title: Liver-specific transcriptional modules identified by genome-wide in silico analysis enable efficient gene therapy in mice and non-human primates.
abstract: The robustness and safety of liver-directed gene therapy can be substantially improved by enhancing expression of the therapeutic transgene in the liver. To achieve this, we developed a new approach of rational in silico vector design. This approach relies on a genome-wide bio-informatics strategy to identify cis-acting regulatory modules (CRMs) containing evolutionary conserved clusters of transcription factor binding site motifs that determine high tissue-specific gene expression. Incorporation of these CRMs into adeno-associated viral (AAV) and non-viral vectors enhanced gene expression in mice liver 10 to 100-fold, depending on the promoter used. Furthermore, these CRMs resulted in robust and sustained liver-specific expression of coagulation factor IX (FIX), validating their immediate therapeutic and translational relevance. Subsequent translational studies indicated that therapeutic FIX expression levels could be attained reaching 20-35% of normal levels after AAV-based liver-directed gene therapy in cynomolgus macaques. This study underscores the potential of rational vector design using computational approaches to improve their robustness and therefore allows for the use of lower and thus safer vector doses for gene therapy, while maximizing therapeutic efficacy.
authors: 1] Department of Gene Therapy & Regenerative Medicine, Free University of Brussels (VUB), Brussels, Belgium [2] Department of Cardiovascular Sciences, Center for Molecular & Vascular Biology, University of Leuven, Leuven, Belgium.
authors: Marinee K
authors: MK
authors: Chuah
authors: Department of Cardiovascular Sciences, Center for Molecular & Vascular Biology, University of Leuven, Leuven, Belgium.
authors: Inge
authors: I
authors: Petrus
authors: Department for Molecular Biomedical Research (DMBR), VIB - Ghent University, Ghent, Belgium.
authors: Pieter
authors: P
authors: De Bleser
authors: 1] INSERM UMR 1089, Atlantic Gene Therapies, Université de Nantes, Nantes, France [2] CHU de Nantes, Nantes, France.
authors: Caroline
authors: C
authors: Le Guiner
authors: 1] INSERM UMR 1089, Atlantic Gene Therapies, Université de Nantes, Nantes, France [2] CHU de Nantes, Nantes, France.
authors: Gwladys
authors: G
authors: Gernoux
authors: 1] INSERM UMR 1089, Atlantic Gene Therapies, Université de Nantes, Nantes, France [2] CHU de Nantes, Nantes, France.
authors: Oumeya
authors: O
authors: Adjali
authors: Department of Gene Therapy & Regenerative Medicine, Free University of Brussels (VUB), Brussels, Belgium.
authors: Nisha
authors: N
authors: Nair
authors: Department of Gene Therapy & Regenerative Medicine, Free University of Brussels (VUB), Brussels, Belgium.
authors: Jessica
authors: J
authors: Willems
authors: Department of Gene Therapy & Regenerative Medicine, Free University of Brussels (VUB), Brussels, Belgium.
authors: Hanneke
authors: H
authors: Evens
authors: 1] Department of Gene Therapy & Regenerative Medicine, Free University of Brussels (VUB), Brussels, Belgium [2] Department of Cardiovascular Sciences, Center for Molecular & Vascular Biology, University of Leuven, Leuven, Belgium.
authors: Melvin Y
authors: MY
authors: Rincon
authors: 1] Department of Gene Therapy & Regenerative Medicine, Free University of Brussels (VUB), Brussels, Belgium [2] Vesalius Research Center, VIB, Leuven, Belgium [3] University of Leuven, Leuven, Belgium.
authors: Janka
authors: J
authors: Matrai
authors: 1] Department of Gene Therapy & Regenerative Medicine, Free University of Brussels (VUB), Brussels, Belgium [2] Department of Cardiovascular Sciences, Center for Molecular & Vascular Biology, University of Leuven, Leuven, Belgium.
authors: Mario
authors: M
authors: Di Matteo
authors: Department of Gene Therapy & Regenerative Medicine, Free University of Brussels (VUB), Brussels, Belgium.
authors: Ermira
authors: E
authors: Samara-Kuko
authors: 1] Vesalius Research Center, VIB, Leuven, Belgium [2] University of Leuven, Leuven, Belgium.
authors: Bing
authors: B
authors: Yan
authors: 1] Vesalius Research Center, VIB, Leuven, Belgium [2] University of Leuven, Leuven, Belgium.
authors: Abel
authors: A
authors: Acosta-Sanchez
authors: 1] Genethon, Evry, France [2] University Pierre and Marie Curie, Paris, France.
authors: Amine
authors: A
authors: Meliani
authors: 1] INSERM, U770, Le Kremlin Bicêtre, France [2] Université Paris-Sud, Le Kremlin Bicêtre, France.
authors: Ghislaine
authors: G
authors: Cherel
authors: 1] INSERM UMR 1089, Atlantic Gene Therapies, Université de Nantes, Nantes, France [2] CHU de Nantes, Nantes, France.
authors: Véronique
authors: V
authors: Blouin
authors: 1] INSERM, U770, Le Kremlin Bicêtre, France [2] Université Paris-Sud, Le Kremlin Bicêtre, France.
authors: Olivier
authors: O
authors: Christophe
authors: 1] INSERM UMR 1089, Atlantic Gene Therapies, Université de Nantes, Nantes, France [2] CHU de Nantes, Nantes, France.
authors: Philippe
authors: P
authors: Moullier
authors: 1] Genethon, Evry, France [2] University Pierre and Marie Curie, Paris, France.
authors: Federico
authors: F
authors: Mingozzi
authors: 1] Department of Gene Therapy & Regenerative Medicine, Free University of Brussels (VUB), Brussels, Belgium [2] Department of Cardiovascular Sciences, Center for Molecular & Vascular Biology, University of Leuven, Leuven, Belgium.
authors: Thierry
authors: T
authors: VandenDriessche
mesh_terms: D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D017124:Conserved Sequence; D000229:Dependovirus / Q000235:genetics*; D005164:Factor IX / Q000235:genetics / Q000378:metabolism; D005822:Genetic Vectors / Q000008:administration & dosage; D016678:Genome; D006801:Humans; D008099:Liver / Q000378:metabolism* / Q000821:virology; D008251:Macaca / Q000235:genetics / Q000821:virology*; D051379:Mice; D009928:Organ Specificity; D050436:Regulatory Elements, Transcriptional; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism
chemical_list: D014157:Transcription Factors; D005164:Factor IX