Development of genome editing tools for basic and therapeutic applications

Dr Doyon established his laboratory at the CHU de Québec–Laval University research center in September 2013 after a seven-year postdoctoral stint in the biotechnology sector (Sangamo Therapeutics, California, USA) devoted to the creation and implementation of genome-editing tools for basic research, agriculture, and therapeutic applications. He has acquired a unique combination of academic and industry experience, holds several patents, and has published some highly-cited scientific articles.

Genome editing

The ability to modify the genomic sequence of living cells through targeted homologous recombination has revolutionized biology. Unfortunately, the effectiveness of the conventional gene targeting tools has been limited to mice and budding yeast. However, the genomes of an ever-growing number of species have now proven amenable to manipulation using a new class of tools termed engineered nucleases (Science’s Breakthrough of the Year 2015). Specifically, three complementary classes of designer enzymes that cleave precise DNA sequences to introduce double-strand breaks (DSBs) have been described; zinc-finger nucleases (ZFNs), transcription activator–like effector nucleases (TALENs), and RNA-guided endonucleases (RGENs-CRISPR/Cas9 system). Independently of the platform, the action of engineered nucleases relies on the cell’s ability to resolve the DNA break via evolutionary conserved pathways, either by a non-templated error-prone process called non-homologous end joining (NHEJ), or using an exogenous template to repair the break by homology directed repair (HDR). Using this core technology, referred to as genome editing, it is possible to accomplish gene disruption, gene correction and targeted gene addition in cells. We aim to further improve those techniques and apply them to address fundamental aspects of the DNA damage response as they are tightly interconnected. Therefore, we study how cells respond to DSBs and choose between alternative types of repair pathways in function of the cell cycle stage, cell type, and the local chromatin architecture at the lesion. This work relies on molecular biology techniques and cell-based assays. Exploiting the novel genome editing technologies based on the use of engineered nucleases allows the elaboration of unique methods for studying DNA repair pathways, which knowledge will, in return, be valuable to implement somatic cell genetics in different species.

In vivo genome editing as a novel class of human therapeutics to treat pediatric metabolic disorders

The development of efficient gene targeting techniques for in vivo genome editing constitutes an independent but complementary research theme in our laboratory. In recent years, technological innovations have led to safe and effective delivery of genome editing reagents into tissues using Adeno-Associated Virus (AAV) vectors. Thus, in vivo genome editing can be contemplated as a potential novel class of human therapeutics that enables precise molecular modification of a genetic defect. It remains of primary importance to define the variables affecting the efficiency of genome editing in neonatal and adult mice, to maximize the therapeutic potential of this gene therapy approach. Following systemic gene delivery of CRISPR nucleases and therapeutic transgene in mice using AAV, we strive to (i) define the variables affecting the efficiency of genome editing, (ii) determine the mode of transgene integration, (iii), ascertain the specificity, and (iv) test if the approach is curative in mouse models of metabolic diseases, such as Tyrosinemia.

Given the rising number of researchers utilizing CRISPR/Cas9 systems across both basic science and biopharmaceutical research, versatile methods that drastically improve the success of genome editing experiments are of significant importance. Our work should enhance fundamental biological research and open novel avenues of treatment, through gene therapy.

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Wang J, Friedman G, Doyon Y, Wang NS, Li CJ, Miller JC, Hua KL, Yan JJ, Babiarz JE, Gregory PD, Holmes MC

Targeted gene addition to a predetermined site in the human genome using a ZFN-based nicking enzyme.

Journal Article

Genome Res, 22 (7), pp. 1316-26, 2012, ISSN: 1088-9051.

Abstract | Links:

Avvakumov N, Lalonde ME, Saksouk N, Paquet E, Glass KC, Landry AJ, Doyon Y, Cayrou C, Robitaille GA, Richard DE, Yang XJ, Kutateladze TG, Cote J

Conserved molecular interactions within the HBO1 acetyltransferase complexes regulate cell proliferation.

Journal Article

Mol Cell Biol, 32 (3), pp. 689-703, 2012, ISSN: 0270-7306.

Abstract | Links:

Li H, Haurigot V, Doyon Y, Li T, Wong SY, Bhagwat AS, Malani N, Anguela XM, Sharma R, Ivanciu L, Murphy SL, Finn JD, Khazi FR, Zhou S, Paschon DE, Rebar EJ, Bushman FD, Gregory PD, Holmes MC, High KA

In vivo genome editing restores haemostasis in a mouse model of haemophilia.

Journal Article

Nature, 475 (7355), pp. 217-21, 2011, ISSN: 0028-0836.

Abstract | Links:

Young JJ, Cherone JM, Doyon Y, Ankoudinova I, Faraji FM, Lee AH, Ngo C, Guschin DY, Paschon DE, Miller JC, Zhang L, Rebar EJ, Gregory PD, Urnov FD, Harland RM, Zeitler B

Efficient targeted gene disruption in the soma and germ line of the frog Xenopus tropicalis using engineered zinc-finger nucleases.

Journal Article

Proc Natl Acad Sci U S A, 108 (17), pp. 7052-7, 2011, ISSN: 0027-8424.

Abstract | Links:

Doyon JB, Zeitler B, Cheng J, Cheng AT, Cherone JM, Santiago Y, Lee AH, Vo TD, Doyon Y, Miller JC, Paschon DE, Zhang L, Rebar EJ, Gregory PD, Urnov FD, Drubin DG

Rapid and efficient clathrin-mediated endocytosis revealed in genome-edited mammalian cells.

Journal Article

Nat Cell Biol, 13 (3), pp. 331-7, 2011, ISSN: 1465-7392.

Abstract | Links:

McCammon JM, Doyon Y, Amacher SL

Inducing high rates of targeted mutagenesis in zebrafish using zinc finger nucleases (ZFNs).

Journal Article

Methods Mol Biol, 770 , pp. 505-27, 2011, ISSN: 1064-3745.

Abstract | Links:

Doyon Y, Vo TD, Mendel MC, Greenberg SG, Wang J, Xia DF, Miller JC, Urnov FD, Gregory PD, Holmes MC

Enhancing zinc-finger-nuclease activity with improved obligate heterodimeric architectures.

Journal Article

Nat Methods, 8 (1), pp. 74-9, 2011, ISSN: 1548-7091.

Abstract | Links:

Doyon Y, Choi VM, Xia DF, Vo TD, Gregory PD, Holmes MC

Transient cold shock enhances zinc-finger nuclease-mediated gene disruption.

Journal Article

Nat Methods, 7 (6), pp. 459-60, 2010, ISSN: 1548-7091.

Abstract | Links:

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.

Journal Article

Nature, 459 (7245), pp. 437-41, 2009, ISSN: 0028-0836.

Abstract | Links:

Cai CQ, Doyon Y, Ainley WM, Miller JC, Dekelver RC, Moehle EA, Rock JM, Lee YL, Garrison R, Schulenberg L, Blue R, Worden A, Baker L, Faraji F, Zhang L, Holmes MC, Rebar EJ, Collingwood TN, Rubin-Wilson B, Gregory PD, Urnov FD, Petolino JF

Targeted transgene integration in plant cells using designed zinc finger nucleases.

Journal Article

Plant Mol Biol, 69 (6), pp. 699-709, 2009, ISSN: 0167-4412.

Abstract | Links:

31 entries « 2 of 4 »
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Active projects

  • Centre de recherche du CHU de Québec - Université Laval, Subvention, Centre hospitalier universitaire de Québec - Université Laval, Centres de recherche affiliés, from 2017-01-01 to 2099-12-31
  • Centre de recherche sur le cancer, Subvention, Institutionnel - BDR, BDR - Centres de recherche reconnus, from 1996-05-01 to 2023-04-30
  • Deciphering DNA repair pathways using engineered nucleases., Subvention, Conseil de recherches en sciences naturelles et génie Canada, Subventions à la découverte SD (individuelles et d'équipe), from 2014-04-01 to 2020-03-31
  • Enabling Targeted Genome Editing in Hematopoietic Stem Cells to Develop Novel Classes of Human Therapeutics, Partenariat, MITACS Inc., Accélération Québec (MITACS et gouvernement provincial), from 2016-07-11 to 2020-01-28
  • Orthologous CRISPR-Cas9 systems for genome editing: discovery, characterization and development for novel biotechnological applications, Subvention, Instituts de recherche en santé du Canada, Subvention Projet, from 2019-10-01 to 2024-09-30
  • Principes fondamentaux et applications thérapeutiques de l'ingénierie des génomes, Subvention, Fonds de recherche du Québec - Santé, Chercheur-boursier Juniors 1 et 2, Seniors, from 2018-07-01 to 2022-06-30

Recently finished projects

  • Basic and therapeutic applications of genome editing technologies, Partenariat, Fondation Canadienne pour l'innovation (La), Fonds des leaders John-R.-Evans (FLJR), from 2016-12-01 to 2018-08-31
  • Développement de thérapies pour les maladies métaboliques rares de l'enfant par correction génique in vivo et étude des mécanismes de réparation de l'ADN., Subvention, Fonds de recherche du Québec - Santé, Chercheur-boursier Juniors 1 et 2, Seniors, from 2014-07-01 to 2018-06-30
  • In vivo genome editing as a novel class of human therapeutics to treat pediatric metabolic disorders., Subvention, Instituts de recherche en santé du Canada, Subvention de fonctionnement, from 2014-07-01 to 2019-06-30
Data provided by the Université Laval research projects registery