Genome Editing Procedure Research Articles

CRISPR/Cas9-Mediated Knockin Application in Cell Therapy: A Non-viral Procedure for Bystander Treatment of Glioma in Mice.

The use of non-viral procedures, together with CRISPR/Cas9 genome-editing technology, allows the insertion of single-copy therapeutic genes at pre-determined genomic sites, overcoming safety limitations resulting from random gene insertions of viral vectors with potential for genome damage. In this study, we demonstrate that combination of non-viral gene delivery and CRISPR/Cas9-mediated knockin via homology-directed repair can replace the use of viral vectors for the generation of genetically modified therapeutic cells. We custom-modified human adipose mesenchymal stem cells (hAMSCs), using electroporation as a transfection method and CRISPR/Cas9-mediated knockin for the introduction and stable expression of a 3 kb DNA fragment including the eGFP (selectable marker) and a variant of the herpes simplex virus 1 thymidine kinase genes (therapeutic gene), under the control of the human elongation factor 1 alpha promoter in exon 5 of the endogenous thymidine kinase 2 gene. Using a U87 glioma model in SCID mice, we show that the therapeutic capacity of the new CRISPR/Cas9-engineered hAMSCs is equivalent to that of therapeutic hAMSCs generated by introduction of the same therapeutic gene by transduction with a lentiviral vector previously published by our group. This strategy should be of general use to other applications requiring genetic modification of therapeutic cells.

Genome Editing in Mouse Zygotes and Embryonic Stem Cells by Introducing SgRNA/Cas9 Expressing Plasmids.

In mammalian cells, genome editing with the single guide RNA (sgRNA)/Cas9 complex allows for high targeting efficiency within a relatively short time frame with the added benefits of being low cost and easy to design. sgRNA/Cas9-mediated editing in mouse zygotes has accelerated the analysis of gene functions and the generation of mouse models of human diseases. Despite the benefits, this method still suffers from several problems, such as mosaicism in the founder generation which complicates genotyping and phenotypical analyses, and the low efficiency of more complicated genome editing. Thus, we recently established the system for genome editing in embryonic stem (ES) cells and its application for chimeric analysis in mice. In this section, we introduce the procedure for genome editing in mouse zygotes and ES cells.

Preservation of Gene Edited Hematopoietic Stem Cells By Transient Overexpression of BCL-2 mRNA

Introduction: Site-specific gene correction of the point mutation causing sickle cell disease (SCD) in hematopoietic stem cells (HSCs) constitutes a precise strategy to generate a life-long source of gene-corrected erythrocytes that do not sickle. However, low efficiency of homology-directed repair (HDR) in primitive reconstituting HSCs is currently a limit to the use of therapeutic genome editing for treatment of severe genetic blood disorders. To identify the mechanism(s) that underlie decreased HDR efficacy in primitive HSCs relative to that in more mature progenitor populations, we assessed: efficiency of gene delivery and expression after electroporation of in vitro transcribed mRNA; functional ZFN-mediated endonuclease activity; cell cycle status; gene expression of key HDR genes; and cytotoxic responses; in the following immunophenotypically-defined human cell populations: HSCs (CD34+/CD38-/CD90+CD45RA-); multipotent progenitors (MPPs) (CD34+/CD38-/CD45RA-/CD90-); and progenitor cells (CD34+/CD38+).Methods: CD34+ cells were enriched from human G-CSF-mobilized peripheral blood and cultured for 1-3 days prior to electroporation of in vitro transcribed mRNA encoding GFP or a pair of zinc finger nucleases (ZFN). The ZFNs, designed to target the sickle mutation in exon 1 of the human beta-globin gene, were co-delivered with one of the homologous donor templates containing the corrective base (A/T): an integrase-deficient lentiviral vector (IDLV) or a 101bp single-stranded oligodeoxynucleotide (oligo). Percentages of alleles containing insertions/deletions (indels) and/or HDR-mediated gene correction were analyzed by high throughput sequencing (HTS). Acute cytotoxicity was determined by flow cytometry, identifying viable cells as 7AAD/AnnexinV neg. cells. To assess HDR-mediated gene correction in vivo after three months, gene-edited cells were transplanted (>1E6 viable CD34+ cells/mouse, I.V.) one day after electroporation into irradiated (250cGy) NOD/SCID/IL2R gamma-/- (NSG) mice.Results: In HSCs, MPPs and progenitor populations, no differences were observed in delivery and expression from electroporated GFP mRNA [%GFP(+) and MFI]. To assess the activity of ZFN mRNA in the stem and progenitor populations, ZFNs were delivered to CD34+ cells through electroporation of in vitrotranscribed mRNA. The CD34+ cells were then FACS-sorted into the respective populations and HTS was used to determine the percentage of alleles containing indels; the frequencies of indels were equivalent among the populations indicating equivalent ZFN mRNA activity. To evaluate the efficacy of site-specific HDR in HSCs and progenitor cells, ZFN mRNA was co-delivered with either an IDLV or an oligodeoxynucleotide donor template to modify the single base-pair involved in SCD. We observed lower percentage of HDR-mediated gene modification in the HSC population compared to progenitors with all donor templates.Due to the cell cycle phase restriction of HDR, we pre-stimulated CD34+ cells for 1-3 days prior to electroporation of ZFN mRNA and the oligo donor, and analyzed the cell cycle phases at the time of electroporation, and the frequencies of HDR and NHEJ produced by HTS. Only a small percentage of the immunophenotypic HSCs were in S/G2 phase after 24 hours of pre-stimulation; no HDR modification was observed in these cells. After 2-3 days of pre-stimulation, the HDR levels increased as the percentage of HSCs in S/G2 phase reached 20%. Importantly, assessment of relative cytotoxicity of the genome editing procedure (electroporation of ZFN mRNA and oligo donor) revealed a heightened sensitivity of HSCs/MPPs compared to progenitors, resulting in ~80% cell death in HSC vs. ~30% in progenitors under the conditions we are using. Transient expression of BCL-2 mRNA, co-electroporated with the genome editing reagents, improved HSC survival and significantly increased the numbers of HDR gene-corrected HSCs both in vitro and in vivo.Conclusions: These data indicate an elevated sensitivity to cytotoxicity from the gene editing process for HSCs compared to the mature progenitor cells under our conditions, which may explain the lower levels of gene modification seen using in vivo compared to in vitro assays. Transient overexpression of BCL-2 mRNA preserves HSC survival after HDR-based gene editing, increasing the frequency of gene-corrected HSCs. DisclosuresBjurström:UCLA: Patents & Royalties: 2016-290. Holmes:Sangamo BioSciences Inc: Employment.

Development of a fast and easy method for Escherichia coli genome editing with CRISPR/Cas9.

BackgroundMicrobial genome editing is a powerful tool to modify chromosome in way of deletion, insertion or replacement, which is one of the most important techniques in metabolic engineering research. The emergence of CRISPR/Cas9 technique inspires various genomic editing methods.ResultsIn this research, the goal of development of a fast and easy method for Escherichia coli genome editing with high efficiency is pursued. For this purpose, we designed modular plasmid assembly strategy, compared effects of different length of homologous arms for recombination, and tested different sets of recombinases. The final technique we developed only requires one plasmid construction and one transformation of practice to edit a genomic locus with 3 days and minimal lab work. In addition, the single temperature sensitive plasmid is easy to eliminate for another round of editing. Especially, process of the modularized editing plasmid construction only takes 4 h.ConclusionIn this study, we developed a fast and easy genome editing procedure based on CRISPR/Cas9 system that only required the work of one plasmid construction and one transformation, which allowed modification of a chromosome locus within 3 days and could be performed continuously for multiple loci.Electronic supplementary materialThe online version of this article (doi:10.1186/s12934-016-0605-5) contains supplementary material, which is available to authorized users.

Specific Destruction of HIV Proviral p17 Gene in T Lymphoid Cells Achieved by the Genome Editing Technology.

Recent development in genome editing technologies has enabled site-directed deprivation of a nucleotide sequence in the chromosome in mammalian cells. Human immunodeficiency (HIV) infection causes integration of proviral DNA into the chromosome, which potentially leads to re-emergence of the virus, but conventional treatment cannot delete the proviral DNA sequence from the cells infected with HIV. In the present study, the transcription activator-like effector nucleases (TALENs) specific for the HIV p17 gene were constructed, and their activities to destroy the target sequence were evaluated. SSA assay showed a high activity of a pair of p17-specific TALENs. A human T lymphoid cell line, Jurkat, was infected with a lentivirus vector followed by transfection with the TALEN–HIV by electroporation. The target sequence was destructed in approximately 10–95% of the p17 polymerase chain reaction clones, and the efficiencies depended on the Jurkat–HIV clones. Because p17 plays essential roles for assembly and budding of HIV, and this gene has relatively low nucleotide sequence diversity, genome editing procedures targeting p17 may provide a therapeutic benefit for HIV infection.

Development of an Efficient Genome Editing Method by CRISPR/Cas9 in a Fish Cell Line.

CRISPR/Cas9 system has been used widely in animals and plants to direct mutagenesis. To date, no such method exists for fish somatic cell lines. We describe an efficient procedure for genome editing in the Chinook salmon Oncorhynchus tshawytscha CHSE. This cell line was genetically modified to firstly overexpress a monomeric form of EGFP (cell line CHSE-E Geneticin resistant) and additionally to overexpress nCas9n, a nuclear version of Cas9 (cell line CHSE-EC, Hygromycin and Geneticin resistant). A pre-validated sgRNA was produced in vitro and used to transfect CHSE-EC cells. The EGFP gene was disrupted in 34.6 % of cells, as estimated by FACS and microscopy. The targeted locus was characterised by PCR amplification, cloning and sequencing of PCR products; inactivation of the EGFP gene by deletions in the expected site was validated in 25 % of clones. This method opens perspectives for functional genomic studies compatible with high-throughput screening.

A Method for Genome Editing in Human Pluripotent Stem Cells.

Human pluripotent stem cells (PSCs) hold great potential for regenerative medicine and currently are being used as a research tool for basic discovery and disease modeling. To evaluate the role of a single genetic variant, a system of genome editing is needed to precisely mutate any desired DNA sequence in isolation and measure its effect on phenotype when compared to the isogenic parental PSC from which it was derived. This protocol describes the general targeting schemes used by researchers to edit PSCs to knock out, knock-in, or precisely alter a single nucleotide, covering conditions for electroporation, clonal isolation, and screening of edited PSCs for the targeted mutation. These recent advances simplify the procedure for genome editing, allowing individual researchers to induce nearly any desired mutation to further study its function or to reverse a disease-causing variant for future applications in regenerative medicine.

Establishment of proprotein convertase, furinA knocked-out lines in medaka, Oryzias latipes, and unique form of medaka furin-like prorprotein convertase (mflPC)

Furin is a member of the subtilisin-like proprotein convertase family. Medaka furin-like proprotein convertase (mflPC), a unique form of medaka FurinA (mFurinA) (GenBank accession no. AB092685.1) was cloned from the ovary cDNA library. Compared to human furin (GenBank accession no. NM_002569.3) and mFurinA in the structural motif of mflPC, only the catalytic domain and the N-terminal region of the P domain are highly conserved, but more C-terminal domains are truncated. Based on our research, there three forms of furin, mFurinA, mflPC and mFurinB that exist in medaka. These three genes are expressed in the developing embryos and ubiquitously in adult tissues.To investigate the function of mFurinA and mflPC, as a first step, mFurinA KO lines were established. The mFurinA KO larvae with abnormal phenotypes exhibit edema, abnormal body fluid accumulation in the pericardial and yolk sacs, enlarged hearts, clogged blood vessels, structurally weak eyes, and a very short life. The data suggests that abnormal processing of TGF-β may be one of the causes of these disorders. FurinA KO medaka is a good model for the study of human diseases such as Fraser Syndrome and Marfan syndrome. The creation of human genomic disorder models using recently advanced genome editing procedures informs us of the function of key molecules and their role in causing equivalent human disorders and will be useful as a tool to identify the mechanisms involved.