Nager syndrome (NS) is a rare congenital disorder primarily characterized by mandibulofacial dysostosis and upper limb anomalies. Pathogenic variants in SF3B4, which encodes a core spliceosomal component, represent the primary known genetic cause of NS. This review synthesizes recent findings from cellular, zebrafish, Xenopus, and mouse models to elucidate how SF3B4 deficiency perturbs neural crest cell (NCC) biology and multi-tissue development. Loss of SF3B4 induces widespread splicing abnormalities, with preferential exon skipping affecting AT-rich and GC-poor exons, thereby altering the expression of genes critical for NCC survival, proliferation, migration, and lineage specification. These cellular defects are further exacerbated by oxidative stress and activation of the p53 pathway, resulting in a broad spectrum of developmental abnormalities involving craniofacial, cardiac, skeletal, and sensory (auditory and ocular) systems. Together, these findings highlight the essential role of SF3B4 in coordinating early morphogenesis. Cross-species comparisons reveal conserved NCC vulnerabilities alongside model-specific phenotypes, highlighting the challenge of linking individual splicing alterations to distinct structural outcomes in NS. Future research directions include defining tissue-specific SF3B4-dependent splicing targets, developing human induced pluripotent stem cell-derived models, and exploring therapeutic strategies aimed at restoring splicing homeostasis or compensating for disrupted developmental signaling pathways. This article is categorized under: Congenital Diseases > Molecular and Cellular Physiology Congenital Diseases > Genetics/Genomics/Epigenetics Congenital Diseases > Stem Cells and Development.

To compare management and outcomes of infants with mandibulofacial dysostosis syndromes (Treacher Collins and Nager syndromes) admitted to neonatal intensive care units (NICUs) to infants with other causes of micrognathia. The Children's Hospitals Neonatal Database from 2010 to 2023 was queried for infants with diagnoses of Treacher Collins syndrome (TCS), Nager syndrome (NS), and other infants in NICUs with micrognathia (n = 4210). We identified 103 infants with TCS and 11 with NS to compare with the micrognathia cohort (n = 4210). Compared with infants with micrognathia, those with TCS were more likely to undergo tracheostomy (54% vs 11%) and gastrostomy tube placement (67% vs 35%) and were less likely to undergo mandibular distraction (9.7% vs 28.2%). The hospital mortality rate in TCS was lower than micrognathia cohort (1.9% vs 7.2%). Apgar scores were similar for TCS and micrognathia cohorts (6 and 8 vs 7 and 8, at 1 and 5 minutes, respectively) but lower for NS (2 and 6). Infants with NS had the highest rate of intubation at birth (91%) and tracheostomy placement (72.7%), and a higher mortality rate than TCS (27.3% vs 1.9%). Hospital length of stay was longer in TCS (47.5 days) and NS (43 days) than the micrognathia cohort (37 days). Infants with mandibulofacial dysostosis (TCS and NS) were more likely to have a tracheostomy and gastrostomy tube, and less likely to undergo mandibular distraction than infants with micrognathia from other causes. NS was most severe with highest mortality rate and lowest Apgar scores. Despite a higher rate of tracheostomy and longer length of stay, the mortality rate for TCS remained low.

Alternative splicing creates diverse RNA isoforms from individual genes, yet single-cell CRISPR screens are limited to gene-level quantification and cannot detect changes in alternative splicing and transcript isoforms. To overcome this limitation, we develop CRISPore-seq, which couples massively-parallel CRISPR perturbations with joint short- and long-read transcriptomics. CRISPore-seq simultaneously captures genetic perturbations and expression of genes, full-length transcripts and surface proteins in single cells. CRISPore-seq long reads identify 80% more transcript isoforms than short reads. Nearly all long reads map to unique transcript isoforms - in contrast to existing single-cell perturbation methods, which rarely distinguish specific isoforms. Using CRISPore-seq, we knock-down 15 different RNA-binding proteins (RBPs) and identify thousands of perturbation-driven alternative splicing events (ASEs). We find that exon skipping is the most common ASE observed and that skipped exons are enriched for binding sites of perturbed RBPs. Loss of the Nager syndrome-associated spliceosomal factor SF3B4 triggers skipping of exon 2 in the cell-cycle regulator CCND1 , preventing formation of a complex with CDK6 and blocking the G1-S transition. After rescue with a CCND1 isoform containing the skipped exon, both holoenzyme complex formation and cell proliferation are restored. By linking genes to transcriptional phenotypes with isoform-level resolution, CRISPore-seq is a highly scalable tool for understanding the impact of genetic perturbations on the human transcriptome.

Nager acrofacial dysostosis (#154400) is a rare and mostly sporadic malformation syndrome characterized by craniofacial and extremity findings. In the study, a new case diagnosed in the neonatal period will be presented. The neonatal intensive care unit consulted with our pediatrics genetic clinic for a 2-week-old male patient, who was being followed up in their unit, due to his dysmorphic findings and extremity defects. In the physical examination, downward palpebral fissures, zygomatic bone hypoplasia, mandibular hypoplasia, retromicrognathia, bilateral microtia, bilateral external auditory canal atresia, and bilateral thumb agenesis were observed. Direct radiographs showed left radius hypoplasia and bilateral thumb agenesis. Nager syndrome was considered in the presence of typical craniofacial findings, preaxial extremity deformities, and radiological findings. In the SF3B4 sequence analysis, c.737dupC p.(V247Sfs*239) heterozygous variant was detected. As a result of the segregation analysis, it was demonstrated that the variant was de novo. Nager acrofacial dysostosis should be considered in the patients with craniofacial malformations and radial ray findings.

Mandibulofacial dysostosis (MFD) is a congenital disorder characterized by defects in facial bones of neural crest origin. Nager syndrome combines many features of MFD with limb defects. Mutations in SF3B4, a gene located on chromosome 1 that encodes a protein of the spliceosome, were identified as a cause for Nager syndrome in approximately 60% of patients. A region of chromosome 9 (9q32) that contains 35 genes has also been linked to Nager syndrome and may account for some affected individuals for which the causes of the disease have not been identified. Because Nager syndrome belongs to a rapidly growing list of craniofacial syndromes caused by pathogenic variants of splicing factors, we focused our attention on two genes in the 9q32 region that encode factors involved in pre-mRNA processing, PRPF4 and PTBP3, and analyzed their role in craniofacial development in Xenopus embryos. Loss-of-function experiments in Xenopus laevis embryos indicate that Ptbp3 is required while Prpf4 is dispensable for neural crest gene expression at the neurula stage, a phenotype that is partially rescued by expression of human PTBP3. At the tadpole stage, Ptbp3-depleted embryos have severely hypoplastic craniofacial cartilages, phenocopying the defects observed in Sf3b4 morphant tadpoles. Furthermore, ptbp3 expression is significantly increased in Xenopus tropicalis sf3b4 Null embryos as compared to wild-type siblings. We propose that dysregulation of PTBP3 expression may cause Nager syndrome in a subset of patients who do not have a mutation in SF3B4.