Search Results (111)

Background: Multiple myeloma (MM) is characterised by clonal expansion of plasma cells (PCs) in the bone marrow (BM). Disease assessment and monitoring typically rely on invasive, single-site procedures, such as BM biopsies (BMBs), which may inadequately capture intra- and extra-medullary spatial heterogeneity. Circulating plasma cells (CPCs), enriched from peripheral blood (PB), may represent a minimally invasive alternative or adjunct for molecular profiling. Objectives: This study aimed to evaluate the feasibility of using CPCs, enriched from PB, for mRNA analysis in plasma cell dyscrasia, including MM. A secondary objective was to assess whether mRNA expression levels of the endoplasmic reticulum (ER) stress sensors X-box-binding protein 1 (uXBP1) and activating transcription factor 6 (ATF6), and the chaperone-mediated autophagy marker Lysosomal-Associated Membrane Protein 2 (LAMP2A) by droplet digital PCR (ddPCR), were associated with resistance to the second-generation proteasome inhibitor (PI) carfilzomib (Cfz). Methods: Multiple myeloma (MM) cell lines (H929 and U266) and their carfilzomib-adapted derivatives were used to establish and validate droplet digital PCR (ddPCR) assays targeting ER stress (uXBP1, ATF6) and autophagy-related (LAMP2A) transcripts. Solid tumour cell lines, including serum-starved HeLa cells, served as biological controls to support assay specificity and sensitivity. Total RNA was extracted and reverse-transcribed to complementary DNA prior to analysis. Transcript levels were normalised to those of β-actin or GAPDH, as appropriate. ddPCR was performed using the BioRad QX200 system, with results reported as the normalised transcript copy number per microlitre of reaction. Matched bone marrow aspirate (BMA) and peripheral blood (PB) samples were collected at a single clinical time point from adults undergoing investigation for plasma cell dyscrasia between January 2021 and December 2023. Samples were obtained as part of standard clinical care and/or during treatment with Bortezomib (Btz) or Cfz. Mononuclear cells were isolated by density gradient centrifugation, and CD138⁺ plasma cells were enriched by fluorescence-activated cell sorting. Enrichment purity was assessed qualitatively by immunofluorescence microscopy using CD138 and CD117 markers. Samples yielding fewer than 1000 CD138⁺ plasma cells were excluded, resulting in 10 evaluable matched patient pairs. Results: Carfilzomib-adapted MM cell lines demonstrated reduced levels of uXBP1, ATF6, and LAMP2A mRNA compared to treatment-naïve cells. In matched BM and PB samples, uXBP1 mRNA levels were consistently lower in circulating PCs than in BM-derived PCs, whereas ATF6 mRNA levels were concordant between compartments. LAMP2A mRNA levels exhibited marked inter-patient heterogeneity. Conclusions: This study demonstrates the feasibility of using CPCs as a minimally invasive source for mRNA-based biomarker assessment and highlights ddPCR as a sensitive platform for quantifying ER stress and chaperone-mediated autophagy related transcripts in CPCs. Cfz adaptation was associated with reduced levels of uXBP1 and LAMP2A mRNA in MM cell lines. Future prospective studies evaluating the clinical utility of ER stress and chaperone-mediated autophagy associated transcripts in CPCs as predictors of resistance to PI are warranted. Full article

Background: Forensic DNA phenotyping (FDP) enables the inference of externally visible characteristics (EVCs) and biogeographic ancestry when conventional STR profiling is inconclusive. The ForenSeq™ Imagen kit (107 SNPs) integrates phenotype-, ancestry-, and Y-SNPs markers; however, its performance under partial genotyping conditions has not been systematically evaluated. Methods: Ninety-four samples from a Mexican mestizo population were analyzed using the ForenSeq™ Imagen kit on the MiSeq FGx™ platform. Due to incomplete genotype recovery, 41 samples with >60% locus detection were selected for downstream analyses. Phenotype prediction was performed using the HIrisPlex-S model, and ancestry inference was assessed through principal component analysis. In silico simulations were conducted to evaluate locus-specific dropout effects. Results: Eye color prediction showed both reduced feasibility (68.3%) and lower overall accuracy (56.1%), primarily driven by systematic prediction failure when rs12913832 (HERC2) was absent, although accuracy among successfully predicted samples remained high (82.1%). In contrast, hair and skin color inference remained feasible in >97% and 100% of evaluable samples, respectively; however, classification accuracy was moderate (70% for hair and 61% for skin), improving substantially when allowing adjacent-category concordance (90.2% for skin). Ancestry inference was robust when at least 27 aiSNPs were detected, and Y-SNPs reliably distinguished male and female samples. In silico analyses confirmed the critical contribution of rs12913832 to eye color model operability. Conclusions: FDP performance under partial genotyping reflects a trade-off between prediction feasibility and accuracy and depends on locus-specific integrity rather than overall genotype completeness. The ForenSeq™ Imagen kit shows robustness for ancestry, sex, hair, and skin prediction, although with variable accuracy, whereas eye color inference remains structurally vulnerable to drop out of high-impact variants. Evaluating FDP systems under realistic non-ideal conditions is essential to define their true operational limits and ensure scientifically robust and responsible implementation. Full article

Ultraviolet (UV) radiation induces DNA damage and oxidative stress in melanocytes, shaping pigmentation phenotypes and elevating photocarcinogenesis risk. Human models that capture donor-linked genetic determinants of UV sensitivity remain limited. Here, we establish a genotype-informed UV response model using induced pluripotent stem cell (iPSC)-derived melanocytes from donors carrying defined MC1R variants. Differentiated cells recapitulated melanocytic morphology, marker expression, and pigmentation consistent with donor sun-sensitivity traits. Following narrowband UVB exposure, melanocyte lines with higher UV sensitivity showed reduced survival, prolonged checkpoint activation, and CPD-associated DNA damage signaling dynamics. Mechanistic analysis suggests that the interferon-regulated GTPase MX2 is associated with amplification of UV-induced p53 and p38 activation while promoting apoptosis independently of AKT. These findings support MX2 as a physiological enhancer of DNA damage signaling in normal melanocytes, distinct from its interferon-mediated role in melanoma. Our study provides a human-relevant platform linking pigmentation genotype to UV resilience and supports iPSC-derived systems as new approach methodologies (NAMs) for mechanistic and translational phototoxicology. Full article

Colorectal cancer (CRC) develops through both conventional adenoma–carcinoma and serrated neoplasia pathways, yet noninvasive screening still under-detects the advanced precursor lesions that enable true cancer prevention. Stool-based screening reduces CRC mortality, but its preventive impact remains constrained by limited detection of advanced precancerous lesions (APLs), including advanced adenomas and sessile serrated lesions. Next-generation multitarget stool DNA assays (mt-sDNA; e.g., Cologuard Plus) have established high sensitivity for CRC and specificity approaching 94%, leaving improved APL detection as the principal opportunity for innovation. This review presents a consensus framework for a multi-omic stool screening paradigm that integrates host epigenetic markers (DNA methylation) with gut microbiome features using artificial intelligence (AI). Multi-omics capture complementary layers of early tumor biology: epithelial shedding and field effects reflected in host methylation signals together with luminal ecological and inflammatory changes represented by microbial features. Evidence from cross-cohort microbiome studies indicates that microbial signatures provide an additive—rather than standalone—axis of information for CRC and its precursor lesions. Because microbiome-based models are highly susceptible to batch effects arising from collection devices, extraction chemistry, sequencing platforms, and bioinformatic pipelines, practical mitigation strategies are outlined, including harmonized pre-analytics, batch-aware study design, leakage-resistant validation, and computational harmonization. A translational roadmap linking analytical validity, locked-model development, and prospective colonoscopy-verified clinical validation is proposed, aligned with TRIPOD + AI, STARD, PROBAST-AI, SPIRIT-AI, CONSORT-AI, and DECIDE-AI reporting standards. Scenario modeling using BLUE-C prevalence estimates suggests that improving APL sensitivity from approximately 43% to 55–65% at ~94% specificity could translate to detecting roughly 13–23 additional advanced precancerous lesions per 1000 individuals screened, highlighting the potential prevention impact of a multi-omic approach. This framework aims to guide developers and clinical investigators toward next-generation stool tests capable of materially improving precursor-lesion detection while maintaining clinically acceptable specificity. Full article

Aspergillus fijiensis is an industrially important filamentous fungus, whose genetic analysis has been limited by the absence of species-specific tools. This study establishes an optimized CRISPR–Cas9 genome editing platform for A. fijiensis, from protoplast preparation to DNA repair pathway engineering. Antibiotic screening first identified hygromycin B and 5-FOA (5-fluoroorotic acid) as effective positive and counter-selection markers. A high-efficiency protoplast regeneration protocol was developed depending on specific osmotic stabilization and mycelial competence. Evaluation of a plasmid-based CRISPR system revealed that while autonomous replication was feasible, gene editing was constrained by low efficiency and a predominant bias toward NHEJ (non-homologous end joining). We implemented a Cas9–sgRNA RNP (ribonucleoprotein) delivery approach, with RNP delivery alone producing frequent indels. However, targeted integration remained inefficient when using conventional MMEJ (Microhomology-mediated end joining) donors. By employing donors containing short (5 bp) microhomology arms between cleavage sites, we effectively engaged the MMEJ pathway, enabling precise insertions and large-fragment deletions in 92% of the analyzed transformants. Donor templates containing minimal 5 bp microhomology sequences could effectively shift the predominant repair pathway from NHEJ to MMEJ. These findings demonstrate that MMEJ is the superior pathway with a unique mechanism for genome engineering in A. fijiensis, providing a versatile toolkit for unlocking the biotechnological potential of this recalcitrant species and a successful paradigm for establishing genetic systems in other species. Full article

Proton therapy offers superior dose localization, yet the biological effects of low-energy protons relevant to superficial tissues remain underexplored. We report the design and validation of a proton irradiation setup developed at the Tandem Accelerator of NCSR “Demokritos” for controlled radiobiological experiments. Monte Carlo simulations using Geant4 and Monte Carlo Damage Simulation (MCDS—Monte Carlo Damage Simulation) were used to determine proton energy spectra, linear energy transfer (LET), and predicted DNA damage yields. A single layer (15–20 μm in thickness) of human keratinocytes (HaCaT) was irradiated at doses from 0.65 to 3.65 Gy, and γ-H2AX foci were quantified as markers of tracks including one or more DNA double-strand breaks. The system achieved a uniform dose rate of 0.37 Gy/min, as calculated with Geant4, with a mean proton energy of 4.1 MeV (LET ≈ 8 keV/μm). A strong correlation (R² = 0.93) was observed between proton dose and γH2AX foci per nucleus (~10 foci/Gy), reflecting damage-inducing proton tracks rather than individual DNA double-strand breaks. At higher doses, an increased fraction of cells exhibited pan-nuclear γH2AX staining, characterized by a diffuse γH2AX signal throughout the nucleus and commonly associated with extensive or clustered DNA damage and global chromatin phosphorylation. These responses are consistent with the well-established dense ionization patterns produced by low-energy protons, as indicated by the LET spectrum and supported by MCDS-predicted clustered damage yields. While the γH2AX assay does not directly resolve simple versus complex DNA lesions, the agreement between Monte Carlo modeling and the observed cellular stress responses indicates that the irradiation platform reliably reproduces the expected biological signatures of low-energy proton exposure. Consequently, the developed system provides a robust experimental tool for systematic investigations of cellular radiosensitivity and radiotoxicity, with potential applications in skin dosimetry and radioprotection. Full article

Forensic DNA profiling commonly relies on polymerase chain reaction (PCR) amplification followed by capillary electrophoresis (CE) or massively parallel sequencing (MPS), which requires expensive, laboratory-based equipment that depends on a stable power supply and is unsuitable for field applications. Here, we present a proof-of-concept assay that uses recombinase polymerase amplification (RPA) combined with exo probe detection for rapid, isothermal genotyping of insertion–deletion (InDel) markers. To the best of our knowledge, this study represents the first demonstration of forensic DNA typing using RPA coupled with exo probes. The reaction proceeds at 39 °C and combines amplification and detection in a single 20 min step. Thirteen DNA samples were genotyped in triplicate across eight InDel loci using allele-specific fluorescent probes. Genotypes were derived from differential endpoint fluorescence between matched and mismatched probes. Compared with benchmark genotyping, 97.07% of genotypes (n = 307) were correct at 1 ng DNA input. Accurate profiles were reliably obtained for DNA inputs as low as 250 pg, and partial profiles were still detectable at 31 pg. The results demonstrate that RPA-based InDel genotyping is fast, sensitive, and reproducible. With further optimization, such as refined probe design and selection of robust loci, the assay has clear potential to achieve complete accuracy and to be integrated into portable lab-on-a-chip platforms for rapid, field-deployable forensic identification. Full article

Background/Objectives: Triple-negative breast cancer (TNBC) is an aggressive subtype, with limited diagnostic options and no targeted early detection tools. Liquid biopsy represents a minimally invasive approach for detecting tumor-derived molecular alterations in body fluids. This scoping review aimed to comprehensively synthesize all liquid biopsy-derived molecular biomarkers evaluated for the diagnosis of TNBC in adults. Methods: This review followed the Arksey and O’Malley framework and PRISMA-ScR guidelines. Systematic searches of PubMed, Scopus, Embase, and Web of Science identified primary human studies evaluating circulating molecular biomarkers for TNBC diagnosis. Non-TNBC, non-human, hereditary, treatment-response, and nonmolecular studies were excluded. Data on study design, patient characteristics, biospecimen type, analytical platforms, biomarker class, and diagnostic performance were extracted and synthesized descriptively by biomolecule class. Results: Thirty-two studies met the inclusion criteria, comprising 15 protein-based, 12 RNA-based, and 6 DNA-based studies (one reporting both protein and RNA). In total, 1532 TNBC cases and 3137 participants in the comparator group were analyzed. Protein biomarkers were the most frequently studied, although only APOA4 appeared in more than one study, with conflicting results. RNA-based biomarkers identified promising candidates, particularly miR-21, but validation cohorts were scarce. DNA methylation markers showed promising diagnostic accuracy yet lacked replication. Most studies were small retrospective case–control designs with heterogeneous comparators and inconsistent diagnostic reporting. Conclusions: Evidence for liquid biopsy-derived biomarkers in TNBC remains limited, heterogeneous, and insufficiently validated. No biomarker currently shows reproducibility suitable for clinical implementation. Robust, prospective, and standardized studies are needed to advance liquid biopsy-based diagnostics in TNBC. Full article

Early cancer detection is crucial for improving survival rates and treatment outcomes. Electrochemical biosensors have emerged as powerful tools for early cancer detection due to their high sensitivity, specificity, and rapid detection capabilities. This review explores recent advancements (2015–2025) in electrochemical biosensors for cancer biomarker detection, their working principles, novel nanomaterial-based enhancements, challenges, and prospects for clinical applications. Specifically, we highlight the electrochemical detection of protein biomarkers (e.g., CEA, PSA, CRP), nucleic acid markers (ctDNA, miRNA, methylation patterns), and metabolic indicators, emphasizing their clinical relevance in early diagnosis and monitoring. Unlike previous reviews which focus on either biomarker classes or sensor platforms, this review uniquely integrates both factors. This review provides a novel perspective on how next-generation electrochemical biosensors can bridge the gap between laboratory development and real-world cancer diagnostics. Full article

The genetic improvement of Phalaenopsis-type Dendrobium, a valuable ornamental and medicinal orchid, is hindered by the lack of a complete reference genome. In this study, a transcriptome-based approach was employed to develop and validate insertion–deletion (InDel) markers for genetic analysis and variety identification. RNA-seq was performed on two distinct varieties, resulting in the de novo assembly of 156,108 unigenes. A bioinformatics pipeline was developed to identify 5083 high-quality InDel loci, from which 1029 potential markers were designed. Fifty primer pairs were selected and validated experimentally, with 84% successfully amplifying clear products, and 76% showing polymorphism. The polymorphism information content (PIC) of the markers ranged from 0.25 to 0.78, indicating their high potential for use in genetic diversity studies. These markers were used to classify 24 Phalaenopsis-type Dendrobium varieties into distinct genetic clusters. This work provides a scalable and robust platform for molecular breeding, DNA fingerprinting, and germplasm management in non-model species that lack a reference genome. By leveraging transcriptome data, these markers will contribute to the efficient genetic improvement of Dendrobium and other similar crops. Full article

Background: Adenomyosis is a benign uterine disorder defined by the invagination of ectopic endometrial-like tissue into the myometrium, causing heavy menstrual bleeding and pain. While its pathogenesis remains unclear, shared-symptomology with endometriosis suggests a common mechanism. Adenomyosis is often diagnosed after age 40 due to its complex presentation and the need for histopathological confirmation, underscoring the need for non-invasive markers. Methods: Ten unrelated women with histopathological diagnosis of adenomyosis were recruited. All recruits completed the WERF-EPHect questionnaire and were additionally questioned about any comorbidities. Genomic DNA isolated from peripheral blood was subjected to whole exome sequencing (WES) on Illumina NovaSeq 6000 and was analyzed using the Pairend NGS Cloud platform. Variants were filtered for MAF < 1% and were prioritized based on functional relevance and impact determined by in silico prediction tools. Variant selection adhered to stringent quality metrics to identify candidate variants associated with adenomyosis. Results: WES analysis did not reveal any variant common to the cohort. A total of eight pathogenic and two likely pathogenic novel variants were identified. Moreover, novel variants of p.(Val331Ile) in EFHB and p.(Phe14Val) in MEIS1 were the most frequently shared genetic variants in the cohort. Conclusions: Our findings suggest novel candidate genes for adenomyosis that warrant validation and functional investigation in larger, independent cohorts. Full article

The global aquaculture industry produces 91 million tons annually, yet achieving sustainable growth optimization remains constrained by incomplete understanding of regulatory system integration, polyploid genomic complexity, and disconnected molecular-environmental approaches. This systematic review synthesizes 180 peer-reviewed articles (1992–2025) from four databases, revealing that growth regulation operates through integrated multi-level networks: the GH-IGF axis, TGF-β/myostatin signaling, and epigenetic mechanisms responding dynamically to environmental inputs. Research acceleration is evident, with 52.2% of studies published during 2020–2025. Whole-genome duplication events created expanded gene repertoires enabling sophisticated regulatory control while presenting breeding challenges in polyploid species. CRISPR-Cas9 myostatin knockout achieves 15–30% growth enhancement, though practical implementation faces regulatory and economic barriers. DNA methylation and microRNAs enable environmental adaptation and transgenerational trait inheritance, offering complementary approaches to conventional breeding. Climate-resilient strain development requires integrating polyploid breeding methodologies, multi-omics phenotyping platforms, and validated epigenetic markers. Sustainable aquaculture intensification through precision genetics demands coordinated infrastructure development, harmonized regulatory frameworks, and international collaboration to address food security while adapting to climate change. This synthesis establishes research priorities bridging molecular mechanisms with practical applications for sustainable production enhancement. Full article

Nonalcoholic fatty liver disease (NAFLD) associated with high-fat diet (HFD) intake involves oxidative stress, inflammation, apoptosis, and genotoxicity. Carvacrol, a natural monoterpenoid phenol, exhibits potent antioxidant, anti-inflammatory, and cytoprotective properties, but its clinical application is limited by poor solubility and bioavailability. Chitosan nanoparticles, known for their biocompatibility and ability to enhance drug delivery, offer a promising nanotherapeutic platform for carvacrol delivery in NAFLD. Given the limited therapeutic options for NAFLD, there is a growing interest in nanotherapeutic strategies to enhance the delivery and efficacy of natural antioxidants. This study examined carvacrol-loaded chitosan nanoparticles (CRV-CNPs) in HFD-induced NAFLD. Sixty rats were assigned to six groups: control, CRV-treated (100 mg/kg), CRV-CNP-treated (100 mg/kg), HFD-fed, and two combination groups receiving HFD with either CRV or CRV-CNPs (100 mg/kg) for six weeks after 14 weeks on HFD. Liver function, metabolic markers, oxidative stress parameters, antioxidant enzyme levels, inflammatory and fibrotic mediators, apoptotic gene expression, genotoxicity indices, and histopathological changes were evaluated. CRV-CNPs showed greater efficacy than free carvacrol in ameliorating hepatic dysfunction and metabolic disturbances in HFD-fed rats. CRV-CNPs significantly reduced malondialdehyde, upregulated Nrf2, and elevated hepatic glutathione peroxidase, superoxide dismutase, catalase, and reduced glutathione. Inflammatory markers (NF-κB, iNOS, IL-1β, CRP) and transforming growth factor-beta were suppressed. Pro-apoptotic genes (Bax, Caspase-3) were downregulated, while antiapoptotic Bcl-2 was upregulated. CRV-CNPs also reduced DNA fragmentation and 8-hydroxy-2′-deoxyguanosine levels, indicating strong antigenotoxic effects. Histopathological and ultrastructural assessments revealed mitigated steatosis, preserved hepatic architecture, and maintained mitochondrial integrity. In conclusion, CRV-CNPs provide potent hepatoprotection by targeting oxidative stress, inflammation, apoptosis, and genotoxicity in NAFLD, demonstrating enhanced bioavailability, solubility, and sustained release, which support their potential as an advanced nanotherapeutic strategy for NAFLD management. 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

Hepatitis C represents a critical global health crisis, causing approximately 1.4 million deaths annually. Although 98% of cases are treatable, only about 20% of infected individuals know their hepatitis C virus (HCV) status, highlighting the urgent need for rapid and more efficient diagnostic management. Viral genetic material can be detected in serum or plasma within just one week of exposure, making it the most reliable marker and the gold standard for active HCV infection diagnosis. In this study, a biosensor was developed to detect conserved nucleotide sequences of HCV using a 3D surface electrode composed of poly-L-lysine (PLL) and carbon nanotubes (CNTs). PLL is a positively charged biocompatible polymer rich in amine groups, attractive for the immobilization of proteins, DNA, and other biomolecules. PLL was employed to construct a 3D surface with vertically aligned CNTs, achieving a high electron transfer rate. Cyclic voltammetry technique and scanning electron microscopy (SEM) were used to characterize the sensor platform, and analytical responses were measured by differential pulse voltammetry. This HCV biosensor detected the hybridization event by a significant reduction in DPV peaks in the presence of the ferri/ferrocyanide redox probe, without any intercalator agents. DNA responses were observed in phosphate-buffered saline (PBS) and cDNA-spiked serum samples, demonstrating its analytical specificity. These findings represent advances in analytical tools that can effectively address the challenges of timely diagnosis for asymptomatic HCV carriers. Full article