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Hammad R, Alzubi J, Rhiel M, Chmielewski KO, Mosti L, Rositzka J, Heugel M, Lawrenz J, Pennucci V, Gläser B, Fischer J, Schambach A, Moritz T, Lachmann N, Cornu TI, Mussolino C, Schäfer R, Cathomen T. CRISPR-Cas12a for Highly Efficient and Marker-Free Targeted Integration in Human Pluripotent Stem Cells. Int J Mol Sci 2024; 25:985. [PMID: 38256061 PMCID: PMC10816062 DOI: 10.3390/ijms25020985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 01/04/2024] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
The CRISPR-Cas12a platform has attracted interest in the genome editing community because the prototypical Acidaminococcus Cas12a generates a staggered DNA double-strand break upon binding to an AT-rich protospacer-adjacent motif (PAM, 5'-TTTV). The broad application of the platform in primary human cells was enabled by the development of an engineered version of the natural Cas12a protein, called Cas12a Ultra. In this study, we confirmed that CRISPR-Cas12a Ultra ribonucleoprotein complexes enabled allelic gene disruption frequencies of over 90% at multiple target sites in human T cells, hematopoietic stem and progenitor cells (HSPCs), and induced pluripotent stem cells (iPSCs). In addition, we demonstrated, for the first time, the efficient knock-in potential of the platform in human iPSCs and achieved targeted integration of a GFP marker gene into the AAVS1 safe harbor site and a CSF2RA super-exon into CSF2RA in up to 90% of alleles without selection. Clonal analysis revealed bi-allelic integration in >50% of the screened iPSC clones without compromising their pluripotency and genomic integrity. Thus, in combination with the adeno-associated virus vector system, CRISPR-Cas12a Ultra provides a highly efficient genome editing platform for performing targeted knock-ins in human iPSCs.
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Affiliation(s)
- Ruba Hammad
- Institute for Transfusion Medicine and Gene Therapy, Medical Center—University of Freiburg, 79106 Freiburg, Germany; (R.H.); (J.A.); (M.R.); (K.O.C.); (L.M.); (J.R.); (M.H.); (V.P.); (T.I.C.); (C.M.); (R.S.)
- Center for Chronic Immunodeficiency (CCI), Medical Center—University of Freiburg, 79106 Freiburg, Germany
- Freiburg iPS Core Facility, Medical Center—University of Freiburg, 79106 Freiburg, Germany
- PhD Program, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Jamal Alzubi
- Institute for Transfusion Medicine and Gene Therapy, Medical Center—University of Freiburg, 79106 Freiburg, Germany; (R.H.); (J.A.); (M.R.); (K.O.C.); (L.M.); (J.R.); (M.H.); (V.P.); (T.I.C.); (C.M.); (R.S.)
- Center for Chronic Immunodeficiency (CCI), Medical Center—University of Freiburg, 79106 Freiburg, Germany
| | - Manuel Rhiel
- Institute for Transfusion Medicine and Gene Therapy, Medical Center—University of Freiburg, 79106 Freiburg, Germany; (R.H.); (J.A.); (M.R.); (K.O.C.); (L.M.); (J.R.); (M.H.); (V.P.); (T.I.C.); (C.M.); (R.S.)
- Center for Chronic Immunodeficiency (CCI), Medical Center—University of Freiburg, 79106 Freiburg, Germany
| | - Kay O. Chmielewski
- Institute for Transfusion Medicine and Gene Therapy, Medical Center—University of Freiburg, 79106 Freiburg, Germany; (R.H.); (J.A.); (M.R.); (K.O.C.); (L.M.); (J.R.); (M.H.); (V.P.); (T.I.C.); (C.M.); (R.S.)
- Center for Chronic Immunodeficiency (CCI), Medical Center—University of Freiburg, 79106 Freiburg, Germany
- PhD Program, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Laura Mosti
- Institute for Transfusion Medicine and Gene Therapy, Medical Center—University of Freiburg, 79106 Freiburg, Germany; (R.H.); (J.A.); (M.R.); (K.O.C.); (L.M.); (J.R.); (M.H.); (V.P.); (T.I.C.); (C.M.); (R.S.)
- Center for Chronic Immunodeficiency (CCI), Medical Center—University of Freiburg, 79106 Freiburg, Germany
| | - Julia Rositzka
- Institute for Transfusion Medicine and Gene Therapy, Medical Center—University of Freiburg, 79106 Freiburg, Germany; (R.H.); (J.A.); (M.R.); (K.O.C.); (L.M.); (J.R.); (M.H.); (V.P.); (T.I.C.); (C.M.); (R.S.)
- Center for Chronic Immunodeficiency (CCI), Medical Center—University of Freiburg, 79106 Freiburg, Germany
| | - Marcel Heugel
- Institute for Transfusion Medicine and Gene Therapy, Medical Center—University of Freiburg, 79106 Freiburg, Germany; (R.H.); (J.A.); (M.R.); (K.O.C.); (L.M.); (J.R.); (M.H.); (V.P.); (T.I.C.); (C.M.); (R.S.)
- Center for Chronic Immunodeficiency (CCI), Medical Center—University of Freiburg, 79106 Freiburg, Germany
| | - Jan Lawrenz
- Institute for Transfusion Medicine and Gene Therapy, Medical Center—University of Freiburg, 79106 Freiburg, Germany; (R.H.); (J.A.); (M.R.); (K.O.C.); (L.M.); (J.R.); (M.H.); (V.P.); (T.I.C.); (C.M.); (R.S.)
- Center for Chronic Immunodeficiency (CCI), Medical Center—University of Freiburg, 79106 Freiburg, Germany
| | - Valentina Pennucci
- Institute for Transfusion Medicine and Gene Therapy, Medical Center—University of Freiburg, 79106 Freiburg, Germany; (R.H.); (J.A.); (M.R.); (K.O.C.); (L.M.); (J.R.); (M.H.); (V.P.); (T.I.C.); (C.M.); (R.S.)
- Center for Chronic Immunodeficiency (CCI), Medical Center—University of Freiburg, 79106 Freiburg, Germany
| | - Birgitta Gläser
- Institute of Human Genetics, Medical Center—University of Freiburg, 79106 Freiburg, Germany; (B.G.); (J.F.)
| | - Judith Fischer
- Institute of Human Genetics, Medical Center—University of Freiburg, 79106 Freiburg, Germany; (B.G.); (J.F.)
- Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Axel Schambach
- Institute for Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; (A.S.); (T.M.)
- REBIRTH Center for Regenerative and Translational Medicine, Hannover Medical School, 30625 Hannover, Germany;
| | - Thomas Moritz
- Institute for Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; (A.S.); (T.M.)
- REBIRTH Center for Regenerative and Translational Medicine, Hannover Medical School, 30625 Hannover, Germany;
| | - Nico Lachmann
- REBIRTH Center for Regenerative and Translational Medicine, Hannover Medical School, 30625 Hannover, Germany;
- Department of Pediatric Pulmonology, Allergology and Neonatology, Hannover Medical School, 30625 Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease, German Center for Lung Research, Hannover Medical School, 30625 Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, 30625 Hannover, Germany
- Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), 30625 Hannover, Germany
| | - Tatjana I. Cornu
- Institute for Transfusion Medicine and Gene Therapy, Medical Center—University of Freiburg, 79106 Freiburg, Germany; (R.H.); (J.A.); (M.R.); (K.O.C.); (L.M.); (J.R.); (M.H.); (V.P.); (T.I.C.); (C.M.); (R.S.)
- Center for Chronic Immunodeficiency (CCI), Medical Center—University of Freiburg, 79106 Freiburg, Germany
- Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Claudio Mussolino
- Institute for Transfusion Medicine and Gene Therapy, Medical Center—University of Freiburg, 79106 Freiburg, Germany; (R.H.); (J.A.); (M.R.); (K.O.C.); (L.M.); (J.R.); (M.H.); (V.P.); (T.I.C.); (C.M.); (R.S.)
- Center for Chronic Immunodeficiency (CCI), Medical Center—University of Freiburg, 79106 Freiburg, Germany
- Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Richard Schäfer
- Institute for Transfusion Medicine and Gene Therapy, Medical Center—University of Freiburg, 79106 Freiburg, Germany; (R.H.); (J.A.); (M.R.); (K.O.C.); (L.M.); (J.R.); (M.H.); (V.P.); (T.I.C.); (C.M.); (R.S.)
- Center for Chronic Immunodeficiency (CCI), Medical Center—University of Freiburg, 79106 Freiburg, Germany
- Freiburg iPS Core Facility, Medical Center—University of Freiburg, 79106 Freiburg, Germany
- Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Medical Center—University of Freiburg, 79106 Freiburg, Germany; (R.H.); (J.A.); (M.R.); (K.O.C.); (L.M.); (J.R.); (M.H.); (V.P.); (T.I.C.); (C.M.); (R.S.)
- Center for Chronic Immunodeficiency (CCI), Medical Center—University of Freiburg, 79106 Freiburg, Germany
- Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
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Validation of Promoters and Codon Optimization on CRISPR/Cas9-Engineered Jurkat Cells Stably Expressing αRep4E3 for Interfering with HIV-1 Replication. Int J Mol Sci 2022; 23:ijms232315049. [PMID: 36499376 PMCID: PMC9738563 DOI: 10.3390/ijms232315049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 11/15/2022] [Accepted: 11/27/2022] [Indexed: 12/05/2022] Open
Abstract
Persistent and efficient therapeutic protein expression in the specific target cell is a significant concern in gene therapy. The controllable integration site, suitable promoter, and proper codon usage influence the effectiveness of the therapeutic outcome. Previously, we developed a non-immunoglobulin scaffold, alpha repeat protein (αRep4E3), as an HIV-1 RNA packaging interference system in SupT1 cells using the lentiviral gene transfer. Although the success of anti-HIV-1 activity was evidenced, the integration site is uncontrollable and may not be practical for clinical translation. In this study, we use the CRISPR/Cas9 gene editing technology to precisely knock-in αRep4E3 genes into the adeno-associated virus integration site 1 (AAVS1) safe harbor locus of the target cells. We compare the αRep4E3 expression under the regulation of three different promoters, including cytomegalovirus (CMV), human elongation factor-1 alpha (EF1α), and ubiquitin C (UbC) promoters with and without codon optimization in HEK293T cells. The results demonstrated that the EF1α promoter with codon-optimized αRep4E3mCherry showed higher protein expression than other promoters with non-optimized codons. We then performed a proof-of-concept study by knocking in the αRep4E3mCherry gene at the AAVS1 locus of the Jurkat cells. The results showed that the αRep4E3mCherry-expressing Jurkat cells exhibited anti-HIV-1 activities against HIV-1NL4-3 strain as evidenced by decreased capsid (p24) protein levels and viral genome copies as compared to the untransfected Jurkat control cells. Altogether, our study demonstrates that the αRep4E3 could interfere with the viral RNA packaging and suggests that the αRep4E3 scaffold protein could be a promising anti-viral molecule that offers a functional cure for people living with HIV-1.
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