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PubMed · 39947136

Activation of the imprinted Prader-Willi syndrome locus by CRISPR-based epigenome editing.

Dahlia Rohm·Joshua B Black·Sean R McCutcheon·Alejandro Barrera·Shanté S Berry·Daniel J Morone·Xander Nuttle·Celine E de Esch·Derek J C Tai·Michael E Talkowski·Nahid Iglesias·Charles A Gersbach
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Abstract

Epigenome editing with DNA-targeting technologies such as CRISPR-dCas9 can be used to dissect gene regulatory mechanisms and potentially treat associated disorders. For example, Prader-Willi syndrome (PWS) results from loss of paternally expressed imprinted genes on chromosome 15q11.2-q13.3, although the maternal allele is intact but epigenetically silenced. Using CRISPR repression and activation screens in human induced pluripotent stem cells (iPSCs), we identified genomic elements that control the expression of the PWS gene SNRPN from the paternal and maternal chromosomes. We showed that either targeted transcriptional activation or DNA demethylation can activate the silenced maternal SNRPN and downstream PWS transcripts. However, these two approaches function at unique regions, preferentially activating different transcript variants and involving distinct epigenetic reprogramming mechanisms. Remarkably, transient expression of the targeted demethylase leads to stable, long-term maternal SNRPN expression in PWS iPSCs. This work uncovers targeted epigenetic manipulations to reprogram a disease-associated imprinted locus and suggests possible therapeutic interventions.

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Prader-Willi SyndromeHumansGenomic ImprintingInduced Pluripotent Stem CellsGene EditingsnRNP Core ProteinsCRISPR-Cas SystemsDNA MethylationEpigenesis, GeneticEpigenomeChromosomes, Human, Pair 15Clustered Regularly Interspaced Short Palindromic RepeatsEpigenome EditingCRISPRDNA methylationdCas9epigenome editingimprintingJournal Article

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Dahlia Rohm, Joshua B Black, Sean R McCutcheon, Alejandro Barrera, Shanté S Berry, Daniel J Morone, Xander Nuttle, Celine E de Esch, Derek J C Tai, Michael E Talkowski, Nahid Iglesias, Charles A Gersbach. 2025-02-12. Activation of the imprinted Prader-Willi syndrome locus by CRISPR-based epigenome editing.. https://doi.org/10.1016/j.xgen.2025.100770

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PubMed2025

Rescue of imprinted genes by epigenome editing in human cellular models of Prader-Willi syndrome.

Prader-Willi syndrome (PWS) is a genomic imprinting disorder caused by the loss of function of the paternal chromosome 15q11-13, resulting in a spectrum of symptoms associated with hypothalamic dysfunction. PWS patients lack the expression of paternally expressed genes (PEGs) in the 15q11-13 locus but possess an epigenetically silenced set of these genes in the maternal allele. Thus, activation of these silenced genes can serve as a therapeutic target for PWS. Here, we leverage CRISPR-based epigenome editing system to modulate the DNA methylation status of the PWS imprinting control region (PWS-ICR) in induced pluripotent stem cells (iPSCs) derived from PWS patients. Successful demethylation in the PWS-ICR restores the PEG expression from the maternal allele and reorganizes the methylation patterns in other PWS-associated imprinted regions beyond the PWS-ICR. Remarkably, these corrected epigenomic patterns and PEG expression are maintained following the differentiation of these cells into hypothalamic organoids. Finally, the single-cell transcriptomic analysis of epigenome-edited organoids demonstrates a partial restoration of the transcriptomic dysregulation observed in PWS. This study highlights the utility of epigenome editing technology as a therapeutic approach in addressing PWS and potentially other imprinting disorders.

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