Hao-Fountain syndrome (HAFOUS) is a rare autosomal dominant neurodevelopmental disorder caused by pathogenic USP7 variants. A diagnostic blood DNA methylation episignature has been established, yet the broader regulatory consequences of USP7 haploinsufficiency and their tissue specificity remain incompletely characterized. We performed genome-wide DNA methylation profiling, RNA sequencing, and cis expression quantitative trait methylation (eQTM) analysis in whole blood (n = 9) and patient-derived skin fibroblasts (n = 4). Differential methylation was assessed and methylation-expression coupling within ±250 kb of each DMR. DMRs were further interpreted using BCOR, H2AK119ub1, and H3K27me3 ChIP-Rx datasets from neural models. Blood reproduced the established USP7 hypermethylation episignature and yielded 17 significant DMRs, accompanied by modest numbers of differentially expressed genes and eQTMs. Fibroblasts displayed internally coherent regulatory patterns, including 2,143 nominal DMRs, 310 differentially expressed genes, and 559 significant eQTMs. Convergent methylation-expression changes prominently involved the HOXB cluster (HOXB3, HOXB5, HOXB6). Both blood- and fibroblast-derived DMRs showed significant enrichment for BCOR- and H2AK119ub1-marked regions, consistent with disruption of non-canonical PRC1.1-associated chromatin. Cross-tissue comparison revealed limited overlap, supporting marked tissue specificity in methylation-expression relationships. USP7 haploinsufficiency is associated with a restricted set of regulatory loci enriched within PRC1-associated chromatin domains. Fibroblasts revealed coherent methylation and expression changes at developmental genes, whereas blood captured the diagnostic episignature and a smaller set of downstream regulatory alterations. Together, this dual-tissue integrative analysis refines the molecular consequences of reduced USP7 dosage and provides a framework for future mechanistic studies in disease-relevant cellular models.

Hao-Fountain Syndrome (HAFOUS) is an autosomal dominant neurodevelopmental disorder caused by pathogenic variants in the USP7 gene. Research into the molecular mechanisms of HAFOUS has been limited by the lack of suitable human model systems. In this study, we introduce induced pluripotent stem cell (iPSC) lines derived from a HAFOUS patient, providing a valuable model to investigate mechanisms of altered cell lineage commitment during disease progression. This model offers a platform to explore the role of USP7 variants in HAFOUS pathogenesis and develop potential therapeutic strategies.

Ubiquitin-specific protease 7 (USP7) is a deubiquitylase essential for cell homeostasis, DNA repair, and regulation of both tumor suppressors and oncogenes. Recently, haploinsufficiency of USP7 has been associated with Hao-Fountain syndrome (HAFOUS), a rare neurodevelopmental disorder. Although a range of USP7 inhibitors have been developed over the last decade, in the context of HAFOUS, USP7 activators may represent a more relevant approach. To address this challenge, we report the identification and characterization of a small-molecule activator of USP7 called MS-8. Structural and functional studies show that MS-8 allosterically activates USP7, mimicking the endogenous autoactivation mechanism of the enzyme. We observed that MS-8 engages and activates mutant USP7 in a cellular context, impacting downstream proteins. Taken together, our study provides validation of the USP7 activator that paves the way toward activation-driven USP7 pharmacology.

Hao-Fountain syndrome is a rare neurodevelopmental disorder caused by mutations in the deubiquitinating enzyme Ubiquitin-Specific Protease 7 (USP7). Due to the novelty of the disease and its poorly understood molecular mechanisms, treatments for the syndrome are currently lacking. This study examines the effects of 11 patient-derived variants located within the catalytic domain of USP7, focusing on their impact on the enzyme's activity, thermodynamic stability, and substrate recognition. Our findings reveal a spectrum of functional consequences, ranging from complete inactivation to hyperactivation of USP7. Notably, we identify a specific subset of pathogenic variants whose catalytic activity can be significantly boosted using an allosteric activator, MS-8. These results provide insight into USP7 malfunction in Hao-Fountain syndrome-linked variants and pave the way for improved prognostic approaches and targeted treatments in the future.

Ubiquitin-specific protease 7 (USP7) is a deubiquitinating enzyme that plays a crucial role in cellular processes, including the maintenance of genome stability and regulation of antiviral and immune responses. Its dysfunction is linked to various cancers and neurodevelopmental disorders such as Hao-Fountain syndrome. Unlike other USP-family enzymes, the triad of catalytic residues in USP7 adopts an inactive conformation and undergoes rearrangement into the active state upon substrate binding. Despite its potential importance for regulating the enzyme's activity, the dynamics of USP7 have not been explored. In this study, we combine advanced CPMG NMR relaxation dispersion measurements with the analysis of enzyme kinetics to investigate the conformational dynamics of USP7 in solution and its role in enzyme activation. Our results suggest that apo-USP7 exists in a dynamic equilibrium, transiently switching between inactive and low-populated active conformations, indicating that enzyme activation can occur spontaneously, even in the absence of a substrate. Furthermore, we show that the Hao-Fountain syndrome-associated variant G392D enhances the conformational dynamics of the enzyme, leading to a significant increase in its catalytic activity. This study captures the sparsely populated, "invisible" active conformation of USP7 and demonstrates how changes in enzyme dynamics can contribute to activity, offering broader insights into enzyme function and disease mechanisms.