Abstract
Purpose
The human chromosome 19q13.11 deletion syndrome is associated with a variable phenotype that includes aplasia cutis congenita (ACC) and ectrodactyly as specific features. UBA2 (ubiquitin-like modifier-activating enzyme 2) lies adjacent to the minimal deletion overlap region. We aimed to define the UBA2-related phenotypic spectrum in humans and zebrafish due to sequence variants and to establish the mechanism of disease.
Methods
Exome sequencing was used to detect UBA2 sequence variants in 16 subjects in 7 unrelated families. uba2 loss of function was modeled in zebrafish. Effects of human missense variants were assessed in zebrafish rescue experiments.
Results
Seven human UBA2 loss-of-function and missense sequence variants were detected. UBA2-phenotypes included ACC, ectrodactyly, neurodevelopmental abnormalities, ectodermal, skeletal, craniofacial, cardiac, renal, and genital anomalies. uba2 was expressed in zebrafish eye, brain, and pectoral fins; uba2-null fish showed deficient growth, microcephaly, microphthalmia, mandibular hypoplasia, and abnormal fins. uba2-mRNAs with human missense variants failed to rescue nullizygous zebrafish phenotypes.
Conclusion
UBA2 variants cause a recognizable syndrome with a wide phenotypic spectrum. Our data suggest that loss of UBA2 function underlies the human UBA2 monogenic disorder and highlights the importance of SUMOylation in the development of affected tissues.
Similar content being viewed by others
INTRODUCTION
Features of the chromosome 19q13.11 deletion syndrome include early growth deficiencies, developmental delay, distinctive facial features, aplasia cutis congenita (ACC), hip dysplasia, digital and limb anomalies including ectrodactyly, and other malformations.1,2,3,4,5,6,7,8 Deletions range in size from 1.37–11 Mb with a minimum overlapping region (MOR) of 324 kb, without clear genotype-phenotype correlation.3,4,6 UBA2 lies adjacent to the MOR and has been proposed to underlie key aspects of the deletion phenotype including ACC and ectrodactyly.1,2,3,5,6 Limited patient data and lack of an animal model have prevented establishing UBA2 as the causative gene.
UBA2 plays a key role in the post-translational modification of protein (SUMOylation) by the addition of SUMO1 (small ubiquitin-like modifier) protein. UBA2 forms a heterodimer with SAE1 (SUMO-Activating Enzyme Subunit 1) and binds with SUMO1 in an ATP-dependent manner.9,10,11 Unlike ubiquitination, SUMOylation does not only target proteins for degradation, but is also involved in cell cycle regulation, subcellular trafficking, signal transduction, stress responses, and chromatin structure dynamics. SUMOylation alters protein kinases and transcription factors to maintain transcriptional regulation of tissue-specific gene expression.12
In this study, we report 16 additional individuals from seven unrelated families with de novo and familial UBA2 sequence variants who have highly variable but overlapping clinical presentations. In silico modeling and a zebrafish uba2 nullizygous phenotype provide further functional evidence for the pathogenicity of UBA2 as the key gene underlying the chromosome 19q13.11 microdeletion syndrome.
MATERIALS AND METHODS
Subject enrollment and clinical evaluations
Each described patient was evaluated by a clinical geneticist. Written informed consent was obtained for exome sequencing either on a clinical or research basis. A written informed consent was also obtained from subjects to publish their photos. Genomic DNA was extracted from whole blood from affected probands and their biological parents for exome sequencing. See supplement for details.
Zebrafish modeling of the phenotypic effects of uba2 variants
All animal experiments were conducted in accordance with recommendations of the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health (protocol NEI-679). Adult AB (Tubingen) and ABTL (Tubingen long fin) zebrafish strains were raised and maintained according to standard protocols as described.13
Whole-mount in situ hybridization
Wild type (WT) zebrafish embryos at different developmental stages (5 somite, 24, 35, 48, 72 hpf [hours postfertilization]), 5 and 7 dpf (days postfertilization) were fixed in preparation for performing in situ hybridization. See Supplemental methods for details.
CRISPR/Cas9 uba2 knockout line generation
CRISPR/Cas9 method was used to generate uba2 knockout zebrafish lines. See Supplemental methods for details.
mRNA rescue
To evaluate the impact of human UBA2 variants on encoded protein products, we utilized uba2-mutant fish to perform rescue studies with capped full-length human WT and missense alleles in messenger RNA (mRNA) transcribed with the T7 mMESSAGE mMACHINE kit (Ambion).
Please see Supplement for other methodology details.
RESULTS
Clinical studies
The cohort was gathered through GeneDx, a clinical molecular laboratory, and GeneMatcher. Investigators independently ascertained families with related phenotypes and rare candidate variants. Table 1 and the Supplement contain additional clinical details.
Family 1: Family 1 (Figs. 1 and 2) is comprised of an affected mother and her four offspring. Two children have ACC. By report, the maternal grandmother and great grandmother also have histories of ACC. Other ectodermal changes are variable including thin scalp hair, xerosis, and dental anomalies. The index case (IV-4, Fig. 1a, b) has unilateral ectrodactyly of the hand. All of the other affected examined individuals have more subtle digital variations including camptodactyly, syndactyly, clinodactyly, and diminished distal flexion creases of the fingers. All affected individuals share a high anterior hairline and mild frontal bossing, and several, including the proband (IV-4), have slightly downslanted palpebral fissures. All have had highly variable neurodevelopmental problems, ranging from hypotonia to autism spectrum disorder in two of the brothers. Hypotonia generally persisted throughout childhood. Affected individuals had early growth deficiencies that improved with age. See Supplement for other details. All affected individuals studied are heterozygous for a UBA2 frameshift variant: c.816_817delAT, p.Trp273Alafs*13.
Family 2: This family consists of three affected brothers (Fig. 1b: II-1, II-2, II-3); neither parent is affected. Parentage was genetically confirmed prior to exome sequencing. All affected individuals have histories of hypotonia through childhood that impeded motor development and even feeding ability in early infancy, and sensory integration problems, but normal cognitive abilities. Neither ACC nor other ectodermal changes are noted, but the youngest brother (II-3) has unilateral cleft hand and polydactyly. More subtle foot, toe, and other minor digital anomalies vary among the three affected males. All three also have histories of cryptorchidism and/or hypospadias. Each is heterozygous for a de novo frameshift UBA2 variant, c.1376_1377insT, p.Thr460Aspfs*24, not detected in blood of either parent with either next-generation (130× coverage at 10× depth) or Sanger sequencing.
Family 3: Clinical details about part of this family were reported previously14 but are now updated and expanded along with results of exome analysis. The male proband (II-2, Fig. 1a, b) has a single area of ACC, supernumerary nipple, cryptorchidism, early developmental delay, astigmatism, learning disability, depression, bipolar disorder, and social phobia. His mother (I-2) has multiple areas of healed ACC, supernumerary nipples, small head circumference, and asymmetric kidneys with reduced renal function. Neither have documented hand or foot anomalies. They are both heterozygous for a nonsense variant in UBA2: c.364C>T, p.Arg122*. Two other affected individuals (II-1 and III-1) have similar facial features, ACC, and supernumerary nipples and were each confirmed to harbor the familial UBA2 variant.
Family 4: The female proband (II-1, Fig. 1b), 21 years old at examination, has a history of delayed motor skills and attention deficit disorder. Height, weight, and head circumference are all currently less than the third percentile; she also had early growth deficiency, delayed dentition and bone age. Features include ACC, thin scalp hair, clinodactyly, and overlapping toes. See Table 1 and supplement for additional endocrine, renal, and ophthalmologic concerns. She is heterozygous for a de novo missense variant in UBA2, c.167A>C: p.Asn56Thr.
Family 5: The female proband (Fig. 1b, II-1), 4 years 9 months old at exam, has developmental delay, absent speech, hemangiomas, ACC, and seizures. She has relative macrocephaly, epicanthal folds, anteriorly placed anus, and pes planus. She carries a de novo missense UBA2 variant: c.1447G>A, p.Glu483Lys.
Family 6: The proband is a male toddler (Fig. 1a, b, II-1) with cryptorchidism, bilateral inguinal hernias, and multiple limb deformities including bilateral ectrodactyly of the feet, complete 2–3 finger syndactyly, clinodactyly, and camptodactyly. He has low-normal growth and normal developmental milestones. Facial features include hypertelorism, bilateral epicanthal folds, and pseudostrabismus. He does not have ACC or other ectodermal abnormalities. He is heterozygous for a de novo UBA2 nonsense variant: c.800T>A, p.Leu267*.
Family 7: The proband (Fig. 1b, II-1) is a 3-year, 11-month-old Caribbean male born at 35 weeks gestational age. At two weeks, height and weight (corrected for prematurity) were normal, but head circumference measured at the 2nd centile. He had global developmental delay and four limb ectrodactyly, tall and prominent forehead, deep-set eyes, broad nasal root, left preauricular tag, narrow palate, and a vertical cleft chin. Presurgery, he had left 2–3 finger syndactyly with a nodule adjacent to the medial aspect of the PIP joint of the 4th finger. The right 3rd digit is missing; other digits are relatively normal. On the left foot, two malformed digits are divided by a deep central cleft; the right foot also has a deep central cleft with three malformed digits, and 4–5 toe syndactyly. He does not have ACC but has large areas of faint hypopigmentation over his torso and limbs. He is heterozygous for a de novo missense variant in UBA2: c.364C>G, p.Arg122Gly.
None of the detected UBA2 variants was found in the gnomAD database.15 Results of in silico predictor analyses for missense variants and variant classification are provided in Supplemental Tables 1 and 2. All would be classified as pathogenic or likely pathogenic using American College of Medical Genetics and Genomics (ACMG)/Association for Molecular Pathology (AMP) guidelines (classification criteria)16 in Supplemental Table 2.
Modeling effects of missense variants on UBA2 function
UBA2 in complex with SAE1 plays a key role in the SUMOylation pathway. Observed human UBA2 variants are distributed across the gene (Fig. 2a, b). All truncating variants are expected to undergo nonsense-mediated decay based on their position within the mRNA. Missense variants occur at residues that are strongly conserved across vertebrates (Fig. 2c). Given the similarities in phenotypes between individuals with truncating and missense alleles, we hypothesized that missense alleles also lead to loss of function.
To understand how missense alleles might disrupt UBA2 function, molecular modeling using published crystal structures17 and simulated substitutions were performed for each detected human missense variant. In the UBA2 protein, p.Gly2418 is directly involved in ATP binding; its substitution with valine results in altered protein conformation and is predicted to result in loss of ATP binding and ectopic interactions with nearby residues (Fig. 2d).17 Similarly, asparagine replacement with threonine at position 56 putatively abolishes ATP-dependent activation. The p.Arg122Gly substitution is predicted to result in loss of interaction with ATP. Human UBA2 protein interacts with a conjugating enzyme called UBC9 (amino acids 6–38) via amino acid residues 478–509, which include Glutamate 483. UBA2 forms a hydrophobic bond with Leu6, Met36, and Leu38 of UBC9; replacing Glutamate 483 with Lysine is predicted to disrupt UBA2–UBC9 binding. In summary, missense alleles observed in patients with UBA2-associated syndrome are observed to occur at functionally critical residues and potentially disrupt ATP binding, protein folding, or protein–protein interactions.
Zebrafish uba2 expression in affected tissues
By whole-mount in situ hybridization, uba2 transcript was detected on the dorsoventral axis of 5-somite stage embryos (Fig. S1a, b). At later stages, uba2 is expressed in developing brain, eye, craniofacial structures, and fins. At 24 hpf, uba2 expression was restricted to the head region, including the eye and nervous system (Fig. S1c). At 35 hpf, prominent signal was observed in pectoral fins (arrows, Fig. S1d). At all other examined stages (48 and 72 hpf, 5 and 7 dpf), uba2 mRNA signal localized to the head region, specifically brain, neural retina, and lens (Fig. S1e–h). Therefore, zebrafish uba2 is expressed in some structures that are analogous to those affected in humans harboring deleterious UBA2 variants.
Variable expressivity observed with uba2 loss of function
uba2 knockout zebrafish lines were generated by CRISPR/Cas9-targeted deletion. The phenotype of homozygous fish was notable for failure to inflate swim bladders. At 5–8 dpf, we observed severe gross morphological defects in uba2-/- zebrafish (Fig. 3) including small eyes, hydrocephalus and craniofacial edema, ventrally curved body axis, and uninflated swim bladder. Faint heartbeat and severe pericardial edema were observed in 41% of embryos (Fig. 3a, b). Edema became generalized at 8 dpf when most lethality was noted. To further examine the effect of uba2 on zebrafish development, we calculated the survival rate of uba2-/- zebrafish which was significantly lower than control (WT) and heterozygous fish. uba2-/- zebrafish showed a mortality rate of approximately 50% at 8 dpf; however, 100% of mutant fish were dead by day 12 (Fig. 3d).
Nullizygous fish exhibited a wide phenotypic range. We observed a pair of normal extended pectoral fins in WT zebrafish versus uba2-/- fish, where pectoral fins were found to be short and upright-oriented (Fig. 3a) confirming uba2 function in fish extremity development. WT zebrafish had thin lines originating from base to fin tips showing normal actinotrichia. In contrast, uba2-/- fish displayed collapsed (Fig. 3b, middle image) and irregular fin fold edges (Fig. 3b, last image).
To better characterize variable expression and the relationship between the zebrafish knockout and the human disorders, we quantified craniofacial (F), brain (B), pectoral fin (PF), tail fin (TF), and swim bladder (SB) defects. Defects at later stages of development were studied in uba2-/- fish bred from the same parent at 8 dpf, when approximately half the fish survive (n = 32; Fig. 3c). Tissue-level malformations were observed in craniofacial structures (9.38%), brain size (90.6%), tail fin (25%), pectoral fin (100%), and swim bladder (93.75%) (Fig. 3c and as described below). Thus, across individual fish with similar genetic backgrounds, total uba2 function loss recapitulates some tissue-level phenotypes and the variable expression observed in human UBA2-related phenotypes.
Neuronal reduction in uba2 zebrafish
Tissue-level analysis was performed in zebrafish to elucidate abnormalities resulting from uba2 loss of function. First, we conducted immunohistochemistry studies on 8 dpf zebrafish cryosections through eye and brain. Compared to WT controls, uba2-null fish showed small heads, reduced midbrain size, low nuclei cell count with high accumulation of actin signal (orange, Fig. S2), implying a decreased proportion of gray to white matter. In addition, uba2-/- fish had smaller eyes, reduced retinal thickness, retinal laminations, and lens defects (see Supplement).
Skeletal and extremity phenotypes in the uba2 zebrafish model
To investigate the impact of uba2 on zebrafish skeletal development, we stained uba2 WT (+/+), heterozygous (+/-), and homozygous (-/-) fish with alcian blue dye at 5 dpf. In both uba2 WT (Fig. 4a) and heterozygous zebrafish (data not shown), alcian staining demonstrated a normal pattern of cartilage element development including typical ceratohyoid, Meckel’s cartilage, ceratobranchials arches, and pectoral fin cartilage. However, complete loss of uba2 in homozygous fish resulted in abnormal craniofacial development. In addition to jaw malformations, other craniofacial malformations included malformed and hypoplastic ventral and dorsal cartilage structures with lack of basihyal and hypohyal development. We also noted an apparently abnormal fusion of Meckel’s cartilage with the palatoquadrate, resulting in a small, narrow mandible (Fig. 4b). Moreover, Meckel’s cartilage was flattened at the midline fusion point with completely absent ceratohyal cartilage and ceratobranchials arches, the equivalent of micrognathia in these fish.
To explore whether uba2 mutation causes skeletal phenotypes in adult fish, we performed microcomputed tomography (CT) comparing WT (n = 3) and uba2+/- (n = 3) fish, as nullizygous fish did not survive to this stage. We noted abnormal, wavy ribs and dysmorphic fin girdles in uba2+/- fish (Fig. S3).
In teleosts, finfolds are typically made of type II collagen matrix structures called actinotrichia that line the epidermis. Brightfield microscopy of uba2-/- fish revealed structural defects in median fins (Fig. 3b). To examine the effect of uba2 truncation on zebrafish median fin structure development, we stained uba2 zebrafish (+/+, +/-, and -/-) larvae with type II collagen (Col2a) and Phalloidin (F-actin) antibodies to label actinotrichia (Fig. 4c).
Actinotrichia fibrils initiate fin development and become the future fin connective tissue. At 5 dpf, both WT (Fig. 4c, top panel) and heterozygous (data not shown) larvae develop median fins showed normally arrayed Col2a-labeled actinotrichia fibers; however, we observed nonrigid, nonparallel and bent actinotrichia in uba2-/- (Fig. 4c, arrows) fish. Phalloidin staining in uba2-/- fish revealed disorganized and disrupted organization, corresponding to areas of this abnormal collagen pattern (Fig. 4c).
Further investigating these extremity defects at a cellular level, we performed ultrastructural analysis of the uba2 zebrafish body wall near the median finfold at 5 dpf. Detailed examination by TEM revealed a typical dynamically assembled dense striated pattern of actinotrichia in WT fish (Fig. S4). Similarly, in WT fish we observed a normal and organized distribution of skeletal muscles with normal nuclei and mitochondria. However, in uba2-/- zebrafish, we observed disorganized (or incompletely developed) and scattered actinotrichia with abnormal epidermal cells (arrow). The skeletal muscle layer in homozygous fish was also observed to be discontinuous or atrophic with degenerated nuclei and mitochondria. Therefore, absent uba2 impacts connective and epithelial tissue and skeletal muscle and causes extremity malformations in developing fish.
Conserved function of UBA2 candidate variants in zebrafish
To further confirm the specificity of the uba2 knockout phenotype, we attempted phenotypic rescue of developmental fish malformations by injecting human UBA2 mRNA. Injected fish were grouped into three phenotypic classes and genotyped at 5 dpf, and the uba2-/- subset was analyzed. Embryos were classified as class I (grossly normal body structure), class II (decreased head size, absent swim bladder), and class III (small head and body, generalized edema) (Fig. 4d). As compared to H2O-injected controls, injecting human WT UBA2 mRNA grossly rescued phenotypes in a significant number of fish. The proportion of class I fish increased from 5% to 33%, and the proportion of class III fish decreased from 47% to 6% (p < 0.0001) (Fig. 4e). Even though WT UBA2 mRNA injection rescued gross phenotypes, most uba2-/- zebrafish still did not show inflated swim bladder (data not shown), suggesting that early uba2 deficiency permanently impacts zebrafish physiology despite substitution with human mRNA.
Human mRNAs encoding p.Gly24Val, p.Arg122Gly and p.Glu483Lys all failed to rescue the uba2-/- phenotypes in contrast to WT mRNA. The p.Asn56Thr substitution demonstrated statistically similar rescue to control mRNA; however, there were more class III fish (23% vs. 6%) and fewer class I fish (18% vs. 33%) following p.Asn56Thr injection, indicating possible partial loss of function for this missense substitution (Fig. 4e). Because the mRNAs containing the missense variants failed to rescue uba2-null phenotypes to a similar level as did WT UBA2 mRNA, we conclude that the most likely mechanism of disease is loss of function.
DISCUSSION
In this study, we describe a cohort of patients harboring deleterious variants in the UBA2 gene. They show highly variable inter- and intrafamilial expression of dermatologic, skeletal, extremity, neurologic, cardiac, and renal features, similar to those of the chromosome 19q13.11 microdeletion syndrome.1,2,3,4,5,6,7,8 These observations further support UBA2 as the critical gene in the microdeletion syndrome and suggest its essential role in early human growth and development. There are only a few other reports of intragenic UBA2 variants (summarized in Table 1). Marble et al.18 reported a de novo UBA2 missense variant (c.71G>T, p.Gly24Val) in a 2.5-year-old female with ACC, thin hair, tall forehead, Duane anomaly, hip dysplasia, clinodactyly, and poor weight gain. Wang et al.18 reported an inherited UBA2 frameshift variant (c.327delT, p.Phe109Leufs*3) in a young boy and his mother. The mother had ACC but was otherwise healthy. The son had ACC, microcephaly, bilateral ectrodactyly, low‐lying conus medullaris, horseshoe kidney, and tracheoesophageal fistula. A de novo UBA2 loss-of-function variant (c.1324dupT, p.Tyr442Leufs*17) was associated with four extremity split hand and foot malformation with tibial deficiency and undermasculinized external genitalia.19 Aerden et al.20 reported a male proband with ectrodactyly of the feet, autism spectrum disorder, craniofacial variations, dry sparse scalp hair, strabismus, and hypermetropia who was heterozygous for a de novo frameshift variant in UBA2 (c.612delA, p.Glu205Lysfs*63); this was considered to be responsible for the phenotype.20
The four patients previously reported with intragenic UBA2 variants were added to our clinical summary table (Table 1) to compare phenotypes.18,19,20,21 We’ve estimated the percentage of key traits in UBA2 subjects (Fig. 1c) based on available clinical information. The most specific aspects of the UBA2-related phenotype are ACC, seen in 61%, and ectrodactyly, which is less common (37%). Early growth deficiency and neurodevelopmental delay are reported in 61% and 80% of affected individuals, respectively. More variable digital and skeletal abnormalities are also present (56%) but are sometimes subtle and potentially overlooked (e.g., Fig. 1a, panels C, D). These include clinodactyly (62%), syndactyly (59%), camptodactyly (57%), and hip abnormality (35%). The most common craniofacial variations are tall forehead/high hairline (76%), downslanted palpebral fissures (47%), hypertelorism (62%), broad nasal root (81%), microcephaly (37%), and micrognathia (53%). Other observed features among our subjects include other ectodermal variations (~82%), ocular abnormalities (53%), and cardiac (43%), genital (50%, in males), and renal (36%) abnormalities.
In C. elegans, Uba-2 is also noted to be a critical element of the SUMOylation pathway; its ablation leads to embryonic lethality.22 UBA2 acute knockdown in xenograft tumors by conditional short hairpin RNA (shRNAs) causes marked growth arrest, cell proliferation defects, and increased apoptosis.23 In mice, loss of any key component of the SUMOylation pathway can lead to severe impairment of cellular functions and lethality.24,25 An in situ hybridization study conducted in mouse embryos (8.5 to 11.5 days postcoitum) revealed Uba2 ample expression at multiple morphogenetic activity sites, e.g., neural folds, branchial arches, and limb buds,24 suggesting that Uba2 is essential for normal cellular function/development. Recently, SUMOylation was reported to regulate differentiation of several ocular tissues.26,27
Phenotypic features in our human UBA2-related syndrome cohort and the uba2 knockout zebrafish are reminiscent of disorders associated with pathogenic variants in DLX5/6 (split hand/foot malformation [SHFM1], OMIM 220600), TP63 (e.g., ectrodactyly, ectodermal dysplasia, and cleft lip/palate syndrome 3 [EEC3], OMIM 604292; split hand/foot malformation syndrome 4 [SHFM4], OMIM 605289; and others), and FBXW4, a candidate for SHFM3 (OMIM 246560). tp63-/- zebrafish embryos have ectodermal defects involving skin, absent pectoral fin buds, and reduced size fin folds at 36 hpf and embryos died between 40–50 hpf.28 tp63 zebrafish morphants affect skin integrity by making the skin more prone to microbial infection.29 fndc3a-/- zebrafish show broken actinotrichia, aberrant collagen localization, and cellular defects in epidermal cells during caudal fin development.30 It is possible that these genes function downstream of the SUMOylation pathway, leading to phenotypes that overlap the UBA2-related syndrome.
In the current study, the mRNA rescue experiments showed that WT UBA2 mRNA injection partially rescued the abnormal head/eye, tail, and uninflated swim bladder phenotype in uba2-/- zebrafish (33%). Notably, three of four human missense UBA2 mRNAs did not rescue the uba2-/- phenotype to a significant degree, suggesting a loss-of-function mechanism for these disease-associated alleles. As wide phenotypic variability is observed in both fish and human UBA2/uba2-related phenotypes, additional studies are warranted to define potential modifiers. Morpholinos (MOs) have been used in reverse genetic studies in a range of animal models.31,32 However, MOs may be hard to interpret as they typically result in more severe phenotypes.33 mRNA rescue in CRISPR-generated stable mutant lines is potentially useful in the interpretation of MO-related inconsistencies. Precise single-nucleotide variant animal models of human diseases can help to better understand underlying molecular processes and may aid in management of UBA2-related abnormalities.34
In conclusion, we report clinical details in 16 individuals from seven unrelated families with inherited or de novo heterozygous UBA2 sequence variants, who present with highly variable phenotypes. Definition of the UBA2-related autosomal dominant phenotypic spectrum in humans, in silico modeling predictions, uba2 expression, and characterization of the knockout phenotype in zebrafish support the significance of UBA2/uba2 in development, potentially by affecting post-translational modification of SHFM-associated genes. mRNA rescue experiments in zebrafish also suggest that loss of gene function is the primary mechanism of disease. The highly variable expressivity of the human UBA2 phenotype, either via sequence alteration or contiguous gene deletion, even within the same family, remains incompletely explained; there are likely other modifiers, still to be identified. However, our studies define a human disorder associated with UBA2 sequence variants with a phenotype that overlaps key aspects of the chromosome 19q13.11 microdeletion syndrome.
Web Resources
ClinVar Database https://www.clinicalgenome.org/data-sharing/clinvar
gnomAD https://gnomad.broadinstitute.org/
GeneMatcher https://genematcher.org/
Pathogenicity predictions https://varsome.com/
OMIM http://www.omim.org/
Clustal omega https://www.ebi.ac.uk/Tools/msa/clustalo/
Data availability
All data is mentioned in the main text and supplement, available to readers.
References
Abe, K. T. et al. 19q13.11 microdeletion: clinical features overlapping ectrodactyly ectodermal dysplasia-clefting syndrome phenotype. Clin. Case Rep. 6, 1300–1307 (2018).
Chowdhury, S. et al. Phenotypic and molecular characterization of 19q12q13.1 deletions: a report of five patients. Am. J. Med. Genet. A. 164A, 62–69 (2014).
Gana, S. et al. 19q13.11 cryptic deletion: description of two new cases and indication for a role of WTIP haploinsufficiency in hypospadias. Eur. J. Hum. Genet. 20, 852–856 (2012).
Malan, V. et al. 19q13.11 deletion syndrome: a novel clinically recognisable genetic condition identified by array comparative genomic hybridisation. J. Med. Genet. 46, 635–640 (2009).
Melo, J. B., Estevinho, A., Saraiva, J., Ramos, L. & Carreira, I. M. Cutis aplasia as a clinical hallmark for the syndrome associated with 19q13.11 deletion: the possible role for UBA2 gene. Mol. Cytogenet. 8, 21 (2015).
Schuurs-Hoeijmakers, J. H. et al. Refining the critical region of the novel 19q13.11 microdeletion syndrome to 750 Kb. J. Med. Genet. 46, 421–423 (2009).
Urquhart, J. E. et al. Deletion of 19q13 reveals clinical overlap with Dubowitz syndrome. J. Hum. Genet. 60, 781–785 (2015).
Venegas-Vega, C. et al. 19q13.11 microdeletion concomitant with ins(2;19)(p25.3;q13.1q13.4)dn in a boy: potential role of UBA2 in the associated phenotype. Mol. Cytogenet. 7, 61 (2014).
Desterro, J. M., Rodriguez, M. S., Kemp, G. D. & Hay, R. T. Identification of the enzyme required for activation of the small ubiquitin-like protein SUMO-1. J. Biol. Chem. 274, 10618–10624 (1999).
He, P. et al. UBA2 promotes proliferation of colorectal cancer. Mol. Med. Rep. 18, 5552–5562 (2018).
Olsen, S. K., Capili, A. D., Lu, X., Tan, D. S. & Lima, C. D. Active site remodelling accompanies thioester bond formation in the SUMO E1. Nature. 463, 906–912 (2010).
Chang, S. C. & Ding, J. L. Ubiquitination and SUMOylation in the chronic inflammatory tumor microenvironment. Biochim. Biophys. Acta Rev. Cancer. 1870, 165–175 (2018).
Westerfield, M. The Zebrafish Book: A Guide for the Laboratory Use of Zebrafish (Danio rerio). (M. Westerfield, Eugene, OR, 2007).
Marble, M. & Pridjian, G. Scalp defects, polythelia, microcephaly, and developmental delay: a new syndrome with apparent autosomal dominant inheritance. Am. J. Med. Genet. 108, 327–332 (2002).
Lek, M. et al. Analysis of protein-coding genetic variation in 60,706 humans. Nature. 536, 285–291 (2016).
Richards, S. et al. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet. Med. 17, 405–424 (2015).
Lois, L. M. & Lima, C. D. Structures of the SUMO E1 provide mechanistic insights into SUMO activation and E2 recruitment to E1. EMBO J. 24, 439–451 (2005).
Marble, M., Guillen Sacoto, M. J., Chikarmane, R., Gargiulo, D. & Juusola, J. Missense variant in UBA2 associated with aplasia cutis congenita, duane anomaly, hip dysplasia and other anomalies: a possible new disorder involving the SUMOylation pathway. Am. J. Med. Genet. A. 173, 758–761 (2017).
Yamoto, K. et al. Comprehensive clinical and molecular studies in split-hand/foot malformation: identification of two plausible candidate genes (LRP6 and UBA2). Eur. J. Hum. Genet. 27, 1845–1857 (2019).
Aerden, M. et al. Genotype-phenotype correlations of UBA2 mutations in patients with ectrodactyly. Eur. J. Med. Genet. 63, 104009 (2020).
Wang, Y., Dupuis, L., Jobling, R. & Kannu, P. Aplasia cutis congenita associated with a heterozygous loss-of-function UBA2 variant. Br. J. Dermatol. 182, 792–794 (2020).
Jones, D., Crowe, E., Stevens, T. A. & Candido, E. P. Functional and phylogenetic analysis of the ubiquitylation system in Caenorhabditis elegans: ubiquitin-conjugating enzymes, ubiquitin-activating enzymes, and ubiquitin-like proteins. Genome Biol. 3, RESEARCH0002 (2002).
Carrington, B., Varshney, G. K., Burgess, S. M. & Sood, R. CRISPR-STAT: an easy and reliable PCR-based method to evaluate target-specific sgRNA activity. Nucleic Acids Res. 43, e157 (2015).
Costa, M. W. et al. Complex SUMO-1 regulation of cardiac transcription factor Nkx2-5. PLoS One. 6, e24812 (2011).
Zhao, J. Sumoylation regulates diverse biological processes. Cell. Mol. Life Sci. 64, 3017–3033 (2007).
Nie, Q. et al. Analysis of the differential expression patterns of sumoylation enzymes E1, E2 and E3 in ocular cell lines. Curr. Mol. Med. 18, 509–515 (2018).
Gong, X. et al. Localization patterns of sumoylation enzymes E1, E2 and E3 in ocular cell lines predict their functional importance. Curr. Mol. Med. 18, 516–522 (2018).
Santos-Pereira, J. M., Gallardo-Fuentes, L., Neto, A., Acemel, R. D. & Tena, J. J. Pioneer and repressive functions of p63 during zebrafish embryonic ectoderm specification. Nat. Commun. 10, 3049 (2019).
Lee, H. & Kimelman, D. A dominant-negative form of p63 is required for epidermal proliferation in zebrafish. Dev. Cell. 2, 607–616 (2002).
Liedtke, D. et al. ECM alterations in Fndc3a (Fibronectin Domain Containing Protein 3A) deficient zebrafish cause temporal fin development and regeneration defects. Sci. Rep. 9, 13383 (2019).
Yousaf, R. et al. Modifier variant of METTL13 suppresses human GAB1-associated profound deafness. J. Clin. Invest. 128, 1509–1522 (2018).
Yousaf, S. et al. Molecular characterization of SLC24A5 variants and evaluation of Nitisinone treatment efficacy in a zebrafish model of OCA6. Pigment Cell Melanoma Res. 33, 556–565 (2020).
Stainier, D. Y. R. et al. Guidelines for morpholino use in zebrafish. PLoS Genet. 13, e1007000 (2017).
Prykhozhij, S. V. & Berman, J. N. Zebrafish knock-ins swim into the mainstream. Dis. Model Mech. 11, dmm037515 (2018).
Acknowledgements
We thank the individuals and families who participated in this project. We express our deepest gratitude to Mary Ella Pierpont for her valuable contribution and dedicate this report to her memory. W.K.C. received financial support from the JPB Foundation. N.S.’s work is supported by National Human Genome Research Institute (NHGRI) grant 1U54HG006542. We would like to thank Sunit Dutta (National Eye Institute, National Institutes of Health [NIH], Bethesda, MD) for assistance in establishing uba2 zebrafish knockout lines. We thank the zebrafish facility, Confocal, transmission electron microscopy, and microcomputed tomography mouse imaging facilities at NIH for their support and technical assistance. The research work carried out at NIH was supported by funds provided by National Eye Institute, NIH (Bethesda, MD).
Author information
Authors and Affiliations
Contributions
R.E.S. and R.B.H. designed and organized the study. S.Y. and J.L. generated and analyzed zebrafish-related data. R.E.S. collated and composed sections describing human clinical data; S.Y. and J.L. composed the core manuscript. R.E.S. and R.B.H. supervised and validated data and reviewed and edited the manuscript. M.F. generated microcomputer tomography data. S.K. performed zebrafish genotyping and alcian staining. L.R. coordinated all clinical collaborations. R.E.S., W.K.C., M.M., R.M.Z., N.S., P.J., M.E.P., M.J.S., P.N.P., R.J.O., G.E.G., M.O., G.A.C.-G., K.A.C.-N., C.A.P.-M., K.N., M.I.S., C.E.P. all contributed clinical patient information. M.J.G.S., I.M.W., J.J. analyzed exome data and provided clinical variant interpretations.
Corresponding authors
Ethics declarations
Competing interests
R.E.S., I.M.W., M.J.G.S., L.R., and J.J. are employees of GeneDx, Inc., Gaithersburg, Maryland. The other authors declare no competing interests.
Ethics declaration
Study participants were enrolled in approved protocols as per the policies of the Institutional Review Board (IRB) Committees of the institutions at which patients were identified, or via GeneDx, following the tenets of the Declaration of Helsinki. The main IRB for this study is Western Institutional Review Board, study number 1175206, WIRB protocol 20171030 (GeneDx). Written informed consent for inclusion in this study was obtained as required from all subjects, including specific consent to use photographs. All zebrafish-related experiments were conducted in accordance with recommendations of the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health, protocol NEI-679.
Additional information
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary information
Rights and permissions
About this article
Cite this article
Schnur, R.E., Yousaf, S., Liu, J. et al. UBA2 variants underlie a recognizable syndrome with variable aplasia cutis congenita and ectrodactyly. Genet Med 23, 1624–1635 (2021). https://doi.org/10.1038/s41436-021-01182-1
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/s41436-021-01182-1
This article is cited by
-
A novel frameshift variant in UBA2 causing split-hand/foot malformations in a Pakistani family
Human Genome Variation (2023)