Search Results (2,342)

Gangliosides are essential for membrane functions, cell recognition, and maintenance of the nervous system. GM2 gangliosidosis is a group of rare genetic lysosomal storage diseases that includes Tay-Sachs disease (TSD), Sandhoff disease (SD), and AB variant. TSD and SD are characterized by deficient β-N-acetyl-hexosaminidase activity. This leads to decreased catabolism of β-N-acetyl-hexosamine-containing ganglioside GM2 in the lysosomes, damage to cells and tissues, and severe neurological symptoms. GM2 is a major ganglioside accumulating in TSD and SD, and is synthesized from GM3 by β1,4-N-acetylgalactosaminyltransferase 1 (B4GALNT1, GM2 synthase). Therapies under development for GM2 gangliosidosis include adeno-associated virus gene therapy, enzyme replacement, and substrate reduction therapy (SRT). The goal of this work was to express and purify human B4GALNT1, characterize its activity, and explore its structural features by protein modeling and substrate docking. We used a panel of synthetic compounds to study their potential inhibition of B4GALNT1 activity. This work can serve to develop SRT for GM2 gangliosidosis. Full article

Background: Bovine mastitis (BM) is a major disease affecting dairy herds (DHs), with Serratia marcescens (S. marcescens) being increasingly implicated as a causative agent. The growing concern over antimicrobial resistance (AMR) extends to BM-associated S. marcescens isolates, where resistance patterns are emerging. Methods: Here, four BM Gram-negative isolates were investigated: 1-DH1, 2-DH1, 3-DH2, and 4-DH3. Phenotypic characterization was performed using the Neg-Urine-Combo98 panel on a MicroScan WalkAway Plus system. Whole-genome sequencing (WGS) was performed to characterize and identify AMR and virulence factors (VF) genes and plasmids in isolates 1-DH1, 3-DH2, and 4-DH3, and phylogenomic analyses were conducted for a visual comparison of the genomes. Results: Phenotypically, isolates 1-DH1, 2-DH1, and 4-DH3 were identified as S. marcescens, and 3-DH2 as Serratia odorifera (confirmed as S. marcescens by WGS). A 28.00% (n = 25) prevalence of phenotypic AMR for isolates 1-DH1, 2-DH1, and 4-DH3 against Aug-E, AM, To, Cfx, Crm, Cl, and Fd was shown, and 24.00% (n = 25) for isolate 3-DH2 against Aug-E, AM, To, Crm, Cl, and Fd. The AMR genes AAC(6′)-Ic, aac(6′)-Ic_1, aac(6′)-Ial, H-NS, SRT-2, oqxB, oqxB_1, oqxB25, mexI, CRP, and blaSST-1, and flgH, fliP, fliM, and fliG VF genes were identified in the whole genome of the S. marcescens sequenced isolates 1-DH1, 2-DH1, and 4-DH3. In addition, a phylogenomic analysis of these three isolates revealed that WGS genomes are more closely related to S. marcescens prevenient from environmental sources. Conclusions: This study reports, for the first time, AMR resistance to tobramycin, cefuroxime, colistin, and nitrofurantoin in BM S. marcescens isolates. Genomic analysis revealed the presence of multiple AMR and VF genes, further highlighting the pathogenic potential of these isolates. Phylogenomic analysis revealed that the genome of the three BM S. marcescens isolates is more closely related to environmental S. marcescens strains. Full article

MicroRNAs (miRNAs) are short, non-coding RNA molecules that play a crucial role in regulating various biological processes by influencing post-transcriptional gene expression and gene silencing. Background/Objectives: In this study, rabbit embryos were utilised as a model system to investigate potential biomarkers relevant to human embryo development. Seven microRNAs (miRNAs) identified in the embryo culture medium were evaluated as biomarkers by analysing the correlation between their expression levels and the developmental quality of rabbit embryos at days 4 and 6. Methods: We analysed the expression of seven development-specific miRNAs (miR-24-3p, miR-28-3p, miR-103a-3p, miR-181a-5p, miR-191-5p, miR-320a-3p, miR-378a-3p) in 4-day-old and 6-day-old rabbit embryos, along with their culture media. Results: Our findings revealed significant differences in the expression levels of these miRNAs between the 4-day-old and 6-day-old embryos. On the other hand, the expression patterns observed in the culture medium samples showed less variation between the two age groups. Nonetheless, analysis of miRNA expression profiles in the spent culture medium from individually cultured embryos enabled the identification of lower-quality embryos, characterised by smaller size and impaired or delayed development. Conclusions: The detection of these miRNAs in embryo culture medium may serve as a reliable indicator of successful progression to the blastocyst stage. Our experimental results identified specific miRNAs whose expression profiles differ according to embryonic stage and quality, thereby reflecting key developmental milestones. Notably, the detectability of these miRNAs in the medium—without prior RNA isolation—indicates their active secretion into the extracellular environment. By synthesising our findings with the existing literature, we refined a panel of miRNAs essential for the development of implantation-competent embryos in both rabbits and humans. Consequently, we developed a non-invasive assay for predicting implantation and pregnancy outcomes, which may have significant applications in human reproductive medicine. Full article

Sugarcane smut, caused by Sporisorium scitamineum, is a globally prevalent disease that severely impacts sugarcane yield and quality. The most cost-effective and sustainable approach to disease control is breeding for smut-resistant varieties. In this study, we conducted a genome-wide association study (GWAS) using a panel of core sugarcane parents and their derived lines to elucidate the genetic basis of smut resistance across seven different environments. We identified 68 new loci significantly associated with smut resistance across all the chromosomes. Based on functional annotations and genomic positions, 164 candidate genes were identified, many of which are related to enzymatic systems, resistance genes, transcription factors, and other pathways implicated in smut defense. Using resistance ratings and associated SNPs, we further selected ten elite parents and derivatives as potential donors for marker-assisted selection (MAS). This study provides a valuable reservoir of genetic resources for improving smut resistance in sugarcane. Full article

Background: Bone tissue decalcification is essential for histopathological evaluation, but conventional methods using inorganic acids degrade nucleic acids, limiting molecular testing. EDTA is known to better preserve DNA, but its suitability for next-generation sequencing (NGS) in clinical settings remains to be validated. Methods: This retrospective study evaluated 752 formalin-fixed paraffin-embedded (FFPE) tissue samples undergoing NGS between January 2022 and October 2024. Of these, 31 were decalcified using EDTA (Osteosoft, Merck, Germany). DNA was extracted using the Qiagen AllPrep^® kit and quantified using Qubit and NanoDrop. Libraries were prepared with a custom 30-gene Ampliseq panel and sequenced on the Ion Torrent platform. Sequencing was deemed suboptimal if <95% of target regions reached ≥250X depth. Results were compared to 721 non-decalcified FFPE samples. Results: Suboptimal sequencing occurred in 9.7% of EDTA-decalcified and 9.0% of non-decalcified cases (p = 0.9). DNA concentration (Qubit) and NanoDrop 260/280 ratios were not significantly different (p = 0.4 and p = 0.8, respectively), though EDTA cases had lower DNA concentrations (NanoDrop, p = 0.006) and 260/230 ratios (p = 0.002). Mutation detection in decalcified samples was consistent with known mutation profiles for respective tumor types. Conclusions: EDTA-decalcified FFPE bone tissues produce NGS results comparable to non-decalcified specimens, with similar sequencing success rates and acceptable DNA quality. These findings support the use of EDTA as a suitable decalcification method for molecular diagnostics, enabling broader inclusion of bone specimens in clinical testing. Full article

Inter-individual variability in response to androgenetic alopecia (AGA) therapies remains a therapeutic challenge. This study evaluated the clinical and mechanistic utility of a 26-SNP pharmacogenetic panel in guiding treatment decisions. By using a database containing data from 252 individuals stratified by genotype, overall response rates were high (85.6–91.0%), exceeding published benchmarks for minoxidil, finasteride, and dutasteride. SNP association analysis identified rs1042028 in SULT1A1 as a robust predictor of poor response across all three drugs (minoxidil: p = 2.4 × 10⁻⁸, OR = 0.09; dutasteride: p = 0.023, OR = 0.21; finasteride: p = 0.025, OR = 0.11). For dutasteride, the TT genotype of rs39848 in SRD5A1 was also associated with reduced efficacy (p = 0.018, OR = 0.02). SNP–SNP interaction analysis revealed significant epistatic effects between genes involved in prostaglandin signalling and oxidative stress response, including PTGFR × MUC1 (p = 5.38 × 10⁻⁶) and GPR44 × FUT2 (p = 9.4 × 10⁻⁵). Network enrichment analyses further supported drug-specific mechanistic clusters. Importantly, no statistically significant differences in response were observed between pharmacogenetically guided treatment groups (p > 0.1), suggesting successful genotype-based alignment. Together, these findings demonstrate that SNP-informed therapy can enhance efficacy, clarify drug mechanisms, and provide a foundation for precision treatment in AGA. Full article

Under physiological and pathological conditions, all cells release extracellular vesicles named exosomes, which act as transporters of lipidic, protein, and genetic material from parent to recipient cells. Neoplastic cells can secrete higher number of exosomes to exert pro-tumoral effects such as microenvironmental changes, disease progression, immunosuppression and drug-resistance. This holds true for both organ-specific cancers and hematologic malignancies. One of the most important components of exosomal cargo are microRNAs which can mediate all the abovementioned effects. More specifically, microRNAs are small non-coding RNAs, routinely detected through quantitative real-time PCR, which act as translational suppressors by regulating protein-coding genes. Considering their high stability in all body fluids and viability in circulation, research is currently focusing on this type of RNAs for the so called “liquid biopsy”, a non-invasive tool for disease diagnosis and longitudinal monitoring. However, several issues remain to be solved including the lack of standardized protocols for exosome isolation and miRNA detection. Starting with this premise, our review aims to provide a wide description of the known microRNA panels employed in the prominent hematological malignancies, which will hopefully redefine the approach to these very challenging diseases in the near future. Full article

Background/Objectives: Inherited platelet disorders (IPDs) are diverse conditions characterized by abnormalities in platelet count and function. Next-Generation Sequencing (NGS) shows promise as a diagnostic tool in the diagnosis of IPDs. This study aims to assess the clinical value and limitations of using a targeted NGS panel in diagnosing children with suspected IPDs. Methods: We conducted a retrospective study of 93 children evaluated for suspected IPDs. A targeted NGS panel of 14 IPD-associated genes (RUNX1, WAS, ADAMTS13, ANKRD26, CYCS, GATA1, GP1BA, GB1BB, GP9, ITGA2B, ITGB3, MASTL, MPL, MYH9) was performed. Results: Genetic variants were identified in 30 patients (32.3% of the cohort). A total of 37 variants, of which 15 (40.5%) were novel, were found across 11 of the 14 genes on the panel (all except MPL, CYCS, and RUNX1). Variants were most frequently found in ITGB3 (18.9% of variants), GP1BA (16.2%), and ADAMTS13 (16.2%) genes. The majority of variants (64.9%) were classified as variants of uncertain significance (VUS), followed by likely pathogenic (LP) (27%) and pathogenic (8.1%) variants. Most variants were in a heterozygous state (73%). Specific cases highlighted complex genetic scenarios, such as co-occurring variants, and the identification of pathogenic and LP variants in patients initially presenting with immune thrombocytopenia. Conclusions: NGS helps to identify genetic causes, assess risk, manage, and provide genetic counseling in the management of IPDs. However, the prevalence of VUS underscores the need for a multidisciplinary approach to evaluate NGS results accurately. Full article

Epithelial ovarian cancer (EOC) is the most lethal gynecologic malignancy, often diagnosed at an advanced stage due to its asymptomatic progression. The high recurrence rate and development of platinum-based chemotherapy resistance contribute to its poor prognosis. Despite advancements in molecular profiling, predictive biomarkers for chemotherapy response and recurrence risk remain limited. In this study, we developed OvarianTag™, a biomarker panel integrating apoptosis and necroptosis pathways, to predict chemotherapy benefit and disease progression in EOC patients. This observational study was conducted in two phases. In the first phase, 45 patients were recruited, and RNA was extracted from fresh ovarian tissues (normal, benign, and malignant). qRT-PCR was performed to assess the relative expression of genes involved in apoptosis and necroptosis-regulated cell death pathways. Machine learning algorithms were applied to identify the relevant prognostic markers, leading to the development of OvarianTag™. In the second phase, 55 additional EOC patients were included, and their formalin-fixed, paraffin-embedded (FFPE) tumor samples were analyzed using qRT-PCR. The classifier algorithm incorporated hierarchical clustering to stratify patients based on gene expression profiles. Significant differences in TNFRSF10C/TRAIL-R3, TNFRSF10B/TRAIL-R2, and CASP8 expression levels were observed between patient groups. CASP8 downregulation was strongly correlated with platinum resistance and a poor prognosis. Decision tree models achieved 83.3% accuracy in predicting platinum response and 79.2% accuracy in recurrence risk stratification. The OvarianTag™ classifier demonstrated high sensitivity and specificity in identifying high-risk patients, supporting its potential as a prognostic tool. The OvarianTag™ panel provides a novel approach for risk stratification in EOC, integrating apoptosis and necroptosis pathways to refine chemotherapy response prediction and recurrence risk assessment. This molecular assay has the potential to guide personalized treatment strategies, enhancing clinical decision-making and improving patient outcomes. Further validation in independent cohorts is warranted to establish its clinical utility. Full article

Identification of two or more pathogenic/likely pathogenic (P/LP) variants in cancer susceptibility genes carried by the same patient have important consequences for patient management. We have limited information about the effect of double heterozygosity (DH) in cancer susceptibility genes. The prevalence of DH among Hungarian cancer patients referred to oncogenetic counselling, and comparison of their phenotypes to single variant carriers were performed. In total, 2050 patients were analysed by multigene panel sequencing. Variants of 48 established cancer predisposition genes by ACMG guidelines were evaluated. In overall, P/LP variants were found in 19.8% of cases. DH was observed in 16 cases, amount to 0.8% of all patients, and to 4.0% of positive cases. Appearance of multiple primary tumours was not associated with DH compared to non-P/LP and single P/LP carriers (p = 0.71 and p = 0.54, respectively). Within a cohort of patients referred with suspected HBOC syndrome, earlier tumour formation was observed when DH cases were compared to non-P/LP carriers (p = 0.01), but difference between single and DH carriers was not statistically significant (p = 0.19; Bonferroni corrected alpha = 0.017). Our observations provide information about the incidence of DH status among Hungarian hereditary cancer patients and suggest that DH did not increase the risk of cancer compared to individuals with single P/LP mutation. Full article

In Brassica napus, hypocotyl elongation under shade conditions poses a significant challenge in intensive agricultural systems, particularly in rice-rapeseed rotation regimes where straw mulching reduces light quality. However, the genetic basis of light-mediated hypocotyl growth responses in B. napus remains poorly understood. In this study, hypocotyl lengths were measured in a panel of 267 diverse rapeseed accessions under five light conditions including white, red, far-red, blue light, and complete darkness. Substantial phenotypic variation was observed among accessions and treatments, with red light exhibiting the weakest inhibitory effect on elongation, and white light showing the strongest suppression. Genome-wide association studies (GWAS) (−log₁₀ (p) > 4.5) identified numerous significant SNPs associated with light response, highlighting candidate genes such as KAN1, ILL2, VQ18, HDA15, and HAT3 involved in photomorphogenesis and hormonal signaling pathways. These findings elucidate the polygenic control of light responsiveness in B. napus and provide molecular targets for breeding shade-tolerant varieties to enhance crop resilience under dense planting and straw mulching systems. Full article

Phenolic compounds contribute significantly to the nutritional and functional properties of wheat, particularly due to their antioxidant activity. In this study, a genome-wide association study was conducted to elucidate the genetic basis of total phenolic content (TPC) and antioxidant activity (AA) in a panel of 144 tetraploid wheat accessions representing diverse subspecies. The panel was evaluated under two different environments, located in Chile and Italy, to assess the influence of genotype, environment, and their interaction. Significant variability was observed for both TPC and AA, with TPC ranging from 0.26 to 0.82 mg gallic acid equivalent (GAE)/g and AA from 0.04 to 0.99 µmol Trolox equivalent (TE)/g. Substantial phenotypic variation and high broad-sense heritability were observed for both traits, underscoring the predominant genetic control. The genome-wide association study, using a mixed linear model (MLM), and the Bayesian information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK) approaches identified 17 significant marker–trait associations, including quantitative trait loci on chromosomes 2B, 3A, 4B, 5A, 5B, and 6B. Notably, QTLs on chromosome 5A were co-localized for both TPC and AA, suggesting potential pleiotropic loci. Candidate genes linked to these loci included flavonol 3-sulfotransferase and peptidylprolyl isomerase, which are involved in phenylpropanoid metabolism and oxidative stress response, respectively. These findings offer valuable insights into the genetic basis of wheat phenolic traits and provide molecular targets for the development of biofortified cultivars through marker-assisted selection. Full article

Background/Objectives: Y-chromosomal short tandem repeats (Y-STR) are genetic markers widely used in forensic and population genetics. However, despite their importance, many populations remain under-represented in published studies and genetic databases. One such population is the Cape Verdean, which, despite its unique history of admixture between European and sub-Saharan African populations, continues to be under-represented in global Y-STR reference databases. This study aims to characterize the Y-STR haplotype diversity and paternal lineage composition of the Cape Verdean population using a high-resolution STR panel. Methods: A total of 143 unrelated Cape Verdean men were analyzed using a set of 26 Y-STR loci, including rapidly mutating markers. Allele and haplotype frequencies were calculated, along with standard forensic parameters such as gene and haplotype diversity. Paternal lineages were inferred, and genetic relationships with other populations were evaluated using distance-based and graphical methods. Results: A total of 135 haplotypes were detected, with 88.8% being unique, yielding a haplotype diversity of 0.999. The most common haplogroups reflected both West African and European ancestry. Genetic distance analysis positioned the Cape Verdean population between African and European groups, supporting its intermediate and admixed genetic background. Conclusions: This study provides the first high-resolution Y-STR dataset for Cape Verdeans, contributing valuable reference data for forensic casework and population genetic studies. The results highlight the utility of extended Y-STR panels in admixed populations and underscore the need to enhance the representation of admixed populations in international forensic reference databases. Full article

Background: Given the limited research on mitochondrial diseases in our area, specifically regarding their genetic variability and diverse clinical manifestations, and considering the significant number of consanguineous marriages in our region, we aimed to investigate the clinical and molecular characteristics of patients with mitochondrial disorders in Saudi Arabia. Methods: This retrospective cross-sectional cohort study involved a chart review of patients diagnosed with mitochondrial disorders at the Ministry of National Guard Health Affairs tertiary health care centers in Saudi Arabia between 2013 and 2022. Results: The study population comprised 116 patients with a mean age of 10 years (±7 SD). Among the study cohort, 34.5% (n = 40) had died. The primary cause of death was cardiopulmonary arrest (55.0%, n = 22). The most prevalent condition was developmental delay (67.9%). Around 56.9% were diagnosed using Whole Exome Sequencing (WES), 10.3% by Whole Genome Sequencing due to negative WES, 23.3% through a single-gene approach, 7.8% were analyzed through a mitochondrial panel, and 1.7% via a gene panel. The distributions of current age and age at diagnosis were significantly different between the nuclear and mitochondrial gene types. Notably, the diagnostic delay time (time taken from symptom onset to genetic diagnosis) averaged 1.5 years for nDNA variants compared to an average of 10 years for mDNA variants. Conclusions: This study shows that gene type affects clinical characteristics, highlighting the importance of genetic studies in disease manifestation. Full article

Magnesium (Mg) alloys, particularly Mg AZ31, have emerged as promising biomaterials for orthopedic applications due to their biodegradability and favorable mechanical characteristics. Among these, the Mg AZ31+SPF alloy, subjected to hydrothermal (HT) treatment, has demonstrated enhanced bioactivity. Our previous research established that this surface modification supports the osteogenic differentiation of human mesenchymal stem cells (hMSCs) by modulating both canonical and non-canonical signaling pathways, including those implicated in osteogenesis, hypoxic response, exosome biogenesis, and lipid metabolism. In the present study, we extended our investigation to assess the effects of Mg AZ31+SPF+HT and Mg AZ31+SPF extracts on murine pre-osteoclasts (RAW 264.7 cells) over 3- and 6-day treatment periods. The primary objectives were to evaluate biocompatibility and to investigate potential impacts on osteoclastogenesis induction and miRNA expression profiles. Methods: To assess cytocompatibility, metabolic activity, DNA integrity, and morphological alterations in RAW 264.7 cells were evaluated. Osteoclast differentiation was quantified using TRAP staining, alongside the assessment of osteoclastogenic marker expression by qRT-PCR and ELISA. The immunomodulatory properties of the extracts were examined using multiplex BioPlex assays to quantify soluble factors involved in bone healing. Additionally, global miRNA expression profiling was performed using a specialized panel targeting 82 microRNAs implicated in bone remodeling and inflammatory signaling. Results: Mg AZ31+SPF+HT extract exhibited high biocompatibility, with no observable adverse effects on cell viability. Notably, a significant reduction in the number of TRAP-positive and multinucleated cells was observed relative to the Mg AZ31+SPF group. This effect was corroborated by the downregulation of osteoclast-specific gene expression and decreased MMP9 protein levels. Cytokine profiling indicated that Mg AZ31+SPF+HT extract promoted an earlier release of key cytokines involved in maintaining the balance between bone formation and resorption, suggesting a beneficial role in bone healing. Furthermore, miRNA profiling revealed a distinct regulatory signature in Mg AZ31+SPF+HT-treated cells, with differentially expressed miRNAs associated with inflammation, osteoclast differentiation, apoptosis, bone resorption, hypoxic response, and metabolic processes compared to Mg AZ31+SPF-treated cells. Conclusions: Collectively, these findings indicate that hydrothermal treatment of Mg AZ31+SPF (resulting in Mg AZ31+SPF+HT) attenuates pre-osteoclast activation by influencing cellular morphology, gene and protein expression, as well as post-transcriptional regulation via modulation of miRNAs. The preliminary identification of miRNAs and the activation of their regulatory networks in pre-osteoclasts exposed to hydrothermally treated Mg alloy are described herein. In the context of orthopedic surgery—where balanced bone remodeling is imperative—our results emphasize the dual significance of promoting bone formation while modulating bone resorption to achieve optimal implant integration and ensure long-term bone health. Full article