1
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Ou L, DeKelver RC, Rohde M, Tom S, Radeke R, St Martin SJ, Santiago Y, Sproul S, Przybilla MJ, Koniar BL, Podetz-Pedersen KM, Laoharawee K, Cooksley RD, Meyer KE, Holmes MC, McIvor RS, Wechsler T, Whitley CB. ZFN-Mediated In Vivo Genome Editing Corrects Murine Hurler Syndrome. Mol Ther 2018; 27:178-187. [PMID: 30528089 PMCID: PMC6319315 DOI: 10.1016/j.ymthe.2018.10.018] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 10/12/2018] [Accepted: 10/26/2018] [Indexed: 11/28/2022] Open
Abstract
Mucopolysaccharidosis type I (MPS I) is a severe disease due to deficiency of the lysosomal hydrolase α-L-iduronidase (IDUA) and the subsequent accumulation of the glycosaminoglycans (GAG), leading to progressive, systemic disease and a shortened lifespan. Current treatment options consist of hematopoietic stem cell transplantation, which carries significant mortality and morbidity risk, and enzyme replacement therapy, which requires lifelong infusions of replacement enzyme; neither provides adequate therapy, even in combination. A novel in vivo genome-editing approach is described in the murine model of Hurler syndrome. A corrective copy of the IDUA gene is inserted at the albumin locus in hepatocytes, leading to sustained enzyme expression, secretion from the liver into circulation, and subsequent uptake systemically at levels sufficient for correction of metabolic disease (GAG substrate accumulation) and prevention of neurobehavioral deficits in MPS I mice. This study serves as a proof-of-concept for this platform-based approach that should be broadly applicable to the treatment of a wide array of monogenic diseases.
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Affiliation(s)
- Li Ou
- Gene Therapy Center, University of Minnesota, Minneapolis, MN, USA
| | | | - Michelle Rohde
- Sangamo Therapeutics, Inc., 501 Canal Boulevard, Richmond, CA, USA
| | - Susan Tom
- Sangamo Therapeutics, Inc., 501 Canal Boulevard, Richmond, CA, USA
| | - Robert Radeke
- Sangamo Therapeutics, Inc., 501 Canal Boulevard, Richmond, CA, USA
| | | | - Yolanda Santiago
- Sangamo Therapeutics, Inc., 501 Canal Boulevard, Richmond, CA, USA
| | - Scott Sproul
- Sangamo Therapeutics, Inc., 501 Canal Boulevard, Richmond, CA, USA
| | - Michelle J Przybilla
- Center for Genome Engineering, Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Brenda L Koniar
- Research Animal Resources, University of Minnesota, Minneapolis, MN, USA
| | - Kelly M Podetz-Pedersen
- Center for Genome Engineering, Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Kanut Laoharawee
- Center for Genome Engineering, Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Renee D Cooksley
- Gene Therapy Center, University of Minnesota, Minneapolis, MN, USA
| | - Kathleen E Meyer
- Sangamo Therapeutics, Inc., 501 Canal Boulevard, Richmond, CA, USA
| | - Michael C Holmes
- Sangamo Therapeutics, Inc., 501 Canal Boulevard, Richmond, CA, USA
| | - R Scott McIvor
- Center for Genome Engineering, Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Thomas Wechsler
- Sangamo Therapeutics, Inc., 501 Canal Boulevard, Richmond, CA, USA
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2
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Laoharawee K, DeKelver RC, Podetz-Pedersen KM, Rohde M, Sproul S, Nguyen HO, Nguyen T, St Martin SJ, Ou L, Tom S, Radeke R, Meyer KE, Holmes MC, Whitley CB, Wechsler T, McIvor RS. Dose-Dependent Prevention of Metabolic and Neurologic Disease in Murine MPS II by ZFN-Mediated In Vivo Genome Editing. Mol Ther 2018; 26:1127-1136. [PMID: 29580682 PMCID: PMC6080131 DOI: 10.1016/j.ymthe.2018.03.002] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 01/31/2018] [Indexed: 12/16/2022] Open
Abstract
Mucopolysaccharidosis type II (MPS II) is an X-linked recessive lysosomal disorder caused by deficiency of iduronate 2-sulfatase (IDS), leading to accumulation of glycosaminoglycans (GAGs) in tissues of affected individuals, progressive disease, and shortened lifespan. Currently available enzyme replacement therapy (ERT) requires lifelong infusions and does not provide neurologic benefit. We utilized a zinc finger nuclease (ZFN)-targeting system to mediate genome editing for insertion of the human IDS (hIDS) coding sequence into a "safe harbor" site, intron 1 of the albumin locus in hepatocytes of an MPS II mouse model. Three dose levels of recombinant AAV2/8 vectors encoding a pair of ZFNs and a hIDS cDNA donor were administered systemically in MPS II mice. Supraphysiological, vector dose-dependent levels of IDS enzyme were observed in the circulation and peripheral organs of ZFN+donor-treated mice. GAG contents were markedly reduced in tissues from all ZFN+donor-treated groups. Surprisingly, we also demonstrate that ZFN-mediated genome editing prevented the development of neurocognitive deficit in young MPS II mice (6-9 weeks old) treated at high vector dose levels. We conclude that this ZFN-based platform for expression of therapeutic proteins from the albumin locus is a promising approach for treatment of MPS II and other lysosomal diseases.
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Affiliation(s)
- Kanut Laoharawee
- Center for Genome Engineering, Department of Genetics Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | | | - Kelly M Podetz-Pedersen
- Center for Genome Engineering, Department of Genetics Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Michelle Rohde
- Sangamo Therapeutics, Inc., 501 Canal Boulevard, Richmond, CA, USA
| | - Scott Sproul
- Sangamo Therapeutics, Inc., 501 Canal Boulevard, Richmond, CA, USA
| | | | - Tam Nguyen
- Center for Genome Engineering, Department of Genetics Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | | | - Li Ou
- Gene Therapy Center, Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
| | - Susan Tom
- Sangamo Therapeutics, Inc., 501 Canal Boulevard, Richmond, CA, USA
| | - Robert Radeke
- Sangamo Therapeutics, Inc., 501 Canal Boulevard, Richmond, CA, USA
| | - Kathleen E Meyer
- Sangamo Therapeutics, Inc., 501 Canal Boulevard, Richmond, CA, USA
| | - Michael C Holmes
- Sangamo Therapeutics, Inc., 501 Canal Boulevard, Richmond, CA, USA
| | - Chester B Whitley
- Gene Therapy Center, Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
| | - Thomas Wechsler
- Sangamo Therapeutics, Inc., 501 Canal Boulevard, Richmond, CA, USA
| | - R Scott McIvor
- Center for Genome Engineering, Department of Genetics Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA.
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3
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Komeno Y, Huang YJ, Qiu J, Lin L, Xu Y, Zhou Y, Chen L, Monterroza DD, Li H, DeKelver RC, Yan M, Fu XD, Zhang DE. SRSF2 Is Essential for Hematopoiesis, and Its Myelodysplastic Syndrome-Related Mutations Dysregulate Alternative Pre-mRNA Splicing. Mol Cell Biol 2015; 35:3071-82. [PMID: 26124281 PMCID: PMC4525309 DOI: 10.1128/mcb.00202-15] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 03/19/2015] [Accepted: 06/19/2015] [Indexed: 01/06/2023] Open
Abstract
Myelodysplastic syndromes (MDS) are a group of neoplasms characterized by ineffective myeloid hematopoiesis and various risks for leukemia. SRSF2, a member of the serine/arginine-rich (SR) family of splicing factors, is one of the mutation targets associated with poor survival in patients suffering from myelodysplastic syndromes. Here we report the biological function of SRSF2 in hematopoiesis by using conditional knockout mouse models. Ablation of SRSF2 in the hematopoietic lineage caused embryonic lethality, and Srsf2-deficient fetal liver cells showed significantly enhanced apoptosis and decreased levels of hematopoietic stem/progenitor cells. Induced ablation of SRSF2 in adult Mx1-Cre Srsf2(flox/flox) mice upon poly(I):poly(C) injection demonstrated a significant decrease in lineage(-) Sca(+) c-Kit(+) cells in bone marrow. To reveal the functional impact of myelodysplastic syndromes-associated mutations in SRSF2, we analyzed splicing responses on the MSD-L cell line and found that the missense mutation of proline 95 to histidine (P95H) and a P95-to-R102 in-frame 8-amino-acid deletion caused significant changes in alternative splicing. The affected genes were enriched in cancer development and apoptosis. These findings suggest that intact SRSF2 is essential for the functional integrity of the hematopoietic system and that its mutations likely contribute to development of myelodysplastic syndromes.
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Affiliation(s)
- Yukiko Komeno
- Moores UCSD Cancer Center, University of California, San Diego, La Jolla, California, USA
| | - Yi-Jou Huang
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Jinsong Qiu
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California, USA
| | - Leo Lin
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - YiJun Xu
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Yu Zhou
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California, USA
| | - Liang Chen
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California, USA
| | - Dora D Monterroza
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Hairi Li
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California, USA
| | - Russell C DeKelver
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Ming Yan
- Moores UCSD Cancer Center, University of California, San Diego, La Jolla, California, USA
| | - Xiang-Dong Fu
- Moores UCSD Cancer Center, University of California, San Diego, La Jolla, California, USA Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California, USA
| | - Dong-Er Zhang
- Moores UCSD Cancer Center, University of California, San Diego, La Jolla, California, USA Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA Department of Pathology, University of California, San Diego, La Jolla, California, USA
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4
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DeKelver RC, Lewin B, Weng S, Yan M, Biggs J, Zhang DE. RUNX1-ETO induces a type I interferon response which negatively effects t(8;21)-induced increased self-renewal and leukemia development. Leuk Lymphoma 2014; 55:884-91. [PMID: 23772668 PMCID: PMC3987666 DOI: 10.3109/10428194.2013.815351] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The 8;21 translocation is the most common chromosomal aberration occurring in acute myeloid leukemia (AML). This translocation causes expression of the RUNX1-ETO (AML1-ETO) fusion protein, which cooperates with additional mutations in leukemia development. We report here that interferons (IFNs) and IFN-stimulated genes are a group of genes consistently up-regulated by RUNX1-ETO in both human and murine models. RUNX1-ETO-induced up-regulation of IFN-stimulated genes occurs primarily via type I IFN signaling with a requirement for the IFNAR complex. Addition of exogenous IFN in vitro significantly reduces the increase in self-renewal potential induced by both RUNX1-ETO and its leukemogenic splicing isoform RUNX1-ETO9a. Finally, loss of type I IFN signaling via knockout of Ifnar1 significantly accelerates leukemogenesis in a t(8;21) murine model. This demonstrates the role of increased IFN signaling as an important factor inhibiting t(8;21) fusion protein function and leukemia development and supports the use of type I IFNs in the treatment of AML.
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MESH Headings
- Animals
- Cell Line, Tumor
- Cell Transformation, Neoplastic/genetics
- Chromosomes, Human, Pair 21
- Chromosomes, Human, Pair 8
- Core Binding Factor Alpha 2 Subunit/genetics
- Disease Models, Animal
- Gene Expression Regulation, Leukemic/drug effects
- Humans
- Interferon Type I/pharmacology
- Leukemia/genetics
- Leukemia/metabolism
- Mice
- Mice, Knockout
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Proto-Oncogene Proteins/genetics
- RUNX1 Translocation Partner 1 Protein
- Receptor, Interferon alpha-beta/deficiency
- Receptor, Interferon alpha-beta/genetics
- Receptor, Interferon alpha-beta/metabolism
- Transcription Factors/genetics
- Translocation, Genetic
- U937 Cells
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Affiliation(s)
- Russell C. DeKelver
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Benjamin Lewin
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Stephanie Weng
- Department of Biomedical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Ming Yan
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Joseph Biggs
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Dong-Er Zhang
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
- Department of Biomedical Sciences, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
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5
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DeKelver RC, Lewin B, Lam K, Komeno Y, Yan M, Rundle C, Lo MC, Zhang DE. Cooperation between RUNX1-ETO9a and novel transcriptional partner KLF6 in upregulation of Alox5 in acute myeloid leukemia. PLoS Genet 2013; 9:e1003765. [PMID: 24130502 PMCID: PMC3794898 DOI: 10.1371/journal.pgen.1003765] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 07/16/2013] [Indexed: 11/18/2022] Open
Abstract
Fusion protein RUNX1-ETO (AML1-ETO, RUNX1-RUNX1T1) is expressed as the result of the 8q22;21q22 translocation [t(8;21)], which is one of the most common chromosomal abnormalities found in acute myeloid leukemia. RUNX1-ETO is thought to promote leukemia development through the aberrant regulation of RUNX1 (AML1) target genes. Repression of these genes occurs via the recruitment of the corepressors N-COR and SMRT due to their interaction with ETO. Mechanisms of RUNX1-ETO target gene upregulation remain less well understood. Here we show that RUNX1-ETO9a, the leukemogenic alternatively spliced transcript expressed from t(8;21), upregulates target gene Alox5, which is a gene critically required for the promotion of chronic myeloid leukemia development by BCR-ABL. Loss of Alox5 expression reduces activity of RUNX1-ETO9a, MLL-AF9 and PML-RARα in vitro. However, Alox5 is not essential for the induction of leukemia by RUNX1-ETO9a in vivo. Finally, we demonstrate that the upregulation of Alox5 by RUNX1-ETO9a occurs via the C2H2 zinc finger transcription factor KLF6, a protein required for early hematopoiesis and yolk sac development. Furthermore, KLF6 is specifically upregulated by RUNX1-ETO in human leukemia cells. This identifies KLF6 as a novel mediator of t(8;21) target gene regulation, providing a new mechanism for RUNX1-ETO transcriptional control. The 8;21 translocation is one of the most common genetic abnormalities present in acute myeloid leukemia (AML). This translocation causes expression of the fusion gene RUNX1-ETO and its splicing isoforms. RUNX1-ETO proteins then reprogram the transcriptional landscape of the cell and cooperate with further mutations to induce leukemia development. In this study, we examine the transcriptional control of the RUNX1-ETO target gene Alox5. Although Alox5 appears to be dispensable for AML development in a mouse model, it is required for some RUNX1-ETO functions. In studying the regulation of Alox5 expression, we have discovered a novel RUNX1-ETO partner protein, KLF6, which is both upregulated by RUNX1-ETO and participates in RUNX1-ETO gene regulation. This provides new insight into the under-studied mechanisms of RUNX1-ETO target gene upregulation and identifies KLF6 as a potentially important protein for further study in t(8;21) AML development.
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Affiliation(s)
- Russell C. DeKelver
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Benjamin Lewin
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Kentson Lam
- Department of Biomedical Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Yukiko Komeno
- Moores Cancer Center, University of California San Diego, La Jolla, California, United States of America
| | - Ming Yan
- Moores Cancer Center, University of California San Diego, La Jolla, California, United States of America
| | - Chandler Rundle
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Miao-Chia Lo
- Moores Cancer Center, University of California San Diego, La Jolla, California, United States of America
| | - Dong-Er Zhang
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
- Department of Biomedical Sciences, University of California San Diego, La Jolla, California, United States of America
- Moores Cancer Center, University of California San Diego, La Jolla, California, United States of America
- Department of Pathology, University of California San Diego, La Jolla, California, United States of America
- * E-mail:
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6
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Ahn EEY, Higashi T, Yan M, Matsuura S, Hickey CJ, Lo MC, Shia WJ, DeKelver RC, Zhang DE. SON protein regulates GATA-2 through transcriptional control of the microRNA 23a~27a~24-2 cluster. J Biol Chem 2013; 288:5381-8. [PMID: 23322776 DOI: 10.1074/jbc.m112.447227] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
SON is a DNA- and RNA-binding protein localized in nuclear speckles. Although its function in RNA splicing for effective cell cycle progression and genome stability was recently unveiled, other mechanisms of SON functions remain unexplored. Here, we report that SON regulates GATA-2, a key transcription factor involved in hematopoietic stem cell maintenance and differentiation. SON is highly expressed in undifferentiated hematopoietic stem/progenitor cells and leukemic blasts. SON knockdown leads to significant depletion of GATA-2 protein with marginal down-regulation of GATA-2 mRNA. We show that miR-27a is up-regulated upon SON knockdown and targets the 3'-UTR of GATA-2 mRNA in hematopoietic cells. Up-regulation of miR-27a was due to activation of the promoter of the miR-23a∼27a∼24-2 cluster, suggesting that SON suppresses this promoter to lower the microRNAs from this cluster. Our data revealed a previously unidentified role of SON in microRNA production via regulating the transcription process, thereby modulating GATA-2 at the protein level during hematopoietic differentiation.
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Affiliation(s)
- Erin Eun-Young Ahn
- Moores UCSD Cancer Center, the University of California San Diego, La Jolla, California 92093, USA
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7
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Gupta M, DeKelver RC, Palta A, Clifford C, Gopalan S, Miller JC, Novak S, Desloover D, Gachotte D, Connell J, Flook J, Patterson T, Robbins K, Rebar EJ, Gregory PD, Urnov FD, Petolino JF. Transcriptional activation of Brassica napus β-ketoacyl-ACP synthase II with an engineered zinc finger protein transcription factor. Plant Biotechnol J 2012; 10:783-791. [PMID: 22520333 DOI: 10.1111/j.1467-7652.2012.00695.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Targeted gene regulation via designed transcription factors has great potential for precise phenotypic modification and acceleration of novel crop trait development. Canola seed oil composition is dictated largely by the expression of genes encoding enzymes in the fatty acid biosynthetic pathway. In the present study, zinc finger proteins (ZFPs) were designed to bind DNA sequences common to two canola β-ketoacyl-ACP Synthase II (KASII) genes downstream of their transcription start site. Transcriptional activators (ZFP-TFs) were constructed by fusing these ZFP DNA-binding domains to the VP16 transcriptional activation domain. Following transformation using Agrobacterium, transgenic events expressing ZFP-TFs were generated and shown to have elevated KASII transcript levels in the leaves of transgenic T(0) plants when compared to 'selectable marker only' controls as well as of T(1) progeny plants when compared to null segregants. In addition, leaves of ZFP-TF-expressing T(1) plants contained statistically significant decreases in palmitic acid (consistent with increased KASII activity) and increased total C18. Similarly, T(2) seed displayed statistically significant decreases in palmitic acid, increased total C18 and reduced total saturated fatty acid contents. These results demonstrate that designed ZFP-TFs can be used to regulate the expression of endogenous genes to elicit specific phenotypic modifications of agronomically relevant traits in a crop species.
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8
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Ahn EY, DeKelver RC, Lo MC, Nguyen TA, Matsuura S, Boyapati A, Pandit S, Fu XD, Zhang DE. SON controls cell-cycle progression by coordinated regulation of RNA splicing. Mol Cell 2011; 42:185-98. [PMID: 21504830 DOI: 10.1016/j.molcel.2011.03.014] [Citation(s) in RCA: 109] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Revised: 12/28/2010] [Accepted: 02/02/2011] [Indexed: 12/15/2022]
Abstract
It has been suspected that cell-cycle progression might be functionally coupled with RNA processing. However, little is known about the role of the precise splicing control in cell-cycle progression. Here, we report that SON, a large Ser/Arg (SR)-related protein, is a splicing cofactor contributing to efficient splicing of cell-cycle regulators. Downregulation of SON leads to severe impairment of spindle pole separation, microtubule dynamics, and genome integrity. These molecular defects result from inadequate RNA splicing of a specific set of cell-cycle-related genes that possess weak splice sites. Furthermore, we show that SON facilitates the interaction of SR proteins with RNA polymerase II and other key spliceosome components, suggesting its function in efficient cotranscriptional RNA processing. These results reveal a mechanism for controlling cell-cycle progression through SON-dependent constitutive splicing at suboptimal splice sites, with strong implications for its role in cancer and other human diseases.
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Affiliation(s)
- Eun-Young Ahn
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
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9
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Orlando SJ, Santiago Y, DeKelver RC, Freyvert Y, Boydston EA, Moehle EA, Choi VM, Gopalan SM, Lou JF, Li J, Miller JC, Holmes MC, Gregory PD, Urnov FD, Cost GJ. Zinc-finger nuclease-driven targeted integration into mammalian genomes using donors with limited chromosomal homology. Nucleic Acids Res 2010; 38:e152. [PMID: 20530528 PMCID: PMC2926620 DOI: 10.1093/nar/gkq512] [Citation(s) in RCA: 165] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We previously demonstrated high-frequency, targeted DNA addition mediated by the homology-directed DNA repair pathway. This method uses a zinc-finger nuclease (ZFN) to create a site-specific double-strand break (DSB) that facilitates copying of genetic information into the chromosome from an exogenous donor molecule. Such donors typically contain two approximately 750 bp regions of chromosomal sequence required for homology-directed DNA repair. Here, we demonstrate that easily-generated linear donors with extremely short (50 bp) homology regions drive transgene integration into 5-10% of chromosomes. Moreover, we measure the overhangs produced by ZFN cleavage and find that oligonucleotide donors with single-stranded 5' overhangs complementary to those made by ZFNs are efficiently ligated in vivo to the DSB. Greater than 10% of all chromosomes directly incorporate this exogenous DNA via a process that is dependent upon and guided by complementary 5' overhangs on the donor DNA. Finally, we extend this non-homologous end-joining (NHEJ)-based technique by directly inserting donor DNA comprising recombinase sites into large deletions created by the simultaneous action of two separate ZFN pairs. Up to 50% of deletions contained a donor insertion. Targeted DNA addition via NHEJ complements our homology-directed targeted integration approaches, adding versatility to the manipulation of mammalian genomes.
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10
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DeKelver RC, Choi VM, Moehle EA, Paschon DE, Hockemeyer D, Meijsing SH, Sancak Y, Cui X, Steine EJ, Miller JC, Tam P, Bartsevich VV, Meng X, Rupniewski I, Gopalan SM, Sun HC, Pitz KJ, Rock JM, Zhang L, Davis GD, Rebar EJ, Cheeseman IM, Yamamoto KR, Sabatini DM, Jaenisch R, Gregory PD, Urnov FD. Functional genomics, proteomics, and regulatory DNA analysis in isogenic settings using zinc finger nuclease-driven transgenesis into a safe harbor locus in the human genome. Genome Res 2010; 20:1133-42. [PMID: 20508142 DOI: 10.1101/gr.106773.110] [Citation(s) in RCA: 260] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Isogenic settings are routine in model organisms, yet remain elusive for genetic experiments on human cells. We describe the use of designed zinc finger nucleases (ZFNs) for efficient transgenesis without drug selection into the PPP1R12C gene, a "safe harbor" locus known as AAVS1. ZFNs enable targeted transgenesis at a frequency of up to 15% following transient transfection of both transformed and primary human cells, including fibroblasts and hES cells. When added to this locus, transgenes such as expression cassettes for shRNAs, small-molecule-responsive cDNA expression cassettes, and reporter constructs, exhibit consistent expression and sustained function over 50 cell generations. By avoiding random integration and drug selection, this method allows bona fide isogenic settings for high-throughput functional genomics, proteomics, and regulatory DNA analysis in essentially any transformed human cell type and in primary cells.
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Affiliation(s)
- Russell C DeKelver
- Sangamo BioSciences, Inc., Point Richmond Tech Center, Richmond, California 94804, USA
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11
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Hockemeyer D, Soldner F, Beard C, Gao Q, Mitalipova M, DeKelver RC, Katibah GE, Amora R, Boydston EA, Zeitler B, Meng X, Miller JC, Zhang L, Rebar EJ, Gregory PD, Urnov FD, Jaenisch R. Efficient targeting of expressed and silent genes in human ESCs and iPSCs using zinc-finger nucleases. Nat Biotechnol 2009; 27:851-7. [PMID: 19680244 PMCID: PMC4142824 DOI: 10.1038/nbt.1562] [Citation(s) in RCA: 792] [Impact Index Per Article: 52.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2009] [Accepted: 08/10/2009] [Indexed: 11/09/2022]
Abstract
Realizing the full potential of human embryonic stem cells (hESCs) and induced pluripotent stem cells (hiPSCs) requires efficient methods for genetic modification. However, techniques to generate cell type-specific lineage reporters, as well as reliable tools to disrupt, repair or overexpress genes by gene targeting, are inefficient at best and thus are not routinely used. Here we report the highly efficient targeting of three genes in human pluripotent cells using zinc-finger nuclease (ZFN)-mediated genome editing. First, using ZFNs specific for the OCT4 (POU5F1) locus, we generated OCT4-eGFP reporter cells to monitor the pluripotent state of hESCs. Second, we inserted a transgene into the AAVS1 locus to generate a robust drug-inducible overexpression system in hESCs. Finally, we targeted the PITX3 gene, demonstrating that ZFNs can be used to generate reporter cells by targeting non-expressed genes in hESCs and hiPSCs.
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Affiliation(s)
- Dirk Hockemeyer
- The Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, 02142 MA, USA
| | - Frank Soldner
- The Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, 02142 MA, USA
| | - Caroline Beard
- The Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, 02142 MA, USA
| | - Qing Gao
- The Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, 02142 MA, USA
| | - Maisam Mitalipova
- The Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, 02142 MA, USA
| | - Russell C. DeKelver
- Sangamo BioSciences, Inc., Pt. Richmond Tech Center, 501 Canal Blvd., Suite A100, Richmond, CA 94804, USA
| | - George E. Katibah
- Sangamo BioSciences, Inc., Pt. Richmond Tech Center, 501 Canal Blvd., Suite A100, Richmond, CA 94804, USA
| | - Ranier Amora
- Sangamo BioSciences, Inc., Pt. Richmond Tech Center, 501 Canal Blvd., Suite A100, Richmond, CA 94804, USA
| | - Elizabeth A. Boydston
- Sangamo BioSciences, Inc., Pt. Richmond Tech Center, 501 Canal Blvd., Suite A100, Richmond, CA 94804, USA
| | - Bryan Zeitler
- Sangamo BioSciences, Inc., Pt. Richmond Tech Center, 501 Canal Blvd., Suite A100, Richmond, CA 94804, USA
| | - Xiangdong Meng
- Sangamo BioSciences, Inc., Pt. Richmond Tech Center, 501 Canal Blvd., Suite A100, Richmond, CA 94804, USA
| | - Jeffrey C. Miller
- Sangamo BioSciences, Inc., Pt. Richmond Tech Center, 501 Canal Blvd., Suite A100, Richmond, CA 94804, USA
| | - Lei Zhang
- Sangamo BioSciences, Inc., Pt. Richmond Tech Center, 501 Canal Blvd., Suite A100, Richmond, CA 94804, USA
| | - Edward J. Rebar
- Sangamo BioSciences, Inc., Pt. Richmond Tech Center, 501 Canal Blvd., Suite A100, Richmond, CA 94804, USA
| | - Philip D. Gregory
- Sangamo BioSciences, Inc., Pt. Richmond Tech Center, 501 Canal Blvd., Suite A100, Richmond, CA 94804, USA
| | - Fyodor D. Urnov
- Sangamo BioSciences, Inc., Pt. Richmond Tech Center, 501 Canal Blvd., Suite A100, Richmond, CA 94804, USA
| | - Rudolf Jaenisch
- The Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, 02142 MA, USA
- Department of Biology, Massachusetts Institute of Technology, 31 Ames Street, Cambridge, MA 02139, USA
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12
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Shukla VK, Doyon Y, Miller JC, DeKelver RC, Moehle EA, Worden SE, Mitchell JC, Arnold NL, Gopalan S, Meng X, Choi VM, Rock JM, Wu YY, Katibah GE, Zhifang G, McCaskill D, Simpson MA, Blakeslee B, Greenwalt SA, Butler HJ, Hinkley SJ, Zhang L, Rebar EJ, Gregory PD, Urnov FD. Precise genome modification in the crop species Zea mays using zinc-finger nucleases. Nature 2009; 459:437-41. [PMID: 19404259 DOI: 10.1038/nature07992] [Citation(s) in RCA: 477] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2008] [Accepted: 03/17/2009] [Indexed: 11/09/2022]
Abstract
Agricultural biotechnology is limited by the inefficiencies of conventional random mutagenesis and transgenesis. Because targeted genome modification in plants has been intractable, plant trait engineering remains a laborious, time-consuming and unpredictable undertaking. Here we report a broadly applicable, versatile solution to this problem: the use of designed zinc-finger nucleases (ZFNs) that induce a double-stranded break at their target locus. We describe the use of ZFNs to modify endogenous loci in plants of the crop species Zea mays. We show that simultaneous expression of ZFNs and delivery of a simple heterologous donor molecule leads to precise targeted addition of an herbicide-tolerance gene at the intended locus in a significant number of isolated events. ZFN-modified maize plants faithfully transmit these genetic changes to the next generation. Insertional disruption of one target locus, IPK1, results in both herbicide tolerance and the expected alteration of the inositol phosphate profile in developing seeds. ZFNs can be used in any plant species amenable to DNA delivery; our results therefore establish a new strategy for plant genetic manipulation in basic science and agricultural applications.
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Affiliation(s)
- Vipula K Shukla
- Dow AgroSciences, 9330 Zionsville Road, Indianapolis, Indiana 46268, USA.
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13
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Geurts AM, Choi V, DeKelver RC, Miller JC, Zeitler B, Rebar EJ, Wood A, Schilling R, Kalloway S, Davis G, Urnov FD, Gregory PD, Jacob H. TARGETED MODIFICATION OF THE RAT GENOME USING ZINC FINGER NUCLEASES. FASEB J 2009. [DOI: 10.1096/fasebj.23.1_supplement.814.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Aron M Geurts
- Human Molecular Genetics CenterMedical College of WisconsinMilwaukeeWI
| | | | | | | | | | | | - Adam Wood
- Research Biotech DivisionSigma AldrichSt. LouisMO
| | - Rebecca Schilling
- Human Molecular Genetics CenterMedical College of WisconsinMilwaukeeWI
| | - Shawn Kalloway
- Human Molecular Genetics CenterMedical College of WisconsinMilwaukeeWI
| | - Greg Davis
- Research Biotech DivisionSigma AldrichSt. LouisMO
| | | | | | - Howard Jacob
- Human Molecular Genetics CenterMedical College of WisconsinMilwaukeeWI
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14
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Moehle EA, Rock JM, Lee YL, Jouvenot Y, DeKelver RC, Gregory PD, Urnov FD, Holmes MC. Targeted gene addition into a specified location in the human genome using designed zinc finger nucleases. Proc Natl Acad Sci U S A 2007; 104:3055-60. [PMID: 17360608 PMCID: PMC1802009 DOI: 10.1073/pnas.0611478104] [Citation(s) in RCA: 306] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Efficient incorporation of novel DNA sequences into a specific site in the genome of living human cells remains a challenge despite its potential utility to genetic medicine, biotechnology, and basic research. We find that a precisely placed double-strand break induced by engineered zinc finger nucleases (ZFNs) can stimulate integration of long DNA stretches into a predetermined genomic location, resulting in high-efficiency site-specific gene addition. Using an extrachromosomal DNA donor carrying a 12-bp tag, a 900-bp ORF, or a 1.5-kb promoter-transcription unit flanked by locus-specific homology arms, we find targeted integration frequencies of 15%, 6%, and 5%, respectively, within 72 h of treatment, and with no selection for the desired event. Importantly, we find that the integration event occurs in a homology-directed manner and leads to the accurate reconstruction of the donor-specified genotype at the endogenous chromosomal locus, and hence presumably results from synthesis-dependent strand annealing repair of the break using the donor DNA as a template. This site-specific gene addition occurs with no measurable increase in the rate of random integration. Remarkably, we also find that ZFNs can drive the addition of an 8-kb sequence carrying three distinct promoter-transcription units into an endogenous locus at a frequency of 6%, also in the absence of any selection. These data reveal the surprising versatility of the specialized polymerase machinery involved in double-strand break repair, illuminate a powerful approach to mammalian cell engineering, and open the possibility of ZFN-driven gene addition therapy for human genetic disease.
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Affiliation(s)
- Erica A. Moehle
- Sangamo BioSciences, Inc., Point Richmond Technology Center, 501 Canal Boulevard, Suite A100, Richmond, CA 94804
| | - Jeremy M. Rock
- Sangamo BioSciences, Inc., Point Richmond Technology Center, 501 Canal Boulevard, Suite A100, Richmond, CA 94804
| | - Ya-Li Lee
- Sangamo BioSciences, Inc., Point Richmond Technology Center, 501 Canal Boulevard, Suite A100, Richmond, CA 94804
| | - Yann Jouvenot
- Sangamo BioSciences, Inc., Point Richmond Technology Center, 501 Canal Boulevard, Suite A100, Richmond, CA 94804
| | - Russell C. DeKelver
- Sangamo BioSciences, Inc., Point Richmond Technology Center, 501 Canal Boulevard, Suite A100, Richmond, CA 94804
| | - Philip D. Gregory
- Sangamo BioSciences, Inc., Point Richmond Technology Center, 501 Canal Boulevard, Suite A100, Richmond, CA 94804
| | - Fyodor D. Urnov
- Sangamo BioSciences, Inc., Point Richmond Technology Center, 501 Canal Boulevard, Suite A100, Richmond, CA 94804
- *To whom correspondence should be addressed. E-mail:
| | - Michael C. Holmes
- Sangamo BioSciences, Inc., Point Richmond Technology Center, 501 Canal Boulevard, Suite A100, Richmond, CA 94804
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