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Henriquez AR, Godbout-Cheliak M, Filiatreault A, Thomson EM. Ozone and particulate matter co-exposure at the air-liquid interface: Establishing an approach to assess pollutant interactions in vitro. Toxicol In Vitro 2025; 107:106060. [PMID: 40179993 DOI: 10.1016/j.tiv.2025.106060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2025] [Revised: 03/22/2025] [Accepted: 03/29/2025] [Indexed: 04/05/2025]
Abstract
BACKGROUND Air pollution is a complex mixture of gases and particulates that varies spatially and temporally, making attribution of adverse effects to specific individual air pollutants a challenge. To disentangle effects of mixtures in a controlled setting, reproducible and realistic co-exposures of human-relevant models to gaseous and particulate pollutants are needed. Although air-liquid interface (ALI) exposures offer considerable promise as non-animal models for inhalation toxicity testing, a lack of studies comparing individual and co-exposures to gaseous and particulate pollutants has thus far prevented assessment of their strengths and limitations for disentangling effects of pollutant mixtures. METHODS Using an integrated ALI exposure system, we characterized the interaction between ozone and particles (25 nm fluorescent polystyrene beads) to assess effects on and reproducibility of critical physical endpoints including temperature, humidity, ozone concentration and particle deposition. Particle deposition and concentration were assessed via three independent methods: fluorescence, quartz crystal microbalance (QCM), and airborne particle count. To evaluate the acute biological effects of an air pollutant mixture in vitro, human lung type 2 epithelial-like cells (A549) were exposed at the ALI to air, ozone (O3), particles, and O3 + particles (co-exposure) for 1 h (n = 4 independent repeats/exposure type). Cell injury and inflammation were quantified by extracellular lactate dehydrogenase (LDH) activity and release of proinflammatory cytokines (interleukin (IL)-8 and IL-6) respectively 0 and 24 h post-exposure. RESULTS Exposures were effective at delivering targeted O3 exposures under controlled temperature and relative humidity. In-well particle deposition and airborne concentration exiting the exposure system, quantified through parallel methods, were consistent, and increased in relation to aerosolized particle concentration. Levels of each pollutant were effectively maintained in the presence of the other. O3 alone, and co-exposure to O3 and particles, increased LDH release from A549 cells, indicating pollutant-specific cytotoxicity. In contrast, IL-8 and IL-6 release (24 h > 0 h) were not changed by exposure to the individual pollutants, but tended to increase following co-exposure. CONCLUSION The present work establishes the utility of ALI exposure systems to disentangle individual effects of pollutants from a mixture, and highlights the importance of direct experimental characterization of dosimetry and exposure conditions.
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Affiliation(s)
- Andres R Henriquez
- Environmental Health Science and Research Bureau, Environmental and Radiation Health Sciences Directorate, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON K1A 0K9, Canada
| | - Marjolaine Godbout-Cheliak
- Environmental Health Science and Research Bureau, Environmental and Radiation Health Sciences Directorate, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON K1A 0K9, Canada
| | - Alain Filiatreault
- Environmental Health Science and Research Bureau, Environmental and Radiation Health Sciences Directorate, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON K1A 0K9, Canada
| | - Errol M Thomson
- Environmental Health Science and Research Bureau, Environmental and Radiation Health Sciences Directorate, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON K1A 0K9, Canada; Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Canada.
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Han Y, Zhang M, Yu S, Jia L. Oxidative Stress in Pediatric Asthma: Sources, Mechanisms, and Therapeutic Potential of Antioxidants. FRONT BIOSCI-LANDMRK 2025; 30:22688. [PMID: 40018915 DOI: 10.31083/fbl22688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 06/08/2024] [Accepted: 07/30/2024] [Indexed: 03/01/2025]
Abstract
Pediatric asthma is a common respiratory condition in children, characterized by a complex interplay of environmental and genetic factors. Evidence shows that the airways of stimulated asthmatic patients have increased oxidative stress, but the exact mechanisms through which this stress contributes to asthma progression are not fully understood. Oxidative stress originates from inflammatory cells in the airways, producing significant amounts of reactive oxygen species (ROS) and reactive nitrogen species (RNS). External factors such as cigarette smoke, particulate matter, and atmospheric pollutants also contribute to ROS and RNS levels. The accumulation of these reactive species disrupts the cellular redox balance, leading to heightened oxidative stress, which activates cellular signaling pathways and modulates the release of inflammatory factors, worsening asthma inflammation. Therefore, understanding the sources and impacts of oxidative stress in pediatric asthma is crucial to developing antioxidant-based treatments. This review examines the sources of oxidative stress in children with asthma, the role of oxidative stress in asthma development, and the potential of antioxidants as a therapeutic strategy for pediatric asthma.
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Affiliation(s)
- Yanhua Han
- Department of Pediatrics, Affiliated Hospital to Changchun University of Chinese Medicine, 130021 Changchun, Jilin, China
| | - Mingyao Zhang
- Department of Pediatrics, The Third Affiliated Hospital of Changchun University of Chinese Medicine, 130117 Changchun, Jilin, China
| | - Shishu Yu
- Department of Pediatrics, The Third Affiliated Hospital of Changchun University of Chinese Medicine, 130117 Changchun, Jilin, China
| | - Lulu Jia
- Department of Pediatrics, The Third Affiliated Hospital of Changchun University of Chinese Medicine, 130117 Changchun, Jilin, China
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Amitrano A, Yuan Q, Agarwal B, Sen A, Dance YW, Zuo Y, Phillip JM, Gu L, Konstantopoulos K. Extracellular fluid viscosity regulates human mesenchymal stem cell lineage and function. SCIENCE ADVANCES 2025; 11:eadr5023. [PMID: 39742493 PMCID: PMC11691697 DOI: 10.1126/sciadv.adr5023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Accepted: 11/20/2024] [Indexed: 01/03/2025]
Abstract
Human mesenchymal stem cells (hMSCs) respond to mechanical stimuli, including stiffness and viscoelasticity. To date, it is unknown how extracellular fluid viscosity affects hMSC function on substrates of different stiffness and viscoelasticity. While hMSCs assume an adipogenic phenotype on gels of low stiffness and prescribed stress relaxation times, elevated fluid viscosity is sufficient to bias hMSCs toward an osteogenic phenotype. Elevated viscosity induces Arp2/3-dependent actin remodeling, enhances NHE1 activity, and promotes hMSC spreading via up-regulation of integrin-linked kinase. The resulting increase in membrane tension triggers the activation of transient receptor potential cation vanilloid 4 to facilitate calcium influx, thereby stimulating RhoA/ROCK and driving YAP-dependent RUNX2 translocation to the nucleus, leading to osteogenic differentiation. hMSCs on soft gels at elevated relative to basal viscosity favor an M2 macrophage phenotype. This study establishes fluid viscosity as a key physical cue that imprints osteogenic memory in hMSCs and promotes an immunosuppressive phenotype.
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Affiliation(s)
- Alice Amitrano
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Qinling Yuan
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Bhawana Agarwal
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Anindya Sen
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Yoseph W. Dance
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Yi Zuo
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
- Deparment of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jude M. Phillip
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21231, USA
| | - Luo Gu
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
- Deparment of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Konstantinos Konstantopoulos
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21231, USA
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González D, Infante A, López L, Ceschin D, Fernández-Sanchez MJ, Cañas A, Zafra-Mejía C, Rojas A. Airborne fine particulate matter exposure induces transcriptomic alterations resembling asthmatic signatures: insights from integrated omics analysis. ENVIRONMENTAL EPIGENETICS 2025; 11:dvae026. [PMID: 39850030 PMCID: PMC11753294 DOI: 10.1093/eep/dvae026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2024] [Revised: 11/20/2024] [Accepted: 12/30/2024] [Indexed: 01/25/2025]
Abstract
Fine particulate matter (PM2.5), an atmospheric pollutant that settles deep in the respiratory tract, is highly harmful to human health. Despite its well-known impact on lung function and its ability to exacerbate asthma, the molecular basis of this effect is not fully understood. This integrated transcriptomic and epigenomic data analysis from publicly available datasets aimed to determine the impact of PM2.5 exposure and its association with asthma in human airway epithelial cells. Differential gene expression and binding analyses identified 349 common differentially expressed genes and genes associated with differentially enriched H3K27ac regions in both conditions. Co-expression network analysis revealed three preserved modules (Protein Folding, Cell Migration, and Hypoxia Response) significantly correlated with PM2.5 exposure and preserved in asthma networks. Pathways dysregulated in both conditions included epithelial function, hypoxia response, interleukin-17 and TNF signaling, and immune/inflammatory processes. Hub genes like TGFB2, EFNA5, and PFKFB3 were implicated in airway remodeling, cell migration, and hypoxia-induced glycolysis. These findings elucidate common altered expression patterns and processes between PM2.5 exposure and asthma, helping to understand their molecular connection. This provides guidance for future research to utilize them as potential biomarkers or therapeutic targets and generates evidence supporting the need for implementing effective air quality management strategies.
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Affiliation(s)
- Daniel González
- Institute of Human Genetics, School of Medicine, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
| | - Alexis Infante
- School of Engineering, Universidad Nacional de Colombia, Bogotá 111321, Colombia
| | - Liliana López
- Department of Statistics, Universidad Nacional de Colombia, Bogotá 111321, Colombia
| | - Danilo Ceschin
- Instituto Universitario de Ciencias Biomédicas de Córdoba (IUCBC), Córdoba X5016KEJ, Argentina
- Centro de Investigación en Medicina Traslacional “Severo R. Amuchástegui” (CIMETSA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba X5016KEJ, Argentina
| | - María José Fernández-Sanchez
- School of Medicine, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
- Pulmonary Unit, Hospital Universitario San Ignacio, Bogotá 110231, Colombia
| | - Alejandra Cañas
- School of Medicine, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
- Pulmonary Unit, Hospital Universitario San Ignacio, Bogotá 110231, Colombia
| | - Carlos Zafra-Mejía
- Grupo de Investigación en Ingeniería Ambiental (GIIAUD), Facultad del Medio Ambiente y Recursos Naturales, Universidad Distrital Francisco José de Caldas, Bogotá 110321, Colombia
| | - Adriana Rojas
- Institute of Human Genetics, School of Medicine, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
- Department of Genetics, University of Córdoba, Córdoba 14071, Spain
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba 14004, Spain
- Reina Sofía University Hospital, Córdoba 14004, Spain
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Martines-Arano H, Valdivia-Flores A, Castillo-Cruz J, García-Pérez BE, Torres-Torres C. Spatially modulated ablation driven by chaotic attractors in human lung epithelial cancer cells. Biomed Phys Eng Express 2024; 10:035041. [PMID: 38569484 DOI: 10.1088/2057-1976/ad39f1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 04/03/2024] [Indexed: 04/05/2024]
Abstract
A significant modification in photoinduced energy transfer in cancer cells is reported by the assistance of a dynamic modulation of the beam size of laser irradiation. Human lung epithelial cancer cells in monolayer form were studied. In contrast to the quantum and thermal ablation effect promoted by a standard focused Gaussian beam, a spatially modulated beam can caused around 15% of decrease in the ablation threshold and formation of a ring-shaped distribution of the photothermal transfer effect. Optical irradiation was conducted in A549 cells by a 532 nm single-beam emerging from a Nd:YVO4 system. Ablation effects derived from spatially modulated convergent waves were controlled by an electrically focus-tunable lens. The proposed chaotic behavior of the spatial modulation followed an Arneodo chaotic oscillator. Fractional dynamic thermal transport was analyzed in order to describe photoenergy in propagation through the samples. Immediate applications of chaos theory for developing phototechnology devices driving biological functions or phototherapy treatments can be considered.
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Affiliation(s)
- Hilario Martines-Arano
- Facultad de Ciencias de la Electrónica, Benemérita Universidad Autónoma de Puebla, 72592, Puebla, Puebla, Mexico
| | - Alejandra Valdivia-Flores
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, 11340, Mexico
| | - Juan Castillo-Cruz
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, 11340, Mexico
| | - Blanca Estela García-Pérez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, 11340, Mexico
| | - Carlos Torres-Torres
- Sección de Estudios de Posgrado e Investigación, Escuela Superior de Ingeniería Mecánica y Eléctrica Unidad Zacatenco, Instituto Politécnico Nacional, Ciudad de México, 07738, Mexico
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Chen W, Ge P, Deng M, Liu X, Lu Z, Yan Z, Chen M, Wang J. Toxicological responses of A549 and HCE-T cells exposed to fine particulate matter at the air-liquid interface. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:27375-27387. [PMID: 38512571 PMCID: PMC11052810 DOI: 10.1007/s11356-024-32944-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 03/12/2024] [Indexed: 03/23/2024]
Abstract
Fine particulate matter (PM2.5) can enter the human body in various ways and have adverse effects on human health. Human lungs and eyes are exposed to the air for a long time and are the first to be exposed to PM2.5. The "liquid immersion exposure method" has some limitations that prevent it from fully reflecting the toxic effects of particulate matter on the human body. In this study, the collected PM2.5 samples were chemically analyzed. An air-liquid interface (ALI) model with a high correlation to the in vivo environment was established based on human lung epithelial cells (A549) and immortalized human corneal epithelial cells (HCE-T). The VITROCELL Cloud 12 system was used to distribute PM2.5 on the cells evenly. After exposure for 6 h and 24 h, cell viability, apoptosis rate, reactive oxygen species (ROS) level, expression of inflammatory factors, and deoxyribonucleic acid (DNA) damage were measured. The results demonstrated significant dose- and time-dependent effects of PM2.5 on cell viability, cell apoptosis, ROS generation, and DNA damage at the ALI, while the inflammatory factors showed dose-dependent effects only. It should be noted that even short exposure to low doses of PM2.5 can cause cell DNA double-strand breaks and increased expression of γ-H2AX, indicating significant genotoxicity of PM2.5. Increased abundance of ROS in cells plays a crucial role in the cytotoxicity induced by PM2.5 exposure These findings emphasize the significant cellular damage and genotoxicity that may result from short-term exposure to low levels of PM2.5.
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Affiliation(s)
- Wankang Chen
- Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, Nanjing, 210044, China
| | - Pengxiang Ge
- Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, Nanjing, 210044, China
| | - Minjun Deng
- Ningxia Meteorological Service Center, Yinchuan, 750002, China
| | - Xiaoming Liu
- Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, Nanjing, 210044, China
| | - Zhenyu Lu
- Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, Nanjing, 210044, China
| | - Zhansheng Yan
- Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, Nanjing, 210044, China
| | - Mindong Chen
- Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, Nanjing, 210044, China.
| | - Junfeng Wang
- Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, Nanjing, 210044, China
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Ahn Y, Yim YH, Yoo HM. Particulate Matter Induces Oxidative Stress and Ferroptosis in Human Lung Epithelial Cells. TOXICS 2024; 12:161. [PMID: 38393256 PMCID: PMC10893167 DOI: 10.3390/toxics12020161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 02/11/2024] [Accepted: 02/18/2024] [Indexed: 02/25/2024]
Abstract
Numerous toxicological studies have highlighted the association between urban particulate matter (PM) and increased respiratory infections and lung diseases. The adverse impact on the lungs is directly linked to the complex composition of particulate matter, initiating reactive oxygen species (ROS) production and consequent lipid peroxidation. Excessive ROS, particularly within mitochondria, can destroy subcellular organelles through various pathways. In this study, we confirmed the induction of ferroptosis, an iron-dependent cell death, upon exposure to an urban PM using RT-qPCR and signaling pathway analysis. We used KRISS CRM 109-02-004, the certified reference material for the analysis of particulate matter, produced by the Korea Research Institute of Standards and Science (KRISS). To validate that ferroptosis causes lung endothelial toxicity, we assessed intracellular mitochondrial potential, ROS overproduction, lipid peroxidation, and specific ferroptosis biomarkers. Following exposure to the urban PM, a significant increase in ROS generation and a decrease in mitochondrial potential were observed. Furthermore, it induced hallmarks of ferroptosis, including the accumulation of lipid peroxidation, the loss of antioxidant defenses, and cellular iron accumulation. In addition, the occurrence of oxidative stress as a key feature of ferroptosis was confirmed by increased expression levels of specific oxidative stress markers such as NQO1, CYP1B1, FTH1, SOD2, and NRF. Finally, a significant increase in key ferroptosis markers was observed, including xCT/SLC7A11, NQO1, TRIM16, HMOX-1, FTL, FTH1, CYP1B1, CHAC1, and GPX4. This provides evidence that elevated ROS levels induce oxidative stress, which ultimately triggers ferroptosis. In conclusion, our results show that the urban PM, KRISS CRM, induces cellular and mitochondrial ROS production, leading to oxidative stress and subsequent ferroptosis. These results suggest that it may induce ferroptosis through ROS generation and may offer potential strategies for the treatment of lung diseases.
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Affiliation(s)
- Yujin Ahn
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
- Department of Precision Measurement, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Yong-Hyeon Yim
- Department of Precision Measurement, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
- Inorganic Metrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
| | - Hee Min Yoo
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
- Department of Precision Measurement, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
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Burroughs MR, Sweet PJ, Contreras LM. Optimized chemical labeling method for isolation of 8-oxoG-modified RNA, ChLoRox-Seq, identifies mRNAs enriched in oxidation and transcriptome-wide distribution biases of oxidation events post environmental stress. RNA Biol 2024; 21:132-148. [PMID: 39559912 PMCID: PMC11581162 DOI: 10.1080/15476286.2024.2427903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 11/02/2024] [Accepted: 11/05/2024] [Indexed: 11/20/2024] Open
Abstract
Bulk increases in nucleobase oxidation, most commonly manifesting as the guanine (G) nucleobase modification 8-oxo-7,8-dihydroguanine (8-oxoG), have been linked to several disease pathologies. Elucidating the effects of RNA oxidation on cellular homoeostasis is limited by a lack of effective tools for detecting specific regions modified with 8-oxoG. Building on a previously published method for studying 8-oxoG in DNA, we developed ChLoRox-Seq, which works by covalently functionalizing 8-oxoG sites in RNA with biotin. Importantly, this method enables antibody-free enrichment of 8-oxoG-containing RNA fragments for Next Generation Sequencing-based detection of modified regions transcriptome-wide. We demonstrate the high specificity of ChLoRox-Seq for functionalizing 8-oxoG over unmodified nucleobases in RNA and benchmark this specificity to a commonly used antibody-based approach. Key advantages of ChLoRox-Seq include: (1) heightened resolution of RNA oxidation regions (e.g. exon-level) and (2) lower experimental costs. By applying ChLoRox-Seq to mRNA extracted from human lung epithelial cells (BEAS-2B) after exposure to environmentally relevant stress, we observe that 8-oxoG modifications tend to cluster in regions that are G-rich and within mRNA transcripts possessing longer 5' UTR and CDS regions. These findings provide new insight into the complex mechanisms that bias the accumulation of RNA oxidation across the transcriptome. Notably, our analysis suggests the possibility that most mRNA oxidation events are probabilistically driven and that mRNAs that possess more favourable intrinsic properties are prone to incur oxidation events at elevated rates. ChLoRox-Seq can be readily applied in future studies to identify regions of elevated RNA oxidation in any cellular model of interest.
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Affiliation(s)
- Matthew R. Burroughs
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Philip J. Sweet
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Lydia M. Contreras
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
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