UFSP2-related spondyloepimetaphyseal dysplasia: A confirmatory report

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Abstract

Spondyloepimetaphyseal dysplasias (SEMDs), which comprise a heterogeneous group of autosomal-dominant, autosomal-recessive and X-linked recessive disorders, are characterized by anomalies of the spine, the epiphyses and metaphyses of the long bones, resulting in short stature and osteoarthritic changes of the joints. UFSP2 gene encodes a highly conserved cysteine protease which cleaves two C-terminal residues from ubiquitin-fold modifier 1, an ubiquitin-like post-translational modifier protein. In 2018, Di Rocco, M reported for the first time that a novel heterozygous variant exon 11: c.1277A > C of the UFSP2 gene was the cause to spondyloepimetaphyseal dysplasia mainly manifested as: short stature, anterior vertebral dysplasia, hip dysplasia, flat vertebra, spinal metaphyseal dysplasia, irregular acetabular apex, distal femoral metaphyseal dysplasia, proximal tibial metaphyseal dysplasia, osteoarthritis and so on. In this report, we describe a boy with spondyloepimetaphyseal dysplasia due to a novel mutation exon 11: c.1283A > G (leading to p. H428R) of the UFSP2 gene. This is the second report to describe children with SEMDs associated with an UFSP2 variant. However, it is the first to describe a UFSP2 gene mutation exon 11: c.1283A > G (leading to p. H428R). Our findings of a novel heterozygous mutation of UFSP2 gene add to the list of 2 reported heterozygous mutations of UFSP2 which led to hereditary osteopathy.

Introduction

Spondyloepimetaphyseal dysplasias (SEMDs), which comprise a heterogeneous group of autosomal-dominant, autosomal-recessive and X-linked recessive disorders, are characterized by anomalies of the spine, the epiphyses and metaphyses of the long bones, resulting in short stature and osteoarthritic changes of the joints (Cho et al., 2016). It can be divided into various types and each type has different clinical characteristics according to OMIM database (https://omim.org/search/?index=entry&start=1&limit=10&sort=score+desc%2C+prefix_sort+desc&search=SPONDYLOEPIMETAPHYSEAL+DYSPLASIA). Like ubiquitin, ubiquitin-fold modifier-1 (UFM1) must be processed by a protease before it can conjugate with its target proteins. UFSP2 is a thiol protease that specifically processes the C terminus of UFM1 (Kang et al., 2007). Ha et al. solved the crystal structure of mouse Ufsp2 to 2.6-Å resolution revealing a C-terminal catalytic domain and an N-terminal substrate recognition domain connected by a linker of about 20 residues. The catalytic domain with tyr282, cys294, asp418, and his420, as well as a regulatory loop, participating in catalysis. The N-terminal domain bound its substrate targeted Ufsp2 to endoplasmic reticulum (Ha et al., 2011).

Spondyloepimetaphyseal dysplasia of the Di Ro cco type (SEMDDR, 617974) characterized by short stature, joint pain, and genu varum, as well as involving primarily the hips but also affecting the wrists, hands, knees, ankles, variable degrees of metaphyseal and spine, is just reported by Di Rocco et al., in 2018 for the first time and heterozygosity for a missense mutation in UFSP2 gene was identified as the pathogenic factor (Di Rocco et al., 2018). According to the report, a heterozygosity for a c.1277A-C transversion (c.1277A-C, NM_018359) in exon 11 of the UFSP2 gene was identified in a 3-year-old Italian girl with SEMDDR and her affected mother and grandmother, resulting in an D426A substitution within the active enzymatic site of the protein, involving one of the four catalytic residues identified by Ha et al. (Di Rocco et al., 2018; Ha et al., 2011).

We herein reported an SEMDDR in a Chinese boy due to a novel mutation also in exon 11 of UFSP2 gene which was initially suspected to be mucopolysaccharidosis type IVA (MPS IVA). The aim of this study is to report a novel missense mutation of UFSP2, to enrich the number of cases of SEMDDR caused by the mutation of UFSP2, and to heighten clinician awareness of SEMDDR.

An 8-year old Chiniese boy came to Zunyi Medical University in March 2019 for evaluation of short stature, skeletal deformities and searching for cause of the disease. The boy born at term from healthy parents with birth weights and birth lengths being within the normal range, came to medical attention at the age of 2 years and 9 months old due to short stature with no obvious retardation in mental and sports development. At that time, a systematic orthopedic workup was carried out and showed that pelvis, femur are the main lesions with mild vertebral abnormalities as Fig. 1. Morphological abnormalities of pituitary gland were excluded by cranial magnetic resonance imaging (MRI) as Supplementary Fig. 1. Stimulation test of growth hormone was normal. Calcium, phosphorus, alkaline phosphatase and growth hormone are all within normal range as Table 1. Gene screening for dwarfism (including 448 genes and 427 diseases as Supplementary Fig. 2) by sequencing of target region capture showed that no other mutations of known pathogenic genes for skeletal system-related dwarfism associated with the clinical manifestations of this boy were identified except for a heterozygous variant: c.1198G > A (leading to p.A400T) of the GALNS gene (NM_000512), associated with MPS IVA. At the age of 5 years and 5 months old, the second visit was made because of the aggravation of growth disorder and joint pain. Enzymological examination associated with MPS IVA by chemiluminescence immunoassay showed that galactosamine-6-sulfate esterase in leukocytes was 65.1 nmol/17h/mgPr, just slightly lower than the low limit of normal range (69.8–221.8) and may not be the primary cause of his problems. This revisit was at the age of 8 years and 3 months old for further clarifying the etiology. Physical examination findings are as followings: he was short-statured with thoracic vertebrae protruding backward, nasal bridge collapse, dysplasia of nostrils and had waddling gait, bowlegs with normal mental development as Fig. 2. There were no abnormalities in heart and lung and no enlargement of liver and spleen. Wechsler intelligence test suggested the score of IQ was 86 score (normal level). The vision was normal. Orthopedic workup was carried out again presenting a progressive aggravation of lesions being involved in vertebrae, pelvics, hip, femur, ankle. See Fig. 3 for details. Delayed carpal bone age progressively worsened. See Fig. 4 and Table 2 for details. High-throughput whole-exome sequencing of genomic DNA was performed and a novel heterozygous variant exon 11: C.1283A > G (leading to p.H428R) of the UFSP2: NM_018359.3, whose heterozygous mutation leads to SEMDs according to a report in 2018, was identified and comfirmed by sanger sequencing as Fig. 5B, which is one of the four catalytic residues identified by Ha et al. (2011) as Fig. 5A (Di Rocco et al., 2018; Ha et al., 2011).

Whole exome sequencing and Sanger sequencing were both performed by BerryGenomics according to a previously described protocol 5 6. PCR amplification fragments were hybridized and captured by IDT's xGen Exome Research Panel (Integrated DNA Technologies, San Diego, USA) according to the manufacturer's Protocol. The size distribution and concentration of the libraries were determined using an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA). Novaseq6000 platform (Illumina, San Diego, USA) was used for sequencing the genomic DNA. Raw image files were processed for base calling and generating raw data using CASAVA v1.82.

Burrows–Wheeler Aligner tool was employed for the sequencing reads aligning to the human reference genome (hg19/GRCh37) and PCR duplicates were removed by using Picard v1.57 (http://picard.sourceforge.net/). Verita Trekker® Variants Detection System by Berry Genomics and the third-party software GATK (https://software.broadinstitute.org/gatk/) were employed for variant calling. Variant annotation and interpretation were conducted by the Enliven® Variants Annotation Interpretation System authorized by Berry Genomics and ANNOVAR (Wang et al., 2010). Annotation databases mainly included: human population databases such as gnomAD (http://gnomad.broadinstitute.org/), the 1000 Genome Project (http://browser.1000genomes.org), Berrybig data population database and dbSNP (http://www.ncbi.nlm.nih.gov/snp); in silico prediction algorithms, such as SIFT (http://sift.jcvi.org), FATHMM (http://fathmm.biocompute.org.uk), MutationAssesso r (http://mutationassessor.org), CADD (http://cadd.gs.washington.edu) and SPIDEX (Xiong et al., 2015); disease and phenotype databases, such as OMIM (http://www.omim.org), ClinVar (http://www.ncbi.nlm.nih.gov/clinvar), HGMD (http://www.hgmd.org), HPO (https://hpo.jax.org/app/).

According to the American College of Medical Genetics and Genomics (ACMG) guidelines (Richards et al., 2015) for interpretation of genetic variants, variants were classified to five categories: pathogenic, likely pathogenic, uncertain significance, likely benign and benign. The variants with splicing impact or with minor allele frequencies (MAF) < 1% in exonic region were taken for further interpretation considering clinical synopsis, inheritance model, ACMG category and evidence of pathogenicity of the associated disease.

Section snippets

Results

According to ACMG, c.1283A > G mutation of UFSP2 is a likely pathogenic mutation site (PM2+PM6+PP3+PP4) of SEMDDR, an autosomal dominant hereditary diseases as Supplementary Fig. 3. The specific is as follows: evidence of moderate pathogenicity PM2: this mutation was not found in the Shenzhou Genome Database of the Berry Genomics Chinese Population Specific Database and The Genome Aggregation Database (gnomAD); Evidence of moderate pathogenicity PM6: results of verification showed that the

Discussion

SEMD usually presenting symptom of disproportionate short stature are a rare heterogeneous group of disorders with differing modes of inheritance, characterized by the combination of vertebral, epiphyseal and metaphyseal abnormalities of which the metaphyseal involvement is variable (Cormier-Daire, 2008). Some entity have been described in a single family and are purely defined on clinical and radiological features, with the molecular basis still unknown. Further clinical, genetic, and

Declaration of competing interest

The authors declare that there are no conflicts of interest.

Acknowledgements

We thank the patient and his guardian for their agree to publish this report.

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    Patients with autosomal dominant Beukes hip dysplasia have a Y290H variant in UFSP2.12 Spondyloepimetaphyseal dysplasia, Di Rocco type (SEMDDR) occurred in an Italian family with a D426A variant in UFSP211 and a Chinese patient with a H428R variant.13 None of the reported patients with these diseases had neurological impairments or seizures.

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