title: Targeted gene correction minimally impacts whole-genome mutational load in human-disease-specific induced pluripotent stem cell clones.
abstract: The utility of genome editing technologies for disease modeling and developing cellular therapies has been extensively documented, but the impact of these technologies on mutational load at the whole-genome level remains unclear. We performed whole-genome sequencing to evaluate the mutational load at single-base resolution in individual gene-corrected human induced pluripotent stem cell (hiPSC) clones in three different disease models. In single-cell clones, gene correction by helper-dependent adenoviral vector (HDAdV) or Transcription Activator-Like Effector Nuclease (TALEN) exhibited few off-target effects and a low level of sequence variation, comparable to that accumulated in routine hiPSC culture. The sequence variants were randomly distributed and unique to individual clones. We also combined both technologies and developed a TALEN-HDAdV hybrid vector, which significantly increased gene-correction efficiency in hiPSCs. Therefore, with careful monitoring via whole-genome sequencing it is possible to apply genome editing to human pluripotent cells with minimal impact on genomic mutational load.
authors.affiliation: Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
authors.forename: Keiichiro
authors.initials: K
authors.lastname: Suzuki
authors.affiliation: BGI, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China.
authors.forename: Chang
authors.initials: C
authors.lastname: Yu
authors.affiliation: Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Qu
authors.affiliation: Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
authors.forename: Mo
authors.initials: M
authors.lastname: Li
authors.affiliation: BGI, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China.
authors.forename: Xiaotian
authors.initials: X
authors.lastname: Yao
authors.affiliation: National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Tingting
authors.initials: T
authors.lastname: Yuan
authors.affiliation: Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
authors.forename: April
authors.initials: A
authors.lastname: Goebl
authors.affiliation: BGI, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China; Institute of Digestive Disease and the Department of Medicine and Therapeutics, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong.
authors.forename: Senwei
authors.initials: S
authors.lastname: Tang
authors.affiliation: National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Ruotong
authors.initials: R
authors.lastname: Ren
authors.affiliation: Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
authors.forename: Emi
authors.initials: E
authors.lastname: Aizawa
authors.affiliation: BGI, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China; Department of Computational Medicine and Bioinformatics, Medical School, University of Michigan, 500 South State Street, Ann Arbor, MI 48109, USA.
authors.forename: Fan
authors.initials: F
authors.lastname: Zhang
authors.affiliation: National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Xiuling
authors.initials: X
authors.lastname: Xu
authors.affiliation: Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
authors.forename: Rupa Devi
authors.initials: RD
authors.lastname: Soligalla
authors.affiliation: BGI, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China.
authors.forename: Feng
authors.initials: F
authors.lastname: Chen
authors.affiliation: Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
authors.forename: Jessica
authors.initials: J
authors.lastname: Kim
authors.affiliation: Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
authors.forename: Na Young
authors.initials: NY
authors.lastname: Kim
authors.affiliation: Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
authors.forename: Hsin-Kai
authors.initials: HK
authors.lastname: Liao
authors.affiliation: Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
authors.forename: Chris
authors.initials: C
authors.lastname: Benner
authors.affiliation: Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
authors.forename: Concepcion Rodriguez
authors.initials: CR
authors.lastname: Esteban
authors.affiliation: BGI, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China.
authors.forename: Yabin
authors.initials: Y
authors.lastname: Jin
authors.affiliation: National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Center for Age-related Diseases (CAD), Beijing, China; Beijing Institute for Brain Disorders, Beijing 100069, China. Electronic address: ghliu@ibp.ac.cn.
authors.forename: Guang-Hui
authors.initials: GH
authors.lastname: Liu
authors.affiliation: BGI, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China. Electronic address: liyr@genomics.cn.
authors.forename: Yingrui
authors.initials: Y
authors.lastname: Li
authors.affiliation: Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA. Electronic address: belmonte@salk.edu.
authors.forename: Juan Carlos
authors.initials: JC
authors.lastname: Izpisua Belmonte
mesh_terms: D000256:Adenoviridae / Q000235:genetics*; D064113:CRISPR-Cas Systems / Q000235:genetics; D002999:Clone Cells; D004260:DNA Repair / Q000235:genetics; D004720:Endonucleases / Q000235:genetics / Q000378:metabolism*; D015316:Genetic Therapy; D005822:Genetic Vectors / Q000235:genetics / Q000378:metabolism*; D016678:Genome / Q000235:genetics; D057809:HEK293 Cells; D006801:Humans; D057026:Induced Pluripotent Stem Cells / Q000502:physiology*; D009154:Mutation / Q000235:genetics; D044968:Regenerative Medicine; D017422:Sequence Analysis, DNA
chemical_list: D004720:Endonucleases