Search Results (563)

Studying intraspecific differentiation in closely related species is essential to clarify the phylogenetic relationships and mechanisms of early stage speciation, particularly in evolutionarily young lineages affected by human-driven population declines. The endangered saker falcon (Falco cherrug), with its ambiguous phylogenetic links to the gyrfalcon (F. rusticolus), exemplifies this scenario. This study presents a comprehensive genetic analysis of F. cherrug and F. rusticolus using mtDNA markers and microsatellite loci, focusing on the diversity of southern Siberian saker falcon populations. The genotyping results for these populations were correlated with phenotypic data obtained from long-term monitoring (1999–2021). Our findings provide novel insights into the current subspecific differentiation and the remnants of a nascent subspecies structure that existed before the recent demographic collapse. Furthermore, our results support the hypothesis of the gyrfalcon’s origin as a descendant species of the Asian saker falcon, i.e., an evolutionarily young lineage undergoing divergence. Our data contribute to the understanding of the Hierofalco evolutionary history, particularly through the analysis of heterogeneous mutation rates among mitochondrial haplogroups. This study underscores the critical importance of conservation efforts for wild endangered populations through long-term monitoring integrated with combined genetic approaches. Full article

Colorectal cancer (CRC) remains one of the leading causes of cancer-related morbidity and mortality worldwide. Despite advances in screening and therapeutic strategies, early detection and individualized treatment remain major challenges. In recent years, an expanding repertoire of biomarkers has emerged, spanning genomic, transcriptomic, proteomic, and metabolomic signatures. Epigenetic features, such as DNA methylation panels, as well as non-coding RNAs and the gut microbiome, hold potential not only for improving early diagnosis but also for refining prognosis and predicting therapeutic responses within the framework of precision oncology. This narrative review provides an updated, integrative overview of CRC diagnostic, prognostic, and predictive biomarkers. We distinguish established markers already in clinical practice, such as RAS and BRAF mutations, HER2 amplification, microsatellite instability/mismatch repair deficiency (MSI/dMMR), and widely investigated molecular alterations including TP53 mutations and immune-checkpoint-related markers, from novel biomarkers with growing translational potential. We also discuss the implementation challenges of these biomarkers in clinical practice, including issues related to validation, standardization, and cost-effectiveness, as well as the multi-modal approach for the development of composite diagnostic panels. Full article

The Balkan mountain ranges are major hotspots of genetic diversity and endemism, yet many species remain poorly studied. One such species is Alyssum bosniacum, a narrow endemic of the Central Dinaric Alps. To fill this gap, we examined 143 individuals from 15 populations across the species’ range using flow-cytometric ploidy determination, amplified fragment length polymorphisms (AFLPs), nuclear microsatellites, and chloroplast DNA sequences. Microsatellite data revealed two genetic clusters, showing moderate differentiation and relatively high diversity. AFLP profiles indicated shallow but geographically structured variation, while chloroplast haplotypes showed limited divergence and regional clustering. Our data suggest possible persistence in multiple microrefugia within the Central Dinaric Alps, although further evidence is needed to confirm this scenario. Despite range fragmentation, genetic variation within the population remains high, indicating evolutionary resilience and supporting the species’ long-term future population stability under current conditions. Full article

Domestic donkeys (Equus africanus asinus) are an important livestock genetic resource that is currently considered at risk. The number of donkey breeds worldwide is declining due to their loss of function as working animals in rural communities. Local breeds with small populations, which are threatened by genetic erosion and are at risk of extinction, require urgent action to characterize and preserve their genetic diversity. As microarrays containing thousands of single-nucleotide polymorphisms (SNPs) are not yet available for these species, traditional molecular markers such as microsatellites and mitochondrial DNA (mtDNA) remain valuable tools for genetic monitoring and management. This study uses different molecular markers to assess and manage genetic variability in endangered Sicilian donkey breeds. This information can support breeding plans and mating schemes, as well as in situ and ex situ conservation programs. The practical application of molecular information in the conservation strategies for these breeds is briefly discussed, and the proposed approach is considered transferable to other threatened breeds. Full article

Background and Objectives: BRCA1-interacting protein C-terminal helicase 1 (BRIP1) encodes a member of the RecQ DEAH helicase family and interacts with the BRCT repeats of breast cancer type 1 (BRCA1). It also participates in DNA damage repair and tumor suppression; thus, its mutations may be associated with an increased risk of several cancers, including fallopian tube and ovarian cancer. Recent research has explored whether BRIP1 dysregulation also contributes to the development and progression of other malignancies. This study investigated the clinical and prognostic value of BRIP1 in colorectal cancer (CRC). Materials and Methods: We first analyzed The Cancer Genome Atlas (TCGA) dataset to evaluate the prognostic significance of BRIP1 mRNA expression in CRC. BRIP1 expression was subsequently examined in tumor tissues from 60 CRC patients, and its associations with clinicopathological characteristics and clinical outcomes were assessed. Results: In rectal cancer, a higher BRIP1 expression was associated with younger age. In colon cancer, BRIP1 expression was correlated with gender, lymphatic invasion, carcinoembryonic antigen (CEA) level, pathological stage, M stage, N stage, microsatellite instability (MSI) status, and anatomical tumor location. Survival analysis showed that low BRIP1 expression was associated with poorer overall survival in both rectal and colon cancers significantly. In CRC patient tissues, lower BRIP1 expression was further related to elevated CEA levels and unfavorable clinical outcomes. Lower BRIP1 mRNA expression is significantly associated with aggressive clinicopathological features and poor prognosis in CRC. Conclusions: BRIP1 may serve as a promising biomarker for risk stratification and a potential therapeutic target in the management of CRC. Full article

Background/Objectives: Comprehensive genomic profiling (CGP) is a cornerstone of personalized oncology. However, large-scale, systematic data on the somatic mutation spectrum in Russian cancer patients are scarce. This study aimed to characterize the genomic landscape and assess the potential for matched therapy in a Russian cohort of patients with solid tumors. Methods: This retrospective study included 204 patients with various solid tumors. CGP was performed using the FoundationOne^®CDx (FFPE tissue) and FoundationOne^®Liquid CDx (cfDNA) platforms. The analysis assessed single-nucleotide variants, indels, copy number alterations, gene fusions, tumor mutational burden (TMB), microsatellite instability (MSI), and PD-L1 expression. Results: The most frequently mutated genes were TP53 (61.5%) and KRAS. The median TMB was 4.0 mut/Mb and was significantly lower in stage IV tumors. Significant co-occurrence was observed between KRAS and TP53 mutations, as well as between APC and KRAS mutations, which were particularly characteristic of colorectal cancer. KRAS mutations were associated with higher combined positive score (CPS) values in cases with lung cancer. Based on the CGP results, 44% of patients had findings that supported the use of an approved matched targeted therapy or immunotherapy for their tumor type. An additional 36% of patients had alterations indicating potential benefit from off-label targeted therapy. Conclusions: This study reveals the distinct genomic characteristics of solid tumors in a Russian cohort and confirms the high clinical utility of CGP for identifying actionable targets. Implementing CGP early in the diagnostic process is a necessary step towards realizing personalized treatment strategies for cancer patients. Full article

The genetic diversity and population structure of Tunisian Arabian horses were assessed using highly polymorphic microsatellite markers, which are critical for conservation and breeding programs. Despite the cultural and economic importance of Arabian horses in Tunisia, molecular data supporting their management remain limited. In this study, DNA from 130 horses was genotyped with 17 ISAG-FAO-recommended microsatellites to evaluate diversity within Eastern and Western Arabian lineages and their relationship to Thoroughbreds. Eastern Arabians showed an average of 5.176 alleles per locus, observed heterozygosity of 0.657, expected heterozygosity of 0.677, and a fixation index of 0.028, while Western Arabians displayed 5.941 alleles, heterozygosity values of 0.689 (Ho) and 0.688 (He), and a fixation index of −0.006. Genetic differentiation was low between Eastern and Western Arabians (0.011) but moderate between Eastern Arabians and Thoroughbreds (0.071), with high gene flow within Arabian subpopulations (0.950). Principal component analysis confirmed distinct subpopulations. These findings highlight high genetic diversity in Western Arabians and variable heterozygosity in Eastern Arabians, providing a molecular basis for targeted breeding strategies to preserve genetic traits, control inbreeding, and ensure the long-term sustainability of Tunisian Arabian horse populations. Full article

Lynch syndrome (LS), also known as hereditary nonpolyposis colorectal cancer (HNPCC), is a hereditary cancer syndrome significantly increasing the risk of colorectal cancer (CRC) and various extracolonic cancers, including endometrial, ovarian, and gastric cancers. LS results from germline pathogenic variants (GPVs) in DNA mismatch repair (MMR) genes, such as MLH1, MSH2, MSH6, and PMS2, leading to microsatellite instability (MSI). This review explores the multifaceted aspects of LS, covering clinical presentation, genetic underpinnings, and emerging therapeutic strategies. The discussion explores the importance of identifying at-risk individuals, facilitating personalized cancer surveillance and prevention strategies. Molecular insights into distinguishing between sporadic and LS-associated cancers are also examined, with a focus on somatic testing methods, including MSI and immunohistochemistry (IHC). The gynecological cancer risks, particularly those related to endometrial and ovarian malignancies, are addressed, underscoring the need for early detection and risk-reducing interventions. Recent advancements in the management of colorectal and other LS-related cancers are highlighted, with particular attention to the growing role of immunotherapy, including immune checkpoint inhibitors, and immunoprevention strategies. With ongoing advances in our understanding of LS, opportunities for earlier detection, more effective prevention, and innovative treatments continue to expand. This narrative review adopts a multidisciplinary approach to provide a comprehensive understanding of LS, from its genetic basis to current clinical and therapeutic practices, with the ultimate goal of improving patient outcomes and enhancing the quality of care. Full article

Background/Objectives: Colorectal cancer (CRC) is the second leading cause of cancer-related death in the US. The presence of deficient DNA mismatch repair and microsatellite instability (dMMR/MSI) in CRC is linked to responses to immune checkpoint inhibitors (ICIs). This study investigates the impact of metformin on the tumor microenvironment (TME) and clinical outcomes of patients with dMMR/MSI CRC treated with ICIs, aiming to better understand its potential role in enhancing ICI efficacy. Methods: Of 25,011 CRC patients in Caris database, 47 received both metformin and ICI therapy (Met-ICI group), and 475 patients received ICI therapy alone (ICI group). Samples underwent genomic or transcriptome sequencing at Caris Life Sciences. Immune cell fractions were estimated using quanTIseq. Univariate and multivariate survival analyses were conducted using the Cox proportional model. Results: The TME analysis of CRC patient samples revealed that TMB-High (≥10 mut/Mb) was more prevalent in the “ICI” group compared to the “Met-ICI” group (99.1% vs. 95.6%, p = 0.036). Mutation rates for most genes between the two groups were similar, but CIC gene mutations were more common in the “ICI” group than in the “Met-ICI” group (23.2% vs. 4.8%, p = 0.006). No significant differences were observed in the PD-L1 positivity rate or immune checkpoint gene expression (including IDO1, IFNG, TIM3, and CTLA4). M1 macrophages and neutrophils showed the highest infiltration among immune cells. However, the fractions of infiltrated immune cells were similar between the two cohorts. Univariate and multivariate analyses showed that there was no significant difference in patient survival between “ICI” and “Met-ICI” cohorts. Conclusions: In this retrospective analysis of real-world clinical outcomes, the concurrent use of metformin with ICIs in patients with dMMR/MSI CRC did not reveal an impact on clinical outcomes. Full article

Circulating tumor DNA (ctDNA) analysis has emerged as a powerful and minimally invasive approach for genomic profiling of metastatic castration-resistant prostate cancer (mCRPC), enabling real-time detection of tumor-derived mutations that guide therapy. Approximately 20% of mCRPC patients harbor alterations in homologous recombination repair (HRR) genes, most commonly BRCA1/2 and ATM, which are actionable with different poly-(ADP-ribose) polymerase inhibitors (PARPIs) used as monotherapy or in combination with androgen receptor signaling inhibitors (ARSIs). A smaller subset of patients with mismatch repair deficiency (MMRd) or microsatellite instability-high (MSI-high) tumors may benefit from immune checkpoint blockade with pembrolizumab. Different FDA-approved liquid biopsy assays detect these actionable alterations when tissue biopsies are unavailable or insufficient. This review summarizes current evidence on ctDNA-based genotyping in mCRPC, highlighting clinically actionable mutations, corresponding targeted therapies, and technical and analytical considerations for clinical implementation. By capturing DNA shed from multiple metastatic sites, ctDNA profiling provides a comprehensive view of tumor heterogeneity and enables serial monitoring of molecular evolution. Overall, ctDNA analysis represents a transformative advance in precision oncology, supporting personalized treatment selection and ongoing assessment of therapeutic response in mCRPC. Full article

Background: Cholangiocarcinoma (CCA) has the highest incidence in Northeastern Thailand, where patients generally present with late diagnosis and poor prognosis. Opisthorchis viverrini (OV) infection is the major cause of CCA, with oxidative stress driving DNA mutations and genetic instability. Microsatellite instability (MSI) is a predictive biomarker in several cancers. This study aimed to investigate MSI status and its association with clinicopathological features and survival of CCA patients. Methods: Tissue and serum samples were collected from 25 surgical CCA patients. MSI status and mismatch repair (MMR) proteins were evaluated using an MSI scanner and immunohistochemistry (IHC). Serum OV IgG was assessed by ELISA, while tumor-infiltrating lymphocytes (TILs) were evaluated by two pathologists. Associations of MSI with clinicopathological features, OV status, MMR, and survival were analyzed. Results: Among CCA patients, 66.7% were MSI-high and 33.3% were MSI-low. MSI-high significantly correlated with age < 57 years, intraductal growth pattern, OV positivity, and early-stage disease. Patients with MSI-high and high TILs showed markedly improved median survival compared to MSI-low with low TILs (94.0 vs. 16.8 and 3.0 months; HR = 6.82 and 14.10; p = 0.004 and 0.001). Incorporation of MSI and TILs remained an independent prognostic factor in multivariate analysis (p < 0.05). Conclusions: MSI-high is highly prevalent in OV-associated CCA and is associated with intraductal growth, OV infection, and early-stage disease. Combined MSI and TIL status may serve as an independent prognostic factor, warranting validation in larger cohorts. 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

Objectives: This study presents a comprehensive molecular investigation of Apis cerana cerana populations inhabiting the Lüliang Mountain region, aiming to evaluate their genetic diversity and population structure using polymorphic microsatellite and mitochondrial DNA (mtDNA) markers. Methods: A total of 23 microsatellite loci and three mtDNA fragments (COI–COII, COI, Cytb) were successfully amplified, of which 21 loci were polymorphic and used for subsequent genetic analyses. Measures of genetic variability, population differentiation, and molecular variance were computed to assess intra- and interpopulation diversity. Results: High levels of genetic variation were detected (mean PIC = 0.349), with observed heterozygosity (Ho = 0.827) exceeding expected heterozygosity (He = 0.608). Analysis of molecular variance (AMOVA) revealed that 95.28% of total genetic variation occurred within populations, while 4.72% was attributed to among-population differences. Mitochondrial analyses identified 20 polymorphic sites forming 19 haplotypes, with high haplotype (Hd = 0.884) and nucleotide diversity (π = 0.00157). Conclusions: These results indicate substantial gene flow and interpopulation connectivity among A. c. cerana populations in the Lüliang region. Collectively, the findings provide critical molecular evidence supporting the conservation and sustainable management of A. c. cerana genetic resources in this area. Full article

In colorectal carcinoma (CRC), 5-fluorouracil (5-FU) remains the cornerstone of adjuvant systemic therapy, with folic acid (FA) serving as an essential adjunct. Expression of genes related to the metabolism and action of 5-FU and FA can be influenced by patient- and tumor-specific biological factors. In this study, we explore differential gene expression profiles of 180 genes representing 14 different gene sets associated with different 5-FU and FA metabolism processes, at both gene and pathway levels across clinical and molecular subgroups. In 71 patients with CRC, paired tumors and normal colonic tissues were analyzed. In CRC tissue, several gene sets (including Cell Cycle Checkpoint, Oxidative Stress Response, and Signaling Pathway, etc.) were upregulated, while three gene sets (Apoptotic, Tumor Suppressor, and Endoplasmic Reticulum Stress) were downregulated. Kirsten rat sarcoma virus (KRAS), tumor protein p53 (TP53), and microsatellite instability (MSI) status impacted gene expression across molecular subgroups. At the individual gene level, among cell cycle genes, the BUB3 mitotic checkpoint protein (BUB3) was upregulated in MSI tumors compared to MSS, whereas SMAD family member 4 (SMAD4) was downregulated in MSS tumors compared to MSI. DNA fragmentation factor alpha (DFFA) was downregulated in MSI and upregulated in MSS. Notably, thymidylate synthetase (TYMS) was more upregulated in MSI tumors (1.65-fold; 95% CI: 1.27–2.13) compared to MSS (1.19-fold; 95% CI: 1.02–1.39). Dysregulation of these genes across these factors will broaden our understanding of 5-FU-based treatment in CRC. Furthermore, targeting dysregulated pathways could form the basis for improved precision therapies tailored to CRC subtypes. Full article

Background/Objectives: Metabolic syndrome (MS) impacts 25% of the adult population worldwide and elevates the risk of colorectal cancer by 40%. Microsatellite instability (MSI) resulting from impaired DNA mismatch repair serves as a critical biomarker for selecting patients for immunotherapy. Methods: This single-center pilot study examined the correlations between MS and MSI in 157 individuals with surgically treated colorectal cancer. Patients were categorized according to the International Diabetes Federation Metabolic Syndrome criteria. The MSI status was assessed using immunohistochemical investigation of mismatch repair proteins. The statistical analysis encompassed chi-square tests and the computation of odds ratios. Results: Patients with MS exhibited a substantially greater prevalence of MSI compared to controls (15.5% vs. 9.8%, p < 0.05) corresponding to a 1.63-fold increase in odds. The co-occurrence of MSI and hepatic steatosis displayed a strong association within the MS group (OR: 5.81), indicating a 2.6-fold increased prevalence relative to controls. Conclusions: This pilot investigation offers initial evidence associating MS with a heightened frequency of MSI in colorectal cancer. The strong association with hepatic steatosis indicates common metabolic-genomic pathways. The findings advocate for the incorporation of metabolic assessment into precision oncology for the selection of immunotherapy, necessitating multicenter validation studies. Full article