Developmental epileptic encephalopathy with hypomyelination and brain atrophy associated with PTPN23 variants affecting the assembly of UsnRNPs.

PTPN23 encodes a ubiquitously expressed non-receptor type, catalytically inactive protein-tyrosine phosphatase found in all cells including neurons. Recently, we have identified PTPN23 in a cellular screen for the systematic identification of novel regulators of survival motor neuron (SMN) function in the assembly of splicing factors (Uridine-rich small nuclear ribonucleoproteins, UsnRNPs). Based on three families, recessive PTPN23 variants have been associated with human disease tentatively, without functional studies. Here, we describe a pediatric proband with severe developmental delay, epilepsy, cortical blindness, hypomyelination and brain atrophy on MRI. Whole exome sequencing and family study showed two novel PTPN23 variants, c.1902C>G (p.(Asn634Lys)) and c.2974delC (p.(Leu992Tyrfs*168)), in compound heterozygous state, which are predicted in silico to be damaging. When studying patient's fibroblasts we found similar expression of SMN but a dramatic reduction of cells displaying SMN accumulation in Cajal bodies (CB). SMN strongly accumulated in CB in more than 50% of unrelated control cell fibroblasts as well as in fibroblasts from the parent carrying only the c.2974delC (p.(Leu992Tyrfs*168)) variant (predicted to cause loss-of-function). In contrast, only 22% of cells showed respective SMN accumulations in patient fibroblasts (p = 1.9-2.5 × 10-7) while showing a higher level of nucleoplasmic SMN. Furthermore, the remaining accumulations in patient cells displayed weaker SMN signals than control or heterozygous wt/c.2974delC (p.(Leu992Tyrfs*168)) fibroblasts. Our report provides the first description of the clinical phenotype of recessive PTPN23 variants with pathogenicity substantiated by a functional study.

Novel mitosis-specific phosphorylation of histone H3 at Thr11 mediated by Dlk/ZIP kinase.

Death-associated protein (DAP)-like kinase (Dlk), also known as Zipper interacting protein (ZIP) kinase, is a nuclear serine/threonine-specific kinase that phosphorylates core histones H3 and H4, and myosine light chain in vitro. It interacts with transcription and splicing factors as well as with pro-apoptotic protein Par-4 suggesting that it participates in multiple cellular processes. To explore the significance of histone phosphorylation by Dlk, we determined the phosphorylation site in H3 and generated phosphospecific antibodies for in vivo analyses. Interestingly, Dlk/ZIP kinase phosphorylated histone H3 at a novel site, Thr11, rather than Ser10, which is characteristic of mitotic chromosomes. Immunoblotting and confocal immunofluorescence analyses demonstrated that phosphorylation of H3 at Thr11 occurred in vivo and was restricted to mitosis as well. It was discernable from prophase to early anaphase and particularly enriched at centromeres. Strikingly, during this time interval, Dlk was associated with centromeres too, as revealed by stable expression of a green fluorescent protein (GFP)-Dlk fusion protein. These findings strongly suggest that Dlk is a centromere-specific histone kinase that might play a role in labeling centromere-specific chromatin for subsequent mitotic processes.