suggestions for how the FDA might target its resources with respect to regulatory oversight. We characterize 169 direct-to-consumer stem cell businesses in the southwest US We show differences in degree of clinic focus on providing stem cell treatments We compare care provider expertise with the stem cell-based interventions they offer We offer suggestions for regulatory oversight of direct-to-consumer stem cell businesses
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Affiliation(s)
- Emma K Frow
- School for the Future of Innovation in Society, Arizona State University, Tempe, AZ 85287, USA; School of Biological & Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA.
| | - David A Brafman
- School of Biological & Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA.
| | - Anna Muldoon
- School for the Future of Innovation in Society, Arizona State University, Tempe, AZ 85287, USA
| | - Logan Krum
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Paige Williams
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85287, USA
| | - Bryson Becker
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - John P Nelson
- School for the Future of Innovation in Society, Arizona State University, Tempe, AZ 85287, USA
| | - Ashley Pritchett
- College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA
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Brookhouser N, Zhang P, Caselli R, Kim JJ, Brafman DA. Generation and characterization of two human induced pluripotent stem cell (hiPSC) lines homozygous for the Apolipoprotein e4 (APOE4) risk variant-Alzheimer's disease (ASUi005-A) and healthy non-demented control (ASUi006-A). Stem Cell Res 2018; 32:145-149. [PMID: 30296667 PMCID: PMC6217860 DOI: 10.1016/j.scr.2018.09.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 08/22/2018] [Accepted: 09/10/2018] [Indexed: 11/08/2022] Open
Abstract
Although the majority of late-onset Alzheimer's disease (AD) patients are labeled sporadic, multiple genetic risk variants have been identified, the most powerful and prevalent of which is the e4 variant of the Apolipoprotein E (APOE) gene. Here, we generated human induced pluripotent stem cell (hiPSC) lines from the peripheral blood mononuclear cells (PBMCs) of a clinically diagnosed AD patient [ASUi005-A] and a non-demented control (NDC) patient [ASUi006-A] homozygous for the APOE4 risk allele. These hiPSCs maintained their original genotype, expressed pluripotency markers, exhibited a normal karyotype, and retained the ability to differentiate into cells representative of the three germ layers.
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Affiliation(s)
- Nicholas Brookhouser
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
| | - Ping Zhang
- Molecular and Cellular Biology, Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard Caselli
- Department of Neurology, Mayo Clinic College of Medicine, Scottsdale, AZ 85259, USA
| | - Jean J Kim
- Molecular and Cellular Biology, Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - David A Brafman
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA.
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26
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Srinivasan G, Morgan D, Varun D, Brookhouser N, Brafman DA. An integrated biomanufacturing platform for the large-scale expansion and neuronal differentiation of human pluripotent stem cell-derived neural progenitor cells. Acta Biomater 2018; 74:168-179. [PMID: 29775730 DOI: 10.1016/j.actbio.2018.05.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 05/03/2018] [Accepted: 05/07/2018] [Indexed: 12/12/2022]
Abstract
Human pluripotent stem cell derived neural progenitor cells (hNPCs) have the unique properties of long-term in vitro expansion as well as differentiation into the various neurons and supporting cell types of the central nervous system (CNS). Because of these characteristics, hNPCs have tremendous potential in the modeling and treatment of various CNS diseases and disorders. However, expansion and neuronal differentiation of hNPCs in quantities necessary for these applications is not possible with current two dimensional (2-D) approaches. Here, we used a fully defined peptide substrate as the basis for a microcarrier (MC)-based suspension culture system. Several independently derived hNPC lines were cultured on MCs for multiple passages as well as efficiently differentiated to neurons. Finally, this MC-based system was used in conjunction with a low shear rotating wall vessel (RWV) bioreactor for the integrated, large-scale expansion and neuronal differentiation of hNPCs. Overall, this fully defined and scalable biomanufacturing system will facilitate the generation of hNPCs and their neuronal derivatives in quantities necessary for basic and translational applications. STATEMENT OF SIGNIFICANCE In this work, we developed a microcarrier (MC)-based culture system that allows for the expansion and neuronal differentiation of human pluripotent stem cell-derived neural progenitor cells (hNPCs) under defined conditions. In turn, this MC approach was implemented in a rotating wall vessel (RWV) bioreactor for the large-scale expansion and neuronal differentiation of hNPCs. This work is of significance as it overcomes current limitations of conventional two dimensional (2-D) culture systems to enable the generation of hNPCs and their neuronal derivatives in quantities required for downstream applications in disease modeling, drug screening, and regenerative medicine.
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Affiliation(s)
- Gayathri Srinivasan
- School of Biological and Health Systems Engineering, Arizona State University, United States
| | - Daylin Morgan
- School of Biological and Health Systems Engineering, Arizona State University, United States
| | - Divya Varun
- School of Biological and Health Systems Engineering, Arizona State University, United States
| | - Nicholas Brookhouser
- School of Biological and Health Systems Engineering, Arizona State University, United States
| | - David A Brafman
- School of Biological and Health Systems Engineering, Arizona State University, United States.
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27
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Brookhouser N, Zhang P, Caselli R, Kim JJ, Brafman DA. Generation and characterization of human induced pluripotent stem cell (hiPSC) lines from an Alzheimer's disease (ASUi003-A) and non-demented control (ASUi004-A) patient homozygous for the Apolipoprotein e4 (APOE4) risk variant. Stem Cell Res 2017; 25:266-269. [PMID: 29246571 DOI: 10.1016/j.scr.2017.07.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 07/07/2017] [Indexed: 12/31/2022] Open
Abstract
Although the majority of late-onset Alzheimer's disease (AD) patients are labeled sporadic, multiple genetic risk variants have been identified, the most powerful and prevalent of which is the e4 variant of the Apolipoprotein E (APOE) gene. Here, we generated human induced pluripotent stem cell (hiPSC) lines from the peripheral blood mononuclear cells (PBMCs) of a clinically diagnosed AD patient [ASUi003-A] and a non-demented control (NDC) patient [ASUi004-A] homozygous for the APOE4 risk allele. These hiPSCs maintained their original genotype, expressed pluripotency markers, exhibited a normal karyotype, and retained the ability to differentiate into cells representative of the three germ layers.
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Affiliation(s)
- Nicholas Brookhouser
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
| | - Ping Zhang
- Molecular and Cellular Biology, Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard Caselli
- Department of Neurology, Mayo Clinic College of Medicine, Scottsdale, AZ 85259, USA
| | - Jean J Kim
- Molecular and Cellular Biology, Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - David A Brafman
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA.
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28
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Brookhouser N, Zhang P, Caselli R, Kim JJ, Brafman DA. Generation and characterization of human induced pluripotent stem cell (hiPSC) lines from an Alzheimer's disease (ASUi001-A) and non-demented control (ASUi002-A) patient homozygous for the Apolipoprotein e4 (APOE4) risk variant. Stem Cell Res 2017; 24:160-163. [PMID: 29034886 DOI: 10.1016/j.scr.2017.06.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 05/20/2017] [Accepted: 06/06/2017] [Indexed: 11/20/2022] Open
Abstract
Although the majority of late-onset Alzheimer's disease (AD) patients are labeled sporadic, multiple genetic risk variants have been identified, the most powerful and prevalent of which is the e4 variant of the Apolipoprotein E (APOE) gene. Here, we generated human induced pluripotent stem cell (hiPSC) lines from the peripheral blood mononuclear cells (PBMCs) of a clinically diagnosed AD patient [ASUi001-A] and a non-demented control (NDC) patient [ASUi002-A] homozygous for the APOE4 risk allele. These hiPSCs maintained their original genotype, expressed pluripotency markers, exhibited a normal karyotype, and demonstrated the ability to differentiate into cells representative of the three germ layers.
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Affiliation(s)
- Nicholas Brookhouser
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
| | - Ping Zhang
- Molecular and Cellular Biology, Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard Caselli
- Department of Neurology, Mayo Clinic College of Medicine, Scottsdale, AZ 85259, USA
| | - Jean J Kim
- Molecular and Cellular Biology, Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - David A Brafman
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA.
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29
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Abstract
In order to efficiently edit eukaryotic genomes, it is critical to test the impact of chromatin dynamics on CRISPR/Cas9 function and develop strategies to adapt the system to eukaryotic contexts. So far, research has extensively characterized the relationship between the CRISPR endonuclease Cas9 and the composition of the RNA-DNA duplex that mediates the system's precision. Evidence suggests that chromatin modifications and DNA packaging can block eukaryotic genome editing by custom-built DNA endonucleases like Cas9; however, the underlying mechanism of Cas9 inhibition is unclear. Here, we demonstrate that closed, gene-silencing-associated chromatin is a mechanism for the interference of Cas9-mediated DNA editing. Our assays use a transgenic cell line with a drug-inducible switch to control chromatin states (open and closed) at a single genomic locus. We show that closed chromatin inhibits binding and editing at specific target sites and that artificial reversal of the silenced state restores editing efficiency. These results provide new insights to improve Cas9-mediated editing in human and other mammalian cells.
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Affiliation(s)
- René M. Daer
- School of Biological and
Health Systems Engineering, Arizona State University, 501 E. Tyler
Mall, ECG 344A, Tempe, Arizona 85287, United States
| | - Josh P. Cutts
- School of Biological and
Health Systems Engineering, Arizona State University, 501 E. Tyler
Mall, ECG 344A, Tempe, Arizona 85287, United States
| | - David A. Brafman
- School of Biological and
Health Systems Engineering, Arizona State University, 501 E. Tyler
Mall, ECG 344A, Tempe, Arizona 85287, United States
| | - Karmella A. Haynes
- School of Biological and
Health Systems Engineering, Arizona State University, 501 E. Tyler
Mall, ECG 344A, Tempe, Arizona 85287, United States
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30
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Varun D, Srinivasan GR, Tsai YH, Kim HJ, Cutts J, Petty F, Merkley R, Stephanopoulos N, Dolezalova D, Marsala M, Brafman DA. A robust vitronectin-derived peptide for the scalable long-term expansion and neuronal differentiation of human pluripotent stem cell (hPSC)-derived neural progenitor cells (hNPCs). Acta Biomater 2017; 48:120-130. [PMID: 27989923 DOI: 10.1016/j.actbio.2016.10.037] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 10/03/2016] [Accepted: 10/26/2016] [Indexed: 12/22/2022]
Abstract
Despite therapeutic advances, neurodegenerative diseases and disorders remain some of the leading causes of mortality and morbidity in the United States. Therefore, cell-based therapies to replace lost or damaged neurons and supporting cells of the central nervous system (CNS) are of great therapeutic interest. To that end, human pluripotent stem cell (hPSC) derived neural progenitor cells (hNPCs) and their neuronal derivatives could provide the cellular 'raw material' needed for regenerative medicine therapies for a variety of CNS disorders. In addition, hNPCs derived from patient-specific hPSCs could be used to elucidate the underlying mechanisms of neurodegenerative diseases and identify potential drug candidates. However, the scientific and clinical application of hNPCs requires the development of robust, defined, and scalable substrates for their long-term expansion and neuronal differentiation. In this study, we rationally designed a vitronectin-derived peptide (VDP) that served as an adhesive growth substrate for the long-term expansion of several hNPC lines. Moreover, VDP-coated surfaces allowed for the directed neuronal differentiation of hNPC at levels similar to cells differentiated on traditional extracellular matrix protein-based substrates. Overall, the ability of VDP to support the long-term expansion and directed neuronal differentiation of hNPCs will significantly advance the future translational application of these cells in treating injuries, disorders, and diseases of the CNS.
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Kharaziha M, Memic A, Akbari M, Brafman DA, Nikkhah M. Tissue Engineering: Nano-Enabled Approaches for Stem Cell-Based Cardiac Tissue Engineering(Adv. Healthcare Mater. 13/2016). Adv Healthc Mater 2016. [DOI: 10.1002/adhm.201670066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Mahshid Kharaziha
- Biomaterials Research Group; Department of Materials Engineering; Isfahan University of Technology; Isfahan 8415683111 Iran
| | - Adnan Memic
- Center of Nanotechnology; King Abdulaziz University; Jeddah 21589 Saudi Arabia
| | - Mohsen Akbari
- Department of Mechanical Engineering; University of Victoria; Victoria BC Canada
| | - David A. Brafman
- School of Biological and Health Systems Engineering (SBHSE) Harington; Bioengineering Program; Arizona State University; Tempe Arizona 85287 USA
| | - Mehdi Nikkhah
- School of Biological and Health Systems Engineering (SBHSE) Harington; Bioengineering Program; Arizona State University; Tempe Arizona 85287 USA
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Kharaziha M, Memic A, Akbari M, Brafman DA, Nikkhah M. Nano-Enabled Approaches for Stem Cell-Based Cardiac Tissue Engineering. Adv Healthc Mater 2016; 5:1533-53. [PMID: 27199266 DOI: 10.1002/adhm.201600088] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 03/01/2016] [Indexed: 12/20/2022]
Abstract
Cardiac diseases are the most prevalent causes of mortality in the world, putting a major economic burden on global healthcare system. Tissue engineering strategies aim at developing efficient therapeutic approaches to overcome the current challenges in prolonging patients survival upon cardiac diseases. The integration of advanced biomaterials and stem cells has offered enormous promises for regeneration of damaged myocardium. Natural or synthetic biomaterials have been extensively used to deliver cells or bioactive molecules to the site of injury in heart. Additionally, nano-enabled approaches (e.g., nanomaterials, nanofeatured surfaces) have been instrumental in developing suitable scaffolding biomaterials and regulating stem cells microenvironment to achieve functional therapeutic outcomes. This review article explores tissue engineering strategies, which have emphasized on the use of nano-enabled approaches in combination with stem cells for regeneration and repair of injured myocardium upon myocardial infarction (MI). Primarily a wide range of biomaterials, along with different types of stem cells, which have utilized in cardiac tissue engineering will be presented. Then integration of nanomaterials and surface nanotopographies with biomaterials and stem cells for myocardial regeneration will be presented. The advantages and challenges of these approaches will be reviewed and future perspective will be discussed.
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Affiliation(s)
- Mahshid Kharaziha
- Biomaterials Research Group; Department of Materials Engineering; Isfahan University of Technology; Isfahan 8415683111 Iran
| | - Adnan Memic
- Center of Nanotechnology; King Abdulaziz University; Jeddah 21589 Saudi Arabia
| | - Mohsen Akbari
- Department of Mechanical Engineering; University of Victoria; Victoria BC Canada
| | - David A. Brafman
- School of Biological and Health Systems Engineering (SBHSE) Harington; Bioengineering Program; Arizona State University; Tempe Arizona 85287 USA
| | - Mehdi Nikkhah
- School of Biological and Health Systems Engineering (SBHSE) Harington; Bioengineering Program; Arizona State University; Tempe Arizona 85287 USA
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33
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Cutts J, Brookhouser N, Brafman DA. Generation of Regionally Specific Neural Progenitor Cells (NPCs) and Neurons from Human Pluripotent Stem Cells (hPSCs). Methods Mol Biol 2016; 1516:121-144. [PMID: 27106497 DOI: 10.1007/7651_2016_357] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Neural progenitor cells (NPCs) derived from human pluripotent stem cells (hPSCs) are a multipotent cell population capable of long-term expansion and differentiation into a variety of neuronal subtypes. As such, NPCs have tremendous potential for disease modeling, drug screening, and regenerative medicine. Current methods for the generation of NPCs results in cell populations homogenous for pan-neural markers such as SOX1 and SOX2 but heterogeneous with respect to regional identity. In order to use NPCs and their neuronal derivatives to investigate mechanisms of neurological disorders and develop more physiologically relevant disease models, methods for generation of regionally specific NPCs and neurons are needed. Here, we describe a protocol in which exogenous manipulation of WNT signaling, through either activation or inhibition, during neural differentiation of hPSCs, promotes the formation of regionally homogenous NPCs and neuronal cultures. In addition, we provide methods to monitor and characterize the efficiency of hPSC differentiation to these regionally specific cell identities.
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Affiliation(s)
- Josh Cutts
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, 85287-9709, USA
| | - Nicholas Brookhouser
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, 85287-9709, USA
| | - David A Brafman
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, 85287-9709, USA.
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Tsai Y, Cutts J, Kimura A, Varun D, Brafman DA. A chemically defined substrate for the expansion and neuronal differentiation of human pluripotent stem cell-derived neural progenitor cells. Stem Cell Res 2015; 15:75-87. [DOI: 10.1016/j.scr.2015.05.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 05/04/2015] [Accepted: 05/04/2015] [Indexed: 01/27/2023] Open
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Cutts J, Nikkhah M, Brafman DA. Biomaterial Approaches for Stem Cell-Based Myocardial Tissue Engineering. Biomark Insights 2015; 10:77-90. [PMID: 26052226 PMCID: PMC4451817 DOI: 10.4137/bmi.s20313] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 05/05/2015] [Accepted: 05/06/2015] [Indexed: 12/21/2022] Open
Abstract
Adult and pluripotent stem cells represent a ready supply of cellular raw materials that can be used to generate the functionally mature cells needed to replace damaged or diseased heart tissue. However, the use of stem cells for cardiac regenerative therapies is limited by the low efficiency by which stem cells are differentiated in vitro to cardiac lineages as well as the inability to effectively deliver stem cells and their derivatives to regions of damaged myocardium. In this review, we discuss the various biomaterial-based approaches that are being implemented to direct stem cell fate both in vitro and in vivo. First, we discuss the stem cell types available for cardiac repair and the engineering of naturally and synthetically derived biomaterials to direct their in vitro differentiation to the cell types that comprise heart tissue. Next, we describe biomaterial-based approaches that are being implemented to enhance the in vivo integration and differentiation of stem cells delivered to areas of cardiac damage. Finally, we present emerging trends of using stem cell-based biomaterial approaches to deliver pro-survival factors and fully vascularized tissue to the damaged and diseased cardiac tissue.
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Affiliation(s)
- Josh Cutts
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA
| | - Mehdi Nikkhah
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA
| | - David A Brafman
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA
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Abstract
Human pluripotent stem cell (hPSC)-derived neural progenitor cells (NPCs), a multipotent cell population that is capable of near indefinite expansion and subsequent differentiation into the various cell types that comprise the central nervous system (CNS), could provide an unlimited source of cells for neural-related cell-based therapies and disease modeling. However, the use of NPCs for the study and treatment of a variety of debilitating neurological diseases requires the development of scalable and reproducible protocols for their generation, expansion, characterization, and neuronal differentiation. Here, we describe a serum-free method for the stepwise generation of NPCs from hPSCs through the sequential formation of embryoid bodies (EBs) and neuro-epithelial-like rosettes. NPCs isolated from neural rosette cultures can be homogenously expanded while maintaining high expression of pan-neural markers such as SOX1, SOX2, and Nestin. Finally, this protocol allows for the robust differentiation of NPCs into microtubule-associated protein 2 (MAP2) and β-Tubulin-III (β3T) positive neurons.
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Affiliation(s)
- David A Brafman
- Department of Cellular and Molecular Medicine, Stem Cell Program, UCSD, 9500 Gilman Drive, La Jolla, CA, 92093-0395, USA,
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37
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Moya N, Cutts J, Gaasterland T, Willert K, Brafman DA. Endogenous WNT signaling regulates hPSC-derived neural progenitor cell heterogeneity and specifies their regional identity. Stem Cell Reports 2014; 3:1015-28. [PMID: 25458891 PMCID: PMC4264562 DOI: 10.1016/j.stemcr.2014.10.004] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Revised: 10/13/2014] [Accepted: 10/14/2014] [Indexed: 11/20/2022] Open
Abstract
Neural progenitor cells (NPCs) derived from human pluripotent stem cells (hPSCs) are a multipotent cell population that is capable of nearly indefinite expansion and subsequent differentiation into the various neuronal and supporting cell types that comprise the CNS. However, current protocols for differentiating NPCs toward neuronal lineages result in a mixture of neurons from various regions of the CNS. In this study, we determined that endogenous WNT signaling is a primary contributor to the heterogeneity observed in NPC cultures and neuronal differentiation. Furthermore, exogenous manipulation of WNT signaling during neural differentiation, through either activation or inhibition, reduces this heterogeneity in NPC cultures, thereby promoting the formation of regionally homogeneous NPC and neuronal cultures. The ability to manipulate WNT signaling to generate regionally specific NPCs and neurons will be useful for studying human neural development and will greatly enhance the translational potential of hPSCs for neural-related therapies. Heterogeneous endogenous WNT signaling regulates hPSC-derived neuronal diversity Endogenous WNT signaling specifies the regional identity of hPSC-derived neurons Exogenous WNT signaling leads to uniform neuronal cultures from hPSCs Effects of WNT signaling on neurogenesis are recapitulated in an hPSC-based system
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Affiliation(s)
- Noel Moya
- Department of Cellular and Molecular Medicine, Stem Cell Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0695, USA
| | - Josh Cutts
- Department of Cellular and Molecular Medicine, Stem Cell Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0695, USA; School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287-9709, USA
| | - Terry Gaasterland
- UCSD and Scripps Institution of Oceanography, Scripps Genome Center, 9500 Gilman Drive, La Jolla, CA 92093-0202, USA
| | - Karl Willert
- Department of Cellular and Molecular Medicine, Stem Cell Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0695, USA.
| | - David A Brafman
- Department of Cellular and Molecular Medicine, Stem Cell Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0695, USA; School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287-9709, USA.
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38
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Brafman DA, Moya N, Allen-Soltero S, Fellner T, Robinson M, McMillen ZL, Gaasterland T, Willert K. Analysis of SOX2-expressing cell populations derived from human pluripotent stem cells. Stem Cell Reports 2013; 1:464-78. [PMID: 24286033 PMCID: PMC3841266 DOI: 10.1016/j.stemcr.2013.09.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 09/24/2013] [Accepted: 09/25/2013] [Indexed: 01/20/2023] Open
Abstract
SOX2 is involved in several cell and developmental processes, including maintenance of embryonic stem cells, differentiation of neural progenitor cells, and patterning of gut endoderm. To study its role in a human system, we generated a human embryonic stem cell (hESC) line harboring a reporter gene encoding GFP in the SOX2 locus. This SOX2 reporter line faithfully recapitulates expression of the SOX2 gene in undifferentiated human pluripotent stem cells (hPSCs), neural progenitor cells (NPCs), and anterior foregut endoderm (AFE). In undifferentiated hESCs, GFP expression corresponds to those cells with highest levels of expression of genes associated with the pluripotent state. In NPCs, expression of GFP can be employed to isolate cells expressing markers associated with NPC multipotency. In AFE, we used transcriptome-wide expression analysis to identify cell surface markers with elevated expression in this population, thereby facilitating isolation and purification of this hPSC-derived cell population. A SOX2-GFP hESC line is used to isolate and characterize multiple cell types A cell surface marker signature allows for the purification of endodermal progeny Targeted gene insertion with adeno-associated virus (AAV) is highly efficient
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Affiliation(s)
- David A Brafman
- Stem Cell Program, Department of Cellular and Molecular Medicine, UCSD, 9500 Gilman Drive, La Jolla, CA 92093-0695, USA
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Abstract
Within the adult organism, stem cells reside in defined anatomical microenvironments called niches. These architecturally diverse microenvironments serve to balance stem cell self-renewal and differentiation. Proper regulation of this balance is instrumental to tissue repair and homeostasis, and any imbalance can potentially lead to diseases such as cancer. Within each of these microenvironments, a myriad of chemical and physical stimuli interact in a complex (synergistic or antagonistic) manner to tightly regulate stem cell fate. The in vitro replication of these in vivo microenvironments will be necessary for the application of stem cells for disease modeling, drug discovery, and regenerative medicine purposes. However, traditional reductionist approaches have only led to the generation of cell culture methods that poorly recapitulate the in vivo microenvironment. To that end, novel engineering and systems biology approaches have allowed for the investigation of the biological and mechanical stimuli that govern stem cell fate. In this review, the application of these technologies for the dissection of stem cell microenvironments will be analyzed. Moreover, the use of these engineering approaches to construct in vitro stem cell microenvironments that precisely control stem cell fate and function will be reviewed. Finally, the emerging trend of using high-throughput, combinatorial methods for the stepwise engineering of stem cell microenvironments will be explored.
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Affiliation(s)
- David A Brafman
- Department of Cellular and Molecular Medicine, Stem Cell Program, University of California at San Diego, La Jolla, California
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Brafman DA, Chien S, Willert K. Arrayed cellular microenvironments for identifying culture and differentiation conditions for stem, primary and rare cell populations. Nat Protoc 2012; 7:703-17. [PMID: 22422316 DOI: 10.1038/nprot.2012.017] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
During the development of an organism, cells are exposed to a myriad of signals, structural components and scaffolds, which collectively make up the cellular microenvironment. The majority of current developmental biology studies examine the effect of individual or small subsets of molecules and parameters on cellular behavior, and they consequently fail to explore the complexity of factors to which cells are exposed. Here we describe a technology, referred to as arrayed cellular microenvironments (ACMEs), that allows for a high-throughput examination of the effects of multiple extracellular components in a combinatorial manner on any cell type of interest. We will specifically focus on the application of this technology to human pluripotent stem cells (hPSCs), a population of cells with tremendous therapeutic potential, and one for which growth and differentiation conditions are poorly characterized and far from defined and optimized. A standard ACME screen uses the technologies previously applied to the manufacture and analysis of DNA microarrays, requires standard cell-culture facilities and can be performed from beginning to end within 5-10 days.
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Affiliation(s)
- David A Brafman
- Cellular and Molecular Medicine, Stem Cell Program, University of California, San Diego, California, USA.
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Brafman DA, Chang CW, Fernandez A, Willert K, Varghese S, Chien S. Long-term human pluripotent stem cell self-renewal on synthetic polymer surfaces. Biomaterials 2010; 31:9135-44. [PMID: 20817292 DOI: 10.1016/j.biomaterials.2010.08.007] [Citation(s) in RCA: 142] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Accepted: 08/04/2010] [Indexed: 01/22/2023]
Abstract
Realization of the full potential of human pluripotent stem cells (hPSCs) in regenerative medicine requires the development of well-defined culture conditions for their long-term growth and directed differentiation. Current practices for maintaining hPSCs generally utilize empirically determined combinations of feeder cells and other animal-based products, which are expensive, difficult to isolate, subject to batch-to-batch variations, and unsuitable for cell-based therapies. Using a high-throughput screening approach, we identified several polymers that can support self-renewal of hPSCs. While most of these polymers provide support for only a short period of time, we identified a synthetic polymer poly(methyl vinyl ether-alt-maleic anhydride) (PMVE-alt-MA) that supported the long-term attachment, proliferation and self-renewal of HUES1, HUES9, and iPSCs. The hPSCs cultured on PMVE-alt-MA maintained their characteristic morphology, expressed high levels of markers of pluripotency, and retained a normal karyotype. Such cost-effective, polymer-based matrices that support long-term self-renewal and proliferation of hPSCs will not only help to accelerate the translational perspectives of hPSCs, but also provide a platform to elucidate the underlying molecular mechanisms that regulate stem cell proliferation and differentiation.
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Affiliation(s)
- David A Brafman
- Department of Bioengineering, University of California-San Diego, 9500 Gilman Dr, La Jolla, CA 92093-0695, United States
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Brafman DA, Shah KD, Fellner T, Chien S, Willert K. Defining long-term maintenance conditions of human embryonic stem cells with arrayed cellular microenvironment technology. Stem Cells Dev 2009; 18:1141-54. [PMID: 19327010 DOI: 10.1089/scd.2008.0410] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The optimization of defined growth conditions is necessary for the development of clinical application of human embryonic stem cells (hESCs). Current research has focused on developing defined media formulations for long-term culture of hESCs with little attention on the establishment of defined substrates for hESC proliferation and self-renewal. Presently available technologies are insufficient to address the full complement of factors that may regulate hESC proliferation and maintenance of pluripotency. Here, we report the application of a multifactorial array technology to identify fully defined and optimized culture conditions for the proliferation of hESCs. Through the systematic screening of extracellular matrix proteins (ECMPs) and other signaling molecules, we developed and characterized a completely defined culture system for the long-term self-renewal of three independent hESC lines. In the future, the novel array platform and analysis procedure presented here will be applied toward the directed differentiation of hESCs and maintenance of other stem and progenitor cell populations.
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Affiliation(s)
- David A Brafman
- Department of Bioengineering, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0412, USA
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Brafman DA, de Minicis S, Seki E, Shah KD, Teng D, Brenner D, Willert K, Chien S. Investigating the role of the extracellular environment in modulating hepatic stellate cell biology with arrayed combinatorial microenvironments. Integr Biol (Camb) 2009; 1:513-24. [PMID: 20023766 DOI: 10.1039/b912926j] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Hepatic stellate cells (HSCs) are a major cell type of the liver that are involved in liver homeostasis. Upon liver damage, HSCs exit their normally quiescent state and become activated, leading to an increase of their proliferation, production of abnormal extracellular matrix proteins (ECMPs) and inflammatory mediators, and eventually liver fibrosis and cirrhosis. Current in vitro approaches to identify components that influence HSC biology typically investigate one factor at a time and generally ignore the complex crosstalk among the myriad of components that comprise the microenvironments of quiescent or activated HSCs. Here we describe a high throughput screening (HTS) approach to identify factors that affect HSC biology. Specifically, we integrated the use of ECMPs and signaling molecules into a combinatorial cellular microarray technology platform, thereby creating comprehensive "microenvironments". Using this technology, we performed real-time simultaneous screening of the effects of hundreds of unique microenvironments composed of ECMPs and signaling molecules on HSC proliferation and activation. From these screens, we identified combinations of microenvironment components that differentially modulate the HSC phenotype. Furthermore, analysis of HSC responses revealed that the influences of Wnt signaling molecules on HSC fate are dependent on the ECMP composition in which they are presented. Collectively, our results demonstrate the utility of high-content, array-based screens to provide a better understanding of HSC biology. Our results indicate that array-based screens may provide an efficient means for identifying candidate signaling pathways to be targeted for anti-fibrotic therapies.
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Affiliation(s)
- David A Brafman
- Department of Bioengineering, University of California, San Diego, USA.
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