Dysfunctional Homozygous VRK1-D263G Variant Impairs the Assembly of Cajal Bodies and DNA Damage Response in Hereditary Spastic Paraplegia

Abstract

Background and ObjectivesTo conduct a genetic and molecular functional study of a family with members affected of hereditary spastic paraplegia (HSP) of unknown origin and carrying a novel pathogenic vaccinia-related kinase 1 (VRK1) variant.MethodsWhole-exome sequencing was performed in 2 patients, and their parents diagnosed with HSP. The novel VRK1 variant was detected by whole-exome sequencing, molecularly modeled and biochemically characterized in kinase assays. Functionally, we studied the role of this VRK1 variant in DNA damage response and its effect on the assembly of Cajal bodies (CBs).ResultsWe have identified a very rare homozygous variant VRK1-D263G with a neurologic phenotype associated with HSP and moderate intellectual disability. The molecular modeling of this VRK1 variant protein predicted an alteration in the folding of a loop that interferes with the access to the kinase catalytic site. The VRK1-D263G variant is kinase inactive and does not phosphorylate histones H2AX and H3, transcription factors activating transcription factor 2 and p53, coilin needed for assembly of CBs, and p53 binding protein 1, a DNA repair protein. Functionally, this VRK1 variant protein impairs CB formation and the DNA damage response.DiscussionThis report expands the neurologic spectrum of neuromotor syndromes associated with a new and rare VRK1 variant, representing a novel pathogenic participant in complicated HSP and demonstrates that CBs and the DNA damage response are impaired in these patients.

Pathogenic effects of Leu200Pro and Arg387His VRK1 protein variants on phosphorylation targets and H4K16 acetylation in distal hereditary motor neuropathy

“…A consequence of alterations of H4K16 acetylation will be the impairment of the DNA damage response (DDR), which can be detected by the formation of 53BP1 foci. This has already been shown to be the case for several of the VRK1 variants studied [ 9 , 39 , 48 ]. The formation of 53BP1 foci in response to doxorubicin is regulated by VRK1, by directly phosphorylating 53BP1 in Ser 25/29 [ 19 ].…”

“…4 ). The R219I, T228M, R241C, W254L, T256I, G257S, D263G, D267G, and W375* were modeled as previously described for other VRK1 variants [ 9 , 39 ].

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“…This epigenetic modification is critical for the dynamic remodeling of chromatin, and is required for correct DNA damage responses. Several variants are known to impair DNA damage responses detected by their effect on γH2AX [ 20 , 47 ] and 53BP1 foci formation [ 7 , 9 , 39 ]. VRK1 specifically phosphorylates Tip60 in The158 and Ser199 facilitating both its acetyltransferase activity and translocation to chromatin [ 27 , 30 ].…”

“…Rare variants of the human VRK1 gene are associated with a heterogeneous group of neurological diseases, affecting motor neurons and the peripheral nerves, sensory and sensory-motor. Among these diseases are spinal muscular atrophy (SMA), amyotrophic lateral sclerosis (ALS), distal hereditary motor neuropathies (dHMN), and Charcot-Marie-Tooth (CMT) disease [ 3 – 9 ]. All VRK1 gene variants associated with these diseases are recessive and their clinical phenotypes are manifested either in homozygous or compound heterozygous individuals [ 3 – 9 ].…”

“…Among these diseases are spinal muscular atrophy (SMA), amyotrophic lateral sclerosis (ALS), distal hereditary motor neuropathies (dHMN), and Charcot-Marie-Tooth (CMT) disease [ 3 – 9 ]. All VRK1 gene variants associated with these diseases are recessive and their clinical phenotypes are manifested either in homozygous or compound heterozygous individuals [ 3 – 9 ]. The evolution of these diseases affecting motor neurons is slowly progressive, often starting early in life, and their clinical manifestations are initially distal.…”