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      Targeted Genome Editing in Human Repopulating Hematopoietic Stem Cells

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          Abstract

          Targeted genome editing by artificial nucleases has brought the goal of site-specific transgene integration and gene correction within the reach of gene therapy. However, its application to long-term repopulating Hematopoietic Stem Cells (HSCs) has remained elusive. Here we show that poor permissiveness to gene transfer and limited proficiency of the homology directed DNA repair pathway constrain gene targeting in human HSCs. By tailoring delivery platforms and culture conditions we overcame these barriers and provide stringent evidence of targeted integration in human HSCs by long-term multilineage repopulation of transplanted mice. We demonstrate the therapeutic potential of our strategy by targeting a corrective cDNA into the IL2RG gene of HSCs from healthy donors and a subject with X-linked Severe Combined Immunodeficiency (SCID-X1). Gene edited HSCs sustained normal hematopoiesis and gave rise to functional lymphoid cells that possess a selective growth advantage over those carrying disruptive IL2RG mutations. These results open new avenues for treating SCID-X1 and other diseases.

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          Aryl hydrocarbon receptor antagonists promote the expansion of human hematopoietic stem cells.

          Although practiced clinically for more than 40 years, the use of hematopoietic stem cell (HSC) transplants remains limited by the ability to expand these cells ex vivo. An unbiased screen with primary human HSCs identified a purine derivative, StemRegenin 1 (SR1), that promotes the ex vivo expansion of CD34+ cells. Culture of HSCs with SR1 led to a 50-fold increase in cells expressing CD34 and a 17-fold increase in cells that retain the ability to engraft immunodeficient mice. Mechanistic studies show that SR1 acts by antagonizing the aryl hydrocarbon receptor (AHR). The identification of SR1 and AHR modulation as a means to induce ex vivo HSC expansion should facilitate the clinical use of HSC therapy.
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            An improved zinc-finger nuclease architecture for highly specific genome editing.

            Genome editing driven by zinc-finger nucleases (ZFNs) yields high gene-modification efficiencies (>10%) by introducing a recombinogenic double-strand break into the targeted gene. The cleavage event is induced using two custom-designed ZFNs that heterodimerize upon binding DNA to form a catalytically active nuclease complex. Using the current ZFN architecture, however, cleavage-competent homodimers may also form that can limit safety or efficacy via off-target cleavage. Here we develop an improved ZFN architecture that eliminates this problem. Using structure-based design, we engineer two variant ZFNs that efficiently cleave DNA only when paired as a heterodimer. These ZFNs modify a native endogenous locus as efficiently as the parental architecture, but with a >40-fold reduction in homodimer function and much lower levels of genome-wide cleavage. This architecture provides a general means for improving the specificity of ZFNs as gene modification reagents.
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              IL-7 and IL-15 instruct the generation of human memory stem T cells from naive precursors.

              Long-living memory stem T cells (T(SCM)) with the ability to self-renew and the plasticity to differentiate into potent effectors could be valuable weapons in adoptive T-cell therapy against cancer. Nonetheless, procedures to specifically target this T-cell population remain elusive. Here, we show that it is possible to differentiate in vitro, expand, and gene modify in clinically compliant conditions CD8(+) T(SCM) lymphocytes starting from naive precursors. Requirements for the generation of this T-cell subset, described as CD62L(+)CCR7(+)CD45RA(+)CD45R0(+)IL-7Rα(+)CD95(+), are CD3/CD28 engagement and culture with IL-7 and IL-15. Accordingly, T(SCM) accumulates early after hematopoietic stem cell transplantation. The gene expression signature and functional phenotype define this population as a distinct memory T-lymphocyte subset, intermediate between naive and central memory cells. When transplanted in immunodeficient mice, gene-modified naive-derived T(SCM) prove superior to other memory lymphocytes for the ability to expand and differentiate into effectors able to mediate a potent xenogeneic GVHD. Furthermore, gene-modified T(SCM) are the only T-cell subset able to expand and mediate GVHD on serial transplantation, suggesting self-renewal capacity in a clinically relevant setting. These findings provide novel insights into the origin and requirements for T(SCM) generation and pave the way for their clinical rapid exploitation in adoptive cell therapy.
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                Author and article information

                Journal
                0410462
                6011
                Nature
                Nature
                Nature
                0028-0836
                1476-4687
                3 June 2014
                28 May 2014
                12 June 2014
                12 December 2014
                : 510
                : 7504
                : 235-240
                Affiliations
                [1 ]TIGET, San Raffaele Telethon Institute for Gene Therapy, San Raffaele Scientific Institute, Milan, Italy
                [2 ]Vita Salute San Raffaele University, Milan, Italy
                [3 ]Experimental Hematology Unit, San Raffaele Scientific Institute, Milan, Italy
                [4 ]Sangamo BioSciences Inc., Richmond, CA, United States.
                [5 ]Dept. of Immunology Erasmus MC, University Medical Center, Rotterdam, The Netherlands
                Author notes
                Correspondence to: naldini.luigi@ 123456hsr.it
                [¶]

                These Authors share senior authorship.

                Author Contributions: PG designed experiments, performed research, interpreted data and wrote the manuscript. GS and GE performed research and interpreted data. TDT performed mRNA production. CF characterized the corrective cDNA. AC and EM performed bioinformatics analysis of ZFN specificity. RM and DM developed the NSG human tumor rejection model. CB contributed to the T cell studies. MvdB provided SCID-X1 patient cells. MCH and PDG provided ZFNs, interpreted data and edited the manuscript. BG set up culture conditions for HSC maintenance. AL and LN designed and supervised research, interpreted data and wrote the manuscript. LN coordinated the study.

                [*]

                Present address: The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland 4102, Australia

                Article
                EMS58323
                10.1038/nature13420
                4082311
                24870228
                a47bded0-d470-45c1-82e4-65ace8a4ebc8
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