Search Results (2,558)

Background: Despite well-established treatment and follow-up protocols for the management of colorectal cancer patients, recurrences are frequent. Post curative therapy, ctDNA-based molecular residual disease assessment has the ability to stratify patients into higher and lower risks of recurrence. Large-scale clinical trials are necessary to establish utility at a broad level, but physicians also need real-world evidence and case reports before utilizing MRD testing in routine practice. Methods: We analyzed real-world utilization patterns of Guardant Reveal in patients with CRC across stages by collating information from the test request form after the test was ordered as a part of routine practice in the AMEA region. Results: We report that 92% of the tests were utilized for stage II and stage III patients. The timing of the first MRD test order varies between stages, with a higher proportion of tests being ordered within the first 12 weeks of surgery for stage II (71.8%), while for stage III (50%) and stage IV oligometastatic (72%), the first test was ordered after 12 weeks of surgery. Conclusions: Case reports delineate physicians’ perspectives on actions taken on the basis of MRD test results and outcomes. Full article

Background: Improved assessment of tumor biology has contributed to better outcomes in colorectal liver metastasis (CLM). Previously, tumor biology was assessed based on clinical factors such as number and size of metastases, primary tumor characteristics, and extent of extrahepatic disease. Currently, tumor biology assessment includes response to chemotherapy, genetic mutations, and circulating tumor DNA (ctDNA). Methods: A review of the literature in Medline/Pubmed, Embase, and Cochrane Library was conducted using keywords and MeSH terms. Results: Tumor response to chemotherapy can be assessed using pathologic and radiologic criteria. Radiologic morphologic response has been associated with more accurate determination of outcomes compared with size-based criteria. Pathologic tumor response can be assessed by the percentage of cancer cells remaining within each tumor, the ratio of cancer cells to fibrosis, and the thickness of the tumor–normal liver interface. Six driver mutations are consistently associated with outcomes in CLM: RAS/BRAF, TP53, SMAD4, FBXW7, and APC. All are associated with decreased overall survival (OS) and recurrence-free survival (RFS) except for APC, which is associated with better survival. More than 50% of patients have co-mutations, and a three-tier pathway-centric risk score integrating these mutations offers a more comprehensive approach. While mutations should be considered when evaluating for locoregional therapy, it should not influence ablation margins, surgical margins, or parenchymal sparing approach. Preoperative ctDNA is associated with worse survival, but clearance after hepatectomy is associated with improved survival. Postoperative ctDNA status is associated with recurrence and has the potential to guide the choice of adjuvant chemotherapy. Conclusion: Tumor biology enables informed, precise, and personalized decision-making. Integration of response to chemotherapy, driver mutations, and ctDNA into routine practice is critical to improve CLM management. Full article

Recurrent spontaneous miscarriages represent a significant reproductive challenge, often associated with inherited thrombophilia. Among the genetic factors involved, methylenetetrahydrofolate reductase (MTHFR) gene polymorphisms have been increasingly studied. The two main variants, MTHFR C677T and MTHFR A1298C, have been suggested to contribute to thrombotic events and adverse pregnancy outcomes. This study aims to evaluate the higher prevalence and potential role of MTHFR gene polymorphisms (C677T and A1298C) in the etiology of recurrent spontaneous miscarriages in pregnant women with inherited thrombophilia, in comparison with the classical thrombophilia-associated SNPs—F5 Leiden and the F2 G20210A gene mutation. In this single-center retrospective observational study, 64 women with recurrent pregnancy loss and confirmed inherited thrombophilia were evaluated. Genomic DNA extracted from peripheral blood samples was analyzed for thrombophilia-associated polymorphisms, including F5 Leiden (G1691A), F2 G20210A, MTHFR C677T, MTHFR A1298C, SERPINE1 4G/5G, and F13A1 V34L, using a real-time PCR-based Bosphore^® Thrombophilia Panel. The presence of MTHFR C677T and A1298C polymorphisms was investigated and compared to the incidence of F5 Leiden and F2 G20210A gene SNPs. Associations between genotypes and clinical characteristics, including the number of pregnancy losses, were assessed using chi-square tests, Kruskal–Wallis analysis, and logistic regression models. The most frequently detected polymorphisms were heterozygous variants of the MTHFR gene, with prevalences of 57.8% for C677T and 53.1% for A1298C. Homozygous MTHFR C677T was significantly associated with a higher number of pregnancy losses (Kruskal–Wallis test, p = 0.001). Similarly, the homozygous MTHFR A1298C genotype showed a significant association with increased miscarriage frequency (p = 0.012). Classical thrombophilic mutations were less frequent, with F2 G20210A identified in only two patients, although its presence was associated with a higher number of pregnancy losses (p = 0.030). These findings suggest that combined thrombophilic polymorphisms may contribute to recurrent pregnancy loss, although larger studies are required to confirm these observations. Full article

Background/Objectives: High-grade endometrial cancer (EC) is associated with poor outcomes, particularly in populations with a high burden of aggressive histologies. There is a critical need for accessible biomarkers to improve prognostic assessment and guide clinical management. Methods: In this study, we evaluated the feasibility and clinical relevance of monitoring circulating tumor DNA (ctDNA) by tracking somatic TP53 mutations using a routine next-generation sequencing (NGS) assay already implemented in diagnostic practice. Results: Among 21 patients with high-grade EC carrying TP53 mutations in the primary tumor, ctDNA was detectable in over 75% during follow-up. Baseline ctDNA detection strongly correlated with advanced disease: none of the FIGO I tumors were ctDNA-positive at diagnosis, whereas 73% of FIGO > I tumors showed detectable ctDNA. Patients with ctDNA detected at baseline had significantly poorer outcomes, with a 2-year recurrence-free survival (RFS) of 18% versus 60% and a 2-year overall survival (OS) of 40% versus 78%. Longitudinal monitoring revealed that postoperative persistence or reappearance of ctDNA was consistently associated with disease progression, often preceding radiological relapse. Conversely, early ctDNA clearance (at M4–M8) was associated with more favorable clinical trajectories. Conclusions: These findings highlight the potential role of ctDNA as a real-time molecular marker of minimal residual disease and tumor dynamics. Our results demonstrate that TP53-based ctDNA tracking using a standard NGS panel is feasible, sensitive, and clinically informative in high-grade EC. This approach may contribute to improving prognostic stratification and enabling more personalized, responsive clinical management, particularly in high-risk populations. Full article

Chryseobacterium indologenes MA9 is a causative agent of root rot disease in Panax notoginseng (P. notoginseng), with its high incidence being a major manifestation of continuous cropping barriers, severely hindering the sustainable development of the P. notoginseng industry. In this study, a novel lytic bacteriophage, MA9V-3, was isolated from wastewater, targeting C. indologenes MA9. The phage produced clear plaques, ranging from 1 to 3 mm in diameter, with a surrounding halo. Phage MA9V-3 achieved an adsorption rate of up to 80% after 30 min of contact with C. indologenes MA9, a latent period of approximately 40 min, and an average burst-size if 160 PFU/cell. Transmission electron microscopy revealed that phage MA9V-3 possesses an icosahedral head and a contractile tail, exhibiting a typical myovirus-like morphology. According to the latest ICTV taxonomy, MA9V-3 belongs to the class Caudoviricetes, and the phage’s biocontrol efficacy and inhibitory capacity were evaluated at different multiplicity of infection (MOI s). The results showed that the highest titer recorded at 1.6 × 10¹⁰ PFU/mL. Whole-genome sequencing revealed that MA9V-3 is a double-stranded circular DNA virus, with a genome length of 103,203 bp, GC content of 34.29%, and 150 open reading frames (ORFs), one of which is related to tRNA. Only 13 of these ORFs encode known functional sequences, likely due to the limited available gene data for such phages in the database, with additional details on hypothetical proteins yet to be uncovered. Comparative database analysis confirmed that the phage genome contains no antibiotic resistance or toxin-related genes. Phage therapy experiments were performed using MA9V-3 and two other phages screened in our laboratory. The experimental results showed that phage MA9V-3 may be a potential candidate for effectively controlling the infection of Panax notoginseng by C. indologenes MA9, and offering valuable insights into the potential application of phage therapy for managing bacterial plant diseases. Full article

The modulation of plant responses to abscisic acid (ABA) and/or abiotic stresses can be manipulated by the expression of ABA-responsive genes, which is affected by phytohormone ABA. While some ABA-responsive genes have been shown to regulate plant responses to ABA and/or abiotic stresses, the functions of numerous ABA-responsive genes remain unknown. Therefore, characterizing these unstudied genes would provide a practical way to identify novel regulators of plant adaptations to ABA and/or abiotic stresses. Here, we characterized four closely related unstudied ABA-responsive genes in Arabidopsis thaliana, named Arabidopsis thaliana ABA-up regulated genes (AtAUGs). We found that ABA treatment induces AtAUGs expression level, and our results in transfected protoplasts show that AtAUGs exhibit nucleus localization and downregulate the co-transfected reporter expression level. The results of ABA sensitivity assays, including seed germination, cotyledon greening, and root extension assay show that transgenic plants overexpressing AtAUGs had increased sensitivity, but ataugs mutants generated by isolating T-DNA insertion lines or through CRISPR/Cas9 gene-editing of AtAUGs had decreased sensitivity; in addition, the greatest decrease in ABA sensitivity was observed in the ataug1 ataug2 ataug3 ataug4 (ataug1234) quadruple mutants. The qRT-PCR results show that the expression levels of several Type 2C Protein Phosphatase (PP2C) genes, the key negative regulator genes of ABA signaling including PP2CA, Hypersensitive to ABA 1 (HAB1), HAB2, Highly ABA-Induced PP2C protein 3 (HAI3), ABA-Hypersensitive Germination 1 (AHG1), and ABA Insensitive 2 (ABI2) decreased in 35S:AtAUGs transgenic plants, but increased in the ataug1234 quadruple mutants. Taken together, these results suggest that AtAUGs are ABA-responsive genes, and AtAUGs positively regulate ABA responses in a redundant manner, by downregulating the expression of crucial negative regulator genes in ABA signaling. Full article

Metastatic colorectal cancer (mCRC) accounts for 90% of CRC-related mortality. This review synthesizes insights from comparative genomics tracing evolutionary trajectories from primary tumor to disseminated disease. Multi-region sequencing reveals metastatic seeding often occurs early—before clinical detection—challenging linear progression models. The metastatic bottleneck reduces clonal diversity while enriching for dissemination-competent traits including SMAD4 loss, PTEN inactivation and metabolic reprogramming. Organ-specific adaptation yields distinct molecular signatures: liver metastases exhibit Wnt hyperactivation and TGF-β-driven immune suppression; peritoneal tumors display mucinous features; brain metastases show HER2 enrichment. The immune microenvironment evolves toward immunosuppressive configurations, with Microsatellite instability high (MSI-H) tumors acquiring B2M or JAK1/2 mutations. Circulating tumor DNA (ctDNA) enables real-time tracking of clonal dynamics, detecting molecular residual disease months before radiographic progression. Therapeutic resistance follows predictable evolutionary trajectories—from RAS/BRAF mutations to EGFR ectodomain alterations, HER2/MET amplifications and lineage plasticity—with metastasis-specific mechanisms including microenvironmental protection and cellular dormancy. The clinical future lies in interception: leveraging liquid biopsies for early detection, targeting both tumor-intrinsic vulnerabilities and permissive metastatic niches and adapting therapy dynamically to anticipate resistance. Understanding this genomic odyssey is essential for transforming mCRC into a controllable chronic condition. Full article

Head and neck squamous cell carcinoma (HNSCC) is biologically and clinically dichotomous according to HPV status, a distinction that fundamentally dictates the design, implementation, and interpretation of liquid biopsy strategies. Conventional anatomical imaging lacks sufficient sensitivity for minimal residual disease (MRD) detection, contributing significantly to treatment failure and suboptimal clinical outcomes. This review provides a critical, evidence-based synthesis of the three principal circulating analytes, circulating tumor DNA (ctDNA), exosomes, and circulating tumor cells (CTCs), and their evolving roles in real-time, non-invasive molecular monitoring. Critically, the clinical readiness of these analytes differs substantially: while ctDNA, particularly HPV-related ctDNA, is approaching clinical validation for MRD detection and recurrence surveillance in HPV-positive HNSCC, exosomes and CTCs remain investigational tools hindered by ongoing technical challenges including lack of standardized assays, limited reproducibility across platforms, and insufficient prospective validation. We review how the presence of a clonal, virally derived DNA target in HPV-positive HNSCC contrasts with the heterogeneous somatic mutational landscape of HPV-negative tumors, necessitating divergent analytical platforms and yielding distinct clinical utility profiles for MRD detection and recurrence surveillance. We further outline a pragmatic translational pathway focused on assay standardization, particularly for exosomes and CTCs where this foundational work is most urgently needed, integration of complementary multimodal liquid biopsy approaches, and rigorously designed prospective interventional clinical trials to establish clinical utility. Collectively, these efforts aim to transition HNSCC management from reactive, anatomy-based surveillance to proactive, molecularly guided precision oncology, with the potential to improve therapeutic decision-making and patient outcomes. Full article

Background: Liquid biopsy using circulating tumor DNA (ctDNA) is rapidly reshaping gastrointestinal (GI) oncology. The highest-impact applications are molecular residual disease (mRD) detection after curative-intent therapy and early recognition of progression or resistance during systemic treatment. Methods: We performed a structured, clinically oriented narrative synthesis by using explicit search, eligibility, evidence prioritization, and clinical interpretation rules, integrating landmark prospective cohorts, randomized ctDNA-guided strategy trials where available, meta-analyses, key methodological research (e.g., pre-analytics, assay design, and clonal hematopoiesis (CH)/clonal hematopoiesis of indeterminate potential (CHIP)), and selected trial registries. Results: In resected colorectal cancer (CRC), postoperative ctDNA positivity is among the strongest known biomarkers of recurrence risk; large prospective studies demonstrate clear separation of disease-free survival (DFS)/overall survival (OS) between mRD+ and mRD− patients. In stage II colon cancer, randomized data (DYNAMIC) show that a ctDNA-guided strategy reduces adjuvant chemotherapy exposure without compromising long-term outcomes. In metastatic CRC, ctDNA supports early response monitoring and resistance tracking; ctDNA-selected anti-EGFR rechallenge provides a model of biomarker-driven actionability (CHRONOS). In gastroesophageal cancers, longitudinal ctDNA dynamics correlate with relapse risk and treatment efficacy, and in esophageal squamous cell carcinoma, ctDNA after neoadjuvant chemoradiotherapy informs residual disease risk and adjuvant stratification. In pancreatic ductal adenocarcinoma and hepatobiliary malignancies, sensitivity is constrained by low shedding and background cell-free DNA (cfDNA), yet ctDNA positivity remains clinically meaningful, and emerging data in resected extrahepatic cholangiocarcinoma (STAMP-linked analyses) show that ctDNA dynamics during adjuvant therapy predict recurrence. Conclusions: ctDNA is a clinically validated biomarker for mRD in CRC, whereas in other GI cancers, it remains a promising but methodologically heterogeneous tool whose clinical utility is tumor- and context-dependent. The next phase requires interventional trials demonstrating outcome improvement, harmonized sampling and reporting standards, and rigorous control of confounders (notably CH/CHIP). Full article

Next-generation sequencing (NGS) has impacted the treatment landscape for mCRC, leading to improved outcomes through the use of molecularly targeted and immune checkpoint inhibitor therapies. The National Comprehensive Cancer Network (NCCN) and the American Society of Clinical Oncology (ASCO) recommend, at a minimum, initial testing to assess RAS, BRAF, HER2, and microsatellite instability (MSI)/mismatch repair (MMR) status, as these results determine therapeutic eligibility. Broader testing to identify the eligibility for tumor-agnostic therapy for a tumor mutation burden (TMB), NTRK gene fusions, and RET fusions is encouraged for all patients with advanced solid tumors. Patients with metastatic disease may develop progressive disease, often as a result of adaptive resistance mechanisms and selective therapeutic pressure on disease heterogeneity. Repeat biomarker testing at progression has the potential to define these resistance mechanisms and to guide the next therapy or clinical trial enrollment. While these practices have become more commonplace, unified guidelines have yet to be established. In this review of the literature, we evaluate the advantages and pitfalls of sequential biomarker testing during disease progression in patients with mCRC. Full article

Background: The etiopathogenesis of juvenile systemic lupus erythematosus (JSLE), a complex and complicated illness, is unknown. Genetic, environmental, and dysregulated immune system responses are all thought to contribute to the disease’s etiology. Important immunological molecules that regulate different immune cells and are associated with autoimmune disorders are TNFSF4 and IKZF1. Thus, our purpose was to discover if TNFSF4 and IKZF1 mutations left the Egyptian population genetically predisposed to SLE. Methods: Using real-time polymerase chain reaction (RT-PCR), polymorphism analysis of the TNFSF4 rs1234315 C/T and IKZF1 rs11980379 C/T genes was performed on extracted DNA from JSLE patients and healthy controls. Results: TNFSF4 frequencies (rs1234315 T allele, CT, TT genotypes, dominant and recessive models) were substantially associated with a higher incidence of JSLE (p < 0.05) compared to healthy controls. Conversely, IKZF1 frequencies (rs11980379 T allele, TC, TT genotypes, and dominant model) significantly correlated with a lower incidence of JSLE. Furthermore, the TC + CC rs11980379 genotype was identified as significantly associated with lower kidney biopsy grades and a lower incidence of lupus nephritis. Conclusions: Our findings suggest that TNFSF4 and IKZF1 polymorphisms affect vulnerability to juvenile SLE. Full article

We synthesized seven carbocyclic nucleoside analogs featuring a cyclopentane ring in place of the (deoxy)ribose sugar, which serves as a linker in DNA/RNA nucleosides. We assessed the stability of cyclopentane nucleosides in 98% w/w sulfuric acid at room temperature via ¹H and ¹³C NMR spectroscopy. We observe that adenine (A1, A4), guanine (G1) and thymine (T1) cyclopentane nucleoside analogs remain stable for at least two weeks at room temperature, with only minor (~4%) degradation in A1. In contrast, the cytosine analog (C1) rapidly degrades to release a soluble cytosine. Methyl-substituted adenine analogs mimicking polymer backbone attachments at positions prone to tertiary carbocation formation (A2, A3) prove unstable and release soluble adenine. Only the 3,3-dimethylcyclopentyl adenine analog (A4) exhibits sufficient stability. Our findings reveal that cyclopentane serves as a viable stable linker in concentrated sulfuric acid for select nucleic acid bases, provided that the backbone connections avoid tertiary carbons susceptible to carbocation-mediated cleavage. We thus identify one potential key structural feature for engineering examples of genetic-like polymers that could potentially persist in Venus’s concentrated sulfuric acid cloud environment. Full article

Functional analysis of SLC22A5 variants can improve diagnostic accuracy in patients with primary carnitine deficiency (PCD). Herein, we performed a genetic analysis of three neonates with PCD. Two of the patients harbored a novel synonymous SLC22A5 variant that has not been previously reported, and the other patient harbored a classical splice site variant. The splicing patterns of the two SLC22A5 variants were evaluated using three in silico tools, and in vitro minigene analysis was performed to verify the impact of variants on RNA splicing mechanisms. All three in silico tools predicted that both SLC22A5 variants could alter normal RNA splicing. Functional studies using minigene assays demonstrated that the c.450C>T (p.F150=) leads to partial exon 2 skipping, and c.394-1G>A leads to intron 1 retention and exon 2 skipping. Intron 1 retention of 65 nucleotides and exon 2 skipping were confirmed by sequencing cDNA amplification products. These results, along with functional evidence, led to reclassification of c.450C>T (p.F150=) and c.394-1G>A as likely pathogenic and pathogenic, respectively. This is the first reported synonymous variant in the SLC22A5 gene that has been functionally validated to affect RNA splicing, thus enriching the variant spectrum of SLC22A5 and aiding accurate PCD diagnosis. Full article

Soft-tissue sarcomas (STSs) comprise a rare, heterogeneous group of mesenchymal malignancies in which histologic grade remains the strongest determinant of outcome, metastatic risk, and therapeutic strategy. Intermediate/high-grade STSs exhibit a pronounced propensity for early distant relapse, yet growing evidence indicates that metastatic behaviour is not uniform. Within this spectrum, an oligometastatic phenotype, characterised by a limited number of metastases, often confined to the lung, has emerged as a clinically and biologically distinct state associated with more indolent metastatic kinetics and improved survival when treated with aggressive local interventions. However, the criteria that define true oligometastatic STSs remain unsettled, and prospective evidence is lacking. Emerging molecular and immunological correlates provide a potential framework for biological triage. Low genomic complexity (low-risk CINSARC), a B-cell/TLS-rich tumour microenvironment, high immune-cytotoxic signatures, and persistently low or undetectable circulating tumour DNA (ctDNA) are each linked to reduced metastatic competence and may underpin oligometastatic trajectories. Conversely, high chromosomal instability, immunosuppressive microenvironments, and elevated ctDNA levels align with covertly polymetastatic biology despite limited radiographic disease. In this context, artificial intelligence and machinelearning approaches applied to computational genomics, immune profiling, imaging, and liquid-biopsy data offer a powerful strategy to integrate these multi-dimensional features and refine predictions of metastatic behaviour in STS. Oligometastatic STS therefore represents a biologically definable subset amenable to multimodal management integrating local ablative therapies, systemic agents, and immune-based strategies. Prospective, biomarker-stratified trials are needed to validate selection frameworks and optimise treatment sequencing in this evolving therapeutic space. Full article

Background/Objectives: Eliciting robust immune responses against the hepatitis B virus (HBV) through therapeutic vaccination holds promise for curing chronic hepatitis B. We previously developed the heterologous protein prime/viral vector boost clinical vaccine candidate, TherVacB. Here, we evaluated a replication-competent chimeric vesicular stomatitis virus vector (VSV-GP) as an alternative viral vector boost vaccine. Methods: A recombinant VSV-GP vector co-expressing HBV surface and core antigens (VSV-GP-HBs/c) was generated and characterized for antigen expression. Its immunogenicity, antiviral efficacy, and durability were assessed in HBV-naïve and HBV-carrier mice, using protein primed, viral vector-primed, and multi-viral vector boost regimens. Results: VSV-GP-HBs/c efficiently expressed both HBV antigens in vitro. A single immunization with VSV-GP-HBs/c induced only weak HBV-specific immune responses in vivo. Replacing protein priming with VSV-GP-HBs/c resulted in modest immune activation and limited antiviral effects in HBV-carrier mice. In contrast, substituting the modified vaccinia virus Ankara (MVA)-HBs/c boost in the TherVacB regimen with VSV-GP-HBs/c elicited robust HBV-specific antibody responses and strong CD4 and CD8 T-cell immunity, assessed by intracellular IFN-γ staining after peptide stimulation. This regimen achieved a substantial reduction in serum HBsAg levels, numbers of HBV-positive hepatocytes, and intrahepatic HBV-DNA, with antiviral efficacy comparable to that of the classical TherVacB regimen. Notably, a second viral vector boost did not enhance HBV-specific immunity or antiviral efficacy; instead, it promoted dominant vector-specific CD8 T-cell responses. Long-term analyses performed 10 weeks after the last vaccination further demonstrated that a single protein-prime/VSV-GP-HBs/c boost was sufficient to achieve sustained antiviral control. Conclusions: These findings identify VSV-GP-HBs/c as an effective boost vector for therapeutic hepatitis B vaccination and establish protein priming followed by a single viral vector boost as an optimal strategy for sustained antiviral immunity. Full article