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Keywords = drug-induced transcriptome data

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17 pages, 2774 KiB  
Article
Chronic Morphine Treatment Leads to a Global DNA Hypomethylation via Active and Passive Demethylation Mechanisms in mESCs
by Manu Araolaza, Iraia Muñoa-Hoyos, Itziar Urizar-Arenaza, Irune Calzado and Nerea Subirán
Int. J. Mol. Sci. 2025, 26(15), 7056; https://doi.org/10.3390/ijms26157056 - 22 Jul 2025
Viewed by 232
Abstract
Epigenetic regulation, particularly DNA methylation, plays a crucial role in embryonic development by controlling gene expression patterns. The disruption of this regulation by environmental factors can have long-lasting consequences. Opioid drugs, such as morphine, are known to cross the placental barrier and affect [...] Read more.
Epigenetic regulation, particularly DNA methylation, plays a crucial role in embryonic development by controlling gene expression patterns. The disruption of this regulation by environmental factors can have long-lasting consequences. Opioid drugs, such as morphine, are known to cross the placental barrier and affect the developing central nervous system, yet their precise epigenetic effects during early development remain unclear. This study aimed to elucidate the impact of chronic morphine exposure on the DNA methylation landscape and gene expression in mouse embryonic stem cells (mESCs). mESCs were chronically exposed to morphine (10 μM for 24 h). Genome-wide bisulfite sequencing was performed to identify DNA methylation changes, while RNA sequencing (RNA-Seq) assessed corresponding gene expression alterations. Global levels of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) were quantified using mass spectrometry. Morphine exposure induced global DNA hypomethylation and identified 16,808 differentially methylated genes (DMGs) related to development, cell signalling, metabolism, and transcriptional regulation. Integrative transcriptomic analysis with RNA-Seq data revealed 651 overlapping genes, including alterations in key epigenetic regulators involved on DNA methylation machinery. Specifically, Tet1 was upregulated with promoter hypomethylation, while Dnmt1 was downregulated, without changes in promoter methylation after morphine exposiure. Mass spectrometry results confirmed a global decrease in 5mC levels alongside increased 5hmC, indicating the involvement of both passive and active demethylation pathways. These findings demonstrate for the first time that morphine disrupts the epigenetic homeostasis of mESCs by promoting global and gene-specific DNA demethylation, which might be key to the phenotypic changes that occur in adulthood. This work provides novel mechanistic insights into how opioid exposure during early development may lead to persistent epigenetic alterations, with potential long-term implications for neurodevelopment and disease susceptibility. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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17 pages, 1350 KiB  
Review
Emerging Therapeutic Strategies Targeting GPX4-Mediated Ferroptosis in Head and Neck Cancer
by Jaewang Lee, Youngin Seo and Jong-Lyel Roh
Int. J. Mol. Sci. 2025, 26(13), 6452; https://doi.org/10.3390/ijms26136452 - 4 Jul 2025
Viewed by 605
Abstract
Ferroptosis, a regulated form of iron-dependent lipid peroxidation-induced cell death, has emerged as a compelling therapeutic strategy to overcome treatment resistance in head and neck cancer (HNC). Glutathione peroxidase 4 (GPX4), a selenoenzyme responsible for detoxifying phospholipid hydroperoxides, plays a central role in [...] Read more.
Ferroptosis, a regulated form of iron-dependent lipid peroxidation-induced cell death, has emerged as a compelling therapeutic strategy to overcome treatment resistance in head and neck cancer (HNC). Glutathione peroxidase 4 (GPX4), a selenoenzyme responsible for detoxifying phospholipid hydroperoxides, plays a central role in blocking ferroptosis and is frequently upregulated in therapy-resistant HNC subtypes. In this review, we examine the multifaceted regulation of GPX4 expression and function, including transcriptional, post-transcriptional, epigenetic, and proteostatic mechanisms. We explore how GPX4 suppression through pharmacologic inhibitors (e.g., RSL3, withaferin A, statins), metabolic stress, or combined therapies (e.g., radiotherapy, EGFR inhibitors, immunotherapy) induces ferroptosis and resensitizes resistant tumors. We also summarize emerging biomarkers, including GPX4, ACSL4, SLC7A11, and NCOA4, that predict ferroptosis sensitivity and may guide patient selection for ferroptosis-targeted therapies. Single-cell and spatial transcriptomics reveal significant intratumoral heterogeneity in ferroptosis susceptibility, underscoring the need for precision approaches. Despite promising preclinical data, challenges such as drug delivery, toxicity, and resistance mechanisms remain. Nevertheless, the ferroptosis-GPX4 axis represents a unique vulnerability in HNC that can be therapeutically exploited. Integrating ferroptosis modulation into personalized oncology may transform outcomes for patients with refractory disease. Full article
(This article belongs to the Special Issue Pathogenesis and Treatments of Head and Neck Cancer)
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26 pages, 3510 KiB  
Article
Comparative Transcriptomics Study of Curcumin and Conventional Therapies in Translocation, Clear Cell, and Papillary Renal Cell Carcinoma Subtypes
by Moses Owoicho Abah, Deborah Oganya Ogenyi, Angelina V. Zhilenkova, Freddy Elad Essogmo, Ikenna Kingsley Uchendu, Yvan Sinclair Ngaha Tchawe, Akaye Madu Pascal, Natalia M. Nikitina, Onoja Solomon Oloche, Maria Pavliv, Alexander S. Rusanov, Varvara D. Sanikovich, Yuliya N. Pirogova, Leonid N. Bagmet, Aleksandra V. Moiseeva and Marina I. Sekacheva
Int. J. Mol. Sci. 2025, 26(13), 6161; https://doi.org/10.3390/ijms26136161 - 26 Jun 2025
Viewed by 1042
Abstract
Currently, there is no standard treatment for renal cell carcinoma (RCC) that is free of side effects and resistance. Additionally, limited information exists on how curcumin affects the gene expression profiles of patients with translocation renal cell carcinoma (tRCC) and papillary renal cell [...] Read more.
Currently, there is no standard treatment for renal cell carcinoma (RCC) that is free of side effects and resistance. Additionally, limited information exists on how curcumin affects the gene expression profiles of patients with translocation renal cell carcinoma (tRCC) and papillary renal cell carcinoma (pRCC). The pathways responsible for metastasis in tRCC are still not well understood, and there is no established treatment or reliable biomarker to predict outcomes for metastatic tRCC. Primary clinical data from patients were retrieved from the TCGA database and analyzed using cBioPortal, stitch, string, R and Python. Various analyses were performed, including differential gene expression, protein-protein interaction (PPI) network analysis, drug-targeted gene analysis, gene ontology (GO), enrichment analyses, and systematic searches to assess the impact of curcumin on the transcriptomic profiles of tRCC, pRCC, and clear cell renal cell carcinoma (ccRCC). No significant impact of sensitive genes on survival in KIRC and KIRP was found, though a trend suggested they may delay disease progression. The combination of curcumin with sunitinib showed promise in overcoming drug resistance in ccRCC by inducing ferroptosis, reducing iron, and increasing ADAMTS18 expression. This study, leveraging data from the TCGA database and other databases explored the impact of curcumin on transcriptomic profiles in tRCC, pRCC, and clear cell RCC (ccRCC). Gene analysis revealed immune and metabolic differences, with KIRC showing a stronger immune response. This study is the first to propose that future research into the miR-148/ADAMTS18 genes and the ferroptosis pathway in tRCC and pRCC could lead to the development of new therapies and the identification of novel therapeutic targets, potentially overcoming drug resistance and metastasis. Full article
(This article belongs to the Section Bioactives and Nutraceuticals)
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31 pages, 12256 KiB  
Article
Inter-Relationship Between Melanoma Vemurafenib Tolerance Thresholds and Metabolic Pathway Choice
by Pratima Nangia-Makker, Madison Ahrens, Neeraja Purandare, Siddhesh Aras, Jing Li, Katherine Gurdziel, Hyejeong Jang, Seongho Kim and Malathy P Shekhar
Cells 2025, 14(12), 923; https://doi.org/10.3390/cells14120923 - 18 Jun 2025
Viewed by 810
Abstract
Melanomas quickly acquire resistance to vemurafenib, an important therapeutic for BRAFV600 mutant melanomas. Although combating vemurafenib resistance (VemR) to counter mitochondrial metabolic shift using mitochondria-targeting therapies has promise, no studies have analyzed the relationship between vemurafenib tolerance levels and metabolic plasticity. To determine [...] Read more.
Melanomas quickly acquire resistance to vemurafenib, an important therapeutic for BRAFV600 mutant melanomas. Although combating vemurafenib resistance (VemR) to counter mitochondrial metabolic shift using mitochondria-targeting therapies has promise, no studies have analyzed the relationship between vemurafenib tolerance levels and metabolic plasticity. To determine how vemurafenib endurance levels drive metabolic plasticity, we developed isogenic BRAFV600E VemR melanoma models with variant vemurafenib tolerances and performed an integrative analysis of metabolomic and transcriptome alterations using metabolome, Mitoplate-S1, Seahorse, and RNA-seq assays. Regardless of drug tolerance differences, both VemR models display resistance to MEK inhibitor and sensitivity to Wnt/β-catenin inhibitor, ICG-001. β-catenin, MITF, and ABCB5 levels are upregulated in both VemR models, and ICG-001 treatment restored vemurafenib sensitivity with reductions in MITF, ABCB5, phospho-ERK1/2, and mitochondrial respiration. Whereas β-catenin signaling induced TCA cycle and OXPHOS in highly drug tolerant A2058VemR cells, it activated pentose phosphate pathway in M14VemR cells with low vemurafenib tolerance, both of which are inhibited by ICG-001. These data implicate an important role for Wnt/β-catenin signaling in VemR-induced metabolic plasticity. Our data demonstrate that drug tolerance thresholds play a direct role in driving metabolic shifts towards specific routes, thus providing a new basis for delineating VemR melanomas for metabolism-targeting therapies. Full article
(This article belongs to the Collection Pathometabolism: Understanding Disease through Metabolism)
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16 pages, 1251 KiB  
Article
The Association Between Dexmedetomidine and Bradycardia: An Analysis of FDA Adverse Event Reporting System (FAERS) Data and Transcriptomic Profiles
by Robert Morris, Suguna Aishwarya Kuppa, Xinran Zhu, Kun Bu, Weiru Han and Feng Cheng
Genes 2025, 16(6), 615; https://doi.org/10.3390/genes16060615 - 22 May 2025
Viewed by 687
Abstract
Background/Objectives: Bradycardia, an uncharacteristically low heart rate below 60 bpm, is a commonly reported adverse drug event (ADE) in individuals administered dexmedetomidine for sedation. Dexmedetomidine is frequently used as a sedative and analgesic for both intubated and non-intubated patients due to its low [...] Read more.
Background/Objectives: Bradycardia, an uncharacteristically low heart rate below 60 bpm, is a commonly reported adverse drug event (ADE) in individuals administered dexmedetomidine for sedation. Dexmedetomidine is frequently used as a sedative and analgesic for both intubated and non-intubated patients due to its low risk of respiratory depression. The purpose of this study was to further characterize the safety profile of dexmedetomidine using safety reports collected from the FDA Adverse Event Reporting System (FAERS) and transcriptomic data. Methods: Association rule mining was used to both identify additional ADEs that presented concurrently with bradycardia in patients sedated with dexmedetomidine, as well as to characterize potential drug–drug interactions (DDIs). Furthermore, public transcriptomic data were analyzed to identify differentially expressed genes that may elucidate the genetic drivers of elevated bradycardia risk in those administered dexmedetomidine. Results: Bradycardia was the most frequently reported ADE for individuals administered dexmedetomidine. Other cardiovascular-related ADEs commonly associated with bradycardia included syncope (lift = 4.711), loss of consciousness (lift = 3.997), cardiac arrest (lift = 2.850), and hypotension (lift = 2.770). Several possible DDIs were identified, including Lactated Ringer’s solution (lift = 5.441), bupivacaine (lift = 2.984), and risperidone (lift = 2.434), which may elevate bradycardia risk. Finally, eight genes related to cardiac muscle contraction were identified as possible regulators of dexmedetomidine-induced bradycardia, including COX5B, COX6A2, COX8B, MYH7, MYH6, MYL2, UQCRQ, and UQCR11 in mouse cardiac cells. Conclusions: Key clinical takeaways include the co-presentation of multiple cardiovascular ADEs, including cardiac arrest, hypotension, and syncope, alongside dexmedetomidine-associated bradycardia. Furthermore, several possible DDIs with dexmedetomidine were also identified. Full article
(This article belongs to the Section Bioinformatics)
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32 pages, 5488 KiB  
Article
Persistent Transcriptome Alterations in Zebrafish Embryos After Discontinued Opioid Exposure
by Ryan J. North, Gwendolyn Cooper, Lucas Mears, Brian Bothner, Mensur Dlakić and Christa S. Merzdorf
Int. J. Mol. Sci. 2025, 26(10), 4840; https://doi.org/10.3390/ijms26104840 - 19 May 2025
Viewed by 593
Abstract
Much attention has been paid to the public health crisis that has resulted from the opioid epidemic. Given the high number of opioid users that are of childbearing age, the impact of utero exposure is a serious concern. Unfortunately, there is little knowledge [...] Read more.
Much attention has been paid to the public health crisis that has resulted from the opioid epidemic. Given the high number of opioid users that are of childbearing age, the impact of utero exposure is a serious concern. Unfortunately, there is little knowledge regarding the consequences of opioid exposure during early development. While neurobehavioral effects of opioid exposure are well-documented, effects of exposure on embryogenesis remain largely unexplored. To address this gap in knowledge, we investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish (Danio rerio) embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant (oxycodone HCl 10.6 ng/L and fentanyl citrate 0.629 ng/L) and therapeutically relevant doses (oxycodone HCl 35.14 μg/L and fentanyl citrate 3.14 μg/L) from 2 to 24 h post-fertilization (hpf), followed by another 24 h of opioid-free development. mRNA profiling at 48 hpf revealed dose- and drug-specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed transcripts (DETs) than higher doses, potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total, 892 DETs (corresponding to 866 genes) were identified across all conditions suggesting continued differential gene expression well after cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix (ECM) organization, cell adhesion, and visual and nervous system formation. Key pathways include those involved in axon guidance, synapse formation, and ECM biosynthesis/remodeling, all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that very early developmental exposure to opioids induces persistent transcriptomic changes which may have lasting implications for vertebrate cellular functions. Overall, these data provide insights into the molecular mechanisms of opioid-induced alterations during development. Full article
(This article belongs to the Special Issue The Zebrafish Model in Animal and Human Health Research, 2nd Edition)
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15 pages, 4436 KiB  
Article
Transcriptomic Plasticity of Human Alveolar Macrophages Revealed by Single-Cell RNA Sequencing Following Drug Exposure: Implications for Therapeutic Development
by Penny L. Groves, Levi Hockey, Brendan J. O’Sullivan, Lai-Ying Zhang, Zherui Xiong, Quan H. Nguyen, Maxine E. Tan, Viviana P. Lutzky, Rohan A. Davis, Daniel C. Chambers and Simon H. Apte
Int. J. Mol. Sci. 2025, 26(9), 4439; https://doi.org/10.3390/ijms26094439 - 7 May 2025
Viewed by 1074
Abstract
Alveolar macrophages (AM) must perform three seemingly opposing roles including homeostasis, driving inflammation, and facilitating tissue repair. Whilst there is now consensus (supported by a large body of human single cell RNA sequencing (scRNA-seq) data) that the cell subsets that perform these tasks [...] Read more.
Alveolar macrophages (AM) must perform three seemingly opposing roles including homeostasis, driving inflammation, and facilitating tissue repair. Whilst there is now consensus (supported by a large body of human single cell RNA sequencing (scRNA-seq) data) that the cell subsets that perform these tasks can readily be found based on their transcriptome, their ontogeny has remained unclear. Moreover, there is agreement that in all types of pulmonary fibrosis (PF) there is an expanded population of profibrotic AM that may aberrantly drive PF. From a therapeutic viewpoint, there is great appeal in the notion that the transcriptional program in different AM subsets is not fixed but remains plastic and amenable to pharmacological reprogramming. Accordingly, this study addresses this question by performing scRNA-seq on human AM following treatment with drugs or perturbagens including pioglitazone, trametinib, nintedanib, lipopolysaccharide and the natural compound endiandrin A. Each treatment induced a unique global transcriptional change, driving the cells towards distinct subsets, further supported by trajectory analysis, confirming a high level of plasticity. Confirmatory experiments using qPCR demonstrated that single exposure to a compound induced a relatively stable transcriptome, whereas serial exposure to a different compound allowed the cells to be reprogrammed yet again to a different phenotype. These findings add new insight into the biology of AM and support the development of novel therapies to treat PF. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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20 pages, 4025 KiB  
Article
Deciphering Nicotine-Driven Oncogenesis in Head and Neck Cancer: Integrative Transcriptomics and Drug Repurposing Insights
by Guo-Rung You, Daniel Yu Chang, Hung-Han Huang, Yin-Ju Chen, Joseph T. Chang and Ann-Joy Cheng
Cancers 2025, 17(9), 1430; https://doi.org/10.3390/cancers17091430 - 24 Apr 2025
Viewed by 588
Abstract
Background: Chronic nicotine exposure drives head and neck cancer (HNC) progression, yet its molecular mechanisms remain underexplored. This study examines nicotine-induced transcriptomic changes and potential therapies via drug repurposing. Methods: HNC cell lines (OECM1, SAS, and CGHNC9) were exposed to an [...] Read more.
Background: Chronic nicotine exposure drives head and neck cancer (HNC) progression, yet its molecular mechanisms remain underexplored. This study examines nicotine-induced transcriptomic changes and potential therapies via drug repurposing. Methods: HNC cell lines (OECM1, SAS, and CGHNC9) were exposed to an IC30 nicotine dose for three months to model chronic exposure in habitual smokers. Transcriptomic profiling of these sublines was integrated with TCGA-HNSC patient data. Differentially expressed genes (DEGs) underwent functional pathway enrichment analysis. Drug repurposing was conducted using gene–drug correlation analysis across GDSC, CTRP, and PRISM databases. Results: Transcriptomic analysis identified 1223 DEGs in nicotine-exposed HNC cells, and integration with TCGA-HNSC data defined a Nic-HNC gene set of 168 genes: 149 oncogenes and 19 tumor suppressors, with 36 oncogenes overexpressed in heavy smokers. Pathway analysis revealed the upregulation of oncogenic signaling, such as PI3K-AKT, alongside the suppression of immune regulation and metabolic reprogramming. Drug repurposing identified five compounds—AZD1332, JAK-8517, NU7441, BRD-K30748066, and neopeltolide—with the first two exhibiting the strongest inverse correlations with nicotine-induced oncogenes in heavy smokers, highlighting their potential as targeted therapies for tobacco-associated HNC. Conclusions: This study comprehensively characterizes nicotine-driven molecular dysregulation in HNC and proposes AZD1332 and JAK-8517 as promising therapeutic candidates through drug repurposing. These insights advance our understanding of nicotine’s oncogenic role and provide a foundation for translational research to develop targeted interventions for tobacco-associated HNC. Full article
(This article belongs to the Special Issue Advances in Drug Repurposing to Overcome Cancers)
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22 pages, 16615 KiB  
Article
The Mechanism of a Novel Mitochondrial-Targeted Icaritin Derivative in Regulating Apoptosis of BEL-7402 Cells Based on the SIRT3 and CypD-Mediated ROS/p38 MAPK Signaling Pathway
by Zenan Chen, Wei Li, Yan Zhao, Dingrui Liu, Jiahong Han and Enbo Cai
Molecules 2025, 30(8), 1667; https://doi.org/10.3390/molecules30081667 - 8 Apr 2025
Viewed by 622
Abstract
Tumorigenesis and progression are closely associated with apoptosis and primarily regulated by mitochondria, which are considered major targets for cancer therapy. In this study, twelve novel icaritin (ICT) derivatives were designed and synthesized, four of which were specifically targeted to mitochondria. Biological studies [...] Read more.
Tumorigenesis and progression are closely associated with apoptosis and primarily regulated by mitochondria, which are considered major targets for cancer therapy. In this study, twelve novel icaritin (ICT) derivatives were designed and synthesized, four of which were specifically targeted to mitochondria. Biological studies demonstrated that all compounds containing triphenylphosphine (TPP+) exhibited a substantial increase in antitumor activity compared to ICT and control compounds while also exhibiting notable selectivity for tumor cells over normal cells. Among these derivatives, Mito-ICT-4 exhibited the strongest antiproliferative effect, with an IC50 value of 0.73 ± 0.06 μM for BEL-7402 cells, which is 29 times lower than that of ICT, and an IC50 value of 67.11 ± 2.09 μM for HEK293 cells, indicating approximately 33-fold selectivity for tumor cells. High-performance liquid chromatography (HPLC) analysis revealed that Mito-ICT-4 significantly accumulated in the mitochondria of BEL-7402 cells, with the level of accumulation approximately 2.5 times greater than that of ICT. Further investigations demonstrated that upon entering the mitochondria of tumor cells, Mito-ICT-4 downregulated SIRT3 protein expression, disrupted intracellular redox homeostasis, and led to a substantial increase in mitochondrial ROS levels, abnormal CypD-dependent MPTP opening, mitochondrial membrane potential depolarization, and ROS release into the cytoplasm, ultimately triggering ROS-mediated apoptosis in BEL-7402 cells. Transcriptomic analysis identified differentially expressed genes and enriched pathways, highlighting the ROS-mediated p38-MAPK signaling pathway as a key mediator of Mito-ICT-4-induced mitochondria-dependent apoptosis. The effects of Mito-ICT-4 on the expression of key genes (SIRT3, CypD, P-MKK6, P-P38, and DDIT3) were further validated by qRT-PCR and Western blot analysis, with results aligning with transcriptomic data. The novel ICT derivatives synthesized in this study, with mitochondria-targeting functionality, provide a basis for the development of targeted antitumor drugs. Full article
(This article belongs to the Special Issue Design, Synthesis and Biological Activity of Novel Antitumor Drugs)
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27 pages, 10658 KiB  
Article
QSAR-Based Drug Repurposing and RNA-Seq Metabolic Networks Highlight Treatment Opportunities for Hepatocellular Carcinoma Through Pyrimidine Starvation
by Nicholas Dale D. Talubo, Emery Wayne B. Dela Cruz, Peter Matthew Paul T. Fowler, Po-Wei Tsai and Lemmuel L. Tayo
Cancers 2025, 17(5), 903; https://doi.org/10.3390/cancers17050903 - 6 Mar 2025
Viewed by 1177
Abstract
Background/Objectives: The molecular heterogeneity and metabolic flexibility of Hepatocellular Carcinoma (HCC) pose significant challenges to the efficacy of systemic therapy for advanced cases. Early screening difficulties often delay diagnosis, leading to more advanced stages at presentation. Combined with the inconsistent responses to [...] Read more.
Background/Objectives: The molecular heterogeneity and metabolic flexibility of Hepatocellular Carcinoma (HCC) pose significant challenges to the efficacy of systemic therapy for advanced cases. Early screening difficulties often delay diagnosis, leading to more advanced stages at presentation. Combined with the inconsistent responses to current systemic therapies, HCC continues to have one of the highest mortality rates among cancers. Thus, this paper seeks to contribute to the development of systemic therapy options through the consideration of HCC’s metabolic vulnerabilities and lay the groundwork for future in vitro studies. Methods: Transcriptomic data were used to calculate single and double knockout options for HCC using genetic Minimal Cut Sets. Furthermore, using QSAR modeling, drug repositioning opportunities were assessed to inhibit the selected genes. Results: Two single knockout options that were also annotated as essential pairs were found within the pyrimidine metabolism pathway of HCC, wherein the knockout of either DHODH or TYMS is potentially disruptive to proliferation. The result of the flux balance analysis and gene knockout simulation indicated a significant decrease in biomass production. Three machine learning algorithms were assessed for their performance in predicting the pIC50 of a given compound for the selected genes. SVM-rbf performed the best on unseen data achieving an R2 of 0.82 for DHODH and 0.81 for TYMS. For DHODH, the drugs Oteseconazole, Tipranavir, and Lusutrombopag were identified as potential inhibitors. For TYMS, the drugs Tadalafil, Dabigatran, Baloxavir Marboxil, and Candesartan Cilexetil showed promise as inhibitors. Conclusions: Overall, this study suggests in vitro testing of the identified drugs to assess their capabilities in inducing pyrimidine starvation on HCC. Full article
(This article belongs to the Section Cancer Drug Development)
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24 pages, 3411 KiB  
Article
Comparative Analysis of Proximal Tubule Cell Sources for In Vitro Studies of Renal Proximal Tubule Toxicity
by Courtney Sakolish, Han-Hsuan D. Tsai, Hsing-Chieh Lin, Piyush Bajaj, Remi Villenave, Stephen S. Ferguson, Jason P. Stanko, Richard A. Becker, Philip Hewitt, Weihsueh A. Chiu and Ivan Rusyn
Biomedicines 2025, 13(3), 563; https://doi.org/10.3390/biomedicines13030563 - 24 Feb 2025
Cited by 1 | Viewed by 1126
Abstract
Background/Objectives: The kidneys are essential for eliminating drugs and chemicals from the human body and renal epithelial cells are particularly vulnerable to damage caused by xenobiotics and their metabolites. Drug-induced kidney toxicity is a major cause of drug attrition during preclinical and clinical [...] Read more.
Background/Objectives: The kidneys are essential for eliminating drugs and chemicals from the human body and renal epithelial cells are particularly vulnerable to damage caused by xenobiotics and their metabolites. Drug-induced kidney toxicity is a major cause of drug attrition during preclinical and clinical development and the ability to predict renal toxicity remains a pressing challenge, necessitating more predictive in vitro models. However, the abundance of commercially available renal proximal tubule epithelial cell (RPTEC) sources complicates the selection of the most predictive cell types. Methods: This study compared a wide range of RPTEC sources, including primary cells (Lonza) and various RPTEC lines from different vendors, such as ciPTECs (Cell4Pharma), TERT1/RPTECs (ATCC), and HEK293 (GenoMembrane), including OAT1-overexpressing variants. HepG2 cells were included for a comparison of organ specificity. The different cells were cultured in 96- or 384-well plates and exposed to 12 drugs for 72 h at a concentration yielding a response (0.3–300 µM) to evaluate their ability to predict clinical outcomes. The CellTiterGlo® assay was used to measure cell viability, and transcriptome data from unexposed cells was analyzed using the TempO-seq® S1500+ platform. Results: Gene expression data showed that the primary kidney cells most closely matched the transcriptome of the human kidney medulla, followed by the TERT1 and ciPTEC lines, with the HEK lines showing the lowest similarity. The RPTEC sources showed clustering by cell type, with OAT1 overexpression driving changes in metabolic, detoxification, and immune pathways, especially in TERT1 cells. Cell viability data were used to determine points of departure (PODs) which were compared to human serum Cmax values to assess safety margins. The TERT1 and ciPTEC RPTEC lines demonstrated the highest predictive performance for nephrotoxicity, with OAT1 overexpression significantly enhancing sensitivity, accuracy, and overall predictive power (MCC scores: 0.764 and 0.667, respectively). In contrast, HepG2 cells showed the lowest performance across all metrics, highlighting the critical role of cell type and transporter expression in nephrotoxicity prediction. Conclusions: This study highlights important differences among RPTEC sources and their utility in drug safety studies of the renal proximal tubule. We show that while improved cell options for renal proximal tubule are needed, OAT1-overexpressing RPTECs are a superior model to the background cell type. Full article
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22 pages, 1816 KiB  
Article
The Association Between Statin Drugs and Rhabdomyolysis: An Analysis of FDA Adverse Event Reporting System (FAERS) Data and Transcriptomic Profiles
by Robert Morris, Kun Bu, Weiru Han, Savanah Wood, Paola M. Hernandez Velez, Jacob Ward, Ariana Crescitelli, Madison Martin and Feng Cheng
Genes 2025, 16(3), 248; https://doi.org/10.3390/genes16030248 - 21 Feb 2025
Cited by 3 | Viewed by 4005
Abstract
Background/Objectives: Rhabdomyolysis, a dangerous breakdown of skeletal muscle, has been reported as an adverse event in those prescribed a statin therapy for the treatment of hypercholesterolemia. Statin drugs are some of the most prescribed treatments for elevated cholesterol levels. The purpose of this [...] Read more.
Background/Objectives: Rhabdomyolysis, a dangerous breakdown of skeletal muscle, has been reported as an adverse event in those prescribed a statin therapy for the treatment of hypercholesterolemia. Statin drugs are some of the most prescribed treatments for elevated cholesterol levels. The purpose of this comparative study was to determine the association between the statin drugs used and the risk of rhabdomyolysis using the FDA Adverse Event Reporting System (FAERS) and transcriptomic data. Methods: A disproportionality analysis was performed to compare the risk of rhabdomyolysis between the reference statin drug (simvastatin) and the treatment group, with patient age assessed as a possible confounder. In addition, association rule mining was utilized to both identify other adverse events that frequently presented with rhabdomyolysis and identify possible drug-drug interactions (DDIs). Finally, public transcriptomic data were explored to identify the possible genetic underpinnings highlighting these differences in rhabdomyolysis risk across statins. Results: Rhabdomyolysis is a commonly reported adverse event for patients treated with statins, particularly those prescribed simvastatin. Simvastatin was associated with a more than 2-fold increased likelihood of rhabdomyolysis compared to other statins. Men were twice as likely to report rhabdomyolysis than women regardless of statin treatment, with the highest risk observed for pravastatin (ROR = 2.30, p < 0.001) and atorvastatin (ROR = 2.03, p < 0.0001). Several possible DDIs were identified, including furosemide/Lasix, allopurinol clopidogrel/Plavix, and pantoprazole, which may elevate rhabdomyolysis risk through impaired muscle function and delayed statin metabolism. Finally, nine myopathic genes were identified as possible regulators of statin-induced rhabdomyolysis, including DYSF, DES, PLEC, CAPN3, SCN4A, TNNT1, SDHA, MYH7, and PYGM in primary human muscle cells. Conclusions: Simvastatin was associated with the highest risk of rhabdomyolysis. The risk of rhabdomyolysis was more pronounced in men than women. Several possible DDIs were identified including furosemide/Lasix, allopurinol clopidogrel/Plavix, and pantoprazole. Full article
(This article belongs to the Section Toxicogenomics)
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24 pages, 3458 KiB  
Article
Unveiling the Mechanisms of a Remission in Major Depressive Disorder (MDD)-like Syndrome: The Role of Hippocampal Palmitoyltransferase Expression and Stress Susceptibility
by Careen A. Schroeter, Anna Gorlova, Michael Sicker, Aleksei Umriukhin, Alisa Burova, Boris Shulgin, Sergey Morozov, Joao P. Costa-Nunes and Tatyana Strekalova
Biomolecules 2025, 15(1), 67; https://doi.org/10.3390/biom15010067 - 5 Jan 2025
Cited by 1 | Viewed by 1406
Abstract
Post-translational modifications of proteins via palmitoylation, a thioester linkage of a 16-carbon fatty acid to a cysteine residue, reversibly increases their affinity for cholesterol-rich lipid rafts in membranes, changing their function. Little is known about how altered palmitoylation affects function at the systemic [...] Read more.
Post-translational modifications of proteins via palmitoylation, a thioester linkage of a 16-carbon fatty acid to a cysteine residue, reversibly increases their affinity for cholesterol-rich lipid rafts in membranes, changing their function. Little is known about how altered palmitoylation affects function at the systemic level and contributes to CNS pathology. However, recent studies suggested a role for the downregulation of palmitoyl acetyltransferase (DHHC) 21 gene expression in the development of Major Depressive Disorder (MDD)-like syndrome. Here, we sought to investigate how susceptibility (sucrose preference below 65%) or resilience (sucrose preference > 65%) to stress-induced anhedonia affects DHHC gene expression in the hippocampus of C57BL/6J mice during the phase of spontaneous recovery from anhedonia. Because MDD is a recurrent disorder, it is important to understand the molecular mechanisms underlying not only the symptomatic phase of the disease but also a state of temporary remission. Indeed, molecular changes associated with the application of pharmacotherapy at the remission stage are currently not well understood. Therefore, we used a mouse model of chronic stress to address these questions. The stress protocol consisted of rat exposure, social defeat, restraint stress, and tail suspension. Mice from the stress group were not treated, received imipramine via drinking water (7 mg/kg/day), or received intraperitoneal injections of dicholine succinate (DS; 25 mg/kg/day) starting 7 days prior to stress and continuing during a 14-day stress procedure. Controls were either untreated or treated with either of the two drugs. At the 1st after-stress week, sucrose preference, forced swim, novel cage, and fear-conditioning tests were carried out; the sucrose test and 5-day Morris water maze test followed by a sacrifice of mice on post-stress day 31 for all mice were performed. Transcriptome Illumina analysis of hippocampi was carried out. Using the RT-PCR, the hippocampal gene expression of Dhhc3, Dhhc7, Dhhc8, Dhhc13, Dhhc14, and Dhhc21 was studied. We found that chronic stress lowered sucrose preference in a subgroup of mice that also exhibited prolonged floating behavior, behavioral invigoration, and impaired contextual fear conditioning, while auditory conditioning was unaltered. At the remission phase, no changes in the sucrose test were found, and the acquisition of the Morris water maze was unchanged in all groups. In anhedonic, but not resilient animals, Dhhc8 expression was lowered, and the expression of Dhhc14 was increased. Antidepressant treatment with either drug partially preserved gene expression changes and behavioral abnormalities. Our data suggest that Dhhc8 and Dhhc14 are likely to be implicated in the mechanisms of depression at the remission stage, serving as targets for preventive therapy. Full article
(This article belongs to the Section Molecular Medicine)
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20 pages, 3030 KiB  
Review
Recent Advances in Omics, Computational Models, and Advanced Screening Methods for Drug Safety and Efficacy
by Ahrum Son, Jongham Park, Woojin Kim, Yoonki Yoon, Sangwoon Lee, Jaeho Ji and Hyunsoo Kim
Toxics 2024, 12(11), 822; https://doi.org/10.3390/toxics12110822 - 16 Nov 2024
Cited by 6 | Viewed by 2432
Abstract
It is imperative to comprehend the mechanisms that underlie drug toxicity in order to enhance the efficacy and safety of novel therapeutic agents. The capacity to identify molecular pathways that contribute to drug-induced toxicity has been significantly enhanced by recent developments in omics [...] Read more.
It is imperative to comprehend the mechanisms that underlie drug toxicity in order to enhance the efficacy and safety of novel therapeutic agents. The capacity to identify molecular pathways that contribute to drug-induced toxicity has been significantly enhanced by recent developments in omics technologies, such as transcriptomics, proteomics, and metabolomics. This has enabled the early identification of potential adverse effects. These insights are further enhanced by computational tools, including quantitative structure–activity relationship (QSAR) analyses and machine learning models, which accurately predict toxicity endpoints. Additionally, technologies such as physiologically based pharmacokinetic (PBPK) modeling and micro-physiological systems (MPS) provide more precise preclinical-to-clinical translation, thereby improving drug safety assessments. This review emphasizes the synergy between sophisticated screening technologies, in silico modeling, and omics data, emphasizing their roles in reducing late-stage drug development failures. Challenges persist in the integration of a variety of data types and the interpretation of intricate biological interactions, despite the progress that has been made. The development of standardized methodologies that further enhance predictive toxicology is contingent upon the ongoing collaboration between researchers, clinicians, and regulatory bodies. This collaboration ensures the development of therapeutic pharmaceuticals that are more effective and safer. Full article
(This article belongs to the Special Issue Advances in Computational Toxicology and Their Exposure)
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24 pages, 1718 KiB  
Article
Functional Assessments of Gynecologic Cancer Models Highlight Differences Between Single-Node Inhibitors of the PI3K/AKT/mTOR Pathway and a Pan-PI3K/mTOR Inhibitor, Gedatolisib
by Aaron Broege, Stefano Rossetti, Adrish Sen, Arul S. Menon, Ian MacNeil, Jhomary Molden and Lance Laing
Cancers 2024, 16(20), 3520; https://doi.org/10.3390/cancers16203520 - 17 Oct 2024
Cited by 2 | Viewed by 3245
Abstract
Background/Objectives: The PI3K/AKT/mTOR (PAM) pathway is frequently activated in gynecological cancers. Many PAM inhibitors selectively target single PAM pathway nodes, which can lead to reduced efficacy and increased drug resistance. To address these limitations, multiple PAM pathway nodes may need to be [...] Read more.
Background/Objectives: The PI3K/AKT/mTOR (PAM) pathway is frequently activated in gynecological cancers. Many PAM inhibitors selectively target single PAM pathway nodes, which can lead to reduced efficacy and increased drug resistance. To address these limitations, multiple PAM pathway nodes may need to be inhibited. Gedatolisib, a well-tolerated panPI3K/mTOR inhibitor targeting all Class I PI3K isoforms, mTORC1 and mTORC2, could represent an effective treatment option for patients with gynecologic cancers. Methods: Gedatolisib and other PAM inhibitors (e.g., alpelisib, capivasertib, and everolimus) were tested in endometrial, ovarian, and cervical cancer cell lines by using cell viability, cell proliferation, and flow cytometry assays. Xenograft studies evaluated gedatolisib in combination with a CDK4/6 inhibitor (palbociclib) or an anti-estrogen (fulvestrant). A pseudo-temporal transcriptomic trajectory of endometrial cancer clinical progression was computationally modeled employing data from 554 patients to correlate non-clinical studies with a potential patient group. Results: Gedatolisib induced a substantial decrease in PAM pathway activity in association with the inhibition of cell cycle progression and the decreased cell viability in vitro. Compared to single-node PAM inhibitors, gedatolisib exhibited greater growth-inhibitory effects in almost all cell lines, regardless of the PAM pathway mutations. Gedatolisib combined with either fulvestrant or palbociclib inhibited tumor growth in endometrial and ovarian cancer xenograft models. Conclusions: Gedatolisib in combination with other therapies has shown an acceptable safety profile and promising preliminary efficacy in clinical studies with various solid tumor types. The non-clinical data presented here support the development of gedatolisib combined with CDK4/6 inhibitors and/or hormonal therapy for gynecologic cancer treatment. Full article
(This article belongs to the Section Molecular Cancer Biology)
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