SF3B4 Gene Research Articles

Transcriptomic analysis reveals mitochondrial dysfunction in the pathogenesis of Nager syndrome in sf3b4-depleted zebrafish

Nager syndrome (NS) is a rare acrofacial dysostosis caused by heterozygous loss-of-function variants in the splicing factor 3B subunit 4 (SF3B4). The main clinical features of patients with NS are characterized by facial-mandibular and preaxial limb malformations. The migration and specification of neural crest cells are crucial for craniofacial development, and mitochondrial fitness appears to play a role in such processes. Here, by analyzing our previously published transcriptome dataset, we aim to investigate the potential involvement of mitochondrial components in the pathogenesis of craniofacial malformations, especially in sf3b4 mutant zebrafish. We identified that oxidative phosphorylation (OXPHOS) defects and overproduction of reactive oxygen species (ROS) due to decreased antioxidants defense activity, which leads to oxidative damage and mitochondrial dysfunction. Furthermore, our results highlight that fish lacking sf3b4 gene, primarily display defects in mitochondrial complex I. Altogether, our findings suggest that mitochondrial dysfunction may contribute to the development of the craniofacial anomalies observed in sf3b4-depleted zebrafish.

Children with Rare Nager Syndrome-Literature Review, Clinical and Physiotherapeutic Management.

Nager syndrome is a rare human developmental disorder characterized by craniofacial defects including the downward slanting of the palpebral fissures, cleft palate, limb deformities, mandibular hypoplasia, hypoplasia or absence of thumbs, microretrognathia, and ankylosis of the temporomandibular joint. The prevalence is very rare and the literature describes only about a hundred cases of Nager syndrome. There is evidence of autosomal dominant and autosomal recessive inheritance for Nager syndrome, suggesting genetic heterogeneity. The majority of the described causes of Nager syndrome include pathogenic variants in the SF3B4 gene, which encodes a component of the spliceosome; therefore, the syndrome belongs to the spliceosomopathy group of diseases. The diagnosis is made on the basis of physical and radiological examination and detection of mutations in the SF3B4 gene. Due to the diversity of defects associated with Nager syndrome, patients require multidisciplinary, complex, and long-lasting treatment. Usually, it starts from birth until the age of twenty years. The surgical procedures vary over a patient's lifetime and are related to the needed function. First, breathing and feeding must be facilitated; then, oral and facial clefts should be addressed, followed by correcting eyelid deformities and cheekbone reconstruction. In later age, a surgery of the nose and external ear is performed. Speech and hearing disorders require specialized logopedic treatment. A defect of the thumb is treated by transplanting a tendon and muscle or transferring the position of the index finger. In addition to surgery, in order to maximize a patient's benefit and to reduce functional insufficiency, complementary treatments such as rehabilitation and physiotherapy are recommended. In our study, we describe eight patients of different ages with various cases of Nager syndrome. The aim of our work was to present the actual genetic knowledge on this disease and its treatment procedures.

A rare case of Rodriguez syndrome caused by a SF3B4 gene deletion

The acrofacial dysostoses are a genetically heterogeneous group of inherited disorders characterized by craniofacial and limb abnormalities. Nager and Rodriguez syndromes, posited as distinct subtypes, have recently been described as a phenotypic spectrum associated with haploinsufficiency of the SF3B4 gene.

Dysregulation of Spliceosomes Complex Induces Retinitis Pigmentosa–Like Characteristics in sf3b4-Depleted Zebrafish

The SF3B4 gene encodes a highly conserved protein that plays a critical role in mRNA splicing, and mutations in this gene are known to cause Nager syndrome, a rare craniofacial disorder. Although SF3B4 expression is detected earlier in the optic vesicle than in the limb and somite, the role of SF3B4 in the eye is not well understood. Here, we investigate the function of sf3b4 in the retina by performing transcriptome profiles, immunostaining, and behavioral analysis of sf3b4-/- mutant zebrafish. Our findings suggest that dysregulation of the spliceosome complex affects not only craniofacial development but also retinogenesis. Our observation points to the fact that zebrafish lacking functional sf3b4 displayed characteristics similar to retinitis pigmentosa (RP), marked by severe retinal pigment epithelium (RPE) defects and rod degeneration. Pathway analysis revealed altered retinol metabolism and retinoic acid (RA) signaling in the sf3b4-/- mutants. Supplementation of RA rescued key cellular phenotypes observed in the sf3b4-/- mutants, offering potential therapeutic strategies for RP in the future. In conclusion, our study sheds light on the previously unknown role of SF3B4 in retinogenesis and provides insights into the underlying mechanisms of RP.

SF3B4 Frameshift Variants Represented a More Severe Clinical Manifestation in Nager Syndrome.

Nager syndrome (NS) is a rare disease marked with craniofacial and preaxial limb anomalies. In this report, we summarized the current evidence to determine a possible genotype-phenotype association among NS individuals. Twenty-four articles comprising of 84 NS (including 9 patients with a severe form of NS [Rodriguez syndrome]) patients were examined, of which 76% were caused by variants in SF3B4 (OMIM *605593, Splicing Factor 3B, Subunit 4). Within the SF3B4 gene, variants located in exon 3 commonly occurred (20%) from a total identified variant, while hotspot location was identified in exon 1 (12%), and primarily occurred as frameshift variants (64%). Thirty-five distinct pathogenic variants within SF3B4 gene were identified with two common sites, c.1A > G and c.1060dupC in exons 1 and 5, respectively. Although no significant genotype-phenotype association was found, it is notable that patients with frameshift SF3B4 variants and predicted to lead to nonsense-mediated RNA decay (NMD) of the transcripts tended to have a more severe clinical manifestation. Additionally, patients harboring variants in exons 2 and 3 displayed a higher proportion of cardiac malformations. Taken together, this article summarizes the pathogenic variants observed in SF3B4 and provides a possible genotype-phenotype relationship in this disease.

Molecular mechanisms of hearing loss in Nager syndrome

Nager syndrome is a rare human developmental disorder characterized by hypoplastic neural crest-derived craniofacial bones and limb defects. Mutations in SF3B4 gene, which encodes a component of the spliceosome, are a major cause for Nager. A review of the literature indicates that 45% of confirmed cases are also affected by conductive, sensorineural or mixed hearing loss. Conductive hearing loss is due to defective middle ear ossicles, which are neural crest derived, while sensorineural hearing loss typically results from defective inner ear or vestibulocochlear nerve, which are both derived from the otic placode. Animal model of Nager syndrome indicates that upon Sf3b4 knockdown cranial neural crest progenitors are depleted, which may account for the conductive hearing loss in these patients. To determine whether Sf3b4 plays a role in otic placode formation we analyzed the impact of Sf3b4 knockdown on otic development. Sf3b4-depleted Xenopus embryos exhibited reduced expression of several pan-placodal genes six1, dmrta1 and foxi4.1. We confirmed the dependence of placode genes expression on Sf3b4 function in animal cap explants expressing noggin, a BMP antagonist critical to induce placode fate in the ectoderm. Later in development, Sf3b4 morphant embryos had reduced expression of pax8, tbx2, otx2, bmp4 and wnt3a at the otic vesicle stage, and altered otic vesicle development. We propose that in addition to the neural crest, Sf3b4 is required for otic development, which may account for sensorineural hearing loss in Nager syndrome.

14. Prenatal diagnosis of Acrofacial Dysostosis type 1 (Nager syndrome) by chromosomal microarray at the exon level

Nager syndrome or Acrofacial Dysostosis type 1 (OMIM #154400) is a rare, autosomal dominant syndrome characterized by craniofacial malformations. Fewer than 100 cases have been reported in the literature and of these, only 11 were suspected prenatally. Major phenotypic findings include micrognathia, ear anomalies and limb malformations; however, the severity is variable. Haploinsufficiency of the SF3B4 (1q21.2) gene is the most commonly recognized etiology of Nager syndrome and can be identified in more than 50% of clinically affected patients. SF3B4 encodes for the SAP49 protein which is a component of the spliceosome and has a role in the bone morphogenic protein pathway. The majority of Nager syndrome cases involve missense and nonsense mutations, or whole gene deletions. We report on a 20 year old primigravida who underwent amniocentesis at 23+1 weeks due to ultrasound findings of severe micrognathia, ear anomalies, mild hypotelorism, and absent left thumb. Chromosome microarray identified a 166kb partial deletion of the SF3B4 gene spanning exons 3-6. Copy number PCR was performed to confirm the finding and to determine whether the deletion was maternally inherited. Both independent DNA extractions of the amniotic fluid sample had a copy number of one and the maternal sample had a copy number of two, confirming the deletion. To the best of our knowledge, this prenatal diagnosis of Nager syndrome by chromosomal microarray is the first partial gene deletion of SF3B4 reported. Further, this demonstrates the importance of chromosomal microarray in correlating fetal ultrasound findings with genetic etiology. Knowledge of this result prior to birth allowed more robust family counseling about the findings and prognosis, along with adequate medical preparation for the anticipated complex interventional needs of the neonate at and after delivery.

Rodriguez acrofacial dysostosis is caused by apparently de novo heterozygous mutations in the SF3B4 gene.

Acrofacial dysostosis syndrome of Rodriguez is characterized by severe mandibular underdevelopment, upper limb phocomelia with absent fingers, absent fibulae, cleft palate, microtia, and abnormal pulmonary function. First reported in three siblings it was assumed to be an autosomal recessive condition. However, subsequent publication reported a further five simplex occurrences and a living patient with a heterozygous mutation in the SF3B4 gene. Exome sequencing was performed on four fetuses with this disorder, including one of the originally described affected siblings. We identified two heterozygous frameshift mutations in the SF3B4 gene in three of the four fetuses investigated. The observed mutation was apparently de novo in one fetus for whom parental DNA was available. Thus, Acrofacial dysostosis syndrome of Rodriguez is an autosomal dominant condition and the recurrences identified in the initial report were likely due to gonadal mosaicism. © 2016 Wiley Periodicals, Inc.

Syndrome de Nager associé à une tétralogie de Fallot : une association fréquente ?

Nager syndrome belongs to a heterogeneous group of disorders involving abnormal development of the extremities, face, and jaw: acrofacial dysostosis (AFD). Fewer than 100 cases of Nager syndrome have been reported to date. Recently, mutations in the 1q21.2 region of the SF3B4 gene (splicing factor 3B subunit 4), which encodes a spliceosomal protein (SAP49) involved in the assembly of the spliceosomal complex U2SNP, have been demonstrated in patients with Nager syndrome. We report the case of a child who had a characteristic association (Pierre Robin sequence, bilateral and symmetrical malar hypoplasia, absent thumbs) clinically diagnosed as Nager syndrome. This child also presented tetralogy of Fallot. This combination is unusual; only two other cases have been described. The karyotype and the CGH-array were normal. After the description in 2012 of several mutations in the SF3B4 gene (1q21.2) in Nager syndrome, a genetic search for our patient revealed the mutation c.1229delC. In 2013, other authors showed the presence of these same mutations in the majority of their patients diagnosed as Nager syndrome. The haploinsufficiency of the SF3B4 region seems to be the major cause of Nager syndrome.

Nager Syndrome Does Not Preclude Organ Donation

Nager Syndrome is characterized by craniofacial and upper limb anomalies. The majority of patients are affected by sporadic disease. Yet, familial cases have been reported where patients are affected by mutations in SF3B4 gene or express 3p14 common fragile site. Aberrations in the first, second branchial arches and limb buds are responsible for the phenotypic presentations [1,2]. The diagnostic features of NS can be categorized into craniofacial, limb and skeletal anomalies that give these patients an atypical appearance. Hallmark of the facial findings are: down slanting palpebral fissures, malar and mandibular hypoplasia, high nasal bridge, micrognathia, external ear anomalies, and cleft palate. Upper limb deformities include thumb anomalies, radial defect and radioulnar synostosis and axial skeletal anomalies with short stature [3]. In addition, other features that have been less often identified in NS are internal organ anomalies associated with cardiovascular, gastrointestinal, genitourinary and central nervous systems [4]. To our knowledge, no previous reports of patients with Nager Syndrome (NS) and solid organ donation have been described in the literature.

Nager syndrome: confirmation of SF3B4 haploinsufficiency as the major cause

Nager syndrome belongs to the group of acrofacial dysostosis, which are characterized by the association of craniofacial and limb malformations. Recently, exome sequencing studies identified the SF3B4 gene as the cause of this condition in most patients. SF3B4 encodes a highly conserved protein implicated in mRNA splicing and bone morphogenic protein (BMP) signaling. We performed SF3B4 sequencing in 14 families (18 patients) whose features were suggestive of Nager syndrome and found nine mutations predicted to result in loss-of-function. SF3B4 is the major gene responsible for autosomal dominant Nager syndrome. All mutations reported predict null alleles, therefore precluding genotype-phenotype correlations. Most mutation-negative patients were phenotypically indistinguishable from patients with mutations, suggesting genetic heterogeneity.

Possible autosomal recessive inheritance in an infant with acrofacial dysostosis similar to nager syndrome

The acrofacial dysostosis syndromes, which are characterized by malformations of the craniofacial region and limbs, are a clinically heterogeneous group of disorders. Based primarily on the of the pattern of limb defects two major groups have emerged: Nager syndrome with predominantly preaxial malformations plus mandibulofacial dysostosis (severe micrognathia and malar hypoplasia) and Miller syndrome with postaxial malformations plus mandibulofacial dysostosis. Among these syndromes, Nager syndrome is a rare condition but the most common form of acrofacial dysostosis. Most cases are sporadic, while autosomal dominant and autosomal recessive inheritance patterns have been reported. Recently, heterozygous mutations in the SF3B4 gene on chromosome 1q12-q21 were found to be responsible for a subset of sporadic and autosomal dominant cases. We present a female infant born to consanguineous parents with craniofacial features resembling Nager syndrome and a unilateral preaxial limb malformation. Mutation analysis of coding exons of SF3B4 did not identify any mutations. This couple also had a deceased child who had similar clinical features. We conclude that, the presence of consanguinity and absence of mutation in SF3B4, provides evidence in support of a recessive form of Nager syndrome.

Clinical and mutation data in 12 patients with the clinical diagnosis of Nager syndrome

Nager syndrome (MIM #154400) is the best-known preaxial acrofacial dysostosis, mainly characterized by craniofacial and preaxial limb anomalies. The craniofacial abnormalities mainly consist of downslanting palpebral fissures, malar hypoplasia, micrognathia, external ear anomalies, and cleft palate. The preaxial limb defects are characterized by radial and thumb hypoplasia or aplasia, duplication of thumbs and proximal radioulnar synostosis. Haploinsufficiency of SF3B4 (MIM *605593), which encodes SAP49, a component of the pre-mRNA spliceosomal complex, has recently been identified as the underlying cause of Nager syndrome. In our study, we performed exome sequencing in two and Sanger sequencing of SF3B4 in further ten previously unreported patients with the clinical diagnosis of Nager syndrome, including one familial case. We identified heterozygous SF3B4 mutations in seven out of twelve patients. Four of the seven mutations were shown to be de novo; in three individuals, DNA of both parents was not available. No familial mutations were discovered. Three mutations were nonsense, three were frameshift mutations and one T>C transition destroyed the translation start signal. In three of four SF3B4 negative families, EFTUD2 was analyzed, but no pathogenic variants were identified. Our results indicate that the SF3B4 gene is mutated in about half of the patients with the clinical diagnosis of Nager syndrome and further support genetic heterogeneity for this condition.

Szanowny Panie Profesorze

Facial dysostoses are clinically and genetically a heterogeneous group of dysmorphic syndromes characterized by malar and mandibular hypoplasia, dysmorphism of external ear with hearing loss and dysmorphism of eyelids (downslanting palpebral fissures, coloboma of lower eyelid with lack of eyelashes). Facial dysostoses are currently divided as two large groups: with normal limbs development – mandibulofacial dysostoses (MFD) – and dysostoses with abnormalities in development and structure, mainly hands and feet – acrofacial dysostoses (AFD). Facial phenotype in all dysostoses is very similar therefore in dysmorphological diagnostics and it is important to assess other dysmorphic features of face, neck, hand and feet. Other important features that differentiate particular dysostoses are intellectual abilities, microcephaly and additional malformations.The most common and most characteristic MFD is Treacher Collins syndrome (TCS), caused by mutations in TCOF1, POLR1D, and POLR1C genes. The best known acrofacial dysostoses are Nager syndrome, caused by mutations in SF3B4 gene, Miller syndrome caused by mutations in DHDH gene and acrofacial dysostosis type Guion-Almeida (MFDGA) caused by mutations in EFTUD2 gene.The aim of this work is presentation of current knowledge about main types of facial dysostoses, clinical description of particular diseases with their genetic bases and delineation of recommended specialist management.