Inducible XIST-mediated trisomy 21 correction uncovers a USP16-p16 senescence axis driving epileptogenesis in Down syndrome

Down syndrome (DS), caused by human chromosome 21 (HSA21) trisomy, carries elevated epilepsy risk with unknown mechanisms. We integrated clinical epidemiology, fetal brain single-nucleus RNA sequencing, patient-derived induced pluripotent stem cell (iPSC) models, cerebral organoids, and in vivo chimeric mice to dissect this link. Clinical analysis of 1,365 DS individuals exhibited an age-stratified epilepsy prevalence pattern, with higher rates in older children. Fetal brain transcriptomes revealed neurogenesis defects, aging-related signatures, synaptic/metabolic dysregulation. We engineered an inducible XIST-mediated extra HSA21 silencing system in female DS iPSCs, showing HSA21 dosage correction reduced neural progenitor cell (NPC) senescence markers and neuronal hyperexcitability. Transcriptomic screening pinpointed USP16 as a key pro-aging candidate. Moreover, USP16 suppression and the senolytic combination dasatinib/quercetin reduced senescence-linked and hyperexcitability-associated readouts, supporting a USP16-p16-NPC aging axis as a therapeutic target for DS-associated epilepsy, with broader implications for aging-linked neurological disorders.