Search Results (615)

Microsatellite instability-high (MSI-H) and deficient mismatch repair (dMMR) define a molecular subtype of colorectal cancer (CRC) and predict benefit from immune checkpoint inhibition. Clinically, MSI/MMR assessment may yield discordant results across assays, anatomic sites, or time points. A challenging scenario occurs when tissue analysis identifies microsatellite-stable (MSS) or mismatch repair-proficient (pMMR) CRC, whereas circulating tumor DNA (ctDNA) analysis indicates MSI-H. This review evaluates evidence for MSI/MMR heterogeneity and subclonality in CRC. We reviewed literature on spatial, temporal and subclonal MSI/MMR heterogeneity across human cancers, focusing on CRC. Explanations for tissue–plasma and tissue–tissue discordance, including assay limitations, sampling bias, lesions misattribution, biological evolution, and treatment-related selection, were assessed. Although discordance more commonly reflects assay limitations, sampling bias, or profiling of different lesions, increasing evidence supports genuine biological heterogeneity. Distinct tumor regions may show retained MMR protein expression in one area and regional loss with MSI in another. Noncanonical MMR defects, epigenetic heterogeneity, post-treatment evolution, adaptive mutator-state, and immune selection may also generate dynamic or subclonal instability. Therapeutic relevance may depend not simply on MSI detection, but on whether the unstable clone is sufficiently dominant to generate broadly shared neoantigens across the disease burden. MSI/MMR discordance requires careful interpretation and should not automatically be considered as true biological heterogeneity. Nevertheless, genuine subclonality occurs in CRC and other cancers and may affect responsiveness to immune checkpoint inhibition. Integrated tissue, plasma, spatial and longitudinal analyses may improve treatment decisions and biomarker development. Full article

Ulleungdo Island harbors several endemic plant lineages commonly interpreted as products of anagenetic speciation following long-distance colonization. Yet plastome phylogenies represent a single organellar genealogy and may conflict with nuclear genomic structure, morphology, or taxonomic boundaries. This critical mini-review evaluates whether plastid-based hypotheses for the origin and diversification of Ulleungdo endemics are supported by independent molecular and phenotypic evidence. We synthesize findings from comparative plastomics, chloroplast haplotype and network analyses, nuclear microsatellites, nrDNA sequencing, genome-wide multiplexed inter-simple sequence repeat genotyping by sequencing (MIG-seq) single-nucleotide polymorphisms (SNP), cytogenetics, morphology, and multicompartment phylogenomics. The evidence reveals heterogeneous evolutionary outcomes. Prunus takesimensis and Phedimus takesimensis are broadly consistent with probable single-origin scenarios, although confidence is constrained by progenitor sampling and marker resolution. Rubus takesimensis exhibits chloroplast non-monophyly and elevated haplotype diversity consistent with multiple maternal origins, whereas Acer takesimense shows signatures of historical drift and loss of rare nuclear alleles. Morphological, chromosomal, plastid, and nuclear–ribosomal evidence strongly support Allium ulleungense, while the delimitation of Viola ulleungdoensis remains unresolved. Plastid–nuclear incongruence in Hepatica maxima and Fagus multinervis further indicates that introgression, hybridization, incomplete lineage sorting, and restricted taxon sampling can complicate evolutionary inference. This comparative framework distinguishes species histories from provisional interpretations based on limited accessions or uniparentally inherited markers. The novelty of this review lies in its cross-taxon assessment of plastome–nuclear–morphological congruence rather than a descriptive plastome inventory. Ulleungdo lineages interpreted as products of anagenetic speciation do not exhibit a uniform genomic signature and that robust taxonomic, evolutionary, and conservation inference requires population-level integration of independently inherited genomic compartments with standardized morphological and reproductive data. Full article

In post-mortem genetic identification, teeth represent one of the most reliable sources of nuclear DNA when other biological samples are unavailable, owing to their ability to protect genetic material from autolysis, microbial degradation, and environmental insults. The present study describes a forensic veterinary case report involving a Staffordshire Bull Terrier litter in which the appearance of blue-coated offspring from a phenotypically black sire and a blue dam prompted parentage verification. The sire died before formal ante-mortem sampling could be carried out. In accordance with Regulation (EC) No. 1069/2009, Article 15, the carcass was interred in the owner’s garden. Before burial, two teeth were collected as the sole biological material available for identification by the official veterinarian, ensuring an unambiguous chain of custody from death certification to laboratory analysis. DNA extraction was performed using two independent protocols: Method A, a silica-membrane-based purification (QIAamp DNA Kit, Qiagen), applied to dental pulp, and Method B, a decalcification-based workflow (T-Bone Ex Kit) followed by DNA extraction using EZ2 Connect Instruments (Qiagen). Quantification of the DNA samples obtained were done by fluorometry. Short Tandem Repeat (STR) genotyping was performed using the Canine Genotypes™ Panel 1.1 by Applied Biosystems (Thermo Fisher Scientific, Waltham, MA, USA) targeting the 18 autosomal ISAG-recommended microsatellite loci. Parentage assignments were carried out against reference STR profiles obtained from peripheral blood of the dam and offspring. The two methods, considering a different biological matrix and different operating conditions, allowed us to obtain the STR profile, but Method B showed quality electropherograms, improving the confidence and interpretation of all the markers analyzed. The differences observed between the two approaches may reflect a combination of factors, including the different dental matrices analysed, the quantity and quality of the starting material, tooth identity and tissue preservation, and differences inherent to the extraction procedures themselves; therefore, in this case, the more complete and clearer STR profile obtained with Method B should be considered a case-specific observation rather than evidence of a direct effect of the extraction method. Overall, regardless of the DNA extraction method used, the results did not exclude the biological paternity of the blue-mantled offspring. Furthermore, this case report provides practical methodological guidance for DNA recovery from canine teeth and supports their use as a reliable source of post-mortem DNA for STR-based parentage testing. Full article

Colorectal cancer (CRC) remains one of the most frequently diagnosed malignancies worldwide and a leading indication for major abdominal surgery, with a rising incidence among younger adults. Because CRC resection is a physiologically demanding procedure performed in a frequently comorbid, often anemic and malnourished population, the preoperative period represents a decisive window in which laboratory and diagnostic testing shapes staging, risk stratification, and optimization. This narrative review is deliberately confined to the preoperative window—from histological diagnosis to the day of elective, curative-intent colon or rectal resection—and synthesizes evidence retrieved from PubMed/MEDLINE, Scopus, and ScienceDirect together with current society guidelines. It is organized around four themes: (i) the core laboratory workup, including the complete blood count and preoperative anemia, iron studies, metabolic and hepatic panels, coagulation testing, and carcinoembryonic antigen (CEA); (ii) the diagnostic and staging workup, encompassing complete colonic evaluation, contrast-enhanced computed tomography, pelvic magnetic resonance imaging for rectal cancer, and the selective role of positron emission tomography; (iii) risk stratification and preoperative optimization, spanning patient blood management, nutritional assessment and albumin, computed-tomography-defined low skeletal muscle mass, frailty, functional capacity, prehabilitation, and glycemic control; and (iv) molecular characterization, distinguishing mismatch-repair/microsatellite-instability (MMR/MSI) testing—an established, widely recommended component of CRC evaluation—from genuinely emerging biomarkers such as circulating tumor DNA (ctDNA) and systemic inflammatory and prognostic nutritional indices. Differences between colon and rectal cancer, elective and emergency presentation, and upfront versus post-neoadjuvant surgery are signposted throughout. We further integrate these elements within contemporary guideline and Enhanced Recovery After Surgery (ERAS) frameworks, including the 2025 ERAS Society recommendations for elective colorectal surgery, and distill them into a practical, evidence-based preoperative checklist specifying thresholds, timing, interventions, and strength of supporting evidence. We emphasize that the prognostic power of postoperative ctDNA does not yet translate into ctDNA-guided treatment decisions outside clinical trials. The central message is that preoperative testing in CRC should be purposeful and stage- and risk-adapted rather than reflexive: each investigation should refine staging, modify perioperative management, or enable measurable optimization. Each risk domain is paired with the intervention it should trigger, the criteria identifying candidates for extended thromboprophylaxis are specified, and the systemic inflammatory indices are framed as a trigger for optimization rather than as prognostic commentary. Full article

DNA mismatch repair (MMR) proteins have been investigated as biomarkers in human oncology, but their role in canine PPCs has not been characterized. Immunohistochemistry for MCK, TTF-1, MSH2, and MSH6 was performed and evaluated in relation to clinicopathological parameters. Affected dogs had a median age of 10.6 years. Histologically, 16 tumors were classified as adenocarcinoma and one as adenosquamous carcinoma, with papillary architecture predominating. MCK and TTF-1 immunoreactivity was detected in all cases, supporting epithelial and pulmonary differentiation when considered with histopathological and available clinical findings. Absent MSH2 immunoreactivity was observed in 17.6% of cases, whereas absent MSH6 immunoreactivity was observed in 11.8%. MSH2 expression showed a significant inverse association with tumor volume (p = 0.006), whereas no significant associations were identified between MSH6 expression and the evaluated clinicopathological parameters. As only MSH2 and MSH6 were assessed and no microsatellite instability or molecular analyses were performed, the observed abnormalities cannot be interpreted as definitive evidence of functional MMR deficiency. These findings provide preliminary data on MSH2 and MSH6 expression in canine PPCs and support further investigation using comprehensive MMR assessment and molecular approaches. Full article

Efficient exploitation of genetic diversity is essential for broadening the genetic base of cucumber (Cucumis sativus L.) breeding. This study evaluated the genetic diversity and population structure of a cucumber breeding collection comprising 60 accessions representing four breeding-origin groups: Eastern Europe (n = 34), Western Europe (n = 14), East Asia (n = 5), and locally developed breeding materials from Kazakhstan (n = 7). Fifteen chromosome-specific SSR markers were screened, of which 10 polymorphic loci were retained for downstream analyses. The marker panel showed moderate informativeness, with a mean polymorphism information content (PIC) of 0.438 ± 0.032, while CS-SSR05723 (PIC = 0.587) and CS-SSR23370 (PIC = 0.528) were the most informative loci. Bayesian clustering and complementary multivariate and network-based analyses revealed extensive intermixing among breeding-origin groups, indicating that geographic origin was only weakly associated with genetic relatedness in the analyzed collection. Eastern European germplasm exhibited the highest genetic diversity (Na = 2.9, Ne = 2.198, He = 0.516, I = 0.856) and was the only group to carry three private alleles. AMOVA revealed that 96.30% of the total molecular variation occurred within geographic groups and 3.70% among groups (F_st = 0.037, p = 0.043). These findings identify informative SSR markers for cucumber DNA fingerprinting and suggest that Eastern European germplasm constitutes an important source of genetic diversity within the analyzed breeding collection. The study provides a baseline molecular characterization of the cucumber breeding collection currently maintained in Kazakhstan and supports its future utilization in breeding and germplasm management. Full article

Metastatic colorectal cancer remains associated with poor prognosis despite major therapeutic advances, highlighting the need for robust biomarkers to refine treatment selection and monitor disease dynamics. This review summarizes emerging predictive and prognostic biomarkers in metastatic colorectal cancer across molecular and cellular layers, encompassing both tissue and circulating biomarkers. At the tissue level, we discuss genomic alterations and mutational signatures, transcriptomic classification systems and immune-related gene expression tools, protein-level immune checkpoint markers, and cellular determinants including immune infiltrates, cancer-associated fibroblasts and microbiome features. At the circulating level, we review biomarkers derived from liquid biopsy and peripheral blood, including circulating tumor DNA kinetics, T-cell receptor repertoire diversity, soluble cytokines and proteins, immune cell phenotyping, and circulating tumor cells. We highlight major challenges limiting clinical translation, including tumor heterogeneity, methodological variability, and the absence of standardized analytical pipelines and thresholds. Finally, we discuss future perspectives, emphasizing the integration of multi-omics biomarkers and artificial intelligence-driven strategies to improve biomarker validation and enable more precise management of metastatic colorectal cancer, particularly for patients with microsatellite-stable tumors who derive limited benefit from immune checkpoint inhibition. Full article

Perioperative treatment for colorectal cancer (CRC) is undergoing a paradigm shift from uniform cytotoxic regimens toward strategies guided by tumor location, microsatellite instability (MSI)/mismatch repair (MMR) status, and recurrence risk. Four clinically relevant subgroups now shape decision-making: microsatellite stable (MSS)/proficient MMR (pMMR) colon cancer, microsatellite instability-high (MSI-H)/deficient MMR (dMMR) colon cancer, MSS/pMMR rectal cancer, and MSI-H/dMMR rectal cancer. In MSS/pMMR colon cancer, adjuvant therapy is being refined through risk-adapted treatment duration and selective use of neoadjuvant chemotherapy. In MSS/pMMR rectal cancer, total neoadjuvant therapy, selective omission of pelvic radiotherapy, and watch-and-wait strategies are redefining treatment sequencing and organ preservation. In MSI-H/dMMR colon cancer, immune checkpoint inhibitor (ICI) therapy has shown marked activity in both adjuvant and neoadjuvant settings. In MSI-H/dMMR rectal cancer, neoadjuvant ICI therapy is being explored as a non-operative organ preservation strategy. In parallel, circulating tumor DNA (ctDNA)-based minimal residual disease (MRD) assessment is emerging as a tool for postoperative escalation, de-escalation, and surveillance. Across these settings, the maturity of the evidence varies widely, ranging from established phase III standards to guideline-endorsed but still single-arm approaches and investigational strategies that require prospective validation before routine adoption. This review summarizes the current evidence and remaining challenges in biology-, site-, and risk-adapted perioperative management of CRC. Full article

Immune checkpoint inhibitors (ICIs) have significantly changed the treatment landscape of several gastrointestinal (GI) malignancies, particularly microsatellite instability-high (MSI-H) and mismatch repair-deficient (dMMR) tumors. However, most GI cancers remain resistant to current PD-1/PD-L1-based immunotherapy because of complex and highly suppressive tumor microenvironments characterized by immune stromal exclusion, myeloid-driven immune suppression, defective antigen presentation, and adaptive immune resistance mechanisms. Emerging evidence suggests that alternative inhibitory pathways, including lymphocyte activation gene-3 (LAG-3), T-cell immunoreceptor with immunoglobulin and ITIM domain (TIGIT), T-cell immunoglobulin and mucin-domain containing-3 (TIM-3), and V-domain Ig suppressor of T-cell activation (VISTA), contribute substantially to persistent T-cell dysfunction and resistance to checkpoint blockade. This review summarizes the immune landscape of GI malignancies and discusses the biological mechanisms underlying resistance to current ICIs. We highlight the evolving role of next-generation immune checkpoints, ongoing clinical development of novel inhibitors, and emerging combination strategies involving chemotherapy, anti-angiogenic therapy, radiation, bispecific antibodies, and tumor microenvironment modulation. In addition, we discuss current limitations in biomarker development and the growing role of circulating tumor DNA, spatial immune profiling, and multi-omics approaches in patient selection. Finally, we explore future directions aimed at improving precision immunotherapy and expanding durable responses across GI cancers. Full article

Colorectal cancer (CRC) remains one of the leading causes of cancer-related morbidity and mortality worldwide despite substantial advances in screening, surgical techniques, systemic therapies, and multidisciplinary care. The increasing implementation of precision oncology has fundamentally transformed CRC management by enabling molecularly guided therapeutic strategies based on tumor-specific genetic alterations. In recent years, the molecular landscape of CRC has expanded considerably beyond traditional histopathological classification, incorporating a growing number of clinically actionable biomarkers with prognostic, predictive, and therapeutic significance. This review provides a comprehensive and up-to-date overview of the genetic landscape of CRC, focusing on established biomarkers currently integrated into clinical practice, including microsatellite instability/mismatch repair deficiency (MSI/dMMR), KRAS, NRAS, BRAF, HER2, and NTRK alterations. In addition, emerging biomarkers such as tumor mutational burden (TMB), POLE/POLD1 mutations, circulating tumor DNA (ctDNA), DNA damage repair (DDR) alterations, transcriptomic signatures, and artificial intelligence-based molecular prediction models are critically discussed. Particular emphasis is placed on their biological significance, diagnostic methodologies, prognostic and predictive value, and potential role in treatment selection. A structured, database-informed narrative review identified 140 relevant publications, primarily published between January 2020 and June 2026, supplemented by earlier seminal studies and major clinical guidelines. Based on the available evidence, we propose a Clinical Actionability Framework for CRC, categorizing biomarkers into three hierarchical tiers according to their level of clinical validation and therapeutic relevance: established standard-of-care biomarkers, emerging clinical biomarkers, and future precision oncology biomarkers. Collectively, current evidence supports a progressive transition from single-gene testing toward integrated multi-omics precision medicine. Advances in comprehensive genomic profiling, liquid biopsy technologies, transcriptomics, radiogenomics, and artificial intelligence are expected to further refine patient stratification, optimize therapeutic decision-making, and facilitate the development of adaptive precision oncology models. Understanding the evolving genetic landscape of CRC is therefore essential for maximizing treatment efficacy and improving patient outcomes in the era of personalized cancer care. Full article

Background: Pancreatic ductal adenocarcinoma (PDAC) remains one of the most lethal solid malignancies, with poor survival driven by late presentation, aggressive tumor biology, and limited responsiveness to conventional systemic therapy. Advances in molecular profiling have expanded opportunities for biomarker-guided and targeted therapeutic approaches. Methods: A literature review was conducted using PubMed and the Cochrane Library through July 2026, supplemented by abstracts and proceedings from major international oncology conferences. Results: Pancreatic cancer is driven mainly by somatic changes in KRAS, TP53, CDKN2A, and SMAD4. Established precision approaches include maintenance olaparib for selected platinum-sensitive tumors with germline BRCA1 or BRCA2 pathogenic variants, immune checkpoint inhibition for mismatch repair-deficient or microsatellite instability-high tumors, and tropomyosin receptor kinase inhibition for cancers with neurotrophic tyrosine receptor kinase gene fusions. Direct inhibition of KRAS and RAS represents a major therapeutic breakthrough. KRAS G12C inhibitors established proof of concept, while agents targeting the more common KRAS G12D mutation are showing encouraging early activity. In the randomized phase III RASolute 302 trial, the multiselective RAS inhibitor daraxonrasib improved survival compared with chemotherapy in previously treated metastatic disease with oncogenic RAS mutations. Early studies of zoldonrasib combinations have extended this progress to KRAS G12D-mutant disease, although confirmation is required. Molecular profiling, next-generation sequencing, patient-derived organoids, and circulating tumor DNA may further improve treatment selection and monitoring. Conclusions: Precision oncology is becoming clinically relevant in pancreatic ductal adenocarcinoma. KRAS- and RAS-directed therapies are central advances, but resistance, toxicity, limited durability, and access to comprehensive testing remain important challenges. Full article

Background/Objectives: Irinotecan is a key late-line agent in metastatic gastric cancer, but its dose-limiting toxicities—severe neutropenia and diarrhea—are strongly influenced by UGT1A1 promoter polymorphisms. Commercial genotyping kits in Japan routinely interrogate only the common *6 and *28 alleles and may fail to resolve rarer TATA-box variants. We report a case in which an indeterminate commercial result unmasked an extremely rare loss-of-function genotype. Methods: A Japanese man in his 60s with HER2-negative, microsatellite-stable metastatic gastric cancer progressing after four prior lines underwent pretreatment UGT1A1 genotyping with a commercial DNA chip in anticipation of irinotecan. When the *28 result returned as indeterminate owing to a TA-ratio error, reflex Sanger sequencing of the UGT1A1 promoter TATA box was performed. Results: The chip reported *6 as wild-type but could not resolve *28. Sanger sequencing identified one allele with seven TA repeats (*28) and one with eight TA repeats (*37), with no wild-type six-repeat allele—a *28/*37 compound heterozygote. The *37 allele is exceptionally rare in Japanese individuals (ToMMo 61KJPN allele frequency 0.000294) and has historically been reported almost exclusively in individuals of African ancestry. This genotype has previously caused fatal neutropenic colitis despite preemptive dose reduction. Given the patient’s frailty and limited expected benefit, irinotecan was withheld entirely. Conclusions: Indeterminate commercial UGT1A1 results may conceal rare loss-of-function alleles with divergent functional consequences. Such results should trigger confirmatory sequencing rather than empiric dose reduction, and institutions should establish reflex pathways in advance to support biomarker-informed, frailty-adapted treatment selection. Full article

Background: Endometrial carcinoma (EC) is one of the most common gynaecological malignancies, with a steadily increasing incidence worldwide. In 2013, a novel molecular classification of ECs enabled patient stratification into four groups with important clinical management implications: (1) DNA Polymerase Epsilon (POLE)-mutated, (2) microsatellite instability-high (MSI-H/dMMR) hypermutated, (3) tumours with low somatic copy number alteration (low-SCNA), and (4) tumours with high SCNA and p53 deficiency. This molecular classification should also be used as a tool to identify hereditary cancer syndromes, as MSI-ECs can be associated with Lynch Syndrome (LS, ORPHA:144) while somatic POLE mutations may reflect polymerase proofreading-associated polyposis (PPAP syndrome, ORPHA:447877). Methods: From 2022 to 2024, molecular classification of ECs was routinely performed on 188 consecutive cases. The results were correlated with family history and constitutional genetic testing. Results: Somatic testing revealed that 45 ECs were dMMR and 23 carried POLE variants. Five POLE-mutated ECs also displayed concomitant MSI. For all 68 patients, cancer genetic counselling was proposed, but only 41 accepted, and of these, 26 patients were eligible for the genetic test. None of the POLE somatic variants were proven to be constitutive, whereas LS was diagnosed in seven patients with dMMR-EC; interestingly, two of these patients displayed a POLE-mutated EC. Conclusions: Our data strongly suggest that molecular classification of ECs is important to improve the identification of LS and highlight the relevance of investigating all molecular markers at once in order to identify overlaps between POLE mutations and MMR defects. Full article

Urban-driven landscape fragmentation is a major factor contributing to amphibian population decline yet its genetic consequences remain incompletely understood. We examined the genetic structure and variability of the common toad (Bufo bufo) in Warsaw, Poland, using seven nuclear microsatellite loci and mitochondrial cytochrome b sequences (800 bp). Samples (N = 97) were collected from six breeding sites representing contrasting urban habitats on both banks of the Vistula River. Genetic analyses revealed low but significant population differentiation, elevated inbreeding coefficients, and a heterozygosity deficit despite relatively high effective population sizes. This pattern is consistent with post-fragmentation genetic inertia, in which demographic buffering temporarily maintains genetic diversity despite reduced connectivity. Consequently, contemporary genetic patterns may underestimate the extent of ecological isolation imposed by urban infrastructure. Mitochondrial analyses identified seven haplotypes, including six previously unreported, forming a star-like network topology indicative of a single postglacial colonization event. The Vistula River did not constitute a significant barrier to gene flow, based on pairwise F_ST and hierarchical AMOVA. Supervised feature selection (MCFS-ID) identified specific alleles and body mass as key discriminants among sites, suggesting emerging responses to local urban conditions. Our results indicate that urban common toad populations can retain substantial genetic variation despite fragmentation, although continued isolation may ultimately increase inbreeding and genetic drift. Full article

The carcinogenic liver fluke Opisthorchis viverrini underlies one of the world’s heaviest burdens of bile duct cancer, yet for decades it was treated as a single, genetically uniform parasite whose transmission was shaped mainly by environment and human behavior. However, advances in molecular biology have fundamentally reshaped this conceptual model. Evidence accumulated over the past three decades demonstrates that O. viverrini comprises geographically structured populations linked to hydrological connectivity, host distribution, and long-term evolutionary processes across interconnected river systems of mainland Southeast Asia, particularly within the Lower Mekong Basin. This review synthesizes research on the systematics and population structure of O. viverrini and its Bithynia snail hosts, tracing the transition from early allozyme studies to contemporary DNA-based and genomic approaches. Collectively, mitochondrial, nuclear, microsatellite, and intron markers reveal strong spatial structuring among parasite populations, while genetic patterns observed in snail hosts show partial geographic concordance with parasite population structure, suggesting that both may be influenced by shared hydrological organization, ecological isolation, and host connectivity across endemic aquatic systems. Population structure is strongly scale-dependent, with local panmixia often occurring within connected aquatic systems but pronounced differentiation emerging across broader geographic regions. Together, these findings indicate that transmission dynamics are shaped not only by environmental and behavioral factors, but also by evolutionary and landscape-level processes influencing host and parasite connectivity. Finally, we emphasize the increasing significance of population genomics and landscape genetics in understanding how transmission systems persist, disperse, reconnect, and respond to environmental change across endemic landscapes. Full article