Biallelic Variants in UBA5 Link Dysfunctional UFM1 Ubiquitin-like Modifier Pathway to Severe Infantile-Onset Encephalopathy

Abstract

The ubiquitin fold modifier 1 (UFM1) cascade is a recently identified evolutionarily conserved ubiquitin-like modification system whose function and link to human disease have remained largely uncharacterized. By using exome sequencing in Finnish individuals with severe epileptic syndromes, we identified pathogenic compound heterozygous variants in UBA5, encoding an activating enzyme for UFM1, in two unrelated families. Two additional individuals with biallelic UBA5 variants were identified from the UK-based Deciphering Developmental Disorders study and one from the Northern Finland Intellectual Disability cohort. The affected individuals (n = 9) presented in early infancy with severe irritability, followed by dystonia and stagnation of development. Furthermore, the majority of individuals display postnatal microcephaly and epilepsy and develop spasticity. The affected individuals were compound heterozygous for a missense substitution, c.1111G>A (p.Ala371Thr; allele frequency of 0.28% in Europeans), and a nonsense variant or c.164G>A that encodes an amino acid substitution p.Arg55His, but also affects splicing by facilitating exon 2 skipping, thus also being in effect a loss-of-function allele. Using an in vitro thioester formation assay and cellular analyses, we show that the p.Ala371Thr variant is hypomorphic with attenuated ability to transfer the activated UFM1 to UFC1. Finally, we show that the CNS-specific knockout of Ufm1 in mice causes neonatal death accompanied by microcephaly and apoptosis in specific neurons, further suggesting that the UFM1 system is essential for CNS development and function. Taken together, our data imply that the combination of a hypomorphic p.Ala371Thr variant in trans with a loss-of-function allele in UBA5 underlies a severe infantile-onset encephalopathy.

The UFM1 cascade times mitosis entry associated with microcephaly

“…17,18,20,26,27 However, the mechanism behind its contribution to microcephaly remains to be defined. 17,18,20,26,27 However, the mechanism behind its contribution to microcephaly remains to be defined.…”

“…17 Other studies have shown that the depletion of the UFM1 cascade in Caenorhabditis elegans altered cholinergic neurotransmission, while its silencing in zebrafish induced abnormal seizure-like movements. Conditional knockout of UFM1 in the central nervous system (CNS) resulted in neonatal death with microcephaly, 20 indicating that this cascade was also essential for CNS development. 13,19 Transgenic expression of UBA5 in the erythroid lineage extended the life span of UBA5-deficient embryos, but only to E18.5, 19 indicating that the UFM1 cascade plays vital roles in not just the hematopoietic system.…”

“…17,18,[20][21][22][23][24][25][26] In 2016, we performed Whole Exome Sequencing on two siblings and observed two compound heterogeneous mutations in UBA5 with significant cerebellar atrophy, gait instability, speech difficulties, and cataract. 17,18,[20][21][22][23][24][25][26] In 2016, we performed Whole Exome Sequencing on two siblings and observed two compound heterogeneous mutations in UBA5 with significant cerebellar atrophy, gait instability, speech difficulties, and cataract.…”

“…17,18,[20][21][22][23][24][25][26] In 2016, we performed Whole Exome Sequencing on two siblings and observed two compound heterogeneous mutations in UBA5 with significant cerebellar atrophy, gait instability, speech difficulties, and cataract. 18,20 More recently, biallelic mutations of UFM1 or UFC1 were reported in cases with microcephaly, global developmental delay, and seizures. 18,20 More recently, biallelic mutations of UFM1 or UFC1 were reported in cases with microcephaly, global developmental delay, and seizures.…”

PEHO syndrome: the endpoint of different genetic epilepsies

“…The c.1111G>A p.Ala371Thr variant is the recorded SNP rs114925667 with a population frequency in EVS of 0.0015 (20/12976) and in ExAC of 0.0018 (223/121150). It has been shown to be a pathogenic hypomorphic variant affecting UBA5 function 36. This pathogenic SNP was found as the second mutation in nine children reported with a severe infantile-onset encephalopathy, and in each of the five families described, the first variant was a nonsense or pathogenic splice site variant.…”