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.

CHUL
2705, boulevard Laurier
T-3-67
Québec, Québec
Canada G1V 4G2
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Agudelo D, Duringer A, Bozoyan L, Huard CC, Carter S, Loehr J, Synodinou D, Drouin M, Salsman J, Dellaire G, Laganiere J, Doyon Y

Marker-free coselection for CRISPR-driven genome editing in human cells.

Journal Article

Nat Methods, 14 (6), pp. 615-620, 2017, ISSN: 1548-7091.

Abstract | Links:

Carter S, Doyon Y

Gene Therapy in Tyrosinemia: Potential and Pitfalls.

Journal Article

Adv Exp Med Biol, 959 , pp. 231-243, 2017, ISSN: 0065-2598.

Abstract | Links:

Jacquet K, Fradet-Turcotte A, Avvakumov N, Lambert JP, Roques C, Pandita RK, Paquet E, Herst P, Gingras AC, Pandita TK, Legube G, Doyon Y, Durocher D, Cote J

The TIP60 Complex Regulates Bivalent Chromatin Recognition by 53BP1 through Direct H4K20me Binding and H2AK15 Acetylation.

Journal Article

Mol Cell, 62 (3), pp. 409-421, 2016, ISSN: 1097-2765.

Abstract | Links:

Doyon Y, Cote J

Preparation and Analysis of Native Chromatin-Modifying Complexes.

Journal Article

Methods Enzymol, 573 , pp. 303-18, 2016, ISSN: 0076-6879.

Abstract | Links:

Dalvai M, Loehr J, Jacquet K, Huard CC, Roques C, Herst P, Cote J, Doyon Y

A Scalable Genome-Editing-Based Approach for Mapping Multiprotein Complexes in Human Cells.

Journal Article

Cell Rep, 13 (3), pp. 621-633, 2015.

Abstract | Links:

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Active 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
  • Centre de recherche sur le cancer, Subvention, Institutionnel - BDR, BDR - Centres de recherche reconnus, from 1996-05-01 to 2023-04-30
  • Centre hospitalier universitaire de Québec - 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
  • 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 2019-03-31
  • Enabling Targeted Genome Editing in Hematopoietic Stem Cells to Develop Novel Classes of Human Therapeutics, Partenariat, MITACS Inc., Accélération Québec (MITACS/MESI), from 2016-07-11 to 2018-09-10
  • 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

Recently finished projects

  • 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, Établissement de jeunes chercheurs - Juniors 1, from 2014-07-01 to 2017-06-30
  • 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
Data provided by the Université Laval research projects registery