Search Results (38)

Neurodevelopmental disorders (NDDs) with ataxia are genetically heterogeneous and remain a diagnostic challenge. Recent advances in genomic technologies have facilitated the identification of rare, potentially causative variants in genes not traditionally associated with classic NDD phenotypes. The DNAH14 gene, encoding a dynein axonemal heavy chain involved in ciliary motility, has recently emerged as a novel candidate in neurological syndromes. Here, we report two Turkish siblings presenting with late-onset balance disorder, progressive ataxia, and cognitive impairment. Initial genetic analysis revealed that both siblings also harbor FXN GAA repeat expansions consistent with pathogenic Friedreich’s ataxia (FRDA). To elucidate the molecular basis of the patients’ cognitive impairment, whole-exome sequencing was performed. This analysis identified a novel homozygous frameshift variant in the DNAH14 gene, located within the conserved linker domain upstream of the motor core, which is critical for ATP hydrolysis and microtubule interactions. The variant is absent from population databases, predicted to be deleterious by multiple in silico algorithms, and segregates in the family in a manner consistent with autosomal recessive inheritance. The coexistence of FRDA expansions and a truncating DNAH14 variant suggests a potential dual genetic contribution to the observed phenotype, in which FRDA-associated pathology likely underlies the ataxia, while DNAH14 disruption may contribute to additional neurodevelopmental features. This is the first report describing the co-occurrence of FRDA and a homozygous truncating DNAH14 variant in the same individuals, broadening our understanding of overlapping neurogenetic mechanisms. Our findings expand the phenotypic spectrum of DNAH14-related disorders and highlight the importance of considering multilocus pathogenic variants in patients with complex or atypical ataxia presentations. Full article

Background: Ovarian cancer is characterized by high mortality rates, primarily due to diagnosis at late stages. Current biomarkers, such as CA125, have demonstrated limited efficacy for early detection. While high-dimensional proteomics offers a more comprehensive view of systemic biology, the analysis of such data, where the number of features far exceeds the number of samples, presents a significant computational challenge. Methods: This study utilized a nested case–control cohort of longitudinal pre-diagnostic serum samples from the UK Collaborative Trial of Ovarian Cancer Screening (UKCTOCS) profiled for eight candidate ovarian cancer biomarkers (CA125, HE4, PEBP4, CHI3L1, FSTL1, AGR2, SLPI, DNAH17) and 92 additional cancer-associated proteins from the Olink Oncology II panel. We employed a Synolitic Graph Neural Network framework that transforms high-dimensional multi-protein data into sample-specific, interconnected graphs using a synolitic network approach. These graphs, which encode the relational patterns between proteins, were then used to train Graph Neural Network (GNN) models for classification. Performance of the network approach was evaluated together with conventional machine learning approaches via 5-fold cross-validation on samples collected within one year of diagnosis and a separate holdout set of samples collected one to two years prior to diagnosis. Results: In samples collected within one year of ovarian cancer diagnosis, conventional machine learning models—including XGBoost, random forests, and logistic regression—achieved the highest discriminative performance, with XGBoost reaching an ROC-AUC of 92%. Graph Convolutional Networks (GCNs) achieved moderate performance in this interval (ROC-AUC ~71%), with balanced sensitivity and specificity comparable to mid-performing conventional models. In the 1–2 year early-detection window, conventional model performance declined sharply (XGBoost ROC-AUC 46%), whereas the GCN maintained robust discriminative ability (ROC-AUC ~74%) with relatively balanced sensitivity and specificity. These findings indicate that while conventional approaches excel at detecting late pre-diagnostic signals, GNNs are more stable and effective at capturing subtle early molecular changes. Conclusions: The synolitic GNN framework demonstrates robust performance in early pre-diagnostic detection of ovarian cancer, maintaining accuracy where conventional methods decline. These results highlight the potential of network-informed machine learning to identify subtle proteomic patterns and pathway-level dysregulation prior to clinical diagnosis. This proof-of-concept study supports further development of GNN approaches for early ovarian cancer detection and warrants validation in larger, independent cohorts. Full article

Background: Hypospadias development is influenced by prenatal androgen levels, with genetic factors typically playing a significant role. Through whole-exome sequencing, we found that rare damaging variants in DNAH8 (dynein axonemal heavy chain 8) were significantly enriched in hypospadias cases. However, the role of DNAH8 deficiency in hypospadias pathogenesis remains unclear. Objectives: This study aimed to clarify the function of DNAH8 in urethral development and fusion. Materials and Methods: Using CRISPR/Cas9, we generated DNAH8 knockout mice and employed a multi-disciplinary approach to evaluate urogenital development, male differentiation, testosterone levels, steroid biosynthesis gene expression, and cellular changes in fetal testes and external genitalia. Results:DNAH8 knockout mice presented abnormal masculinization phenotype, and fetal mice exhibited urethral fusion defects and hypoplastic glans during early urethral development. DNAH8 knockout was found to reduce prenatal testosterone levels and steroid biosynthesis in the testes. Based on single-cell sequencing and multicolor immunofluorescence, we demonstrated that in the early stage of fetal testis development, the loss of DNAH8 function affected the differentiation of Sertoli and steroidogenic cell lineages, thereby impairing testosterone synthesis ability during the masculinization programming window. Meanwhile, we identified two key distal glans cell populations that cause abnormal urethral fusion and hypoplastic glans. Furthermore, DNAH8 knockout could synergistically interact with low-dose endocrine-disrupting chemicals, increasing the incidence of urethral fusion defects at E16.5, and led to clear hypospadias phenotypes at E18.5. Conclusions: Loss of DNAH8 delays differentiation of Sertoli and steroidogenic lineages, reduces prenatal testosterone, and, with environmental exposure, increases hypospadias risk. Full article

Primary ciliary dyskinesia (PCD) is a rare hereditary disorder belonging to the group of ciliopathies, with autosomal recessive, autosomal dominant, and, less frequently, X-linked inheritance patterns. The aim of this study was to investigate the genetic heterogeneity of the Russian population of PCD patients based on national registry data. The study included patients with PCD confirmed by molecular genetic testing. Quantitative data were analyzed using non-parametric statistical methods. Differences were considered statistically significant at p < 0.05. The study included 109 patients with PCD. Molecular genetic testing identified pathogenic variants in 29 autosomal recessive genes. The analysis of pathogenic variant distribution in the Russian PCD cohort revealed the highest number of changes in the DNAH5 and DNAH11 genes. 26 genetic variants in 13 genes were identified for the first time in the Russian population. Variants in the DNAH5 gene were significantly more frequent in Kartagener’s syndrome (KS) patients (32/55%) compared to those without KS (11/21.5%) (χ² = 12.8; p = 0.0004; OR = 4.48). Preliminary data indicate that the frequency spectrum of DNAH5 and DNAH11 genes in Russian patients is similar to international trends. Additionally, there is an accumulation of pathogenic variants in the DNAH5, DNAH11, CCDC39, and CFAP300 genes. Full article

Background: Hypospadias is a common congenital condition in male infants, characterised by incomplete development of the underside of the penile shaft. Genetic factors play a major role in its development. Therefore, studying genetic contributions, especially in familial cases, can enhance our understanding of disease causes and guide targeted interventions. Materials and Methods: Through a structured biobank for hypospadias, we collected blood samples from individuals with familial hypospadias and their relatives. Whole-genome sequencing (WGS) was performed on 27 individuals across seven families to identify potential genetic causes. Bioinformatics analysis, including the GEMINI tool, was used to assess inheritance patterns of single-nucleotide variants (SNVs) within families and identify potential causative SNVs. Results: We identified three likely pathogenic variants in genes not previously associated with hypospadias in EIF2B5, INO80, and ACADVL genes, in three index patients. These variants co-segregated with the condition within the families. Additionally, we detected variants of uncertain significance in hypospadias-related gene families (DNAH12 and LHFP) and in other genes, such as COL6A3, which may cause the phenotype. No potential causative variants were found in two of the seven studied families, indicating the need for further analysis, including the assessment of copy number variants (CNVs). Functional studies will be crucial to establish the role of the identified variants in the development of hypospadias. Conclusions: This study underscores the importance of disease biobanking and genetic analysis in identifying potential underlying causes of congenital conditions, such as hypospadias. The identified variants provide new opportunities for functional research and may enhance our understanding of hypospadias pathophysiology. These findings broaden the genetic landscape of hypospadias and lay the groundwork for functional validation, improved risk assessment, and personalised medicine strategies. Full article

Background: Reproductive efficiency is a significant hurdle to the sustainability of the beef cattle industry. Method: This study employed transcriptomic profiling to investigate endometrial gene expression differences in heifers with divergent fertility outcomes. Caruncular endometrial samples from fertile (n = 7) and subfertile (n = 5) heifers were subjected to RNA-Seq analysis, yielding 894 differentially expressed genes (DEGs) (p ≤ 0.05 and |log2FC| ≥ 0.5). Results: The MAPK (Mitogen-activated protein kinase) and Rap1 (Ras-associated protein 1) signaling pathways and immune response regulation were identified among the over-represented pathways underlying the DEGs. Transcriptional regulators, such as DUSP2, DUSP10, and MAPK13, were downregulated in subfertile heifers, suggesting disrupted signal transduction and immune function. Gene co-expression network analysis showed network rewiring and increased connectivity of genes related to cilium organization, motility, and microtubule-based processes in the subfertile group. Over-represented hub genes were enriched in the subfertile endometrium, including DNAH2, DNAI2, DNAAF4, CCDC65, and the transcription factor FOXJ1. Our results suggest that impaired ciliary function and disrupted MAPK and immune signaling could potentially contribute to subfertility. Conclusions: This study highlights novel molecular signatures in the uterine endometrium that may serve as predictive markers of fertility potential in beef heifers, providing a foundation for targeted strategies to improve reproductive performance in cattle. Full article

Background/Objectives: Although biallelic pathogenic variants in different DNAH gene family members have been associated with infertility, the role of DNAH12 in this disorder is still incompletely understood. To date, few patients have been shown to have infertility due to biallelic variants in this gene. Here, we report two more unrelated patients with infertility who carry homozygous variants in DNAH12. Methods: This study included two male patients with primary infertility and oligoasthenoteratozoospermia (OAT). Patient 1 was a 32-year-old with 1.5 years of infertility and no chronic illnesses or prior assisted reproductive technologies (ARTs). Patient 2 was a 49-year-old with 24 years of infertility, a history of varicocelectomy, and the occasional use of PRN analgesics for bone pain. Using genome sequencing, we identified two homozygous variants: c.3757C>A, p. Pro1253Thr, and c.11086-1G>A, p.?, in patients 1 and 2, respectively. Results: Our findings add supportive evidence that DNAH12 is a gene implicated in rare cases of male infertility. The identification of these homozygous variants in two additional patients supports the association between DNAH12 variants and reproductive dysfunction. Conclusions: This study highlights the need for further research on the role of DNAH12, including functional studies to clarify the mechanisms contributing to infertility. Full article

Background: Primary ciliary dyskinesia (PCD) is a rare genetic disorder characterized by recurrent sinopulmonary infections due to motile cilia defects. The disease is genetically heterogeneous, with abnormalities in structural ciliary proteins. Zinc finger MYND-type containing 10 (ZMYND10) is essential for the assembly of outer dynein arms (ODA), with chaperones like Glucose-regulated protein 78 (GRP78) facilitating protein folding. This study investigates ZMYND10 and Dynein axonemal heavy chain 5 (DNAH5) mutations in individuals with PCD. Methods: Eight individuals aged 14–22 with clinical PCD symptoms and confirmed DNAH5 mutations were included. We analyzed the correlation between DNAH5 abnormalities and preassembly/chaperone proteins using immunofluorescence labeling. Nasal swabs were double-labeled (DNAH5–β-tubulin, β-tubulin–ZMYND10, β-tubulin–GRP78) and examined via fluorescence microscopy. Serum metabolomics and proteomics were also assessed. Results: The corrected total cell fluorescence (CTCF) levels of DNAH5, ZMYND10, and GRP78 were significantly different between PCD individuals and controls. Metabolomic analysis showed reduced valine, leucine, and isoleucine biosynthesis, with increased malate and triacylglycerol biosynthesis, malate-aspartate and glycerol phosphate shuttles, and arginine/proline metabolism, suggesting mitochondrial and ER stress. Conclusions: The altered expression of DNAH5, ZMYND10, and GRP78, along with metabolic shifts, points to a complex link between ciliary dysfunction and cellular stress in PCD. Further studies are needed to clarify the underlying mechanisms. Full article

Multiple myeloma ranks as the second most common hematopoietic malignancy in terms of both incidence and mortality. Prognostic stratification is critical for optimizing therapeutic strategies, as certain genetic alterations can significantly influence disease progression and treatment response. The meta-analysis analyzed data from 3421 multiple myeloma patients and 14,720 controls. PubMed, Web of Science, and Scopus were used as databases. Associations between the SNPs and multiple myeloma were calculated as a measure of pooled odds ratios (ORs) and 95% confidence intervals. Statistical analysis was performed using Review Manager (RevMan). DNAH11 rs4487645 A/C genotype (OR = 1.35; 95% CI: 1.24–1.46; p < 0.00001; I² = 0%), ULK4 rs1052501 G/G genotype (OR = 1.21; 95% CI: 0.98–1.50; p = 0.08; I² = 64%), ULK4 rs1052501 A/G genotype (OR = 1.23; 95% CI: 1.13–1.34; p < 0.00001; I² = 0%), DTNB rs6746082 A/A genotype (OR = 1.10; 95% CI: 1.01–1.20; p = 0.03; I² = 45%), and VDR rs1544410 A/G genotype (OR = 1.87; 95% CI: 1.04–3.36; p = 0.04; I² = 0%) increased multiple myeloma risk. Our study concludes that DNAH11, ULK4, DTNB, and VDR may serve as predictive biomarkers for MM risk. Full article

Background/Objectives: Primary ciliary dyskinesia (PCD) (OMIM: 244400) is a hereditary, rare disorder with a high prevalence in Turkey due to a high rate of consanguinity. The disorder is caused by malfunctioning motile cilia and is characterized by a variety of clinical symptoms including sinusitis, otitis media and chronic obstructive pulmonary disease. This study presents the first assessment of the efficacy of immunofluorescence (IF) labeling for diagnosing PCD in Turkey by correlating IF with clinical observations when genetic data are scarce. Methods: We have a cohort of 54 PCD-suspected individuals with an age range of 5–27 years classified into two groups: group A with available genomic data (8 individuals) and group B with no available genomic data (46 individuals). We performed immunofluorescence analysis to confirm the pathogenicity of the variants in individuals with a prior genetic diagnosis and to confirm a PCD diagnosis in individuals with typical PCD symptoms and no genetic diagnosis. Results: All individuals had airway infections and displayed clinical symptoms of PCD. Our data revealed an absence of outer dynein arm dynein heavy chain DNAH5 in individuals with pathogenic variants in DNAH5 and DNAAF1 and in 17 other PCD-suspected individuals, an absence of nexin–dynein regulatory complex component GAS8 in 8 PCD-suspected individuals, an absence of outer dynein arm dynein heavy chain DNAH11 in 6 PCD-suspected individuals and an absence of radial spoke head component RSPH9 in 2 PCD-suspected individuals. Furthermore, the pathogenicity of ARMC4 variants was confirmed by the absence of the outer dynein arm docking complex component ARMC4 and the proximal localization of DNAH5. Conclusions: Immunofluorescence analysis, owing to its lower cost and quicker turnaround time, proves to be a powerful tool for diagnosing PCD even in the absence of genetic data or electron microscopy results. Full article

Background: Individuals with Down syndrome exhibit a higher prevalence of periodontal disease, which can lead to implant loss. This study aims to identify genetic markers associated with implant loss in these patients, providing insight into potential predictive and therapeutic approaches. Methods: A systematic analysis was conducted, including both clinical and genetic data from Down syndrome patients with a history of dental implants. Genetic profiling was performed using Transcriptome Analysis Console (TAC version 4.0 Applied Biosystems^TM, Thermo Fisher Scientific, Waltham, MA, USA), focusing on genes previously implicated in periodontal disease and bone metabolism. Statistical analysis identified correlations between genetic variants and implant survival rates. Results: The analysis revealed statistically significant alterations in several genes related to inflammation and bone remodeling. Key findings included alterations in the expression of the genes MMP15, MMP17, S100B, GHR, DNAH6, and ZCCHC14 in patients with implant failure. These genetic markers were strongly correlated with compromised osseointegration and implant loss. These findings underline the role of genetic predisposition in the failure of dental implants among individuals with Down syndrome. Conclusions: Genetic markers, particularly those involved in inflammation and bone metabolism, play a critical role in implant loss among Down syndrome patients with periodontal disease. Recognizing these markers can aid in early diagnosis and personalized treatment strategies, potentially improving implant success rates. Full article

Dnah5 is associated with primary ciliary dyskinesia in humans. Dnah5-knockout (Dnah5−/− mice develop acute hydrocephalus shortly after birth owing to impaired ciliary motility and cerebrospinal fluid (CSF) stagnation. In contrast to chronic adult-onset hydrocephalus observed in other models, this rapid ventricular enlargement indicates additional factors beyond CSF stagnation. Herein, we investigated the contributors to rapid ventricular enlargement in congenital hydrocephalus. Dnah5−/− mice were generated using CRISPR/Cas9. The expression of dynein, N-cadherin, and nestin in the cerebral cortex was assessed using microarrays and immunostaining. Real-time PCR and Western blotting were performed for gene and protein quantification, respectively. All Dnah5−/− mice developed hydrocephalus, confirmed by electron microscopy, indicating the absence of axonemal outer dynein arms. Ventricular enlargement occurred rapidly, with a 25% reduction in the number of mature neurons in the motor cortex. Dync1h1 expression was decreased, while cytoplasmic dynein levels were 56.3% lower. Levels of nestin and N-cadherin in the lateral ventricular walls decreased by 31.7% and 33.3%, respectively. Reduced cytoplasmic dynein disrupts neurogenesis and axonal growth and reduces neuron cortical density. Hydrocephalus in Dnah5−/− mice may result from cortical maldevelopment due to cytoplasmic dynein deficiency, further exacerbating ventricular enlargement due to CSF stagnation caused by impaired motile ciliary function. Full article

Disease-causing bi-allelic DNA variants in CCDC39 and CCDC40 are frequent causes of the hereditary disorder of primary ciliary dyskinesia (PCD). The encoded proteins form a molecular ruler complex, crucial for maintaining the 96 nm repeat units along the ciliary axonemes. Defects of those proteins cause a stiff, rapid, and flickery ciliary beating pattern, recurrent respiratory infections, axonemal disorganization, and abnormal assembly of GAS8, CCDC39, and DNALI1. We performed molecular characterization of the defects in the 96 nm axonemal ruler due to disease-causing variants in CCDC39 and CCDC40 and analyzed the effect on additional axonemal components. We identified a cohort of 51 individuals with disease-causing variants in CCDC39 and CCDC40 via next-generation sequencing techniques and demonstrated that the IDA heavy chains DNAH1, DNAH6, and DNAH7 are conspicuously absent within the respiratory ciliary axonemes by immunofluorescence analyses. Hence, we show for the first time that the centrin2 (CETN2) containing IDAs are also affected. These findings underscore the crucial role of CCDC39 and CCDC40 in the assembly and function of IDAs in human respiratory cilia. Thus, our data improve the diagnostics of axonemal ruler defects by further characterizing the associated molecular IDA defects. Full article

Premalignant lesions within the bronchial epithelium signify the initial phases of squamous cell lung carcinoma, posing challenges for detection via conventional methods. Instead of focusing solely on gene expression, in this study, we explore transcriptomic alterations linked to lesion progression, with an emphasis on protein-coding transcripts. We reanalyzed a publicly available RNA-Seq dataset on airway epithelial cells from 82 smokers with and without premalignant lesions. Transcript and gene abundance were quantified using kallisto, while differential expression and transcript usage analysis was performed utilizing sleuth and RATs packages. Functional characterization involved overrepresentation analysis via clusterProfiler, weighted coexpression network analysis (WGCNA), and network analysis via Enrichr-KG. We detected 5906 differentially expressed transcripts and 4626 genes, exhibiting significant enrichment within pathways associated with oxidative phosphorylation and mitochondrial function. Remarkably, transcript-level WGCNA revealed a single module correlated with dysplasia status, notably enriched in cilium-related biological processes. Notable hub transcripts included RABL2B (ENST00000395590), DNAH1 (ENST00000420323), EFHC1 (ENST00000635996), and VWA3A (ENST00000563389) along with transcription factors such as FOXJ1 and ZNF474 as potential regulators. Our findings underscore the value of transcript-level analysis in uncovering novel insights into premalignant bronchial lesion biology, including identification of potential biomarkers associated with early lung carcinogenesis. Full article

Porcine hemagglutinating encephalomyelitis virus (PHEV) replicates in the upper respiratory tract and tonsils of pigs. Using an air–liquid interface porcine respiratory epithelial cells (ALI-PRECs) culture system, we demonstrated that PHEV disrupts respiratory epithelia homeostasis by impairing ciliary function and inducing antiviral, pro-inflammatory cytokine, and chemokine responses. This study explores the mechanisms driving early innate immune responses during PHEV infection through host transcriptome analysis. Total RNA was collected from ALI-PRECs at 24, 36, and 48 h post inoculation (hpi). RNA-seq analysis was performed using an Illumina Hiseq 600 to generate 100 bp paired-end reads. Differential gene expression was analyzed using DeSeq2. PHEV replicated actively in ALI-PRECs, causing cytopathic changes and progressive mucociliary disruption. Transcriptome analysis revealed downregulation of cilia-associated genes such as CILK1, DNAH11, LRRC-23, -49, and -51, and acidic sialomucin CD164L2. PHEV also activated antiviral signaling pathways, significantly increasing the expression of interferon-stimulated genes (RSAD2, MX1, IFIT, and ISG15) and chemokine genes (CCL5 and CXCL10), highlighting inflammatory regulation. This study contributes to elucidating the molecular mechanisms of the innate immune response to PHEV infection of the airway epithelium, emphasizing the critical roles of the mucociliary, interferon, and chemokine responses. Full article