Search Results (468)

Objective: Asthma is a complex and heterogeneous syndrome, making it hard to predict disease progression and suitable treatments. One strategy for reducing this uncertainty is to define genetic subtypes, or endophenotypes, that capture shared biological mechanisms. Most genome-wide studies, however, compare one subgroup against all others within a single cohort and rarely replicate their findings. We aimed to determine whether simultaneously modeling all asthma endophenotypes improves the discovery and replication of genetic associations compared with the standard one-versus-rest approach. Methods: We analyzed common single-nucleotide polymorphisms (SNPs) in the Childhood Asthma Management Program (CAMP) using an analysis of covariance (ANCOVA) across all severity-related endophenotypes, adjusting for age, sex, and ancestry principal components. SNPs showing genome-wide significance were tested for replication in the Genetics of Asthma in Costa Rican Children Study (GACRS). For comparison, we performed traditional one-versus-rest logistic regression analyses within each cohort, using identical covariates and endophenotype labels. Results: The ANCOVA identified 244 genome-wide significant SNPs in CAMP, of which six unique loci replicated in GACRS. In contrast, logistic regression recovered only four significant contrasts from those six loci in CAMP and replicated just one in GACRS. Conclusions: Our findings highlight genetic variants that are associated with asthma severity endophenotypes and demonstrate that modeling all clinical subtypes simultaneously can reveal biologically meaningful signals that are missed by standard pairwise design. Full article

Metabolic syndrome (MetS) represents a global health challenge mainly driven by chronic low-grade inflammation and persistent oxidative stress (OS). Current therapeutic and nutritional strategies often fail to resolve these interconnected core pathologies due to the multifactorial nature of MetS. Anthocyanins (ACNs), a class of potent dietary flavonoids, offer significant promise due to their established pleiotropic effects, including robust antioxidant activity through modulation of the Nrf2/ARE pathway, anti-inflammatory effects via NF-κB suppression, and overall support for glucose and lipid homeostasis. However, the therapeutic efficacy of ACNs is characterized by interindividual variability, which is intrinsically linked to their low systemic bioavailability. This heterogeneity in the response is due to the complex interplay between genetic polymorphisms affecting absorption, distribution, metabolism, and excretion (ADME), as well as the specific biotransformation capacity of the gut microbiome. This review proposes that achieving the full clinical potential of ACNs requires moving beyond conventional nutritional advice. We propose that precision nutrition, which integrates multi-omics data (e.g., genomics, metagenomics, and metabolomics), can determine the individual phenotype, predict functional metabolic response, and tailor safer and effective ACN-rich interventions. This integrated, multifactorial approach is essential for optimizing the antioxidant and metabolic benefits of ACNs for the prevention and management of MetS and its associated pathologies. Full article

Background/Objectives: Systemic lupus erythematosus (SLE) is a complex autoimmune disease with a multifactorial origin involving genetic, epigenetic, and environmental determinants as well as some risk factors. Genetic predisposition has been quantified through polygenic risk scores (PRS), which integrate the cumulative effect of multiple single nucleotide variants (SNVs) associated with disease risk. Despite extensive research on immune and inflammatory pathways in SLE, the interplay between genetic susceptibility and metabolic dysfunction remains poorly understood. This study aimed to explore associations between SLE-related PRS and metabolic, inflammatory, and clinical parameters in adults participating in the METAINFLAMACIÓN-CM project (Hospital Universitario Puerta de Hierro Majadahonda, Madrid, Spain). Methods: Ninety-three participants were included: 56 SLE patients and 37 individuals with metabolic syndrome (MetS) as a reference group. PRS were computed based on validated lupus-associated SNVs. Results: SLE patients showed a distinct metabolic profile compared with the MetS group, characterized by lower BMI, visceral fat, blood pressure, glucose, and liver enzyme levels. Within the SLE cohort, PRS values varied markedly and correlated with specific clinical and biochemical features. Linear regression models revealed a significant inverse association between PRS in SLE and ferritin levels, whereas other metabolic and inflammatory markers (glucose, IL-6, LDL, CRP, neutrophils) were directly influenced by clinical factors. Conclusions: Polygenic predisposition contributes to variability in SLE metabolic phenotype but does not independently drive most inflammatory parameters. SLE patients displayed metabolic and inflammatory alterations relevant to cardiovascular risk, highlighting the importance of comprehensive cardiometabolic assessment. Integrating PRS with metabolic profiling may support precision personalized management and improve cardiovascular risk evaluation in SLE. Full article

Background/Objectives: Prenatal Exome Sequencing (pES) has revolutionized prenatal diagnosis in fetuses with congenital anomalies. Although its performance is very promising, previous pES studies have mainly focused on diagnostic yield, often without considering the actual impact on ongoing pregnancies. In this study, we aim to (1) assess whether a prenatal molecular diagnosis can reliably predict the clinical features of the unborn child and (2) determine the gestational age (gw) at which ultrasound (US) findings are sufficient to support the pathogenicity of genetic variants detected by pES. Methods: We retrospectively selected 47 cases complicated by US anomalies that underwent Exome Sequencing (ES) and for which complete clinical assessment was available. A blinded reanalysis of ES data was performed, considering only prenatal features. Results: In our cohort, standard ES led to a molecular diagnosis in 43% of cases. The blinded reanalysis revealed that a complete or partial retrospective prenatal diagnosis was achievable in 95% of diagnosed cases. The mean gestational week at which US data would have supported molecular diagnosis was 22 + 5 weeks. The clinical follow-up confirmed a syndromic presentation in 21 out of 23 newborns and in all terminated pregnancies. Conclusions: Our study further confirms that pES is a valuable diagnostic tool for detecting genetic etiology in fetuses with congenital malformations. In most cases, pES results accurately predict the postnatal phenotype. However, the prenatal setting requires specific adjustments and precautions, and a negative pES result cannot be considered reassuring. Full article

Background: Wolfram syndrome (WS) is an ultrarare neuroendocrine disorder caused by pathogenic variants in WFS1, frequently leading to progressive neurological, autonomic, and cognitive impairment. Anticipating neurological trajectories remains challenging due to marked phenotypic variability and limited genotype–phenotype data. Methods: Forty-five genetically confirmed patients with WS were evaluated between 1998 and 2024 in Spain. All WFS1 variants were systematically classified by exon, zygosity, protein-level functional impact, and predicted wolframin production (Classes 0–3). Machine learning models (Random Forests with engineered gene–gene interaction terms) were applied to predict neurological manifestations and identify the strongest genetic determinants of symptom severity. Results: Neurological involvement was present in 93% of patients. The most prevalent manifestations were absence of gag reflex (67%), gait instability (64%), dysphagia (60%), and sialorrhea (60%), followed by dysmetria (56%), impaired tandem gait (53%), anosmia (44%), dysarthria (44%), and adiadochokinesia (42%). Most symptoms emerged in early adulthood (23–26 years), whereas cognitive decline occurred later (29.9 ± 12.2 years). Homozygosity for truncating variants—particularly c.409_424dup16 (Val142fsX110)—and complete loss of wolframin production (Class 0; 67–83% across symptoms) were the strongest predictors of early and severe neurological involvement. Machine learning models achieved high discrimination for ataxia, gait instability, and absent gag reflex (AUC 0.63–0.86; calibrated AUC up to 0.97), identifying Mut1_Protein_Class and Mut2_Protein_Class as dominant predictors across all phenotypes, followed by coherent secondary effects from zygosity × exon interaction terms (Prod_mgm). Conclusions: Integrating detailed genetic classification with machine learning methods enables accurate prediction of neurological outcomes in WS. Protein-level dysfunction and allele interaction structure are the principal drivers of neurological vulnerability. This framework enhances precision diagnosis and offers a foundation for individualized surveillance, clinical risk stratification, and future therapeutic trial design in WFS1-related disorders. Full article

Background/Objectives: Children with hearing loss (HL) could experience significant fatigue which compromises their performance. The effort related to the combination of HL and visual impairment in children affected by Usher syndrome (USH) could compromise mental health, socio-emotional behavior and academic achievement. The aim of the present study was to analyse the listening effort in USH cases types 1 and 2 and its relation to age, molecular diagnosis, visual field, visual acuity, degree of HL, vestibular impairment and spatial orientation. Methods: This was a retrospective monocentric study. Twenty children with genetically confirmed USH (USH2 in 15/20–75% and USH1 in 5/20–25%), age range 3–17 years (mean 9.6 ± 4.7), underwent: the Vanderbilt fatigue scale questionnaire (VFS), audiological and vestibular assessment including the Oldenburg Matrix test in Italian and video head impulse test (VHIT), sound localization test and ophthalmologic examination. Results: We observed a more pronounced HL and deteriorated vestibular function in those with USH1. They also employed significantly more time and head movements to localize sounds compared to USH2 and had the worst visual field on eye examination. The VFS did not show significant differences between the two groups, with the exception of the physical fatigue reported by parents. Mean VFS was linearly related to age, the hearing threshold of the worse ear, data logging hours of hearing device, time and head movements of the localization test, VHIT asymmetry and balance problems referred by parents and the visual field. USH type 1 had no greater risk of fatigue than USH2. Profound hearing loss, data logging of hearing device < 8 h a day, difficult localization test, balance problems and low retinal sensitivity represented risk factors for listening effort measured with VFS. Conclusions: Listening effort in difficult environments such as school rooms in USH patients is not only associated to hearing function but also to the spatial awareness determined in part by vestibular and visual function. Teachers should be informed and made aware of multiple comorbidities in order to facilitate learning. Full article

Background/Objectives: Genetic abnormalities are critical for the diagnosis, prognosis, and therapeutic management of myelodysplastic syndromes (MDS). This study aims to evaluate the clinical utility of Multiplex Ligation-dependent Probe Amplification (MLPA) as a rapid and cost-effective method, determining its place alongside Next-Generation Sequencing (NGS) for the initial genetic assessment of patients with MDS. Methods: Bone marrow samples from 68 patients newly diagnosed with MDS were analyzed. Genomic DNA was investigated using the SALSA MLPA P414-C1 MDS probe mix to detect common copy number variations (CNVs). Results: MLPA detected genetic variants in 25 patients (36.8%). The most common finding was a single chromosomal abnormality (26.5%). Multiple pathological findings were observed in only 1.5% of patients, and a JAK2 mutation was observed in 8.8% of the cohort. However, the presence of these aberrations did not show a statistically significant association with overall survival (OS) in the cohort. Patient sex was identified as the only variable that was associated with a marginal level of statistical significance regarding OS, indicating a worse prognosis for males. Conclusions: MLPA is a valuable, rapid, and cost-effective tool for initial genetic screening in low-resource settings. This was highlighted by our finding that sex was the sole significant prognostic factor, while the MLPA-detected variants were not found to be significant. The findings suggest that comprehensive risk stratification aligned with international standards requires more advanced molecular technologies. Full article

Human growth hormone (GH) exerts its pleiotropic effects by binding to its receptor (GHR), leading to receptor dimerization and activation. We combined structural, evolutionary, and genetic analyses to elucidate the critical determinants of GH-GHR interaction and the impact of disease-causing mutations. Protein contact analysis revealed the specific amino acid residues involved in two distinct binding interfaces between GH and two chains of GHR. ConSurf analysis demonstrated significant sequence conservation in the receptor-binding regions of GH across species, highlighting their functional importance. A comprehensive list of known disease-causing mutations in GH was compiled and mapped to these binding interfaces and conserved regions. Computational site-directed mutagenesis (SDM) analysis predicted the impact of several mutations on protein stability, revealing both stabilizing and destabilizing effects. Sequence comparisons with orthologs from various species further supported the evolutionary conservation of key functional residues. Integrated analysis of contact residues between GH and GHR showed a strong correlation between receptor-binding residues, evolutionary conservation, and the occurrence of disease-associated mutations. These findings underscore the critical role of specific GH residues in mediating high-affinity interactions with its receptor and how mutations in these conserved contact points can disrupt binding affinity and/or protein stability, ultimately leading to growth disorders. This multi-faceted approach provides valuable insights into the molecular mechanisms underlying growth hormone deficiency and related syndromes. Full article

Background: Endometrial hyperplasia (EH) represents a precursor lesion in the development of endometrial carcinoma, particularly the endometrioid subtype. Among the molecular pathways involved, microsatellite instability (MSI) resulting from DNA mismatch repair (MMR) deficiency has gained increasing attention as an early event in endometrial carcinogenesis. Objective: This study aimed to evaluate the expression of key MMR proteins (MLH1, PMS2, MSH2, and MSH6) in endometrial hyperplasia without atypia and endometrial atypical hyperplasia/endometrioid intraepithelial neoplasia (EAH/EIN) to determine the prevalence and potential implications of MMR deficiency at the precancerous stage. Methods: Fifty-six cases of EH were analyzed, including 28 endometrial hyperplasia without atypia and 28 EAH/EIN. Immunohistochemical (IHC) analysis was performed to assess the nuclear expression of MMR proteins. Loss of expression was defined as complete absence of epithelial nuclear staining with retained stromal positivity. Results: MMR protein expression was retained in all cases of endometrial hyperplasia without atypia, while total loss of one or more MMR proteins was observed in 3 of 28 (10.7%) EAH/EIN. The most frequent pattern involved concurrent MLH1/PMS2 loss, consistent with sporadic MLH1 promoter hypermethylation. One case exhibited isolated MSH6 loss, suggesting a potential Lynch syndrome, and another showed combined MSH6/PMS2 loss. Conclusions: MMR deficiency appears confined to atypical EH, supporting its role as an early molecular alteration in the neoplastic sequence leading to endometrioid carcinoma. Identification of abnormal MMR expression in EH may facilitate risk stratification, guide reflex testing for MLH1 methylation, and prompt genetic counseling for hereditary cancer predisposition. Full article

The Middle East Respiratory Syndrome coronavirus (MERS-CoV) remains a highly significant threat to global public health. Dromedary camels are the zoonotic source of human infection. All cases of zoonotic Middle East Respiratory Syndrome (MERS) have occurred in Middle Eastern countries despite MERS-CoV infection of camels being widespread in Africa. This disparity in the geographic burden of the disease may be due to genomic differences between MERS-CoV circulating in Middle Eastern countries (clades A and B) versus those infecting camels in Africa (clade C), although the precise genetic determinants of virulence remain to be elucidated. The objective of the studies reported here was to evaluate differences in the magnitude of virus shedding and in transmissibility of clades A/B and C viruses using alpacas as a surrogate for dromedary camels. We found that two of three African-origin, clade C strains of MERS-CoV induced very reduced levels of virus shedding and were transmitted inefficiently to contact control animals as compared to one other clade C virus and representative viruses from clade A and B. Lower virus titers in the nasopharynx may be associated with lower zoonotic transmission and human disease severity and may explain the observed epidemiology of MERS-CoV in Africa where zoonotic disease appears rare. These results add to our understanding of the transmission of different lineages of MERS CoV in camelids and zoonotic transmission. Full article

The process of aging is fundamentally driven by genomic instability and the accumulation of DNA damage, which progressively impair cellular and tissue function. In order to counteract these challenges, cells rely on the DNA damage response (DDR), a multilayered signaling and repair network that preserves genomic integrity and sustains homeostasis. Within this framework, nucleases and helicases have pivotal and complementary roles by remodeling aberrant DNA structures, generating accessible repair intermediates, and determining whether a cell achieves faithful repair, undergoes apoptosis, or enters senescence. Defects in these enzymes are exemplified in human progeroid syndromes, where inherited mutations lead to premature aging phenotypes. This phenomenon is also replicated in genetically engineered mouse models that exhibit tissue degeneration, stem cell exhaustion, and metabolic dysfunction. Beyond their canonical repair functions, helicases and nucleases also interface with the epigenome, as DNA damage-induced chromatin remodeling alters enzyme accessibility, disrupts transcriptional regulation, and drives progressive epigenetic drift and chronic inflammatory signaling. Moreover, their dysfunction accelerates the exhaustion of adult stem cell populations, such as hematopoietic, neural, and mesenchymal stem cells. As a result, tissue regeneration is undermined, establishing a self-perpetuating cycle of senescence, impaired repair, and organismal aging. Current research is focused on developing therapeutic strategies that target the DDR–aging axis on several fronts: by directly modulating repair pathways, by regulating the downstream consequences of senescence, or by preventing DNA damage from accumulating upstream. Taken together, evidence from human disease, animal models, molecular studies, and pharmacological interventions demonstrates that nucleases and helicases are not only essential for genome maintenance but also decisive in shaping aging trajectories. This provides valuable knowledge into how molecular repair pathways influence organismal longevity and age-related diseases. Full article

Background/Objectives: Non-syndromic tooth agenesis (NSTA) is a congenital condition that causes the absence of one or more teeth without accompanying systemic abnormalities, which significantly affects quality of life. Genetic factors, including mutations in several specific genes, contribute to the pathogenesis of NSTA. This study investigates a novel EVC2 mutation in a patient with NSTA and explores its potential pathogenic mechanism, with the aim of enriching the spectrum of pathogenic genes. Methods: Whole-exome sequencing (WES) was performed on peripheral blood samples from a patient diagnosed with NSTA. Bioinformatics analysis was utilized to identify the mutation and assess its potential impact on protein structure and function. Molecular dynamics simulations were conducted to analyze structural alterations in the EVC2 protein. The binding affinity between EVC2, EVC, and Smoothened (SMO) was to determine the effect of mutation on protein–protein interaction. Protein localization and expression were analyzed using immunofluorescence and Western blotting. Reverse transcription quantitative PCR (RT-qPCR) was employed to evaluate downstream signaling pathway alterations. Results: A novel EVC2 mutation (c.1657_1660delinsA, p.Glu553_leu554delinsMet) was identified in the proband, and the mutation was maternally inherited. Molecular dynamics simulations revealed that the mutation resulted in a decrease in α-helical content and significant conformational changes in the protein structure. This led to reduced binding affinity between EVC2 and its ligands EVC and SMO, destabilizing the structural integrity of the protein complex. Despite these structural changes, EVC2 protein localization and expression were unaffected. Furthermore, a downregulation of GLI1 and SHH expression was observed, indicating impaired Hedgehog (Hh) signaling. The downregulation of the Hh signaling pathway impairs the tooth development process and may lead to the occurrence of tooth agenesis. Conclusions: A novel EVC2 mutation was identified in a patient with NSTA. Based on molecular dynamics simulations, it is hypothesized that this EVC2 variant could contribute to the pathogenesis of NSTA by impairing the EVC2-EVC-SMO complex formation, which may lead to downregulation of downstream GLI1 and SHH. These findings provide new insights into the molecular mechanisms underlying EVC2-mediated NSTA, suggesting that disruption of Hh signaling may represent a critical pathogenic mechanism. Full article

Background/Objectives: Friedreich’s ataxia (FA) is a rare neurodegenerative disorder caused by GAA repeat expansions in the FXN gene. While well-studied in larger populations, data from Southeastern Europe are limited. This study aimed to characterize the clinical and genetic features of FA in a Serbian cohort and explore genotype–phenotype correlations. Methods: A multi-center, retrospective analysis was conducted on 30 genetically confirmed FA patients. Clinical assessments included neurological, cardiological, and metabolic evaluations. GAA repeat sizes were determined in 26 patients, and correlations with clinical features were analyzed. Results: The mean age at disease onset was 9.0 ± 3.0 years, with ataxia as the initial symptom in 80% of patients. Hypertrophic cardiomyopathy was present in 73.3%, and 43.3% of patients lost ambulation within 1.5 to 15 years after symptom onset. Two patients developed diabetes, and two were diagnosed with nephrotic syndrome. Genetic analysis revealed an average GAA1 repeat length of 805 and GAA2 of 1024 alleles. Larger GAA1 expansions were associated with extensor plantar responses, while longer GAA2 repeats correlated with impaired vibration sense. Disease duration was strongly linked to multiple neurological signs and loss of ambulation. No significant correlation was found between GAA repeat length and age at onset. Conclusions: This study provides the first genotype–phenotype analysis of FA in Serbia, confirming known patterns and revealing new comorbidities, such as nephrotic syndrome. GAA repeat length influences some clinical features but does not fully predict disease onset or progression, indicating the need for broader genetic and environmental studies. Full article

Background/Objectives: With the emergence of accessible and affordable next-generation sequencing platforms, pediatric oncologists are now accountable to diligently ascertain genetic causes of cancer, with an amenable opportunity to test for cancer predisposition syndromes. Methods: This study incorporates triangulated interviews of family members diagnosed with Li–Fraumeni syndrome through clinical TP53 testing. The interview content was coded using NVivo 10.0 software to determine psychosocial themes relevant to genetic testing, diagnosis, and surveillance. Results: Interview content revealed opportunities to apply social themes analogous to TP53 biologic language. Conclusions: This report models the systematic inclusion of patient, parent, and health care provider perspectives when testing individuals for familial cancer predisposition syndromes. Full article

Accessory breasts denote the formation of extra breast tissue along the milk line, and are known to be more prevalent among Black and Asian populations, affecting both genders. This first-ever study aimed to determine the genetic aetiology of accessory breasts in a multiplex family, where all female siblings present with bilateral accessory breasts. The study also ascertained secondary findings (SFs) responsible for comorbidities. Clinical data and saliva samples were obtained from all family members. Ultrasound and histopathology confirmed the diagnosis. Whole-exome sequencing was conducted on DNA samples obtained from the saliva, with variant calling conducted utilising the Sentieon workflow. Variant classification was based on American College of Medical Genetics and Genomics guidelines. After segregation analysis, 12 candidate genes emerged. Among these, PRSS50 and FANCC emerged as top candidates, being implicated in breast diseases. However, two variants in FANCC (c.360del; p.His120GlnfsTer24 and c.355_358del; p.Ser119IlefsTer24) were selected as the most probable causal variants because of the role of this gene in hereditary breast and ovarian cancer syndromes. The remaining ten genes were reported as potentially accounting for comorbidities segregating with accessory breasts. Reported SFs involve TTR and RYR1. In conclusion, pathogenic variants in FANCC cause familial accessory breasts. These novel observations impact pathophysiology, genetic counselling, and personalised medicine. Full article