Search Results (424)

Treatment-refractory rectal cancer liver metastasis represents a major therapeutic challenge, particularly in the absence of actionable genomic biomarkers. Functional precision oncology approaches integrating genomic profiling with patient-derived organoid (PDO) drug testing may provide biologically informed therapeutic prioritization. A 50-year-old female patient with KRAS/TP53-mutant, microsatellite-stable (MSS) rectal adenocarcinoma refractory to FOLFIRINOX was enrolled. A liver metastasis from a treatment-refractory rectal cancer patient was processed to establish three-dimensional patient-derived organoids. Histopathological concordance was assessed using H&E and p53 immunohistochemistry. Comprehensive genomic profiling was performed using a 637-gene targeted next-generation sequencing panel, enabling detection of single-nucleotide variants, indels, copy number variations, microsatellite instability, and tumor mutational burden. Functional drug sensitivity profiling was conducted in parallel 2D and 3D platforms using a customized 17-agent panel, followed by exploratory combinatorial validation. The organoids demonstrated high phenotypic and genomic concordance with the parental tumor, preserving key driver alterations (KRAS^A146T, TP53^R175H, APC frameshifts, CCNE1 amplification), microsatellite stability, and low tumor mutational burden (TMB: 6.37 mut/Mb). Functional screening identified selective sensitivity to bevacizumab (IC₅₀: 0.130 μM), doxorubicin (IC₅₀: 0.570 μM), carboplatin (IC₅₀: 0.950 μM), and topotecan (IC₅₀: 1.600 μM) in the 3D organoid model, with consistent cross-platform validation. An exploratory combination assay further supported enhanced viability suppression under bevacizumab-based regimens. Critically, at the time of manuscript preparation, the patient demonstrated radiological disease stabilization under bevacizumab plus trastuzumab deruxtecan, consistent with the organoid-derived response profile. These findings highlight the capacity of integrated genomic and organoid-based profiling to uncover therapeutic vulnerabilities beyond standard biomarker assessment. This proof-of-concept case report study demonstrates the feasibility and translational relevance of an established organoid-based functional precision oncology platform for therapeutic prioritization in metastatic rectal cancer. Full article

Background/objectives: Infections caused by multidrug-resistant (MDR) bacteria are becoming increasingly difficult to treat with recommended antimicrobials. Considering the critical and growing challenge of antimicrobial resistance (AMR), this study aims to evaluate the antimicrobial susceptibility patterns of Escherichia coli clinical isolates from dogs in Grenada. This research project consists of two distinct studies: a retrospective analysis of AMR in canine E. coli isolates collected between 2010 and 2020, and a cross-sectional study characterizing the genotypic AMR profiles of E. coli isolates obtained between April and June 2023. Methods: A retrospective analysis of antibacterial sensitivity test (ABST) reports from canine clinical samples submitted to the Small Animal Clinic at St. George’s University (SGU), St. George’s, Grenada, between 2010 and 2020 revealed a notable prevalence of AMR among canine E. coli isolates. To further investigate the underlying mechanisms of this resistance, the study analyzed canine E. coli isolates that exhibited phenotypic resistance in ABST assays. These isolates were subsequently screened for AMR-associated genes using polymerase chain reaction (PCR) and next-generation sequencing (NGS). Results: The retrospective study identified 153 canine clinical isolates positive for E. coli. The antimicrobial drugs, imipenem, cefotaxime and ciprofloxacin were found to be highly effective against these isolates. However, a gradual increase in AMR was observed for amoxicillin–clavulanic acid (34.88%), ampicillin–sulbactam (17.31%), cephalexin (43.08%), cefpodoxime (22.31%), cephalothin (68.42%), and doxycycline (37.04%). In the prospective study, PCR analysis of resistant canine E. coli isolates detected the tetA (577 bp) and blaTEM (686 bp) genes. These AMR determinants were further confirmed through analysis of NGS reads and assembled contigs. Additionally, NGS-based predictions identified genes associated with resistance to aminoglycosides and potentiated sulfonamides. Conclusions: This study demonstrates that E. coli from dogs in Grenada exhibits resistance to tetracycline and several β-lactam antimicrobials. These findings underscore the need for rational antimicrobial stewardship and continuous AMR surveillance in small animal practice within the region. Full article

Background: Pulmonary arterial hypertension is a rare but life-threatening condition in children, with hereditary forms often being linked to mutations in genes such as bone morphogenetic protein receptor type 2 (BMPR2), caveolin 1 (CAV1), and potassium channel subfamily K member 3 (KCNK3). Among these, CAV1 mutations are associated with severe disease phenotypes, though cases resulting from de novo heterozygous CAV1 mutations with multi-system involvement remain rarely reported. The CAV1 mutation (c.424C > T, p.Q142X) disrupts caveolin-1 function, leading to dysregulated pulmonary vascular remodeling and multi-system abnormalities. Methods: This was a retrospective case study of a pediatric patient with hereditary PAH. The patient was followed at our hospital from initial presentation until death. Clinical data were collected from medical records, including physical examinations, laboratory tests, echocardiography, chest X-ray, computed tomography pulmonary angiography (CTPA), and genetic analysis. The patient was treated sequentially with various PAH-targeted medications. This report also includes a review of the relevant literature on CAV1-associated PAH. Results: A female aged 3 years and 11 months was diagnosed with hereditary PAH associated with a de novo heterozygous CAV1 mutation (c.424C > T, p.Q142X). Both parents underwent genetic testing and were negative for the mutation, confirming its de novo origin. Clinical manifestations included special facial features, congenital telangiectasia, cutis marmorata (marbled skin), congenital cataract, hereditary lipodystrophy, and severe PAH. The patient presented with progressive exercise intolerance, syncope, and worsening dyspnea over nine years. Echocardiography revealed pulmonary hypertension with an estimated pulmonary artery systolic pressure of 69–105 mmHg, right heart enlargement, right ventricular hypertrophy, and moderate tricuspid regurgitation. Blood and urine metabolic screenings were normal. A chest X-ray showed progressive enlargement of the cardiac silhouette and bulging of the pulmonary artery segment. CTPA demonstrated pulmonary hypertension, secondary right heart dysfunction, decompensated right ventricular function, and mosaic perfusion in both lungs, suggestive of small arterial branch occlusion. Right heart catheterization was declined by the parents. Thus, the diagnosis of PAH was established based on clinical, echocardiographic, CTPA, and genetic findings. The patient was hospitalized four times and lost to follow-up from 2017 to 2023. She received sequential treatment with digoxin, hydrochlorothiazide, tadalafil, ambrisentan, selexipag, and treprostinil. Despite these therapies, pulmonary artery pressure continued to rise with progressive clinical deterioration. The patient ultimately died at 13 years of age due to a pulmonary hypertensive crisis and multiple organ failure following a severe episode of gastroenteritis. Conclusions: Despite aggressive treatment with multiple targeted reduced pulmonary artery pressure drug therapies, managing hereditary PAH caused by CAV1 mutations in children remains a significant challenge, with a high mortality rate. Early genetic diagnosis, regular follow-up, and individualized treatment are crucial. It requires the joint efforts of patients, parents, and healthcare providers. Full article

Leishmaniasis remains a major neglected tropical disease with limited therapeutic options, challenged by drug toxicity and emerging resistance to current treatments like miltefosine. In this study, a virtual library of approximately 150 azole-derived compounds was screened in silico to identify promising thiazole and imidazole scaffolds, leading to the rational design of novel hybrid molecules. Molecular docking against thioredoxin reductase (PDB ID: 4CBQ), a key enzyme in the redox metabolism of Leishmania mexicana, showed improved binding affinity compared to miltefosine, with compound 3f showing the most favourable interaction profile. Among the synthesized series 3a–f, compound 3f (4-NO₂Ph) exhibited the most favourable predicted binding parameters within the series (∆G = −16.08, Ki = 0.0019 nM). Biological evaluation was performed against L. mexicana promastigotes as an early-stage phenotypic screening model to identify active compounds with potential relevance during the initial infective phase, and a markedly improved in vitro inhibitory effect (IC₅₀ = 22.41 µM) compared to miltefosine (IC₅₀ = 132.42 µM), representing a six-fold increase in molar potency. Furthermore, hybrid thiazolyl–imidazole systems (series 3) consistently outperformed single-core analogues, likely due to enhanced molecular planarity and lipophilicity provided by the imine linkage. Cytotoxicity assays in Vero cells revealed a high safety margin for the lead compounds, with compound 3f achieving a Selectivity Index (SI) of around 89, significantly outperforming the reference drug. Acute toxicity studies (LD₅₀) in murine models further confirmed the safety profile, with values exceeding 2000 mg/kg for the most active derivatives. These findings identify thiazolyl–imidazole hybrids as promising early-stage scaffolds for antileishmanial drug discovery, particularly for early infection/prophylactic screening. Full article

Restless legs syndrome (RLS) is a common sensorimotor disorder with limited treatment options and incompletely understood pathophysiology. Genome-wide association studies have identified numerous risk loci, but translating these findings into causal genes and therapeutic targets remains challenging. We performed a proteome-wide association study (PWAS) integrating RLS genome-wide association study (GWAS) data from FinnGen with two brain pQTL datasets (ROSMAP and Banner). We validated the identified proteins using TWAS, SMR, and colocalization analyses using brain pQTL and eQTL datasets. To further investigate peripheral protein associations, we performed SMR using plasma pQTL data from the UK Biobank Pharma Proteomics Project (UKB-PPP). We also conducted a phenome-wide association study (PheWAS) to screen for potential off-target effects of the prioritized genes, followed by drug prediction using DSigDB and molecular docking. PWAS identified GLO1, along with GRWD1 and MAP2K5, as significantly associated with RLS. GLO1 was identified by brain-based SMR (p = 0.0001), colocalization (PP.H4 = 0.96), TWAS (p = 0.048), and was confirmed by plasma-based SMR (p = 3.16 × 10⁻⁹) as the only protein associated with RLS. PheWAS analysis, without associations for 783 non-RLS phenotypes, confirmed the specificity of GLO1. Among 27 predicted GLO1-targeting compounds, Gambierol had the strongest binding affinity (−8.3 kcal/mol). This proteogenomic study identifies GLO1 as a prioritized causal gene and promising drug target for RLS, combining brain and plasma data to provide new insights into pathogenesis and candidate drug development. Full article

Background/Objectives: Familial hyperaldosteronism type IV (FH-IV) is an extremely rare, clinically heterogeneous condition representing the least characterized familial subtype of primary aldosteronism (PA) caused by germline gain-of-function CACNA1H mutations. Despite growing molecular insights, optimal diagnostic and therapeutic strategies remain poorly defined. This systematic review aims to synthesize available evidence regarding the clinical, biochemical, and genetic characteristics of FH-IV, and to evaluate the efficacy of current pharmacological and surgical treatments. Methods: A systematic review was conducted in accordance with PRISMA guidelines and preregistered in PROSPERO (CRD420261324945). A comprehensive search of MEDLINE, Embase, and Web of Science identified studies reporting genetically confirmed FH-IV patients. Data concerning clinical phenotypes, diagnostic evaluations, treatment outcomes, and genetic backgrounds were extracted and analyzed. Results: The primary cohort included 31 fully characterized symptomatic patients, alongside 8 mutation-positive relatives (4 asymptomatic carriers and 4 symptomatic individuals). The genetic landscape was remarkably heterogeneous, encompassing 17 distinct CACNA1H mutations. Clinically, diagnosis was frequently delayed, often complicated by atypical normokalaemic presentations and misleading adrenal imaging. Surgical treatment was generally ineffective, frequently resulting in persistent or recurrent hypertension and biochemical dysregulation. Pharmacologically, patients often required multiple antihypertensive drugs, most frequently a combination of mineralocorticoid receptor antagonists (MRAs) and calcium channel blockers (CCBs). Conclusions: FH-IV is best conceptualized as a systemic adrenal channelopathy. While standard screening parameters are usually elevated, atypical biochemical profiles and misleading structural imaging can complicate the diagnostic process. Optimal management relies on multigene Next-Generation Sequencing (NGS) panels for definitive diagnosis and cascade screening of relatives. Finally, while the combination of MRAs and CCBs is commonly used in PA, it represents a valuable therapy for FH-IV, with dual L-/T-type CCBs emerging as a potential disease-specific option. Full article

Biofilms on meat-contact surfaces pose critical food safety risks. This study investigates the interplay between biofilm architecture, metabolic vigor, and antimicrobial resistance on retail surfaces in Pakistan. Screening 300 isolates from 120 surfaces identified 42 high-risk biofilm formers. Comprehensive phenotypic screening revealed that standard visual assays severely underestimate the viability of environmental strains. Biofilm biomass and metabolic activity correlated positively (Spearman’s ρ = 0.656, p < 0.001). Crucially, Ordinary Least Squares regression established that metabolic vigor, rather than physical biomass, independently predicts resistance severity. Phenotypic profiling revealed a high-risk landscape with 81.8% multidrug-resistant and 18.2% extensively drug-resistant isolates, including resistance to colistin and Linezolid. Alarmingly, 79.5% of critical resistance phenotypes compromised WHO Reserve category antibiotics, escalating to 100% on mincer machines. Ecological analysis demonstrated surface-driven partitioning; porous wood boards fostered diverse Enterobacteriaceae, while mincers selected for uniformly resistant clades. These findings highlight processing machinery as resilient reservoirs for untreatable pathogens, necessitating targeted anti-biofilm measures, such as matrix-degrading enzymes. Bridging a critical knowledge gap, this study is among the earliest integrated ecological analyses combining phylogenetic, metabolic, and resistance profiling in Pakistan’s non-poultry meat sector. Full article

Pesticide manufacturing industry wastewater is a complex mixture of potentially harmful components. If not properly treated, discharged effluents may pose serious risks to environment and organisms. In this study, influent and effluent wastewater samples from a pesticide factory were comprehensively non-screened by liquid chromatography high-resolution mass spectrometry, coupled with zebrafish embryo toxicity testing to assess whole effluent toxicity. A total of eight chemical groups were identified, including pesticides, antibiotics, nitrogen compounds, ketones, esters, amines and derivatives, other drugs, and other organic compounds. While wastewater treatment processes reduced most of the analyzed groups of compounds, compounds (e.g., 2-aminophenol, N-Nitrosodipropylamine, and carbamazepine) increased during the treatments. The influent samples were more toxic to zebrafish than the effluent samples in terms of lethality, teratogenic effects, developmental impacts, locomotor behavior, and neurotoxicity. The results showed that locomotor behavior was the most sensitive phenotypic toxicity endpoint, with significantly higher sensitivity than traditional acute lethal or teratogenic endpoints. Through a multi-dimensional assessment approach combining chemical screening, literature-based, risk ranking, and targeted quantification, we identified three predominant pesticide residues in the wastewater samples (both influents and effluents): hexaconazole, fenobucarb and isoprocarb. All three compounds exhibited additive or synergistic toxicity in zebrafish embryos. Exposure to ≥0.08% influent or ≥2% effluent increased inflammation (interleukin-1 beta, IL-1β), oxidative stress (copper/zinc superoxide dismutase, Cu/Zn-Sod), apoptosis (tumor protein p53, p53), and significantly impaired neurodevelopment in zebrafish larvae by altering the expression of sonic hedgehog a (shha), synapsin IIa (syn2a), and glial fibrillary acidic protein (gfap). This study suggests the necessity of incorporating non-apical endpoint (locomotor behavior) into whole effluent toxicity test, as this approach is essential for reducing the environmental risks posed by pesticide factory wastewater. Full article

Acute mountain sickness (AMS) arises from hypobaric hypoxia at high altitude and still lacks effective pharmacological treatments. Although hypoxic preconditioning via gradual ascent prevents AMS, the underlying molecular adaptations have not yielded therapeutics. Here, inspired by metabolic reprogramming during stepwise altitude adaptation, we screened for anti-hypoxia compounds and identified H0802 (N-(pyridin-2-yl) pyridine-2-carbothioamide) as the most promising candidate. H0802 markedly enhances hypoxic tolerance in mice, prolongs survival under acute hypoxia, improves survival during simulated high-altitude exposure, and attenuates hypoxia-induced lung injury, accompanied by combined anti-inflammatory and antioxidant effects. Transcriptomic profiling shows that H0802 elicits a gene expression signature resembling hypoxia, including key hypoxia-related genes (Edn1, Angptl4, Mt1, Gdf15, Slc7a5, and Hif-3α) involved in glucose and oxygen metabolism. Mechanistically, H0802 stabilizes endogenous hypoxia-inducible factor (HIF) proteins under normoxia by preventing ubiquitin-dependent degradation, thereby activating hypoxia-responsive genes. In vivo, H0802 pretreatment lowers circulating glucose and hepatic glycogen while increasing brain glucose uptake, suggesting a metabolic shift that preserves cerebral energy during acute hypoxic stress; it also modulates whole-body oxygen consumption. H0802 represents a candidate for anti-AMS therapy, and phenotypic optimization of H0802 provides a potential route for drug discovery. Full article

Reproducible morphological profiling, particularly for drug discovery, has become an important tool for compound evaluation. Established workflows such as CellProfiler provide a widely adopted foundation for Cell Painting analysis. However, conventional pipelines often require substantial manual configuration and technical expertise, which can limit scalability and accessibility. In this study, a fully automated deep learning-based workflow is presented for segmentation-driven morphological profiling from raw microscopy data. Using a curated subset of the JUMP Cell Painting pilot dataset, ground-truth masks were generated and used to train a U-net–based segmentation model in the IKOSA platform. Post-processing strategies were introduced to improve instance separation and reduce segmentation artifacts. The final model achieved strong segmentation performance (precision/recall/AP up to 0.98/0.94/0.92 for nuclei), with an average runtime of 2.2 s per 1080 × 1080 image. Segmentation outputs enabled large-scale feature extraction, yielding 3664 morphological descriptors that showed high correlation with CellProfiler-derived measurements (normalized MAE: 0.0298). Feature prioritization further reduced redundancy to 1145 informative descriptors. These results demonstrate that automated deep learning pipelines can complement established Cell Painting workflows by reducing configuration overhead while maintaining compatibility with validated morphological profiling standards. The proposed workflow may help improve resource efficiency in drug discovery and personalized medicine. Full article

In pancreatic cancer, cancer stem-like cells (CSCs) contribute to tumor initiation, reduced drug sensitivity, and recurrence. Limited strategies are currently available to target this cell population. Here we used a proteasome-low CSC enrichment system to identify microRNAs that negatively regulate CSC-like properties. From PANC-1 cells expressing a ZsGreen–ODC degron reporter, a proteasome-low population was isolated through sequential fluorescence-activated cell sorting of ZsGreen-positive cells. Molecular and functional analyses confirmed the CSC-like phenotype of this cell population. Integrated in silico analysis was used to select 31 microRNAs predicted to target CSC-related molecules, which were then evaluated by in vitro viability-based screening to identify candidates that selectively suppressed the viability of CSC-like cells, relative to non-CSCs. Moreover, comprehensive miRNA expression profiling revealed that miR-136-5p was downregulated in the CSC-like population and was therefore selected for further analysis. Mechanistically, miR-136-5p directly targets the 3′ untranslated region of DCLK1 and reduces its expression, with a greater reduction in the short isoform. Finally, in a CSC-derived xenograft mouse model, systemic delivery of miR-136-5p using super carbonate apatite nanoparticles significantly suppressed tumor growth. Taken together, these findings suggest that miR-136-5p restoration may provide a therapeutic approach for targeting CSC-driven tumor growth in pancreatic cancer. Full article

Background: Osteosarcoma (OS) is an aggressive bone tumor. The lack of physiologically relevant three-dimensional models that recapitulate the native tumor microenvironment hampers drug development and mechanistic studies. The study aimed to develop bone-mimetic microspheres for the construction of an OS model. Materials and Methods: We employed droplet microfluidics to fabricate bone-mimetic microspheres (named MSHA) from a composite of gelatin methacryloyl, polyethylene glycol diacrylate, and nano-hydroxyapatite (nHA). MNNG/HOS cells were cultured on MSHA microspheres and subsequently evaluated for their bioactivity and capabilities of stemness, migration, and invasion. Results: The microfluidic platform enabled efficient and scalable production of highly uniform MSHA microspheres with controlled sizes. MNNG/HOS cells cultured on MSHA maintained high viability and spontaneously formed compact tumor spheroids after 7 days. Compared with two-dimensional cultures, cells cultured on these microsphere-based platforms exhibited enhanced migration and invasion capacities, along with increased expression of relevant biomarkers. RNA sequencing further revealed the activation of cancer-related pathways. Notably, the incorporation of nHA into microspheres amplified these malignant phenotypes, potentially through the activation of ECM–receptor interaction and calcium signaling pathways. Conclusions: The microfluidics-fabricated MSHA microspheres, as biomimetic three-dimensional culture scaffolds, offer a promising platform for applications in mechanistic studies of osteosarcoma progression and drug screening. Full article

Background/Objectives: NF2-related schwannomatosis (NF2-SWN) is a genetic tumor predisposition syndrome of the nervous system caused by pathogenic variants in NF2 encoding the merlin tumor suppressor. Truncating variants in NF2 cause severe phenotypes with higher tumor burden, early mortality, and a lifetime need for multiple surgeries due to lack of medications that control schwannoma growth. Methods: We developed a functional precision medicine (FPM)-inspired workflow to identify drug sensitivities in cells isolated from a pediatric severe NF2-SWN patient’s spinal and peripheral schwannomas. Transcriptomic profiling, high-content drug sensitivity assays, tissue and isolated cell immunostaining, flow cytometry, and capillary-based immunoblotting were used to study the available tissues. Results: Aberrant merlin-dependent pathway expression was conserved between the spinal schwannoma and its cultured primary cells. Drug sensitivity screens in 2- and 3-dimensional formats revealed cytotoxic effects of fimepinostat in primary cells; dasatinib with brigatinib was the most effective cytostatic combination. Ineffective therapies attempted in the patient were also ineffective ex vivo. Conclusions: These data support the idea of using the FPM workflow to improve and individualize the standard of care for severe NF2-SWN patients using surgical samples. Full article

The anticancer ruthenium complex indazolium trans-[tetrachlorobis(1H-indazole) ruthenate (III)—also known as KP1019—inhibits cancer cell proliferation in vitro, causes tumor regression in animal models, and showed no dose-limiting toxicity in a phase I clinical trial. Previous studies found that KP1019 damages DNA in both cancer cells and the budding yeast Saccharomyces cerevisiae. To identify other potential targets of KP1019 along with pathways that modulate the drug’s cellular effects, we screened the yeast gene deletion strain library by quantitative high-throughput cell array phenotyping (Q-HTCP). Fitness differences, as judged by growth curve analysis, identified genes for which loss of function (gene deletion) interacts with (enhances or suppresses) KP1019 effects. Drug-enhancing deletions were enriched for DNA repair functions, consistent with DNA damage being a primary target of KP1019 in yeast. pH homeostasis also modified the effects of KP1019. Drug-suppressing deletions prominently involved ribosomal proteins. A mechanistic link between ribosomal protein function and KP1019 toxicity was supported by dose-dependent accumulation of Rpl7a-GFP in the nucleolus, which is a hallmark of ribosomal biogenesis stress. Furthermore, KP1019 acted synergistically with the TOR pathway inhibitor everolimus to inhibit cell proliferation. The resulting model, wherein KP1019 perturbs ribosome assembly, can inform the design of future combination therapies. Full article

Glioblastoma (GBM) is one of the most aggressive and therapy-resistant primary brain tumors, mainly due to its pronounced intratumoral heterogeneity and highly invasive phenotype. Patient-derived three-dimensional (3D) culture models, including tumor spheroids, represent valuable tools to preserve the cellular complexity, phenotypic plasticity, and microenvironmental features of GBM ex vivo. However, standardized and reproducible protocols for the generation and maintenance of GBM spheroids from surgical specimens are still limited. Here, we describe a detailed and robust protocol for the isolation, 3D cultures, and expansion of primary GBM cells obtained from patient biopsies, leading to the formation of stable and morphologically consistent spheroids. The protocol provides step-by-step instructions for tissue dissociation, cell seeding under low-adhesion conditions, optimization of culture density, and long-term spheroid maintenance. In addition, we include guidelines for the morpho-phenotypical characterization of the resulting 3D structures. This methodological workflow offers a reproducible platform for modeling GBM in vitro, enabling the study of tumor biology and supporting translational applications such as drug screening, biomarker validation, and patient-specific therapeutic testing in a 3D context. Full article