Efficient SNP editing in haploid human pluripotent stem cells

J Assist Reprod Genet. 2020 Apr;37(4):735-745. doi: 10.1007/s10815-020-01723-8. Epub 2020 Mar 11.


Purpose: To correct a potentially damaging mutation in haploid human embryonic stem cells.

Methods: Exome sequencing was performed on DNA extracted from parthenogenetically derived embryonic stem cell line (pES12). An SLC10A2 gene mutation, which affects bile acid transport, was chosen as mutation of interest in this proof of concept study to attempt correction in human pluripotent haploid cells. Confirmation of the mutation was verified, and guide RNA and a correction template was designed in preparation of performing CRISPR. Haploid cells underwent serial fluorescence activated cell sorting (FACS) with Hoechst 33342 to create an increasingly haploid (1n) enriched culture. Nucleofection was performed on p. 37 and then cells were sorted for 1n DNA content with +GFP to identify the haploid cells that expressed Cas9 tagged with GFP.

Results: 104,686 haploid GFP + cells were collected. Cells were cultured, individual colonies picked, and 48 clones were sent for Sanger sequencing. CRIPSR efficiency was 77.1%, with 7/48 (14.6%) clones resulting in a corrected SLC10A2 mutation. Confirmation of persistence of haploid cells was achieved with repeated FACS sorting and centromere quantification. Given the large number of passages and exposure to CRISPR, we also performed analysis of karyotypes and of off-target effects. Cells evaluated were karyotypically normal and there was no evident off target effects.

Conclusions: CRISPR/Cas9 can be effectively utilized to edit mutations in haploid human embryonic stem cells. Establishment and maintenance of a haploid cell culture provides a novel way to utilize CRISPR/Cas9 in gene editing, particularly in the study of recessive alleles.

Keywords: CRISPR/Cas-9; Gene editing; Haploid stem cells.

MeSH terms

  • CRISPR-Cas Systems / genetics*
  • Cell Line
  • Centromere / genetics
  • Embryonic Stem Cells / cytology
  • Exome Sequencing
  • Gene Editing
  • Haploidy
  • Humans
  • Induced Pluripotent Stem Cells / cytology*
  • Mutation / genetics
  • Organic Anion Transporters, Sodium-Dependent / genetics*
  • Parthenogenesis / genetics
  • RNA, Guide, Kinetoplastida / genetics*
  • Symporters / genetics*


  • Organic Anion Transporters, Sodium-Dependent
  • RNA, Guide
  • Symporters
  • sodium-bile acid cotransporter