Genes

Background/Objectives: Formalin-fixed paraffin-embedded (FFPE) tissues are sometimes the only DNA source for forensic applications. The quantity and integrity of the DNA extracted from these samples depend on multiple factors. In this work, we analyzed, for the first time, whether Masson’s trichrome (MT) staining alters the results of genetic profiles obtained from DNA extracted from FFPE tissue sections. Methods: Three pairs of sections from the year 2024 and three pairs from the year 2001 were analyzed. Each pair consisted of serial sections, one stained with hematoxylin and eosin and the other with MT. DNA was extracted using the PrepFiler Express BTA™ Forensic DNA Extraction Kit and quantified by real-time PCR using the Quantifiler™ HP DNA Quantification Kit. DNA samples were processed for short tandem repeat (STR) profiling using the GlobalFiler™ PCR Amplification Kit. The amplified alleles were separated and analyzed using an ABI PRISM^® 3500 genetic analyzer. Results: All MT-stained samples showed deficiency in most or all of the parameters assessed: DNA yield, degradation index, number of alleles detected, random match probability value, and intensity of the electropherogram peaks. In fact, DNA could not even be quantified in the samples processed in 2001. Conclusions: These results could be due to the large number of acids used in MT staining, which cause chemical modification and hydrolysis of DNA, affecting the success of PCR-based methods used subsequently. In conclusion, DNA obtained from MT-stained FFPE tissue sections may be highly degraded and should therefore be used with great caution in forensic settings.

Non-syndromic Inherited Retinal Dystrophies (IRDs) are a set of degenerative retinal diseases that vary clinically and genetically, including Leber congenital amaurosis (LCA) and retinitis pigmentosa (RP). IRDs are a significant cause of vision loss in young adults globally. To date, more than 280 genes have been associated with IRD pathogenesis. This study aims to investigate the genetic basis of non-syndromic IRD in the Qatari population and to assess the diagnostic yield of various genetic tests through a retrospective cohort study. Our study identified 49 eligible patients with IRD, 61.2% of whom were Qatari. Rod-dominated phenotypes accounted for 51% of the hereditary retinal diseases in this cohort. Whole-exome sequencing with mitochondrial genome testing (WES Plus) was the most frequently utilized genetic test. A total of 55 variants were identified across 32 IRD-associated genes. Of the 49 cases, 34 (69.4%) were initially classified as solved, and an additional five were likely to be solved based on familial segregation analysis. Variants in the ABCA4 gene were the most commonly observed, present in eight patients, with the c.5882G>A variant being the most recurrent, identified in three of these cases. Specific genes exhibited recurrent variations, including pan-ethnic variants that are common across multiple populations. These variants merit prioritization in testing due to their global prevalence. WES is recommended as a first-tier test for non-syndromic IRD cases, as it accelerates diagnosis, facilitates earlier interventions, and provides a comprehensive genetic picture by incorporating information from family members. Moreover, our study highlighted the significance of performing family segregation analyses in identifying possible causative variants. This is the first genetic study of IRD in Qatar, laying the groundwork for further research on the epidemiology and genetics of non-syndromic IRD in this understudied region.

Background: Exercise is a promising non-pharmacological intervention for cocaine addiction but molecular mechanisms of exercise-related genes in addiction remain unclear. This study aimed to identify exercise-related signature genes for cocaine addiction and to assess the potential causal relationship between exercise and cocaine addiction using two-sample Mendelian randomization (MR) analysis. Methods: Midbrain transcriptomic data were analyzed for differentially expressed genes (DEGs) and intersected with exercise-related genes. Functional enrichment, protein-protein interaction (PPI) and immune infiltration analyses explored their roles while signature genes were screened via LASSO/Random Forest and validated by ROC curves. GSEA explored pathways and MR confirmed exercise’s causal effect. Results: A total of 244 DEGs were identified,including 27 exercise-related, and six signature genes (CALM3, CCL2, CD44, CLIC1, JUN, VCAM1) showed AUC values between 0.714 and 0.868 in distinguishing cocaine-addicted individuals from controls. Functional analyses revealed enrichment in immune-inflammatory pathways, metabolic processes and neuro-immune interactions and immune infiltration analysis showed cocaine addicts had elevated pro-inflammatory cells, reduced regulatory cells and signature genes correlated with immune dysregulations. MR analysis suggested a statistically significant protective association between genetically proxied higher levels of exercise and cocaine addiction risk (p < 0.05). Conclusions: These six genes may be potential biomarkers and therapeutic targets, and exercise may protect against cocaine addiction by regulating immune-inflammatory responses, metabolic pathways and neuroplasticity, although further validation in larger, independent cohorts and experimental models is required.