Toxicological Sciences最新文献

{"title":"The aryl hydrocarbon receptor as a tissue-specific modulator of insulin sensitivity: evidence from conditional deletion studies.","authors":"Mauricio Di Fulvio","doi":"10.1093/toxsci/kfag103","DOIUrl":"10.1093/toxsci/kfag103","url":null,"abstract":"<p><p>The aryl hydrocarbon receptor (AhR) has emerged as a consequential regulator of fuel homeostasis and insulin action, yet its tissue-specific contributions remain incompletely resolved. Using evidence from conditional and inducible AhR deletion models, the purpose of this review is to evaluate the role of AhR in metabolically active tissues including adipose, liver, skeletal muscle, intestinal epithelium, kidney, pancreatic β-cells and the central nervous system. Tissue-specific phenotypes reveal that AhR may modulate insulin sensitivity in a context-dependent manner shaped by at least 3 critical variables: (i) the timing of receptor deletion (developmental vs. post-developmental), (ii) sex (with divergent mechanisms operating in males vs. females), and (iii) dietary context (chow vs. metabolic challenge). In adipocytes, for instance, post-developmental AhR deletion protects females against diet-induced metabolic dysfunction by mechanisms potentially associated with estrogen receptor-dependent enhancement of hypothalamic leptin sensitivity, while males show only partial protection mediated in part through reduced adipose tissue inflammation. Hepatocyte-specific AhR deletion worsens steatosis but may improve systemic metabolism through FGF21-dependent mechanisms, suggesting opposing local vs. endocrine effects. Specific deletion in insulin-secreting β-cells suggests that AhR may contribute to dioxin-induced glucose dysregulation in a sex-contingent manner. Collectively, these tissue-specific phenotypes suggest that physiological AhR signaling contributes to metabolic homeostasis under basal conditions, whereas dietary lipid excess or xenobiotic exposure may reveal tissue-specific functions that either impair or preserve insulin sensitivity. These observations position AhR as a tissue-restricted modulator of insulin action whose physiological impact is shaped by cellular context, hormonal milieu and ligand environment.</p>","PeriodicalId":23178,"journal":{"name":"Toxicological Sciences","volume":" ","pages":""},"PeriodicalIF":5.2,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148809088","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Proteomic characterization of ocular tear fluid reveals preclinical markers of sulfur mustard toxicity.","authors":"Sreekala P V Shenoy, Cameron A Sousa, Aaron T Doney, Adrienne B Stone, Christel Y Anthony, Steven Cayea, Hadi Pourhadi, Jingyun Lee, Saleh Ahmed, Ashok Sharma, Sarfaraz Ahmad, Ratnakar Tripathi, Patrick M McNutt","doi":"10.1093/toxsci/kfag108","DOIUrl":"10.1093/toxsci/kfag108","url":null,"abstract":"<p><p>Sulfur mustard (SM) vapor causes ocular injury after a short latent period, when molecular damage has occurred, but clinical signs are not yet apparent. Characterizing ocular responses during this early phase is important for understanding SM pathogenesis, identifying molecular readouts of injury progression, and developing biomarkers of exposure. Tear fluid is well-suited for this purpose because it can be collected noninvasively and captures responses from injured ocular tissues. We tested whether temporal changes in the tear fluid proteome reflect cellular and molecular responses to corneal SM exposure. Rabbits were exposed to SM vapor using a corneal vapor cap, and tear fluid was collected at baseline, 4 h, 1 d, and 5 d, corresponding to the latent period, acute lesion, and early recovery. A large proteomic response was detected at 4 h, involving extracellular injury signaling, epithelial injury, and innate immune activation. By 1 d, the tear fluid proteome transitioned to inflammatory cell activation with metabolic, redox, and proteostasis stress. By 5 d, evidence of acute injury response was reduced but the proteome retained a residual signature of immune, epithelial, and stress responses. This temporal progression is consistent with the molecular mechanisms of SM toxicity and provides insight into acute ocular vesicant injury. These findings establish tear fluid as a noninvasive molecular reporter of ocular SM injury progression. They also reveal a molecular signature of vesicant exposure, which emerges prior to clinical signs, and provide foundational data for developing tear-based biomarkers of chemical exposure, injury assessment, and therapeutic testing.</p>","PeriodicalId":23178,"journal":{"name":"Toxicological Sciences","volume":" ","pages":""},"PeriodicalIF":5.2,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148798220","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deposition of polyethylene micro- and nano-plastics is associated with accumulation of cadmium in lungs of smokers: a pilot study.","authors":"Gagandeep Kaur, Md Imam Faizan, Felix Effah, Aerlin D Decker, Marcus A Garcia, Matthew J Campen, Irfan Rahman","doi":"10.1093/toxsci/kfag121","DOIUrl":"10.1093/toxsci/kfag121","url":null,"abstract":"<p><p>Airborne micro- and nano-plastics (MNPs) are emerging environmental toxicants which may affect lung cellular functions. Deposition of MNPs in lungs of susceptible individuals, e.g. smokers, is not known. We determined the deposition of MNPs in the lungs of smokers and nonsmokers. Lung tissues from age- and sex-matched smokers (n = 9) and nonsmokers (n = 10) were analyzed to quantify: (i) microplastic levels using pyro-GC/MS, and (ii) heavy metal accumulation using ICP-MS, given the synergistic environmental effects of these pollutants. Py-GC/MS analysis showed a relatively higher level of MNPs in the lungs of smokers (43.67 mcg/gm) as compared with nonsmokers (34.53 mcg/gm). We observed a significant increase in the levels of polyethylene (PE; q = 0.0128), polyvinyl chloride (PVC; q = 0.0013), and polyurethane (PU; q = 0.0485) polymers in the lungs of smokers. Pairwise comparisons of elemental analyses results found an increase in the levels of cadmium (Cd) in the lungs of smokers. Importantly, we observed a strong association (R2 = 0.6392; P = 0.005) between the amounts of accumulated PE and levels of Cd in the lungs of nonsmokers versus smokers. Overall, our results show a positive correlation between bioaccumulation of PE and Cd in the lungs based on smoking status.</p>","PeriodicalId":23178,"journal":{"name":"Toxicological Sciences","volume":" ","pages":""},"PeriodicalIF":5.2,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148920960","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Detecting drug-induced nephrotoxicity using simultaneous label-free autofluorescence multiharmonic microscopy.","authors":"Aneesh Alex, Jindou Shi, Eric J Chaney, Minh Doan, Ciarán P Fisher, Leslie Obert, Crysthiane Ishiy, Alexander Ho, Darold R Spillman, Marina Marjanovic, Jan Roger, M Reid Groseclose, Steve R Hood, Stephen A Boppart","doi":"10.1093/toxsci/kfag098","DOIUrl":"10.1093/toxsci/kfag098","url":null,"abstract":"<p><p>Drug-induced nephrotoxicity (DIN) is a major cause of drug development failure, yet many cases are detected only late in clinical trials or after approval. Conventional methods to detect DIN often lack sensitivity and specificity, particularly for early or region-specific kidney injury. Here, we evaluate Simultaneous Label-free Autofluorescence Multiharmonic (SLAM) microscopy as a rapid, label-free imaging approach to quantify kidney microstructural and functional metabolic changes associated with DIN. SLAM simultaneously captures endogenous NAD(P)H and FAD autofluorescence, collagen-derived second harmonic generation, and third-harmonic generation from structural interfaces. SLAM images were acquired from the cortex and outer medulla (OM) of rat kidneys after cisplatin dosing at days 1, 6, and 29 post-administration. Imaging revealed region-specific injury, with the OM showing greater sensitivity to DIN than the cortex. The most prominent changes-tubular degeneration and hyaline casts-peaked at day 6, whereas tubular dilation and fibrosis-related features persisted to day 29. Feature-based classification captured these spatial and temporal patterns, achieving higher balanced accuracy in the OM (0.944) than in the cortex (0.860). Key model drivers included granularity and inter-channel correlations, underscoring the value of multi-channel SLAM data. Overall, these results demonstrate the potential of SLAM microscopy for sensitive, region-specific detection and characterization of DIN in preclinical safety studies. SLAM microscopy provides a rapid, label-free way to detect, localize, and classify drug-induced nephrotoxicity with improved sensitivity and regional specificity, potentially strengthening preclinical kidney safety screening and reducing late-stage development failures.</p>","PeriodicalId":23178,"journal":{"name":"Toxicological Sciences","volume":" ","pages":""},"PeriodicalIF":5.2,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13537822/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148798203","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Assessing drug-induced liver injury liabilities in human and animal hepatocytes under static and perfused spheroid culture conditions.","authors":"Chander K Negi, Chi Lam T Chan, Han-Hsuan D Tsai, Ibrahim Alshammari, Courtney Sakolish, Weihsueh A Chiu, Philip Hewitt, Stephen S Ferguson, Remi Villenave, Dimitrios Bitounis, Ivan Rusyn","doi":"10.1093/toxsci/kfag114","DOIUrl":"10.1093/toxsci/kfag114","url":null,"abstract":"<p><p>Drug-induced liver injury (DILI) remains a major challenge in drug development, highlighting the need for reliable in vitro tools to assess hepatotoxicity and improve translation from animal to human studies. Models using hepatocytes from preclinical species are also needed to evaluate species-specific toxicity. In this study, we evaluated the basal function and DILI sensitivity of primary hepatocytes from human, monkey, rat, and dog cultured for up to 14 d in static monolayers, static spheroids, and spheroids cultured in a microfluidics-based microphysiological system (MPS). Hepatocyte function and injury responses were assessed using albumin, urea, and liver enzymes. Cells were exposed to species-specific DILI compounds chlorpromazine (CPZ), bosentan (BOS), and fialuridine (FIAU). Across platforms, human and monkey hepatocytes exhibited greater functional stability and sensitivity to DILI compounds than rat and dog hepatocytes. CPZ and BOS induced cytotoxicity primarily in human and monkey hepatocytes, while FIAU produced species-dependent effects consistent with known in vivo outcomes. The microfluidics-based MPS exhibited modestly improved hepatocyte spheroid function relative to static models, although limited MPS throughput constrained our ability for testing drugs beyond FIAU. Overall, these results demonstrate that integrating multi-species hepatocyte spheroids across static and microfluidic platforms enables comparative DILI assessment and supports improved preclinical-to-clinical translation. This study demonstrates that static primary hepatocyte spheroids provide a robust, scalable, and physiologically relevant platform for detecting species-specific drug-induced liver injury, with gene expression profiling offering stronger mechanistic insight than traditional functional biomarkers. By showing that perfused microphysiological systems may not substantially improve performance over static spheroids for the tested hepatocyte preparations, the work supports a pragmatic tiered testing strategy that balances throughput, cost, and biological complexity in preclinical safety assessments.</p>","PeriodicalId":23178,"journal":{"name":"Toxicological Sciences","volume":" ","pages":""},"PeriodicalIF":5.2,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13600685/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148892274","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In vitro approaches to assess respiratory toxicity from volatile organic compounds: an in-depth review.","authors":"Olivia C G Lampe, Eva C M Vitucci, Carolyn L Cannon, Kyle Holland, Margaret J Foster, Natalie M Johnson","doi":"10.1093/toxsci/kfag110","DOIUrl":"10.1093/toxsci/kfag110","url":null,"abstract":"<p><p>Volatile organic compounds (VOCs) are ubiquitous inhaled pollutants. This review showcases current literature utilizing in vitro models of the human respiratory system to characterize the toxicity of VOCs. To map the existing evidence base, we conducted a scoping review following systematic search and screening procedures. Comprehensive searches of MEDLINE, Embase, Web of Science, CINAHL, PubMed, and CENTRAL identified 3,052 records. After screening, 144 original studies evaluating VOC exposures in human lung epithelial models met inclusion criteria. Overall, the current literature reflects substantial heterogeneity in cell models, exposure systems, and endpoints. Among 105 unique VOCs evaluated, acrolein, formaldehyde, toluene diisocyanate, and benzene were most frequently studied. Most investigations used submerged culture systems with liquid-phase VOC application, whereas fewer employed air-liquid interface (ALI) exposures that better mimic inhalation. Cytotoxicity, oxidative stress, proinflammatory signaling, and apoptosis were the most commonly measured endpoints, with oxidative stress frequently identified as an upstream driver of inflammatory and cytotoxic responses. However, mechanistic depth varied, and studies examining metabolism, barrier function, morphology, or transcriptomic regulation were relatively uncommon. Notably, chronic or repeated exposures were rarely conducted. Overall, this review highlights the variety of VOC exposure methods and commonly assessed biological endpoints, as well as the critical lack of more detailed mechanistic studies and somewhat limited VOC/mixture evaluation. The field is expansive but methodologically fragmented, underscoring the need for broader use of human respiratory cell models, more physiologically relevant exposure systems, improved dose characterization, and greater mechanistic resolution to advance understanding and throughput for VOC-induced pulmonary toxicity studies.</p>","PeriodicalId":23178,"journal":{"name":"Toxicological Sciences","volume":" ","pages":""},"PeriodicalIF":5.2,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13557630/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148798175","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Nonclinical investigation of the potential of MHAA4549A, an anti-influenza A therapeutic antibody, to mediate antibody-dependent enhancement.","authors":"Gautham K Rao, Min Xu, Rodney A Prell, Man-Wah Tan, Lee R Swem, Jenny Jiang, Olga Li, Summer Park, Donghong Yan, Daniel Sheinson, Lynn Kamen, Wendy G Halpern, Jacqueline M McBride","doi":"10.1093/toxsci/kfag109","DOIUrl":"10.1093/toxsci/kfag109","url":null,"abstract":"<p><p>Antibody-dependent enhancement (ADE) of infection and disease is a theoretical safety risk for antiviral antibodies against seasonal viruses with antigenic drift, such as influenza. ADE of infection may occur if virus-specific antibodies at subtherapeutic, nonneutralizing concentrations facilitate virus uptake, thus potentially enhancing virus replication. In contrast, ADE of disease reflects exacerbation of viral disease severity through viral replication-dependent or -independent mechanisms. Because of the theoretical concern of ADE, nonclinical safety assessment of therapeutic anti-influenza antibodies includes a thorough evaluation of ADE potential. The current set of studies was conducted to investigate the potential of MHAA4549A-a broadly specific, neutralizing, therapeutic anti-influenza A antibody-to elicit ADE of infection and disease of influenza H3N2 A/Aichi/2/68 (X31) across a broad dose range. Assessment of ADE was based on totality of results from both in vitro and mouse influenza studies with integration across study endpoints. In vitro studies demonstrated that MHAA4549A can mediate increased X31 entry into human and murine monocytic cells, but increased uptake did not result in enhanced viral replication or release under physiologic conditions. In a mouse model of X31 infection, intravenous administration of MHAA4549A resulted in delayed body weight recovery, but no exacerbation in orthogonal endpoints including mortality, lung viral titers or genomes, lung weights, or severity of influenza pneumonia. Overall, the totality of nonclinical data did not demonstrate any clear indication of ADE of infection at nonneutralizing concentrations, suggesting a low risk for MHAA4549A to cause enhanced influenza A-mediated disease at subtherapeutic doses.</p>","PeriodicalId":23178,"journal":{"name":"Toxicological Sciences","volume":" ","pages":""},"PeriodicalIF":5.2,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13573589/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148798228","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cigarette smoke and e-cigarette aerosol extracts induce myelopoiesis and suppress inflammatory cytokine production.","authors":"Jeanette Y C Sullivan, Helen X Huang, Jianhong C Heidmann, Francisco Diaz, Camille Brzechffa, Jane H Chen, Eli M Soyfer, Nneamaka Iwobi, Irene Hasen, Amanda Ting, Nicole Sparks, Michael T Kleinman, Angela G Fleischman","doi":"10.1093/toxsci/kfag096","DOIUrl":"10.1093/toxsci/kfag096","url":null,"abstract":"<p><p>Tobacco and nicotine use remain leading preventable drivers of cancer risk, and both combustible cigarettes and electronic nicotine devices perturb immune function and hematopoiesis. However, side-by-side comparisons of their effects across the hematopoietic hierarchy remain limited. Here, we evaluate the impact of cigarette smoke extract (CSE) and e-cigarette vapor extract (EVE) on inflammatory responses in mature myeloid cells and on hematopoietic stem and progenitor cell function using complementary in vitro and in vivo approaches. Using a standardized protocol applied across multiple macrophage models, including RAW264.7 cells, THP-1 macrophages, primary mouse bone marrow-derived macrophages, and human peripheral blood mononuclear cells, we found that CSE consistently suppressed LPS-induced TNF-α secretion in a dose-dependent manner, whereas EVE alone had minimal effect. CSE also induced foam cell formation in macrophages through a reactive oxygen species-dependent mechanism. Additionally, both CSE and EVE suppressed hematopoietic progenitor colony formation. To model real-world exposure patterns, we used a nose-only inhalation system to deliver combustible cigarette smoke followed by e-cigarette aerosol to mice. Sequential smoke and e-cigarette exposure increased platelet counts and myeloid cell frequency, effects not observed with smoking cessation alone. Myeloid skewing persisted through secondary transplantation, indicating durable, cell-intrinsic changes to the hematopoietic stem cell compartment. Together, these findings demonstrate that tobacco and e-cigarette exposures blunt innate immune responsiveness while driving lasting myeloid-biased hematopoiesis, with implications for infection susceptibility, cardiovascular disease, and hematologic malignancy risk.</p>","PeriodicalId":23178,"journal":{"name":"Toxicological Sciences","volume":" ","pages":""},"PeriodicalIF":5.2,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13553112/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148888398","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Nicotine analogs in e-cigarettes: unrecognized health risks and insufficient regulatory oversight.","authors":"Alexis A Graham, Elizabeth M Corteselli","doi":"10.1093/toxsci/kfag104","DOIUrl":"10.1093/toxsci/kfag104","url":null,"abstract":"","PeriodicalId":23178,"journal":{"name":"Toxicological Sciences","volume":" ","pages":""},"PeriodicalIF":5.2,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13543675/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148832350","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Analytical choices drive toxicogenomic potency estimates: a systematic evaluation of transcriptomic points of departure.","authors":"Imke B Bruns, Dayna R Schultz, Emmanuel Demuynck, Friedel Dewulf, Ioannis Theologidis, Steven J Kunnen, Lukas S Wijaya, Ilias Frydas, Nafsika Papaioannou, Elisavet Renieri, Thanasis Papageorgiou, Dimosthenis Sarigiannis, Kyriaki Machera, Birgit Mertens, Jana Asselman, Carsten Weiss, Bob van de Water, Giulia Callegaro","doi":"10.1093/toxsci/kfag115","DOIUrl":"10.1093/toxsci/kfag115","url":null,"abstract":"<p><p>Omics technologies are increasingly integrated into next-generation risk assessment, yet quantitative toxicogenomics outcomes remain highly dependent on analytical choices, motivating a systematic evaluation of how bioinformatics workflows influence hazard characterization and transcriptomic Points of Departure (tPOD). Here, we applied 5 independent transcriptomics pipelines to a shared dataset of RPTEC/TERT1 kidney cells exposed to cisplatin across multiple concentrations and time points, comparing effects of pre-processing, benchmark concentration modeling, and pathway-based interpretation strategies. Across workflows, substantial variability was observed in gene-level benchmark concentrations (BMCs). This variability was associated with differences in normalization, filtering, and modeling software, although the present design does not isolate the contribution of individual workflow choices. Despite this variability, convergence increased at later time points as transcriptional responses strengthened, with 24 h consistently identified as the most sensitive time point at the gene level. Aggregation of gene-level BMCs into pathway-based metrics reduced variability but did not eliminate it, with pathway definition emerging as a major determinant of tPOD estimates. Notably, distinct pathway resources showed minimal gene overlap, and smaller, biologically coherent gene sets (e.g. co-expression modules and biomarker panels) produced lower and less dispersed BMCs compared with broader pathway annotations. Furthermore, direct modeling of pathway activity scores yielded systematically different tPODs relative to median-based aggregation, with method-dependent conservativeness influenced by pathway coverage and response strength. Overall, our findings demonstrate that both analytical workflow design and pathway selection critically shape toxicogenomic-derived potency estimates, highlighting the need for harmonized, transparent methodologies to enable robust application of transcriptomics in chemical safety assessment and regulatory decision-making.</p>","PeriodicalId":23178,"journal":{"name":"Toxicological Sciences","volume":" ","pages":""},"PeriodicalIF":5.2,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13623630/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148906743","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}