Downregulation of SNCA Expression by Targeted Editing of DNA Methylation: A Potential Strategy for Precision Therapy in PD

Mol Ther. 2018 Nov 7;26(11):2638-2649. doi: 10.1016/j.ymthe.2018.08.019. Epub 2018 Aug 29.


Elevated levels of SNCA have been implicated in the pathogenesis of Parkinson's disease (PD), while normal physiological levels of SNCA are needed to maintain neuronal function. We ought to develop new therapeutic strategies targeting the regulation of SNCA expression. DNA methylation at SNCA intron 1 regulates SNCA transcription, and PD brains showed differential methylation levels compared to controls. Thus, DNA methylation at SNCA intron 1 is an attractive target for fine-tuned downregulation of SNCA levels. Here we developed a system, comprising an all-in-one lentiviral vector, for targeted DNA methylation editing within intron 1. The system is based on CRISPR-deactivated Cas9 (dCas9) fused with the catalytic domain of DNA-methyltransferase 3A (DNMT3A). Applying the system to human induced pluripotent stem cell (hiPSC)-derived dopaminergic neurons from a PD patient with the SNCA triplication resulted in fine downregulation of SNCA mRNA and protein mediated by targeted DNA methylation at intron 1. Furthermore, the reduction in SNCA levels by the guide RNA (gRNA)-dCas9-DMNT3A system rescued disease-related cellular phenotype characteristics of the SNCA triplication hiPSC-derived dopaminergic neurons, e.g., mitochondrial ROS production and cellular viability. We established that DNA hypermethylation at SNCA intron 1 allows an effective and sufficient tight downregulation of SNCA expression levels, suggesting the potential of this target sequence combined with the CRISPR-dCas9 technology as a novel epigenetic-based therapeutic approach for PD.

Keywords: CRISPR/dCas9; DNA methylation; Parkinson's disease; SNCA; hiPSC-derived neurons; lentiviral vector; targeted epigenome editing.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Brain / metabolism
  • Brain / pathology
  • CRISPR-Cas Systems / genetics*
  • Cell Culture Techniques
  • Cell Differentiation / genetics
  • DNA (Cytosine-5-)-Methyltransferases / genetics
  • DNA Methylation / genetics*
  • DNA Methyltransferase 3A
  • Dopaminergic Neurons / metabolism
  • Dopaminergic Neurons / pathology
  • Gene Editing
  • Gene Expression Regulation / genetics
  • Genetic Therapy*
  • Humans
  • Induced Pluripotent Stem Cells / metabolism
  • Induced Pluripotent Stem Cells / transplantation
  • Introns / genetics
  • Parkinson Disease / genetics*
  • Parkinson Disease / pathology
  • Parkinson Disease / therapy
  • RNA, Guide, Kinetoplastida / genetics
  • alpha-Synuclein / genetics*


  • DNMT3A protein, human
  • RNA, Guide
  • SNCA protein, human
  • alpha-Synuclein
  • DNA (Cytosine-5-)-Methyltransferases
  • DNA Methyltransferase 3A