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Wang M, Krueger JB, Gilkey AK, Stelljes EM, Kluesner MG, Pomeroy EJ, Skeate JG, Slipek NJ, Lahr WS, Vázquez PNC, Zhao Y, Eaton EJ, Laoharawee K, Webber BR, Moriarity BS. Precision Enhancement of CAR-NK Cells through Non-Viral Engineering and Highly Multiplexed Base Editing. bioRxiv 2024:2024.03.05.582637. [PMID: 38496503 PMCID: PMC10942345 DOI: 10.1101/2024.03.05.582637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Natural killer (NK) cells' unique ability to kill transformed cells expressing stress ligands or lacking major histocompatibility complexes (MHC) has prompted their development for immunotherapy. However, NK cells have demonstrated only moderate responses against cancer in clinical trials and likely require advanced genome engineering to reach their full potential as a cancer therapeutic. Multiplex genome editing with CRISPR/Cas9 base editors (BE) has been used to enhance T cell function and has already entered clinical trials but has not been reported in human NK cells. Here, we report the first application of BE in primary NK cells to achieve both loss-of-function and gain-of-function mutations. We observed highly efficient single and multiplex base editing, resulting in significantly enhanced NK cell function. Next, we combined multiplex BE with non-viral TcBuster transposon-based integration to generate IL-15 armored CD19 CAR-NK cells with significantly improved functionality in a highly suppressive model of Burkitt's lymphoma both in vitro and in vivo. The use of concomitant non-viral transposon engineering with multiplex base editing thus represents a highly versatile and efficient platform to generate CAR-NK products for cell-based immunotherapy and affords the flexibility to tailor multiple gene edits to maximize the effectiveness of the therapy for the cancer type being treated.
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Affiliation(s)
- Minjing Wang
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Joshua B Krueger
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Alexandria K Gilkey
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Erin M Stelljes
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Mitchell G Kluesner
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Molecular and Cellular Biology Graduate Program, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Emily J Pomeroy
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Joseph G Skeate
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Nicholas J Slipek
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Walker S Lahr
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Patricia N Claudio Vázquez
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Yueting Zhao
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Ella J Eaton
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Kanut Laoharawee
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Beau R Webber
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Branden S Moriarity
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
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2
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Jaeger-Ruckstuhl CA, Lo Y, Fulton E, Waltner OG, Shabaneh TB, Simon S, Muthuraman PV, Correnti CE, Newsom OJ, Engstrom IA, Kanaan SB, Bhise SS, Peralta JMC, Ruff R, Price JP, Stull SM, Stevens AR, Bugos G, Kluesner MG, Voillet V, Muhunthan V, Morrish F, Olson JM, Gottardo R, Sarthy JF, Henikoff S, Sullivan LB, Furlan SN, Riddell SR. Signaling via a CD27-TRAF2-SHP-1 axis during naive T cell activation promotes memory-associated gene regulatory networks. Immunity 2024; 57:287-302.e12. [PMID: 38354704 DOI: 10.1016/j.immuni.2024.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 09/26/2023] [Accepted: 01/11/2024] [Indexed: 02/16/2024]
Abstract
The interaction of the tumor necrosis factor receptor (TNFR) family member CD27 on naive CD8+ T (Tn) cells with homotrimeric CD70 on antigen-presenting cells (APCs) is necessary for T cell memory fate determination. Here, we examined CD27 signaling during Tn cell activation and differentiation. In conjunction with T cell receptor (TCR) stimulation, ligation of CD27 by a synthetic trimeric CD70 ligand triggered CD27 internalization and degradation, suggesting active regulation of this signaling axis. Internalized CD27 recruited the signaling adaptor TRAF2 and the phosphatase SHP-1, thereby modulating TCR and CD28 signals. CD27-mediated modulation of TCR signals promoted transcription factor circuits that induced memory rather than effector associated gene programs, which are induced by CD28 costimulation. CD27-costimulated chimeric antigen receptor (CAR)-engineered T cells exhibited improved tumor control compared with CD28-costimulated CAR-T cells. Thus, CD27 signaling during Tn cell activation promotes memory properties with relevance to T cell immunotherapy.
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Affiliation(s)
- Carla A Jaeger-Ruckstuhl
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.
| | - Yun Lo
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Elena Fulton
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Olivia G Waltner
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Tamer B Shabaneh
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Sylvain Simon
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Pranav V Muthuraman
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Colin E Correnti
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Oliver J Newsom
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Ian A Engstrom
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Sami B Kanaan
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Shruti S Bhise
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Jobelle M C Peralta
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Raymond Ruff
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Jason P Price
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Sylvia M Stull
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Andrew R Stevens
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Grace Bugos
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Mitchell G Kluesner
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Valentin Voillet
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Vishaka Muhunthan
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Fionnuala Morrish
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - James M Olson
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Raphaël Gottardo
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Department of Statistics, University of Washington, Seattle, WA 98195, USA; Swiss Institute of Bioinformatics, University of Lausanne and Lausanne University Hospital, Lausanne 1011, Switzerland
| | - Jay F Sarthy
- Seattle Children's Hospital, Seattle, WA 98105, USA; Basic Science Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Steven Henikoff
- Basic Science Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Lucas B Sullivan
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Scott N Furlan
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Stanley R Riddell
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Department of Medicine, University of Washington, Seattle, WA 98195, USA.
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3
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Becklin KL, Draper GM, Madden RA, Kluesner MG, Koga T, Huang M, Weiss WA, Spector LG, Largaespada DA, Moriarity BS, Webber BR. Developing Bottom-Up Induced Pluripotent Stem Cell Derived Solid Tumor Models Using Precision Genome Editing Technologies. CRISPR J 2022; 5:517-535. [PMID: 35972367 PMCID: PMC9529369 DOI: 10.1089/crispr.2022.0032] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 03/10/2022] [Accepted: 07/29/2022] [Indexed: 11/13/2022] Open
Abstract
Advances in genome and tissue engineering have spurred significant progress and opportunity for innovation in cancer modeling. Human induced pluripotent stem cells (iPSCs) are an established and powerful tool to study cellular processes in the context of disease-specific genetic backgrounds; however, their application to cancer has been limited by the resistance of many transformed cells to undergo successful reprogramming. Here, we review the status of human iPSC modeling of solid tumors in the context of genetic engineering, including how base and prime editing can be incorporated into "bottom-up" cancer modeling, a term we coined for iPSC-based cancer models using genetic engineering to induce transformation. This approach circumvents the need to reprogram cancer cells while allowing for dissection of the genetic mechanisms underlying transformation, progression, and metastasis with a high degree of precision and control. We also discuss the strengths and limitations of respective engineering approaches and outline experimental considerations for establishing future models.
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Affiliation(s)
- Kelsie L. Becklin
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
| | - Garrett M. Draper
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
| | - Rebecca A. Madden
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
| | - Mitchell G. Kluesner
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
| | - Tomoyuki Koga
- Ludwig Cancer Research San Diego Branch, La Jolla, California, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Department of Neurosurgery, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
| | - Miller Huang
- Department of Pediatrics, University of Southern California, Los Angeles, California, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Cancer and Blood Disease Institute, Children's Hospital Los Angeles and The Saban Research Institute, Los Angeles, California, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
| | - William A. Weiss
- Departments of Neurology, Pediatrics, Neurosurgery, Brain Tumor Research Center, and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California, USA; and Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Departments of Pediatrics, Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
| | - Logan G. Spector
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
| | - David A. Largaespada
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
| | - Branden S. Moriarity
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
| | - Beau R. Webber
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
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4
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Sipe CJ, Kluesner MG, Bingea SP, Lahr WS, Andrew AA, Wang M, DeFeo AP, Hinkel TL, Laoharawee K, Wagner JE, MacMillan ML, Vercellotti GM, Tolar J, Osborn MJ, McIvor RS, Webber BR, Moriarity BS. Correction of Fanconi Anemia Mutations Using Digital Genome Engineering. Int J Mol Sci 2022; 23:8416. [PMID: 35955545 PMCID: PMC9369391 DOI: 10.3390/ijms23158416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/20/2022] [Accepted: 07/25/2022] [Indexed: 12/10/2022] Open
Abstract
Fanconi anemia (FA) is a rare genetic disease in which genes essential for DNA repair are mutated. Both the interstrand crosslink (ICL) and double-strand break (DSB) repair pathways are disrupted in FA, leading to patient bone marrow failure (BMF) and cancer predisposition. The only curative therapy for the hematological manifestations of FA is an allogeneic hematopoietic cell transplant (HCT); however, many (>70%) patients lack a suitable human leukocyte antigen (HLA)-matched donor, often resulting in increased rates of graft-versus-host disease (GvHD) and, potentially, the exacerbation of cancer risk. Successful engraftment of gene-corrected autologous hematopoietic stem cells (HSC) circumvents the need for an allogeneic HCT and has been achieved in other genetic diseases using targeted nucleases to induce site specific DSBs and the correction of mutated genes through homology-directed repair (HDR). However, this process is extremely inefficient in FA cells, as they are inherently deficient in DNA repair. Here, we demonstrate the correction of FANCA mutations in primary patient cells using ‘digital’ genome editing with the cytosine and adenine base editors (BEs). These Cas9-based tools allow for C:G > T:A or A:T > C:G base transitions without the induction of a toxic DSB or the need for a DNA donor molecule. These genetic corrections or conservative codon substitution strategies lead to phenotypic rescue as illustrated by a resistance to the alkylating crosslinking agent Mitomycin C (MMC). Further, FANCA protein expression was restored, and an intact FA pathway was demonstrated by downstream FANCD2 monoubiquitination induction. This BE digital correction strategy will enable the use of gene-corrected FA patient hematopoietic stem and progenitor cells (HSPCs) for autologous HCT, obviating the risks associated with allogeneic HCT and DSB induction during autologous HSC gene therapy.
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Affiliation(s)
- Christopher J. Sipe
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.S.); (M.G.K.); (S.P.B.); (W.S.L.); (A.A.A.); (M.W.); (A.P.D.); (T.L.H.); (K.L.); (J.E.W.); (M.L.M.); (J.T.); (M.J.O.); (R.S.M.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Mitchell G. Kluesner
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.S.); (M.G.K.); (S.P.B.); (W.S.L.); (A.A.A.); (M.W.); (A.P.D.); (T.L.H.); (K.L.); (J.E.W.); (M.L.M.); (J.T.); (M.J.O.); (R.S.M.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Samuel P. Bingea
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.S.); (M.G.K.); (S.P.B.); (W.S.L.); (A.A.A.); (M.W.); (A.P.D.); (T.L.H.); (K.L.); (J.E.W.); (M.L.M.); (J.T.); (M.J.O.); (R.S.M.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Walker S. Lahr
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.S.); (M.G.K.); (S.P.B.); (W.S.L.); (A.A.A.); (M.W.); (A.P.D.); (T.L.H.); (K.L.); (J.E.W.); (M.L.M.); (J.T.); (M.J.O.); (R.S.M.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Aneesha A. Andrew
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.S.); (M.G.K.); (S.P.B.); (W.S.L.); (A.A.A.); (M.W.); (A.P.D.); (T.L.H.); (K.L.); (J.E.W.); (M.L.M.); (J.T.); (M.J.O.); (R.S.M.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Minjing Wang
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.S.); (M.G.K.); (S.P.B.); (W.S.L.); (A.A.A.); (M.W.); (A.P.D.); (T.L.H.); (K.L.); (J.E.W.); (M.L.M.); (J.T.); (M.J.O.); (R.S.M.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Anthony P. DeFeo
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.S.); (M.G.K.); (S.P.B.); (W.S.L.); (A.A.A.); (M.W.); (A.P.D.); (T.L.H.); (K.L.); (J.E.W.); (M.L.M.); (J.T.); (M.J.O.); (R.S.M.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Timothy L. Hinkel
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.S.); (M.G.K.); (S.P.B.); (W.S.L.); (A.A.A.); (M.W.); (A.P.D.); (T.L.H.); (K.L.); (J.E.W.); (M.L.M.); (J.T.); (M.J.O.); (R.S.M.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Kanut Laoharawee
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.S.); (M.G.K.); (S.P.B.); (W.S.L.); (A.A.A.); (M.W.); (A.P.D.); (T.L.H.); (K.L.); (J.E.W.); (M.L.M.); (J.T.); (M.J.O.); (R.S.M.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - John E. Wagner
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.S.); (M.G.K.); (S.P.B.); (W.S.L.); (A.A.A.); (M.W.); (A.P.D.); (T.L.H.); (K.L.); (J.E.W.); (M.L.M.); (J.T.); (M.J.O.); (R.S.M.)
- Division of Blood and Marrow Transplantation, University of Minnesota, Minneapolis, MN 55455, USA
| | - Margaret L. MacMillan
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.S.); (M.G.K.); (S.P.B.); (W.S.L.); (A.A.A.); (M.W.); (A.P.D.); (T.L.H.); (K.L.); (J.E.W.); (M.L.M.); (J.T.); (M.J.O.); (R.S.M.)
- Division of Blood and Marrow Transplantation, University of Minnesota, Minneapolis, MN 55455, USA
| | - Gregory M. Vercellotti
- Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, MN 55455, USA;
| | - Jakub Tolar
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.S.); (M.G.K.); (S.P.B.); (W.S.L.); (A.A.A.); (M.W.); (A.P.D.); (T.L.H.); (K.L.); (J.E.W.); (M.L.M.); (J.T.); (M.J.O.); (R.S.M.)
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
- Division of Blood and Marrow Transplantation, University of Minnesota, Minneapolis, MN 55455, USA
| | - Mark J. Osborn
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.S.); (M.G.K.); (S.P.B.); (W.S.L.); (A.A.A.); (M.W.); (A.P.D.); (T.L.H.); (K.L.); (J.E.W.); (M.L.M.); (J.T.); (M.J.O.); (R.S.M.)
- Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, MN 55455, USA;
| | - R. Scott McIvor
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.S.); (M.G.K.); (S.P.B.); (W.S.L.); (A.A.A.); (M.W.); (A.P.D.); (T.L.H.); (K.L.); (J.E.W.); (M.L.M.); (J.T.); (M.J.O.); (R.S.M.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Beau R. Webber
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.S.); (M.G.K.); (S.P.B.); (W.S.L.); (A.A.A.); (M.W.); (A.P.D.); (T.L.H.); (K.L.); (J.E.W.); (M.L.M.); (J.T.); (M.J.O.); (R.S.M.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Branden S. Moriarity
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.S.); (M.G.K.); (S.P.B.); (W.S.L.); (A.A.A.); (M.W.); (A.P.D.); (T.L.H.); (K.L.); (J.E.W.); (M.L.M.); (J.T.); (M.J.O.); (R.S.M.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
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5
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Kluesner MG, Lahr WS, Lonetree CL, Smeester BA, Qiu X, Slipek NJ, Claudio Vázquez PN, Pitzen SP, Pomeroy EJ, Vignes MJ, Lee SC, Bingea SP, Andrew AA, Webber BR, Moriarity BS. CRISPR-Cas9 cytidine and adenosine base editing of splice-sites mediates highly-efficient disruption of proteins in primary and immortalized cells. Nat Commun 2021; 12:2437. [PMID: 33893286 PMCID: PMC8065034 DOI: 10.1038/s41467-021-22009-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 02/24/2021] [Indexed: 12/19/2022] Open
Abstract
CRISPR-Cas9 cytidine and adenosine base editors (CBEs and ABEs) can disrupt genes without introducing double-stranded breaks by inactivating splice sites (BE-splice) or by introducing premature stop (pmSTOP) codons. However, no in-depth comparison of these methods or a modular tool for designing BE-splice sgRNAs exists. To address these needs, we develop SpliceR ( http://z.umn.edu/spliceR ) to design and rank BE-splice sgRNAs for any Ensembl annotated genome, and compared disruption approaches in T cells using a screen against the TCR-CD3 MHC Class I immune synapse. Among the targeted genes, we find that targeting splice-donors is the most reliable disruption method, followed by targeting splice-acceptors, and introducing pmSTOPs. Further, the CBE BE4 is more effective for disruption than the ABE ABE7.10, however this disparity is eliminated by employing ABE8e. Collectively, we demonstrate a robust method for gene disruption, accompanied by a modular design tool that is of use to basic and translational researchers alike.
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Affiliation(s)
- Mitchell G Kluesner
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
| | - Walker S Lahr
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
| | - Cara-Lin Lonetree
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
| | - Branden A Smeester
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
| | - Xiaohong Qiu
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
| | - Nicholas J Slipek
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
| | - Patricia N Claudio Vázquez
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | - Samuel P Pitzen
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | - Emily J Pomeroy
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
| | - Madison J Vignes
- College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
| | - Samantha C Lee
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
- College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
| | - Samuel P Bingea
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
| | - Aneesha A Andrew
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
- College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
| | - Beau R Webber
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA.
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA.
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA.
| | - Branden S Moriarity
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA.
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA.
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA.
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6
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Webber BR, Lonetree CL, Kluesner MG, Johnson MJ, Pomeroy EJ, Diers MD, Lahr WS, Draper GM, Slipek NJ, Smeester BA, Lovendahl KN, McElroy AN, Gordon WR, Osborn MJ, Moriarity BS. Author Correction: Highly efficient multiplex human T cell engineering without double-strand breaks using Cas9 base editors. Nat Commun 2019; 10:5659. [PMID: 31811147 PMCID: PMC6898206 DOI: 10.1038/s41467-019-13778-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Beau R Webber
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA.,Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.,Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA.,Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
| | - Cara-Lin Lonetree
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA.,Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.,Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Mitchell G Kluesner
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA.,Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.,Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Matthew J Johnson
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA.,Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.,Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Emily J Pomeroy
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA.,Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.,Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Miechaleen D Diers
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA.,Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.,Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Walker S Lahr
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA.,Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.,Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Garrett M Draper
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA.,Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.,Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Nicholas J Slipek
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA.,Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.,Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Branden A Smeester
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA.,Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.,Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Klaus N Lovendahl
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Amber N McElroy
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA.,Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA.,Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
| | - Wendy R Gordon
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Mark J Osborn
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA.,Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA.,Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
| | - Branden S Moriarity
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA. .,Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA. .,Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA.
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7
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Pomeroy EJ, Hunzeker JT, Kluesner MG, Lahr WS, Smeester BA, Crosby MR, Lonetree CL, Yamamoto K, Bendzick L, Miller JS, Geller MA, Walcheck B, Felices M, Webber BR, Starr TK, Moriarity BS. A Genetically Engineered Primary Human Natural Killer Cell Platform for Cancer Immunotherapy. Mol Ther 2019; 28:52-63. [PMID: 31704085 DOI: 10.1016/j.ymthe.2019.10.009] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [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: 04/15/2019] [Revised: 10/08/2019] [Accepted: 10/10/2019] [Indexed: 11/18/2022] Open
Abstract
Enhancing natural killer (NK) cell cytotoxicity by blocking inhibitory signaling could lead to improved NK-based cancer immunotherapy. Thus, we have developed a highly efficient method for editing the genome of human NK cells using CRISPR/Cas9 to knock out inhibitory signaling molecules. Our method efficiently edits up to 90% of primary peripheral blood NK cells. As a proof-of-principle we demonstrate highly efficient knockout of ADAM17 and PDCD1, genes that have a functional impact on NK cells, and demonstrate that these gene-edited NK cells have significantly improved activity, cytokine production, and cancer cell cytotoxicity. Furthermore, we were able to expand cells to clinically relevant numbers, without loss of activity. We also demonstrate that our CRISPR/Cas9 method can be used for efficient knockin of genes by delivering homologous recombination template DNA using recombinant adeno-associated virus serotype 6 (rAAV6). Our platform represents a feasible method for generating engineered primary NK cells as a universal therapeutic for cancer immunotherapy.
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Affiliation(s)
- Emily J Pomeroy
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - John T Hunzeker
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Mitchell G Kluesner
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Walker S Lahr
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Branden A Smeester
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Margaret R Crosby
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Cara-Lin Lonetree
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Kenta Yamamoto
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Laura Bendzick
- Department of Obstetrics, Gynecology, and Women's Health, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jeffrey S Miller
- Department of Medicine, Division of Hematology, Oncology, and Transplantation, University of Minnesota, Minneapolis, MN 55455, USA
| | - Melissa A Geller
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Department of Obstetrics, Gynecology, and Women's Health, University of Minnesota, Minneapolis, MN 55455, USA
| | - Bruce Walcheck
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55455, USA
| | - Martin Felices
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Department of Medicine, Division of Hematology, Oncology, and Transplantation, University of Minnesota, Minneapolis, MN 55455, USA
| | - Beau R Webber
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Timothy K Starr
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA; Department of Obstetrics, Gynecology, and Women's Health, University of Minnesota, Minneapolis, MN 55455, USA
| | - Branden S Moriarity
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA.
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8
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Kurata M, Wolf NK, Lahr WS, Weg MT, Kluesner MG, Lee S, Hui K, Shiraiwa M, Webber BR, Moriarity BS. Highly multiplexed genome engineering using CRISPR/Cas9 gRNA arrays. PLoS One 2018; 13:e0198714. [PMID: 30222773 PMCID: PMC6141065 DOI: 10.1371/journal.pone.0198714] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [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: 05/23/2018] [Accepted: 08/22/2018] [Indexed: 01/08/2023] Open
Abstract
The CRISPR/Cas9 system is an RNA guided nuclease system that evolved as a mechanism of adaptive immunity in bacteria. This system has been adopted for numerous genome engineering applications in research and recently, therapeutics. The CRISPR/Cas9 system has been largely implemented by delivery of Cas9 as protein, RNA, or plasmid along with a chimeric crRNA-tracrRNA guide RNA (gRNA) under the expression of a pol III promoter, such as U6. Using this approach, multiplex genome engineering has been achieved by delivering several U6-gRNA plasmids targeting multiple loci. However, this approach is limited due to the efficiently of delivering multiple plasmids to a single cell at one time. To augment the capability and accessibility of multiplexed genome engineering, we developed an efficient golden gate based method to assemble gRNAs linked by optimal Csy4 ribonuclease sequences to deliver up to 10 gRNAs as a single gRNA array transcript. Here we report the optimal expression of our guide RNA array under a strong pol II promoter. This system can be implemented alongside the myriad of CRISPR applications, allowing users to model complex biological processes requiring numerous gRNAs.
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Affiliation(s)
- Morito Kurata
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States of America
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, United States of America
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Natalie K. Wolf
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States of America
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States of America
| | - Walker S. Lahr
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States of America
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, United States of America
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States of America
| | - Madison T. Weg
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States of America
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States of America
| | - Mitchell G. Kluesner
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States of America
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, United States of America
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States of America
| | - Samantha Lee
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States of America
- College of Biological Sciences, University of Minnesota, Minneapolis, MN, United States of America
| | - Kai Hui
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States of America
- College of Biological Sciences, University of Minnesota, Minneapolis, MN, United States of America
| | - Masano Shiraiwa
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Beau R. Webber
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States of America
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, United States of America
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States of America
| | - Branden S. Moriarity
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States of America
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, United States of America
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States of America
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9
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Kluesner MG, Nedveck DA, Lahr WS, Garbe JR, Abrahante JE, Webber BR, Moriarity BS. EditR: A Method to Quantify Base Editing from Sanger Sequencing. CRISPR J 2018; 1:239-250. [PMID: 31021262 PMCID: PMC6694769 DOI: 10.1089/crispr.2018.0014] [Citation(s) in RCA: 250] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas9-Cytidine deaminase fusion enzymes—termed “base editors”—allow targeted editing of genomic deoxycytidine to deoxythymidine (C:G→T:A) without the need for double-stranded break induction. Base editors represent a paradigm shift in gene editing technology due to their unprecedented efficiency to mediate targeted, single-base conversion. However, current analysis of base editing outcomes rely on methods that are either imprecise or expensive and time-consuming. To overcome these limitations, we developed a simple, cost-effective, and accurate program to measure base editing efficiency from fluorescence-based Sanger sequencing, termed “EditR.” We provide EditR as a free online tool or downloadable desktop application requiring a single Sanger sequencing file and guide RNA sequence. EditR is more accurate than enzymatic assays, and provides added insight to the position, type, and efficiency of base editing. Furthermore, EditR is likely amenable to quantify base editing from the recently developed adenosine deaminase base editors that act on either DNA (adenosine deaminase base editors [ABEs]) or RNA (REPAIRs) (catalyzes A:T→G:C). Collectively, we demonstrate that EditR is a robust, inexpensive tool that will facilitate the broad application of base editing technology, thereby fostering further innovation in this burgeoning field.
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Affiliation(s)
- Mitchell G Kluesner
- 1 Masonic Cancer Center, University of Minnesota , Minneapolis, Minnesota.,2 Department of Pediatrics, University of Minnesota , Minneapolis, Minnesota.,3 Center for Genome Engineering, University of Minnesota , Minneapolis, Minnesota
| | - Derek A Nedveck
- 4 Department of Plant Biology, University of Minnesota , Minneapolis, Minnesota
| | - Walker S Lahr
- 1 Masonic Cancer Center, University of Minnesota , Minneapolis, Minnesota.,2 Department of Pediatrics, University of Minnesota , Minneapolis, Minnesota.,3 Center for Genome Engineering, University of Minnesota , Minneapolis, Minnesota
| | - John R Garbe
- 5 Genomics Center, University of Minnesota , Minneapolis, Minnesota
| | - Juan E Abrahante
- 6 Informatics Institute, University of Minnesota , Minneapolis, Minnesota
| | - Beau R Webber
- 1 Masonic Cancer Center, University of Minnesota , Minneapolis, Minnesota.,2 Department of Pediatrics, University of Minnesota , Minneapolis, Minnesota.,3 Center for Genome Engineering, University of Minnesota , Minneapolis, Minnesota
| | - Branden S Moriarity
- 1 Masonic Cancer Center, University of Minnesota , Minneapolis, Minnesota.,2 Department of Pediatrics, University of Minnesota , Minneapolis, Minnesota.,3 Center for Genome Engineering, University of Minnesota , Minneapolis, Minnesota
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