Search Results (27)

Background: Intellectual disability (ID) is a heterogeneous condition caused by diverse genetic factors, including single-nucleotide variants (SNVs) and copy number variants (CNVs). Whole-exome sequencing (WES) and clinical exome sequencing (CES) have become essential tools for identifying pathogenic variants; however, their relative diagnostic performance in ID has not been fully characterized. Methods: Children diagnosed with ID or related neurodevelopmental disorders underwent WES or CES. Identified variants were classified according to ACMG/AMP and ClinGen guidelines, with segregation analysis performed when parental samples were available. Diagnostic yields were compared across demographic, prenatal, and phenotypic subgroups. A multidimensional semi-quantitative scoring system encompassing 15 clinical domains (e.g., age at onset, neuro-motor function, seizures, MRI findings, vision, and dysmorphic features) was developed. Z-scores were calculated for each parameter, followed by hierarchical cluster analysis (HCA) and correlation modeling to define genotype–phenotype associations and pathway-level clustering. Results: A broad spectrum of pathogenic and likely pathogenic variants across multiple genes and biological pathways was identified in our study. CNV-associated cases frequently exhibited prenatal anomalies or multisystem phenotypes associated with large chromosomal rearrangements. Monogenic variants and their corresponding phenotypic profiles were identified through clinical exome sequencing (CES) and whole-exome sequencing (WES). Phenotypic HCA based on Z-scores revealed three major biological groups of patients with coherent genotype–phenotype relationships: Group 1, severe multisystem neurodevelopmental disorders dominated by transcriptional and RNA-processing genes (POLR1C, TCF4, HNRNPU, NIPBL, ACTG1); Group 2, intermediate epileptic and metabolic forms associated with ion-channel and excitability-related genes (SCN2A, PAH, IQSEC2, GNPAT); and Group 3, milder or focal neurodevelopmental phenotypes involving myelination and signaling-related genes (NKX6-2, PLP1, PGAP3, SMAD6, ATP1A3). Gene distribution significantly differed among these biological categories (χ² = 54.566, df = 34, p = 0.0141), confirming non-random, biologically consistent grouping. Higher Z-scores correlated with earlier onset and greater neurological severity, underscoring the clinical relevance of the multidimensional analytical framework. Conclusions: This study highlights the genetic complexity and clinical heterogeneity of intellectual disability and demonstrates the superior diagnostic resolution of WES and CES. Integrating multidimensional phenotypic profiling with genomic analysis enhances genotype–phenotype integration and enables data-driven phenotype stratification and pathway-based re-analysis. This combined diagnostic and analytical framework offers a more comprehensive approach to diagnosing monogenic ID and provides a foundation for future predictive and functional studies. Full article

Cornelia de Lange Syndrome (CdLS) is a rare congenital disorder characterised by distinctive facial features, growth retardation, limb abnormalities and developmental delays. It is characterised by genetic heterogeneity and also presents a broad clinical variability, with a spectrum of manifestations ranging from mild to severe, with milder phenotypes that can be difficult to ascertain based on physical characteristics. Pathogenic variations in the NIPBL gene account for the majority of cases, but variations in several other genes, including BRD4, have been identified as causative factors for non-classic or milder forms of the syndrome. This review aims to analyse the roles that BRD4 plays in the various pathways in which it is involved and to summarise current knowledge on atypical CdLS associated with BRD4 gene alterations, highlighting clinical features, molecular mechanisms, and implications for diagnostic assessment and patient care. Full article

Neurodevelopmental disorders (NDDs) represent a heterogeneous group of diseases with a variety of clinical presentations related to different genetic, epigenetic, and environmental etiologies. Numerous pathogenic variants have been identified by comprehensive genetic approaches such as next-generation sequencing and chromosomal microarray analyses. This study included eleven pediatric patients with NDDs who were referred to our Molecular Medicine (MM) unit for further diagnostic workup. Whole exome sequencing (WES) was performed, and data were analyzed as part of a contracted service with the National Genomic Center and iBioScience LTD. Likely pathogenic single nucleotide variants in genes DDX3X c.869C>A, p.S290* and CNOT1 c.920delG, p.G307Afs*32 in two patients, and pathogenic copy number variants in the 16p11.2 (16:29,690,418-30,200,285)x3 and 16p12.1-p11.2 (16:27,078,317-29,001,333)x3 regions in a third patient with NDDs were identified. In a fourth patient, the c.6839A>G, p.Gln2280Arg variant of uncertain significance was found in the NIPBL gene. Altogether, our study has revealed four novel variants in genes previously linked to NDDs. Identification of genetic causes of NDDs not only promotes establishing a more precise diagnosis and improves our understanding of disease pathogenesis but may also provide better means for developing preventive measures for the recurrence of this serious condition. Full article

Autism spectrum disorder (ASD) is a heritable neurodevelopmental condition with a complex genetic architecture. Dissecting the interplay between inherited variants and high-impact de novo variants is critical for understanding its etiology. We conducted a family-based study involving 42 families with ASD (139 individuals). Using a targeted next-generation sequencing (NGS) panel of 236 genes, we identified and characterized rare inherited and de novo variants in affected probands, parents, and unaffected siblings. Our analysis revealed a complex genetic landscape marked by diverse inheritance patterns. De novo variants were predominantly observed in individuals with atypical autism, while biparental (homozygous) inheritance was more common in Asperger syndrome. Maternally inherited variants showed significant enrichment in intronic regions, pointing to a potential regulatory role. We also detected variants in several high-confidence ASD risk genes, including SHANK3, MYT1L, MCPH1, NIPBL, and TSC2, converging on pathways central to synaptic function and neurogenesis. Across the cohort, five variants of uncertain significance (VUS) were identified, comprising two inherited variants in ABCC8 and additional variants in CUL23, TSC2, and MCPH1. Our findings underscore the profound genetic heterogeneity of ASD and suggest that distinct genetic mechanisms and inheritance patterns may contribute to different clinical presentations within the spectrum. This highlights the power of family-based genomic analyses in elucidating the complex interplay of inherited and de novo variants that underlies ASD. Full article

High-risk neuroblastoma remains a major clinical challenge, with a five-year survival rate below 50% despite intensive multimodal therapies. MYCN amplification, a hallmark of high-risk disease, drives an aggressive transcriptional program that maintains undifferentiated and proliferative states in neuroblastoma cells. Given its central role in oncogenic transcription, MYCN represents an attractive therapeutic target; however, its undruggable nature has prompted efforts to identify upstream regulators or cofactors that sustain MYCN expression and oncogenic function. In this study, we investigate the role of the cohesin loading factor NIPBL in supporting the MYCN-driven transcriptional program. We demonstrate that elevated NIPBL expression is associated with undifferentiated, proliferative neuroblastoma cell states and poor clinical outcomes in neuroblastoma patients. Functionally, NIPBL depletion reduces MYCN mRNA and protein levels and induces widespread transcriptional reprogramming consistent with neuronal differentiation. These transcriptional changes are accompanied by decreased neuroblastoma cell proliferation and increased neuronal differentiation, reflecting impaired regulation of MYCN target genes upon NIPBL loss. Collectively, we have established a mechanistic link between NIPBL and the MYCN-driven transcriptome, highlighting NIPBL as a potential therapeutic vulnerability to promote differentiation in high-risk neuroblastoma. Full article

The shape of the skull plays a crucial role in the evolution and adaptation of species to their environments. In the case of aquaculture fish, the size of the head is also an important economic trait, as it is linked to fillet yield and ornamental value. This study applies our GRAMMAR-Lambda method to perform a genome-wide association study analysis on loci related to head size in catfish. Compared with traditional GWAS methods, the GRAMMAR-Lambda method offers higher computational efficiency, statistical power, and stability, especially in complex population structures. This research identifies many candidate genes closely related to cranial morphology in terms of head length, width, and depth in catfish, including bmpr1bb, fgfrl1b, nipbl, foxp2, and pax5, etc. Based on the results of gene–gene interaction analysis, we speculate that there may be frequent genetic interactions between chromosome 19 and chromosome 29 in bone development. Additionally, many candidate genes, gene families, and mechanisms (such as SOCE mechanisms) affecting skeletal development and morphology have been identified. These findings contribute to our understanding of the genetic architecture of head size and will support marker-assisted breeding in aquaculture, also reflecting the potential application of the GRAMMAR-Lambda method in genetic studies of complex traits. Full article

Cornelia de Lange syndrome (CdLS) is a rare, dominantly inherited multisystem developmental disorder. Pathogenic variants in genes encoding the structural subunits and regulatory proteins of the cohesin complex (NIPBL, SMC1A, SMC3, HDAC8, and RAD21) are the primary contributors to the pathogenesis of CdLS. Pathogenic variations in these genes disrupt normal cohesin function, leading to the syndrome’s diverse and complex clinical presentation. In this study, we discovered that cells harboring variants in the NIPBL, SMC1A and HDAC8 genes exhibit spontaneous genome instability, elevated oxidative stress and premature cellular aging. These findings suggest that cohesin plays a critical role in maintaining proper cellular function and highlight its contribution to the pathophysiology seen in the related diagnoses. Full article

Cornelia de Lange syndrome (CdLS) is a rare genetic disorder characterized by a distinctive facial appearance, growth/cognitive retardation, developmental delay, skeletal malformation, hypertrichosis, and other abnormalities. Patients with mild CdLS have less severe phenotypes, while retaining representative facial features. Mutations in the genes NIPBL, SMC1A, SMC3, HDAC8, and RAD21 have been associated with CdLS, with mutations in NIPBL accounting for approximately 60% of cases. Herein, we present a case of CdLS accompanied by cholelithiasis and nephrolithiasis. A 9-year-old Korean boy presented with vomiting and abdominal pain. Abdominal ultrasonography revealed several gallstones and renal stones. Extracorporeal shock wave lithotripsy failed; therefore, cholecystectomy and nephrolithotomy were performed. Postoperative stone composition analysis revealed calcium oxalate as the primary component. CdLS was suspected based on the characteristic appearance and physical examination, with genetic testing confirming an NIPBL gene mutation. Simultaneous CdLS, cholelithiasis, and nephrolithiasis requires careful management and treatment tailored to each patient’s specific needs and challenges. Full article

Cannabinoids are reported to have neuroprotective properties and play a role in neurogenesis and neuroplasticity in in vitro and in vivo models. Cannabinol (CBN) is a minor cannabinoid produced by the degradation of Δ⁹-tetrahydrocannabinol in Cannabis sativa L. and exhibits anti-oxidant, analgesic, anti-bacterial, and anti-inflammatory effects. In this study, we explored the biological effects of 20 µM CBN (6.20 µg/mL) on differentiated NSC-34 cells by MTT assay and next-generation sequencing analysis on the transcriptome. KEGG and Gene Ontology enrichment analyses have been performed to evaluate potential CBN-associated processes. Our results highlighted the absence of any cytotoxic effect of CBN. The comparative transcriptomic analysis pointed out the downregulation of Cdkn2a, Cdkn2c and Cdkn2d genes, which are known to suppress the cell cycle. Ccne2, Cdk2, Cdk7, Anapc11, Anapc10, Cdc23, Cdc16, Anapc4, Cdc27, Stag1, Smc3, Smc1a, Nipbl, Pds5a, Pds5b, and Wapl genes, renowned for their role as cell cycle progression activators, were instead upregulated. Our work suggests that CBN regulates the expression of many genes related to the cell cycle, which are required for axonal maturation, migration, and synaptic plasticity, while not affecting the expression of genes involved in cell death or tumorigenesis. Full article

Cohesin is a highly conserved ring-shaped complex involved in topologically embracing chromatids, gene expression regulation, genome compartmentalization, and genome stability maintenance. Genomic analyses have detected mutations in the cohesin complex in a wide array of human tumors. These findings have led to increased interest in cohesin as a potential target in cancer therapy. Synthetic lethality has been suggested as an approach to exploit genetic differences in cancer cells to influence their selective killing. In this study, we show that mutations in ESCO1, NIPBL, PDS5B, RAD21, SMC1A, SMC3, STAG2, and WAPL genes are synthetically lethal with stimulation of WNT signaling obtained following LY2090314 treatment, a GSK3 inhibitor, in several cancer cell lines. Moreover, treatment led to the stabilization of β-catenin and affected the expression of c-MYC, probably due to the occupancy decrease in cohesin at the c-MYC promoter. Finally, LY2090314 caused gene expression dysregulation mainly involving pathways related to transcription regulation, cell proliferation, and chromatin remodeling. For the first time, our work provides the underlying molecular basis for synthetic lethality due to cohesin mutations and suggests that targeting the WNT may be a promising therapeutic approach for tumors carrying mutated cohesin. Full article

The human STAG2 protein is an essential component of the cohesin complex involved in cellular processes of gene expression, DNA repair, and genomic integrity. Somatic mutations in the STAG2 sequence have been associated with various types of cancer, while congenital variants have been linked to developmental disorders such as Mullegama–Klein–Martinez syndrome, X-linked holoprosencephaly-13, and Cornelia de Lange syndrome. In the cohesin complex, the direct interaction of STAG2 with DNA and with NIPBL, RAD21, and CTCF proteins has been described. The function of STAG2 within the complex is still unknown, but it is related to its DNA binding capacity and is modulated by its binding to the other three proteins. Every missense variant described for STAG2 is located in regions involved in one of these interactions. In the present work, we model the structure of 12 missense variants described for STAG2, as well as two other variants of NIPBl and two of RAD21 located at STAG2 interaction zone, and then analyze their behavior through molecular dynamic simulations, comparing them with the same simulation of the wild-type protein. This will allow the effects of variants to be rationalized at the atomic level and provide clues as to how STAG2 functions in the cohesin complex. Full article

Cornelia de Lange Syndrome (CdLS) patients, who frequently carry a mutation in NIPBL, present an increased incidence of outflow tract (OFT)-related congenital heart defects (CHDs). Nipbl+/- mice recapitulate a number of phenotypic traits of CdLS patients, including a small body size and cardiac defects, but no study has specifically focused on the valves. Here, we show that adult Nipbl+/- mice present aortic valve thickening, a condition that has been associated with stenosis. During development, we observed that OFT septation and neural crest cell condensation was delayed in Nipbl+/- embryos. However, we did not observe defects in the deployment of the main lineages contributing to the semilunar valves. Indeed, endocardial endothelial-to-mesenchymal transition (EndMT), analysed via outflow tract explants, and neural crest migration, analysed via genetic lineage tracing, did not significantly differ in Nipbl+/- mice and their wild-type littermates. Our study provides the first direct evidence for valve formation defects in Nipbl+/- mice and points to specific developmental defects as an origin for valve disease in patients. Full article

Ningxiang pig is a breed renowned for its exceptional meat quality, but it possesses suboptimal carcass traits. To elucidate the genetic architecture of meat quality and carcass traits in Ningxiang pigs, we assessed heritability and executed a genome-wide association study (GWAS) concerning carcass length, backfat thickness, meat color parameters (L.LD, a.LD, b.LD), and pH at two postmortem intervals (45 min and 24 h) within a Ningxiang pig population. Heritability estimates ranged from moderate to high (0.30~0.80) for carcass traits and from low to high (0.11~0.48) for meat quality traits. We identified 21 significant SNPs, the majority of which were situated within previously documented QTL regions. Furthermore, the GRM4 gene emerged as a pleiotropic gene that correlated with carcass length and backfat thickness. The ADGRF1, FKBP5, and PRIM2 genes were associated with carcass length, while the NIPBL gene was linked to backfat thickness. These genes hold the potential for use in selective breeding programs targeting carcass traits in Ningxiang pigs. Full article

Novel approaches to uncover the molecular etiology of neurodevelopmental disorders (NDD) are highly needed. Even using a powerful tool such as whole exome sequencing (WES), the diagnostic process may still prove long and arduous due to the high clinical and genetic heterogeneity of these conditions. The main strategies to improve the diagnostic rate are based on family segregation, re-evaluation of the clinical features by reverse-phenotyping, re-analysis of unsolved NGS-based cases and epigenetic functional studies. In this article, we described three selected cases from a cohort of patients with NDD in which trio WES was applied, in order to underline the typical challenges encountered during the diagnostic process: (1) an ultra-rare condition caused by a missense variant in MEIS2, identified through the updated Solve-RD re-analysis; (2) a patient with Noonan-like features in which the NGS analysis revealed a novel variant in NIPBL causing Cornelia de Lange syndrome; and (3) a case with de novo variants in genes involved in the chromatin-remodeling complex, for which the study of the epigenetic signature excluded a pathogenic role. In this perspective, we aimed to (i) provide an example of the relevance of the genetic re-analysis of all unsolved cases through network projects on rare diseases; (ii) point out the role and the uncertainties of the reverse phenotyping in the interpretation of the genetic results; and (iii) describe the use of methylation signatures in neurodevelopmental syndromes for the validation of the variants of uncertain significance. Full article

Cornelia de Lange syndrome (CdLS) is a multisystemic genetic disorder characterized by distinctive facial features, growth retardation, and intellectual disability, as well as various systemic conditions. It is caused by genetic variants in genes related to the cohesin complex. Single-nucleotide variations are the best-known genetic cause of CdLS; however, copy number variants (CNVs) clearly underlie a substantial proportion of cases of the syndrome. The NIPBL gene was thought to be the locus within which clinically relevant CNVs contributed to CdLS. However, in the last few years, pathogenic CNVs have been identified in other genes such as HDAC8, RAD21, and SMC1A. Here, we studied an affected girl presenting with a classic CdLS phenotype heterozygous for a de novo ~32 kbp intragenic duplication affecting exon 10 of HDAC8. Molecular analyses revealed an alteration in the physiological splicing that included a 96 bp insertion between exons 9 and 10 of the main transcript of HDAC8. The aberrant transcript was predicted to generate a truncated protein whose accessibility to the active center was restricted, showing reduced ease of substrate entry into the mutated enzyme. Lastly, we conclude that the duplication is responsible for the patient’s phenotype, highlighting the contribution of CNVs as a molecular cause underlying CdLS. Full article