A Recurrent De Novo PACS2 Heterozygous Missense Variant Causes Neonatal-Onset Developmental Epileptic Encephalopathy, Facial Dysmorphism, and Cerebellar Dysgenesis

Abstract

Developmental and epileptic encephalopathies (DEEs) represent a large clinical and genetic heterogeneous group of neurodevelopmental diseases. The identification of pathogenic genetic variants in DEEs remains crucial for deciphering this complex group and for accurately caring for affected individuals (clinical diagnosis, genetic counseling, impacting medical, precision therapy, clinical trials, etc.). Whole-exome sequencing and intensive data sharing identified a recurrent de novo PACS2 heterozygous missense variant in 14 unrelated individuals. Their phenotype was characterized by epilepsy, global developmental delay with or without autism, common cerebellar dysgenesis, and facial dysmorphism. Mixed focal and generalized epilepsy occurred in the neonatal period, controlled with difficulty in the first year, but many improved in early childhood. PACS2 is an important PACS1 paralog and encodes a multifunctional sorting protein involved in nuclear gene expression and pathway traffic regulation. Both proteins harbor cargo(furin)-binding regions (FBRs) that bind cargo proteins, sorting adaptors, and cellular kinase. Compared to the defined PACS1 recurrent variant series, individuals with PACS2 variant have more consistently neonatal/early-infantile-onset epilepsy that can be challenging to control. Cerebellar abnormalities may be similar but PACS2 individuals exhibit a pattern of clear dysgenesis ranging from mild to severe. Functional studies demonstrated that the PACS2 recurrent variant reduces the ability of the predicted autoregulatory domain to modulate the interaction between the PACS2 FBR and client proteins, which may disturb cellular function. These findings support the causality of this recurrent de novo PACS2 heterozygous missense in DEEs with facial dysmorphim and cerebellar dysgenesis.

Keywords: PACS-2; PACS2; cerebellar dysgenesis; epilepsy; intellectual disability.

Figure 1

Clinical and Imaging Features (A) Pictures of individuals 1 (a, b), 2 (c, d), 3 (e, f), 5 (g, h), 7 (i, j), and 11 (k, l): variable facial dysmorphism. (B) Spectrum of posterior fossa abnormalities in the PACS2 cohort. Sagittal T1 weighted (m–p, u–x), axial T2 weighted (t, y–ab), axial T1 weighted (q, s), and coronal T2 weighted (r) imaging for subject 2 at 5 years of age (m, q), subject 4 at 3 weeks of age (n, r), subject 5 at 7 days of age (o, s), subject 9 at 1 week of age (p, t), subject 10 at 1 month of age (u, y), subject 12 at 3 months of age (v, z), subject 13 at 23 months of age (w, aa), and subject 14 at 2.5 years of age (x, ab). Of 8 subjects with centrally reviewed imaging, there was prominence of the cisterna magna (asterisk in o) in all but subject 13 (w) and widening of the foramen Magendie in all subjects except subject 12 (v). Mild inferior vermian hypoplasia was also evident in subjects 2 (m), 4 (n), 5 (o), and 14 (x). Cerebellar hemisphere dysplasia was present in subjects 2 (q), 4 (r), 5 (s), 12 (z), and 13 (aa) manifest as unusual centrifugal orientation of the folia bilaterally in subjects 2 (q, arrows) and 12 (z, arrows) and on the left side only in subject 5 (s, arrow). Distortion of the foliar pattern was present without centrifugal orientation in subjects 4 (r) and 13 (aa). Subtler foliar distortion was visible in subjects 9 (t) and 14 (ab).

Figure 2

PACS2 Variant Location (A) Schematic of PACS1 and PACS2 illustrating the proposed domains (ARR, atrophin-1-related region; FBR, furin (cargo)-binding region; MR, middle region; CTR, C-terminal region) and residues important for partner protein binding (AP-1, adaptor protein complex 1; CK2, protein kinase CK2; GGA, Golgi-associated γ-adaptin ear homology domain ARF-interacting protein), with location of PACS1 and PACS2 missense variants responsible for intellectual disability. (B) HCT116 cells, which can be efficiently transfected with plasmids, expressing the indicated proteins were harvested in mRIPA (50 mM Tris-HCl [pH 8.0] plus 1% NP-40, 1% deoxycholate, and 150 mM NaCl) containing proteinase inhibitors (0.5 mM PMSF, 0.1 μM each of aprotinin, E-64, and leupeptin) and phosphatase inhibitors (1 mM Na₃VO₄ and 20 mM NaF). The FLAG-tagged cargo proteins SIRT1, HDAC1, or TRPV1 were immunoprecipitated with anti-Flag antibody (Sigma #F7425) and co-precipitating HA-tagged PACS2 or PACS2 p.Glu209Lys was detected by western blot using anti-HA antibody (Cell Signaling Technology #3724S) and developed with the Pierce ECL Western Blotting Substrate (ThermoFisher) using a FluorChem E image acquisition system (ProteinSimple). Signals were quantified using the AlphaView image analysis software package (ProteinSimple) and normalized to wild-type PACS2. Data are mean ± standard deviation, n = 4.