Search Results (652)

Background: Colorectal cancer (CRC) is the third most diagnosed malignancy and the second leading cause of cancer-related mortality worldwide. Recent therapeutic advancements have significantly improved clinical management, underscoring the importance of routine molecular profiling to guide personalised treatment strategies. This study aims to evaluate the prognostic impact of main molecular alterations—including allele frequency (AF) of RAS mutations—on survival outcomes in a real-world hospital-based cohort of patients with metastatic CRC. Methods: A total of 208 consecutive patients with a histologically confirmed diagnosis of CRC and complete clinical, molecular, and survival data were retrospectively analysed. Somatic mutations in KRAS, NRAS, BRAF, and the occurrence of microsatellite instability (MSI) were assessed using pyrosequencing and real-time PCR assays, respectively, on formalin-fixed, paraffin-embedded tumour samples. Associations between mutational status, clinicopathological parameters, and overall survival (OS) were evaluated. Results: Overall, 138 patients (66.3%) harboured at least one somatic mutation: 115 (55.3%) in KRAS, 8 (3.8%) in NRAS, and 15 (7.2%) in BRAF. MSI was detected in 17/208 (8.2%) patients. A statistically significant improvement in OS was observed in patients lacking mutations in any of the three genes—referred to as wild-type (WT) patients—with BRAF mutated cases showing the worst survival (p = 0.041). Increasing age at the time of first-line therapy for advanced disease stage was associated with a statistically significant increase in the hazard of death (p = 0.031). Conclusions: In the advanced disease stage, RAS/BRAF wild-type colorectal cancers were significantly associated with a survival advantage. Full article

Background: Lymphocyte-activation gene 3 (LAG3) and cytotoxic T-lymphocyte-associated protein 4 (CTLA4) are immune checkpoint receptors and inhibitory regulators of T-cells. Methods: Here, we analyzed the prevalence and potential impact of the LAG3 gene variant rs870849 and the CTLA4 gene variant rs231775 in AML patients eligible for autologous stem cell transplantation. Results: While CTLA4 rs231775 was prevalent at reduced minor allele frequencies (MAF 0.33), LAG3 rs870849 was prevalent at elevated minor allele frequencies (MAF 0.58) in AML patients, compared to the allele frequencies in the European population (MAF 0.37 and MAF 0.39). The gene risk analysis indicated a dose-dependent risk of AML disease associated with LAG3 rs870849, but no risk associated with CTLA4 rs231775. Baseline blood count profiles differed across LAG3 genotypes, suggesting a link between LAG3 rs870849 and disease-associated levels of anemia, thrombocytopenia and peripheral blast percentage. Conslusions: The germline LAG3 variant rs870849 may be associated with AML disease risk and specific hematological disease features. Full article

This study used three complementary datasets to investigate the relationship between human Campylobacter infections in Estonia and potential sources. A targeted dataset of 15 C. jejuni genomes with overlapping sequence types from human cases and broiler chicken meat was analysed using genotyping and in silico antimicrobial resistance profiling, alongside 20 human isolates for source attribution. Additionally, 12,111 isolates were analysed to provide population-level context. The core genome multilocus sequence typing showed a high similarity (less than three allelic differences) between the human and broiler isolates of ST122, ST464, and ST7355, indicating poultry as a likely source, whereas ST9882 was more divergent (13–18 allelic differences). The resistance profiles were consistent within ST122, ST464, and ST7355, and all were resistant to ciprofloxacin, nalidixic acid, ampicillin, and tetracycline, while ST9882 additionally exhibited aminoglycoside (streptomycin) resistance. The source attribution linked 77.8% of the human cases to chicken and 22.2% to cattle. A novel genotype, ST11001, was identified in humans and attributed to cattle source, while C. coli isolates were linked to birds and sheep. Poultry dominated the larger dataset (87.3%). Gastroenteritis was the predominant clinical presentation (98.5%), whereas ST22 and ST122 were associated with Guillain–Barré syndrome. These findings support poultry as a major reservoir of human Campylobacter infections and highlight the need for coordinated cross-border surveillance. Full article

Lactococcosis has emerged as an economically and ecologically significant disease in aquatic animals worldwide. This study employed multilocus sequence typing (MLST) to investigate the genetic diversity of Lactococcus spp. strains from Brazilian fish species and evaluate their phylogenetic relationships with global isolates to elucidate potential epidemiological connections involving multiple host species and distinct geographic regions. A total of 55 isolates from different laboratories had their DNA extracted, followed by the amplification and sequencing of the internal fragments of seven housekeeping genes (als, atpA, tuf, gapC, gyrB, rpoC and galP). Sequence types (STs) and clonal complexes (CCs) were defined. An unrooted neighbor-joining phylogenetic tree was generated using allele profiles from this study and those previously reported from other aquatic animal species. The isolates comprised 29 STs (11 previously reported, 18 novel ones), which were grouped into species-specific CCs: CC5 (L. formosensis); CC4, CC17, CC62 (L. garvieae); CC24, CC29, CC97 (L. petauri). Considerable genetic divergence was observed, with L. formosensis and L. garvieae forming heterogeneous populations, while L. petauri was more homogeneous. These findings describe the MLST structure of the sampled isolates and should be interpreted as hypothesis-generating rather than population-level estimates of genotype prevalence. Phylogenetics confirmed groupings within the CCs and revealed additional phylogenetic clustering patterns. In conclusion, the Brazilian Lactococcus spp. strains analyzed in this study constitute a genetically diverse population based on their STs. MLST and phylogenetic analysis demonstrated genetic relatedness between the L. garvieae and L. formosensis isolates from this study and those from other aquatic animal species. In contrast, all the STs identified for L. petauri in this study were unrelated to the MLST lineages responsible for outbreaks in Brazilian Nile tilapia (Oreochromis niloticus) and North American rainbow trout (Oncorhynchus mykiss). This suggests that piscine L. petauri populations in the Americas evolved from distinct ancestral origins. Full article

In the scenario of ongoing climate changes, the selection of plant genotypes with high salt tolerance is emerging as the most sustainable strategy to safeguard crop yield and quality and make productive use of salinized soils. Glassworts are annual and perennial halophytes found in inner and coastal wastelands, indistinctly consumed as high-nutritional green vegetables. Traditional taxonomic classification based on morphological traits can be very challenging in glasswort, due to phenotypic plasticity, reduced plant morphology, and inbreeding. In this work, we used DNA-based molecular tools to overcome such constraints and assess inter-generic and inter-specific genetic diversity in a collection of ecotypes from different Apulian areas. A fast and reliable Allele-Specific PCR assay was optimized to enable molecular detection of annual and perennial genera. Species-level classification was obtained through a similarity- and phylogeny-based approach relying on matK and rbcL DNA barcoding. Combined DNA tools identified perennial samples as Sarcocornia fruticosa and Arthrocaulon macrostachyum, along with annual Salicornia europaea, and phylogenetic trees unveiled genetic distances between glassworts, which clustered according to life cycle. The relationship between genotypes and nutritional profiles was finally investigated, suggesting that environmental factors may play a predominant role over taxonomic relatedness in shaping interspecific differences in nutrient composition of the analyzed samples. Full article

Indigenous sheep breeds represent valuable reservoirs of genetic diversity shaped by long-term adaptation to local environments and management systems. Greek autochthonous sheep breeds remain underrepresented in genomic and functional studies. The objective of this study was to characterize and compare coding sequence variation in three indigenous Greek sheep breeds—Lesvos (LES), Serres (SER), and Thrace (THR)—and to identify shared and breed-associated functional patterns. The study was designed using a two-stage approach, comprising a discovery (exploratory) phase and a validation phase. In the discovery phase, whole genome sequencing data (one animal per breed; total n = 3; mean sequencing depth ~36.9×) were analyzed to identify protein-altering exonic variants, focusing on missense single-nucleotide polymorphisms (SNPs) and exonic insertions/deletions (indels). Variants were examined at breed-specific and comparative levels, followed by functional enrichment analyses using Gene Ontology (GO) and KEGG pathways. Normalized variant density metrics identified genes with elevated polymorphism levels. In the validation phase, a subset of prioritized missense SNPs was genotyped in an independent cohort of 54 animals (18 per breed) using MassARRAY genotyping. Genes harboring prioritized missense SNPs showed a conserved enrichment profile across breeds, dominated by genome maintenance, DNA repair, cytoskeletal organization, and core regulatory functions. Distinct breed-associated patterns were also observed. LES showed enrichment in metabolic, biosynthetic, and sensory-related processes, SER in regulatory and signaling functions, and THR in cytoskeletal, extracellular matrix, and organelle-associated pathways. Polymorphism density analyses highlighted highly variable genes across breeds, including olfactory receptor (OR) gene families, keratin-associated protein genes (KRTAPs), and loci involved in immune and regulatory functions (e.g., PRKDC, CDH15). The validation phase confirmed the expected allele frequency patterns for most prioritized SNPs, supporting the robustness of the approach. This study identifies functionally relevant coding variation across Greek indigenous sheep breeds, revealing conserved genomic patterns and breed-associated signatures linked to metabolic, structural, and regulatory processes. Full article

Psoriasis is a chronic immune-mediated disease driven by genetic susceptibility and environmental factors, including microbial exposure. While HLA-C-linked variants represent the strongest genetic risk factors, their relationship with the cutaneous microbiome remains incompletely understood. This study aimed to investigate host–microbiome interactions in psoriasis through integrative multi-omics analysis. Skin microbiome profiling using 16S rRNA sequencing and targeted genotyping of psoriasis-associated single-nucleotide polymorphisms (SNPs) was performed in lesional and non-lesional skin from patients with plaque psoriasis and in healthy controls. Integrated analysis was conducted using supervised multivariate modeling (DIABLO) to identify coordinated genetic and microbial features associated with disease status. Combined genetic and microbial signatures differentiated lesional, non-lesional, and healthy skin. Variants within the HLA-C susceptibility region, including rs12191877, rs10484554, and rs4406273, showed contributions to group separation and demonstrated positive associations with Peptostreptococcus anaerobius. Associations involving ERAP1 variants linked antigen-processing pathways with inflammation-associated microbial taxa in lesional skin. Importantly, genotype–microbiome correlations were also detected in clinically non-lesional skin, where an increased psoriasis risk allele dosage co-varied with a higher relative abundance of P. anaerobius and Aerococcus urinae. In contrast, commensal-associated taxa were enriched in healthy controls and formed genotype-linked clusters only in non-lesional skin. These findings suggest that psoriasis is characterized by coordinated host genetic and microbial interaction patterns centered on antigen presentation pathways. The presence of a genotype–microbiome coupling in non-lesional skin may indicate that genetically determined immune configurations could shape microbial community structure prior to visible lesion development. Rather than reflecting uniform dysbiosis, psoriasis may represent a dynamic host–microbe ecosystem in which genetic susceptibility influences microbial persistence and inflammatory readiness. Full article

The use of fresh and dried figs has increased markedly in Tunisia in recent years, leading to a rise in public subsidies to support the further development of fig cultivation, especially in well-adapted production areas and with the adoption of innovative agronomic practices. This study aimed to carry out a comprehensive morphological and genetic characterization of fig germplasm from the Kesra region in north-western Tunisia, which is widely recognized for its long-standing tradition of fig production, in particular of the ‘Zidi’ cultivar. Field surveys and prospections enabled the identification of 26 distinct local fig cultivars, which were morphologically characterized and genotyped using 12 microsatellite (SSR) markers. All cultivars showed a specific allelic profile, including ‘Zidi’. The results provided valuable information for the conservation and management of Tunisian fig genetic resources. Moreover, the data will support the valorization of local fig production in the area through the establishment of the Protected Designation of Origin (PDO) ‘Fig of Kesra’, thereby contributing to the sustainable development of traditional orchards and the preservation of local agrobiodiversity. Full article

Objective: Current knowledge surrounding the diagnosis and mechanisms that result in immune checkpoint inhibitor-associated diabetes (ICI-DM) remain to be fully defined. We present clinical vignettes of patients that have presented to our hospital to illustrate the heterogenous clinical profiles that patients with ICI-DM can experience. We also provide an update on ICI-DM, focusing on current and future perspectives and emerging therapies. Methods: We performed a retrospective review of the electronic records of five ICI-DM patients who presented to St. Vincent’s Hospital Melbourne between 2020 and 2024, with patients identified from the hospital endocrinology and oncology databases. We also performed a literature review via a PubMed search using the keywords “checkpoint inhibitors” and “diabetes” between the years 2015 and 2025 to allow us to collate a descriptive review on ICI-DM. Results: Our cases show some heterogeneity in presentation, with biochemical evidence of diabetic ketoacidosis (DKA) in 4/5 patients, presentation 18–253 days (median 47 days) from ICI commencement, HbA1c 59–78 mmol/mol (median 66 mmol/mol), and c-peptide 0.06–0.77 pmol/mL (median 0.09 pmol/mL). Islet autoantibodies were present in 4/5 cases and high-risk HLA alleles identified in 1/2 tested patients. The findings from our descriptive review support a similar heterogeneity in ICI-DM presentations. Inconsistent diagnostic criteria for ICI-DM were noted with low c-peptide being the most common biochemical presentation. Pancreatic volume is emerging as a useful predictive marker of ICI-DM development. We found no reports of the reversal of ICI-DM with immunosuppression in humans, although recent preclinical studies suggest that this approach is feasible. Conclusions: Diagnostic criteria should include new-onset hyperglycaemia with low paired c-peptide, and may be supported with T1DM-associated autoantibodies and evidence of pancreatic atrophy on imaging. Further research is needed in the realm of predicting ICI-DM and considering the role of immunosuppression as a treatment modality. Full article

Acute myeloid leukemia (AML) is a heterogeneous malignancy, with clonal complexity and somatic mutations critically influencing prognosis and treatment. While global genomic profiling efforts have revolutionized AML classification and risk stratification, the molecular landscape in Pakistani patients remains underexplored. Our aim is to perform targeted next-generation sequencing (NGS) for somatic mutational profiling of newly diagnosed AML patients in Pakistan. This prospective study was conducted at the Armed Forces Institute of Pathology, Pakistan, from January 2021 to January 2026. Among 104 patients, 204 somatic variants were identified (mean: 1.96 variants/patient), predominantly single-nucleotide variants (49.5%). Missense mutations (38.2%) were most common, with enriched transitions (Ti/Tv: 1.27:1). Frequently mutated genes included TP53 (22.1%), KIT (9.8%), CEBPA (8.8%), and NRAS (5.9%). Cell-signaling genes (30.4%) and tumor suppressor genes (27.0%) were the most affected functional groups. Co-mutation analysis showed clustering led by DNMT3A–IDH1 co-occurrence (ρ ≈ 0.43). DNA-methylation alterations frequently co-occurred with tumor suppressors (OR ≈ 4.6, p = 0.007), transcription factors (OR ≈ 3.9, p = 0.023), and NPM1 (ρ = 0.32). This study provides the first comprehensive genomic map of Pakistani AML patients, revealing unique mutational signatures. The findings lay the groundwork for population-specific precision oncology in low- and middle-income countries. Full article

Background: High-grade serous ovarian carcinoma (HG-SOC) remains the most lethal gynecological malignancy, largely due to intrinsic or acquired resistance to platinum-based chemotherapy. Although large-scale sequencing studies have delineated the genomic landscape of HG-SOC, clinically actionable biomarkers predictive of platinum response and outcome are still lacking. This study aimed to identify genomic alterations associated with platinum sensitivity, resistance, or refractoriness, and to assess their prognostic relevance. Methods: Tumor DNA from 24 HG-SOC patients with optimal cytoreductive resection, classified as platinum-sensitive (n = 9), platinum-resistant (n = 8), or platinum-refractory (n = 7) underwent targeted next-generation sequencing of 409 cancer-associated genes. Somatic variants were filtered and classified for oncogenicity using established criteria incorporating predicted functional impact, REVEL scores, and population allele frequencies. Associations between mutational profiles, platinum response, and overall survival (OS) were evaluated using Kaplan–Meier and Cox regression analyses. Key findings were validated in the TCGA ovarian serous carcinoma (TCGA-OV) dataset using survival analyses. Results: A total of 1367 protein-altering somatic variants across 301 genes were identified. While TP53 mutations were ubiquitous, platinum-resistant and platinum-refractory tumors showed enrichment of pathogenic alterations affecting DNA repair, transcriptional regulation, epigenetic modification, and oncogenic signaling, including FANCA, ATF1, MAF, NCOA2, PIK3CA, and TET1. Mutations in these genes were associated with reduced overall survival in exploratory analyses (median 2.5–9 months vs. 27.5–45 months). Multivariate analysis identified FANCA and ATF1 as potential independent predictors in exploratory modeling. In the TCGA-OV cohort, patients harboring pathogenic variants in a multi-gene panel derived from this study (excluding BRCA1/2) exhibited significantly worse survival compared with both BRCA1/2-mutated cases and the overall cohort. Conclusions: This exploratory study identifies a set of genomic alterations converging on transcriptional and epigenetic regulation, DNA repair, and oncogenic signaling that are associated with platinum resistance and adverse prognosis in HG-SOC. Independent validation in TCGA supports the potential clinical relevance of this mutational signature. These findings warrant further validation in larger prospective cohorts and functional studies to clarify their role as biomarkers of aggressive disease and therapeutic vulnerability. Full article

GDSL esterase/lipase (GELP) proteins constitute an evolutionarily conserved yet functionally diversified hydrolase family in land plants. They participate in cuticle and secondary cell wall biosynthesis, seed lipid remobilization, reproductive development, and hormone-mediated responses to biotic and abiotic stresses. Despite extensive genome-wide and comparative genomic studies that have categorized large GELPs across numerous crops and model species, only a fraction of members have been functionally characterized in plants, and their catalytic mechanisms and regulatory architectures remain poorly understood. Recent population genomics and cross-species orthogroup analyses in 46 angiosperms have uncovered substantial natural variation within GELP coding sequences and regulatory regions, providing a powerful framework to link allelic diversity to evolutionary trajectories and physiological functions. This review synthesizes current knowledge on GELP evolution, biochemical properties, and roles in development and stress adaptation, and critically evaluates how these insights can be translated into biotechnology and molecular breeding strategies. It highlights emerging resources and concepts from orthogroup-based classification and multi-species datasets that enable systematic discovery of GELP alleles affecting agronomic traits. It further outlines research exploiting GELPs in crop improvement, emphasizing the integration of reverse and forward genetics with multi-omics profiling, biochemical and structural characterization, and gene regulatory network reconstruction. Systematic assessment of the phenotypic impacts of single and combinatorial GELP perturbations on yield, quality, and stress resilience is proposed as a key step toward translating basic insights into breeding and engineering strategies. Full article

Staphylococcus pseudintermedius is an opportunistic bacterium previously associated with dogs but has recently been found in human infections, raising zoonotic concerns. Genomic characterization of human S. pseudintermedius isolates can provide preliminary information on antibiotic resistance, pathogenicity, and genomic features relevant to host range. Two S. pseudintermedius isolates (hereafter referred to as S. pseudintermedius EGH1 and S. pseudintermedius EGH2) from human clinical samples in Egypt were sequenced using the Illumina NovaSeq X Plus platform. To assess genetic relatedness to human S. pseudintermedius isolates worldwide, multilocus sequence typing (MLST), pangenome analysis, and antimicrobial resistance gene profiling were performed. The sequencing produced a total of 9,499,989 reads for S. pseudintermedius EGH1 and 9,567,531 reads for S. pseudintermedius EGH2. Sequences were assembled with Geneious Prime^® 2025 and annotated using NCBI Prokaryotic Genome Annotation Pipeline v6.10. Pangenome analysis identified 9574 genes, comprising 1681 core genes (17.56%), 180 soft-core genes (1.88%), 837 shell genes (8.74%), and 6876 cloud genes (71.82%). MLST was conducted on human S. pseudintermedius genome assemblies using MLST v2.23.0. The analysis revealed both isolates as novel sequence types: S. pseudintermedius EGH1 was assigned ST-3037 with a new allele (purA-107), and S. pseudintermedius EGH2 was assigned ST-2874. Clonal relationships among S. pseudintermedius isolates were evaluated using the eBURST algorithm. This study presents the first next-generation genome sequencing and comparative genomic analysis of S. pseudintermedius isolates from humans in Egypt. Future studies integrating genomic, epidemiological, and phenotypic data are required. Full article

Pharmaceutical care provides the conceptual foundation for integrating pharmacogenetics into everyday pharmacy practice. Defined by Hepler and Strand as “the responsible provision of drug therapy for the purpose of achieving specific outcomes that improve a patient’s quality of life”, pharmaceutical care emphasizes a patient-centered approach in which the pharmacist collaborates with the patient, physician, and other healthcare professionals to design, implement, and monitor individualized therapeutic plans. In this context, pharmacogenetics can be regarded as an extension of pharmaceutical care: while the traditional model relies on monitoring patient outcomes and adherence, PGx adds a genetic dimension that allows treatment to be optimized from the very beginning. The pharmacist’s role therefore evolves from not only ensuring safe and effective use of medicines, but also interpreting genetic test results, supporting adherence to genetically guided therapy, and educating patients about the implications of their personal genetic profile. The introduction of pharmacogenetics testing as one of the potential services offered by community pharmacies is a promising proposition that may revolutionize the approach to drug therapy. Pharmacogenetics, a subset of pharmacogenomics, focuses on the study of DNA sequence variations that influence response to drugs. Thanks to advances in the field of genomics, it has become possible to study the genetic basis of variability in drug response. The identification of alleles responsible for the rapid or slow metabolism of xenobiotics has ushered in a new era in pharmacology. The aim of this interdisciplinary field, combining genetics and pharmacology, is to adapt treatment to a specific patient based on the analysis of their genome and gene polymorphism. Throughout the world, pharmacogenetics is gaining importance as a tool for personalizing medicine. In countries such as the United States, Canada, and the United Kingdom, programs integrating pharmacogenetics with healthcare are being developed. Clinical trials and the implementation of genetic tests into medical practice allow for better matching of medications and reducing the risk of side effects. Pharmacists will play a key role in integrating pharmacogenetics into healthcare. As specialists in the field of pharmacotherapy, they will support physicians in interpreting the results of genetic tests and adapting drug therapy to the individual needs of the patient. Additionally, pharmacists can educate patients and healthcare professionals about the benefits of pharmacogenetics and monitor the effects and safety of medications. Their involvement in the process of personalization of treatment may contribute to improving the effectiveness and safety of pharmacological therapies. Full article

Background/Objectives: Operational DNA databases traditionally rely on static locus-count thresholds to determine search eligibility and report matches. While computationally straightforward, these rigid criteria routinely discard high-value investigative leads from degraded forensic profiles while simultaneously permitting adventitious matches when common alleles are involved. To overcome the limitations of static rules, this study introduces an automated framework for dynamic likelihood ratio (LR) thresholding. Methods: Utilizing a Fast Fourier Transform (FFT) algorithm, the system calculates the Probability Mass Function (PMF) for any specific combination of shared loci in real-time, natively incorporating the Balding–Nichols model to account for population substructure. Instead of applying an arbitrary locus count or fixed LR cutoff, the framework defines admissibility based on a user-defined maximum upper bound of acceptable false positives at a specified confidence (probability) level (e.g., 95%). Results: This empowers database custodians to precisely predict and adapt their search criteria to match an acceptable administrative workload, dynamically adjusting the required LR threshold to the exact size of the searched database. This approach was validated through massive-scale empirical simulations across five reference population groups. Receiver Operating Characteristic (ROC) and Poisson distribution analyses reveal that static thresholds inevitably collapse under the multiplicity effect of large-scale comparisons; for instance, a static locus rule that maintains safety within a small DNA database yields an unmanageable false positive risk when scaled to larger DNA databases or international networks like the Prüm DNA Exchange. Conclusions: By explicitly coupling the decision threshold to the database size and the genetic rarity of the evidence, this dynamic framework provides a mathematically rigorous and scalable solution. Most notably, it identifies rare, low-locus matches that static rules typically discard, offering a method to maintain a predefined expected false positive rate. Full article