A Homozygous PPP1R21 Splice Variant Associated with Severe Developmental Delay, Absence of Speech, and Muscle Weakness Leads to Activated Proteasome Function

Abstract

PPP1R21 acts as a co-factor for protein phosphatase 1 (PP1), an important serine/threonine phosphatase known to be essential for cell division, control of glycogen metabolism, protein synthesis, and muscle contractility. Bi-allelic pathogenic variants in PPP1R21 were linked to a neurodevelopmental disorder with hypotonia, facial dysmorphism, and brain abnormalities (NEDHFBA) with pediatric onset. Functional studies unraveled impaired vesicular transport as being part of PPP1R21-related pathomechanism. To decipher further the pathophysiological processes leading to the clinical manifestation of NEDHFBA, we investigated the proteomic signature of fibroblasts derived from the first NEDHFBA patient harboring a splice-site mutation in PPP1R21 and presenting with a milder phenotype. Proteomic findings and further functional studies demonstrate a profound activation of the ubiquitin–proteasome system with presence of protein aggregates and impact on cellular fitness and moreover suggest a cross-link between activation of the proteolytic system and cytoskeletal architecture (including filopodia) as exemplified on paradigmatic proteins including actin, thus extending the pathophysiological spectrum of the disease. In addition, the proteomic signature of PPP1R21-mutant fibroblasts displayed a dysregulation of a variety of proteins of neurological relevance. This includes increase proteins which might act toward antagonization of cellular stress burden in terms of pro-survival, a molecular finding which might accord with the presentation of a milder phenotype of our NEDHFBA patient.

Expanding the phenotype of PPP1R21‐related neurodevelopmental disorder

“…In fibroblasts from a patient with a splice-site mutation in PPP1R21, immunoblot studies revealed accumulation of autophagy adaptor p62, proteomic analyses revealed an overactivation of the ubiquitin-proteasome system (UPS), and cell morphological measurements indicated spatial rearrangement in the actin cytoskeleton. The authors hypothesized overactivation of the UPS represents an attempt to counteract protein aggregates resulting from endosolysosomal stall and thereby prevent cellular degeneration 7. While we report the first two missense variants in PPP1R21 associated with this recognizable disorder, we did not observe any clear indication of allelism that would account for any milder spectrum of the disorders in a genotype-phenotype spectrum.In conclusion, here we present the clinical, molecular, and radiological features of PPP1R21-related NDD in 11 new subjects with six novel variants and two recurrent variants.…”

“…We proposed that null, frameshift, and splicing variants result in complete loss‐of‐function (LoF) while the missense variants result in partial LoF thus behaving as hypomorphic alleles. Previous reports have only reported complete LoF variants (nonsense, frameshift, and splicing variants) 5–9 . Here were report the first two subjects with PPP1R21 missense variant alleles and neurodevelopmental phenotype which along with the other novel variant expand the allelic spectrum of the disease.…”

“…Previous reports have only reported complete LoF variants (nonsense, frameshift, and splicing variants). [5][6][7][8][9] Here were report the first two subjects with PPP1R21 missense variant alleles and neurodevelopmental phenotype which along with the other novel variant expand the allelic spectrum of the disease. PPP1R21 has two domains, an N-terminus KLRAQ domain and a C-terminus TTKRSYEDQ domain.…”

“…6 Recently, four more individuals were reported, including one asymptomatic newborn diagnosed with exome-based carrier screening, making the total reported cases with PPP1R21-related NDD with hypotonia, facial dysmorphism, and brain abnormalities (OMIM #619383) to date 13 cases. [7][8][9][10] In this report, we present clinical, radiological, and molecular details of 11 previously unpublished individuals with PPP1R21related NDD from nine unrelated families with six novel variants in PPP1R21. The molecular diagnosis of PPP1R21-related NDD was made from clinical(cES) or research exome sequencing (rES).…”

“…Furthermore, they showed localization of PPP1R21 protein to the early endosome suggesting a role for PPP1R21 in the endosomal maturation 6 . Recently, four more individuals were reported, including one asymptomatic newborn diagnosed with exome‐based carrier screening, making the total reported cases with PPP1R21 ‐related NDD with hypotonia, facial dysmorphism, and brain abnormalities (OMIM #619383) to date 13 cases 7–10 …”