Search Results (1,951)

Introduction: Current treatments for patients with stage III non-small-cell lung cancer (NSCLC) are not sufficiently personalized, resulting in suboptimal outcomes and high mortality rates. The Developing Circulating and Imaging Biomarkers Towards Personalized Radiotherapy in Lung Cancer (VIGILANCE) study employs innovative health technologies to collect a range of clinical data and features. This includes longitudinal analyses of cell-free and circulating tumor DNA from blood samples and radiomic features extracted from standard-of-care imaging. Additionally, patient-reported outcome measures will be collected to capture patients’ symptoms and quality of life. This will provide invaluable insight into the patient experience during and after radiotherapy. We aim to evaluate whether the data, including patient-reported outcomes, can serve as biomarkers to refine treatment strategies, improve post-treatment follow-up and provide patients with realistic outcome predictions. Key endpoints include the following: (1) assessing whether baseline ctDNA status and its early on-treatment dynamics can identify patients with radioresistant disease who could benefit from treatment intensification; (2) determining whether post-radiotherapy ctDNA clearance can predict benefit from consolidation durvalumab, potentially sparing ctDNA-negative patients from unnecessary immunotherapy; and (3) developing integrated models combining novel ctDNA and radiomic biomarkers to distinguish between radiation fibrosis and tumor recurrence and to predict survival. We adopt a pragmatic approach by recruiting patients receiving standard-of-care treatments in a real-world setting. In addition, most of the clinical data is already routinely collected in our center, except for the blood tests for cell-free and circulating tumor DNA analysis. Methods and analysis: This is a single-center, prospective, exploratory, longitudinal, follow-up study, recruiting patients with stage III NSCLC undergoing standard-of-care curative-intent radiotherapy (with or without systemic therapy). Data collection spans from baseline to during radiotherapy and is extended up to 1 year following radiotherapy. The longitudinal analysis aims to describe and characterize dynamic changes in the collected features and assess their utility as prognostic and response biomarkers. Trial registration number: NCT06086574. Full article

The adoption of liquid biopsy approaches in clinical practice has triggered a significant paradigm shift in the diagnostic, prognostic, and predictive outcomes for cancer patients. Circulating tumor DNA (ctDNA) is considered a valuable biomarker for monitoring tumor burden and its mutational dynamics. In this context, not all cell-free DNA (cfDNA) molecules are derived from tumor cells. Furthermore, due to tumor heterogeneity, not all ctDNA molecules contain cancer-associated alleles, complicating the direct quantification of the circulating tumor allele fraction (cTF) within the total cfDNA. Cancer arises from the accumulation of multiple genetic and epigenetic changes. Each of these molecular features can be exploited as the basis of methodological strategies used in ctDNA quantification. Different layers of omics data, from genomics, evaluating mutational analysis of somatic single-nucleotide variants and copy number alterations, to epigenomics, primarily consisting of the evaluation of methylation profiles and fragmentation patterns, can be used for this purpose. Some of these approaches can be effective in a multi-modal manner. To date, the quantification approaches for estimating cTF vary enormously, making direct comparisons and an assessment of their translational value challenging. Moreover, the lack of regulatory approval for many of these assays is a critical barrier to their widespread clinical adoption. This review explores the different omics approaches described for ctDNA quantification, outlining strengths and limitations, and highlighting their valuable applications in clinical settings. Full article

DNA is continuously exposed to endogenous and exogenous factors that induce oxidative modifications leading to mutations and genomic instability. Oxidative DNA damage plays a dual role, contributing to physiological signaling at low levels while promoting mutagenesis, carcinogenesis and degenerative diseases when unpaired. Among various lesions, an oxidized base, such as 8-oxo-2′-deoxyguanosine (8-oxodG), is one of the major biomarkers of oxidative stress and genomic damage. Cells have evolved sophisticated repair processes, including base excision repair (BER), nucleotide excision repair (NER), and mismatch repair (MMR), to maintain genomic integrity. Dysregulation or polymorphism of these repair genes has been linked with cancer, neurologic, and cardiovascular disorders. This review discusses an overview of what is presently known concerning oxidative DNA damage and repair mechanisms, particularly emphasizing their molecular players, signaling routes, and human disease implications. It further refers to the latest advances in CRISPR-based technologies and multi-omics approaches that are redefining our understanding of DNA damage response (DDR) networks and creating new frontiers for therapeutic interventions. Full article

Woody plants, comprising forest and fruit tree species, provide essential ecological and economic benefits to society. Their genetic improvement is challenging due to long generation intervals and high heterozygosity. Genetic transformation, which combines targeted DNA delivery with plant regeneration from transformed cells, offers a powerful alternative to accelerating their domestication and improvement. Agrobacterium tumefaciens, Rhizobium rhizogenes, and particle bombardment have been widely used for DNA delivery into a wide variety of explants, including leaves, stems, hypocotyls, roots, and embryos, with regeneration occurring via direct organogenesis, callus-mediated organogenesis, somatic embryogenesis, or hairy root formation. Despite successes, conventional approaches are hampered by low efficiency, genotype dependency, and a reliance on challenging tissue culture. This review provides a critical analysis of the current landscape in woody plant transformation, moving beyond a simple summary of techniques to evaluate the co-evolution of established platforms with disruptive technologies. Key advances among these include the use of developmental regulators to engineer regeneration, the rise in in planta systems to bypass tissue culture, and the imperative for DNA-free genome editing to meet regulatory and public expectations. By examining species-specific breakthroughs in key genera, including Populus, Malus, Citrus, and Pinus, this review highlights a paradigm shift from empirical optimization towards rational, predictable engineering of woody plants for a sustainable future. Full article

Ischemic stroke remains one of the most catastrophic diseases in neurology, in which, due to a disturbance in the cerebral blood flow, the brain is acutely deprived of its oxygen and glucose oligomer, which in turn rapidly leads to energetic collapse and progressive cellular death. There is now increasing evidence that this type of stroke is not simply a type of ‘oxidative stress’ but rather a programmable loss-of-redox homeostasis, within which electron flow and the balance of oxidants/reductants are cumulatively displaced at the level of the single molecule and at the level of the cellular area. The advances being made in cryo-electron microscopy, lipidomics, and spatial omics are coupled with the introduction of a redox code produced by the interaction of the couples NADH/NAD⁺, NADPH/NADP⁺, GSH/GSSG, BH₄/BH₂, and NO/SNO, which determine the end results of the fates of the neurons, glia, endothelium, and pericytes. Within the mitochondria, pathophysiological events, including reverse electron transport, succinate overflow, and permeability transition, are found to be the first events after reperfusion, while signals intercommunicating via ER–mitochondria contact, peroxisomes, and nanotunnels control injury propagation. At the level of the tissue, events such as the constriction of the pericytes, the degradation of the glycocalyx, and the formation of neutrophil extracellular traps underlie microvascular failure (at least), despite the effective recanalization of the vessels. Systemic influences such as microbiome products, oxidized lipids, and free mitochondrial DNA in cells determine the redox imbalance, but this generally occurs outside the brain. We aim to synthesize how the progressive stages of ischemic injury evolve from the cessation of flow to the collapse of the cell structure. Within seconds of injury, there is reverse electron transport (RET) through mitochondrial complex I, with bursts of superoxide (O₂•⁻) and hydrogen peroxide (H₂O₂) being produced, which depletes the stores of superoxide dismutase, catalase, and glutathione peroxidase. Accumulated succinate and iron-induced lipid peroxidation trigger ferroptosis, while xanthine oxidase and NOX2/NOX4, as well as uncoupled eNOS/nNOS, lead to oxidative and nitrosative stress. These cascades compromise the function of neuronal mitochondria, the glial antioxidant capacity, and endothelial–pericyte integrity, leading to the degradation of the glycocalyx with microvascular constriction. Stroke, therefore, represents a continuum of redox disequilibrium, a coordinated biochemical failure linking the mitochondrial metabolism with membrane integrity and vascular homeostasis. Full article

Background: Non-invasive prenatal testing (NIPT) based on cell-free fetal DNA (cfDNA) in maternal blood has revolutionized prenatal screening for trisomies 21, 18, and 13. This approach, based on next-generation sequencing (NGS), usually allows the detection of other chromosomal abnormalities; however, their clinical value in routine practice requires further evidence. Objectives: This study aimed to assess the experience and clinical utility of genome-wide NIPT in pregnant women at intermediate risk in the autonomous communities of Aragón and Valencia, Spain. Methods: For this purpose, a retrospective cohort study was conducted between 2020 and 2024 across two public hospitals. Pregnant women at intermediate risk for trisomies 21, 18, or 13, were included, as well as those meeting specific clinical criteria. Participants were offered either basic or expanded NIPT, and positive results were confirmed by invasive prenatal testing or placental analysis. Results: Among 9,059 expanded NIPT tests, 132 (1.45%) indicated a high-risk result for less common chromosomal anomalies, comprising 60 rare autosomal aneuploidies (RAAs), 39 copy number variants (CNVs), 23 sex chromosome aneuploidies (SCAs), and 10 multiple abnormalities. The positive predictive value (PPV) was 5.5% for RAAs in the fetus, 12.8% for CNVs (31% for deletions), and 58% for SCAs. Conclusions: Several confirmed anomalies were clinically significant and would not have been detected through conventional screening. Opportunistic use of expanded NIPT enables the detection of additional clinically relevant abnormalities, potentially improving obstetric management without substantially increasing invasive testing. Full article

Background: Poxviruses constitute a family of large dsDNA viruses that can infect a plethora of species including humans. Historically, poxviruses have caused a health burden in multiple outbreaks. The large genome of poxviruses favors reverse vaccinology approaches that can determine potential antigens and epitopes. Here, we propose the modeling of a user-friendly database containing the predicted antigens and epitopes of a large cohort of poxvirus proteomes using the existing PoxiPred method for reverse vaccinology of poxviruses. Methods: In the present study, we obtained the whole proteomes of as many as 37 distinct poxviruses. We utilized each proteome to predict both antigenic proteins and T-cell epitopes of poxviruses with the aid of an Artificial Intelligence method, namely the PoxiPred method. Results: In total, we predicted 3966 proteins as potential antigen targets. Of note, we considered that this protein may exist in a set of proteoforms. Subsets of these proteins constituted a comprehensive repository of 54,291 linear T-cell epitopes. We combined the outcome of the predictions in the format of a web tool that delivers a database of antigens and epitopes of poxviruses. We also developed a comprehensive repository dedicated to providing access to end-users to obtain AI-based screened antigens and T-cell epitopes of poxviruses in a user-friendly manner. These antigens and epitopes can be utilized to design experiments for the development of effective vaccines against a plethora of poxviruses. Conclusions: The TCEPVDB repository, already deployed to the web under an open-source coding philosophy, is free to use, does not require any login, does not store any information from its users. Full article

Cell-free DNA (cfDNA) promoter hypermethylation shows promise as a blood-based biomarker for pancreatic cancer, and similar alterations may occur in acute pancreatitis (AP). This study investigated the cfDNA hypermethylation profile of AP patients over time, compared with healthy controls, and its association with AP severity markers. A prospective longitudinal study including hospitalized AP patients and healthy controls was conducted. Methylation-specific PCR of a 23-gene panel was performed on plasma collected at inclusion (T0), 6 weeks (T6W), 6 months (T6M), and 7–8 years (T8Y). Associations between gene hypermethylation and clinical markers of AP severity—CRP, leukocyte count, creatinine, hospital stay, and complications—were evaluated. AP patients had a significantly higher mean number of hypermethylated genes at T0 (7.4, 95% CI: 6.8–8.0) compared with the controls (3.3, 95% CI: 2.8–3.8; p < 0.01). The mean number decreased over time to 3.2 (95% CI: 2.4–4.1) at T8Y. Total hypermethylation was positively associated with CRP (ρ = 0.39; p = 0.0018), leukocytes (ρ = 0.35; p = 0.0052), and hospital stay (ρ = 0.27; p = 0.0375). AP patients exhibited significantly higher cfDNA hypermethylation at disease onset, which normalized over time. Total hypermethylation showed positive associations with several markers of AP severity. Full article

Background/Objectives: Conventional imaging assesses therapy response in stage IV solid-tumor patients in 8- to 12-week intervals, delaying detection of non-responders. We evaluated a quantitative PCR (qPCR) assay that interrogates size-distributed cell-free DNA (cfDNA) fragments to provide earlier insights into treatment efficacy. Methods: In this prospective study, 128 patients with metastatic lung, breast, or colorectal cancer provided plasma 12–21 days after the first dose of a new systemic regimen. The qPCR targets multi-copy retrotransposon element fragments of greater than 80 bp, greater than 105 bp, and greater than 265 bp, as well as an internal control. A model integrates these quantities into a Progression Score (PS) ranging from 0 to 100; higher values indicate probable disease progression. Results: The PS model yielded an area under (AUC) the receiver-operating-characteristic (ROC) curve of 0.93 for predicting radiographic progression at first imaging. Scores were strongly bimodal: 92% of patients with PS > 90 progressed, whereas 95% with PS < 10 did not. Intermediate scores (10–90) comprised a mixed cohort. Assay performance was unaffected by tumor genomic profile. Conclusions: This cfDNA-based Progression Score (PS) assay enables tumor- and therapy-agnostic, non-invasive monitoring of treatment response as early as two weeks after initiation. By flagging ineffective regimens well before standard imaging, the test can accelerate clinical decision-making, reduce exposure to futile therapy, and potentially improve outcomes in stage IV cancer. Early treatment plan changes may also avoid the high costs of ineffective treatments, prevent downstream toxicity-related hospitalizations, and free up limited imaging and infusion-suite capacity—yielding savings for patients, payers, and healthcare systems. Full article

Background/Objectives: Here, we report the design, synthesis, and in vitro biological evaluation of a novel stimuli-sensitive nanotherapeutics based on cisplatin analog, cis-[PtCl₂(NH₃)(2-(3-oxobutyl)pyridine)] (Pt-OBP), covalently linked to a N-(2-hydroxypropyl)methacrylamide (HPMA) copolymer via a pH-sensitive hydrazone bond. Methods: Two polymer–drug conjugates, P-Pt-A and P-Pt-B, were synthesized, differing in spacer length between the polymer chain and hydrazone bond, which in turn modulates their drug release kinetics. Results: The spacer based on hydrazone bond demonstrated satisfactory stability under blood-mimicking conditions while enabling selective release of the active drug intracellularly or even in the mildly acidic tumor microenvironment. Pt-OBP exhibits comparable or even superior cytostatic and cytotoxic activity to carboplatin across a panel of murine and human cancer cell lines, with the highest potency observed in FaDu cells representing human head and neck squamous cell carcinoma. Mechanistically, Pt-OBP induced significant phosphorylation of γ-H2AX and activation of caspase-3, indicating its ability to cause DNA damage with subsequent apoptosis induction. P-Pt-A retained moderate biological activity, whereas the slower-releasing P-Pt-B exhibited reduced potency in vitro, consistent with its drug release profile. Conclusions: Notably, free Pt-OBP induced rapid apoptotic cell death, surpassing carboplatin at early time points, and the polymeric conjugates achieved comparable pro-apoptotic activity after extended incubation, suggesting effective intracellular release of the active drug. Full article

Guava fruit is widely consumed in tropical countries and beyond. The phenolic fraction of guava pulp and processing waste (a single fraction containing seeds, skins, and pulp residues) have been reported to carry in vitro biological activities, acting on biomarkers of metabolic diseases such as type 2 diabetes and obesity (enzymatic inhibition of α-glucosidase and pancreatic lipase), atherosclerosis (mitigation of LDL-cholesterol oxidation), and mutagenesis (suppression of DNA strand scission). However, such bioactivities may be compromised by the exposure of guava phenolics to the harsh conditions found along the human gastrointestinal (GI) tract. To overcome this limitation, guava phenolic extracts were microencapsulated with maltodextrin through freeze-drying. The effect of crude and microencapsulated extracts on biomarkers of metabolic diseases was compared before and after in vitro simulated GI digestion. Moreover, guava waste extracts were tested for their ability to interfere with the intracellular redox status of Caco-2 and HeLa cells incubated with free radicals. Microencapsulation considerably improved the bioaccessibility of guava phenolics across digestion stages, which reflected on the enhancement of most bioactivities measured, with the exception of pancreatic lipase inhibition (both pulp and waste extracts) and LDL oxidative protection (pulp extract). Meanwhile, microencapsulation accentuated intracellular antioxidant activity in Caco-2 cells induced by guava waste extract whereas a prooxidant effect in HeLa cells was intensified. This highlights the selectivity of the same extract toward different cell lines. Overall, microencapsulation was demonstrated as a promising tool for protecting and even enhancing the nutraceutical power of guava phenolics, reinforcing their relevance in the development of functional foods and nutraceutical products. Full article

Lung cancer is the most frequently diagnosed cancer and the leading cause of cancer death worldwide. Early detection of lung cancer can lead to identification of the cancer at its initial treatable stages and improves survival. Low-dose CT scan (LDCT) is currently the gold standard for lung cancer screening in high-risk individuals. Despite the observed stage migration and consistently demonstrated disease-specific overall survival benefit, LDCT has inherent limitations, including false-positive results, radiation exposure, and low compliance. Recently, new techniques have been investigated for early detection of lung cancer. Several studies have shown that liquid biopsy biomarkers such as circulating cell-free DNA (cfDNA), microRNA molecules (miRNA), circulating tumor cells (CTCs), tumor-derived exosomes (TDEs), and tumor-educated platelets (TEPs), as well as volatile organic compounds (VOCs), have the power to distinguish lung cancer patients from healthy subjects, offering potential for minimally invasive and non-invasive means of early cancer detection. Furthermore, recent studies have shown that the integration of artificial intelligence (AI) with clinical, imaging, and laboratory data has provided significant advancements and can offer potential solutions to some challenges related to early detection of lung cancer. Adopting AI-based multimodality strategies, such as multi-omics liquid biopsy and/or VOCs’ detection, with LDCT augmented by advanced AI, could revolutionize early lung cancer screening by improving accuracy, efficiency, and personalization, especially when combined with patient clinical data. However, challenges remain in validating, standardizing, and integrating these approaches into clinical practice. In this review, we described these innovative milestones and methods, as well as their advantages and limitations in screening and early diagnosis of lung cancer. Full article

Gastroesophageal cancers including esophageal and gastric cancer remain major causes of global cancer mortality, primarily due to late diagnosis and high recurrence rates after curative treatment. Current surveillance methods, such as endoscopy and imaging, are invasive, costly, and often inadequate for detection. Blood-based biomarkers (“liquid biopsies”) offer a minimally invasive alternative capable of real-time tumor monitoring. In this review, we summarize recent advances across all major classes of blood-derived biomarkers: circulating tumor DNA (ctDNA), methylated DNA, cell-free RNAs (microRNAs, lncRNAs, circRNAs), circulating proteins, autoantibodies, circulating tumor cells, extracellular vesicles, and metabolites. Reviewing the existing literature on gastroesophageal cancers, we highlight current evidence, validation phases, performance metrics, and limitations. Special attention is given to clinical trial evidence, including ctDNA monitoring studies, that demonstrated earlier recurrence detection compared to imaging. While blood-based biomarker analysis has not yet supplanted endoscopy as standard of care in gastroesophageal cancer surveillance, the convergence of multi-analyte assays, AI, and clinical validation trials positions liquid biopsy as a transformative tool in the surveillance of gastroesophageal cancers. Full article

Malaria remains a considerable challenge to international health, especially in returning travelers from endemic regions where exposure risk may be downplayed. Prompt and accurate diagnosis is crucial, especially when conventional diagnostic techniques are insufficient. This case report presents a 59-year-old man who developed fever, rash, and myalgia after returning from the Amazon rainforest. Initial laboratory tests demonstrated leukopenia, thrombocytopenia, transaminitis, and hyperbilirubinemia. Despite these abnormal results and a clinically suspicious presentation, malaria smears were negative. Since the symptoms did not resolve, a Karius test—a plasma-based microbial cell-free DNA sequencing assay—successfully detected the presence of Plasmodium vivax, thus establishing the diagnosis. The patient needed several treatment regimens for the recurrent attacks, including chloroquine and primaquine, artemether-lumefantrine, and eventually a combination of quinine and doxycycline together with a prolonged course of primaquine. His symptoms resolved completely after the last treatment regimen, along with the normalization of the blood counts and liver function tests. This case demonstrates the limitations of smear microscopy diagnosis in P. vivax infections, highlights the role of molecular diagnostics like the Karius test, and stresses the importance of preventing relapses with adequate hypnozoite clearance. It further highlights the importance of clinician awareness and diligent follow-up in cases of travel-related Malaria, especially those with unusual presentations or recurrent symptoms. Full article

Cervical cancer remains a significant public health priority, particularly in low- and middle-income countries. In this context, liquid biopsy has emerged as a minimally invasive method for detecting and monitoring molecular biomarkers, offering advantages over traditional screening approaches. This systematic review included 21 studies published between 2015 and 2025 and was conducted in accordance with the PRISMA 2020 statement. The analysis examined the role of serum cytokines, circulating microRNAs (miRNAs), and circulating cell-free HPV DNA (cfHPV-DNA) in patients with cervical cancer or high-grade intraepithelial lesions. Circulating miRNAs—particularly miR-21, miR-29a, and miR-34a—are consistently associated with recurrence, tumor progression, and reduced survival. However, their immediate clinical translation remains limited by methodological variability and the lack of universal normalizers. In contrast, cfHPV-DNA, especially with ddPCR, exhibited the best study-level performance, with a specificity of 100% and a sensitivity of approximately 80–88%, across heterogeneous endpoints and analytic conditions. Consequently, cfHPV-DNA represents a promising tool for post-treatment surveillance and early detection of recurrence. Serum cytokines, such as TNF-α, IL-6, and IL-10, reflect inflammation and the tumor microenvironment. Nevertheless, their lack of standardization and variability across detection platforms restricts their reproducibility, positioning them as complementary rather than stand-alone markers. In conclusion, the evidence supports liquid biopsy as a promising tool in cervical cancer management; nonetheless, only cfHPV-DNA is currently ready for clinical application, whereas miRNAs and cytokines require multicenter validation and technical standardization before implementation. Full article