Abstract Objectives Glutaric aciduria type I (GA-I) is an inborn error of metabolism caused by biallelic variants in the GCDH gene, disrupting lysine and tryptophan catabolism. While exonic variants are well-characterized, the clinical and molecular consequences of intronic splice-site variants remain poorly understood, especially in underrepresented populations. Here, we report a novel homozygous intronic variant in GCDH in a 5-year-old Iranian girl. Methods We investigated a 5-year-old Iranian patient with severe GA-I symptoms (macrocephaly, seizures, developmental delay) using Gas chromatography–mass spectrometry (GC–MS) for biochemical profiling, Targeted GCDH sequencing (Sanger) and segregation analysis and Computational splice prediction tools (MutationTaster, SpliceAI). Twenty-one splice-site variants from 77 GA-I patients were also analyzed in silico. Results Genetic testing identified a novel intronic variant (c.957-1G>C) in the GCDH gene in our patient, who presented with severe neurological symptoms including seizures, macrocephaly, and developmental delay. Biochemical analysis revealed elevated levels of glutaric acid (560 µmol/mol creatinine) and 3-hydroxyglutaric acid (18 µmol/mol creatinine). Parental testing confirmed carrier status for this variant. Seventy-six patients with intronic variants were also investigated from the previous reported patients; splice variants account for 27% (21/77) of cases. The most common clinical manifestations included neurological disorders (40%), macrocephaly (16%), and seizures (15%). Geographically, most affected individuals were of North American (50%) or Asian (32%) descent. Conclusions The c.957-1G>C variant expands the mutational spectrum of GA-I and underscores the importance of intronic analysis in diagnostic workflows. Splice-site variants demonstrate significant phenotypic heterogeneity, necessitating early surveillance for neurological sequelae. Population-specific variant patterns suggest founder effects in high-risk groups.

Abstract Background Lipoprotein-associated phospholipase A₂ (Lp-PLA₂) is a vascular-specific enzyme that hydrolyzes oxidized phospholipids on low-density lipoprotein (LDL-C), thereby promoting vascular inflammation and atherosclerosis. Sex-related differences in lipid metabolism and genetic polymorphisms may influence cardiovascular disease (CVD) risk. This study aimed to evaluate sex-specific variations in lipid profiles, cardiac biomarkers, Lp-PLA₂ activity, and the Ala379Val (rs1051931, G/A) polymorphism in healthy Egyptian adults. Methods One hundred healthy individuals (50 males and 50 females) were recruited. Serum concentrations of triglycerides, total cholesterol (T-C), high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), total creatine kinase (T-CK), and creatine kinase-MB (CK-MB) were measured. Lp-PLA₂ activity was determined using a colorimetric assay, and genotyping of rs1051931 was performed via PCR-RFLP. Results Males exhibited significantly higher levels of triglycerides, low-density lipoprotein cholesterol (LDL-C), total creatine kinase (T-CK), and creatine kinase-MB (CK-MB), along with lower high-density lipoprotein cholesterol (HDL-C) levels compared to females ( P < 0.05). After adjusting for body mass index (BMI), Lp-PLA₂ activity was elevated in males across all genotypes, with the highest activity observed in individuals carrying the AA genotype. The A allele was more prevalent in males (31%) than in females (25%) ( P < 0.05). Conclusion Sex-specific disparities favoring males in lipid metabolism, cardiac enzyme activity, and the Lp-PLA₂ (G/A) variation may augment their heightened cardiovascular risk. Specifically, Egyptian males possessing the A allele of rs1051931 seem to exhibit increased vulnerability to lipid-induced cardiovascular problems, presumably due to elevated Lp-PLA₂ activity. These findings underscore the need to incorporate sex and genetic profiling into cardiovascular disease risk evaluation and preventive measures, enabling more precise and individualized therapies. Graphical abstract

Abstract Background Whole-genome sequencing (WGS) is an efficient, accurate, and high-throughput technique used for the discovery of exonic as well as non-exonic variants causing different genetic anomalies, improving clinical management for the disease. This study was designed to evaluate pathogenic genetic variants related to male infertility in male infertile families in remote rural areas of Pakistan. Methods For the five families recruited, WGS was conducted on 14 patients and 6healthy controls. WGS was performed using the Illumina TruSeq DNA Nano Library Prep workflow protocol. DNA was assessed with TapeStation and sequenced using the TruSeq kit (Illumina). Bioinformatics tools were then used to identify potential causative variants, including indels and single-nucleotide variants. Results In family 1, five homozygous nonsynonymous SNVs were identified in FMR1 , PHF8 , TOPBP1 , and DAB2IP . These X-linked or recessive variants cause amino acid changes that affect key cellular pathways. In family 10, homozygous nonsynonymous SNVs were detected in FOS , MIR452 , PDHA1 , and SERPINB1 , implicating roles in structural, transcriptional, metabolic, and synaptic processes. In family 11, a frameshift deletion in PRDM9 and nonsynonymous SNVs in KIAA1210 , suggesting possible disruption of gene regulation and protein stability. In family 13, multiple nonsynonymous variants were identified in SPATA20 , and G6PD ,, with implications in reproductive function, angiogenesis, enzymatic activity, and neuromuscular disorders. SNV Variant was detected in SLC12A4 in Family 15. Conclusion The study contributes to a systematic understanding of the problem and provides a basis for identifying causal variations in idiopathic cases of male infertility, setting targets for future therapeutic development.

Abstract Background The c-ros oncogene 1 (ROS1) rearrangement is one of the actionable targets in non-small cell lung carcinoma (NSCLC), particularly the adenocarcinoma subtype. Early detection of this mutation is crucial for determining appropriate therapy. While Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) remains the gold standard for ROS1 rearrangement detection, immunohistochemistry (IHC) is often used as a screening method due to its accessibility and rapid processing time. Aim This study evaluates the sensitivity and specificity of IHC compared to RT-PCR in detecting ROS1 rearrangement. Materials and methods This was a diagnostic cross-sectional study conducted at H. Adam Malik Hospital and Santa Elisabeth Hospital in Medan between December 2022 and December 2023. A total of 90 patients with NSCLC adenocarcinoma who met the inclusion and exclusion criteria were enrolled. Collected data included clinical characteristics and results of ROS1 rearrangement testing using RT-PCR and IHC. The validity of IHC was assessed by calculating sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and diagnostic accuracy, using RT-PCR as the reference method. Results Most patients were male (66.7%), with a mean age of 56.46 years, and the majority were former smokers (67.8%). Among the 90 patients, 8 (8.9%) were ROS1-positive by RT-PCR and 7 (7.8%) were ROS1-positive by IHC. The sensitivity of IHC compared to RT-PCR was 37.5%, specificity was 95.1%, PPV was 42.9%, and NPV was 94.0%. The overall diagnostic accuracy of IHC was 90.0%. Conclusion Immunohistochemistry shows high specificity and negative predictive value, making it a reasonably effective screening tool for ROS1 rearrangement detection. However, its low sensitivity and positive predictive value indicate that IHC should not be used as a standalone diagnostic method for determining ROS1 status.

Abstract Recurrent pregnancy loss (RPL), defined as two or more consecutive miscarriages, poses significant challenges in reproductive medicine due to its multifactorial etiology, including genetic, immunologic, and environmental factors. Emerging evidence highlights the critical role of epigenetic modifications, particularly DNA methylation, in RPL. This review explores the involvement of DNA methyltransferase (DNMT1, DNMT3A, DNMT3B) and ten-eleven translocation (TET1, TET2, TET3) enzymes in regulating embryonic and placental development. Dysregulation of these enzymes disrupts the balance between methylation and demethylation, leading to aberrant gene expression and increased miscarriage risk. In recurrent pregnancy loss, excessive oxidative stress and disrupted metabolic homeostasis can impair the enzymatic machinery maintaining DNA methylation turnover. DNMT downregulation has been associated with depleted cellular levels of S-adenosylmethionine (SAM), the principal methyl donor, whereas reduced TET activity may result from an imbalance in α-ketoglutarate (αKG) and Fe²⁺ availability cofactors required for 5-methylcytosine oxidation. These conditions collectively attenuate methylation-demethylation dynamics and contribute to aberrant epigenetic programming in trophoblast and decidual tissues. Studies demonstrate altered DNMT and TET expression in chorionic and decidual tissues of RPL patients, correlating with global hypomethylation or hypermethylation of key developmental genes. Genetic polymorphisms in DNMT and TET genes further elevate RPL susceptibility. Diagnostic approaches, including RT-qPCR, bisulfite sequencing, and methylation microarrays, enable precise assessment of epigenetic profiles, offering potential biomarkers for early risk prediction. Therapeutically, DNMT inhibitors like 5-azacytidine, TET activators such as vitamin C, and emerging CRISPR-based epigenetic editing present promising avenues for restoring epigenetic balance, though challenges like safety and specificity remain.

Abstract This critical appraisal reviews the article by Sidiq et al. on transporter gene polymorphisms and metformin efficacy in type 2 diabetes. The study strengthens evidence linking SLC22A1 and SLC47A1 variants to treatment response. We highlight the limited clinical use of genetic screening, particularly in low-resource settings, and call for inclusion of diverse populations and multi-omic approaches to enhance predictive value. Affordable genotyping and decision-support tools are essential for translating these findings into practice and advancing personalized diabetes therapy.

Abstract Background Although Genome-Wide Association Studies (GWAS) link genetic variants to kidney disease, the specific role of phase separation-related genes (PSGs) in renal failure pathogenesis is unknown. This study investigates the potential of PSGs as novel biomarkers to improve the early detection and treatment of renal failure. Methods We created ten gene co-expression modules and associated cluster trees using enrichment and differential expression analysis. The final phase separation-related biomarkers were screened using three machine classification algorithms, and each gene's functional pathways and relationship to immune function were examined. In order to thoroughly confirm the link between potentially linked genes and the onset of renal failure, the study also employed Mendelian Randomization (MR) and supervised and unsupervised machine learning. It also showed the statistical power of unsupervised learning and the results of additional verification. Results According to the correlation of gene expression, ten genes that may be related to renal failure were screened out. Linking phase separation to renal failure identified two core phase separation-related genes, ARL6IP4 and MRRF . Mendelian randomization provided suggestive evidence of a potential causal association between genetically predicted constipation and increased risk of renal failure. Conclusions This study points to a higher potential of MRRF as a biomarker for renal failure than ARL6IP4 . There may also be a potential causal association between the prevalence of constipation and the incidence of renal failure.

Abstract Background Breast cancer is the leading cause of cancer death in women in Morocco and worldwide. The development of anti-HER2 therapies has improved the management of HER2-positive breast cancers. However, cardiotoxicity remains the major complication observed in patients undergoing this treatment and genetic factors appear to be involved in the predisposition to these cardiovascular toxicities. The present systematic review aims to further elucidate the relationship between some genetic polymorphisms and cardiotoxicity in HER2-positive breast cancers. Methods All relevant studies, that investigated the association between genetic variants and cardiotoxicity in adult patients with HER2-positive breast cancer treated with anti-HER2 targeted therapy, have been extracted from PubMed, Scopus, and Google Scholar databases up to February 2025. Results 15 studies were enrolled after strict literature screening. Most of them have analyzed HER2 gene polymorphisms, which are most likely associated with cardiotoxicity induced by anti-HER2 treatments; nevertheless, some findings are still inconclusive. Conclusion The current evidence does not yet justify clinical implementation of HER2 polymorphism testing. Larger studies such as multi-center cohorts including biomarkers and pharmacokinetic data are needed to confirm the effects of these genetic variants in predicting cardiotoxicity in patients with HER2-positive breast cancer.

Abstract Background The cause of chromosome 21nondisjunction and subsequent Down syndrome birth are not all stochastic and there are certain genetic predispositions for meiotic recombination anomalies that increase the risk of trisomy21 conception. This entire etiology is complicated, enigmatic and needs to be addressed with explicit experimental approach. Result We genotyped recombination regulators RNF212 , PRDM9 and SPO11 from the genome of women having trisomy 21 child stratifying them according to their age at conception and origin of meiotic errors. Out of 34 variants nineteen unique sequence alterations exhibited association with meiosis I error ( N = 700), while four exhibited association with meiosis II error ( N = 125) and this association was maternal age independent. These risk variants were found associated with reduced recombination on long arm of chromosome 21 among the women of all age groups. In addition, variants of RNF212 and PRDM9 exhibited association with the altered position of single recombinant event on the nondisjoined chromosome 21. Conclusion Our novel results revealed that the risk variants of RNF212 , PRDM9 , but not the SPO11 may reduce recombination on chromosome 21 and cause altered placement of single recombinant events on chromosome 21 and make the homologues vulnerable for nondisjunction. The variant of RNF212 increase the risk of peri-telomeric single recombination that in turn makes the chromosome susceptible to meiosis I nondisjunction in maternal age-independent manner. On the other hand variants of PRDM9 increase risk of pericentromeric recombination on chromosome that nondisjoined at meiosis II in maternal age-dependent manner and also elevate the chance of pertelomeric exchange that increase the risk of meiosis I nondisjunction in maternal age independent manner. We for the first time provide evidence that some important recombination regulators in human oocyte, when carry risk variants, increase chance anomalous positioning of chiasma on the pairing homologues that reduces frequency of recombination and challenges faithful segregation of the chromosomes. This underpins the aneuploidy birth.

Abstract Background SRY-box transcription factor 2 ( SOX2 ) is implicated in diverse pathological conditions; however, its contribution to vascular calcification (VC) is not well define. This research explored the influence of SOX2 on VC and associated molecular mechanisms utilizing a β-Glycerophosphate (β-GP)-driven calcification model in human aortic vascular smooth muscle cell (HA-VSMC). Results One in vitro VC model was established by exposing HA-VSMCs to β-GP. The experimental design comprised several key groups: an untreated control, a β-GP-induced calcification model group, a group receiving β-GP and SOX2 -targeting siRNA (si- SOX2 ), a group treated with β-GP and 3-Methyladenine (3-MA), an autophagy inhibitor, and a group co-treated with β-GP, si- SOX2 , and the Wnt pathway activator BML-284. Relative to controls, the β-GP model group exhibited increased calcification, elevated protein levels of SOX2 and osteogenic markers (Runx2, BMP2), enhanced autophagic activity, reduced expression of contractile markers (SM22α, α-SMA), and suppression of Wnt pathway signaling. Transfection with si- SOX2 significantly counteracted these β-GP-induced alterations. Conversely, the beneficial impact of si- SOX2 on β-GP-induced VC was negated by BML-284-mediated activation of the Wnt pathway. Conclusion The findings indicate that suppressing SOX2 alleviates β-GP-induced VC by influencing the activation status of the Wnt pathway.