A chemically modified promoter-targeted duplex RNA activates TCF4 expression

ABSTRACT Pitt-Hopkins syndrome (PTHS) is a severe neurodevelopmental disorder caused by haploinsufficient expression of transcription factor 4 ( TCF4 ). Increasing expression from the remaining functional TCF4 allele could provide a mutation-independent strategy for patients with diverse pathogenic variants. We integrated genomic datasets with strand-specific RNA analysis to identify transcribed regions of the TCF4 promoter suitable for targeting by activating double-stranded RNAs (dsRNAs). Screening of overlapping promoter-targeted dsRNAs identified a hotspot for increased TCF4 expression. Activation was retained by a lead dsRNA containing extensive 2′-fluoro, 2′-O-methyl, and phosphorothioate modifications used in therapeutic oligonucleotides. Anti-AGO2 immunoprecipitation showed association with RNA transcribed from the targeted promoter region. dsRNA-mediated activation was associated with increased RNA polymerase II occupancy. These findings establish promoter-targeted dsRNAs as chemically tractable starting points for increasing TCF4 expression and support their investigation as a mutation-independent strategy for haploinsufficient disease.