scholarly journals P53 toxicity is a hurdle to CRISPR/CAS9 screening and engineering in human pluripotent stem cells

2017 ◽  
Author(s):  
Robert J. Ihry ◽  
Kathleen A. Worringer ◽  
Max R. Salick ◽  
Elizabeth Frias ◽  
Daniel Ho ◽  
...  
Keyword(s):  
Stem Cells ◽  
Pluripotent Stem Cells ◽  
Genome Engineering ◽  
High Efficiency ◽  
Cell Types ◽  
Human Pluripotent Stem Cells ◽  
Double Strand Breaks ◽  
Toxic Response ◽  
Strand Breaks ◽  
Genome Wide

SUMMARYCRISPR/Cas9 has revolutionized our ability to engineer genomes and to conduct genome-wide screens in human cells. While some cell types are easily modified with Cas9, human pluripotent stem cells (hPSCs) poorly tolerate Cas9 and are difficult to engineer. Using a stable Cas9 cell line or transient delivery of ribonucleoproteins (RNPs) we achieved an average insertion or deletion efficiency greater than 80%. This high efficiency made it apparent that double strand breaks (DSBs) induced by Cas9 are toxic and kill most treated hPSCs. Cas9 toxicity creates an obstacle to the high-throughput use CRISPR/Cas9 for genome-engineering and screening in hPSCs. We demonstrated the toxic response istp53-dependent and the toxic effect oftp53severely reduces the efficiency of precise genome-engineering in hPSCs. Our results highlight that CRISPR-based therapies derived from hPSCs should proceed with caution. Following engineering, it is critical to monitor fortp53function, especially in hPSCs which spontaneously acquiretp53mutations.

scholarly journals Multiplexed and Inducible Gene Modulation in Human Pluripotent Stem Cells by CRISPR Interference and Activation

2019 ◽  
Author(s):  
Dane Z. Hazelbaker ◽  
Amanda Beccard ◽  
Patrizia Mazzucato ◽  
Gabriella Angelini ◽  
Angelica Messana ◽  
...  
Keyword(s):  
Stem Cells ◽  
Pluripotent Stem Cells ◽  
Genome Engineering ◽  
Human Pluripotent Stem Cells ◽  
Guide Rna ◽  
Genome Wide ◽  
Cas9 Nuclease ◽  
Genomic Studies ◽  
A Cell ◽  
Accurate Quantification

ABSTRACTCRISPR-Cas9-mediated gene interference (CRISPRi) and activation (CRISPRa) approaches hold promise for functional genomic studies and genome-wide screens in human pluripotent stem cells (hPSCs). However, in contrast to CRISPR-Cas9 nuclease approaches, the efficiency of CRISPRi/a depends on continued expression of the dead Cas9 (dCas9) effector and guide RNA (gRNA), which can vary substantially depending on transgene design and delivery. Here, we design new fluorescently labeledpiggyBac(PB) vectors to deliver robust and stable expression of multiplexed gRNAs. In addition, we generate hPSC lines harboring AAVS1-integrated, inducible and fluorescent dCas9-KRAB and dCas9-VPR transgenes to allow for accurate quantification and tracking of cells that express both the dCas9 effectors and gRNAs. We then employ these systems to target theTCF4gene and conduct a rigorous assessment of expression levels of the dCas9 effectors, gRNAs and targeted gene. Collectively, these data provide proof-of-principle application of a stable, multiplexed PB gRNA delivery system that can be widely exploited to further enable genome engineering studies in hPSCs. Paired with diverse CRISPR tools including our dual fluorescence CRISPRi/a cell lines, this system would facilitate functional dissection of individual genes and pathways as well as larger-scale screens for studies of development and disease.

Parallel generation of easily selectable multiple nephronal cell types from human pluripotent stem cells

2018 ◽  
Vol 76 (1) ◽  
pp. 179-192 ◽  
Author(s):  
Krithika Hariharan ◽  
Harald Stachelscheid ◽  
Bella Rossbach ◽  
Su-Jun Oh ◽  
Nancy Mah ◽  
...  
Keyword(s):  
Stem Cells ◽  
Pluripotent Stem Cells ◽  
Cell Types ◽  
Human Pluripotent Stem Cells

Identification of stable reference genes in differentiating human pluripotent stem cells

2015 ◽  
Vol 47 (6) ◽  
pp. 232-239 ◽  
Author(s):  
Gustav Holmgren ◽  
Nidal Ghosheh ◽  
Xianmin Zeng ◽  
Yalda Bogestål ◽  
Peter Sartipy ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stem Cells ◽  
Gene Expression Data ◽  
Pluripotent Stem Cells ◽  
Reference Genes ◽  
Cell Types ◽  
Human Pluripotent Stem Cells ◽  
Expression Data ◽  
Large Variability ◽  
The Stability

Reference genes, often referred to as housekeeping genes (HKGs), are frequently used to normalize gene expression data based on the assumption that they are expressed at a constant level in the cells. However, several studies have shown that there may be a large variability in the gene expression levels of HKGs in various cell types. In a previous study, employing human embryonic stem cells (hESCs) subjected to spontaneous differentiation, we observed that the expression of commonly used HKG varied to a degree that rendered them inappropriate to use as reference genes under those experimental settings. Here we present a substantially extended study of the HKG signature in human pluripotent stem cells (hPSC), including nine global gene expression datasets from both hESC and human induced pluripotent stem cells, obtained during directed differentiation toward endoderm-, mesoderm-, and ectoderm derivatives. Sets of stably expressed genes were compiled, and a handful of genes (e.g., EID2, ZNF324B, CAPN10, and RABEP2) were identified as generally applicable reference genes in hPSCs across all cell lines and experimental conditions. The stability in gene expression profiles was confirmed by reverse transcription quantitative PCR analysis. Taken together, the current results suggest that differentiating hPSCs have a distinct HKG signature, which in some aspects is different from somatic cell types, and underscore the necessity to validate the stability of reference genes under the actual experimental setup used. In addition, the novel putative HKGs identified in this study can preferentially be used for normalization of gene expression data obtained from differentiating hPSCs.

scholarly journals Modulating cell state to enhance suspension expansion of human pluripotent stem cells

2018 ◽  
Vol 115 (25) ◽  
pp. 6369-6374 ◽  
Author(s):  
Yonatan Y. Lipsitz ◽  
Curtis Woodford ◽  
Ting Yin ◽  
Jacob H. Hanna ◽  
Peter W. Zandstra
Keyword(s):  
Stem Cells ◽  
Pluripotent Stem Cells ◽  
Large Scale ◽  
Cell Types ◽  
Human Pluripotent Stem Cells ◽  
The Body ◽  
Altered Expression ◽  
Pancreatic Progenitors ◽  
Erk Inhibition

The development of cell-based therapies to replace missing or damaged tissues within the body or generate cells with a unique biological activity requires a reliable and accessible source of cells. Human pluripotent stem cells (hPSC) have emerged as a strong candidate cell source capable of extended propagation in vitro and differentiation to clinically relevant cell types. However, the application of hPSC in cell-based therapies requires overcoming yield limitations in large-scale hPSC manufacturing. We explored methods to convert hPSC to alternative states of pluripotency with advantageous bioprocessing properties, identifying a suspension-based small-molecule and cytokine combination that supports increased single-cell survival efficiency, faster growth rates, higher densities, and greater expansion than control hPSC cultures. ERK inhibition was found to be essential for conversion to this altered state, but once converted, ERK inhibition led to a loss of pluripotent phenotype in suspension. The resulting suspension medium formulation enabled hPSC suspension yields 5.7 ± 0.2-fold greater than conventional hPSC in 6 d, for at least five passages. Treated cells remained pluripotent, karyotypically normal, and capable of differentiating into all germ layers. Treated cells could also be integrated into directed differentiated strategies as demonstrated by the generation of pancreatic progenitors (NKX6.1+/PDX1+ cells). Enhanced suspension-yield hPSC displayed higher oxidative metabolism and altered expression of adhesion-related genes. The enhanced bioprocess properties of this alternative pluripotent state provide a strategy to overcome cell manufacturing limitations of hPSC.

scholarly journals Genome-wide Screen for Culture Adaptation and Tumorigenicity-Related Genes in Human Pluripotent Stem Cells

iScience ◽  
2019 ◽  
Vol 11 ◽  
pp. 398-408 ◽  
Author(s):  
Uri Weissbein ◽  
Mordecai Peretz ◽  
Omer Plotnik ◽  
Ofra Yanuka ◽  
Ido Sagi ◽  
...  
Keyword(s):  
Stem Cells ◽  
Pluripotent Stem Cells ◽  
Human Pluripotent Stem Cells ◽  
Culture Adaptation ◽  
Genome Wide

scholarly journals The Opportunities and Challenges regarding Induced Platelets from Human Pluripotent Stem Cells

2021 ◽  
Vol 2021 ◽  
pp. 1-10
Author(s):  
Meng-Xue Xu ◽  
Li-Ping Liu ◽  
Yu-Mei Li ◽  
Yun-Wen Zheng
Keyword(s):  
Stem Cells ◽  
Clinical Application ◽  
Pluripotent Stem Cells ◽  
High Efficiency ◽  
Storage Temperature ◽  
Scale Up ◽  
Human Pluripotent Stem Cells ◽  
Scale Production ◽  
Platelet Production ◽  
Platelet Transfusions

As a standard clinical treatment, platelet transfusion has been employed to prevent hemorrhage in patients with thrombocytopenia or platelet dysfunctions. Platelets also show therapeutic potential for aiding liver regeneration and bone healing and regeneration and for treating dermatological conditions. However, the supply of platelets rarely meets the rising clinical demand. Other issues, including short shelf life, strict storage temperature, and allogeneic immunity caused by frequent platelet transfusions, have become serious challenges that require the development of high-yielding alternative sources of platelets. Human pluripotent stem cells (hPSCs) are an unlimited substitution source for regenerative medicine, and patient-derived iPSCs can provide novel research models to explore the pathogenesis of some diseases. Many studies have focused on establishing and modifying protocols for generating functional induced platelets (iPlatelets) from hPSCs. To reach high efficiency production and eliminate the exogenous antigens, media supplements and matrix have been optimized. In addition, the introduction of some critical transgenes, such as c-MYC, BMI1, and BCL-XL, can also significantly increase hPSC-derived platelet production; however, this may pose some safety concerns. Furthermore, many novel culture systems have been developed to scale up the production of iPlatelets, including 2D flow systems, 3D rotary systems, and vertical reciprocal motion liquid culture bioreactors. The development of new gene-editing techniques, such as CRISPR/Cas9, can be used to solve allogeneic immunity of platelet transfusions by knocking out the expression of B2M. Additionally, the functions of iPlatelets were also evaluated from multiple aspects, including but not limited to morphology, structure, cytoskeletal organization, granule content, DNA content, and gene expression. Although the production and functions of iPlatelets are close to meeting clinical application requirements in both quantity and quality, there is still a long way to go for their large-scale production and clinical application. Here, we summarize the diverse methods of platelet production and update the progresses of iPlatelets. Furthermore, we highlight recent advances in our understanding of key transcription factors or molecules that determine the platelet differentiation direction.

scholarly journals Generation of CD34+CD43+ hematopoietic progenitors to induce thymocytes from human pluripotent stem cells

2021 ◽  
Author(s):  
Lea Flippe ◽  
Anne Gaignerie ◽  
Celine Serazin ◽  
Olivier Baron ◽  
Xavier Saulquin ◽  
...  
Keyword(s):  
Stem Cells ◽  
T Cells ◽  
Pluripotent Stem Cells ◽  
High Efficiency ◽  
Embryonic Stem ◽  
Human Pluripotent Stem Cells ◽  
Blood Type ◽  
Hematopoietic Stem ◽  
Similar Profile

Immunotherapy using primary T cells has revolutionized medical care in some pathologies in recent years but limitations associated to challenging cell genome edition, insufficient cell number production, the use of only autologous cells and lack of product standardization have limited its uses in the clinic. The alternative use of T cells generated in vitro from human pluripotent stem cells (hPSCs) offers great advantages by providing a self-renewing source of T cells that can be readily genetically modified and facilitate the use of standardized universal off-the-shelf allogeneic cell products and rapid clinic access. However, despite their potential, the feasibility and functionality of T-cells differentiated from hPSCs needs better comprehension before moving to the clinic. In this study, we generated human induced pluripotent stem cells from T-cells (T-iPSCs) allowing preservation of already recombined TCR, with the same properties as human embryonic stem cells (hESCs). Based on these cells, we differentiated with high efficiency hematopoietic progenitor stem cells (HPSCs), capable of self-renewal and differentiation into any cell blood type, and then DN3a thymic progenitors from several T-iPSC lines. To better comprehend differentiation, we analyzed the transcriptomic profiles of the different cell types and demonstrated that HPSCs differentiated from hiPSCs had a very similar profile to cord blood hematopoietic stem cells (HSCs). Furthermore, differentiated T-cell progenitors had a similar profile to thymocytes at the DN3a stage of thymic lymphopoiesis. Therefore, with this approach, we were able to regenerate precursors of therapeutic human T cells to potentially treat a wide number of diseases.

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