Abstract Background Machine-learning models based on tissue transcriptomic data are powerful tools for disease classification. However, their clinical adoption is limited by the invasive nature of tissue sampling. Furthermore, transcriptomic datasets are often affected by batch effects and gene-level noise, which compromise model generalizability across platforms and clinical cohorts. Methods We developed WBT-DC (Whole Blood Transcriptomics–based Disease Classification), a computational pipeline designed to overcome these challenges. WBT-DC integrates rank-based feature extraction to mitigate batch effects with an ensemble machine-learning framework that incorporates cross-validation and hyperparameter optimization. Its performance was systematically evaluated across five independent cohorts involving 2,164 participants and three disease contexts: Crohn’s disease (CD), ulcerative colitis (UC), and amyotrophic lateral sclerosis (ALS). We tested the model’s robustness across RNA-sequencing and microarray platforms. Additionally, an internal rheumatoid arthritis (RA) cohort (n = 165) was utilized for real-world prospective validation. Results WBT-DC demonstrated high accuracy, achieving ROC–AUC values of 0.90–0.94 in independent datasets when training and testing were conducted on the same platform. In cross-platform evaluations, the pipeline maintained robust performance with ROC–AUC values ranging from 0.71 to 0.84, consistently outperforming conventional gene expression-based models. In the RA validation cohort, WBT-DC achieved an ROC–AUC of 0.81, supporting its applicability in a real-world clinical setting. Conclusions WBT-DC provides a robust, non-invasive, and platform-agnostic framework for disease classification using whole-blood transcriptomics. By effectively addressing batch effects and platform variability, this pipeline offers a scalable solution for translating systems-level transcriptomic insights into applications.

Clear cell Renal Cell Carcinoma (ccRCC) is the most common subtype of renal malignancy and remains a major clinical challenge. This challenge underscores the urgent need to identify novel molecules with potential as therapeutic targets in ccRCC. Therefore, in this study, four novel pyrimidine-based derivatives of TG-101,209 (3a-d) were designed and synthesized as potential inhibitors of BUB1B (Budding Uninhibited by Benzimidazoles 1 Mitotic Checkpoint Serine/Threonine Kinase B), a mitotic checkpoint kinase involved in ccRCC pathogenesis. Complete structural characterization of all synthesized compounds was achieved using Fourier-transform infrared (FT-IR) spectroscopy, nuclear magnetic resonance (1H and 13C NMR), and mass spectrometry (MS). The crystalline architecture and intermolecular interactions of compound 3a were further elucidated by single-crystal X-ray diffraction. Theoretical computations were performed using Density Functional Theory (DFT) at the B3LYP/6-311++G(d,p) level of theory to investigate the electronic and structural properties of the most active compound. The computed IR spectrum of compound 3a showed excellent agreement with experimental data, supporting the structural findings from X-ray analysis. Hirshfeld surfaces (HS) analyses were carried out to visualize the intermolecular interactions in the crystal packing of 3a. This analysis highlighted key N-H & sdot;& sdot;& sdot;O and N-H & sdot;& sdot;& sdot;N hydrogen bonds, which were found to be in excellent agreement with the experimental single-crystal X-ray diffraction data. Multiple noncovalent interactions (N-H & sdot;& sdot;& sdot;O/N, C-H & sdot;& sdot;& sdot;O, C-H & sdot;& sdot;& sdot;pi) were identified in the solid state and quantitatively examined using Independent Gradient Model based on Hirshfeld partition (IGMH) analysis, confirming N-H & sdot;& sdot;& sdot;N as the strongest interaction. In vitro cytotoxicity assays on Caki-1 cells revealed that compounds 3a, 3c, and 3d exerted significant antiproliferative effects. Compound 3a exhibited superior BUB1B inhibition compared to the other derivatives, eliciting a robust apoptotic response as evidenced by enhanced PARP cleavage and caspase activation. Molecular docking and dynamics studies revealed stable and favorable binding affinity of the compound 3a within the BUB1B active site, consistent with experimental observations. The combined experimental and computational findings indicate that these pyrimidine derivatives, particularly compound 3a, act as promising BUB1B inhibitors with potential therapeutic relevance in ccRCC therapy.

Human tissues exhibit specialized metabolic functions that are essential for maintaining whole-body metabolic homeostasis. To systematically characterize organ- and cell-type-specific metabolic heterogeneity, we constructed 32 tissue-specific and 81 cell-type-specific enzyme-constrained genome-scale metabolic models (ecGEMs) by integrating the global human metabolic network with the tissue- and single-cell transcriptomic data from the Human Protein Atlas (HPA). Our analysis revealed pronounced differences in metabolic network architecture and activity across the human body, identifying key cell types that drive tissue metabolic functions. To demonstrate the applicability of these models, we employed the liver-specific ecGEM to investigate the metabolic reprogramming induced by a high-sugar, high-fat (HSHF) diet, a primary driver of metabolic dysfunction-associated fatty liver disease (MAFLD). Flux balance analysis revealed a fundamental transition in hepatic metabolism: from a flexible, multi-functional system toward a constrained, lipid-centric regime. This state is characterized by carbohydrate and lipid overload, mitochondrial respiratory dysfunction, and a compromised capacity for reactive oxygen species (ROS) detoxification. These computational predictions were validated through integrative analysis of transcriptomic data from a human MAFLD cohort and metabolomic profiles from an in vivo HSHF rat model. Together, this work provides a comprehensive atlas of human metabolic models, enabling the systematic investigation of metabolic features across tissues and conditions from a systems-level perspective.

Extremely low-frequency (ELF) magnetic fields generated by power-line sources are ubiquitous, yet their long-term effects on neuronal cells remain unclear. We investigated whether continuous exposure (72 - 96 h) to a 60 Hz ELF magnetic field induces oxidative DNA damage and alters cell death pathways in differentiated SH-SY5Y human neuroblastoma cells. Neuron-like cells generated by retinoic acid and brain-derived neurotrophic factor were exposed to 1-3 mT ELF magnetic fields for 96 h, with sham-exposed cells as controls. Chromosomal integrity (Hoechst 33258 staining), apoptosis/necrosis (Annexin V-FITC/propidium iodide flow cytometry), oxidative DNA damage (apurinic/apyrimidinic site analysis), and redox balance (total oxidant and total antioxidant status) were assessed. ELF magnetic field exposure caused intensity dependent nuclear abnormalities, increased oxidative DNA lesions, early oxidative imbalance, and a predominance of necrotic over apoptotic cell death. These findings indicate that continuous low-intensity ELF magnetic field exposure disrupts redox homeostasis and compromises genomic stability in differentiated neuronal cells.

Hepatocellular carcinoma (HCC) remains difficult to treat due to its limited targets. Hence, we introduced phosphorylated c-Jun N-terminal kinase (p-JNK) as an anti-HCC target protein and investigated JNK-IN-5A and six derivatives (SET135, SET156, SET158, SET159, SET171, and SET172) which stabilize p-JNK. In vitro, these compounds outperformed sorafenib and regorafenib, inducing stronger p53-mediated cell-cycle arrest, autophagy, apoptosis, and reduced invasiveness via JNK/c-Jun pathways. RNA-seq profiling revealed distinct mechanisms: SET135 triggered autophagic necrosis via p62/SQSTM1, while SET171 induced reactive oxygen species (ROS)-driven necrosis. Systems biology analysis confirmed their enhanced efficacy. A 7-day GLP-like rat toxicity study showed SET135 and SET171 were well-tolerated. In vivo study performed with 21-day treatment of SET135 or SET171 showed superior anti-tumor effects compared to sorafenib via apoptotic mechanisms in HCC-transplanted mice. These findings highlight JNK-IN-5A derivatives as promising HCC therapeutic candidates capable of inducing both apoptotic and necrotic cell death.

Fish processing by-products represent a valuable and sustainable source of collagen for biomedical and functional applications. In the present study, collagen was extracted from the scales of red mullet (Mullus barbatus), gilthead sea bream (Sparus aurata), and European sea bass (Dicentrarchus labrax) using a green extraction approach based on a natural deep eutectic solvent (NADES) system composed of citric acid, xylitol, and water. The extracted collagens were comprehensively characterized by SDS-PAGE, Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), and X-ray diffraction (XRD) analyses. The results confirmed the presence of Type I collagen and demonstrated that the characteristic triple-helical structure and molecular organization were preserved throughout the extraction process. To preliminarily evaluate their potential as matrices for incorporating bioactive compounds, collagen matrices were combined with Zingiber officinale (ginger) extract at different ratios. The resulting combinations were evaluated for antioxidant, antimicrobial, and cytocompatibility properties. Antioxidant activity increased significantly with increasing ginger concentration, with the highest radical scavenging activity observed in combinations containing the greatest proportion of ginger extract. Similarly, antimicrobial activity against Escherichia coli and Staphylococcus aureus was enhanced by ginger incorporation, with stronger inhibition observed against the Gram-positive bacterium. Cytocompatibility studies performed on human dermal fibroblast (HDFa) cells revealed that selected collagen-ginger combinations maintained high cell viability and did not induce substantial membrane damage, nuclear abnormalities, apoptosis, or necrosis at appropriate concentrations. Overall, the findings demonstrate that fish scale-derived collagen obtained through a sustainable NADES-based extraction process possesses favorable structural and biological properties and may serve as a potential carrier matrix for plant-derived bioactive compounds. These findings provide preliminary evidence supporting the future development of environmentally friendly functional biomaterials with prospective applications in pharmaceutical, biomedical, and tissue engineering fields.

Carrier and newborn screenings are foundational components of preventive genomic medicine. With the growing demand for standardized sequencing-based carrier and newborn screening programs, a unified platform is needed to comprehensively assess genomic risks from the preconception stage through postnatal life, thereby facilitating screening management and program development. Here, we present FamilyRisk (https://www.phenomeportal.org/familyrisk), a standalone web server supporting comprehensive sequencing-based carrier and newborn screening data analysis at the individual, family, and population levels. The platform enables efficient evaluation of variants and generates clinically oriented personalized reports that summarize key findings and clinical interpretations. FamilyRisk also integrates an expandable database for referencing screening panels and clinical outcomes. Additionally, it provides complex disease risk assessment through polygenic risk score calculation and therapeutic recommendations based on pharmacogenomic profiles. The feasibility of FamilyRisk was demonstrated through applying newborn screening on a trio family, where the newborn was diagnosed with IDH3A -related mitochondrial encephalopathy. FamilyRisk successfully identified the homozygous pathogenic variant IDH3A c.802G > A inherited from two heterozygous parents. Additional cases further demonstrate its utility across diverse screening contexts. In conclusion, FamilyRisk is an integrated web server bridging genomic analysis and clinical screening to assist clinicians and researchers, support scalable sequencing-based screening programs, and advance precision medicine.

Objective: Epstein-Barr virus (EBV)-derived microRNAs (miRNAs) have been proposed as potential circulating biomarkers in EBV-associated malignancies. This study aimed to quantify the expression levels of four EBV-miRNAs (ebv-miR-BHRF1-2-5p, BHRF1-3, BART1-3p, and BART2-5p) in peripheral blood and to explore their possible diagnostic value in distinguishing lymphoma patients from healthy individuals. Methodology: This case control study included 50 newly diagnosed lymphoma patients (22 Hodgkin lymphoma, 28 Non-Hodgkin lymphoma) and 50 healthy controls recruited in 2025 at the Department of Internal Medicine (Hematology), Atatürk University. qRT-PCR analyses were performed at the Department of Medical Biology. EBV-miRNA expression levels were calculated using the ΔCt method with U6 snRNA as an internal control. Statistical analyses included FDR correction and ROC curve evaluation. Results: Ct values for U6 snRNA and all four EBV-miRNAs were significantly lower in lymphoma patients compared with controls (all p < 0.001, FDR < 0.001), indicating increased levels of circulating viral transcripts. ROC analyses showed that some miRNAs, particularly BHRF1-3 and BART1-3p, demonstrated notable discriminatory ability between patients and controls. No significant overall differences were observed between Hodgkin and Non-Hodgkin lymphoma; however, subtype analysis revealed significant variation in BHRF1-3 and BART2-5p expression (FDR = 0.005). Conclusion: Circulating EBV-miRNAs were elevated in lymphoma patients, and several miRNAs showed promising discriminatory performance. However, this study is limited by its single-center design and the absence of external validation. Therefore, these findings should be considered preliminary, and further research in larger and independent cohorts is needed to confirm the diagnostic utility of EBV-derived miRNAs in lymphoma.

Numerous web-based tools have been developed to support large-scale genomics research, whereas challenges remain due to their limited functionality. Therefore, we developed VarXOmics, an end-to-end, versatile web server for querying variants and genes, streamlining germline variant analysis, prioritizing variants with multi-omics insights, and providing interactive visualizations. The utility of VarXOmics was demonstrated by analyzing multiple small variants of the whole genome sequencing data from a breast cancer patient. It prioritized BRCA2 c.3751dup as the most likely pathogenic variant, and highlighted disease associations with cell cycle regulation, DNA repair pathways, and type 2 diabetes through multi-omics evidence, gene set enrichment, and network analysis. Overall, VarXOmics serves as a practical genomics platform for researchers and clinicians. It shows potential in identifying pathogenic variants and causal genes, uncovering the molecular mechanisms of disease pathogenesis, providing valuable references for clinical decision-making and therapeutic strategies, thus advancing precision medicine. VarXOmics is publicly available at https://www.phenomeportal.org/varxomics.

Bilacunaria microcarpa, a traditionally consumed yet underexplored species of the Apiaceae family, was evaluated for its neuroprotective potential in an in vitro Parkinson’s disease model induced by 1-methyl-4-phenylpyridinium (MPP⁺). Differentiated SH-SY5Y neuronal cells were co-treated with MPP⁺ and aqueous extracts derived from the plant’s flowers, stems, and leaves. Cell viability was assessed using the MTT assay, while nuclear morphology was examined via Hoechst 33258 staining. Enzymatic activities of AChE and caspase-3 were analyzed to investigate cholinergic and apoptotic responses, respectively. The antioxidant and oxidant status of the samples was determined by measuring the total antioxidant status and total oxidant levels. Chemical profiling analysis by HPLC-DAD identified chlorogenic acid as the predominant compound across all plant parts. The extracts demonstrated substantial enhancement in cell viability and were non-cytotoxic in fibroblast cultures. Moreover, all sample extracts caused a statistically significant reduction in caspase − 3 activity (p < 0.05). Furthermore, in silico blood-brain barrier permeability predictions indicated that some phytochemicals present in the extracts, such as resveratrol, o-coumaric acid, hydroxybenzoic acid, and vanillin, have the potential to permeate the blood-brain barrier. These outcomes indicate that Bilacunaria microcarpa exhibits considerable potential as a neuroprotective agent, warranting further exploration as a candidate for the development of therapeutic interventions for Parkinson’s disease.

Chronic kidney disease (CKD) characterized by the progressive loss of renal, represents a significant global health challenge. Central to CKD progression is kidney fibrosis, an irreversible process marked by the accumulation of extracellular matrix proteins. The development of effective antifibrotic therapies is thus crucial for improving patient outcomes. We conducted a comprehensive analysis of bulk RNA sequencing data from unilateral ureteral obstruction (UUO) and folic acid (FA)-induced nephropathy mice models, combined with single-cell RNA sequencing (scRNA-seq) to explore cellular heterogeneity and molecular mechanisms of kidney fibrosis. Differential gene expression analysis, gene co-expression network (CN) analysis, time-series clustering, and cell marker analysis were employed to identify core fibrosis-related genes. Our analyses revealed a set of 37 core fibrosis-related genes which are largely associated with inflammation and immune response and contributed to the production of extracellular matrix (ECM), with Ckap4 standing out as a key marker of kidney fibrosis. In vivo experiments demonstrated that knockdown of Ckap4 significantly reduced kidney fibrosis in UUO mice, as evidenced by decreased collagen deposition and improved renal function. Additionally, the repurposed small molecule drugs, especially CGP-60474, showed promising antifibrotic effects, further highlighting the potential of Ckap4 as a therapeutic target.

Neurodegenerative disorders are characterized by progressive neuronal dysfunction, cholinergic impairment, and disruption of cellular homeostasis. Ionic balance and metabolic stability are increasingly recognized as critical contributors to neuronal resilience under injurious conditions. The present study aimed to evaluate the potential protective effects of selected sodium (Na⁺) and potassium (K⁺) salts in differentiated SH-SY5Y neuronal cells subjected to hydrogen peroxide (H₂O₂; 100 µM), a widely used model of neuronal injury. Following H₂O₂ exposure, cells were treated with non-toxic concentrations of the following salts: Sodium citrate tribasic dihydrate (Na₃C₆H₅O₇·2H₂O), Sodium hydrogen carbonate (NaHCO₃), Disodium hydrogen phosphate (Na₂HPO₄), Potassium sodium tartrate tetrahydrate (KNaC₄H₄O₆·4H₂O). Salt treatments ameliorated the decline in cell viability and partially reversed changes in total antioxidant status (TAS), total oxidant status (TOS), and acetylcholinesterase (AChE) activity induced by H₂O₂. To further explore potential mechanistic interactions, molecular docking and molecular dynamics (MD) simulations were conducted on human AChE. The salts were found to interact primarily with peripheral residues surrounding the active-site gorge, suggesting a possible allosteric influence rather than direct engagement with the catalytic triad. Among the tested compounds, disodium hydrogen phosphate (Na₂HPO₄) exhibited the most stable binding profile over 100 ns MD simulations. Overall, these findings provide preliminary evidence that selected Na⁺- and K⁺-based salts may attenuate neuronal injury and support cellular function under stress conditions. Given their established safety profiles and accessibility, these compounds warrant further investigation as potential adjunctive agents for mitigating processes relevant to neurodegeneration.

Alzheimer's disease (AD) is a debilitating neurodegenerative disorder characterized by cognitive decline and memory loss. Current treatments offer limited efficacy, necessitating the development of innovative multitarget therapeutic strategies. Here, we present N 3,N 5-bis(2-(5-methoxy-1H-indol-3-yl)ethyl)-2,6-dimethyl-4-(2-nitrophenyl)pyridine-3,5-dicarboxamide (HCM-01), a novel compound developed to target multiple neurodegenerative pathways implicated in AD. In vitro assays included MTT-based cell viability analyses performed in two complementary experimental settings: primary neuronal cultures and astrocyte-based in vitro cell culture models exposed to glutamate. In primary hippocampal neuronal cultures, glutamate exposure induced a statistically significant reduction in cell viability compared with vehicle-treated controls, consistent with glutamate-induced excitotoxicity. Under these conditions, HCM-01 treatment resulted in a statistically significant improvement in neuronal viability, showing a greater protective effect compared with donepezil and memantine. In contrast, in astrocyte-based in vitro cultures, the applied glutamate concentration did not induce overt cytotoxicity, in line with the intrinsic neuroprotective and glutamate-buffering role of astrocytes. Accordingly, astrocytic experiments were designed to assess functional modulation of glutamate-handling mechanisms rather than cell survival. Western blot analysis in C8-D1A astrocytic cells demonstrated increased expression of excitatory amino acid transporter 2 (EAAT2) following HCM-01 treatment compared with control and reference drug-treated groups, suggesting modulation of astrocyte-mediated glutamate homeostasis. In parallel, redox analyses revealed that HCM-01 improved oxidative/antioxidative balance, as evidenced by increased total antioxidant capacity (TAC) and reduced total oxidant status (TOS), supporting an indirect antioxidant contribution to its functional effects. In vivo behavioral assessment of HCM-01 in a streptozotocin (STZ)-induced Alzheimer's model in female Sprague-Dawley rats demonstrated that administration of HCM-01 at doses of 50 mg/kg orally (oral, P.O. and intraperitoneal, I.P.) and 100 mg/kg (P.O.), significantly improved cognitive and memory functions in the passive avoidance (PA), Morris water maze (MWM), and locomotor activity tests. Moreover, histopathological and immunohistochemical analyses of different hippocampal regions revealed reduced neuronal damage, attenuation of tau pathology, antiamyloidogenic effect, and restoration of cholinergic function. Complementary in silico studies, including molecular docking, molecular dynamics simulations (MDS), and free energy calculations, suggested potential interactions of HCM-01 with the allosteric site of EAAT2. Taken together, these findings suggest that HCM-01 exerts neuroprotective effects against glutamate-induced excitotoxicity in primary hippocampal neurons while additionally modulating glutamatergic homeostasis and redox balance through functional mechanisms in astrocyte-based models, supporting its relevance as a multitarget preclinical candidate for early stage AD mechanisms.

Sarcopenia is a chronic disease characterized by loss of skeletal muscle mass and strength, posing a rising societal health challenge among the elderly, leading to increased risks of disability, fractures, falls, and mortality. Despite its clinical significance, there are currently no approved medicinal interventions for this condition. In this study, we used a systems biology framework to uncover potential therapeutic targets for sarcopenia. Based on computational analysis, CYC1 was identified as a key druggable protein. Following bioinformatic screening, ML-167 was selected as a candidate for repurposing. Guided by this insight, we have rationally designed and synthesized a novel series of ML-167-based derivatives, intending to modulate CYC1 activity. For structural validations, comprehensive spectroscopic techniques, including 1H and 13C NMR, MS, and, where applicable, single-crystal X-ray crystallography techniques were used. In vitro evaluation of the ML-167 derivatives in C2C12 cells established structure-dependent effects on cell viability. Several derivatives exhibited proliferation levels similar to the control group and indicate differences in biological activity among the derivatives. Computational studies, including molecular docking, density functional theory (DFT) calculations, and analyses of frontier molecular orbitals (FMOs), disclosed favorable electronic features, charge-transfer characteristics, and binding interactions with CYC1. Noncovalent interaction (NCI), reduced density gradient (RDG), electron localization function (ELF), and quantum theory of atoms in molecules (QTAIM) analyses highlighted the role of dispersive forces and hydrogen bonding in stabilizing the ligand-protein complex. Structure–activity relationship (SAR) analysis and in vitro cell proliferation assays identified compounds 3a, 3f, and 5a as the most promising leads, demonstrating optimal binding profiles and favorable biological activity.

The development of multifunctional implant coatings that promote biocompatibility while inhibiting bacterial adhesion is of critical importance in orthopedic and dental applications. In this study, Tantalum-Boron Nitride (Ta-BN) composite thin films were fabricated via dual-target magnetron sputtering at power levels of 15 W, 20 W, and 25 W, and their structural, biological, and antibacterial properties were evaluated. X-ray diffraction revealed amorphous structures for all coatings, while SEM confirmed dense, void-free morphologies. EDS showed a power-dependent compositional shift, with the 20 W group displaying the most balanced distribution (57.45% Ta, 32.55% B, 10.00% N). Biocompatibility testing with Saos-2 cells demonstrated the highest viability for the 20 W coating (91.3 f 5.2%), closely approximating the control (100 f 4.7%), whereas 15 W and 25 W coatings showed reduced values. Fluorescence microscopy further confirmed superior cell adhesion and uniform coverage on the 20 W surface. Antibacterial assays against E. coli revealed the strongest effect at 20 W, with bacterial viability reduced to 53.4 f 4.2%, outperforming both 15 W (79.5 f 6.3%) and 25 W (66.7 f 5.1%). These results indicate that Ta-BN coatings deposited at 20 W offer the optimal balance of biocompatibility and antibacterial performance, making them strong candidates for next-generation implant surface modifications.

Monastrol, a DHPM-based Eg5 inhibitor with well-known antiproliferative activity but limited therapeutic potential due to poor solubility and low bioavailability, was selected as the lead compound for the design of styryl-modified 3,4-dihydropyrimidin-2(1H)-ones with an improved pharmaceutical profile. Twelve derivatives (10-21) were synthesized via the Biginelli reaction and evaluated for cytotoxicity in HeLa and MCF-7 cells. Styryl derivatives 16 and 17 emerged as the most active. In HeLa cells, derivatives 17 (IC50 = 1.3 µM) and 16 (IC50 = 3.7 µM) were approximately 85-fold and 30-fold more potent than monastrol (IC50 = 111 µM), respectively. In MCF-7 cells, derivatives 16 and 17 displayed 18- to 20-fold higher potency than monastrol, respectively. Biological results also indicate that styryl derivatives 16 and 17 induce apoptosis in both HeLa and MCF-7 cells. In HeLa cells, activation of caspase-8, -9, and -3 suggests the involvement of both intrinsic and extrinsic pathways. In contrast, in MCF-7 cells, the increased expression of p53 and p21, together with PARP cleavage, suggests a p53-dependent apoptotic response. Derivatives 16 and 17 emerged as promising Eg5 inhibitors from docking studies, but their poor aqueous solubility (0.2-0.7 µM), despite high biological stability, highlights the need for formulation strategies to improve drug-like properties.

Glioblastoma (GBM) remains one of the most lethal primary brain tumors, characterized by aggressive proliferation, marked therapeutic resistance, and limited responsiveness to standard chemoradiotherapy. Therefore, identifying combination strategies capable of enhancing cytotoxic efficacy while minimizing toxicity is of considerable interest. In this study, we investigated the antitumor potential of Farnesene, a sesquiterpene natural compound, alone and in combination with the anthracycline chemotherapeutic Daunorubicin in U87MG glioblastoma cells. MTT assays demonstrated that Farnesene exerts strong tumor-selective cytotoxicity, with an IC₅₀ value of 4.65 µM in U87MG cells compared with 264.0 µM in non-malignant HDFa fibroblasts. Daunorubicin also reduced viability in a dose-dependent manner (IC₅₀ = 9.81 µM in U87MG), although with lower selectivity. Fixed-ratio combination analyses revealed pronounced synergism, as evidenced by markedly negative Bliss scores, high Highest Single Agent (HSA) advantages, and Combination Index values below 1 at submaximal concentrations. Flow cytometry using Annexin V/PI staining confirmed that the combination significantly increased both early and late apoptotic populations relative to monotherapies. FDA/PI fluorescent imaging supported these findings, showing a substantial elevation in non-viable PI-positive cells, whereas Hoechst 33,258 staining indicated preserved nuclear morphology at 24 h, consistent with early apoptotic engagement rather than immediate genotoxic collapse. Our results suggest that Farnesene not only exhibits potent and selective cytotoxicity toward glioblastoma cells but also enhances Daunorubicin-induced apoptosis through synergistic interactions. These findings highlight the preclinical potential of this combination and provide a rationale for further mechanistic and in vivo evaluation in experimental GBM models.

While single-omics analyses of Parkinson's Disease (PD) have demonstrated their ability in revealing the underlying molecular mechanisms, they often fail to provide a comprehensive view of the complete disease mechanisms. In this study, we leveraged multi-omics data from 64 heterogeneous, well-phenotyped PD patients, generated plasma metabolomics data and Olink proteomics data together with the gut and saliva metagenomics data, and investigated the altered molecular mechanisms and their interactions in association with the severity of motor function disorders in PD patients. Based on our multi-omics approach, we identified a panel of 58 biomarkers comprising one clinical variable, 10 proteins, and 17 metabolites from plasma, 26 gut species, and 4 saliva species for PD severity. These biomarkers exhibited superior predictive performance for assessing PD severity compared to those derived from single-omics datasets. The predictive power of our machine learning models based on these biomarkers was validated using additional multi-omics data from the same group of PD patients after a 3-month follow-up. The contribution of each omics dataset was evaluated by both supervised and unsupervised machine learning approaches, highlighting the importance of plasma metabolomics in disease stratification. Our study unveiled disease-related molecular alterations across multiple omics datasets, offering potential diagnostic and therapeutic insights for PD. Moreover, it underpinned the significance of employing multi-omics analyses when studying complex diseases like PD.

Mitochondria play a central role in energy metabolism, redox balance, and cellular homeostasis, and their dysfunction has been implicated in the pathogenesis of complex human diseases. Advances in systems biology and omics technologies have elucidated the mechanisms underlying these conditions, including metabolic dysfunction, mitochondrial impairment, inflammation, and redox imbalance. Preclinical and early clinical studies of combined metabolic activators (CMA), a formulation of bioactive metabolites, have demonstrated improvements in mitochondrial function and systemic metabolic profiles across multiple diseases. In this review, we provide a comprehensive overview of the mechanistic rationale for CMA, summarize evidence from preclinical models and clinical studies investigating CMA and its components, and evaluate its translational potential and challenges as a mitochondrial-targeted therapeutic strategy for complex human diseases.

Despite rapid advances in whole-genome sequencing (WGS), translating genomic findings into individualized insights remains challenging. We present GenRiskPro, a clinical decision-support and research platform, which automates WGS variant calling, annotation, prioritization, and reporting to deliver actionable findings and facilitate precision wellness. (To test the GenRiskPro platform, log on to https://www.phenomeportal.org/dashboard using the following credentials: Username: user@test.com; Password: test.) GenRiskPro integrates rare and common variant prioritization in a unified pipeline and in-house database, enabling both rare and complex disease and trait association analyses. Variant reporting is supported via LongevityCloud, which features a web portal for clinicians to review, adjust, and authorize the return of results in tabular and PDF formats, alongside a mobile app with artificial intelligence (AI) integration for sequenced individuals. Case studies using Turkish (TR, n = 275) and Swedish (SW, n = 101) WGS data assessed platform performance and variant prioritization: (a) predefined gene panels yielded a 1.82% positive rate for actionable findings per American College of Medical Genetics and Genomics (ACMG) secondary findings guidelines; (b) phenotype-driven support diagnosed cases including muscular dystrophy and microcephaly; (c) cohort-level ClinVar reassessment identified potentially misclassified pathogenic variants; (d) rare variant burden analysis revealed enrichment in ABCA4 for TR and SMPD1 in SW; and (e) population analysis highlighted carrier differences in trait-associated SNPs (rs12913832 and rs4988235) and PGx variants (CYP2B64 and CYP2B66). GenRiskPro unifies databases, literature, web development, and AI for rapid, user-friendly genomic analysis and reporting, which fosters collaboration among hospitals, researchers, clinicians, and patients.