Methods in enzymology
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Methods in enzymology · Jan 2014
The iCRISPR platform for rapid genome editing in human pluripotent stem cells.
Human pluripotent stem cells (hPSCs) have the potential to generate all adult cell types, including rare or inaccessible human cell populations, thus providing a unique platform for disease studies. To realize this promise, it is essential to develop methods for efficient genetic manipulations in hPSCs. Established using TALEN (transcription activator-like effector nuclease) and CRISPR (clustered regularly interspaced short palindromic repeats)/Cas (CRISPR-associated) systems, the iCRISPR platform supports a variety of genome-engineering approaches with high efficiencies. ⋯ We have successfully used these protocols in four different hPSC lines, including human embryonic stem cells and induced pluripotent stem cells. Once the iCRISPR platform is established, clonal lines with desired genetic modifications can be established in as little as 1 month. The methods described here enable a wide range of genome-engineering applications in hPSCs, thus providing a valuable resource for the creation of diverse hPSC-based disease models with superior speed and ease.
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Methods in enzymology · Jan 2014
Methods to monitor ROS production by fluorescence microscopy and fluorometry.
Mitochondria are considered one of the main sources of reactive oxygen species (ROS). The overgeneration of ROS can evoke an intracellular state of oxidative stress, leading to permanent cell damage. ⋯ Here, we describe the use of chemical probes for the rapid detection of ROS in intact and permeabilized adherent cells by fluorescence microscopy and fluorometry. Moreover, after discussing the limitations described in the literature for the fluorescent probes presented herein, we recommend methods to assess the production of specific ROS in various fields of investigation, including the study of oncometabolism.
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Methods in enzymology · Jan 2014
Targeted genome editing in human cells using CRISPR/Cas nucleases and truncated guide RNAs.
CRISPR RNA-guided nucleases have recently emerged as a robust genome-editing platform that functions in a wide range of organisms. To reduce off-target effects of these nucleases, we developed and validated a modified system that uses truncated guide RNAs (tru-gRNAs). The use of tru-gRNAs leads to decreases in off-target effects and does not generally compromise the on-target efficiencies of these genome-editing nucleases. In this chapter, we describe guidelines for identifying potential tru-gRNA target sites and protocols for measuring the on-target efficiencies of CRISPR RNA-guided nucleases in human cells.
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Methods in enzymology · Jan 2014
3-D adipocyte differentiation and peri-adipocyte collagen turnover.
Peri-adipocyte extracellular matrix (ECM) remodeling is a key biological process observed during adipose tissue development and expansion. The genetic loss of a pericellular collagenase, MMP14 (also known as MT1-MMP), renders mice lipodystrophic with the accumulation of undigested collagen fibers in adipose tissues. ⋯ Studying adipogenesis in 3-D may serve as an effective experimental approach to bridge gaps in our understanding of in vivo adipocyte biology. Moreover, by assessing the content of collagen family members and their rate of degradation in adipose tissues, we should be able to better define the role of dynamic ECM remodeling in the pathogenesis of obesity and diabetes.
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Methods in enzymology · Jan 2012
Clinical TrialLentiviral hematopoietic cell gene therapy for X-linked adrenoleukodystrophy.
X-linked adrenoleukodystrophy (X-ALD) is a severe genetic demyelinating disease caused by a deficiency in ALD protein, an adenosine triphosphate-binding cassette transporter encoded by the ABCD1 gene. When performed at an early stage of the disease, allogeneic hematopoietic stem cell transplantation (HCT) can arrest the progression of cerebral demyelinating lesions. To overcome the limitations of allogeneic HCT, hematopoietic stem cell (HSC) gene therapy strategy aiming to perform autologous transplantation of lentivirally corrected cells was developed. ⋯ There was no evidence of clonal dominance or skewing based on the retrieval of lentiviral insertion repertoire in different hematopoietic lineages by deep sequencing. Cerebral demyelination was arrested 14 and 16months, respectively, in the two treated patients, without further progression up to the last follow-up, a clinical outcome that is comparable to that observed after allogeneic HCT. Longer follow-up of these two treated patients and HSC gene therapy performed in additional ALD patients are however needed to evaluate the safety and efficacy of lentiviral HSC gene therapy in cerebral forms of X-ALD.