CRISPR/Cas9-mediated Knockout of the Neuropsychiatric Risk Gene KCTD13 Causes Developmental Deficits in Human Cortical Neurons Derived from Induced Pluripotent Stem Cells

Mol Neurobiol. 2020 Feb;57(2):616-634. doi: 10.1007/s12035-019-01727-1. Epub 2019 Aug 11.


The human KCTD13 gene is located within the 16p11.2 locus and copy number variants of this locus are associated with a high risk for neuropsychiatric diseases including autism spectrum disorder and schizophrenia. Studies in zebrafish point to a role of KCTD13 in proliferation of neural precursor cells which may contribute to macrocephaly in 16p11.2 deletion carriers. KCTD13 is highly expressed in the fetal human brain and in mouse cortical neurons, but its contribution to the development and function of mammalian neurons is not completely understood. In the present study, we deleted the KCTD13 gene in human-induced pluripotent stem cells (iPSCs) using CRISPR/Cas9 nickase. Following neural differentiation of KCTD13 deficient and isogenic control iPSC lines, we detected a moderate but significant inhibition of DNA synthesis and proliferation in KCTD13 deficient human neural precursor cells. KCTD13 deficient cortical neurons derived from iPSCs showed decreased neurite formation and reduced spontaneous network activity. RNA-sequencing and pathway analysis pointed to a role for ERBB signaling in these phenotypic changes. Consistently, activating and inhibiting ERBB kinases rescued and aggravated, respectively, impaired neurite formation. In contrast to findings in non-neuronal human HeLa cells, we did not detect an accumulation of the putative KCTD13/Cullin-3 substrate RhoA, and treatment with inhibitors of RhoA signaling did not rescue decreased neurite formation in human KCTD13 knockout neurons. Taken together, our data provide insight into the role of KCTD13 in neurodevelopmental disorders, and point to ERBB signaling as a potential target for neuropsychiatric disorders associated with KCTD13 deficiency.

Keywords: 16p11.2; CRISPR/Cas9; Induced pluripotent stem cells; KCTD13; Neurodevelopment; Neuropsychiatric disorders.

MeSH terms

  • Base Sequence
  • CRISPR-Associated Protein 9 / metabolism
  • CRISPR-Cas Systems / genetics*
  • Cell Differentiation
  • Cell Proliferation
  • Cerebral Cortex / pathology*
  • DNA / biosynthesis
  • Gene Knockout Techniques*
  • Genetic Predisposition to Disease*
  • Humans
  • Induced Pluripotent Stem Cells / pathology*
  • Mental Disorders / genetics*
  • Neural Stem Cells / metabolism
  • Neurites / metabolism
  • Neurons / pathology*
  • Nuclear Proteins / deficiency
  • Nuclear Proteins / genetics*
  • Receptor, ErbB-2 / metabolism
  • Risk Factors
  • rhoA GTP-Binding Protein / metabolism


  • KCTD13 protein, human
  • Nuclear Proteins
  • RHOA protein, human
  • DNA
  • Receptor, ErbB-2
  • CRISPR-Associated Protein 9
  • rhoA GTP-Binding Protein