Search Results (149)

Sex chromosome imbalance is a genetic challenge in species with unequal X-chromosome numbers. Organisms have developed distinct strategies to control this imbalance through a process called dosage compensation. These strategies include X-chromosome inactivation in mammals mediated by the XIST long noncoding RNA and proteins recruited by XIST, and X-linked hypertranscription in male Drosophila driven by the Male-Specific Lethal (MSL) complex. In Caenorhabditis elegans, gene expression is downregulated from each of the two X chromosomes of hermaphrodites by half, thereby matching the levels in XO males. This is mediated by a specialized condensin-containing protein complex, the Dosage Compensation Complex (DCC). In all cases, the chromatin states on the sex chromosomes must be first established and then maintained for the entire lifetime of the organism. Although mammals and nematodes both use repression to achieve dosage compensation, the mechanisms are very different. Here, we summarize recent advances on how repressive chromatin states are established and maintained, with a focus on contrasting C. elegans dosage compensation to XIST-mediated X-chromosome inactivation. We review how specialized chromosome topology, repressive chromatin modifications, and higher-order nuclear architecture are established and maintained to achieve sex-specific regulation of the X chromosomes and highlight key outstanding questions and future research directions. Full article

NKAP (NF-kappa-B-activating protein) is a ubiquitously expressed nuclear protein involved in multiple biological processes. Males with missense NKAP mutations have been reported to present with marfanoid features and behavioral and musculoskeletal abnormalities. We have previously reported that a disruptive NKAP mutation resulted in extremely skewed X chromosome inactivation (XCI), leading to phenotypic manifestation of hemophilia A (HA) in a HA carrier. In this study, with the aim of exploring the phenotypic manifestations of deleterious NKAP mutations in males, as well as their involvement in the mechanism of XCI regulation in females, we generated NKAP mutant mice using CRISPR/Cas9 technology. Gait analysis studies conducted in male mice hemizygous for mutant NKAP by the CatWalk XT system revealed significant alterations in gait parameters, consistent with hypotonia reported in human mutant NKAP patients. By breeding mutant NKAP mice with HA mice, we generated a double heterozygous mutant NKAP/HA mouse model, i.e., female mice carrying mutant NKAP with a WT F8 copy on one X chromosome, and WT NKAP with a mutant F8 copy on the other X chromosome. XCI pattern analysis using methylation-sensitive restriction enzymes demonstrated that mutant NKAP/HA females exhibited significant XCI skewing of the X chromosome bearing the mutant NKAP copy. Furthermore, these females exhibited significantly reduced F8 mRNA levels and FVIII (factor VIII) antigen levels, as demonstrated by quantitative RT-PCR and ELISA, respectively. Murine embryonic fibroblasts (MEFs) derived from a hemizygous mutant NKAP embryo exhibited markedly reduced proliferation rate and increased senescence compared to WT NKAP MEFs, suggesting that XCI skewing induced by mutant NKAP results from secondary selection against cells with an active X chromosome bearing the mutant NKAP copy. Full article

This study aimed to establish a model for investigating X chromosome inactivation using transgenic mouse strains expressing green fluorescent protein (GFP). The D4/XGFP-Tg (XGFP) strain carries the GFP transgene on the X chromosome; therefore, due to random X chromosome inactivation, female offspring from crosses between XGFP males and CD-1 females exhibit mosaic GFP expression. In contrast, the B5/EGFP-Tg (EGFP) strain harbours autosomal integration of the same reporter construct, resulting in uniform GFP expression in progenies. Analysis of CD-1 × XGFP attached blastocysts revealed strong GFP expression in giant trophoblast cells and primordial germ cells (PGCs) at E6.5, demonstrating paternal X-chromosome reactivation. In 14.5-day-old CD-1 × XGFP female embryos and CD-1 × EGFP embryos, intense CAG promoter-driven GFP signals were detected in the brain, heart, gonads, somites, and limbs. In line with random X-chromosome inactivation, only 56% of embryonic fibroblast cells, derived from CD-1 × XGFP female embryos, exhibited GFP expression. These findings validate that CD-1 × XGFP mice represent a valuable in vivo model for studying X chromosome inactivation during early embryonic development and PGC specification. Furthermore, CD-1 × XGFP embryonic fibroblasts represent a valuable in vitro model for investigating the molecular mechanisms governing X-chromosome activation and inactivation. Full article

Background/Objectives: Factors modulating phenotypic variability in Rett syndrome (RTT, OMIM 312750) include X chromosome inactivation (XCI), type of MECP2 variant, and/or disease modifiers. Emerging evidence also points to multi-locus genetic variants. Understanding the phenotypic variability associated with multi-locus genetic diagnoses in individuals with RTT and MECP2-related disorders would be important not only for accurate diagnosis, risk stratification and clinical management but also to explain symptoms that might not be typically associated with RTT. Methods: We present a case series of five individuals with a diagnosis of RTT or an MECP2-related disorder with co-occurring genetic findings, including pathogenic variants, variants of unknown significance and chromosome duplications. Clinical features such as neurodevelopmental history and comorbid medical conditions were assessed alongside the genetic findings. Results: A review of 200 cases with RTT identified five cases (all females aged 7–27 years) with a co-occurring genetic finding. Each case harboured at least one additional genetic variant that included a beta thalassaemia trait, Calmodulin 3 (CALM3) missense variant, maternally inherited 22q12.3 to q13.1 duplication, 7p14.3 and Dynein Cytoplasmic 1 Heavy Chain 1 (DYNC1H1) variants of uncertain significance and a pathogenic Set Domain-containing protein 5 (SETD5) variant. A rare triple genetic finding was illustrated in a single case, combining MECP2, CALM3, and DYNC1H1 variants. Conclusions: This case series supports the premise that RTT and MECP2-related disorders exist in a more complex neurogenetic spectrum than previously defined. It also emphasises the complexity within MECP2-related disorders. They are not static, and in the context of severe treatment resistant epilepsy, MECP2 disorders can evolve over time, necessitating diagnostic reclassification. Although the co-occurrence of multiple genetic disorders in RTT and MECP2-related disorders is rare, these cases underscore the importance of considering cumulative genetic burden when evaluating individuals with atypical features or evolving neurodevelopmental phenotypes. Full article

Background: ALG13-CDG is an X-linked N-linked glycosylation disorder caused by pathogenic variants in the glycosyltransferase ALG13, leading to severe neurological manifestations. Despite the clear CNS involvement, the impact of ALG13 dysfunction on human brain glycosylation and neurodevelopment remains unknown. We hypothesize that ALG13-CDG causes brain-specific hypoglycosylation that disrupts neurodevelopmental pathways and contributes directly to cortical network dysfunction. Methods: We generated iPSC-derived human cortical organoids (hCOs) from individuals with ALG13-CDG to define the impact of hypoglycosylation on cortical development and function. Electrophysiological activity was assessed using MEA recordings and integrated with multiomic profiling, including scRNA-seq, proteomics, glycoproteomics, N-glycan imaging, lipidomics, and metabolomics. X-inactivation status was evaluated in both iPSCs and hCOs. Results: ALG13-CDG hCOs showed reduced glycosylation of proteins involved in ECM organization, neuronal migration, lipid metabolism, calcium homeostasis, and neuronal excitability. These pathway disruptions were supported by proteomic and scRNA-seq data and included altered intercellular communication. Trajectory analyses revealed mistimed neuronal maturation with early inhibitory and delayed excitatory development, indicating an E/I imbalance. MEA recordings demonstrated early network hypoactivity with reduced firing rates, immature burst structure, and shortened axonal projections, while transcriptomic and proteomic signatures suggested emerging hyperexcitability. Altered lipid and GlcNAc metabolism, along with skewed X-inactivation, were also observed. Conclusions: Our study reveals that ALG13-CDG is a disorder of brain-specific hypoglycosylation that disrupts key neurodevelopmental pathways and destabilizes cortical network function. Through integrated multiomic and functional analyses, we identify early network hypoactivity, mistimed neuronal maturation, and evolving E/I imbalance that progresses to compensatory hyperexcitability, providing a mechanistic basis for seizure vulnerability. These findings redefine ALG13-CDG as disorders of cortical network instability, offering a new framework for targeted therapeutic intervention. Full article

Background: The immunoglobulin superfamily member 1 (IGSF1) gene encodes for a transmembrane glycoprotein involved in crucial processes such as growth, metabolism, and reproductive function. Loss-of-Function (LOF) mutations in the IGSF1 gene have been reported to cause the X-linked IGSF1 deficiency syndrome, a rare genetic condition that primarily affects males, characterized by hypothyroidism, macroorchidism, delayed puberty, obesity, and infertility. Case Report: In this study, we identified a novel hemizygous nonsense IGSF1 variant c.1989G>A (p.Trp663Ter) in a male patient who initially presented with growth impairment and growth hormone deficiency (GHD), with a positive family history on the maternal lineage. Notably, the proband does not present with macroorchidism, a feature typically associated with IGSF1 deficiency. The variant was also found in his heterozygous sister, who presented with isolated growth hormone deficiency, and in his mother, who displayed hypertension and thyroid dysfunction but no significant growth impairment. Discussion: This phenotypic variability suggests a differential expression of IGSF1-related symptoms depending on zygosity and sex within the same family, probably explained by X-chromosome inactivation (XCI) in females, which can lead to varying degrees of functional IGSF1 expression in different tissues. Conclusions: This case highlights the intrafamilial phenotypic variability associated with IGSF1 mutations, illustrating differences between male and female carriers and highlighting the importance of genetic testing in patients with similar clinical presentations. Full article

Hemophilia A (HA) is an X-linked recessive bleeding disorder that predominantly affects males but rarely manifests clinically in females. We report an unusual case of a woman with HA carrying a de novo heterozygous F8 variant, skewed X chromosome inactivation (XCI), and mosaic monosomy X without the Turner syndrome phenotype. DNA was extracted from whole blood. After excluding F8 inversions and large rearrangements, Sanger sequencing of coding regions was performed. XCI was assessed by STR analysis of the AR gene. Haplotypes were identified by fragment analysis of three polymorphic sites. Karyotyping was performed using G-banding. A heterozygous missense variant in the F8 gene, c.6545G>A (p.Arg2182His), was detected with allelic imbalance. STR analysis confirmed ~93% skewed XCI. Karyotyping revealed mosaicism: 45,X [7]/46,XX [14]. Neither parent carried the c.6545G>A variant or karyotype aberrations. We suggest that 46,XX cells carried c.6545G/A with preferential inactivation of the normal X chromosome, whereas 45,X0 cells carried the mutant allele only. The limited proportion of active normal X chromosomes led to a mild rather than severe phenotype. This case highlights complex genetic mechanisms underlying HA in females and underscores the importance of comprehensive molecular and cytogenetic testing for accurate diagnosis, clinical management, and genetic counseling. Full article

Background/Objectives: In digenic populations, all females produce males and females in their offspring. Monogenic populations are composed of gynogenic (female-producing) and androgenic (male-producing) females. A theoretical population genetic model for evolution of digenic to monogenic populations is presented here. Methods: A controlling gene was associated with each of the four processes that characterise monogenic populations: (1) oogenesis is conventional, whereas spermatogenesis is unusual and it is characterised by the exclusive formation of X-bearing sperm (gene (s)), i.e., the paternal chromosomes are eliminated so that only the maternal ones are transmitted to the next generation; (2) the X chromosome that is eliminated in the zygote is the one inherited from the father (gene r); (3) an imprinting process occurs in the mother (gene g), which protects the maternally inherited X chromosome from elimination in the zygote and the whole maternal chromosome complement in spermatogenesis; (4) a maternal factor is produced during oogenesis (gene e), which inactivates the elimination factor [r] in the zygote, thus controlling the elimination of the paternal X chromosome. The sequences of emergence of the genes (e s r g) that transform a digenic population into a monogenic one were analysed. Results: The following evolutionary sequences were found: (1) the sequence (r s e) under dominant conditions of gene (s) and recessive conditions of gene (r); and (2) the sequences (s r e), (r s e), and (e s r) under recessive conditions of gene (s) and gene (r). It was also found that the process of genomic imprinting is a necessary condition for the generation of a monogenic population. Furthermore, a quantitative change in the interaction between the elimination factor and its maternal inhibitor modifies the genotypic formula of the monogenic state. Conclusions: The number and types of evolutionary transitions of a digenic to a monogenic population depends on the dominant or recessive characteristic of the newly emerging genes. The imprinting process must already be present in the digenic population from which the monogenic one evolves; otherwise, the population cannot reach the monogenic state. Full article

Fragile X syndrome (FXS, OMIM#300624) is the most common inherited cause of X-linked intellectual disability and behavior difficulties. In 99% of cases, it is caused by the pathological expansion (>200 repeats, full mutation -FM) of the CGG trinucleotide located at the 5′ UTR of the FMR1 (Fragile X Messenger Ribonucleoprotein 1) gene, leading to the lack of production of the FMRP. Clinical manifestations are well known in boys but are sometimes overlooked in girls, who may remain underdiagnosed. Premutation (PM) populations (55–200 repeats) may present other medical issues, such as FXPOI or FXTAS. Mosaic conditions, such as a combination of PM and FM lines in the same patient, may lead to milder phenotypes. With the improvement of genetic testing, information regarding the exact number of CGG triplet repeats and methylation status could help explain milder phenotypes in patients who may produce some FMRP. Chromosome X preferential inactivation (XCI) in FXS women can also play a role in clinical severity. We present four non-related families who were followed up in our FXS clinic. Some of their members showed FM on Southern blot, but had milder symptoms than expected. To rule out size mosaicism, a RT-PCR was performed, giving a different and more consistent molecular diagnosis. When mosaicism was not present, methylation status was performed, excluding full methylation. For females, XCI showed preferential inactivation in one case. Revisiting old molecular diagnoses should be considered in clinical practice, especially for patients with a milder phenotype than expected from their molecular reports. This personalized follow up may change their former diagnosis, prognosis, and expectations. Full article

Background/Objectives: Fabry disease is an X-linked lysosomal storage disorder. It is characterised by impaired metabolism of glycosphingolipids whose accumulation causes irreversible organ damage and life-threatening complications. Genotype–phenotype correlations have a limited scope in Fabry disease as the disorder presents with wide-ranging clinical variability. In other X-linked disorders, epigenetic profiling has identified methylation patterns and disease modifiers that may explain clinical heterogeneity. In this narrative review and thematic analysis, the role of DNA methylation and epigenetics on the clinical phenotype in Fabry disease was investigated. Methods: Embase, PubMed, and PsycINFO were searched to identify literature on DNA methylation and epigenetics in Fabry disease. Based on the eligibility criteria, 20 articles were identified, and a thematic analysis was performed on the extracted data to identify themes. Results: Three themes emerged: (I) genetic modifiers, (II) methylation profiling, and (III) insights into X chromosome inactivation (XCI). The evidence synthesis revealed that telomere length, especially in early disease stages, bidirectional promoter (BDP) methylation by sphingolipids, epigenetic reader proteins, mitochondrial DNA haplogroups, and DNA methylation of the promoter region of the calcitonin receptor gene are potential genetic modifiers in Fabry disease. Methylation patterns also reveal episignatures in Fabry disease evolution and genes implicated in the maintenance of basement membranes. Studies on XCI further emphasise disease heterogeneity and draw attention to methodological issues in the assessment of XCI. Conclusions: This thematic review shows that DNA methylation and genetic modifiers are key factors modifying clinical variability in Fabry disease. More broadly, it underscores a crucial role for epigenetic processes in driving disease onset, progression, and severity in X-linked disorders. Full article

Germline mutations in the X-linked cohesin subunit gene SMC1A have been increasingly recognized as a cause of developmental and epileptic encephalopathy (DEE); however, the underlying basis of its marked phenotypic heterogeneity remains elusive. In our narrative review, starting from all literature-reported clinical cases of SMC1A-related DEE, we propose an integrative framework summarizing all the clinical and genetic features, stratified by mutation type, mosaic fraction, and X-chromosome inactivation (XCI) patterns to provide valuable support for genetic diagnosis and variants, found to date. Also, we discuss how somatic mosaicism and epigenetic variability underlie the clinical diversity of SMC1A-associated epilepsy and systematically describe the entire phenotypic spectrum, from early-onset, therapy-resistant seizures to milder intellectual disability profiles. We further examine how SMC1A mutations perturb cohesin’s canonical roles in chromatin loop formation and sister-chromatid cohesion, leading to widespread transcriptional dysregulation of neurodevelopmental gene networks. Evidence that XCI skewing can ameliorate or exacerbate neuronal cohesin deficits and, thus modulate seizure threshold, is presented. Full article

X chromosome inactivation (XCI) is a fundamental epigenetic process that balances X-linked gene expression between females and males by silencing one X chromosome in female cells. Variability or skewing of XCI can influence the clinical presentation of X-linked disorders. Bain type X-linked intellectual disability syndrome (MRXSB), caused by mutations in the X-linked HNRNPH2 gene, is characterized by intellectual disability, developmental delay, and neurological abnormalities. In female patients, XCI heterogeneity complicates disease modeling and therapeutic development. Induced pluripotent stem cells (iPSCs) offer a unique platform to study patient-specific disease mechanisms, but the dynamics of XCI during iPSC reprogramming, maintenance, and differentiation are not fully understood. In this study, we generated 12 iPSC clones from fibroblasts of a female MRXSB patient heterozygous for the HNRNPH2 c.340C > T mutation. Four clones expressed the mutant HNRNPH2 allele and eight expressed the wild-type allele, indicating X chromosome reactivation (XCR) followed by random XCI during reprogramming. Importantly, these XCI patterns remained stable during long-term iPSC propagation and subsequent differentiation into the three germ layers and neural stem cells. Our findings provide new insights into XCI and XCR dynamics in the context of X-linked neurodevelopmental disorders and emphasize the importance of careful clone selection for accurate disease modeling using iPSC-based approaches. Full article

Background/Objectives: The X-inactivation specific transcript (XIST) is a long noncoding RNA playing a crucial regulatory role in X chromosome inactivation (XCI)—a transcriptional regulatory process that silences one of the two X chromosomes in females to ensure proper dosage compensation between male and female mammals. The transcription of XIST is maintained throughout a female’s lifespan in all somatic cells, where XIST RNA binds to the X chromosome in cis and ensures chromosome-wide gene silencing. Disrupting XIST expression can lead to transcriptional reactivation of X-linked genes and epigenetic changes affecting cell development. The prevalence of XIST regulatory effects on mammalian transcription, however, remains unclarified. Methods: Here we performed a comparative expression analysis using RNA-sequencing datasets from recently published studies and examined the consequences of XIST-deletion on transcription at the whole genome, individual chromosome, and specific gene levels. We investigated the common differentially expressed genes (DEGs) and biological pathways following XIST loss across cell types, together with differential transcriptional analysis comparing the X chromosome and autosomes using cumulative distribution fractions. We analyzed the distribution of DEGs along the X chromosome with scatterplots and correlation analysis incorporating gene density and transposable elements. Results: Our findings indicate that the loss of XIST causes transcriptional changes in the X chromosome and autosomes that differ depending on cell type and state. XIST-deletion results in differential expression of genes subject to XCI-silencing as well as genes escaping XCI. In all the cell types we analyzed, X-linked genes show differential expression across the entire X chromosome in a cluster-like pattern according to gene density and, in certain cell types, correlate strongly with short interspersed nuclear element (SINE) distributions. Conclusions: Our results demonstrate that transcriptional roles of XIST can be highly associated with cell state: stem cells have different transcriptional responses compared to differentiated cells following XIST loss. Full article

Rett syndrome is a severe neurodevelopmental disorder that occurs primarily in females and is caused by mutations in the methyl-CpG-binding protein 2 (MECP2) gene located on the X chromosome. Though MECP2 acts as a representative transcriptional regulator and affects gene expression both directly and indirectly, a complete understanding of this disease and the treatment mechanism has not been established yet. MECP2 plays a particularly important role in synaptic development, neuronal maturation, and epigenetic regulation in the brain. In this study, we summarize the molecular structure of MECP2, mutation-specific pathogenesis, and the role of MECP2 in regulating chromatin remodeling, RNA splicing, and miRNA processing to provide a comprehensive understanding of Rett syndrome. Additionally, we describe abnormal phenotypes manifested in various brain regions and other tissues owing to MECP2 dysfunction. Finally, we discuss current and future therapeutic approaches, including AAV-based gene therapy, RNA editing, X chromosome reactivation, and pharmacological interventions. Understanding the diverse functions and pathological mechanisms of MECP2 provides an important foundation for developing targeted therapies for Rett syndrome. Full article

Congenital cataracts (CCs) are a leading cause of preventable childhood blindness, with genetic factors playing a crucial role in their etiology. Nance–Horan syndrome (NHS) is a rare X-linked dominant disorder associated with CCs but is often underdiagnosed due to variable expressivity, particularly in female carriers. Objective: This study aimed to explore the genetic landscape of CCs in a Swiss cohort, focusing on two novel NHS and one novel GJA8 variants and their phenotypic presentation. Methods: Whole-exome sequencing (WES) was conducted on 20 unrelated Swiss families diagnosed with CCs. Variants were analyzed for pathogenicity using genetic databases, and segregation analysis was performed. Clinical data, including cataract phenotype and associated systemic anomalies, were assessed to establish genotype–phenotype correlations. Results: Potentially pathogenic DNA sequence variants were identified in 10 families, including three novel variants, one in GJA8 (c.584T>C) and two NHS variants (c.250_252insA and c.484del). Additional previously reported variants were detected in CRYBA1, CRYGC, CRYAA, MIP, EPHA2, and MAF, reflecting genetic heterogeneity in the cohort. Notably, NHS variants displayed significant phenotypic variability, suggesting dose-dependent effects and X-chromosome inactivation in female carriers. Conclusions: NHS remains underdiagnosed due to its variable expressivity and the late manifestation of systemic features, often leading to misclassification as isolated CC. This study highlights the importance of genetic testing in unexplained CC cases to improve early detection of syndromic forms. The identification of novel NHS and GJA8 variants provides new insights into the genetic complexity of CCs, emphasizing the need for further research on genotype–phenotype correlations. Full article