Heterozygous DLX5 nonsense mutation associated with isolated split-hand/foot malformation with reduced penetrance and variable expressivity in two unrelated families

A genotype-phenotype correlation in split-hand/foot malformation type 1: further refinement of the phenotypic subregions within the 7q21.3 locus

Background: Split-hand/foot malformation type 1 (SHFM1) refers to the group of rare congenital limb disorders defined by the absence or hypoplasia of the central rays of the autopods with or without accompanying anomalies, such as hearing loss, craniofacial malformation, and ectodermal dysplasia. Consequently, the condition is characterized by clinical variability that hinders diagnostic and counseling procedures. SHFM1 is caused by pathogenic variants affecting the DLX5/6 genes and/or their tissue-specific enhancers at the 7q21.3 locus. Herein, we report on seven patients from five unrelated Polish families affected by variable symptoms of the SHFM1 spectrum, all harboring 7q21.3 or 7q21.2-q21.3 rearrangements, and provide a genotype-phenotype correlation in the studied cohort. Methods: We applied GTG banding, array-based comparative genomic hybridization (aCGH), and whole-genome sequencing (WGS) in order to identify the causative aberrations in all affected patients. Results: The identified pathogenic structural variants included deletions and/or translocations involving the 7q21.3 locus, i.e., t(7;10)(q21.3;q22.2) and t(7;12)(q21.3;q21.2) in all affected individuals. Interestingly, a sporadic carrier of the latter aberration presented the SHFM1 phenotype with additional features overlapping with Baker-Gordon syndrome (BAGOS), which resulted from the translocation breakpoint at chromosome 12 within the SYT1 gene. Conclusion: Clinical variability of the studied cohort reflects the composition of the DLX5/6 regulatory elements that were dislocated from their target genes by chromosomal rearrangements. The correlation of our data with the previously published observations enabled us to update the phenotypic subregions and regulatory units within the SHFM1 locus. In addition, we present the first case of SHFM1 and BAGOS-like phenotype that resulted from translocation breakpoints at chromosomes 7 and 12, both of which were pathogenic, and consequently, we show the first evidence that BAGOS can also result from the regulatory loss-of-function SYT1 mutations. In this paper, we emphasize the utility of sequence-based approaches in molecular diagnostics of disorders caused by regulatory structural variants.

Split Hand-Foot and Deafness in a Patient with 7q21.13-q21.3 Deletion Not Including the DLX5/6 Genes

Split Hand-Foot Malformation (SHFM) is a congenital limb defect characterized by a median cleft of the hands and/or feet due to the absence/hypoplasia of the central rays. It may occur as part of a syndromic condition or as an isolated malformation. The most common of the six genetic loci identified for this condition is correlated to SHFM1 and maps in the 7q21q22 region. SHFM1 is characterized by autosomal dominant transmission, incomplete penetrance and variable expressivity. Associated features often include hearing loss, intellectual disability/developmental delay and craniofacial abnormalities. Disruption of the DLX5/DLX6 genes, mapping within the SHFM1 locus, is now known to be responsible for the phenotype. Through SNP array, we analyzed a patient affected by SHFM1 associated with deafness and an abnormality of the inner ear (incomplete partition type I); we identified a deletion in 7q21, not involving the DLX5/6 genes, but including exons 15 and 17 of DYNC1I1, known to act as exonic enhancers (eExons) of the DLX5/6 genes. We further demonstrated the role of DYNC1I1 eExons in regulating DLX5/6 expression by means of showing a reduced expression of the DLX5/6 genes through RT-PCR in a patient-derived lymphoblastoid cell line. Furthermore, our data and a review of published cases do not support the hypothesis that DLX5/6 are imprinted in humans. This work is an example of how the disruption of regulatory elements can be responsible for congenital malformations.

New pathogenic variant in DLX5: New clues for a clinical spectrum from split-hand-foot malformation to fibular aplasia, tibial campomelia and oligosyndactyly

Introduction: FATCO (Fibular Aplasia, Tibial Campomelia and Oligosyndactyly) is a very infrequent skeletal dysplasia classified within the limb hypoplasia-reduction defects group whose genetic cause has not yet been identified. The advent of next-generation sequencing is enabling the diagnosis of diseases with no previously known genetic cause. Methods: We performed a thorough autopsy on a fetus whose pregnancy was legally terminated due to severe malformations detected by ultrasound. A trio exome was run to identify the genetic cause and risk of recurrence. Previous literature of similar cases was systematically searched. Results: Anatomopathological analyses revealed complete fibular aplasia, shortened and campomelic tibia, absent ankle joint, club right foot and a split foot malformation, leading to the diagnosis of FATCO. Exome sequencing showed that the female fetus carried a de novo nonsense variant in DLX5. The literature search permitted the collection of information on 43 patients with FATCO, the majority of whom were males diagnosed postnatally. In most cases, lower limbs were affected exclusively, but in 39.5% of cases the upper limbs were also affected. Conclusion: The pathologies associated with DLX5 variants encompass a wide spectrum of manifestations ranging from abnormalities exclusively in the hands and feet to long bones such as the tibia and fibula.

Distal Dorsal Dimelia: A Disturbance of Dorsal-Ventral Digit Development

PURPOSE

Congenital palmar nail (distal dorsal dimelia [dDD]) of the hand is a rare malformation most commonly affecting the little finger. The purpose of this report was to review the features and associations of this rare disorder and discuss the suspected underlying etiology in light of our current understanding of developmental biology.

METHODS

In this retrospective cohort study from 3 practices, we describe our collective experience and review the reported literature on this disorder both as an isolated condition and in conjunction with other anomalies.

RESULTS

We examined 15 fingers with dDD, 5 of which involved little fingers. We also found dDD in 6 cases with radial polydactyly (preaxial polydactyl type II [PPD2]) and in 1 case of cleft hand involving digits adjacent to the clefted web space (the index and middle fingers). Cases of little finger dDD were also associated with prominent clefting of the adjacent web space in 4 of 5 cases. All cases had stiffness of the interphalangeal joints and loss of palmar creases consistent with dorsalization of the palmar aspect of the digit. When combined with 63 fingers reported in the literature with dDD, 3 patterns were evident. The most common form occurred in little fingers (n = 50; 64%; dDDu). The next most common form was reported in association with cleft hands (n = 16; 21%; dDDc). Radial digits in association with either radial polydactyly (PPD2) or radial longitudinal deficiency were also susceptible to dDD (n = 12; 15%; dDDr).

CONCLUSIONS

Congenital dDD is a disturbance of terminal dorsal-ventral digit patterning. The distribution of this condition with little fingers, clefting, and altered radial digit formation (PPD2 or radial longitudinal deficiency), as well as recent genetic and animal studies, suggests that dDD and altered dorsal-ventral patterning are linked to abnormal apical ectodermal ridge boundary formation.

TYPE OF STUDY/LEVEL OF EVIDENCE

Diagnostic IV.

Deletion 7q21.2-q22.1 in a case with split hand-split foot malformation, sensorineural hearing loss and intellectual disability: Phenotype subtypes and the correlation with genotypes

The split hand/split foot malformation (SHFM) or ectrodactyly is a rare congenital heterogeneous limb developmental disorder with at least 6 associated loci. It is characterized by absence of central rays of hands and feet and fusion of remaining digits. It can present as an isolated malformation or in combination with additional anomalies (non-syndromic or syndromic ectrodactyly). This is a report of a 4 year old male child with SHFM with facial dysmorphism, profound sensorineural hearing loss, microcephaly and developmental delay associated with a large deletion of 7.242 MB on chromosome 7q21.2-q22.1. This is the region of SHFM1 (OMIM No. 183600) and deletions of varying sizes have been reported. We have reviewed the phenotypes and genotypes of this locus. The deletions with this severe phenotype are large and some of them detected on traditional karyotyping. The cases with submicroscopic deletions are few but show some correlation of genotype with phenotype which will help in counseling the families with prenatally or neonatally detected deletion at this locus.

Homozygous sequence variants in the WNT10B gene underlie split hand/foot malformation

Split-hand/split-foot malformation (SHFM), also known as ectrodactyly is a rare genetic disorder. It is a clinically and genetically heterogeneous group of limb malformations characterized by absence/hypoplasia and/or median cleft of hands and/or feet. To date, seven genes underlying SHFM have been identified. This study described four consanguineous families (A-D) segregating SHFM in an autosomal recessive manner. Linkage in the families was established to chromosome 12p11.1-q13.13 harboring WNT10B gene. Sequence analysis identified a novel homozygous nonsense variant (p.Gln154*) in exon 4 of the WNT10B gene in two families (A and B). In the other two families (C and D), a previously reported variant (c.300_306dupAGGGCGG; p.Leu103Argfs*53) was detected. This study further expands the spectrum of the sequence variants reported in the WNT10B gene, which result in the split hand/foot malformation.

Deletion of a Long-Range Dlx5 Enhancer Disrupts Inner Ear Development in Mice

Distal enhancers are thought to play important roles in the spatiotemporal regulation of gene expression during embryonic development, but few predicted enhancer elements have been shown to affect transcription of their endogenous genes or to alter phenotypes when disrupted. Here, we demonstrate that a 123.6-kb deletion within the mouse Slc25a13 gene is associated with reduced transcription of Dlx5, a gene located 660 kb away. Mice homozygous for the Slc25a13 deletion mutation [named hyperspin (hspn)] have malformed inner ears and are deaf with balance defects, whereas previously reported Slc25a13 knockout mice showed no phenotypic abnormalities. Inner ears of Slc25a13^hspn/hspn mice have malformations similar to those of Dlx5^-/- embryos, and Dlx5 expression is severely reduced in the otocyst but not the branchial arches of Slc25a13^hspn/hspn embryos, indicating that the Slc25a13^hspn deletion affects otic-specific enhancers of Dlx5 In addition, transheterozygous Slc25a13^+/hspn Dlx5^+/- mice exhibit noncomplementation with inner ear dysmorphologies similar to those of Slc25a13^hspn/hspn and Dlx5^-/-embryos, verifying a cis-acting effect of the Slc25a13^hspn deletion on Dlx5 expression. CRISPR/Cas9-mediated deletions of putative enhancer elements located within the Slc25a13^hspn deleted region failed to phenocopy the defects of Slc25a13^hspn/hspn mice, suggesting the possibility of multiple enhancers with redundant functions. Our findings in mice suggest that analogous enhancer elements in the human SLC25A13 gene may regulate DLX5 expression and underlie the hearing loss that is associated with split-hand/-foot malformation 1 syndrome. Slc25a13^hspn/hspn mice provide a new animal model for studying long-range enhancer effects on Dlx5 expression in the developing inner ear.

Identification of Associated Genes and Diseases in Patients With Congenital Upper-Limb Anomalies: A Novel Application of the OMT Classification

PURPOSE

Congenital upper-limb anomalies (CULA) can present as a part of a syndrome or association. There is a wide spectrum of CULA, each of which might be related to different diseases. The structure provided by the Oberg, Manske, and Tonkin (OMT) classification could aid in differential diagnosis formulation in patients with CULA. The aims of this study were to review the Human Phenotype Ontology (HPO) project database for diseases and causative genes related to the CULA described in the OMT classification and to develop a methodology for differential diagnosis formulation based on the observed congenital anomalies, CulaPhen.

METHODS

We reviewed the HPO database for all diseases, including causative genes related to CULA. All CULA were classified according to the OMT classification; associated non-hand phenotypes were classified into 12 anatomical groups. We analyzed the contribution of each anatomical group to a given disease and developed a tool for differential diagnosis formulation based on these contributions. We compared our results with cases from the literature and with a current HPO tool, Phenomizer.

RESULTS

In total, 514 hand phenotypes were obtained, 384 of which could be classified in the OMT classification. A total of 1,403 diseases could be related to those CULA. A comparison with 10 recently published cases with CULA revealed that the presented phenotype matched the descriptions in our dataset. The differential diagnosis produced using our methodology was more accurate than Phenomizer in 4 of 5 examples.

CONCLUSIONS

The OMT classification can be used to describe hand anomalies that may present in over 1,400 diseases. CulaPhen was developed to provide a (hand) phenotype-based differential diagnosis. Differential diagnosis formulation based on the proposed system outperforms the system in current use.

CLINICAL RELEVANCE

This study illustrates that the OMT diagnoses, either individually or combined, can be cross-referenced with different diseases and syndromes. Therefore, use of the OMT classification can aid differential diagnosis formulation for CULA patients.

Limb development: a paradigm of gene regulation

The limb is a commonly used model system for developmental biology. Given the need for precise control of complex signalling pathways to achieve proper patterning, the limb is also becoming a model system for gene regulation studies. Recent developments in genomic technologies have enabled the genome-wide identification of regulatory elements that control limb development, yielding insights into the determination of limb morphology and forelimb versus hindlimb identity. The modulation of regulatory interactions - for example, through the modification of regulatory sequences or chromatin architecture - can lead to morphological evolution, acquired regeneration capacity or limb malformations in diverse species, including humans.

A Novel Heterozygous Intragenic Sequence Variant in DLX6 Probably Underlies First Case of Autosomal Dominant Split-Hand/Foot Malformation Type 1

Split-hand and foot malformation (SHFM; MIM 183600) is a rare human genetic limb malformation. It is characterized by missing digital rays in the hands and feet. SHFMs vary in severity from mild abnormalities affecting a single limb to acute malformations involving all 4 limbs. It is inherited, as part of both a syndromic and nonsyndromic disorder, in an autosomal recessive, autosomal dominant, and X-linked patterns. So far, 9 loci of hand and foot malformation have been mapped on human chromosomes. The present study describes a family with 2 affected individuals segregating SHFM in an autosomal dominant fashion. Sanger sequencing of the genes involved in SHFM was performed to identify the disease-causing variant. Sequence analysis revealed the first heterozygous missense variant (c.632T>A, p.Val211Glu) in the distal-less homeobox 6 (DLX6) gene, located in chromosome 7q21, causing SHFM in the present family. This study supports the evidence of DLX6 as an SHFM-causing gene.

Altered mRNA Splicing, Chondrocyte Gene Expression and Abnormal Skeletal Development due to SF3B4 Mutations in Rodriguez Acrofacial Dysostosis

The acrofacial dysostoses (AFD) are a genetically heterogeneous group of inherited disorders with craniofacial and limb abnormalities. Rodriguez syndrome is a severe, usually perinatal lethal AFD, characterized by severe retrognathia, oligodactyly and lower limb abnormalities. Rodriguez syndrome has been proposed to be a severe form of Nager syndrome, a non-lethal AFD that results from mutations in SF3B4, a component of the U2 small nuclear ribonucleoprotein particle (U2 snRNP). Furthermore, a case with a phenotype intermediate between Rodriguez and Nager syndromes has been shown to have an SF3B4 mutation. We identified heterozygosity for SF3B4 mutations in Rodriguez syndrome, confirming that the phenotype is a dominant disorder that is allelic with Nager syndrome. The mutations led to reduced SF3B4 synthesis and defects in mRNA splicing, primarily exon skipping. The mutations also led to reduced expression in growth plate chondrocytes of target genes, including the DLX5, DLX6, SOX9, and SOX6 transcription factor genes, which are known to be important for skeletal development. These data provide mechanistic insight toward understanding how SF3B4 mutations lead to the skeletal abnormalities observed in the acrofacial dysostoses.

The acrofacial dysostoses (AFD) are inherited disorders with abnormalities of the facial and limb bones. Rodriguez syndrome is a severe type of AFD that is usually lethal in the immediate perinatal period. Rodriguez syndrome has been proposed to be a severe form of Nager syndrome, a non-lethal AFD that results from mutations in SF3B4, a component of mRNA splicing machinery needed for proper maturation of primary transcripts. Furthermore, a case with a phenotype intermediate between Rodriguez and Nager syndromes has been shown to have an SF3B4 mutation. We found that mutations in SF3B4 produce Rodriguez syndrome, further demonstrating that it is allelic with Nager syndrome. The consequences of the mutations include abnormal splicing and reduced expression in growth plate chondrocytes of genes that are important for proper development of the skeleton, providing mechanistic insight toward understanding how SF3B4 mutations lead to the skeletal abnormalities observed in the acrofacial dysostoses.

7q21.3 Deletion involving enhancer sequences within the gene DYNC1I1 presents with intellectual disability and split hand-split foot malformation with decreased penetrance

Split hand-split food malformation (SHFM) is a congenital defect of limb development that involves the central rays of the autopod and presents with median clefts of the hands and feet. It often includes syndactyly and aplasia/hypoplasia of the phalanges. SHFM is a genetic condition with high genetic heterogeneity, with at least 6 associated chromosomal loci. A locus in chromosomal region 7q21.3, associated with SHFM is referred to as SHFM1. Genes considered to be associated with SHFM1 are DLX5 and DLX6. These two genes participate in the Wnt pathway that has a role in limb development. The gene DYNC1I1, located proximally (centromeric) to the SHFM1 locus was recently reported to include enhancer sequences involved in limb development in its exons 15 and 17. These sequences were shown to cis-regulate the function of the adjacent SHFM associated genes. We report a family, in which the father and three of his sons carry an approximately 1 Mb deletion in this chromosomal region, arr[hg19]7q21.3(94,769,383-95,801,045)x1. The deleted region is located proximally (centromerically) adjacent to the SHFM region at 7q21.3. It does not include the SHFM candidate genes DLX5 and DLX6, but includes the enhancer sequences within DYNC111 and six other genes centromeric to DYNC1I1. All deletion carriers have various degrees of intellectual disability while two of them have SHFM. This family is the eighth reported family where a chromosome 7q21.3 deletion co-segregating with SHFM involves the enhancer regions within gene DYNC111, but does not involve the genes DLX5 and DLX 6. This is also the third family where decreased penetrance of enhancer-associated SHFM is demonstrated. Intellectual disability was not observed in the previously reported families and may be associated with deficiency of one or more of the 6 genes included in the reported deletion centromeric to DYNC1I1.

DLX4 is associated with orofacial clefting and abnormal jaw development

Cleft lip and/or palate (CL/P) are common structural birth defects in humans. We used exome sequencing to study a patient with bilateral CL/P and identified a single nucleotide deletion in the patient and her similarly affected son—c.546_546delG, predicting p.Gln183Argfs*57 in the Distal-less 4 (DLX4) gene. The sequence variant was absent from databases, predicted to be deleterious and was verified by Sanger sequencing. In mammals, there are three Dlx homeobox clusters with closely located gene pairs (Dlx1/Dlx2, Dlx3/Dlx4, Dlx5/Dlx6). In situ hybridization showed that Dlx4 was expressed in the mesenchyme of the murine palatal shelves at E12.5, prior to palate closure. Wild-type human DLX4, but not mutant DLX4_c.546delG, could activate two murine Dlx conserved regulatory elements, implying that the mutation caused haploinsufficiency. We showed that reduced DLX4 expression after short interfering RNA treatment in a human cell line resulted in significant up-regulation of DLX3, DLX5 and DLX6, with reduced expression of DLX2 and significant up-regulation of BMP4, although the increased BMP4 expression was demonstrated only in HeLa cells. We used antisense morpholino oligonucleotides to target the orthologous Danio rerio gene, dlx4b, and found reduced cranial size and abnormal cartilaginous elements. We sequenced DLX4 in 155 patients with non-syndromic CL/P and CP, but observed no sequence variants. From the published literature, Dlx1/Dlx2 double homozygous null mice and Dlx5 homozygous null mice both have clefts of the secondary palate. This first finding of a DLX4 mutation in a family with CL/P establishes DLX4 as a potential cause of human clefts.