Variability in Genome Editing Outcomes: Challenges for Research Reproducibility and Clinical Safety

Genome editing tools have already revolutionized biomedical research and are also expected to have an important impact in the clinic. However, their extensive use in research has revealed much unpredictability, both off and on target, in the outcome of their application. We discuss the challenges associated with this unpredictability, both for research and in the clinic. For the former, an extensive validation of the model is essential. For the latter, potential unpredicted activity does not preclude the use of these tools but requires that molecular evidence to underpin the relevant risk:benefit evaluation is available. Safe and successful clinical application will also depend on the mode of delivery and the cellular context.

[1]  J Keith Joung,et al.  Correction of the Crb1rd8 allele and retinal phenotype in C57BL/6N mice via TALEN-mediated homology-directed repair. , 2014, Investigative ophthalmology & visual science.

[2]  Jonathan Y. Hsu,et al.  Response to “Unexpected mutations after CRISPR–Cas9 editing in vivo” , 2018, Nature Methods.

[3]  Heidi Ledford,et al.  CRISPR treatment inserted directly into the body for first time , 2020, Nature.

[4]  Sheila Jasanoff,et al.  A global observatory for gene editing , 2018, Nature.

[5]  R. Cohn,et al.  Therapeutic Applications of CRISPR/Cas for Duchenne Muscular Dystrophy. , 2018, Current gene therapy.

[6]  Steve D. M. Brown,et al.  Response to "unexpected mutations after CRISPR-Cas9 editing in vivo" , 2018 .

[7]  Annemieke Aartsma-Rus,et al.  The use of genetically humanized animal models for personalized medicine approaches , 2019, Disease Models & Mechanisms.

[8]  Howard Y. Chang,et al.  CRISPR-engineered T cells in patients with refractory cancer , 2020, Science.

[9]  Cameron S. Osborne,et al.  LMO2-Associated Clonal T Cell Proliferation in Two Patients after Gene Therapy for SCID-X1 , 2003, Science.

[10]  David R. Liu,et al.  Revealing Off-Target Cleavage Specificities of Zinc Finger Nucleases by In Vitro Selection , 2011, Nature Methods.

[11]  Ian Tomlinson,et al.  CRISPR-Cas9 Causes Chromosomal Instability and Rearrangements in Cancer Cell Lines, Detectable by Cytogenetic Methods , 2019, The CRISPR journal.

[12]  Christof von Kalle,et al.  A serious adverse event after successful gene therapy for X-linked severe combined immunodeficiency. , 2003, The New England journal of medicine.

[13]  Li Zhang,et al.  Induction of site-specific chromosomal translocations in embryonic stem cells by CRISPR/Cas9 , 2016, Scientific Reports.

[14]  Tomas W. Fitzgerald,et al.  Origins and functional impact of copy number variation in the human genome , 2010, Nature.

[15]  Tao Zhang,et al.  A large-scale whole-genome sequencing analysis reveals highly specific genome editing by both Cas9 and Cpf1 (Cas12a) nucleases in rice , 2018, Genome Biology.

[16]  Mark S. Anderson,et al.  A large CRISPR-induced bystander mutation causes immune dysregulation , 2019, Communications Biology.

[17]  Andy Greenfield,et al.  CRISPR-Cas9-Mediated Mutagenesis: Mind the Gap? , 2018, The CRISPR Journal.

[18]  Alessandro Aiuti,et al.  Gene therapy for immunodeficiency due to adenosine deaminase deficiency. , 2009, The New England journal of medicine.

[19]  Gang Bao,et al.  A high-fidelity Cas9 mutant delivered as a ribonucleoprotein complex enables efficient gene editing in human haematopoietic stem and progenitor cells , 2018, Nature Medicine.

[20]  Christof von Kalle,et al.  Evaluation of TCR Gene Editing Achieved by TALENs, CRISPR/Cas9, and megaTAL Nucleases. , 2016, Molecular therapy : the journal of the American Society of Gene Therapy.

[21]  Wei-Ting Hwang,et al.  Gene editing of CCR5 in autologous CD4 T cells of persons infected with HIV. , 2014, The New England journal of medicine.

[22]  Sruthi Mantri,et al.  Identification of preexisting adaptive immunity to Cas9 proteins in humans , 2018, Nature Medicine.

[23]  P. Jeggo,et al.  The repair and signaling responses to DNA double-strand breaks. , 2013, Advances in genetics.

[24]  M. Mahfouz,et al.  CRISPR base editors: genome editing without double-stranded breaks , 2018, The Biochemical journal.

[25]  Daesik Kim,et al.  Genome editing reveals a role for OCT4 in human embryogenesis , 2017, Nature.

[26]  David R. Liu,et al.  Search-and-replace genome editing without double-strand breaks or donor DNA , 2019, Nature.

[27]  Alan E. Tomkinson,et al.  Repair of DNA double-strand breaks by mammalian alternative end-joining pathways , 2018, The Journal of Biological Chemistry.

[28]  Mark A. Kay,et al.  Progress and problems with the use of viral vectors for gene therapy , 2003, Nature Reviews Genetics.

[29]  Christof von Kalle,et al.  Genome-wide Specificity of Highly Efficient TALENs and CRISPR/Cas9 for T Cell Receptor Modification , 2017, Molecular therapy. Methods & clinical development.

[30]  Sara Reardon,et al.  Leukaemia success heralds wave of gene-editing therapies , 2015, Nature.

[31]  Bo Huang,et al.  Deep profiling reveals substantial heterogeneity of integration outcomes in CRISPR knock-in experiments , 2019, bioRxiv.

[32]  M. Nair,et al.  Current application of CRISPR/Cas9 gene-editing technique to eradication of HIV/AIDS , 2017, Gene Therapy.

[33]  Michael C. Holmes,et al.  Targeted Correction and Restored Function of the CFTR Gene in Cystic Fibrosis Induced Pluripotent Stem Cells , 2015, Stem cell reports.

[34]  A. Thrasher,et al.  Progress and prospects: gene therapy for inherited immunodeficiencies , 2009, Gene Therapy.

[35]  Sheng Tong,et al.  Engineered materials for in vivo delivery of genome-editing machinery , 2019, Nature Reviews Materials.

[36]  Ying Sun,et al.  CRISPR/Cas9-mediated gene editing in human tripronuclear zygotes , 2015, Protein & Cell.

[37]  Jin-Soo Kim,et al.  Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases , 2014, Genome research.

[38]  Alessandro Romanel,et al.  A highly specific SpCas9 variant is identified by in vivo screening in yeast , 2018, Nature Biotechnology.

[39]  Jong-il Kim,et al.  Digenome-seq: genome-wide profiling of CRISPR-Cas9 off-target effects in human cells , 2015, Nature Methods.

[40]  Said Assou,et al.  Concise Review: Assessing the Genome Integrity of Human Induced Pluripotent Stem Cells: What Quality Control Metrics? , 2018, Stem cells.

[41]  Dennis Normile,et al.  China sprints ahead in CRISPR therapy race. , 2017, Science.

[42]  Jussi Taipale,et al.  CRISPR–Cas9 genome editing induces a p53-mediated DNA damage response , 2018, Nature Medicine.

[43]  Chad A. Cowan,et al.  Low incidence of off-target mutations in individual CRISPR-Cas9 and TALEN targeted human stem cell clones detected by whole-genome sequencing. , 2014, Cell stem cell.

[44]  Aymeric Duclert,et al.  Multiplex Genome-Edited T-cell Manufacturing Platform for "Off-the-Shelf" Adoptive T-cell Immunotherapies. , 2015, Cancer research.

[45]  Yazdan Rahmati,et al.  Promising therapeutic approaches using CRISPR/Cas9 genome editing technology in the treatment of Duchenne muscular dystrophy , 2020, Genes & diseases.

[46]  Philip R. Johnson,et al.  Recombinant Adeno-Associated Virus Vector Genomes Take the Form of Long-Lived, Transcriptionally Competent Episomes in Human Muscle. , 2016, Human gene therapy.

[47]  Hans A. Kestler,et al.  Chromosomal Integration of Adenoviral Vector DNA In Vivo , 2010, Journal of Virology.

[48]  Waseem Qasim,et al.  Preliminary Data on Safety, Cellular Kinetics and Anti-Leukemic Activity of UCART19, an Allogeneic Anti-CD19 CAR T-Cell Product, in a Pool of Adult and Pediatric Patients with High-Risk CD19+ Relapsed/Refractory B-Cell Acute Lymphoblastic Leukemia , 2018, Blood.

[49]  David R. Liu,et al.  High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity , 2013, Nature Biotechnology.

[50]  Akino Shiroma,et al.  Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area , 2017, Human Cell.

[51]  James E Haber,et al.  Sources of DNA double-strand breaks and models of recombinational DNA repair. , 2014, Cold Spring Harbor perspectives in biology.

[52]  Richard L. Frock,et al.  Genome-wide detection of DNA double-stranded breaks induced by engineered nucleases , 2014, Nature Biotechnology.

[53]  Yu-Kyoung Oh,et al.  Therapeutic gene editing: delivery and regulatory perspectives , 2017, Acta Pharmacologica Sinica.

[54]  Sara Reardon First CRISPR editing trial results assuage safety concerns. , 2019, Nature medicine.

[55]  Z. Glass,et al.  Non-viral delivery of genome-editing nucleases for gene therapy , 2016, Gene Therapy.

[56]  Yang Du,et al.  Correction of X-linked chronic granulomatous disease by gene therapy, augmented by insertional activation of MDS1-EVI1, PRDM16 or SETBP1 , 2006, Nature Medicine.

[57]  A. Bradley,et al.  Repair of double-strand breaks induced by CRISPR–Cas9 leads to large deletions and complex rearrangements , 2018, Nature Biotechnology.

[58]  Asher Mullard First in vivo CRISPR candidate enters the clinic , 2019, Nature Reviews Drug Discovery.

[59]  Adrian Pickar-Oliver,et al.  The next generation of CRISPR–Cas technologies and applications , 2019, Nature Reviews Molecular Cell Biology.

[60]  Adrian J. Thrasher,et al.  Molecular remission of infant B-ALL after infusion of universal TALEN gene-edited CAR T cells , 2017, Science Translational Medicine.

[61]  Jian‐Kang Zhu,et al.  The CRISPR/Cas9 system produces specific and homozygous targeted gene editing in rice in one generation. , 2014, Plant biotechnology journal.

[62]  Christopher Baum,et al.  A modified γ-retrovirus vector for X-linked severe combined immunodeficiency. , 2014, The New England journal of medicine.

[63]  Sushil Devkota,et al.  The road less traveled: strategies to enhance the frequency of homology-directed repair (HDR) for increased efficiency of CRISPR/Cas-mediated transgenesis , 2018, BMB reports.

[64]  Michael Rothe,et al.  Gene Therapy for Wiskott-Aldrich Syndrome—Long-Term Efficacy and Genotoxicity , 2014, Science Translational Medicine.

[65]  Eunji Kim,et al.  Targeted chromosomal duplications and inversions in the human genome using zinc finger nucleases. , 2012, Genome research.

[66]  Jocelyn Kaiser A human has been injected with gene-editing tools to cure his disabling disease. Here’s what you need to know , 2017 .

[67]  Detlef Weigel,et al.  Rapid generation of a transgene-free powdery mildew resistant tomato by genome deletion , 2017, Scientific Reports.

[68]  Jennifer A. Doudna,et al.  Knocking out barriers to engineered cell activity , 2020, Science.

[69]  Bin Zhang,et al.  CRISPR-Edited Stem Cells in a Patient with HIV and Acute Lymphocytic Leukemia. , 2019, The New England journal of medicine.

[70]  Jean-Paul Concordet,et al.  Improved Genome Editing Efficiency and Flexibility Using Modified Oligonucleotides with TALEN and CRISPR-Cas9 Nucleases. , 2016, Cell reports.

[71]  Monica J Justice,et al.  Using the mouse to model human disease: increasing validity and reproducibility , 2016, Disease Models & Mechanisms.

[72]  David R. Liu,et al.  Evaluation and minimization of Cas9-independent off-target DNA editing by cytosine base editors , 2020, Nature Biotechnology.

[73]  J. Keith Joung,et al.  High frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells , 2013, Nature Biotechnology.

[74]  Yoshio Koyanagi,et al.  Harnessing the CRISPR/Cas9 system to disrupt latent HIV-1 provirus , 2013, Scientific Reports.

[75]  Kun Zhang,et al.  Whole-genome sequencing analysis reveals high specificity of CRISPR/Cas9 and TALEN-based genome editing in human iPSCs. , 2014, Cell stem cell.

[76]  Jerilyn A Timlin,et al.  Delivering CRISPR: a review of the challenges and approaches , 2018, Drug delivery.

[77]  Andrea Ng,et al.  Second malignant neoplasms: assessment and strategies for risk reduction. , 2012, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[78]  Martin J. Aryee,et al.  GUIDE-Seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases , 2014, Nature Biotechnology.

[79]  Eytan Ruppin,et al.  A systematic genome-wide mapping of the oncogenic risks associated with CRISPR-Cas9 editing , 2018 .

[80]  Enrico Mastrobattista,et al.  Delivery Aspects of CRISPR/Cas for in Vivo Genome Editing , 2019, Accounts of chemical research.

[81]  Petra Reinke,et al.  High prevalence of Streptococcus pyogenes Cas9-reactive T cells within the adult human population , 2018, Nature Medicine.

[82]  Rudolf Jaenisch,et al.  One-Step Generation of Mice Carrying Mutations in Multiple Genes by CRISPR/Cas-Mediated Genome Engineering , 2013, Cell.

[83]  R. Myers,et al.  Advancements in Next-Generation Sequencing. , 2016, Annual review of genomics and human genetics.

[84]  J. Kent,et al.  Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR , 2016, Genome Biology.

[85]  Eric Vilain,et al.  Next-generation mapping: a novel approach for detection of pathogenic structural variants with a potential utility in clinical diagnosis , 2017, Genome Medicine.

[86]  David Cyranoski,et al.  Genome-edited baby claim provokes international outcry , 2018, Nature.

[87]  David A. Scott,et al.  Double Nicking by RNA-Guided CRISPR Cas9 for Enhanced Genome Editing Specificity , 2013, Cell.

[88]  Yoshitaka Fujihara,et al.  Double strand break repair by capture of retrotransposon sequences and reverse-transcribed spliced mRNA sequences in mouse zygotes , 2015, Scientific Reports.

[89]  Thomas M. Keane,et al.  Off-target mutations are rare in Cas9-modified mice , 2015, Nature Methods.

[90]  Gregory McAllister,et al.  p53 inhibits CRISPR–Cas9 engineering in human pluripotent stem cells , 2018, Nature Medicine.

[91]  Peter Krawitz,et al.  Efficient CRISPR/Cas9 genome editing with low off-target effects in zebrafish , 2013, Development.

[92]  Xiaoling Wang,et al.  Unbiased detection of off-target cleavage by CRISPR-Cas9 and TALENs using integrase-defective lentiviral vectors , 2015, Nature Biotechnology.

[93]  A. Bassuk,et al.  Unexpected mutations after CRISPR–Cas9 editing in vivo , 2017, Nature Methods.

[94]  Guillaume Pavlovic,et al.  Efficient and rapid generation of large genomic variants in rats and mice using CRISMERE , 2017, Scientific Reports.

[95]  Philippe Leboulch,et al.  Highly efficient in vitro and in vivo delivery of functional RNAs using new versatile MS2-chimeric retrovirus-like particles , 2015, Molecular therapy. Methods & clinical development.

[96]  L. Mir,et al.  Molecular signature of the immune and tissue response to non-coding plasmid DNA in skeletal muscle after electrotransfer , 2011, Gene Therapy.

[97]  Stefan Mundlos,et al.  Deletions, Inversions, Duplications: Engineering of Structural Variants using CRISPR/Cas in Mice. , 2015, Cell reports.

[98]  Botao Zhang,et al.  Multigeneration analysis reveals the inheritance, specificity, and patterns of CRISPR/Cas-induced gene modifications in Arabidopsis , 2014, Proceedings of the National Academy of Sciences.

[99]  Andrew R. Bassett,et al.  Predicting the mutations generated by repair of Cas9-induced double-strand breaks , 2018, Nature Biotechnology.

[100]  Heidi Ledford Quest to use CRISPR against disease gains ground , 2020, Nature.

[101]  Lothar Hennighausen,et al.  CRISPR/Cas9 targeting events cause complex deletions and insertions at 17 sites in the mouse genome , 2017, Nature Communications.

[102]  M. Porteus,et al.  A New Class of Medicines through DNA Editing , 2019, The New England journal of medicine.

[103]  Lydia Teboul,et al.  Phenotyping first-generation genome editing mutants: a new standard? , 2017, Mammalian Genome.

[104]  Christof von Kalle,et al.  The genotoxic potential of retroviral vectors is strongly modulated by vector design and integration site selection in a mouse model of HSC gene therapy. , 2009, The Journal of clinical investigation.

[105]  Eytan Ruppin,et al.  Integrated computational and experimental identification of p53, KRAS and VHL mutant selection associated with CRISPR-Cas9 editing , 2018 .

[106]  Lydia Teboul,et al.  Application of long single-stranded DNA donors in genome editing: generation and validation of mouse mutants , 2018, BMC Biology.

[107]  John Kelsoe,et al.  Exome sequencing in the knockin mice generated using the CRISPR/Cas system , 2016, Scientific Reports.

[108]  Matthew Meyerson,et al.  Targeted genomic rearrangements using CRISPR/Cas technology , 2014, Nature Communications.

[109]  Dominik Wodarz,et al.  Multiploid Inheritance of HIV-1 during Cell-to-Cell Infection , 2011, Journal of Virology.

[110]  Lydia Teboul,et al.  Microhomologies are prevalent at Cas9-induced larger deletions , 2019, Nucleic acids research.

[111]  J. Nickoloff,et al.  Regulation of DNA double-strand break repair pathway choice , 2008, Cell Research.

[112]  Mark Thomas,et al.  No unexpected CRISPR-Cas9 off-target activity revealed by trio sequencing of gene-edited mice , 2018, bioRxiv.

[113]  Wolfgang Wurst,et al.  Control of gene editing by manipulation of DNA repair mechanisms , 2017, Mammalian Genome.

[114]  M. Lynch Evolution of the mutation rate. , 2010, Trends in genetics : TIG.